Title: classes and methods for spatial data
Diff between sp versions 1.0-9 dated 2013-04-22 and 1.0-11 dated 2013-06-30
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson
[ctb], Virgilio Gomez-Rubio [ctb]
Maintainer: Edzer Pebesma
sp-1.0-11/sp/DESCRIPTION | 13
sp-1.0-11/sp/MD5 | 89
sp-1.0-11/sp/NAMESPACE | 5
sp-1.0-11/sp/R/CRS-methods.R | 8
sp-1.0-11/sp/R/Spatial-methods.R | 7
sp-1.0-11/sp/R/SpatialGridDataFrame-methods.R | 25
sp-1.0-11/sp/R/SpatialLines-methods.R | 6
sp-1.0-11/sp/R/SpatialPoints-methods.R | 16
sp-1.0-11/sp/R/disaggregate.R |only
sp-1.0-11/sp/R/gridlines.R | 23
sp-1.0-11/sp/R/sp_spat1.R |only
sp-1.0-11/sp/R/zerodist.R | 7
sp-1.0-11/sp/inst/ChangeLog | 3228 ++++++++------------
sp-1.0-11/sp/inst/doc/csdacm.R |only
sp-1.0-11/sp/inst/doc/csdacm.Rnw |only
sp-1.0-11/sp/inst/doc/csdacm.pdf |only
sp-1.0-11/sp/inst/doc/intro_sp.pdf |binary
sp-1.0-11/sp/inst/doc/over.pdf |binary
sp-1.0-11/sp/inst/external/seamap105_mod.csv |only
sp-1.0-11/sp/inst/include/sp_xports.c | 6
sp-1.0-11/sp/man/CRS-class.Rd | 8
sp-1.0-11/sp/man/Spatial-class.Rd | 4
sp-1.0-11/sp/man/SpatialGridDataFrame-class.Rd | 2
sp-1.0-11/sp/man/SpatialPoints-class.Rd | 3
sp-1.0-11/sp/man/SpatialPointsDataFrame-class.Rd | 1
sp-1.0-11/sp/man/SpatialPolygons-class.Rd | 17
sp-1.0-11/sp/man/SpatialPolygonsDataFrame-class.Rd | 4
sp-1.0-11/sp/man/as.SpatialPolygons.GridTopology.Rd | 3
sp-1.0-11/sp/man/disaggregate.Rd |only
sp-1.0-11/sp/man/gridlines.Rd | 6
sp-1.0-11/sp/man/is.projected.Rd | 4
sp-1.0-11/sp/man/nowrapSpatialLines.Rd | 3
sp-1.0-11/sp/man/polygons.Rd | 8
sp-1.0-11/sp/man/recenter-methods.Rd | 6
sp-1.0-11/sp/man/spDistsN1.Rd | 4
sp-1.0-11/sp/man/spTransform.Rd | 2
sp-1.0-11/sp/man/spplot.Rd | 26
sp-1.0-11/sp/man/zerodist.Rd | 4
sp-1.0-11/sp/src/gcdist.c | 14
sp-1.0-11/sp/src/init.c | 2
sp-1.0-11/sp/src/sp.h | 3
sp-1.0-11/sp/src/sp_xports.c | 6
sp-1.0-11/sp/src/zerodist.c | 18
sp-1.0-11/sp/tests/Examples/sp-Ex.Rout.save | 89
sp-1.0-11/sp/tests/fail1.R | 3
sp-1.0-11/sp/tests/fail1.Rout.save | 8
sp-1.0-11/sp/vignettes |only
sp-1.0-9/sp/ChangeLog |only
sp-1.0-9/sp/x |only
sp-1.0-9/sp/xx |only
50 files changed, 1668 insertions(+), 2013 deletions(-)
Title: Adapt numerical records to fit (in)equality restrictions with
the Successive Projection Algorithm
Diff between rspa versions 0.1-2 dated 2013-05-08 and 0.1-3 dated 2013-06-30
Description: Based on (optionally sparse) quadratic optimization with
the main algorithms implemented in C. Includes features for
easy processing of many (smaller) records. The algorithm has
been tested on fairly large optimization problems with up to a
few million variables and several hundred thousand
restrictions.
Author: Mark van der Loo
Maintainer: Mark van der Loo
DESCRIPTION | 6 +++---
MD5 | 15 ++++++++-------
NEWS | 5 ++++-
inst/doc/getting_started.R |only
inst/doc/getting_started.Rnw | 1 -
inst/doc/getting_started.pdf |binary
vignettes/Rplots.pdf |binary
vignettes/figure/unnamed-chunk-11.pdf |binary
vignettes/getting_started.Rnw | 1 -
9 files changed, 15 insertions(+), 13 deletions(-)
Title: Sample Generation by Replacement
Diff between sgr versions 1.0 dated 2013-03-18 and 1.0.1 dated 2013-06-30
Description: The library for Sample Generation by Replacement
simulations. The package can be used to perform fake data
analysis according to the sample generation by replacement
approach. It includes functions for making simple inferences
about discrete/ordinal fake data. The package allows to study
the implications of fake data for empirical results.
Author: Massimiliano Pastore & Luigi Lombardi
Maintainer: Massimiliano Pastore
DESCRIPTION | 14 +++++++++-----
MD5 | 28 ++++++++++++++--------------
R/partition.replacement.R | 2 ++
data/smokers.rda |binary
man/model.fake.par.Rd | 4 ++--
man/partition.replacement.Rd | 14 +++++++-------
man/pfake.Rd | 8 ++++----
man/pfakebad.Rd | 4 ++--
man/pfakegood.Rd | 4 ++--
man/rdatagen.Rd | 15 +++++++--------
man/rdatarepl.Rd | 2 +-
man/replacement.matrix.Rd | 10 +++++-----
man/sgr-package.Rd | 7 ++++---
man/smokers.Rd | 10 +++++-----
sgr-Ex.R | 17 +++++++++--------
15 files changed, 73 insertions(+), 66 deletions(-)
Title: Utility function for defining S3 methods
Diff between R.methodsS3 versions 1.4.2 dated 2012-06-27 and 1.4.4 dated 2013-06-30
Description: Methods that simplify the setup of S3 generic functions
and S3 methods. Major effort has been made in making
definition of methods as simple as possible with a minimum of
maintenance for package developers. For example, generic
functions are created automatically, if missing, and naming
conflict are automatically solved, if possible. The method
setMethodS3() is a good start for those who in the future may
want to migrate to S4. This is a cross-platform package
implemented in pure R that generates standard S3 methods.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
R.methodsS3-1.4.2/R.methodsS3/incl |only
R.methodsS3-1.4.4/R.methodsS3/DESCRIPTION | 21
R.methodsS3-1.4.4/R.methodsS3/MD5 | 30 -
R.methodsS3-1.4.4/R.methodsS3/inst/NEWS | 8
R.methodsS3-1.4.4/R.methodsS3/man/Non-documented_objects.Rd | 82 +--
R.methodsS3-1.4.4/R.methodsS3/man/R.KEYWORDS.Rd | 60 +-
R.methodsS3-1.4.4/R.methodsS3/man/R.methodsS3-package.Rd | 156 +++----
R.methodsS3-1.4.4/R.methodsS3/man/findDispatchMethodsS3.Rd | 86 ++--
R.methodsS3-1.4.4/R.methodsS3/man/getDispatchMethodS3.Rd | 84 ++-
R.methodsS3-1.4.4/R.methodsS3/man/getGenericS3.Rd | 80 +--
R.methodsS3-1.4.4/R.methodsS3/man/getMethodS3.Rd | 82 +--
R.methodsS3-1.4.4/R.methodsS3/man/isGenericS3.Rd | 92 ++--
R.methodsS3-1.4.4/R.methodsS3/man/isGenericS4.Rd | 88 ++--
R.methodsS3-1.4.4/R.methodsS3/man/setGenericS3.Rd | 158 +++----
R.methodsS3-1.4.4/R.methodsS3/man/setMethodS3.Rd | 256 ++++++------
R.methodsS3-1.4.4/R.methodsS3/man/throw.Rd | 112 ++---
16 files changed, 712 insertions(+), 683 deletions(-)
Title: Miscellaneous useful functions
Diff between rje versions 1.5 dated 2013-05-18 and 1.6 dated 2013-06-30
Description: A series of useful functions, some available in different
forms in other packages, but which have been extended or
modified in some way considered useful to the author.
Author: Robin Evans
Maintainer: Robin Evans
rje-1.5/rje/R/and0.R |only
rje-1.5/rje/R/arrayInd.R |only
rje-1.5/rje/R/combinations.R |only
rje-1.5/rje/R/condition.table.R |only
rje-1.5/rje/R/condition.table2.R |only
rje-1.5/rje/R/ddirichlet.R |only
rje-1.5/rje/R/expit.R |only
rje-1.5/rje/R/fsapply.R |only
rje-1.5/rje/R/greaterThan.R |only
rje-1.5/rje/R/indexBox.R |only
rje-1.5/rje/R/intervention.table.R |only
rje-1.5/rje/R/is.subset.R |only
rje-1.5/rje/R/is.wholenumber.R |only
rje-1.5/rje/R/last.R |only
rje-1.5/rje/R/logit.R |only
rje-1.5/rje/R/or0.R |only
rje-1.5/rje/R/patternRepeat.R |only
rje-1.5/rje/R/powerSet.R |only
rje-1.5/rje/R/powerSetMat.R |only
rje-1.5/rje/R/printPercentage.R |only
rje-1.5/rje/R/quickSort.R |only
rje-1.5/rje/R/rdirichlet.R |only
rje-1.5/rje/R/setmatch.R |only
rje-1.5/rje/R/setsetdiff.R |only
rje-1.5/rje/R/setsetequal.R |only
rje-1.5/rje/R/subarray.R |only
rje-1.5/rje/R/subsetMatrix.R |only
rje-1.5/rje/R/subsetOrder.R |only
rje-1.5/rje/R/subsetmatch.R |only
rje-1.5/rje/R/subtable.R |only
rje-1.5/rje/R/z%subof%.R |only
rje-1.6/rje/ChangeLog | 10 +-
rje-1.6/rje/DESCRIPTION | 10 +-
rje-1.6/rje/MD5 | 56 +++-----------
rje-1.6/rje/R/rje.R |only
rje-1.6/rje/man/Dirichlet.Rd | 132 +++++++++++++++++-----------------
rje-1.6/rje/man/and0.Rd | 5 -
rje-1.6/rje/man/armijo.Rd |only
rje-1.6/rje/man/arrayInd.Rd | 4 -
rje-1.6/rje/man/condition.table.Rd | 6 -
rje-1.6/rje/man/cubeHelix.Rd |only
rje-1.6/rje/man/fsapply.Rd | 60 +++++++--------
rje-1.6/rje/man/greaterThan.Rd | 2
rje-1.6/rje/man/intervention.table.Rd | 4 -
rje-1.6/rje/man/quickSort.Rd | 4 -
rje-1.6/rje/man/rje-package.Rd | 5 -
46 files changed, 135 insertions(+), 163 deletions(-)
Title: Rank Estimation for Linear Models
Diff between Rfit versions 0.14 dated 2011-10-13 and 0.17 dated 2013-06-30
Description: R estimation and inference for linear models. Estimation
is for general scores and a library of commonly used score
functions is included.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke
Rfit-0.14/Rfit/R/default.rfit.R |only
Rfit-0.17/Rfit/DESCRIPTION | 9 +++++----
Rfit-0.17/Rfit/MD5 | 26 +++++++++++++++++---------
Rfit-0.17/Rfit/NAMESPACE |only
Rfit-0.17/Rfit/R/gettau.R | 2 +-
Rfit-0.17/Rfit/R/gettauF0.R |only
Rfit-0.17/Rfit/R/jaeckel.R | 26 +++++++++++++++++++++-----
Rfit-0.17/Rfit/R/oneway.rfit.R | 4 ++++
Rfit-0.17/Rfit/R/print.summary.rfit.R | 2 +-
Rfit-0.17/Rfit/R/rfit.default.R |only
Rfit-0.17/Rfit/R/summary.rfit.R | 17 +++++++++++------
Rfit-0.17/Rfit/data/CardioRiskFactors.rda |only
Rfit-0.17/Rfit/man/CardioRiskFactors.Rd |only
Rfit-0.17/Rfit/man/gettau.Rd | 19 ++++---------------
Rfit-0.17/Rfit/man/rfit.Rd | 6 ++++--
Rfit-0.17/Rfit/src |only
16 files changed, 68 insertions(+), 43 deletions(-)
Title: Access to The Dataverse Network API
Diff between dvn versions 0.1 dated 2013-01-31 and 0.2 dated 2013-06-30
Description: Provides access to The Dataverse Network API via the RCurl
package, enabling access to archived data (and metadata), along
with a number of functions to translate responses to API calls
into R data structures using the XML package.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper
DESCRIPTION | 9 +++++----
MD5 | 9 +++++----
NEWS | 4 ++++
R/dvn.r | 33 +++++++++++++++++++++------------
README.md |only
man/dvn-package.Rd | 38 +++++++++++++++++++++++---------------
6 files changed, 58 insertions(+), 35 deletions(-)
Title: Allele Retention, Inbreeding, and Demography
Diff between AlleleRetain versions 1.3 dated 2013-01-02 and 1.3.1 dated 2013-06-30
Description: Simulate the effect of management or demography on allele
retention and inbreeding accumulation in bottlenecked
populations of animals with overlapping generations.
Author: Emily Weiser
Maintainer: Emily Weiser
DESCRIPTION | 7 ++++---
MD5 | 6 +++---
R/AlleleRetain.R | 1 +
inst/doc/AlleleRetain_User_Guide.pdf |binary
4 files changed, 8 insertions(+), 6 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 4.05 dated 2013-06-19 and 4.06 dated 2013-06-30
Description: Methods and tools for displaying and analysing univariate
time series forecasts including exponential smoothing via state
space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/errors.R | 4 ++--
4 files changed, 12 insertions(+), 9 deletions(-)
Title: RSDA - R to Symbolic Data Analysis
Diff between RSDA versions 1.0 dated 2013-05-29 and 1.1 dated 2013-06-30
Description: Symbolic Data Analysis (SDA) was proposed by professor
Edwin DIDAY in 1987, the main purpose of SDA is to substitute
the set of rows (cases) in the data table for a concept (second
order statistical unit). This package implements, to the
symbolic case, certain techniques of automatic classification,
as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Johnny Villalobos
M.
Maintainer: Oldemar Rodriguez
DESCRIPTION | 14 +++--
MD5 | 118 ++++++++++++++++++++++++++++++++++++----------
NAMESPACE | 7 +-
R/Dbload.R |only
R/R2.L.R |only
R/R2.U.R |only
R/RMSE.L.R |only
R/RMSE.U.R |only
R/Scon.R |only
R/Sconcept.R |only
R/Shis.R |only
R/Sint.R |only
R/Sobject.R |only
R/Sset.R |only
R/cfa.CVPRealz.R |only
R/cfa.Czz.R |only
R/cfa.MatrixZ.R |only
R/cfa.minmax.R |only
R/cfa.scatterplot.R |only
R/cfa.totals.R |only
R/deter.coefficient.R |only
R/interscal.B.R |only
R/interscal.R |only
R/interscal.delta.R |only
R/interval.dist.R | 61 +++++++++++++++--------
R/interval.dist.tobj.R | 93 +++++++++++++++++++++---------------
R/predictsym.glm.R |only
R/predictsym.lm.R |only
R/sym.cfa.R |only
R/sym.glm.R |only
R/sym.lm.R | 91 +++++++++++++++--------------------
R/sym.lm.bi.R |only
R/sym.normalize.R |only
data/Cardiological.rda |only
data/StudentsGrades.rda |binary
data/USCrime.rda |only
data/VeterinaryData.rda |binary
data/ex1_db2so.rda |only
data/ex_cfa1.rda |only
data/ex_cfa2.rda |only
data/example1.rda |binary
data/example2.rda |binary
data/example3.rda |binary
data/example4.rda |binary
data/example5.rda |binary
data/example6.rda |binary
data/example7.rda |binary
data/int_prost_test.rda |only
data/int_prost_train.rda |only
data/lynne1.rda |binary
data/lynne2.rda |binary
data/oils.rda |binary
data/uscrime_int.rda |only
man/Cardiological.Rd |only
man/Dbload.Rd |only
man/R2.L.Rd |only
man/R2.U.Rd |only
man/RMSE.L.Rd |only
man/RMSE.U.Rd |only
man/RSDA-package.Rd | 4 -
man/Scon.Rd |only
man/Sconcept.Rd |only
man/Shis.Rd |only
man/Sint.Rd |only
man/Sobject.Rd |only
man/Sset.Rd |only
man/USCrime.Rd |only
man/cfa.CVPRealz.Rd |only
man/cfa.Czz.Rd |only
man/cfa.MatrixZ.Rd |only
man/cfa.minmax.Rd |only
man/cfa.scatterplot.Rd |only
man/cfa.totals.Rd |only
man/deter.coefficient.Rd |only
man/display.sym.table.Rd | 1
man/ex1_db2so.Rd |only
man/ex_cfa1.Rd |only
man/ex_cfa2.Rd |only
man/int_prost_test.Rd |only
man/int_prost_train.Rd |only
man/interscal.B.Rd |only
man/interscal.Rd |only
man/interscal.delta.Rd |only
man/interval.dist.Rd | 2
man/interval.dist.tobj.Rd | 3 -
man/predictsym.glm.Rd |only
man/predictsym.lm.Rd |only
man/sym.cfa.Rd |only
man/sym.cov.Rd | 4 -
man/sym.glm.Rd |only
man/sym.lm.Rd | 101 +++++++++++++++++----------------------
man/sym.lm.bi.Rd |only
man/sym.normalize.Rd |only
man/sym.variance.Rd | 4 -
man/uscrime_int.Rd |only
95 files changed, 298 insertions(+), 205 deletions(-)
Title: vcd extensions and additions
Diff between vcdExtra versions 0.5-7 dated 2013-03-05 and 0.5-10 dated 2013-06-30
Description: Provides additional data sets, methods and documentation
to complement the vcd package for Visualizing Categorical Data
and the gnm package for Generalized Nonlinear Models. In
particular, vcdExtra extends mosaic, assoc and sieve plots from
vcd to handle glm() and gnm() models and adds a 3D version in
mosaic3d.
Author: Michael Friendly with Heather Turner, Achim Zeileis, Duncan
Murdoch and David Firth
Maintainer: Michael Friendly
vcdExtra-0.5-10/vcdExtra/DESCRIPTION | 15
vcdExtra-0.5-10/vcdExtra/MD5 | 103 +++---
vcdExtra-0.5-10/vcdExtra/NEWS | 10
vcdExtra-0.5-10/vcdExtra/R/datasets.R | 28 +
vcdExtra-0.5-10/vcdExtra/data/Abortion.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Alligator.RData |binary
vcdExtra-0.5-10/vcdExtra/data/Bartlett.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Caesar.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Cancer.rda |binary
vcdExtra-0.5-10/vcdExtra/data/DaytonSurvey.RData |binary
vcdExtra-0.5-10/vcdExtra/data/Detergent.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Donner.RData |only
vcdExtra-0.5-10/vcdExtra/data/Draft1970.RData |only
vcdExtra-0.5-10/vcdExtra/data/Draft1970table.RData |only
vcdExtra-0.5-10/vcdExtra/data/Dyke.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Fungicide.rda |binary
vcdExtra-0.5-10/vcdExtra/data/GSS.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Gilby.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Hauser79.RData |binary
vcdExtra-0.5-10/vcdExtra/data/Heart.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Heckman.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Hoyt.rda |binary
vcdExtra-0.5-10/vcdExtra/data/ICU.rda |binary
vcdExtra-0.5-10/vcdExtra/data/JobSat.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Mammograms.RData |binary
vcdExtra-0.5-10/vcdExtra/data/Mental.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Mobility.rda |binary
vcdExtra-0.5-10/vcdExtra/data/TV.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Vietnam.rda |binary
vcdExtra-0.5-10/vcdExtra/data/Yamaguchi87.RData |binary
vcdExtra-0.5-10/vcdExtra/inst/doc/vcd-tutorial.R |only
vcdExtra-0.5-10/vcdExtra/inst/doc/vcd-tutorial.Rnw | 312 +++++++++++++++++---
vcdExtra-0.5-10/vcdExtra/inst/doc/vcd-tutorial.pdf |binary
vcdExtra-0.5-10/vcdExtra/man/CMHtest.Rd | 11
vcdExtra-0.5-10/vcdExtra/man/Donner.Rd |only
vcdExtra-0.5-10/vcdExtra/man/Draft1970.Rd |only
vcdExtra-0.5-10/vcdExtra/man/Draft1970table.Rd |only
vcdExtra-0.5-10/vcdExtra/man/Dyke.Rd | 31 +
vcdExtra-0.5-10/vcdExtra/man/Hauser79.Rd | 5
vcdExtra-0.5-10/vcdExtra/man/Kway.Rd | 8
vcdExtra-0.5-10/vcdExtra/man/Vietnam.Rd | 7
vcdExtra-0.5-10/vcdExtra/man/Yamaguchi87.Rd | 3
vcdExtra-0.5-10/vcdExtra/man/collapse.table.Rd | 49 +++
vcdExtra-0.5-10/vcdExtra/man/datasets.Rd | 14
vcdExtra-0.5-10/vcdExtra/man/mosaic.glm.Rd | 7
vcdExtra-0.5-10/vcdExtra/man/mosaic3d.Rd | 3
vcdExtra-0.5-10/vcdExtra/man/vcdExtra-package.Rd | 8
vcdExtra-0.5-10/vcdExtra/vignettes/vcd-tutorial.Rnw | 312 +++++++++++++++++---
vcdExtra-0.5-7/vcdExtra/vignettes/fig |only
49 files changed, 763 insertions(+), 163 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.2-80 dated 2013-05-31 and 0.2-90 dated 2013-06-30
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
phytools-0.2-80/phytools/R/bind.tip.R |only
phytools-0.2-90/phytools/DESCRIPTION | 8
phytools-0.2-90/phytools/MD5 | 33 +-
phytools-0.2-90/phytools/NAMESPACE | 6
phytools-0.2-90/phytools/R/brownieREML.R | 44 +--
phytools-0.2-90/phytools/R/evol.vcv.R | 315 +++++++---------------
phytools-0.2-90/phytools/R/fancyTree.R | 5
phytools-0.2-90/phytools/R/phylomorphospace.R | 8
phytools-0.2-90/phytools/R/phylomorphospace3d.R | 9
phytools-0.2-90/phytools/R/plotSimmap.R | 49 +++
phytools-0.2-90/phytools/R/plotTree.R | 6
phytools-0.2-90/phytools/R/read.newick.R | 184 +++++++-----
phytools-0.2-90/phytools/R/utilities.R | 71 ++++
phytools-0.2-90/phytools/man/add.simmap.legend.Rd |only
phytools-0.2-90/phytools/man/collapse.to.star.Rd |only
phytools-0.2-90/phytools/man/findMRCA.Rd | 15 -
phytools-0.2-90/phytools/man/phylomorphospace.Rd | 2
phytools-0.2-90/phytools/man/plotSimmap.Rd | 3
phytools-0.2-90/phytools/man/read.newick.Rd | 8
19 files changed, 414 insertions(+), 352 deletions(-)
Title: A collection of methods for singular spectrum analysis
Diff between Rssa versions 0.9.9 dated 2013-03-12 and 0.9.10 dated 2013-06-29
Description: This package provides various Singular Spectrum Analysis
routines.
Author: Anton Korobeynikov
Maintainer: Anton Korobeynikov
DESCRIPTION | 10
MD5 | 55 ++--
NAMESPACE | 5
R/common.R | 37 ++
R/hankel.R | 176 ++++++-------
R/hbhankel.R | 106 ++++----
R/init.R | 2
R/plot.R | 480 ++++++++++++++++++++++++++++++-------
R/ssa.R | 9
R/toeplitz.R | 194 ++++++++------
R/wcor.R | 46 ++-
inst/extdata/2dssa.testdata.rda |only
inst/extdata/common.test.methods.R | 4
inst/extdata/gentest-2dssa.R |only
inst/extdata/gentest-toeplitz.R | 1
inst/extdata/toeplitz.testdata.rda |binary
inst/tests/test-2dssa.R |only
inst/tests/test-is.fft.plan.R |only
inst/tests/test-parest.R | 26 +-
inst/tests/test-serialize.R |only
inst/tests/test-wcor.R |only
man/hankel.Rd | 2
man/hbhankel.Rd | 2
man/plot.Rd | 41 +++
man/plot.reconstruct.Rd | 41 +++
man/toeplitz.Rd | 2
man/wcor.Rd | 32 +-
man/wnorm.Rd |only
src/config.h | 2
src/extmat.c | 10
src/hankel.c | 264 ++++++++++----------
src/toeplitz.c | 150 ++++-------
32 files changed, 1075 insertions(+), 622 deletions(-)
Title: Big Random Forests: Classification and Regression Forests for
Large Data Sets
Diff between bigrf versions 0.1-5 dated 2013-04-12 and 0.1-6 dated 2013-06-29
Description: This is an implementation of Leo Breiman's and Adele
Cutler's Random Forest algorithms for classification and
regression, with optimizations for performance and for handling
of data sets that are too large to be processed in memory.
Forests can be built in parallel at two levels. First, trees
can be grown in parallel on a single machine using foreach.
Second, multiple forests can be built in parallel on multiple
machines, then merged into one. For large data sets, disk-based
big.matrix's may be used for storing data and intermediate
computations, to prevent excessive virtual memory swapping by
the operating system. Currently, only classification forests
with a subset of the functionality in Breiman and Cutler's
original code are implemented. More functionality and
regression trees will be added in the future. See file
INSTALL-WINDOWS in the source package for Windows installation
instructions.
Author: Aloysius Lim, Leo Breiman, Adele Cutler
Maintainer: Aloysius Lim
DESCRIPTION | 8 ++---
MD5 | 10 +++---
NEWS | 8 +++++
man/bigrf-package.Rd | 4 +-
src/bigrfc.h | 17 +++++------
src/growtree.cpp | 77 +++++++++++++++++++++++++++++----------------------
6 files changed, 72 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-18 1.0-12
2013-04-17 1.0-11
2013-02-11 1.0-10
2012-10-30 1.0-9
2011-09-30 1.0-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-04 0.1.5
2013-02-07 0.1.4
2012-12-17 0.1.3
2012-04-04 0.1.2
2011-11-07 0.1.1
2011-08-03 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-01 1.4.1
2013-05-23 1.4
2013-04-03 1.3.2
2013-03-23 1.3.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-13 1.6
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Diff between Matching versions 4.8-2 dated 2013-04-27 and 4.8-3.1 dated 2013-06-28
Description: Provides functions for multivariate and propensity score
matching and for finding optimal balance based on a genetic
search algorithm. A variety of univariate and multivariate
metrics to determine if balance has been obtained are also
provided.
Author: Jasjeet Singh Sekhon
Maintainer: Jasjeet Singh Sekhon
ChangeLog | 10
DESCRIPTION | 12
MD5 | 34 -
R/GenMatching.R | 18
data/lalonde.rda |binary
man/GenMatch.Rd | 12
man/Match.Rd | 10
man/MatchBalance.Rd | 8
man/ks.boot.Rd | 9
man/qqstats.Rd | 7
tests/AbadieImbens.R | 2
tests/AbadieImbens.Rout.save | 28 -
tests/DehejiaWahba.R | 2
tests/DehejiaWahba.Rout.save | 28 -
tests/GenMatch.R | 5
tests/GenMatch.Rout.save | 1153 ++++++++++++++++++++++++++-----------------
tests/Matchby.R | 2
tests/Matchby.Rout.save | 28 -
18 files changed, 793 insertions(+), 575 deletions(-)
Title: Greg's Miscellaneous Functions
Diff between gregmisc versions 2.1.2 dated 2011-09-02 and 2.1.5 dated 2013-06-28
Description: Description: The former gregmisc bundle is a repository
for a variety of useful functions. The gregmisc package has
been split into a set of more focused packages: gdata, gmodels,
gplots, gtools. The purpose of this 'new' gregmisc is to
provide an easy way to access the original combined
functionality. To this end, it simply depends on all of the
new packages so that these will installed/loaded when this
package is installed/loaded.
Author: Gregory R. Warnes.
Maintainer: Gregory R. Warnes
gregmisc-2.1.2/gregmisc/R/First.R |only
gregmisc-2.1.2/gregmisc/man |only
gregmisc-2.1.5/gregmisc/.Rinstignore |only
gregmisc-2.1.5/gregmisc/ChangeLog |only
gregmisc-2.1.5/gregmisc/DESCRIPTION | 23 ++++++++++++-----------
gregmisc-2.1.5/gregmisc/MD5 | 12 ++++++++----
gregmisc-2.1.5/gregmisc/NAMESPACE |only
gregmisc-2.1.5/gregmisc/NEWS | 7 ++++++-
gregmisc-2.1.5/gregmisc/R/onAttach.R |only
gregmisc-2.1.5/gregmisc/inst/ChangeLog |only
gregmisc-2.1.5/gregmisc/inst/NEWS |only
gregmisc-2.1.5/gregmisc/inst/doc/gregmisc.pdf |only
12 files changed, 26 insertions(+), 16 deletions(-)
Title: Robust gridding and quantifying of pinned genetic screens
Diff between gitter versions 1.0 dated 2013-06-14 and 1.0.1 dated 2013-06-28
Description: gitter is a image analysis package for R. Its primary goal
is to allow users to robustly and quickly grid and quantify
biological images of pinned colonies. It includes several image
pre-processing techniques, such as autorotation of plates,
noise removal, contrast adjustment and image resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih
CHANGES |only
DESCRIPTION | 8 +-
MD5 | 19 +++---
R/Help.R | 90 ++++++++++++++++++------------
R/Main.R | 77 ++++++++++++++++---------
R/Peaks.R | 128 +++++++++++++++++++++++++++++++------------
build/BUILD.R | 6 +-
inst/extdata/sample.jpg |binary
inst/extdata/sample_dead.jpg |binary
man/gitter.Rd | 24 ++++----
man/gitter.batch.Rd | 7 --
11 files changed, 228 insertions(+), 131 deletions(-)
Title: Calculate agreement
Diff between agrmt versions 1.30 dated 2013-03-13 and 1.31 dated 2013-06-28
Description: This package calculates agreement or consensus in ordered
rating scales. It implements van der Eijk's (2001) measure of
agreement A, which can be used to describe agreement,
consensus, or polarization among respondents. It also
implements measures of consensus (dispersion) by Leik, Tatsle
and Wierman, Blair and Lacy, Kvalseth, and Berry and Mielke.
Furthermore, an implementation of Galtungs AJUS-system is
provided to classify distributions, as well as a function to
identify the position of multiple modes.
Author: Didier Ruedin
Maintainer: Didier Ruedin
DESCRIPTION | 19 ++++++++++---------
MD5 | 15 +++++++++++++--
R/BerryMielke.R |only
R/BlairLacy.R |only
R/Kvalseth.R |only
R/dsquared.R |only
R/lsquared.R |only
inst/doc/agrmt.R |only
man/BerryMielke.Rd |only
man/BlairLacy.Rd |only
man/Kvalseth.Rd |only
man/agrmt-package.Rd | 2 +-
man/dsquared.Rd |only
man/lsquared.Rd |only
14 files changed, 24 insertions(+), 12 deletions(-)
Title: Various R programming tools for plotting data
Diff between gplots versions 2.11.0.1 dated 2013-04-02 and 2.11.3 dated 2013-06-28
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes
ChangeLog | 950 +++++++++----------------------------------
DESCRIPTION | 22
MD5 | 36 -
NEWS | 73 ++-
R/barplot2.R | 108 +++-
R/heatmap.2.R | 10
R/plot.venn.R | 109 +++-
R/sinkplot.R | 26 -
R/venn.R | 23 -
inst/ChangeLog | 950 +++++++++----------------------------------
inst/NEWS | 73 ++-
inst/doc/BalloonPlot.pdf |binary
inst/doc/venn.R |only
inst/doc/venn.Rnw |only
inst/doc/venn.pdf |only
man/barplot2.Rd | 11
man/plotmeans.Rd | 6
man/sinkplot.Rd | 6
tests/heatmap2Test.R | 6
tests/heatmap2Test.Rout.save | 12
vignettes |only
21 files changed, 759 insertions(+), 1662 deletions(-)
Title: The Fisher-EM algorithm
Diff between FisherEM versions 1.3.2 dated 2013-02-21 and 1.4 dated 2013-06-28
Description: The FisherEM package provides an efficient algorithm for
the unsupervised classification of high-dimensional data. This
FisherEM algorithm models and clusters the data in a
discriminative and low-dimensional latent subspace. It also
provides a low-dimensional representation of the clustered
data. A sparse version of Fisher-EM algorithm is also provided.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Camille Brunet
FisherEM-1.3.2/FisherEM/R/FisherEM-internal.R |only
FisherEM-1.3.2/FisherEM/R/criteria.R |only
FisherEM-1.3.2/FisherEM/R/estep.R |only
FisherEM-1.3.2/FisherEM/R/evalEM.R |only
FisherEM-1.3.2/FisherEM/R/fem_main.R |only
FisherEM-1.3.2/FisherEM/R/fem_sparse.R |only
FisherEM-1.3.2/FisherEM/R/mstep.R |only
FisherEM-1.3.2/FisherEM/man/evalEM.Rd |only
FisherEM-1.4/FisherEM/DESCRIPTION | 12 +-
FisherEM-1.4/FisherEM/MD5 | 41 ++++-----
FisherEM-1.4/FisherEM/NAMESPACE | 5 -
FisherEM-1.4/FisherEM/R/fem.R | 109 ++++++++++--------------
FisherEM-1.4/FisherEM/R/fem.ari.R |only
FisherEM-1.4/FisherEM/R/fem.criteria.R |only
FisherEM-1.4/FisherEM/R/fem.estep.R |only
FisherEM-1.4/FisherEM/R/fem.main.R |only
FisherEM-1.4/FisherEM/R/fem.mstep.R |only
FisherEM-1.4/FisherEM/R/fem.sparse.R |only
FisherEM-1.4/FisherEM/R/fstep.GramSc.R | 30 +++---
FisherEM-1.4/FisherEM/R/fstep.fisher.R | 3
FisherEM-1.4/FisherEM/R/fstep.qiao.R | 3
FisherEM-1.4/FisherEM/R/fstep.sparse.R | 4
FisherEM-1.4/FisherEM/R/plot.fem.R | 77 +++++++++++++----
FisherEM-1.4/FisherEM/R/sfem.R |only
FisherEM-1.4/FisherEM/R/summary.fem.R |only
FisherEM-1.4/FisherEM/demo/FisherEM.r | 101 +++++++++++-----------
FisherEM-1.4/FisherEM/man/fem.Rd | 116 ++++++++++----------------
FisherEM-1.4/FisherEM/man/fem.ari.Rd |only
FisherEM-1.4/FisherEM/man/plot.fem.Rd | 29 +++---
FisherEM-1.4/FisherEM/man/sfem.Rd |only
FisherEM-1.4/FisherEM/man/summary.fem.Rd |only
31 files changed, 270 insertions(+), 260 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.5.1 dated 2013-06-17 and 0.8.5.2 dated 2013-06-28
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 12 +++---
MD5 | 17 ++++++---
R/impCalc.R | 87 +++++++++----------------------------------------
R/regVarImp.R | 4 +-
R/requiredPackages.R | 2 -
inst |only
man/fscaret-package.Rd | 6 +--
man/fscaret.Rd | 2 -
vignettes |only
9 files changed, 41 insertions(+), 89 deletions(-)
Title: Double log normal distribution functions
Diff between loglognorm versions 1.0.0 dated 2008-08-07 and 1.0.1 dated 2013-06-28
Description: r,d,p,q functions for the double log normal distribution
Author: Heike Trautmann, Detlef Steuer and Olaf Mersmann
Maintainer: Olaf Mersmann
DESCRIPTION | 19 ++++++++-----------
MD5 |only
2 files changed, 8 insertions(+), 11 deletions(-)
Title: Functions and data for "Data Mining with R"
Diff between DMwR versions 0.3.1 dated 2013-03-22 and 0.4.0 dated 2013-06-28
Description: This package includes functions and data accompanying the
book "Data Mining with R, learning with case studies" by Luis
Torgo, CRC Press 2010.
Author: Luis Torgo
Maintainer: Luis Torgo
DMwR-0.3.1/DMwR/inst/doc |only
DMwR-0.3.1/DMwR/man/standardWF.Rd |only
DMwR-0.3.1/DMwR/man/timeseriesWF.Rd |only
DMwR-0.4.0/DMwR/CHANGES | 7
DMwR-0.4.0/DMwR/DESCRIPTION | 8
DMwR-0.4.0/DMwR/MD5 | 33 +-
DMwR-0.4.0/DMwR/NAMESPACE | 4
DMwR-0.4.0/DMwR/R/DMwR-defunct.R | 43 +--
DMwR-0.4.0/DMwR/R/classes.R | 113 +++------
DMwR-0.4.0/DMwR/R/experiments.R | 318 ++++++++++----------------
DMwR-0.4.0/DMwR/inst/CITATION | 2
DMwR-0.4.0/DMwR/man/DMwR-defunct.Rd | 14 -
DMwR-0.4.0/DMwR/man/bootSettings-class.Rd | 6
DMwR-0.4.0/DMwR/man/cvSettings-class.Rd | 6
DMwR-0.4.0/DMwR/man/experimentalComparison.Rd | 6
DMwR-0.4.0/DMwR/man/growingWindowTest.Rd |only
DMwR-0.4.0/DMwR/man/hldSettings-class.Rd | 6
DMwR-0.4.0/DMwR/man/mcSettings-class.Rd | 6
DMwR-0.4.0/DMwR/man/monteCarlo.Rd | 66 +++--
DMwR-0.4.0/DMwR/man/slidingWindowTest.Rd |only
20 files changed, 269 insertions(+), 369 deletions(-)
Title: R version of GENetic Optimization Using Derivatives
Diff between rgenoud versions 5.7-9 dated 2013-05-07 and 5.7-12 dated 2013-06-28
Description: A genetic algorithm plus derivative optimizer
Author: Walter R. Mebane, Jr.
Maintainer: Jasjeet Singh Sekhon
rgenoud-5.7-12/rgenoud/ChangeLog | 28
rgenoud-5.7-12/rgenoud/DESCRIPTION | 11
rgenoud-5.7-12/rgenoud/MD5 | 23
rgenoud-5.7-12/rgenoud/R/rgenoud.R | 70 --
rgenoud-5.7-12/rgenoud/inst/doc/rgenoud.pdf |binary
rgenoud-5.7-12/rgenoud/man/genoud.Rd | 23
rgenoud-5.7-12/rgenoud/src/evaluate.cpp | 16
rgenoud-5.7-12/rgenoud/tests/tests.R | 20
rgenoud-5.7-12/rgenoud/tests/tests.Rout.save | 757 +--------------------------
rgenoud-5.7-12/rgenoud/vignettes |only
rgenoud-5.7-9/rgenoud/inst/doc/Figures |only
rgenoud-5.7-9/rgenoud/inst/doc/rgenoud.bib |only
12 files changed, 131 insertions(+), 817 deletions(-)
Title: 2d Rain Use Efficience model
Diff between r2dRue versions 1.0.3 dated 2011-04-26 and 1.0.4 dated 2013-06-28
Description: 2dRUE is a methodology to make a diagnostic of land
condition in a large territory during a given time period. The
following projects have funded this package: DeSurvey IP (EC
FP6 Integrated Project contract No. 003950), DesertWatch (ESA
DUE contract No. 18487/04/I-LG) and MesoTopos (Junta de
Andalucia PE ref. RNM-4023).
Author: Gabriel del Barrio, Juan Puigdefabregas, Maria E. Sanjuan &
Alberto Ruiz
Maintainer: Alberto Ruiz Moreno
r2dRue-1.0.3/r2dRue/.project |only
r2dRue-1.0.3/r2dRue/inst |only
r2dRue-1.0.4/r2dRue/DESCRIPTION | 16 +++++---
r2dRue-1.0.4/r2dRue/MD5 |only
r2dRue-1.0.4/r2dRue/R/etp.R | 57 ------------------------------
r2dRue-1.0.4/r2dRue/R/rgf.R | 10 ++++-
r2dRue-1.0.4/r2dRue/R/solarRadiation.R | 13 +++++-
r2dRue-1.0.4/r2dRue/man/r2dRplot.Rd | 3 +
r2dRue-1.0.4/r2dRue/man/r2dRue-package.Rd | 6 +--
r2dRue-1.0.4/r2dRue/man/rasterStack.Rd | 3 +
10 files changed, 36 insertions(+), 72 deletions(-)
Title: GUI for biodiversity, suitability and community ecology analysis
Diff between BiodiversityR versions 2.3 dated 2013-04-11 and 2.3-6 dated 2013-06-28
Description: This package provides a GUI (Graphical User Interface, via
the R-Commander) and some utility functions (often based on the
vegan package) for statistical analysis of biodiversity and
ecological communities, including species accumulation curves,
diversity indices, Renyi profiles, GLMs for analysis of species
abundance and presence-absence, distance matrices, Mantel
tests, and cluster, constrained and unconstrained ordination
analysis. A book on biodiversity and community ecology analysis
is available for free download from the website. In 2012,
methods for (ensemble) suitability modelling and mapping were
expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt
BiodiversityR-2.3-6/BiodiversityR/DESCRIPTION | 8
BiodiversityR-2.3-6/BiodiversityR/MD5 | 53
BiodiversityR-2.3-6/BiodiversityR/NAMESPACE | 2
BiodiversityR-2.3-6/BiodiversityR/R/check.datasets.R | 39
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.batch.R | 271 +
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.drop1.R | 465 +-
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.formulae.R | 2
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.raster.R | 1789 +++++++----
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.strategy.R |only
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.test.R | 1308 +++++---
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.test.gbm.R | 187 -
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.test.nnet.R | 200 -
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.test.splits.R | 506 ++-
BiodiversityR-2.3-6/BiodiversityR/R/ensemble.weights.R | 21
BiodiversityR-2.3-6/BiodiversityR/R/evaluation.strip.data.R | 5
BiodiversityR-2.3-6/BiodiversityR/R/evaluation.strip.plot.R | 21
BiodiversityR-2.3-6/BiodiversityR/R/ordicoeno.R | 40
BiodiversityR-2.3-6/BiodiversityR/R/ordisymbol.R | 10
BiodiversityR-2.3-6/BiodiversityR/inst/etc/BiodiversityGUI.R | 22
BiodiversityR-2.3-6/BiodiversityR/man/add.spec.scores.Rd | 3
BiodiversityR-2.3-6/BiodiversityR/man/caprescale.Rd | 3
BiodiversityR-2.3-6/BiodiversityR/man/ensemble.Rd | 331 +-
BiodiversityR-2.3-6/BiodiversityR/man/ensemble.raster.Rd | 239 +
BiodiversityR-2.3-6/BiodiversityR/man/evaluation.strip.Rd | 13
BiodiversityR-2.3-6/BiodiversityR/man/ordicoeno.Rd | 7
BiodiversityR-2.3-6/BiodiversityR/man/ordisymbol.Rd | 20
BiodiversityR-2.3-6/BiodiversityR/man/removeNAcomm.Rd | 23
BiodiversityR-2.3/BiodiversityR/R/evaluation.strip.newdata.R |only
BiodiversityR-2.3/BiodiversityR/R/evaluation.strip.plot2.R |only
29 files changed, 3844 insertions(+), 1744 deletions(-)
Title: Conditional Density Estimation Network Construction and
Evaluation
Diff between CaDENCE versions 1.2.0 dated 2013-06-27 and 1.2.1 dated 2013-06-28
Description: A probabilistic extension of the standard multi-layer
perceptron neural network
Author: Alex J. Cannon
Maintainer: Alex J. Cannon
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/cadence.evaluate.R | 1 +
R/cadence.fit.R | 14 +++++++-------
man/cadence.fit.Rd | 2 +-
5 files changed, 16 insertions(+), 15 deletions(-)
More information about tibbrConnector at CRAN
Permanent link
Title: Spatially explicit capture-recapture
Diff between secr versions 2.6.0 dated 2013-06-12 and 2.6.1 dated 2013-06-27
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive
detectors, such as traps, or by searching polygons or
transects. Models incorporating distance-dependent detection
are fitted by maximizing the likelihood. Tools are included for
data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 8 +-
MD5 | 61 ++++++++--------
NAMESPACE | 10 ++
NEWS | 15 ++++
R/DENSITY.R | 12 ---
R/autoini.R | 3
R/derivedMS.R | 9 +-
R/esa.R | 4 -
R/make.capthist.R | 1
R/methods.R | 10 ++
R/regionN.R | 3
R/secr.fit.R | 10 +-
R/secrloglik.R | 10 +-
R/sim.capthist.R | 169 +++++++++++++++++++++++++++++++----------------
R/telemetry.R | 81 ++++++++++++++++++++++
R/utility.R | 23 ++++++
inst/doc/secr-manual.pdf |binary
man/DENSITY.Rd | 14 +--
man/addTelemetry.Rd | 5 -
man/make.capthist.Rd | 8 +-
man/make.traps.Rd | 6 -
man/mask.check.Rd | 6 -
man/model.average.Rd | 4 -
man/plot.capthist.Rd | 8 +-
man/read.telemetry.Rd |only
man/read.traps.Rd | 8 +-
man/secr-package.Rd | 4 -
man/secrdemo.Rd | 10 +-
man/suggest.buffer.Rd | 4 -
man/transformations.Rd | 3
man/traps.Rd | 6 -
src/secr.h | 20 +++++
32 files changed, 373 insertions(+), 162 deletions(-)
Title: MatchIt: Nonparametric Preprocessing for Parametric Casual
Inference
Diff between MatchIt versions 2.4-20 dated 2011-10-24 and 2.4-21 dated 2013-06-27
Description: MatchIt selects matched samples of the the original
treated and control groups with similar covariate distributions
-- can be used to match exactly on covariates, to match on
propensity scores, or perform a variety of other matching
procedures.
Author: Daniel Ho
Maintainer: Kosuke Imai
MatchIt-2.4-20/MatchIt/R/load.first.R |only
MatchIt-2.4-20/MatchIt/inst/doc |only
MatchIt-2.4-21/MatchIt/DESCRIPTION | 38 ++++++++-------
MatchIt-2.4-21/MatchIt/MD5 | 71 ++++++++++++-----------------
MatchIt-2.4-21/MatchIt/R/discard.R | 4 -
MatchIt-2.4-21/MatchIt/R/matchit2cem.R | 4 -
MatchIt-2.4-21/MatchIt/R/matchit2full.R | 4 -
MatchIt-2.4-21/MatchIt/R/matchit2genetic.R | 4 -
MatchIt-2.4-21/MatchIt/R/matchit2optimal.R | 4 -
MatchIt-2.4-21/MatchIt/data/lalonde.tab.gz |binary
MatchIt-2.4-21/MatchIt/vignettes |only
11 files changed, 60 insertions(+), 69 deletions(-)
Title: Multitaper spectral analysis tools
Diff between multitaper versions 1.0-5 dated 2013-05-14 and 1.0-6 dated 2013-06-27
Description: Generates Discrete Prolate Spheroidal Sequences, provides
functions and utilities for multitaper spectral analysis and
related problems.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 11 +++++------
MD5 | 8 ++++++--
inst |only
man/demod.dpss.Rd | 5 +++--
4 files changed, 14 insertions(+), 10 deletions(-)
More information about knitrBootstrap at CRAN
Permanent link
Title: PCIC implementation of Climdex routines
Diff between climdex.pcic versions 0.6-2 dated 2013-02-07 and 0.7-2 dated 2013-06-27
Description: The pcic_climdex package provides PCIC's implementation of
Climdex routines for computation of climate indices.
Author: David Bronaugh
Maintainer: David Bronaugh
climdex.pcic-0.6-2/climdex.pcic/comparison |only
climdex.pcic-0.7-2/climdex.pcic/CHANGELOG | 6
climdex.pcic-0.7-2/climdex.pcic/DESCRIPTION | 12
climdex.pcic-0.7-2/climdex.pcic/MD5 | 19
climdex.pcic-0.7-2/climdex.pcic/R/climdex.r | 19
climdex.pcic-0.7-2/climdex.pcic/man/climdexInput.raw.Rd | 15
climdex.pcic-0.7-2/climdex.pcic/man/growing.season.length.Rd | 7
climdex.pcic-0.7-2/climdex.pcic/man/percent.days.op.threshold.Rd | 9
climdex.pcic-0.7-2/climdex.pcic/man/threshold.exceedance.duration.index.Rd | 4
climdex.pcic-0.7-2/climdex.pcic/src/Makevars |only
climdex.pcic-0.7-2/climdex.pcic/src/Makevars.win |only
climdex.pcic-0.7-2/climdex.pcic/src/zhang_running_quantile.cc | 406 +++++++---
12 files changed, 367 insertions(+), 130 deletions(-)
Title: Conditional Density Estimation Network Construction and
Evaluation
Diff between CaDENCE versions 1.1.1 dated 2013-02-09 and 1.2.0 dated 2013-06-27
Description: A probabilistic extension of the standard multi-layer
perceptron neural network
Author: Alex J. Cannon
Maintainer: Alex J. Cannon
DESCRIPTION | 9 +
MD5 | 14 +--
R/cadence.evaluate.R | 13 +-
R/cadence.fit.R | 223 +++++++++++++++++++++++++++++--------------------
man/CaDENCE-package.Rd | 7 +
man/cadence.fit.Rd | 66 +++++++++++---
man/cadence.predict.Rd | 3
man/gam.style.Rd | 9 +
8 files changed, 220 insertions(+), 124 deletions(-)
Title: Functions for wind resource assessment
Diff between bReeze versions 0.2-1 dated 2013-02-28 and 0.2-2 dated 2013-06-27
Description: A collection of functions to analyse, visualize and
interpret wind data and to calculate the potential energy
production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul
bReeze-0.2-1/bReeze/inst/NEWS |only
bReeze-0.2-1/bReeze/man/bReezeNews.Rd |only
bReeze-0.2-2/bReeze/DESCRIPTION | 8
bReeze-0.2-2/bReeze/MD5 | 113 ++---
bReeze-0.2-2/bReeze/NAMESPACE | 31 +
bReeze-0.2-2/bReeze/R/availability.R | 85 +++-
bReeze-0.2-2/bReeze/R/clean.R | 3
bReeze-0.2-2/bReeze/R/formatTS.R | 2
bReeze-0.2-2/bReeze/R/frequency.R | 7
bReeze-0.2-2/bReeze/R/monthStats.R | 3
bReeze-0.2-2/bReeze/R/plotAvailability.R | 3
bReeze-0.2-2/bReeze/R/plotDay.R | 3
bReeze-0.2-2/bReeze/R/plotMonthStats.R | 3
bReeze-0.2-2/bReeze/R/plotPC.R | 211 +++++++---
bReeze-0.2-2/bReeze/R/plotPolar.R | 10
bReeze-0.2-2/bReeze/R/plotTimeSeries.R | 4
bReeze-0.2-2/bReeze/R/plotTurbIEC.R | 3
bReeze-0.2-2/bReeze/R/printObject.R | 7
bReeze-0.2-2/bReeze/R/profile.R | 6
bReeze-0.2-2/bReeze/R/turbulence.R | 6
bReeze-0.2-2/bReeze/R/weibull.R | 7
bReeze-0.2-2/bReeze/R/wrapper.R |only
bReeze-0.2-2/bReeze/R/zzz.R | 125 +++++
bReeze-0.2-2/bReeze/inst/CHANGES |only
bReeze-0.2-2/bReeze/inst/powercurves/EWT_DW90_2MW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/EWT_DW96_2MW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Enercon_E40_500kW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Enercon_E66_1870kW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Enercon_E66_2000kW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Siemens_SWT-3.6MW-120m.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Vensys_100_2.5MW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Vensys_109_2.5MW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Vensys_112_2.5MW.pow |only
bReeze-0.2-2/bReeze/inst/powercurves/Vensys_82_1.5MW.pow |only
bReeze-0.2-2/bReeze/man/availability.Rd | 19
bReeze-0.2-2/bReeze/man/availabilityInt.Rd | 5
bReeze-0.2-2/bReeze/man/bReeze-package.Rd | 6
bReeze-0.2-2/bReeze/man/changes.Rd |only
bReeze-0.2-2/bReeze/man/clean.Rd | 7
bReeze-0.2-2/bReeze/man/createMast.Rd | 6
bReeze-0.2-2/bReeze/man/createPC.Rd | 8
bReeze-0.2-2/bReeze/man/createSet.Rd | 3
bReeze-0.2-2/bReeze/man/energy.Rd | 9
bReeze-0.2-2/bReeze/man/formatTS.Rd | 6
bReeze-0.2-2/bReeze/man/frequency.Rd | 8
bReeze-0.2-2/bReeze/man/monthStats.Rd | 9
bReeze-0.2-2/bReeze/man/plotAep.Rd | 6
bReeze-0.2-2/bReeze/man/plotAvailability.Rd | 10
bReeze-0.2-2/bReeze/man/plotDay.Rd | 9
bReeze-0.2-2/bReeze/man/plotEnergy.Rd | 6
bReeze-0.2-2/bReeze/man/plotFrequency.Rd | 6
bReeze-0.2-2/bReeze/man/plotMonthStats.Rd | 9
bReeze-0.2-2/bReeze/man/plotPC.Rd | 21
bReeze-0.2-2/bReeze/man/plotPolar.Rd | 11
bReeze-0.2-2/bReeze/man/plotProfile.Rd | 6
bReeze-0.2-2/bReeze/man/plotTimeSeries.Rd | 6
bReeze-0.2-2/bReeze/man/plotTurbIEC.Rd | 9
bReeze-0.2-2/bReeze/man/plotTurbulence.Rd | 6
bReeze-0.2-2/bReeze/man/plotWbDir.Rd | 6
bReeze-0.2-2/bReeze/man/plotWeibull.Rd | 6
bReeze-0.2-2/bReeze/man/printObject.Rd | 6
bReeze-0.2-2/bReeze/man/profile.Rd | 15
bReeze-0.2-2/bReeze/man/readPC.Rd | 41 +
bReeze-0.2-2/bReeze/man/turbulence.Rd | 10
bReeze-0.2-2/bReeze/man/weibull.Rd | 14
65 files changed, 719 insertions(+), 210 deletions(-)
Title: parallel implementation of the "segment" function of package
"DNAcopy"
Diff between ParDNAcopy versions 1.1 dated 2013-06-23 and 1.3 dated 2013-06-27
Description: parallelized version of the "segment" function from
Bioconductor package "DNAcopy", utilizing multi-core
computation on host CPU
Author: Alex krasnitz, Guoli Sun
Maintainer: Guoli Sun
DESCRIPTION | 6 +++---
MD5 | 4 ++--
man/parSegment.Rd | 2 --
3 files changed, 5 insertions(+), 7 deletions(-)
Title: cold: a package for Count Longitudinal Data
Diff between cold versions 1.0 dated 2013-06-20 and 1.0-1 dated 2013-06-27
Description: cold performs regression analysis for longitudinal count
data using a self-decomposable probability distribution, a
random intercept term is also allowed. Estimation is via
maximization of the exact likelihood of a suitably defined
model.
Author: M. Helena Gonçalves and M. Salomé Cabral, apart from a set of
Fortran-77 subroutines written by R. Piessens and E. de
Doncker, belonging to the suite "Quadpack"
Maintainer: M. Helena Gonçalves
DESCRIPTION | 8 ++++----
MD5 | 19 ++++++++++---------
R/coldControl.R | 2 +-
history.txt |only
man/anova-methods.Rd | 2 +-
man/cold.Rd | 4 ++--
man/coldControl.Rd | 2 +-
man/coldIntegrate.Rd | 2 +-
man/fitted-methods.Rd | 2 +-
man/resid-methods.Rd | 2 +-
man/seizure.rd | 11 ++++++-----
11 files changed, 28 insertions(+), 26 deletions(-)
Title: Grain-size Statistics and Description of Sediment
Diff between G2Sd versions 1.2 dated 2012-01-10 and 2.0 dated 2013-06-27
Description: G2Sd package gives full descriptive statistics and a
physical description of sediment obtained with metric or phi
sieves according to the grain size distribution.
Author: Regis K. Gallon (MNHN), Jerome Fournier (CNRS|MNHN)
Maintainer: Regis K. Gallon
G2Sd-1.2/G2Sd/man/G2Sd-internal.Rd |only
G2Sd-1.2/G2Sd/man/plotgran.Rd |only
G2Sd-2.0/G2Sd/DESCRIPTION | 19
G2Sd-2.0/G2Sd/MD5 | 30 -
G2Sd-2.0/G2Sd/NAMESPACE | 8
G2Sd-2.0/G2Sd/NEWS |only
G2Sd-2.0/G2Sd/R/G2Sd-internal.R | 985 +++++++++++++++++++------------------
G2Sd-2.0/G2Sd/R/grandistrib.R |only
G2Sd-2.0/G2Sd/R/granplot.R | 77 +-
G2Sd-2.0/G2Sd/R/granstat.R | 11
G2Sd-2.0/G2Sd/data/coord_gran.rda |only
G2Sd-2.0/G2Sd/data/granulo.rda |binary
G2Sd-2.0/G2Sd/inst/CITATION | 39 -
G2Sd-2.0/G2Sd/inst/INDEX | 14
G2Sd-2.0/G2Sd/man/G2Sd-package.Rd | 21
G2Sd-2.0/G2Sd/man/coord_gran.Rd |only
G2Sd-2.0/G2Sd/man/grandistrib.Rd |only
G2Sd-2.0/G2Sd/man/granplot.Rd |only
G2Sd-2.0/G2Sd/man/granstat.Rd | 30 -
G2Sd-2.0/G2Sd/man/granulo.Rd | 25
20 files changed, 652 insertions(+), 607 deletions(-)
Title: Aggregation Operators and Preordered Sets
Diff between agop versions 0.1-1 dated 2013-06-27 and 0.1-3 dated 2013-06-27
Description: Tools supporting multi-criteria decision making, including
variable number of criteria, by means of aggregation operators
and preordered sets. Possible applications include, but are not
limited to, scientometrics and bibliometrics.
Author: Marek Gagolewski [aut, cre], Anna Cena [ctb]
Maintainer: Marek Gagolewski
DESCRIPTION | 8 +--
MD5 | 16 +++---
NEWS | 6 ++
inst/doc/agop-Tutorial.pdf |binary
src/agop.h | 26 +++++++----
src/agops_classical.cpp | 28 ++++++------
src/agops_impact.cpp | 68 ++++++++++++++---------------
src/preorders.cpp | 18 +++----
src/prepare_arg.cpp | 104 ++++++++++++++++++++++-----------------------
9 files changed, 145 insertions(+), 129 deletions(-)
Title: An R package to interact with the Project Vote Smart API for
scientific research
Diff between pvsR versions 0.1 dated 2013-05-29 and 0.1.1 dated 2013-06-27
Description: The pvsR package facilitates data retrieval from Project
Vote Smart's rich online data base on US politics via the
Project Vote Smart application programming interface (PVS API).
The functions in this package cover most PVS API classes and
methods and return the requested data in a data frame.
Author: Ulrich Matter
Maintainer: Ulrich Matter
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NAMESPACE | 4 ++--
NEWS | 6 ++++++
R/pvsRequest.R | 2 +-
5 files changed, 17 insertions(+), 11 deletions(-)
Title: Measuring Association and Testing Independence Efficiently
Diff between matie versions 1.0 dated 2013-01-20 and 1.1 dated 2013-06-27
Description: Uses a ratio of weighted distributions to estimate
association between variables in a data set.
Author: Ben Murrell, Dan Murrell & Hugh Murrell.
Maintainer: Hugh Murrell
DESCRIPTION | 12 ++++++------
MD5 | 46 +++++++++++++++++++++++-----------------------
NAMESPACE | 9 +++++++++
R/agram.R | 35 +++++++++++++++++++----------------
R/fdg.R | 18 +++++++++++-------
R/ma.R | 20 +++++++++++++++-----
R/rwt.R | 6 ++++--
R/tap.R | 2 +-
man/agram.Rd | 21 ++++++++++-----------
man/baseballData.Rd | 2 +-
man/fbvs.Rd | 5 +++--
man/fdg.Rd | 11 +++++------
man/ma.Rd | 28 ++++++++++++++++++----------
man/ma.nl.Rd | 5 ++---
man/ma.test.Rd | 20 ++++++++++----------
man/matie-package.Rd | 29 ++++++++++++++++++++++++-----
man/pd.Rd | 4 ++--
man/rwt.Rd | 2 +-
man/sbd.Rd | 4 ++--
man/shpd.Rd | 4 ++--
man/spa.Rd | 49 +++++++++++++++++++++++++++++++------------------
man/std.Rd | 4 ++--
man/tap.Rd | 4 ++--
src/maxlike.c | 9 +++++----
24 files changed, 208 insertions(+), 141 deletions(-)
Title: Visualising bipartite networks and calculating some (ecological)
indices.
Diff between bipartite versions 2.00 dated 2013-03-17 and 2.01 dated 2013-06-27
Description: Bipartite provides functions to visualise webs and
calculate a series of indices commonly used to describe pattern
in ecological webs. It focuses on webs consisting of only two
trophic levels, e.g. pollination webs or predator-prey-webs.
Visualisation is important to get an idea of what we are
actually looking at, while the indices summarise different
aspects of the webs topology.
Author: Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with
additional code from Mariano Devoto, Jose Iriondo, Rouven
Strauss and Diego Vazquez, also based on C-code developed by
Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel
Rodriguez-Girones.
Maintainer: Carsten F. Dormann
bipartite-2.00/bipartite/R/nested.R |only
bipartite-2.01/bipartite/DESCRIPTION | 9
bipartite-2.01/bipartite/MD5 | 72 -
bipartite-2.01/bipartite/NAMESPACE | 2
bipartite-2.01/bipartite/R/C.score.R | 8
bipartite-2.01/bipartite/R/ND.r | 8
bipartite-2.01/bipartite/R/computeModules.R | 6
bipartite-2.01/bipartite/R/degreedistr.R | 47
bipartite-2.01/bipartite/R/nested.r |only
bipartite-2.01/bipartite/R/nestedrank.R |only
bipartite-2.01/bipartite/R/plotweb.R | 820 +++++++++++------
bipartite-2.01/bipartite/R/second.extinct.R | 33
bipartite-2.01/bipartite/R/slope.bipartite.R | 1
bipartite-2.01/bipartite/R/specieslevel.R | 32
bipartite-2.01/bipartite/R/web2edges.R | 2
bipartite-2.01/bipartite/data/junker2013.rda |only
bipartite-2.01/bipartite/inst/doc/Dormann2008Rnews.pdf |binary
bipartite-2.01/bipartite/man/C.score.Rd | 2
bipartite-2.01/bipartite/man/ND.rd | 4
bipartite-2.01/bipartite/man/bipartite-package.Rd | 23
bipartite-2.01/bipartite/man/closeness_w.Rd | 2
bipartite-2.01/bipartite/man/clustering_tm.Rd | 7
bipartite-2.01/bipartite/man/degreedistr.Rd | 6
bipartite-2.01/bipartite/man/extinction.Rd | 3
bipartite-2.01/bipartite/man/fd.Rd | 2
bipartite-2.01/bipartite/man/grouplevel.Rd | 8
bipartite-2.01/bipartite/man/junker2013.Rd |only
bipartite-2.01/bipartite/man/nested.Rd | 4
bipartite-2.01/bipartite/man/nestedrank.Rd |only
bipartite-2.01/bipartite/man/networklevel.Rd | 10
bipartite-2.01/bipartite/man/plotweb.Rd | 20
bipartite-2.01/bipartite/man/second.extinct.Rd | 8
bipartite-2.01/bipartite/man/slope.bipartite.Rd | 6
bipartite-2.01/bipartite/man/specieslevel.Rd | 36
bipartite-2.01/bipartite/man/versionlog.Rd | 2
bipartite-2.01/bipartite/man/visweb.Rd | 3
bipartite-2.01/bipartite/man/webs2array.Rd | 3
bipartite-2.01/bipartite/man/wine.rd | 6
bipartite-2.01/bipartite/src/dendro.h | 6
bipartite-2.01/bipartite/src/identifyModules.cc | 10
40 files changed, 813 insertions(+), 398 deletions(-)
Title: Interfaces to various state-of-art SVD and eigensolvers
Diff between svd versions 0.3.1-2 dated 2013-04-14 and 0.3.2 dated 2013-06-27
Description: This package provides various R bindings to various SVD
and eigensolvers (PROPACK, nuTRLan)
Author: Anton Korobeynikov
Maintainer: Anton Korobeynikov
DESCRIPTION | 6
MD5 | 16 -
NAMESPACE | 1
R/extmat.R | 6
man/extmat.Rd | 14 -
src/extmat.c | 40 +++
src/trlan/trlan.c | 566 ++++++++++++++++++++++++++++++++++------------------
src/trlan/trlaux.c | 192 ++++++++++++-----
src/trlan/trlcore.c | 16 +
9 files changed, 595 insertions(+), 262 deletions(-)
Title: (Standardised) Major Axis Estimation and Testing Routines
Diff between smatr versions 3.3 dated 2013-04-05 and 3.4 dated 2013-06-27
Description: This package provides methods of fitting bivariate lines
in allometry using the major axis (MA) or standardised major
axis (SMA), and for making inferences about such lines. The
available methods of inference include confidence intervals and
one-sample tests for slope and elevation, testing for a common
slope or elevation amongst several allometric lines,
constructing a confidence interval for a common slope or
elevation, and testing for no shift along a common axis,
amongst several samples.
Author: David Warton
Maintainer: Remko Duursma
DESCRIPTION | 8 ++---
MD5 | 22 +++++++------
NAMESPACE | 14 +++++---
R/alpha.fun.R | 32 ++++++++++----------
R/fitted.sma.R | 83 ++++++++++++++++++++++++++++++++++++++++------------
R/logLik_sma.R |only
R/nicePlot.R | 12 ++++++-
R/predict.sma.R |only
R/sma.R | 21 ++++++-------
data/leaflife.RData |binary
data/leafmeas.RData |binary
man/fitted.sma.Rd | 14 +++++---
man/sma.Rd | 5 +--
13 files changed, 137 insertions(+), 74 deletions(-)
Title: Implementation of POSIXct work-alike for 365 and 360 day
calendars.
Diff between PCICt versions 0.5-3 dated 2013-02-07 and 0.5-4 dated 2013-06-27
Description: This package implements a work-alike to R's POSIXct class
which implements 360- and 365-day calendars in addition to the
gregorian calendar.
Author: David Bronaugh
Maintainer: David Bronaugh
CHANGELOG | 4 ++++
DESCRIPTION | 13 +++++++------
MD5 | 6 +++---
tests/bootstrap.R | 12 +++++++-----
4 files changed, 21 insertions(+), 14 deletions(-)
Title: Markdown rendering for R
Diff between markdown versions 0.6 dated 2013-06-18 and 0.6.1 dated 2013-06-27
Description: Markdown is a plain-text formatting syntax that can be
converted to XHTML or other formats. This package provides R
bindings to the Sundown markdown rendering library.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie
DESCRIPTION | 10
MD5 | 22
NEWS | 2
R/renderMarkdown.R | 6
R/rpubsUpload.R | 6
inst/COPYING | 916 +++++++++++++----------------------------
inst/doc/markdown-examples.R | 16
inst/include/markdown_rstubs.c | 6
inst/include/markdown_rstubs.h | 6
src/Rinit.c | 6
src/Rmarkdown.c | 6
src/Rmarkdown.h | 6
12 files changed, 342 insertions(+), 666 deletions(-)
Title: Sequential Parametric and Nonparametric Change Detection
Diff between cpm versions 1.0 dated 2012-02-06 and 1.1 dated 2013-06-27
Description: Sequential and batch change detection for univariate data
streams, using the change point model framework. Functions are
provided to allow the parametric monitoring of sequences of
Gaussian and Bernoulli random variables, along with more
general nonparametric functions for monitoring sequences which
have an unspecified or unknown distribution.
Author: Gordon J. Ross
Maintainer: Gordon J. Ross
cpm-1.0/cpm/inst/CITATION |only
cpm-1.0/cpm/inst/doc/chap1_changemean.pdf |only
cpm-1.0/cpm/inst/doc/chap1_changevar.pdf |only
cpm-1.0/cpm/inst/doc/jabref.bib |only
cpm-1.0/cpm/inst/doc/multiplechanges.pdf |only
cpm-1.0/cpm/inst/doc/realdata1.pdf |only
cpm-1.0/cpm/inst/doc/realdata2.pdf |only
cpm-1.0/cpm/inst/doc/realdata3.pdf |only
cpm-1.0/cpm/inst/doc/singlechange1.pdf |only
cpm-1.0/cpm/inst/doc/singlechange2.pdf |only
cpm-1.0/cpm/src/hyper.c |only
cpm-1.0/cpm/src/hyper.h |only
cpm-1.0/cpm/src/hypercpp.cpp |only
cpm-1.1/cpm/DESCRIPTION | 24
cpm-1.1/cpm/MD5 | 97 +-
cpm-1.1/cpm/NAMESPACE | 2
cpm-1.1/cpm/R/ChangePointModeljoint.R |only
cpm-1.1/cpm/R/detectChangePoint.R | 3
cpm-1.1/cpm/R/detectChangePointBatch.R |only
cpm-1.1/cpm/R/getBatchThreshold.R |only
cpm-1.1/cpm/R/loadThresholds.R | 3
cpm-1.1/cpm/R/sysdata.rda |binary
cpm-1.1/cpm/R/verifyArguments.R | 10
cpm-1.1/cpm/inst/doc/cpm.R |only
cpm-1.1/cpm/inst/doc/cpm.Rnw | 564 ----------------
cpm-1.1/cpm/inst/doc/cpm.pdf |binary
cpm-1.1/cpm/man/cpmPackage.Rd | 13
cpm-1.1/cpm/man/detectChangePoint.Rd | 34
cpm-1.1/cpm/man/detectChangePointBatch.Rd |only
cpm-1.1/cpm/man/getBatchThreshold.Rd |only
cpm-1.1/cpm/man/makeChangePointModel.Rd | 11
cpm-1.1/cpm/man/processStream.Rd | 14
cpm-1.1/cpm/src/ChangePointModel.cpp | 7
cpm-1.1/cpm/src/ChangePointModel.h | 6
cpm-1.1/cpm/src/ChangePointModelCVM.cpp | 2
cpm-1.1/cpm/src/ChangePointModelCVM.h | 2
cpm-1.1/cpm/src/ChangePointModelExponential.cpp |only
cpm-1.1/cpm/src/ChangePointModelExponential.h |only
cpm-1.1/cpm/src/ChangePointModelExponentialAdjusted.cpp |only
cpm-1.1/cpm/src/ChangePointModelExponentialAdjusted.h |only
cpm-1.1/cpm/src/ChangePointModelF.h | 2
cpm-1.1/cpm/src/ChangePointModelFET.cpp | 5
cpm-1.1/cpm/src/ChangePointModelFET.h | 2
cpm-1.1/cpm/src/ChangePointModelJointNormal.cpp | 3
cpm-1.1/cpm/src/ChangePointModelJointNormal.h | 4
cpm-1.1/cpm/src/ChangePointModelJointNormalAdjusted.cpp |only
cpm-1.1/cpm/src/ChangePointModelJointNormalAdjusted.h |only
cpm-1.1/cpm/src/ChangePointModelJointNormalHawkins.cpp |only
cpm-1.1/cpm/src/ChangePointModelJointNormalHawkins.h |only
cpm-1.1/cpm/src/ChangePointModelKS.cpp | 2
cpm-1.1/cpm/src/ChangePointModelKS.h | 2
cpm-1.1/cpm/src/ChangePointModelLepage.h | 2
cpm-1.1/cpm/src/ChangePointModelMW.cpp | 2
cpm-1.1/cpm/src/ChangePointModelMW.h | 2
cpm-1.1/cpm/src/ChangePointModelMood.cpp | 2
cpm-1.1/cpm/src/ChangePointModelMood.h | 2
cpm-1.1/cpm/src/ChangePointModelPoisson.cpp |only
cpm-1.1/cpm/src/ChangePointModelPoisson.h |only
cpm-1.1/cpm/src/ChangePointModelRInterface.cpp | 84 ++
cpm-1.1/cpm/src/ChangePointModelT.cpp | 10
cpm-1.1/cpm/src/ChangePointModelT.h | 2
cpm-1.1/cpm/src/ChangePointModelWithOrders.h | 2
cpm-1.1/cpm/src/ChangePointModelWithRanks.h | 2
cpm-1.1/cpm/src/cpmMLE.c | 54 +
64 files changed, 299 insertions(+), 677 deletions(-)
Title: Average bioequivalence and bioavailability data analysis tool
Diff between bear versions 2.5.5 dated 2013-05-07 and 2.5.6 dated 2013-06-27
Description: An average bioequivalence (ABE) and bioavailability data
analysis tool including sample size estimation,
noncompartmental analysis (NCA), ANOVA (lm) for a standard
RT/TR 2x2x2 crossover design or a parallel study. And linear
mixed effect model (lme of nlme) for a 2-treatment, 2-sequence
with 2 periods or more (i.e. 2x2x3/2x2x4) replicate crossover
design.
Author: Hsin-ya Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
DESCRIPTION | 8 +-
MD5 | 82 ++++++++++++-----------
NEWS | 31 ++++++++
R/ARS.r | 143 ++++++++++++++++++++++++++++++----------
R/NCA.BANOVAmenu.r | 4 -
R/NCA.r | 55 ++++++++++++++-
R/NCAoutput.r | 84 ++++++++++++++++--------
R/NCAplot.r | 2
R/NCAreglplot.r | 136 ++++++++++++++++++++++----------------
R/NCAsave.r | 4 -
R/NCAselect.r | 42 ++++++------
R/NCAselectsave.r | 4 -
R/OutputFilez.r | 4 -
R/Singlego.r | 2
R/TTT.r | 154 +++++++++++++++++++++++++++++++++++---------
R/TTTAIC.r | 141 ++++++++++++++++++++++++++++++----------
R/TTTARS.r | 138 ++++++++++++++++++++++++++++++---------
R/about.bear.r | 2
R/aic.r | 141 ++++++++++++++++++++++++++++++----------
R/bye.r | 4 -
R/description_AIC.r | 10 +-
R/description_ARS.r | 2
R/description_BANOVA.r | 2
R/description_NCA.r | 20 ++---
R/description_NCAinput.r | 6 -
R/description_ParaMIX.r | 2
R/description_TOST_lnCmax.r | 2
R/description_TTT.r | 10 +-
R/description_TTTAIC.r | 2
R/description_TTTARS.r | 2
R/description_drugcode.r | 23 +++---
R/description_import.r | 4 -
R/description_load.r | 4 -
R/description_plot.r | 4 -
R/description_pointselect.r | 24 ++++--
R/description_version.r | 4 -
R/go.r | 68 +------------------
R/go2menu.r |only
R/logo_plot_desc.r | 6 -
R/sizemenu.r | 2
R/test.nca_stat.r | 2
R/zzz.R | 2
man/go2menu.rd |only
43 files changed, 927 insertions(+), 455 deletions(-)
Title: Adaptive differential evolution, b6e6rl variant
Diff between b6e6rl versions 1.0 dated 2013-06-20 and 1.1 dated 2013-06-27
Description: This package contains b6e6rl algorithm, adaptive
differential evolution for global optimization.
Author: Marek Spruzina
Maintainer: Marek Spruzina
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/CRexp_set.R | 30 +++++++++++++++---------------
R/b6e6rl.R | 3 +--
4 files changed, 23 insertions(+), 24 deletions(-)
Title: Model selection and multimodel inference based on (Q)AIC(c)
Diff between AICcmodavg versions 1.30 dated 2013-05-16 and 1.31 dated 2013-06-27
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also features functions to
conduct classic model averaging (multimodel inference) for a
given parameter of interest and predicted values, as well as a
shrinkage version of model averaging parameter estimates.
Other handy functions enable the computation of relative
variable importance, evidence ratios, and confidence sets for
the best model. The present version works with Cox regression
('coxph' class), linear models ('lm' class), generalized linear
models ('glm' class), linear models fit by generalized least
squares ('gls' class), linear mixed models ('lme' class),
generalized linear mixed models ('mer' and 'merMod' classes),
multinomial and ordinal logistic regressions ('multinom',
'polr', 'clm', and 'clmm' classes), robust regression models
('rlm' class), nonlinear models ('nls' class), and nonlinear
mixed models ('nlme' class). The package also supports various
models incorporating detection probabilities such as
single-season occupancy models ('unmarkedFitOccu' and
'unmarkedFitOccuFP classes), multiple-season occupancy models
('unmarkedFitColExt' class), single-season heterogeneity models
('unmarkedFitOccuRN' class), single-season and multiple-season
N-mixture models for repeated counts ('unmarkedFitPCount' and
'unmarkedFitPCO' classes, respectively), and distance sampling
models ('unmarkedFitDS' and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
DESCRIPTION | 34 +--
MD5 | 52 ++--
R/AICc.R | 6
R/AICc.mer.R | 23 ++
R/aictab.R | 36 +--
R/aictab.mer.R | 68 ++++++
R/fam.link.mer.r | 128 ++++++++----
R/importance.R | 29 +-
R/modavg.R | 35 ++-
R/modavg.effect.mer.r | 140 +++++++++++++
R/modavg.effect.r | 25 +-
R/modavg.mer.R | 242 ++++++++++++++++++++++
R/modavg.shrink.R | 34 +--
R/modavg.shrink.mer.R | 110 ++++++++++
R/modavgpred.R | 138 ++++++++++++-
R/predictSE.mer.r | 488 +++++++++++++++++++++++++++++++++++++++++++++-
inst/NEWS | 9
man/AICc.Rd | 42 ++-
man/AICcmodavg-package.Rd | 51 ++--
man/aictab.Rd | 35 +--
man/extractSE.mer.Rd | 10
man/fam.link.mer.Rd | 14 -
man/modavg.Rd | 47 ++--
man/modavg.effect.Rd | 23 +-
man/modavg.shrink.Rd | 29 +-
man/modavgpred.Rd | 28 +-
man/predictSE.mer.Rd | 12 -
27 files changed, 1609 insertions(+), 279 deletions(-)
Title: Tools for spatial data analysis
Diff between SpatialTools versions 0.5.1 dated 2013-05-07 and 0.5.3 dated 2013-06-26
Description: Tools for spatial data analysis. Emphasis on kriging.
Provides functions for prediction and simulation. Intended to
be relatively straightforward, fast, and flexible.
Author: Joshua French
Maintainer: Joshua French
DESCRIPTION | 11 +-
MD5 | 20 ++---
NAMESPACE | 1
NEWS | 4 +
R/bayesian.R |only
R/cov.R | 2
R/preamble.R | 2
man/spLMPredictJoint.Rd |only
src/krige.cpp | 87 ++++++++++++++++++++++
src/krige.h | 7 +
src/utils.cpp | 187 +++++++++++++++++++++++++++++++++++++-----------
src/utils.h | 10 ++
12 files changed, 272 insertions(+), 59 deletions(-)
Title: Bridging the gap between qualitative data and quantitative
analysis
Diff between qdap versions 0.2.2 dated 2013-05-18 and 0.2.3 dated 2013-06-26
Description: This package automates many of the tasks associated with
quantitative discourse analysis of transcripts containing
discourse including frequency counts of sentence types, words,
sentences, turns of talk, syllables and other assorted analysis
tasks. The package provides parsing tools for preparing
transcript data. Many functions enable the user to aggregate
data by any number of grouping variables providing analysis and
seamless integration with other R packages that undertake
higher level analysis and visualization of text. This affords
the user a more efficient and targeted analysis. qdap is
designed for transcript analysis, however, many functions are
applicable to other areas of Text Mining /Natural Language
Processing
Author: Tyler Rinker
Maintainer: Tyler Rinker
qdap-0.2.2/qdap/man/print.ngram.Rd |only
qdap-0.2.3/qdap/DESCRIPTION | 67 -
qdap-0.2.3/qdap/MD5 | 402 +++++------
qdap-0.2.3/qdap/NAMESPACE | 4
qdap-0.2.3/qdap/NEWS | 40 +
qdap-0.2.3/qdap/R/Ldist.R |only
qdap-0.2.3/qdap/R/automated_readability_index.R | 8
qdap-0.2.3/qdap/R/bag.o.words.R | 3
qdap-0.2.3/qdap/R/beg2char.R | 36
qdap-0.2.3/qdap/R/blank2NA.R | 2
qdap-0.2.3/qdap/R/bracketX.R | 6
qdap-0.2.3/qdap/R/capitalizer.R | 6
qdap-0.2.3/qdap/R/cm_code.blank.R | 9
qdap-0.2.3/qdap/R/cm_combine.dummy.R | 8
qdap-0.2.3/qdap/R/cm_df.fill.R | 4
qdap-0.2.3/qdap/R/cm_df.temp.R | 14
qdap-0.2.3/qdap/R/cm_df.transcript.R | 6
qdap-0.2.3/qdap/R/cm_df2long.R | 27
qdap-0.2.3/qdap/R/cm_distance.R | 7
qdap-0.2.3/qdap/R/cm_dummy2long.R | 3
qdap-0.2.3/qdap/R/cm_r2l.R | 2
qdap-0.2.3/qdap/R/cm_range2long.R | 6
qdap-0.2.3/qdap/R/cm_t2l.R | 2
qdap-0.2.3/qdap/R/cm_time2long.R | 8
qdap-0.2.3/qdap/R/colsplit2df.R | 2
qdap-0.2.3/qdap/R/dir_map.R | 2
qdap-0.2.3/qdap/R/dissimilarity.R | 13
qdap-0.2.3/qdap/R/diversity.R | 6
qdap-0.2.3/qdap/R/end_inc.R | 8
qdap-0.2.3/qdap/R/formality.R | 10
qdap-0.2.3/qdap/R/gantt_wrap.R | 26
qdap-0.2.3/qdap/R/imperative.R | 15
qdap-0.2.3/qdap/R/incomplete.replace.R | 5
qdap-0.2.3/qdap/R/key_merge.R | 6
qdap-0.2.3/qdap/R/kullback.leibler.R | 3
qdap-0.2.3/qdap/R/left.just.R | 9
qdap-0.2.3/qdap/R/list2df.R |only
qdap-0.2.3/qdap/R/lookup.R | 36
qdap-0.2.3/qdap/R/mcsv_r.R | 11
qdap-0.2.3/qdap/R/multigsub.R | 21
qdap-0.2.3/qdap/R/multiscale.R | 10
qdap-0.2.3/qdap/R/name2sex.R |only
qdap-0.2.3/qdap/R/new_project.R | 44 -
qdap-0.2.3/qdap/R/ngrams.R | 20
qdap-0.2.3/qdap/R/outlier.detect.R | 6
qdap-0.2.3/qdap/R/outlier.labeler.R | 6
qdap-0.2.3/qdap/R/paste2.R | 6
qdap-0.2.3/qdap/R/polarity.R | 8
qdap-0.2.3/qdap/R/pos.R | 25
qdap-0.2.3/qdap/R/prop.R | 12
qdap-0.2.3/qdap/R/qcombine.R | 6
qdap-0.2.3/qdap/R/qcv.R | 9
qdap-0.2.3/qdap/R/qdap-package.R | 68 +
qdap-0.2.3/qdap/R/qheat.R | 21
qdap-0.2.3/qdap/R/qprep.R | 10
qdap-0.2.3/qdap/R/question_type.R | 14
qdap-0.2.3/qdap/R/rank_freq_plot.R | 17
qdap-0.2.3/qdap/R/raw_pro_comb.R | 10
qdap-0.2.3/qdap/R/read.transcript.R | 20
qdap-0.2.3/qdap/R/replace_abbreviation.R | 2
qdap-0.2.3/qdap/R/replace_contraction.R | 6
qdap-0.2.3/qdap/R/replace_symbol.R | 16
qdap-0.2.3/qdap/R/scrubber.R | 10
qdap-0.2.3/qdap/R/sentSplit.R | 18
qdap-0.2.3/qdap/R/space_fill.R | 8
qdap-0.2.3/qdap/R/spaste.R | 5
qdap-0.2.3/qdap/R/speakerSplit.R | 4
qdap-0.2.3/qdap/R/stemmer.R | 8
qdap-0.2.3/qdap/R/stopwords.R | 37 -
qdap-0.2.3/qdap/R/strWrap.R | 2
qdap-0.2.3/qdap/R/strip.R | 15
qdap-0.2.3/qdap/R/syllable.sum.R | 15
qdap-0.2.3/qdap/R/synonyms.R | 13
qdap-0.2.3/qdap/R/tdm.R |only
qdap-0.2.3/qdap/R/termco.R | 30
qdap-0.2.3/qdap/R/termco.c.R | 11
qdap-0.2.3/qdap/R/tot_plot.R | 14
qdap-0.2.3/qdap/R/trans.cloud.R | 38 -
qdap-0.2.3/qdap/R/trans.venn.R | 31
qdap-0.2.3/qdap/R/wfm.R | 21
qdap-0.2.3/qdap/R/word.count.R | 58 -
qdap-0.2.3/qdap/R/word.network.plot.R | 29
qdap-0.2.3/qdap/R/word_associate.R | 31
qdap-0.2.3/qdap/R/word_diff_list.R | 22
qdap-0.2.3/qdap/R/word_list.R | 20
qdap-0.2.3/qdap/R/word_stats.R | 29
qdap-0.2.3/qdap/README.md | 4
qdap-0.2.3/qdap/data/BuckleySaltonSWL.rda |binary
qdap-0.2.3/qdap/data/DATA.rda |binary
qdap-0.2.3/qdap/data/DATA2.rda |binary
qdap-0.2.3/qdap/data/DICTIONARY.rda |binary
qdap-0.2.3/qdap/data/NAMES.rda |only
qdap-0.2.3/qdap/data/NAMES_LIST.rda |only
qdap-0.2.3/qdap/data/NAMES_SEX.rda |only
qdap-0.2.3/qdap/data/OnixTxtRetToolkitSWL1.rda |binary
qdap-0.2.3/qdap/data/SYNONYM.rda |binary
qdap-0.2.3/qdap/data/Top100Words.rda |binary
qdap-0.2.3/qdap/data/Top200Words.rda |binary
qdap-0.2.3/qdap/data/Top25Words.rda |binary
qdap-0.2.3/qdap/data/abbreviations.rda |binary
qdap-0.2.3/qdap/data/action.verbs.rda |binary
qdap-0.2.3/qdap/data/adverb.rda |binary
qdap-0.2.3/qdap/data/contractions.rda |binary
qdap-0.2.3/qdap/data/datalist | 3
qdap-0.2.3/qdap/data/emoticon.rda |binary
qdap-0.2.3/qdap/data/env.syl.rda |binary
qdap-0.2.3/qdap/data/env.syn.rda |binary
qdap-0.2.3/qdap/data/increase.amplification.words.rda |binary
qdap-0.2.3/qdap/data/interjections.rda |binary
qdap-0.2.3/qdap/data/labMT.rda |binary
qdap-0.2.3/qdap/data/mraja1.rda |binary
qdap-0.2.3/qdap/data/mraja1spl.rda |binary
qdap-0.2.3/qdap/data/negation.words.rda |binary
qdap-0.2.3/qdap/data/negative.words.rda |binary
qdap-0.2.3/qdap/data/positive.words.rda |binary
qdap-0.2.3/qdap/data/preposition.rda |binary
qdap-0.2.3/qdap/data/raj.act.1.rda |binary
qdap-0.2.3/qdap/data/raj.act.2.rda |binary
qdap-0.2.3/qdap/data/raj.act.3.rda |binary
qdap-0.2.3/qdap/data/raj.act.4.rda |binary
qdap-0.2.3/qdap/data/raj.act.5.rda |binary
qdap-0.2.3/qdap/data/raj.demographics.rda |binary
qdap-0.2.3/qdap/data/raj.rda |binary
qdap-0.2.3/qdap/data/rajPOS.rda |binary
qdap-0.2.3/qdap/data/rajSPLIT.rda |binary
qdap-0.2.3/qdap/inst/CITATION | 4
qdap-0.2.3/qdap/inst/extdata/docs/PROJECT_WORKFLOW_GUIDE.pdf |binary
qdap-0.2.3/qdap/inst/extdata/docs/extra_functions.R | 4
qdap-0.2.3/qdap/man/NAMES.Rd |only
qdap-0.2.3/qdap/man/NAMES_LIST.Rd |only
qdap-0.2.3/qdap/man/NAMES_SEX.Rd |only
qdap-0.2.3/qdap/man/Readability.Rd | 12
qdap-0.2.3/qdap/man/Word_Frequency_Matrix.Rd | 20
qdap-0.2.3/qdap/man/bag.o.words.Rd | 2
qdap-0.2.3/qdap/man/beg2char.Rd | 11
qdap-0.2.3/qdap/man/blank2NA.Rd | 2
qdap-0.2.3/qdap/man/bracketX.Rd | 8
qdap-0.2.3/qdap/man/capitalizer.Rd | 6
qdap-0.2.3/qdap/man/cm_code.blank.Rd | 11
qdap-0.2.3/qdap/man/cm_combine.dummy.Rd | 11
qdap-0.2.3/qdap/man/cm_df.fill.Rd | 4
qdap-0.2.3/qdap/man/cm_df.temp.Rd | 12
qdap-0.2.3/qdap/man/cm_df.transcript.Rd | 8
qdap-0.2.3/qdap/man/cm_df2long.Rd | 28
qdap-0.2.3/qdap/man/cm_distance.Rd | 11
qdap-0.2.3/qdap/man/cm_dummy2long.Rd | 2
qdap-0.2.3/qdap/man/cm_range2long.Rd | 8
qdap-0.2.3/qdap/man/cm_time2long.Rd | 12
qdap-0.2.3/qdap/man/colsplit2df.Rd | 4
qdap-0.2.3/qdap/man/dir_map.Rd | 4
qdap-0.2.3/qdap/man/dissimilarity.Rd | 20
qdap-0.2.3/qdap/man/diversity.Rd | 8
qdap-0.2.3/qdap/man/end_inc.Rd | 12
qdap-0.2.3/qdap/man/formality.Rd | 12
qdap-0.2.3/qdap/man/gantt_wrap.Rd | 36
qdap-0.2.3/qdap/man/imperative.Rd | 22
qdap-0.2.3/qdap/man/incomplete.replace.Rd | 8
qdap-0.2.3/qdap/man/justification.Rd | 8
qdap-0.2.3/qdap/man/key_merge.Rd | 8
qdap-0.2.3/qdap/man/kullback.leibler.Rd | 2
qdap-0.2.3/qdap/man/lookup.Rd | 32
qdap-0.2.3/qdap/man/multicsv.Rd | 16
qdap-0.2.3/qdap/man/multigsub.Rd | 20
qdap-0.2.3/qdap/man/multiscale.Rd | 12
qdap-0.2.3/qdap/man/name2sex.Rd |only
qdap-0.2.3/qdap/man/new_project.Rd | 6
qdap-0.2.3/qdap/man/ngrams.Rd | 8
qdap-0.2.3/qdap/man/outlier.detect.Rd | 8
qdap-0.2.3/qdap/man/outlier.labeler.Rd | 4
qdap-0.2.3/qdap/man/paste2.Rd | 8
qdap-0.2.3/qdap/man/plot.character.table.Rd | 23
qdap-0.2.3/qdap/man/polarity.Rd | 14
qdap-0.2.3/qdap/man/pos.Rd | 30
qdap-0.2.3/qdap/man/print.character.table.Rd | 14
qdap-0.2.3/qdap/man/print.ngrams.Rd |only
qdap-0.2.3/qdap/man/prop.Rd | 12
qdap-0.2.3/qdap/man/qcombine.Rd | 8
qdap-0.2.3/qdap/man/qcv.Rd | 16
qdap-0.2.3/qdap/man/qheat.Rd | 22
qdap-0.2.3/qdap/man/qprep.Rd | 13
qdap-0.2.3/qdap/man/question_type.Rd | 16
qdap-0.2.3/qdap/man/rank_freq_plot.Rd | 24
qdap-0.2.3/qdap/man/read.transcript.Rd | 31
qdap-0.2.3/qdap/man/replace_abbreviation.Rd | 4
qdap-0.2.3/qdap/man/replace_contraction.Rd | 6
qdap-0.2.3/qdap/man/replace_symbol.Rd | 24
qdap-0.2.3/qdap/man/scrubber.Rd | 15
qdap-0.2.3/qdap/man/sentSplit.Rd | 23
qdap-0.2.3/qdap/man/space_fill.Rd | 11
qdap-0.2.3/qdap/man/spaste.Rd | 8
qdap-0.2.3/qdap/man/speakerSplit.Rd | 4
qdap-0.2.3/qdap/man/stemmer.Rd | 12
qdap-0.2.3/qdap/man/stopwords.Rd | 53 -
qdap-0.2.3/qdap/man/strWrap.Rd | 4
qdap-0.2.3/qdap/man/strip.Rd | 12
qdap-0.2.3/qdap/man/syllabication.Rd | 8
qdap-0.2.3/qdap/man/synonyms.Rd | 12
qdap-0.2.3/qdap/man/tdm.Rd |only
qdap-0.2.3/qdap/man/termco.Rd | 44 -
qdap-0.2.3/qdap/man/termco.c.Rd | 15
qdap-0.2.3/qdap/man/tot_plot.Rd | 16
qdap-0.2.3/qdap/man/trans.cloud.Rd | 39 -
qdap-0.2.3/qdap/man/trans.venn.Rd | 27
qdap-0.2.3/qdap/man/word.count.Rd | 37 -
qdap-0.2.3/qdap/man/word.network.plot.Rd | 34
qdap-0.2.3/qdap/man/word_associate.Rd | 43 -
qdap-0.2.3/qdap/man/word_diff_list.Rd | 28
qdap-0.2.3/qdap/man/word_list.Rd | 24
qdap-0.2.3/qdap/man/word_stats.Rd | 30
209 files changed, 1560 insertions(+), 1285 deletions(-)
Title: Functions to create and manipulate discrete random variables
Diff between discreteRV versions 1.0 dated 2013-04-17 and 1.0.1 dated 2013-06-26
Description: discreteRV implements a set of functions that allow
computations involving discrete random variables. It uses a
syntax which is familiar to that which is used in mathematical
statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare
DESCRIPTION | 15
MD5 | 51 +--
NAMESPACE | 43 +-
R/discreteRV-Probabilities.r | 662 +++++++++++++++++++++++--------------------
R/discreteRV-Simulations.r | 170 +++++------
man/E.Rd | 40 +-
man/KURT.Rd | 34 +-
man/P.Rd | 44 +-
man/Prop.Rd | 46 +-
man/SD.Rd | 34 +-
man/SKEW.Rd | 34 +-
man/SofI.Rd | 58 +--
man/SofIID.Rd | 65 ++--
man/V.Rd | 34 +-
man/as.RV.Rd | 32 +-
man/make.RV.Rd | 74 ++--
man/margins.Rd |only
man/mult.Rd | 66 ++--
man/multN.Rd | 64 ++--
man/plot.RV.Rd | 104 +++---
man/plot.RVsim.Rd | 46 +-
man/print.RV.Rd | 43 +-
man/probs.Rd | 74 ++--
man/props.Rd | 58 +--
man/qqnorm.RV.Rd | 76 ++--
man/rsim.Rd | 54 +--
man/skewSim.Rd | 40 +-
27 files changed, 1069 insertions(+), 992 deletions(-)
Title: Firth's bias reduced logistic regression
Diff between logistf versions 1.20 dated 2013-05-16 and 1.21 dated 2013-06-26
Description: Firth's bias reduced logistic regression approach with
penalized profile likelihood based confidence intervals for
parameter estimates.
Author: Georg Heinze
Maintainer: Georg Heinze
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/logistf.control.R | 2 +-
R/logistf.fit.R | 23 ++++++++++++-----------
4 files changed, 20 insertions(+), 19 deletions(-)
Title: JudgeIt: A Program for Evaluating Electoral Systems and
Redistricting Plans
Diff between JudgeIt versions 1.5.0 dated 2013-06-19 and 1.5.1 dated 2013-06-26
Description: Examines two-party electoral systems and calculates
quantities of interest based on the behaviour of their
districts.
Author: Andrew Gelman, Gary King and Andrew C. Thomas
Maintainer: Andrew C. Thomas
DESCRIPTION | 11 ++++++-----
MD5 | 4 ++--
inst/doc/judgeit.pdf |binary
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Wrapper for fftw3: includes 1-D, univariate and multivariate,
and 2-D transform
Diff between fftwtools versions 0.9-3 dated 2013-05-05 and 0.9-5 dated 2013-06-26
Description: This package is a wrapper for several fftw functions.
