Title: Beta Regression
Diff between betareg versions 2.4-1 dated 2012-01-27 and 3.0-0 dated 2012-05-08
Description: Beta regression for modeling beta-distributed dependent
variables, e.g., rates and proportions. In addition to maximum
likelihood regression (for both mean and precision of a
beta-distributed response), bias-corrected and bias-reduced
estimation as well as finite mixture models and recursive
partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre], Francisco Cribari-Neto [aut], Bettina
Gruen [aut], Ioannis Kosmidis [aut], Alexandre B. Simas [ctb]
(earlier version by), Andrea V. Rocha [ctb] (earlier version
by)
Maintainer: Achim Zeileis
DESCRIPTION | 8 ++++----
MD5 | 44 ++++++++++++++++++++++----------------------
NEWS | 12 ++++++++++++
data/CarTask.rda |binary
data/FoodExpenditure.rda |binary
data/GasolineYield.rda |binary
data/ImpreciseTask.rda |binary
data/MockJurors.rda |binary
data/ReadingSkills.rda |binary
data/StressAnxiety.rda |binary
data/WeatherTask.rda |binary
inst/CITATION | 32 +++++++++++++++-----------------
inst/doc/betareg-ext.Rnw | 27 ++++++++++++++++-----------
inst/doc/betareg-ext.pdf |binary
inst/doc/betareg.Rnw | 2 +-
inst/doc/betareg.pdf |binary
man/ReadingSkills.Rd | 7 +++----
man/betamix.Rd | 9 ++++-----
man/betareg.Rd | 9 ++++-----
man/betatree.Rd | 9 ++++-----
vignettes/betareg-ext.Rnw | 27 ++++++++++++++++-----------
vignettes/betareg.Rnw | 2 +-
vignettes/betareg.bib | 21 +++++++++------------
23 files changed, 111 insertions(+), 98 deletions(-)
Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-6 dated 2012-03-31 and 2.2-7 dated 2012-05-08
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also
provides compatibility functions that facilitate writing code
for ff and ram objects and support for batch processing on ff
objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely
with functionality from package 'bit': chunked looping, fast
bit operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Author: Daniel Adler
Maintainer: Jens Oehlschlägel
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NEWS | 9 +++++++++
src/ordermerge.c | 2 +-
4 files changed, 17 insertions(+), 8 deletions(-)
Title: Bayesian Spectrum Analysis in R
Diff between BaSAR versions 1.2 dated 2012-04-15 and 1.3 dated 2012-05-08
Description: Bayesian Spectrum Analysis of time series data
Author: Emma Granqvist, Matthew Hartley and Richard J Morris
Maintainer: Emma Granqvist
DESCRIPTION | 8 ++++----
MD5 | 6 +++++-
data |only
man/tutorial.2.Rd |only
man/tutorial.Rd |only
5 files changed, 9 insertions(+), 5 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.1 dated 2012-03-02 and 3.2 dated 2012-05-08
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate probit models with
semiparametric predictors (including linear, nonlinear and
nonparametric random effects) in the presence of correlated
error equations, endogeneity or sample selection.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 6 +
DESCRIPTION | 6 -
MD5 | 32 ++++---
R/AT.r | 4
R/LM.bpm.r |only
R/SemiParBIVProbit.r | 21 +++-
R/bprob.r | 4
R/bprobH.r |only
R/bprobNP.H.r | 22 ++---
R/bprobNP.r | 24 ++---
R/bprobSS.r | 14 +--
R/bprobSSH.r |only
R/zzz.r | 16 ---
man/LM.bpm.Rd |only
man/SemiParBIVProbit.Rd | 176 +++++++++++++++++-----------------------
man/SemiParBIVProbitObject.Rd | 6 -
man/bprobH.Rd |only
man/bprobSSH.Rd |only
man/plot.SemiParBIVProbit.Rd | 4
man/summary.SemiParBIVProbit.Rd | 4
20 files changed, 162 insertions(+), 177 deletions(-)
Permanent link
Title: 3D visualization device system (OpenGL)
Diff between rgl versions 0.92.879 dated 2012-04-08 and 0.92.880 dated 2012-05-08
Description: 3D visualization device (OpenGL)
Author: Daniel Adler
Maintainer: Duncan Murdoch
DESCRIPTION | 6 +++---
MD5 | 6 +++---
inst/NEWS | 4 +++-
src/types.h | 20 ++++++++++----------
4 files changed, 19 insertions(+), 17 deletions(-)
Title: Network representations of relationships in data
Diff between qgraph versions 1.0.3 dated 2012-04-19 and 1.0.4 dated 2012-05-08
Description: The qgraph package can be used to visualize data as
networks.
Author: Sacha Epskamp, Angelique O. J. Cramer, Lourens J. Waldorp,
Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp
DESCRIPTION | 8 ++---
MD5 | 43 +++++++++++++++----------------
NEWS | 4 ++
R/qgraph.R | 6 ++--
inst/CITATION |only
inst/COPYRIGHTS | 2 -
man/plot.qgraph.Rd | 2 -
man/print.qgraph.Rd | 2 -
man/qgraph-package.Rd | 9 +++++-
man/qgraph.Rd | 9 +++++-
man/qgraph.animate.Rd | 7 +++++
man/qgraph.arrow.Rd | 2 -
man/qgraph.cfa.Rd | 8 +++++
man/qgraph.lavaan.Rd | 8 ++++-
man/qgraph.layout.fruchtermanreingold.Rd | 9 +++++-
man/qgraph.panel.Rd | 9 +++++-
man/qgraph.semModel.Rd | 11 +++++--
man/qgraph_efa.Rd | 9 +++++-
man/qgraph_loadings.Rd | 9 +++++-
man/qgraph_pca.Rd | 11 +++++--
man/qgraph_sem.Rd | 8 ++++-
man/qgraph_svg.Rd | 8 ++++-
man/summary.qgraph.Rd | 2 -
23 files changed, 129 insertions(+), 57 deletions(-)
More information about SunterSampling at CRAN
Permanent link
Title: vcd additions
Diff between vcdExtra versions 0.5-2 dated 2011-03-24 and 0.5-3 dated 2012-05-08
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-0.5-2/vcdExtra/R/aperm.R |only
vcdExtra-0.5-2/vcdExtra/inst/doc/Z.cls |only
vcdExtra-0.5-2/vcdExtra/inst/doc/fig |only
vcdExtra-0.5-2/vcdExtra/inst/doc/jss.bst |only
vcdExtra-0.5-2/vcdExtra/inst/doc/vcd.bib |only
vcdExtra-0.5-2/vcdExtra/inst/doc/vcdExtra.bib |only
vcdExtra-0.5-2/vcdExtra/man/aperm.Rd |only
vcdExtra-0.5-3/vcdExtra/DESCRIPTION | 26 +-
vcdExtra-0.5-3/vcdExtra/MD5 |only
vcdExtra-0.5-3/vcdExtra/NAMESPACE | 10 -
vcdExtra-0.5-3/vcdExtra/NEWS | 9
vcdExtra-0.5-3/vcdExtra/R/GKgamma.R | 2
vcdExtra-0.5-3/vcdExtra/data/Alligator.RData |only
vcdExtra-0.5-3/vcdExtra/data/DaytonSurvey.RData |only
vcdExtra-0.5-3/vcdExtra/data/Mammograms.RData |only
vcdExtra-0.5-3/vcdExtra/inst/doc/vcd-tutorial.Rnw | 217 +++++++++++++++-------
vcdExtra-0.5-3/vcdExtra/inst/doc/vcd-tutorial.pdf |binary
vcdExtra-0.5-3/vcdExtra/man/Alligator.Rd |only
vcdExtra-0.5-3/vcdExtra/man/DaytonSurvey.Rd |only
vcdExtra-0.5-3/vcdExtra/man/Mammograms.Rd |only
vcdExtra-0.5-3/vcdExtra/man/mosaic.glm.Rd | 29 ++
vcdExtra-0.5-3/vcdExtra/man/vcdExtra-package.Rd | 4
vcdExtra-0.5-3/vcdExtra/vignettes |only
23 files changed, 217 insertions(+), 80 deletions(-)
Title: Time Series Database Interface extensions for PostgreSQL
Diff between TSPostgreSQL versions 2012.3-1 dated 2012-03-29 and 2012.5-1 dated 2012-05-08
Description: TSPostgreSQL provides a PostgreSQL interface for TSdbi.
Author: Paul Gilbert
Maintainer: Paul Gilbert
TSPostgreSQL-2012.3-1/TSPostgreSQL/LICENSE |only
TSPostgreSQL-2012.5-1/TSPostgreSQL/DESCRIPTION | 14 +++++++-------
TSPostgreSQL-2012.5-1/TSPostgreSQL/MD5 | 11 +++++------
TSPostgreSQL-2012.5-1/TSPostgreSQL/NEWS | 8 +++++++-
TSPostgreSQL-2012.5-1/TSPostgreSQL/inst/doc/Guide.pdf |binary
TSPostgreSQL-2012.5-1/TSPostgreSQL/man/TSdbiMethods.Rd | 1 +
TSPostgreSQL-2012.5-1/TSPostgreSQL/vignettes/Guide.Stex | 6 ++----
7 files changed, 22 insertions(+), 18 deletions(-)
Title: Scale functions for graphics.
Diff between scales versions 0.2.0 dated 2012-02-27 and 0.2.1 dated 2012-05-08
Description: Scales map data to aesthetics, and provide methods for
automatically determining breaks and labels for axes and
legends.
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 8 ++++----
MD5 | 27 +++++++++++++++------------
NAMESPACE | 2 ++
NEWS | 19 +++++++++++++++++++
R/breaks.r | 29 ++++++++++++++++++++++-------
R/colour-manip.r | 9 +++++----
R/formatter.r | 22 ++++++++++++++++++----
R/pal-gradient.r | 2 ++
R/scale-continuous.r | 2 +-
build/partial.rdb |binary
inst/tests/test-alpha.r |only
inst/tests/test-breaks-log.r |only
inst/tests/test-formatter.r | 38 ++++++++++++++++++++++++++++++++++++++
man/alpha.Rd | 5 +++--
man/dollar_format.Rd | 14 +++++++++++---
man/extended_breaks.Rd |only
16 files changed, 140 insertions(+), 37 deletions(-)
Title: Download content from NCBI databases
Diff between RISmed versions 2.0 dated 2012-05-06 and 2.0.1 dated 2012-05-08
Description: Download content from NCBI databases. This package is
intended to facilitate analyses of NCBI database content. This
package is not intended for reference management.
Author: Stephanie Kovalchik
Maintainer: S. A. Kovalchik
DESCRIPTION | 6 +-
MD5 | 105 ++++++++++++++++++++++++++++++------
NAMESPACE | 13 +++-
NEWS | 10 +++
R/AllGenerics.R | 42 +++++++++++++-
R/EUtils.R | 27 ++++++---
R/EUtilsSummary.R | 7 +-
R/Medline.R |only
data/myeloma.RData |binary
dev |only
man/AbstractText-methods.Rd |only
man/AbstractText.Rd |only
man/Acronym-methods.Rd |only
man/Acronym.Rd |only
man/Affiliation-methods.Rd |only
man/Affiliation.Rd |only
man/Agency-methods.Rd |only
man/Agency.Rd |only
man/ArticleId-methods.Rd |only
man/ArticleId.Rd |only
man/ArticleTitle-methods.Rd |only
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man/Author-methods.Rd |only
man/Author.Rd |only
man/CollectiveName-methods.Rd |only
man/CollectiveName.Rd |only
man/CopyrightInformation-methods.Rd |only
man/CopyrightInformation.Rd |only
man/Country-methods.Rd |only
man/Country.Rd |only
man/Day-methods.Rd |only
man/Day.Rd |only
man/DescriptorName-methods.Rd |only
man/DescriptorName.Rd |only
man/ELocationID-methods.Rd |only
man/ELocationID.Rd |only
man/EUtilsGet.Rd | 19 ++++--
man/EUtilsSummary-class.Rd | 6 +-
man/EUtilsSummary.Rd | 6 +-
man/GrantID-methods.Rd |only
man/GrantID.Rd |only
man/Hour-methods.Rd |only
man/Hour.Rd |only
man/ISOAbbreviation-methods.Rd |only
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man/ISSN.Rd |only
man/ISSNLinking-methods.Rd |only
man/ISSNLinking.Rd |only
man/Issue-methods.Rd |only
man/Issue.Rd |only
man/Language-methods.Rd |only
man/Language.Rd |only
man/Medline.Rd |only
man/MedlinePgn-methods.Rd |only
man/MedlinePgn.Rd |only
man/MedlineTA-methods.Rd |only
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man/Minute-methods.Rd |only
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man/Month-methods.Rd |only
man/Month.Rd |only
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man/PMID.Rd |only
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man/QualifierName-methods.Rd |only
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man/Query-methods.Rd |only
man/Query.Rd |only
man/RISmed-package.Rd | 6 +-
man/RefSource-methods.Rd |only
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man/Title-methods.Rd |only
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man/Volume.Rd |only
man/Year-methods.Rd |only
man/Year.Rd |only
man/count.Rd | 8 +-
man/id.Rd | 8 +-
man/myeloma.Rd | 4 -
man/print-method.Rd |only
man/show-Medline-methods.Rd |only
man/translation.Rd | 8 +-
91 files changed, 215 insertions(+), 60 deletions(-)
Title: The GSC Applied Geochemistry EDA Package
Diff between rgr versions 1.1.5 dated 2012-04-07 and 1.1.6 dated 2012-05-08
Description: Geological Survey of Canada (GSC) R functions for
exploratory data analysis with applied geochemical data, with
special application to the estimation of background ranges and
identification of outliers, 'anomalies', to support both
environmental studies and mineral exploration.