Please see the fftw package for additional tools. This package
provides access to the two-dimensional fft, the multivariate
fft, and the one-dimensional real to complex fft using fftw3.
The package includes the functions fftw and mvfftw which are
designed to mimic the functionality of the R functions fftw and
mvfft. The fft functions have a parameter that allows them to
not return the redundant complex conjugate when the input is
real data. Please see the package fftw for general
one-dimensional use of fftw, the discrete cosine transform, and
for more detailed use of performance enhancing plans when using
fftw. The calls to fftw and mvfftw in this package mimic the
standard routines in R.
Author: Karim Rahim
Maintainer: Karim Rahim
DESCRIPTION | 27 +++++++++++++++------------
MD5 | 10 +++++-----
inst/doc/testTimeAndSimpleUse.R | 2 ++
inst/doc/testTimeAndSimpleUse.Rnw | 2 ++
inst/doc/testTimeAndSimpleUse.pdf |binary
src/Makevars | 9 ++++++++-
6 files changed, 32 insertions(+), 18 deletions(-)
Title: Method Functions for Confidence Intervals and to Distill
Information from an Object
Diff between distillery versions 1.0 dated 2013-05-30 and 1.0-1 dated 2013-06-26
Description: Some very simple method functions for confidence interval
calculation and to distill pertinent information from a
potentially complex object; primarily used in common with
packages extRemes and SpatialVx.
Author: Eric Gilleland
Maintainer: Eric Gilleland
DESCRIPTION | 13 ++++++++-----
MD5 | 3 ++-
man/distillery-package.Rd |only
3 files changed, 10 insertions(+), 6 deletions(-)
Title: Mediation analysis with missing data using bootstrap
Diff between bmem versions 1.3 dated 2012-06-26 and 1.4 dated 2013-06-26
Description: Four methods for mediation analysis with missing data:
Listwise deletion, Pairwise deletion, Multiple imputation, and
Two Stage Maximum Likelihood algorithm. For MI and TS-ML,
auxiliary variables can be included. Bootstrap confidence
intervals for mediation effects are obtained. The robust method
is also implemented for TS-ML. Since version 1.4, bmem adds the
capability to conduct power analysis for mediation models.
Author: Zhiyong Zhang and Lijuan Wang
Maintainer: Zhiyong Zhang
DESCRIPTION | 16
MD5 | 87 -
NAMESPACE | 23
R/bmem.R | 3011 ++++++++++++++++++++++++++++++--------------------
man/bmem-package.Rd | 52
man/bmem.Rd | 84 -
man/bmem.bs.Rd | 78 -
man/bmem.ci.bc.Rd | 56
man/bmem.ci.bc1.Rd | 46
man/bmem.ci.bca.Rd | 56
man/bmem.ci.bca1.Rd | 38
man/bmem.ci.norm.Rd | 52
man/bmem.ci.p.Rd | 52
man/bmem.cov.Rd | 38
man/bmem.em.Rd | 54
man/bmem.em.boot.Rd | 74 -
man/bmem.em.cov.Rd | 36
man/bmem.em.jack.Rd | 56
man/bmem.em.rcov.Rd | 54
man/bmem.list.Rd | 40
man/bmem.list.boot.Rd | 42
man/bmem.list.cov.Rd | 34
man/bmem.list.jack.Rd | 40
man/bmem.mi.Rd | 44
man/bmem.mi.boot.Rd | 48
man/bmem.mi.cov.Rd | 36
man/bmem.mi.jack.Rd | 36
man/bmem.moments.Rd | 32
man/bmem.pair.Rd | 32
man/bmem.pair.boot.Rd | 34
man/bmem.pair.cov.Rd | 26
man/bmem.pair.jack.Rd | 32
man/bmem.pattern.Rd | 24
man/bmem.plot.Rd | 60
man/bmem.raw2cov.Rd | 54
man/bmem.sem.Rd | 46
man/bmem.sobel.Rd | 66 -
man/bmem.sobel.ind.Rd | 58
man/bmem.ssq.Rd | 32
man/bmem.v.Rd | 36
man/plot.bmem.Rd | 62 -
man/popPar.Rd |only
man/power.basic.Rd |only
man/power.boot.Rd |only
man/power.curve.Rd |only
man/summary.bmem.Rd | 44
man/summary.power.Rd |only
47 files changed, 2778 insertions(+), 2143 deletions(-)
Title: Sequential Parameter Optimization
Diff between SPOT versions 1.0.4045 dated 2013-04-11 and 1.0.4184 dated 2013-06-26
Description: R-Package for Sequential Parameter Optimization Toolbox
Author: T. Bartz-Beielstein with contributions from: J. Ziegenhirt, W.
Konen, O. Flasch, M. Friese, P. Koch, M. Zaefferer, B. Naujoks
Maintainer: Martin Zaefferer
SPOT-1.0.4045/SPOT/R/esOptim.R |only
SPOT-1.0.4184/SPOT/DESCRIPTION | 38 -
SPOT-1.0.4184/SPOT/MD5 | 111 ++-
SPOT-1.0.4184/SPOT/NAMESPACE | 8
SPOT-1.0.4184/SPOT/NEWS | 3
SPOT-1.0.4184/SPOT/R/spot.R | 8
SPOT-1.0.4184/SPOT/R/spotAlgStartEs.R | 78 +-
SPOT-1.0.4184/SPOT/R/spotAlgStartRgp.R | 3
SPOT-1.0.4184/SPOT/R/spotAlgStartSmsEmoaGlg.R |only
SPOT-1.0.4184/SPOT/R/spotCreateDesignLhsOpt.R | 4
SPOT-1.0.4184/SPOT/R/spotGaussianLandscapeGenerator.R | 297 +++++++++-
SPOT-1.0.4184/SPOT/R/spotHelpFunctions.R | 14
SPOT-1.0.4184/SPOT/R/spotOptimEs.R |only
SPOT-1.0.4184/SPOT/R/spotOptimizationFunctions.R | 3
SPOT-1.0.4184/SPOT/R/spotPredictCoForrester.R | 107 +--
SPOT-1.0.4184/SPOT/R/spotPredictDace.R | 6
SPOT-1.0.4184/SPOT/R/spotPredictEsvm.R | 19
SPOT-1.0.4184/SPOT/R/spotPredictForrester.R | 18
SPOT-1.0.4184/SPOT/R/spotPredictKsvm.R | 27
SPOT-1.0.4184/SPOT/R/spotReportMAMP.R | 91 ++-
SPOT-1.0.4184/SPOT/R/spotReportSAMP.R | 88 ++
SPOT-1.0.4184/SPOT/R/spotSurf.R | 15
SPOT-1.0.4184/SPOT/inst/demo01TreeBranin/demo01TreeBranin.conf | 24
SPOT-1.0.4184/SPOT/inst/demo02RandomForestBranin/demo02RandomForestBranin.conf | 24
SPOT-1.0.4184/SPOT/inst/demo03LmBranin/demo03LmBranin.conf | 26
SPOT-1.0.4184/SPOT/inst/demo04MlegpBranin/demo04MlegpBranin.conf | 32 -
SPOT-1.0.4184/SPOT/inst/demo05TgpBranin/demo05TgpBranin.conf | 32 -
SPOT-1.0.4184/SPOT/inst/demo06TreeSann/demo06TreeSann.conf | 26
SPOT-1.0.4184/SPOT/inst/demo07RandomForestSann/demo07RandomForestSann.conf | 28
SPOT-1.0.4184/SPOT/inst/demo08LmSann/demo08LmSann.conf | 28
SPOT-1.0.4184/SPOT/inst/demo09MlegpSann/demo09MlegpSann.conf | 32 -
SPOT-1.0.4184/SPOT/inst/demo10TgpSann/demo10TgpSann.conf | 28
SPOT-1.0.4184/SPOT/inst/demo11Java/demo11Java.conf | 50 -
SPOT-1.0.4184/SPOT/inst/demo12Sann/sann0001.conf | 36 -
SPOT-1.0.4184/SPOT/inst/demo13RandomForestMlegpSann/demo13RandomForestMlegpSann.conf | 28
SPOT-1.0.4184/SPOT/inst/demo14LmOptimSann/demo14LmOptimSann.conf | 38 -
SPOT-1.0.4184/SPOT/inst/demo16EsBranin/es1.conf | 28
SPOT-1.0.4184/SPOT/inst/demo17Rgp/rgp0001.conf | 26
SPOT-1.0.4184/SPOT/inst/demoMixedModelAnalysis/glges01.conf | 38 -
SPOT-1.0.4184/SPOT/inst/demoMixedModelAnalysis/glges02.conf | 38 -
SPOT-1.0.4184/SPOT/inst/doc/SPOT.pdf |binary
SPOT-1.0.4184/SPOT/man/SPOT-package.Rd | 2
SPOT-1.0.4184/SPOT/man/daceBuilder.Rd | 7
SPOT-1.0.4184/SPOT/man/forrBuilder.Rd | 7
SPOT-1.0.4184/SPOT/man/forrCoBuilder.Rd | 21
SPOT-1.0.4184/SPOT/man/spotAlgEsQuickTest.Rd | 9
SPOT-1.0.4184/SPOT/man/spotAlgStartSmsEmoaGlg.Rd |only
SPOT-1.0.4184/SPOT/man/spotCreateDesignLhsOpt.Rd | 2
SPOT-1.0.4184/SPOT/man/spotGlgCore.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgCreate.Rd | 5
SPOT-1.0.4184/SPOT/man/spotGlgCreateN.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgCreateRot.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgCreateRotSearched.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgEval.Rd | 3
SPOT-1.0.4184/SPOT/man/spotGlgEvalN.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgEvalRot.Rd |only
SPOT-1.0.4184/SPOT/man/spotGlgInit.Rd | 3
SPOT-1.0.4184/SPOT/man/spotGlgInitN.Rd |only
SPOT-1.0.4184/SPOT/man/spotPredictCoForrester.Rd | 5
SPOT-1.0.4184/SPOT/man/spotPredictForrester.Rd | 5
SPOT-1.0.4184/SPOT/man/spotSurfContour.Rd | 6
SPOT-1.0.4184/SPOT/vignettes/SPOT.Rnw | 13
62 files changed, 1007 insertions(+), 581 deletions(-)
Title: Structural Equation Modeling using RAM Notation
Diff between RAMpath versions 0.3.5 dated 2013-03-07 and 0.3.6 dated 2013-06-26
Description: RAMpath is a rewrite of RAMpath software developed by John
McArdle and Steven Boker. However, it does more than the
original software by providing flexible fit of growth curve
models, univariate and bivariate latent change score models. It
can also generate the vector field plot for the bivariate
latent change score models.
Author: Zhiyong Zhang, Jack McArdle, Aki Hamagami, & Kevin Grimm
Maintainer: Zhiyong Zhang
DESCRIPTION | 14 +++++++-------
MD5 | 20 ++++++++++----------
R/blcs.R | 25 +++++++++++++++++++++++++
data/ex1.txt.gz |binary
data/ex2.txt.gz |binary
data/ex3.txt.gz |binary
man/plot.RAMpath.Rd | 5 ++++-
man/ramBLCS.Rd | 5 ++++-
man/ramLCM.Rd | 4 +++-
man/ramLCS.Rd | 3 ++-
man/ramVF.Rd | 3 ++-
11 files changed, 57 insertions(+), 22 deletions(-)
Title: Package for Plotting Categorical Longitudinal and Time-Series
Data
Diff between longCatEDA versions 0.13 dated 2013-03-30 and 0.16 dated 2013-06-26
Description: Package for Plotting Categorical Longitudinal and
Time-Series Data
Author: Stephen Tueller. Funded by the National Institute on Drug Abuse
(NIDA) Award number 1R03DA030850 and the National Institute on
Alcohol Abuse and Alcoholism (NIAAA) Award Number R03 AA019775.
Maintainer: Stephen Tueller
longCatEDA-0.13/longCatEDA/R/longCatEDA_0.13.r |only
longCatEDA-0.16/longCatEDA/DESCRIPTION | 12 +++---
longCatEDA-0.16/longCatEDA/MD5 | 15 ++++---
longCatEDA-0.16/longCatEDA/NEWS |only
longCatEDA-0.16/longCatEDA/R/longCatEDA_0.16.r |only
longCatEDA-0.16/longCatEDA/man/colChoose.Rd | 36 ++++++++++++-------
longCatEDA-0.16/longCatEDA/man/longCat-class.Rd | 2 -
longCatEDA-0.16/longCatEDA/man/longCatEDA-package.Rd | 2 -
longCatEDA-0.16/longCatEDA/man/longCatPlot.Rd | 16 ++++++--
longCatEDA-0.16/longCatEDA/man/sorter.Rd | 10 ++---
10 files changed, 58 insertions(+), 35 deletions(-)
Title: Exact (Restricted) Likelihood Ratio tests for mixed and additive
models.
Diff between RLRsim versions 2.0-12 dated 2013-02-26 and 2.1-0 dated 2013-06-26
Description: Rapid, simulation-based exact (restricted) likelihood
ratio tests for testing the presence of variance
components/nonparametric terms for models fit with
nlme::lme(),lme4::lmer(), mgcv::gamm() and SemiPar:spm()
Author: Fabian Scheipl, Ben Bolker
Maintainer: Fabian Scheipl
DESCRIPTION | 10 -
MD5 | 24 +--
R/LRTSim.R | 132 ++++++++++++------
R/RLRTSim.R | 320 +++++++++++++++++++++++++++-------------------
R/exactLRT.R | 131 ++++++++++--------
R/exactRLRT.R | 167 ++++++++++++------------
R/extract.lmeDesign.R | 124 ++++++++---------
R/extract.lmerDesign.R | 102 +++++++-------
R/extract.lmerModDesign.R | 68 ++++-----
man/LRTSim.Rd | 166 ++++++++++++-----------
man/RLRsim-package.Rd | 50 +++----
man/exactLRT.Rd | 129 +++++++++---------
man/exactRLRT.Rd | 169 ++++++++++++------------
13 files changed, 866 insertions(+), 726 deletions(-)
Title: Functions for medical statistics book with some demographic data
Diff between fmsb versions 0.3.9 dated 2013-06-10 and 0.4.0 dated 2013-06-26
Description: Several utility functions for the book entitled "Practices
of Medical and Health Data Analysis using R" (Pearson Education
Japan, 2007) with Japanese demographic data and some
demographic analysis related functions.
Author: Minato Nakazawa
Maintainer: Minato Nakazawa
DESCRIPTION | 8 +--
MD5 | 16 +++---
NEWS | 4 +
R/demogjpn.R | 124 +++++++++++++++++++++++++++++++++---------------------
man/CT.Rd | 5 ++
man/Denny.Rd | 5 ++
man/Hadwiger.Rd | 6 ++
man/Nagelkerke.Rd | 7 +++
man/lifetable.Rd | 15 +++++-
9 files changed, 127 insertions(+), 63 deletions(-)
Title: Gene Set Analysis Exploiting Pathway Topology
Diff between topologyGSA versions 1.2.0 dated 2013-03-01 and 1.2.1 dated 2013-06-26
Description: Using Gaussian graphical models we propose a novel
approach to perform pathway analysis using gene expression.
Given the structure of a graph (a pathway) we introduce two
statistical tests to compare the mean and the concentration
matrices between two groups. Specifically, these tests can be
performed on the graph and on its connected components
(cliques).
Author: Sofia Massa, Gabriele Sales
Maintainer: Gabriele Sales
DESCRIPTION | 19 +++++++++++++------
MD5 | 6 +++---
NAMESPACE | 1 +
R/cliques.R | 2 +-
4 files changed, 18 insertions(+), 10 deletions(-)
Title: R/Weka interface
Diff between RWeka versions 0.4-17 dated 2013-04-16 and 0.4-18 dated 2013-06-26
Description: An R interface to Weka (Version 3.7.9). Weka is a
collection of machine learning algorithms for data mining tasks
written in Java, containing tools for data pre-processing,
classification, regression, clustering, association rules, and
visualization. Package RWeka contains the interface code, the
Weka jar is in a separate package RWekajars. For more
information on Weka see http://www.cs.waikato.ac.nz/~ml/weka/.
Author: Kurt Hornik [aut, cre], Christian Buchta [ctb], Torsten Hothorn
[ctb], Alexandros Karatzoglou [ctb], David Meyer [ctb], Achim
Zeileis [ctb]
Maintainer: Kurt Hornik
CHANGELOG | 5 +++++
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
inst/doc/RWeka.R | 20 ++++++++++----------
inst/doc/RWeka.Rnw | 9 +++++++--
inst/doc/RWeka.pdf |binary
man/WPM.Rd | 9 +++++++++
vignettes/RWeka.Rnw | 9 +++++++--
8 files changed, 48 insertions(+), 24 deletions(-)
Title: Surrogate variable analysis using partial least squares in a
gene expression study.
Diff between svapls versions 1.1 dated 2013-03-13 and 1.2 dated 2013-06-26
Description: Accurate identification of genes that are truly
differentially expressed over two sample varieties, after
adjusting for hidden subject-specific effects of residual
heterogeneity.
Author: Sutirtha Chakraborty, Somnath Datta and Susmita Datta
Maintainer: Sutirtha Chakraborty
DESCRIPTION | 14 -
MD5 | 22 +-
NAMESPACE | 3
R/fitModel.R | 380 +++++++++++++++++++++++++-----------------------
R/hfp.R | 23 +-
R/svpls.R | 164 ++++++++++----------
data/hidden_fac.dat.rda |binary
man/fitModel.Rd | 4
man/hfp.Rd | 12 -
man/hidden_fac.dat.Rd | 27 +++
man/svapls-package.Rd | 12 -
man/svpls.Rd | 19 +-
12 files changed, 367 insertions(+), 313 deletions(-)
Title: Mark-Recapture Distance Sampling (mrds)
Diff between mrds versions 2.1.0 dated 2012-12-11 and 2.1.2 dated 2013-06-26
Description: This package implements mark-recapture distance sampling
methods as described in D.L. Borchers, W. Zucchini and Fewster,
R.M. (1988), "Mark-recapture models for line transect surveys",
Biometrics 54: 1207-1220. and Laake, J.L. (1999) "Distance
sampling with independent observers: Reducing bias from
heterogeneity by weakening the conditional independence
assumption." in Amstrup, G.W., Garner, S.C., Laake, J.L.,
Manly, B.F.J., McDonald, L.L. and Robertson, D.G. (eds) "Marine
mammal survey and assessment methods", Balkema, Rotterdam:
137-148 and Borchers, D.L., Laake, J.L., Southwell, C. and
Paxton, C.L.G. "Accommodating unmodelled heterogeneity in
double-observer distance sampling surveys". 2006. Biometrics
62:372-378.)
Author: Jeff Laake
Maintainer: Jeff Laake
DESCRIPTION | 11 ++-
MD5 | 117 ++++++++++++++++++++--------------------
NEWS | 27 +++++++++
R/create.ddfobj.R | 6 +-
R/ddf.R | 25 +++++---
R/ddf.gof.R | 8 +-
R/ddf.io.fi.R | 34 +++++++----
R/ddf.rem.fi.R | 20 +++++-
R/ddf.trial.fi.R | 19 +++++-
R/det.tables.R | 4 +
R/detfct.R | 23 +++++--
R/flpt.lnl.r | 11 ++-
R/histline.R | 2
R/integratelogistic.R | 4 -
R/integratelogisticdup.R | 4 -
R/integratepdf.r | 9 ++-
R/keyfct.th.R |only
R/mcds.R | 2
R/model.description.R | 4 +
R/mrds-package.R | 36 ++++++++----
R/pdot.dsr.integrate.logistic.R | 23 +++++--
R/plot.det.tables.R | 3 -
R/plot.ds.R | 3 -
R/plot.io.R | 30 +++-------
R/plot.io.fi.R | 29 +++------
R/plot.rem.R | 23 ++-----
R/plot.rem.fi.R | 24 ++------
R/plot.trial.R | 22 ++-----
R/plot.trial.fi.R | 23 ++-----
R/plot_cond.R | 9 ++-
R/plot_uncond.R | 30 ++--------
R/predict.ds.R | 2
R/predict.io.fi.R | 6 --
R/print.summary.ds.R | 2
R/summary.ds.R | 2
data/book.tee.data.rda |binary
man/ddf.Rd | 26 ++++++--
man/det.tables.Rd | 4 +
man/distpdf.Rd | 3 -
man/histline.Rd | 2
man/integratepdf.Rd | 3 -
man/plot.det.tables.Rd | 3 -
man/plot.ds.Rd | 3 -
man/plot.io.Rd | 21 ++-----
man/plot.io.fi.Rd | 20 ++----
man/plot.rem.Rd | 21 ++-----
man/plot.rem.fi.Rd | 21 ++-----
man/plot.trial.Rd | 20 ++----
man/plot.trial.fi.Rd | 21 ++-----
man/plot_cond.Rd | 10 ++-
man/plot_uncond.Rd | 10 ++-
man/predict.ds.Rd | 2
man/predict.io.fi.Rd | 2
man/ptdata.distance.Rd | 3 -
man/ptdata.dual.Rd | 3 -
man/ptdata.removal.Rd | 3 -
man/ptdata.single.Rd | 3 -
man/stake77.Rd | 12 ++--
man/stake78.Rd | 12 ++--
tests/run-all.R | 2
60 files changed, 429 insertions(+), 398 deletions(-)
Title: Get energy data from the UK Dept of Energy and Climate Change
Diff between decctools versions 0.1.0 dated 2013-06-24 and 0.1.1 dated 2013-06-26
Description: decctools provides functions for retrieving energy
statistics from the United Kingdom Department of Energy and
Climate Change and related data sources. The current version
focuses on total final energy consumption statistics at the
local authority, MSOA, and LSOA geographies. Methods for
calculating the generation mix of grid electricity and its
associated carbon intensity are also provided.
Author: James Keirstead
Maintainer: James Keirstead
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
NEWS | 5 +++++
R/utils.r | 4 +++-
README.md | 4 +++-
5 files changed, 21 insertions(+), 12 deletions(-)
Title: Fitting heavy tailed distributions: the poweRlaw package
Diff between poweRlaw versions 0.20.0 dated 2013-06-07 and 0.20.1 dated 2013-06-25
Description: This package implements both the discrete and continuous
maximum likelihood estimators for fitting the power-law
distribution to data. Additionally, a goodness-of-fit based
approach is used to estimate the lower cut-off for the scaling
region.
Author: Colin Gillespie
Maintainer: Colin Gillespie
poweRlaw-0.20.0/poweRlaw/data/NativeAmerican.RData |only
poweRlaw-0.20.0/poweRlaw/data/USAmerican.RData |only
poweRlaw-0.20.0/poweRlaw/man/NativeAmerican.Rd |only
poweRlaw-0.20.1/poweRlaw/DESCRIPTION | 10 +--
poweRlaw-0.20.1/poweRlaw/MD5 | 33 +++++-----
poweRlaw-0.20.1/poweRlaw/NEWS | 9 ++
poweRlaw-0.20.1/poweRlaw/R/aaa_all_classes.R | 4 -
poweRlaw-0.20.1/poweRlaw/R/data_help_files.R | 23 +++++-
poweRlaw-0.20.1/poweRlaw/R/estimate_xmin.R | 6 +
poweRlaw-0.20.1/poweRlaw/R/lines-methods.R | 2
poweRlaw-0.20.1/poweRlaw/R/plot-methods.R | 8 +-
poweRlaw-0.20.1/poweRlaw/R/points-methods.R | 2
poweRlaw-0.20.1/poweRlaw/data/native_american.RData |only
poweRlaw-0.20.1/poweRlaw/data/swiss_prot.RData |only
poweRlaw-0.20.1/poweRlaw/data/us_american.RData |only
poweRlaw-0.20.1/poweRlaw/inst/CITATION |only
poweRlaw-0.20.1/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.20.1/poweRlaw/inst/doc/poweRlaw.pdf |binary
poweRlaw-0.20.1/poweRlaw/man/estimate_xmin.Rd | 7 +-
poweRlaw-0.20.1/poweRlaw/man/native_american.Rd |only
poweRlaw-0.20.1/poweRlaw/man/plotting-methods-distribution.Rd | 14 ++--
poweRlaw-0.20.1/poweRlaw/man/swiss_prot.Rd |only
22 files changed, 76 insertions(+), 42 deletions(-)
Title: Independent Components Analysis (ICA) based artifact correction.
Diff between icaOcularCorrection versions 2.1 dated 2013-06-12 and 2.2.4 dated 2013-06-25
More information about icaOcularCorrection at CRAN
Description: Removes eye-movement and other types of known (i.e.,
recorded) or unknown (i.e., not recorded) artifacts using the
fastICA package. The correction method proposed in this package
is largely based on the method described in on Flexer, Bauer,
Pripfl, and Dorffner (2005). The process of correcting electro-
and magneto-encephalographic data (EEG/MEG) begins by running
function ``icac'', which first performs independent components
analysis (ICA) to decompose the data frame into independent
components (ICs) using function ``fastICA'' from the package of
the same name. It then calculates for each trial the
correlation between each IC and each one of the noise signals
-- there can be one or more, e.g., vertical and horizontal
electro-oculograms (VEOG and HEOG), electro-myograms (EMG),
electro-cardiograms (ECG), galvanic skin responses (GSR), and
other noise signals. Subsequently, portions of an IC
corresponding to trials at which the correlation between it and
a noise signal was at or above threshold (set to 0.4 by
default; Flexer et al., 2005, p. 1001) are zeroed-out in the
source matrix, ``S''. The user can then identify which ICs
correlate with the noise signals the most by looking at the
summary of the ``icac'' object (using function
``summary.icac''), the scalp topography of the ICs (using
function ``topo_ic''), the time courses of the ICs (using
functions ``plot_tric'' and ``plot_nic''), and other diagnostic
plots. Once these ICs have been identified, they can be
completely zeroed-out using function ``update.icac'' and the
resulting correction checked using functions ``plot_avgba'' and
``plot_trba''. Some worked-out examples with R code are
provided in the package vignette.
Author: Antoine Tremblay, NeuroCognitive Imaging Lab, Dalhousie
University
Maintainer: Antoine Tremblay
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.avgba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.nic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.trba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.tric.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/topo.ic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/inst/doc/vignette_v1.pdf |only
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icaOcularCorrection-2.2.4/icaOcularCorrection/DESCRIPTION | 32 +--
icaOcularCorrection-2.2.4/icaOcularCorrection/MD5 | 86 ++++-----
icaOcularCorrection-2.2.4/icaOcularCorrection/NEWS | 94 ----------
icaOcularCorrection-2.2.4/icaOcularCorrection/R/plot_avgba.R |only
icaOcularCorrection-2.2.4/icaOcularCorrection/R/plot_nic.R |only
icaOcularCorrection-2.2.4/icaOcularCorrection/R/plot_trba.R |only
icaOcularCorrection-2.2.4/icaOcularCorrection/R/plot_tric.R |only
icaOcularCorrection-2.2.4/icaOcularCorrection/R/topo_ic.R |only
icaOcularCorrection-2.2.4/icaOcularCorrection/inst/doc/vignette.R |only
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icaOcularCorrection-2.2.4/icaOcularCorrection/man/icac.Rd | 10 -
icaOcularCorrection-2.2.4/icaOcularCorrection/man/plot_avgba.Rd |only
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icaOcularCorrection-2.2.4/icaOcularCorrection/man/plot_trba.Rd |only
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icaOcularCorrection-2.2.4/icaOcularCorrection/man/summary.icac.Rd | 10 -
icaOcularCorrection-2.2.4/icaOcularCorrection/man/topo_ic.Rd |only
icaOcularCorrection-2.2.4/icaOcularCorrection/man/update.icac.Rd | 10 -
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/EEGLABuncorrectedCorrected.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/EEGLABvsICAocularCorrection.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/IC43E21.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/IC52E14.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/IC6E126.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/ICNumTrials12.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/ICNumTrials3.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/ICNumTrials5.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/beforeAfter5IC.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/plotNICIC43E21.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/plotNICIC52E14.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/plotNICIC6E126.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/smryEGI129.rda |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/smryEGI129IC43.rda |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/smryEGI129IC52.rda |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/smryEGI129IC6.rda |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/topomapIC43.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/topomapIC52.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/topomapIC6.pdf |only
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icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/uncorrectedCorrected3.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/uncorrectedCorrected5.pdf |only
icaOcularCorrection-2.2.4/icaOcularCorrection/vignettes/vignette.Rnw |only
60 files changed, 89 insertions(+), 171 deletions(-)
Permanent link
Title: A package for graphical modelling in R
Diff between gRbase versions 1.6-9 dated 2013-06-18 and 1.6-10 dated 2013-06-25
Description: The gRbase package provides certain general constructs
which are used by other graphical modelling packages, in
particular by the packages gRain, gRim and gRc.
gRbase contains several datasets relevant for use in connection with
graphical models. Almost all datasets used in the book
Graphical Models with R (2012) are contained in gRbase.
gRbase implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph algorithms
are: (i) maximum cardinality search (for marked and unmarked
graphs). (ii) moralize. (iii) triangulate. (iv)
junctionTree.
gRbase facilities for array operations,
gRbase implements functions for testing for conditional independence.
gRbase illustrates how hierarchical log-linear models (hllm) may be
implemented and describes concept of gmData (graphical meta
data). These features, however, are not maintained anymore and
remains in gRbase only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The gRbase Package, Journal of Statistical Software, Vol 14, No
17, 2005.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRbase-1.6-10/gRbase/ChangeLog | 9
gRbase-1.6-10/gRbase/DESCRIPTION | 13
gRbase-1.6-10/gRbase/MD5 | 40
gRbase-1.6-10/gRbase/NAMESPACE | 14
gRbase-1.6-10/gRbase/gRbase-Ex.R | 2464 +++++++++++-----------
gRbase-1.6-10/gRbase/man/GraphAlgo-coerce.Rd | 9
gRbase-1.6-10/gRbase/man/GraphAlgo-operations1.Rd | 6
gRbase-1.6-10/gRbase/man/gRbase-internal.Rd | 2
gRbase-1.6-10/gRbase/vignette |only
gRbase-1.6-9/gRbase/inst/doc |only
10 files changed, 1285 insertions(+), 1272 deletions(-)
Title: Variational Bayesian mixture models
Diff between VBmix versions 0.2.12 dated 2013-06-25 and 0.2.13 dated 2013-06-25
Description: Variational algorithms and methods for fitting mixture
models. Main functions are varbayes, vbcomp, vbconstr, mppca,
mmppca and gmmkmsock.
Author: Pierrick Bruneau
Maintainer: Pierrick Bruneau
DESCRIPTION | 6 +++---
MD5 | 16 ++++++++--------
configure | 2 --
configure.ac | 2 --
man/dat1sample.Rd | 11 +----------
src/gmmkmsock.cpp | 9 ++++++---
src/knn.c | 3 ++-
src/utils.c | 19 +++++++++++--------
src/utils.h | 2 +-
9 files changed, 32 insertions(+), 38 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.3.2 dated 2013-06-20 and 0.3.3 dated 2013-06-25
Description: Basic R package to access data structures offered by any
BEFdata portal instance.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
DESCRIPTION | 10 ++---
MD5 | 50 +++++++++++++--------------
NEWS | 8 ++++
R/bef.portal.get.R | 5 +-
R/bef.portal.get.attachment.R | 4 +-
R/bef.portal.get.dataset.R | 6 +--
R/bef.portal.get.dataset_list.R | 5 +-
R/bef.portal.get.keywords.R | 5 +-
R/bef.portal.get.metadata.R | 4 +-
R/bef.portal.get.proposal.R | 4 +-
R/bef.tematres.search.R | 3 +
R/bef.tematres.search.broader_keywords.R | 3 +
R/bef.tematres.search.keywords.R | 3 +
R/bef.tematres.search.narrower_keywords.R | 3 +
R/zzz.R | 3 +
man/bef.portal.get.Rd | 1
man/bef.portal.get.attachment.Rd | 1
man/bef.portal.get.dataset.Rd | 1
man/bef.portal.get.dataset_list.Rd | 1
man/bef.portal.get.keywords.Rd | 1
man/bef.portal.get.metadata.Rd | 1
man/bef.portal.get.proposal.Rd | 1
man/bef.tematres.search.Rd | 1
man/bef.tematres.search.broader_keywords.Rd | 1
man/bef.tematres.search.keywords.Rd | 1
man/bef.tematres.search.narrower_keywords.Rd | 1
26 files changed, 73 insertions(+), 54 deletions(-)
Title: R genetic programming framework
Diff between rgp versions 0.2-4 dated 2011-10-20 and 0.3-4 dated 2013-06-25
Description: RGP is a simple modular Genetic Programming (GP) system
build in pure R. In addition to general GP tasks, the system
supports Symbolic Regression by GP through the familiar R model
formula interface. GP individuals are represented as R
expressions, an (optional) type system enables domain-specific
function sets containing functions of diverse domain- and range
types. A basic set of genetic operators for variation (mutation
and crossover) and selection is provided.
Author: Oliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein, Joerg
Stork, Martin Zaefferer
Maintainer: Oliver Flasch
rgp-0.2-4/rgp/R/breeding.r |only
rgp-0.2-4/rgp/R/building_blocks.r |only
rgp-0.2-4/rgp/R/complexity.r |only
rgp-0.2-4/rgp/R/creation.r |only
rgp-0.2-4/rgp/R/data_driven_gp.r |only
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rgp-0.3-4/rgp/DESCRIPTION | 37 -
rgp-0.3-4/rgp/MD5 | 275 +++++----
rgp-0.3-4/rgp/NAMESPACE | 262 ++++----
rgp-0.3-4/rgp/R/breeding.R |only
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rgp-0.3-4/rgp/R/complexity.R |only
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rgp-0.3-4/rgp/R/function_utils.R |only
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rgp-0.3-4/rgp/R/plot_utils.R |only
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rgp-0.3-4/rgp/R/recombination.R |only
rgp-0.3-4/rgp/R/rgp.R |only
rgp-0.3-4/rgp/R/search_heuristics.R |only
rgp-0.3-4/rgp/R/search_space.R |only
rgp-0.3-4/rgp/R/selection.R |only
rgp-0.3-4/rgp/R/similarity.R |only
rgp-0.3-4/rgp/R/stypes.R |only
rgp-0.3-4/rgp/R/symbolic_regression.R |only
rgp-0.3-4/rgp/R/test_utils.R |only
rgp-0.3-4/rgp/R/time_utils.R |only
rgp-0.3-4/rgp/inst/doc |only
rgp-0.3-4/rgp/man/arity.Rd | 17
rgp-0.3-4/rgp/man/arity.primitive.Rd | 19
rgp-0.3-4/rgp/man/booleanFunctionManipulation.Rd |only
rgp-0.3-4/rgp/man/breeding.Rd | 74 +-
rgp-0.3-4/rgp/man/buildingBlockTags.Rd | 31 -
rgp-0.3-4/rgp/man/buildingBlocks.Rd | 69 +-
rgp-0.3-4/rgp/man/customDist.Rd | 46 -
rgp-0.3-4/rgp/man/dataDrivenGeneticProgramming.Rd | 223 ++++---
rgp-0.3-4/rgp/man/defaultGPFunctionAndConstantSets.Rd | 42 -
rgp-0.3-4/rgp/man/do.call.ignore.unused.arguments.Rd | 30
rgp-0.3-4/rgp/man/embedDataFrame.Rd | 28
rgp-0.3-4/rgp/man/evolutionRestartConditions.Rd | 88 +-
rgp-0.3-4/rgp/man/evolutionRestartStrategies.Rd | 54 +
rgp-0.3-4/rgp/man/evolutionStopConditions.Rd | 100 ++-
rgp-0.3-4/rgp/man/exprChildrenOrEmptyList.Rd | 28
rgp-0.3-4/rgp/man/exprLabel.Rd | 20
rgp-0.3-4/rgp/man/exprToPlotmathExpr.Rd | 22
rgp-0.3-4/rgp/man/expressionComplexityMeasures.Rd | 105 ++-
rgp-0.3-4/rgp/man/expressionComposing.Rd | 21
rgp-0.3-4/rgp/man/expressionCounts.Rd | 89 +-
rgp-0.3-4/rgp/man/expressionCrossover.Rd | 93 ++-
rgp-0.3-4/rgp/man/expressionMutation.Rd | 304 ++++++----
rgp-0.3-4/rgp/man/expressionNames.Rd | 42 -
rgp-0.3-4/rgp/man/expressionSimilarityMeasures.Rd | 193 +++---
rgp-0.3-4/rgp/man/expressionTransformation.Rd | 120 ++-
rgp-0.3-4/rgp/man/extractAttributes.Rd | 36 -
rgp-0.3-4/rgp/man/formatSeconds.Rd | 33 -
rgp-0.3-4/rgp/man/funcToPlotmathExpr.Rd | 25
rgp-0.3-4/rgp/man/geneticProgramming.Rd | 267 +++++---
rgp-0.3-4/rgp/man/gpIndividualVisualization.Rd | 48 -
rgp-0.3-4/rgp/man/gridDesign.Rd |only
rgp-0.3-4/rgp/man/individualAnalysis.Rd | 21
rgp-0.3-4/rgp/man/inversePermutation.Rd | 24
rgp-0.3-4/rgp/man/is.sType.Rd | 17
rgp-0.3-4/rgp/man/iterate.Rd | 34 -
rgp-0.3-4/rgp/man/joinElites.Rd | 36 -
rgp-0.3-4/rgp/man/latinHypercubeDesign.Rd |only
rgp-0.3-4/rgp/man/lispLists.Rd | 78 +-
rgp-0.3-4/rgp/man/listSplittingAndGrouping.Rd | 90 +-
rgp-0.3-4/rgp/man/mae.Rd |only
rgp-0.3-4/rgp/man/makeAgeFitnessComplexityParetoGpSearchHeuristic.Rd |only
rgp-0.3-4/rgp/man/makeArchiveBasedParetoTournamentSearchHeuristic.Rd |only
rgp-0.3-4/rgp/man/makeClosure.Rd |only
rgp-0.3-4/rgp/man/makeCommaEvolutionStrategySearchHeuristic.Rd |only
rgp-0.3-4/rgp/man/makeFunctionFitnessFunction.Rd | 47 +
rgp-0.3-4/rgp/man/makeNaryFunctionFitnessFunction.Rd |only
rgp-0.3-4/rgp/man/makeRegressionFitnessFunction.Rd | 59 +
rgp-0.3-4/rgp/man/makeSeSymbolicFitnessFunction.Rd |only
rgp-0.3-4/rgp/man/makeTinyGpSearchHeuristic.Rd |only
rgp-0.3-4/rgp/man/mse.Rd | 19
rgp-0.3-4/rgp/man/multiNicheGeneticProgramming.Rd | 219 ++++---
rgp-0.3-4/rgp/man/multiNicheSymbolicRegression.Rd | 198 ++++--
rgp-0.3-4/rgp/man/new.alist.Rd | 21
rgp-0.3-4/rgp/man/new.function.Rd | 27
rgp-0.3-4/rgp/man/nmse.Rd |only
rgp-0.3-4/rgp/man/nondeterministicRanking.Rd | 40 -
rgp-0.3-4/rgp/man/normalize.Rd | 18
rgp-0.3-4/rgp/man/normalizedDesign.Rd |only
rgp-0.3-4/rgp/man/orderByParetoMeasure.Rd | 32 -
rgp-0.3-4/rgp/man/paretoSorting.Rd | 38 -
rgp-0.3-4/rgp/man/plotFunction3d.Rd |only
rgp-0.3-4/rgp/man/plotFunctions.Rd | 94 ++-
rgp-0.3-4/rgp/man/plotPopulationFitnessComplexity.Rd | 43 -
rgp-0.3-4/rgp/man/popfitness.Rd | 21
rgp-0.3-4/rgp/man/populationClustering.Rd | 41 -
rgp-0.3-4/rgp/man/populationCreation.Rd | 120 ++-
rgp-0.3-4/rgp/man/predict.symbolicRegressionModel.Rd | 53 +
rgp-0.3-4/rgp/man/print.sType.Rd | 14
rgp-0.3-4/rgp/man/randelt.Rd | 23
rgp-0.3-4/rgp/man/randomExpressionChilds.Rd | 30
rgp-0.3-4/rgp/man/randomExpressionCreation.Rd | 75 +-
rgp-0.3-4/rgp/man/randomExpressionCreationTyped.Rd | 86 +-
rgp-0.3-4/rgp/man/randomFunctionCreation.Rd | 62 +-
rgp-0.3-4/rgp/man/randomFunctionCreationTyped.Rd | 66 +-
rgp-0.3-4/rgp/man/randterminalTyped.Rd | 28
rgp-0.3-4/rgp/man/rangeTypeOfType.Rd | 17
rgp-0.3-4/rgp/man/rgp-package.Rd | 24
rgp-0.3-4/rgp/man/rgpTestingAndBenchmarking.Rd | 52 +
rgp-0.3-4/rgp/man/rmse.Rd | 19
rgp-0.3-4/rgp/man/sTypeConstructors.Rd | 73 +-
rgp-0.3-4/rgp/man/sTypeInference.Rd | 77 +-
rgp-0.3-4/rgp/man/safeGPfunctions.Rd | 74 +-
rgp-0.3-4/rgp/man/seSymbolic.Rd |only
rgp-0.3-4/rgp/man/seSymbolicFunction.Rd |only
rgp-0.3-4/rgp/man/searchSpaceDefinition.Rd | 168 +++--
rgp-0.3-4/rgp/man/selectionFunctions.Rd | 149 ++--
rgp-0.3-4/rgp/man/smse.Rd | 26
rgp-0.3-4/rgp/man/sortBy.Rd | 22
rgp-0.3-4/rgp/man/sortByRange.Rd | 18
rgp-0.3-4/rgp/man/sortByRanking.Rd | 22
rgp-0.3-4/rgp/man/sortByType.Rd | 18
rgp-0.3-4/rgp/man/sortingAlgorithms.Rd | 35 -
rgp-0.3-4/rgp/man/sse.Rd |only
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rgp-0.3-4/rgp/man/subDataFrame.Rd | 29
rgp-0.3-4/rgp/man/summary.geneticProgrammingResult.Rd | 44 -
rgp-0.3-4/rgp/man/symbolicRegression.Rd | 227 ++++---
rgp-0.3-4/rgp/man/tabulateFunction.Rd | 34 -
rgp-0.3-4/rgp/man/variablePresenceMaps.Rd |only
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rgp-0.3-4/rgp/src/initialization.h |only
rgp-0.3-4/rgp/src/list_utils.c | 10
rgp-0.3-4/rgp/src/list_utils.h | 8
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rgp-0.3-4/rgp/src/random_utils.h |only
rgp-0.3-4/rgp/src/sexp_utils.c | 203 ++++++
rgp-0.3-4/rgp/src/sexp_utils.h | 40 +
rgp-0.3-4/rgp/src/unification.c | 29
rgp-0.3-4/rgp/src/unification.h | 5
rgp-0.3-4/rgp/vignettes |only
172 files changed, 3885 insertions(+), 2153 deletions(-)
Title: Package for statistical age models analysis in optically
stimulated luminescence dating
Diff between RadialPlotter versions 1.7 dated 2013-06-19 and 1.8 dated 2013-06-25
Description: Package for estimating parameters of statistical age
models in optically stimulated luminescence dating dynamically.
Author: Peng Jun
Maintainer: Peng Jun
RadialPlotter-1.7/RadialPlotter/man/SGCED.Rd |only
RadialPlotter-1.7/RadialPlotter/src/sgc.f90 |only
RadialPlotter-1.8/RadialPlotter/DESCRIPTION | 8
RadialPlotter-1.8/RadialPlotter/MD5 | 23
RadialPlotter-1.8/RadialPlotter/NEWS | 2
RadialPlotter-1.8/RadialPlotter/R/RadialPlotter.R | 663 +++++------
RadialPlotter-1.8/RadialPlotter/licences/minpack |only
RadialPlotter-1.8/RadialPlotter/man/CW.Signal.data.Rd | 2
RadialPlotter-1.8/RadialPlotter/man/RadialPlotter-package.Rd | 12
RadialPlotter-1.8/RadialPlotter/man/RadialPlotter.Rd | 8
RadialPlotter-1.8/RadialPlotter/man/calED.Rd |only
RadialPlotter-1.8/RadialPlotter/man/decomp.Rd | 17
RadialPlotter-1.8/RadialPlotter/man/sgcED.Rd |only
RadialPlotter-1.8/RadialPlotter/src/calED.f90 |only
RadialPlotter-1.8/RadialPlotter/src/fmin.f90 |only
RadialPlotter-1.8/RadialPlotter/src/interpolate.f90 | 238 ---
16 files changed, 413 insertions(+), 560 deletions(-)
Title: Moving Epidemics Method R Package.
Diff between mem versions 1.2 dated 2012-10-01 and 1.3 dated 2013-06-25
Description: Modelization of influenza epidemics in order to monitor
future activity.
Author: Jose E. Lozano Alonso
Maintainer: Jose E. Lozano Alonso
DESCRIPTION | 11 ++++----
MD5 | 23 ++++++++++-------
NAMESPACE | 2 -
R/iconfianza.completo.R |only
R/iconfianza.percentil.boot.R | 16 +++++++-----
R/memintensity.R |only
R/memtrend.R |only
data/flucyl.rda |binary
man/epimem.Rd | 54 +++++++++++++++++++++++++++++++-----------
man/epitiming.Rd | 48 +++++++++++++++++++++++++++++--------
man/flucyl.Rd | 23 +++++++++++++----
man/mem-internal.Rd | 4 ++-
man/mem-package.Rd | 30 ++++++++++++++++-------
man/memintensity.Rd |only
man/memtrend.Rd |only
15 files changed, 149 insertions(+), 62 deletions(-)
Title: Provides tools for dimension reduction methods
Diff between edrGraphicalTools versions 1.0 dated 2010-04-27 and 2.0 dated 2013-06-25
More information about edrGraphicalTools at CRAN
Description: This package comes to illustrate the articles "A graphical
tool for selecting the number of slices and the dimension of
the model in SIR and SAVE approaches" and "Comparison of sliced
inverse regression approaches for underdetermined cases"
Author: Raphaël Coudret, Benoît Liquet and Jérôme Saracco
Maintainer:
DESCRIPTION | 21 +-
MD5 |only
NAMESPACE | 4
R/criterionRkh.R | 143 ++++++++------
R/edr.R | 388 ++++++++++++++++++++++++++++++++-------
R/edrGraphicalTools-internal.R | 89 ++++++++
R/edrSelec.R |only
R/plot.criterionRkh.R | 22 +-
R/plot.edr.R | 63 +++---
R/print.criterionRkh.R | 2
R/print.edr.R | 37 ++-
R/summary.criterionRkh.R | 2
R/summary.edr.R | 55 +++--
edrGraphicalTools-Ex.R |only
man/criterionRkh.Rd | 15 -
man/edr.Rd | 36 ++-
man/edrGraphicalTools-package.Rd | 61 ++++--
man/edrSelec.Rd |only
man/edrUnderdet.Rd |only
man/plot.criterionRkh.Rd | 5
man/plot.edr.Rd | 4
man/print.criterionRkh.Rd | 2
man/print.edr.Rd | 4
man/print.edrSelec.Rd |only
man/sliceMat.Rd |only
man/summary.criterionRkh.Rd | 4
man/summary.edr.Rd | 6
src |only
28 files changed, 704 insertions(+), 259 deletions(-)
Permanent link
Title: Variational Bayesian mixture models
Diff between VBmix versions 0.2.11 dated 2013-03-11 and 0.2.12 dated 2013-06-25
Description: Variational algorithms and methods for fitting mixture
models. Main functions are varbayes, vbcomp, vbconstr, mppca,
mmppca and gmmkmsock.
Author: Pierrick Bruneau
Maintainer: Pierrick Bruneau
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
man/RGBtoLab.Rd | 3 ++-
man/dat1sample.Rd | 16 +++++++++++++++-
man/datagen.Rd | 3 ++-
man/displayNnet.Rd | 3 ++-
man/displaySVM.Rd | 3 ++-
man/displayScatter.Rd | 5 ++++-
man/mymvn2plot.Rd | 3 ++-
src/utils.c | 35 +++++++++++++++++++++++------------
10 files changed, 65 insertions(+), 32 deletions(-)
Title: GUI for obtaining raw & transformed tests scores. Saves results
in tabular format.
Diff between TestScorer versions 1.1-0 dated 2013-04-19 and 1.2 dated 2013-06-24
Description: GUI for entering tests items and obtaining raw and
transformed scores. The results are shown in the console and
can be saved to a text file for further statistical analysis.
The GUI also generates scripts for scoring tests defined by the
user.
Author: Manel Salamero
Maintainer: Manel Salamero
DESCRIPTION | 15
MD5 | 16
NEWS | 8
R/TestScorer.R | 3379 +++++++++++++++++++++++++-------------------
inst/doc/TestScorerHelp.pdf |binary
inst/some.stuff/TST_DASS.r | 115 -
inst/some.stuff/TST_MHLC.r | 79 -
inst/some.stuff/TST_RAAS.r | 163 +-
man/TestScorer-internal.Rd | 2
9 files changed, 2225 insertions(+), 1552 deletions(-)
Title: Event History Analysis
Diff between eha versions 2.2-5 dated 2013-05-13 and 2.2-6 dated 2013-06-24
Description: Event history analysis: Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Parametric proportional hazards fitting with left truncation
and right censoring for common families of distributions,
piecewise constant hazards, and discrete models. AFT regression
for left truncated and right censored data. Binary and Poisson
regression for clustered data, fixed and random effects with
bootstrapping.
Author: Göran Broström
Maintainer: Göran Broström
ChangeLog | 10 ++++++++++
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++++----------
NAMESPACE | 2 +-
R/BCoxreg.R |only
R/check.dist.R | 4 ++++
R/coxreg.R | 15 ++++++++++++---
R/phreg.R | 8 ++++++++
R/plot.coxreg.R | 16 ++++++++++++----
R/plot.hazards.R |only
R/plot.hazdata.R | 21 +++++++++++++++++----
R/plot.phreg.R | 35 +++++++++++++++++++++++++++++------
eha-Ex.R |only
man/BCoxreg.Rd |only
man/plot.hazdata.Rd | 4 +++-
15 files changed, 114 insertions(+), 33 deletions(-)
Title: Generalized Eigenvalues and QZ Decomposition
Diff between QZ versions 0.1-1 dated 2013-06-04 and 0.1-2 dated 2013-06-24
Description: QZ package provides generalized eigenvalues and QZ
decomposition (generalized Schur form) for an N-by-N
non-symmetric matrix A or paired matrices (A,B) with
eigenvalues reordering mechanism. The package is mainly based
complex*16 and double precision of LAPACK library (version
3.4.2.)
Author: Wei-Chen Chen, partly adapted and using routines from LAPACK.
Maintainer: Wei-Chen Chen
QZ-0.1-1/QZ/demo/ex1_qz_geigen.r |only
QZ-0.1-1/QZ/man/22_fda_geigen.Rd |only
QZ-0.1-2/QZ/ChangeLog | 6 +++
QZ-0.1-2/QZ/DESCRIPTION | 8 ++---
QZ-0.1-2/QZ/MD5 | 28 +++++++++---------
QZ-0.1-2/QZ/R/s3_ordqz.r |only
QZ-0.1-2/QZ/R/s3_qz_geigen.r | 2 +
QZ-0.1-2/QZ/demo/00Index | 2 -
QZ-0.1-2/QZ/demo/ex1_geigen.r |only
QZ-0.1-2/QZ/demo/ex3_ordqz.r | 7 +++-
QZ-0.1-2/QZ/inst/doc/QZ-guide.pdf |binary
QZ-0.1-2/QZ/inst/doc/QZ-include/01-introduction.tex | 4 +-
QZ-0.1-2/QZ/inst/doc/QZ-include/03-implementation.tex | 6 +--
QZ-0.1-2/QZ/man/00_QZ-package.Rd | 2 -
QZ-0.1-2/QZ/man/21_qz_geigen.Rd | 7 +++-
QZ-0.1-2/QZ/man/23_qz.Rd | 4 +-
QZ-0.1-2/QZ/man/24_ordqz.Rd |only
QZ-0.1-2/QZ/man/30_fda_geigen.Rd |only
18 files changed, 47 insertions(+), 29 deletions(-)
Title: Probability Models for Ranking Data
Diff between pmr versions 1.2.0 dated 2013-05-20 and 1.2.1 dated 2013-06-24
Description: Descriptive statistics (mean rank, pairwise frequencies,
and marginal matrix), Analytic Hierarchy Process models (with
Saaty's and Koczkodaj's inconsistencies), probability models
(Luce models, distance-based models, and rank-ordered logit
models) and visualization with multidimensional preference
analysis for ranking data are provided. Current, only complete
rankings are supported by this package.
Author: Paul H. Lee and Philip L. H. Yu
Maintainer: Paul H. Lee
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/pmr-package.Rd | 4 ++--
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Global Soil Information Facilities
Diff between GSIF versions 0.3-2 dated 2013-04-24 and 0.3-3 dated 2013-06-24
Description: Global Soil Information Facilities - tools (standards and
functions) and sample datasets for global soil mapping.
Author: Tomislav Hengl [cre, aut], Bas Kempen [aut], Gerard Heuvelink
[aut], Brendan Malone [ctb], Hannes Reuter [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 12 +++++-----
MD5 | 55 ++++++++++++++++++++++++----------------------
NAMESPACE | 7 +++--
R/AAAA.R | 4 +++
R/FWTools.path.R | 4 +--
R/ZZZ.R | 2 -
R/fit.gstatModel.R | 8 +++---
R/fit.regModel.R | 17 +++++++++-----
R/fit.vgmModel.R | 7 ++++-
R/make.3Dgrid.R | 11 +++++----
R/predict.gstatModel.R | 43 ++++++++++++++++++++++++++---------
R/summary.R | 2 -
R/test.gstatModel.R |only
R/validate.R | 46 ++++++++++++++++++++------------------
man/GlobalSoilMap.Rd | 1
man/WPS.Rd | 1
man/fit.gstatModel.Rd | 20 +++++++++-------
man/fit.regModel.Rd | 7 ++---
man/fit.vgmModel.Rd | 1
man/gdalwarp.Rd |only
man/getID.Rd | 1
man/gstatModel.Rd | 2 +
man/make.3Dgrid.Rd | 7 ++---
man/makeGstatCmd.Rd | 3 +-
man/merge.Rd | 7 ++---
man/mpspline.Rd | 4 ++-
man/predict.gstatModel.Rd | 7 +++++
man/spfkm.Rd | 1
man/summary.Rd | 3 +-
man/test.gstatModel.Rd |only
30 files changed, 170 insertions(+), 113 deletions(-)
Title: Copula based cluster analysis
Diff between CoClust versions 0.2-7 dated 2012-08-05 and 0.2-9 dated 2013-06-24
Description: Copula based cluster analysis.
Author: Francesca Marta Lilja Di Lascio, Simone Giannerini
Maintainer: Simone Giannerini
ChangeLog.txt | 6 +
DESCRIPTION | 11 +
MD5 | 8 -
R/CoClust.R | 285 +++++++++++++++++++++++++------------------------
R/Internal_functions.R | 23 ++-
5 files changed, 183 insertions(+), 150 deletions(-)
Title: An R client for interacting with the White House's "We The
People" petition API.
Diff between wethepeople versions 0.5 dated 2013-06-04 and 0.6.1 dated 2013-06-24
Description: Implements an R client for the We The People petitions
API. The client supports loading petitions, signatures, and
users. Additionally, the package includes petition and
signature data samples. There are also several functions for
analyzing and visualizing the data. Term frequency calculations
and word clouds are supported using the tm and wordcloud
package, respectively. Petition and issue summary plots are
also implemented using the ggplot2 package. For additional
information about the We The People project, see
https://petitions.whitehouse.gov. Note that the API limits
requests to 10/second. For bulk data loading, please use the
data dump provided by the White House:
https://petitions.whitehouse.gov/developers
Author: Yoni Ben-Meshulam
Maintainer: Yoni Ben-Meshulam
DESCRIPTION | 8 +++++---
MD5 | 22 +++++++++++++++-------
NAMESPACE | 6 ++++++
NEWS | 10 ++++++++++
R/WeTheEntitiesAPIClient.r |only
R/WeThePeopleAPIClient.r | 9 ++++-----
R/melt_issues.r | 9 ++++++++-
R/plot_issue_signatures.r |only
R/plot_sentiment_analysis.r |only
R/plot_sentiment_density.r |only
R/wethepeople-package.r | 11 ++++++++++-
data/petitions.RData |binary
man/WeTheEntitiesAPIClient.Rd |only
man/plot_issue_signatures.Rd |only
man/plot_sentiment_analysis.Rd |only
man/plot_sentiment_density.Rd |only
16 files changed, 58 insertions(+), 17 deletions(-)
Title: Linear Predictive Models Based On The Liblinear C/C++ Library.
Diff between LiblineaR versions 1.80-6 dated 2013-03-26 and 1.80-7 dated 2013-06-24
Description: This R package is a wrapper around the liblinear C/C++
library for machine learning. LIBLINEAR is a linear classifier
for data with millions of instances and features. It supports
L2-regularized classifiers (such as L2-loss linear SVM, L1-loss
linear SVM, and logistic regression) as well as L1-regularized
classifiers (such as L2-loss linear SVM and logistic
regression). The main features of LiblineaR include multi-class
classification (one-vs-the rest, and Crammer & Singer method),
cross validation for model selection, probability estimates
(logistic regression only) or weights for unbalanced data. The
estimation of the models is particularly fast as compared to
other libraries. For more information on the C/C++ liblinear
library itself, refer to R.-E. Fan, K.-W. Chang, C.-J. Hsieh,
X.-R. Wang, and C.-J. Lin. LIBLINEAR: A Library for Large
Linear Classification, Journal of Machine Learning Research
9(2008), 1871-1874, available at
http://www.csie.ntu.edu.tw/~cjlin/liblinear . The two first
blocks of the package version indicates which version of
liblinear is currently supported. For example: 1.32-14 means
that the package supports the version 1.32 of liblinear.
Author: Thibault Helleputte
Maintainer: Thibault Helleputte
DESCRIPTION | 9 +++---
MD5 | 18 ++++++------
NEWS | 13 +++++++++
R/LiblineaR.R | 24 ++++++++++++----
R/predict.R | 27 ++++++++++++++----
man/LiblineaR-package.Rd | 4 +-
man/LiblineaR.Rd | 26 +++++++++++++++++-
man/predict.LiblineaR.Rd | 1
src/predictLinear.c | 30 ++++++++++++++++-----
src/trainLinear.c | 67 ++++++++++++++++++++++++++++++++---------------
10 files changed, 162 insertions(+), 57 deletions(-)
Title: eXtensible Time Series
Diff between xts versions 0.9-4 dated 2013-06-09 and 0.9-5 dated 2013-06-24
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Author: Jeffrey A. Ryan, Joshua M. Ulrich
Maintainer: Jeffrey A. Ryan
xts-0.9-4/xts/inst/doc/xts-faq.R |only
xts-0.9-4/xts/inst/doc/xts.R |only
xts-0.9-5/xts/DESCRIPTION | 10 +++++-----
xts-0.9-5/xts/MD5 | 14 ++++++--------
xts-0.9-5/xts/inst/doc/xts-faq.pdf |binary
xts-0.9-5/xts/inst/doc/xts.pdf |binary
xts-0.9-5/xts/inst/include/xts.h | 2 +-
xts-0.9-5/xts/inst/include/xtsAPI.h | 2 +-
xts-0.9-5/xts/src/endpoints.c | 2 +-
9 files changed, 14 insertions(+), 16 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.10.3 dated 2013-03-23 and 0.10.4 dated 2013-06-24
Description: The Rcpp package provides R functions as well as a C++
library which facilitate the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy.
All R types are supported (vectors, functions, environment, etc
...) and each type is mapped to a dedicated class. For
example, numeric vectors are represented as instances of the
Rcpp::NumericVector class, environments are represented as
instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette
provides a good entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as
documented in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing C++
functions and classes to the R level. The "Rcpp-modules"
vignette details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and
expression templates to achieve great performance while
exposing a syntax that is much nicer to use than the equivalent
low-level loop code. The "Rcpp-sugar" vignette gives an
overview of the feature.
Rcpp attributes provide a high-level syntax for declaring C++ functions
as callable from R and automatically generating the code
required to invoke them. Attributes are intended to facilitate
both interactive use of C++ within R sessions as well as to
support R package development. Attributes are built on top of
Rcpp modules and their implementation is based on previous work
in the inline package.
Many examples are included, and around 881 unit tests in 412 unit test
functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic
Rcpp API' was written during 2005 and 2006 by Dominick Samperi.
This code has been factored out of Rcpp into the package
RcppClassic, and it is still available for code relying on the
older interface. New development should always use this Rcpp
package instead.
Additional documentation is available via the paper by Eddelbuettel and
Francois (2011, JSS) paper and the book by Eddelbuettel (2013,
Springer); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by
Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel
ChangeLog | 174 ++
DESCRIPTION | 20
MD5 | 136 +-
R/Attributes.R | 31
TODO | 11
inst/CITATION | 2
inst/NEWS.Rd | 67 +
inst/THANKS | 2
inst/doc/Makefile | 15
inst/doc/Rcpp-FAQ.R |only
inst/doc/Rcpp-FAQ.pdf |binary
inst/doc/Rcpp-FAQ/Rcpp-FAQ.Rnw | 20
inst/doc/Rcpp-attributes.R |only
inst/doc/Rcpp-attributes.pdf |binary
inst/doc/Rcpp-extending.R |only
inst/doc/Rcpp-extending.pdf |binary
inst/doc/Rcpp-introduction.R |only
inst/doc/Rcpp-introduction.Rnw | 13
inst/doc/Rcpp-introduction.pdf |binary
inst/doc/Rcpp-modules.R |only
inst/doc/Rcpp-modules.pdf |binary
inst/doc/Rcpp-package.R |only
inst/doc/Rcpp-package.pdf |binary
inst/doc/Rcpp-quickref.R |only
inst/doc/Rcpp-quickref.pdf |binary
inst/doc/Rcpp-sugar.R |only
inst/doc/Rcpp-sugar.pdf |binary
inst/doc/Rcpp-unitTests.R |only
inst/doc/Rcpp-unitTests.pdf |binary
inst/doc/Rcpp.bib | 55
inst/doc/unitTests-results/Rcpp-unitTests.html | 24
inst/doc/unitTests-results/Rcpp-unitTests.txt | 47
inst/include/Rcpp/DataFrame.h | 3
inst/include/Rcpp/Date.h | 18
inst/include/Rcpp/DottedPair.h | 6
inst/include/Rcpp/Named.h | 2
inst/include/Rcpp/api/meat/DottedPair.h | 12
inst/include/Rcpp/api/meat/Vector.h | 33
inst/include/Rcpp/config.h | 2
inst/include/Rcpp/generated/DataFrame_generated.h | 122 -
inst/include/Rcpp/grow.h | 2
inst/include/Rcpp/module/Module_generated_CppFunction.h | 660 ++++++++--
inst/include/Rcpp/module/Module_generated_CppMethod.h | 398 ++++--
inst/include/Rcpp/module/Module_generated_Pointer_CppMethod.h | 390 +++--
inst/include/Rcpp/module/class.h | 3
inst/include/Rcpp/stats/random/rf.h | 6
inst/include/Rcpp/stats/random/runif.h | 7
inst/include/Rcpp/sugar/functions/all.h | 4
inst/include/Rcpp/sugar/functions/functions.h | 6
inst/include/Rcpp/sugar/functions/is_finite.h |only
inst/include/Rcpp/sugar/functions/is_infinite.h |only
inst/include/Rcpp/sugar/functions/is_na.h | 4
inst/include/Rcpp/sugar/functions/is_nan.h |only
inst/include/Rcpp/sugar/functions/na_omit.h |only
inst/include/Rcpp/traits/is_finite.h |only
inst/include/Rcpp/traits/is_infinite.h |only
inst/include/Rcpp/traits/is_na.h | 13
inst/include/Rcpp/traits/is_nan.h |only
inst/include/Rcpp/traits/named_object.h | 16
inst/include/Rcpp/traits/traits.h | 5
inst/include/Rcpp/vector/MatrixRow.h | 3
inst/include/Rcpp/vector/string_proxy.h | 13
inst/unitTests/cpp/Reference.cpp |only
inst/unitTests/cpp/S4.cpp |only
inst/unitTests/cpp/Vector.cpp | 47
inst/unitTests/cpp/dates.cpp |only
inst/unitTests/cpp/sugar.cpp | 17
inst/unitTests/runit.Date.R | 196 --
inst/unitTests/runit.Reference.R |only
inst/unitTests/runit.S4.R | 146 --
inst/unitTests/runit.Vector.R | 43
inst/unitTests/runit.sugar.R | 27
man/pluginsAttribute.Rd | 3
man/setRcppClass.Rd | 6
src/Date.cpp | 6
src/Makevars | 6
src/Module.cpp | 4
src/api.cpp | 118 +
src/attributes.cpp | 72 -
79 files changed, 1999 insertions(+), 1037 deletions(-)
Title: Generate LaTeX tables of descriptive statistics
Diff between reporttools versions 1.0.8 dated 2012-03-23 and 1.0.9 dated 2013-06-24
Description: The functions in this package are especially helpful when
writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach
reporttools-1.0.8/reporttools/inst/doc/jss.dtx |only
reporttools-1.0.8/reporttools/inst/doc/jsslogo.jpg |only
reporttools-1.0.8/reporttools/inst/doc/report.bib |only
reporttools-1.0.9/reporttools/DESCRIPTION | 9
reporttools-1.0.9/reporttools/MD5 | 46 -
reporttools-1.0.9/reporttools/NAMESPACE | 5
reporttools-1.0.9/reporttools/NEWS | 8
reporttools-1.0.9/reporttools/R/checkDateSuccession.r | 49 +
reporttools-1.0.9/reporttools/R/displayCrossTabs.r | 21
reporttools-1.0.9/reporttools/R/displayKbyC.r | 3
reporttools-1.0.9/reporttools/R/formatPval.R | 168 +++---
reporttools-1.0.9/reporttools/R/pairwise.fisher.test.r |only
reporttools-1.0.9/reporttools/R/tableContinuous.r | 386 +++++++-------
reporttools-1.0.9/reporttools/R/tableDate.r | 8
reporttools-1.0.9/reporttools/R/tableNominal.R | 13
reporttools-1.0.9/reporttools/R/transformVarNames.r | 11
reporttools-1.0.9/reporttools/R/twoGroupComparisons.r | 6
reporttools-1.0.9/reporttools/inst/doc/reporttools.R |only
reporttools-1.0.9/reporttools/inst/doc/reporttools.pdf |binary
reporttools-1.0.9/reporttools/man/checkDateSuccession.Rd | 6
reporttools-1.0.9/reporttools/man/pairwise.fisher.test.Rd |only
reporttools-1.0.9/reporttools/man/reporttools-package.Rd | 6
reporttools-1.0.9/reporttools/man/tableContinuous.Rd | 3
reporttools-1.0.9/reporttools/man/tableDate.Rd | 3
reporttools-1.0.9/reporttools/man/tableNominal.Rd | 12
reporttools-1.0.9/reporttools/vignettes |only
26 files changed, 408 insertions(+), 355 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.47 dated 2013-06-03 and 3.49 dated 2013-06-23
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++++++--------
NAMESPACE | 4 ++++
NEWS | 9 +++++++++
R/ChangeCoordinate.R |only
R/ScalePreviousPlot.R |only
R/add_phenology.R | 36 ++++++++++++------------------------
R/phenology-package.R | 4 ++--
R/plot_add.R |only
R/plot_errbar.R |only
R/read_phenology.R | 8 +++++---
man/ChangeCoordinate.Rd |only
man/ScalePreviousPlot.Rd |only
man/add_phenology.Rd | 27 +++++++++++++++------------
man/phenology-package.Rd | 2 +-
man/plot_add.Rd |only
man/plot_errbar.Rd |only
17 files changed, 68 insertions(+), 54 deletions(-)
Title: parallel implementation of the "segment" function of package
"DNAcopy"
Diff between ParDNAcopy versions 1.0 dated 2013-06-21 and 1.1 dated 2013-06-23
Description: parallelized version of the "segment" function from
Bioconductor package "DNAcopy", utilizing multi-core
computation on host CPU
Author: Alex krasnitz, Guoli Sun
Maintainer: Guoli Sun
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/parSegment.Rd | 4 +++-
3 files changed, 9 insertions(+), 7 deletions(-)
Title: Parameter estimation and prediction for hidden Markov and
semi-Markov models for data with multiple observation
sequences.
Diff between mhsmm versions 0.4.10 dated 2013-06-13 and 0.4.11 dated 2013-06-23
Description: Parameter estimation and prediction for hidden Markov and
semi-Markov models for data with multiple observation
sequences. Suitable for equidistant time series data, with
multivariate and/or missing data.
Author: Jared O'Connell
Maintainer: Jared O'Connell
mhsmm-0.4.10/mhsmm/vignettes/DHMM1.tex |only
mhsmm-0.4.11/mhsmm/ChangeLog | 4 +++-
mhsmm-0.4.11/mhsmm/DESCRIPTION | 8 ++++----
mhsmm-0.4.11/mhsmm/MD5 | 19 +++++++++----------
mhsmm-0.4.11/mhsmm/R/hmm_functions.R | 4 ++--
mhsmm-0.4.11/mhsmm/R/hsmm_functions.R | 10 ++++------
mhsmm-0.4.11/mhsmm/inst/doc/DHMM2.pdf |binary
mhsmm-0.4.11/mhsmm/man/hsmmfit.Rd | 14 ++++++++++++++
mhsmm-0.4.11/mhsmm/mhsmm-Ex.R | 14 ++++++++++++++
mhsmm-0.4.11/mhsmm/vignettes/fig/dhmm-clsfig1.pdf |binary
mhsmm-0.4.11/mhsmm/vignettes/fig/dhmm-clsfig2.pdf |binary
11 files changed, 50 insertions(+), 23 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models with Local
Dependence
Diff between hergm versions 1.3-7 dated 2013-05-27 and 1.3-8 dated 2013-06-23
Description: The R package 'hergm' implements Hierarchical
Exponential-Family Random Graph Models (HERGMs), which can be
used to model a wide range of relational data (networks).
'hergm' implements both simulation and Bayesian inference.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/hergm.R | 21 ---------------------
R/hergm.mcmc.R | 1 +
R/hergm.postprocess.R | 3 ++-
R/hergm.preprocess.R | 26 ++++++++++++++++++++++++--
R/hergm.set.mcmc.R | 2 +-
7 files changed, 38 insertions(+), 35 deletions(-)
Title: Trends and Unit Roots
Diff between fUnitRoots versions 2160.77 dated 2012-12-10 and 3010.78 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
ChangeLog | 6 ++++++
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
R/zzz.R | 27 +++++++++++++--------------
src/Makevars | 1 -
5 files changed, 29 insertions(+), 24 deletions(-)
Title: Regression Based Decision and Prediction
Diff between fRegression versions 2160.77 dated 2012-12-10 and 3010.78 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz (for the Rmetrics port), R core team (for lm()
from R's base and nnet() from nnet package); B.R. Ripley (for
glm() from R's base); S.N. Wood (for gam() from mgcv package);
N.N. (for ppr() from modreg package); M. O' Connors (for
functions from polspline package); and T. Hothorn, A. Zeileis
G. Millo and D. Mitchell (for bgtest(), bptest(), dwtest(),
gqtest(), harvtest(), hmctest(), raintest(), reset() and
resettest() from lmtest package)
Maintainer: Yohan Chalabi
ChangeLog | 7 +++++++
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
R/zzz.R | 29 ++++++++++++++---------------
src/Makevars | 1 -
5 files changed, 31 insertions(+), 25 deletions(-)
Title: Basics of Option Valuation
Diff between fOptions versions 2160.82 dated 2012-11-07 and 3010.83 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
ChangeLog | 6 ++++++
DESCRIPTION | 17 +++++++++--------
MD5 | 8 ++++----
R/zzz.R | 36 +++++++++++++++++++++---------------
src/Makevars | 1 -
5 files changed, 40 insertions(+), 28 deletions(-)
Title: Nonlinear and Chaotic Time Series Modelling
Diff between fNonlinear versions 2160.77 dated 2012-12-10 and 3010.78 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
ChangeLog | 6 ++++++
DESCRIPTION | 11 ++++++-----
MD5 | 8 ++++----
R/zzz.R | 29 ++++++++++++++---------------
src/Makevars | 1 -
5 files changed, 30 insertions(+), 25 deletions(-)
Title: EBM and Asian Option Valuation
Diff between fAsianOptions versions 3000.78 dated 2013-02-08 and 3010.79 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
ChangeLog | 9 +++++++++
DESCRIPTION | 11 ++++++-----
MD5 | 6 +++---
src/Makevars | 1 -
4 files changed, 18 insertions(+), 9 deletions(-)
Title: ARMA Time Series Modelling
Diff between fArma versions 2160.78 dated 2012-09-17 and 3010.79 dated 2013-06-23
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
ChangeLog | 11
DESCRIPTION | 17
MD5 | 14
NAMESPACE | 28
R/whittle.R | 1387 ++++++++++++++----------------
R/zzz.R | 31
inst/unitTests/runit.LongRangeModelling.R | 103 +-
src/Makevars | 1
8 files changed, 799 insertions(+), 793 deletions(-)
Title: Cores of Recurrent Events
Diff between CORE versions 1.0 dated 2013-06-21 and 1.1 dated 2013-06-23
Description: given a collection of intervals with integer start and end
positions, find recurrently targeted regions and estimate the
significance of finding. Randomization is implemented by
parallel methods, either using local host machines, or
submitting grid engine jobs.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun
DESCRIPTION | 9 +++++----
MD5 | 10 +++++-----
NAMESPACE | 2 +-
inst/doc/CORE.Rnw | 6 +++---
inst/doc/CORE.pdf |binary
vignettes/CORE.Rnw | 6 +++---
6 files changed, 17 insertions(+), 16 deletions(-)
Title: Tools to deal with fuzzy numbers
Diff between FuzzyNumbers versions 0.02 dated 2012-12-27 and 0.3-1 dated 2013-06-23
Description: The FuzzyNumbers package provides S4 classes and methods
to deal with Fuzzy Numbers: computations of arithmetic
operations, approximation by trapezoidal and piecewise linear
FNs, visualization, etc.
Author: Marek Gagolewski [aut, cre], Jan Caha [ctb]
Maintainer: Marek Gagolewski
FuzzyNumbers-0.02/FuzzyNumbers/LICENSE |only
FuzzyNumbers-0.02/FuzzyNumbers/R/Arithmetic-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/DiscontinuousFuzzyNumber.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/Extract-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/FuzzyNumber.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/PiecewiseLinearFuzzyNumber.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/PowerFuzzyNumber.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/TrapezoidalFuzzyNumber.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/alphaInterval-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/alphacut-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/ambiguity-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/convert-generators.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/core-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/distance-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/evaluate-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/expectedInterval-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/expectedValue-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/integrate.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/invert-generators.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/piecewiseLinearApproximation-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/plot-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/show-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/supp-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/trapezoidalApproximation-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/value-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/weightedExpectedValue-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/R/width-methods.R |only
FuzzyNumbers-0.02/FuzzyNumbers/man/approx.invert.Rd |only
FuzzyNumbers-0.02/FuzzyNumbers/man/convert.alpha.Rd |only
FuzzyNumbers-0.02/FuzzyNumbers/man/convert.side.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/.Rinstignore |only
FuzzyNumbers-0.3-1/FuzzyNumbers/DESCRIPTION | 65 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/MD5 | 156 +++++-----
FuzzyNumbers-0.3-1/FuzzyNumbers/NAMESPACE | 24 -
FuzzyNumbers-0.3-1/FuzzyNumbers/NEWS | 71 ++++
FuzzyNumbers-0.3-1/FuzzyNumbers/R/FuzzyNumbers-package.R | 64 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/R/auxiliary-convert.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/auxiliary-invert.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/class-DiscontinuousFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/class-FuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/class-PiecewiseLinearFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/class-PowerFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/class-TrapezoidalFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-Arithmetic.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-Extract.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-alphaInterval.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-alphacut.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-ambiguity.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-as.FuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-as.PiecewiseLinearFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-as.PowerFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-as.TrapezoidalFuzzyNumber.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-as.character.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-core.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-distance.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-evaluate.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-expectedInterval.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-expectedValue.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-fapply.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-integrate.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-piecewiseLinearApproximation.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-plot.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-show.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-supp.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-trapezoidalApproximation.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-value.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-weightedExpectedValue.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/R/methods-width.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/CITATION | 12
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/doc/FuzzyNumbers-Tutorial.Rnw |only
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/doc/FuzzyNumbers-Tutorial.pdf |binary
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/tests/run_package_test.R |only
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/tests/test-convgen.R | 28 -
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/tests/test-fn.R | 16 -
FuzzyNumbers-0.3-1/FuzzyNumbers/inst/tests/test-invert.R | 12
FuzzyNumbers-0.3-1/FuzzyNumbers/man/Arithmetic-methods.Rd | 139 +++++++-
FuzzyNumbers-0.3-1/FuzzyNumbers/man/DiscontinuousFuzzyNumber-class.Rd | 42 +-
FuzzyNumbers-0.3-1/FuzzyNumbers/man/DiscontinuousFuzzyNumber.Rd | 8
FuzzyNumbers-0.3-1/FuzzyNumbers/man/Extract-methods.Rd | 60 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/FuzzyNumber-class.Rd | 72 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/FuzzyNumber.Rd | 26 +
FuzzyNumbers-0.3-1/FuzzyNumbers/man/FuzzyNumbers-package.Rd | 119 ++++---
FuzzyNumbers-0.3-1/FuzzyNumbers/man/PiecewiseLinearFuzzyNumber-class.Rd | 48 ++-
FuzzyNumbers-0.3-1/FuzzyNumbers/man/PiecewiseLinearFuzzyNumber.Rd | 27 +
FuzzyNumbers-0.3-1/FuzzyNumbers/man/PowerFuzzyNumber-class.Rd | 42 ++
FuzzyNumbers-0.3-1/FuzzyNumbers/man/PowerFuzzyNumber.Rd | 10
FuzzyNumbers-0.3-1/FuzzyNumbers/man/TrapezoidalFuzzyNumber-class.Rd | 37 ++
FuzzyNumbers-0.3-1/FuzzyNumbers/man/TrapezoidalFuzzyNumber.Rd | 12
FuzzyNumbers-0.3-1/FuzzyNumbers/man/TriangularFuzzyNumber.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/alphaInterval-methods.Rd | 94 +++---
FuzzyNumbers-0.3-1/FuzzyNumbers/man/alphacut-methods.Rd | 56 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/ambiguity-methods.Rd | 58 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/approxInvert.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/as.FuzzyNumber.Rd | 49 ++-
FuzzyNumbers-0.3-1/FuzzyNumbers/man/as.PiecewiseLinearFuzzyNumber.Rd | 77 ++++
FuzzyNumbers-0.3-1/FuzzyNumbers/man/as.PowerFuzzyNumber.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/as.TrapezoidalFuzzyNumber.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/as.character-methods.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/convertAlpha.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/convertSide.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/core-methods.Rd | 54 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/distance-methods.Rd | 77 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/evaluate-methods.Rd | 48 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/expectedInterval-methods.Rd | 94 +++---
FuzzyNumbers-0.3-1/FuzzyNumbers/man/expectedValue-methods.Rd | 64 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/fapply-methods.Rd |only
FuzzyNumbers-0.3-1/FuzzyNumbers/man/integrateAlpha-methods.Rd | 72 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/integrate_discont_val.Rd | 7
FuzzyNumbers-0.3-1/FuzzyNumbers/man/piecewiseLinearApproximation-methods.Rd | 91 +++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/plot-methods.Rd | 139 ++++++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/show-methods.Rd | 55 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/supp-methods.Rd | 54 +--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/trapezoidalApproximation-methods.Rd | 75 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/value-methods.Rd | 61 ++-
FuzzyNumbers-0.3-1/FuzzyNumbers/man/weightedExpectedValue-methods.Rd | 76 ++--
FuzzyNumbers-0.3-1/FuzzyNumbers/man/width-methods.Rd | 62 +--
116 files changed, 1531 insertions(+), 922 deletions(-)
Title: Coupled dipole approximation in electromagnetic scattering
Diff between cda versions 1.3 dated 2012-11-28 and 1.3.3 dated 2013-06-23
Description: The cda package implements the coupled-dipole
approximation for electromagnetic scattering by sparse
collections of subwavelength particles, with a particular focus
on plasmonic nanoparticles in the visible regime. The
interaction matrix, and the solution of the linear system of
coupled-dipole equations are executed in C++ code for speed;
convenient wrapper functions are provided at the R level to
generate the particle clusters, calculate the extinction,
scattering, and absorption of light by particles with linearly
and circularly polarised light. Functions are also provided to
calculate orientation-averaged circular dichroism, and display
clusters of nanoparticles in three dimensions using OpenGL or
povray.
Author: Baptiste Auguie [aut, cre], LAPACK authors [cph] (copyrights
apply to src/zgels.f)
Maintainer: Baptiste Auguie
cda-1.3.3/cda/DESCRIPTION | 33 +++++++++++++--------------
cda-1.3.3/cda/MD5 | 21 ++++++++---------
cda-1.3.3/cda/NAMESPACE | 2 -
cda-1.3.3/cda/NEWS | 11 +++++++++
cda-1.3.3/cda/R/array_factor.R | 4 +--
cda-1.3.3/cda/inst/COPYRIGHTS |only
cda-1.3.3/cda/inst/doc/CD-theory.R |only
cda-1.3.3/cda/inst/tests/lowlevel.r | 11 ---------
cda-1.3.3/cda/inst/wiki/diffractive_chain2.R |only
cda-1.3.3/cda/inst/wiki/helix_cd.rmd | 2 -
cda-1.3.3/cda/man/array_factor.Rd | 2 -
cda-1.3/cda/LICENCE |only
cda-1.3/cda/R/epsilon.r |only
cda-1.3/cda/man/epsAg.Rd |only
cda-1.3/cda/man/epsAu.Rd |only
15 files changed, 42 insertions(+), 44 deletions(-)
Title: Competing risks regression for Stratified and Clustered data
Diff between crrSC versions 1.0.3 dated 2012-11-06 and 1.1 dated 2013-06-22
Description: Extension of cmprsk to Stratified and Clustered data.
Goodness of fit test for Fine-Gray model.
Author: Bingqing Zhou and Aurelien Latouche
Maintainer: Aurelien Latouche
DESCRIPTION | 10 +
MD5 | 13 +-
NAMESPACE | 10 -
R/pshtest.r |only
data/bce.RData |only
man/bce.Rd |only
man/pshtest.Rd |only
src/crrc.c |only
src/crrcc.c | 157 +++++++++++++++-----------
src/crrcs.c | 337 ++++++++++++++++++++++-----------------------------------
10 files changed, 247 insertions(+), 280 deletions(-)
Title: C++ implementations of phylogenetic calculations
Diff between cladoRcpp versions 0.11 dated 2013-04-11 and 0.14 dated 2013-06-22
Description: This package implements in C++/Rcpp various
cladogenesis-related calculations that are slow in pure R.
These include the calculation of the probability of various
scenarios for the inheritance of geographic range at the
divergence events on a phylogenetic tree, and other
calculations necessary for models which are not continuous-time
markov chains (CTMC), but where change instead occurs
instantaneously at speciation events. Typically these models
must assess the probability of every possible combination of
(ancestor state, left descendent state, right descendent
state). This means that there are up to (# of states)^3
combinations to investigate, and in biogeographical models,
there can easily be hundreds of states, so calculation time
becomes an issue. C++ implementation plus clever tricks (many
combinations can be eliminated a priori) can greatly speed the
computation time over naive R implementations.
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke
cladoRcpp-0.11/cladoRcpp/inst |only
cladoRcpp-0.14/cladoRcpp/DESCRIPTION | 8
cladoRcpp-0.14/cladoRcpp/MD5 | 39 -
cladoRcpp-0.14/cladoRcpp/R/cladoRcpp-package.R | 337 ++++++---
cladoRcpp-0.14/cladoRcpp/R/cladoRcpp.R | 132 ++-
cladoRcpp-0.14/cladoRcpp/man/Rcpp_combn_zerostart.Rd | 12
cladoRcpp-0.14/cladoRcpp/man/areas_list_to_states_list_old.Rd | 54 -
cladoRcpp-0.14/cladoRcpp/man/cladoRcpp-package.Rd | 363 ++++++----
cladoRcpp-0.14/cladoRcpp/man/numstates_from_numareas.Rd | 58 -
cladoRcpp-0.14/cladoRcpp/man/rcpp_areas_list_to_states_list.Rd | 34
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp.Rd | 19
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp_COOprobs.Rd | 19
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp_COOweights_faster.Rd | 29
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp_prebyte.Rd | 19
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp_rowsums.Rd | 19
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_anclikes_sp_using_COOprobs.Rd | 12
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_rowsums_for_COOweights_columnar.Rd | 16
cladoRcpp-0.14/cladoRcpp/man/rcpp_calc_splitlikes_using_COOweights_columnar.Rd | 16
cladoRcpp-0.14/cladoRcpp/man/rcpp_convolve.Rd | 8
cladoRcpp-0.14/cladoRcpp/man/rcpp_states_list_to_DEmat.Rd | 39 -
cladoRcpp-0.14/cladoRcpp/src/calc_anclikes_sp.cpp | 7
21 files changed, 648 insertions(+), 592 deletions(-)
Title: Spatial and Space-Time Point Pattern Analysis
Diff between splancs versions 2.01-32 dated 2013-01-16 and 2.01-33 dated 2013-06-22
Description: Spatial and Space-Time Point Pattern Analysis Functions
Author: Roger Bivand [cre], Barry Rowlingson [aut], Peter Diggle [aut],
Giovanni Petris [ctb], Stephen Eglen [ctb]
Maintainer: Roger Bivand
splancs-2.01-32/splancs/LICENCE |only
splancs-2.01-32/splancs/inst/LICENCE |only
splancs-2.01-33/splancs/ChangeLog | 17 +++++++++++++++++
splancs-2.01-33/splancs/DESCRIPTION | 21 +++++++++++++--------
splancs-2.01-33/splancs/MD5 | 13 ++++++-------
splancs-2.01-33/splancs/inst/ChangeLog | 17 +++++++++++++++++
splancs-2.01-33/splancs/inst/README |only
splancs-2.01-33/splancs/man/burkitt.Rd | 8 ++++++--
splancs-2.01-33/splancs/src/ptinpoly.c | 4 ++--
9 files changed, 61 insertions(+), 19 deletions(-)
Title: Interface between GRASS 6+ geographical information system and R
Diff between spgrass6 versions 0.8-1 dated 2013-05-02 and 0.8-2 dated 2013-06-22
Description: Interpreted interface between GRASS 6+ geographical
information system and R, based on starting R from within the
GRASS environment, or running free-standing R in a temporary
GRASS location; the package provides facilities for using all
GRASS commands from the R command line.
Author: Roger Bivand [cre, aut], Rainer Krug [ctb], Markus Neteler
[ctb]
Maintainer: Roger Bivand
ChangeLog | 9 +++++++++
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
inst/ChangeLog | 9 +++++++++
inst/doc/spgrass6_0.3.pdf |binary
man/initGRASS.Rd | 3 ++-
man/readRAST6.Rd | 7 +++++--
man/spgrass6.Rd | 3 ++-
8 files changed, 38 insertions(+), 15 deletions(-)
Title: Choose univariate class intervals
Diff between classInt versions 0.1-19 dated 2012-11-05 and 0.1-20 dated 2013-06-22
Description: A package for choosing univariate class intervals for
mapping or other graphics purposes
Author: Roger Bivand [aut, cre], Hisaji Ono [ctb], Richard Dunlap
[ctb], Matthieu Stigler [ctb]
Maintainer: Roger Bivand
ChangeLog | 31 +++++++++++++++++++++++++++++++
DESCRIPTION | 9 +++++----
MD5 | 16 ++++++++--------
R/classInt.R | 2 +-
inst/ChangeLog | 31 +++++++++++++++++++++++++++++++
man/classIntervals.Rd | 25 +++++++++++++++----------
man/findColours.Rd | 15 +++++++++------
man/findCols.Rd | 3 ++-
man/jenks.tests.Rd | 3 ++-
9 files changed, 104 insertions(+), 31 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Diff between rgeos versions 0.2-17 dated 2013-05-02 and 0.2-19 dated 2013-06-22
Description: Interface to Geometry Engine - Open Source (GEOS) using
the C API for topology operations on geometries. The GEOS
library is external to the package, and, when installing the
package from source, must be correctly installed first. Windows
and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut], Colin Rundel [aut], Edzer Pebesma
[ctb], Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand
ChangeLog | 43 ++++++
DESCRIPTION | 8 -
MD5 | 56 +++----
NAMESPACE | 2
R/labelpt.R | 217 +++++++++++++++++++++++++-----
R/rgeos_misc.R | 21 +-
R/rgeos_predicate_binary.R | 37 ++++-
R/rgeos_predicate_unary.R | 14 +
R/rgeos_topology.R | 18 ++
R/rgeos_topology_binary.R | 10 +
configure | 28 +++
configure.ac | 8 -
inst/ChangeLog | 43 ++++++
inst/SVN_VERSION | 2
man/comment-functions.Rd | 55 ++++---
man/constructor-SpatialCollections.Rd | 3
man/labelpt.Rd | 239 +++++++++++++++++++++++++---------
man/misc-gBuffer.Rd | 12 +
man/misc-gDistance.Rd | 5
man/pred-binary-gIntersects.Rd | 6
man/pred-binary-gRelate.Rd | 27 ++-
man/pred-unary-gIsValid.Rd | 23 ++-
man/topo-bin-gIntersection.Rd | 3
man/topo-bin-gUnion.Rd | 3
man/topo-unary-gCentroid.Rd | 3
man/topo-unary-gConvexHull.Rd | 3
man/topo-unary-gEnvelope.Rd | 3
man/topo-unary-gPointOnSurface.Rd | 10 -
man/topo-unary-gSimplify.Rd | 3
29 files changed, 694 insertions(+), 211 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.8-9 dated 2013-05-02 and 0.8-10 dated 2013-06-22
Description: Provides bindings to Frank Warmerdam's Geospatial Data
Abstraction Library (GDAL) (>= 1.6.3) and access to
projection/transformation operations from the PROJ.4 library.
The GDAL and PROJ.4 libraries are external to the package, and,
when installing the package from source, must be correctly
installed first. Both GDAL raster and OGR vector map data can
be imported into R, and GDAL raster data and OGR vector data
exported. Use is made of classes defined in the sp package.
Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and
Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut], Tim Keitt [aut], Barry Rowlingson
[aut], Edzer Pebesma [ctb], Michael Sumner [ctb], Robert
Hijmans [ctb]
Maintainer: Roger Bivand
ChangeLog | 33 +++++++++++++++++++++++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
R/ogr_sp.R | 9 ++++++++-
R/ogr_write.R | 2 +-
configure | 2 +-
configure.ac | 2 +-
inst/ChangeLog | 33 +++++++++++++++++++++++++++++++++
inst/SVN_VERSION | 2 +-
inst/doc/OGR_shape_encoding.pdf |binary
man/readGDAL.Rd | 2 +-
man/readOGR.Rd | 2 ++
man/spTransform-methods.Rd | 2 +-
man/writeOGR.Rd | 3 ++-
14 files changed, 101 insertions(+), 25 deletions(-)
Title: Geographically weighted regression
Diff between spgwr versions 0.6-19 dated 2013-01-10 and 0.6-21 dated 2013-06-22
Description: Functions for computing geographically weighted
regressions based on work by Chris Brunsdon, Martin Charlton
and Stewart Fortheringham, http://gwr.nuim.ie/
Author: Roger Bivand [cre, aut], Danlin Yu [aut], Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand
ChangeLog | 37 +++++++++++++++++++++++++++++++++++++
DESCRIPTION | 23 +++++++++++++----------
MD5 | 43 ++++++++++++++++++++++++-------------------
R/gwe.R | 22 ++++++++++++++--------
R/gwr.R | 11 +++++++----
R/gwr.cv.R | 11 +++++++----
R/gwr1.R | 11 +++++++----
R/gwr1.cv.R | 11 +++++++----
inst/ChangeLog | 37 +++++++++++++++++++++++++++++++++++++
inst/backstore |only
inst/doc |only
man/LMZ.F3GWR.test.Rd | 2 +-
man/georgia.Rd | 2 +-
man/ggwr.Rd | 2 +-
man/ggwr.sel.Rd | 2 +-
man/gw.cov.Rd | 2 +-
man/gwr.Rd | 2 +-
man/gwr.bisquare.Rd | 2 +-
man/gwr.cv.Rd | 2 +-
man/gwr.gauss.Rd | 2 +-
man/gwr.tricube.Rd | 2 +-
src/gwe.c | 2 +-
vignettes |only
23 files changed, 164 insertions(+), 64 deletions(-)
Title: GGEBiplotGUI: Interactive GGE Biplots in R
Diff between GGEBiplotGUI versions 1.0-5 dated 2013-05-01 and 1.0-6 dated 2013-06-22
Description: A GUI with which to construct and interact with GGE
biplots.
Author: Elisa Frutos Bernal
Maintainer: Elisa Frutos Bernal
ChangeLog | 1 +
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/GGEBiplot.R | 3 ++-
4 files changed, 10 insertions(+), 8 deletions(-)
Title: Discrete Beta Kernel Graduation of mortality data
Diff between DBKGrad versions 1.01 dated 2012-09-19 and 1.2 dated 2013-06-22
Description: This package allows for nonparametric graduation of
mortality rates using fixed or adaptive discrete beta kernel
estimator.
Author: Angelo Mazza and Antonio Punzo
Maintainer: Angelo Mazza
DBKGrad-1.01/DBKGrad/data/Sicily2008M.rda |only
DBKGrad-1.01/DBKGrad/man/Sicily2008M.Rd |only
DBKGrad-1.2/DBKGrad/DESCRIPTION | 12
DBKGrad-1.2/DBKGrad/MD5 | 16
DBKGrad-1.2/DBKGrad/NAMESPACE | 10
DBKGrad-1.2/DBKGrad/R/dbkGrad.R | 735 ++++++++++++++++++++++-------
DBKGrad-1.2/DBKGrad/data/ItalyM.RData |only
DBKGrad-1.2/DBKGrad/man/DBKGrad-package.Rd | 4
DBKGrad-1.2/DBKGrad/man/ItalyM.Rd |only
DBKGrad-1.2/DBKGrad/man/dbkGrad.Rd | 174 +++---
DBKGrad-1.2/DBKGrad/man/plot.dbkGrad.Rd | 115 ++--
11 files changed, 751 insertions(+), 315 deletions(-)
Title: Entropy and Mutual Information Estimation
Description: This package implements various estimators of entropy,
such as the shrinkage estimator by Hausser and Strimmer, the
maximum likelihood and the Millow-Madow estimator, various
Bayesian estimators, and the Chao-Shen estimator. It also
offers an R interface to the NSB estimator. Furthermore, it
provides functions for estimating mutual information.