Author: Robert G. Garrett
Maintainer: Robert G. Garrett
rgr-1.1.5/rgr/inst/doc/What_is_in_rgr_1-1-5.pdf |only
rgr-1.1.5/rgr/inst/doc/rgr_Overview_1-1-5.pdf |only
rgr-1.1.5/rgr/inst/doc/rgr_func_list_1-1-5.pdf |only
rgr-1.1.5/rgr/man/rgr_1.1.5-package.Rd |only
rgr-1.1.6/rgr/DESCRIPTION | 6
rgr-1.1.6/rgr/MD5 | 122 ++++++-------
rgr-1.1.6/rgr/NAMESPACE | 2
rgr-1.1.6/rgr/R/ad.plot1.R | 33 ++-
rgr-1.1.6/rgr/R/ad.plot2.R | 8
rgr-1.1.6/rgr/R/bwplots.R | 221 +++++++++++++-----------
rgr-1.1.6/rgr/R/fences.R | 19 +-
rgr-1.1.6/rgr/R/fences.summary.R | 40 ++--
rgr-1.1.6/rgr/R/framework.summary.R | 76 +++++---
rgr-1.1.6/rgr/R/gx.md.display.R | 53 ++++-
rgr-1.1.6/rgr/R/gx.md.print.R | 41 ++--
rgr-1.1.6/rgr/R/gx.mva.closed.R |only
rgr-1.1.6/rgr/R/gx.mvalloc.R | 95 ++++++----
rgr-1.1.6/rgr/R/gx.mvalloc.print.R | 63 +++---
rgr-1.1.6/rgr/R/gx.rqpca.print.R | 131 +++++++++-----
rgr-1.1.6/rgr/R/map.z.R | 101 ++++++----
rgr-1.1.6/rgr/R/tbplots.R | 13 -
rgr-1.1.6/rgr/data/ad.test.rda |binary
rgr-1.1.6/rgr/data/crm.test.rda |binary
rgr-1.1.6/rgr/data/fix.test.asis.rda |binary
rgr-1.1.6/rgr/data/fix.test.rda |binary
rgr-1.1.6/rgr/data/kola.c.rda |binary
rgr-1.1.6/rgr/data/kola.o.rda |binary
rgr-1.1.6/rgr/data/ms.data1.rda |binary
rgr-1.1.6/rgr/data/ms.data2.rda |binary
rgr-1.1.6/rgr/data/ms.data3.rda |binary
rgr-1.1.6/rgr/data/ogrady.mat2open.rda |binary
rgr-1.1.6/rgr/data/ogrady.rda |binary
rgr-1.1.6/rgr/data/sind.mat2open.rda |binary
rgr-1.1.6/rgr/data/sind.rda |binary
rgr-1.1.6/rgr/data/triples.test1.rda |binary
rgr-1.1.6/rgr/data/triples.test2.rda |binary
rgr-1.1.6/rgr/inst/doc/What_is_in_rgr_1-1-6.pdf |only
rgr-1.1.6/rgr/inst/doc/rgr_Overview_1-1-6.pdf |only
rgr-1.1.6/rgr/inst/doc/rgr_func_list_1-1-6.pdf |only
rgr-1.1.6/rgr/man/ad.plot1.Rd | 7
rgr-1.1.6/rgr/man/ad.plot2.Rd | 5
rgr-1.1.6/rgr/man/bwplots.Rd | 2
rgr-1.1.6/rgr/man/fences.Rd | 2
rgr-1.1.6/rgr/man/fences.summary.Rd | 6
rgr-1.1.6/rgr/man/framework.summary.Rd | 4
rgr-1.1.6/rgr/man/gx.md.display.Rd | 6
rgr-1.1.6/rgr/man/gx.md.plot.Rd | 6
rgr-1.1.6/rgr/man/gx.md.print.Rd | 6
rgr-1.1.6/rgr/man/gx.mva.Rd | 39 ++--
rgr-1.1.6/rgr/man/gx.mva.closed.Rd |only
rgr-1.1.6/rgr/man/gx.mvalloc.Rd | 4
rgr-1.1.6/rgr/man/gx.mvalloc.closed.Rd | 4
rgr-1.1.6/rgr/man/gx.mvalloc.print.Rd | 6
rgr-1.1.6/rgr/man/gx.pearson.Rd | 4
rgr-1.1.6/rgr/man/gx.robmva.Rd | 8
rgr-1.1.6/rgr/man/gx.robmva.closed.Rd | 8
rgr-1.1.6/rgr/man/gx.rotate.Rd | 6
rgr-1.1.6/rgr/man/gx.rqpca.loadplot.Rd | 4
rgr-1.1.6/rgr/man/gx.rqpca.plot.Rd | 6
rgr-1.1.6/rgr/man/gx.rqpca.print.Rd | 19 +-
rgr-1.1.6/rgr/man/gx.rqpca.screeplot.Rd | 6
rgr-1.1.6/rgr/man/gx.spearman.Rd | 7
rgr-1.1.6/rgr/man/gx.triples.aov.Rd | 2
rgr-1.1.6/rgr/man/gx.triples.fgx.Rd | 3
rgr-1.1.6/rgr/man/orthonorm.Rd | 2
rgr-1.1.6/rgr/man/rgr_1.1.6-package.Rd |only
rgr-1.1.6/rgr/man/tbplots.Rd | 4
67 files changed, 705 insertions(+), 495 deletions(-)
Title: R interface to the Levenberg-Marquardt nonlinear least-squares
algorithm found in MINPACK, plus support for bounds
Diff between minpack.lm versions 1.1-5 dated 2010-09-29 and 1.1-6 dated 2012-05-08
Description: The nls.lm function provides an R interface to lmder and
lmdif from the MINPACK library, for solving nonlinear
least-squares problems by a modification of the
Levenberg-Marquardt algorithm, with support for lower and upper
parameter bounds. The implementation can be used via nls-like
calls using the nlsLM function.
Author: Timur V. Elzhov, Katharine M. Mullen, Andrej-Nikolai Spiess,
Ben Bolker
Maintainer: Katharine M. Mullen
DESCRIPTION | 22 +++++++++++++---------
MD5 |only
NAMESPACE | 2 +-
NEWS |only
R/nls.lm.R | 14 ++++++++++++--
R/nlsLM.R |only
THANKS |only
man/nls.lm.Rd | 9 ++++++++-
man/nlsLM.Rd |only
src/fcn_lmder.c | 8 ++++++++
src/fcn_lmdif.c | 13 ++++++++++---
src/minpack_lm.h | 15 +++++++++++----
src/nls_lm.c | 37 ++++++++++++++++++++++++++++++-------
13 files changed, 93 insertions(+), 27 deletions(-)
Title: Software for Bayesian Inference
Diff between LaplacesDemon versions 12.04.02 dated 2012-04-02 and 12.05.07 dated 2012-05-08
Description: Laplace's Demon is software for Bayesian inference.
Author: Byron Hall
Maintainer: Byron Hall
CHANGELOG | 19 +
DESCRIPTION | 8
MD5 | 88 +++---
NAMESPACE | 9
R/ESS.R | 14
R/KLD.R | 2
R/LaplacesDemon.R | 104 +++----
R/Levene.Test.R |only
R/OnLoad.R | 5
R/Stick.R |only
R/distributions.R | 104 ++++++-
R/plot.demonoid.ppc.R | 300 ++++++++++++++++++++
R/plot.laplace.ppc.R | 306 ++++++++++++++++++++
R/summary.demonoid.ppc.R | 33 +-
R/summary.laplace.ppc.R | 28 +
inst/doc/BayesianInference.pdf |binary
inst/doc/Examples.Stex | 439 ++++++++++++++++++++++++------
inst/doc/Examples.pdf |binary
inst/doc/LaplacesDemonTutorial.Stex | 52 +--
inst/doc/LaplacesDemonTutorial.pdf |binary
inst/doc/References.bib | 68 +++-
man/CSF.Rd | 21 +
man/Consort.Rd | 12
man/ESS.Rd | 27 +
man/Geweke.Diagnostic.Rd | 7
man/IAT.Rd | 12
man/Importance.Rd | 4
man/KS.Diagnostic.Rd | 10
man/LaplacesDemon-package.Rd | 15 -
man/LaplacesDemon.Rd | 6
man/Levene.Test.Rd |only
man/MCSE.Rd | 6
man/Matrices.Rd | 2
man/Model.Spec.Time.Rd | 6
man/SIR.Rd | 7
man/Stick.Rd |only
man/burnin.Rd | 10
man/dist.Multivariate.Normal.Precision.Rd | 9
man/dist.Multivariate.Normal.Rd | 9
man/dist.Normal.Precision.Rd | 9
man/dist.Normal.Variance.Rd | 9
man/dist.Skew.Discrete.Laplace.Rd |only
man/dist.Stick.Rd |only
man/plot.demonoid.Rd | 3
man/plot.demonoid.ppc.Rd | 152 +++++++++-
man/plot.laplace.ppc.Rd | 154 +++++++++-
man/summary.demonoid.ppc.Rd | 128 +++++++-
man/summary.laplace.ppc.Rd | 128 +++++++-
48 files changed, 1982 insertions(+), 343 deletions(-)
Title: Integrative clustering of multiple genomic data types
Diff between iCluster versions 1.2.0 dated 2010-04-05 and 2.1.0 dated 2012-05-08
Description: Integrative clustering of multiple genomic data types
using a joint latent variable model.
Author: Ronglai Shen
Maintainer: Ronglai Shen
iCluster-1.2.0/iCluster/R/compute.pod.R |only
iCluster-2.1.0/iCluster/DESCRIPTION | 16 -
iCluster-2.1.0/iCluster/MD5 |only
iCluster-2.1.0/iCluster/NAMESPACE | 2
iCluster-2.1.0/iCluster/R/computePOD.R |only
iCluster-2.1.0/iCluster/R/iCluster.R | 226 ++++++++++++-------------
iCluster-2.1.0/iCluster/R/iCluster2.R |only
iCluster-2.1.0/iCluster/R/plotHeatmap.R |only
iCluster-2.1.0/iCluster/R/plotRI.R |only
iCluster-2.1.0/iCluster/R/plotiCluster.R | 74 ++++----
iCluster-2.1.0/iCluster/R/tune.iCluster2.R |only
iCluster-2.1.0/iCluster/data/breast.chr17.rda |binary
iCluster-2.1.0/iCluster/data/coord.rda |only
iCluster-2.1.0/iCluster/data/datalist |only
iCluster-2.1.0/iCluster/data/gbm.rda |only
iCluster-2.1.0/iCluster/data/glp.rda |only
iCluster-2.1.0/iCluster/data/simu.datasets.rda |only
iCluster-2.1.0/iCluster/demo/00Index | 2
iCluster-2.1.0/iCluster/demo/iCluster.demo.R | 76 +++++---
iCluster-2.1.0/iCluster/man/compute.pod.Rd | 68 +++----
iCluster-2.1.0/iCluster/man/coord.Rd |only
iCluster-2.1.0/iCluster/man/gbm.Rd |only
iCluster-2.1.0/iCluster/man/glp.Rd |only
iCluster-2.1.0/iCluster/man/iCluster.Rd | 98 +++++-----
iCluster-2.1.0/iCluster/man/iCluster2.Rd |only
iCluster-2.1.0/iCluster/man/plotHeatmap.Rd |only
iCluster-2.1.0/iCluster/man/plotRI.Rd |only
iCluster-2.1.0/iCluster/man/plotiCluster.Rd | 70 +++----
iCluster-2.1.0/iCluster/man/simu.datasets.Rd |only
iCluster-2.1.0/iCluster/man/tuneiCluster2.Rd |only
30 files changed, 325 insertions(+), 307 deletions(-)
Title: An implementation of the Grammar of Graphics
Diff between ggplot2 versions 0.9.0 dated 2012-01-26 and 0.9.1 dated 2012-05-08
Description: An implementation of the grammar of graphics in R. It
combines the advantages of both base and lattice graphics:
conditioning and shared axes are handled automatically, and you
can still build up a plot step by step from multiple data
sources. It also implements a sophisticated multidimensional
conditioning system and a consistent interface to map data to
aesthetic attributes. See the ggplot2 website for more
information, documentation and examples.