Author: Jean Hausser and Korbinian Strimmer
Maintainer: Korbinian Strimmer
Diff between entropy versions 1.1.8 dated 2013-03-25 and 1.1.9 dated 2013-06-22
DESCRIPTION | 10 +++++-----
MD5 | 18 ++++++++++--------
NAMESPACE | 1 +
NEWS | 7 +++++++
R/discretize.R |only
man/discretize.Rd |only
man/entropy.Dirichlet.Rd | 2 +-
man/entropy.Rd | 9 ++++++---
man/entropy.empirical.Rd | 2 +-
man/entropy.plugin.Rd | 2 +-
man/entropy.shrink.Rd | 8 +++++---
11 files changed, 37 insertions(+), 22 deletions(-)
Title: Compiling the NHL Real Time Scoring System Database for easy use
in R
Description: Compiling the NHL Real Time Scoring System Database for
easy use in R
Author: A.C. Thomas, Samuel L. Ventura
Maintainer: A.C. Thomas
Diff between nhlscrapr versions 1.0 dated 2013-06-17 and 1.0.2 dated 2013-06-22
DESCRIPTION | 8 +--
MD5 | 14 +++---
R/convert-html.R | 109 ++++++++++++++++++++++++-----------------------
R/integrate.R | 25 +++++-----
data/nhl20022013.RData |binary
man/nhl20022013.Rd | 10 +++-
man/nhlscrapr-package.Rd | 4 -
man/process-games.Rd | 2
8 files changed, 91 insertions(+), 81 deletions(-)
Title: Generating and fitting truncated (gamlss.family) distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to defined truncated distributions in
GAMLSS models. The main function gen.trun() generates truncated
version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
Diff between gamlss.tr versions 4.1-0 dated 2012-02-21 and 4.2-6 dated 2013-06-21
gamlss.tr-4.1-0/gamlss.tr/R/gen.trun.R |only
gamlss.tr-4.1-0/gamlss.tr/R/trun.R |only
gamlss.tr-4.1-0/gamlss.tr/R/trun.d.R |only
gamlss.tr-4.1-0/gamlss.tr/R/trun.p.R |only
gamlss.tr-4.1-0/gamlss.tr/R/trun.q.R |only
gamlss.tr-4.1-0/gamlss.tr/R/trun.r.R |only
gamlss.tr-4.2-6/gamlss.tr/DESCRIPTION | 9
gamlss.tr-4.2-6/gamlss.tr/MD5 | 28 +-
gamlss.tr-4.2-6/gamlss.tr/R/gen.trun-21-06-13.R |only
gamlss.tr-4.2-6/gamlss.tr/R/trun-21-06-13.R |only
gamlss.tr-4.2-6/gamlss.tr/R/trun.d-27-12-12.R |only
gamlss.tr-4.2-6/gamlss.tr/R/trun.p-27-12-12.R |only
gamlss.tr-4.2-6/gamlss.tr/R/trun.q-27-12-12.R |only
gamlss.tr-4.2-6/gamlss.tr/R/trun.r-28-12-12.R |only
gamlss.tr-4.2-6/gamlss.tr/man/gamlss.tr.package.Rd | 19 -
gamlss.tr-4.2-6/gamlss.tr/man/gen.trun.Rd | 118 ++++----
gamlss.tr-4.2-6/gamlss.tr/man/trun.Rd | 9
gamlss.tr-4.2-6/gamlss.tr/man/trun.d.Rd | 291 ++++++++++++---------
gamlss.tr-4.2-6/gamlss.tr/man/trun.p.Rd | 279 ++++++++++++--------
gamlss.tr-4.2-6/gamlss.tr/man/trun.q.Rd | 116 +++++---
gamlss.tr-4.2-6/gamlss.tr/man/trun.r.Rd | 192 ++++++++-----
21 files changed, 624 insertions(+), 437 deletions(-)
Title: Fitting an interval response variable using gamlss.family
distributions
Description: This is an add on package to GAMLSS. The purpose of this
package is to allow users to fit interval response variables in
GAMLSS models. The main function gen.cens() generates a
censored version of an existing GAMLSS family distribution.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
Diff between gamlss.cens versions 4.1.0 dated 2012-02-21 and 4.2.6 dated 2013-06-21
DESCRIPTION | 9
MD5 | 20 +-
R/cens.R | 532 ++++++++++++++++++++++++++++----------------------------
R/cens.d.R | 86 ++++-----
R/cens.p.R | 96 +++++-----
R/gen.cens.R | 98 +++++-----
data/lip.rda |binary
man/cens.Rd | 261 ++++++++++++++-------------
man/cens.d.Rd | 90 ++++-----
man/cens.p.Rd | 86 ++++-----
man/gen.cens.Rd | 103 +++++-----
11 files changed, 703 insertions(+), 678 deletions(-)
Title: Download, manipulate, and present data from the US Census
American Community Survey
Description: Provides a general toolkit for downloading, managing,
analyzing, and presenting data from the U.S. Census American
Community Survey (ACS). Confidence intervals provided with the
data are converted to standard errors to be bundled with
estimates in complex acs objects. Package provides new methods
to conduct standard operations and tests of significance on acs
objects in statistically appropriate ways. Current version is
1.0 +/- .05.
Author: Ezra Haber Glenn
Maintainer: Ezra Haber Glenn
Diff between acs versions 0.8 dated 2012-03-18 and 1.0 dated 2013-06-21
DESCRIPTION | 31
MD5 | 58 +
NAMESPACE | 17
R-bkp |only
R/acs.R | 1305 +++++++++++++++++++++++++++++++++------
data/cpi.rda |binary
data/fips.county.rda |only
data/fips.county.subdivision.rda |only
data/fips.place.rda |only
data/fips.state.rda |only
data/kansas07.rda |binary
data/kansas09.rda |binary
data/lawrence10.rda |binary
inst |only
man/acs-class.Rd | 23
man/acs-package.Rd | 22
man/acs.fetch.Rd |only
man/acs.lookup-class.Rd |only
man/acs.lookup.Rd |only
man/api.key.install.Rd |only
man/currency.convert.Rd | 4
man/currency.year.Rd | 4
man/divide.acs.Rd |only
man/endyear.Rd | 5
man/fips.state.Rd |only
man/flatten.geo.set.Rd |only
man/geo.lookup.Rd |only
man/geo.make.Rd |only
man/geo.set-class.Rd |only
man/geography.Rd | 15
man/kansas07.Rd | 6
man/kansas09.Rd | 4
man/lawrence10.Rd | 2
man/plot-methods.Rd | 28
man/prompt.acs.Rd | 4
man/read.acs.Rd | 68 +-
man/sum-methods.Rd | 45 +
37 files changed, 1362 insertions(+), 279 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial
responses using a local odds ratios parameterization.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
Diff between multgee versions 1.2 dated 2013-05-30 and 1.3 dated 2013-06-21
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 3 +++
R/nomLORgee.R | 2 +-
R/ordLORgee.R | 2 +-
5 files changed, 13 insertions(+), 10 deletions(-)
Title: Meta-Analysis Package for R
Description: The metafor package provides a comprehensive collection of
functions for conducting meta-analyses in R. The package
includes functions to calculate various effect size or outcome
measures, fit fixed-, random-, and mixed-effects models to such
data, carry out moderator and meta-regression analyses, and
create various types of meta-analytical plots (e.g., forest,
funnel, radial, and L'Abbe plots). For meta-analyses of 2x2
tables, proportions, incidence rates, and incidence rate
ratios, the package also provides functions that implement
specialized methods, including the Mantel-Haenszel method,
Peto's method, and a variety of suitable generalized linear
(mixed-effects) models (i.e., mixed-effects (conditional)
logistic and Poisson regression models).
Author: Wolfgang Viechtbauer
Maintainer: Wolfgang Viechtbauer
Diff between metafor versions 1.8-0 dated 2013-04-11 and 1.9-0 dated 2013-06-21
metafor-1.8-0/metafor/inst/doc/viechtbauer2010.pdf |only
metafor-1.8-0/metafor/vignettes/viechtbauer2010.Rnw |only
metafor-1.9-0/metafor/DESCRIPTION | 12
metafor-1.9-0/metafor/MD5 | 74 -
metafor-1.9-0/metafor/NAMESPACE | 1
metafor-1.9-0/metafor/NEWS | 103 +-
metafor-1.9-0/metafor/R/metafor.R | 978 +++++++++++++------
metafor-1.9-0/metafor/data/dat.bangertdrowns2004.rda |only
metafor-1.9-0/metafor/data/dat.bcg.rda |binary
metafor-1.9-0/metafor/data/dat.bonett2010.rda |binary
metafor-1.9-0/metafor/data/dat.colditz1994.rda |binary
metafor-1.9-0/metafor/data/dat.collins1985a.rda |binary
metafor-1.9-0/metafor/data/dat.collins1985b.rda |binary
metafor-1.9-0/metafor/data/dat.curtis1998.rda |binary
metafor-1.9-0/metafor/data/dat.hackshaw1998.rda |binary
metafor-1.9-0/metafor/data/dat.hart1999.rda |binary
metafor-1.9-0/metafor/data/dat.hine1989.rda |binary
metafor-1.9-0/metafor/data/dat.lee2004.rda |only
metafor-1.9-0/metafor/data/dat.mcdaniel1994.rda |binary
metafor-1.9-0/metafor/data/dat.nielweise2007.rda |binary
metafor-1.9-0/metafor/data/dat.nielweise2008.rda |binary
metafor-1.9-0/metafor/data/dat.normand1999.rda |binary
metafor-1.9-0/metafor/data/dat.pritz1997.rda |binary
metafor-1.9-0/metafor/data/dat.raudenbush1985.rda |binary
metafor-1.9-0/metafor/data/dat.yusuf1985.rda |binary
metafor-1.9-0/metafor/inst/doc/metafor.pdf |only
metafor-1.9-0/metafor/inst/doc/metafor_diagram.pdf |only
metafor-1.9-0/metafor/man/anova.rma.uni.Rd | 32
metafor-1.9-0/metafor/man/confint.rma.uni.Rd | 2
metafor-1.9-0/metafor/man/dat.bangertdrowns2004.Rd |only
metafor-1.9-0/metafor/man/dat.lee2004.Rd |only
metafor-1.9-0/metafor/man/escalc.Rd | 2
metafor-1.9-0/metafor/man/fsn.Rd | 13
metafor-1.9-0/metafor/man/hc.Rd |only
metafor-1.9-0/metafor/man/metafor-package.Rd | 8
metafor-1.9-0/metafor/man/print.anova.rma.uni.Rd | 2
metafor-1.9-0/metafor/man/print.hc.rma.uni.Rd |only
metafor-1.9-0/metafor/man/print.rma.uni.Rd | 15
metafor-1.9-0/metafor/man/qqnorm.rma.uni.Rd | 2
metafor-1.9-0/metafor/man/rma.glmm.Rd | 32
metafor-1.9-0/metafor/man/rma.uni.Rd | 13
metafor-1.9-0/metafor/man/trimfill.rma.uni.Rd | 15
metafor-1.9-0/metafor/vignettes/metafor.Rnw |only
metafor-1.9-0/metafor/vignettes/metafor_diagram.Rnw |only
44 files changed, 913 insertions(+), 391 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
Diff between gamlss versions 4.2-5 dated 2013-05-26 and 4.2-6 dated 2013-06-21
gamlss-4.2-5/gamlss/R/LR-test.R |only
gamlss-4.2-5/gamlss/R/SUMMARY-26-03-13.R |only
gamlss-4.2-5/gamlss/R/confint-gamlss-02-05-13.R |only
gamlss-4.2-5/gamlss/R/gen-Likelihood-22-03-13.R |only
gamlss-4.2-5/gamlss/R/lms-23-5-13.r |only
gamlss-4.2-5/gamlss/R/lms.r |only
gamlss-4.2-5/gamlss/R/vcoc-gamlss-22-03-13.R |only
gamlss-4.2-6/gamlss/DESCRIPTION | 8 -
gamlss-4.2-6/gamlss/MD5 | 34 +++--
gamlss-4.2-6/gamlss/NAMESPACE | 152 ++++++++++++------------
gamlss-4.2-6/gamlss/R/LR-test-12-06-2013.R |only
gamlss-4.2-6/gamlss/R/SUMMARY-15-06-13.R |only
gamlss-4.2-6/gamlss/R/confint-gamlss-17-06-13.R |only
gamlss-4.2-6/gamlss/R/extra.R | 3
gamlss-4.2-6/gamlss/R/fitDist17-05-13.R |only
gamlss-4.2-6/gamlss/R/gen-Likelihood-12-06-13.R |only
gamlss-4.2-6/gamlss/R/get-K-rvcov-16-06-2913.R |only
gamlss-4.2-6/gamlss/R/getSmo-18-6-13.R |only
gamlss-4.2-6/gamlss/R/lms-20-6-13.r |only
gamlss-4.2-6/gamlss/R/vcoc-gamlss-16-06-13.R |only
gamlss-4.2-6/gamlss/inst/doc/NEWS.txt | 18 ++
gamlss-4.2-6/gamlss/man/LR.test.Rd | 100 +++++++--------
gamlss-4.2-6/gamlss/man/getSmo.Rd |only
gamlss-4.2-6/gamlss/man/lms.Rd | 36 +++--
gamlss-4.2-6/gamlss/man/lpred.Rd | 122 +++++++++----------
gamlss-4.2-6/gamlss/man/rvcov.Rd |only
gamlss-4.2-6/gamlss/man/summary.gamlss.Rd | 104 ++++++++--------
27 files changed, 307 insertions(+), 270 deletions(-)
Title: String distance functions for R
Diff between stringdist versions 0.4-2 dated 2013-02-11 and 0.5.0 dated 2013-06-21
Description: Implements the following string distance functions: Q-gram
distance, Hamming distance, (weighted) Levenshtein, (weighted)
restricted Damerau-Levenshtein (a.k.a. optimal string
alignment), (weighted) Damerau-Levenshtein distance, longest
common substring distance.
Author: Mark van der Loo
Maintainer: Mark van der Loo
stringdist-0.4-2/stringdist/x.R |only
stringdist-0.5.0/stringdist/DESCRIPTION | 19 +
stringdist-0.5.0/stringdist/MD5 | 30 +--
stringdist-0.5.0/stringdist/NAMESPACE | 1
stringdist-0.5.0/stringdist/NEWS | 11 +
stringdist-0.5.0/stringdist/R/stringdist.R | 112 ++++++++---
stringdist-0.5.0/stringdist/R/utils.R |only
stringdist-0.5.0/stringdist/inst/tests/testQgrams.R |only
stringdist-0.5.0/stringdist/inst/tests/testStringdist.R | 77 +++++++
stringdist-0.5.0/stringdist/man/qgrams.Rd |only
stringdist-0.5.0/stringdist/man/stringdist.Rd | 158 ++++++++++++----
stringdist-0.5.0/stringdist/src/dl.c | 33 ++-
stringdist-0.5.0/stringdist/src/hamming.c | 69 +++---
stringdist-0.5.0/stringdist/src/lcs.c |only
stringdist-0.5.0/stringdist/src/lv.c | 41 ++--
stringdist-0.5.0/stringdist/src/osa.c | 37 ++-
stringdist-0.5.0/stringdist/src/qgram.c |only
stringdist-0.5.0/stringdist/src/qgram2.c |only
stringdist-0.5.0/stringdist/src/utils.c | 1
stringdist-0.5.0/stringdist/tmp |only
20 files changed, 436 insertions(+), 153 deletions(-)
Title: Seismic Time Series Analysis Tools
Diff between RSEIS versions 3.0-9 dated 2012-07-30 and 3.2-1 dated 2013-06-21
Description: Multiple interactive codes to view and analyze seismic
data, via spectrum analysis, wavelet transforms, particle
motion, hodograms. Includes general time-series tools,
plotting, filtering, interactive display.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees
DESCRIPTION | 11 -
MD5 | 439 ++++++++++++++++++++++-----------------------
NEWS | 15 +
R/CHOP.SEISN.R | 1
R/FmakeDB.R |only
R/GETARAIC.R | 29 ++
R/JGET.seis.R | 19 +
R/JSAC.seis.R | 22 +-
R/JSEGY.seis.R | 62 +++++-
R/Mine.seis.R | 7
R/PICK.DOC.R | 139 ++++++--------
R/ReadInstr.R |only
R/YPIX.R | 2
R/buttonFUNCS.R | 6
R/getseis24.R | 8
R/hilbert.R | 4
R/makeDB.R | 24 +-
R/pickFUNCS.R | 23 +-
R/plotDB.R | 2
R/repairWPX.R | 21 ++
R/setupDB.R | 6
R/swig.R | 2
R/view.seis.R | 4
R/wigFUNCS.R | 64 ++++++
R/wlet.drive.R | 24 +-
R/write1sac.R | 9
R/xtract.trace.R | 10 +
inst/doc/hodo.R |only
inst/doc/hodo.pdf |binary
inst/doc/rseis.R |only
inst/doc/rseis.pdf |binary
man/ASCII.SEISN.Rd | 2
man/BUTREPLOT.Rd | 8
man/CE1.Rd | 2
man/CHOP.SEISN.Rd | 4
man/Comp1Dvel.Rd | 32 +--
man/Comp1Dvels.Rd | 32 +--
man/DAYSperYEAR.Rd | 2
man/DISPLACE.SEISN.Rd | 30 +--
man/DOsgram.Rd | 27 +-
man/EPOCHday.Rd | 4
man/EPOCHyear.Rd | 8
man/ETECTG.Rd | 5
man/FILT.SEISN.Rd | 16 -
man/FILT.spread.Rd | 17 +
man/FRWDft.Rd | 6
man/GAZI.Rd | 19 +
man/GETARAIC.Rd | 20 +-
man/GH.Rd | 14 -
man/GreatDist.Rd | 10 -
man/INSTFREQS.Rd | 6
man/INSTresponse.Rd | 4
man/INVRft.Rd | 6
man/JBLACK.Rd | 2
man/JGET.seis.Rd | 31 +--
man/JGRAY.Rd | 2
man/JSAC.seis.Rd | 32 +--
man/KH.Rd | 18 +
man/LocalUnwrap.Rd | 13 -
man/MTM.drive.Rd | 25 +-
man/MTMdisp.Rd | 6
man/MTMgabor.Rd | 22 +-
man/MTMplot.Rd | 4
man/Mine.seis.Rd | 8
man/Mmorlet.Rd | 2
man/NEWPLOT.WPX.Rd | 4
man/OH.Rd | 23 +-
man/P2GH.Rd | 4
man/PICK.DOC.Rd | 4
man/PLOT.ALLPX.Rd | 6
man/PLOT.MATN.Rd | 20 +-
man/PLOT.SEISN.Rd | 34 +--
man/PLOT.TTCURVE.Rd | 9
man/PLTpicks.Rd | 4
man/PMOT.drive.Rd | 8
man/PSTLTcurve.Rd | 20 +-
man/PreSet.Instr.Rd | 2
man/RSEIS-package.Rd | 4
man/Ray.time1D.Rd | 9
man/ReadInstr.Rd |only
man/ReadSet.Instr.Rd | 4
man/SELBUT.Rd | 5
man/SNET.drive.Rd | 4
man/SPECT.drive.Rd | 22 +-
man/STLTcurve.Rd | 6
man/TOCART.Rd | 4
man/VELMOD1D.Rd | 2
man/VELOCITY.SEISN.Rd | 31 +--
man/XTR.Rd | 14 -
man/YPIX.Rd | 8
man/YRsecdif.Rd | 8
man/ZOOM.SEISN.Rd | 6
man/Zdate.Rd | 8
man/addWPX.Rd | 6
man/addtix.Rd | 4
man/applytaper.Rd | 4
man/attime12.Rd | 11 -
man/autoreg.Rd | 4
man/brune.doom.Rd | 4
man/brune.search.Rd | 19 +
man/butfilt.Rd | 7
man/catWPX.Rd | 6
man/checkWPX.Rd | 2
man/choosfilt.Rd | 6
man/cleanWPX.Rd | 2
man/cleanpickfile.Rd | 2
man/colorwig.Rd | 4
man/comp.env.Rd | 6
man/complex.hodo.Rd | 10 -
man/contwlet.Rd | 4
man/convert2Rseis.Rd | 32 +--
man/deconinst.Rd | 8
man/deleteWPX.Rd | 8
man/detail.pick.Rd | 4
man/detrend.Rd | 10 -
man/distseisnXY.Rd | 6
man/doGABOR.AR.Rd | 18 -
man/doGABOR.MTM.Rd | 9
man/editDB.Rd | 24 --
man/envelope.Rd | 4
man/evolAR.Rd | 27 +-
man/evolMTM.Rd | 24 +-
man/evolfft.Rd | 14 -
man/filedatetime.Rd | 4
man/filterstamp.Rd | 12 -
man/finteg.Rd | 4
man/fixUWstasLL.Rd | 4
man/fixcomps.Rd | 2
man/fromjul.Rd | 8
man/gaddtix.Rd | 10 -
man/genrick.Rd | 10 -
man/get.corner.Rd | 20 +-
man/get.slepians.Rd | 8
man/getIRIS.Rd | 6
man/getPDEcsv.Rd | 10 -
man/getphaselag2.Rd | 14 -
man/getseis24.Rd | 9
man/getvertsorder.Rd | 6
man/gpoly.Rd | 2
man/grotseis.Rd | 66 +++---
man/hilbert.Rd | 4
man/hilow.Rd | 6
man/hodogram.Rd | 10 -
man/hypot.Rd | 9
man/idpoints.hodo.Rd | 18 +
man/infoDB.Rd | 6
man/insertNAs.Rd | 4
man/jadjust.length.Rd | 2
man/jitter.lab.Rd | 56 ++---
man/jlegend.Rd | 6
man/jstats.Rd | 2
man/leests.Rd | 2
man/letter.it.Rd | 4
man/logspace.Rd | 4
man/longfft.Rd | 22 +-
man/makeDB.Rd | 80 +++++---
man/makefreq.Rd | 6
man/markseis24.Rd | 18 +
man/matsquiggle.Rd | 23 +-
man/mirror.matrix.Rd | 2
man/mtapspec.Rd | 5
man/next2.Rd | 4
man/parseFN2STA.Rd | 2
man/partmotnet.Rd | 8
man/peaks.Rd | 8
man/pickit.Rd | 8
man/pickseis24.Rd | 12 -
man/plocator.Rd | 4
man/plotDB.Rd | 6
man/plotJGET.Rd | 4
man/plotarrivals.Rd | 2
man/plotevol.Rd | 36 +--
man/plotseis24.Rd | 6
man/plotwlet.Rd | 7
man/plt.MTM0.Rd | 49 ++---
man/prep1wig.Rd | 56 +++--
man/prepSEIS.Rd | 52 ++---
man/pwlet2freqs.Rd | 10 -
man/rDUMPLOC.Rd | 8
man/rdistaz.Rd | 12 -
man/recdate.Rd | 8
man/repairWPX.Rd | 6
man/replaceWPX.Rd | 6
man/rsspec.taper.Rd | 4
man/ruler.Rd | 2
man/saveWPX.Rd | 4
man/scal2freqs.Rd | 14 -
man/secdif.Rd | 11 -
man/secdifL.Rd | 11 -
man/secdifv.Rd | 11 -
man/seiscols.Rd | 6
man/seisorder.Rd | 9
man/selAPX.Rd | 4
man/setWPX.Rd | 6
man/setstas.Rd | 8
man/setupDB.Rd | 8
man/setwelch.Rd | 43 ++--
man/setwpix.Rd | 28 +-
man/setypx.Rd | 2
man/showdatetime.Rd | 5
man/sigconv.Rd | 20 +-
man/sigconvGR.Rd | 24 +-
man/swig.ALLPX.Rd | 6
man/swig.Rd | 17 +
man/symshot1.Rd | 2
man/trapz.Rd | 2
man/travel.time1D.Rd | 4
man/tung.pulse.Rd | 4
man/varsquig.Rd | 8
man/varsquiggle.Rd | 14 -
man/view.seis.Rd | 61 +++---
man/wiggle.env.Rd | 2
man/winmark.Rd | 23 +-
man/winseis24.Rd | 6
man/wlet.do.Rd | 25 +-
man/write1sac.Rd | 45 ++--
man/writeUW.Commentcard.Rd | 4
man/writeUW.DOTcard.Rd | 4
man/writeUW.Fcard.Rd | 2
man/xcor2.Rd | 16 -
man/xprod.Rd | 6
man/xtract.trace.Rd | 2
src/ARAIC.c | 14 -
223 files changed, 1834 insertions(+), 1405 deletions(-)
Title: Continuous Time Autoregressive Models
Diff between cts versions 1.0-16 dated 2013-06-13 and 1.0-17 dated 2013-06-21
Description: Continuous Time Autoregressive Models and the Kalman
Filter
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port
by Zhu Wang with contribution from John Nash, Netlib and NAG
authors
Maintainer: Zhu Wang
cts-1.0-16/cts/inst/doc/kf.bib |only
cts-1.0-16/cts/src/dgetrf.f |only
cts-1.0-16/cts/src/dgetrs.f |only
cts-1.0-17/cts/DESCRIPTION | 9 +++++----
cts-1.0-17/cts/MD5 | 12 ++++++------
cts-1.0-17/cts/NEWS | 7 ++++++-
cts-1.0-17/cts/inst/COPYRIGHTS |only
cts-1.0-17/cts/inst/doc/kf.pdf |binary
cts-1.0-17/cts/vignettes |only
9 files changed, 17 insertions(+), 11 deletions(-)
Title: Analysis of configuration frequencies (CFA)
Diff between cfa versions 0.9-2 dated 2011-05-24 and 0.9-3 dated 2013-06-21
Description: Analysis of configuration frequencies for simple and
repeated measures, more sample CFa, hierarchical CFA,
bootstrap-CFA, functional CFA, Kieser-Victor CFA and various
plots, and Lindner's test using a conventional and an
accelerated algorithm
Author: Stefan Funke
Maintainer: Stefan Funke
cfa-0.9-2/cfa/R/lcfa.R |only
cfa-0.9-2/cfa/man/lcfa.Rd |only
cfa-0.9-3/cfa/DESCRIPTION | 16 +++++++++-------
cfa-0.9-3/cfa/MD5 |only
cfa-0.9-3/cfa/NAMESPACE | 3 ++-
cfa-0.9-3/cfa/R/PXisM.R |only
cfa-0.9-3/cfa/R/PXisMclassic.R |only
cfa-0.9-3/cfa/R/cfa.r | 22 +++++++++++-----------
cfa-0.9-3/cfa/man/PXisM.Rd |only
cfa-0.9-3/cfa/man/PXisMclassic.Rd |only
cfa-0.9-3/cfa/man/fCFA.Rd | 15 ++++++++++-----
cfa-0.9-3/cfa/man/hcfa.Rd | 4 +++-
12 files changed, 35 insertions(+), 25 deletions(-)
Title: Tools for reading and handling spatial objects
Diff between maptools versions 0.8-23 dated 2013-02-10 and 0.8-24 dated 2013-06-21
Description: Set of tools for manipulating and reading geographic data,
in particular ESRI shapefiles; C code used from shapelib. It
includes binary access to GSHHS shoreline files. The package
also provides interface wrappers for exchanging spatial objects
with packages such as PBSmapping, spatstat, maps, RArcInfo,
Stata tmap, WinBUGS, Mondrian, and others.
Author: Roger Bivand [cre, aut], Nicholas Lewin-Koh [aut], Edzer
Pebesma [ctb], Eric Archer [ctb], Adrian Baddeley [ctb],
Hans-Jörg Bibiko [ctb], Steven Brey [ctb], Jonathan Callahan
[ctb], German Carrillo [ctb], Stéphane Dray [ctb], David
Forrest [ctb], Michael Friendly [ctb], Patrick Giraudoux [ctb],
Duncan Golicher [ctb], Virgilio Gómez Rubio [ctb], Patrick
Hausmann [ctb], Karl Ove Hufthammer [ctb], Thomas Jagger [ctb],
Sebastian Luque [ctb], Don MacQueen [ctb], Andrew Niccolai
[ctb], Oscar Perpiñán Lamigueiro [ctb], Tom Short [ctb], Greg
Snow [ctb], Ben Stabler [ctb], Murray Stokely [ctb], Rolf
Turner [ctb]
Maintainer: Roger Bivand
maptools-0.8-23/maptools/LICENSE |only
maptools-0.8-24/maptools/ChangeLog | 41 ++++++++
maptools-0.8-24/maptools/DESCRIPTION | 51 +++++-----
maptools-0.8-24/maptools/MD5 | 59 ++++++++----
maptools-0.8-24/maptools/NAMESPACE | 2
maptools-0.8-24/maptools/R/Spatial-methods.R | 4
maptools-0.8-24/maptools/R/SpatialLines-methods.R | 1
maptools-0.8-24/maptools/R/SpatialPoints-methods.R | 1
maptools-0.8-24/maptools/R/SpatialPolys-methods.R | 2
maptools-0.8-24/maptools/R/kmlLines.R |only
maptools-0.8-24/maptools/R/kmlPolygons.R |only
maptools-0.8-24/maptools/inst/ChangeLog | 41 ++++++++
maptools-0.8-24/maptools/inst/doc |only
maptools-0.8-24/maptools/inst/shapes/co37_d90.dbf |only
maptools-0.8-24/maptools/inst/shapes/co37_d90.shp |only
maptools-0.8-24/maptools/inst/shapes/co37_d90.shx |only
maptools-0.8-24/maptools/inst/shapes/co45_d90.dbf |only
maptools-0.8-24/maptools/inst/shapes/co45_d90.shp |only
maptools-0.8-24/maptools/inst/shapes/co45_d90.shx |only
maptools-0.8-24/maptools/inst/shapes/co51_d90.dbf |only
maptools-0.8-24/maptools/inst/shapes/co51_d90.shp |only
maptools-0.8-24/maptools/inst/shapes/co51_d90.shx |only
maptools-0.8-24/maptools/inst/share/90mfips.txt |only
maptools-0.8-24/maptools/man/CCmaps.Rd | 5 -
maptools-0.8-24/maptools/man/kmlLines.Rd |only
maptools-0.8-24/maptools/man/kmlPoints.Rd | 6 -
maptools-0.8-24/maptools/man/kmlPolygons.Rd |only
maptools-0.8-24/maptools/man/map2SpatialPolygons.Rd | 4
maptools-0.8-24/maptools/man/sun-methods.Rd | 2
maptools-0.8-24/maptools/maptools-Ex.R | 74 ++++++++++++++-
maptools-0.8-24/maptools/src/Rcentroid.c | 2
maptools-0.8-24/maptools/src/Rgshhs.c | 18 +--
maptools-0.8-24/maptools/src/Rshapewrite1.c | 30 +++---
maptools-0.8-24/maptools/src/insiders.c | 2
maptools-0.8-24/maptools/src/shapefil.h | 14 +-
maptools-0.8-24/maptools/src/shpopen.c | 94 ++++++++++----------
maptools-0.8-24/maptools/src/shptree.c | 46 ++++-----
maptools-0.8-24/maptools/vignettes |only
38 files changed, 337 insertions(+), 162 deletions(-)
Title: Spatial dependence: weighting schemes, statistics and models
Diff between spdep versions 0.5-56 dated 2013-01-11 and 0.5-57 dated 2013-06-21
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by
distance and tessellations, for summarizing these objects, and
for permitting their use in spatial data analysis, including
regional aggregation by minimum spanning tree; a collection of
tests for spatial autocorrelation, including global Moran's I,
APLE, Geary's C, Hubert/Mantel general cross product statistic,
Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord
G and multicoloured join count statistics, local Moran's I and
Getis/Ord G, saddlepoint approximations and exact tests for
global and local Moran's I; and functions for estimating
spatial simultaneous autoregressive (SAR) lag and error models,
impact measures for lag models, weighted and unweighted SAR and
CAR spatial regression models, semi-parametric and Moran
eigenvector spatial filtering, GM SAR error models, and
generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut], Micah Altman [ctb], Luc Anselin [ctb],
Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb],
Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia
Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb],
Carsten Dormann [ctb], Stéphane Dray [ctb], Rein Halbersma
[ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas
Lewin-Koh [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Giovanni
Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro
Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb],
Michael Tiefelsdorf [ctb], Danlin Yu [ctb]
Maintainer: Roger Bivand
spdep-0.5-56/spdep/LICENCE |only
spdep-0.5-56/spdep/inst/etc/shapes/columbusRegression.txt |only
spdep-0.5-56/spdep/inst/etc/weights/e80_queen.gal |only
spdep-0.5-57/spdep/ChangeLog | 42 +++++++++
spdep-0.5-57/spdep/DESCRIPTION | 53 ++++++++---
spdep-0.5-57/spdep/MD5 | 62 ++++++++------
spdep-0.5-57/spdep/R/error.spsarlm.R | 1
spdep-0.5-57/spdep/R/mcmcsamp.R | 2
spdep-0.5-57/spdep/inst/ChangeLog | 42 +++++++++
spdep-0.5-57/spdep/inst/doc/CO69.R |only
spdep-0.5-57/spdep/inst/doc/CO69.Rnw | 1
spdep-0.5-57/spdep/inst/doc/CO69.pdf |binary
spdep-0.5-57/spdep/inst/doc/SpatialFiltering.R |only
spdep-0.5-57/spdep/inst/doc/SpatialFiltering.Rnw |only
spdep-0.5-57/spdep/inst/doc/SpatialFiltering.pdf |only
spdep-0.5-57/spdep/inst/doc/nb.R |only
spdep-0.5-57/spdep/inst/doc/nb.Rnw |only
spdep-0.5-57/spdep/inst/doc/nb.pdf |only
spdep-0.5-57/spdep/inst/doc/sids.R |only
spdep-0.5-57/spdep/inst/doc/sids.Rnw | 1
spdep-0.5-57/spdep/inst/doc/sids.pdf |binary
spdep-0.5-57/spdep/inst/etc/shapes/NY8_utm18.dbf |only
spdep-0.5-57/spdep/inst/etc/shapes/NY8_utm18.prj |only
spdep-0.5-57/spdep/inst/etc/shapes/NY8_utm18.shp |only
spdep-0.5-57/spdep/inst/etc/shapes/NY8_utm18.shx |only
spdep-0.5-57/spdep/inst/etc/weights/NY_nb.gal |only
spdep-0.5-57/spdep/man/MCMCsamp.Rd | 1
spdep-0.5-57/spdep/man/impacts.sarlm.Rd | 9 +-
spdep-0.5-57/spdep/man/lagmess.Rd | 3
spdep-0.5-57/spdep/man/lm.morantest.exact.Rd | 4
spdep-0.5-57/spdep/man/localmoran.exact.Rd | 10 +-
spdep-0.5-57/spdep/man/spautolm.Rd | 6 -
spdep-0.5-57/spdep/man/tolerance.nb.Rd | 28 ++++--
spdep-0.5-57/spdep/man/trW.Rd | 5 -
spdep-0.5-57/spdep/spdep-Ex.R | 5 -
spdep-0.5-57/spdep/src/dnn.c | 6 -
spdep-0.5-57/spdep/src/ml_sse.c | 11 +-
spdep-0.5-57/spdep/src/polypoly.c | 4
spdep-0.5-57/spdep/src/skater.c | 2
spdep-0.5-57/spdep/src/spdep.h | 1
40 files changed, 227 insertions(+), 72 deletions(-)
Title: Outlier Detection using Quantile Regression for Censored Data
Diff between OutlierDC versions 0.2.1 dated 2013-03-18 and 0.2.5 dated 2013-06-21
Description: This provides three algorithms to detect outliers based on
censored quantile regression.
Author: Soo-Heang Eo
Maintainer: Soo-Heang Eo
OutlierDC-0.2.1/OutlierDC/COPYING |only
OutlierDC-0.2.5/OutlierDC/DESCRIPTION | 12 -
OutlierDC-0.2.5/OutlierDC/MD5 | 19 +-
OutlierDC-0.2.5/OutlierDC/NEWS | 16 ++
OutlierDC-0.2.5/OutlierDC/R/LCRQ.R | 154 +++++++++++------------
OutlierDC-0.2.5/OutlierDC/R/class.R | 8 -
OutlierDC-0.2.5/OutlierDC/R/odc.R | 42 ++++--
OutlierDC-0.2.5/OutlierDC/R/subfunctions.R | 104 ++++++++++-----
OutlierDC-0.2.5/OutlierDC/man/OutlierDC-class.Rd | 9 -
OutlierDC-0.2.5/OutlierDC/man/odc.Rd | 50 ++++---
OutlierDC-0.2.5/OutlierDC/man/update.Rd | 9 -
11 files changed, 258 insertions(+), 165 deletions(-)
Title: Nonlinear Calibration
Diff between nCal versions 0.1-1 dated 2013-05-10 and 0.2-1 dated 2013-06-21
Description: nCal is a package that performs nonlinear calibration and
curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc.
Additional documentation can be found on
http://research.fhcrc.org/youyifong/en/resources/ncal.html.
Author: Youyi Fong
Maintainer: Youyi Fong
ChangeLog | 9
DESCRIPTION | 21 -
MD5 | 56 +-
NAMESPACE | 4
R/5pl.R | 635 +++++++++-----------------------
R/5pl_parameterization_calculus.R |only
R/bcrm.R | 163 ++++++--
R/drm.fit.R | 1
R/ncal.R | 123 +++---
R/ncalGUI.R | 135 +++++-
R/read.luminex.xls.R | 19
R/youtilcopy.R | 28 +
inst/doc |only
inst/jags_script/model_gh_norm_4pl.txt |only
inst/jags_script/model_gh_t4_4pl.txt |only
inst/misc/02-14A22-IgA-Biotin-short.xls |only
inst/misc/02-14A22-IgA-Biotin-tiny.xls |only
inst/misc/02-14A22-IgA-Biotin.xls |binary
inst/unitTests |only
man/5PL.Rd | 23 -
man/bcrm.Rd | 23 -
man/get.S1.Rd | 49 ++
man/getConc.Rd |only
man/ncal.Rd | 69 +--
man/plot.bcrm.Rd | 12
man/read.luminex.xls.Rd | 20 -
tests |only
vignettes |only
28 files changed, 710 insertions(+), 680 deletions(-)
Title: Seasonal analysis and graphics, especially for climatology
Diff between seas versions 0.4-1 dated 2013-01-08 and 0.4-2 dated 2013-06-21
Description: Capable of deriving seasonal statistics, such as
"normals", and analysis of seasonal data, such as departures.
This package also has graphics capabilities for representing
seasonal data, including boxplots for seasonal parameters, and
bars for summed normals. There are many specific functions
related to climatology, including precipitation normals,
temperature normals, cumulative precipitation departures and
precipitation interarrivals. However, this package is designed
to represent any time-varying parameter with a discernible
seasonal signal, such as found in hydrology and ecology.
Author: Mike Toews
Maintainer: Mike Toews
seas-0.4-1/seas/seas_0.4-0.tar.gz |only
seas-0.4-2/seas/DESCRIPTION | 11 +++++++----
seas-0.4-2/seas/MD5 | 14 +++++++-------
seas-0.4-2/seas/R/getstnname.R | 9 +++++----
seas-0.4-2/seas/R/sysdata.rda |only
seas-0.4-2/seas/data/mscdata.rda |binary
seas-0.4-2/seas/data/mscstn.rda |binary
seas-0.4-2/seas/inst/ChangeLog | 5 +++++
seas-0.4-2/seas/man/mksub.Rd | 1 -
9 files changed, 24 insertions(+), 16 deletions(-)
Title: Power and Sample size based on two one-sided t-tests (TOST) for
(bio)equivalence studies
Diff between PowerTOST versions 1.1-05 dated 2013-06-17 and 1.1-06 dated 2013-06-21
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies. See
function known.designs() for study designs covered. Moreover
the package contains functions for power and sample size based
on 'expected' power in case of uncertain (estimated)
variability. ----- Added are functions for the power and
sample size for the ratio of two means with normally
distributed data on the original scale (based on Fieller's
confidence ('fiducial') interval). ----- Contains further
functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but
eventually useful if the question of 'non-superiority' must be
evaluated. The power and sample size calculations based on
non-inferiority test may also performed via 'expected' power in
case of uncertain (estimated) variability. ----- Contains
functions power.scABEL() and sampleN.scABEL() to calculate
power and sample size for the BE decision via scaled (widened)
BE acceptance limits based on simulations. Contains functions
power.RSABE() and sampleN.RSABE() to calculate power and sample
size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations. Contains
further functions power.NTIDFDA() and sampleN.NTIDFDA() to
calculate power and sample size for the BE decision via the FDA
procedure for NTID's based on simulations.
Author: Detlew Labes
Maintainer: Detlew Labes
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
NEWS | 5 +++++
R/power_RSABE_NTID.R | 1 +
R/samplesize_RSABE_NTID.R | 2 ++
man/PowerTOST-package.Rd | 11 ++++++-----
man/power.NTIDFDA.Rd | 18 ++++++++++++------
man/power.RSABE.Rd | 19 +++++++++++--------
man/power.scABEL.Rd | 9 +++++----
man/sampleN.NTIDFDA.Rd | 22 ++++++++++++----------
man/sampleN.RSABE.Rd | 9 ++++++---
man/sampleN.scABEL.Rd | 12 +++++++++---
12 files changed, 84 insertions(+), 54 deletions(-)
Title: Binarization of numeric data arrays
Diff between ArrayBin versions 0.1 dated 2013-02-01 and 0.2 dated 2013-06-21
Description: Fast adaptive binarization for numeric data arrays,
particularly designed for high-throughput biological datasets.
Includes options to filter out rows of the array with
insufficient magnitude or variation (based on gap statistic).
Author: Ed Curry
Maintainer: Ed Curry
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
R/binarize_array.R | 10 ++++++++--
R/clusterDisc.R | 38 +++++++++++++++++++++-----------------
man/binarize_array.Rd | 4 +++-
5 files changed, 41 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-06 1.2
2011-04-11 1.1
2010-02-03 1.0-1
2010-02-03 1.0-2
2010-02-02 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-02 0.3
2010-11-30 0.2
2010-11-13 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-10-14 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-05-17 0.2.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-19 1.2.1
2011-05-10 1.2
2011-05-09 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-06-24 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-02-03 0.1
Title: Estimation of spatial autoregressive models with and without
heteroskedastic innovations
Diff between sphet versions 1.1-12 dated 2012-04-13 and 1.4 dated 2013-06-21
Description: Generalized Method of Moment estimation of Cliff-Ord-type
spatial autoregressive models with and without heteroskedastic
innovations
Author: Gianfranco Piras
Maintainer: Gianfranco Piras
sphet-1.1-12/sphet/data/knn10columbus.txt.xz |only
sphet-1.4/sphet/ChangeLog | 12 +++++++-
sphet-1.4/sphet/DESCRIPTION | 20 +++++++------
sphet-1.4/sphet/MD5 | 35 ++++++++++++++---------
sphet-1.4/sphet/NAMESPACE | 2 -
sphet-1.4/sphet/R/Omega.R | 29 ++++++++++++++-----
sphet-1.4/sphet/R/circular.R |only
sphet-1.4/sphet/R/gm_functions.R |only
sphet-1.4/sphet/R/gs2slshet.R | 21 +++++++++-----
sphet-1.4/sphet/R/ivreg.R |only
sphet-1.4/sphet/R/s2slshac.R | 14 ++++-----
sphet-1.4/sphet/R/spreg.R |only
sphet-1.4/sphet/R/twostagels.R | 8 +++--
sphet-1.4/sphet/R/utilities.R | 40 ++++++++++++++++-----------
sphet-1.4/sphet/data/coldis.rda |binary
sphet-1.4/sphet/data/knn10columbus.txt.gz |only
sphet-1.4/sphet/inst/doc/sphet.R |only
sphet-1.4/sphet/inst/doc/sphet.pdf |binary
sphet-1.4/sphet/man/circular.Rd |only
sphet-1.4/sphet/man/distance.Rd | 1
sphet-1.4/sphet/man/gstslshet.Rd | 8 +++--
sphet-1.4/sphet/man/spreg.Rd |only
sphet-1.4/sphet/man/stslshac.Rd | 4 +-
23 files changed, 122 insertions(+), 72 deletions(-)
Title: Easy analysis and visualization of factorial experiments.
Diff between ez versions 4.1-1 dated 2012-08-11 and 4.2-0 dated 2013-06-21
Description: This package facilitates easy analysis of factorial
experiments, including purely within-Ss designs (a.k.a.
"repeated measures"), purely between-Ss designs, and mixed
within-and-between-Ss designs. The functions in this package
aim to provide simple, intuitive and consistent specification
of data analysis and visualization. Visualization functions
also include design visualization for pre-analysis data
auditing, and correlation matrix visualization. Finally, this
package includes functions for non-parametric analysis,
including permutation tests and bootstrap resampling. The
bootstrap function obtains predictions either by cell means or
by more advanced/powerful mixed effects models, yielding
predictions and confidence intervals that may be easily
visualized at any level of the experiment's design.
Author: Michael A. Lawrence
Maintainer: Michael A. Lawrence
ez-4.1-1/ez/R/progress_time.R |only
ez-4.1-1/ez/man/progress_time.Rd |only
ez-4.2-0/ez/CHANGES | 5 +++++
ez-4.2-0/ez/DESCRIPTION | 9 +++++----
ez-4.2-0/ez/MD5 | 16 +++++++---------
ez-4.2-0/ez/NAMESPACE | 2 +-
ez-4.2-0/ez/R/ez-internal.R | 2 ++
ez-4.2-0/ez/R/ezCor.R | 4 ++--
ez-4.2-0/ez/R/ezPredict.R | 4 ++--
ez-4.2-0/ez/man/ez-package.Rd | 9 ++++-----
10 files changed, 28 insertions(+), 23 deletions(-)
Title: Constrained, covariance-matching constrained and universal point
or block kriging
Diff between constrainedKriging versions 0.2.0 dated 2013-06-17 and 0.2.1 dated 2013-06-21
More information about constrainedKriging at CRAN
Description: The constrainedKriging package provides functions for
efficient computations of nonlinear spatial predictions with
local change of support. The package supplies functions for
tow-dimensional spatial interpolation by constrained,
covariance-matching constrained and universal (external drift)
kriging for points or block of any shape for data with a
nonstationary mean function and an isotropic weakly stationary
variogram. The linear spatial interpolation methods,
constrained and covariance-matching constrained kriging,
provide approximately unbiased prediction for nonlinear target
values under change of support. The constrainedKriging package
extends the range of geostatistical tools available in R and
provides a veritable alternative to conditional simulation for
nonlinear spatial prediction problems with local change of
support.
Author: Christoph Hofer
Maintainer: Christoph Hofer
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/covmodlist.R | 2 +-
R/f.intersect.area.R | 12 +-----------
inst/ChangeLog.txt | 3 +++
5 files changed, 14 insertions(+), 21 deletions(-)
Permanent link
Title: Axis Labeling
Diff between labeling versions 0.1 dated 2010-11-22 and 0.2 dated 2013-06-20
Description: Provides a range of axis labeling algorithms
Author: Justin Talbot
Maintainer: Justin Talbot
DESCRIPTION | 16 ++++----
MD5 | 28 +++++++--------
NAMESPACE | 15 +++++---
R/labeling.R | 19 ++++++++--
man/extended.Rd | 52 ++++++++++++++++++++--------
man/extended.figures.Rd | 31 ++++++++++++-----
man/gnuplot.Rd | 33 +++++++++++++-----
man/heckbert.Rd | 34 +++++++++++++-----
man/labeling-package.Rd | 64 +++++++++++++++++++++++------------
man/matplotlib.Rd | 33 +++++++++++++-----
man/nelder.Rd | 39 ++++++++++++++++-----
man/rpretty.Rd | 62 +++++++++++++++++++++++++---------
man/sparks.Rd | 35 ++++++++++++++-----
man/thayer.Rd | 35 ++++++++++++++-----
man/wilkinson.Rd | 87 +++++++++++++++++++++++++++++++++---------------
15 files changed, 413 insertions(+), 170 deletions(-)
Title: Dive analysis and calibration
Diff between diveMove versions 1.3.6 dated 2013-03-28 and 1.3.7 dated 2013-06-20
Description: Utilities to represent, visualize, filter, analyse, and
summarize time-depth recorder (TDR) data. Miscellaneous
functions for handling location data are also provided.
Author: Sebastian P. Luque
Maintainer: Sebastian P. Luque
ChangeLog | 88 +++++++++++++++++++++++++++++++++++++-----------
DESCRIPTION | 12 +++---
MD5 | 45 ++++++++++++------------
NAMESPACE | 10 ++++-
NEWS | 21 ++++++++++-
R/AllMethod.R | 6 ++-
R/austFilter.R | 44 ++++++++++++------------
R/calibrate.R | 5 --
R/distSpeed.R | 43 ++++++++---------------
R/plotTDR.R | 4 +-
R/zoc.R | 3 -
R/zzz.R | 15 ++++++--
inst/doc/diveMove.R |only
inst/doc/diveMove.pdf |binary
man/austFilter.Rd | 12 ++++--
man/distSpeed.Rd | 17 +++++++--
man/diveMove-package.Rd | 4 +-
man/dives.Rd | 10 ++---
man/readLocs.Rd | 7 ++-
man/readTDR.Rd | 11 +++---
man/sealLocs.Rd | 7 +--
tests/calibrations.R | 2 -
tests/class-tests.R | 58 ++++++++++++++++---------------
tests/final-stats.R | 4 --
24 files changed, 258 insertions(+), 170 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 5.16-04 dated 2013-05-17 and 5.16-24 dated 2013-06-20
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer, Allan Engelhardt and Tony Cooper
Maintainer: Max Kuhn
DESCRIPTION | 31 +++++-------
MD5 | 36 +++++++-------
R/classLevels.R | 1
R/createGrid.R | 25 +++------
R/createModel.R | 123 +++++++++++++++++++++++++++++--------------------
R/misc.R | 44 +++++++++++++++--
R/modelLookup.R | 114 ++++++++++++++++++++++++++++++---------------
R/predictionFunction.R | 30 ++++++++---
R/print.train.R | 7 --
R/probFunction.R | 9 ---
R/rfe.R | 3 +
R/selection.R | 15 +++++
R/train.default.R | 13 +++--
R/workflows.R | 18 +++----
inst/NEWS.Rd | 49 +++++++++++++++++++
inst/doc/caret.pdf |binary
inst/modelKey.txt | 2
man/calibration.Rd | 3 -
man/train.Rd | 3 -
19 files changed, 346 insertions(+), 180 deletions(-)
Title: Truncated Maximum Likelihood fit and Robust Accelerated Failure
Time regression for Gaussian and log-Weibull case.
Diff between RobustAFT versions 1.0 dated 2011-08-20 and 1.2 dated 2013-06-20
Description: R functions for the computation of the truncated maximum
likelihood and the robust accelerated failure time regression
for gaussian and log-Weibull case.
Author: Alfio Marazzi
Maintainer: A. Randriamiharisoa
RobustAFT-1.0/RobustAFT/R/comval.R |only
RobustAFT-1.0/RobustAFT/R/dfcomn.R |only
RobustAFT-1.2/RobustAFT/DESCRIPTION | 11
RobustAFT-1.2/RobustAFT/MD5 | 227 ++++++--------
RobustAFT-1.2/RobustAFT/NAMESPACE | 2
RobustAFT-1.2/RobustAFT/R/AV.MM.gauss.R | 8
RobustAFT-1.2/RobustAFT/R/BtamatG.r | 26 -
RobustAFT-1.2/RobustAFT/R/BtamatW.r | 28 -
RobustAFT-1.2/RobustAFT/R/CandidateG.r | 49 +--
RobustAFT-1.2/RobustAFT/R/ChiSG.r | 10
RobustAFT-1.2/RobustAFT/R/ChiSN.r | 10
RobustAFT-1.2/RobustAFT/R/ChiSw.r | 10
RobustAFT-1.2/RobustAFT/R/Chidlweibul.r | 8
RobustAFT-1.2/RobustAFT/R/Chidnorm.r | 7
RobustAFT-1.2/RobustAFT/R/CutoffW.r | 20 -
RobustAFT-1.2/RobustAFT/R/IChidlweibul.r | 16
RobustAFT-1.2/RobustAFT/R/IChidnorm.r | 14
RobustAFT-1.2/RobustAFT/R/IPsidnorm.r | 14
RobustAFT-1.2/RobustAFT/R/MM.E.gauss.R | 14
RobustAFT-1.2/RobustAFT/R/PsiSG.r | 10
RobustAFT-1.2/RobustAFT/R/PsiSN.r | 10
RobustAFT-1.2/RobustAFT/R/PsiSw.r | 10
RobustAFT-1.2/RobustAFT/R/Psidnorm.r | 7
RobustAFT-1.2/RobustAFT/R/PspSG.r | 12
RobustAFT-1.2/RobustAFT/R/PspSN.r | 12
RobustAFT-1.2/RobustAFT/R/PspSw.r | 12
RobustAFT-1.2/RobustAFT/R/QMatrix.G.r | 67 ++--
RobustAFT-1.2/RobustAFT/R/Qmatrix.W.r | 69 ++--
RobustAFT-1.2/RobustAFT/R/RappN.r | 35 +-
RobustAFT-1.2/RobustAFT/R/RappW.r | 37 +-
RobustAFT-1.2/RobustAFT/R/RefAve2G.r | 30 -
RobustAFT-1.2/RobustAFT/R/RefAve2W.r | 32 -
RobustAFT-1.2/RobustAFT/R/RefBetaG.r | 82 ++---
RobustAFT-1.2/RobustAFT/R/RefBetaW.r | 83 ++---
RobustAFT-1.2/RobustAFT/R/RefSG.r | 94 ++---
RobustAFT-1.2/RobustAFT/R/RefSW.r | 89 ++---
RobustAFT-1.2/RobustAFT/R/RefSigmaG.r | 19 -
RobustAFT-1.2/RobustAFT/R/RefSigmaW.r | 19 -
RobustAFT-1.2/RobustAFT/R/ResExpG.r | 15
RobustAFT-1.2/RobustAFT/R/ResExpW.r | 20 -
RobustAFT-1.2/RobustAFT/R/SparamG.S.r | 128 +++----
RobustAFT-1.2/RobustAFT/R/SparamW.S.r | 138 ++++----
RobustAFT-1.2/RobustAFT/R/TML.Ave2G.r | 46 +-
RobustAFT-1.2/RobustAFT/R/TML.Ave2W.r | 49 +--
RobustAFT-1.2/RobustAFT/R/TML.BetaG.r | 82 ++---
RobustAFT-1.2/RobustAFT/R/TML.BetaW.r | 91 ++---
RobustAFT-1.2/RobustAFT/R/TML.SigmaG.r | 19 -
RobustAFT-1.2/RobustAFT/R/TML.SigmaW.r | 21 -
RobustAFT-1.2/RobustAFT/R/TML.censored.R | 14
RobustAFT-1.2/RobustAFT/R/TML.gauss.R | 2
RobustAFT-1.2/RobustAFT/R/TML.logweibull.R | 2
RobustAFT-1.2/RobustAFT/R/TML.noncensored.R | 8
RobustAFT-1.2/RobustAFT/R/TML1.control.R | 4
RobustAFT-1.2/RobustAFT/R/TML1.noncensored.R | 8
RobustAFT-1.2/RobustAFT/R/TMLG.r | 105 +++---
RobustAFT-1.2/RobustAFT/R/TMLW.r | 112 +++---
RobustAFT-1.2/RobustAFT/R/TMLeqn2W.r | 49 +--
RobustAFT-1.2/RobustAFT/R/TMLjac11.G.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac11.W.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac12.G.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac12.W.r | 41 +-
RobustAFT-1.2/RobustAFT/R/TMLjac21.G.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac21.W.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac22.G.r | 45 +-
RobustAFT-1.2/RobustAFT/R/TMLjac22.W.R | 45 +-
RobustAFT-1.2/RobustAFT/R/comval2.R |only
RobustAFT-1.2/RobustAFT/R/dfcomn2.R | 38 --
RobustAFT-1.2/RobustAFT/R/dfvals.R | 94 ++---
RobustAFT-1.2/RobustAFT/R/dlweibul.r | 7
RobustAFT-1.2/RobustAFT/R/ezez.R | 7
RobustAFT-1.2/RobustAFT/R/hysest.R | 6
RobustAFT-1.2/RobustAFT/R/intg0.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg0.r | 12
RobustAFT-1.2/RobustAFT/R/intg1.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg2.TMLW.r | 7
RobustAFT-1.2/RobustAFT/R/intg2.r | 7
RobustAFT-1.2/RobustAFT/R/intw0.r | 15
RobustAFT-1.2/RobustAFT/R/intw1.r | 8
RobustAFT-1.2/RobustAFT/R/intxlwbl.r | 10
RobustAFT-1.2/RobustAFT/R/liepsu.R | 2
RobustAFT-1.2/RobustAFT/R/lywalg.R | 4
RobustAFT-1.2/RobustAFT/R/plot.TML.R | 2
RobustAFT-1.2/RobustAFT/R/plot.fits.compare.R | 2
RobustAFT-1.2/RobustAFT/R/plweibul.r | 7
RobustAFT-1.2/RobustAFT/R/ps0.r | 7
RobustAFT-1.2/RobustAFT/R/ps0W.r | 7
RobustAFT-1.2/RobustAFT/R/ps1.r | 7
RobustAFT-1.2/RobustAFT/R/ps1W.r | 7
RobustAFT-1.2/RobustAFT/R/psp0W.r | 7
RobustAFT-1.2/RobustAFT/R/psp1W.r | 7
RobustAFT-1.2/RobustAFT/R/regfal.r | 60 +--
RobustAFT-1.2/RobustAFT/R/rysigm.R | 4
RobustAFT-1.2/RobustAFT/R/rywalg.R | 4
RobustAFT-1.2/RobustAFT/R/s.estim.R | 2
RobustAFT-1.2/RobustAFT/R/summary.TML.R | 6
RobustAFT-1.2/RobustAFT/R/tutl.R | 10
RobustAFT-1.2/RobustAFT/R/ww.r | 8
RobustAFT-1.2/RobustAFT/R/xlwbl.r | 7
RobustAFT-1.2/RobustAFT/R/zez.R | 7
RobustAFT-1.2/RobustAFT/man/RobustAFT.package.Rd | 155 +++++----
RobustAFT-1.2/RobustAFT/man/TML.censored.control.S.rd | 29 +
RobustAFT-1.2/RobustAFT/man/TML.censored.control.ref.rd | 35 +-
RobustAFT-1.2/RobustAFT/man/TML.censored.control.tml.rd | 25 -
RobustAFT-1.2/RobustAFT/man/TML.censored.rd | 97 +++--
RobustAFT-1.2/RobustAFT/man/TML.noncensored.control.rd | 38 +-
RobustAFT-1.2/RobustAFT/man/TML.noncensored.rd | 75 ++--
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.Rd | 55 ++-
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.control.S.Rd | 8
RobustAFT-1.2/RobustAFT/man/TML1.noncensored.control.rd | 9
RobustAFT-1.2/RobustAFT/man/fits.compare.rd | 28 -
RobustAFT-1.2/RobustAFT/man/plot.TML.rd | 39 +-
RobustAFT-1.2/RobustAFT/man/plot.fits.compare.rd | 37 +-
RobustAFT-1.2/RobustAFT/man/predict.TML.rd | 26 -
RobustAFT-1.2/RobustAFT/man/summary.TML.rd | 51 ++-
RobustAFT-1.2/RobustAFT/src/robaft.f | 50 ++-
RobustAFT-1.2/RobustAFT/src/robcom.f | 108 +-----
116 files changed, 1878 insertions(+), 1839 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 2.4-0 dated 2013-06-17 and 2.4-1 dated 2013-06-20
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer
DESCRIPTION | 8 +--
MD5 | 30 +++++++-------
NEWS | 32 +++++++++++++++
R/asin2p.R | 56 ++++++++++++++------------
R/forest.meta.R | 88 +++++++++++++++++++++++++++---------------
R/metaprop.R | 3 +
R/print.meta.R | 16 +++++++
R/print.summary.meta.R | 102 ++++++++++++++++++++++++++++++-------------------
man/forest.meta.Rd | 23 +++++++++++
man/metabin.Rd | 1
man/metacont.Rd | 1
man/metacor.Rd | 2
man/metacr.Rd | 2
man/metagen.Rd | 2
man/metaprop.Rd | 4 +
man/print.meta.Rd | 1
16 files changed, 255 insertions(+), 116 deletions(-)
Title: Syntax highlighter
Diff between highlight versions 0.4.2 dated 2013-06-19 and 0.4.3 dated 2013-06-20
Description: Syntax highlighter for R code based on the results of the
R parser. Rendering in HTML and latex markup. Custom Sweave
driver performing syntax highlighting of R code chunks
Author: Romain Francois
Maintainer: Romain Francois
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/SweaveLatexDriver.R | 9 ++++++---
R/zzz.R | 2 +-
build/highlight.pdf |binary
man/Hweave.Rd | 15 +++++++++++----
man/highlight-package.Rd | 4 ++--
7 files changed, 30 insertions(+), 20 deletions(-)
Title: Tools of the Trade for Discriminant Analysis
Diff between DiscriMiner versions 0.1-22 dated 2012-09-14 and 0.1-25 dated 2013-06-20
Description: Functions for Discriminant Analysis and Classification
purposes covering various methods such as descriptive,
geometric, linear, quadratic, PLS, as well as qualitative
discriminant analyses
Author: Gaston Sanchez [aut, cre], Charles Determan [ctb]
Maintainer: Gaston Sanchez
DESCRIPTION | 30 +++++++---
MD5 | 133 +++++++++++++++++++++++----------------------
NAMESPACE | 84 ++++++++++------------------
R/DiscriMiner-package.R |only
R/FRatio.R | 24 ++++++++
R/betweenCov.R | 33 +++++++++--
R/betweenSS.R | 24 ++++++++
R/binarize.R | 27 ++++++++-
R/classify.R | 47 ++++++++++++++-
R/corRatio.R | 23 +++++++
R/desDA.R | 64 +++++++++++++++++++--
R/discPower.R | 30 +++++++++-
R/disqual.R | 60 ++++++++++++++++++++
R/easyMCA.R | 30 ++++++++++
R/geoDA.R | 56 ++++++++++++++++++
R/getWithin.R | 31 ++++++++++
R/groupMeans.R | 25 ++++++++
R/groupMedians.R | 25 ++++++++
R/groupQuants.R | 26 ++++++++
R/groupStds.R | 25 ++++++++
R/groupVars.R | 25 ++++++++
R/linDA.R | 65 +++++++++++++++++++++
R/my_plsDA.R | 107 +++++++++++++++++++++++++-----------
R/my_plsDA_old.R |only
R/plot.plsda.R | 1
R/plsDA.R | 96 ++++++++++++++++++++++++++++----
R/plsDA_old.R |only
R/print.desda.R | 1
R/print.disqual.R | 1
R/print.geoda.R | 1
R/print.linda.R | 1
R/print.plsda.R | 1
R/print.quada.R | 1
R/print.qualmca.R | 1
R/quaDA.R | 69 ++++++++++++++++++++++-
R/totalCov.R | 27 +++++++++
R/totalSS.R | 21 +++++++
R/withinCov.R | 29 +++++++++
R/withinSS.R | 24 ++++++++
README.md | 45 ++++++++-------
man/DiscriMiner-package.Rd | 51 +++++++++--------
man/FRatio.Rd | 35 ++++++-----
man/betweenCov.Rd | 54 ++++++++++--------
man/betweenSS.Rd | 35 ++++++-----
man/binarize.Rd | 34 ++++++-----
man/bordeaux.Rd | 38 +++++-------
man/classify.Rd | 45 +++++++++------
man/corRatio.Rd | 39 ++++++-------
man/desDA.Rd | 84 +++++++++++++++++-----------
man/discPower.Rd | 44 ++++++++------
man/disqual.Rd | 102 +++++++++++++++++++++++-----------
man/easyMCA.Rd | 45 ++++++++-------
man/geoDA.Rd | 82 +++++++++++++++++----------
man/getWithin.Rd | 41 +++++++------
man/groupMeans.Rd | 36 ++++++------
man/groupMedians.Rd | 36 ++++++------
man/groupQuants.Rd | 41 ++++++++-----
man/groupStds.Rd | 36 ++++++------
man/groupVars.Rd | 37 +++++++-----
man/infarctus.Rd | 44 ++++++--------
man/insurance.Rd | 59 ++++++++++---------
man/linDA.Rd | 93 ++++++++++++++++++++-----------
man/my_plsDA.Rd |only
man/plsDA.Rd | 114 +++++++++++++++++++++++++++-----------
man/plsDA_old.Rd |only
man/quaDA.Rd | 91 +++++++++++++++++++-----------
man/totalCov.Rd | 40 +++++++------
man/totalSS.Rd | 31 +++++-----
man/withinCov.Rd | 44 ++++++++------
man/withinSS.Rd | 35 ++++++-----
70 files changed, 1968 insertions(+), 811 deletions(-)
Title: Tools for parsing and generating XML within R and S-Plus.
Diff between XML versions 3.96-1.1 dated 2013-03-28 and 3.98-1.1 dated 2013-06-20
Description: This package provides many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. It also offers access to an
XPath "interpreter".
Author: Duncan Temple Lang (duncan@r-project.org)
Maintainer: Duncan Temple Lang
XML-3.96-1.1/XML/INSTALL_R |only
XML-3.96-1.1/XML/INSTALL_S |only
XML-3.98-1.1/XML/Changes | 19 +++++
XML-3.98-1.1/XML/DESCRIPTION | 10 +-
XML-3.98-1.1/XML/DESCRIPTION.in | 6 +
XML-3.98-1.1/XML/MD5 | 83 +++++++++++-----------
XML-3.98-1.1/XML/NAMESPACE | 4 -
XML-3.98-1.1/XML/R/getRelativeURL.R | 12 +--
XML-3.98-1.1/XML/R/namespaces.R | 23 ++++++
XML-3.98-1.1/XML/R/simplifyPath.R |only
XML-3.98-1.1/XML/R/xincludes.R | 2
XML-3.98-1.1/XML/R/xmlIncludes.R |only
XML-3.98-1.1/XML/R/xmlInternalSource.R | 52 +++++++------
XML-3.98-1.1/XML/Todo.xml | 10 ++
XML-3.98-1.1/XML/VersionInfo | 2
XML-3.98-1.1/XML/a.out.dSYM |only
XML-3.98-1.1/XML/index.html | 22 ++---
XML-3.98-1.1/XML/inst/exampleData/redundantNS.xml |only
XML-3.98-1.1/XML/libxml2.9.R |only
XML-3.98-1.1/XML/man/Doctype-class.Rd | 4 -
XML-3.98-1.1/XML/man/Doctype.Rd | 8 +-
XML-3.98-1.1/XML/man/SAXState-class.Rd | 3
XML-3.98-1.1/XML/man/addChildren.Rd | 7 +
XML-3.98-1.1/XML/man/asXMLTreeNode.Rd | 3
XML-3.98-1.1/XML/man/catalogs.Rd | 33 ++++----
XML-3.98-1.1/XML/man/getChildrenStrings.Rd | 4 -
XML-3.98-1.1/XML/man/getNodeSet.Rd | 14 ++-
XML-3.98-1.1/XML/man/getRelativeURL.Rd | 4 -
XML-3.98-1.1/XML/man/getXIncludes.Rd | 21 +++++
XML-3.98-1.1/XML/man/makeClassTemplate.Rd | 4 -
XML-3.98-1.1/XML/man/newXMLDoc.Rd | 5 +
XML-3.98-1.1/XML/man/readHTMLTable.Rd | 12 +--
XML-3.98-1.1/XML/man/xmlAttrs.Rd | 3
XML-3.98-1.1/XML/man/xmlCleanNamespaces.Rd |only
XML-3.98-1.1/XML/man/xmlClone.Rd | 3
XML-3.98-1.1/XML/man/xmlEventParse.Rd | 13 ++-
XML-3.98-1.1/XML/man/xmlFlatListTree.Rd | 3
XML-3.98-1.1/XML/man/xmlNode.Rd | 3
XML-3.98-1.1/XML/man/xmlParseDoc.Rd | 3
XML-3.98-1.1/XML/man/xmlSource.Rd | 14 ++-
XML-3.98-1.1/XML/man/xmlTree.Rd | 11 ++
XML-3.98-1.1/XML/man/xmlTreeParse.Rd | 8 +-
XML-3.98-1.1/XML/src/XMLEventParse.c | 51 ++++++++++---
XML-3.98-1.1/XML/src/XMLHashTree.c | 4 -
XML-3.98-1.1/XML/src/XMLTree.c | 60 ++++++++++++---
XML-3.98-1.1/XML/src/xpath.c | 2
46 files changed, 365 insertions(+), 180 deletions(-)
Title: A swiss army knife for population genetic & genomic analysis
Diff between PopGenome versions 1.2.3 dated 2013-02-21 and 1.2.5 dated 2013-06-20
Description: PopGenome is an R-package for Population Genetic & Genomic
Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer
PopGenome-1.2.3/PopGenome/man/concatenate_to_whole_genome.Rd |only
PopGenome-1.2.3/PopGenome/man/popGetBial-methods.Rd |only
PopGenome-1.2.3/PopGenome/vignettes/XXX.png |only
PopGenome-1.2.3/PopGenome/vignettes/ZZZ2.png |only
PopGenome-1.2.5/PopGenome/DESCRIPTION | 17
PopGenome-1.2.5/PopGenome/MD5 | 114 ++-
PopGenome-1.2.5/PopGenome/NAMESPACE | 12
PopGenome-1.2.5/PopGenome/NEWS | 43 +
PopGenome-1.2.5/PopGenome/R/BAYESRETURN.R | 3
PopGenome-1.2.5/PopGenome/R/GENOME.R | 94 ++
PopGenome-1.2.5/PopGenome/R/PG_plot.biallelic.matrix.R |only
PopGenome-1.2.5/PopGenome/R/calc.R2.R |only
PopGenome-1.2.5/PopGenome/R/calc_sxsfss.R | 14
PopGenome-1.2.5/PopGenome/R/complike.R | 37 -
PopGenome-1.2.5/PopGenome/R/concatenate.R | 16
PopGenome-1.2.5/PopGenome/R/concatenate.classes.R |only
PopGenome-1.2.5/PopGenome/R/concatenate.regions.R |only
PopGenome-1.2.5/PopGenome/R/fisherextest.R | 6
PopGenome-1.2.5/PopGenome/R/fstcalc.R | 18
PopGenome-1.2.5/PopGenome/R/get.biallelic.matrix.R |only
PopGenome-1.2.5/PopGenome/R/get.codons.R |only
PopGenome-1.2.5/PopGenome/R/get.individuals.R |only
PopGenome-1.2.5/PopGenome/R/get_data.R | 8
PopGenome-1.2.5/PopGenome/R/get_gff_info.R | 18
PopGenome-1.2.5/PopGenome/R/getsyn.R | 2
PopGenome-1.2.5/PopGenome/R/import_export_slim.R | 7
PopGenome-1.2.5/PopGenome/R/intern.calc.R2.R |only
PopGenome-1.2.5/PopGenome/R/mult.linkage.stats.R | 71 --
PopGenome-1.2.5/PopGenome/R/my_math.R | 1
PopGenome-1.2.5/PopGenome/R/pair_linkdisequ_FAST.R |only
PopGenome-1.2.5/PopGenome/R/read.ms.output.R | 3
PopGenome-1.2.5/PopGenome/R/readData.R | 24
PopGenome-1.2.5/PopGenome/R/readMS.R |only
PopGenome-1.2.5/PopGenome/R/readSNP.R | 14
PopGenome-1.2.5/PopGenome/R/readVCF.R | 9
PopGenome-1.2.5/PopGenome/R/set.outgroup.R |only
PopGenome-1.2.5/PopGenome/R/slim.R | 17
PopGenome-1.2.5/PopGenome/R/splitting.data.R | 5
PopGenome-1.2.5/PopGenome/R/splitting.data.sep.R | 2
PopGenome-1.2.5/PopGenome/R/sweeps.stats.R | 23
PopGenome-1.2.5/PopGenome/R/update_slim.R | 9
PopGenome-1.2.5/PopGenome/inst/doc/Integration_of_new_Methods.R |only
PopGenome-1.2.5/PopGenome/inst/doc/Integration_of_new_Methods.Rnw | 2
PopGenome-1.2.5/PopGenome/inst/doc/Integration_of_new_Methods.pdf |binary
PopGenome-1.2.5/PopGenome/inst/doc/PopGenome_Vignette.R |only
PopGenome-1.2.5/PopGenome/inst/doc/PopGenome_Vignette.pdf |binary
PopGenome-1.2.5/PopGenome/man/BayeScanR.Rd | 4
PopGenome-1.2.5/PopGenome/man/GENOME-class.Rd | 14
PopGenome-1.2.5/PopGenome/man/PG_plot.biallelic.matrix.Rd |only
PopGenome-1.2.5/PopGenome/man/calc.R2-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/concatenate.classes.Rd |only
PopGenome-1.2.5/PopGenome/man/concatenate.regions.Rd |only
PopGenome-1.2.5/PopGenome/man/detail.stats-methods.Rd | 19
PopGenome-1.2.5/PopGenome/man/get.biallelic.matrix-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get.codons-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get.individuals-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/get_gff_info.Rd | 6
PopGenome-1.2.5/PopGenome/man/linkage.stats-methods.Rd | 3
PopGenome-1.2.5/PopGenome/man/mult.linkage.stats.Rd | 19
PopGenome-1.2.5/PopGenome/man/readData.Rd | 6
PopGenome-1.2.5/PopGenome/man/readMS.Rd |only
PopGenome-1.2.5/PopGenome/man/readSNP.Rd | 7
PopGenome-1.2.5/PopGenome/man/region.as.fasta.Rd | 6
PopGenome-1.2.5/PopGenome/man/set.outgroup-methods.Rd |only
PopGenome-1.2.5/PopGenome/man/sliding.window.transform-methods.Rd | 9
PopGenome-1.2.5/PopGenome/man/sweeps.stats-methods.Rd | 40 -
PopGenome-1.2.5/PopGenome/src/R2_C.c | 330 +++++++++-
PopGenome-1.2.5/PopGenome/src/get_gff_info_C.c | 12
PopGenome-1.2.5/PopGenome/src/whopgenome/readdnapp.cpp | 2
PopGenome-1.2.5/PopGenome/vignettes/Integration_of_new_Methods.Rnw | 2
PopGenome-1.2.5/PopGenome/vignettes/XXX.pdf |only
PopGenome-1.2.5/PopGenome/vignettes/XYZ.pdf |only
72 files changed, 824 insertions(+), 244 deletions(-)
Title: Fit high dimensional mixtures of Poisson GLMs
Diff between poisson.glm.mix versions 1.0 dated 2012-07-29 and 1.1 dated 2013-06-20
More information about poisson.glm.mix at CRAN
Description: High dimensional mixtures of Poisson Generalized Linear
models with three different parameterizations of Poisson means
are considered. Moreover, partitioning the response variables
into a set of blocks is possible. The package estimates
parameters via EM algorithm. For an efficient initialization, a
random splitting small-EM is introduced.
Author: Panagiotis Papastamoulis, Marie-Laure Martin-Magniette, Cathy
Maugis-Rabusseau
Maintainer: Panagiotis Papastamoulis
DESCRIPTION | 11 ++++++-----
MD5 | 34 +++++++++++++++++-----------------
R/bjkmodel.R | 4 ++--
R/bjmodel.R | 4 ++--
R/bkmodel.R | 4 ++--
R/init1.1.jk.j.R | 7 ++++---
R/init1.2.jk.j.R | 12 +++++++-----
R/init1.k.R | 6 ++++--
R/init2.jk.j.R | 16 ++++++++++------
R/init2.k.R | 10 +++++++---
R/pois.glm.mix.R | 15 ++++++++-------
man/init1.1.jk.j.Rd | 9 ++++++---
man/init1.2.jk.j.Rd | 19 +++++++++++--------
man/init1.k.Rd | 7 +++++--
man/init2.jk.j.Rd | 15 +++++++++------
man/init2.k.Rd | 9 ++++++---
man/pois.glm.mix.Rd | 7 +++++--
man/poisson.glm.mix.Rd | 2 +-
18 files changed, 112 insertions(+), 79 deletions(-)
Permanent link
Title: basic tools for the analysis of disease outbreaks.
Diff between epibase versions 0.1-0 dated 2013-05-22 and 0.1-1 dated 2013-06-20
Description: basic tools for the analysis of disease outbreaks.
Author: {The Hackout team (In alphabetic order: David Aanensen, Marc
Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho,
Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames,
Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues,
Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel
Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)}
Maintainer: Thibaut Jombart
epibase-0.1-0/epibase/vignettes/cache |only
epibase-0.1-0/epibase/vignettes/epibase.aux |only
epibase-0.1-0/epibase/vignettes/epibase.log |only
epibase-0.1-0/epibase/vignettes/epibase.out |only
epibase-0.1-0/epibase/vignettes/epibase.toc |only
epibase-0.1-0/epibase/vignettes/figs |only
epibase-0.1-1/epibase/DESCRIPTION | 14 -
epibase-0.1-1/epibase/MD5 | 285 ----------------------------
epibase-0.1-1/epibase/NAMESPACE | 58 +++--
epibase-0.1-1/epibase/R/make.phylo.R | 8
epibase-0.1-1/epibase/inst/doc/epibase.R | 3
epibase-0.1-1/epibase/inst/doc/epibase.Rnw | 3
epibase-0.1-1/epibase/inst/doc/epibase.pdf |binary
epibase-0.1-1/epibase/man/make.phylo.Rd | 7
epibase-0.1-1/epibase/man/uniqSequences.Rd | 5
epibase-0.1-1/epibase/vignettes/epibase.Rnw | 3
epibase-0.1-1/epibase/vignettes/texput.log |only
17 files changed, 75 insertions(+), 311 deletions(-)
Title: Analysis of animal movements
Diff between adehabitatLT versions 0.3.11 dated 2013-03-22 and 0.3.12 dated 2013-06-20
Description: A collection of tools for the analysis of animal movements
Author: Clement Calenge, contributions from Stephane Dray and Manuela
Royer
Maintainer: Clement Calenge
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/gdltraj.r | 4 ++--
inst/doc/adehabitatLT.R |only
src/tests.c | 2 +-
5 files changed, 11 insertions(+), 10 deletions(-)
Title: An R package for changepoint analysis
Diff between changepoint versions 1.0.6 dated 2013-06-08 and 1.1 dated 2013-06-20
Description: Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within
data. Many popular non-parametric and frequentist methods are
included. The cpt.mean, cpt.var, cpt.meanvar functions should
be your first point of call.
Author: Rebecca Killick
Maintainer: Rebecca Killick
DESCRIPTION | 8 ++---
MD5 | 30 +++++++++++-----------
NEWS | 6 ++++
R/exp.R | 27 +++++++++++++++----
R/gamma.R | 10 +++++--
R/multiple.nonparametric.R | 5 ++-
R/multiple.norm.R | 6 ++++
R/poisson.R | 2 +
R/single.norm.R | 61 ++++++++++++++++++++++++++++++++++++---------
man/cpt.mean.Rd | 2 -
man/cpt.meanvar.Rd | 2 -
man/cpt.var.Rd | 2 -
man/single.mean.norm.Rd | 2 -
man/single.meanvar.exp.Rd | 2 -
man/single.meanvar.norm.Rd | 2 -
man/single.var.norm.Rd | 2 -
16 files changed, 122 insertions(+), 47 deletions(-)
Title: Bradley-Terry Models
Diff between BradleyTerry2 versions 1.0-0 dated 2012-05-14 and 1.0-1 dated 2013-06-20
Description: Specify and fit the Bradley-Terry model and structured
versions
Author: Heather Turner and David Firth
Maintainer: Heather Turner
BradleyTerry2-1.0-0/BradleyTerry2/R/predict.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/print.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/summary.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/R/vcov.glmmPQL.R |only
BradleyTerry2-1.0-0/BradleyTerry2/man/predict.glmmPQL.Rd |only
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BradleyTerry2-1.0-0/BradleyTerry2/vignettes/BradleyTerry.blg |only
BradleyTerry2-1.0-1/BradleyTerry2/DESCRIPTION | 16
BradleyTerry2-1.0-1/BradleyTerry2/MD5 | 57
BradleyTerry2-1.0-1/BradleyTerry2/NAMESPACE | 11
BradleyTerry2-1.0-1/BradleyTerry2/R/BTm.R | 4
BradleyTerry2-1.0-1/BradleyTerry2/R/glmmPQL.R | 2
BradleyTerry2-1.0-1/BradleyTerry2/R/predict.BTglmmPQL.R |only
BradleyTerry2-1.0-1/BradleyTerry2/R/print.BTglmmPQL.R |only
BradleyTerry2-1.0-1/BradleyTerry2/R/print.summary.glmmPQL.R | 2
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BradleyTerry2-1.0-1/BradleyTerry2/data/baseball.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/chameleons.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/citations.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/flatlizards.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/icehockey.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/seeds.rda |binary
BradleyTerry2-1.0-1/BradleyTerry2/data/sound.fields.rda |binary
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BradleyTerry2-1.0-1/BradleyTerry2/inst/doc/BradleyTerry.Rnw | 2
BradleyTerry2-1.0-1/BradleyTerry2/inst/doc/BradleyTerry.pdf |binary
BradleyTerry2-1.0-1/BradleyTerry2/man/glmmPQL.Rd | 4
BradleyTerry2-1.0-1/BradleyTerry2/man/predict.BTglmmPQL.Rd |only
BradleyTerry2-1.0-1/BradleyTerry2/tests/flatlizards.R | 1
BradleyTerry2-1.0-1/BradleyTerry2/tests/flatlizards.Rout.save | 742 +++++-----
BradleyTerry2-1.0-1/BradleyTerry2/tests/predict.R | 2
BradleyTerry2-1.0-1/BradleyTerry2/tests/predict.Rout.save | 51
BradleyTerry2-1.0-1/BradleyTerry2/vignettes/BradleyTerry.Rnw | 2
37 files changed, 457 insertions(+), 439 deletions(-)
Title: Using gene expression data to improve flux balance analysis
predictions
Diff between sybilEFBA versions 0.0.1 dated 2013-06-05 and 1.0.0 dated 2013-06-20
Description: three different approaches to use gene expression data (or
protein measurements) for improving FBA predictions.
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 15 ++++-----
MD5 | 20 ++++++------
NAMESPACE | 3 -
R/eFBA_gene.R | 78 ++++++++++++++++++++++++------------------------
R/eFBA_rxn.R | 64 +++++++++++++++++++--------------------
R/findFluxGeneExpr.R |only
R/findMDCFlux.R | 26 ++++++++--------
man/FECorr.Rd | 1
man/eFBA_gene.Rd | 4 +-
man/findFluxGeneExpr.Rd |only
man/findMDCFlux.Rd | 4 --
man/iND750.Rd | 2 -
12 files changed, 107 insertions(+), 110 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.3.1 dated 2013-06-12 and 0.3.2 dated 2013-06-20
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
rbefdata-0.3.1/rbefdata/R/rbefdata-defunct.R |only
rbefdata-0.3.1/rbefdata/man/rbefdata-defunct.Rd |only
rbefdata-0.3.2/rbefdata/DESCRIPTION | 10 +-
rbefdata-0.3.2/rbefdata/MD5 | 37 +++++-----
rbefdata-0.3.2/rbefdata/NEWS | 7 +
rbefdata-0.3.2/rbefdata/R/bef.portal.get.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.attachment.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.dataset.R | 2
rbefdata-0.3.2/rbefdata/R/bef.portal.get.dataset_list.R | 5 -
rbefdata-0.3.2/rbefdata/R/bef.portal.get.keywords.R | 1
rbefdata-0.3.2/rbefdata/R/bef.portal.get.metadata.R | 21 ++++-
rbefdata-0.3.2/rbefdata/R/bef.portal.get.proposal.R | 2
rbefdata-0.3.2/rbefdata/R/helper.R | 21 ++++-
rbefdata-0.3.2/rbefdata/R/rbefdata-deprecated.R |only
rbefdata-0.3.2/rbefdata/R/rbefdata-package.R | 13 ++-
rbefdata-0.3.2/rbefdata/inst/fixtures |only
rbefdata-0.3.2/rbefdata/inst/tests/test.1.bef.options.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.attachment.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.dataset.R | 25 ++++--
rbefdata-0.3.2/rbefdata/inst/tests/test.bef.portal.get.metadata.R |only
rbefdata-0.3.2/rbefdata/inst/tests/test.helpers.R |only
rbefdata-0.3.2/rbefdata/man/rbefdata-deprecated.Rd |only
rbefdata-0.3.2/rbefdata/man/rbefdata-package.Rd | 12 ++-
rbefdata-0.3.2/rbefdata/tests/run-all.R | 1
24 files changed, 114 insertions(+), 47 deletions(-)
Title: L-moments
Diff between lmom versions 2.0 dated 2013-06-17 and 2.1 dated 2013-06-20
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples;
parameter estimation; L-moment ratio diagram; plot vs.
quantiles of an extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 6 ++++++
src/dqagie.f | 7 +++----
src/dqagse.f | 7 +++----
src/dqk15i.f | 13 ++++++-------
src/dqk21.f | 13 ++++++-------
7 files changed, 34 insertions(+), 32 deletions(-)
More information about SmithWilsonYieldCurve at CRAN
Permanent link
Title: Siena - Simulation Investigation for Empirical Network Analysis
Diff between RSiena versions 1.1-212 dated 2012-03-30 and 1.1-232 dated 2013-06-19
Description: Fits models to longitudinal network data
Author: Ruth Ripley, Krists Boitmanis, Tom A.B. Snijders
Maintainer: Tom A.B. Snijders
RSiena-1.1-212/RSiena/R/bayes.r |only
RSiena-1.1-212/RSiena/man/bayes.Rd |only
RSiena-1.1-212/RSiena/man/sienaModelCreate.Rd |only
RSiena-1.1-212/RSiena/man/sienaNet.Rd |only
RSiena-1.1-232/RSiena/.Rinstignore | 20
RSiena-1.1-232/RSiena/DESCRIPTION | 25
RSiena-1.1-232/RSiena/MD5 | 320
RSiena-1.1-232/RSiena/NAMESPACE | 92
RSiena-1.1-232/RSiena/R/RSienaRDocumentation.r | 584
RSiena-1.1-232/RSiena/R/Sienatest.r | 562
RSiena-1.1-232/RSiena/R/effects.r | 2929 -
RSiena-1.1-232/RSiena/R/effectsDocumentation.r | 303
RSiena-1.1-232/RSiena/R/effectsMethods.r | 346
RSiena-1.1-232/RSiena/R/getTargets.r | 84
RSiena-1.1-232/RSiena/R/globals.r | 414
RSiena-1.1-232/RSiena/R/initializeFRAN.r | 3946 -
RSiena-1.1-232/RSiena/R/iwlsm.R | 894
RSiena-1.1-232/RSiena/R/maxlike.r | 1688
RSiena-1.1-232/RSiena/R/maxlikec.r | 450
RSiena-1.1-232/RSiena/R/maxlikecalc.r | 302
RSiena-1.1-232/RSiena/R/observationErrors.r | 406
RSiena-1.1-232/RSiena/R/phase1.r | 971
RSiena-1.1-232/RSiena/R/phase2.r | 715
RSiena-1.1-232/RSiena/R/phase3.r | 1454
RSiena-1.1-232/RSiena/R/print01Report.r | 2767 -
RSiena-1.1-232/RSiena/R/print07Report.r | 386
RSiena-1.1-232/RSiena/R/printDataReport.r | 498
RSiena-1.1-232/RSiena/R/printInitialDescription.r | 1070
RSiena-1.1-232/RSiena/R/robmon.r | 679
RSiena-1.1-232/RSiena/R/siena01.r | 2468 -
RSiena-1.1-232/RSiena/R/siena07.r | 912
RSiena-1.1-232/RSiena/R/siena07gui.r | 210
RSiena-1.1-232/RSiena/R/siena08.r | 1364
RSiena-1.1-232/RSiena/R/sienaDataCreate.r | 4475 +-
RSiena-1.1-232/RSiena/R/sienaDataCreateFromSession.r | 1451
RSiena-1.1-232/RSiena/R/sienaGOF.r |only
RSiena-1.1-232/RSiena/R/sienaModelCreate.r | 212
RSiena-1.1-232/RSiena/R/sienaTimeTest.r | 2174
RSiena-1.1-232/RSiena/R/sienaeffects.r | 493
RSiena-1.1-232/RSiena/R/sienaprint.r | 1421
RSiena-1.1-232/RSiena/R/sienatable.r |only
RSiena-1.1-232/RSiena/R/sienautils.r | 969
RSiena-1.1-232/RSiena/R/simstatsc.r | 300
RSiena-1.1-232/RSiena/R/terminateFRAN.r | 67
RSiena-1.1-232/RSiena/R/zzz.R | 102
RSiena-1.1-232/RSiena/changeLog | 4802 +-
RSiena-1.1-232/RSiena/cleanup | 6
RSiena-1.1-232/RSiena/cleanup.win | 16
RSiena-1.1-232/RSiena/data/RSiena.rda |binary
RSiena-1.1-232/RSiena/data/allEffects.R | 2
RSiena-1.1-232/RSiena/data/allEffects.csv | 425
RSiena-1.1-232/RSiena/inst/doc/RSiena.bib | 8492 ++-
RSiena-1.1-232/RSiena/inst/doc/RSiena_Manual.pdf |binary
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RSiena-1.1-232/RSiena/inst/doc/effects.pdf |binary
RSiena-1.1-232/RSiena/inst/examples/Sampson_t2.txt | 210
RSiena-1.1-232/RSiena/inst/examples/Sampson_t3.txt | 266
RSiena-1.1-232/RSiena/inst/examples/Sampson_t4.txt | 202
RSiena-1.1-232/RSiena/inst/examples/arclistdata.dat | 700
RSiena-1.1-232/RSiena/inst/examples/vtextexoreal.dat | 64
RSiena-1.1-232/RSiena/inst/scripts/RSienaSNADescriptives.R | 296
RSiena-1.1-232/RSiena/inst/scripts/Rscript01DataFormat.R | 843
RSiena-1.1-232/RSiena/inst/scripts/Rscript02SienaVariableFormat.R | 965
RSiena-1.1-232/RSiena/inst/scripts/Rscript03SienaRunModel.R | 732
RSiena-1.1-232/RSiena/inst/scripts/Rscript04SienaBehaviour.R | 256
RSiena-1.1-232/RSiena/man/RSiena-package.Rd | 154
RSiena-1.1-232/RSiena/man/allEffects.Rd | 88
RSiena-1.1-232/RSiena/man/coCovar.Rd | 65
RSiena-1.1-232/RSiena/man/coDyadCovar.Rd | 76
RSiena-1.1-232/RSiena/man/edit.sienaEffects.Rd | 77
RSiena-1.1-232/RSiena/man/effectsDocumentation.Rd | 107
RSiena-1.1-232/RSiena/man/getEffects.Rd | 172
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RSiena-1.1-232/RSiena/man/includeInteraction.Rd | 155
RSiena-1.1-232/RSiena/man/includeTimeDummy.Rd | 225
RSiena-1.1-232/RSiena/man/installGui.Rd | 46
RSiena-1.1-232/RSiena/man/iwlsm.Rd | 408
RSiena-1.1-232/RSiena/man/maxlikefn.Rd | 160
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RSiena-1.1-232/RSiena/man/print.sienaEffects.Rd | 118
RSiena-1.1-232/RSiena/man/print.sienaMeta.Rd | 188
RSiena-1.1-232/RSiena/man/print01Report.Rd | 97
RSiena-1.1-232/RSiena/man/s50.Rd | 70
RSiena-1.1-232/RSiena/man/s501.Rd | 50
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RSiena-1.1-232/RSiena/man/s503.Rd | 58
RSiena-1.1-232/RSiena/man/s50a.Rd | 62
RSiena-1.1-232/RSiena/man/setEffect.Rd | 169
RSiena-1.1-232/RSiena/man/siena01Gui.Rd | 129
RSiena-1.1-232/RSiena/man/siena07.Rd | 267
RSiena-1.1-232/RSiena/man/siena08.Rd | 251
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RSiena-1.1-232/RSiena/man/sienaDataConstraint.Rd | 88
RSiena-1.1-232/RSiena/man/sienaDataCreate.Rd | 102
RSiena-1.1-232/RSiena/man/sienaDataCreateFromSession.Rd | 228
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RSiena-1.1-232/RSiena/man/sienaGroupCreate.Rd | 229
RSiena-1.1-232/RSiena/man/sienaModelOptions.Rd | 144
RSiena-1.1-232/RSiena/man/sienaNodeSet.Rd | 62
RSiena-1.1-232/RSiena/man/sienaTimeTest.Rd | 295
RSiena-1.1-232/RSiena/man/simstats0c.Rd | 252
RSiena-1.1-232/RSiena/man/summary.iwlsm.Rd | 208
RSiena-1.1-232/RSiena/man/tmp3.Rd | 37
RSiena-1.1-232/RSiena/man/tmp4.Rd | 37
RSiena-1.1-232/RSiena/man/updateTheta.Rd | 105
RSiena-1.1-232/RSiena/man/varCovar.Rd | 67
RSiena-1.1-232/RSiena/man/varDyadCovar.Rd | 84
RSiena-1.1-232/RSiena/man/xtable.Rd | 94
RSiena-1.1-232/RSiena/po/R-RSiena.pot | 1392
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RSiena-1.1-232/RSiena/src/Makevars.win | 60
RSiena-1.1-232/RSiena/src/data/ChangingDyadicCovariate.cpp | 9
RSiena-1.1-232/RSiena/src/data/ChangingDyadicCovariate.h | 1
RSiena-1.1-232/RSiena/src/data/ConstantDyadicCovariate.cpp | 8
RSiena-1.1-232/RSiena/src/data/ConstantDyadicCovariate.h | 1
RSiena-1.1-232/RSiena/src/data/NetworkLongitudinalData.cpp | 15
RSiena-1.1-232/RSiena/src/data/NetworkLongitudinalData.h | 7
RSiena-1.1-232/RSiena/src/model/EffectInfo.cpp | 4
RSiena-1.1-232/RSiena/src/model/Model.cpp | 64
RSiena-1.1-232/RSiena/src/model/Model.h | 18
RSiena-1.1-232/RSiena/src/model/StatisticCalculator.cpp | 309
RSiena-1.1-232/RSiena/src/model/StatisticCalculator.h | 18
RSiena-1.1-232/RSiena/src/model/effects/AllEffects.h | 7
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RSiena-1.1-232/RSiena/src/model/effects/OutdegreePopularityEffect.cpp | 4
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RSiena-1.1-232/RSiena/src/model/effects/WWXClosureEffect.cpp | 90
RSiena-1.1-232/RSiena/src/model/effects/WWXClosureEffect.h | 13
RSiena-1.1-232/RSiena/src/model/effects/generic/AlterPredicate.h | 27
RSiena-1.1-232/RSiena/src/model/effects/generic/CovariateMixedNetworkAlterFunction.cpp |only
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RSiena-1.1-232/RSiena/src/model/effects/generic/MixedNetworkAlterFunction.cpp | 4
RSiena-1.1-232/RSiena/src/model/effects/generic/OutDegreeFunction.cpp | 2
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RSiena-1.1-232/RSiena/src/model/filters/PermittedChangeFilter.h | 4
RSiena-1.1-232/RSiena/src/model/variables/DependentVariable.cpp | 521
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RSiena-1.1-232/RSiena/src/model/variables/NetworkVariable.cpp | 311
RSiena-1.1-232/RSiena/src/model/variables/NetworkVariable.h | 2
RSiena-1.1-232/RSiena/src/network/NetworkUtils.cpp | 32
RSiena-1.1-232/RSiena/src/network/NetworkUtils.h | 3
RSiena-1.1-232/RSiena/src/siena07internals.cpp | 231
RSiena-1.1-232/RSiena/src/siena07internals.h | 5
RSiena-1.1-232/RSiena/src/siena07setup.cpp | 11
RSiena-1.1-232/RSiena/tests/parallel.R | 24
RSiena-1.1-232/RSiena/tests/parallel.Rout.save | 105
RSiena-1.1-232/RSiena/tests/scriptfile.Rout.save | 215
RSiena-1.1-232/RSiena/tests/scriptfile.Rout.win | 5809 +-
RSiena-1.1-232/RSiena/tests/scripts.Rout.save | 10
184 files changed, 49319 insertions(+), 44807 deletions(-)
Title: Package for statistical age models analysis in optically
stimulated luminescence dating
Diff between RadialPlotter versions 1.6 dated 2013-05-20 and 1.7 dated 2013-06-19
Description: Package for estimating parameters of statistical age
models in optically stimulated luminescence dating dynamically.
Author: Peng Jun
Maintainer: Peng Jun
DESCRIPTION | 8
MD5 | 42 ++-
NEWS | 2
R/RadialPlotter.R | 475 ++++++++++++++++++++++++++++++++++++++++++-
THANKS | 1
data/CW.Signal.data.RData |only
man/CW.Signal.data.Rd |only
man/EDdata.Rd | 5
man/RadialPlotter-package.Rd | 22 +
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man/SGCED.Rd |only
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src/MamED.f90 | 26 +-
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src/diag.f90 | 2
src/diffev.f90 |only
src/fdhessian.f90 | 92 +++++---
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src/inverse.f90 | 2
src/leaveone.f90 |only
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Title: R package to compute the FastPCS outlyingness index.
Diff between FastPCS versions 0.0.2 dated 2013-05-25 and 0.0.3 dated 2013-06-19
Description: R implementation of the FastPCS algorithm for computing
the FastPCS outlyingness index.
Author: Kaveh Vakili [aut, cre]
Maintainer: Kaveh Vakili
DESCRIPTION | 7 ++++---
MD5 | 10 +++++-----
NAMESPACE | 1 +
R/FastPCS.R | 38 +++++++++++++++++++++++---------------
man/FastPCS.Rd | 53 ++++++++++++++++++++++++++++++++++++-----------------
src/FastPCS.cpp | 44 ++++++++++++++++----------------------------
6 files changed, 85 insertions(+), 68 deletions(-)
Title: Fits geographically weighted regression models with diagnostic
tools
Diff between gwrr versions 0.1-2 dated 2011-11-29 and 0.2-1 dated 2013-06-19
Description: Fits geographically weighted regression (GWR) models and
has tools to diagnose and remediate collinearity in the GWR
models. Also fits geographically weighted ridge regression
(GWRR) and geographically weighted lasso (GWL) models.