Author: Hadley Wickham
Maintainer: Hadley Wickham
ggplot2-0.9.0/ggplot2/R/utilities-position.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-aspect-ratio.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-coord-cartesian-with-limits.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-dotplot.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-geom-raster.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-guide-axis.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-guide-position.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-lines.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-minor-breaks.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-scale-breaks.r |only
ggplot2-0.9.0/ggplot2/inst/tests/visual-violin.r |only
ggplot2-0.9.0/ggplot2/test |only
ggplot2-0.9.1/ggplot2/DESCRIPTION | 28
ggplot2-0.9.1/ggplot2/MD5 | 1239 ++++++++--
ggplot2-0.9.1/ggplot2/NAMESPACE | 15
ggplot2-0.9.1/ggplot2/NEWS | 92
ggplot2-0.9.1/ggplot2/R/aes.r | 2
ggplot2-0.9.1/ggplot2/R/annotation-logticks.r |only
ggplot2-0.9.1/ggplot2/R/annotation-raster.r | 25
ggplot2-0.9.1/ggplot2/R/annotation.r | 18
ggplot2-0.9.1/ggplot2/R/autoplot.r | 14
ggplot2-0.9.1/ggplot2/R/coord-.r | 33
ggplot2-0.9.1/ggplot2/R/coord-cartesian-.r | 55
ggplot2-0.9.1/ggplot2/R/coord-fixed.r | 15
ggplot2-0.9.1/ggplot2/R/coord-flip.r | 2
ggplot2-0.9.1/ggplot2/R/coord-map.r | 110
ggplot2-0.9.1/ggplot2/R/coord-munch.r | 11
ggplot2-0.9.1/ggplot2/R/coord-polar.r | 83
ggplot2-0.9.1/ggplot2/R/coord-transform.r | 85
ggplot2-0.9.1/ggplot2/R/facet-grid-.r | 55
ggplot2-0.9.1/ggplot2/R/facet-layout.r | 12
ggplot2-0.9.1/ggplot2/R/facet-locate.r | 17
ggplot2-0.9.1/ggplot2/R/facet-null.r | 5
ggplot2-0.9.1/ggplot2/R/fortify-lm.r | 1
ggplot2-0.9.1/ggplot2/R/fortify-map.r | 3
ggplot2-0.9.1/ggplot2/R/fortify.r | 2
ggplot2-0.9.1/ggplot2/R/geom-abline.r | 2
ggplot2-0.9.1/ggplot2/R/geom-bar-.r | 2
ggplot2-0.9.1/ggplot2/R/geom-bin2d.r | 2
ggplot2-0.9.1/ggplot2/R/geom-boxplot.r | 8
ggplot2-0.9.1/ggplot2/R/geom-crossbar.r | 4
ggplot2-0.9.1/ggplot2/R/geom-dotplot.r | 86
ggplot2-0.9.1/ggplot2/R/geom-error.r | 2
ggplot2-0.9.1/ggplot2/R/geom-errorh.r | 2
ggplot2-0.9.1/ggplot2/R/geom-hex.r | 2
ggplot2-0.9.1/ggplot2/R/geom-hline.r | 2
ggplot2-0.9.1/ggplot2/R/geom-linerange.r | 2
ggplot2-0.9.1/ggplot2/R/geom-map.r | 15
ggplot2-0.9.1/ggplot2/R/geom-path-.r | 9
ggplot2-0.9.1/ggplot2/R/geom-path-contour.r | 2
ggplot2-0.9.1/ggplot2/R/geom-path-density2d.r | 2
ggplot2-0.9.1/ggplot2/R/geom-path-step.r | 2
ggplot2-0.9.1/ggplot2/R/geom-point-.r | 4
ggplot2-0.9.1/ggplot2/R/geom-pointrange.r | 2
ggplot2-0.9.1/ggplot2/R/geom-polygon.r | 2
ggplot2-0.9.1/ggplot2/R/geom-raster.r | 41
ggplot2-0.9.1/ggplot2/R/geom-rect.r | 2
ggplot2-0.9.1/ggplot2/R/geom-ribbon-.r | 4
ggplot2-0.9.1/ggplot2/R/geom-ribbon-density.r | 2
ggplot2-0.9.1/ggplot2/R/geom-rug.r | 53
ggplot2-0.9.1/ggplot2/R/geom-segment.r | 2
ggplot2-0.9.1/ggplot2/R/geom-smooth.r | 2
ggplot2-0.9.1/ggplot2/R/geom-text.r | 6
ggplot2-0.9.1/ggplot2/R/geom-tile.r | 2
ggplot2-0.9.1/ggplot2/R/geom-violin.r | 2
ggplot2-0.9.1/ggplot2/R/geom-vline.r | 2
ggplot2-0.9.1/ggplot2/R/guide-colorbar.r | 71
ggplot2-0.9.1/ggplot2/R/guide-legend.r | 132 -
ggplot2-0.9.1/ggplot2/R/guides-.r | 135 -
ggplot2-0.9.1/ggplot2/R/labels.r | 1
ggplot2-0.9.1/ggplot2/R/layer.r | 23
ggplot2-0.9.1/ggplot2/R/limits.r | 8
ggplot2-0.9.1/ggplot2/R/panel.r | 7
ggplot2-0.9.1/ggplot2/R/plot-render.r | 46
ggplot2-0.9.1/ggplot2/R/plot.r | 68
ggplot2-0.9.1/ggplot2/R/position-collide.r | 13
ggplot2-0.9.1/ggplot2/R/position-identity.r | 1
ggplot2-0.9.1/ggplot2/R/quick-plot.r | 19
ggplot2-0.9.1/ggplot2/R/scale-.r | 242 +
ggplot2-0.9.1/ggplot2/R/scale-continuous.r | 13
ggplot2-0.9.1/ggplot2/R/scale-date.r | 51
ggplot2-0.9.1/ggplot2/R/scale-datetime.r | 48
ggplot2-0.9.1/ggplot2/R/scale-discrete-.r | 12
ggplot2-0.9.1/ggplot2/R/scale-gradient2.r | 4
ggplot2-0.9.1/ggplot2/R/scale-gradientn.r | 4
ggplot2-0.9.1/ggplot2/R/scale-hue.r | 2
ggplot2-0.9.1/ggplot2/R/scale-identity.r | 20
ggplot2-0.9.1/ggplot2/R/scale-manual.r | 29
ggplot2-0.9.1/ggplot2/R/stat-bin.r | 2
ggplot2-0.9.1/ggplot2/R/stat-bin2d.r | 10
ggplot2-0.9.1/ggplot2/R/stat-bindot.r | 4
ggplot2-0.9.1/ggplot2/R/stat-density-2d.r | 3
ggplot2-0.9.1/ggplot2/R/stat-smooth.r | 2
ggplot2-0.9.1/ggplot2/R/stat-sum.r | 10
ggplot2-0.9.1/ggplot2/R/stat-vline.r | 1
ggplot2-0.9.1/ggplot2/R/stat-ydensity.r | 1
ggplot2-0.9.1/ggplot2/R/templates.r | 24
ggplot2-0.9.1/ggplot2/R/theme.r | 8
ggplot2-0.9.1/ggplot2/R/utilities-layer.r | 3
ggplot2-0.9.1/ggplot2/data/diamonds.rda |binary
ggplot2-0.9.1/ggplot2/data/midwest.rda |binary
ggplot2-0.9.1/ggplot2/data/movies.rda |binary
ggplot2-0.9.1/ggplot2/data/msleep.rda |binary
ggplot2-0.9.1/ggplot2/inst/tests/test-aes-grouping.r | 8
ggplot2-0.9.1/ggplot2/inst/tests/test-coord-train.r |only
ggplot2-0.9.1/ggplot2/inst/tests/test-empty-data.r |only
ggplot2-0.9.1/ggplot2/inst/tests/test-facet-layout.r | 9
ggplot2-0.9.1/ggplot2/inst/tests/test-facet-locate.r | 2
ggplot2-0.9.1/ggplot2/inst/tests/test-labels.r |only
ggplot2-0.9.1/ggplot2/inst/tests/test-qplot.r |only
ggplot2-0.9.1/ggplot2/inst/tests/test-scale-manual.r | 51
ggplot2-0.9.1/ggplot2/inst/tests/test-scales-breaks-labels.r | 106
ggplot2-0.9.1/ggplot2/inst/tests/test-scales.r | 55
ggplot2-0.9.1/ggplot2/inst/tests/test-stats.r | 100
ggplot2-0.9.1/ggplot2/man/annotate.Rd | 21
ggplot2-0.9.1/ggplot2/man/annotation_logticks.Rd |only
ggplot2-0.9.1/ggplot2/man/annotation_raster.Rd | 21
ggplot2-0.9.1/ggplot2/man/autoplot.Rd | 11
ggplot2-0.9.1/ggplot2/man/continuous_scale.Rd | 14
ggplot2-0.9.1/ggplot2/man/coord_cartesian.Rd | 8
ggplot2-0.9.1/ggplot2/man/coord_expand_defaults.Rd |only
ggplot2-0.9.1/ggplot2/man/coord_fixed.Rd | 14
ggplot2-0.9.1/ggplot2/man/coord_polar.Rd | 6
ggplot2-0.9.1/ggplot2/man/coord_trans.Rd | 8
ggplot2-0.9.1/ggplot2/man/discrete_scale.Rd | 11
ggplot2-0.9.1/ggplot2/man/facet_grid.Rd | 25
ggplot2-0.9.1/ggplot2/man/facet_wrap.Rd | 2
ggplot2-0.9.1/ggplot2/man/fortify.lm.Rd | 3
ggplot2-0.9.1/ggplot2/man/fortify.map.Rd | 2
ggplot2-0.9.1/ggplot2/man/geom_dotplot.Rd | 23
ggplot2-0.9.1/ggplot2/man/geom_map.Rd | 1
ggplot2-0.9.1/ggplot2/man/geom_raster.Rd | 12
ggplot2-0.9.1/ggplot2/man/geom_rug.Rd | 9
ggplot2-0.9.1/ggplot2/man/geom_text.Rd | 4
ggplot2-0.9.1/ggplot2/man/ggfluctuation.Rd | 8
ggplot2-0.9.1/ggplot2/man/ggmissing.Rd | 6
ggplot2-0.9.1/ggplot2/man/ggorder.Rd | 5
ggplot2-0.9.1/ggplot2/man/ggpcp.Rd | 2
ggplot2-0.9.1/ggplot2/man/ggplot.Rd | 68
ggplot2-0.9.1/ggplot2/man/ggstructure.Rd | 5
ggplot2-0.9.1/ggplot2/man/guide_colourbar.Rd | 3
ggplot2-0.9.1/ggplot2/man/guide_legend.Rd | 3
ggplot2-0.9.1/ggplot2/man/guides.Rd | 8
ggplot2-0.9.1/ggplot2/man/opts.Rd | 6
ggplot2-0.9.1/ggplot2/man/print.ggplot.Rd | 4
ggplot2-0.9.1/ggplot2/man/qplot.Rd | 12
ggplot2-0.9.1/ggplot2/man/scale_brewer.Rd | 2
ggplot2-0.9.1/ggplot2/man/scale_continuous.Rd | 9
ggplot2-0.9.1/ggplot2/man/scale_date.Rd | 24
ggplot2-0.9.1/ggplot2/man/scale_datetime.Rd | 21
ggplot2-0.9.1/ggplot2/man/scale_discrete.Rd | 4
ggplot2-0.9.1/ggplot2/man/scale_gradient.Rd | 2
ggplot2-0.9.1/ggplot2/man/scale_gradient2.Rd | 2
ggplot2-0.9.1/ggplot2/man/scale_gradientn.Rd | 6
ggplot2-0.9.1/ggplot2/man/scale_grey.Rd | 2
ggplot2-0.9.1/ggplot2/man/scale_hue.Rd | 2
ggplot2-0.9.1/ggplot2/man/scale_identity.Rd | 8
ggplot2-0.9.1/ggplot2/man/scale_manual.Rd | 7
ggplot2-0.9.1/ggplot2/man/xlim.Rd | 4
ggplot2-0.9.1/ggplot2/man/ylim.Rd | 4
ggplot2-0.9.1/ggplot2/tests |only
ggplot2-0.9.1/ggplot2/visual_test |only
162 files changed, 3042 insertions(+), 920 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
(fda.usc)
Diff between fda.usc versions 0.9.6 dated 2012-03-06 and 0.9.7 dated 2012-05-08
Description: This package implements functional data methods.