Author: David Wheeler
Maintainer: David Wheeler
DESCRIPTION | 18 +-
MD5 | 24 ++-
NAMESPACE | 3
R/gwl.est.r |only
R/gwr.bw.est.R | 4
R/gwr.est.R | 4
R/gwr.vdp.R | 4
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Title: Mixtures of von Mises-Fisher Distributions
Diff between movMF versions 0.1-0 dated 2012-10-23 and 0.1-1 dated 2013-06-19
Description: Fit and simulate mixtures of von Mises-Fisher
distributions.
Author: Kurt Hornik [aut, cre], Bettina Grün [aut]
Maintainer: Kurt Hornik
DESCRIPTION | 19 +--
MD5 | 19 +--
R/dmovMF.R | 5
R/movMF.R | 316 +++++++++++++++++++++++++++++++++++++++-------------
R/rmovMF.R | 5
inst/NEWS.Rd | 6
inst/doc/movMF.R |only
inst/doc/movMF.Rnw | 2
inst/doc/movMF.pdf |binary
vignettes/movMF.Rnw | 2
vignettes/vMF.bib | 166 ++++++++++++++++++---------
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Title: Syntax highlighter
Diff between highlight versions 0.4.1 dated 2013-04-09 and 0.4.2 dated 2013-06-19
Description: Syntax highlighter for R code based on the results of the
R parser. Rendering in HTML and latex markup. Custom Sweave
driver performing syntax highlighting of R code chunks
Author: Romain Francois
Maintainer: Romain Francois
DESCRIPTION | 6 +-
MD5 | 31 ++++++------
NAMESPACE | 4 +
NEWS | 10 +++
R/SweaveLatexDriver.R | 26 +++++++++-
R/external_highlight.R | 13 +----
R/highlight.R | 111 +++++++++++++++++++++-----------------------
R/renderer.R | 2
R/zzz.R | 3 +
build/highlight.pdf |binary
inst/stylesheet/default.css | 2
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man/renderer_latex.Rd | 15 +++--
src/configurationreader.cpp | 2
src/render.cpp | 10 +--
17 files changed, 148 insertions(+), 111 deletions(-)
Title: Differential Geometric LARS (dgLARS) method
Diff between dglars versions 1.0 dated 2012-11-08 and 1.0.1 dated 2013-06-19
Description: dglars implements the differential geometric extension of
the least angle regression method for logistic and Poisson
regression models. To compute the implicitly defined solution
curve, two different algorithms are implemented, i.e. the
predictor-corrector method and the cyclic coordinate descent
method.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro
dglars-1.0.1/dglars/ChangeLog |only
dglars-1.0.1/dglars/DESCRIPTION | 7 +++---
dglars-1.0.1/dglars/MD5 | 34 +++++++++++++++---------------
dglars-1.0.1/dglars/man/breast.Rd | 6 ++---
dglars-1.0.1/dglars/man/coef.cvdglars.Rd | 6 +++--
dglars-1.0.1/dglars/man/coef.dglars.Rd | 2 +
dglars-1.0.1/dglars/man/cvdglars.Rd | 13 ++++++-----
dglars-1.0.1/dglars/man/dglars-package.Rd | 14 ++++++------
dglars-1.0.1/dglars/man/dglars.Rd | 19 ++++++++--------
dglars-1.0.1/dglars/man/gdf.Rd | 12 ++++++----
dglars-1.0.1/dglars/man/plot.cvdglars.Rd | 6 +++--
dglars-1.0.1/dglars/man/plot.dglars.Rd | 4 ++-
dglars-1.0.1/dglars/man/print.cvdglars.Rd | 4 ++-
dglars-1.0.1/dglars/man/print.dglars.Rd | 19 +++++++++++++++-
dglars-1.0.1/dglars/man/summary.dglars.Rd | 10 +++++---
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21 files changed, 96 insertions(+), 62 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 2.1 dated 2013-06-03 and 2.2 dated 2013-06-19
Description: Performs the colocalisation tests described in Plagnol et
al (2009), Wallace et al (2013) and Giambartolomei et al
(2013).
Author: Chris Wallace and Claudia Giambartolemei with contributions
from Vincent Plagnol
Maintainer: Chris Wallace
coloc-2.1/coloc/R/coloc.abf.imputed.R |only
coloc-2.1/coloc/man/coloc.abf.imputed.Rd |only
coloc-2.2/coloc/ChangeLog | 10 +
coloc-2.2/coloc/DESCRIPTION | 7 -
coloc-2.2/coloc/MD5 | 25 +--
coloc-2.2/coloc/NAMESPACE | 1
coloc-2.2/coloc/R/claudia.R | 190 +++++++++++++++++++++---------
coloc-2.2/coloc/inst/doc/vignette.R | 17 +-
coloc-2.2/coloc/inst/doc/vignette.Rnw | 38 ++++--
coloc-2.2/coloc/inst/doc/vignette.pdf |binary
coloc-2.2/coloc/man/approx.bf.imputed.Rd | 2
coloc-2.2/coloc/man/coloc.abf.Rd | 79 +++++++-----
coloc-2.2/coloc/man/coloc.abf.datasets.Rd | 3
coloc-2.2/coloc/man/coloc.abf.snpStats.Rd | 14 ++
coloc-2.2/coloc/man/process.dataset.Rd |only
15 files changed, 260 insertions(+), 126 deletions(-)
Title: Generalized multistate simulation model
Diff between gems versions 0.9.1 dated 2013-02-18 and 0.9.2 dated 2013-06-19
Description: This package allows to simulating and analyzing multistate
models with general hazard functions. It provides functionality
for the preparation of hazard functions and parameters,
simulation from a general multistate model and predicting
future events. The multistate model is not required to be a
Markov model and may take the history of previous events into
account. In the basic version, it allows to simulate from
transition-specific hazard function, whose parameters are
multivariable normally distributed.
Author: Luisa Salazar Vizcaya, Nello Blaser, Thomas Gsponer
Maintainer: Luisa Salazar Vizcaya
DESCRIPTION | 6 ++---
MD5 | 8 +++----
R/gems.r | 56 +++++++++++++++++++++++++-------------------------
changeLog | 4 +++
man/simulateCohort.Rd | 6 ++---
5 files changed, 42 insertions(+), 38 deletions(-)
Title: Data from the M-competitions
Diff between Mcomp versions 2.04 dated 2012-03-19 and 2.05 dated 2013-06-19
Description: The 1001 time series from the M-competition (Makridakis et
al. 1982) and the 3003 time series from the IJF-M3 competition
(Makridakis and Hibon, 2000).
Author: Rob J Hyndman with assistance from Muhammad Akram and Christoph
Bergmeir.
Maintainer: Rob J Hyndman
ChangeLog | 4 ++++
DESCRIPTION | 12 +++++++-----
MD5 | 13 ++++++++-----
data/M3.rda |binary
data/M3Forecast.rda |only
data/datalist |only
man/M1.Rd | 4 ++--
man/M3Forecast.Rd |only
man/Mcomp-package.Rd | 9 ++++-----
9 files changed, 25 insertions(+), 17 deletions(-)
Title: JudgeIt
Diff between JudgeIt versions 1.3.3 dated 2008-08-27 and 1.5.0 dated 2013-06-19
Description: Examines two-party electoral systems and calculates
quantities of interest based on the behaviour of their
districts.
Author: Andrew Gelman, Gary King and Andrew C. Thomas
Maintainer: Andrew C. Thomas
JudgeIt-1.3.3/JudgeIt/inst/doc/.latex2html-init |only
JudgeIt-1.3.3/JudgeIt/inst/doc/Makefile |only
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JudgeIt-1.3.3/JudgeIt/inst/doc/judgeit.toc |only
JudgeIt-1.5.0/JudgeIt/.Rinstignore |only
JudgeIt-1.5.0/JudgeIt/DESCRIPTION | 27 +
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JudgeIt-1.5.0/JudgeIt/NAMESPACE | 14 -
JudgeIt-1.5.0/JudgeIt/R/operators.R | 2
JudgeIt-1.5.0/JudgeIt/R/quantities.R | 189 +++++++++++++
JudgeIt-1.5.0/JudgeIt/R/visibles.R | 259 ++++++++++++++-----
JudgeIt-1.5.0/JudgeIt/data/StateLeg.RData |only
JudgeIt-1.5.0/JudgeIt/data/house6311.RData |binary
JudgeIt-1.5.0/JudgeIt/data/pres.elect.15.RData |only
JudgeIt-1.5.0/JudgeIt/demo/distreportdemo.R | 4
JudgeIt-1.5.0/JudgeIt/demo/judgeit.primer.R | 4
JudgeIt-1.5.0/JudgeIt/demo/probdemo.R | 4
JudgeIt-1.5.0/JudgeIt/demo/seatsdemo.R | 6
JudgeIt-1.5.0/JudgeIt/demo/svsumdemo.R | 6
JudgeIt-1.5.0/JudgeIt/inst/doc/index.shtml | 162 +++++------
JudgeIt-1.5.0/JudgeIt/inst/doc/judgeit.pdf |binary
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JudgeIt-1.5.0/JudgeIt/inst/doc/judgeittechniques.pdf |only
JudgeIt-1.5.0/JudgeIt/inst/doc/judgeittechniques.tex |only
JudgeIt-1.5.0/JudgeIt/man/StateLeg.Rd |only
JudgeIt-1.5.0/JudgeIt/man/judgeit.Rd | 10
JudgeIt-1.5.0/JudgeIt/man/pres-elect-15.Rd |only
JudgeIt-1.5.0/JudgeIt/man/seats.Rd | 10
33 files changed, 632 insertions(+), 307 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 4.04 dated 2013-04-22 and 4.05 dated 2013-06-19
Description: Methods and tools for displaying and analysing univariate
time series forecasts including exponential smoothing via state
space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 12
DESCRIPTION | 14
MD5 | 39 -
R/HoltWintersNew.R | 8
R/arima.R | 2
R/bats.R | 71 +-
R/errors.R | 149 +++-
R/ets.R | 1294 +++++++++++++++++++++++----------------
R/forecast.R | 5
R/forecast2.R | 45 -
R/fpp.R | 8
R/guerrero.R | 6
R/lm.R | 9
R/simulate.R | 10
R/tbats.R | 99 +-
README.md |only
man/accuracy.Rd | 6
man/ets.Rd | 3
man/simulate.Rd | 3
src/etsTargetFunction.cpp |only
src/etsTargetFunction.h |only
src/etsTargetFunctionWrapper.cpp |only
src/etspolyroot.c |only
23 files changed, 1069 insertions(+), 714 deletions(-)
Title: A fast solver for constrained l1 minimization approach to sparse
precision matrix estimation
Diff between fastclime versions 1.0 dated 2013-05-30 and 1.1 dated 2013-06-19
Description: The package "fastclime" provides a method of recover the
precision matrix efficiently by applying parametric simplex
method. The computation is based on a linear optimization
solver. It also contains a generic LP solver using parametric
simplex method.
Author: Haotian Pang, Han Liu and Robert Vanderbei
Maintainer: Haotian Pang
DESCRIPTION | 11 +++--
MD5 | 27 ++++++++-----
NAMESPACE | 3 +
R/fastclime.R | 16 +-------
R/fastclime.generator.R | 4 +-
R/fastclime.plot.R | 4 +-
R/fastclime.roc.R | 4 +-
R/fastlp.R |only
inst/doc/fastclime.pdf |only
inst/doc/vignette.Rnw |only
inst/doc/vignette.pdf |binary
man/fastclime.Rd | 7 ++-
man/fastlp.Rd |only
src/fastlp.c |only
src/linalg.c | 84 ++++++++++++++++++++++++++++++++++++++++++
src/linalg.h | 14 +++++++
src/parametric.c | 94 ------------------------------------------------
17 files changed, 136 insertions(+), 132 deletions(-)
Title: Quality Assurance Toolkit
Diff between qat versions 0.71 dated 2013-03-30 and 0.72 dated 2013-06-18
Description: This package delivers some functions to provide a
scientific quality assurance of meteorological data.
Author: Andre Duesterhus
Maintainer: Andre Duesterhus
ChangeLog.txt | 3
DESCRIPTION | 8 -
MD5 | 200 +++++++++++++++---------------
R/qat_analyse_histogram_test_1d.R |only
R/qat_analyse_histogram_test_2d.R |only
R/qat_analyse_histogram_test_emd_1d.R | 29 ----
R/qat_analyse_histogram_test_emd_2d.R | 31 ----
R/qat_analyse_histogram_test_jsd_1d.R | 48 -------
R/qat_analyse_histogram_test_jsd_2d.R | 48 -------
R/qat_analyse_histogram_test_kld_1d.R | 55 --------
R/qat_analyse_histogram_test_kld_2d.R | 55 --------
R/qat_analyse_histogram_test_ms_1d.R | 27 ----
R/qat_analyse_histogram_test_ms_2d.R | 27 ----
R/qat_analyse_histogram_test_rms_1d.R | 27 ----
R/qat_analyse_histogram_test_rms_2d.R | 27 ----
R/qat_data_close_ncdf.R |only
R/qat_measure_histogram_difference.R |only
inst/doc/qatdoku.pdf |binary
inst/extdata/workflowexample.xml | 83 ------------
man/qat-package.Rd | 17 +-
man/qat_analyse_histogram_test_1d.Rd |only
man/qat_analyse_histogram_test_2d.Rd |only
man/qat_analyse_histogram_test_emd_1d.Rd | 3
man/qat_analyse_histogram_test_emd_2d.Rd | 3
man/qat_analyse_histogram_test_jsd_1d.Rd | 6
man/qat_analyse_histogram_test_jsd_2d.Rd | 6
man/qat_analyse_histogram_test_kld_1d.Rd | 6
man/qat_analyse_histogram_test_kld_2d.Rd | 6
man/qat_analyse_histogram_test_ms_1d.Rd | 3
man/qat_analyse_histogram_test_ms_2d.Rd | 3
man/qat_analyse_histogram_test_rms_1d.Rd | 3
man/qat_analyse_histogram_test_rms_2d.Rd | 3
man/qat_analyse_lim_rule_dynamic_1d.Rd | 7 -
man/qat_analyse_lim_rule_dynamic_2d.Rd | 7 -
man/qat_analyse_roc_rule_dynamic_1d.Rd | 7 -
man/qat_analyse_roc_rule_dynamic_2d.Rd | 7 -
man/qat_analyse_roc_rule_static_1d.Rd | 3
man/qat_analyse_roc_rule_static_2d.Rd | 3
man/qat_call_block_distribution.Rd | 4
man/qat_call_boot_distribution.Rd | 4
man/qat_call_distribution.Rd | 4
man/qat_call_histogram_test.Rd | 4
man/qat_call_lim_rule.Rd | 8 -
man/qat_call_noc_rule.Rd | 4
man/qat_call_plot_block_distribution.Rd | 10 +
man/qat_call_plot_boot_distribution.Rd | 11 +
man/qat_call_plot_distribution.Rd | 7 -
man/qat_call_plot_histogram_test.Rd | 10 +
man/qat_call_plot_lim_rule.Rd | 17 +-
man/qat_call_plot_noc_rule.Rd | 7 -
man/qat_call_plot_roc_rule.Rd | 17 +-
man/qat_call_plot_slide_distribution.Rd | 10 +
man/qat_call_plot_trimmed_distribution.Rd | 7 -
man/qat_call_roc_rule.Rd | 7 -
man/qat_call_save_block_distribution.Rd | 4
man/qat_call_save_boot_distribution.Rd | 4
man/qat_call_save_distribution.Rd | 7 -
man/qat_call_save_histogram_test.Rd | 4
man/qat_call_save_lim_rule.Rd | 14 +-
man/qat_call_save_noc_rule.Rd | 4
man/qat_call_save_roc_rule.Rd | 14 +-
man/qat_call_save_set_addup.Rd | 4
man/qat_call_save_set_mean.Rd | 4
man/qat_call_save_set_nans.Rd | 4
man/qat_call_save_slide_distribution.Rd | 5
man/qat_call_save_trimmed_distribution.Rd | 5
man/qat_call_set_addup.Rd | 4
man/qat_call_set_mean.Rd | 4
man/qat_call_set_nans.Rd | 4
man/qat_call_slide_distribution.Rd | 4
man/qat_call_trimmed_distribution.Rd | 4
man/qat_config_write_workflow.Rd | 4
man/qat_data_close_ncdf.Rd |only
man/qat_measure_histogram_difference.Rd |only
man/qat_plot_block_distribution_1d.Rd | 6
man/qat_plot_block_distribution_2d.Rd | 6
man/qat_plot_boot_distribution_1d.Rd | 10 -
man/qat_plot_distribution_1d.Rd | 6
man/qat_plot_histogram_test.Rd | 7 -
man/qat_plot_lim_rule_dynamic_1d.Rd | 12 +
man/qat_plot_lim_rule_dynamic_2d.Rd | 12 +
man/qat_plot_lim_rule_sigma_1d.Rd | 8 -
man/qat_plot_lim_rule_sigma_2d.Rd | 9 +
man/qat_plot_lim_rule_static_1d.Rd | 8 -
man/qat_plot_lim_rule_static_2d.Rd | 8 -
man/qat_plot_noc_rule_1d.Rd | 7 -
man/qat_plot_noc_rule_2d.Rd | 7 -
man/qat_plot_roc_rule_dynamic_1d.Rd | 13 +
man/qat_plot_roc_rule_dynamic_2d.Rd | 13 +
man/qat_plot_roc_rule_static_1d.Rd | 8 -
man/qat_plot_roc_rule_static_2d.Rd | 8 -
man/qat_plot_slide_distribution_1d.Rd | 6
man/qat_plot_slide_distribution_2d.Rd | 6
man/qat_plot_trimmed_distribution_1d.Rd | 6
man/qat_plot_trimmed_distribution_2d.Rd | 6
man/qat_run_workflow_check.Rd | 6
man/qat_run_workflow_plot.Rd | 6
man/qat_run_workflow_save.Rd | 9 -
man/qat_save_boot_distribution_2d.Rd | 2
man/qat_save_lim_rule_dynamic_1d.Rd | 3
man/qat_save_lim_rule_dynamic_2d.Rd | 3
man/qat_save_result_ncdf.Rd | 14 +-
man/qat_save_roc_rule_dynamic_1d.Rd | 4
man/qat_save_roc_rule_dynamic_2d.Rd | 3
man/qat_style_plot.Rd | 7 -
105 files changed, 511 insertions(+), 707 deletions(-)
Title: Markdown rendering for R
Diff between markdown versions 0.5.5 dated 2013-06-07 and 0.6 dated 2013-06-18
Description: Markdown is a plain-text formatting syntax that can be
converted to XHTML or other formats. This package provides R
bindings to the Sundown markdown rendering library.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie
DESCRIPTION | 17 +-
MD5 | 40 ++--
NAMESPACE | 22 +-
NEWS | 6
R/markdown-package.R |only
R/renderMarkdown.R | 365 +++++++++++++++++++++++++++++++++++++++++++--
R/rpubsUpload.R | 202 ++++++++++++------------
inst/doc |only
inst/examples |only
man/markdown.Rd | 43 +++--
man/markdownExtensions.Rd | 210 +++++++++++--------------
man/markdownHTMLOptions.Rd | 197 ++++++++++++------------
man/markdownToHTML.Rd | 164 ++++++++++----------
man/registeredRenderers.Rd | 38 +---
man/renderMarkdown.Rd | 99 ++++++------
man/rendererExists.Rd | 16 -
man/rendererOutputType.Rd | 33 +---
man/rpubsUpload.Rd | 3
man/smartypants.Rd | 61 +++----
tests/tests.R | 130 ----------------
tests/tests.Rout.save | 249 ++++++++++++++----------------
21 files changed, 1039 insertions(+), 856 deletions(-)
Title: Interface to HDF5 Files
Diff between h5r versions 1.4.1 dated 2012-08-07 and 1.4.5 dated 2013-06-18
Description: A package for reading and writing HDF5 files.
Author: James Bullard
Maintainer: James Bullard
h5r-1.4.1/h5r/src/Makevars |only
h5r-1.4.5/h5r/DESCRIPTION | 9
h5r-1.4.5/h5r/INSTALL | 33 ++-
h5r-1.4.5/h5r/MD5 | 21 +-
h5r-1.4.5/h5r/NEWS | 10
h5r-1.4.5/h5r/R/h5R.R | 12 +
h5r-1.4.5/h5r/inst/h5_files/compound.h5 |only
h5r-1.4.5/h5r/inst/h5_files/ex_1.h5 |binary
h5r-1.4.5/h5r/inst/h5_files/makeH5.py | 42 ++++
h5r-1.4.5/h5r/src/h5_debug.c | 11 -
h5r-1.4.5/h5r/src/h5_wrap.c | 332 ++++++++++++++++++++++----------
h5r-1.4.5/h5r/tests/testCompound.R |only
h5r-1.4.5/h5r/tests/testMemory.R | 89 +++++---
13 files changed, 404 insertions(+), 155 deletions(-)
Title: Financial Risk Modelling and Portfolio Optimisation with R
Diff between FRAPO versions 0.3-7 dated 2013-06-08 and 0.3-8 dated 2013-06-18
Description: Accompanying package of the book 'Financial Risk Modelling
and Portfolio Optimisation with R'. The data sets used in the
book are contained in this package.
Author: Bernhard Pfaff [aut, cre], Miguel Sousa Lobo [ctb] (SOCP),
Lieven Vandenberghe [ctb] (SOCP), Stephen Boyd [ctb] (SOCP),
Herve Lebret [ctb] (SOCP)
Maintainer: Bernhard Pfaff
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
NAMESPACE | 1 +
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Ridge regression and other kernels for genomic selection
Diff between rrBLUP versions 4.1 dated 2012-12-21 and 4.2 dated 2013-06-18
Description: Software for genomic prediction with the RR-BLUP mixed
model. One application is to estimate marker effects by ridge
regression; alternatively, BLUPs can be calculated based on an
additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman
DESCRIPTION | 12 +++++++-----
MD5 | 28 +++++++++++++++-------------
NEWS | 4 ++++
R/A.mat.R | 28 ++++++++++++++++++----------
R/GWAS.R | 4 ++--
R/kin.blup.R | 4 ++--
R/kinship.BLUP.R | 4 ++--
inst/doc/GS_tutorial.R |only
inst/doc/GS_tutorial.pdf |binary
inst/doc/GWAS_tutorial.R |only
inst/doc/GWAS_tutorial.pdf |binary
man/A.mat.Rd | 12 +++++-------
man/GWAS.Rd | 2 +-
man/kin.blup.Rd | 2 +-
man/kinship.BLUP.Rd | 2 +-
man/rrBLUP-package.Rd | 4 +---
16 files changed, 59 insertions(+), 47 deletions(-)
Title: an R package for analyzing multivariate longitudinal data with
multivariate marginal models
Diff between mmm versions 1.2 dated 2013-02-04 and 1.3 dated 2013-06-18
Description: fits multivariate marginal models for multivariate
longitudinal data for both continuous and discrete responses
Author: Ozgur Asar, Ozlem Ilk
Maintainer: Ozgur Asar
mmm-1.2/mmm/data/mlcd.rda |only
mmm-1.2/mmm/data/mlgd.rda |only
mmm-1.2/mmm/data/mscm.rda |only
mmm-1.2/mmm/man/mlcd.Rd |only
mmm-1.2/mmm/man/mlgd.Rd |only
mmm-1.2/mmm/man/mscm.Rd |only
mmm-1.3/mmm/DESCRIPTION | 12 -
mmm-1.3/mmm/MD5 | 20 +-
mmm-1.3/mmm/R/mmm.R | 10 -
mmm-1.3/mmm/data/motherStress.rda |only
mmm-1.3/mmm/data/multiLongCount.rda |only
mmm-1.3/mmm/data/multiLongGaussian.rda |only
mmm-1.3/mmm/man/mmm-package.Rd | 6
mmm-1.3/mmm/man/mmm.Rd | 235 ++++++++++++++++++++++++++++++---
mmm-1.3/mmm/man/motherStress.Rd |only
mmm-1.3/mmm/man/multiLongCount.Rd |only
mmm-1.3/mmm/man/multiLongGaussian.Rd |only
17 files changed, 239 insertions(+), 44 deletions(-)
Title: Robust estimation of location and scatter
Diff between restlos versions 0.1-1 dated 2013-03-11 and 0.1-2 dated 2013-06-18
Description: The package implements some recently introduced
methodology for robust estimation of location and scatter as
well as outlier identification.
Author: Steffen Liebscher and Thomas Kirschstein
Maintainer: Steffen Liebscher
restlos-0.1-1/restlos/R/pMST.R |only
restlos-0.1-2/restlos/DESCRIPTION | 10 +++++-----
restlos-0.1-2/restlos/MD5 | 20 ++++++++++----------
restlos-0.1-2/restlos/NAMESPACE | 3 ++-
restlos-0.1-2/restlos/R/pMST.r |only
restlos-0.1-2/restlos/man/flood.Rd | 2 +-
restlos-0.1-2/restlos/man/pMST.Rd | 2 +-
restlos-0.1-2/restlos/man/plot.flood.Rd | 2 +-
restlos-0.1-2/restlos/man/plot.pMST.Rd | 2 +-
restlos-0.1-2/restlos/man/plot.rdela.Rd | 2 +-
restlos-0.1-2/restlos/man/rdela.Rd | 2 +-
restlos-0.1-2/restlos/man/restlos-package.Rd | 10 +++++-----
12 files changed, 28 insertions(+), 27 deletions(-)
Title: Calculate generalized eigenvalues of a matrix pair
Diff between geigen versions 1.1 dated 2013-05-23 and 1.2 dated 2013-06-18
Description: Compute generalized eigenvalues and eigenvectors of a pair
of matrices, using routines from Lapack (dggev and zggev).
Compute the generalized Schur decomposition of a pair of
matrices using Lapack routines. In the latter case options for
ordering the generalized eigenvalues are provided.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman
DESCRIPTION | 10 ++---
MD5 | 36 +++++++++---------
NEWS | 10 +++++
R/geigen.R | 83 +++++++++++++++++++------------------------
R/gqz.R | 72 +++++++++++++++++++------------------
R/lapackerror.R |only
inst |only
man/geigen.Rd | 15 ++++++-
man/gqz.Rd | 2 -
src/xdgges.f | 96 ++++++++++++++++++++++++++++++--------------------
src/xdggev.f | 22 +++++------
src/xzgges.f | 86 +++++++++++++++++++++++++++-----------------
src/xzggev.f | 17 ++++----
tests/testgv.R | 4 +-
tests/tgqz2.R | 2 -
tests/tgqz2.Rout | 6 +--
tests/tgqz2.Rout.save | 6 +--
tests/tgqz6.R | 6 +--
tests/tgqz6.Rout | 10 ++---
tests/tgqz6.Rout.save | 10 ++---
20 files changed, 275 insertions(+), 218 deletions(-)
Title: Topic models
Diff between topicmodels versions 0.1-9 dated 2012-12-13 and 0.1-11 dated 2013-06-18
Description: Provides an interface to the C code for Latent Dirichlet
Allocation (LDA) models and Correlated Topics Models (CTM) by
David M. Blei and co-authors and the C++ code for fitting LDA
models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Grün and Kurt Hornik
Maintainer: Bettina Grün
DESCRIPTION | 14 +++++++-------
MD5 | 19 ++++++++++---------
R/control.R | 2 +-
R/ctm.R | 14 ++++++++------
R/lda.R | 17 +++++++++--------
data/AssociatedPress.rda |binary
inst/NEWS.Rd | 15 +++++++++++++++
inst/doc/topicmodels.R |only
inst/doc/topicmodels.pdf |binary
src/gsl-wrappers.c | 4 ++--
src/gsl-wrappers.h | 4 ++--
11 files changed, 54 insertions(+), 35 deletions(-)
Title: Text Mining Package
Diff between tm versions 0.5-8.3 dated 2013-01-28 and 0.5-9 dated 2013-06-18
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre], Kurt Hornik [aut]
Maintainer: Ingo Feinerer
tm-0.5-8.3/tm/R/cluster.R |only
tm-0.5-8.3/tm/man/cluster.Rd |only
tm-0.5-9/tm/DESCRIPTION | 13
tm-0.5-9/tm/MD5 | 62 +--
tm-0.5-9/tm/NAMESPACE | 2
tm-0.5-9/tm/R/filter.R | 15
tm-0.5-9/tm/R/matrix.R | 14
tm-0.5-9/tm/R/plot.R | 1
tm-0.5-9/tm/R/score.R | 6
tm-0.5-9/tm/R/transform.R | 19
tm-0.5-9/tm/R/utils.R | 2
tm-0.5-9/tm/data/acq.rda |binary
tm-0.5-9/tm/data/crude.rda |binary
tm-0.5-9/tm/inst/NEWS.Rd | 21 +
tm-0.5-9/tm/inst/doc/extensions.R |only
tm-0.5-9/tm/inst/doc/extensions.pdf |binary
tm-0.5-9/tm/inst/doc/tm.R |only
tm-0.5-9/tm/inst/doc/tm.pdf |binary
tm-0.5-9/tm/inst/stopwords/danish.dat | 211 +++-------
tm-0.5-9/tm/inst/stopwords/dutch.dat | 173 ++++----
tm-0.5-9/tm/inst/stopwords/english.dat | 610 +++++++-----------------------
tm-0.5-9/tm/inst/stopwords/finnish.dat | 263 ++----------
tm-0.5-9/tm/inst/stopwords/french.dat | 290 +++++---------
tm-0.5-9/tm/inst/stopwords/german.dat | 73 ---
tm-0.5-9/tm/inst/stopwords/hungarian.dat | 88 +---
tm-0.5-9/tm/inst/stopwords/italian.dat | 540 +++++++++++---------------
tm-0.5-9/tm/inst/stopwords/norwegian.dat | 300 ++++++--------
tm-0.5-9/tm/inst/stopwords/portuguese.dat | 406 +++++++------------
tm-0.5-9/tm/inst/stopwords/russian.dat | 316 +++++++--------
tm-0.5-9/tm/inst/stopwords/spanish.dat | 608 ++++++++++++-----------------
tm-0.5-9/tm/inst/stopwords/swedish.dat | 190 ++++-----
tm-0.5-9/tm/man/stemDocument.Rd | 6
tm-0.5-9/tm/man/stopwords.Rd | 19
tm-0.5-9/tm/man/weightSMART.Rd | 6
34 files changed, 1636 insertions(+), 2618 deletions(-)
Title: Analysis of Overdispersed Data using S3 methods
Diff between aods3 versions 0.4.0 dated 2013-06-15 and 0.4-1 dated 2013-06-18
Description: This package provides functions to analyse overdispersed
counts or proportions. These functions should be considered as
complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect
models (GLMM). aods3 is an S3 re-implementation of the
deprecated S4 package aod.
Author: Matthieu Lesnoff
Maintainer: Renaud Lancelot
DESCRIPTION | 10 ++---
MD5 | 17 +++++----
NEWS |only
R/aodml.R | 51 ++++++++++++++--------------
R/print.anova.aodml.R | 14 +++----
R/print.summary.aodml.R | 16 +++++++--
R/summary.aodml.R | 3 +
man/aodml.Rd | 85 +++++++++++++++++++++++++++++++++++-------------
man/iccbin.Rd | 6 ++-
man/varbin.Rd | 11 +++++-
10 files changed, 138 insertions(+), 75 deletions(-)
Title: Spatial analysis of animal track data
Diff between trip versions 1.1-14 dated 2013-05-16 and 1.1-15 dated 2013-06-18
Description: Functions for accessing and manipulating spatial data for
animal tracking. Filter for speed and create time spent plots
from animal track data.
Author: Michael Sumner[aut, cre], Sebastian Luque [ctb]
Maintainer: Michael D. Sumner
trip-1.1-14/trip/ChangeLog |only
trip-1.1-14/trip/TODO |only
trip-1.1-15/trip/DESCRIPTION | 6
trip-1.1-15/trip/MD5 | 27 -
trip-1.1-15/trip/NAMESPACE | 2
trip-1.1-15/trip/NEWS | 21
trip-1.1-15/trip/R/AllClass.R | 132 +++---
trip-1.1-15/trip/R/AllGenerics.R | 62 +-
trip-1.1-15/trip/R/AllMethod.R | 683 ++++++++++++++++----------------
trip-1.1-15/trip/R/trackDistance.R | 77 +++
trip-1.1-15/trip/R/trip.R | 60 ++
trip-1.1-15/trip/man/trackAngle.Rd |only
trip-1.1-15/trip/man/trackDistance.Rd | 9
trip-1.1-15/trip/man/trip-class.Rd | 14
trip-1.1-15/trip/man/trip-deprecated.Rd | 102 ++--
trip-1.1-15/trip/man/trip-internal.Rd | 9
16 files changed, 680 insertions(+), 524 deletions(-)
Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Diff between rsgcc versions 1.0.5 dated 2013-06-12 and 1.0.6 dated 2013-06-18
Description: This package provides functions for calculating
associations between two genes with five correlation
methods(e.g., the Gini correlation coefficient [GCC], the
Pearson's product moment correlation coefficient [PCC], the
Kendall tau rank correlation coefficient [KCC], the Spearman's
rank correlation coefficient [SCC] and the Tukey's biweight
correlation coefficient [BiWt], and three non-correlation
methods (e.g., mutual information [MI] and the maximal
information-based nonparametric exploration [MINE], and the
euclidean distance [ED]). It can also been implemented to
perform the correlation and clustering analysis of
transcriptomic data profiled by microarray and RNA-Seq
technologies. Additionally, this package can be further applied
to construct gene co-expression networks (GCNs).
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma
DESCRIPTION | 14 +++++++-------
MD5 | 10 +++++-----
data/rsgcc.rda |binary
man/getsgene.Rd | 11 ++++++-----
man/rsgcc-package.Rd | 6 +++---
src/bridge.c | 12 ++++++++----
6 files changed, 29 insertions(+), 24 deletions(-)
Title: A package for graphical modelling in R
Diff between gRbase versions 1.6-8 dated 2013-03-11 and 1.6-9 dated 2013-06-18
Description: The gRbase package provides certain general constructs
which are used by other graphical modelling packages, in
particular by the packages gRain, gRim and gRc.
gRbase contains several datasets relevant for use in connection with
graphical models. Almost all datasets used in the book
Graphical Models with R (2012) are contained in gRbase.
gRbase implements several graph algorithms (based mainly on
representing graphs as adjacency matrices - either in the form
of a standard matrix or a sparse matrix). Some graph algorithms
are: (i) maximum cardinality search (for marked and unmarked
graphs). (ii) moralize. (iii) triangulate. (iv)
junctionTree.
gRbase facilities for array operations,
gRbase implements functions for testing for conditional independence.
gRbase illustrates how hierarchical log-linear models (hllm) may be
implemented and describes concept of gmData (graphical meta
data). These features, however, are not maintained anymore and
remains in gRbase only because there exists a paper describing
these facilities: A Common Platform for Graphical Models in R:
The gRbase Package, Journal of Statistical Software, Vol 14, No
17, 2005.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 16
DESCRIPTION | 9
MD5 | 51
NAMESPACE | 2
R/GraphAlgo-mcs.R | 2
R/GraphAlgo-rip.R | 119 +-
R/table-operations.R | 20
R/yyyPrim.R | 4
data/Nutrimouse.RData |binary
data/ashtrees.RData |binary
data/breastcancer.RData |binary
data/chestSim1000.RData |binary
data/chestSim10000.RData |binary
data/chestSim100000.RData |binary
data/chestSim500.RData |binary
data/chestSim50000.RData |binary
data/dumping.RData |binary
data/lizard.RData |binary
data/mildew.RData |binary
data/reinis.RData |binary
gRbase-Ex.R | 2464 +++++++++++++++++++++---------------------
inst/doc/gRbase-arrayops1.R |only
inst/doc/gRbase-arrayops1.pdf |binary
inst/doc/gRbase-arrayops2.R |only
inst/doc/gRbase-arrayops2.pdf |binary
inst/doc/gRbase-graphs.R |only
inst/doc/gRbase-graphs.pdf |binary
man/GraphAlgo-triangulate.Rd | 10
28 files changed, 1359 insertions(+), 1338 deletions(-)
Title: Format R Code Automatically
Diff between formatR versions 0.7 dated 2012-12-02 and 0.8 dated 2013-06-18
Description: This package provides a function tidy.source() and
optionally a GUI (by gWidgets and preferably gWidgetsRGtk2) to
format R source code. Spaces and indent will be added to the
code automatically, and comments will be preserved under
certain conditions, so that R code will be more human-readable
and tidy.
Author: Yihui Xie
Maintainer: Yihui Xie
formatR-0.7/formatR/inst/doc/Makefile |only
formatR-0.7/formatR/inst/doc/formatR.Rnw |only
formatR-0.7/formatR/inst/doc/formatR.bib |only
formatR-0.7/formatR/inst/doc/formatR.lyx |only
formatR-0.7/formatR/inst/doc/formatR.pdf |only
formatR-0.7/formatR/man/InLiNe_IdEnTiFiEr.Rd |only
formatR-0.7/formatR/man/parse.tidy.Rd |only
formatR-0.7/formatR/man/unmask.source.Rd |only
formatR-0.8/formatR/DESCRIPTION | 12 +-
formatR-0.8/formatR/MD5 | 30 ++---
formatR-0.8/formatR/NAMESPACE | 4
formatR-0.8/formatR/NEWS | 14 ++
formatR-0.8/formatR/R/tidy.R | 134 ++-----------------------
formatR-0.8/formatR/inst/doc/formatR-intro.R |only
formatR-0.8/formatR/inst/doc/formatR-intro.Rnw |only
formatR-0.8/formatR/inst/doc/formatR-intro.bib |only
formatR-0.8/formatR/inst/doc/formatR-intro.pdf |only
formatR-0.8/formatR/inst/doc/formatR.R |only
formatR-0.8/formatR/inst/doc/formatR.Rmd |only
formatR-0.8/formatR/inst/doc/formatR.html |only
formatR-0.8/formatR/inst/format |only
formatR-0.8/formatR/man/tidy.eval.Rd | 3
formatR-0.8/formatR/man/tidy.gui.Rd | 9 -
formatR-0.8/formatR/man/tidy.source.Rd | 28 ++---
24 files changed, 65 insertions(+), 169 deletions(-)
Title: Various Methods for Measuring Agreement.
Diff between agRee versions 0.2-0 dated 2013-05-08 and 0.2-1 dated 2013-06-18
Description: Plots for visualization and point and interval estimates
for different metrics of agreement.
Author: Dai Feng
Maintainer: Dai Feng
ChangeLog | 7 +++++++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/agree.plot.Rd | 4 ++--
4 files changed, 16 insertions(+), 9 deletions(-)
Title: ZeBook Working with dynamic models for agriculture and
environment
Diff between ZeBook versions 0.4 dated 2013-04-09 and 0.5 dated 2013-06-17
Description: R package accompanying the book Working with dynamic
models for agriculture and environment, by Daniel Wallach
(INRA), David Makowski (INRA), James W. Jones (U.of Florida),
Francois Brun (ACTA), in preparation for June 2013.
Author: Francois Brun (ACTA), David Makowski (INRA), Daniel Wallach
(INRA), James W. Jones (U.of Florida).
Maintainer: Francois Brun
ZeBook-0.4/ZeBook/R/grain.filling_data.r |only
ZeBook-0.4/ZeBook/data/grain.filling.rda |only
ZeBook-0.4/ZeBook/man/epirice.multi.simul.Rd |only
ZeBook-0.4/ZeBook/man/grain.filling.Rd |only
ZeBook-0.5/ZeBook/DESCRIPTION | 21 +
ZeBook-0.5/ZeBook/MD5 | 198 ++++++++++------
ZeBook-0.5/ZeBook/NAMESPACE | 26 ++
ZeBook-0.5/ZeBook/R/AIC.r | 4
ZeBook-0.5/ZeBook/R/Sunflower_Phomopsis_data.r | 2
ZeBook-0.5/ZeBook/R/WheatYieldGreece_data.r | 2
ZeBook-0.5/ZeBook/R/Wheat_GPC_data.r | 2
ZeBook-0.5/ZeBook/R/ZeBook.r | 21 +
ZeBook-0.5/ZeBook/R/carbon.model.r |only
ZeBook-0.5/ZeBook/R/carcass.EMI.model.r |only
ZeBook-0.5/ZeBook/R/carcass.model.r |only
ZeBook-0.5/ZeBook/R/carcass_data.r |only
ZeBook-0.5/ZeBook/R/chicks_data.r |only
ZeBook-0.5/ZeBook/R/cotton.model.r |only
ZeBook-0.5/ZeBook/R/epirice.model.r | 31 --
ZeBook-0.5/ZeBook/R/evaluation.criteria.r | 4
ZeBook-0.5/ZeBook/R/exponential.model.r |only
ZeBook-0.5/ZeBook/R/goodness.of.fit.r | 4
ZeBook-0.5/ZeBook/R/lactation.calf.model.r |only
ZeBook-0.5/ZeBook/R/lactation.machine.model.r |only
ZeBook-0.5/ZeBook/R/magarey.model.r | 43 ++-
ZeBook-0.5/ZeBook/R/maize.data_EuropeEU.r | 2
ZeBook-0.5/ZeBook/R/maize.model.r | 37 +-
ZeBook-0.5/ZeBook/R/population.age.model.r |only
ZeBook-0.5/ZeBook/R/prey.predator.model.r |only
ZeBook-0.5/ZeBook/R/sample.r | 8
ZeBook-0.5/ZeBook/R/seedweight.data_data.r |only
ZeBook-0.5/ZeBook/R/seedweight.model.r |only
ZeBook-0.5/ZeBook/R/verhulst.model.r | 10
ZeBook-0.5/ZeBook/R/watbal.model.r | 84 ++++++
ZeBook-0.5/ZeBook/R/watbal.simobsdata.r | 4
ZeBook-0.5/ZeBook/R/weather_EuropeEU_data.r | 12
ZeBook-0.5/ZeBook/R/weather_FranceWest_data.r | 4
ZeBook-0.5/ZeBook/R/weather_SouthAsia_data.r | 4
ZeBook-0.5/ZeBook/R/weed.model.r | 33 +-
ZeBook-0.5/ZeBook/data/carcass_data.rda |only
ZeBook-0.5/ZeBook/data/chicks_data.rda |only
ZeBook-0.5/ZeBook/data/datalist | 4
ZeBook-0.5/ZeBook/data/seedweight.data.rda |only
ZeBook-0.5/ZeBook/demo/00Index | 49 ++-
ZeBook-0.5/ZeBook/demo/ch04Simulation.epirice.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.exponential.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.maize.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.population.age.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.prey.predator.r |only
ZeBook-0.5/ZeBook/demo/ch04Simulation.watbal.r |only
ZeBook-0.5/ZeBook/demo/ch05USA_Carcass.r |only
ZeBook-0.5/ZeBook/demo/ch05USA_Lactation.r |only
ZeBook-0.5/ZeBook/demo/ch08DLM_CarbonSoil.r | 7
ZeBook-0.5/ZeBook/demo/ch08DLM_WheatYieldGreece.r | 6
ZeBook-0.5/ZeBook/demo/ch08DLM_watbal.r |only
ZeBook-0.5/ZeBook/demo/ch10maize1data.r | 4
ZeBook-0.5/ZeBook/demo/ch10maize2evaluation.r | 3
ZeBook-0.5/ZeBook/demo/ch10maize5cparameterConcL.r | 52 +++-
ZeBook-0.5/ZeBook/demo/ch10maize5dparameterConcL_log.r |only
ZeBook-0.5/ZeBook/demo/ch10maizeB5aBayesEstimRUE.r | 2
ZeBook-0.5/ZeBook/demo/ch10maizeB5bBayesEstimAllparam.r | 2
ZeBook-0.5/ZeBook/demo/ch10maizeB7Bayes_functionsMH.r | 5
ZeBook-0.5/ZeBook/man/AICf.Rd | 2
ZeBook-0.5/ZeBook/man/ZeBook-package.Rd | 38 +--
ZeBook-0.5/ZeBook/man/carbonsoil.model.Rd |only
ZeBook-0.5/ZeBook/man/carbonsoil.update.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.model.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.model2.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.multi.Rd |only
ZeBook-0.5/ZeBook/man/carcass.EMI.simule.Rd |only
ZeBook-0.5/ZeBook/man/carcass.define.param.Rd |only
ZeBook-0.5/ZeBook/man/carcass.model.Rd |only
ZeBook-0.5/ZeBook/man/carcass_data.Rd |only
ZeBook-0.5/ZeBook/man/chicks_data.Rd |only
ZeBook-0.5/ZeBook/man/cotton.model.Rd |only
ZeBook-0.5/ZeBook/man/epirice.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/epirice.model.Rd | 4
ZeBook-0.5/ZeBook/man/epirice.multi.simule.Rd |only
ZeBook-0.5/ZeBook/man/epirice.weather.Rd | 5
ZeBook-0.5/ZeBook/man/evaluation.criteria.Rd | 2
ZeBook-0.5/ZeBook/man/exponential.model.Rd |only
ZeBook-0.5/ZeBook/man/exponential.model.bis.Rd |only
ZeBook-0.5/ZeBook/man/exponential.model.ie.Rd |only
ZeBook-0.5/ZeBook/man/goodness.of.fit.Rd | 5
ZeBook-0.5/ZeBook/man/lactation.calf.model.Rd |only
ZeBook-0.5/ZeBook/man/lactation.calf.model2.Rd |only
ZeBook-0.5/ZeBook/man/lactation.calf.simule.Rd |only
ZeBook-0.5/ZeBook/man/lactation.define.param.Rd |only
ZeBook-0.5/ZeBook/man/lactation.model.machine.Rd |only
ZeBook-0.5/ZeBook/man/lactation.model.machine2.Rd |only
ZeBook-0.5/ZeBook/man/magarey.define.param.Rd | 15 -
ZeBook-0.5/ZeBook/man/magarey.model2.Rd | 2
ZeBook-0.5/ZeBook/man/magarey.simule.Rd | 2
ZeBook-0.5/ZeBook/man/maize.RUEtemp.Rd | 4
ZeBook-0.5/ZeBook/man/maize.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/maize.model.Rd | 11
ZeBook-0.5/ZeBook/man/maize.model2.Rd | 5
ZeBook-0.5/ZeBook/man/maize.multisy240.Rd | 6
ZeBook-0.5/ZeBook/man/maize.simule.Rd | 6
ZeBook-0.5/ZeBook/man/maize.simule240.Rd | 10
ZeBook-0.5/ZeBook/man/maize.simule_multisy240.Rd | 11
ZeBook-0.5/ZeBook/man/maize.weather.Rd | 5
ZeBook-0.5/ZeBook/man/maize_cir.model.Rd | 5
ZeBook-0.5/ZeBook/man/maize_cir_rue.model.Rd | 4
ZeBook-0.5/ZeBook/man/maize_cir_rue_ear.model.Rd | 5
ZeBook-0.5/ZeBook/man/param.rtriangle.Rd | 2
ZeBook-0.5/ZeBook/man/param.runif.Rd | 2
ZeBook-0.5/ZeBook/man/population.age.matrix.model.Rd |only
ZeBook-0.5/ZeBook/man/population.age.model.Rd |only
ZeBook-0.5/ZeBook/man/population.age.model.ode.Rd |only
ZeBook-0.5/ZeBook/man/predator.prey.model.Rd |only
ZeBook-0.5/ZeBook/man/q.arg.fast.runif.Rd | 2
ZeBook-0.5/ZeBook/man/seedweight.data.Rd |only
ZeBook-0.5/ZeBook/man/seedweight.model.Rd |only
ZeBook-0.5/ZeBook/man/verhulst.model.Rd | 9
ZeBook-0.5/ZeBook/man/verhulst.update.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.define.param.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.model.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.model.arid.Rd |only
ZeBook-0.5/ZeBook/man/watbal.simobsdata.Rd | 2
ZeBook-0.5/ZeBook/man/watbal.update.Rd | 5
ZeBook-0.5/ZeBook/man/watbal.weather.Rd | 6
ZeBook-0.5/ZeBook/man/weather_EuropeEU.Rd | 12
ZeBook-0.5/ZeBook/man/weather_FranceWest.Rd | 2
ZeBook-0.5/ZeBook/man/weather_SouthAsia.Rd | 2
ZeBook-0.5/ZeBook/man/weed.define.param.Rd | 4
ZeBook-0.5/ZeBook/man/weed.model.Rd | 2
ZeBook-0.5/ZeBook/man/weed.simule.Rd | 6
ZeBook-0.5/ZeBook/man/weed.update.Rd | 2
129 files changed, 595 insertions(+), 323 deletions(-)
Title: Robust Library
Diff between robust versions 0.4-11 dated 2013-02-24 and 0.4-15 dated 2013-06-17
Description: A package of robust methods.
Author: Jiahui Wang, Ruben Zamar
Maintainer: Kjell Konis
robust-0.4-11/robust/R/covMLE.q |only
robust-0.4-11/robust/R/plot.covMLE.q |only
robust-0.4-11/robust/R/summary.covMLE.q |only
robust-0.4-11/robust/man/covMLE.Rd |only
robust-0.4-15/robust/DESCRIPTION | 18 -
robust-0.4-15/robust/MD5 | 63 ++---
robust-0.4-15/robust/NAMESPACE | 39 +--
robust-0.4-15/robust/R/covClassic.q |only
robust-0.4-15/robust/R/covRob.control.q | 85 ++-----
robust-0.4-15/robust/R/gen.data.q | 2
robust-0.4-15/robust/R/glm.methods.q | 4
robust-0.4-15/robust/R/globalVariables.q |only
robust-0.4-15/robust/R/library.q | 2
robust-0.4-15/robust/R/plot.covClassic.q |only
robust-0.4-15/robust/R/print.covMLE.q | 2
robust-0.4-15/robust/R/print.summary.covMLE.q | 5
robust-0.4-15/robust/R/robLev.q | 35 +-
robust-0.4-15/robust/R/summary.covClassic.q |only
robust-0.4-15/robust/README | 2
robust-0.4-15/robust/inst/tests_S/plots.covrob.t | 4
robust-0.4-15/robust/man/covClassic.Rd |only
robust-0.4-15/robust/man/covRob.Rd | 2
robust-0.4-15/robust/man/ddPlot.covfm.Rd | 2
robust-0.4-15/robust/man/distancePlot.covfm.Rd | 2
robust-0.4-15/robust/man/ellipsesPlot.covfm.Rd | 2
robust-0.4-15/robust/man/lmRob.control.Rd | 48 ++--
robust-0.4-15/robust/man/plot.covfm.Rd | 18 -
robust-0.4-15/robust/man/predict.glmRob.Rd | 6
robust-0.4-15/robust/man/screePlot.covfm.Rd | 2
robust-0.4-15/robust/man/summary.covfm.Rd | 16 -
robust-0.4-15/robust/src/glmrob.f | 188 ++++++++--------
robust-0.4-15/robust/src/lmrobfs.f | 4
robust-0.4-15/robust/src/lmrobml.f | 2
robust-0.4-15/robust/src/lmrobmm.f | 6
robust-0.4-15/robust/src/tdmean.f | 179 +++++++--------
robust-0.4-15/robust/src/tmlfor.f | 108 ++++-----
robust-0.4-15/robust/tests/Examples/robust-Ex.Rout.save | 59 ++---
37 files changed, 446 insertions(+), 459 deletions(-)
Title: Moment and Inverse Moment Bayes factors
Diff between mombf versions 1.4.1 dated 2013-04-05 and 1.5.2 dated 2013-06-17
Description: This package performs model selection based on non-local
priors, including MOM, eMOM and iMOM priors. Routines are
provided to compute Bayes factors, marginal densities and to
perform variable selection in regression setups. Routines to
evaluate prior densities, distribution functions, quantiles and
modes are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell
DESCRIPTION | 18 ++--
INDEX |only
MD5 | 54 ++++++++------
NAMESPACE | 11 ++
R/AllClasses.R | 3
R/AllGenerics.R | 9 ++
R/margpemom.R |only
R/margpimom.R | 8 +-
R/margpmom.R | 2
R/modelSelection.R | 33 ++++++++
R/msPriorSpec.R | 31 ++++++++
R/pplProbit.R | 15 ----
R/rmom.R | 41 +++++++++--
changeLog | 6 +
data/hald.rda |binary
inst/doc/mombf.R |only
inst/doc/mombf.Rnw | 8 +-
inst/doc/mombf.pdf |binary
man/dmom.Rd | 3
man/modelSelection.Rd | 22 +++--
man/msPriorSpec-class.Rd | 45 +++++++++++-
man/msfit-class.Rd |only
man/pmomLM.Rd | 30 ++++----
man/postProb.Rd |only
man/rnlp.Rd |only
src/cstat.cpp | 174 +++++++++++++++++++++++++++++++++++++++++------
src/cstat.h | 36 +++++++--
src/do_mombf.h | 2
src/modelSel.cpp | 115 ++++++++++++++++---------------
src/modelSel.h | 1
vignettes/mombf.Rnw | 8 +-
31 files changed, 501 insertions(+), 174 deletions(-)
Title: Regional frequency analysis using L-moments
Diff between lmomRFA versions 2.4 dated 2012-01-24 and 2.5 dated 2013-06-17
Description: Functions for regional frequency analysis using the
methods of J. R. M. Hosking and J. R. Wallis (1997), "Regional
frequency analysis: an approach based on L-moments".
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
lmomRFA-2.4/lmomRFA/LICENSE |only
lmomRFA-2.5/lmomRFA/DESCRIPTION | 13 +--
lmomRFA-2.5/lmomRFA/MD5 | 51 ++++++-------
lmomRFA-2.5/lmomRFA/NAMESPACE | 1
lmomRFA-2.5/lmomRFA/NEWS | 25 ++++++
lmomRFA-2.5/lmomRFA/R/lmomRFA.r | 111 +++++++++++++++++++++++++++--
lmomRFA-2.5/lmomRFA/data/Appalach.rda |binary
lmomRFA-2.5/lmomRFA/data/Cascades.rda |binary
lmomRFA-2.5/lmomRFA/data/Maxwind.rda |binary
lmomRFA-2.5/lmomRFA/man/cluagg.Rd | 2
lmomRFA-2.5/lmomRFA/man/cluinf.Rd | 2
lmomRFA-2.5/lmomRFA/man/clukm.Rd | 2
lmomRFA-2.5/lmomRFA/man/evplot.rfd.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/lmomRFA-package.Rd | 2
lmomRFA-2.5/lmomRFA/man/regavlmom.Rd | 2
lmomRFA-2.5/lmomRFA/man/regdata.Rd | 2
lmomRFA-2.5/lmomRFA/man/regfit.Rd | 2
lmomRFA-2.5/lmomRFA/man/reglmr.Rd | 2
lmomRFA-2.5/lmomRFA/man/regquant.Rd | 2
lmomRFA-2.5/lmomRFA/man/regquantbounds.Rd | 8 --
lmomRFA-2.5/lmomRFA/man/regsamlmu.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/regsimh.Rd | 6 -
lmomRFA-2.5/lmomRFA/man/regsimq.Rd | 4 -
lmomRFA-2.5/lmomRFA/man/regtst.Rd | 15 ++-
lmomRFA-2.5/lmomRFA/man/sitequant.Rd | 2
lmomRFA-2.5/lmomRFA/man/summary.regtst.Rd | 5 -
lmomRFA-2.5/lmomRFA/src/lmomRFA.f | 98 ++++++++-----------------
27 files changed, 232 insertions(+), 133 deletions(-)
Title: L-moments
Diff between lmom versions 1.6 dated 2012-01-24 and 2.0 dated 2013-06-17
Description: Functions related to L-moments: computation of L-moments
and trimmed L-moments of distributions and data samples;
parameter estimation; L-moment ratio diagram; plot vs.
quantiles of an extreme-value distribution.
Author: J. R. M. Hosking
Maintainer: J. R. M. Hosking
lmom-1.6/lmom/LICENSE |only
lmom-1.6/lmom/src/lmom.f |only
lmom-2.0/lmom/DESCRIPTION | 17
lmom-2.0/lmom/MD5 | 40 -
lmom-2.0/lmom/NAMESPACE | 2
lmom-2.0/lmom/NEWS | 24
lmom-2.0/lmom/R/lmom.r | 1225 ++++++++++++++++++++++++-------------
lmom-2.0/lmom/man/cdfln3.Rd | 6
lmom-2.0/lmom/man/evplot.Rd | 2
lmom-2.0/lmom/man/lmom-package.Rd | 73 +-
lmom-2.0/lmom/man/lmr-functions.Rd | 58 -
lmom-2.0/lmom/man/lmrd.Rd | 50 -
lmom-2.0/lmom/man/lmrdpoints.Rd | 2
lmom-2.0/lmom/man/lmrp.Rd | 154 ++--
lmom-2.0/lmom/man/pel-functions.Rd | 58 -
lmom-2.0/lmom/man/pelp.Rd | 128 ++-
lmom-2.0/lmom/man/samlmu.Rd | 80 +-
lmom-2.0/lmom/src/d1mach.f |only
lmom-2.0/lmom/src/dqagie.f |only
lmom-2.0/lmom/src/dqagse.f |only
lmom-2.0/lmom/src/dqelg.f |only
lmom-2.0/lmom/src/dqk15i.f |only
lmom-2.0/lmom/src/dqk21.f |only
lmom-2.0/lmom/src/dqpsrt.f |only
lmom-2.0/lmom/src/lmomc.c |only
lmom-2.0/lmom/src/lmoments.f |only
lmom-2.0/lmom/src/samlm.f |only
27 files changed, 1234 insertions(+), 685 deletions(-)
Title: Tests for random and fixed effects for linear mixed effect
models (lmer objects of lme4 package).
Diff between lmerTest versions 1.2-0 dated 2013-03-20 and 1.2-1 dated 2013-06-17
Description: The package provides different kinds of tests on lmer
objects(of lme4 package). Tests comprise type 3 F tests for
fixed effects, LRT tests for random effects, calculation of
population means for fixed factors with confidence intervals
and corresponding plots. Package also provides backward
elimination of non-significant effects
Author: Alexandra Kuznetsova, Per Bruun Brockhoff, Rune Haubo Bojesen
Christensen
Maintainer: Alexandra Kuznetsova
DESCRIPTION | 8 +-
MD5 | 12 +--
R/utils.R | 10 +-
man/lmer.Rd | 3
man/merLmerTest-class.Rd | 1
man/step.Rd | 3
tests/Examples/lmerTest-Ex.Rout.save | 125 +++++++++++++++++++++++------------
7 files changed, 106 insertions(+), 56 deletions(-)
Title: Two functions for Generalized SARIMA time series simulation
Diff between gsarima versions 0.1-3 dated 2013-01-17 and 0.1-4 dated 2013-06-17
Description: Write SARIMA models in (finite) AR representation and
simulate generalized multiplicative seasonal autoregressive
moving average (time) series with Normal / Gaussian, Poisson or
negative binomial distribution.
Author: Olivier Briet
Maintainer: Olivier Briet
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
man/arrep.Rd | 8 +++++---
man/garsim.Rd | 29 ++++++++++++++++++++---------
man/gsarima-package.Rd | 8 ++++++--
5 files changed, 40 insertions(+), 22 deletions(-)
Title: Baseline identification and peak decomposition for x-ray
diffractograms
Diff between diffractometry versions 0.1-03 dated 2011-03-11 and 0.1-7 dated 2013-06-17
More information about diffractometry at CRAN
Description: Residual-based baseline identification and peak
decomposition for x-ray diffractograms as introduced in
Davies/Gather/Mergel/Meise/Mildenberger (2008).
Author: P.L. Davies, U. Gather, M. Meise, D.Mergel, T. Mildenberger.
Additional Code by T. Bernholt and T. Hofmeister
Maintainer: T. Mildenberger
DESCRIPTION | 9
MD5 |only
R/baselinefit.r | 12 -
R/fitint.r | 601 +++++++++++++++++++++++++--------------------------
man/diffractogram.Rd | 4
man/pkdecomp.Rd | 4
man/pkdecompint.Rd | 2
src/Cbaselinefit.c | 25 +-
src/Fbaselinefit.f | 37 ++-
9 files changed, 358 insertions(+), 336 deletions(-)
Permanent link
Title: Bolstad functions
Diff between Bolstad versions 0.2-24 dated 2013-04-30 and 0.2-25 dated 2013-06-17
Description: A set of R functions and data sets for the book
Introduction to Bayesian Statistics, Bolstad, W.M. (2007), John
Wiley & Sons ISBN 0-471-27020-2
Author: James Curran
Maintainer: James Curran
DESCRIPTION | 8 +++---
MD5 | 40 +++++++++++++++++----------------
NAMESPACE | 1
R/binobp.r | 8 ++++--
R/binodp.r | 50 +++++++++++++++++++++++++----------------
R/binogcp.r | 8 ++++--
R/binomixp.r | 6 ++++-
R/normdp.r | 7 ++++-
R/normgcp.r | 8 +++++-
R/normnp.r | 9 +++++--
R/nvaricp.r | 8 +++++-
R/plot.Bolstad.r |only
R/poisdp.r | 6 ++++-
R/poisgamp.r | 62 ++++++++++++++++++++++++++++++----------------------
R/poisgcp.r | 26 +++++++++++++--------
R/xdesign.r | 37 ++++++++++++-------------------
man/binobp.Rd | 10 ++++----
man/binodp.Rd | 3 +-
man/plot.Bolstad.Rd |only
man/poisgamp.Rd | 7 +++--
man/poisgcp.Rd | 3 +-
man/xdesign.Rd | 13 +++++++---
22 files changed, 188 insertions(+), 132 deletions(-)
Title: Interactive manipulation of R expressions
Diff between twiddler versions 0.4-0 dated 2012-09-13 and 0.5-0 dated 2013-06-17
Description: Twiddler is an interactive tool that automatically creates
a Tcl/Tk GUI for manipulating variables in any R expression.
See the documentation of the function twiddle to get started.
Author: Oliver Flasch, Olaf Mersmann
Maintainer: Oliver Flasch
twiddler-0.4-0/twiddler/man/print-dot-twiddlerControl.Rd |only
twiddler-0.4-0/twiddler/man/twiddle-sub-print.Rd |only
twiddler-0.5-0/twiddler/DESCRIPTION | 17 +-
twiddler-0.5-0/twiddler/MD5 | 26 +--
twiddler-0.5-0/twiddler/NAMESPACE | 10 -
twiddler-0.5-0/twiddler/R/twiddler.R | 7
twiddler-0.5-0/twiddler/man/combo.Rd | 32 ++-
twiddler-0.5-0/twiddler/man/entry.Rd | 47 +++--
twiddler-0.5-0/twiddler/man/filer.Rd | 34 ++--
twiddler-0.5-0/twiddler/man/knob.Rd | 58 ++++--
twiddler-0.5-0/twiddler/man/print.twiddlerControl.Rd |only
twiddler-0.5-0/twiddler/man/shortenString.Rd | 23 +-
twiddler-0.5-0/twiddler/man/toggle.Rd | 29 ++-
twiddler-0.5-0/twiddler/man/twiddle_print.Rd |only
twiddler-0.5-0/twiddler/man/twiddler.Rd | 125 +++++++++------
twiddler-0.5-0/twiddler/man/unboundVariables.Rd | 23 +-
16 files changed, 275 insertions(+), 156 deletions(-)
Title: R functions for robust statistics
Diff between robeth versions 2.2 dated 2011-08-20 and 2.6 dated 2013-06-17
Description: Locations problems, M-estimates of coefficients and scale
in linear regression, Weights for bounded influence regression,
Covariance matrix of the coefficient estimates, Asymptotic
relative efficiency of regression M-estimates, Robust testing
in linear models, High breakdown point regression, M-estimates
of covariance matrices, M-estimates for discrete generalized
linear models.
Author: Alfio Marazzi
Maintainer: A. Randriamiharisoa
DESCRIPTION | 9 -
MD5 | 212 ++++++++++++++++++-------------------
NAMESPACE | 12 +-
R/Fn.Exp.f.R | 4
R/QD2coef.f.R | 6 -
R/QD2funC.f.R | 6 -
R/Qn.Exp.f.R | 6 -
R/Random.R | 8 -
R/Regtau.f.R | 4
R/RegtauW.f.R | 4
R/airefq.R | 10 -
R/cerfd.R | 4
R/cfrcov.R | 2
R/cimedv.R | 2
R/cyfalg.R | 10 -
R/cygalg.R | 20 +--
R/cynalg.R | 14 +-
R/dfcomn.R | 18 +--
R/dfrpar.R | 20 +--
R/dfvals.R | 90 +++++++--------
R/dotpd.R | 6 -
R/exchd.R | 2
R/gaussd.R | 4
R/gintac.R | 4
R/gyastp.R | 11 +
R/gymain.R | 11 +
R/h12d.R | 6 -
R/machd.R | 2
R/mchld.R | 2
R/mffd.R | 6 -
R/mfyd.R | 6 -
R/minvd.R | 2
R/mlyd.R | 4
R/msf1d.R | 6 -
R/msfd.R | 6 -
R/mssd.R | 6 -
R/mtt1d.R | 4
R/mtt2d.R | 4
R/mtt3d.R | 6 -
R/mtyd.R | 4
R/nrm2d.R | 4
R/precd.R | 2
R/probin.R |only
R/rimtrd.R | 8 -
R/rybifr.R | 2
R/scald.R | 2
R/swapd.R | 4
R/to.double.R | 1
R/ucv_1.R | 2
R/upcv_1.R | 2
R/wcv_1.R | 2
R/wimedv.R | 2
R/wpcv_1.R | 2
R/www_1.R | 2
R/wyfalg.R | 12 +-
R/wyfcol.R | 20 +--
R/wygalg.R | 18 +--
R/wynalg.R | 14 +-
R/xsyd.R | 8 -
R/zemll.R |only
man/QD2coef.f.Rd | 3
man/Regtau.f.Rd | 3
man/RegtauW.f.Rd | 3
man/airef0.Rd | 4
man/airefq.Rd | 5
man/cifact.Rd | 7 -
man/cyfalg.Rd | 4
man/cygalg.Rd | 5
man/cynalg.Rd | 5
man/dfcomn.Rd | 19 ++-
man/gintac.Rd | 4
man/gyastp.Rd | 5
man/gycstp.Rd | 3
man/gymain.Rd | 9 +
man/gytstp.Rd | 5
man/hylmse.Rd | 4
man/hyltse.Rd | 4
man/hysest.Rd | 6 -
man/hysestw.Rd | 6 -
man/kiedcu.Rd | 3
man/ktaskw.Rd | 3
man/lyhalg.Rd | 4
man/lyhdle.Rd | 3
man/lymnwt.Rd | 3
man/lytau2.Rd | 4
man/lywalg.Rd | 13 +-
man/messagena.Rd |only
man/mfragr.Rd | 4
man/mirtsr.Rd | 5
man/mymvlm.Rd | 5
man/ribet0.Rd | 3
man/ribetu.Rd | 3
man/riclls.Rd | 3
man/robeth.package.Rd | 38 +++---
man/rybifr.Rd | 4
man/ryhalg.Rd | 7 +
man/rynalg.Rd | 6 -
man/rysalg.Rd | 6 -
man/rysigm.Rd | 4
man/rywalg.Rd | 6 -
man/tauare.Rd | 4
man/wimedv.Rd | 3
man/wyfalg.Rd | 5
man/wyfcol.Rd | 5
man/wygalg.Rd | 5
man/wynalg.Rd | 5
man/zemll.Rd |only
src/fastcens.f | 78 +++++++++++++
src/robeth.f | 285 ++++++++++++++++++++++++++++++++++++--------------
109 files changed, 809 insertions(+), 482 deletions(-)
Title: Sample size calculations for longitudinal data
Diff between longpower versions 1.0-8 dated 2013-05-28 and 1.0-9 dated 2013-06-17
Description: The longpower package contains functions for computing
power and sample size for linear models of longitudinal data
based on the formula due to Liu and Liang (1997) and Diggle et
al (2002). Either formula is expressed in terms of marginal
model or Generalized Estimating Equations (GEE) parameters.
This package contains functions which translate pilot mixed
effect model parameters (e.g. random intercept and/or slope)
into marginal model parameters so that the formulas of Diggle
et al or Liu and Liang formula can be applied to produce sample
size calculations for two sample longitudinal designs assuming
known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/lmmpower.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Multivariate Permutation Tests
Diff between flip versions 2.1 dated 2013-05-07 and 2.2 dated 2013-06-17
Description: It implements many univariate and multivariate permutation
(and rotation) tests. Allowed tests: the t one and two samples,
ANOVA, linear models, Chi Squared test, rank tests (i.e.
Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar.
Test on Linear Models are performed also in presence of
covariates (i.e. nuisance parameters). The permutation and the
rotation methods to get the null distribution of the test
statistics are available. It also implements methods for
multiplicity control such as Westfall-Young minP procedure and
Closed Testing (Marcus, 1976). Moreover, it allows to test for
fixed effects in mixed effects models.
Author: Livio Finos, with contributions by Dario Basso, Aldo Solari and
Jelle Goeman
Maintainer: Livio Finos
flip-2.1/flip/R/rotation.R |only
flip-2.2/flip/DESCRIPTION | 18 +++---
flip-2.2/flip/MD5 | 34 ++++++-----
flip-2.2/flip/NAMESPACE | 6 +-
flip-2.2/flip/R/Padjust.R | 13 +++-
flip-2.2/flip/R/between.R |only
flip-2.2/flip/R/dependence.R | 52 +++++++----------
flip-2.2/flip/R/estimateSu.R |only
flip-2.2/flip/R/flip-object.R | 97 ++++++++++++++++-----------------
flip-2.2/flip/R/flip.R | 8 +-
flip-2.2/flip/R/flipMix.R |only
flip-2.2/flip/R/obs2coeffWithin.R |only
flip-2.2/flip/R/permSpace.R | 4 -
flip-2.2/flip/R/symmetry.R | 39 ++++++++++++-
flip-2.2/flip/R/utilities.R | 90 +++++++++++++++++-------------
flip-2.2/flip/changelog.txt | 7 ++
flip-2.2/flip/man/flip.Rd | 39 +++++++++----
flip-2.2/flip/man/flip.object-class.Rd | 40 ++++++++++++-
flip-2.2/flip/man/flipMix.Rd |only
flip-2.2/flip/man/multiplicity.Rd | 11 ++-
flip-2.2/flip/man/permutationSpace.Rd | 1
21 files changed, 286 insertions(+), 173 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 2.3-0 dated 2013-05-12 and 2.4-0 dated 2013-06-17
Description: Fixed and random effects meta-analysis. Functions for
tests of bias, forest and funnel plot.
Author: Guido Schwarzer
Maintainer: Guido Schwarzer
DESCRIPTION | 8 -
MD5 | 46 +++---
NAMESPACE | 2
NEWS | 42 ++++++
R/catmeth.R | 6
R/forest.meta.R | 330 ++++++++++++++++++++++++++++++++++++-------------
R/metabin.R | 124 +++++++++++++++---
R/metacont.R | 72 +++++++++-
R/metacor.R | 87 ++++++++++++
R/metagen.R | 91 ++++++++++++-
R/metaprop.R | 82 ++++++++++--
R/print.meta.R | 8 -
R/print.summary.meta.R | 83 ++++++++----
R/read.rm5.R | 17 --
R/summary.meta.R | 73 ++++++++++
R/trimfill.default.R | 1
R/trimfill.meta.R | 1
man/forest.meta.Rd | 32 +++-
man/metabin.Rd | 32 ++++
man/metacont.Rd | 26 +++
man/metacor.Rd | 28 +++-
man/metagen.Rd | 38 ++++-
man/metaprop.Rd | 38 ++++-
man/print.meta.Rd | 47 +++++-
24 files changed, 1051 insertions(+), 263 deletions(-)
Title: A Monte Carlo permutation method for multiple test correlation
Diff between MCPerm versions 1.1.3 dated 2013-01-28 and 1.1.4 dated 2013-06-17
Description: A Monte Carlo permutation method for multiple test
correlation.
Author: Lanying Zhang and Yongshuai Jiang
Maintainer: Yongshuai Jiang
MCPerm-1.1.3/MCPerm/R/MCPerm-internal.R |only
MCPerm-1.1.3/MCPerm/R/permuteData.R |only
MCPerm-1.1.3/MCPerm/data/exampleData.rda |only
MCPerm-1.1.3/MCPerm/man/exampleData.Rd |only
MCPerm-1.1.3/MCPerm/man/permuteData.Rd |only
MCPerm-1.1.4/MCPerm/DESCRIPTION | 13 -
MCPerm-1.1.4/MCPerm/MD5 | 95 ++++++++++--
MCPerm-1.1.4/MCPerm/R/HW.test.R |only
MCPerm-1.1.4/MCPerm/R/I2.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/I2.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.Hist.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.CDC.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.Hist.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.boxplot.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.LnOR.qqnorm.R |only
MCPerm-1.1.4/MCPerm/R/PermMeta.boxplot.R |only
MCPerm-1.1.4/MCPerm/R/Q.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/Q.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.Allele.QQ.R |only
MCPerm-1.1.4/MCPerm/R/VS.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.CDC.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.Genotype.QQ.R |only
MCPerm-1.1.4/MCPerm/R/VS.Hist.R |only
MCPerm-1.1.4/MCPerm/R/VS.KS.R |only
MCPerm-1.1.4/MCPerm/R/VS.QQ.R |only
MCPerm-1.1.4/MCPerm/R/meta.MCPerm.R |only
MCPerm-1.1.4/MCPerm/R/meta.R |only
MCPerm-1.1.4/MCPerm/R/meta.TradPerm.R |only
MCPerm-1.1.4/MCPerm/R/pearson_scatter.R |only
MCPerm-1.1.4/MCPerm/R/permuteGenotype.R | 49 +-----
MCPerm-1.1.4/MCPerm/R/permuteGenotypeCount.R |only
MCPerm-1.1.4/MCPerm/R/print.PermMeta.R |only
MCPerm-1.1.4/MCPerm/data/MetaGenotypeCount.rda |only
MCPerm-1.1.4/MCPerm/data/MetaGenotypeData.rda |only
MCPerm-1.1.4/MCPerm/data/genotypeData.rda |only
MCPerm-1.1.4/MCPerm/man/Armitage.MCPerm.Rd | 35 ++--
MCPerm-1.1.4/MCPerm/man/Armitage.Rd | 39 ++---
MCPerm-1.1.4/MCPerm/man/Armitage.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/HW.test.Rd |only
MCPerm-1.1.4/MCPerm/man/I2.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/I2.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/MCPerm-package.Rd | 172 +++++++++++++----------
MCPerm-1.1.4/MCPerm/man/MetaGenotypeCount.Rd |only
MCPerm-1.1.4/MCPerm/man/MetaGenotypeData.Rd |only
MCPerm-1.1.4/MCPerm/man/OR.MCPerm.Rd | 39 ++---
MCPerm-1.1.4/MCPerm/man/OR.Rd | 35 ++--
MCPerm-1.1.4/MCPerm/man/OR.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/PermMeta.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.boxplot.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.LnOR.qqnorm.Rd |only
MCPerm-1.1.4/MCPerm/man/PermMeta.boxplot.Rd |only
MCPerm-1.1.4/MCPerm/man/Q.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/Q.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Allele.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.CDC.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Genotype.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.Hist.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.KS.Rd |only
MCPerm-1.1.4/MCPerm/man/VS.QQ.Rd |only
MCPerm-1.1.4/MCPerm/man/chisq.MCPerm.Rd | 46 +++---
MCPerm-1.1.4/MCPerm/man/chisq.TradPerm.Rd | 47 +++---
MCPerm-1.1.4/MCPerm/man/fisher.MCPerm.Rd | 50 +++---
MCPerm-1.1.4/MCPerm/man/fisher.TradPerm.Rd | 49 +++---
MCPerm-1.1.4/MCPerm/man/genotypeData.Rd |only
MCPerm-1.1.4/MCPerm/man/genotypeStat.Rd | 50 +++---
MCPerm-1.1.4/MCPerm/man/meta.MCPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/meta.Rd |only
MCPerm-1.1.4/MCPerm/man/meta.TradPerm.Rd |only
MCPerm-1.1.4/MCPerm/man/pearson_scatter.Rd |only
MCPerm-1.1.4/MCPerm/man/permuteGenotype.Rd | 63 ++------
MCPerm-1.1.4/MCPerm/man/permuteGenotypeCount.Rd |only
MCPerm-1.1.4/MCPerm/man/print.PermMeta.Rd |only
81 files changed, 469 insertions(+), 411 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.4 dated 2013-06-13 and 0.8.5.1 dated 2013-06-17
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 10 ++--
MD5 | 20 ++++-----
NAMESPACE | 2
R/fscaret.R | 36 ++++++++--------
R/funcReg.all.R | 2
R/regVarImp.R | 104 ++++++++++++-------------------------------------
man/fscaret-package.Rd | 5 +-
man/fscaret.Rd | 14 ++++++
man/impCalc.Rd | 7 ++-
man/regVarImp.Rd | 12 ++++-
man/timeout.Rd | 1
11 files changed, 95 insertions(+), 118 deletions(-)
Title: Analysis of music and speech
Diff between tuneR versions 0.4-1 dated 2012-08-28 and 0.4-2 dated 2013-06-17
Description: Collection of tools to analyze music, extract features
like MFCCs, handling wave files, read mp3, transcription, ...
Also contains functions ported from the rastamat Matlab
package.
Author: Uwe Ligges
Maintainer: Uwe Ligges
tuneR-0.4-1/tuneR/R/levinson.R |only
tuneR-0.4-1/tuneR/R/zzz.R |only
tuneR-0.4-1/tuneR/man/levinson.Rd |only
tuneR-0.4-2/tuneR/DESCRIPTION | 13 +++++++------
tuneR-0.4-2/tuneR/MD5 | 13 +++++--------
tuneR-0.4-2/tuneR/NAMESPACE | 2 +-
tuneR-0.4-2/tuneR/R/Wave.R | 1 -
tuneR-0.4-2/tuneR/R/plot-Wave.R | 27 +++++++++++++++++----------
tuneR-0.4-2/tuneR/man/plot-Wave.Rd | 7 +++++--
9 files changed, 35 insertions(+), 28 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Diff between evtree versions 0.1-2 dated 2012-04-11 and 0.1-3 dated 2013-06-17
Description: Commonly used classification and regression tree methods
like the CART algorithm are recursive partitioning methods that
build the model in a forward stepwise search. Although this
approach is known to be an efficient heuristic, the results of
recursive tree methods are only locally optimal, as splits are
chosen to maximize homogeneity at the next step only. An
alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary
algorithms. The evtree package implements an evolutionary
algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully
computed in C++ while the partykit package is leveraged to
represent the resulting trees in R, providing unified
infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre], Achim Zeileis [aut], Karl-Peter
Pfeiffer [aut]
Maintainer: Thomas Grubinger
DESCRIPTION | 18 -
MD5 | 51 ++
NEWS | 5
R/evtree.R | 2
data/BBBClub.rda |binary
data/ContraceptiveChoice.RData |binary
data/GermanCredit.RData |binary
data/MAGICGammaTelescope.RData |binary
data/StatlogHeart.RData |binary
inst/doc/evtree.R |only
inst/doc/evtree.Rnw | 650 ++++++++++++++++++++++++++++++-------
inst/doc/evtree.pdf |binary
tests/Examples/evtree-Ex.Rout.save | 11
vignettes/.install_extras | 2
vignettes/evtree.Rnw | 650 ++++++++++++++++++++++++++++++-------
vignettes/evtree.bib | 71 +++-
vignettes/results_j48 |only
vignettes/results_parameter |only
18 files changed, 1192 insertions(+), 268 deletions(-)
Title: Robust Linear Mixed Effects Models
Diff between robustlmm versions 1.0 dated 2013-03-08 and 1.1 dated 2013-06-17
Description: Robust mixed effects modeling by robustification of
scoring equations using the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller
DESCRIPTION | 8
MD5 | 149
NAMESPACE | 162 -
R/AllClass.R | 1574 ++++-----
R/AllGeneric.R | 80
R/DAS-scale.R | 1010 +++---
R/accessors.R | 796 ++--
R/fit.effects.R | 90
R/fromLme4.R | 464 +-
R/helpers.R | 1264 +++----
R/lmer.R | 78
R/multiroot.R | 204 -
R/mutators.R | 226 -
R/psiFunc2.R | 544 +--
R/rlmer.R | 799 ++---
R/zero.theta.R | 120
README.md | 50
ToDo | 34
inst/doc/ggplot.theme.R | 26
inst/doc/plots.R | 353 +-
inst/doc/rlmer.pdf |binary
inst/doc/sleepstudy.R | 66
man/VarCorr.Rd | 102
man/cPsi.Rd | 24
man/compare.Rd | 50
man/fixef.Rd | 64
man/getInfo.Rd | 58
man/getME.Rd | 227 -
man/lmerNoFit.Rd | 46
man/nobs-methods.Rd | 30
man/print.xtable.comparison.table.Rd | 80
man/psi2propII.Rd | 34
man/psiFuncCached.Rd | 70
man/psi_func_cached-class.Rd | 150
man/residuals.rlmerMod.Rd | 42
man/rho.b.Rd | 30
man/rho.e.Rd | 30
man/rlmer.Rd | 215 -
man/rlmerMod-class.Rd | 86
man/sigma.Rd | 30
man/smoothPsi.Rd | 48
man/theta.Rd | 26
man/wgt.Rd | 74
man/xtable.comparison.table.Rd | 78
tests/DAS-scale.R | 416 +-
tests/compare-methods.R | 242 -
tests/compare-methods.Rout.save | 941 ++---
tests/expectations.R | 92
tests/genericFunctions.R | 124
tests/getME.R | 30
tests/getME.Rout.save | 763 ++--
tests/psi-rho-funs.R | 186 -
tests/rlmerMod.R | 196 -
tests/subset.R |only
tests/tau.R | 164 -
tests/testMatrices.R | 374 +-
vignettes/cache/03451c9f666591b6ac41dc9a9ed06ce40b992c72 |binary
vignettes/cache/3eedbad1dba67d608f15fff9c8483ecb74f5b750 |binary
vignettes/cache/5d35c874f80664a261be32f6c0cc9ad6cf912ab0 |binary
vignettes/cache/6b459128b6f80b01986ff6c4115e7dfb52f962fb |binary
vignettes/cache/6c12e8730fa7df924a4b57a4258f7d876dd3cc7f |binary
vignettes/cache/e514dc7b17af4b19dcabad5cf474029c569fca86 |binary
vignettes/efficiency-table-B-optimal.tex | 44
vignettes/efficiency-table-lqq-locationScale.tex | 40
vignettes/efficiency-table-lqq.tex | 44
vignettes/efficiency-table.tex | 28
vignettes/figs |only
vignettes/rlmer.Rnw | 2394 +++++++--------
vignettes/rlmer.bib | 882 ++---
vignettes/rlmer.tex |only
vignettes/tuning-constants-table.tex | 28
71 files changed, 8364 insertions(+), 8315 deletions(-)
Title: Power and Sample size based on two one-sided t-tests (TOST) for
(bio)equivalence studies
Diff between PowerTOST versions 1.1-03 dated 2013-05-03 and 1.1-05 dated 2013-06-17
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies. See
function known.designs() for study designs covered. Moreover
the package contains functions for power and sample size based
on 'expected' power in case of uncertain (estimated)
variability. ----- Added are functions for the power and
sample size for the ratio of two means with normally
distributed data on the original scale (based on Fieller's
confidence ('fiducial') interval). ----- Contains further
functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but
eventually useful if the question of 'non-superiority' must be
evaluated. The power and sample size calculations based on
non-inferiority test may also performed via 'expected' power in
case of uncertain (estimated) variability. ----- Contains
functions power.scABEL() and sampleN.scABEL() to calculate
power and sample size for the BE decision via scaled (widened)
BE acceptance limits based on simulations. Contains functions
power.RSABE() and sampleN.RSABE() to calculate power and sample
size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations. Contains
further functions power.NTIDFDA() and sampleN.NTIDFDA() to
calculate power and sample size for the BE decision via the FDA
procedure for NTID's based on simulations.
Author: Detlew Labes
Maintainer: Detlew Labes
PowerTOST-1.1-03/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.02.pdf |only
PowerTOST-1.1-05/PowerTOST/DESCRIPTION | 19 +-
PowerTOST-1.1-05/PowerTOST/MD5 | 32 ++--
PowerTOST-1.1-05/PowerTOST/NAMESPACE | 2
PowerTOST-1.1-05/PowerTOST/NEWS | 18 ++
PowerTOST-1.1-05/PowerTOST/R/SampleSize.R | 22 ++-
PowerTOST-1.1-05/PowerTOST/R/power_RSABE_NTID.R |only
PowerTOST-1.1-05/PowerTOST/R/power_scABEL.R | 6
PowerTOST-1.1-05/PowerTOST/R/samplesize_RSABE.R | 69 +++++++---
PowerTOST-1.1-05/PowerTOST/R/samplesize_RSABE_NTID.R |only
PowerTOST-1.1-05/PowerTOST/R/samplesize_scABEL.R | 68 +++++++--
PowerTOST-1.1-05/PowerTOST/inst/doc/Implementation_scaledABE_simsV0.03.pdf |only
PowerTOST-1.1-05/PowerTOST/man/PowerTOST-package.Rd | 19 ++
PowerTOST-1.1-05/PowerTOST/man/power.NTIDFDA.Rd |only
PowerTOST-1.1-05/PowerTOST/man/power.RSABE.Rd | 12 -
PowerTOST-1.1-05/PowerTOST/man/power.scABEL.Rd | 17 +-
PowerTOST-1.1-05/PowerTOST/man/sampleN.NTIDFDA.Rd |only
PowerTOST-1.1-05/PowerTOST/man/sampleN.RSABE.Rd | 33 ++--
PowerTOST-1.1-05/PowerTOST/man/sampleN.TOST.Rd | 3
PowerTOST-1.1-05/PowerTOST/man/sampleN.scABEL.Rd | 22 +--
20 files changed, 226 insertions(+), 116 deletions(-)
Title: Calculations and visualizations related to Geometric
Morphometrics
Diff between Morpho versions 0.23.3 dated 2013-03-21 and 0.24.1 dated 2013-06-17
Description: A toolset for Geometric Morphometrics and mesh processing.
Author: Stefan Schlager
Maintainer: Stefan Schlager
Morpho-0.23.3/Morpho/R/crestlines.r |only
Morpho-0.23.3/Morpho/R/face.r |only
Morpho-0.23.3/Morpho/R/minClost.r |only
Morpho-0.23.3/Morpho/R/unbias.r |only
Morpho-0.23.3/Morpho/src/gauss_displace.f90 |only
Morpho-0.23.3/Morpho/src/minClost.f90 |only
Morpho-0.24.1/Morpho/DESCRIPTION | 8 +--
Morpho-0.24.1/Morpho/MD5 | 70 ++++++++++++++--------------
Morpho-0.24.1/Morpho/NAMESPACE | 6 +-
Morpho-0.24.1/Morpho/R/adnormals.r | 24 +++++++++
Morpho-0.24.1/Morpho/R/bindArr.r |only
Morpho-0.24.1/Morpho/R/covDist.r |only
Morpho-0.24.1/Morpho/R/histGroup.r | 17 ++++--
Morpho-0.24.1/Morpho/R/kendalldist.r |only
Morpho-0.24.1/Morpho/R/mcNNindex.r | 4 +
Morpho-0.24.1/Morpho/R/name2.r | 2
Morpho-0.24.1/Morpho/R/pls2B.r | 32 ++++++++++--
Morpho-0.24.1/Morpho/R/procAOV.r | 13 +++--
Morpho-0.24.1/Morpho/R/procSym.r | 18 +++++--
Morpho-0.24.1/Morpho/R/regdist.r | 4 -
Morpho-0.24.1/Morpho/R/regdist.raw.r | 10 +---
Morpho-0.24.1/Morpho/R/scaleproc.r | 4 +
Morpho-0.24.1/Morpho/man/CVA.Rd | 35 ++++++++------
Morpho-0.24.1/Morpho/man/Morpho-package.Rd | 12 ++--
Morpho-0.24.1/Morpho/man/adnormals.Rd | 23 ++++++++-
Morpho-0.24.1/Morpho/man/covDist.Rd |only
Morpho-0.24.1/Morpho/man/deformGrid.Rd | 4 +
Morpho-0.24.1/Morpho/man/groupPCA.Rd | 6 +-
Morpho-0.24.1/Morpho/man/histGroup.Rd | 11 +++-
Morpho-0.24.1/Morpho/man/internal.Rd | 16 ------
Morpho-0.24.1/Morpho/man/mesh2ply.Rd | 4 +
Morpho-0.24.1/Morpho/man/meshDist.Rd | 4 +
Morpho-0.24.1/Morpho/man/name2factor.Rd | 6 +-
Morpho-0.24.1/Morpho/man/pls2B.Rd |only
Morpho-0.24.1/Morpho/man/procSym.Rd | 13 ++++-
Morpho-0.24.1/Morpho/man/regdist.raw.Rd | 8 ++-
Morpho-0.24.1/Morpho/man/relaxLM.Rd | 6 +-
Morpho-0.24.1/Morpho/man/rotonto.Rd | 6 +-
Morpho-0.24.1/Morpho/man/tobedoc.Rd | 3 -
Morpho-0.24.1/Morpho/man/typprob.Rd | 2
Morpho-0.24.1/Morpho/man/warpmovie3d.Rd | 6 +-
Morpho-0.24.1/Morpho/src/facenormals.f90 |only
42 files changed, 240 insertions(+), 137 deletions(-)
Title: Bolstad functions
Diff between Bolstad2 versions 1.0-27 dated 2011-11-18 and 1.0-28 dated 2013-06-17
Description: A set of R functions and data sets for the book
Understanding Computational Bayesian Statistics, Bolstad, W.M.
(2009), John Wiley & Sons ISBN 978-0470046098
Author: James M. Curran
Maintainer: James M. Curran
DESCRIPTION | 17 +++--
MD5 | 12 +--
R/BayesCPH.r | 180 +++++++++++++++++++++++++++---------------------------
R/BayesLogistic.r | 14 ++--
R/BayesPois.r | 180 +++++++++++++++++++++++++++---------------------------
R/bivnormMH.r | 16 ++--
R/hierMeanReg.r | 174 ++++++++++++++++++++++++++--------------------------
7 files changed, 298 insertions(+), 295 deletions(-)
Title: A collection of miscellaneous tools for reproducible research
with R.
Diff between repmis versions 0.2.5 dated 2013-04-24 and 0.2.6 dated 2013-06-17
Description: A collection of miscellaneous tools for reproducible
research with R. Currently the package includes tools to load R
packages and automatically generate BibTeX files citing them as
well as load plain-text data stored on Dropbox, GitHub, and
from other sources.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 12 ++---
MD5 | 24 +++++------
NAMESPACE | 5 --
NEWS | 6 ++
R/InstallOldPackages.R | 15 +++----
R/LoadandCite.R | 96 +++++++++++++++++++++++++++++++++++++++-------
R/source_DropboxData.R | 4 -
R/source_GitHubData.R | 4 -
R/source_data.R | 7 +--
README.md | 5 +-
man/InstallOldPackages.Rd | 9 ++--
man/LoadandCite.Rd | 32 ++++++++-------
man/source_data.Rd | 3 -
13 files changed, 153 insertions(+), 69 deletions(-)
Title: Relaxation of glmnet models (as in relaxed lasso, Meinshausen
2007)
Diff between relaxnet versions 0.2-1 dated 2013-05-13 and 0.3-1 dated 2013-06-17
Description: Extends the glmnet package with "relaxation", done by
running glmnet once on the entire predictor matrix, then again
on each different subset of variables from along the
regularization path. Relaxation may lead to improved prediction
accuracy for truly sparse data generating models, as well as
fewer false positives (i.e. fewer noncontributing predictors in
the final model). Penalty may be lasso (alpha = 1) or elastic
net (0 < alpha < 1). For this version, family may be "gaussian"
or "binomial" only. Takes advantage of fast fortran code from
the glmnet package.
Author: Stephan Ritter, Alan Hubbard
Maintainer: Stephan Ritter
ChangeLog |only
DESCRIPTION | 20 ++++----
MD5 | 15 +++---
NAMESPACE | 3 +
R/cv.alpha.relaxnet.R | 125 +++++++++++++++++++++++++++++++++++++-------------
R/cv.relaxnet.R | 110 ++++++++++++++++++++++++++++++++++++--------
R/predict.relaxnet.R | 37 ++++++++++++--
R/relaxnet.R | 5 +-
man/cv.relaxnet.Rd | 15 ++++++
9 files changed, 260 insertions(+), 70 deletions(-)
Title: Dynamic Deterministic Effects Propagation Networks: Infer
signalling networks for timecourse RPPA data.
Diff between ddepn versions 2.1.2 dated 2012-06-21 and 2.1.4 dated 2013-06-17
Description: DDEPN (Dynamic Deterministic Effects Propagation
Networks): Infer signalling networks for timecourse data. Given
a matrix of high-throughput genomic or proteomic timecourse
data, generated after external perturbation of the biological
system, DDEPN models the time-dependent propagation of active
and passive states depending on a network structure. Optimal
network structures given the experimental data are
reconstructed. Two network inference algorithms can be used:
inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA,
a Genetic Algorithm network optimisation. Inclusion of prior
biological knowledge can be done using different network prior
models.
Author: Christian Bender
Maintainer: Christian Bender
DESCRIPTION | 14 +++++-----
MD5 | 45 ++++++++++++++++-----------------
R/ddepn.R | 7 +++--
R/perform.hmmsearch.R | 4 ++
R/samplephi.R | 2 -
data/hcc1954.RData |binary
data/hcc1954raw.RData |binary
data/kegggraphs.RData |binary
inst/doc/ddepn.R |only
inst/doc/ddepn.pdf |binary
man/adjacencyMatrix_to_logicalRules.Rd | 9 ++++--
man/create_signetwork.Rd | 29 ++++++++++++++-------
man/ddepn.Rd | 21 ++++++++++-----
man/getfirstphi.Rd | 3 +-
man/makedata.Rd | 8 +++--
man/mcmc_ddepn.Rd | 15 ++++++-----
man/netga.Rd | 10 +++----
man/plot_edgeconfidences.Rd | 3 +-
man/plot_profiles.Rd | 5 ++-
man/plotdetailed.Rd | 11 +++++---
man/plotdetailed_Rgraphviz.Rd | 6 ++--
man/posterior.Rd | 3 +-
man/samplephi.Rd | 8 +++--
man/signalnetwork.Rd | 3 +-
24 files changed, 127 insertions(+), 79 deletions(-)
Title: Constrained, covariance-matching constrained and universal point
or block kriging
Diff between constrainedKriging versions 0.1.9 dated 2012-12-24 and 0.2.0 dated 2013-06-17
More information about constrainedKriging at CRAN
Description: The constrainedKriging package provides functions for
efficient computations of nonlinear spatial predictions with
local change of support. The package supplies functions for
tow-dimensional spatial interpolation by constrained,
covariance-matching constrained and universal (external drift)
kriging for points or block of any shape for data with a
nonstationary mean function and an isotropic weakly stationary
variogram. The linear spatial interpolation methods,
constrained and covariance-matching constrained kriging,
provide approximately unbiased prediction for nonlinear target
values under change of support. The constrainedKriging package
extends the range of geostatistical tools available in R and
provides a veritable alternative to conditional simulation for
nonlinear spatial prediction problems with local change of
support.