Author: Febrero-Bande, M. and Oviedo de la Fuente, M.
Maintainer: Oviedo de la Fuente, M.
fda.usc-0.9.6/fda.usc/man/classif.kernel.Rd |only
fda.usc-0.9.6/fda.usc/man/classif.knn.Rd |only
fda.usc-0.9.7/fda.usc/DESCRIPTION | 10
fda.usc-0.9.7/fda.usc/MD5 | 114 +++--
fda.usc-0.9.7/fda.usc/NEWS | 16
fda.usc-0.9.7/fda.usc/R/CV.S.R | 25 -
fda.usc-0.9.7/fda.usc/R/GCV.S.R | 38 -
fda.usc-0.9.7/fda.usc/R/S.KNN.R | 4
fda.usc-0.9.7/fda.usc/R/S.NW.R | 10
fda.usc-0.9.7/fda.usc/R/classif.gsam.R |only
fda.usc-0.9.7/fda.usc/R/classif.kgam.R |only
fda.usc-0.9.7/fda.usc/R/classif.np.r |only
fda.usc-0.9.7/fda.usc/R/create.fdata.basis.R | 72 ++-
fda.usc-0.9.7/fda.usc/R/dev.S.R |only
fda.usc-0.9.7/fda.usc/R/fda.usc.internal.R | 18
fda.usc-0.9.7/fda.usc/R/fdata.R | 8
fda.usc-0.9.7/fda.usc/R/fdata2pc.r | 88 ++--
fda.usc-0.9.7/fda.usc/R/fdata2pls.r | 138 ++++--
fda.usc-0.9.7/fda.usc/R/fregre.bootstrap.R | 27 -
fda.usc-0.9.7/fda.usc/R/fregre.glm.R | 9
fda.usc-0.9.7/fda.usc/R/fregre.gsam.R |only
fda.usc-0.9.7/fda.usc/R/fregre.kgam.R |only
fda.usc-0.9.7/fda.usc/R/fregre.np.cv.r | 29 +
fda.usc-0.9.7/fda.usc/R/fregre.pc.R | 180 +++++---
fda.usc-0.9.7/fda.usc/R/fregre.pc.cv.R | 262 +++++++-----
fda.usc-0.9.7/fda.usc/R/fregre.pls.R | 94 ++--
fda.usc-0.9.7/fda.usc/R/fregre.pls.cv.R | 180 +++-----
fda.usc-0.9.7/fda.usc/R/h.default.R | 26 -
fda.usc-0.9.7/fda.usc/R/inprod.fdata.R | 2
fda.usc-0.9.7/fda.usc/R/int.simpson.R | 24 -
fda.usc-0.9.7/fda.usc/R/omit.fdata.R |only
fda.usc-0.9.7/fda.usc/R/predict.classif.R | 494 +++++++++++++----------
fda.usc-0.9.7/fda.usc/R/predict.fregre.fd.R | 4
fda.usc-0.9.7/fda.usc/R/predict.fregre.glm.R | 2
fda.usc-0.9.7/fda.usc/R/predict.fregre.gsam.R |only
fda.usc-0.9.7/fda.usc/R/predict.fregre.kgam.R |only
fda.usc-0.9.7/fda.usc/R/print.classif.r | 8
fda.usc-0.9.7/fda.usc/R/semimetric.basis.R | 2
fda.usc-0.9.7/fda.usc/R/summary.classif.R | 24 -
fda.usc-0.9.7/fda.usc/R/summary.fdata.comp.r | 38 +
fda.usc-0.9.7/fda.usc/R/summary.fregre.fd.r | 348 +++++++++++++++-
fda.usc-0.9.7/fda.usc/man/CV.S.Rd | 3
fda.usc-0.9.7/fda.usc/man/GCV.S.Rd | 3
fda.usc-0.9.7/fda.usc/man/classif.glm.Rd | 3
fda.usc-0.9.7/fda.usc/man/classif.gsam.Rd |only
fda.usc-0.9.7/fda.usc/man/classif.kgam.Rd |only
fda.usc-0.9.7/fda.usc/man/classif.np.Rd |only
fda.usc-0.9.7/fda.usc/man/create.fdata.basis.Rd | 7
fda.usc-0.9.7/fda.usc/man/dev.S.Rd |only
fda.usc-0.9.7/fda.usc/man/fda.usc-package.Rd | 28 -
fda.usc-0.9.7/fda.usc/man/fda.usc.internal.Rd | 10
fda.usc-0.9.7/fda.usc/man/fdata2pc.Rd | 19
fda.usc-0.9.7/fda.usc/man/fdata2pls.Rd | 24 -
fda.usc-0.9.7/fda.usc/man/fregre.bootstrap.Rd | 10
fda.usc-0.9.7/fda.usc/man/fregre.gsam.Rd |only
fda.usc-0.9.7/fda.usc/man/fregre.kgam.Rd |only
fda.usc-0.9.7/fda.usc/man/fregre.pc.Rd | 49 +-
fda.usc-0.9.7/fda.usc/man/fregre.pc.cv.Rd | 43 +-
fda.usc-0.9.7/fda.usc/man/fregre.pls.Rd | 28 -
fda.usc-0.9.7/fda.usc/man/fregre.pls.cv.Rd | 7
fda.usc-0.9.7/fda.usc/man/influence.quan.Rd | 4
fda.usc-0.9.7/fda.usc/man/int.simpson.Rd | 4
fda.usc-0.9.7/fda.usc/man/predict.classif.Rd | 2
fda.usc-0.9.7/fda.usc/man/predict.fregre.gsam.Rd |only
fda.usc-0.9.7/fda.usc/man/predict.fregre.kgam.Rd |only
fda.usc-0.9.7/fda.usc/man/rproc2fdata.Rd | 15
fda.usc-0.9.7/fda.usc/man/semimetric.basis.Rd | 2
fda.usc-0.9.7/fda.usc/man/summary.fregre.kgam.Rd |only
68 files changed, 1616 insertions(+), 939 deletions(-)
Title: diversitree: comparative phylogenetic analyses of
diversification
Diff between diversitree versions 0.9-1 dated 2012-03-15 and 0.9-3 dated 2012-05-08
Description: Contains a number of comparative phylogenetic methods,
mostly focussing 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-0.9-1/diversitree/R/asr-bisse-split.R |only
diversitree-0.9-1/diversitree/R/asr-bisse-t.R |only
diversitree-0.9-1/diversitree/R/asr-musse-split.R |only
diversitree-0.9-1/diversitree/R/combine.R |only
diversitree-0.9-1/diversitree/R/model-bm-direct.R |only
diversitree-0.9-1/diversitree/TAGS |only
diversitree-0.9-1/diversitree/data |only
diversitree-0.9-3/diversitree/ChangeLog | 64 +