Author: Christoph Hofer
Maintainer: Christoph Hofer
constrainedKriging-0.1.9/constrainedKriging/LICENCE |only
constrainedKriging-0.2.0/constrainedKriging/DESCRIPTION | 9 -
constrainedKriging-0.2.0/constrainedKriging/MD5 | 20 +--
constrainedKriging-0.2.0/constrainedKriging/R/covmodlist.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.point.block.cov.R | 58 +++++-----
constrainedKriging-0.2.0/constrainedKriging/R/f.point.rec.covmat.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.polygons.preCKrige.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/f.preCKrige.check.and.test.R | 2
constrainedKriging-0.2.0/constrainedKriging/R/z#f.build.pixel.R |only
constrainedKriging-0.2.0/constrainedKriging/inst/ChangeLog.txt | 8 +
constrainedKriging-0.2.0/constrainedKriging/src/covariancefunctions.h | 30 ++++-
constrainedKriging-0.2.0/constrainedKriging/src/point_block_cov.c | 6 +
12 files changed, 90 insertions(+), 49 deletions(-)
Permanent link
Title: Modeling and Inferring Gene Networks
Diff between GeneNet versions 1.2.6 dated 2013-03-08 and 1.2.7 dated 2013-06-16
Description: GeneNet is a package for analyzing gene expression (time
series) data with focus on the inference of gene networks. In
particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
GeneNet-1.2.6/GeneNet/R/ggm.make.graph.R |only
GeneNet-1.2.6/GeneNet/man/ggm.make.graph.Rd |only
GeneNet-1.2.7/GeneNet/DESCRIPTION | 14 ++---
GeneNet-1.2.7/GeneNet/MD5 | 22 ++++-----
GeneNet-1.2.7/GeneNet/NAMESPACE | 4 -
GeneNet-1.2.7/GeneNet/NEWS | 10 ++++
GeneNet-1.2.7/GeneNet/R/ggm.make.igraph.R |only
GeneNet-1.2.7/GeneNet/R/ggm.simulate.data.R | 16 +++---
GeneNet-1.2.7/GeneNet/data/ecoli.rda |binary
GeneNet-1.2.7/GeneNet/inst/doc/arabidopsis-net.R | 36 +++++++--------
GeneNet-1.2.7/GeneNet/inst/doc/ecoli-net.R | 54 ++++++++++-------------
GeneNet-1.2.7/GeneNet/inst/doc/tcell-net.R | 52 +++++++++-------------
GeneNet-1.2.7/GeneNet/man/GeneNet-internal.Rd | 3 -
GeneNet-1.2.7/GeneNet/man/ggm.make.igraph.Rd |only
14 files changed, 103 insertions(+), 108 deletions(-)
Title: Distribution function of quadratic forms in normal variables
Diff between CompQuadForm versions 1.4 dated 2012-08-10 and 1.4.1 dated 2013-06-16
Description: Computes the distribution function of quadratic forms in
normal variables using Imhof's method, Davies's algorithm,
Farebrother's algorithm or Liu et al.'s algorithm.
Author: P. Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux
DESCRIPTION | 9 +++++----
MD5 | 12 ++++++------
R/zzz.R | 4 ++--
inst/HISTORY | 13 +++++++++++++
man/davies.Rd | 3 ++-
man/farebrother.Rd | 3 ++-
man/imhof.Rd | 7 ++++---
7 files changed, 34 insertions(+), 17 deletions(-)
Title: Statistical methods for visual fields
Diff between visualFields versions 0.3-2 dated 2013-06-08 and 0.3-3 dated 2013-06-16
Description: A collection of tools for analyzing the field of vision.
It provides a framework for development and use of innovative
methods for visualization, statistical analysis, and clinical
interpretation of visual-field loss and its change over time.
It is intended to be a tool for collaborative research.
Author: The visualFields Development Team
Maintainer: Ivan Marin-Franch
DESCRIPTION | 6 +++---
MD5 | 24 ++++++++++++------------
R/agecalc.R | 9 ++++++---
R/loadvfxml.R | 4 ++--
R/vflayout.R | 26 +++++++++-----------------
R/vflayout_legoplot.R | 31 +++++++++++--------------------
R/vflayout_poplr.R | 32 ++++++++++++--------------------
doc/news.txt | 5 ++++-
man/agecalc.Rd | 3 ++-
man/loadvfxml.Rd | 3 ++-
man/vflayout.Rd | 23 ++++++++++++++++++++---
man/vflayout_legoplot.Rd | 30 +++++++++++++++++++++++++++++-
man/vflayout_poplr.Rd | 41 +++++++++++++++++++++++++++++++++++------
13 files changed, 147 insertions(+), 90 deletions(-)
Title: Quantile Regression Using Asymmetric Laplace Distribution
Diff between ALDqr versions 0.1 dated 2013-06-08 and 0.2 dated 2013-06-16
Description: EM algorithm for estimation of parameters and other
methods in a quantile regression.
Author: Luis Benites Sanchez
Maintainer: Luis Benites Sanchez
DESCRIPTION | 10 +-
MD5 | 6 -
R/EM.qr.r | 292 +++++++++++++++++++++++++++++------------------------------
man/EM.qr.Rd | 10 +-
4 files changed, 161 insertions(+), 157 deletions(-)
Title: Two-table ExPosition
Diff between TExPosition versions 1.1 dated 2012-07-12 and 2.0.2 dated 2013-06-15
Description: TExPosition is an extension of ExPosition for two table
analyses, specifically, discriminant analyses.
Author: Derek Beaton, Jenny Rieck, Cherise R. Chin Fatt, Herve Abdi
Maintainer: Derek Beaton
TExPosition-1.1/TExPosition/R/TExPosition-internal.R |only
TExPosition-1.1/TExPosition/R/supplementaryRows.R |only
TExPosition-1.1/TExPosition/R/tepGraphHandler.R |only
TExPosition-1.1/TExPosition/man/supplementaryRows.Rd |only
TExPosition-2.0.2/TExPosition/DESCRIPTION | 11 -
TExPosition-2.0.2/TExPosition/MD5 | 26 +-
TExPosition-2.0.2/TExPosition/NAMESPACE | 2
TExPosition-2.0.2/TExPosition/R/print.tepDICA.R | 11 -
TExPosition-2.0.2/TExPosition/R/tepBADA.R | 34 +--
TExPosition-2.0.2/TExPosition/R/tepDICA.R | 10 -
TExPosition-2.0.2/TExPosition/R/tepGraphs.R | 136 ++++++++++-----
TExPosition-2.0.2/TExPosition/R/texpoDesignCheck.R | 7
TExPosition-2.0.2/TExPosition/man/TExPosition-package.Rd | 6
TExPosition-2.0.2/TExPosition/man/tepBADA.Rd | 13 -
TExPosition-2.0.2/TExPosition/man/tepDICA.Rd | 8
TExPosition-2.0.2/TExPosition/man/tepGraphs.Rd | 27 ++
16 files changed, 176 insertions(+), 115 deletions(-)
Title: Analysis of Quaternary Science Data
Diff between rioja versions 0.7-3 dated 2012-01-05 and 0.8-3 dated 2013-06-15
Description: Functions for the analysis of Quaternary science data,
including constrained clustering, WA, WAPLS, IKFA, MLRC and MAT
transfer functions, and stratigraphic diagrams.
Author: Steve Juggins
Maintainer: Steve Juggins
DESCRIPTION | 15 ++++----
MD5 | 62 ++++++++++++++++++------------------
NAMESPACE | 1
R/IKFA.r | 8 ++--
R/LWR.r | 10 ++---
R/MAT.r | 9 +++--
R/MLRC.r | 57 ++++++++++++++++++++-------------
R/PTF.r | 61 ++++++++++++++++++++++++++++++-----
R/WA.r | 13 ++++---
R/WAPLS.r | 54 ++++++++++++++++++-------------
R/internals.r | 2 -
R/strat.plot.r | 82 +++++++++++++++++++++++++++++++++++-------------
R/zzz.r | 2 -
inst/CITATION | 11 +++---
man/IKFA.Rd | 4 +-
man/LWR.Rd | 6 ++-
man/MAT.Rd | 4 +-
man/MLRC.Rd | 5 +-
man/PTF.Rd | 2 -
man/RLGH.Rd | 4 +-
man/WA.Rd | 10 +++--
man/WAPLS.Rd | 8 ++--
man/chclust.Rd | 2 -
man/compare.datasets.Rd | 2 -
man/interp.dataset.Rd | 2 -
man/rioja.package.Rd | 4 +-
man/strat.plot.Rd | 14 +++++---
src/chclust.cpp | 7 ++--
src/mat.cpp | 4 +-
src/mlrc.cpp | 9 ++++-
src/rdfmt.c | 7 +++-
src/wa.cpp | 5 ++
32 files changed, 313 insertions(+), 173 deletions(-)
Title: Multi-table ExPosition
Diff between MExPosition versions 1.0 dated 2012-07-13 and 2.0.3 dated 2013-06-15
Description: MExPosition is for descriptive (i.e., fixed-effects)
multi-table multivariate analysis the singular value
decomposition.
Author: Cherise R. Chin Fatt, Derek Beaton, Herve Abdi.
Maintainer: Cherise R. Chin Fatt
MExPosition-1.0/MExPosition/R/MExPosition-internal.R |only
MExPosition-1.0/MExPosition/R/matrixTrace.R |only
MExPosition-1.0/MExPosition/R/mpGraphHandler.r |only
MExPosition-1.0/MExPosition/R/print.mpDISTATIS.R |only
MExPosition-1.0/MExPosition/R/rvCoeff.R |only
MExPosition-1.0/MExPosition/man/matrixTrace.Rd |only
MExPosition-1.0/MExPosition/man/mpDISTATIS.Rd |only
MExPosition-1.0/MExPosition/man/mpDISTATIS.core.Rd |only
MExPosition-2.0.3/MExPosition/DESCRIPTION | 11
MExPosition-2.0.3/MExPosition/MD5 | 141 +++++--
MExPosition-2.0.3/MExPosition/NAMESPACE | 56 ++
MExPosition-2.0.3/MExPosition/R/mpANISOSTATIS.core.R | 187 +++-------
MExPosition-2.0.3/MExPosition/R/mpANISOTATIS.R |only
MExPosition-2.0.3/MExPosition/R/mpCANOSTATIS.R |only
MExPosition-2.0.3/MExPosition/R/mpCANOSTATIS.core.R |only
MExPosition-2.0.3/MExPosition/R/mpCOVSTATIS.R |only
MExPosition-2.0.3/MExPosition/R/mpCOVSTATIS.core.R |only
MExPosition-2.0.3/MExPosition/R/mpDISTATIS.R | 40 +-
MExPosition-2.0.3/MExPosition/R/mpDISTATIS.core.r | 157 +++-----
MExPosition-2.0.3/MExPosition/R/mpDOACT.STATIS.R |only
MExPosition-2.0.3/MExPosition/R/mpDOACT.STATIS.core.R |only
MExPosition-2.0.3/MExPosition/R/mpGraphs.R | 166 ++++++--
MExPosition-2.0.3/MExPosition/R/mpKPlus1STATIS.R |only
MExPosition-2.0.3/MExPosition/R/mpKPlus1STATIS.core.R |only
MExPosition-2.0.3/MExPosition/R/mpMFA.R | 19 -
MExPosition-2.0.3/MExPosition/R/mpMahalanobis.R |only
MExPosition-2.0.3/MExPosition/R/mpMultitable.R |only
MExPosition-2.0.3/MExPosition/R/mpOutputHandler.R | 18
MExPosition-2.0.3/MExPosition/R/mpPTA.R |only
MExPosition-2.0.3/MExPosition/R/mpPTA.core.R |only
MExPosition-2.0.3/MExPosition/R/mpSTATIS.R | 145 ++++---
MExPosition-2.0.3/MExPosition/R/mpSTATIS.columnPreproc.R | 3
MExPosition-2.0.3/MExPosition/R/mpSTATIS.core.R | 170 ++++-----
MExPosition-2.0.3/MExPosition/R/mpSTATIS.optimize.R | 51 +-
MExPosition-2.0.3/MExPosition/R/mpSTATIS.preprocess.R | 27 -
MExPosition-2.0.3/MExPosition/R/mpSTATIS.rowPreproc.R | 2
MExPosition-2.0.3/MExPosition/R/mpSTATIS.tablePreproc.R | 103 ++---
MExPosition-2.0.3/MExPosition/R/mpSumPCA.R |only
MExPosition-2.0.3/MExPosition/R/print.KPlus1.statis.compromise.R |only
MExPosition-2.0.3/MExPosition/R/print.KPlus1.statis.innerproduct.R |only
MExPosition-2.0.3/MExPosition/R/print.KPlus1.statis.overview.R |only
MExPosition-2.0.3/MExPosition/R/print.KPlus1.statis.table.R |only
MExPosition-2.0.3/MExPosition/R/print.covstatis.compromise.R |only
MExPosition-2.0.3/MExPosition/R/print.covstatis.innerproduct.R |only
MExPosition-2.0.3/MExPosition/R/print.covstatis.overview.R |only
MExPosition-2.0.3/MExPosition/R/print.covstatis.table.R |only
MExPosition-2.0.3/MExPosition/R/print.distatis.compromise.R | 20 -
MExPosition-2.0.3/MExPosition/R/print.distatis.innerproduct.R | 17
MExPosition-2.0.3/MExPosition/R/print.distatis.overview.R | 5
MExPosition-2.0.3/MExPosition/R/print.distatis.table.R | 21 -
MExPosition-2.0.3/MExPosition/R/print.doact.statis.compromise.R |only
MExPosition-2.0.3/MExPosition/R/print.doact.statis.innerproduct.R |only
MExPosition-2.0.3/MExPosition/R/print.doact.statis.overview.R |only
MExPosition-2.0.3/MExPosition/R/print.doact.statis.table.R |only
MExPosition-2.0.3/MExPosition/R/print.mexPosition.Output.R | 3
MExPosition-2.0.3/MExPosition/R/print.mpANISOSTATIS.R |only
MExPosition-2.0.3/MExPosition/R/print.mpCOVSTATIS.R |only
MExPosition-2.0.3/MExPosition/R/print.mpDISTATIS.r |only
MExPosition-2.0.3/MExPosition/R/print.mpDOACT.STATIS.R |only
MExPosition-2.0.3/MExPosition/R/print.mpKPlus1STATIS.R |only
MExPosition-2.0.3/MExPosition/R/print.mpSTATIS.R | 8
MExPosition-2.0.3/MExPosition/R/print.statis.compromise.R |only
MExPosition-2.0.3/MExPosition/R/print.statis.innerproduct.R | 6
MExPosition-2.0.3/MExPosition/R/print.statis.table.R | 18
MExPosition-2.0.3/MExPosition/man/MExPosition-package.Rd | 8
MExPosition-2.0.3/MExPosition/man/mpANISOSTATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/mpANISOSTATIS.core.Rd | 63 +--
MExPosition-2.0.3/MExPosition/man/mpCANOSTATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/mpCANOSTATIS.core.Rd |only
MExPosition-2.0.3/MExPosition/man/mpCOVSTATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/mpCOVSTATIS.core.Rd |only
MExPosition-2.0.3/MExPosition/man/mpDISTATIS.core.rd |only
MExPosition-2.0.3/MExPosition/man/mpDISTATIS.rd |only
MExPosition-2.0.3/MExPosition/man/mpDOACT.STATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/mpDOACT.STATIS.core.Rd |only
MExPosition-2.0.3/MExPosition/man/mpGraphs.Rd | 13
MExPosition-2.0.3/MExPosition/man/mpKPlus1STATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/mpKPlus1STATIS.core.Rd |only
MExPosition-2.0.3/MExPosition/man/mpMFA.Rd | 32 +
MExPosition-2.0.3/MExPosition/man/mpMahalanobis.Rd |only
MExPosition-2.0.3/MExPosition/man/mpMultitable.Rd |only
MExPosition-2.0.3/MExPosition/man/mpPTA.Rd |only
MExPosition-2.0.3/MExPosition/man/mpPTA.core.Rd |only
MExPosition-2.0.3/MExPosition/man/mpSTATIS.Rd | 33 +
MExPosition-2.0.3/MExPosition/man/mpSTATIS.columnPreproc.Rd | 7
MExPosition-2.0.3/MExPosition/man/mpSTATIS.core.Rd | 41 +-
MExPosition-2.0.3/MExPosition/man/mpSTATIS.optimize.Rd | 7
MExPosition-2.0.3/MExPosition/man/mpSTATIS.preprocess.Rd | 15
MExPosition-2.0.3/MExPosition/man/mpSTATIS.rowPreproc.Rd | 7
MExPosition-2.0.3/MExPosition/man/mpSTATIS.tablePreproc.Rd | 4
MExPosition-2.0.3/MExPosition/man/mpSumPCA.Rd |only
MExPosition-2.0.3/MExPosition/man/print.KPlus1.statis.compromise.Rd |only
MExPosition-2.0.3/MExPosition/man/print.KPlus1.statis.innerproduct.Rd |only
MExPosition-2.0.3/MExPosition/man/print.KPlus1.statis.overview.Rd |only
MExPosition-2.0.3/MExPosition/man/print.KPlus1.statis.table.Rd |only
MExPosition-2.0.3/MExPosition/man/print.covstatis.compromise.Rd |only
MExPosition-2.0.3/MExPosition/man/print.covstatis.innerproduct.Rd |only
MExPosition-2.0.3/MExPosition/man/print.covstatis.overview.Rd |only
MExPosition-2.0.3/MExPosition/man/print.covstatis.table.Rd |only
MExPosition-2.0.3/MExPosition/man/print.doact.statis.compromise.Rd |only
MExPosition-2.0.3/MExPosition/man/print.doact.statis.innerproduct.Rd |only
MExPosition-2.0.3/MExPosition/man/print.doact.statis.overview.Rd |only
MExPosition-2.0.3/MExPosition/man/print.doact.statis.table.Rd |only
MExPosition-2.0.3/MExPosition/man/print.mpANISOSTATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/print.mpCOVSTATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/print.mpDOACT.STATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/print.mpKPlus1STATIS.Rd |only
MExPosition-2.0.3/MExPosition/man/print.statis.compromise.Rd |only
108 files changed, 912 insertions(+), 712 deletions(-)
Title: Pretty scientific plotting with minor-tick and log minor-tick
support
Diff between magicaxis versions 1.4 dated 2013-04-03 and 1.5 dated 2013-06-15
Description: Functions to make useful (and pretty) plots for scientific
plotting. Additional plotting features are added for base
plotting, with particular emphasis on making attractive log
axis plots.
Author: Aaron Robotham
Maintainer: Aaron Robotham
CHANGELOG | 25 ++++++++++++++++++++---
DESCRIPTION | 8 +++----
MD5 | 22 ++++++++++++---------
R/magaxis.R | 23 +++++++++++++++-------
R/magerr.R |only
R/maglab.R | 49 ++++++++++++++++++++++++++++++++++++-----------
R/magmap.R |only
R/magplot.R | 4 +--
man/magaxis.Rd | 12 +++++++++--
man/magerr.Rd |only
man/magicaxis-package.Rd | 4 +--
man/maglab.Rd | 11 ++++++++--
man/magmap.Rd |only
man/magplot.Rd | 10 ++++++++-
14 files changed, 124 insertions(+), 44 deletions(-)
Title: Analysis of Overdispersed Data using S3 methods
Diff between aods3 versions 0.3-11 dated 2013-05-29 and 0.4.0 dated 2013-06-15
Description: This package provides functions to analyse overdispersed
counts or proportions. These functions should be considered as
complements to more sophisticated methods such as generalized
estimating equations (GEE) or generalized linear mixed effect
models (GLMM). Package aods3 is an S3 re-implementation of the
deprecated S4 package aod.
Author: Matthieu Lesnoff
Maintainer: Renaud Lancelot
DESCRIPTION | 8 +-
MD5 | 36 +++++------
R/AIC.aodml.R | 11 ++-
R/anova.aodml.R | 41 +++++++-----
R/aodml.R | 152 +++++++++++++++++++++---------------------------
R/deviance.R | 2
R/drs.R | 6 +
R/fitted.R | 8 +-
R/iccbin.R | 4 -
R/invlink.R | 7 +-
R/link.R | 5 -
R/logLik.R | 4 -
R/predict.R | 9 +-
R/print.anova.aodml.R | 6 +
R/print.aodml.R | 3
R/print.summary.aodml.R | 2
R/vcov.R | 4 -
R/wald.test.R | 4 -
man/aodml.Rd | 120 ++++++++++++++++++++++---------------
19 files changed, 232 insertions(+), 200 deletions(-)
Title: Clustering Indices
Diff between clusterCrit versions 1.2.1 dated 2013-04-25 and 1.2.2 dated 2013-06-15
Description: compute clustering validation indices
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes
clusterCrit-1.2.1/clusterCrit/inst/doc/clusterCrit.R |only
clusterCrit-1.2.2/clusterCrit/DESCRIPTION | 8
clusterCrit-1.2.2/clusterCrit/MD5 | 19 -
clusterCrit-1.2.2/clusterCrit/R/main.R | 5
clusterCrit-1.2.2/clusterCrit/build/clusterCrit.pdf |binary
clusterCrit-1.2.2/clusterCrit/build/partial.rdb |binary
clusterCrit-1.2.2/clusterCrit/inst/unitTests/Makefile | 6
clusterCrit-1.2.2/clusterCrit/src/Makevars.in | 5
clusterCrit-1.2.2/clusterCrit/src/critCalc.f95 | 257 +++++++++---------
clusterCrit-1.2.2/clusterCrit/src/criteria.c | 110 ++++++-
clusterCrit-1.2.2/clusterCrit/src/criteria.h | 10
11 files changed, 257 insertions(+), 163 deletions(-)
Title: Basic Robust Statistics
Diff between robustbase versions 0.9-7 dated 2013-03-06 and 0.9-8 dated 2013-06-15
Description: "Essential" Robust Statistics. The goal is to provide
tools allowing to analyze data with robust methods. This
includes regression methodology including model selections and
multivariate statistics where we strive to cover the book
"Robust Statistics, Theory and Methods" by Maronna, Martin and
Yohai; Wiley 2006.
Author: Original code by many authors, notably Peter Rousseeuw and
Christophe Croux, see file 'Copyrights'; Valentin Todorov
Maintainer: Martin Maechler
robustbase-0.9-7/robustbase/man/glmrobMqle.control.Rd |only
robustbase-0.9-7/robustbase/man/tukeyChi.Rd |only
robustbase-0.9-8/robustbase/ChangeLog | 25
robustbase-0.9-8/robustbase/DESCRIPTION | 15
robustbase-0.9-8/robustbase/Done | 19
robustbase-0.9-8/robustbase/MD5 | 189 +--
robustbase-0.9-8/robustbase/NAMESPACE | 16
robustbase-0.9-8/robustbase/R/BYlogreg.R |only
robustbase-0.9-8/robustbase/R/MTestimador2.R |only
robustbase-0.9-8/robustbase/R/adjbox.R | 2
robustbase-0.9-8/robustbase/R/anova-glmrob.R | 1
robustbase-0.9-8/robustbase/R/anova.lmrob.R | 4
robustbase-0.9-8/robustbase/R/biweight-funs.R | 30
robustbase-0.9-8/robustbase/R/covMcd.R | 199 +--
robustbase-0.9-8/robustbase/R/glmrob.R | 68 -
robustbase-0.9-8/robustbase/R/glmrobMqle-DQD.R | 13
robustbase-0.9-8/robustbase/R/glmrobMqle.R | 101 +
robustbase-0.9-8/robustbase/R/lmrob.M.S.R | 31
robustbase-0.9-8/robustbase/R/lmrob.MM.R | 372 +++---
robustbase-0.9-8/robustbase/R/lmrob.R | 195 +--
robustbase-0.9-8/robustbase/R/ltsReg.R | 177 +-
robustbase-0.9-8/robustbase/R/nlrob.R | 8
robustbase-0.9-8/robustbase/R/plot.lmrob.R | 2
robustbase-0.9-8/robustbase/R/psi-rho-funs.R | 41
robustbase-0.9-8/robustbase/R/rrcov.control.R | 21
robustbase-0.9-8/robustbase/R/zzz.R | 6
robustbase-0.9-8/robustbase/TODO | 89 +
robustbase-0.9-8/robustbase/data/foodstamp.rda |only
robustbase-0.9-8/robustbase/experi-psi-rho-funs.R | 20
robustbase-0.9-8/robustbase/inst/doc/estimating.functions.R | 81 -
robustbase-0.9-8/robustbase/inst/doc/lmrob_simulation.R |only
robustbase-0.9-8/robustbase/inst/doc/lmrob_simulation.Rnw | 16
robustbase-0.9-8/robustbase/inst/doc/lmrob_simulation.bib | 51
robustbase-0.9-8/robustbase/inst/doc/lmrob_simulation.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-GGW.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-Hampel.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-Huber.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-LQQ.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-Welsh.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-bisquare.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi-optimal.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/psi_functions.R |only
robustbase-0.9-8/robustbase/inst/doc/psi_functions.Rnw | 331 +++--
robustbase-0.9-8/robustbase/inst/doc/psi_functions.pdf |binary
robustbase-0.9-8/robustbase/inst/doc/simulation.functions.R | 9
robustbase-0.9-8/robustbase/inst/xtraR/ex-funs.R | 19
robustbase-0.9-8/robustbase/inst/xtraR/lmrob-trace_lev.R |only
robustbase-0.9-8/robustbase/inst/xtraR/m-s_fns.R | 48
robustbase-0.9-8/robustbase/inst/xtraR/plot-psiFun.R | 81 +
robustbase-0.9-8/robustbase/inst/xtraR/subsample-fns.R | 301 ++--
robustbase-0.9-8/robustbase/man/BYlogreg.Rd |only
robustbase-0.9-8/robustbase/man/M.psi.Rd |only
robustbase-0.9-8/robustbase/man/Qn.Rd | 11
robustbase-0.9-8/robustbase/man/chgDefaults-methods.Rd | 3
robustbase-0.9-8/robustbase/man/covMcd.Rd | 56
robustbase-0.9-8/robustbase/man/education.Rd | 2
robustbase-0.9-8/robustbase/man/epilepsy.Rd | 9
robustbase-0.9-8/robustbase/man/foodstamp.Rd |only
robustbase-0.9-8/robustbase/man/glmrob.Rd | 55
robustbase-0.9-8/robustbase/man/glmrob.control.Rd |only
robustbase-0.9-8/robustbase/man/lmrob..M..fit.Rd | 9
robustbase-0.9-8/robustbase/man/lmrob.M.S.Rd | 11
robustbase-0.9-8/robustbase/man/lmrob.Rd | 57
robustbase-0.9-8/robustbase/man/lmrob.control.Rd | 7
robustbase-0.9-8/robustbase/man/los.Rd | 14
robustbase-0.9-8/robustbase/man/ltsReg.Rd | 11
robustbase-0.9-8/robustbase/man/pkg-internal.Rd | 5
robustbase-0.9-8/robustbase/man/plot-methods.Rd | 18
robustbase-0.9-8/robustbase/man/possumDiv.Rd | 23
robustbase-0.9-8/robustbase/man/psi_func-class.Rd | 10
robustbase-0.9-8/robustbase/man/rrcov.control.Rd | 38
robustbase-0.9-8/robustbase/man/summarizeRobWeights.Rd | 11
robustbase-0.9-8/robustbase/man/tukeyPsi1.Rd | 37
robustbase-0.9-8/robustbase/man/vaso.Rd | 2
robustbase-0.9-8/robustbase/man/weights.lmrob.Rd | 32
robustbase-0.9-8/robustbase/src/init.c | 34
robustbase-0.9-8/robustbase/src/lmrob.c | 735 ++++++++----
robustbase-0.9-8/robustbase/src/mc.c | 5
robustbase-0.9-8/robustbase/src/qn_sn.c | 1
robustbase-0.9-8/robustbase/src/rffastmcd.f | 9
robustbase-0.9-8/robustbase/src/robustbase.h | 31
robustbase-0.9-8/robustbase/src/wgt_himed.c | 1
robustbase-0.9-8/robustbase/tests/MCD-specials.Rout.save | 22
robustbase-0.9-8/robustbase/tests/MT-tst.R |only
robustbase-0.9-8/robustbase/tests/NAcoef.Rout.save | 48
robustbase-0.9-8/robustbase/tests/binom-ni-small.R | 1
robustbase-0.9-8/robustbase/tests/binom-ni-small.Rout.save | 27
robustbase-0.9-8/robustbase/tests/glmrob-1.R | 107 +
robustbase-0.9-8/robustbase/tests/lmrob-data.R | 4
robustbase-0.9-8/robustbase/tests/lmrob-data.Rout.save | 303 ++--
robustbase-0.9-8/robustbase/tests/lmrob-methods.Rout.save | 325 ++---
robustbase-0.9-8/robustbase/tests/lmrob-psifns.R | 76 -
robustbase-0.9-8/robustbase/tests/lmrob-psifns.Rout.save | 695 ++++++-----
robustbase-0.9-8/robustbase/tests/m-s-estimator.R | 42
robustbase-0.9-8/robustbase/tests/m-s-estimator.Rout.save | 318 +++--
robustbase-0.9-8/robustbase/tests/nlrob-tst.R | 6
robustbase-0.9-8/robustbase/tests/poisson-ex.R | 125 +-
robustbase-0.9-8/robustbase/tests/psi-rho-etc.R | 29
robustbase-0.9-8/robustbase/tests/psi-rho-etc.Rout.save | 36
robustbase-0.9-8/robustbase/tests/tlts.Rout.save | 36
robustbase-0.9-8/robustbase/tests/weights.R | 3
robustbase-0.9-8/robustbase/tests/weights.Rout.save | 60
102 files changed, 3698 insertions(+), 2383 deletions(-)
Title: Various plotting functions
Diff between plotrix versions 3.4-7 dated 2013-04-13 and 3.4-8 dated 2013-06-15
Description: Lots of plots, various labeling, axis and color scaling
functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry
Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi,
Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl
Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa
Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby
Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann,Ted Toal
Maintainer: Jim Lemon
DESCRIPTION | 8 -
INDEX | 1
MD5 | 53 +++++-----
NEWS | 14 ++
R/addtable2plot.R | 3
R/barp.R | 2
R/box.heresy.R | 2
R/floatpie.R | 12 +-
R/gap.barplot.R | 4
R/gap.plot.R | 37 ++++---
R/kiteChart.R | 6 -
R/plot_bg.R |only
R/pyramid.plot.R | 4
R/radial.plot.R | 4
R/twoord.plot.R | 66 ++++++++-----
data/soils.rda |binary
man/add.ps.Rd | 66 +++++++------
man/addtable2plot.Rd | 5 -
man/barp.Rd | 10 +-
man/do.first.Rd |only
man/draw.ellipse.Rd | 21 ++--
man/floating.pie.Rd | 10 +-
man/gap.plot.Rd | 12 +-
man/kiteChart.Rd | 11 +-
man/plot_bg.Rd |only
man/pyramid.plot.Rd | 5 -
man/radial.plot.Rd | 7 -
man/raw.means.plot.Rd | 248 +++++++++++++++++++++++++++++++++++---------------
man/twoord.plot.Rd | 54 ++++++----
29 files changed, 423 insertions(+), 242 deletions(-)
Title: Exploratory analysis with the singular value decomposition.
Diff between ExPosition versions 1.1 dated 2012-07-12 and 2.1.3 dated 2013-06-15
Description: ExPosition is for descriptive (i.e., fixed-effects)
multivariate analysis with the singular value decomposition.
Author: Derek Beaton, Cherise R. Chin Fatt, Herve Abdi
Maintainer: Derek Beaton
ExPosition-1.1/ExPosition/R/ExPosition-internal.R |only
ExPosition-1.1/ExPosition/R/epGraphHandler.R |only
ExPosition-2.1.3/ExPosition/DESCRIPTION | 11
ExPosition-2.1.3/ExPosition/MD5 | 109 +++++--
ExPosition-2.1.3/ExPosition/NAMESPACE | 2
ExPosition-2.1.3/ExPosition/R/PDQ.R | 4
ExPosition-2.1.3/ExPosition/R/acknowledgements.R |only
ExPosition-2.1.3/ExPosition/R/basePDQ.R | 26 -
ExPosition-2.1.3/ExPosition/R/caSupplementalElementsPreProcessing.R |only
ExPosition-2.1.3/ExPosition/R/calculateConstraints.R | 8
ExPosition-2.1.3/ExPosition/R/chi2Dist.R |only
ExPosition-2.1.3/ExPosition/R/computeConstraints.R | 18 -
ExPosition-2.1.3/ExPosition/R/computeMW.R | 59 ++--
ExPosition-2.1.3/ExPosition/R/coreCA.R | 16 -
ExPosition-2.1.3/ExPosition/R/coreMDS.R |only
ExPosition-2.1.3/ExPosition/R/corePCA.R | 50 +--
ExPosition-2.1.3/ExPosition/R/designCheck.R | 6
ExPosition-2.1.3/ExPosition/R/epCA.R | 8
ExPosition-2.1.3/ExPosition/R/epGPCA.R | 18 -
ExPosition-2.1.3/ExPosition/R/epGraphs.R | 139 ++++++----
ExPosition-2.1.3/ExPosition/R/epMCA.R | 12
ExPosition-2.1.3/ExPosition/R/epMDS.R | 33 --
ExPosition-2.1.3/ExPosition/R/epOutputHandler.R | 7
ExPosition-2.1.3/ExPosition/R/epPCA.R | 21 -
ExPosition-2.1.3/ExPosition/R/expo.scale.R |only
ExPosition-2.1.3/ExPosition/R/genPDQ.R | 4
ExPosition-2.1.3/ExPosition/R/makeDistancesAndWeights.R |only
ExPosition-2.1.3/ExPosition/R/mca.eigen.fix.R | 8
ExPosition-2.1.3/ExPosition/R/mdsSupplementalElementsPreProcessing.R |only
ExPosition-2.1.3/ExPosition/R/mdsTransform.R |only
ExPosition-2.1.3/ExPosition/R/nominalCheck.R |only
ExPosition-2.1.3/ExPosition/R/pcaSupplementaryColsPreProcessing.R |only
ExPosition-2.1.3/ExPosition/R/pcaSupplementaryRowsPreProcessing.R |only
ExPosition-2.1.3/ExPosition/R/pickSVD.R | 85 ++++--
ExPosition-2.1.3/ExPosition/R/print.epCA.R | 3
ExPosition-2.1.3/ExPosition/R/print.epGraphs.R | 12
ExPosition-2.1.3/ExPosition/R/print.epMCA.R | 3
ExPosition-2.1.3/ExPosition/R/print.epMDS.R | 3
ExPosition-2.1.3/ExPosition/R/print.epSVD.R | 3
ExPosition-2.1.3/ExPosition/R/rvCoeff.R |only
ExPosition-2.1.3/ExPosition/R/supplementalProjection.R |only
ExPosition-2.1.3/ExPosition/R/supplementaryCols.R |only
ExPosition-2.1.3/ExPosition/R/supplementaryRows.R |only
ExPosition-2.1.3/ExPosition/data/beer.tasting.notes.rda |binary
ExPosition-2.1.3/ExPosition/data/coffee.data.rda |only
ExPosition-2.1.3/ExPosition/man/ExPosition-package.Rd | 6
ExPosition-2.1.3/ExPosition/man/acknowledgements.Rd |only
ExPosition-2.1.3/ExPosition/man/caSupplementalElementsPreProcessing.Rd |only
ExPosition-2.1.3/ExPosition/man/chi2Dist.Rd |only
ExPosition-2.1.3/ExPosition/man/coffee.data.Rd |only
ExPosition-2.1.3/ExPosition/man/coreCA.Rd | 5
ExPosition-2.1.3/ExPosition/man/coreMDS.Rd |only
ExPosition-2.1.3/ExPosition/man/corePCA.Rd | 9
ExPosition-2.1.3/ExPosition/man/designCheck.Rd | 8
ExPosition-2.1.3/ExPosition/man/epCA.Rd | 3
ExPosition-2.1.3/ExPosition/man/epGPCA.Rd | 9
ExPosition-2.1.3/ExPosition/man/epGraphs.Rd | 28 +-
ExPosition-2.1.3/ExPosition/man/epMCA.Rd | 6
ExPosition-2.1.3/ExPosition/man/epMDS.Rd | 27 +
ExPosition-2.1.3/ExPosition/man/epPCA.Rd | 7
ExPosition-2.1.3/ExPosition/man/expo.scale.Rd |only
ExPosition-2.1.3/ExPosition/man/makeDistancesAndWeights.Rd |only
ExPosition-2.1.3/ExPosition/man/mca.eigen.fix.Rd | 13
ExPosition-2.1.3/ExPosition/man/mdsSupplementalElementsPreProcessing.Rd |only
ExPosition-2.1.3/ExPosition/man/mdsTransform.Rd |only
ExPosition-2.1.3/ExPosition/man/nominalCheck.Rd |only
ExPosition-2.1.3/ExPosition/man/pcaSupplementaryColsPreProcessing.Rd |only
ExPosition-2.1.3/ExPosition/man/pcaSupplementaryRowsPreProcessing.Rd |only
ExPosition-2.1.3/ExPosition/man/pickSVD.Rd |only
ExPosition-2.1.3/ExPosition/man/rvCoeff.Rd |only
ExPosition-2.1.3/ExPosition/man/supplementalProjection.Rd |only
ExPosition-2.1.3/ExPosition/man/supplementaryCols.Rd |only
ExPosition-2.1.3/ExPosition/man/supplementaryRows.Rd |only
73 files changed, 442 insertions(+), 347 deletions(-)
Title: Read and Write SAS XPORT Files
Diff between SASxport versions 1.3.4 dated 2013-06-01 and 1.3.5 dated 2013-06-15
Description: This package provides functions for reading, listing the
contents of, and writing SAS xport format files. The functions
support reading and writing of either individual data frames or
sets of data frames. Further, a mechanism has been provided
for customizing how variables of different data types are
stored.
Author: Unless otherwise noted, the contents of this package were
written by Gregory R. Warnes
Maintainer: Gregory R. Warnes
ChangeLog | 25 ++++++
DESCRIPTION | 8 +-
MD5 | 50 +++++++------
NEWS | 8 ++
R/fstr.R | 6 +
R/lookup.xport.R | 1
R/read.xport.R | 122 ++++++++++++++++------------------
R/write.xport.R | 33 +++++----
inst/ChangeLog | 25 ++++++
inst/NEWS | 8 ++
src/SASxport.c | 5 +
src/writeSAS.c | 2
tests/Alfalfa_Test.Rout.save | 4 -
tests/Theoph.Rout.save | 4 -
tests/cars.Rout.save | 4 -
tests/testDates.Rout.save | 4 -
tests/testDuplicateNames.Rout.save | 4 -
tests/testEmpty.R |only
tests/testEmpty.Rout.save |only
tests/testManyNames.Rout.save | 4 -
tests/testNegative.Rout.save | 4 -
tests/testNumeric.Rout.save | 4 -
tests/testUnnamedComponents.Rout.save | 4 -
tests/test_as_is.Rout.save | 4 -
tests/test_fields.Rout.save | 4 -
tests/xport.Rout.save | 4 -
tests/xxx.Rout.save | 4 -
27 files changed, 211 insertions(+), 134 deletions(-)
Title: raster: Geographic data analysis and modeling
Diff between raster versions 2.1-25 dated 2013-04-12 and 2.1-37 dated 2013-06-15
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions and processing of very large files is
supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
raster-2.1-25/raster/man/shp.Rd |only
raster-2.1-37/raster/ChangeLog | 11
raster-2.1-37/raster/DESCRIPTION | 13
raster-2.1-37/raster/MD5 | 184 +++---
raster-2.1-37/raster/NAMESPACE | 2
raster-2.1-37/raster/R/AAAClasses.R | 34 -
raster-2.1-37/raster/R/aggregate.R | 10
raster-2.1-37/raster/R/artith.R | 20
raster-2.1-37/raster/R/brick.R | 3
raster-2.1-37/raster/R/calc.R | 2
raster-2.1-37/raster/R/canProcessInMemory.R | 4
raster-2.1-37/raster/R/cellValues.R | 2
raster-2.1-37/raster/R/compare.R | 55 +-
raster-2.1-37/raster/R/compareCRS.R | 13
raster-2.1-37/raster/R/connection.R | 109 +++-
raster-2.1-37/raster/R/crop.R | 2
raster-2.1-37/raster/R/crosstab.R | 39 -
raster-2.1-37/raster/R/cut.R | 2
raster-2.1-37/raster/R/depracated.R | 13
raster-2.1-37/raster/R/dim.R | 4
raster-2.1-37/raster/R/disaggregate.R | 2
raster-2.1-37/raster/R/extend.R | 10
raster-2.1-37/raster/R/extent.R | 76 ++
raster-2.1-37/raster/R/extractPolygons.R | 8
raster-2.1-37/raster/R/factor.R | 4
raster-2.1-37/raster/R/filler.R |only
raster-2.1-37/raster/R/focal.R | 18
raster-2.1-37/raster/R/focalWeight.R |only
raster-2.1-37/raster/R/getValuesBlock.R | 2
raster-2.1-37/raster/R/hdr.R | 13
raster-2.1-37/raster/R/hist.R | 8
raster-2.1-37/raster/R/imageplot2.R | 8
raster-2.1-37/raster/R/indexReplace.R | 140 +++--
raster-2.1-37/raster/R/indexReplaceBrick.R | 52 +
raster-2.1-37/raster/R/init.R | 2
raster-2.1-37/raster/R/kml.R | 7
raster-2.1-37/raster/R/layerize.R | 70 +-
raster-2.1-37/raster/R/math.R | 15
raster-2.1-37/raster/R/mean.R | 23
raster-2.1-37/raster/R/minValue.R | 103 ++-
raster-2.1-37/raster/R/netCDFread.R | 38 +
raster-2.1-37/raster/R/netCDFtoRasterCD.R | 35 -
raster-2.1-37/raster/R/notused.R | 4
raster-2.1-37/raster/R/raster.R | 9
raster-2.1-37/raster/R/rasterOptions.R | 4
raster-2.1-37/raster/R/rasterizePolygons.R | 21
raster-2.1-37/raster/R/ratify.R | 2
raster-2.1-37/raster/R/readAscii.R | 18
raster-2.1-37/raster/R/readCells.R | 14
raster-2.1-37/raster/R/readRasterBrick.R | 9
raster-2.1-37/raster/R/readRasterLayer.R | 42 -
raster-2.1-37/raster/R/rotate.R | 2
raster-2.1-37/raster/R/sampleRandom.R | 79 +-
raster-2.1-37/raster/R/show.R | 7
raster-2.1-37/raster/R/stretch.R | 7
raster-2.1-37/raster/R/subs.R | 2
raster-2.1-37/raster/R/subset.R | 2
raster-2.1-37/raster/R/summary-methods.R | 3
raster-2.1-37/raster/R/trim.R | 18
raster-2.1-37/raster/R/which.max.R |only
raster-2.1-37/raster/R/writeRaster.R | 2
raster-2.1-37/raster/R/zonal.R | 83 ++-
raster-2.1-37/raster/inst/doc/Raster.R | 732 +++++++++++++--------------
raster-2.1-37/raster/inst/doc/Raster.pdf |binary
raster-2.1-37/raster/inst/doc/functions.R | 686 ++++++++++++-------------
raster-2.1-37/raster/inst/doc/functions.Rnw | 54 +
raster-2.1-37/raster/inst/doc/functions.pdf |binary
raster-2.1-37/raster/inst/doc/rasterfile.R | 6
raster-2.1-37/raster/inst/doc/rasterfile.pdf |binary
raster-2.1-37/raster/man/area.Rd | 8
raster-2.1-37/raster/man/as.data.frame.Rd | 6
raster-2.1-37/raster/man/compare.Rd | 13
raster-2.1-37/raster/man/crosstab.Rd | 20
raster-2.1-37/raster/man/extend.Rd | 8
raster-2.1-37/raster/man/extent.Rd | 10
raster-2.1-37/raster/man/extract.Rd | 3
raster-2.1-37/raster/man/flip.Rd | 2
raster-2.1-37/raster/man/focal.Rd | 26
raster-2.1-37/raster/man/focalWeight.Rd |only
raster-2.1-37/raster/man/merge.Rd | 7
raster-2.1-37/raster/man/plotRGB.Rd | 6
raster-2.1-37/raster/man/predict.Rd | 38 +
raster-2.1-37/raster/man/programming.Rd | 18
raster-2.1-37/raster/man/projectRaster.Rd | 3
raster-2.1-37/raster/man/raster-package.Rd | 5
raster-2.1-37/raster/man/raster.Rd | 1
raster-2.1-37/raster/man/rasterize.Rd | 7
raster-2.1-37/raster/man/replacement.Rd | 9
raster-2.1-37/raster/man/shapefile.Rd |only
raster-2.1-37/raster/man/strech.Rd |only
raster-2.1-37/raster/man/subset.Rd | 20
raster-2.1-37/raster/man/trim.Rd | 35 -
raster-2.1-37/raster/man/which.Rd | 2
raster-2.1-37/raster/man/which.minmax.Rd |only
raster-2.1-37/raster/man/zonal.Rd | 8
raster-2.1-37/raster/src/edge.c | 73 +-
raster-2.1-37/raster/src/terrain.c | 2
97 files changed, 1928 insertions(+), 1364 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
ordered observations)
Diff between zoo versions 1.7-9 dated 2012-11-04 and 1.7-10 dated 2013-06-14
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre], Gabor Grothendieck [aut], Jeffrey A.
Ryan [aut], Felix Andrews [ctb]
Maintainer: Achim Zeileis
DESCRIPTION | 11 ++---
MD5 | 61 +++++++++++++++--------------
NAMESPACE | 71 ++++++++++++++++++++++++++--------
NEWS | 31 ++++++++++++++
R/aggregate.zoo.R | 5 +-
R/ggplot2.zoo.R | 31 +++++++++++++-
R/merge.zoo.R | 12 +++--
R/na.fill.R | 4 -
R/plot.zoo.R | 2
R/yearmon.R | 28 +++++++++----
R/yearqtr.R | 28 +++++++++----
R/zoo.R | 6 ++
inst/doc/zoo-design.R |only
inst/doc/zoo-design.pdf |binary
inst/doc/zoo-faq.R |only
inst/doc/zoo-faq.Rnw | 66 +++++++++++++++++--------------
inst/doc/zoo-faq.pdf |binary
inst/doc/zoo-quickref.R |only
inst/doc/zoo-quickref.pdf |binary
inst/doc/zoo-read.R |only
inst/doc/zoo-read.pdf |binary
inst/doc/zoo.R |only
inst/doc/zoo.pdf |binary
man/ggplot2.zoo.Rd | 57 +++++++++++++++++++--------
man/yearmon.Rd | 1
man/yearqtr.Rd | 1
man/zoo.Rd | 1
man/zooreg.Rd | 3 -
tests/Examples/zoo-Ex.Rout.save | 68 +++++++++++++++++++-------------
tests/as.Date.Rout.save | 18 +++-----
tests/bugfixes.Rout.save | 9 +---
tests/vignette-zoo-quickref.Rout.save | 11 ++---
tests/vignette-zoo.Rout.save | 20 ++++-----
vignettes/zoo-faq.Rnw | 66 +++++++++++++++++--------------
34 files changed, 399 insertions(+), 212 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3-1 dated 2013-06-11 and 1.3-2 dated 2013-06-14
Description: Spatial and spatio-temporal modelling of point patterns
using the log-Gaussian Cox process
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle.
Additional code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NEWS | 8 ++++++++
R/SpatioTemporalPlusParameters.R | 32 +++++++++++++++++++++++---------
R/lgcpMethods.R | 2 +-
5 files changed, 39 insertions(+), 17 deletions(-)
Title: Analysis of binary character evolution
Diff between corHMM versions 1.10 dated 2013-05-13 and 1.11 dated 2013-06-14
Description: Fits a hidden rates model that allows different transition
rate classes on different portions of a phylogeny by treating
rate classes as hidden states in a Markov process and various
other functions for evaluating models of binary character
evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 13 ++---
MD5 | 12 ++---
R/ancRECON.R | 69 ++++++++++-------------------
R/corHMM.R | 124 ++++++++++++++++++++++++++++++++++++++++++++++++-----
R/rate.mat.maker.R | 8 +++
man/corDISC.Rd | 2
man/corHMM.Rd | 2
7 files changed, 158 insertions(+), 72 deletions(-)
Title: Selection and/or Smoothing of Ordinal Predictors
Diff between ordPens versions 0.1-7 dated 2011-11-02 and 0.2-1 dated 2013-06-14
Description: Selection and/or smoothing of ordinally scaled independent
variables using a group lasso or generalized ridge penalty
Author: Jan Gertheiss
Maintainer: Jan Gertheiss
DESCRIPTION | 16 +-
MD5 | 25 ++--
NAMESPACE |only
R/ordAOV.R |only
R/ordPens-internal.R | 257 +++++++++++++++++++++++++++++++++++++++++++++++-
R/ordSelect.R | 2
R/ordSmooth.R | 2
R/plot.ordPen.R | 6 -
man/ordAOV.Rd |only
man/ordPens-internal.Rd | 8 +
man/ordPens-package.Rd | 27 ++---
man/ordSelect.Rd | 18 +--
man/ordSmooth.Rd | 7 -
man/plot.ordPen.Rd | 2
man/predict.ordPen.Rd | 2
15 files changed, 320 insertions(+), 52 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.8-1 dated 2013-04-06 and 0.8-3 dated 2013-06-14
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests,
adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer
gMCP-0.8-1/gMCP/inst/doc/gMCP.loa |only
gMCP-0.8-1/gMCP/inst/doc/gMCP.lof |only
gMCP-0.8-1/gMCP/inst/doc/gMCP.lot |only
gMCP-0.8-3/gMCP/DESCRIPTION | 6
gMCP-0.8-3/gMCP/MD5 | 74 ++---
gMCP-0.8-3/gMCP/NEWS | 34 ++
gMCP-0.8-3/gMCP/R/calcPower.R | 15 -
gMCP-0.8-3/gMCP/R/graph2latex.R | 143 +++++++++-
gMCP-0.8-3/gMCP/R/graphTest.R | 4
gMCP-0.8-3/gMCP/R/misc.R | 2
gMCP-0.8-3/gMCP/R/startGUIs.R | 17 -
gMCP-0.8-3/gMCP/TODO | 32 --
gMCP-0.8-3/gMCP/inst/doc/AQuickStart.R |only
gMCP-0.8-3/gMCP/inst/doc/AQuickStart.Rnw | 2
gMCP-0.8-3/gMCP/inst/doc/AQuickStart.pdf |binary
gMCP-0.8-3/gMCP/inst/doc/Makefile | 2
gMCP-0.8-3/gMCP/inst/doc/figure/unnamed-chunk-23.pdf |binary
gMCP-0.8-3/gMCP/inst/doc/gMCP.R |only
gMCP-0.8-3/gMCP/inst/doc/gMCP.pdf |binary
gMCP-0.8-3/gMCP/inst/doc/gMCP/gMCP.Rnw | 2
gMCP-0.8-3/gMCP/inst/doc/parametric.R |only
gMCP-0.8-3/gMCP/inst/doc/parametric.Rnw | 2
gMCP-0.8-3/gMCP/inst/doc/parametric.pdf |binary
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/config/GeneralConfig.java | 9
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java | 2
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/MenuBarMGraph.java | 4
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/dialogs/PowerDialogParameterUncertainty.java | 110 ++++++-
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/graph/Edge.java | 9
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/graph/NetList.java | 2
gMCP-0.8-3/gMCP/inst/java-src/org/af/gMCP/gui/graph/Node.java | 5
gMCP-0.8-3/gMCP/inst/java/gsrmtp.jar |binary
gMCP-0.8-3/gMCP/inst/unitTests/runit.LaTeX.R | 5
gMCP-0.8-3/gMCP/inst/unitTests/runit.power.R | 2
gMCP-0.8-3/gMCP/man/calcPower.Rd | 15 -
gMCP-0.8-3/gMCP/man/confint.Rd | 3
gMCP-0.8-3/gMCP/man/corMatWizard.Rd | 3
gMCP-0.8-3/gMCP/man/doUnitTestsForGMCP.Rd | 6
gMCP-0.8-3/gMCP/man/graph2latex.Rd | 6
gMCP-0.8-3/gMCP/man/graphGUI.Rd | 33 +-
gMCP-0.8-3/gMCP/man/graphTest.Rd | 10
gMCP-0.8-3/gMCP/man/secondStageTest.Rd | 3
41 files changed, 422 insertions(+), 140 deletions(-)
Title: Response surface analysis
Diff between RSA versions 0.6.1 dated 2013-03-28 and 0.7.1 dated 2013-06-14
Description: Advanced response surface analysis. The main function RSA
compares several nested models (full polynomial, shifted and
rotated squared differences, shifted squared differences,
rising ridge surfaces, basic squared differences) and provides
plotting functions for 3d wireframe surfaces, interactive 3d
plots, and contour plots. Calculates many surface parameters
(a1 to a4, principal axes, stationary point, eigenvalues) and
provides standard, robust, or bootstrapped standard errors and
confidence intervals for them.
Author: Felix Schönbrodt
Maintainer: Felix Schönbrodt
DESCRIPTION | 31 +++++-----
MD5 | 30 +++++----
NAMESPACE | 1
NEWS | 30 +++++++++
R/RSA.R | 170 +++++++++++++++++++++-----------------------------------
R/bootRSA.R | 10 +--
R/compare.R | 60 +++++++++++++++++--
R/demoRSA.R | 2
R/getPar.R | 13 +++-
R/movieRSA.R |only
R/plot.RSA.R | 90 +++++++++++++++++++----------
R/print.RSA.R | 2
man/RSA.Rd | 23 +++++--
man/bootRSA.Rd | 10 +--
man/getPar.Rd | 4 -
man/movieRSA.Rd |only
man/plotRSA.Rd | 30 ++++-----
17 files changed, 300 insertions(+), 206 deletions(-)
Title: MultiChIPmixHMM
Diff between MultiChIPmixHMM versions 3.0 dated 2013-02-04 and 4.0 dated 2013-06-14
More information about MultiChIPmixHMM at CRAN
Description: Linear regression mixture model to ChIP-chip data
analysis, taking into account the dependence (HMM), and for
multiple biological samples.
Author: Caroline Berard
Maintainer: Caroline Berard
MultiChIPmixHMM-3.0/MultiChIPmixHMM/data/dataHMM_Rep1.RData |only
MultiChIPmixHMM-3.0/MultiChIPmixHMM/data/dataHMM_Rep2.RData |only
MultiChIPmixHMM-3.0/MultiChIPmixHMM/man/dataHMM_Rep1.Rd |only
MultiChIPmixHMM-3.0/MultiChIPmixHMM/man/dataHMM_Rep2.Rd |only
MultiChIPmixHMM-4.0/MultiChIPmixHMM/DESCRIPTION | 10 +-
MultiChIPmixHMM-4.0/MultiChIPmixHMM/MD5 | 31 ++++---
MultiChIPmixHMM-4.0/MultiChIPmixHMM/R/Internal.R | 48 +++++++++++-
MultiChIPmixHMM-4.0/MultiChIPmixHMM/R/multiChIPmix.R | 31 +++----
MultiChIPmixHMM-4.0/MultiChIPmixHMM/R/multiChIPmixHMM.R | 18 +++-
MultiChIPmixHMM-4.0/MultiChIPmixHMM/data/data_Rep1.RData |binary
MultiChIPmixHMM-4.0/MultiChIPmixHMM/data/data_Rep2.RData |binary
MultiChIPmixHMM-4.0/MultiChIPmixHMM/inst |only
MultiChIPmixHMM-4.0/MultiChIPmixHMM/man/data_Rep1.Rd | 22 ++---
MultiChIPmixHMM-4.0/MultiChIPmixHMM/man/data_Rep2.Rd | 22 ++---
MultiChIPmixHMM-4.0/MultiChIPmixHMM/man/multiChIPmix.Rd | 25 +++---
MultiChIPmixHMM-4.0/MultiChIPmixHMM/man/multiChIPmixHMM.Rd | 29 ++++---
MultiChIPmixHMM-4.0/MultiChIPmixHMM/vignettes |only
MultiChIPmixHMM-4.0/MultiChIPmixHMM/zzz.r |only
18 files changed, 145 insertions(+), 91 deletions(-)
Permanent link
Title: Calibration functions for analytical chemistry
Diff between chemCal versions 0.1-28 dated 2012-09-12 and 0.1-29 dated 2013-06-14
Description: chemCal provides simple functions for plotting linear
calibration functions and estimating standard errors for
measurements according to the Handbook of Chemometrics and
Qualimetrics: Part A by Massart et al. There are also functions
estimating the limit of detection (LOD) and limit of
quantification (LOQ). The functions work on model objects from
- optionally weighted - linear regression (lm) or robust linear
regression (rlm from the MASS package).
Author: Johannes Ranke
Maintainer: Johannes Ranke
DESCRIPTION | 13 +++++++------
MD5 | 10 +++++-----
data/din32645.rda |binary
inst/doc/chemCal.pdf |binary
vignettes/chemCal-001.pdf |binary
vignettes/chemCal-002.pdf |binary
6 files changed, 12 insertions(+), 11 deletions(-)
Title: Tools to analyse repertory grid data
Diff between OpenRepGrid versions 0.1.7 dated 2013-05-26 and 0.1.8 dated 2013-06-14
Description: Tools to analyse repertory grid data
Author: Mark Heckmann
Maintainer: Mark Heckmann
CHANGELOG | 10 ++++-
DESCRIPTION | 8 ++--
MD5 | 17 ++++----
NAMESPACE | 39 ++++++++++---------
NEWS | 4 ++
R/calc.r | 53 +++++++++++++++++---------
R/import.r | 65 ++++++++++++++++++++++++++------
man/clusterBoot.Rd | 67 ++++++++++++++++++++++------------
man/importTxtInternal.Rd | 3 +
man/multigridFileToSinglegridFiles.Rd |only
10 files changed, 181 insertions(+), 85 deletions(-)
Title: Miscellaneous Functions
Diff between miscF versions 0.1-1 dated 2013-05-01 and 0.1-2 dated 2013-06-14
Description: Various functions for random number generation, density
estimation, classification, curve fitting, and spatial data
analysis.
Author: Dai Feng
Maintainer: Dai Feng
ChangeLog | 11 ++
DESCRIPTION | 10 +-
MD5 | 11 +-
R/mvt.mcmc.R | 202 ++++++++++++-------------------------------------------
man/mvt.mcmc.Rd | 2
src/Makevars |only
src/Makevars.win |only
src/mvtmcmc.cpp |only
8 files changed, 68 insertions(+), 168 deletions(-)
Title: Least-squares means
Diff between lsmeans versions 1.06-05 dated 2013-02-14 and 1.06-06 dated 2013-06-14
Description: This package provides the function 'lsmeans' for
outputting so-called least-squares means for factor
combinations in an 'lm', 'lme', or 'lmer' object. It can also
compute contrasts or linear combinations of these least-squares
means, and several standard contrast families are provided.
Author: Russell V. Lenth
Maintainer: Russ Lenth
DESCRIPTION | 9 +++++----
MD5 | 9 +++++----
R/lsmeans.R | 19 +++++++------------
inst/NEWS | 5 +++++
inst/doc/using-lsmeans.R |only
lsmeans-Ex.R | 25 ++++++++++++++++++++++---
6 files changed, 44 insertions(+), 23 deletions(-)
Title: Foreach parallel adaptor for the Rmpi package
Diff between doMPI versions 0.1-5 dated 2010-08-10 and 0.2 dated 2013-06-14
Description: Provides a parallel backend for the %dopar% function using
the Rmpi package.
Author: Steve Weston
Maintainer: Steve Weston
doMPI-0.1-5/doMPI/R/nwsworkers.R |only
doMPI-0.1-5/doMPI/README |only
doMPI-0.1-5/doMPI/man/startNWScluster.Rd |only
doMPI-0.2/doMPI/DESCRIPTION | 16 +++---
doMPI-0.2/doMPI/MD5 |only
doMPI-0.2/doMPI/NAMESPACE | 11 ++--
doMPI-0.2/doMPI/NEWS | 12 ++++
doMPI-0.2/doMPI/R/doMPI.R | 66 ++++++++++++++++++++++---
doMPI-0.2/doMPI/R/dompiWorkerLoop.R | 60 ++++++++++++++++++----
doMPI-0.2/doMPI/R/exportDoMPI.R |only
doMPI-0.2/doMPI/R/master.R | 21 ++++++-
doMPI-0.2/doMPI/R/mpiworkers.R | 8 +--
doMPI-0.2/doMPI/R/profile.R | 2
doMPI-0.2/doMPI/R/rng.R |only
doMPI-0.2/doMPI/R/workers.R | 2
doMPI-0.2/doMPI/inst/RMPIworker.R | 31 +++--------
doMPI-0.2/doMPI/inst/doc/doMPI.R |only
doMPI-0.2/doMPI/inst/doc/doMPI.Rnw | 49 +++++++-----------
doMPI-0.2/doMPI/inst/doc/doMPI.pdf |binary
doMPI-0.2/doMPI/inst/examples/clusterexport.R |only
doMPI-0.2/doMPI/inst/examples/clusterexport2.R |only
doMPI-0.2/doMPI/inst/examples/file.R | 3 +
doMPI-0.2/doMPI/inst/examples/file2.R |only
doMPI-0.2/doMPI/inst/examples/initEnvir.R | 22 ++++++--
doMPI-0.2/doMPI/inst/examples/pi2.R | 2
doMPI-0.2/doMPI/inst/examples/prng.R |only
doMPI-0.2/doMPI/inst/examples/prng2.R |only
doMPI-0.2/doMPI/inst/examples/resample.R | 1
doMPI-0.2/doMPI/man/doMPI-package.Rd | 22 ++++++++
doMPI-0.2/doMPI/man/dompiWorkerLoop.Rd | 3 -
doMPI-0.2/doMPI/man/exportDoMPI.Rd |only
doMPI-0.2/doMPI/man/registerDoMPI.Rd | 3 -
doMPI-0.2/doMPI/man/setRngDoMPI.Rd |only
doMPI-0.2/doMPI/man/startMPIcluster.Rd | 4 -
doMPI-0.2/doMPI/test |only
doMPI-0.2/doMPI/vignettes |only
36 files changed, 236 insertions(+), 102 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-03 0.6
2013-04-03 0.7
2012-09-18 0.4
2012-06-21 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-23 0.48
2012-04-21 0.47
2012-01-02 0.46
2011-10-20 0.45
2011-03-24 0.43
2010-12-23 0.41
2010-11-18 0.40
2010-10-09 0.34
2010-07-24 0.32
2010-01-05 0.20.2
2009-12-28 0.20.1
Title: R commander Depth Tools Plug-In
Diff between RcmdrPlugin.depthTools versions 1.2 dated 2013-04-03 and 1.3 dated 2013-06-13
More information about RcmdrPlugin.depthTools at CRAN
Description: This package provides an Rcmdr plug-in based on the
depthTools package, which implements different robust
statistical tools for the description and analysis of gene
expression data based on the Modified Band Depth, namely, the
scale curves for visualizing the dispersion of one or various
groups of samples (e.g. types of tumors), a rank test to decide
whether two groups of samples come from a single distribution
and two methods of supervised classification techniques, the DS
and TAD methods.
Author: Sara Lopez-Pintado
Maintainer: Aurora Torrente
DESCRIPTION | 6 -
MD5 | 10 +-
R/RcmdrPlugin.depthTools.R | 158 +++++++++++++++++++++++++++++++++++++++++----
inst/etc/menus.txt | 2
man/computeMBD.Rd | 2
man/plotCentralCurves.Rd | 2
6 files changed, 158 insertions(+), 22 deletions(-)
Permanent link
Title: Depth Tools Package
Diff between depthTools versions 0.3 dated 2013-04-03 and 0.4 dated 2013-06-13
Description: depthTools is a package that implements different
statistical tools for the description and analysis of gene
expression data based on the concept of data depth, namely, the
scale curves for visualizing the dispersion of one or various
groups of samples (e.g. types of tumors), a rank test to decide
whether two groups of samples come from a single distribution
and two methods of supervised classification techniques, the DS
and TAD methods. All these techniques are based on the Modified
Band Depth, which is a recent notion of depth with a low
computational cost, what renders it very appropriate for high
dimensional data such as gene expression data.
Author: Sara Lopez-Pintado
Maintainer: Aurora Torrente
DESCRIPTION | 8 +-
MD5 | 14 ++--
R/centralPlot.R | 47 +++++++++++---
R/mbd.R | 170 +++++++++++++++++++++++++++++++++++++++--------------
R/tmean.R | 62 +++++++++++++++++--
man/MBD.Rd | 39 ++++++------
man/centralPlot.Rd | 23 ++++---
man/tmean.Rd | 22 +++---
8 files changed, 277 insertions(+), 108 deletions(-)
Title: Companion package to "Learning Statistics with R"
Diff between lsr versions 0.2.3 dated 2013-04-19 and 0.2.4 dated 2013-06-13
Description: Functions that I have found useful for teaching purposes.
Author: Daniel Navarro
Maintainer: Daniel Navarro
DESCRIPTION | 8 +-
MD5 | 12 +--
NEWS | 6 +
R/lsr.R | 173 +++++++++++++++++++++++++++++++----------------------
inst/CITATION | 2
man/cohensD.Rd | 3
man/lsr-package.Rd | 4 -
7 files changed, 125 insertions(+), 83 deletions(-)
Title: diversitree: comparative phylogenetic analyses of
diversification
Diff between diversitree versions 0.9-5 dated 2013-06-13 and 0.9-6 dated 2013-06-13
Description: Contains a number of comparative phylogenetic methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of BiSSE (Binary State
Speciation and Extinction; Maddison et al. 2007: Syst. Biol.
56: 701) and its unresolved tree extensions (FitzJohn et al.
2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation
and Extinction), QuaSSE (Quantitative State Speciation and
Extinction; FitzJohn 2010: Syst. Biol. 59: 619), GeoSSE
(Geographic State Speciation and Extinction; Goldberg et al.
2011: Syst. Biol. 60: 451), and BiSSE-ness (Magnuson-Ford and
Otto 2012: Am. Nat.) Other included methods include Markov
models of discrete and continuous trait evolution and constant
rate speciation and extinction.
Author: Richard G. FitzJohn
Maintainer: Richard G. FitzJohn
DESCRIPTION | 6 +++---
MD5 | 6 +++---
src/Makevars.in | 2 +-
src/TimeMachine.cpp | 2 +-
4 files changed, 8 insertions(+), 8 deletions(-)
Title: Flexible regression models for survival data.
Diff between timereg versions 1.7.6 dated 2013-05-23 and 1.7.7 dated 2013-06-13
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparametric proportional odds model, fast cumulative
residuals, excess risk models and more. Flexible competing
risks regression including GOF-tests. Two-stage frailty
modelling. PLS for the additive risk model. Lasso in ahaz
package.
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Maintainer: Thomas Scheike
DESCRIPTION | 29 ++++++++++++----------
MD5 | 27 +++++++++++++++------
NAMESPACE | 62 ++++++++++++++++++++++++-------------------------
R/dynadd.r |only
R/new.cox-aalen.r | 2 -
R/new.dynreg.r |only
R/new.prop-excess.r |only
R/new.timecox.r |only
R/prop-excess.r |only
R/timecox.r |only
R/two-stage-reg.r | 15 +++++++----
man/cox.Rd |only
man/dynreg.Rd |only
man/internal-addreg.Rd | 6 ++++
man/plot.dynreg.Rd |only
man/prop.excess.Rd |only
man/timecox.Rd |only
man/two.stage.reg.Rd | 6 ++--
src/Makevars | 24 +++++++++---------
src/cox-aalen.c | 12 ++++-----
20 files changed, 103 insertions(+), 80 deletions(-)
Title: Parameter estimation and prediction for hidden Markov and
semi-Markov models for data with multiple observation
sequences.
Diff between mhsmm versions 0.4.8 dated 2013-01-26 and 0.4.10 dated 2013-06-13
Description: Parameter estimation and prediction for hidden Markov and
semi-Markov models for data with multiple observation
sequences. Suitable for equidistant time series data, with
multivariate and/or missing data.
Author: Jared O'Connell
Maintainer: Jared O'Connell
ChangeLog | 6 +++++-
DESCRIPTION | 7 ++++---
MD5 | 26 ++++++++++++++------------
R/hmm_functions.R | 3 ++-
R/hsmm_functions.R | 3 ++-
inst/doc/DHMM1.R |only
inst/doc/DHMM2.R |only
inst/doc/DHMM2.pdf |binary
man/addStates.Rd | 9 ++++-----
man/hsmmfit.Rd | 3 ++-
man/hsmmspec.Rd | 3 ++-
man/smooth.discrete.Rd | 3 ++-
mhsmm-Ex.R | 5 +++--
vignettes/fig/dhmm-clsfig1.pdf |binary
vignettes/fig/dhmm-clsfig2.pdf |binary
15 files changed, 40 insertions(+), 28 deletions(-)
Title: diversitree: comparative phylogenetic analyses of
diversification
Diff between diversitree versions 0.9-3 dated 2012-05-08 and 0.9-5 dated 2013-06-13
Description: Contains a number of comparative phylogenetic methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of BiSSE (Binary State
Speciation and Extinction; Maddison et al. 2007: Syst. Biol.
56: 701) and its unresolved tree extensions (FitzJohn et al.
2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation
and Extinction), QuaSSE (Quantitative State Speciation and
Extinction; FitzJohn 2010: Syst. Biol. 59: 619), GeoSSE
(Geographic State Speciation and Extinction; Goldberg et al.
2011: Syst. Biol. 60: 451), and BiSSE-ness (Magnuson-Ford and
Otto 2012: Am. Nat.) Other included methods include Markov
models of discrete and continuous trait evolution and constant
rate speciation and extinction.
Author: Richard G. FitzJohn
Maintainer: Richard G. FitzJohn
diversitree-0.9-3/diversitree/R/cvodes.R |only
diversitree-0.9-3/diversitree/R/diversitree-branches-C.R |only
diversitree-0.9-3/diversitree/R/mle-tgp.R |only
diversitree-0.9-3/diversitree/R/model-linear-deriv.R |only
diversitree-0.9-3/diversitree/R/model-mkn-exp.R |only
diversitree-0.9-3/diversitree/cvodes-notes.txt |only
diversitree-0.9-3/diversitree/inst/include |only
diversitree-0.9-3/diversitree/man/make.mkn.deriv.Rd |only
diversitree-0.9-3/diversitree/man/time.Rd |only
diversitree-0.9-3/diversitree/src/cvodes |only
diversitree-0.9-3/diversitree/src/cvodes_all_branches.c |only
diversitree-0.9-3/diversitree/src/cvodes_all_branches.h |only
diversitree-0.9-3/diversitree/src/cvodes_asr_marginal.c |only
diversitree-0.9-3/diversitree/src/cvodes_interface.c |only
diversitree-0.9-3/diversitree/src/cvodes_interface_fwd.c |only
diversitree-0.9-3/diversitree/src/cvodes_obj.c |only
diversitree-0.9-3/diversitree/src/cvodes_obj.h |only
diversitree-0.9-3/diversitree/src/cvodes_obj_fwd.c |only
diversitree-0.9-3/diversitree/src/cvodes_obj_fwd.h |only
diversitree-0.9-3/diversitree/src/linear-deriv.c |only
diversitree-0.9-3/diversitree/src/linear-deriv.h |only
diversitree-0.9-3/diversitree/src/mkn.c |only
diversitree-0.9-3/diversitree/src/mkn.h |only
diversitree-0.9-3/diversitree/src/util-complex.c |only
diversitree-0.9-3/diversitree/src/util-complex.h |only
diversitree-0.9-3/diversitree/src/util-linalg.c |only
diversitree-0.9-5/diversitree/ChangeLog | 4
diversitree-0.9-5/diversitree/DESCRIPTION | 22
diversitree-0.9-5/diversitree/MD5 | 355 -
diversitree-0.9-5/diversitree/NAMESPACE | 30
diversitree-0.9-5/diversitree/R/asr-geosse.R |only
diversitree-0.9-5/diversitree/R/asr-mkn.R | 4
diversitree-0.9-5/diversitree/R/asr-t.R |only
diversitree-0.9-5/diversitree/R/asr.R | 47
diversitree-0.9-5/diversitree/R/check.R | 48
diversitree-0.9-5/diversitree/R/clade-tree.R | 53
diversitree-0.9-5/diversitree/R/constrain.R | 73
diversitree-0.9-5/diversitree/R/continuous.R | 3
diversitree-0.9-5/diversitree/R/desolve.R | 131
diversitree-0.9-5/diversitree/R/diversitree-branches.R | 45
diversitree-0.9-5/diversitree/R/drop.tip.fixed.R | 5
diversitree-0.9-5/diversitree/R/dtlik.R | 8
diversitree-0.9-5/diversitree/R/expm.R |only
diversitree-0.9-5/diversitree/R/gslode.R |only
diversitree-0.9-5/diversitree/R/mcmc.R | 201
diversitree-0.9-5/diversitree/R/mle.R | 6
diversitree-0.9-5/diversitree/R/model-bd-nee.R | 15
diversitree-0.9-5/diversitree/R/model-bd-ode.R | 17
diversitree-0.9-5/diversitree/R/model-bd-t.R | 30
diversitree-0.9-5/diversitree/R/model-bd.R | 23
diversitree-0.9-5/diversitree/R/model-bisse-split.R | 29
diversitree-0.9-5/diversitree/R/model-bisse-t.R | 34
diversitree-0.9-5/diversitree/R/model-bisse.R | 21
diversitree-0.9-5/diversitree/R/model-bisseness.R | 43
diversitree-0.9-5/diversitree/R/model-classe.R | 12
diversitree-0.9-5/diversitree/R/model-geosse-split.R | 22
diversitree-0.9-5/diversitree/R/model-geosse.R | 61
diversitree-0.9-5/diversitree/R/model-mkn-expokit.R |only
diversitree-0.9-5/diversitree/R/model-mkn-meristic.R |only
diversitree-0.9-5/diversitree/R/model-mkn-multitrait.R | 10
diversitree-0.9-5/diversitree/R/model-mkn-ode.R | 15
diversitree-0.9-5/diversitree/R/model-mkn-pij.R |only
diversitree-0.9-5/diversitree/R/model-mkn.R | 32
diversitree-0.9-5/diversitree/R/model-musse-t.R | 95
diversitree-0.9-5/diversitree/R/model-musse.R | 48
diversitree-0.9-5/diversitree/R/model-quasse-common.R | 11
diversitree-0.9-5/diversitree/R/model-quasse-fftR.R | 10
diversitree-0.9-5/diversitree/R/model-quasse-mol.R | 2
diversitree-0.9-5/diversitree/R/model-quasse.R | 52
diversitree-0.9-5/diversitree/R/plot-alt-extra.R | 189
diversitree-0.9-5/diversitree/R/profiles-plot.R | 97
diversitree-0.9-5/diversitree/R/split.R | 49
diversitree-0.9-5/diversitree/R/t.R | 296
diversitree-0.9-5/diversitree/R/td.R | 16
diversitree-0.9-5/diversitree/R/time-machine.R |only
diversitree-0.9-5/diversitree/R/util-tree.R | 27
diversitree-0.9-5/diversitree/R/util.R | 34
diversitree-0.9-5/diversitree/R/zzz.R |only
diversitree-0.9-5/diversitree/README | 4
diversitree-0.9-5/diversitree/cleanup | 3
diversitree-0.9-5/diversitree/configure | 4162 ++++++-------
diversitree-0.9-5/diversitree/configure.ac | 64
diversitree-0.9-5/diversitree/configure.win | 2
diversitree-0.9-5/diversitree/inst/CITATION |only
diversitree-0.9-5/diversitree/inst/tests |only
diversitree-0.9-5/diversitree/man/big.brother.Rd | 3
diversitree-0.9-5/diversitree/man/check.Rd | 8
diversitree-0.9-5/diversitree/man/make.bd.Rd | 12
diversitree-0.9-5/diversitree/man/make.bd.t.Rd | 34
diversitree-0.9-5/diversitree/man/make.bisse.Rd | 52
diversitree-0.9-5/diversitree/man/make.bisse.split.Rd | 15
diversitree-0.9-5/diversitree/man/make.bisse.td.Rd | 39
diversitree-0.9-5/diversitree/man/make.bisseness.Rd | 8
diversitree-0.9-5/diversitree/man/make.bm.Rd | 6
diversitree-0.9-5/diversitree/man/make.geosse.split.Rd | 127
diversitree-0.9-5/diversitree/man/make.mkn.Rd | 5
diversitree-0.9-5/diversitree/man/make.musse.multitrait.Rd | 4
diversitree-0.9-5/diversitree/man/make.musse.td.Rd | 11
diversitree-0.9-5/diversitree/man/make.prior.Rd | 3
diversitree-0.9-5/diversitree/man/make.quasse.Rd | 2
diversitree-0.9-5/diversitree/man/mcmc.Rd | 37
diversitree-0.9-5/diversitree/man/profiles.plot.Rd | 6
diversitree-0.9-5/diversitree/man/trait.plot.Rd | 21
diversitree-0.9-5/diversitree/man/utils.Rd |only
diversitree-0.9-5/diversitree/src/GslOdeBase.cpp |only
diversitree-0.9-5/diversitree/src/GslOdeBase.h |only
diversitree-0.9-5/diversitree/src/GslOdeCompiled.cpp |only
diversitree-0.9-5/diversitree/src/GslOdeCompiled.h |only
diversitree-0.9-5/diversitree/src/GslOdeR.cpp |only
diversitree-0.9-5/diversitree/src/GslOdeR.h |only
diversitree-0.9-5/diversitree/src/GslOdeTime.cpp |only
diversitree-0.9-5/diversitree/src/GslOdeTime.h |only
diversitree-0.9-5/diversitree/src/Makevars.in | 11
diversitree-0.9-5/diversitree/src/Makevars.win | 17
diversitree-0.9-5/diversitree/src/Spline.cpp |only
diversitree-0.9-5/diversitree/src/Spline.h |only
diversitree-0.9-5/diversitree/src/TimeMachine.cpp |only
diversitree-0.9-5/diversitree/src/TimeMachine.h |only
diversitree-0.9-5/diversitree/src/bd-eqs.c | 105
diversitree-0.9-5/diversitree/src/bisse-eqs.c | 190
diversitree-0.9-5/diversitree/src/bisseness-eqs.c | 48
diversitree-0.9-5/diversitree/src/classe-eqs.c | 52
diversitree-0.9-5/diversitree/src/config.h.in | 6
diversitree-0.9-5/diversitree/src/config.h.win | 3
diversitree-0.9-5/diversitree/src/continuous.c | 6
diversitree-0.9-5/diversitree/src/continuous.h | 4
diversitree-0.9-5/diversitree/src/derivs.c |only
diversitree-0.9-5/diversitree/src/derivs.h |only
diversitree-0.9-5/diversitree/src/dgexpvi.f |only
diversitree-0.9-5/diversitree/src/dsexpvi.f | 4
diversitree-0.9-5/diversitree/src/expm.f |only
diversitree-0.9-5/diversitree/src/geosse-eqs.c | 53
diversitree-0.9-5/diversitree/src/hdr.c |only
diversitree-0.9-5/diversitree/src/hdr.h |only
diversitree-0.9-5/diversitree/src/interface.cpp |only
diversitree-0.9-5/diversitree/src/mkn-eqs.c | 43
diversitree-0.9-5/diversitree/src/mkn-expokit.c |only
diversitree-0.9-5/diversitree/src/mkn-expokit.h |only
diversitree-0.9-5/diversitree/src/mkn-meristic-eqs.c |only
diversitree-0.9-5/diversitree/src/mkn-pij.c |only
diversitree-0.9-5/diversitree/src/mkn-pij.h |only
diversitree-0.9-5/diversitree/src/musse-eqs.c | 178
diversitree-0.9-5/diversitree/src/quasse-eqs-mol.c | 1
diversitree-0.9-5/diversitree/src/util-matrix.c | 50
diversitree-0.9-5/diversitree/src/util-matrix.h | 7
diversitree-0.9-5/diversitree/src/util-splines.c |only
diversitree-0.9-5/diversitree/src/util-splines.h |only
diversitree-0.9-5/diversitree/src/util.c | 57
diversitree-0.9-5/diversitree/src/util.h | 21
149 files changed, 3910 insertions(+), 3899 deletions(-)
Title: Testset for differential equations
Diff between deTestSet versions 1.0 dated 2011-12-20 and 1.1 dated 2013-06-13
Description: Solvers and testset for stiff and nonstiff differential
equations, and differential algebraic equations
Author: Karline Soetaert
Maintainer: Karline Soetaert
DESCRIPTION | 21 +-
MD5 | 162 +++++++--------
R/bimd.R | 2
R/dae.R | 11 -
R/dopri5.R | 8
R/ex_andrews.R | 81 ++++++-
R/ex_beam.R | 32 ++-
R/ex_caraxis.R | 51 +++-
R/ex_crank.R | 53 ++++-
R/ex_e5.R | 28 ++
R/ex_emep.R | 48 ++++
R/ex_fekete.R | 39 ++-
R/ex_hires.R | 154 +++++++++-----
R/ex_nand.R | 32 ++-
R/ex_orego.R | 31 ++
R/ex_pleiades.R | 35 ++-
R/ex_pollution.R | 46 +++-
R/ex_reference.R | 22 +-
R/ex_ring.R | 36 ++-
R/ex_rober.R | 33 ++-
R/ex_transistor.R | 171 +++++++++-------
R/ex_tube.R | 44 +++-
R/ex_twobit.R | 39 ++-
R/ex_vdpol.R | 28 ++
R/ex_wheelset.R | 30 ++
R/functions.R | 26 ++
R/gam.R | 8
inst/doc/car.f | 2
inst/doc/deTestSet.R |only
inst/doc/deTestSet.Rnw | 12 -
inst/doc/deTestSet.pdf |binary
man/bimd.Rd | 2
man/dae.Rd | 2
man/deTestSet.Rd | 2
man/dopri5.Rd | 9
man/dopri853.Rd | 3
man/ex_E5.Rd | 10
man/ex_andrews.Rd | 183 ++++++++---------
man/ex_beam.Rd | 139 +++++++------
man/ex_caraxis.Rd | 151 +++++++-------
man/ex_crank.Rd | 182 +++++++++--------
man/ex_emep.Rd | 204 ++++++++++---------
man/ex_fekete.Rd | 144 +++++++------
man/ex_hires.Rd | 196 +++++++++---------
man/ex_nand.Rd | 162 ++++++++-------
man/ex_orego.Rd | 15 +
man/ex_pleiades.Rd | 147 +++++++-------
man/ex_pollution.Rd | 179 +++++++++--------
man/ex_reference.Rd | 2
man/ex_ring.Rd | 213 ++++++++++----------
man/ex_rober.Rd | 9
man/ex_transistor.Rd | 164 ++++++++-------
man/ex_tube.Rd | 158 ++++++++-------
man/ex_twobit.Rd | 167 ++++++++-------
man/ex_vdpol.Rd | 17 +
man/ex_wheelset.Rd | 166 ++++++++-------
man/gamd.Rd | 4
man/mebdfi.Rd | 2
src/Ex_andrews.f | 49 +++-
src/Ex_beam.f | 4
src/Ex_crank.f | 8
src/Ex_emep.f | 67 +++++-
src/Ex_hires.f | 2
src/Ex_nand.f | 1
src/Ex_pleiades.f | 4
src/Ex_pollution.f | 52 ++++
src/Ex_ring.f | 4
src/Ex_transistor.f | 19 -
src/Ex_tube.f | 5
src/Ex_twobit.f | 55 +++--
src/Ex_wheelset.f | 7
src/bimd.f | 296 ++++++++++------------------
src/bimda.f | 10
src/call_dopri.c | 7
src/call_gam.c | 159 +++++++--------
src/call_mebdfi.c | 7
src/cashkarp.f | 416 +++++++++++++++++++--------------------
src/de_utils.c | 47 ++++
src/dopri6.f | 73 ++----
src/dopri8.f | 79 ++-----
src/errmsg.f |only
src/gamd.f90 | 202 +++++++++----------
src/mebdfi.f | 512 ++++++++++++-------------------------------------
83 files changed, 3249 insertions(+), 2753 deletions(-)
Title: Solar Photovoltaic Systems
Diff between solaR versions 0.33 dated 2012-08-16 and 0.36 dated 2013-06-13
Description: Calculation methods of solar radiation and performance of
photovoltaic systems from daily and intradaily irradiation data
sources.
Author: Oscar Perpiñán Lamigueiro
Maintainer: Oscar Perpiñán Lamigueiro
solaR-0.33/solaR/NEWS |only
solaR-0.36/solaR/ChangeLog |only
solaR-0.36/solaR/DESCRIPTION | 9
solaR-0.36/solaR/MD5 | 51 -
solaR-0.36/solaR/NAMESPACE | 217 ++--
solaR-0.36/solaR/R/AllMethods.R | 1316 -----------------------------
solaR-0.36/solaR/R/HQCurve.R | 28
solaR-0.36/solaR/R/NmgSFB.R | 179 +--
solaR-0.36/solaR/R/asDataFrame.R |only
solaR-0.36/solaR/R/asZoo.R |only
solaR-0.36/solaR/R/calcG0.R | 375 ++++----
solaR-0.36/solaR/R/compare.R |only
solaR-0.36/solaR/R/horizon.R |only
solaR-0.36/solaR/R/levelplot.R |only
solaR-0.36/solaR/R/losses.R |only
solaR-0.36/solaR/R/markovG0.R |only
solaR-0.36/solaR/R/mergeSolar.R |only
solaR-0.36/solaR/R/shadeplot.R |only
solaR-0.36/solaR/R/show.R |only
solaR-0.36/solaR/R/splom.R |only
solaR-0.36/solaR/R/window.R |only
solaR-0.36/solaR/R/writeSolar.R |only
solaR-0.36/solaR/R/xyplot.R |only
solaR-0.36/solaR/R/zzz.R | 2
solaR-0.36/solaR/data/MTM.RData |only
solaR-0.36/solaR/man/aguiar.Rd |only
solaR-0.36/solaR/man/calcG0.Rd | 93 +-
solaR-0.36/solaR/man/calcGef.Rd | 26
solaR-0.36/solaR/man/compare-methods.Rd | 1
solaR-0.36/solaR/man/local2UTC.Rd | 4
solaR-0.36/solaR/man/mergesolaR-methods.Rd | 1
solaR-0.36/solaR/man/prodGCPV.Rd | 32
solaR-0.36/solaR/man/readSIAR.Rd | 28
solaR-0.36/solaR/man/window-methods.Rd | 4
solaR-0.36/solaR/man/writeSolar.Rd |only
solaR-0.36/solaR/solaR-Ex.R | 239 ++---
36 files changed, 680 insertions(+), 1925 deletions(-)
Title: Positive definite sparse covariance estimators
Diff between PDSCE versions 1.1 dated 2012-08-25 and 1.2 dated 2013-06-13
Description: A package to compute and tune some positive definite and
sparse covariance estimators
Author: Adam J. Rothman
Maintainer: Adam J. Rothman
DESCRIPTION | 12 -
MD5 | 10 -
R/pdsoft.R | 18 +
R/safe.band.R | 9
man/PDSCE-package.Rd | 9
src/pdsc.c | 463 ++++++++++++++++++++++++++++++++++++---------------
6 files changed, 354 insertions(+), 167 deletions(-)
Title: Continuous Time Autoregressive Models
Diff between cts versions 1.0-15 dated 2013-04-08 and 1.0-16 dated 2013-06-13
Description: Continuous Time Autoregressive Models and the Kalman
Filter
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port
by Zhu Wang with contribution from John Nash.
Maintainer: Zhu Wang
DESCRIPTION | 6 +++---
MD5 | 49 +++++++++++++++++++++++++------------------------
NEWS | 4 ++++
R/car.R | 8 +++++++-
inst/doc/kf.R |only
inst/doc/kf.pdf |binary
man/car.Rd | 2 +-
man/control.Rd | 8 +++++---
src/d1rply.f | 10 +++++-----
src/d2rply.f | 2 +-
src/d3rply.f | 4 ++--
src/d4rply.f | 2 +-
src/d5rply.f | 4 ++--
src/d7rply.f | 4 ++--
src/d9rply.f | 4 ++--
src/forecast.f | 6 +++++-
src/kfilsm.f | 3 ++-
src/kfilsm1.f | 3 ++-
src/resg0new.f | 3 ++-
src/resg1d.f | 3 ++-
src/resg1dpre.f | 3 ++-
src/resg1dpre1.f | 3 ++-
src/revg1.f | 3 ++-
src/setfor.f | 9 +++++----
src/setkfilsm.f | 3 ++-
src/setup1.f | 3 ++-
26 files changed, 88 insertions(+), 61 deletions(-)
Title: Companion to Applied Regression
Diff between car versions 2.0-17 dated 2013-05-05 and 2.0-18 dated 2013-06-13
Description: This package accompanies J. Fox and S. Weisberg, An R
Companion to Applied Regression, Second Edition, Sage, 2011.
Author: John Fox [aut, cre], Sanford Weisberg [aut], Douglas Bates
[ctb], Steve Ellison [ctb], David Firth [ctb], Michael Friendly
[ctb], Gregor Gorjanc [ctb], Spencer Graves [ctb], Richard
Heiberger [ctb], Rafael Laboissiere [ctb], Georges Monette
[ctb], Henric Nilsson [ctb], Derek Ogle [ctb], Brian Ripley
[ctb], Achim Zeileis [ctb], R-Core [ctb]
Maintainer: John Fox
DESCRIPTION | 13 +++--
MD5 | 112 +++++++++++++++++++++++++-------------------------
NAMESPACE | 5 +-
NEWS | 6 ++
R/Boot.R | 2
R/densityPlot.R |only
data/AMSsurvey.rda |binary
data/Adler.rda |binary
data/Angell.rda |binary
data/Anscombe.rda |binary
data/Baumann.rda |binary
data/Bfox.rda |binary
data/Blackmoor.rda |binary
data/Burt.rda |binary
data/CanPop.rda |binary
data/Chile.rda |binary
data/Chirot.rda |binary
data/Cowles.rda |binary
data/Davis.rda |binary
data/DavisThin.rda |binary
data/Depredations.rda |binary
data/Duncan.rda |binary
data/Ericksen.rda |binary
data/Florida.rda |binary
data/Freedman.rda |binary
data/Friendly.rda |binary
data/Ginzberg.rda |binary
data/Greene.rda |binary
data/Guyer.rda |binary
data/Hartnagel.rda |binary
data/Highway1.rda |binary
data/Leinhardt.rda |binary
data/Mandel.rda |binary
data/Migration.rda |binary
data/Moore.rda |binary
data/Mroz.rda |binary
data/OBrienKaiser.rda |binary
data/Ornstein.rda |binary
data/Pottery.rda |binary
data/Prestige.rda |binary
data/Quartet.rda |binary
data/Robey.rda |binary
data/SLID.rda |binary
data/Sahlins.rda |binary
data/Salaries.rda |binary
data/Soils.rda |binary
data/States.rda |binary
data/Transact.rda |binary
data/UN.rda |binary
data/USPop.rda |binary
data/Vocab.rda |binary
data/WeightLoss.rda |binary
data/Womenlf.rda |binary
data/Wool.rda |binary
man/car-package.Rd | 4 -
man/densityPlot.Rd |only
man/scatter3d.Rd | 5 +-
man/scatterplot.Rd | 3 -
58 files changed, 83 insertions(+), 67 deletions(-)
Title: Trust region nonlinear optimization, efficient for sparse
Hessians
Diff between trustOptim versions 0.8.0 dated 2012-12-28 and 0.8.1 dated 2013-06-12
Description: Trust region algorithm for nonlinear optimization. In
addition to being more stable and robust than optim, this
package includes methods that are scalable and efficient (in
terms of both speed and memory usage) when the Hessian is
sparse.
Author: Michael Braun
Maintainer: Michael Braun
trustOptim-0.8.0/trustOptim/inst/examples |only
trustOptim-0.8.1/trustOptim/DESCRIPTION | 13 +-
trustOptim-0.8.1/trustOptim/MD5 | 37 +++---
trustOptim-0.8.1/trustOptim/NEWS | 19 +++
trustOptim-0.8.1/trustOptim/R/demo_funcs.R |only
trustOptim-0.8.1/trustOptim/demo |only
trustOptim-0.8.1/trustOptim/inst/doc/trustOptim-vignette.R |only
trustOptim-0.8.1/trustOptim/inst/doc/trustOptim-vignette.pdf |binary
trustOptim-0.8.1/trustOptim/inst/include/CG-base.h | 62 +++++------
trustOptim-0.8.1/trustOptim/inst/include/CG-quasi.h | 2
trustOptim-0.8.1/trustOptim/inst/include/CG-sparse.h | 6 -
trustOptim-0.8.1/trustOptim/inst/include/Rfunc.cpp | 2
trustOptim-0.8.1/trustOptim/inst/include/RfuncHess.cpp | 2
trustOptim-0.8.1/trustOptim/inst/include/common_R.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/defines_optim.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/exceptions.hpp | 2
trustOptim-0.8.1/trustOptim/inst/include/include_eigen.hpp | 2
trustOptim-0.8.1/trustOptim/man/demo.funcs.Rd |only
trustOptim-0.8.1/trustOptim/man/trustOptim-package.Rd | 4
trustOptim-0.8.1/trustOptim/src/Rinterface.cpp | 5
20 files changed, 93 insertions(+), 67 deletions(-)
Title: Functions and Examples for "Software for Data Analysis"
Diff between SoDA versions 1.0-5 dated 2012-12-16 and 1.0-6 dated 2013-06-12
Description: Functions, examples and other software related to the book
"Software for Data Analysis: Programming with R". See
package?SoDA for an overview.
Author: John M Chambers
Maintainer: John M Chambers
DESCRIPTION | 11 ++++++-----
MD5 | 4 ++--
src/geodistv.f | 2 +-
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Transforms input data from a PMML perspective
Diff between pmmlTransformations versions 1.0 dated 2013-01-23 and 1.1 dated 2013-06-12
More information about pmmlTransformations at CRAN
Description: Allows for data to be transformed before using it to
construct models. Builds structures to allow functions in the
PMML package to output transformation details in addition to
the model in the resulting PMML file.
Author: Tridivesh Jena
Maintainer: Tridivesh Jena
DESCRIPTION | 11 ++++---
MD5 | 32 ++++++++++++----------
R/DiscretizeXform.R |only
R/Initialize.R | 45 +++++++++++++++++++++++--------
R/MapXform.R | 35 +++++++++++++++++++-----
R/MinMaxXform.R | 34 ++++++++++++++---------
R/NormDiscreteXform.R | 36 +++++++++++++++++++++----
R/RenameVar.R |only
R/WrapData.R | 22 +++++++++++++++
R/ZScoreXform.R | 53 +++++++++++++++++++++++++++----------
man/DiscretizeXform.Rd |only
man/Initialize.Rd | 3 ++
man/MapXform.Rd | 7 +++-
man/MinMaxXform.Rd | 10 +++++-
man/NormDiscreteXform.Rd | 10 +++++-
man/RenameVar.Rd |only
man/WrapData.Rd | 5 ++-
man/ZScoreXform.Rd | 10 +++++-
man/pmmlTransformations-package.Rd | 26 ++++++++++++------
19 files changed, 253 insertions(+), 86 deletions(-)
Permanent link
Title: Independent Components Analysis (ICA) based artifact correction.
Diff between icaOcularCorrection versions 1.3 dated 2011-11-03 and 2.1 dated 2013-06-12
More information about icaOcularCorrection at CRAN
Description: Removes eye-movement and other types of known (i.e.,
recorded) or unknown (i.e., not recorded) artifacts using the
fastICA package. The correction method proposed in this package
is largely based on the method described in on Flexer, Bauer,
Pripfl, and Dorffner (2005). The process of correcting electro-
and magneto-encephalographic data (EEG/MEG) begins by running
function ``icac'', which first performs independent components
analysis (ICA) to decompose the data frame into independent
components (ICs) using function ``fastICA'' from the package of
the same name. It then calculates for each trial the
correlation between each IC and each one of the noise signals
-- there can be one or more, e.g., vertical and horizontal
electro-oculograms (VEOG and HEOG), electro-myograms (EMG),
electro-cardiograms (ECG), galvanic skin responses (GSR), and
other noise signals. Subsequently, portions of an IC
corresponding to trials at which the correlation between it and
a noise signal was at or above threshold (set to 0.4 by
default; Flexer et al., 2005, p. 1001) are either zeroed-out in
the source matrix, ``S'', or subtracted from the data that was
passed to function ``icac''. The user can then identify which
ICs correlate with the noise signals the most by looking at the
summary of the ``icac'' object (using function
``summary.icac''), the scalp topography of the ICs (using
function ``topo.ic''), the time courses of the ICs (using
functions (``plot.tric'') and ``plot.nic'', and other
diagnostic plots. Once these ICs have been identified, they can
be completely zeroed-out or subtracted using function
``update.icac'' and the resulting correction checked using
functions ``plot.avgba'' and ``plot.trba''. Some worked-out
examples with R code are provided in the following sections.
Please contact the package maintainer to obtain the data to run
the examples.
Author: Antoine Tremblay, NeuroCognitive Imaging Lab, Dalhousie
University
Maintainer: Antoine Tremblay
icaOcularCorrection-1.3/icaOcularCorrection/R/batch.icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/batch.plotICs.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/defineElectrodeSet.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/mc.batch.icaDEN.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/R/plotICs.fnc.R |only
icaOcularCorrection-1.3/icaOcularCorrection/data |only
icaOcularCorrection-1.3/icaOcularCorrection/man/batch.icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/batch.plotICs.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/defineElectrodeSet.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/den.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/eeg.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/mc.batch.icaDEN.fnc.Rd |only
icaOcularCorrection-1.3/icaOcularCorrection/man/plotICs.fnc.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/DESCRIPTION | 53 +++++-
icaOcularCorrection-2.1/icaOcularCorrection/MD5 | 73 ++++++---
icaOcularCorrection-2.1/icaOcularCorrection/NAMESPACE | 1
icaOcularCorrection-2.1/icaOcularCorrection/NEWS | 76 +++++++++
icaOcularCorrection-2.1/icaOcularCorrection/R/get.peaks.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/mwd.thrsh.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.avgba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.nic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.trba.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/plot.tric.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/summary.icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/topo.ic.R |only
icaOcularCorrection-2.1/icaOcularCorrection/R/update.icac.R |only
icaOcularCorrection-2.1/icaOcularCorrection/inst |only
icaOcularCorrection-2.1/icaOcularCorrection/man/get.peaks.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/icaOcularCorrection-package.Rd | 81 ++++------
icaOcularCorrection-2.1/icaOcularCorrection/man/icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/mwd.thrsh.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.avgba.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.nic.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.trba.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/plot.tric.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/summary.icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/topo.ic.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/man/update.icac.Rd |only
icaOcularCorrection-2.1/icaOcularCorrection/vignettes |only
42 files changed, 207 insertions(+), 77 deletions(-)
Permanent link
Title: Species distribution modelling using latent Gaussian random
fields
Diff between GRaF versions 0.1-1 dated 2013-05-15 and 0.1-11 dated 2013-06-12
Description: Functions to fit, visualise and compare Gaussian random
field species distribution models.
Author: Nick Golding
Maintainer: Nick Golding
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/graf.R | 2 +-
man/GRaF-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.10-0 dated 2013-04-16 and 0.10-1 dated 2013-06-12
Description: Unmarked fits hierarchical models of animal abundance and
occurrence to data collected using survey methods such as point
counts, site occupancy sampling, distance sampling, removal
sampling, and double observer sampling. Parameters governing
the state and observation processes can be modeled as functions
of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc
Kery
Maintainer: Richard Chandler
unmarked-0.10-0/unmarked/inst/doc/cap-recap.R |only
unmarked-0.10-0/unmarked/inst/doc/colext.R |only
unmarked-0.10-0/unmarked/inst/doc/distsamp.R |only
unmarked-0.10-0/unmarked/inst/doc/spp-dist.R |only
unmarked-0.10-0/unmarked/inst/doc/unmarked.R |only
unmarked-0.10-0/unmarked/inst/unitTests/simout3.pdf |only
unmarked-0.10-0/unmarked/inst/unitTests/simout4.pdf |only
unmarked-0.10-1/unmarked/DESCRIPTION | 7 +--
unmarked-0.10-1/unmarked/MD5 | 37 ++++++++------------
unmarked-0.10-1/unmarked/inst/doc/cap-recap.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/colext.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/distsamp.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/spp-dist.pdf |binary
unmarked-0.10-1/unmarked/inst/doc/unmarked.pdf |binary
unmarked-0.10-1/unmarked/inst/unitTests/simout1.pdf |binary
unmarked-0.10-1/unmarked/inst/unitTests/simout2.pdf |binary
unmarked-0.10-1/unmarked/man/Switzerland.Rd | 6 ++-
unmarked-0.10-1/unmarked/man/mallard.Rd | 2 -
unmarked-0.10-1/unmarked/man/occuFP.Rd | 6 ++-
unmarked-0.10-1/unmarked/man/occuRN.Rd | 2 -
unmarked-0.10-1/unmarked/man/pcount.Rd | 6 +--
unmarked-0.10-1/unmarked/man/unmarked-package.Rd | 4 +-
unmarked-0.10-1/unmarked/src/Makevars | 2 -
23 files changed, 34 insertions(+), 38 deletions(-)
Title: analysis of complex survey samples
Diff between survey versions 3.29-4 dated 2013-03-11 and 3.29-5 dated 2013-06-12
Description: Summary statistics, two-sample tests, generalised linear
models, cumulative link models, Cox models, loglinear models,
and general maximum pseudolikelihood estimation for multistage
stratified, cluster-sampled, unequally weighted survey samples.
Variances by Taylor series linearisation or replicate weights.
Post-stratification, calibration, and raking. Two-phase
subsampling designs. Graphics. Predictive margins by direct
standardization. PPS sampling without replacement. Principal
components, factor analysis.
Author: Thomas Lumley
Maintainer: Thomas Lumley
DESCRIPTION | 8 +++----
MD5 | 55 ++++++++++++++++++++++++++++------------------------
R/mrb.R | 2 -
R/olr.R | 4 +--
R/survey.R | 2 -
R/surveyby.R | 4 +--
R/surveygraph.R | 3 +-
R/surveyrep.R | 8 +++----
R/svykm.R | 2 -
R/svymi.R | 8 +++----
R/sysdata.rda |binary
data/api.rda |binary
data/crowd.rda |binary
data/election.rda |binary
data/fpc.rda |binary
data/hospital.rda |binary
data/mu284.rda |binary
data/nhanes.rda |binary
data/scd.rda |binary
inst/NEWS | 9 ++++++++
inst/doc/domain.R |only
inst/doc/domain.pdf |binary
inst/doc/epi.R |only
inst/doc/epi.pdf |binary
inst/doc/phase1.R |only
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inst/doc/survey.R |only
inst/doc/survey.pdf |binary
man/svyplot.Rd | 7 ++++++
31 files changed, 67 insertions(+), 45 deletions(-)
Title: Bayesian variable selection and model choice for generalized
additive mixed models
Diff between spikeSlabGAM versions 1.1-5 dated 2013-03-13 and 1.1-6 dated 2013-06-12
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression
models via SSVS with spike-and-slab priors.
Author: Fabian Scheipl
Maintainer: Fabian Scheipl
DESCRIPTION | 10
MD5 | 10
R/spikeAndSlab.R | 1575 ++++++++++++++++++++---------------------
R/spikeSlabGAM.R | 289 +++----
inst/doc/UsingSpikeSlabGAM.pdf |binary
man/spikeSlabGAM.Rd | 3
6 files changed, 947 insertions(+), 940 deletions(-)
Title: R package for simulating biological sequence evolution
Diff between phylosim versions 2.0.1 dated 2013-03-20 and 2.0.2 dated 2013-06-12
Description: PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,
insertions and deletions.
Author: Botond Sipos
Maintainer: Botond Sipos
DESCRIPTION | 10
MD5 | 1014 +++++++++++++-------------
R/AminoAcidSubst.R | 4
R/BrownianInsertor.R | 18
R/Event.R | 8
R/GeneralInDel.R | 62 +
R/GeneralSubstitution.R | 16
R/PhyloSim.R | 18
R/PhyloSimSource.R |only
R/Sequence.R | 43 -
inst/doc/PhyloSim.R |only
inst/doc/PhyloSim.Rnw | 8
inst/doc/PhyloSim.pdf |binary
man/000==.Alphabet.Rd | 10
man/000==.Process.Rd | 10
man/Alphabet.Rd | 8
man/AminoAcidAlphabet.Rd | 8
man/AminoAcidSequence.Rd | 8
man/AminoAcidSubst.Rd | 8
man/AnyAlphabet.Rd | 8
man/BinaryAlphabet.Rd | 8
man/BinarySequence.Rd | 8
man/BinarySubst.Rd | 8
man/BrownianInsertor.Rd | 16
man/BrownianPath.BrownianInsertor.Rd | 10
man/CodonAlphabet.Rd | 8
man/CodonSequence.Rd | 11
man/CodonUNREST.Rd | 8
man/ContinuousDeletor.Rd | 8
man/ContinuousInsertor.Rd | 8
man/Debug.PhyloSim.Rd | 10
man/DiscreteDeletor.Rd | 8
man/DiscreteInsertor.Rd | 8
man/Event.Rd | 8
man/F81.Rd | 8
man/F84.Rd | 8
man/FastFieldDeletor.Rd | 11
man/GTR.Rd | 11
man/GY94.Rd | 11
man/GeneralDeletor.Rd | 11
man/GeneralInDel.Rd | 14
man/GeneralInsertor.Rd | 33
man/GeneralSubstitution.Rd | 8
man/HKY.Rd | 11
man/JC69.Rd | 8
man/JTT.Rd | 8
man/JTT.dcmut.Rd | 8
man/K80.Rd | 8
man/K81.Rd | 8
man/LG.Rd | 8
man/Log.PhyloSim.Rd | 10
man/MtZoa.Rd | 8
man/NucleotideAlphabet.Rd | 8
man/NucleotideSequence.Rd | 8
man/PAM.Rd | 8
man/PAM.dcmut.Rd | 8
man/PSRoot.Rd | 8
man/PSRootSummary.Rd | 8
man/Perform.Event.Rd | 14
man/PhyloSim.Rd | 11
man/Process.Rd | 8
man/QMatrix.Rd | 8
man/Scale.QMatrix.Rd | 10
man/Sequence.Rd | 8
man/Simulate.PhyloSim.Rd | 10
man/Site.Rd | 8
man/T92.Rd | 8
man/TN93.Rd | 11
man/Translate.CodonSequence.Rd | 10
man/UNREST.Rd | 8
man/Undocumented.PhyloSim.Rd | 10
man/WAG.Rd | 8
man/areSynonymous.CodonAlphabet.Rd | 10
man/as.character.Alphabet.Rd | 10
man/as.character.Event.Rd | 10
man/as.character.GeneralSubstitution.Rd | 10
man/as.character.PhyloSim.Rd | 10
man/as.character.Process.Rd | 10
man/as.character.QMatrix.Rd | 10
man/as.character.Sequence.Rd | 10
man/as.character.Site.Rd | 10
man/attachHookToNode.PhyloSim.Rd | 10
man/attachProcess.Sequence.Rd | 10
man/attachProcess.Site.Rd | 10
man/attachSeqToNode.PhyloSim.Rd | 10
man/buildFromPAML.AminoAcidSubst.Rd | 10
man/checkConsistency.Alphabet.Rd | 10
man/checkConsistency.AminoAcidSubst.Rd | 10
man/checkConsistency.BinarySubst.Rd | 10
man/checkConsistency.BrownianInsertor.Rd | 10
man/checkConsistency.CodonAlphabet.Rd | 10
man/checkConsistency.CodonSequence.Rd | 10
man/checkConsistency.CodonUNREST.Rd | 10
man/checkConsistency.ContinuousDeletor.Rd | 10
man/checkConsistency.ContinuousInsertor.Rd | 10
man/checkConsistency.DiscreteDeletor.Rd | 10
man/checkConsistency.DiscreteInsertor.Rd | 10
man/checkConsistency.Event.Rd | 10
man/checkConsistency.F81.Rd | 10
man/checkConsistency.F84.Rd | 10
man/checkConsistency.FastFieldDeletor.Rd | 10
man/checkConsistency.GTR.Rd | 10
man/checkConsistency.GY94.Rd | 10
man/checkConsistency.GeneralDeletor.Rd | 10
man/checkConsistency.GeneralInDel.Rd | 10
man/checkConsistency.GeneralInsertor.Rd | 10
man/checkConsistency.GeneralSubstitution.Rd | 10
man/checkConsistency.HKY.Rd | 10
man/checkConsistency.JC69.Rd | 10
man/checkConsistency.K80.Rd | 10
man/checkConsistency.K81.Rd | 10
man/checkConsistency.PSRoot.Rd | 10
man/checkConsistency.PSRootSummary.Rd | 10
man/checkConsistency.PhyloSim.Rd | 10
man/checkConsistency.Process.Rd | 10
man/checkConsistency.QMatrix.Rd | 10
man/checkConsistency.Sequence.Rd | 10
man/checkConsistency.Site.Rd | 10
man/checkConsistency.T92.Rd | 10
man/checkConsistency.TN93.Rd | 10
man/checkConsistency.UNREST.Rd | 10
man/clearStates.Sequence.Rd | 10
man/clone.GeneralSubstitution.Rd | 16
man/clone.Process.Rd | 10
man/clone.Sequence.Rd | 10
man/copySubSequence.Sequence.Rd | 10
man/cpREV.Rd | 8
man/deleteSubSequence.Sequence.Rd | 10
man/detachHookFromNode.PhyloSim.Rd | 10
man/detachProcess.Sequence.Rd | 10
man/detachProcess.Site.Rd | 10
man/detachSeqFromNode.PhyloSim.Rd | 10
man/enableVirtual.PSRoot.Rd | 10
man/exportStatTree.PhyloSim.Rd | 15
man/flagTotalRate.Site.Rd | 10
man/generateInsert.GeneralInsertor.Rd | 10
man/getAcceptBy.GeneralInDel.Rd | 16
man/getAcceptWin.GeneralInsertor.Rd | 10
man/getAlignment.PhyloSim.Rd | 10
man/getAlignmentLength.PhyloSim.Rd | 13
man/getAlphabet.GeneralSubstitution.Rd | 10
man/getAlphabet.Process.Rd | 10
man/getAlphabet.QMatrix.Rd | 10
man/getAlphabet.Site.Rd | 10
man/getAlphabets.Sequence.Rd | 10
man/getAncestral.Sequence.Rd | 10
man/getAncestral.Site.Rd | 10
man/getBaseFreqs.F81.Rd | 10
man/getBaseFreqs.F84.Rd | 10
man/getBaseFreqs.GTR.Rd | 10
man/getBaseFreqs.HKY.Rd | 10
man/getBaseFreqs.K80.Rd | 10
man/getBaseFreqs.K81.Rd | 10
man/getBaseFreqs.TN93.Rd | 10
man/getBigRate.Sequence.Rd | 10
man/getBranchEvents.PhyloSim.Rd | 14
man/getCodonFreqs.GY94.Rd | 10
man/getComments.PSRoot.Rd | 10
man/getCumulativeRates.Sequence.Rd | 10
man/getCumulativeRatesFromRange.Sequence.Rd | 16
man/getDeletionTolerance.Sequence.Rd | 10
man/getDist.ContinuousDeletor.Rd | 10
man/getDist.ContinuousInsertor.Rd | 10
man/getEdge.PhyloSim.Rd | 10
man/getEdges.PhyloSim.Rd | 10
man/getEquDist.GeneralSubstitution.Rd | 15
man/getEventRate.GeneralSubstitution.Rd | 10
man/getEventRate.QMatrix.Rd | 10
man/getEventRateAtSite.GeneralSubstitution.Rd | 10
man/getEvents.Sequence.Rd | 16
man/getEvents.Site.Rd | 10
man/getEventsAtSite.FastFieldDeletor.Rd | 10
man/getEventsAtSite.GY94.Rd | 10
man/getEventsAtSite.GeneralDeletor.Rd | 10
man/getEventsAtSite.GeneralInsertor.Rd | 10
man/getEventsAtSite.GeneralSubstitution.Rd | 10
man/getEventsAtSite.Process.Rd | 10
man/getGenerateBy.GeneralInsertor.Rd | 20
man/getHandler.Event.Rd | 14
man/getId.PhyloSim.Rd | 10
man/getId.Process.Rd | 10
man/getId.QMatrix.Rd | 10
man/getId.Sequence.Rd | 10
man/getInsertHook.GeneralInsertor.Rd | 10
man/getInsertionTolerance.Sequence.Rd | 10
man/getKappa.F84.Rd | 10
man/getKappa.GY94.Rd | 10
man/getLength.Sequence.Rd | 10
man/getLengthParam1.FastFieldDeletor.Rd | 10
man/getLengthParam2.FastFieldDeletor.Rd | 10
man/getLogFile.PhyloSim.Rd | 10
man/getLogLevel.PhyloSim.Rd | 10
man/getMatrix.QMatrix.Rd | 10
man/getMaxLength.ContinuousDeletor.Rd | 10
man/getMaxLength.ContinuousInsertor.Rd | 10
man/getMethodsList.PSRoot.Rd | 10
man/getName.Event.Rd | 10
man/getName.PhyloSim.Rd | 10
man/getName.Process.Rd | 10
man/getName.QMatrix.Rd | 10
man/getName.Sequence.Rd | 10
man/getNedges.PhyloSim.Rd | 10
man/getNodes.PhyloSim.Rd | 10
man/getNtips.PhyloSim.Rd | 10
man/getOmegaScalingFactor.GY94.Rd | 10
man/getOmegas.CodonSequence.Rd | 10
man/getParameterAtSite.Process.Rd | 10
man/getParameterAtSites.Sequence.Rd | 13
man/getPhylo.PhyloSim.Rd | 10
man/getPosition.Event.Rd | 10
man/getProbs.DiscreteDeletor.Rd | 10
man/getProbs.DiscreteInsertor.Rd | 10
man/getProcess.Event.Rd | 10
man/getProcess.QMatrix.Rd | 10
man/getProcesses.Sequence.Rd | 16
man/getProcesses.Site.Rd | 10
man/getProposeBy.GeneralInDel.Rd | 10
man/getQMatrix.GeneralSubstitution.Rd | 10
man/getRate.Event.Rd | 10
man/getRate.GeneralInDel.Rd | 10
man/getRate.GeneralSubstitution.Rd | 10
man/getRate.QMatrix.Rd | 8
man/getRateList.GeneralSubstitution.Rd | 10
man/getRateList.QMatrix.Rd | 10
man/getRateMultipliers.Sequence.Rd | 10
man/getRateParam.F81.Rd | 10
man/getRateParam.F84.Rd | 10
man/getRateParam.GTR.Rd | 10
man/getRateParam.HKY.Rd | 10
man/getRateParam.K80.Rd | 10
man/getRateParam.K81.Rd | 10
man/getRateParam.T92.Rd | 10
man/getRateParam.TN93.Rd | 10
man/getRateParamList.F81.Rd | 10
man/getRateParamList.F84.Rd | 10
man/getRateParamList.GTR.Rd | 10
man/getRateParamList.HKY.Rd | 10
man/getRateParamList.K80.Rd | 10
man/getRateParamList.K81.Rd | 10
man/getRateParamList.T92.Rd | 10
man/getRateParamList.TN93.Rd | 10
man/getRootNode.PhyloSim.Rd | 10
man/getRootSeq.PhyloSim.Rd | 10
man/getScale.BrownianInsertor.Rd | 10
man/getScaledMatrix.QMatrix.Rd | 10
man/getSeqFromNode.PhyloSim.Rd | 10
man/getSequence.Site.Rd | 10
man/getSequences.PhyloSim.Rd | 10
man/getSite.Event.Rd | 10
man/getSiteSpecificParamIds.Process.Rd | 10
man/getSiteSpecificParamList.Process.Rd | 10
man/getSites.Sequence.Rd | 10
man/getSize.Alphabet.Rd | 10
man/getSizes.DiscreteDeletor.Rd | 10
man/getSizes.DiscreteInsertor.Rd | 10
man/getState.Site.Rd | 10
man/getStates.Sequence.Rd | 10
man/getString.Sequence.Rd | 10
man/getSymbolFreqs.Sequence.Rd | 10
man/getSymbolLength.Alphabet.Rd | 10
man/getSymbols.Alphabet.Rd | 10
man/getTableId.CodonAlphabet.Rd | 10
man/getTemplateSeq.GeneralInsertor.Rd | 10
man/getTheta.T92.Rd | 10
man/getTipLabels.PhyloSim.Rd | 10
man/getTips.PhyloSim.Rd | 10
man/getToleranceMargin.FastFieldDeletor.Rd | 10
man/getTotalRate.Site.Rd | 10
man/getTotalRates.Sequence.Rd | 10
man/getTotalRatesFromRange.Sequence.Rd | 16
man/getTransTable.CodonAlphabet.Rd | 10
man/getTreeLength.PhyloSim.Rd | 10
man/getType.Alphabet.Rd | 10
man/getType.BrownianInsertor.Rd | 10
man/getType.FastFieldDeletor.Rd | 10
man/getUniqueAlphabets.Sequence.Rd | 17
man/getUniqueProcesses.Sequence.Rd | 16
man/getWriteProtected.Alphabet.Rd | 10
man/getWriteProtected.Event.Rd | 10
man/getWriteProtected.Process.Rd | 10
man/getWriteProtected.QMatrix.Rd | 10
man/getWriteProtected.Sequence.Rd | 10
man/globalConsistencyCheck.PSRoot.Rd | 10
man/hasSiteSpecificParameter.Process.Rd | 10
man/hasSymbols.Alphabet.Rd | 10
man/hasUndefinedRate.GeneralInDel.Rd | 10
man/hasUndefinedRate.GeneralSubstitution.Rd | 10
man/hasUndefinedRate.Process.Rd | 10
man/insertSequence.Sequence.Rd | 10
man/intersect.list.PSRoot.Rd | 10
man/is.Alphabet.Rd | 8
man/is.CodonAlphabet.Rd | 8
man/is.CodonUNREST.Rd | 8
man/is.Event.Rd | 8
man/is.GY94.Rd | 8
man/is.GeneralDeletor.Rd | 8
man/is.GeneralInDel.Rd | 8
man/is.GeneralInsertor.Rd | 8
man/is.GeneralSubstitution.Rd | 8
man/is.PSRoot.Rd | 8
man/is.Process.Rd | 8
man/is.QMatrix.Rd | 8
man/is.Sequence.Rd | 8
man/is.Site.Rd | 8
man/is.na.PSRoot.Rd | 10
man/is.phylo.Rd | 8
man/is.tip.PhyloSim.Rd | 10
man/isAttached.Site.Rd | 10
man/isEmpty.Alphabet.Rd | 10
man/isStartCodon.CodonAlphabet.Rd | 10
man/isStopCodon.CodonAlphabet.Rd | 10
man/ll.PSRoot.Rd | 10
man/mtArt.Rd | 8
man/mtMam.Rd | 8
man/mtREV24.Rd | 8
man/my.all.equal.PSRoot.Rd | 10
man/newAAMatrix.AminoAcidSubst.Rd | 10
man/omegaHist.CodonSequence.Rd | 10
man/omegaVarM0.CodonSequence.Rd | 10
man/omegaVarM1.CodonSequence.Rd | 10
man/omegaVarM2.CodonSequence.Rd | 10
man/omegaVarM3.CodonSequence.Rd | 10
man/omegaVarM4.CodonSequence.Rd | 10
man/plot.ContinuousDeletor.Rd | 10
man/plot.ContinuousInsertor.Rd | 10
man/plot.DiscreteDeletor.Rd | 10
man/plot.DiscreteInsertor.Rd | 10
man/plot.GeneralSubstitution.Rd | 10
man/plot.PhyloSim.Rd | 18
man/plot.Sequence.Rd | 10
man/plotParametersAtSites.Sequence.Rd | 10
man/plusGamma.Sequence.Rd | 10
man/plusInvGamma.Sequence.Rd | 10
man/print.PSRootSummary.Rd | 10
man/print.QMatrix.Rd | 10
man/proposeLength.GeneralInDel.Rd | 10
man/readAlignment.PhyloSim.Rd | 10
man/readTree.PhyloSim.Rd | 10
man/rescaleQMatrix.GeneralSubstitution.Rd | 10
man/revComp.NucleotideSequence.Rd | 10
man/sampleState.GeneralSubstitution.Rd | 10
man/sampleStates.Sequence.Rd | 10
man/saveAlignment.PhyloSim.Rd | 10
man/scaleTree.PhyloSim.Rd | 10
man/setAcceptBy.GeneralInDel.Rd | 16
man/setAcceptWin.GeneralInsertor.Rd | 10
man/setAlignment.PhyloSim.Rd | 10
man/setAlphabet.GeneralSubstitution.Rd | 10
man/setAlphabet.Process.Rd | 10
man/setAlphabet.QMatrix.Rd | 10
man/setAlphabet.Site.Rd | 10
man/setAlphabets.Sequence.Rd | 10
man/setAncestral.Sequence.Rd | 10
man/setAncestral.Site.Rd | 10
man/setBaseFreqs.F81.Rd | 10
man/setBaseFreqs.F84.Rd | 10
man/setBaseFreqs.GTR.Rd | 10
man/setBaseFreqs.HKY.Rd | 10
man/setBaseFreqs.K80.Rd | 10
man/setBaseFreqs.K81.Rd | 10
man/setBaseFreqs.TN93.Rd | 10
man/setBigRate.Sequence.Rd | 10
man/setBranchEvents.PhyloSim.Rd | 10
man/setCodonFreqs.GY94.Rd | 10
man/setComments.PSRoot.Rd | 10
man/setCumulativeRates.Sequence.Rd | 10
man/setDeletionTolerance.Sequence.Rd | 10
man/setDist.ContinuousDeletor.Rd | 10
man/setDist.ContinuousInsertor.Rd | 10
man/setEdges.PhyloSim.Rd | 10
man/setEquDist.GeneralSubstitution.Rd | 15
man/setEvents.Site.Rd | 10
man/setGenerateBy.GeneralInsertor.Rd | 19
man/setHandler.Event.Rd | 10
man/setId.PhyloSim.Rd | 10
man/setId.Process.Rd | 10
man/setId.QMatrix.Rd | 10
man/setId.Sequence.Rd | 10
man/setInsertHook.GeneralInsertor.Rd | 10
man/setInsertionTolerance.Sequence.Rd | 10
man/setKappa.F84.Rd | 10
man/setKappa.GY94.Rd | 10
man/setLength.Sequence.Rd | 10
man/setLengthParam1.FastFieldDeletor.Rd | 10
man/setLengthParam2.FastFieldDeletor.Rd | 10
man/setLogFile.PhyloSim.Rd | 10
man/setLogLevel.PhyloSim.Rd | 10
man/setMatrix.QMatrix.Rd | 10
man/setMaxLength.ContinuousDeletor.Rd | 10
man/setMaxLength.ContinuousInsertor.Rd | 10
man/setMethodsList.PSRoot.Rd | 10
man/setName.Event.Rd | 10
man/setName.PhyloSim.Rd | 10
man/setName.Process.Rd | 10
man/setName.QMatrix.Rd | 10
man/setName.Sequence.Rd | 10
man/setNedges.PhyloSim.Rd | 10
man/setNodes.PhyloSim.Rd | 10
man/setNtips.PhyloSim.Rd | 10
man/setOmegas.CodonSequence.Rd | 10
man/setParameterAtSite.Process.Rd | 10
man/setParameterAtSites.Sequence.Rd | 13
man/setPhylo.PhyloSim.Rd | 10
man/setPosition.Event.Rd | 10
man/setProbs.DiscreteDeletor.Rd | 10
man/setProbs.DiscreteInsertor.Rd | 10
man/setProcess.Event.Rd | 10
man/setProcess.QMatrix.Rd | 10
man/setProcesses.Sequence.Rd | 10
man/setProcesses.Site.Rd | 10
man/setProposeBy.GeneralInDel.Rd | 10
man/setQMatrix.GeneralSubstitution.Rd | 10
man/setRate.Event.Rd | 10
man/setRate.GY94.Rd | 10
man/setRate.GeneralInDel.Rd | 10
man/setRate.GeneralSubstitution.Rd | 10
man/setRate.QMatrix.Rd | 10
man/setRateList.GeneralSubstitution.Rd | 10
man/setRateList.QMatrix.Rd | 10
man/setRateMultipliers.Sequence.Rd | 10
man/setRateParam.F81.Rd | 10
man/setRateParam.F84.Rd | 10
man/setRateParam.GTR.Rd | 10
man/setRateParam.HKY.Rd | 10
man/setRateParam.K80.Rd | 10
man/setRateParam.K81.Rd | 10
man/setRateParam.T92.Rd | 10
man/setRateParam.TN93.Rd | 10
man/setRateParamList.F81.Rd | 10
man/setRateParamList.F84.Rd | 10
man/setRateParamList.GTR.Rd | 10
man/setRateParamList.HKY.Rd | 10
man/setRateParamList.K80.Rd | 10
man/setRateParamList.K81.Rd | 10
man/setRateParamList.T92.Rd | 10
man/setRateParamList.TN93.Rd | 10
man/setRootNode.PhyloSim.Rd | 10
man/setRootSeq.PhyloSim.Rd | 10
man/setScale.BrownianInsertor.Rd | 10
man/setScaledMatrix.QMatrix.Rd | 10
man/setSequence.Site.Rd | 10
man/setSequences.PhyloSim.Rd | 10
man/setSite.Event.Rd | 10
man/setSiteSpecificParamIds.Process.Rd | 10
man/setSiteSpecificParamList.Process.Rd | 10
man/setSize.Alphabet.Rd | 10
man/setSizes.DiscreteDeletor.Rd | 10
man/setSizes.DiscreteInsertor.Rd | 10
man/setState.Site.Rd | 10
man/setStates.Sequence.Rd | 10
man/setString.Sequence.Rd | 10
man/setSymbolLength.Alphabet.Rd | 10
man/setSymbols.Alphabet.Rd | 10
man/setTableId.CodonAlphabet.Rd | 10
man/setTemplateSeq.GeneralInsertor.Rd | 10
man/setTheta.T92.Rd | 10
man/setTipLabels.PhyloSim.Rd | 10
man/setTips.PhyloSim.Rd | 10
man/setToleranceMargin.FastFieldDeletor.Rd | 10
man/setTotalRate.Site.Rd | 10
man/setTotalRates.Sequence.Rd | 10
man/setTransTable.CodonAlphabet.Rd | 10
man/setTreeLength.PhyloSim.Rd | 10
man/setType.Alphabet.Rd | 10
man/setType.BrownianInsertor.Rd | 10
man/setType.FastFieldDeletor.Rd | 10
man/setUniqueAlphabets.Sequence.Rd | 10
man/setUniqueProcesses.Sequence.Rd | 10
man/setWriteProtected.Alphabet.Rd | 10
man/setWriteProtected.Event.Rd | 10
man/setWriteProtected.Process.Rd | 10
man/setWriteProtected.QMatrix.Rd | 10
man/setWriteProtected.Sequence.Rd | 10
man/stringLength.Rd | 8
man/stringLengthVector.Rd | 8
man/summary.Alphabet.Rd | 10
man/summary.AminoAcidSubst.Rd | 10
man/summary.BinarySubst.Rd | 10
man/summary.BrownianInsertor.Rd | 18
man/summary.CodonAlphabet.Rd | 10
man/summary.ContinuousDeletor.Rd | 10
man/summary.ContinuousInsertor.Rd | 10
man/summary.DiscreteDeletor.Rd | 10
man/summary.DiscreteInsertor.Rd | 10
man/summary.Event.Rd | 10
man/summary.F81.Rd | 10
man/summary.F84.Rd | 10
man/summary.FastFieldDeletor.Rd | 10
man/summary.GTR.Rd | 10
man/summary.GY94.Rd | 10
man/summary.GeneralDeletor.Rd | 10
man/summary.GeneralInDel.Rd | 10
man/summary.GeneralInsertor.Rd | 10
man/summary.GeneralSubstitution.Rd | 10
man/summary.HKY.Rd | 10
man/summary.JC69.Rd | 10
man/summary.K80.Rd | 10
man/summary.K81.Rd | 10
man/summary.PSRoot.Rd | 10
man/summary.PhyloSim.Rd | 10
man/summary.Process.Rd | 10
man/summary.QMatrix.Rd | 10
man/summary.Sequence.Rd | 10
man/summary.Site.Rd | 10
man/summary.T92.Rd | 10
man/summary.TN93.Rd | 10
man/summary.UNREST.Rd | 10
man/translateCodon.CodonAlphabet.Rd | 10
man/virtualAssignmentForbidden.PSRoot.Rd | 10
509 files changed, 3285 insertions(+), 2923 deletions(-)
Title: Generate PMML for various models
Diff between pmml versions 1.2.34 dated 2013-01-26 and 1.2.35 dated 2013-06-12
Description: The Predictive Modelling Markup Language (PMML) is a
language for representing models, in an application independent
way. Such models can then be loaded into other applications
supporting PMML, including ADAPA from Zementis, Teradata
Warehouse Miner and IBM's DB2. The package provides a generic
pmml function to generate pmml for an object. Using a S3
generic function the appropriate method for the class of the
supplied object is dispatched. The package currently supports
the export of PMML for linear regression, generalized linear
regression, multinomial logistic regression, SVMs, rpart
classification trees, randomSurvivalForest, randomForest, naive
bayes models and kmeans clusters. This package is part of the
Rattle toolkit.
Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant
Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Maintainer: Tridivesh Jena
pmml-1.2.34/pmml/R/pmml.rsf.R |only
pmml-1.2.34/pmml/man/pmml.rsf.Rd |only
pmml-1.2.35/pmml/DESCRIPTION | 18 -
pmml-1.2.35/pmml/MD5 | 22 +-
pmml-1.2.35/pmml/R/pmml.R | 309 +++++++++++++++++++++++++----
pmml-1.2.35/pmml/R/pmml.coxph.R | 16 +
pmml-1.2.35/pmml/R/pmml.cv.glmnet.R |only
pmml-1.2.35/pmml/R/pmml.multinom.R | 17 -
pmml-1.2.35/pmml/R/pmml.naiveBayes.R |only
pmml-1.2.35/pmml/R/pmml.randomForest.R | 332 ++++++++++++++++++--------------
pmml-1.2.35/pmml/R/pmml.rfsrc.R |only
pmml-1.2.35/pmml/R/pmml.rules.R | 2
pmml-1.2.35/pmml/man/pmml.Rd | 4
pmml-1.2.35/pmml/man/pmml.cv.glmnet.Rd |only
pmml-1.2.35/pmml/man/pmml.naiveBayes.Rd |only
pmml-1.2.35/pmml/man/pmml.rfsrc.Rd |only
16 files changed, 506 insertions(+), 214 deletions(-)
Title: Estimating network indices, including trophic structure of
foodwebs in R
Diff between NetIndices versions 1.4 dated 2011-08-11 and 1.4.2 dated 2013-06-12
Description: Given a network (e.g. a food web), estimates several
network indices. These include: Ascendency network indices,
Direct and indirect dependencies, Effective measures, Environ
network indices, General network indices, Pathway analysis,
Network uncertainty indices and constraint efficiencies and the
trophic level and omnivory indices of food webs.
Author: Karline Soetaert
Maintainer: Karline Soetaert
DESCRIPTION | 15 ++++++++-------
MD5 | 30 +++++++++++++++---------------
R/TrophInd.R | 4 +++-
data/Conesprings.rda |binary
data/Takapoto.rda |binary
inst/doc/NetIndices.pdf |binary
man/AscInd.Rd | 2 +-
man/Conesprings.Rd | 2 +-
man/Dependency.Rd | 2 +-
man/EffInd.Rd | 2 +-
man/EnvInd.Rd | 2 +-
man/GenInd.Rd | 2 +-
man/PathInd.Rd | 2 +-
man/Takapoto.Rd | 2 +-
man/TrophInd.Rd | 10 ++++++++--
man/UncInd.Rd | 2 +-
16 files changed, 43 insertions(+), 34 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.4-963 dated 2013-05-07 and 1.5-1026 dated 2013-06-12
Description: Transforms away factors with many levels prior to doing an
OLS. Useful for estimating linear models with multiple group
fixed effects, and for estimating linear models which uses
factors as pure control variables.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
lfe-1.4-963/lfe/inst/doc/CHANGELOG |only
lfe-1.5-1026/lfe/DESCRIPTION | 8
lfe-1.5-1026/lfe/MD5 | 65 ++--
lfe-1.5-1026/lfe/R/kaczmarz.R | 27 +
lfe-1.5-1026/lfe/R/lfe.R | 35 +-
lfe-1.5-1026/lfe/R/utils.R | 12
lfe-1.5-1026/lfe/inst/doc/identification.R | 195 +++++++++++---
lfe-1.5-1026/lfe/inst/doc/identification.Rnw | 361 ++++++++++++++++++++------
lfe-1.5-1026/lfe/inst/doc/identification.pdf |binary
lfe-1.5-1026/lfe/inst/doc/lfehow.Rnw | 30 +-
lfe-1.5-1026/lfe/inst/doc/lfehow.pdf |binary
lfe-1.5-1026/lfe/inst/doc/speed.R |only
lfe-1.5-1026/lfe/inst/doc/speed.Rnw |only
lfe-1.5-1026/lfe/inst/doc/speed.pdf |only
lfe-1.5-1026/lfe/man/btrap.Rd | 6
lfe-1.5-1026/lfe/man/compfactor.Rd | 16 +
lfe-1.5-1026/lfe/man/efactory.Rd | 8
lfe-1.5-1026/lfe/man/felm.Rd | 27 +
lfe-1.5-1026/lfe/man/getfe.Rd | 6
lfe-1.5-1026/lfe/man/is.estimable.Rd | 6
lfe-1.5-1026/lfe/man/kaczmarz.Rd | 5
lfe-1.5-1026/lfe/man/lfe-package.Rd | 15 -
lfe-1.5-1026/lfe/src/lfe.c | 279 +++++++++++++++++---
lfe-1.5-1026/lfe/tests/comparelm.Rout.save | 4
lfe-1.5-1026/lfe/tests/degenerate.Rout.save | 58 ++--
lfe-1.5-1026/lfe/tests/efcheck.R | 2
lfe-1.5-1026/lfe/tests/efcheck.Rout.save | 186 ++++++-------
lfe-1.5-1026/lfe/tests/fourfac.Rout.save | 24 -
lfe-1.5-1026/lfe/tests/ivtest.Rout.save | 4
lfe-1.5-1026/lfe/tests/lfetest.Rout.save | 4
lfe-1.5-1026/lfe/tests/nonest.Rout.save | 18 -
lfe-1.5-1026/lfe/tests/onefac.Rout.save | 4
lfe-1.5-1026/lfe/tests/verify.Rout.save | 10
lfe-1.5-1026/lfe/vignettes/identification.Rnw | 361 ++++++++++++++++++++------
lfe-1.5-1026/lfe/vignettes/lfehow.Rnw | 30 +-
lfe-1.5-1026/lfe/vignettes/speed.Rnw |only
36 files changed, 1318 insertions(+), 488 deletions(-)
Title: Inline C, C++, Fortran function calls from R
Diff between inline versions 0.3.11 dated 2013-02-27 and 0.3.12 dated 2013-06-12
Description: Functionality to dynamically define R functions and S4
methods with in-lined C, C++ or Fortran code supporting .C and
.Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel,
Romain Francois
Maintainer: Dirk Eddelbuettel
inline-0.3.11/inline/LICENSE |only
inline-0.3.12/inline/DESCRIPTION | 8 ++++----
inline-0.3.12/inline/MD5 | 9 ++++-----
inline-0.3.12/inline/R/package.skeleton.R | 8 ++++----
inline-0.3.12/inline/inst/NEWS.Rd | 18 ++++++++++++++----
inline-0.3.12/inline/man/cfunction.Rd | 3 ++-
6 files changed, 28 insertions(+), 18 deletions(-)
Title: Analysis of fMRI experiments
Diff between fmri versions 1.4-8 dated 2012-06-11 and 1.5-0 dated 2013-06-12
Description: The package contains R-functions to perform an fmri
analysis as described in K. Tabelow, J. Polzehl, H.U. Voss, and
V. Spokoiny, Analysing fMRI experiments with structure adaptive
smoothing procedures, NeuroImage, 33:55-62 (2006), J. Polzehl,
H.U. Voss, K. Tabelow, Structural adaptive segmentation for
statistical parametric mapping, NeuroImage, 52:515-523 (2010)
and K. Tabelow, J. Polzehl, Statistical Parametric Maps for
Functional MRI Experiments in {R}: The Package {fmri}}, Journal
of Statistical Software, 44(11):1--21 (2011).
Author: Karsten Tabelow
Maintainer: Karsten Tabelow
DESCRIPTION | 21 +++---
HISTORY | 12 +++
MD5 | 34 +++++-----
NAMESPACE | 2
R/fmri.R | 8 +-
R/io.R | 2
R/lm.R | 1
R/plot.r | 119 ++++++++++++++++++++++++++++++++----
R/segm.r | 92 +++++++++------------------
R/segmkrv.r | 89 +++++++++++++--------------
R/view23D.r | 168 +++++++++++++++++++++++++++++++++++++++++++++++++++
man/cutroi.Rd | 3
man/fmri.smooth.Rd | 8 +-
man/plot.fmridata.Rd | 12 +++
src/misc.f | 49 ++++++++++++++
src/segm3D.f | 77 ++++++++++++++++-------
src/segm3Dkrv.f | 17 ++---
src/vaws3D.f | 10 +--
18 files changed, 531 insertions(+), 193 deletions(-)
Title: Stable Distribution Functions
Diff between stabledist versions 0.6-5 dated 2012-10-01 and 0.6-6 dated 2013-06-12
Description: Density, Probability and Quantile functions, and random
number generation for (skew) stable distributions, using the
parametrizations of Nolan.
Author: Diethelm Wuertz, Martin Maechler and Rmetrics core team
members.
Maintainer: Martin Maechler
DESCRIPTION | 9 +++++----
MD5 | 8 ++++----
R/dpqr-stable.R | 6 +++---
TODO | 2 +-
tests/dstab-ex.R | 9 +++++++++
5 files changed, 22 insertions(+), 12 deletions(-)
Title: Graphical user interface for package sdcMicro
Diff between sdcMicroGUI versions 1.0.1 dated 2013-04-23 and 1.0.2 dated 2013-06-12
Description: A point and click graphical user interface based on top of
the sdcMicro package to create anonymized data set. The
graphical user interface provides full reproducibility of any
result via the script menu in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois
Fonteneau
Maintainer: Matthias Templ
DESCRIPTION | 10 ++++----
MD5 | 6 ++---
R/aux_functions.R | 16 +++----------
R/sdcGUI.r | 62 ++++++++++++++++++++++++++----------------------------
4 files changed, 42 insertions(+), 52 deletions(-)
Title: Reactive transport modelling in 1D, 2D and 3D
Diff between ReacTran versions 1.3.2 dated 2011-08-11 and 1.4.1 dated 2013-06-12
Description: Routines for developing models that describe reaction and
advective-diffusive transport in one, two or three dimensions.
Includes transport routines in porous media, in estuaries, and
in bodies with variable shape.
Author: Karline Soetaert
Maintainer: Karline Soetaert
ReacTran-1.3.2/ReacTran/inst/doc/bibs.bib |only
ReacTran-1.3.2/ReacTran/inst/doc/diffusion.jpeg |only
ReacTran-1.3.2/ReacTran/inst/doc/jss.bst |only
ReacTran-1.3.2/ReacTran/inst/doc/jss.cls |only
ReacTran-1.3.2/ReacTran/inst/doc/perspwave.jpeg |only
ReacTran-1.3.2/ReacTran/inst/doc/reactran-fig1.pdf |only
ReacTran-1.3.2/ReacTran/inst/doc/reactran-phase.pdf |only
ReacTran-1.4.1/ReacTran/.Rinstignore |only
ReacTran-1.4.1/ReacTran/DESCRIPTION | 15
ReacTran-1.4.1/ReacTran/MD5 | 76 +-
ReacTran-1.4.1/ReacTran/NAMESPACE | 6
ReacTran-1.4.1/ReacTran/NEWS | 7
ReacTran-1.4.1/ReacTran/R/advection.R | 31
ReacTran-1.4.1/ReacTran/R/tran.2D.R | 16
ReacTran-1.4.1/ReacTran/R/tran.3D.R | 184 ++---
ReacTran-1.4.1/ReacTran/R/tran.cylspher.R | 18
ReacTran-1.4.1/ReacTran/R/tran.volume.1D.R | 9
ReacTran-1.4.1/ReacTran/R/tran.volume.2D.R |only
ReacTran-1.4.1/ReacTran/R/tran.volume.3D.R |only
ReacTran-1.4.1/ReacTran/inst/CITATION |only
ReacTran-1.4.1/ReacTran/inst/doc/PDE.R |only
ReacTran-1.4.1/ReacTran/inst/doc/PDE.Rnw | 20
ReacTran-1.4.1/ReacTran/inst/doc/PDE.pdf |binary
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.R |only
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.pdf |binary
ReacTran-1.4.1/ReacTran/inst/doc/ReacTran.rnw | 19
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.1D.f |only
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.2D.f |only
ReacTran-1.4.1/ReacTran/inst/doc/fortran/tran.volume.3D.f |only
ReacTran-1.4.1/ReacTran/man/advection.Rd | 14
ReacTran-1.4.1/ReacTran/man/fiadeiro.Rd | 5
ReacTran-1.4.1/ReacTran/man/geometries.Rd | 4
ReacTran-1.4.1/ReacTran/man/properties.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.compaction.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.grid.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.grid.2D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.prop.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/setup.prop.2D.Rd | 4
ReacTran-1.4.1/ReacTran/man/tran.1D.Rd | 4
ReacTran-1.4.1/ReacTran/man/tran.2D.Rd | 6
ReacTran-1.4.1/ReacTran/man/tran.3D.Rd | 9
ReacTran-1.4.1/ReacTran/man/tran.volume.1D.Rd | 155 ++++
ReacTran-1.4.1/ReacTran/src/advection.f | 481 ++++++++++----
ReacTran-1.4.1/ReacTran/src/tran3D.f | 7
ReacTran-1.4.1/ReacTran/vignettes |only
45 files changed, 773 insertions(+), 337 deletions(-)
Title: Constrained B-splines -- outdated 1999 version
Diff between cobs99 versions 0.9-11 dated 2012-12-10 and 0.9-12 dated 2013-06-12
Description: Qualitatively Constrained (Regression) Smoothing via
Linear Programming. OUTDATED version based on He & Ng (1999),
the modified "non-simplex" algorithm of Bartels and Conn
(1980). Use 'cobs' instead, unless for historical comparisons.
Author: Pin T. Ng
Maintainer: Martin Maechler
DESCRIPTION | 9 +-
MD5 | 8 +-
R/drqssbc.R | 10 +-
data/globtemp.rda |binary
src/drqssbc.f | 216 +++++++++++++++++++++++++++++-------------------------
5 files changed, 131 insertions(+), 112 deletions(-)
Title: Statistical Disclosure Control methods for the production of
public- and scientific-use files.
Diff between sdcMicro versions 4.0.2 dated 2013-04-22 and 4.0.3 dated 2013-06-12
Description: Data from statistical agencies and other institutions are
mostly confidential. This package can be used for the
generation of anonymized (micro)data, i.e. for the creation of
public- and scientific-use files. The package sdcMicroGUI
includes a graphical user interface for the methods in this
package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ
sdcMicro-4.0.2/sdcMicro/vignettes/guidelines.R |only
sdcMicro-4.0.3/sdcMicro/DESCRIPTION | 10
sdcMicro-4.0.3/sdcMicro/MD5 | 133 ++--
sdcMicro-4.0.3/sdcMicro/NAMESPACE | 7
sdcMicro-4.0.3/sdcMicro/R/0classes.r | 2
sdcMicro-4.0.3/sdcMicro/R/LLmodGlobalRisk.R | 72 +-
sdcMicro-4.0.3/sdcMicro/R/aux_functions.r | 46 +
sdcMicro-4.0.3/sdcMicro/R/dRisk.R | 4
sdcMicro-4.0.3/sdcMicro/R/dUtility.R | 8
sdcMicro-4.0.3/sdcMicro/R/indivRisk.R | 4
sdcMicro-4.0.3/sdcMicro/R/localSuppression.R | 14
sdcMicro-4.0.3/sdcMicro/R/mafast.R |only
sdcMicro-4.0.3/sdcMicro/R/mdav.R | 8
sdcMicro-4.0.3/sdcMicro/R/measure_risk.R | 8
sdcMicro-4.0.3/sdcMicro/R/methods.r | 4
sdcMicro-4.0.3/sdcMicro/R/microaggregation.R | 37 -
sdcMicro-4.0.3/sdcMicro/R/pram.r | 10
sdcMicro-4.0.3/sdcMicro/R/pram_strata.R | 35 -
sdcMicro-4.0.3/sdcMicro/R/rankSwap.R | 34 -
sdcMicro-4.0.3/sdcMicro/R/report.R | 468 ++++++++--------
sdcMicro-4.0.3/sdcMicro/R/shuffle.R | 19
sdcMicro-4.0.3/sdcMicro/R/timeEstimation.R | 2
sdcMicro-4.0.3/sdcMicro/R/topBotCoding.R | 41 -
sdcMicro-4.0.3/sdcMicro/R/valTable.R | 2
sdcMicro-4.0.3/sdcMicro/data/CASCrefmicrodata.rda |binary
sdcMicro-4.0.3/sdcMicro/data/EIA.rda |binary
sdcMicro-4.0.3/sdcMicro/data/Tarragona.rda |binary
sdcMicro-4.0.3/sdcMicro/data/casc1.rda |binary
sdcMicro-4.0.3/sdcMicro/data/francdat.rda |binary
sdcMicro-4.0.3/sdcMicro/data/free1.rda |binary
sdcMicro-4.0.3/sdcMicro/data/microData.rda |binary
sdcMicro-4.0.3/sdcMicro/data/testdata.RData |binary
sdcMicro-4.0.3/sdcMicro/data/testdata2.RData |binary
sdcMicro-4.0.3/sdcMicro/inst/doc/guidelines.R |only
sdcMicro-4.0.3/sdcMicro/inst/doc/guidelines.pdf |binary
sdcMicro-4.0.3/sdcMicro/inst/doc/sdcMicroPaper.R |only
sdcMicro-4.0.3/sdcMicro/inst/doc/sdcMicroPaper.pdf |binary
sdcMicro-4.0.3/sdcMicro/man/LLmodGlobalRisk.Rd | 26
sdcMicro-4.0.3/sdcMicro/man/LocalRecProg.Rd | 25
sdcMicro-4.0.3/sdcMicro/man/addNoise.Rd | 11
sdcMicro-4.0.3/sdcMicro/man/calcRisks.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dRisk.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dRiskRMD.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dUtility.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/dataGen.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/extractManipData-methods.Rd |only
sdcMicro-4.0.3/sdcMicro/man/globalRecode.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/groupVars-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/localSupp.Rd | 8
sdcMicro-4.0.3/sdcMicro/man/localSupp2.Rd | 3
sdcMicro-4.0.3/sdcMicro/man/localSupp2Wrapper.Rd | 3
sdcMicro-4.0.3/sdcMicro/man/localSuppression.Rd | 11
sdcMicro-4.0.3/sdcMicro/man/mafast.Rd |only
sdcMicro-4.0.3/sdcMicro/man/measure_risk.Rd | 67 +-
sdcMicro-4.0.3/sdcMicro/man/microaggregation.Rd | 17
sdcMicro-4.0.3/sdcMicro/man/pram.Rd | 14
sdcMicro-4.0.3/sdcMicro/man/pram_strata.Rd | 43 -
sdcMicro-4.0.3/sdcMicro/man/print.sdcMicroObj.Rd | 20
sdcMicro-4.0.3/sdcMicro/man/rankSwap.Rd | 10
sdcMicro-4.0.3/sdcMicro/man/renameVars-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/report.Rd | 13
sdcMicro-4.0.3/sdcMicro/man/sdcMicro-deprecated.Rd | 6
sdcMicro-4.0.3/sdcMicro/man/sdcMicro-package.Rd | 29
sdcMicro-4.0.3/sdcMicro/man/sdcMicroObj-class.Rd | 8
sdcMicro-4.0.3/sdcMicro/man/shuffle.Rd | 9
sdcMicro-4.0.3/sdcMicro/man/suda2.Rd | 5
sdcMicro-4.0.3/sdcMicro/man/topBotCoding.Rd | 7
sdcMicro-4.0.3/sdcMicro/man/valTable.Rd | 17
sdcMicro-4.0.3/sdcMicro/man/varToFactor-methods.Rd | 5
sdcMicro-4.0.3/sdcMicro/src/Measure_Risk.h | 15
sdcMicro-4.0.3/sdcMicro/vignettes/guidelines.tex |only
71 files changed, 772 insertions(+), 608 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.3 dated 2013-06-09 and 0.3.1 dated 2013-06-12
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
DESCRIPTION | 15 ++++++++-------
MD5 | 6 +++---
NEWS | 5 +++++
R/zzz.R | 2 +-
4 files changed, 17 insertions(+), 11 deletions(-)
Title: Survival Regression with Smoothed Error Distribution
Diff between smoothSurv versions 1.2.1 dated 2013-03-29 and 1.3-2 dated 2013-06-12
Description: This package contains primarily a function to fit a
regression model with possibly right, left or interval censored
observations and with the error distribution expressed as a
mixture of G-splines. Core part of the computation is done in
compiled C++ written using the Scythe Statistical Library
Version 0.3.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/minPenalty.R | 12 +++---------
R/smoothSurvReg.fit.R | 8 ++------
man/smoothSurvReg.Rd | 6 +++---
man/smoothSurvReg.control.Rd | 6 ++++--
src/AKmatrix.cpp | 6 +++---
src/Scythe_Error.h | 23 +++++++++++++++++++----
src/convertCAD.h | 6 +++---
src/penalLogLik.h | 6 +++---
src/smoothSurvReg84.h | 6 +++---
11 files changed, 59 insertions(+), 52 deletions(-)
Title: Spatially explicit capture-recapture
Diff between secr versions 2.5.0 dated 2013-01-23 and 2.6.0 dated 2013-06-12
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive
detectors, such as traps, or by searching polygons or
transects. Models incorporating distance-dependent detection
are fitted by maximizing the likelihood. Tools are included for
data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
secr-2.5.0/secr/LICENSE |only
secr-2.6.0/secr/DESCRIPTION | 14
secr-2.6.0/secr/MD5 | 165 +--
secr-2.6.0/secr/NEWS | 959 ++-------------------
secr-2.6.0/secr/ONEWS | 854 ++++++++++++++++++
secr-2.6.0/secr/R/ClosedN.R | 6
secr-2.6.0/secr/R/D.designdata.R | 3
secr-2.6.0/secr/R/autoini.R | 3
secr-2.6.0/secr/R/circular.R | 97 +-
secr-2.6.0/secr/R/confint.secr.R | 2
secr-2.6.0/secr/R/esa.R | 13
secr-2.6.0/secr/R/fxi.R | 1
secr-2.6.0/secr/R/mask.check.R | 3
secr-2.6.0/secr/R/methods.R | 195 ++--
secr-2.6.0/secr/R/model.average.R | 100 +-
secr-2.6.0/secr/R/onAttach.R | 6
secr-2.6.0/secr/R/pdot.R | 6
secr-2.6.0/secr/R/plot.secr.R | 26
secr-2.6.0/secr/R/regionN.R | 11
secr-2.6.0/secr/R/score.test.R | 16
secr-2.6.0/secr/R/secr.design.MS.R | 236 +++--
secr-2.6.0/secr/R/secr.fit.R | 194 ++--
secr-2.6.0/secr/R/secr.make.newdata.R | 5
secr-2.6.0/secr/R/secrloglik.R | 69 -
secr-2.6.0/secr/R/sim.capthist.R | 83 +
secr-2.6.0/secr/R/sim.secr.R | 4
secr-2.6.0/secr/R/suggest.buffer.R | 19
secr-2.6.0/secr/R/telemetry.R | 16
secr-2.6.0/secr/R/trap.builder.R | 104 +-
secr-2.6.0/secr/R/utility.R | 373 +++++---
secr-2.6.0/secr/R/verify.R | 68 +
secr-2.6.0/secr/data/deermouse.RData |binary
secr-2.6.0/secr/data/hornedlizard.RData |binary
secr-2.6.0/secr/data/housemouse.RData |binary
secr-2.6.0/secr/data/ovenbird.RData |binary
secr-2.6.0/secr/data/ovensong.RData |binary
secr-2.6.0/secr/data/possum.RData |binary
secr-2.6.0/secr/data/secrdemo.RData |binary
secr-2.6.0/secr/data/skink.RData |binary
secr-2.6.0/secr/data/stoatDNA.RData |binary
secr-2.6.0/secr/inst/doc/secr-datainput.pdf |binary
secr-2.6.0/secr/inst/doc/secr-finitemixtures.pdf |binary
secr-2.6.0/secr/inst/doc/secr-manual.pdf |binary
secr-2.6.0/secr/inst/doc/secr-overview.pdf |binary
secr-2.6.0/secr/inst/doc/secr-polygondetectors.pdf |binary
secr-2.6.0/secr/inst/doc/secr-varyingeffort.pdf |binary
secr-2.6.0/secr/man/AIC.secr.Rd | 35
secr-2.6.0/secr/man/FAQ.Rd | 50 -
secr-2.6.0/secr/man/circular.Rd | 54 +
secr-2.6.0/secr/man/details.Rd |only
secr-2.6.0/secr/man/detectfn.Rd | 187 ++--
secr-2.6.0/secr/man/distancetotrap.Rd | 5
secr-2.6.0/secr/man/esaplot.Rd | 2
secr-2.6.0/secr/man/esaplotsecr.Rd | 2
secr-2.6.0/secr/man/ip.secr.Rd | 2
secr-2.6.0/secr/man/make.mask.Rd | 2
secr-2.6.0/secr/man/make.systematic.Rd | 2
secr-2.6.0/secr/man/model.average.Rd | 49 -
secr-2.6.0/secr/man/ovensong.Rd | 2
secr-2.6.0/secr/man/pdot.Rd | 2
secr-2.6.0/secr/man/plot.capthist.Rd | 4
secr-2.6.0/secr/man/plot.secr.Rd | 2
secr-2.6.0/secr/man/predict.secr.Rd | 30
secr-2.6.0/secr/man/rbind.capthist.Rd | 4
secr-2.6.0/secr/man/read.mask.Rd | 9
secr-2.6.0/secr/man/region.N.Rd | 5
secr-2.6.0/secr/man/score.test.Rd | 9
secr-2.6.0/secr/man/secr-package.Rd | 14
secr-2.6.0/secr/man/secr.design.MS.Rd | 57 +
secr-2.6.0/secr/man/secr.fit.Rd | 93 --
secr-2.6.0/secr/man/sim.capthist.Rd | 16
secr-2.6.0/secr/man/speed.Rd |only
secr-2.6.0/secr/man/stoatDNA.Rd | 2
secr-2.6.0/secr/man/subset.capthist.Rd | 15
secr-2.6.0/secr/man/suggest.buffer.Rd | 10
secr-2.6.0/secr/man/trap.builder.Rd | 31
secr-2.6.0/secr/man/troubleshooting.Rd | 18
secr-2.6.0/secr/man/usage.Rd | 8
secr-2.6.0/secr/man/usagePlot.Rd | 2
secr-2.6.0/secr/man/verify.Rd | 3
secr-2.6.0/secr/man/writeGPS.Rd | 2
secr-2.6.0/secr/src/detectfn.c | 142 ++-
secr-2.6.0/secr/src/secr.c | 388 ++++++--
secr-2.6.0/secr/src/secr.h | 30
secr-2.6.0/secr/src/trapping.c | 30
85 files changed, 3052 insertions(+), 1917 deletions(-)
Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Diff between rsgcc versions 1.0.4 dated 2012-09-22 and 1.0.5 dated 2013-06-12
Description: This package provides functions for calculating
associations between two genes with five correlation
methods(e.g., the Gini correlation coefficient [GCC], the
Pearson's product moment correlation coefficient [PCC], the
Kendall tau rank correlation coefficient [KCC], the Spearman's
rank correlation coefficient [SCC] and the Tukey's biweight
correlation coefficient [BiWt], and three non-correlation
methods (e.g., mutual information [MI] and the maximal
information-based nonparametric exploration [MINE], and the
euclidean distance [ED]). It can also been implemented to
perform the correlation and clustering analysis of
transcriptomic data profiled by microarray and RNA-Seq
technologies. Additionally, this package can be further applied
to construct gene co-expression networks (GCNs).
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma
DESCRIPTION | 40 +++++-----
MD5 | 40 +++++-----
R/getdist.R | 7 +
R/gethclust.R | 11 +-
R/rsgcc.R | 193 ++++++++++++++++++++++++++++++++++++-------------
R/rsgccgui.R | 14 +--
R/tsgene.R | 97 +++++++++++++++---------
R/tsheatmap.R | 19 ++--
data/rsgcc.rda |binary
man/adjacencymatrix.Rd | 48 +++++++++---
man/gcc.corfinal.Rd | 3
man/gcc.dist.Rd | 7 -
man/gcc.hclust.Rd | 9 +-
man/gcc.heatmap.Rd | 8 +-
man/gcc.tsheatmap.Rd | 12 +--
man/getsgene.Rd | 15 ++-
man/rsgcc-package.Rd | 13 ++-
man/uniqueTissues.Rd | 4 +
src/bridge.c | 83 ++++++++++++++++++---
src/mi.c | 108 +++++++--------------------
src/mi.h | 2
21 files changed, 464 insertions(+), 269 deletions(-)
Title: publication-quality graphics.
Diff between prettyGraphs versions 1.0 dated 2012-06-19 and 2.0.3 dated 2013-06-12
Description: prettyGraphs contains simple, crisp graphics. Graphics
produced by prettyGraphs are publication-quality.
Author: Derek Beaton
Maintainer: Derek Beaton
prettyGraphs-1.0/prettyGraphs/R/colorPoints.R |only
prettyGraphs-1.0/prettyGraphs/R/createOriginalPointList.R |only
prettyGraphs-1.0/prettyGraphs/R/createOriginalPointsAndColors.R |only
prettyGraphs-1.0/prettyGraphs/R/createSingleColorVector.R |only
prettyGraphs-1.0/prettyGraphs/R/makeNewPlotWindow.R |only
prettyGraphs-1.0/prettyGraphs/R/prettyGraphs-internal.R |only
prettyGraphs-2.0.3/prettyGraphs/DESCRIPTION | 11 -
prettyGraphs-2.0.3/prettyGraphs/MD5 | 51 ++---
prettyGraphs-2.0.3/prettyGraphs/NAMESPACE | 2
prettyGraphs-2.0.3/prettyGraphs/R/colorVectorIsNull.R | 4
prettyGraphs-2.0.3/prettyGraphs/R/contributionBars.R | 80 ++++----
prettyGraphs-2.0.3/prettyGraphs/R/correlationPlotter.R | 44 ++--
prettyGraphs-2.0.3/prettyGraphs/R/createColorVectorsByDesign.R | 19 +
prettyGraphs-2.0.3/prettyGraphs/R/makeAxes.R |only
prettyGraphs-2.0.3/prettyGraphs/R/minmaxHelper.R | 50 +++--
prettyGraphs-2.0.3/prettyGraphs/R/plotCircle.R | 11 -
prettyGraphs-2.0.3/prettyGraphs/R/plotPoints.R | 77 ++++----
prettyGraphs-2.0.3/prettyGraphs/R/plotText.R | 22 +-
prettyGraphs-2.0.3/prettyGraphs/R/prettyBars.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsColorSelection.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsColors.R | 1
prettyGraphs-2.0.3/prettyGraphs/R/prettyGraphsHSVColorSelection.R |only
prettyGraphs-2.0.3/prettyGraphs/R/prettyPlot.R | 96 +++++++---
prettyGraphs-2.0.3/prettyGraphs/man/contributionBars.Rd | 13 -
prettyGraphs-2.0.3/prettyGraphs/man/correlationPlotter.Rd | 13 +
prettyGraphs-2.0.3/prettyGraphs/man/createColorVectorsByDesign.Rd | 8
prettyGraphs-2.0.3/prettyGraphs/man/minmaxHelper.Rd | 5
prettyGraphs-2.0.3/prettyGraphs/man/peeledHull.Rd | 3
prettyGraphs-2.0.3/prettyGraphs/man/prettyBars.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphs-package.Rd | 4
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphsColorSelection.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyGraphsHSVColorSelection.Rd |only
prettyGraphs-2.0.3/prettyGraphs/man/prettyPlot.Rd | 76 +++++--
33 files changed, 356 insertions(+), 234 deletions(-)
More information about migration.indices at CRAN
Permanent link
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Diff between candisc versions 0.6-3 dated 2013-03-15 and 0.6-5 dated 2013-06-12
Description: This package includes functions for computing and
visualizing generalized canonical discriminant analyses and
canonical correlation analysis for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a
one-way MANOVA design and is equivalent to canonical
correlation analysis between a set of quantitative response
variables and a set of dummy variables coded from the factor
variable. The candisc package generalizes this to multi-way
MANOVA designs for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The
graphic functions provide low-rank (1D, 2D, 3D) visualizations
of terms in an mlm via the plot.candisc and heplot.candisc
methods. Related plots are now provided for canonical
correlation analysis when all predictors are quantitative.
Author: Michael Friendly and John Fox
Maintainer: Michael Friendly
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
NEWS | 9 +++++++++
R/cancor.R | 9 +++++----
R/candisc.R | 5 +++++
R/plot.candisc.R | 22 ++++++++++++----------
data/Grass.rda |binary
data/HSB.rda |binary
data/Wolves.rda |binary
man/cancor.Rd | 5 +++--
man/candisc-package.Rd | 4 ++--
11 files changed, 52 insertions(+), 34 deletions(-)
Title: Conditional logistic regression: A two-step estimation method
Diff between TwoStepCLogit versions 1.2.1 dated 2012-09-18 and 1.2.2 dated 2013-06-11
Description: Conditional logistic regression with longitudinal follow
up and individual-level random coefficients: A stable and
efficient two-step estimation method
Author: Radu V. Craiu, Thierry Duchesne, Daniel Fortin and Sophie
Baillargeon
Maintainer: Thierry Duchesne
TwoStepCLogit-1.2.1/TwoStepCLogit/TwoStepCLogit.Rproj |only
TwoStepCLogit-1.2.1/TwoStepCLogit/inst/tests |only
TwoStepCLogit-1.2.1/TwoStepCLogit/tests |only
TwoStepCLogit-1.2.2/TwoStepCLogit/DESCRIPTION | 10 +-
TwoStepCLogit-1.2.2/TwoStepCLogit/MD5 | 20 +---
TwoStepCLogit-1.2.2/TwoStepCLogit/R/Ts.estim.R | 42 +++++++---
TwoStepCLogit-1.2.2/TwoStepCLogit/R/TwoStepCLogit.R | 4
TwoStepCLogit-1.2.2/TwoStepCLogit/R/ddim.R | 14 +--
TwoStepCLogit-1.2.2/TwoStepCLogit/R/internal.R | 25 ++---
TwoStepCLogit-1.2.2/TwoStepCLogit/inst/NEWS.Rd | 11 ++
TwoStepCLogit-1.2.2/TwoStepCLogit/man/TwoStepCLogit-package.Rd | 4
11 files changed, 75 insertions(+), 55 deletions(-)
Title: R Commander Plug-in for MPA Statistics
Diff between RcmdrPlugin.MPAStats versions 1.0.2 dated 2013-02-01 and 1.1.0 dated 2013-06-11
More information about RcmdrPlugin.MPAStats at CRAN
Description: This package provides an R Commander plugin that offers a
unified menu of new and pre-existing statistical functions
related to public management and policy analysis statistics.
Functions and menus have been renamed according to the usage in
PMGT 630 in the Master of Public Administration program at
Brigham Young University.
Author: Andrew Heiss, Richard Payne
Maintainer: Andrew Heiss
CHANGELOG | 5
DESCRIPTION | 13 +
MD5 | 30 +++-
R/RcmdrPlugin.MPAStats.R | 10 +
R/anova.R |only
R/bivariate-analysis.R | 231 ++++++++++++++++++++++++++++++++++-
R/chi-square.R |only
R/confidence-intervals.R | 85 ++++++++++--
R/kruskal-wallis.R |only
R/logistic-regression.R |only
R/multiple-regression.R |only
R/ologit-regression.R |only
R/t-test.R |only
R/wilcoxon-mann-whitney.R |only
R/wilcoxon-rank.R |only
inst/CHANGELOG | 5
inst/etc/menus.txt | 44 +++---
man/DataframeSummary.Rd | 2
man/RcmdrPlugin.MPAStats-internal.Rd | 1
man/RcmdrPlugin.MPAStats-package.Rd | 12 -
man/interpretations.Rd |only
21 files changed, 369 insertions(+), 69 deletions(-)
Permanent link
Title: multicore higher-order functions
Diff between mchof versions 0.2 dated 2013-05-07 and 0.3 dated 2013-06-11
Description: mchof (read: mac'hoff) is a utility library that provides
composable, consistent parallel implementations of functionals
such as Filter, Fold, ZipWith and Partition.
Author: Ryan Grannell
Maintainer: Ryan Grannell
mchof-0.2/mchof/inst/tests/test-filter.r |only
mchof-0.2/mchof/inst/tests/test-find.r |only
mchof-0.2/mchof/inst/tests/test-matching.r |only
mchof-0.2/mchof/inst/tests/test-partition.r |only
mchof-0.2/mchof/inst/tests/test-position.r |only
mchof-0.2/mchof/inst/tests/test-reduce.r |only
mchof-0.2/mchof/inst/tests/test-speed.r |only
mchof-0.2/mchof/inst/tests/test-unzip.r |only
mchof-0.2/mchof/inst/tests/test-zip.r |only
mchof-0.2/mchof/man/plyr.Rd |only
mchof-0.3/mchof/DESCRIPTION | 26 +-
mchof-0.3/mchof/MD5 | 96 ++++++----
mchof-0.3/mchof/NAMESPACE | 6
mchof-0.3/mchof/NEWS | 42 +++-
mchof-0.3/mchof/R/call_mclapply.R | 100 ++++++----
mchof-0.3/mchof/R/filter.R | 94 ++++-----
mchof-0.3/mchof/R/fold.R |only
mchof-0.3/mchof/R/mchof.R | 68 ++++++-
mchof-0.3/mchof/R/partition.R | 70 +++----
mchof-0.3/mchof/R/position.R | 164 +++++++++--------
mchof-0.3/mchof/R/quantify.R |only
mchof-0.3/mchof/R/reduce.R | 118 ++++++------
mchof-0.3/mchof/R/reject.R |only
mchof-0.3/mchof/R/test_generators.R |only
mchof-0.3/mchof/R/test_utils.R |only
mchof-0.3/mchof/R/unzip.R | 117 +++++++-----
mchof-0.3/mchof/R/utils.R |only
mchof-0.3/mchof/R/zip.R | 161 ++++++++--------
mchof-0.3/mchof/README.md | 31 +--
mchof-0.3/mchof/inst/benchmark |only
mchof-0.3/mchof/inst/examples |only
mchof-0.3/mchof/inst/tests/test-backend.r | 98 +++++-----
mchof-0.3/mchof/inst/tests/test-factors.r | 54 +----
mchof-0.3/mchof/inst/tests/test-filters.r |only
mchof-0.3/mchof/inst/tests/test-folds.r |only
mchof-0.3/mchof/inst/tests/test-len-x.r | 259 ++++++++++++++++++---------
mchof-0.3/mchof/inst/tests/test-positions.r |only
mchof-0.3/mchof/inst/tests/test-quantifier.r |only
mchof-0.3/mchof/inst/tests/test-utils.r |only
mchof-0.3/mchof/inst/tests/test-windows.r |only
mchof-0.3/mchof/inst/tests/test-zips.r |only
mchof-0.3/mchof/man/mcAll.Rd |only
mchof-0.3/mchof/man/mcAny.Rd |only
mchof-0.3/mchof/man/mcFilter.Rd | 75 ++++---
mchof-0.3/mchof/man/mcFind.Rd | 57 +++--
mchof-0.3/mchof/man/mcFold.Rd |only
mchof-0.3/mchof/man/mcOne.Rd |only
mchof-0.3/mchof/man/mcPartition.Rd | 51 +++--
mchof-0.3/mchof/man/mcPosition.Rd | 61 ++++--
mchof-0.3/mchof/man/mcReduce.Rd | 79 ++++++--
mchof-0.3/mchof/man/mcReject.Rd |only
mchof-0.3/mchof/man/mcUnzip.Rd | 28 ++
mchof-0.3/mchof/man/mcUnzipWith.Rd | 70 +++++--
mchof-0.3/mchof/man/mcZip.Rd | 51 +++--
mchof-0.3/mchof/man/mcZipWith.Rd | 102 +++++++---
mchof-0.3/mchof/man/mchof.Rd | 86 +++++++-
mchof-0.3/mchof/tests/run_tests.R | 7
57 files changed, 1359 insertions(+), 812 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 1.3 dated 2013-05-31 and 1.3-1 dated 2013-06-11
Description: Spatial and spatio-temporal modelling of point patterns
using the log-Gaussian Cox process
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle.
Additional code contributions from E. Pebesma.
Maintainer: Benjamin M. Taylor
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
R/AggregateSpatialOnlyPlusParameters.R | 1 -
R/SpatialOnlyPlusParameters.R | 1 -
R/SpatioTemporalPlusParameters.R | 13 +++++++++----
R/lgcpStructures.R | 4 +++-
inst/doc/lgcp.pdf |binary
7 files changed, 21 insertions(+), 16 deletions(-)
Title: Multivariate likelihood ratio calculation and evaluation
Diff between comparison versions 1.0-0 dated 2012-07-16 and 1.0-2 dated 2013-06-11
Description: Functions for calculating and evaluating likelihood ratios
from uni/multivariate continuous observations
Author: David Lucy
Maintainer: David Lucy
comparison-1.0-0/comparison/LICENCE |only
comparison-1.0-2/comparison/DESCRIPTION | 9 +++++----
comparison-1.0-2/comparison/MD5 | 7 +++----
comparison-1.0-2/comparison/data/glass.rda |binary
comparison-1.0-2/comparison/man/two.level.normal.LR.Rd | 2 +-
5 files changed, 9 insertions(+), 9 deletions(-)
Title: Three-way component analysis
Diff between ThreeWay versions 1.1 dated 2013-03-13 and 1.1.1 dated 2013-06-11
Description: Component analysis for three-way data arrays by means of
Candecomp/Parafac, Tucker3, Tucker2 and Tucker1 models
Author: Maria Antonietta Del Ferraro, Henk A.L. Kiers, Paolo Giordani
Maintainer: Paolo Giordani
DESCRIPTION | 8 ++++----
MD5 | 22 +++++++++++-----------
R/CP.R | 17 -----------------
R/T3.R | 16 ----------------
R/bootstrapCP.R | 13 -------------
R/bootstrapT3.R | 18 ------------------
man/CPfunc.Rd | 10 ++++++----
man/CPfuncrep.Rd | 6 ++----
man/T2func.Rd | 9 ++++-----
man/T2funcrep.Rd | 6 ++----
man/T3func.Rd | 6 ++----
man/T3funcrep.Rd | 6 ++----
12 files changed, 33 insertions(+), 104 deletions(-)
Title: toolbox for pseudo and quasi random number generation and RNG
tests.
Diff between randtoolbox versions 1.13 dated 2013-04-02 and 1.14 dated 2013-06-11
Description: The package provides (1) pseudo random generators -
general linear congruential generators (Park Miller) and
multiple recursive generators (Knuth TAOCP), generalized
feedback shift register (SF-Mersenne Twister algorithm and WELL
generators); (2) quasi random generators - the Torus algorithm,
the Sobol sequence, the Halton sequence (thus include Van der
Corput sequence) and (3) some additional tests such as the gap
test, the serial test, the poker test... The package depends on
rngWELL package but it can be provided without this dependency
on demand to the maintainer. For true random number generation,
use the 'random' package, for Latin Hypercube Sampling (a
hybrid QMC method), use the 'lhs' package, a number of RNGs and
tests for RNGs are provided by 'RDieHarder', all available on
CRAN. There is also a small stand-alone package 'rngwell19937'
for the WELL19937a RNG.
Author: Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm
Wuertz (except underlying C codes of (i) the SFMT algorithm
from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from
D. Knuth). See LICENSE file for details.
Maintainer: Christophe Dutang
DESCRIPTION | 8 ++++----
MD5 | 20 +++++++++++---------
inst/doc/fullpres.R |only
inst/doc/fullpres.pdf |binary
inst/doc/shortintro.R |only
inst/doc/shortintro.pdf |binary
man/colltest.Rd | 5 +++--
man/colltestsparse.Rd | 5 +++--
man/pseudoRNG.Rd | 3 ++-
man/quasiRNG.Rd | 3 ++-
man/runifInterface.Rd | 4 ++--
src/Makevars | 3 +--
12 files changed, 28 insertions(+), 23 deletions(-)
Title: toolbox for WELL random number generators.
Diff between rngWELL versions 0.10-1 dated 2013-03-27 and 0.10-2 dated 2013-06-11
Description: It is a dedicated package to WELL pseudo random
generators, which were introduced in Panneton et al. (2006),
``Improved Long-Period Generators Based on Linear Recurrences
Modulo 2'', ACM Transactions on Mathematical Software. But this
package is not intended to be used directly, you are strongly
__encouraged__ to use the 'randtoolbox' package, which depends
on this package.
Author: all C code by F. Panneton, P. L'Ecuyer and M. Matsumoto and R
port by Christophe Dutang and Petr Savicky
Maintainer: Christophe Dutang
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 2 +-
src/Makevars | 3 +--
4 files changed, 9 insertions(+), 10 deletions(-)
Title: Modern measures of population differentiation
Diff between mmod versions 1.01 dated 2012-10-18 and 1.2 dated 2013-06-11
Description: mmod provides functions for measuring population
divergence from genotypic data
Author: David Winter
Maintainer: David Winter
mmod-1.01/mmod/LICENSE |only
mmod-1.01/mmod/REFERENCES.bib |only
mmod-1.01/mmod/mmod_1.01.tar.gz |only
mmod-1.01/mmod/sandbox |only
mmod-1.01/mmod/test |only
mmod-1.2/mmod/DESCRIPTION | 13 +-
mmod-1.2/mmod/MD5 | 81 ++++++++--------
mmod-1.2/mmod/NAMESPACE | 1
mmod-1.2/mmod/NEWS | 7 +
mmod-1.2/mmod/R/D_Jost.R | 15 +-
mmod-1.2/mmod/R/Gst_Hedrick.R | 14 +-
mmod-1.2/mmod/R/Gst_Nei.R | 4
mmod-1.2/mmod/R/HsHt.R | 8 -
mmod-1.2/mmod/R/as.genind.DNAbin.R |only
mmod-1.2/mmod/R/diff_stats.R | 18 +--
mmod-1.2/mmod/R/dist.codom.R | 8 -
mmod-1.2/mmod/R/harmonic_mean.R | 7 -
mmod-1.2/mmod/R/pairwise_D.R | 3
mmod-1.2/mmod/R/pairwise_Gst_Hedrick.R | 5
mmod-1.2/mmod/R/pairwise_Gst_Nei.R | 5
mmod-1.2/mmod/inst/doc/mmod-demo.R |only
mmod-1.2/mmod/inst/staticdocs/D_Jost.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/Gst_Hedrick.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/Gst_Nei.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/Phi_st_Meirmans.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/as.genind.DNAbin.html |only
mmod-1.2/mmod/inst/staticdocs/chao_bootstrap.html | 6 -
mmod-1.2/mmod/inst/staticdocs/diff_stats.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/diff_test.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/dist.codom.html | 13 +-
mmod-1.2/mmod/inst/staticdocs/harmonic_mean.html | 13 +-
mmod-1.2/mmod/inst/staticdocs/img |only
mmod-1.2/mmod/inst/staticdocs/index.html | 15 +-
mmod-1.2/mmod/inst/staticdocs/jacknife_populations.html | 6 -
mmod-1.2/mmod/inst/staticdocs/js |only
mmod-1.2/mmod/inst/staticdocs/mmod.html | 4
mmod-1.2/mmod/inst/staticdocs/pairwise_D.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/pairwise_Gst_Hedrick.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/pairwise_Gst_Nei.html | 11 +-
mmod-1.2/mmod/inst/staticdocs/rgenotypes.html | 35 +++---
mmod-1.2/mmod/inst/staticdocs/summarise_bootstrap.html | 6 -
mmod-1.2/mmod/inst/tests |only
mmod-1.2/mmod/man/as.genind.DNAbin.Rd |only
mmod-1.2/mmod/tests |only
44 files changed, 209 insertions(+), 177 deletions(-)
Title: Multivariate normal mixture models and mixtures of generalized
linear mixed models including model based clustering
Diff between mixAK versions 3.0-1 dated 2013-02-08 and 3.1 dated 2013-06-11
Description: This package contains a mixture of statistical methods
including the MCMC methods to analyze normal mixtures.
Additionally, model based clustering methods are implemented to
perform classification based on (multivariate) longitudinal (or
otherwise correlated) data. The basis for such clustering is a
mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
DESCRIPTION | 18 ++++++++++++------
MD5 | 40 +++++++++++++++++++++-------------------
R/GLMM_MCMC.R | 46 +++++++++++++++++++++++++---------------------
R/GLMM_MCMCdata.R | 19 +++++++++++++++----
R/GLMM_MCMCwrapper.R | 12 +++++++-----
R/NMixRelabel.GLMM_MCMC.R | 8 ++++++--
data/Acidity.rda |binary
data/Enzyme.rda |binary
data/Galaxy.rda |binary
data/PBC910.RData |only
inst/CITATION | 10 +++++-----
man/GLMMMCMC.Rd | 27 ++++++++++++++-------------
man/GLMMMCMCwrapper.Rd | 8 +++++---
man/MVNmixture.Rd | 9 ++++++---
man/NMixRelabel.Rd | 13 ++++++++-----
man/PBC910.Rd |only
man/TMVN.Rd | 18 ++++++++++++------
man/Tandmob.Rd | 9 ++++-----
src/GLMM_MCMC.cpp | 35 ++++++++++++++++++-----------------
src/GLMM_MCMC.h | 9 +++++----
src/GLMM_NMixRelabel.cpp | 19 ++++++++++---------
src/GLMM_NMixRelabel.h | 3 +++
22 files changed, 176 insertions(+), 127 deletions(-)
Title: Bayesian Survival Regression with Flexible Error and Random
Effects Distributions
Diff between bayesSurv versions 1.1 dated 2012-12-27 and 2.1-1 dated 2013-06-11
Description: Later
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
CHANGES | 6
DESCRIPTION | 9
MD5 | 62 ++---
R/bayesBisurvreg.priorInit.R | 1
R/bayessurvreg2.R | 12 -
R/bayessurvreg3.R | 199 +++++++++++++++--
R/bayessurvreg3.priorInit.R | 4
R/bayessurvreg3.priorb.R | 2
R/bayessurvreg3.writeHeaders.R | 26 ++
R/files2coda.R | 15 +
R/give.init.Gspline.R | 37 +--
R/predictive.R | 6
R/predictive2.control.R | 3
man/bayesBisurvreg.Rd | 2
man/bayessurvreg2.Rd | 4
man/bayessurvreg3.Rd | 149 +++++++++---
man/bayessurvreg3.help.Rd | 8
man/densplot2.Rd | 3
src/AK_BasicFun.h | 4
src/Gspline.cpp | 20 +
src/Gspline_update_Scale.cpp | 20 +
src/Gspline_update_a.cpp | 4
src/arms.cpp | 4
src/bayessurvreg1.cpp | 3
src/bayessurvreg1.h | 4
src/bayessurvreg2.cpp | 183 +++++++++++++--
src/bayessurvreg2.h | 77 ++++--
src/constants.h | 3
src/covMatrix.cpp | 5
src/update_Data_GS.cpp | 338 ++++++++++++++++++++++++++++-
src/update_Data_GS.h | 56 +++-
src/update_sens_spec_misclassification.cpp |only
src/update_sens_spec_misclassification.h |only
33 files changed, 1067 insertions(+), 202 deletions(-)
Title: R front-end to PostgreSQL and Pivotal (Greenplum) database,
wrapper for MADlib
Diff between PivotalR versions 0.1.0 dated 2013-06-07 and 0.1.1 dated 2013-06-11
Description: R wrapper of Pivotal Data Fabrics running on PostgreSQL or
Pivotal (Greenplum) database with parallel and distributed
computation ability for big data analytics. PivotalR is a
package that enables users of R to interact with the Pivotal
(Greenplum) Database as well as Pivotal HD/HAWQ for Big Data
analytics. It does so by providing an interface to the
operations on tables/views in the database. These operations
are almost the same as those of data.frame. Thus the users of R
do not need to learn SQL when they operate on the objects in
the database. It also provides a wrapper for MADlib, which is
an open-source library for parallel and scalable in-database
analytics.
Author: Predictive Analytics Team at Pivotal Inc.
Maintainer: Hai Qian
DESCRIPTION | 8 ++--
MD5 | 71 ++++++++++++++++++-----------------
NAMESPACE | 9 +++-
R/db_conn-generic.R | 35 ++++++++++++++---
R/defs-pkg.R | 3 +
R/madlib-glm.R | 4 +-
R/madlib-lm.R | 2 +
R/madlib-summary.R | 16 ++++++++
R/method-aggregates_.R | 64 ++++++++++++++++++++++++--------
R/method-as.db.data.frame_.R | 25 +++++++++---
R/method-as.factor_.R | 17 ++++++++
R/method-by_.R | 1
R/method-db.data.frame_.R | 6 +--
R/method-db.data.frame_props_.R | 80 ++++++++++++++++++++++++++++++++++++++--
R/method-delete_.R | 60 ++++++++++++++++++++++++------
R/method-extraction_.R | 5 +-
R/method-merge_.R | 6 +++
R/method-ops.R | 10 +++--
R/method-replacement_.R | 8 ++++
R/method-sort_.R | 1
R/predict.R | 22 ++++++++---
R/utilities.R | 4 ++
R/utility-generic.R | 9 ++--
man/aggregate-methods.Rd | 2 +
man/as.db.data.frame-methods.Rd | 13 +++++-
man/as.factor-methods.Rd | 4 +-
man/db.Rquery-class.Rd | 11 +++++
man/db.data.frame-class.Rd | 15 +++++++
man/db.objects.Rd | 11 +++++
man/db.table-class.Rd | 2 -
man/delete-methods.Rd | 9 +++-
man/dim-methods.Rd | 16 ++++++--
man/is.factor-methods.Rd |only
man/madlib.summary.Rd | 9 +++-
man/names-methods.Rd | 8 +++-
man/pkg-package.Rd | 62 ++++++++++++++++++++++++++++---
man/predict.Rd | 8 ++++
37 files changed, 508 insertions(+), 128 deletions(-)
Title: The Right Editor to Write R
Diff between rite versions 0.1 dated 2013-06-05 and 0.2 dated 2013-06-10
Description: A simple yet powerful script editor built natively in R
with tcltk.
Author: Thomas J. Leeper
Maintainer: Thomas J. Leeper
rite-0.1/rite/inst/logo/favicon.ico |only
rite-0.2/rite/DESCRIPTION | 10
rite-0.2/rite/MD5 | 12
rite-0.2/rite/NEWS | 19 +
rite-0.2/rite/R/rite.r | 500 +++++++++++++++++++++---------------
rite-0.2/rite/inst/logo/rlogo.gif |only
rite-0.2/rite/man/rite-package.Rd | 4
rite-0.2/rite/man/rite.Rd | 39 ++
8 files changed, 372 insertions(+), 212 deletions(-)
Title: Multivariate regression with covariance estimation
Diff between MRCE versions 1.0 dated 2012-01-07 and 2.0 dated 2013-06-10
Description: Multivariate regression with covariance estimation
Author: Adam J. Rothman
Maintainer: Adam J. Rothman
MRCE-1.0/MRCE/R/compute.mrce.approx.R |only
MRCE-1.0/MRCE/R/mrce.approx.cv.R |only
MRCE-1.0/MRCE/R/multi.lasso.R |only
MRCE-1.0/MRCE/R/multi.lasso.cv.R |only
MRCE-2.0/MRCE/DESCRIPTION | 16 +-
MRCE-2.0/MRCE/MD5 | 21 +--
MRCE-2.0/MRCE/R/compute.fixed.R |only
MRCE-2.0/MRCE/R/compute.mrce.R | 116 +++++++++++++-----
MRCE-2.0/MRCE/R/mrce.R | 76 ++----------
MRCE-2.0/MRCE/R/mrce.cv.R | 105 +++++++++-------
MRCE-2.0/MRCE/R/rblasso.R | 40 +++---
MRCE-2.0/MRCE/man/MRCE-package.Rd | 48 +++----
MRCE-2.0/MRCE/man/mrce.Rd | 215 +++++++++++++++++++++++-----------
MRCE-2.0/MRCE/src/mrce-solveb.c | 180 ++++++++++++----------------
14 files changed, 443 insertions(+), 374 deletions(-)
Title: A package to perform actuarial mathematics for life
contingencies insurances
Diff between lifecontingencies versions 0.9.8 dated 2013-05-06 and 0.9.8.5 dated 2013-06-10
More information about lifecontingencies at CRAN
Description: Financial and actuarial functions to evaluate life
contingencies.
Author: Giorgio A. Spedicato
Maintainer: Giorgio A. Spedicato
lifecontingencies-0.9.8.5/lifecontingencies/ChangeLog | 3
lifecontingencies-0.9.8.5/lifecontingencies/DESCRIPTION | 8
lifecontingencies-0.9.8.5/lifecontingencies/MD5 | 51
lifecontingencies-0.9.8.5/lifecontingencies/NEWS | 7
lifecontingencies-0.9.8.5/lifecontingencies/R/actuarialFunctions.R | 5
lifecontingencies-0.9.8.5/lifecontingencies/inst/CITATION | 4
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.R |only
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.Rnw | 3215 ++++------
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.R |only
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.Rnw | 37
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/lifecontingencies_numerical_checks.pdf |binary
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/mortality_projection.R |only
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/mortality_projection.Rnw | 52
lifecontingencies-0.9.8.5/lifecontingencies/inst/doc/mortality_projection.pdf |binary
lifecontingencies-0.9.8.5/lifecontingencies/man/DAxn.Rd | 4
lifecontingencies-0.9.8.5/lifecontingencies/man/Multiple-life-insurances.Rd | 3
lifecontingencies-0.9.8.5/lifecontingencies/man/annuity.Rd | 6
lifecontingencies-0.9.8.5/lifecontingencies/man/lifecontingencies-package.Rd | 4
lifecontingencies-0.9.8.5/lifecontingencies/man/rLifeContingencies.Rd | 6
lifecontingencies-0.9.8.5/lifecontingencies/man/rLifeContingenciesXyz.Rd | 6
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/Sweave.sty |only
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.Rnw | 3215 ++++------
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 580 -
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/lifecontingencies_numerical_checks.Rnw | 37
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/mortality_projection.Rnw | 52
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/mortality_projection.bbl |only
lifecontingencies-0.9.8.5/lifecontingencies/vignettes/mortality_projection.blg |only
lifecontingencies-0.9.8/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package-figBalanceDue.pdf |only
lifecontingencies-0.9.8/lifecontingencies/vignettes/an_introduction_to_lifecontingencies_package.R |only
lifecontingencies-0.9.8/lifecontingencies/vignettes/mortality_projection.R |only
31 files changed, 3683 insertions(+), 3612 deletions(-)
Permanent link
Title: Affinity Propagation Clustering
Diff between apcluster versions 1.3.1 dated 2013-04-22 and 1.3.2 dated 2013-06-10
Description: The apcluster package implements Frey's and Dueck's
Affinity Propagation clustering in R. The algorithms are
largely analogous to the Matlab code published by Frey and
Dueck. The package further provides leveraged affinity
propagation and an algorithm for exemplar-based agglomerative
clustering that can also be used to join clusters obtained from
affinity propagation. Various plotting functions are available
for analyzing clustering results.
Author: Ulrich Bodenhofer, Andreas Kothmeier, Johannes Palme
Maintainer: Ulrich Bodenhofer
DESCRIPTION | 8 -
MD5 | 22 ++--
NEWS | 11 ++
R/apcluster-methods.R | 22 ++--
R/apclusterL-methods.R | 15 +--
R/plot-methods.R | 83 ++++++++++++++---
inst/doc/apcluster.R | 153 ++++++++++++++++++++++----------
inst/doc/apcluster.Rnw | 223 ++++++++++++++++++++++++++++++++----------------
inst/doc/apcluster.pdf |binary
man/heatmap-methods.Rd | 3
man/plot-methods.Rd | 41 +++++++-
vignettes/apcluster.Rnw | 223 ++++++++++++++++++++++++++++++++----------------
12 files changed, 555 insertions(+), 249 deletions(-)
Title: Safe implementation of Monte Carlo tests.
Diff between simctest versions 2.2 dated 2013-02-20 and 2.3 dated 2013-06-10
Description: Algorithms for the implementation and evaluation of Monte
Carlo tests, as well as for their use in multiple testing
procedures.
Author: Axel Gandy
Maintainer: Axel Gandy
DESCRIPTION | 6 +--
MD5 | 42 +++++++++++-----------
R/mmctest.R | 68 +++++++++++++++++++-----------------
inst/doc/papers.bib | 7 +++
inst/doc/simctest-intro.R |only
inst/doc/simctest-intro.pdf |binary
inst/doc/simctest-mmctest-intro.R |only
inst/doc/simctest-mmctest-intro.Rnw | 40 ++++++++++++---------
inst/doc/simctest-mmctest-intro.pdf |binary
man/confidenceLimits-methods.Rd | 2 -
man/getNumber-methods.Rd | 2 -
man/getSamples-methods.Rd | 4 +-
man/hBH-methods.Rd | 2 -
man/hBonferroni-methods.Rd | 2 -
man/hPC-methods.Rd | 2 -
man/mmctSampler-class.Rd | 7 ++-
man/mmctSampler-methods.Rd | 8 ++--
man/mmctest-class.Rd | 2 -
man/mmctest-methods.Rd | 8 ++--
man/mmctestres-class.Rd | 3 +
man/pEstimate-methods.Rd | 2 -
man/summary.mmctestres-methods.Rd | 2 -
man/testResult-methods.Rd | 4 +-
23 files changed, 121 insertions(+), 92 deletions(-)
Title: Functions for medical statistics book with some demographic data
Diff between fmsb versions 0.3.8 dated 2013-02-28 and 0.3.9 dated 2013-06-10
Description: Several utility functions for the book entitled "Practices
of Medical and Health Data Analysis using R" (Pearson Education
Japan, 2007) with Japanese demographic data and some
demographic analysis related functions.
Author: Minato Nakazawa
Maintainer: Minato Nakazawa
DESCRIPTION | 8 +++----
MD5 | 50 ++++++++++++++++++++++++-------------------------
NEWS | 4 +++
R/demogjpn.R | 5 ++--
man/CT.Rd | 4 +--
man/CronbachAlpha.Rd | 6 ++---
man/Denny.Rd | 2 -
man/GompertzMakeham.Rd | 2 -
man/Hadwiger.Rd | 2 -
man/Jvital.Rd | 10 +++++++--
man/Kappatest.Rd | 4 +--
man/SIQR.Rd | 4 +--
man/Siler.Rd | 2 -
man/gstem.Rd | 6 ++---
man/lifetable.Rd | 3 +-
man/mhchart.Rd | 8 +++----
man/oddsratio.Rd | 2 -
man/pairwisefisher.Rd | 8 +++----
man/percentile.Rd | 2 -
man/pvalueplot.Rd | 6 ++---
man/ratedifference.Rd | 2 -
man/rateratio.Rd | 2 -
man/riskdifference.Rd | 2 -
man/riskratio.Rd | 2 -
man/roc.Rd | 4 +--
man/truemedian.Rd | 4 +--
26 files changed, 83 insertions(+), 71 deletions(-)
Title: Numerical Methods and Optimization in Finance
Diff between NMOF versions 0.27-0 dated 2012-11-29 and 0.28-0 dated 2013-06-10
Description: Functions, examples and data from the book 'Numerical
Methods and Optimization in Finance' by M. Gilli, D. Maringer
and E. Schumann. The package contains, in particular,
implementations of several optimisation heuristics (such as
Differential Evolution, Genetic Algorithms and Threshold
Accepting).
Author: Enrico Schumann
Maintainer: Enrico Schumann
NMOF-0.27-0/NMOF/inst/book/ChangeLog |only
NMOF-0.28-0/NMOF/DESCRIPTION | 19
NMOF-0.28-0/NMOF/MD5 | 108 +-
NMOF-0.28-0/NMOF/NAMESPACE | 56 -
NMOF-0.28-0/NMOF/NEWS | 54 +
NMOF-0.28-0/NMOF/R/GAopt.R | 8
NMOF-0.28-0/NMOF/R/MA.R | 22
NMOF-0.28-0/NMOF/R/NS.R | 40
NMOF-0.28-0/NMOF/R/NSf.R | 34
NMOF-0.28-0/NMOF/R/bonds.R |only
NMOF-0.28-0/NMOF/R/bracket.R | 144 +-
NMOF-0.28-0/NMOF/R/callCF.R | 1
NMOF-0.28-0/NMOF/R/gridSearch.R | 246 ++--
NMOF-0.28-0/NMOF/R/internals.R | 24
NMOF-0.28-0/NMOF/R/mc.R |only
NMOF-0.28-0/NMOF/R/options.R | 223 +++-
NMOF-0.28-0/NMOF/R/repairMatrix.R | 38
NMOF-0.28-0/NMOF/R/restartOpt.R | 112 +-
NMOF-0.28-0/NMOF/data/bundData.RData |binary
NMOF-0.28-0/NMOF/data/fundData.RData |binary
NMOF-0.28-0/NMOF/data/optionData.RData |binary
NMOF-0.28-0/NMOF/inst/NMOFex/NMOFdist.R | 907 ++++++++++--------
NMOF-0.28-0/NMOF/inst/NMOFex/README | 28
NMOF-0.28-0/NMOF/inst/doc/DEnss.Rnw | 8
NMOF-0.28-0/NMOF/inst/doc/DEnss.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/LSselect.Rnw | 328 +++---
NMOF-0.28-0/NMOF/inst/doc/LSselect.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/PSlms.Rnw | 364 +++----
NMOF-0.28-0/NMOF/inst/doc/PSlms.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/TAportfolio.Rnw | 586 +++++------
NMOF-0.28-0/NMOF/inst/doc/TAportfolio.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/qTableEx.R |only
NMOF-0.28-0/NMOF/inst/doc/qTableEx.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/repair.pdf |binary
NMOF-0.28-0/NMOF/inst/doc/vectorise.Rnw | 552 +++++-----
NMOF-0.28-0/NMOF/inst/doc/vectorise.pdf |binary
NMOF-0.28-0/NMOF/inst/unitTests/report.txt | 53 -
NMOF-0.28-0/NMOF/inst/unitTests/runTests.R | 5
NMOF-0.28-0/NMOF/inst/unitTests/unitTests1.R | 184 +--
NMOF-0.28-0/NMOF/inst/unitTests/unitTestsMA.R |only
NMOF-0.28-0/NMOF/inst/unitTests/unitTestsPCparity.R |only
NMOF-0.28-0/NMOF/inst/unitTests/unitTestsRestartOpt.R |only
NMOF-0.28-0/NMOF/inst/unitTests/unitTestscallCF.R | 400 +++----
NMOF-0.28-0/NMOF/man/GAopt.Rd | 365 ++++---
NMOF-0.28-0/NMOF/man/LSopt.Rd | 5
NMOF-0.28-0/NMOF/man/NMOF-internal.Rd | 106 +-
NMOF-0.28-0/NMOF/man/NMOF-package.Rd | 32
NMOF-0.28-0/NMOF/man/PSopt.Rd | 515 +++++-----
NMOF-0.28-0/NMOF/man/TAopt.Rd | 22
NMOF-0.28-0/NMOF/man/bonds.Rd |only
NMOF-0.28-0/NMOF/man/bracketing.Rd | 19
NMOF-0.28-0/NMOF/man/bundData.Rd | 7
NMOF-0.28-0/NMOF/man/callCF.Rd | 20
NMOF-0.28-0/NMOF/man/gridSearch.Rd | 313 +++---
NMOF-0.28-0/NMOF/man/mc.Rd |only
NMOF-0.28-0/NMOF/man/options.Rd | 31
NMOF-0.28-0/NMOF/man/putCallParity.Rd |only
NMOF-0.28-0/NMOF/man/qTable.Rd | 6
NMOF-0.28-0/NMOF/man/repairMatrix.Rd | 4
NMOF-0.28-0/NMOF/man/restartOpt.Rd | 29
60 files changed, 3254 insertions(+), 2764 deletions(-)
Title: Extract information from an html document with CSS selectors
Diff between CSS versions 1.0 dated 2013-05-28 and 1.0.1 dated 2013-06-10
Description: The package provides functions that facilitate extraction
of information from an html document by using css selectors
instead of xpath queries.
Author: Francois Guillem
Maintainer: Francois Guillem
DESCRIPTION | 6 +++---
MD5 | 7 ++++---
NEWS |only
R/CSS.R | 8 ++++----
inst/tests/testDataExtraction.R | 25 +++++++++++++++++++++----
5 files changed, 32 insertions(+), 14 deletions(-)
Title: TeX to HTML/MathML Translators tth/ttm
Diff between tth versions 4.03-0 dated 2012-12-14 and 4.3-1 dated 2013-06-10
Description: C source code and R wrappers for the tth/ttm TeX to
HTML/MathML translators.
Author: Ian H. Hutchinson [aut] (author of tth/ttm C sources),
Friedrich Leisch [aut, cre] (author of R wrappers to tth/ttm),
Achim Zeileis [aut] (author of R wrappers to tth/ttm)
Maintainer: Friedrich Leisch
tth-4.03-0/tth/MD5 |only
tth-4.3-1/tth/DESCRIPTION | 31 +++++++++++++++----------------
tth-4.3-1/tth/NEWS | 6 ++++++
tth-4.3-1/tth/R/tex2html.R | 38 +++++++++++++++++++++++++-------------
tth-4.3-1/tth/Rplots.pdf |only
tth-4.3-1/tth/man/tth.Rd | 8 +++++---
6 files changed, 51 insertions(+), 32 deletions(-)
Title: Probabilistic Knowledge Structures
Diff between pks versions 0.2-0 dated 2012-03-07 and 0.2-1 dated 2013-06-10
Description: Fitting and testing probabilistic knowledge structures,
especially the basic local independence model (BLIM, Doignon &
Flamagne, 1999), using the minimum discrepancy maximum
likelihood (MDML) method.
Author: Florian Wickelmaier [cre, aut], Juergen Heller [aut], Pasquale
Anselmi [ctb]
Maintainer: Florian Wickelmaier
ChangeLog | 6 ++++++
DESCRIPTION | 9 +++++----
MD5 | 24 +++++++++++++-----------
R/blim.R | 12 ++++++------
data/DoignonFalmagne7.rda |binary
data/Taagepera.rda |binary
data/endm.rda |only
inst/CITATION | 27 ++++++++++++++-------------
man/blim.Rd | 24 +++++++++++-------------
man/chess.Rd | 2 +-
man/endm.Rd |only
man/plot.blim.Rd | 4 ++--
man/print.blim.Rd | 2 +-
man/simulate.blim.Rd | 6 +++---
14 files changed, 62 insertions(+), 54 deletions(-)
Title: Multivariate Chebyshev interpolation
Diff between chebpol versions 1.3-952 dated 2013-04-10 and 1.3-1017 dated 2013-06-10
Description: The package contains methods for creating multivariate
Chebyshev approximation of functions on a hypercube. Some
methods for non-Chebyshev grids are also provided.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo,
Norway
Maintainer: Simen Gaure
DESCRIPTION | 8 ++++----
MD5 | 13 +++++++------
R/chebpol.R | 2 +-
inst/doc/chebpol.R |only
inst/doc/chebpol.pdf |binary
src/chebpol.c | 18 +++++++++---------
tests/all.R | 12 ++++++++++++
tests/all.Rout.save | 28 ++++++++++++++++++++++++----
8 files changed, 57 insertions(+), 24 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-25 1.1
2011-10-19 1.0
Title: Generation of regular factorial designs
Diff between planor versions 0.1-5 dated 2013-03-08 and 0.1-8 dated 2013-06-10
Description: planor is a package dedicated to the automatic generation
of regular factorial designs, including fractional designs,
orthogonal block designs, row-column designs and split-plots.
Author: Hervé Monod, Annie Bouvier, André Kobilinsky
Maintainer: Annie Bouvier
planor-0.1-5/planor/tests/compar.R |only
planor-0.1-5/planor/tests/compar.Rout.save |only
planor-0.1-5/planor/tests/hmtestsKobi0 |only
planor-0.1-5/planor/tests/hmtestsKobi1 |only
planor-0.1-5/planor/tests/hmtestsKobi2 |only
planor-0.1-5/planor/tests/hmtestsKobi3 |only
planor-0.1-5/planor/tests/hmtestsKobiRecursive |only
planor-0.1-5/planor/tests/hmtestsSTouzeau2 |only
planor-0.1-5/planor/tests/hmtestsSTouzeau4 |only
planor-0.1-8/planor/ChangeLog | 28
planor-0.1-8/planor/DESCRIPTION | 13
planor-0.1-8/planor/MD5 | 126 +-
planor-0.1-8/planor/NAMESPACE | 9
planor-0.1-8/planor/R/basep.R | 941 ++++++++----------
planor-0.1-8/planor/R/bigm.R | 96 +
planor-0.1-8/planor/R/designfactors.R | 12
planor-0.1-8/planor/R/designkey.R | 38
planor-0.1-8/planor/R/generic.R | 2
planor-0.1-8/planor/R/keymatrix.R | 27
planor-0.1-8/planor/R/keyring.R | 12
planor-0.1-8/planor/R/listofdesignkeys.R | 15
planor-0.1-8/planor/R/listofkeyrings.R | 25
planor-0.1-8/planor/R/makedesignkey.R |only
planor-0.1-8/planor/R/planor.R | 182 +--
planor-0.1-8/planor/R/planordesign.R | 23
planor-0.1-8/planor/R/randomize.R | 276 ++---
planor-0.1-8/planor/R/zzz.R | 1
planor-0.1-8/planor/inst/doc/planor-manual.pdf |binary
planor-0.1-8/planor/inst/doc/planorVignette.pdf |binary
planor-0.1-8/planor/man/alias-methods.Rd | 12
planor-0.1-8/planor/man/as.data.frame.planordesign.Rd |only
planor-0.1-8/planor/man/bind-methods.Rd | 3
planor-0.1-8/planor/man/designfactors-class.Rd | 4
planor-0.1-8/planor/man/designkey-class.Rd | 10
planor-0.1-8/planor/man/getDesign-methods.Rd | 5
planor-0.1-8/planor/man/keymatrix-class.Rd | 6
planor-0.1-8/planor/man/keyring-class.Rd | 4
planor-0.1-8/planor/man/listofdesignkeys-class.Rd | 10
planor-0.1-8/planor/man/listofkeyrings-class.Rd | 12
planor-0.1-8/planor/man/makedesignkey.Rd |only
planor-0.1-8/planor/man/pick-methods.Rd | 10
planor-0.1-8/planor/man/planor-package.Rd | 7
planor-0.1-8/planor/man/planor.design-methods.Rd | 3
planor-0.1-8/planor/man/planor.designkey.Rd | 2
planor-0.1-8/planor/man/planordesign-class.Rd | 21
planor-0.1-8/planor/man/regular.design.Rd | 6
planor-0.1-8/planor/man/summary-methods.Rd | 7
planor-0.1-8/planor/src/planor.cpp | 189 +--
planor-0.1-8/planor/tests/AB.Rout.save | 9
planor-0.1-8/planor/tests/BU_mai2011_2.Rout.save | 9
planor-0.1-8/planor/tests/Kobi0.R | 9
planor-0.1-8/planor/tests/Kobi0.Rout.save | 23
planor-0.1-8/planor/tests/Kobi1.R | 5
planor-0.1-8/planor/tests/Kobi1.Rout.save | 19
planor-0.1-8/planor/tests/Kobi2.R | 4
planor-0.1-8/planor/tests/Kobi2.Rout.save | 18
planor-0.1-8/planor/tests/Kobi3.R | 7
planor-0.1-8/planor/tests/Kobi3.Rout.save | 30
planor-0.1-8/planor/tests/KobiRecursive.R | 5
planor-0.1-8/planor/tests/KobiRecursive.Rout.save | 14
planor-0.1-8/planor/tests/NewKobi1.Rout.save | 9
planor-0.1-8/planor/tests/Touzeau2.R | 29
planor-0.1-8/planor/tests/Touzeau2.Rout.save | 43
planor-0.1-8/planor/tests/exsimple.Rout.save | 9
planor-0.1-8/planor/tests/generate.Rout.save | 57 -
planor-0.1-8/planor/tests/haies.Rout.save | 9
planor-0.1-8/planor/tests/mixkey.R |only
planor-0.1-8/planor/tests/mixkey.Rout.save |only
planor-0.1-8/planor/tests/noineligible.R | 1
planor-0.1-8/planor/tests/noineligible.Rout.save | 10
planor-0.1-8/planor/tests/testSummary.Rout.save | 9
71 files changed, 1194 insertions(+), 1271 deletions(-)
Title: Construction and evaluation of metamodels
Diff between DiceEval versions 1.1 dated 2011-08-26 and 1.2 dated 2013-06-10
Description: Estimation, validation and prediction of metamodels
(linear models, additive models, MARS,PolyMARS and Kriging)
Author: D. Dupuy and C. Helbert
Maintainer: C. Helbert
DESCRIPTION | 13
DiceEval-Ex.R | 941 ++++++++++++++++++++++++-------------------------
MD5 | 18
R/modelComparison.R | 3
R/penaltyPolyMARS.R | 42 +-
R/residualsStudy.R | 11
R/stepEvolution.R | 85 +++-
demo/IRSN5D.R | 2
man/penaltyPolyMARS.Rd | 83 ++--
man/stepEvolution.Rd | 92 ++--
10 files changed, 673 insertions(+), 617 deletions(-)
Title: Convert Rd to roxygen documentation and utilities to improve
documentation
Diff between Rd2roxygen versions 1.1 dated 2012-07-13 and 1.2 dated 2013-06-10
Description: Functions to convert Rd to roxygen documentation. It can
parse an Rd file to a list, create the roxygen documentation
and update the original R script (e.g. the one containing the
definition of the function) accordingly. This package also
provides utilities which can help developers build packages
using roxygen more easily. The formatR package can be used to
reformat the R code in the examples sections so that the code
will be more readable.
Author: Hadley Wickham and Yihui Xie
Maintainer: Yihui Xie
Rd2roxygen-1.1/Rd2roxygen/.gitignore |only
Rd2roxygen-1.1/Rd2roxygen/inst/doc/Makefile |only
Rd2roxygen-1.1/Rd2roxygen/inst/doc/Rd2roxygen.bib |only
Rd2roxygen-1.2/Rd2roxygen/DESCRIPTION | 10 ++-
Rd2roxygen-1.2/Rd2roxygen/MD5 | 26 ++++-----
Rd2roxygen-1.2/Rd2roxygen/NEWS | 16 +++++
Rd2roxygen-1.2/Rd2roxygen/R/Rd2roxygen-package.R | 2
Rd2roxygen-1.2/Rd2roxygen/R/build.R | 25 +++++++-
Rd2roxygen-1.2/Rd2roxygen/R/rd2roxygen.R | 34 ++++++++++--
Rd2roxygen-1.2/Rd2roxygen/R/utils.R | 2
Rd2roxygen-1.2/Rd2roxygen/inst/doc/Rd2roxygen.R |only
Rd2roxygen-1.2/Rd2roxygen/inst/doc/Rd2roxygen.Rnw | 8 +-
Rd2roxygen-1.2/Rd2roxygen/inst/doc/Rd2roxygen.lyx | 12 +++-
Rd2roxygen-1.2/Rd2roxygen/inst/doc/Rd2roxygen.pdf |binary
Rd2roxygen-1.2/Rd2roxygen/inst/examples/pkgDemo/man/data.Rd |only
Rd2roxygen-1.2/Rd2roxygen/man/Rd2roxygen-package.Rd | 2
Rd2roxygen-1.2/Rd2roxygen/man/roxygen_and_build.Rd | 4 -
17 files changed, 103 insertions(+), 38 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-12 0.1.1
Title: R Package for Fitting the Multinomial Probit Model
Diff between MNP versions 2.6-3 dated 2011-12-07 and 2.6-4 dated 2013-06-09
Description: MNP is a publicly available R package that fits the
Bayesian multinomial probit model via Markov chain Monte Carlo.
The multinomial probit model is often used to analyze the
discrete choices made by individuals recorded in survey data.
Examples where the multinomial probit model may be useful
include the analysis of product choice by consumers in market
research and the analysis of candidate or party choice by
voters in electoral studies. The MNP software can also fit the
model with different choice sets for each individual, and
complete or partial individual choice orderings of the
available alternatives from the choice set. The estimation is
based on the efficient marginal data augmentation algorithm
that is developed by Imai and van Dyk (2005). ``A Bayesian
Analysis of the Multinomial Probit Model Using the Data
Augmentation,'' Journal of Econometrics, Vol. 124, No. 2
(February), pp. 311-334. Detailed examples are given in Imai
and van Dyk (2005). ``MNP: R Package for Fitting the
Multinomial Probit Model.'' Journal of Statistical Software,
Vol. 14, No. 3 (May), pp. 1-32.
Author: Kosuke Imai
Maintainer: Kosuke Imai
DESCRIPTION | 49 ++++++++++++++++++++++++++-----------------------
MD5 | 10 +++++-----
MNP.pdf |binary
R/mnp.R | 4 ++--
R/onAttach.R | 7 ++++---
R/xmatrix.mnp.R | 2 +-
6 files changed, 38 insertions(+), 34 deletions(-)
Title: eXtensible Time Series
Diff between xts versions 0.9-3 dated 2013-01-20 and 0.9-4 dated 2013-06-09
Description: Provide for uniform handling of R's different time-based
data classes by extending zoo, maximizing native format
information preservation and allowing for user level
customization and extension, while simplifying cross-class
interoperability.
Author: Jeffrey A. Ryan, Joshua M. Ulrich
Maintainer: Jeffrey A. Ryan
DESCRIPTION | 9 ++++----
MD5 | 44 ++++++++++++++++++++++---------------------
R/bind.R | 2 -
R/index.R | 8 +++++--
R/indexClass.R | 4 +++
R/merge.R | 4 ++-
R/parse8601.R | 6 ++---
R/rollapply.xts.R | 14 +++++++------
R/toperiod.R | 4 +--
R/xts.methods.R | 4 +--
inst/api_example/DESCRIPTION | 2 -
inst/doc/xts-faq.R |only
inst/doc/xts-faq.pdf |binary
inst/doc/xts.R |only
inst/doc/xts.pdf |binary
inst/include/xts.h | 10 ++++++++-
inst/include/xtsAPI.h | 43 ++++++++++++++++++++++++++++++++++++++++++
man/merge.Rd | 6 ++++-
man/xts-package.Rd | 2 -
src/init.c | 13 ++++++++----
src/period.max.f | 2 -
src/period.sum.f | 2 -
src/rbind.c | 1
src/xts.h | 10 ++++++++-
24 files changed, 137 insertions(+), 53 deletions(-)
Title: Simulating trees under the birth-death model
Diff between TreeSim versions 1.8 dated 2013-04-16 and 1.9 dated 2013-06-09
Description: The package simulates phylogenetic trees where (i) all
tips are sampled at one time point or (ii) tips are sampled
sequentially through time. (i) For sampling at one time point,
simulations are performed under a constant-rate birth-death
process, conditioned on having a fixed number of final tips
(sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and
number of tips (sim.bd.taxa.age). When conditioning on the
number of final tips, the method allows for shifts in rates and
mass extinction events during the birth-death process
(sim.rateshift.taxa).sim.bd.age (and sim.rateshift.taxa without
extinction) allow the speciation rate to change in a
density-dependent way. The LTT plots of the simulations can be
displayed using LTT.plot, LTT.plot.gen and LTT.average.root.
TreeSim further samples appropriately trees with n final tips
from a set of trees generated by the common sampling algorithm
stopping when a fixed number m>>n of leaves is first reached
(sim.gsa.taxa). This latter method is appropriate for m-tip
trees generated under a big class of models (details in the
sim.gsa.taxa man page). For incomplete phylogeny, the missing
speciation events can be added through simulations (corsim).
(ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for
serially sampled trees, where the trees are conditioned on
either the number of sampled tips or the age. Furthermore, for
a multitype-branching process with sequential sampling, trees
on a fixed number of tips can be simulated using
sim.bdtypes.stt.taxa.
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/sim2.bd.fast.single.mrca.R | 6 +++++-
R/sim2.bd.fast.single.origin.R | 1 +
man/TreeSim-package.Rd | 4 ++--
man/corsim.Rd | 3 ++-
man/sim.bdsky.stt.Rd | 3 ++-
man/sim.bdtypes.stt.taxa.Rd | 3 ++-
8 files changed, 25 insertions(+), 17 deletions(-)
Title: Perceptual analysis, visualization and organization of spectral
color data in R
Diff between pavo versions 0.3-1 dated 2013-05-06 and 0.5 dated 2013-06-09
Description: A cohesive framework for parsing, analyzing and organizing
color from spectral data
Author: Rafael Maia [aut, cre], Chad Eliason [aut], Pierre-Paul Bitton
[aut]
Maintainer: Rafael Maia
DESCRIPTION | 6 +-
MD5 | 28 +++++-----
NEWS | 11 +++
R/coldist.R | 23 ++++++--
R/internal.R | 23 ++++++++
R/plot.rspec.r | 15 +++--
R/spec2rgb.R | 5 +
R/summary.rspec.R | 142 ++++++++++++++++++++++++++++++++++++---------------
R/tcsplot.R | 31 +++++++----
R/vismodel.R | 48 +++++++++++------
inst/CITATION | 8 +-
man/coldist.Rd | 3 -
man/summary.rspec.Rd | 17 +++---
man/tcsplot.Rd | 16 +++++
man/vismodel.Rd | 5 +
15 files changed, 275 insertions(+), 106 deletions(-)
Title: BEFdata R package
Diff between rbefdata versions 0.2 dated 2013-04-17 and 0.3 dated 2013-06-09
Description: Basic R package to access the data structures offered by
the BEFdata portal.
Author: Claas-Thido Pfaff
Maintainer: Claas-Thido Pfaff
rbefdata-0.2/rbefdata/R/bef.combineObjects.R |only
rbefdata-0.2/rbefdata/R/bef.getDataset.R |only
rbefdata-0.2/rbefdata/R/bef.getKeywords.R |only
rbefdata-0.2/rbefdata/R/bef.getMetadata.R |only
rbefdata-0.2/rbefdata/R/bef.getProposal.R |only
rbefdata-0.2/rbefdata/R/bef.getdata.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematres.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematresLower.R |only
rbefdata-0.2/rbefdata/R/bef.searchTematresUpper.R |only
rbefdata-0.2/rbefdata/man/bef.combineObjects.Rd |only
rbefdata-0.2/rbefdata/man/bef.getDataset.Rd |only
rbefdata-0.2/rbefdata/man/bef.getKeywords.Rd |only
rbefdata-0.2/rbefdata/man/bef.getMetadata.Rd |only
rbefdata-0.2/rbefdata/man/bef.getProposal.Rd |only
rbefdata-0.2/rbefdata/man/bef.getdata.Rd |only
rbefdata-0.2/rbefdata/man/bef.searchTematres.Rd |only
rbefdata-0.2/rbefdata/man/bef.searchTematresLower.Rd |only
rbefdata-0.2/rbefdata/man/bef.searchTematresUpper.Rd |only
rbefdata-0.3/rbefdata/DESCRIPTION | 37 ++++--
rbefdata-0.3/rbefdata/MD5 | 55 +++++-----
rbefdata-0.3/rbefdata/NAMESPACE | 12 ++
rbefdata-0.3/rbefdata/NEWS | 21 +++
rbefdata-0.3/rbefdata/R/bef.options.R | 4
rbefdata-0.3/rbefdata/R/bef.portal.get.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.attachment.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.dataset.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.dataset_list.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.keywords.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.metadata.R |only
rbefdata-0.3/rbefdata/R/bef.portal.get.proposal.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.broader_keywords.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.keywords.R |only
rbefdata-0.3/rbefdata/R/bef.tematres.search.narrower_keywords.R |only
rbefdata-0.3/rbefdata/R/helper.R |only
rbefdata-0.3/rbefdata/R/rbefdata-defunct.R |only
rbefdata-0.3/rbefdata/R/zzz.R | 3
rbefdata-0.3/rbefdata/inst |only
rbefdata-0.3/rbefdata/man/bef.portal.get.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.attachment.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.dataset.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.dataset_list.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.metadata.Rd |only
rbefdata-0.3/rbefdata/man/bef.portal.get.proposal.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.broader_keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.keywords.Rd |only
rbefdata-0.3/rbefdata/man/bef.tematres.search.narrower_keywords.Rd |only
rbefdata-0.3/rbefdata/man/rbefdata-defunct.Rd |only
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51 files changed, 90 insertions(+), 42 deletions(-)
Title: Calculate observed and expected disease incidence counts from a
case file and population data.
Diff between diseasemapping versions 0.6 dated 2012-01-17 and 0.7.3 dated 2013-06-09
More information about diseasemapping at CRAN
Description: Tools for calculating rates and Standardized Incidence
Ratios from case and population data.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 22 +++++++++++++---------
MD5 | 41 ++++++++++++++++++++++-------------------
R/cancerRates.R | 8 +++-----
R/computeArea.r | 5 ++---
R/formatCases.R | 8 --------
R/getBreaks.R | 6 +++++-
R/getSMR.data.frame.R | 17 ++++++++++++++---
R/getStdRate.R | 24 +++++++-----------------
R/mergeBugsData.R | 1 +
data/casedata.RData |binary
data/datalist |only
data/kentucky.RData |only
data/popdata.RData |binary
data/referencepop.RData |binary
man/diseasemapping-package.Rd | 35 +++++++++++++++++++++++++++++++++++
man/expandCensus.Rd | 3 ++-
man/formatCases.Rd | 3 ++-
man/formatPopulation.Rd | 15 +++++++++------
man/getBreaks.Rd | 4 ++--
man/getSMR.Rd | 11 ++++++++---
man/getStdRate.Rd | 6 +++---
man/kentucky.Rd |only
man/referencepop.Rd | 9 ++++++---
23 files changed, 134 insertions(+), 84 deletions(-)
Permanent link
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.14 dated 2013-05-22 and 0.9.15 dated 2013-06-09
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 -
MD5 | 106 +++++++++----------
NEWS | 7 +
R/IBD.r | 215 +++++++++++++++++++++++++---------------
R/SNPRelate_Main.r | 12 +-
inst/doc/SNPRelateTutorial.R | 125 ++++++++++++++---------
inst/doc/SNPRelateTutorial.Rnw | 65 +++++++++---
inst/doc/SNPRelateTutorial.pdf |binary
man/SNPRelate-package.Rd | 19 +--
man/snpgdsBED2GDS.Rd | 2
man/snpgdsCombineGeno.Rd | 2
man/snpgdsCreateGeno.Rd | 2
man/snpgdsCreateGenoSet.Rd | 2
man/snpgdsCutTree.Rd | 2
man/snpgdsDiss.Rd | 2
man/snpgdsDrawTree.Rd | 2
man/snpgdsErrMsg.Rd | 2
man/snpgdsExampleFileName.Rd | 2
man/snpgdsGDS2BED.Rd | 2
man/snpgdsGDS2Eigen.Rd | 2
man/snpgdsGDS2PED.Rd | 2
man/snpgdsGetGeno.Rd | 2
man/snpgdsHCluster.Rd | 2
man/snpgdsIBDKING.Rd | 101 +++++++++++-------
man/snpgdsIBDMLE.Rd | 11 +-
man/snpgdsIBDMLELogLik.Rd | 2
man/snpgdsIBDMoM.Rd | 13 ++
man/snpgdsIBDSelection.Rd | 38 +++----
man/snpgdsIBS.Rd | 2
man/snpgdsIBSNum.Rd | 2
man/snpgdsIndInb.Rd | 2
man/snpgdsIndInbCoef.Rd | 2
man/snpgdsLDMat.Rd | 2
man/snpgdsLDpair.Rd | 2
man/snpgdsLDpruning.Rd | 2
man/snpgdsOption.Rd | 2
man/snpgdsPCA.Rd | 72 ++++++++++---
man/snpgdsPCACorr.Rd | 2
man/snpgdsPCASNPLoading.Rd | 2
man/snpgdsPCASampLoading.Rd | 2
man/snpgdsPairIBD.Rd | 2
man/snpgdsPairIBDMLELogLik.Rd | 2
man/snpgdsSNPList.Rd | 2
man/snpgdsSNPListClass.Rd | 2
man/snpgdsSNPListIntersect.Rd | 2
man/snpgdsSNPListStrand.Rd | 2
man/snpgdsSNPRateFreq.Rd | 2
man/snpgdsSampMissrate.Rd | 2
man/snpgdsSelectSNP.Rd | 2
man/snpgdsSummary.Rd | 2
man/snpgdsVCF2GDS.Rd | 2
src/SNPRelate.cpp | 142 ++++++++++++--------------
src/genIBS.cpp | 35 +-----
vignettes/SNPRelateTutorial.Rnw | 65 +++++++++---
54 files changed, 669 insertions(+), 439 deletions(-)
Title: Iterated Racing Procedures
Diff between irace versions 1.03 dated 2013-01-15 and 1.04 dated 2013-06-09
Description: Iterated racing for automatic algorithm configuration
Author: Manuel López-Ibáñez, Jérémie Dubois-Lacoste, Thomas Stützle,
Mauro Birattari, Eric Yuan and Prasanna Balaprakash
Maintainer: Manuel López-Ibáñez
DESCRIPTION | 13 +++++-----
MD5 | 27 +++++++++++----------
NAMESPACE | 1
NEWS | 7 +++++
R/irace.R | 2 -
R/main.R | 6 ++--
R/model.R | 2 -
R/race-wrapper.R | 51 +++++++++++++++++++++++++++++------------
R/version.R | 2 -
README | 9 ++++++-
inst/examples/acotsp/tune-conf | 5 +---
inst/examples/tune-main-tmp |only
inst/templates/tune-conf.tmpl | 5 +---
man/irace-package.Rd | 4 +--
svn_version | 2 -
15 files changed, 86 insertions(+), 50 deletions(-)
Title: Statistical methods for visual fields
Diff between visualFields versions 0.3 dated 2013-03-18 and 0.3-2 dated 2013-06-08
Description: A collection of tools for analyzing the field of vision.
It provides a framework for development and use of innovative
methods for visualization, statistical analysis, and clinical
interpretation of visual-field loss and its change over time.
It is intended to be a tool for collaborative research.
Author: The visualFields Development Team
Maintainer: Ivan Marin-Franch
DESCRIPTION | 10 +++++-----
MD5 | 16 +++++++++-------
NAMESPACE | 3 ++-
R/agecalc.R |only
R/loadvfxml.R | 4 +++-
R/poplr.R | 4 +++-
R/vflayout.R | 4 ++--
doc/news.txt | 5 +++++
man/agecalc.Rd |only
man/vfobject.Rd | 6 +++---
10 files changed, 32 insertions(+), 20 deletions(-)
Title: R functions for working with spatial data.
Diff between spatial.tools versions 1.0.2 dated 2013-06-01 and 1.0.6 dated 2013-06-08
Description: Spatial functions meant to enhance the core functionality
of the package "raster", including a parallel processing engine
for use with rasters.
Author: Jonathan Asher Greenberg
Maintainer: Jonathan Asher Greenberg
DESCRIPTION | 16 +++---
MD5 | 37 ++++++++------
NAMESPACE | 2
R/Rgdal_translate.R |only
R/binary_image_write.R | 3 -
R/build_raster_header.R | 3 -
R/by.Raster.R |only
R/create_blank_raster.R | 5 +
R/focal_hpc.R | 10 +--
R/getValuesBlock_stackfix.R | 6 +-
R/get_gdal_installation.R | 105 ++++++++++++++++++++++++++---------------
R/modis_hdf4_subdatasets.R |only
R/sfQuickInit.R | 20 ++-----
man/Rgdal_translate.Rd |only
man/binary_image_write.Rd | 2
man/build_raster_header.Rd | 2
man/create_blank_raster.Rd | 4 +
man/focal_hpc.Rd | 11 ++--
man/getValuesBlock_stackfix.Rd | 2
man/get_gdal_installation.Rd | 35 +++++++++++--
man/modis_hdf4_subdatasets.Rd |only
man/sfQuickInit.Rd | 13 +++--
22 files changed, 173 insertions(+), 103 deletions(-)
Title: Financial Risk Modelling and Portfolio Optimisation with R
Diff between FRAPO versions 0.3-6 dated 2012-12-06 and 0.3-7 dated 2013-06-08
Description: Accompanying package of the book 'Financial Risk Modelling
and Portfolio Optimisation with R'. The data sets used in the
book are contained in this package.
Author: Bernhard Pfaff [aut, cre], Miguel Sousa Lobo [ctb] (SOCP),
Lieven Vandenberghe [ctb] (SOCP), Stephen Boyd [ctb] (SOCP),
Herve Lebret [ctb] (SOCP)
Maintainer: Bernhard Pfaff
FRAPO-0.3-6/FRAPO/inst/BookEx.tar.gz |only
FRAPO-0.3-7/FRAPO/DESCRIPTION | 16 +++++++-----
FRAPO-0.3-7/FRAPO/MD5 | 39 ++++++++++++++----------------
FRAPO-0.3-7/FRAPO/NAMESPACE | 1
FRAPO-0.3-7/FRAPO/R/zzz.R | 2 -
FRAPO-0.3-7/FRAPO/data/ESCBFX.rda |binary
FRAPO-0.3-7/FRAPO/data/EuroStoxx50.rda |binary
FRAPO-0.3-7/FRAPO/data/FTSE100.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK1.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK2.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK3.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK4.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK5.rda |binary
FRAPO-0.3-7/FRAPO/data/INDTRACK6.rda |binary
FRAPO-0.3-7/FRAPO/data/MIBTEL.rda |binary
FRAPO-0.3-7/FRAPO/data/MultiAsset.rda |binary
FRAPO-0.3-7/FRAPO/data/NASDAQ.rda |binary
FRAPO-0.3-7/FRAPO/data/SP500.rda |binary
FRAPO-0.3-7/FRAPO/data/StockIndex.rda |binary
FRAPO-0.3-7/FRAPO/data/StockIndexAdj.rda |binary
FRAPO-0.3-7/FRAPO/data/StockIndexAdjD.rda |binary
21 files changed, 30 insertions(+), 28 deletions(-)
Title: Quantile Regression Using Asymmetric Laplace Distribution
Diff between ALDqr versions 0.0 dated 2013-05-15 and 0.1 dated 2013-06-08
Description: EM algorithm for estimating the parameters and other
methods in a quantile regression.
Author: Luis Benites Sanchez
Maintainer: Luis Benites Sanchez
ALDqr-0.0/ALDqr/R/EMqr.r |only
ALDqr-0.0/ALDqr/man/EMqr.Rd |only
ALDqr-0.1/ALDqr/DESCRIPTION | 8 ++++----
ALDqr-0.1/ALDqr/MD5 | 6 +++---
ALDqr-0.1/ALDqr/R/EM.qr.r |only
ALDqr-0.1/ALDqr/man/EM.qr.Rd |only
6 files changed, 7 insertions(+), 7 deletions(-)
Title: Nonparametric Multiple Change Point Analysis of Multivariate
Data
Diff between ecp versions 1.5.3 dated 2013-05-21 and 1.5.4 dated 2013-06-08
Description: This package performs hierarchical change point analysis
through the use of U-statistics. Both agglomerative and
divisive procedures return the set of change points estimates,
and other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James
ecp-1.5.3/ecp/data/STPP.RData |only
ecp-1.5.3/ecp/data/datalist |only
ecp-1.5.3/ecp/man/STPP.RData.Rd |only
ecp-1.5.4/ecp/DESCRIPTION | 6 +-
ecp-1.5.4/ecp/MD5 | 17 ++-----
ecp-1.5.4/ecp/NEWS | 22 ++++++++-
ecp-1.5.4/ecp/R/e_agglomerative.R | 28 ++++++++---
ecp-1.5.4/ecp/R/e_divisive.R | 76 +++++++++++++++-----------------
ecp-1.5.4/ecp/man/e.agglo.Rd | 8 +--
ecp-1.5.4/ecp/man/e.divisive.Rd | 12 +----
ecp-1.5.4/ecp/src/energyChangePoint.cpp | 35 ++++++++------
11 files changed, 112 insertions(+), 92 deletions(-)
Title: An R package for changepoint analysis
Diff between changepoint versions 1.0.5 dated 2013-03-07 and 1.0.6 dated 2013-06-08
Description: Implements various mainstream and specialised changepoint
methods for finding single and multiple changepoints within
data. Many popular non-parametric and frequentist methods are
included. The cpt.mean, cpt.var, cpt.meanvar functions should
be your first point of call.
Author: Rebecca Killick
Maintainer: Rebecca Killick
DESCRIPTION | 8 +-
MD5 | 114 ++++++++++++++++++-------------------
NEWS | 6 +
R/cpt.class.R | 14 ++--
man/PELT.meanvar.exp.Rd | 3
man/PELT.meanvar.gamma.Rd | 6 +
man/PELT.meanvar.norm.Rd | 3
man/PELT.meanvar.poisson.Rd | 3
man/binseg.mean.cusum.Rd | 4 -
man/binseg.mean.norm.Rd | 7 +-
man/binseg.meanvar.exp.Rd | 7 +-
man/binseg.meanvar.gamma.Rd | 10 ++-
man/binseg.meanvar.norm.Rd | 7 +-
man/binseg.meanvar.poisson.Rd | 7 +-
man/binseg.var.css.Rd | 4 -
man/binseg.var.norm.Rd | 7 +-
man/changepoint-package.Rd | 4 -
man/cpt.mean.Rd | 22 ++++---
man/cpt.meanvar.Rd | 19 ++++--
man/cpt.var.Rd | 19 ++++--
man/cpts.ts.Rd | 3
man/likelihood.Rd | 3
man/logLik-methods.Rd | 3
man/multiple.mean.cusum.Rd | 13 ++--
man/multiple.mean.norm.Rd | 13 ++--
man/multiple.meanvar.exp.Rd | 13 ++--
man/multiple.meanvar.gamma.Rd | 19 ++++--
man/multiple.meanvar.norm.Rd | 13 ++--
man/multiple.meanvar.poisson.Rd | 13 ++--
man/multiple.var.css.Rd | 13 ++--
man/multiple.var.norm.Rd | 13 ++--
man/param.Rd | 3
man/segneigh.mean.cusum.Rd | 4 -
man/segneigh.mean.norm.Rd | 7 +-
man/segneigh.meanvar.exp.Rd | 7 +-
man/segneigh.meanvar.gamma.Rd | 10 ++-
man/segneigh.meanvar.norm.Rd | 7 +-
man/segneigh.meanvar.poisson.Rd | 7 +-
man/segneigh.var.css.Rd | 4 -
man/segneigh.var.norm.Rd | 7 +-
man/single.mean.cusum.Rd | 16 +++--
man/single.mean.cusum.calc.Rd | 3
man/single.mean.norm.Rd | 12 ++-
man/single.mean.norm.calc.Rd | 6 +
man/single.meanvar.exp.Rd | 16 +++--
man/single.meanvar.exp.calc.Rd | 6 +
man/single.meanvar.gamma.Rd | 19 ++++--
man/single.meanvar.gamma.calc.Rd | 6 +
man/single.meanvar.norm.Rd | 20 ++++--
man/single.meanvar.norm.calc.Rd | 6 +
man/single.meanvar.poisson.Rd | 16 +++--
man/single.meanvar.poisson.calc.Rd | 6 +
man/single.var.css.Rd | 13 ++--
man/single.var.css.calc.Rd | 3
man/single.var.norm.Rd | 16 +++--
man/single.var.norm.calc.Rd | 6 +
man/summary-methods.Rd | 6 -
man/test.stat--methods.Rd | 4 -
58 files changed, 408 insertions(+), 221 deletions(-)
Title: RFinanceYJ
Diff between RFinanceYJ versions 0.1.6 dated 2011-03-27 and 0.2.0 dated 2013-06-08
Description: Japanese stock market from Yahoo!-finance-Japan
Author: Yohei Sato, Nobuaki Oshiro, Shinichi Takayanagi
Maintainer: Yohei Sato
DESCRIPTION | 9 +++++----
MD5 |only
R/quoteStockTsData.R | 45 +++++++++++++++++++++++++++++++--------------
man/RFinanceYJ-package.Rd | 10 ++++------
man/quoteFXTsData.Rd | 9 ---------
man/quoteFundTsData.Rd | 10 ----------
man/quoteStockTsData.Rd | 14 ++------------
man/quoteStockXtsData.Rd | 7 -------
man/toXts.Rd | 10 ----------
9 files changed, 42 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-15 1.0-2
2006-11-02 1.0-0
Title: VAR Modelling
Diff between vars versions 1.5-0 dated 2012-07-26 and 1.5-1 dated 2013-06-08
Description: Estimation, lag selection, diagnostic testing,
forecasting, causality analysis, forecast error variance
decomposition and impulse response functions of VAR models and
estimation of SVAR/SVEC models.
Author: Bernhard Pfaff [aut, cre], Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff
DESCRIPTION | 12 +++++++-----
MD5 | 17 +++++++++--------
R/VARselect.R | 2 +-
R/logLik.varest.R | 3 +++
R/logLik.vec2var.R | 3 +++
data/Canada.RData |binary
inst/doc/vars.R |only
inst/doc/vars.pdf |binary
man/SVEC.Rd | 3 ++-
man/summary.Rd | 3 ++-
10 files changed, 27 insertions(+), 16 deletions(-)
Title: Amelia II: A Program for Missing Data
Diff between Amelia versions 1.7.1 dated 2013-04-02 and 1.7.2 dated 2013-06-08
Description: Amelia II "multiply imputes" missing data in a single
cross-section (such as a survey), from a time series (like
variables collected for each year in a country), or from a
time-series-cross-sectional data set (such as collected by
years for each of several countries). Amelia II implements our
bootstrapping-based algorithm that gives essentially the same
answers as the standard IP or EMis approaches, is usually
considerably faster than existing approaches and can handle
many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but
please let us know if you find to the contrary!). The program
also generalizes existing approaches by allowing for trends in
time series across observations within a cross-sectional unit,
as well as priors that allow experts to incorporate beliefs
they have about the values of missing cells in their data.
Amelia II also includes useful diagnostics of the fit of
multiple imputation models. The program works from the R
command line or via a graphical user interface that does not
require users to know R.
Author: James Honaker
Maintainer: Matthew Blackwell
Amelia-1.7.1/Amelia/inst/doc/amelia.R |only
Amelia-1.7.2/Amelia/DESCRIPTION | 8 ++++----
Amelia-1.7.2/Amelia/MD5 | 15 +++++++--------
Amelia-1.7.2/Amelia/NEWS | 4 ++++
Amelia-1.7.2/Amelia/R/emb.r | 2 ++
Amelia-1.7.2/Amelia/R/prep.r | 4 ++--
Amelia-1.7.2/Amelia/inst/doc/amelia.pdf |binary
Amelia-1.7.2/Amelia/src/em.cpp | 12 ++++++------
Amelia-1.7.2/Amelia/vignettes/Rplots.pdf |binary
9 files changed, 25 insertions(+), 20 deletions(-)
Title: Foreach parallel adaptor for the parallel package
Diff between doParallel versions 1.0.1 dated 2012-04-16 and 1.0.3 dated 2013-06-07
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Revolution Analytics, Steve Weston
Maintainer: Revolution Analytics
DESCRIPTION | 12 ++-
MD5 | 14 ++--
NEWS |only
R/doParallel.R | 112 +++++++++++++++++++++++++++++-------
R/zzz.R | 6 -
inst/doc/gettingstartedParallel.R |only
inst/doc/gettingstartedParallel.pdf |binary
inst/examples/bootParallel.R | 72 ++++++++++++++++++++---
man/registerDoParallel.Rd | 24 +++++--
9 files changed, 188 insertions(+), 52 deletions(-)
Title: Reaction Time Analysis
Diff between retimes versions 0.1-0 dated 2012-11-10 and 0.1-1 dated 2013-06-07
Description: Reaction time analysis by maximum likelihood
Author: Davide Massidda
Maintainer: Davide Massidda
ChangeLog | 1 +
DESCRIPTION | 9 +++++----
MD5 | 10 +++++-----
R/distributions.R | 4 ++--
R/retimes.R | 7 +++++--
man/ex-gaussian.Rd | 4 ++--
6 files changed, 20 insertions(+), 15 deletions(-)
Title: Markdown rendering for R
Diff between markdown versions 0.5.4 dated 2013-01-25 and 0.5.5 dated 2013-06-07
Description: Markdown is a plain-text formatting syntax that can be
converted to XHTML or other formats. This package provides R
bindings to the Sundown markdown rendering library.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Yihui Xie
DESCRIPTION | 12 +++++---
MD5 | 26 +++++++++----------
NEWS | 22 ++++++++++++++++
R/renderMarkdown.R | 32 ++++++++++++++++-------
inst/resources/markdown.html | 8 +++--
man/markdownHTMLOptions.Rd | 58 +++++++++++++++++++++----------------------
man/markdownToHTML.Rd | 9 ++++--
man/renderMarkdown.Rd | 2 -
man/rendererOutputType.Rd | 2 -
man/rpubsUpload.Rd | 7 +----
man/smartypants.Rd | 2 -
src/buffer.c | 4 +-
src/buffer.h | 5 ---
tests/tests.Rout.save | 10 ++-----
14 files changed, 114 insertions(+), 85 deletions(-)
Title: geotopbricks: Analyzes raster maps as input/output files from
the Hydrological Distributed Model GEOtop
Diff between geotopbricks versions 1.3.4 dated 2013-05-31 and 1.3.4.2 dated 2013-06-07
Description: geotopbricks: Analyzes raster maps and other information
as input/output files from the Hydrological Distributed Model
GEOtop. It contains functions and methods to import maps and
other keywords from geotop.inpts file. Any information about
the GEOtop Distributed Hydrological Model is available on
www.geotop.org. The examples are tested on two simulation cases
run with GEOtop built 1.225-9 mostly developed by Stefano
Endrizzi. Bugs/comments/questions/collaboration of any kind are
warmly welcomed.
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/geotopbricks-package.R | 2 +-
R/get.keyword.value.R | 15 +++++++++++++--
man/geotopbricks-package.Rd | 2 +-
man/get.geotop.inpts.keyword.value.Rd | 12 ++++++++++--
6 files changed, 34 insertions(+), 15 deletions(-)
Title: Genome-wide association/interaction analysis and rare variant
analysis with family data
Diff between GWAF versions 2.0 dated 2012-04-17 and 2.1 dated 2013-06-07
Description: Functions for genome-wide association/interaction analysis
and rare variant analysis on a continuous/dichotomous trait
using family data, and for making genome-wide p-value plot and
QQ plot.
Author: Ming-Huei Chen
Maintainer: Ming-Huei Chen
GWAF-2.0/GWAF/GWAF |only
GWAF-2.0/GWAF/R/BDSmatrix.R |only
GWAF-2.0/GWAF/R/BDSmatrix_%_%.R |only
GWAF-2.0/GWAF/R/align.pedigree.R |only
GWAF-2.0/GWAF/R/alignped1.R |only
GWAF-2.0/GWAF/R/alignped2.R |only
GWAF-2.0/GWAF/R/alignped3.R |only
GWAF-2.0/GWAF/R/alignped4.R |only
GWAF-2.0/GWAF/R/as.matrix.bdsmatrix.R |only
GWAF-2.0/GWAF/R/autohint.R |only
GWAF-2.0/GWAF/R/bdsBlock.R |only
GWAF-2.0/GWAF/R/bdsI.R |only
GWAF-2.0/GWAF/R/bdsmatrix.ibd.R |only
GWAF-2.0/GWAF/R/bdsmatrix.reconcile.R |only
GWAF-2.0/GWAF/R/besthint.R |only
GWAF-2.0/GWAF/R/check.hint.R |only
GWAF-2.0/GWAF/R/coxme.R |only
GWAF-2.0/GWAF/R/coxme.control.R |only
GWAF-2.0/GWAF/R/coxme.fit.R |only
GWAF-2.0/GWAF/R/coxme.varcheck.R |only
GWAF-2.0/GWAF/R/coxph.wtest.R |only
GWAF-2.0/GWAF/R/diag.bdsmatrix.R |only
GWAF-2.0/GWAF/R/familycheck.R |only
GWAF-2.0/GWAF/R/gchol.R |only
GWAF-2.0/GWAF/R/gchol.bdsmatrix.R |only
GWAF-2.0/GWAF/R/getCovariateFormula2.R |only
GWAF-2.0/GWAF/R/getCrossedTerms.R |only
GWAF-2.0/GWAF/R/getGroupsFormula2.R |only
GWAF-2.0/GWAF/R/kindepth.R |only
GWAF-2.0/GWAF/R/kinship.R |only
GWAF-2.0/GWAF/R/lmekin.R |only
GWAF-2.0/GWAF/R/makefamid.R |only
GWAF-2.0/GWAF/R/makekinship.R |only
GWAF-2.0/GWAF/R/pedigree.R |only
GWAF-2.0/GWAF/R/plot.pedigree.R |only
GWAF-2.0/GWAF/R/print.coxme.R |only
GWAF-2.0/GWAF/R/print.lmekin.R |only
GWAF-2.0/GWAF/R/solve.bdsmatrix.R |only
GWAF-2.0/GWAF/R/solve.gchol.R |only
GWAF-2.0/GWAF/R/solve.gchol.bdsmatrix.R |only
GWAF-2.0/GWAF/R/strata2.R |only
GWAF-2.0/GWAF/man/bdsmatrix-class.Rd |only
GWAF-2.0/GWAF/man/gchol-class.Rd |only
GWAF-2.0/GWAF/man/gchol-methods.Rd |only
GWAF-2.0/GWAF/man/gchol.Rd |only
GWAF-2.0/GWAF/man/gchol.bdsmatrix-class.Rd |only
GWAF-2.0/GWAF/man/lmekin.Rd |only
GWAF-2.0/GWAF/man/lmepack.batch.Rd |only
GWAF-2.0/GWAF/man/lmepack.batch.imputed.Rd |only
GWAF-2.0/GWAF/man/lmepack.int.batch.Rd |only
GWAF-2.0/GWAF/man/lmepack.int.batch.imputed.Rd |only
GWAF-2.0/GWAF/man/makekinship.Rd |only
GWAF-2.0/GWAF/src |only
GWAF-2.1/GWAF/ChangeLog | 13
GWAF-2.1/GWAF/DESCRIPTION | 22
GWAF-2.1/GWAF/MD5 | 171 +---
GWAF-2.1/GWAF/NAMESPACE | 25
GWAF-2.1/GWAF/R/auto.R | 675 ++++++++++---------
GWAF-2.1/GWAF/R/geepack.lgst.batch.R | 209 ++---
GWAF-2.1/GWAF/R/geepack.lgst.batch.imputed.R | 185 ++---
GWAF-2.1/GWAF/R/geepack.lgst.int.batch.R | 203 ++---
GWAF-2.1/GWAF/R/geepack.lgst.int.batch.imputed.R | 203 ++---
GWAF-2.1/GWAF/R/geepack.quant.R | 31
GWAF-2.1/GWAF/R/geepack.quant.imputed.R | 13
GWAF-2.1/GWAF/R/geepack.quant.int.R | 301 ++++----
GWAF-2.1/GWAF/R/geepack.quant.int.imputed.R | 290 ++++----
GWAF-2.1/GWAF/R/glmm.lgst.R |only
GWAF-2.1/GWAF/R/glmm.lgst.batch.R |only
GWAF-2.1/GWAF/R/lme.R | 79 +-
GWAF-2.1/GWAF/R/lme.imputed.R | 35
GWAF-2.1/GWAF/R/lme.int.R | 102 +-
GWAF-2.1/GWAF/R/lme.int.imputed.R | 62 -
GWAF-2.1/GWAF/R/lmeV.imputed.R |only
GWAF-2.1/GWAF/inst/doc/UsingGWAF.pdf |binary
GWAF-2.1/GWAF/man/GWAF-package.Rd | 15
GWAF-2.1/GWAF/man/GWplot.Rd | 9
GWAF-2.1/GWAF/man/auto.Rd | 17
GWAF-2.1/GWAF/man/geepack.lgst.Rd | 5
GWAF-2.1/GWAF/man/geepack.lgst.batch.Rd | 13
GWAF-2.1/GWAF/man/geepack.lgst.batch.imputed.Rd | 14
GWAF-2.1/GWAF/man/geepack.lgst.imputed.Rd | 8
GWAF-2.1/GWAF/man/geepack.lgst.int.Rd | 6
GWAF-2.1/GWAF/man/geepack.lgst.int.batch.Rd | 14
GWAF-2.1/GWAF/man/geepack.lgst.int.batch.imputed.Rd | 19
GWAF-2.1/GWAF/man/geepack.lgst.int.imputed.Rd | 9
GWAF-2.1/GWAF/man/geepack.quant.batch.Rd | 11
GWAF-2.1/GWAF/man/geepack.quant.batch.imputed.Rd | 120 +--
GWAF-2.1/GWAF/man/geepack.quant.int.batch.Rd | 14
GWAF-2.1/GWAF/man/geepack.quant.int.batch.imputed.Rd | 18
GWAF-2.1/GWAF/man/glmm.lgst.Rd |only
GWAF-2.1/GWAF/man/glmm.lgst.batch.Rd |only
GWAF-2.1/GWAF/man/lme.batch.Rd |only
GWAF-2.1/GWAF/man/lme.batch.imputed.Rd |only
GWAF-2.1/GWAF/man/lme.int.batch.Rd |only
GWAF-2.1/GWAF/man/lme.int.batch.imputed.Rd |only
GWAF-2.1/GWAF/man/lmeV.batch.imputed.Rd |only
GWAF-2.1/GWAF/man/qq.Rd | 5
97 files changed, 1497 insertions(+), 1419 deletions(-)
Title: Spatial utility functions from the Dyer laboratory
Diff between gstudio versions 0.8 dated 2012-01-31 and 1.0 dated 2013-06-07
Description: This package contains classes and functions for the
spatial analysis of marker data to include structure
statistics, analyses based upon allele frequencies, and
Population Graphs network analysis of spatial conditional
genetic covariance. This package supersedes the original
studio package by interfacing with raster and sp objects
directly.
Author: Rodney J. Dyer
Maintainer: Rodney J. Dyer
gstudio-0.8/gstudio/.Rinstignore |only
gstudio-0.8/gstudio/.tm_properties |only
gstudio-0.8/gstudio/ChangeLog |only
gstudio-0.8/gstudio/R/Frequencies-class.R |only
gstudio-0.8/gstudio/R/Locus-class.R |only
gstudio-0.8/gstudio/R/Population-class.R |only
gstudio-0.8/gstudio/R/congruence.graph.R |only
gstudio-0.8/gstudio/R/congruence.probability.R |only
gstudio-0.8/gstudio/R/exclusion.probability.R |only
gstudio-0.8/gstudio/R/genetic.distance.R |only
gstudio-0.8/gstudio/R/genetic.diversity.R |only
gstudio-0.8/gstudio/R/genetic.structure.R |only
gstudio-0.8/gstudio/R/google.pie.chart.R |only
gstudio-0.8/gstudio/R/great.circle.distance.R |only
gstudio-0.8/gstudio/R/minus.mom.R |only
gstudio-0.8/gstudio/R/offspring.array.R |only
gstudio-0.8/gstudio/R/paternity.spiderplot.R |only
gstudio-0.8/gstudio/R/pies.on.map.R |only
gstudio-0.8/gstudio/R/popgraph.on.map.R |only
gstudio-0.8/gstudio/R/population.graph.R |only
gstudio-0.8/gstudio/R/print.summary.dyerlab.R |only
gstudio-0.8/gstudio/R/read.pgraph.R |only
gstudio-0.8/gstudio/R/read.population.R |only
gstudio-0.8/gstudio/R/stratum.distance.R |only
gstudio-0.8/gstudio/R/transition.probability.R |only
gstudio-0.8/gstudio/R/validate_gstudio_package.R |only
gstudio-0.8/gstudio/data/araptus_attenuatus.rda |only
gstudio-0.8/gstudio/data/cornus_florida.rda |only
gstudio-0.8/gstudio/inst/doc/Using_GStudio.Rnw |only
gstudio-0.8/gstudio/inst/doc/Using_GStudio.pdf |only
gstudio-0.8/gstudio/man/Frequencies-class.Rd |only
gstudio-0.8/gstudio/man/Frequencies.Rd |only
gstudio-0.8/gstudio/man/Locus-accessors.Rd |only
gstudio-0.8/gstudio/man/Locus-class.Rd |only
gstudio-0.8/gstudio/man/Locus.Rd |only
gstudio-0.8/gstudio/man/Population-accessors.Rd |only
gstudio-0.8/gstudio/man/Population-class.Rd |only
gstudio-0.8/gstudio/man/Population.Rd |only
gstudio-0.8/gstudio/man/allele.frequencies_Population.Rd |only
gstudio-0.8/gstudio/man/araptus_attenuatus.Rd |only
gstudio-0.8/gstudio/man/as.character.Rd |only
gstudio-0.8/gstudio/man/as.vector.Rd |only
gstudio-0.8/gstudio/man/column.class_Population.Rd |only
gstudio-0.8/gstudio/man/column.names_Population.Rd |only
gstudio-0.8/gstudio/man/congruence.graph.Rd |only
gstudio-0.8/gstudio/man/congruence.probability.Rd |only
gstudio-0.8/gstudio/man/cornus_florida.Rd |only
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gstudio-0.8/gstudio/man/exclusion.probability.Rd |only
gstudio-0.8/gstudio/man/genetic.distance.Rd |only
gstudio-0.8/gstudio/man/genetic.diversity.Rd |only
gstudio-0.8/gstudio/man/genetic.structure.Rd |only
gstudio-0.8/gstudio/man/genotype.counts_Population.Rd |only
gstudio-0.8/gstudio/man/get.frequencies_Frequencies.Rd |only
gstudio-0.8/gstudio/man/google.pie.chart.Rd |only
gstudio-0.8/gstudio/man/great.circle.distance.Rd |only
gstudio-0.8/gstudio/man/he_Frequencies.Rd |only
gstudio-0.8/gstudio/man/ho_Frequencies.Rd |only
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gstudio-1.0/gstudio/man/paternity.Rd | 68 +--
gstudio-1.0/gstudio/man/permute_ci.Rd |only
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gstudio-1.0/gstudio/tests/run-testthat-gstudio.R |only
224 files changed, 512 insertions(+), 378 deletions(-)
Title: Regularization paths for regression models with grouped
covariates
Diff between grpreg versions 2.3-0 dated 2013-02-10 and 2.4-0 dated 2013-06-07
Description: Efficient algorithms for fitting the regularization path
of linear or logistic regression models with grouped penalties,
such as group lasso, group MCP, and group SCAD. The algorithms
are based on the idea of either locally approximated coordinate
descent or group descent, depending on the penalty.
Author: Patrick Breheny
Maintainer: Patrick Breheny
DESCRIPTION | 9 +++--
FAQ.md |only
MD5 | 53 ++++++++++++++++++-------------
NAMESPACE | 4 ++
NEWS | 18 ++++++++++
R/calcNullDev.R |only
R/cv.grpreg.R | 40 ++++++++++++++++++------
R/gBridge.R | 53 ++++++++++++++++++++++++-------
R/grpreg.R | 33 ++++++++++++++-----
R/loss.R | 15 ++++++---
R/multi.R |only
R/orthogonalize.R | 13 +------
R/plot.R | 12 +++----
R/plot.cv.R | 64 +++++++++++++++++++++++++++++++++-----
R/predict.R | 64 +++++++++++++++++++++++++-------------
R/predict.cv.R |only
R/summary.cv.grpreg.R |only
inst/CITATION | 2 -
inst/tests/extra-features.R | 73 +++++++++++++++++++++++++++++++++++++++++---
inst/tests/multitask.R |only
man/cv.grpreg.Rd | 34 +++++++++++++-------
man/gBridge.Rd | 4 +-
man/grpreg-internal.Rd | 6 ++-
man/grpreg-package.Rd | 8 ++--
man/grpreg.Rd | 30 ++++++++++++------
man/plot.cv.grpreg.Rd | 42 ++++++++++++++++++++-----
man/plot.grpreg.Rd | 4 +-
man/predict.Rd | 33 ++++++++++++++++---
man/select.grpreg.Rd | 3 +
man/summary.cv.grpreg.Rd |only
src/grpreg.c | 1
31 files changed, 462 insertions(+), 156 deletions(-)
Title: R Package for Covariate Balancing Propensity Score
Diff between CBPS versions 0.5 dated 2013-05-08 and 0.6 dated 2013-06-07
Description: CBPS is an R package that implements the covariate
balancing propensity score proposed by Imai and Ratkovic (2013;
JRSSB). The propensity score is estimated such that it
maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore,
avoids an iteration between model fitting and balance checking.
The package also implements several extensions of the CBPS
beyond the cross-sectional, binary treatment setting. The
current version implements the CBPS for longitudinal settings
so that it can be used in conjunction with marginal structural
models (Imai and Ratkovic, 2013a), treatments with three- and
four-valued treatment variables (Fong, 2013), and the situation
with multiple distinct binary treatments administered
simultaneously. In the future it will be extended to other
settings including continuous treatments and the generalization
of experimental and instrumental variable estimates.
Author: Marc Ratkovic
Maintainer: Marc Ratkovic
ChangeLog | 3
DESCRIPTION | 23 +-
MD5 | 31 +--
NAMESPACE | 17 +
R/CBMSMFunction.R | 134 ++++++++++---
R/CBPSBinary.R | 21 +-
R/CBPSMain.R | 496 ++++++++++++++++++++++++++++++++++++++++++++++++---
R/CBPSMultiTreat.r | 131 ++++++++-----
data/LaLonde.tab.gz |binary
man/CBPS.Rd | 80 +++++++-
man/DR.rd | 3
man/IPW.Rd | 3
man/balance.CBMB.Rd |only
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man/balance.CBPS.Rd |only
man/balance.Rd |only
man/plot.CBMB.Rd |only
man/plot.CBMSM.Rd |only
man/plot.CBPS.Rd |only
man/summary.CBPS.Rd | 2
20 files changed, 795 insertions(+), 149 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between metrumrg versions 5.49 dated 2013-05-23 and 5.50 dated 2013-06-06
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of
detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/first.R | 2 +-
man/metrumrg-package.Rd | 4 ++--
5 files changed, 15 insertions(+), 11 deletions(-)
Title: Foreach looping construct for R
Diff between foreach versions 1.4.0 dated 2012-04-16 and 1.4.1 dated 2013-06-06
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation of
a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Revolution Analytics, Steve Weston
Maintainer: Revolution Analytics
DESCRIPTION | 12 +++++++-----
MD5 | 12 +++++++-----
NEWS | 4 ++++
R/getsyms.R | 4 +++-
inst/doc/foreach.R |only
inst/doc/foreach.pdf |binary
inst/doc/nested.R |only
inst/doc/nested.pdf |binary
8 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools for Approximate Bayesian Computation (ABC)
Diff between abc versions 1.6 dated 2012-08-14 and 1.7 dated 2013-06-06
Description: The package implements several ABC algorithms for
performing parameter estimation and model selection.
Cross-validation tools are also available for measuring the
accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.
Author: Katalin Csillery, Michael Blum and Olivier Francois
Maintainer: Michael Blum
CHANGES | 15 +++++++++++++++
DESCRIPTION | 9 +++++----
MD5 | 19 ++++++++++---------
R/abc.R | 2 +-
R/cv4postpr.R | 10 ++++++----
R/postpr.R | 2 ++
inst/doc/abcvignette.R |only
man/abc.Rd | 13 +++----------
man/cv4abc.Rd | 4 ++--
man/cv4postpr.Rd | 3 ++-
man/postpr.Rd | 19 +++++++++++--------
11 files changed, 57 insertions(+), 39 deletions(-)
Title: R interface to the Encyclopedia of Life
Diff between Reol versions 1.8 dated 2013-04-23 and 1.14 dated 2013-06-06
Description: An R interface to the EOL API. Includes functions for
downloading and extracting information off the EOL pages.
Author: Barb Banbury
Maintainer: Barb Banbury
DESCRIPTION | 12 ++++++------
MD5 | 10 ++++++----
NAMESPACE | 2 +-
R/MatchHierPageToEOLdata.R | 4 +++-
doc |only
man/MakeEdgeLabels.Rd | 3 ++-
6 files changed, 18 insertions(+), 13 deletions(-)
Title: Calculation of rarity indices for species and assemblages of
species
Diff between Rarity versions 1.1 dated 2013-05-10 and 1.2 dated 2013-06-06
Description: This package allows calculation of rarity weights for
species and indices of rarity for assemblages of species
according to different methods (Leroy et al. 2012, In Press).
Author: Boris Leroy
Maintainer: Boris Leroy
Rarity-1.1/Rarity/R/funcRarity.R |only
Rarity-1.2/Rarity/DESCRIPTION | 10 ++--
Rarity-1.2/Rarity/MD5 | 15 ++++--
Rarity-1.2/Rarity/R/correlation_plots.R |only
Rarity-1.2/Rarity/R/rarity_indices.R |only
Rarity-1.2/Rarity/R/rarity_weights.R |only
Rarity-1.2/Rarity/data |only
Rarity-1.2/Rarity/man/Irr.Rd | 34 ++++++++------
Rarity-1.2/Rarity/man/Rarity-package.Rd | 30 +++++++------
Rarity-1.2/Rarity/man/corPlot.Rd |only
Rarity-1.2/Rarity/man/rWeights.Rd | 73 ++++++++++++++++----------------
Rarity-1.2/Rarity/man/spid.occ.Rd |only
12 files changed, 90 insertions(+), 72 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Diff between pegas versions 0.4-4 dated 2013-01-23 and 0.4-5 dated 2013-06-06
Description: pegas provides functions for reading, writing, plotting,
analysing, and manipulating allelic and haplotypic data, and
for the analysis of population nucleotide sequences including
coalescence analyses.
Author: Emmanuel Paradis, Alastair Potts
Maintainer: Emmanuel Paradis
pegas-0.4-4/pegas/COPYING |only
pegas-0.4-5/pegas/DESCRIPTION | 11 ++++++-----
pegas-0.4-5/pegas/MD5 | 10 +++++-----
pegas-0.4-5/pegas/NAMESPACE | 22 +++++++++++++++++++++-
pegas-0.4-5/pegas/NEWS | 9 +++++++++
pegas-0.4-5/pegas/inst/doc/ReadingFiles.R |only
pegas-0.4-5/pegas/man/bind.loci.Rd | 7 ++++---
7 files changed, 45 insertions(+), 14 deletions(-)
Title: Pedigree functions
Diff between kinship2 versions 1.3.7 dated 2012-10-31 and 1.5.0 dated 2013-06-06
Description: Routines to handle family data with a pedigree object. The
initial purpose was to create correlation structures that
describe family relationships such as kinship and
identity-by-descent, which can be used to model family data in
mixed effects models, such as in the coxme function. Also
includes a tool for pedigree drawing which is focused on
producing compact layouts without intervention. Recent
additions include utilities to trim the pedigree object with
various criteria, and kinship for the X chromosome
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Martha
Matsumoto, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell
DESCRIPTION | 11
MD5 | 43 +-
R/alignped1.R | 5
R/autohint.R | 6
R/kinship.R | 168 ++++++++-
R/pedigree.R | 8
R/pedigree.trim.R | 59 ---
R/pedtrim.R |only
R/plot.pedigree.shrink.R | 24 -
inst/NEWS.Rd | 20 +
inst/doc/pedigree.pdf |binary
man/autohint.Rd | 9
man/kinship.Rd | 35 +
noweb/align.Rnw | 16
noweb/align2.Rnw | 11
noweb/all.nw | 685 +++++++++++++++++++++++--------------
noweb/kinship.Rnw | 526 ++++++++++++++++++++--------
noweb/pedigree.Rnw | 45 +-
noweb/pedigree.shrink.Rnw | 83 ----
tests/kin1.R | 8
tests/kin1.Rout.save | 17
tests/test.kinX.R |only
tests/test.kinX.Rout.save |only
tests/test.pedigree.trim.Rout.save | 4
24 files changed, 1174 insertions(+), 609 deletions(-)
Title: Automatic Generation of Exams in R
Diff between exams versions 1.9-5 dated 2013-06-04 and 1.9-6 dated 2013-06-06
Description: Sweave-based automatic generation of exams including
multiple-choice questions and arithmetic problems. Exams can be
produced in various formats, including PDF, HTML, Moodle XML,
QTI 1.2 (for OLAT).
Author: Achim Zeileis [aut, cre], Bettina Gruen [aut], Friedrich Leisch
[aut], Nikolaus Umlauf [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 ++++++
inst/doc/exams.pdf |binary
inst/doc/exams2.pdf |binary
tests/encodings.R | 4 ++--
6 files changed, 17 insertions(+), 11 deletions(-)
Title: CLAG: an unsupervised non hierarchical clustering algorithm
handling biological data
Diff between CLAG versions 2.10 dated 2013-05-02 and 2.16.1 dated 2013-06-06
Description: CLAG (for CLusters AGgregation) is an unsupervised non
hierarchical clustering algorithm designed to cluster a large
variety of biological data and to provide a clustered matrix
and numerical values indicating cluster strength. CLAG
clusterizes correlation matrices for residues in protein
families, gene-expression and miRNA data related to various
cancer types, sets of species described by multidimensional
vectors of characters, binary matrices. It does not ask to all
data points to cluster and it converges yielding the same
result at each run. Its simplicity and speed allows it to run
on reasonably large datasets.
Author: Linda DIB, Raphael CHAMPEIMONT, Alessandra CARBONE
Maintainer: Raphael CHAMPEIMONT
DESCRIPTION | 8 +--
MD5 | 29 ++++++-----
NAMESPACE | 2
NEWS | 25 ++++++++++
R/CLAG.R | 47 +++++--------------
R/CLAG_compareclust.R |only
inst/Perl/TOOLCLAG-minimal/AnyMatrix/Aggregation.pl | 4 -
inst/Perl/TOOLCLAG-minimal/AnyMatrix/exe-RCommand.pl | 2
inst/Perl/TOOLCLAG-minimal/Binary/Aggregation.pl | 2
inst/doc/CLAG-tutorial.pdf |binary
man/BREAST.Rd | 2
man/CLAG.clust.Rd | 31 +++++-------
man/DIM128.Rd | 2
man/DIM128_subset.Rd | 2
man/GLOBINE.Rd | 2
man/compareClusterings.Rd |only
man/mapClusterings.Rd |only
17 files changed, 82 insertions(+), 76 deletions(-)
Title: Spatial point patterns analysis
Diff between ads versions 1.2-13 dated 2013-05-16 and 1.3-1 dated 2013-06-06
Description: Perform first- and second-order multi-scale analyses
derived from Ripley's K-function, for univariate, multivariate
and marked mapped data in rectangular, circular or irregular
shaped sampling windows, with test of statistical significance
based on Monte Carlo simulations.
Author: R. Pelissier and F. Goreaud
Maintainer: Raphael Pelissier
DESCRIPTION | 8
MD5 | 65 +-
R/fads.R | 178 ++++++-
R/plot.fads.R | 74 ++
R/print.fads.R | 5
data/BPoirier.rda |binary
data/Couepia.rda |binary
man/Allogny.Rd | 6
man/BPoirier.Rd | 2
man/Couepia.Rd | 2
man/area.swin.Rd | 10
man/dval.Rd | 14
man/inside.swin.Rd | 14
man/internal.Rd | 17
man/k12fun.Rd | 18
man/k12val.Rd | 16
man/kfun.Rd | 16
man/ki.fun.Rd | 14
man/kijfun.Rd | 16
man/kmfun.Rd | 22
man/ksfun.Rd |only
man/kval.Rd | 14
man/plot.fads.Rd | 28 -
man/plot.spp.Rd | 24
man/plot.vads.Rd | 17
man/spp.Rd | 16
man/swin.Rd | 28 -
man/triangulate.Rd | 12
src/Zlibs.c | 1315 ++++++++++++++++++++++++++++++++++++++++++++++++++++-
src/Zlibs.h | 17
src/adssub.c | 27 +
src/adssub.h | 2
src/triangulate.c | 32 -
src/triangulate.h | 2
34 files changed, 1809 insertions(+), 222 deletions(-)
Title: Particle Swarm Optimisation, with focus on Environmental Models
Diff between hydroPSO versions 0.3-2 dated 2013-05-29 and 0.3-3 dated 2013-06-06
Description: This package implements a state-of-the-art version of the
Particle Swarm Optimisation (PSO) algorithm (SPSO-2011 and
SPSO-2007 capable). hydroPSO can be used as a replacement of
the 'optim' R function for (global) optimization of non-smooth
and non-linear functions. However, the main focus of hydroPSO
is the calibration of environmental and other real-world models
that need to be executed from the system console. hydroPSO is
model-independent, allowing the user to easily interface any
computer simulation model with the calibration engine (PSO).
hydroPSO communicates with the model through the model's own
input and output files, without requiring access to the model's
source code. Several PSO variants and controlling options are
included to fine-tune the performance of the calibration engine
to different calibration problems. An advanced sensitivity
analysis function together with user-friendly plotting
summaries facilitate the interpretation and assessment of the
calibration results. hydroPSO is parallel-capable, to alleviate
the computational burden of complex models with "long"
execution time. Bugs reports/comments/questions are very
welcomed (in English, Spanish or Italian).
Author: Mauricio Zambrano-Bigiarini [aut, cre], Rodrigo Rojas [ctb]
Maintainer: Mauricio Zambrano-Bigiarini
DESCRIPTION | 8 ++--
MD5 | 28 +++++++--------
NAMESPACE | 6 ++-
NEWS | 20 +++++++++-
R/PSO_v2013.R | 12 +++---
R/hydroPSO2pest.R | 2 -
R/hydromod.R | 11 +++---
R/lhoat.R | 26 +++++++-------
R/pest2hydroPSO.R | 71 ++++++++++++++++++++++++---------------
R/plot_out.R | 4 +-
R/plot_results.R | 2 -
R/read_out.R | 5 +-
inst/Rscripts/hydroPSO-Rscript.R | 7 ++-
man/hydroPSO-internal.Rd | 1
man/hydroPSO-package.Rd | 8 ++--
15 files changed, 124 insertions(+), 87 deletions(-)
Title: Unit root and cointegration tests for time series data
Diff between urca versions 1.2-7 dated 2012-07-26 and 1.2-8 dated 2013-06-06
Description: Unit root and cointegration tests encountered in applied
econometric analysis are implemented.
Author: Bernhard Pfaff [aut, cre], Matthieu Stigler [ctb]
Maintainer: Bernhard Pfaff
DESCRIPTION | 12 +++++++-----
MD5 | 34 +++++++++++++++++-----------------
data/Raotbl1.rda |binary
data/Raotbl2.rda |binary
data/Raotbl3.rda |binary
data/Raotbl4.rda |binary
data/Raotbl5.rda |binary
data/Raotbl6.rda |binary
data/Raotbl7.rda |binary
data/UKconinc.rda |binary
data/UKconsumption.rda |binary
data/UKpppuip.rda |binary
data/denmark.rda |binary
data/ecb.rda |binary
data/finland.rda |binary
data/npext.rda |binary
data/nporg.rda |binary
src/Makevars | 1 -
18 files changed, 24 insertions(+), 23 deletions(-)
Title: Statistical Analysis of Mixed Ploidy Populations
Diff between StAMPP versions 1.0 dated 2013-05-29 and 1.1 dated 2013-06-06
Description: StAMPP allows users to calculate pairwise Nei's Genetic
Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir &
Cockerham 1984) and also Genomic Relationship matrixes
following Yang et al. (2010) in mixed and single ploidy
populations. Bootstrapping across loci is implemented during
Fst calculation to generate confidence intervals and p-values
around pairwise Fst values. StAMPP utilises SNP genotype data
of any ploidy level (with the ability to handle missing data)
and is coded to utilise multithreading where available to allow
efficient analysis of large datasets. StAMPP is able to handle
genotype data from genlight objects allowing integration with
other packages such adegenet. Please refer to LW Pembleton,
NOI Cogan & JW Forster, 2013, Molecular Ecology Resources,
doi:10.1111/1755-0998.12129 for the appropriate citation and
user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/stampp2genlight.R | 2 +-
man/StAMPP-package.Rd | 4 ++--
5 files changed, 11 insertions(+), 10 deletions(-)
Title: Gene region-level testing procedure for SNP data, using the min
P test resampling approach
Diff between minPtest versions 1.5 dated 2012-11-26 and 1.6 dated 2013-06-06
Description: Package minPtest is designed for estimating a gene
region-level summary for SNP data from case-control studies
using a permutation-based resampling method, called min P test,
allowing execution on a compute cluster or multicore computer.
Author: Stefanie Hieke
Maintainer: Stefanie Hieke
DESCRIPTION | 15 +++++----
MD5 | 21 +++++++------
R/minPtest.R | 46 ++++++++++++++----------------
inst/doc/plots/plot_minPtest1_object1.pdf |binary
inst/doc/plots/plot_minPtest2_object2.pdf |binary
inst/doc/vignette.R |only
inst/doc/vignette.Snw | 21 ++++++-------
inst/doc/vignette.pdf |binary
man/generateSNPs.Rd | 2 -
man/minPtest.Rd | 21 +++++++------
man/plot.minPtest.Rd | 14 +++++----
man/summary.minPtest.Rd | 7 ++--
12 files changed, 76 insertions(+), 71 deletions(-)
Title: This package contains an implementation of continuous convex
piecewise (linear and quadratic) functions
Diff between ConConPiWiFun versions 0.3 dated 2013-02-13 and 0.4.1 dated 2013-06-06
Description: Continuous convex piecewise linear (ccpl) resp. quadratic
(ccpq) functions can be implemented with sorted breakpoints and
slopes. This includes functions that are ccpl (resp. ccpq) on a
convex set (i.e. an interval or a point) and infinite out of
the domain. These functions can be very useful for a large
class of optimisation problems. Efficient manipulation (such as
log(N) insertion) of such data structure is obtained with map
standard template library of C++ (that hides balanced trees).
This package is a wrapper on such a class based on Rcpp
modules.
Author: Robin Girard
Maintainer: Robin Girard
ConConPiWiFun-0.3/ConConPiWiFun/inst/include/cpfunction.h |only
ConConPiWiFun-0.3/ConConPiWiFun/src/cplfunction.cc |only
ConConPiWiFun-0.4.1/ConConPiWiFun/DESCRIPTION | 15 -
ConConPiWiFun-0.4.1/ConConPiWiFun/MD5 | 33 ++-
ConConPiWiFun-0.4.1/ConConPiWiFun/R/zzz.R | 92 +++++++---
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/ConConPiWiFun.h |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/convex_function_manip.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/convex_functions_tools.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/cplfunction.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/cplfunctionvec.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/cpqfunction.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/inst/include/cpqfunctionvec.hpp |only
ConConPiWiFun-0.4.1/ConConPiWiFun/man/cplfunction.Rd | 20 +-
ConConPiWiFun-0.4.1/ConConPiWiFun/man/cplfunctionvec.Rd | 28 +--
ConConPiWiFun-0.4.1/ConConPiWiFun/man/cpqfunction.Rd |only
ConConPiWiFun-0.4.1/ConConPiWiFun/man/cpqfunctionvec.Rd |only
ConConPiWiFun-0.4.1/ConConPiWiFun/src/Makevars.win | 1
ConConPiWiFun-0.4.1/ConConPiWiFun/src/Modules.cc |only
ConConPiWiFun-0.4.1/ConConPiWiFun/test |only
19 files changed, 124 insertions(+), 65 deletions(-)
Title: Foreach parallel adaptor for the snow package
Diff between doSNOW versions 1.0.6 dated 2012-04-16 and 1.0.7 dated 2013-06-06
Description: Provides a parallel backend for the %dopar% function using
Luke Tierney's snow package.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 10 +++---
MD5 | 5 +--
R/doSNOW.R | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++---------
inst |only
4 files changed, 90 insertions(+), 19 deletions(-)
Title: Joint Modeling of Longitudinal and Time-to-Event Data under a
Bayesian Approach
Diff between JMbayes versions 0.4-0 dated 2013-05-15 and 0.4-1 dated 2013-06-06
Description: Shared parameter models for the joint modeling of
longitudinal and time-to-event data using JAGS, WinBUGS, or
OpenBUGS.
Author: Dimitris Rizopoulos [aut, cre]
Maintainer: Dimitris Rizopoulos
DESCRIPTION | 9 ++++---
MD5 | 58 ++++++++++++++++++++++++++----------------------
NAMESPACE | 4 ++-
R/aucJM.JMbayes.R | 2 -
R/aucJM.coxph.R | 10 ++++----
R/dataLM.R |only
R/dbs.R | 1
R/dns.R | 1
R/dynCJM.coxph.R | 17 +++++++++-----
R/fitted.JMbayes.R |only
R/globals.R | 2 -
R/ibs.R | 9 +++++--
R/ins.R | 8 ++++--
R/jointModelBayes.R | 2 -
R/makepredictcall.dbs.R | 4 +--
R/makepredictcall.dns.R | 4 +--
R/makepredictcall.ibs.R | 4 +--
R/makepredictcall.ins.R | 4 +--
R/prederrJM.JMbayes.R | 6 ++--
R/prederrJM.coxph.R | 37 ++++++++++++++----------------
R/residuals.JMbayes.R |only
R/survPriors.R | 6 +++-
R/xtable.JMbayes.R |only
data/aids.id.rda |binary
data/aids.rda |binary
data/pbc2.id.rda |binary
data/pbc2.rda |binary
data/prothro.rda |binary
data/prothros.rda |binary
inst/NEWS | 12 +++++++++
man/JMbayes.Rd | 4 +--
man/fitted.Rd |only
man/xtable.Rd |only
33 files changed, 121 insertions(+), 83 deletions(-)
Title: Joint Modeling of Longitudinal and Survival Data
Diff between JM versions 1.1-0 dated 2012-12-07 and 1.2-0 dated 2013-06-06
Description: Shared parameter models for the joint modeling of
longitudinal and time-to-event data.
Author: Dimitris Rizopoulos
Maintainer: Dimitris Rizopoulos
JM-1.1-0/JM/R/dynC.R |only
JM-1.1-0/JM/R/dynC.coxph.R |only
JM-1.1-0/JM/R/dynC.jointModel.R |only
JM-1.1-0/JM/R/print.dynC.R |only
JM-1.1-0/JM/man/dynC.Rd |only
JM-1.2-0/JM/DESCRIPTION | 9 -
JM-1.2-0/JM/MD5 | 66 +++++----
JM-1.2-0/JM/NAMESPACE | 17 +-
JM-1.2-0/JM/R/aucJM.R |only
JM-1.2-0/JM/R/aucJM.coxph.R |only
JM-1.2-0/JM/R/aucJM.jointModel.R |only
JM-1.2-0/JM/R/dataLM.R |only
JM-1.2-0/JM/R/dbs.R | 1
JM-1.2-0/JM/R/dns.R | 1
JM-1.2-0/JM/R/dynCJM.R |only
JM-1.2-0/JM/R/dynCJM.coxph.R |only
JM-1.2-0/JM/R/dynCJM.jointModel.R |only
JM-1.2-0/JM/R/ibs.R | 11 +
JM-1.2-0/JM/R/ins.R | 10 -
JM-1.2-0/JM/R/makepredictcall.dbs.R | 4
JM-1.2-0/JM/R/makepredictcall.dns.R | 4
JM-1.2-0/JM/R/makepredictcall.ibs.R | 4
JM-1.2-0/JM/R/makepredictcall.ins.R | 4
JM-1.2-0/JM/R/prederrJM.R |only
JM-1.2-0/JM/R/prederrJM.coxph.R |only
JM-1.2-0/JM/R/prederrJM.jointModel.R |only
JM-1.2-0/JM/R/print.aucJM.R |only
JM-1.2-0/JM/R/print.dynCJM.R |only
JM-1.2-0/JM/R/print.prederrJM.R |only
JM-1.2-0/JM/R/survfitJM.R | 252 -----------------------------------
JM-1.2-0/JM/R/survfitJM.jointModel.R |only
JM-1.2-0/JM/data/aids.id.rda |binary
JM-1.2-0/JM/data/aids.rda |binary
JM-1.2-0/JM/data/pbc2.id.rda |binary
JM-1.2-0/JM/data/pbc2.rda |binary
JM-1.2-0/JM/data/prothro.rda |binary
JM-1.2-0/JM/data/prothros.rda |binary
JM-1.2-0/JM/inst/NEWS | 17 ++
JM-1.2-0/JM/man/JM.Rd | 8 -
JM-1.2-0/JM/man/aucJM.Rd |only
JM-1.2-0/JM/man/dynCJM.Rd |only
JM-1.2-0/JM/man/jointModel.Rd | 4
JM-1.2-0/JM/man/prederrJM.Rd |only
JM-1.2-0/JM/man/rocJM.Rd | 4
JM-1.2-0/JM/man/survfitJM.Rd | 8 -
45 files changed, 118 insertions(+), 306 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Diff between FactoClass versions 1.0.8 dated 2012-02-01 and 1.0.9 dated 2013-06-06
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
Author: Campo Elias Pardo
Maintainer: Campo Elias Pardo
DESCRIPTION | 15 ++++++++-------
MD5 | 6 +++---
R/plotFactoClass.R | 2 +-
man/plotFactoClass.Rd | 24 +++++++++++++-----------
4 files changed, 25 insertions(+), 22 deletions(-)
Title: Combined analysis of pleiotropy and epistasis
Diff between cape versions 1.0 dated 2013-04-04 and 1.1 dated 2013-06-05
Description: This package combines complementary information across
multiple related phenotypes to infer directed epistatic
interactions between genetic markers. The analysis in this
package can be applied to a variety of engineered and natural
populations.
Author: Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and
Greg W. Carter
Maintainer: Anna L. Tyler
cape-1.0/cape/R/plotSelectedMarkers.R |only
cape-1.0/cape/man/plotSelectedMarkers.Rd |only
cape-1.1/cape/DESCRIPTION | 10
cape-1.1/cape/MD5 | 71 ++---
cape-1.1/cape/R/calc.p.R | 49 ++-
cape-1.1/cape/R/consec.pairs.R |only
cape-1.1/cape/R/create.covar.R | 10
cape-1.1/cape/R/direct.influence.R | 326 +++++++++++------------
cape-1.1/cape/R/get.covar.R | 11
cape-1.1/cape/R/get.network.R |only
cape-1.1/cape/R/linkage.blocks.R |only
cape-1.1/cape/R/one.pairscan.R | 6
cape-1.1/cape/R/plotCollapsedVarInf.R |only
cape-1.1/cape/R/plotNetwork.R |only
cape-1.1/cape/R/plotPairscan.R | 43 ++-
cape-1.1/cape/R/plotSinglescan.R | 234 ++++++++++++----
cape-1.1/cape/R/plotVariantInfluences.R | 34 +-
cape-1.1/cape/R/read.population.R | 13
cape-1.1/cape/R/segment.region.R |only
cape-1.1/cape/R/select.by.ind.R | 5
cape-1.1/cape/R/select.markers.for.pairscan.R | 4
cape-1.1/cape/R/set.covar.R | 21 +
cape-1.1/cape/R/singlescan.R | 18 +
cape-1.1/cape/R/writeVariantInfluences.R | 34 +-
cape-1.1/cape/data/obesity.cross.rda |binary
cape-1.1/cape/inst/doc/cape.Rnw |only
cape-1.1/cape/inst/doc/cape.pdf |binary
cape-1.1/cape/man/calc.p.Rd | 10
cape-1.1/cape/man/consec.pairs.Rd |only
cape-1.1/cape/man/direct.influence.Rd | 12
cape-1.1/cape/man/genome.wide.threshold.1D.Rd | 4
cape-1.1/cape/man/get.network.Rd |only
cape-1.1/cape/man/linkage.blocks.Rd |only
cape-1.1/cape/man/one.pairscan.Rd | 3
cape-1.1/cape/man/plotCollapsedVarInf.Rd |only
cape-1.1/cape/man/plotNetwork.Rd |only
cape-1.1/cape/man/plotPairscan.Rd | 4
cape-1.1/cape/man/plotSinglescan.Rd | 22 +
cape-1.1/cape/man/plotVariantInfluences.Rd | 6
cape-1.1/cape/man/rz.transform.Rd | 6
cape-1.1/cape/man/segment.region.Rd |only
cape-1.1/cape/man/select.markers.for.pairscan.Rd | 6
cape-1.1/cape/man/set.covar.Rd | 8
cape-1.1/cape/man/writeVariantInfluences.Rd | 6
44 files changed, 635 insertions(+), 341 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.5.0 dated 2013-03-29 and 0.6.0 dated 2013-06-05
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between
inputs and outputs and extensive pre-built widgets make it
possible to build beautiful, responsive, and powerful
applications with minimal effort.
Author: RStudio, Inc.
Maintainer: Winston Chang
DESCRIPTION | 14
MD5 | 144 +-
NAMESPACE | 15
NEWS | 38
R/bootstrap.R | 360 +++++
R/fileupload.R | 9
R/imageutils.R | 9
R/priorityqueue.R |only
R/react.R | 17
R/reactives.R | 107 +
R/shiny.R | 263 +++-
R/tags.R | 259 ++--
R/update-input.R |only
R/utils.R | 42
inst/NOTICE | 3
inst/tests-js |only
inst/tests/test-bootstrap.r | 43
inst/tests/test-reactivity.r | 13
inst/tests/test-tags.r | 27
inst/www/shared/datepicker |only
inst/www/shared/shiny.js | 1184 +++++++++++++++++--
inst/www/shared/slider/img/jslider.blue.png |binary
inst/www/shared/slider/img/jslider.plastic.png |binary
inst/www/shared/slider/img/jslider.png |binary
inst/www/shared/slider/img/jslider.round.plastic.png |binary
inst/www/shared/slider/img/jslider.round.png |binary
man-roxygen |only
man/actionButton.Rd |only
man/bootstrapPage.Rd | 9
man/checkboxGroupInput.Rd | 3
man/checkboxInput.Rd | 3
man/dateInput.Rd |only
man/dateRangeInput.Rd |only
man/invalidateLater.Rd | 31
man/numericInput.Rd | 3
man/observe.Rd | 8
man/outputOptions.Rd | 8
man/radioButtons.Rd | 3
man/reactiveTimer.Rd | 35
man/runApp.Rd | 21
man/runExample.Rd | 12
man/selectInput.Rd | 3
man/shinyServer.Rd | 6
man/sliderInput.Rd | 3
man/tabPanel.Rd | 3
man/tabsetPanel.Rd | 10
man/tag.Rd | 13
man/textInput.Rd | 3
man/updateCheckboxGroupInput.Rd |only
man/updateCheckboxInput.Rd |only
man/updateDateInput.Rd |only
man/updateDateRangeInput.Rd |only
man/updateNumericInput.Rd |only
man/updateRadioButtons.Rd |only
man/updateSelectInput.Rd |only
man/updateSliderInput.Rd |only
man/updateTabsetPanel.Rd |only
man/updateTextInput.Rd |only
man/withTags.Rd |only
59 files changed, 2331 insertions(+), 393 deletions(-)
Title: Bayesian inference of outbreak dynamics based on epidemiological
and genetic information.
Diff between outbreaker versions 1.0-0 dated 2013-02-19 and 1.0-1 dated 2013-06-05
Description: Bayesian inference of outbreak dynamics based on
epidemiological and genetic information.
Author: Thibaut Jombart
Maintainer: Thibaut Jombart
ChangeLog | 7 +++++++
DESCRIPTION | 15 ++++++++-------
MD5 | 30 ++++++++++++++++--------------
NAMESPACE | 21 +++++++++++----------
R/interface.R | 2 +-
R/plot.R | 27 ++++++++++++---------------
R/reproRate.R | 4 ++--
R/selectChains.R |only
R/simOutbreak.R | 12 ++++++------
R/tTree.R | 6 +++---
R/zzz.R | 2 +-
man/mainplots.Rd | 26 ++++++++++++++++++--------
man/outbreaker.Rd | 6 ++++--
man/selectChains.Rd |only
man/simOutbreak.Rd | 17 ++++++++++-------
man/tTree.Rd | 6 ++++--
man/toyOutbreak.Rd | 15 ++++++++++-----
17 files changed, 113 insertions(+), 83 deletions(-)
Title: Weighted Logrank Tests and NPMLE for interval censored data
Diff between interval versions 1.0-1.2 dated 2011-04-07 and 1.1-0.0 dated 2013-06-05
Description: Functions to fit nonparametric survival curves, plot them,
and perform logrank or Wilcoxon type tests.
Author: Michael P. Fay
Maintainer: Michael P. Fay
DESCRIPTION | 9 +--
MD5 |only
NAMESPACE | 2
NEWS | 12 +++-
R/getsurv.R | 15 +++--
R/icfit.R | 99 +++++++++++++++++++++++++++++++++-
R/icfitControl.R | 11 +++
R/methods.icfit.R | 117 ++++++++++++++++++++++++++++++++++-------
inst/doc/intervalCensoring.R |only
inst/doc/intervalCensoring.pdf |binary
man/icfit.Rd | 16 +++++
man/icfitControl.Rd | 14 ++++
man/ictest.Rd | 7 ++
man/interval-internal.Rd | 8 ++
man/interval-package.Rd | 4 -
man/plot.icfit.Rd | 10 +++
16 files changed, 285 insertions(+), 39 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Diff between bpcp versions 0.5.0 dated 2012-06-29 and 1.0.0 dated 2013-06-05
Description: Calculates nonparametric pointwise confidence intervals
for the survival distribution for right censored data.
Especially important for small sample sizes or heavily censored
data.
Author: Michael Fay
Maintainer: Michael Fay
DESCRIPTION | 11 ++++++-----
MD5 | 18 ++++++++++--------
NEWS |only
R/kmciFunctions.R | 26 ++++++++++++++++++++++++++
demo/00Index | 4 +++-
demo/Simulation.R | 6 ++++--
demo/SimulationBootOnly.R |only
man/bpcp-package.Rd | 7 ++++---
man/kmci.object.Rd | 2 +-
man/kmciALL.Rd | 16 +++++++++++-----
man/plot.kmciLR.Rd | 9 ++++++---
11 files changed, 71 insertions(+), 28 deletions(-)
Title: Graphical Integrated Text Mining Solution
Diff between RcmdrPlugin.temis versions 0.6 dated 2013-02-10 and 0.6.1 dated 2013-06-05
More information about RcmdrPlugin.temis at CRAN
Description: An Rcommander plug-in providing an integrated solution to
perform a series of text mining tasks such as importing and
cleaning a corpus, and analyses like terms and documents
counts, vocabulary tables, terms co-occurrences and documents
similarity measures, time series analysis, correspondence
analysis and hierarchical clustering.
Author: Milan Bouchet-Valat [aut, cre], Gilles Bastin [aut]
Maintainer: Milan Bouchet-Valat
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/DESCRIPTION | 18
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/MD5 | 27
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/NAMESPACE | 1
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/NEWS |only
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/SnowballC.R |only
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/common.R | 13
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/corpusClustering.R | 77 +
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/dictionary.R | 8
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/importCorpus.R | 195 ++-
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/R/time.R | 20
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/inst/po/fr/LC_MESSAGES/R-RcmdrPlugin.temis.mo |binary
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/man/importCorpusDlg.rd | 9
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/man/stemDocumentSnowballC.Rd |only
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/po/R-RcmdrPlugin.temis.pot | 479 +++++----
RcmdrPlugin.temis-0.6.1/RcmdrPlugin.temis/po/R-fr.po | 525 +++++-----
RcmdrPlugin.temis-0.6/RcmdrPlugin.temis/R/Rstem.R |only
RcmdrPlugin.temis-0.6/RcmdrPlugin.temis/man/stemDocumentRstem.Rd |only
17 files changed, 784 insertions(+), 588 deletions(-)
Permanent link
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-6 dated 2013-01-09 and 1.0-7 dated 2013-06-05
Description: A computational toolbox for recursive partitioning. The
core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems,
including nominal, ordinal, numeric, censored as well as
multivariate response variables and arbitrary measurement
scales of the covariates. Based on conditional inference
trees, cforest() provides an implementation of Breiman's random
forests. The function mob() implements an algorithm for
recursive partitioning based on parametric models (e.g. linear
models, GLMs or survival regression) employing parameter
instability tests for split selection. Extensible functionality
for visualizing tree-structured regression models is available.
Author: Torsten Hothorn [aut, cre], Kurt Hornik [aut], Carolin Strobl
[aut], Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 9 +++++----
MD5 | 28 +++++++++++++++-------------
R/ConditionalTree.R | 5 +++--
R/Plot.R | 2 +-
data/mammoexp.rda |binary
inst/NEWS | 7 +++++++
inst/doc/MOB.R |only
inst/doc/MOB.pdf |binary
inst/doc/party.R |only
inst/doc/party.pdf |binary
man/varimp.Rd | 7 +++----
src/RandomForest.c | 4 ++--
src/Utils.c | 4 ++--
tests/Examples/party-Ex.Rout.save | 27 ++++++++++++---------------
tests/bugfixes.R | 7 +++++++
tests/bugfixes.Rout.save | 14 ++++++++++----
16 files changed, 67 insertions(+), 47 deletions(-)
Title: Statistical Tests for Evaluating Conformity to Benford's Law
Diff between BenfordTests versions 1.0.0 dated 2013-05-14 and 1.0.1 dated 2013-06-05
Description: This package contains seven specialized statistical tests
and support functions for determining if numerical data could
conform to Benford's law.
Author: Dieter William Joenssen, with contributions from Thomas
Muellerleile
Maintainer: Dieter William Joenssen
BenfordTests-manual.pdf |binary
DESCRIPTION | 8 +++----
MD5 | 10 ++++-----
NEWS | 45 +++++++++++++++++++++++---------------------
man/BenfordTests-package.Rd | 4 +--
src/NULLH_BfT.c | 10 ++++++++-
6 files changed, 44 insertions(+), 33 deletions(-)
Title: Implementation of the 3D alpha-shape for the reconstruction of
3D sets from a point cloud
Diff between alphashape3d versions 1.0-2 dated 2013-04-22 and 1.0-3 dated 2013-06-05
Description: The package alphashape3d presents the implementation in R
of the alpha-shape of a finite set of points in the
three-dimensional space. This geometric structure generalizes
the convex hull and allows to recover the shape of non-convex
and even non-connected sets in 3D, given a random sample of
points taken into it. Besides the computation of the
alpha-shape, the package alphashape3d provides users with
functions to compute the volume of the alpha-shape, identify
the connected components and facilitate the three-dimensional
graphical visualization of the estimated set.
Author: Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer: Beatriz Pateiro-Lopez
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/inashape3d.R | 13 ++++++++++++-
R/rtorus.R | 42 ++++++++++++++++++++++++++++++------------
man/alphashape3d-package.Rd | 4 ++--
man/ashape3d.Rd | 3 ++-
6 files changed, 55 insertions(+), 25 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.820 dated 2013-05-13 and 0.3.900.0 dated 2013-06-05
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims towards a good balance between speed and ease of use.
Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions.
Various matrix decompositions are provided through optional
integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library (currently version 3.820). Thus users do not
need to install Armadillo itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL
version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
RcppArmadillo-0.3.820/RcppArmadillo/inst/examples/kalman/KalmanCpp.R |only
RcppArmadillo-0.3.900.0/RcppArmadillo/ChangeLog | 13
RcppArmadillo-0.3.900.0/RcppArmadillo/DESCRIPTION | 8
RcppArmadillo-0.3.900.0/RcppArmadillo/MD5 | 115 -
RcppArmadillo-0.3.900.0/RcppArmadillo/debian/changelog | 12
RcppArmadillo-0.3.900.0/RcppArmadillo/debian/control | 4
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/NEWS.Rd | 18
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/doc/RcppArmadillo-intro.pdf |binary
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 16
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 2
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/examples/kalman/Kalman.cpp | 13
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/examples/kalman/benchmark.R | 3
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo | 3
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Col_bones.hpp | 36
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp | 56
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Cube_bones.hpp | 50
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Cube_meat.hpp | 57
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/GenCube_meat.hpp | 14
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Gen_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Gen_meat.hpp | 14
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Mat_bones.hpp | 58
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp | 158 +-
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Proxy.hpp | 762 +++++++++-
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/ProxyCube.hpp | 67
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Row_bones.hpp | 40
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/Row_meat.hpp | 56
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/access.hpp | 8
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 4
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_bones.hpp | 25
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/arrayops_meat.hpp | 344 +++-
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 35
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 4
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/diagview_bones.hpp | 6
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/diagview_meat.hpp | 14
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/diskio_bones.hpp | 4
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 216 ++
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_bones.hpp | 7
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eGlueCube_meat.hpp | 18
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eGlue_meat.hpp | 19
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eOpCube_meat.hpp | 14
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eOp_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eOp_meat.hpp | 14
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eglue_core_meat.hpp | 464 +++++-
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/eop_core_meat.hpp | 291 +++
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/fn_as_scalar.hpp | 3
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/forward_bones.hpp | 5
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/hdf5_misc.hpp | 126 -
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/memory.hpp | 116 +
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/op_median_meat.hpp | 166 +-
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/podarray_bones.hpp | 4
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/subview_bones.hpp | 76
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_bones.hpp | 2
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/subview_cube_meat.hpp | 10
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/subview_meat.hpp | 236 +++
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_bones.hpp |only
RcppArmadillo-0.3.900.0/RcppArmadillo/inst/include/armadillo_bits/xvec_htrans_meat.hpp |only
60 files changed, 3213 insertions(+), 618 deletions(-)
Title: A few useful functions for statisticians
Diff between packHV versions 1.5 dated 2013-05-10 and 1.6 dated 2013-06-05
Description: Various useful functions for statisticians: describe data,
plot Kaplan-Meier curves with numbers of subjects at risk,
compare data sets, display spaghetti-plot, build
multi-contingency tables...
Author: Hugo Varet
Maintainer: Hugo Varet
DESCRIPTION | 13 ++++++++-----
MD5 | 26 +++++++++++++-------------
R/desc.R | 23 +++++++++++++++--------
R/plot_km.R | 41 ++++++++++++++++++++++++-----------------
R/plot_mm.R | 14 +++++---------
man/convert_zero_NA.Rd | 6 +++---
man/cut_quanti.Rd | 6 +++---
man/desc.Rd | 6 ++++--
man/hist_boxplot.Rd | 1 +
man/multi.table.Rd | 6 +++++-
man/packHV-package.Rd | 6 +++---
man/plot_km.Rd | 6 +++---
man/plot_mm.Rd | 12 ++++++------
man/plot_reg.Rd | 2 +-
14 files changed, 94 insertions(+), 74 deletions(-)
Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness
estimation
Diff between mgcv versions 1.7-23 dated 2013-05-20 and 1.7-24 dated 2013-06-05
Description: Routines for GAMs and other generalized ridge regression
with multiple smoothing parameter selection by GCV, REML or
UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood
DESCRIPTION | 6 ++---
MD5 | 22 +++++++++----------
R/fast-REML.r | 2 -
R/gam.fit3.r | 8 ++++---
R/gamm.r | 37 +++++++++++++++++++++++++--------
R/mgcv.r | 5 ++--
changeLog | 34 ++++++++++++++++++++++++++++--
man/bam.Rd | 16 +++++++++-----
man/negbin.Rd | 3 +-
man/smooth.construct.ad.smooth.spec.Rd | 6 +++--
man/smooth.construct.so.smooth.spec.Rd | 7 +++---
src/mgcv.c | 7 ++++--
12 files changed, 110 insertions(+), 43 deletions(-)
Title: Post-Hoc Interaction Analysis
Diff between phia versions 0.1-1 dated 2013-05-11 and 0.1-2 dated 2013-06-05
Description: Analysis of terms in linear, generalized and mixed linear
models, on the basis of multiple comparisons of factor
contrasts. Specially suited for the analysis of interaction
terms.
Author: Helios De Rosario-Martinez
Maintainer: Helios De Rosario-Martinez
ChangeLog | 8 ++++++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/getElements.R | 2 +-
R/testFactors.R | 2 +-
inst/doc/phia.pdf |binary
6 files changed, 19 insertions(+), 11 deletions(-)
Title: Batching Routines in Parallel and Passing Command-Line Arguments
to R
Diff between batch versions 1.1-3 dated 2011-04-14 and 1.1-4 dated 2013-06-05
Description: Functions to allow you to easily pass command-line
arguments into R, and functions to aid in submitting your R
code in parallel on a cluster and joining the results afterward
(e.g. multiple parameter values for simulations running in
parallel, splitting up a permutation test in parallel, etc.).
See `parseCommandArgs(...)' for the main example of how to use
this package.
Author: Thomas Hoffmann
Maintainer: Thomas Hoffmann
DESCRIPTION | 12 +++++++-----
MD5 |only
NAMESPACE | 4 ++--
R/batch.R | 10 +++++-----
4 files changed, 14 insertions(+), 12 deletions(-)
Title: Automatic Generation of Exams in R
Diff between exams versions 1.9-4 dated 2013-03-15 and 1.9-5 dated 2013-06-04
Description: Sweave-based automatic generation of exams including
multiple-choice questions and arithmetic problems. Exams can be
produced in various formats, including PDF, HTML, Moodle XML,
QTI 1.2 (for OLAT).
Author: Achim Zeileis [aut, cre], Bettina Gruen [aut], Friedrich Leisch
[aut], Nikolaus Umlauf [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8
MD5 | 81 +++---
NAMESPACE | 3
NEWS | 43 +++
R/exams.R | 16 +
R/exams2html.R | 27 +-
R/exams2lops.R | 4
R/exams2moodle.R | 150 ++++++++---
R/exams2pdf.R | 41 ++-
R/exams2qti12.R | 175 +++++++++++--
R/exams_eval.R |only
R/exams_skeleton.R |only
R/read_exercise.R | 10
R/read_metainfo.R | 21 +
R/search_files.R |only
R/transformers.R | 1
R/xexams.R | 7
inst/doc/exams.R |only
inst/doc/exams.Rnw | 47 ++-
inst/doc/exams.pdf |binary
inst/doc/exams2.R |only
inst/doc/exams2.Rnw | 548 ++++++++++++++++++++++++++++++-------------
inst/doc/exams2.pdf |binary
inst/exercises/boxhist.Rnw | 14 -
inst/exercises/boxhist2.Rnw |only
inst/exercises/currency1.Rnw |only
inst/exercises/currency8.Rnw |only
inst/exercises/currency9.Rnw |only
inst/exercises/function.Rnw |only
inst/tex/exam.tex | 18 -
inst/tex/oexam.tex |only
inst/tex/osolution.tex |only
inst/tex/plain8.tex |only
inst/tex/plain9.tex |only
inst/tex/solution.tex | 18 -
inst/xml/plain.html | 6
inst/xml/plain8.html |only
inst/xml/plain9.html |only
inst/xml/qti12.xml | 24 -
man/exams.Rd | 2
man/exams2html.Rd | 19 +
man/exams2lops.Rd | 3
man/exams2moodle.Rd | 17 +
man/exams2pdf.Rd | 3
man/exams2qti12.Rd | 38 +-
man/exams_eval.Rd |only
man/exams_skeleton.Rd |only
tests |only
vignettes/exams.Rnw | 47 ++-
vignettes/exams.bib | 112 +++++---
vignettes/exams2.Rnw | 548 ++++++++++++++++++++++++++++++-------------
51 files changed, 1457 insertions(+), 594 deletions(-)
Title: An R client for interacting with the White House's "We The
People" petition API.
Diff between wethepeople versions 0.4 dated 2013-05-01 and 0.5 dated 2013-06-04
Description: Implements an R client for the We The People petitions
API. The client supports loading petitions, signatures, and
users. Additionally, the package includes petition and
signature data samples. There are also several functions for
analyzing and visualizing the data. Term frequency calculations
and word clouds are supported using the tm and wordcloud
package, respectively. Petition and issue summary plots are
also implemented using the ggplot2 package. For additional
information about the We The People project, see
https://petitions.whitehouse.gov. Note that the API limits
requests to 10/second. For bulk data loading, please use the
data dump provided by the White House:
https://petitions.whitehouse.gov/developers
Author: Yoni Ben-Meshulam
Maintainer: Yoni Ben-Meshulam
wethepeople-0.4/wethepeople/R/WeThePeopleClient.r |only
wethepeople-0.4/wethepeople/man/WeThePeopleClient.Rd |only
wethepeople-0.5/wethepeople/DESCRIPTION | 20 +++--
wethepeople-0.5/wethepeople/MD5 | 34 +++++-----
wethepeople-0.5/wethepeople/NAMESPACE | 3
wethepeople-0.5/wethepeople/NEWS | 6 +
wethepeople-0.5/wethepeople/R/WeThePeopleAPIClient.r |only
wethepeople-0.5/wethepeople/R/WeThePeopleMySQLClient.r |only
wethepeople-0.5/wethepeople/R/petition_term_document_matrix.r | 1
wethepeople-0.5/wethepeople/R/plot_issues_over_time.r | 4 -
wethepeople-0.5/wethepeople/R/plot_issues_pending_response.r | 4 -
wethepeople-0.5/wethepeople/R/plot_signatures_by_time_of_day.r | 2
wethepeople-0.5/wethepeople/R/plot_status_by_creation.r | 4 -
wethepeople-0.5/wethepeople/R/wethepeople-package.r | 15 ++--
wethepeople-0.5/wethepeople/README.md | 4 -
wethepeople-0.5/wethepeople/data/petitions.RData |binary
wethepeople-0.5/wethepeople/man/WeThePeopleAPIClient.Rd |only
wethepeople-0.5/wethepeople/man/WeThePeopleMySQLClient.Rd |only
wethepeople-0.5/wethepeople/man/petition_term_document_matrix.Rd | 1
wethepeople-0.5/wethepeople/man/plot_signatures_by_time_of_day.Rd | 4 -
wethepeople-0.5/wethepeople/man/wethepeople.Rd | 12 ++-
21 files changed, 69 insertions(+), 45 deletions(-)
Title: Differentially private regularized logistic regression
Diff between PrivateLR versions 1.0-21 dated 2012-03-23 and 1.1-69 dated 2013-06-04
Description: Differentially private regularized logistic regression
Author: Staal A. Vinterbo
Maintainer: Staal A. Vinterbo
DESCRIPTION | 9 -
MD5 | 8
NAMESPACE | 4
R/dplr.r | 514 +++++++++++++++++++++++++++++++++++++++++++++---------------
man/dplr.Rd | 121 +++++++++++---
5 files changed, 497 insertions(+), 159 deletions(-)
Title: netClass: An R Package for Network-Based Biomarker Discovery
Diff between netClass versions 1.0 dated 2013-05-30 and 1.1 dated 2013-06-04
Description: netClass is an R package for network-based feature (gene)
selection for biomarkers discovery via integrating biological
information. This package adapts the following 5 algorithms
for classifying and predicting gene expression data using prior
knowledge: 1) average gene expression of pathway (aep); 2)
pathway activities classification (PAC); 3) Hub network
Classification (hubc); 4) filter via top ranked genes (FrSVM);
5) smoothed t-statistic (stSVM).
Author: Yupeng Cun
Maintainer: Yupeng Cun
DESCRIPTION | 30 +++++++++++++++---------------
MD5 | 14 +++++++-------
R/FrSVM.R | 11 ++++-------
R/averageExpressionPathwaySVM.R | 11 ++++-------
R/hubNetworkAnalysisCV.R | 12 +++++-------
R/pacCV.R | 17 ++++++-----------
R/stSVM.R | 12 ++++--------
man/netClass-package.Rd | 2 +-
8 files changed, 46 insertions(+), 63 deletions(-)
Title: Estimation and simulation of CARMA(p,q)
Diff between ctarma versions 0.1.4 dated 2013-02-07 and 0.1.5 dated 2013-06-04
Description: Estimation and simulation of CARMA(p,q),
continuous-time-autoregressive-moving-average models
Author: Helgi Tomasson
Maintainer: Helgi Tomasson
DESCRIPTION | 9 ++++----
MD5 | 14 ++++++-------
NEWS | 8 ++++++-
man/carma.covm.rd | 2 -
man/carma.var.lspectrum.rd | 14 +++++++++----
src/blas.f | 30 ++++++++++++++---------------
src/fftest.f | 46 ++++++++++++++++++++++-----------------------
src/zexpm.f | 32 +++++++++++++++----------------
8 files changed, 84 insertions(+), 71 deletions(-)
Title: adegenet: an R package for the exploratory analysis of genetic
and genomic data.
Diff between adegenet versions 1.3-8 dated 2013-05-15 and 1.3-9 dated 2013-06-04
Description: Classes and functions for genetic data analysis within the
multivariate framework.
Author: Thibaut Jombart, Ismail Ahmed, Federico Calboli, Anne Cori,
Tobias Erik Reiners, Peter Solymos
Maintainer: Thibaut Jombart
adegenet-1.3-8/adegenet/TODO |only
adegenet-1.3-9/adegenet/DESCRIPTION | 15 +-
adegenet-1.3-9/adegenet/MD5 | 112 ++++++++--------
adegenet-1.3-9/adegenet/NAMESPACE | 24 +--
adegenet-1.3-9/adegenet/R/SNPbin.R | 12 -
adegenet-1.3-9/adegenet/R/auxil.R | 24 ++-
adegenet-1.3-9/adegenet/R/dapc.R | 107 ++++++++++++---
adegenet-1.3-9/adegenet/R/find.clust.R | 22 +--
adegenet-1.3-9/adegenet/R/gengraph.R | 12 -
adegenet-1.3-9/adegenet/R/glFunctions.R | 34 ++--
adegenet-1.3-9/adegenet/R/glHandle.R | 10 -
adegenet-1.3-9/adegenet/R/glSim.R | 2
adegenet-1.3-9/adegenet/R/gstat.randtest.R | 1
adegenet-1.3-9/adegenet/R/haploGen.R | 8 -
adegenet-1.3-9/adegenet/R/import.R | 33 ++--
adegenet-1.3-9/adegenet/R/monmonier.R | 2
adegenet-1.3-9/adegenet/R/mutations.R | 2
adegenet-1.3-9/adegenet/R/seqTrack.R | 2
adegenet-1.3-9/adegenet/R/sequences.R | 1
adegenet-1.3-9/adegenet/R/setAs.R | 4
adegenet-1.3-9/adegenet/R/spca.R | 6
adegenet-1.3-9/adegenet/R/spca.rtests.R | 4
adegenet-1.3-9/adegenet/R/xvalDapc.R |only
adegenet-1.3-9/adegenet/data/H3N2.RData |binary
adegenet-1.3-9/adegenet/data/dapcIllus.RData |binary
adegenet-1.3-9/adegenet/data/datalist | 2
adegenet-1.3-9/adegenet/data/eHGDP.RData |binary
adegenet-1.3-9/adegenet/data/microbov.RData |binary
adegenet-1.3-9/adegenet/data/nancycats.RData |binary
adegenet-1.3-9/adegenet/data/rupica.RData |binary
adegenet-1.3-9/adegenet/data/sim2pop.RData |binary
adegenet-1.3-9/adegenet/data/spcaIllus.RData |binary
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.R | 34 ++--
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.Rnw | 38 ++---
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.pdf |binary
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.R | 92 ++++++-------
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.Rnw | 2
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.pdf |binary
adegenet-1.3-9/adegenet/man/adegenet.package.Rd | 7 -
adegenet-1.3-9/adegenet/man/auxil.Rd | 26 ++-
adegenet-1.3-9/adegenet/man/dapc.Rd | 32 +---
adegenet-1.3-9/adegenet/man/dapcGraphics.Rd | 4
adegenet-1.3-9/adegenet/man/dapcIllus.Rd | 2
adegenet-1.3-9/adegenet/man/fasta2genlight.Rd | 17 +-
adegenet-1.3-9/adegenet/man/glAux.Rd | 8 -
adegenet-1.3-9/adegenet/man/glPca.Rd | 24 +--
adegenet-1.3-9/adegenet/man/monmonier.Rd | 2
adegenet-1.3-9/adegenet/man/nancycats.Rd | 3
adegenet-1.3-9/adegenet/man/read.PLINK.Rd | 21 ---
adegenet-1.3-9/adegenet/man/read.snp.Rd | 22 ---
adegenet-1.3-9/adegenet/man/seploc.Rd | 8 -
adegenet-1.3-9/adegenet/man/xvalDapc.Rd |only
adegenet-1.3-9/adegenet/vignettes/adegenet-genomics.Rnw | 38 ++---
adegenet-1.3-9/adegenet/vignettes/adegenet-spca.Rnw | 2
adegenet-1.3-9/adegenet/vignettes/base-045.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-068.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-070.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-073.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-080.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-083.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-085.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-088.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-104.pdf |only
63 files changed, 434 insertions(+), 387 deletions(-)
Title: The R-to-MOSEK Optimization Interface
Diff between Rmosek versions 1.2.4 dated 2012-09-04 and 1.2.5 dated 2013-06-04
Description: An interface to the MOSEK optimization library designed to
solve large-scale mathematical optimization problems. Supports
linear, quadratic and second order cone optimization
with/without integer variables, in addition to the more general
separable convex problems. Trial and free academic licenses
available at http://www.mosek.com.
Author: Henrik Alsing Friberg
Maintainer: Henrik Alsing Friberg
DESCRIPTION | 10 +++++++---
MD5 | 18 +++++++++---------
NEWS | 9 +++++++++
configure | 2 +-
configure.win | 6 +++---
inst/doc/userguide.pdf |binary
man/mosek_qptoprob.Rd | 11 +++++++++--
src/Rmosek.cc | 1 +
src/compatibility/pkgMatrixVersion.h | 2 +-
src/rmsk_obj_sexp.h | 2 +-
10 files changed, 41 insertions(+), 20 deletions(-)
Title: Varying stimulus coefficient fMRI models in R
Diff between RfmriVC versions 1.0 dated 2012-04-26 and 1.0.4 dated 2013-06-04
Description: A varying coefficient on the stimulus effect is introduced
into the voxelwise fMRI regression model. By this the effects
of the canonical hemodynamic response function are allowed to
vary with another variable, like for example time or a
vigilance parameter.
Author: Ludwig Bothmann, Stefanie Kalus
Maintainer: Stefanie Kalus
RfmriVC-1.0.4/RfmriVC/DESCRIPTION | 9 -
RfmriVC-1.0.4/RfmriVC/MD5 | 28 ++--
RfmriVC-1.0.4/RfmriVC/R/Fct_designmatrix.R | 2
RfmriVC-1.0.4/RfmriVC/R/RfmriVCConfig.R | 106 ++++++++++++++----
RfmriVC-1.0.4/RfmriVC/R/RfmriVCResults.R | 127 +++++++++++++++++++++-
RfmriVC-1.0.4/RfmriVC/R/calc.ImagePars.R |only
RfmriVC-1.0.4/RfmriVC/R/calcDeviceHeight.R |only
RfmriVC-1.0.4/RfmriVC/R/plotNifti.R |only
RfmriVC-1.0.4/RfmriVC/man/ConfigVC-class.Rd | 5
RfmriVC-1.0.4/RfmriVC/man/ConfigVC-setConfigVC.Rd | 7 -
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-class.Rd | 8 +
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-hrfHat.Rd | 3
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-setters.Rd | 4
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-internal.Rd | 2
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-package.Rd | 9 +
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-saveload.rd |only
RfmriVC-1.0.4/RfmriVC/man/calcDeviceHeight.Rd |only
RfmriVC-1.0.4/RfmriVC/man/plotNifti.Rd |only
RfmriVC-1.0/RfmriVC/.project |only
RfmriVC-1.0/RfmriVC/.settings |only
20 files changed, 260 insertions(+), 50 deletions(-)
Title: Time series costationarity determination
Diff between costat versions 2.1 dated 2012-11-27 and 2.2 dated 2013-06-04
Description: Contains functions that can determine whether a time
series is second-order stationary or not (and hence evidence
for locally stationarity). Given two non-stationary series
(i.e. locally stationary series) this package can then
discover time-varying linear combinations that are second-order
stationary.
Author: Guy Nason, Alessandro Cardinali
Maintainer: Guy Nason
costat-2.1/costat/NEWS |only
costat-2.2/costat/DESCRIPTION | 11 ++++++-----
costat-2.2/costat/MD5 | 4 ++--
costat-2.2/costat/inst |only
4 files changed, 8 insertions(+), 7 deletions(-)
Title: Generalized Diffusion Magnetic Resonance Imaging
Diff between gdimap versions 0.0-3 dated 2013-03-20 and 0.1-1 dated 2013-06-04
Description: Diffusion anisotropy has been used to characterize white
matter neuronal pathways in the human brain, and infer global
connectivity in the central nervous system. The package
implements algorithms to estimate and visualize the orientation
of neuronal pathways in model-free methods (q-space imaging
methods). For estimating fibre orientations two methods have
been implemented. One method implements fibre orientation
detection through local maxima extraction. A second more robust
method is based on directional statistical clustering of ODF
voxel data. Fibre orientations in multiple fibre voxels are
estimated using a mixture of von Mises-Fisher (vMF)
distributions. This statistical estimation procedure is used to
resolve crossing fibre configurations. Reconstruction of
orientation distribution function (ODF) profiles may be
performed using the standard generalized q-sampling imaging
(GQI) approach, Garyfallidis' GQI (GQI2) approach, or Aganj's
variant of the Q-ball imaging (CSA-QBI) approach. Procedures
for the visualization of RGB-maps, line-maps and glyph-maps of
real diffusion magnetic resonance imaging (dMRI) data-sets are
included in the package.
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
gdimap-0.0-3/gdimap/inst/extdata/data_V1_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_V2_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_brain.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_gfa_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/dsi203_bmax4000.txt |only
gdimap-0.0-3/gdimap/man/data_V1_gqi.Rd |only
gdimap-0.0-3/gdimap/man/data_V2_gqi.Rd |only
gdimap-0.0-3/gdimap/man/data_brain.Rd |only
gdimap-0.0-3/gdimap/man/data_gfa_gqi.Rd |only
gdimap-0.0-3/gdimap/man/dsi203_bmax4000.Rd |only
gdimap-0.1-1/gdimap/DESCRIPTION | 38 +--
gdimap-0.1-1/gdimap/MD5 | 91 ++++----
gdimap-0.1-1/gdimap/NAMESPACE | 2
gdimap-0.1-1/gdimap/NEWS | 19 +
gdimap-0.1-1/gdimap/R/gdiutils.R | 22 +-
gdimap-0.1-1/gdimap/R/gqi.odfpeaklines.R | 31 +-
gdimap-0.1-1/gdimap/R/gqi.odfpeaks.R | 30 +-
gdimap-0.1-1/gdimap/R/gqi.odfvmf.R | 34 ++-
gdimap-0.1-1/gdimap/R/gqi.odfvmflines.R | 31 +-
gdimap-0.1-1/gdimap/R/gqi.odfvxgrid.R | 30 +-
gdimap-0.1-1/gdimap/R/readutils.R | 89 ++++++++
gdimap-0.1-1/gdimap/R/rgbvolmap.R | 29 +-
gdimap-0.1-1/gdimap/R/simul.fandtasia.R | 20 +
gdimap-0.1-1/gdimap/R/simul.simplefield.R | 28 +-
gdimap-0.1-1/gdimap/R/simulglyph.vmf.R | 70 +++++-
gdimap-0.1-1/gdimap/R/sph.odfpeaklines.R |only
gdimap-0.1-1/gdimap/R/sph.odfpeaks.R |only
gdimap-0.1-1/gdimap/R/sph.odfvmf.R |only
gdimap-0.1-1/gdimap/R/sph.odfvmflines.R |only
gdimap-0.1-1/gdimap/R/sph.odfvxgrid.R |only
gdimap-0.1-1/gdimap/R/sphutils.R |only
gdimap-0.1-1/gdimap/R/synthfiberss2z.R | 18 +
gdimap-0.1-1/gdimap/inst/extdata/btable.txt |only
gdimap-0.1-1/gdimap/inst/extdata/data.bvec | 206 -------------------
gdimap-0.1-1/gdimap/inst/extdata/data_V1.nii.gz |only
gdimap-0.1-1/gdimap/inst/extdata/data_V2.nii.gz |only
gdimap-0.1-1/gdimap/inst/extdata/data_gfa.nii.gz |only
gdimap-0.1-1/gdimap/man/btable.Rd |only
gdimap-0.1-1/gdimap/man/data.Rd | 9
gdimap-0.1-1/gdimap/man/data.bval.Rd | 6
gdimap-0.1-1/gdimap/man/data.bvec.Rd | 10
gdimap-0.1-1/gdimap/man/data_V1.Rd |only
gdimap-0.1-1/gdimap/man/data_V2.Rd |only
gdimap-0.1-1/gdimap/man/data_brain_mask.Rd | 9
gdimap-0.1-1/gdimap/man/data_gfa.Rd |only
gdimap-0.1-1/gdimap/man/gdimap-package.Rd | 60 +++++
gdimap-0.1-1/gdimap/man/gqi.odfpeaklines.Rd | 61 +----
gdimap-0.1-1/gdimap/man/gqi.odfpeaks.Rd | 46 +---
gdimap-0.1-1/gdimap/man/gqi.odfvmf.Rd | 51 +---
gdimap-0.1-1/gdimap/man/gqi.odfvmflines.Rd | 54 +---
gdimap-0.1-1/gdimap/man/gqi.odfvxgrid.Rd | 11 -
gdimap-0.1-1/gdimap/man/rgbvolmap.Rd | 2
gdimap-0.1-1/gdimap/man/simul.fandtasia.Rd | 5
gdimap-0.1-1/gdimap/man/simul.simplefield.Rd | 13 -
gdimap-0.1-1/gdimap/man/simulglyph.vmf.Rd | 75 ++++--
gdimap-0.1-1/gdimap/man/sph.odfpeaklines.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfpeaks.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfvmf.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfvmflines.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfvxgrid.Rd |only
gdimap-0.1-1/gdimap/man/synthfiberss2z.Rd | 11 -
61 files changed, 639 insertions(+), 572 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-19 1.1
2011-11-25 1.0
Title: Statistical methods to model and adjust for bias in
meta-analysis
Diff between copas versions 0.6-5 dated 2012-03-20 and 0.7-0 dated 2013-06-04
Description: Copas selection model.
Author: James Carpenter
Maintainer: Guido Schwarzer
COPYRIGHT | 2 +-
DESCRIPTION | 9 +++++----
MD5 | 22 ++++++++++++----------
NAMESPACE | 3 +++
NEWS | 28 +++++++++++++++++++++++++++-
R/copas-interal.R |only
R/copas.R | 9 +++++++++
R/crtitle.R |only
R/print.copas.R | 11 ++++++++---
R/print.summary.copas.R | 11 +++++++----
R/summary.copas.R | 6 ++++++
man/copas.Rd | 4 ++++
man/print.copas.Rd | 14 ++++++++++----
13 files changed, 92 insertions(+), 27 deletions(-)
Title: EasyABC: performing efficient approximate Bayesian computation
sampling schemes
Diff between EasyABC versions 1.2 dated 2013-02-27 and 1.2.2 dated 2013-06-04
Description: The package EasyABC enables to launch a series of
simulations of a computer code from the R platform, and to
retrieve the simulation outputs in an appropriate format for
post-processing treatments. Four sequential sampling schemes
and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot, Thierry Faure, Nicolas Dumoullin
Maintainer: Nicolas Dumoulin
CHANGELOG | 14 +++++++++++
DESCRIPTION | 12 ++++-----
MD5 | 25 ++++++++++----------
R/binary_model.R | 3 +-
R/binary_model_cluster.R | 3 +-
inst/doc/EasyABC.R |only
inst/doc/EasyABC.pdf |binary
man/ABC_mcmc.Rd | 41 ++++++++++++++++++++++-----------
man/ABC_rejection.Rd | 54 +++++++++++++++++++++++++++++---------------
man/ABC_sequential.Rd | 36 +++++++++++++++++++----------
man/EasyABC-package.Rd | 4 +--
man/binary_model.Rd | 3 +-
man/binary_model_cluster.Rd | 9 ++++---
src/trait_model_rc.cpp | 2 -
14 files changed, 136 insertions(+), 70 deletions(-)
Title: Efficient meta analysis for the SKAT test
Diff between skatMeta versions 1.3.1 dated 2013-04-01 and 1.4.3 dated 2013-06-04
Description: Computes necessary information to meta analyze SKAT
statistics in each individual cohort, and then performs the
meta analysis.
Author: Arend Voorman, Jennifer Brody, Thomas Lumley
Maintainer: Arend Voorman
DESCRIPTION | 10 -
MD5 | 44 +++++---
NAMESPACE | 2
R/burdenMeta.R | 211 ++++++++++++++++++++---------------------
R/cohortAdjust.R |only
R/pchisqsum2.R |only
R/singlesnpMeta.R | 215 +++++++++++++++++++++---------------------
R/skatCohort.R | 230 +++++++++++++++++++++++----------------------
R/skatCoxCohort.R | 220 +++++++++++++++++++++++--------------------
R/skatFamCohort.R | 257 ++++++++++++++++++++++++++-------------------------
R/skatMeta.R | 227 ++++++++++++++++++++++-----------------------
R/skatOMeta.R |only
R/sparseBlockInv.R | 24 ++--
data/SNPInfo.rda |binary
data/skatExample.rda |binary
inst |only
man/SNPInfo.Rd | 3
man/burdenMeta.Rd | 13 +-
man/singlesnpMeta.Rd | 21 ++--
man/skatCohort.Rd | 20 ++-
man/skatCohortAdj.Rd |only
man/skatExample.Rd | 7 -
man/skatMeta.Rd | 22 ++--
man/skatOMeta.Rd |only
vignettes |only
25 files changed, 794 insertions(+), 732 deletions(-)
Title: R/GNU Linear Programming Kit Interface
Diff between Rglpk versions 0.3-10 dated 2012-09-12 and 0.4-1 dated 2013-06-04
Description: R interface to the GNU Linear Programming Kit (GLPK
version 4.50 is shipped with the source package). GLPK is open
source software for solving large-scale linear programming
(LP), mixed integer linear programming (MILP) and other related
problems.
Author: Stefan Theussl [aut, cre], Kurt Hornik [aut], Christian Buchta
[ctb]
Maintainer: Stefan Theussl
Rglpk-0.3-10/Rglpk/src/GLPK/glpfhv.c |only
Rglpk-0.3-10/Rglpk/src/GLPK/glpfhv.h |only
Rglpk-0.4-1/Rglpk/DESCRIPTION | 20
Rglpk-0.4-1/Rglpk/MD5 | 279 ++--
Rglpk-0.4-1/Rglpk/inst/CHANGELOG | 5
Rglpk-0.4-1/Rglpk/man/Rglpk_solve.Rd | 2
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile | 211 +--
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.am | 15
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.in | 1493 ++++++++++++++++++++------
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.win | 211 +--
Rglpk-0.4-1/Rglpk/src/GLPK/amd/amd_internal.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/bflib |only
Rglpk-0.4-1/Rglpk/src/GLPK/colamd/colamd.c | 24
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi.h | 16
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi09.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi10.c | 30
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi11.c | 27
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi12.c | 24
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi13.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi14.c | 11
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi15.c | 7
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi16.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi17.c | 224 +++
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi18.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi19.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi20.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi21.c | 33
Rglpk-0.4-1/Rglpk/src/GLPK/glpavl.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpavl.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfd.c | 92 +
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfd.h | 10
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpcpx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv.h | 53
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv01.c | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv01.c.orig | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv05.c | 206 ++-
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpgmp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpgmp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glphbm.c | 63 -
Rglpk-0.4-1/Rglpk/src/GLPK/glphbm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpini01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpini02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios.h | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glpios01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios03.c | 15
Rglpk-0.4-1/Rglpk/src/GLPK/glpios04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios09.c | 8
Rglpk-0.4-1/Rglpk/src/GLPK/glpios10.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios11.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios12.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpipm.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpipm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpk.h | 772 -------------
Rglpk-0.4-1/Rglpk/src/GLPK/glplib.h | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glplib01.c | 48
Rglpk-0.4-1/Rglpk/src/GLPK/glplib02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplib03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpf.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx01.c | 18
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpluf.c | 40
Rglpk-0.4-1/Rglpk/src/GLPK/glpluf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplux.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplux.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmat.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmat.h | 70 -
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl.h | 14
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmps.c | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet03.c | 243 ++++
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet09.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpqmd.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprgr.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprgr.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprlx.c |only
Rglpk-0.4-1/Rglpk/src/GLPK/glprlx.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glprng.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprng02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscf.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscl.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsdf.c | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpsdf.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glpspm.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsql.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsql.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpstd.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glptsp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glptsp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/zlib/gzwrite.c | 2
139 files changed, 2873 insertions(+), 2040 deletions(-)
Title: HIBAG -- HLA Genotype Imputation with Attribute Bagging
Diff between HIBAG versions 1.0.0 dated 2013-03-26 and 1.1.0 dated 2013-06-04
Description: To impute HLA types from unphased SNP data using an
attribute bagging method.
Author: Xiuwen Zheng, Bruce S. Weir
Maintainer: Xiuwen Zheng
HIBAG-1.0.0/HIBAG/data/hla.snp.geno.rdata |only
HIBAG-1.0.0/HIBAG/data/hla.type.table.rdata |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.bed |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.bim |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.fam |only
HIBAG-1.0.0/HIBAG/man/hla.snp.geno.Rd |only
HIBAG-1.0.0/HIBAG/man/hla.type.table.Rd |only
HIBAG-1.0.0/HIBAG/man/hlaAnonymize.Rd |only
HIBAG-1.0.0/HIBAG/man/hlaModelfromObj.Rd |only
HIBAG-1.1.0/HIBAG/DESCRIPTION | 12
HIBAG-1.1.0/HIBAG/MD5 | 140 +--
HIBAG-1.1.0/HIBAG/NEWS | 25
HIBAG-1.1.0/HIBAG/R/HIBAG.r | 805 ++++++++++++++++------
HIBAG-1.1.0/HIBAG/data/HLA_Type_Table.rdata |only
HIBAG-1.1.0/HIBAG/data/HapMap_CEU_Geno.rdata |only
HIBAG-1.1.0/HIBAG/inst/CITATION | 7
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.R |only
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.Rnw | 32
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.pdf |binary
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.bed |only
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.bim |only
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.fam |only
HIBAG-1.1.0/HIBAG/man/HIBAG-package.Rd | 78 --
HIBAG-1.1.0/HIBAG/man/HLA_Type_Table.Rd |only
HIBAG-1.1.0/HIBAG/man/HapMap_CEU_Geno.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaAllele.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaAlleleClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaAlleleDigit.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaAlleleSubset.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaAttrBagClass.Rd | 9
HIBAG-1.1.0/HIBAG/man/hlaAttrBagObj.Rd | 11
HIBAG-1.1.0/HIBAG/man/hlaAttrBagging.Rd | 37 -
HIBAG-1.1.0/HIBAG/man/hlaBED2Geno.Rd | 22
HIBAG-1.1.0/HIBAG/man/hlaCheckSNPs.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaClose.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaCombineAllele.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaCombineModelObj.Rd | 17
HIBAG-1.1.0/HIBAG/man/hlaCompareAllele.Rd | 5
HIBAG-1.1.0/HIBAG/man/hlaErrMsg.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaFlankingSNP.Rd | 21
HIBAG-1.1.0/HIBAG/man/hlaGeno2PED.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaGenoAFreq.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoCombine.Rd | 18
HIBAG-1.1.0/HIBAG/man/hlaGenoLD.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaGenoMFreq.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoMRate.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoMRate_Samp.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoSubset.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoSwitchStrand.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaHaplo2Geno.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaHaploSubset.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaLociInfo.Rd | 13
HIBAG-1.1.0/HIBAG/man/hlaMakeSNPGeno.Rd | 19
HIBAG-1.1.0/HIBAG/man/hlaMakeSNPHaplo.Rd | 7
HIBAG-1.1.0/HIBAG/man/hlaModelFiles.Rd | 24
HIBAG-1.1.0/HIBAG/man/hlaModelFromObj.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaModelToObj.Rd | 4
HIBAG-1.1.0/HIBAG/man/hlaParallelAttrBagging.Rd | 62 -
HIBAG-1.1.0/HIBAG/man/hlaPublish.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaSNPGenoClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaSNPHaploClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaSNPID.Rd | 9
HIBAG-1.1.0/HIBAG/man/hlaSampleAllele.Rd | 6
HIBAG-1.1.0/HIBAG/man/hlaSplitAllele.Rd | 10
HIBAG-1.1.0/HIBAG/man/hlaSubModelObj.Rd | 19
HIBAG-1.1.0/HIBAG/man/hlaUniqueAllele.Rd | 8
HIBAG-1.1.0/HIBAG/man/plot.hlaAttrBagClass.Rd | 28
HIBAG-1.1.0/HIBAG/man/plot.hlaAttrBagObj.Rd | 33
HIBAG-1.1.0/HIBAG/man/predict.hlaAttrBagClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/print.hlaAttrBagClass.Rd | 2
HIBAG-1.1.0/HIBAG/man/print.hlaAttrBagObj.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaAlleleClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/summary.hlaAttrBagClass.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaAttrBagObj.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaSNPGenoClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/summary.hlaSNPHaploClass.Rd | 2
HIBAG-1.1.0/HIBAG/src/HIBAG.cpp | 90 +-
HIBAG-1.1.0/HIBAG/src/LibHLA.cpp | 56 +
HIBAG-1.1.0/HIBAG/src/LibHLA.h | 33
HIBAG-1.1.0/HIBAG/vignettes/HIBAG_Ref.bib | 7
HIBAG-1.1.0/HIBAG/vignettes/HIBAG_Tutorial.Rnw | 32
81 files changed, 1188 insertions(+), 688 deletions(-)
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
Diff between EMD versions 1.5.3 dated 2013-04-25 and 1.5.5 dated 2013-06-04
Description: This package carries out empirical mode decomposition and
Hilbert spectral analysis. For usage of EMD, see Kim and Oh,
2009 (Kim, D and Oh, H.-S. (2009) EMD: A Package for Empirical
Mode Decomposition and Hilbert Spectrum, The R Journal, 1,
40-46).
Author: Donghoh Kim and Hee-Seok Oh
Maintainer: Donghoh Kim
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/Hilbert.R | 2 +-
man/semd.Rd | 26 +++++++++++++-------------
4 files changed, 22 insertions(+), 22 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.1.5 dated 2013-05-21 and 0.1.5.2 dated 2013-06-04
Description: R tools for combining and cleaning data sets, including
filling in missing observations with data from another data
frame.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NAMESPACE | 1 +
NEWS | 12 ++++++++++--
R/FillIn.R | 35 +++++++++++++++++++++++------------
R/slide.R | 5 +++--
README.md | 2 +-
man/FillIn.Rd | 18 ++++++++++++++----
8 files changed, 63 insertions(+), 32 deletions(-)
Title: Agricultural datasets
Diff between agridat versions 1.5 dated 2013-04-26 and 1.6 dated 2013-06-04
Description: Datasets from books and papers related to agriculture.
Example analyses included.
Author: Kevin Wright
Maintainer: Kevin Wright
agridat-1.5/agridat/data/batchelor.apple.txt.gz |only
agridat-1.5/agridat/data/batchelor.lemon.txt.gz |only
agridat-1.5/agridat/data/batchelor.navel1.txt.gz |only
agridat-1.5/agridat/data/batchelor.navel2.txt.gz |only
agridat-1.5/agridat/data/batchelor.valencia.txt.gz |only
agridat-1.5/agridat/data/batchelor.walnut.txt.gz |only
agridat-1.5/agridat/data/gomez.uniformity.txt.gz |only
agridat-1.5/agridat/data/goulden.barley.txt.gz |only
agridat-1.5/agridat/data/immer.sugarbeet.txt.gz |only
agridat-1.5/agridat/data/kempton.uniformity.txt.gz |only
agridat-1.5/agridat/data/lyon.potato.txt.gz |only
agridat-1.5/agridat/data/mercer.wheat.txt.gz |only
agridat-1.5/agridat/data/smith.uniformity3.txt.gz |only
agridat-1.5/agridat/data/wiebe.wheat.txt.gz |only
agridat-1.5/agridat/data/williams.barley.txt.gz |only
agridat-1.5/agridat/data/williams.cotton.txt.gz |only
agridat-1.5/agridat/man/batchelor.Rd |only
agridat-1.5/agridat/man/gomez.uniformity.Rd |only
agridat-1.5/agridat/man/goulden.barley.Rd |only
agridat-1.5/agridat/man/immer.sugarbeet.Rd |only
agridat-1.5/agridat/man/kempton.uniformity.Rd |only
agridat-1.5/agridat/man/lyon.potato.Rd |only
agridat-1.5/agridat/man/mercer.wheat.Rd |only
agridat-1.5/agridat/man/smith.uniformity3.Rd |only
agridat-1.5/agridat/man/wiebe.wheat.Rd |only
agridat-1.5/agridat/man/williams.barley.Rd |only
agridat-1.5/agridat/man/williams.cotton.Rd |only
agridat-1.6/agridat/DESCRIPTION | 14
agridat-1.6/agridat/MD5 | 289 +++++-----
agridat-1.6/agridat/NEWS | 39 -
agridat-1.6/agridat/data/batchelor.apple.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.lemon.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.navel1.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.navel2.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.valencia.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.walnut.uniformity.txt.gz |only
agridat-1.6/agridat/data/crossa.wheat.txt.gz |only
agridat-1.6/agridat/data/datalist | 41 -
agridat-1.6/agridat/data/garber.multi.uniformity.txt.gz |only
agridat-1.6/agridat/data/gomez.nitrogen.txt.gz |only
agridat-1.6/agridat/data/gomez.rice.uniformity.txt.gz |only
agridat-1.6/agridat/data/goulden.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/harris.multi.uniformity.txt.gz |only
agridat-1.6/agridat/data/immer.sugarbeet.uniformity.txt.gz |only
agridat-1.6/agridat/data/kempton.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/li.millet.uniformity.txt.gz |only
agridat-1.6/agridat/data/lyon.potato.uniformity.txt.gz |only
agridat-1.6/agridat/data/mercer.wheat.uniformity.txt.gz |only
agridat-1.6/agridat/data/odland.soybean.uniformity.txt.gz |only
agridat-1.6/agridat/data/odland.soyhay.uniformity.txt.gz |only
agridat-1.6/agridat/data/ratkowsky.onions.txt.gz |only
agridat-1.6/agridat/data/smith.corn.uniformity.txt.gz |only
agridat-1.6/agridat/data/stephens.sorghum.uniformity.txt.gz |only
agridat-1.6/agridat/data/wiebe.wheat.uniformity.txt.gz |only
agridat-1.6/agridat/data/williams.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/williams.cotton.uniformity.txt.gz |only
agridat-1.6/agridat/man/aastveit.barley.Rd | 6
agridat-1.6/agridat/man/adugna.sorghum.Rd | 7
agridat-1.6/agridat/man/agridat.Rd | 68 +-
agridat-1.6/agridat/man/allcroft.lodging.Rd | 5
agridat-1.6/agridat/man/archbold.apple.Rd | 25
agridat-1.6/agridat/man/ars.earlywhitecorn96.Rd | 11
agridat-1.6/agridat/man/australia.soybean.Rd | 2
agridat-1.6/agridat/man/batchelor.uniformity.Rd |only
agridat-1.6/agridat/man/besag.bayesian.Rd | 2
agridat-1.6/agridat/man/besag.elbatan.Rd | 4
agridat-1.6/agridat/man/besag.met.Rd | 4
agridat-1.6/agridat/man/blackman.wheat.Rd | 8
agridat-1.6/agridat/man/bond.diallel.Rd | 2
agridat-1.6/agridat/man/box.cork.Rd | 2
agridat-1.6/agridat/man/bridges.cucmber.Rd | 5
agridat-1.6/agridat/man/broadbalk.wheat.Rd | 2
agridat-1.6/agridat/man/byers.apple.Rd | 2
agridat-1.6/agridat/man/caribbean.maize.Rd | 2
agridat-1.6/agridat/man/carmer.density.Rd | 3
agridat-1.6/agridat/man/cate.potassium.Rd | 5
agridat-1.6/agridat/man/cleveland.soil.Rd | 3
agridat-1.6/agridat/man/cochran.bib.Rd | 2
agridat-1.6/agridat/man/cochran.crd.Rd | 4
agridat-1.6/agridat/man/cochran.eelworms.Rd | 4
agridat-1.6/agridat/man/cochran.latin.Rd | 4
agridat-1.6/agridat/man/cochran.wireworms.Rd | 2
agridat-1.6/agridat/man/corsten.interaction.Rd | 2
agridat-1.6/agridat/man/cox.stripsplit.Rd | 2
agridat-1.6/agridat/man/crossa.wheat.Rd |only
agridat-1.6/agridat/man/crowder.seeds.Rd | 2
agridat-1.6/agridat/man/darwin.maize.Rd | 2
agridat-1.6/agridat/man/denis.missing.Rd | 2
agridat-1.6/agridat/man/denis.ryegrass.Rd | 2
agridat-1.6/agridat/man/desplot.Rd | 28
agridat-1.6/agridat/man/digby.jointregression.Rd | 2
agridat-1.6/agridat/man/diggle.cow.Rd | 10
agridat-1.6/agridat/man/durban.competition.Rd | 5
agridat-1.6/agridat/man/durban.rowcol.Rd | 4
agridat-1.6/agridat/man/durban.splitplot.Rd | 5
agridat-1.6/agridat/man/eden.potato.Rd | 2
agridat-1.6/agridat/man/engelstad.nitro.Rd | 2
agridat-1.6/agridat/man/fan.stability.Rd | 4
agridat-1.6/agridat/man/federer.diagcheck.Rd | 3
agridat-1.6/agridat/man/federer.tobacco.Rd | 2
agridat-1.6/agridat/man/garber.mulit.uniformity.Rd |only
agridat-1.6/agridat/man/gathmann.bt.Rd | 4
agridat-1.6/agridat/man/gauch.soy.Rd | 4
agridat-1.6/agridat/man/gilmour.serpentine.Rd | 5
agridat-1.6/agridat/man/gilmour.slatehall.Rd | 4
agridat-1.6/agridat/man/gomez.fractionalfactorial.Rd | 5
agridat-1.6/agridat/man/gomez.groupsplit.Rd | 2
agridat-1.6/agridat/man/gomez.multilocsplitplot.Rd | 2
agridat-1.6/agridat/man/gomez.nitrogen.Rd |only
agridat-1.6/agridat/man/gomez.rice.uniformity.Rd |only
agridat-1.6/agridat/man/gomez.seedrate.Rd | 3
agridat-1.6/agridat/man/gomez.splitsplit.Rd | 5
agridat-1.6/agridat/man/gomez.stripplot.Rd | 2
agridat-1.6/agridat/man/gomez.stripsplitplot.Rd | 2
agridat-1.6/agridat/man/gotway.hessianfly.Rd | 5
agridat-1.6/agridat/man/goulden.barley.uniformity.Rd |only
agridat-1.6/agridat/man/graybill.heteroskedastic.Rd | 2
agridat-1.6/agridat/man/hanks.sprinkler.Rd | 9
agridat-1.6/agridat/man/harris.multi.uniformity.Rd |only
agridat-1.6/agridat/man/henderson.milkfat.Rd | 3
agridat-1.6/agridat/man/hernandez.nitrogen.Rd | 5
agridat-1.6/agridat/man/hessling.argentina.Rd | 2
agridat-1.6/agridat/man/hildebrand.systems.Rd | 2
agridat-1.6/agridat/man/hughes.grapes.Rd | 2
agridat-1.6/agridat/man/ilri.sheep.Rd | 2
agridat-1.6/agridat/man/immer.sugarbeet.uniformity.Rd |only
agridat-1.6/agridat/man/ivins.herbs.Rd | 2
agridat-1.6/agridat/man/jenkyn.mildew.Rd | 3
agridat-1.6/agridat/man/john.alpha.Rd | 2
agridat-1.6/agridat/man/johnson.blight.Rd | 3
agridat-1.6/agridat/man/kempton.barley.uniformity.Rd |only
agridat-1.6/agridat/man/kempton.competition.Rd | 5
agridat-1.6/agridat/man/kempton.rowcol.Rd | 5
agridat-1.6/agridat/man/kempton.slatehall.Rd | 5
agridat-1.6/agridat/man/lambert.soiltemp.Rd | 2
agridat-1.6/agridat/man/lavoranti.eucalyptus.Rd | 3
agridat-1.6/agridat/man/li.millet.uniformity.Rd |only
agridat-1.6/agridat/man/lyon.potato.uniformity.Rd |only
agridat-1.6/agridat/man/lyons.wheat.Rd | 2
agridat-1.6/agridat/man/mcconway.turnip.Rd | 2
agridat-1.6/agridat/man/mead.cowpeamaize.Rd | 2
agridat-1.6/agridat/man/mead.germination.Rd | 3
agridat-1.6/agridat/man/mead.strawberry.Rd | 5
agridat-1.6/agridat/man/mercer.wheat.uniformity.Rd |only
agridat-1.6/agridat/man/minnesota.barley.weather.Rd | 38 +
agridat-1.6/agridat/man/minnesota.barley.yield.Rd | 25
agridat-1.6/agridat/man/nass.corn.Rd | 2
agridat-1.6/agridat/man/nebraska.farmincome.Rd | 2
agridat-1.6/agridat/man/odland.soy.uniformity.Rd |only
agridat-1.6/agridat/man/ortiz.tomato.Rd | 5
agridat-1.6/agridat/man/pacheco.soybean.Rd | 3
agridat-1.6/agridat/man/pearl.kernels.Rd | 4
agridat-1.6/agridat/man/ratkowsky.onions.Rd |only
agridat-1.6/agridat/man/rothamsted.brussels.Rd | 5
agridat-1.6/agridat/man/ryder.groundnut.Rd | 4
agridat-1.6/agridat/man/senshu.rice.Rd | 2
agridat-1.6/agridat/man/shafii.rapeseed.Rd | 2
agridat-1.6/agridat/man/smith.corn.uniformity.Rd |only
agridat-1.6/agridat/man/snedecor.asparagus.Rd | 3
agridat-1.6/agridat/man/steel.soybeanmet.Rd | 15
agridat-1.6/agridat/man/stephens.sorghum.uniformity.Rd |only
agridat-1.6/agridat/man/streibig.competition.Rd | 4
agridat-1.6/agridat/man/stroup.nin.Rd | 2
agridat-1.6/agridat/man/stroup.splitplot.Rd | 2
agridat-1.6/agridat/man/student.barley.Rd | 2
agridat-1.6/agridat/man/talbot.potato.Rd | 2
agridat-1.6/agridat/man/theobald.covariate.Rd | 2
agridat-1.6/agridat/man/thompson.cornsoy.Rd | 8
agridat-1.6/agridat/man/vargas.wheat1.Rd | 2
agridat-1.6/agridat/man/vargas.wheat2.Rd | 3
agridat-1.6/agridat/man/verbyla.lupin.Rd | 2
agridat-1.6/agridat/man/vsn.lupin3.Rd | 4
agridat-1.6/agridat/man/wedderburn.barley.Rd | 4
agridat-1.6/agridat/man/wiebe.wheat.uniformity.Rd |only
agridat-1.6/agridat/man/williams.barley.uniformity.Rd |only
agridat-1.6/agridat/man/williams.cotton.uniformity.Rd |only
agridat-1.6/agridat/man/williams.trees.Rd | 2
agridat-1.6/agridat/man/yan.winterwheat.Rd | 2
agridat-1.6/agridat/man/yates.missing.Rd | 2
agridat-1.6/agridat/man/yates.oats.Rd | 5
agridat-1.6/agridat/man/zuidhof.broiler.Rd | 2
181 files changed, 503 insertions(+), 417 deletions(-)
Title: Circos 2D Track Plot
Diff between RCircos versions 1.1.0 dated 2013-05-17 and 1.1.1 dated 2013-06-03
Description: RCircos package provides a simple and flexible way to
generate Circos 2D track plot images for genomic data
visualization. The types of plots include: heatmap, histogram,
lines, scatterplot, tiles and plot items for further
decorations include connector, links, and text (gene) label.
All functions require only R graphics package that comes with R
base installation.
Author: Hongen Zhang
Maintainer: Hongen Zhang
RCircos-1.1.0/RCircos/inst/doc/RCircos.pdf |only
RCircos-1.1.1/RCircos/DESCRIPTION | 8 ++++----
RCircos-1.1.1/RCircos/MD5 | 8 +++++---
RCircos-1.1.1/RCircos/inst/doc/RCircos-manual.pdf |binary
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.R |only
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.Rnw |only
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.pdf |only
7 files changed, 9 insertions(+), 7 deletions(-)
Title: SYNCSA - Analysis of functional and phylogenetic patterns in
metacommunities.
Diff between SYNCSA versions 1.3 dated 2013-02-22 and 1.3.1 dated 2013-06-03
Description: Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are
offered here implement for the R environment methods that have
been available in the SYNCSA application written in C++ (by
Valerio Pillar, available at
http://ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/matrix.x.R | 16 ++++++++++++----
man/cor.matrix.Rd | 3 ++-
man/cor.matrix.partial.Rd | 3 ++-
man/optimal.Rd | 7 +++++--
man/syncsa.Rd | 4 +++-
7 files changed, 34 insertions(+), 19 deletions(-)
Title: Read and write JPEG images
Diff between jpeg versions 0.1-4 dated 2013-04-26 and 0.1-6 dated 2013-06-03
Description: This package provides an easy and simple way to read,
write and display bitmap images stored in the JPEG format. It
can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 6 ++--
MD5 | 9 ++++---
NEWS | 10 ++++++++
configure.win | 63 +++++++++++++++++++++++++++++++++++++++-------------
src/Makevars-ls.win |only
src/rjcommon.h | 11 +++++++++
6 files changed, 77 insertions(+), 22 deletions(-)
Title: R functions in Chapter 3,4,6,7,9,10,11,12,14,15
Diff between TrialSize versions 1.0 dated 2012-07-11 and 1.3 dated 2013-06-03
Description: functions and examples in Sample Size Calculation in
Clinical Research.
Author: Ed Zhang ; Vicky Qian Wu ; Shein-Chung Chow ; Harry G.Zhang
(Quality check)
Maintainer: Vicky Qian Wu
DESCRIPTION | 14 +-
MD5 | 168 +++++++++++++++----------------
R/TwoSampleSurvival.Conditional.R | 5
man/AB.withDescalation.Rd | 11 +-
man/AB.withoutDescalation.Rd | 12 +-
man/ABE.Rd | 19 +--
man/ANOVA.Repeat.Measure.Rd | 8 -
man/Cochran.Armitage.Trend.Rd | 22 +---
man/Cox.Equality.Rd | 4
man/Cox.Equivalence.Rd | 4
man/Cox.NIS.Rd | 6 -
man/CrossOver.ISV.Equivalence.Rd | 6 -
man/CrossOver.ISV.NIS.Rd | 10 -
man/Dose.Min.Effect.Rd | 18 ---
man/Dose.Response.Linear.Rd | 19 +--
man/Dose.Response.binary.Rd | 17 +--
man/Dose.Response.time.to.event.Rd | 36 ++----
man/IBE.Rd | 31 -----
man/ISCV.Equality.Rd | 11 --
man/ISCV.Equivalence.Rd | 14 --
man/ISCV.NIS.Rd | 8 -
man/ISV.Equivalence.Rd | 4
man/ISV.NIS.Rd | 8 -
man/InterSV.Equality.Rd | 10 -
man/McNemar.Test.Rd | 6 -
man/MeanWilliamsDesign.Equality.Rd | 5
man/MeanWilliamsDesign.Equivalence.Rd | 9 -
man/MeanWilliamsDesign.NIS.Rd | 13 +-
man/Multiple.Testing.Rd | 10 -
man/Nonpara.Independ.Rd | 10 -
man/Nonpara.One.Sample.Rd | 14 +-
man/Nonpara.Two.Sample.Rd | 14 +-
man/OneSampleMean.Equality.Rd | 6 -
man/OneSampleMean.Equivalence.Rd | 10 +
man/OneSampleMean.NIS.Rd | 9 -
man/OneSampleProportion.Equality.Rd | 7 -
man/OneSampleProportion.Equivalence.Rd | 7 -
man/OneSampleProportion.NIS.Rd | 7 -
man/OneSide.fixEffect.Rd | 18 ---
man/OneSide.varyEffect.Rd | 15 +-
man/OneWayANOVA.PairwiseComparison.Rd | 9 -
man/OneWayANOVA.pairwise.Rd | 8 -
man/PBE.Rd | 19 +--
man/Propensity.Score.nostrata.Rd | 29 +----
man/Propensity.Score.strata.Rd | 21 +--
man/QOL.Rd | 12 --
man/QT.PK.crossover.Rd | 14 --
man/QT.PK.parallel.Rd | 12 --
man/QT.crossover.Rd | 14 --
man/QT.parallel.Rd | 13 --
man/RelativeRisk.Equality.Rd | 7 -
man/RelativeRisk.Equivalence.Rd | 9 -
man/RelativeRisk.NIS.Rd | 7 -
man/RelativeRiskCrossOver.Equality.Rd | 9 -
man/RelativeRiskCrossOver.Equivalence.Rd | 9 -
man/RelativeRiskCrossOver.NIS.Rd | 10 -
man/Sensitivity.Index.Rd | 9 -
man/Stuart.Maxwell.Test.Rd | 10 -
man/TrialSize-package.Rd | 14 +-
man/TwoSampleCrossOver.Equality.Rd | 4
man/TwoSampleCrossOver.Equivalence.Rd | 6 -
man/TwoSampleCrossOver.NIS.Rd | 6 -
man/TwoSampleMean.Equality.Rd | 2
man/TwoSampleMean.Equivalence.Rd | 6 -
man/TwoSampleMean.NIS.Rd | 6 -
man/TwoSampleProportion.Equality.Rd | 6 -
man/TwoSampleProportion.Equivalence.Rd | 8 -
man/TwoSampleProportion.NIS.Rd | 10 -
man/TwoSampleSeqCrossOver.Equivalence.Rd | 5
man/TwoSampleSurvival.Conditional.Rd | 6 -
man/TwoSampleSurvival.Equality.Rd | 10 -
man/TwoSampleSurvival.NIS.Rd | 10 -
man/TwoSide.fixEffect.Rd | 10 +
man/TwoSide.varyEffect.Rd | 12 +-
man/Vaccine.CEM.Rd | 2
man/Vaccine.ELDI.Rd | 9 -
man/Vaccine.RDI.Rd | 4
man/Vitro.BE.Rd | 38 +------
man/WilliamsDesign.Equality.Rd | 9 -
man/WilliamsDesign.Equivalence.Rd | 11 --
man/WilliamsDesign.NIS.Rd | 11 --
man/gof.Pearson.Rd | 2
man/gof.Pearson.twoway.Rd | 2
src/TrialSize.cc | 2
src/TrialSize_main.cc | 4
85 files changed, 384 insertions(+), 677 deletions(-)
Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.90 dated 2013-05-23 and 0.91 dated 2013-06-03
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/Main_SSD.R | 8 ++++----
inst/doc/SKAT.pdf |binary
4 files changed, 11 insertions(+), 11 deletions(-)
Title: Methods for robust rank aggregation
Diff between RobustRankAggreg versions 1.0 dated 2011-03-28 and 1.1 dated 2013-06-03
More information about RobustRankAggreg at CRAN
Description: Methods for aggregating ranked lists, especially lists of
genes. It implements the Robust Rank Aggregation (Kolde et. al
in preparation) and some other simple algorithms for the task.
RRA method uses a probabilistic model for aggregation that is
robust to noise and also facilitates the calculation of
significance probabilities for all the elements in the final
ranking.
Author: Raivo Kolde, Sven Laur
Maintainer: Raivo Kolde
RobustRankAggreg-1.0/RobustRankAggreg/run_roxygen.r |only
RobustRankAggreg-1.1/RobustRankAggreg/DESCRIPTION | 7
RobustRankAggreg-1.1/RobustRankAggreg/MD5 |only
RobustRankAggreg-1.1/RobustRankAggreg/NAMESPACE | 4
RobustRankAggreg-1.1/RobustRankAggreg/R/aggregateRanks.R | 117 +++++---
RobustRankAggreg-1.1/RobustRankAggreg/man/aggregateRanks.Rd | 157 +++++++-----
RobustRankAggreg-1.1/RobustRankAggreg/man/betaScores.Rd | 57 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/cellCycleKO.Rd | 56 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/rankMatrix.Rd | 57 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/rhoScores.Rd | 43 ++-
10 files changed, 324 insertions(+), 174 deletions(-)
Permanent link
Title: Read and write PNG images
Diff between png versions 0.1-4 dated 2011-12-11 and 0.1-5 dated 2013-06-03
Description: This package provides an easy and simple way to read,
write and display bitmap images stored in the PNG format. It
can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 11 ++++++----
MD5 | 22 ++++++++++----------
NAMESPACE | 2 -
NEWS | 14 ++++++++++++
R/read.R | 4 +--
R/write.R | 6 ++---
configure.win | 60 +++++++++++++++++++++++++++++++++++++++++--------------
man/readPNG.Rd | 5 +++-
man/writePNG.Rd | 21 ++++++++++++++-----
src/Makevars.win | 16 +++++++-------
src/read.c | 48 +++++++++++++++++++++++++++++++++++++++++---
src/write.c | 39 +++++++++++++++++++++++++++++++++--
12 files changed, 193 insertions(+), 55 deletions(-)
Title: Spatial Probit Models
Diff between spatialprobit versions 0.9-8 dated 2013-03-02 and 0.9-9 dated 2013-06-03
Description: Bayesian Estimation of Spatial Probit and Tobit Models
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
.Rinstignore | 1 +
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NEWS | 4 ++++
R/SpatialProbit-MCMC.R | 4 ++++
R/semprobit.R | 4 ++++
inst/tests/test-sarprobit.R |only
inst/tests/test-semprobit.R |only
man/sarprobit.Rd | 19 ++++++++++++-------
9 files changed, 36 insertions(+), 16 deletions(-)
Title: Visualization methods for the raster package
Diff between rasterVis versions 0.20-07 dated 2013-05-06 and 0.21 dated 2013-06-03
Description: The raster package defines classes and methods for spatial
raster data access and manipulation. The rasterVis package
complements raster providing a set of methods for enhanced
visualization and interaction.
Author: Oscar Perpinan Lamigueiro [cre, aut], Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro
ChangeLog | 416 ++---------------------------------------------
DESCRIPTION | 8
MD5 | 11 -
R/horizonplot.R | 2
R/levelplot.R | 8
man/levelplot-methods.Rd | 21 ++
rasterVis-Ex.R |only
7 files changed, 60 insertions(+), 406 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.44 dated 2013-01-29 and 3.47 dated 2013-06-03
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 9 +-
MD5 | 138 ++++++++++++++++++++++---------------------
NAMESPACE | 3
NEWS | 18 +++++
R/BE_to_LBLE.R | 7 +-
R/Gratiot.R | 4 -
R/LBLE_to_BE.R | 5 -
R/LBLE_to_L.R | 6 +
R/L_to_LBLE.R | 4 -
R/Likelihood_phenology.R | 3
R/Script_MCMC.r | 31 +++++----
R/adapt_parameters.R | 6 +
R/add_phenology.R | 9 +-
R/as.mcmc.mcmcComposite.R |only
R/as.par.mcmcComposite.R |only
R/compare_AIC.R | 72 ++++++++++++++--------
R/extract_result.R | 9 +-
R/fit_phenology.R | 8 +-
R/map_phenology.R | 23 +++++--
R/moon_phase.R | 6 +
R/onAttach.R | 8 ++
R/par_init.R | 6 +
R/phenology-package.R | 10 +--
R/phenology_MHmcmc_p.R | 28 +++++---
R/phenology_fonctionMCMC.R | 3
R/plot.mcmcComposite.R | 34 +++++-----
R/plot.phenology.R | 6 +
R/plot.phenologymap.R | 18 +++--
R/plot_delta.R | 16 +++-
R/plot_phi.R | 21 ++++--
R/print.phenology.R | 6 +
R/print.phenologymap.R | 24 +++++--
R/print.phenologyout.R | 12 ++-
R/remove_site.R | 12 ++-
R/shift_sinusoid.R | 28 ++++++--
R/summary.mcmcComposite.R | 32 +++++----
R/summary.phenology.R | 12 ++-
R/summary.phenologymap.R | 24 +++++--
R/summary.phenologyout.R | 12 ++-
man/BE_to_LBLE.Rd | 7 +-
man/Gratiot.Rd | 4 -
man/LBLE_to_BE.Rd | 3
man/LBLE_to_L.Rd | 6 +
man/L_to_LBLE.Rd | 4 -
man/adapt_parameters.Rd | 6 +
man/add_phenology.Rd | 9 +-
man/as.mcmc.mcmcComposite.Rd |only
man/as.par.mcmcComposite.Rd |only
man/compare_AIC.Rd | 27 +++++---
man/extract_result.Rd | 9 +-
man/fit_phenology.Rd | 8 +-
man/likelihood_phenology.Rd | 3
man/map_phenology.Rd | 23 +++++--
man/moon_phase.Rd | 6 +
man/par_init.Rd | 6 +
man/phenology-package.Rd | 8 +-
man/phenology_MHmcmc.Rd | 28 ++++----
man/phenology_MHmcmc_p.Rd | 25 ++++---
man/plot.mcmcComposite.Rd | 32 +++++----
man/plot.phenology.Rd | 6 +
man/plot.phenologymap.Rd | 18 +++--
man/plot_delta.Rd | 16 +++-
man/plot_phi.Rd | 21 ++++--
man/print.phenology.Rd | 6 +
man/print.phenologymap.Rd | 24 +++++--
man/print.phenologyout.Rd | 12 ++-
man/remove_site.Rd | 12 ++-
man/shift_sinusoid.Rd | 28 ++++++--
man/summary.mcmcComposite.Rd | 32 +++++----
man/summary.phenology.Rd | 12 ++-
man/summary.phenologymap.Rd | 24 +++++--
man/summary.phenologyout.Rd | 12 ++-
72 files changed, 730 insertions(+), 380 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 2.0 dated 2013-05-23 and 2.1 dated 2013-06-03
Description: Performs the colocalisation tests described in Plagnol et
al (2009), Wallace et al (2013) and Giambartolomei et al
(2013).
Author: Chris Wallace and Claudia Giambartolemei with contributions
from Vincent Plagnol
Maintainer: Chris Wallace
ChangeLog | 9 ++++++
DESCRIPTION | 10 ++++--
MD5 | 16 ++++++----
NAMESPACE | 1
R/claudia.R | 70 ++++++++++++++++++++++++-----------------------
R/coloc.abf.imputed.R |only
inst/CITATION | 29 ++++++++-----------
man/approx.bf.imputed.Rd |only
man/coloc.abf.Rd | 24 +++++++++-------
man/coloc.abf.imputed.Rd |only
man/combine.abf.Rd |only
11 files changed, 90 insertions(+), 69 deletions(-)
Title: Regularization for semiparametric additive hazards regression
Diff between ahaz versions 1.13 dated 2013-04-25 and 1.14 dated 2013-06-03
Description: Computationally efficient procedures for regularized
estimation with the semiparametric additive hazards regression
model.
Author: Anders Gorst-Rasmussen
Maintainer: Anders Gorst-Rasmussen
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/ahaz.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Text Mining Distributed Corpus Plug-In
Diff between tm.plugin.dc versions 0.2-4 dated 2012-11-11 and 0.2-5 dated 2013-06-03
Description: A plug-in for the text mining framework tm to support text
mining in a distributed way. The package provides a convenient
interface for handling distributed corpus objects based on
distributed list objects.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl
DESCRIPTION | 13 +++++++------
MD5 | 4 ++--
R/mapper.R | 4 ++--
3 files changed, 11 insertions(+), 10 deletions(-)
Title: Latent position and cluster models for statistical networks
Diff between latentnet versions 2.4-4 dated 2013-03-06 and 2.4-5 dated 2013-06-03
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre], Mark S. Handcock [aut], Susan M.
Shortreed [ctb], Jeremy Tantrum [ctb], Peter D. Hoff [ctb]
Maintainer: Pavel N. Krivitsky
ChangeLog | 5 ++++
DESCRIPTION | 8 +++----
MD5 | 18 ++++++++---------
R/mcmc.diagnostics.ergmm.R | 4 +++
data/davis.RData |binary
man/latentnet-internal.Rd | 3 ++
man/plot.ergmm.Rd | 3 +-
man/summary.ergmm.Rd | 9 ++++++--
man/tribes.Rd | 7 +++---
tests/examples.R | 46 +++++++++++++++++++++++++++++++--------------
10 files changed, 70 insertions(+), 33 deletions(-)
Title: Goodness-of-fit functions for comparison of simulated and
observed hydrological time series
Diff between hydroGOF versions 0.3-6 dated 2013-03-25 and 0.3-7 dated 2013-06-03
Description: S3 functions implementing both statistical and graphical
goodness-of-fit measures between observed and simulated values,
mainly oriented to be used during the calibration, validation,
and application of hydrological models. Missing values in
observed and/or simulated values can be removed before
computations. Comments / questions / collaboration of any kind
are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre]
Maintainer: Mauricio Zambrano Bigiarini
DESCRIPTION | 8 -
MD5 | 33 +++---
NAMESPACE | 2
NEWS | 24 ++++-
R/ggof.R | 195 ++++++++++++++++++++++++++++++++---------
R/pbiasfdc.R | 24 +++--
R/plot2.R | 108 +++++++++++++---------
R/plotbands.R | 33 ++++--
R/plotbandsonly.R | 24 +++--
R/valindex.R | 4
inst/doc/hydroGOF_Vignette.R |only
inst/doc/hydroGOF_Vignette.pdf |binary
man/KGE.Rd | 2
man/VE.Rd | 2
man/ggof.Rd | 35 ++++++-
man/hydroGOF-package.Rd | 8 -
man/plot2.Rd | 8 +
man/valindex.Rd | 2
18 files changed, 363 insertions(+), 149 deletions(-)
Title: Distributed Storage and List
Diff between DSL versions 0.1-3 dated 2013-06-01 and 0.1-4 dated 2013-06-03
Description: A package providing functions and methods for handling
distributed storage (DStorage) and lists (DLlist). It
implements an abstract DList class for storing large list-type
objects in a distributed manner. In doing so it uses a well
defined storage backend implemented based on the DStorage
class. It allows for processing such DLists on distributed
systems efficiently.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre], Christian
Buchta [ctb]
Maintainer: Stefan Theussl
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/storage.R | 8 ++++----
inst/doc/DSL.pdf |binary
4 files changed, 11 insertions(+), 11 deletions(-)
Title: circos layout in R
Diff between circlize versions 0.0.2 dated 2013-05-26 and 0.0.3 dated 2013-06-02
Description: circlize is an R package which implements circos layout
(http://circos.ca/) in R. It can do almost everything that
circos can do. And due to the natural born feature of drawing
statistical graphics in R, this package can provide a more
flexible way to visualize information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu
CHANGES | 13
DESCRIPTION | 12
MD5 | 81 +-
NAMESPACE | 2
R/global.R | 256 +++---
R/link.R |only
R/overview.R | 31
R/plot.R | 464 +++++------
R/utils.R | 161 ----
inst/doc/circlize.R | 1401 ++++++++++++++++++++++-------------
inst/doc/circlize.Rnw | 833 +++++++++++---------
inst/doc/circlize.pdf |binary
inst/doc/draw-ideogram.R | 690 +++++++++++------
inst/doc/draw-ideogram.Rnw | 522 +++++--------
inst/doc/draw-ideogram.pdf |binary
inst/doc/draw-relations.R | 279 +++---
inst/doc/draw-relations.Rnw | 135 +--
inst/doc/draw-relations.pdf |binary
inst/doc/interesting-graphics.R | 262 +++---
inst/doc/interesting-graphics.Rnw | 98 +-
inst/doc/interesting-graphics.pdf |binary
man/circlize.rd | 85 +-
man/circos.axis.rd | 26
man/circos.clear.rd | 6
man/circos.initialize.rd | 4
man/circos.initializeWithIdeogram.rd | 67 -
man/circos.lines.rd | 30
man/circos.link.rd | 37
man/circos.par.rd | 27
man/circos.points.rd | 4
man/circos.polygon.rd | 2
man/circos.rect.rd | 5
man/circos.text.rd | 26
man/circos.trackHist.rd | 22
man/circos.trackLines.rd | 14
man/circos.trackPlotRegion.rd | 10
man/circos.trackPoints.rd | 8
man/circos.trackText.rd | 9
man/circos.updatePlotRegion.rd | 2
man/draw.sector.rd | 69 +
man/get.cell.meta.data.rd | 18
man/show.index.rd | 10
42 files changed, 3186 insertions(+), 2535 deletions(-)
Title: Classes for Spatial Data
Diff between ngspatial versions 0.5-2 dated 2012-12-09 and 1.0 dated 2013-06-02
Description: ngspatial provides tools for analyzing spatial data,
especially non-Gaussian areal data.
Author: John Hughes
Maintainer: John Hughes
COPYING | 2
DESCRIPTION | 11
MD5 | 34 -
R/autologistic.R | 941 ++++++++++++++++++++++++++++----------------
R/misc.R | 46 --
R/moller.R | 67 +--
R/sparse.sglmm.R | 682 ++++++++++++++++++-------------
R/zzz.R | 8
inst/CITATION | 1
man/autologistic.Rd | 206 +++++----
man/rautologistic.Rd | 44 +-
man/sparse.sglmm.Rd | 70 ++-
man/summary.autologistic.Rd | 15
man/summary.sparse.sglmm.Rd | 13
man/vcov.autologistic.Rd | 3
src/moller.cpp | 194 ++++-----
src/moller.h | 11
src/perfsampler.cpp | 38 -
18 files changed, 1407 insertions(+), 979 deletions(-)
Title: A Lasso for Hierarchical Interactions
Diff between hierNet versions 1.2 dated 2013-03-15 and 1.3 dated 2013-06-01
Description: Fits sparse interaction models for continuous and binary
responses subject to the strong (or weak) hierarchy restriction
that an interaction between two variables only be included if
both (or at least one of) the variables is included as a main
effect. For more details, see Bien, J., Taylor, J.,
Tibshirani, R., (2012) "A Lasso for Hierarchical Interactions"
accepted for publication in Annals of Statistics.
Author: Jacob Bien and Rob Tibshirani
Maintainer: Jacob Bien
DESCRIPTION | 6 ++--
MD5 | 4 +-
R/funcs.R | 84 ++++++++++++++++++++++++++++++++++++------------------------
3 files changed, 56 insertions(+), 38 deletions(-)
Title: Univariate and Multivariate Spatial-temporal Modeling
Diff between spBayes versions 0.3-6 dated 2013-03-19 and 0.3-7 dated 2013-06-01
Description: spBayes fits univariate and multivariate spatio-temporal
models with Markov chain Monte Carlo (MCMC).
Author: Andrew O. Finley
Maintainer: Andrew O. Finley
DESCRIPTION | 8 +-
MD5 | 33 ++++----
R/spDiag.R | 7 -
R/spDynLM.R | 108 ++++++++++++++++++++++++++--
R/spLM.R | 35 ---------
R/spMvLM.R | 41 +---------
data/NYOzone.dat.tab.gz |only
inst/ChangeLog | 10 ++
man/NYOzone.dat.Rd |only
man/spDynLM.Rd | 25 ++++--
man/spLM.Rd | 3
man/spMvLM.Rd | 3
src/spDynLM.cpp | 180 +++++++++++++++++++++++-------------------------
src/spLM.cpp | 136 ++++++++----------------------------
src/spLMRecover.cpp | 97 ++++++++++++++++++++++---
src/spMvLM.cpp | 142 ++++++++-----------------------------
src/spMvLMRecover.cpp | 173 +++++++++++++++++++++++++++++++++++++---------
src/spPPDynLM.cpp |only
src/spPPMvLM.cpp | 4 -
19 files changed, 538 insertions(+), 467 deletions(-)
Title: Sean Lahman's Baseball Database
Diff between Lahman versions 2.0-1 dated 2013-04-25 and 2.0-3 dated 2013-06-01
Description: This package provides the tables from Sean Lahman's
Baseball Database as a set of R data.frames. It uses the data
on pitching, hitting and fielding performance and other tables
from 1871 through 2012, as recorded in the 2012 version of the
database.
Author: Michael Friendly and Dennis Murphy and Martin Monkman
Maintainer: Michael Friendly
DESCRIPTION | 19 +++++++-----
MD5 | 64 ++++++++++++++++++++---------------------
NEWS | 7 ++++
data/AllstarFull.RData |binary
data/Appearances.RData |binary
data/AwardsManagers.RData |binary
data/AwardsPlayers.RData |binary
data/AwardsShareManagers.RData |binary
data/AwardsSharePlayers.RData |binary
data/Batting.RData |binary
data/BattingPost.RData |binary
data/Fielding.RData |binary
data/FieldingOF.RData |binary
data/FieldingPost.RData |binary
data/HallOfFame.RData |binary
data/LahmanData.RData |binary
data/Managers.RData |binary
data/ManagersHalf.RData |binary
data/Master.RData |binary
data/Pitching.RData |binary
data/PitchingPost.RData |binary
data/Salaries.RData |binary
data/Schools.RData |binary
data/SchoolsPlayers.RData |binary
data/SeriesPost.RData |binary
data/Teams.RData |binary
data/TeamsFranchises.RData |binary
data/TeamsHalf.RData |binary
data/battingLabels.RData |binary
data/fieldingLabels.RData |binary
data/pitchingLabels.RData |binary
man/Lahman-package.Rd | 10 +++---
man/Schools.Rd | 35 +++++++++++-----------
33 files changed, 74 insertions(+), 61 deletions(-)
Title: R functions for working with spatial data.
Diff between spatial.tools versions 0.9.4 dated 2013-02-24 and 1.0.2 dated 2013-06-01
Description: Spatial functions meant to enhance the core functionality
of the package "raster", including a parallel processing engine
for use with rasters.
Author: Jonathan Asher Greenberg
Maintainer: Jonathan Asher Greenberg
DESCRIPTION | 15 +--
MD5 | 62 ++++++++-----
NAMESPACE | 33 ++++---
R/bbox_to_SpatialPolygons.R |only
R/binary_image_write.R | 5 -
R/brickstack_to_raster_list.R |only
R/fix_extent.R | 12 ++
R/focal_hpc.R | 176 +++++++++++++++++++++++---------------
R/getValuesBlock_enhanced.R | 10 +-
R/getValuesBlock_stackfix.R |only
R/get_gdal_installation.R |only
R/is.Raster.R |only
R/modify_raster_margins.R |only
R/projectRaster_rigorous.R |only
R/sfQuickInit.R | 1
R/sfQuickStop.R | 1
R/spatial_sync_raster.R | 23 +++-
R/spatial_sync_vector.R | 10 +-
R/tahoe_highrez_training_data.R | 10 +-
R/tahoe_lidar_bareearth_data.R | 3
R/tahoe_lidar_highesthit_data.R | 3
man/bbox_to_SpatialPolygons.Rd |only
man/binary_image_write.Rd | 5 -
man/brickstack_to_raster_list.Rd |only
man/fix_extent.Rd | 9 +
man/focal_hpc.Rd | 11 +-
man/getValuesBlock_enhanced.Rd | 8 +
man/getValuesBlock_stackfix.Rd |only
man/get_gdal_installation.Rd |only
man/is.Raster.Rd |only
man/modify_raster_margins.Rd |only
man/projectRaster_rigorous.Rd |only
man/sfQuickInit.Rd | 3
man/sfQuickStop.Rd | 3
man/spatial_sync_raster.Rd | 4
man/spatial_sync_vector.Rd | 10 +-
man/tahoe_highrez_training.Rd | 10 +-
man/tahoe_lidar_bareearth.tif.Rd | 3
man/tahoe_lidar_highesthit.tif.Rd | 3
39 files changed, 277 insertions(+), 156 deletions(-)
Title: Distributed Storage and List
Diff between DSL versions 0.1-2.1 dated 2013-04-25 and 0.1-3 dated 2013-06-01
Description: A package providing functions and methods for handling
distributed storage (DStorage) and lists (DLlist). It
implements an abstract DList class for storing large list-type
objects in a distributed manner. In doing so it uses a well
defined storage backend implemented based on the DStorage
class. It allows for processing such DLists on distributed
systems efficiently.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre], Christian
Buchta [ctb]
Maintainer: Stefan Theussl
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
R/map.R | 2 +-
R/storage.R | 8 ++++----
inst/doc/DSL.Rnw | 34 +++++++++++++++++++---------------
inst/doc/DSL.pdf |binary
man/map.Rd | 3 ++-
vignettes/DSL.Rnw | 34 +++++++++++++++++++---------------
8 files changed, 57 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-11-04 0.0-2
Title: Relational Class Analysis
Diff between RCA versions 1.4 dated 2013-05-23 and 1.4.1 dated 2013-06-01
Description: Relational Class Analysis (RCA) is a method for detecting
heterogeneity in attitudinal data. (as described in Goldberg
A., 2011, Am. J. Soc, 116(5)) . src/ also contains the source
files of igraph-C which was written by Gabor.
Author: Amir Goldberg
Maintainer: Yuan Wang
DESCRIPTION | 8 ++---
MD5 | 19 +++++++----
configure |only
configure.in |only
configure.win |only
man/RCA-package.Rd | 4 +-
man/RCA.Rd | 75 ++++++++++-------------------------------------
man/Result.Rd | 21 +++----------
man/SampleInputMatrix.Rd | 9 +++--
src/Makevars | 1
src/Makevars.in |only
src/Makevars.win | 1
src/config.h.in |only
13 files changed, 46 insertions(+), 92 deletions(-)
Title: Read and Write SAS XPORT Files
Diff between SASxport versions 1.3.2 dated 2013-05-12 and 1.3.4 dated 2013-06-01
Description: This package provides functions for reading, listing the
contents of, and writing SAS xport format files. The functions
support reading and writing of either individual data frames or
sets of data frames. Further, a mechanism has been provided
for customizing how variables of different data types are
stored.
Author: Unless otherwise noted, the contents of this package were
written by Gregory R. Warnes
Maintainer: Gregory R. Warnes
ChangeLog | 51 +++++++++++++++++++++++++
DESCRIPTION | 8 +--
MD5 | 69 +++++++++++++++++-----------------
NEWS | 11 +++++
R/make.formats.R | 18 ++++----
inst/ChangeLog | 51 +++++++++++++++++++++++++
inst/NEWS | 11 +++++
tests/Alfalfa_Test.R | 1
tests/Alfalfa_Test.Rout.save | 7 +--
tests/Theoph.R | 1
tests/Theoph.Rout.save | 7 +--
tests/cars.R | 1
tests/cars.Rout.save | 7 +--
tests/dfAttributes.R | 1
tests/testBlockBoundary.R | 2
tests/testDates.R | 1
tests/testDates.Rout.save | 7 +--
tests/testDuplicateNames.R | 2
tests/testDuplicateNames.Rout.save | 32 +++++++--------
tests/testFactorAllNA.R |only
tests/testManyNames.R | 1
tests/testManyNames.Rout.save | 7 +--
tests/testNegative.R | 1
tests/testNegative.Rout.save | 7 +--
tests/testNumeric.R | 1
tests/testNumeric.Rout.save | 7 +--
tests/testUnnamedComponents.R | 2
tests/testUnnamedComponents.Rout.save | 64 +++++++++++++++----------------
tests/test_as_is.R | 1
tests/test_as_is.Rout.save | 7 +--
tests/test_fields.R | 1
tests/test_fields.Rout.save | 7 +--
tests/xport.R | 1
tests/xport.Rout.save | 7 +--
tests/xxx.R | 1
tests/xxx.Rout.save | 7 +--
36 files changed, 281 insertions(+), 129 deletions(-)
Title: High dimensional multiclass classification using sparse group
lasso
Diff between msgl versions 0.1.3 dated 2013-05-27 and 0.1.4 dated 2013-06-01
Description: Sparse group lasso multiclass classification, suitable for
high dimensional problems with many classes. Fast algorithm for
solving the multinomial sparse group lasso convex optimization
problem. This package apply template metaprogramming
techniques, therefore -- when compiling the package from source
-- a high level of optimization is needed to gain full speed
(e.g. for the GCC compiler use -O3). Use of multiple processors
for cross validation and subsampling is supported through
OpenMP. The Armadillo C++ library is used as the primary linear
algebra engine. Armadillo is licensed under the MPL 2.0. The
Armadillo C++ library is primarily developed at NICTA
(Australia) by Conrad Sanderson, with contributions from around
the world. Furthermore the package utilize various Boost
libraries, in particular the Tuple library by Jaakko Jarvi and
the Random library by Jens Maurer. The Boost libraries are
licensed under the Boost Software License.
Author: Martin Vincent
Maintainer: Martin Vincent
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
src/include/msgl_R_interface.h | 5 +++++
src/include/sgl/interface_basic.h | 4 ++--
4 files changed, 14 insertions(+), 9 deletions(-)
Title: Time series management, analysis and interpolation for
hydrological modelling
Diff between hydroTSM versions 0.3-6 dated 2012-10-18 and 0.4-1 dated 2013-06-01
Description: S3 functions for management, analysis, interpolation and
plotting of time series used in hydrology and related
environmental sciences. In particular, this package is highly
oriented to hydrological modelling tasks. The focus of this
package has been put in providing a collection of tools useful
for the daily work of hydrologists (although an effort was made
to optimise each function as much as possible, functionality
has had priority over speed). Bugs / comments / questions /
collaboration of any kind are very welcomed, and in particular,
datasets that can be included in this package for academic
purposes.
Author: Mauricio Zambrano-Bigiarini [aut, cre]
Maintainer: Mauricio Zambrano-Bigiarini
hydroTSM-0.3-6/hydroTSM/LICENSE |only
hydroTSM-0.4-1/hydroTSM/DESCRIPTION | 17
hydroTSM-0.4-1/hydroTSM/MD5 | 171 +++---
hydroTSM-0.4-1/hydroTSM/NAMESPACE | 8
hydroTSM-0.4-1/hydroTSM/NEWS | 198 ++-----
hydroTSM-0.4-1/hydroTSM/R/annualfunction.R | 84 +--
hydroTSM-0.4-1/hydroTSM/R/daily2annual.R | 469 ++++++++---------
hydroTSM-0.4-1/hydroTSM/R/daily2monthly.R | 461 ++++++++--------
hydroTSM-0.4-1/hydroTSM/R/dip.R | 53 +
hydroTSM-0.4-1/hydroTSM/R/diy.R | 23
hydroTSM-0.4-1/hydroTSM/R/dm2seasonal.R | 89 +--
hydroTSM-0.4-1/hydroTSM/R/drawxaxis.R | 10
hydroTSM-0.4-1/hydroTSM/R/dwdays.R | 53 +
hydroTSM-0.4-1/hydroTSM/R/dwi.R | 22
hydroTSM-0.4-1/hydroTSM/R/extract.R | 32 -
hydroTSM-0.4-1/hydroTSM/R/fdc.R | 2
hydroTSM-0.4-1/hydroTSM/R/fdcu.R | 14
hydroTSM-0.4-1/hydroTSM/R/gists2spt.R | 6
hydroTSM-0.4-1/hydroTSM/R/hip.R |only
hydroTSM-0.4-1/hydroTSM/R/hydrokrige.R | 33 -
hydroTSM-0.4-1/hydroTSM/R/hydropairs.R | 20
hydroTSM-0.4-1/hydroTSM/R/hydroplot.R | 144 ++---
hydroTSM-0.4-1/hydroTSM/R/hypsometric.R | 2
hydroTSM-0.4-1/hydroTSM/R/infillxy.R | 22
hydroTSM-0.4-1/hydroTSM/R/istdx.R | 28 -
hydroTSM-0.4-1/hydroTSM/R/izoo2rzoo.R | 11
hydroTSM-0.4-1/hydroTSM/R/ma.R | 45 +
hydroTSM-0.4-1/hydroTSM/R/matrixplot.R | 8
hydroTSM-0.4-1/hydroTSM/R/mip.R | 51 +
hydroTSM-0.4-1/hydroTSM/R/monthly2annual.R | 20
hydroTSM-0.4-1/hydroTSM/R/monthlyfunction.R | 469 ++++++++---------
hydroTSM-0.4-1/hydroTSM/R/mspplot.R | 19
hydroTSM-0.4-1/hydroTSM/R/rm1stchar.R | 19
hydroTSM-0.4-1/hydroTSM/R/seasonalfunction.R | 87 +--
hydroTSM-0.4-1/hydroTSM/R/sfreq.R | 7
hydroTSM-0.4-1/hydroTSM/R/smry.R | 71 +-
hydroTSM-0.4-1/hydroTSM/R/sname2plot.R | 333 ++++++------
hydroTSM-0.4-1/hydroTSM/R/sname2ts.R | 15
hydroTSM-0.4-1/hydroTSM/R/stdx.R | 35 -
hydroTSM-0.4-1/hydroTSM/R/subdaily2annual.R |only
hydroTSM-0.4-1/hydroTSM/R/subdaily2daily.R |only
hydroTSM-0.4-1/hydroTSM/R/subdaily2monthly.R |only
hydroTSM-0.4-1/hydroTSM/R/subdaily2seasonal.R |only
hydroTSM-0.4-1/hydroTSM/R/time2season.R | 34 -
hydroTSM-0.4-1/hydroTSM/R/vector2zoo.R | 8
hydroTSM-0.4-1/hydroTSM/R/yip.R | 57 +-
hydroTSM-0.4-1/hydroTSM/WhatsNew.txt | 146 +++++
hydroTSM-0.4-1/hydroTSM/data/KarameaAtGorgeQts.RData |only
hydroTSM-0.4-1/hydroTSM/inst/doc/hydroTSM_Vignette.R |only
hydroTSM-0.4-1/hydroTSM/inst/doc/hydroTSM_Vignette.Rnw | 141 ++++-
hydroTSM-0.4-1/hydroTSM/inst/doc/hydroTSM_Vignette.pdf |binary
hydroTSM-0.4-1/hydroTSM/man/KarameaAtGorgeQts.Rd |only
hydroTSM-0.4-1/hydroTSM/man/OcaEnOnaQts.Rd | 6
hydroTSM-0.4-1/hydroTSM/man/SanMartinoPPts.Rd | 6
hydroTSM-0.4-1/hydroTSM/man/annualfunction.Rd | 14
hydroTSM-0.4-1/hydroTSM/man/daily2annual.Rd | 48 +
hydroTSM-0.4-1/hydroTSM/man/daily2monthly.Rd | 37 -
hydroTSM-0.4-1/hydroTSM/man/dip.Rd | 14
hydroTSM-0.4-1/hydroTSM/man/diy.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/dm2seasonal.Rd | 47 +
hydroTSM-0.4-1/hydroTSM/man/drawxaxis.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/dwdays.Rd | 14
hydroTSM-0.4-1/hydroTSM/man/dwi.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/extract.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/fdc.Rd | 34 -
hydroTSM-0.4-1/hydroTSM/man/fdcu.Rd | 2
hydroTSM-0.4-1/hydroTSM/man/gists2spt.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/hip.Rd |only
hydroTSM-0.4-1/hydroTSM/man/hydroTSM-package.Rd | 16
hydroTSM-0.4-1/hydroTSM/man/hydrokrige.Rd | 12
hydroTSM-0.4-1/hydroTSM/man/hydropairs.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/hydroplot.Rd | 46 +
hydroTSM-0.4-1/hydroTSM/man/hypsometric.Rd | 4
hydroTSM-0.4-1/hydroTSM/man/infillxy.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/istdx.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/izoo2rzoo.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/ma.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/matrixplot.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/mip.Rd | 12
hydroTSM-0.4-1/hydroTSM/man/monthlyfunction.Rd | 18
hydroTSM-0.4-1/hydroTSM/man/mspplot.Rd | 9
hydroTSM-0.4-1/hydroTSM/man/rm1stchar.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/seasonalfunction.Rd | 14
hydroTSM-0.4-1/hydroTSM/man/sfreq.Rd | 4
hydroTSM-0.4-1/hydroTSM/man/smry.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/sname2ts.Rd | 12
hydroTSM-0.4-1/hydroTSM/man/stdx.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/subdaily2daily.Rd |only
hydroTSM-0.4-1/hydroTSM/man/time2season.Rd | 12
hydroTSM-0.4-1/hydroTSM/man/vector2zoo.Rd | 8
hydroTSM-0.4-1/hydroTSM/man/yip.Rd | 14
hydroTSM-0.4-1/hydroTSM/man/zoo2RHtest.Rd | 18
92 files changed, 2421 insertions(+), 1649 deletions(-)
Title: HTTP and WebSocket server library
Diff between httpuv versions 1.0.5 dated 2013-03-11 and 1.0.6.3 dated 2013-06-01
Description: httpuv provides low-level socket and protocol support for
handling HTTP and WebSocket requests directly from within R. It
is primarily intended as a building block for other packages,
rather than making it particularly easy to create complete web
applications using httpuv alone. httpuv is built on top of the
libuv and http-parser C libraries, both of which were developed
by Joyent, Inc. (See LICENSE file for libuv and http-parser
license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng
DESCRIPTION | 11 ++---
LICENSE | 4 +
MD5 | 32 +++++++-------
NAMESPACE | 1
NEWS |only
R/RcppExports.R | 8 ++-
R/httpuv.R | 73 +++++++++++++++++++++++++++------
configure |only
man/WebSocket.Rd | 6 ++
man/startServer.Rd | 37 ++++++++++++++---
src/RcppExports.cpp | 25 +++++++++--
src/http.cpp | 112 ++++++++++++++++++++++++++++++++++------------------
src/http.h | 28 +++++++++----
src/httpuv.cpp | 74 +++++++++++++++++++---------------
src/sha1/sha1.c | 26 ++++++------
src/sha1/sha1.h | 6 +-
src/websockets.cpp | 28 ++++---------
src/websockets.h | 2
18 files changed, 313 insertions(+), 160 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-11-05 1.0