diversitree-0.9-3/diversitree/DESCRIPTION | 8
diversitree-0.9-3/diversitree/MD5 | 219 +++--
diversitree-0.9-3/diversitree/NAMESPACE | 126 ---
diversitree-0.9-3/diversitree/R/asr-bisse.R | 55 -
diversitree-0.9-3/diversitree/R/asr-mkn.R | 67 -
diversitree-0.9-3/diversitree/R/asr-musse.R | 51 -
diversitree-0.9-3/diversitree/R/asr.R | 69 +
diversitree-0.9-3/diversitree/R/check.R | 158 ++--
diversitree-0.9-3/diversitree/R/clade-tree.R | 15
diversitree-0.9-3/diversitree/R/constrain.R | 238 +++---
diversitree-0.9-3/diversitree/R/continuous.R |only
diversitree-0.9-3/diversitree/R/cvodes.R | 44 -
diversitree-0.9-3/diversitree/R/desolve.R |only
diversitree-0.9-3/diversitree/R/diversitree-branches-C.R | 101 +-
diversitree-0.9-3/diversitree/R/diversitree-branches.R | 222 +++---
diversitree-0.9-3/diversitree/R/dtlik.R |only
diversitree-0.9-3/diversitree/R/mcmc-hmc.R | 7
diversitree-0.9-3/diversitree/R/mcmc.R | 45 +
diversitree-0.9-3/diversitree/R/mle-methods.R |only
diversitree-0.9-3/diversitree/R/mle-mixed.R | 13
diversitree-0.9-3/diversitree/R/mle.R | 196 +----
diversitree-0.9-3/diversitree/R/model-bd-nee.R | 136 +--
diversitree-0.9-3/diversitree/R/model-bd-ode.R | 112 +--
diversitree-0.9-3/diversitree/R/model-bd-split.R | 155 +---
diversitree-0.9-3/diversitree/R/model-bd-t.R | 79 --
diversitree-0.9-3/diversitree/R/model-bd.R | 231 +++---
diversitree-0.9-3/diversitree/R/model-bisse-split.R | 142 ---
diversitree-0.9-3/diversitree/R/model-bisse-t.R | 73 -
diversitree-0.9-3/diversitree/R/model-bisse-td.R | 88 --
diversitree-0.9-3/diversitree/R/model-bisse.R | 309 +++-----
diversitree-0.9-3/diversitree/R/model-bisseness.R | 431 +++--------
diversitree-0.9-3/diversitree/R/model-bm-pruning.R |only
diversitree-0.9-3/diversitree/R/model-bm-vcv.R | 81 --
diversitree-0.9-3/diversitree/R/model-bm.R | 113 +--
diversitree-0.9-3/diversitree/R/model-classe.R | 443 +++++-------
diversitree-0.9-3/diversitree/R/model-geosse-split.R | 136 ---
diversitree-0.9-3/diversitree/R/model-geosse.R | 266 ++-----
diversitree-0.9-3/diversitree/R/model-linear-deriv.R | 59 -
diversitree-0.9-3/diversitree/R/model-mkn-exp.R | 206 +----
diversitree-0.9-3/diversitree/R/model-mkn-multitrait.R | 148 ++--
diversitree-0.9-3/diversitree/R/model-mkn-ode.R | 129 ---
diversitree-0.9-3/diversitree/R/model-mkn.R | 292 +++----
diversitree-0.9-3/diversitree/R/model-musse-multitrait.R | 208 ++---
diversitree-0.9-3/diversitree/R/model-musse-split.R | 118 ---
diversitree-0.9-3/diversitree/R/model-musse-t.R | 136 +--
diversitree-0.9-3/diversitree/R/model-musse-td.R | 96 --
diversitree-0.9-3/diversitree/R/model-musse.R | 252 ++----
diversitree-0.9-3/diversitree/R/model-ou-pruning.R |only
diversitree-0.9-3/diversitree/R/model-ou-vcv.R |only
diversitree-0.9-3/diversitree/R/model-ou.R | 162 +---
diversitree-0.9-3/diversitree/R/model-quasse-common.R | 101 ++
diversitree-0.9-3/diversitree/R/model-quasse-fftC.R | 4
diversitree-0.9-3/diversitree/R/model-quasse-fftR.R | 2
diversitree-0.9-3/diversitree/R/model-quasse-mol.R | 2
diversitree-0.9-3/diversitree/R/model-quasse-split.R | 269 ++-----
diversitree-0.9-3/diversitree/R/model-quasse.R | 333 +++------
diversitree-0.9-3/diversitree/R/plot-alt-extra.R | 64 +
diversitree-0.9-3/diversitree/R/plot-alt.R | 10
diversitree-0.9-3/diversitree/R/profiles-plot.R | 13
diversitree-0.9-3/diversitree/R/sim-character.R | 58 +
diversitree-0.9-3/diversitree/R/simulate-bisse.R | 28
diversitree-0.9-3/diversitree/R/simulate-bisseness.R |only
diversitree-0.9-3/diversitree/R/simulate-classe.R |only
diversitree-0.9-3/diversitree/R/simulate-geosse.R |only
diversitree-0.9-3/diversitree/R/simulate-musse.R | 3
diversitree-0.9-3/diversitree/R/simulation.R | 6
diversitree-0.9-3/diversitree/R/split.R | 358 +++++----
diversitree-0.9-3/diversitree/R/t.R | 199 +++--
diversitree-0.9-3/diversitree/R/td.R | 85 +-
diversitree-0.9-3/diversitree/R/util-tree.R |only
diversitree-0.9-3/diversitree/R/util.R | 328 ++------
diversitree-0.9-3/diversitree/TODO |only
diversitree-0.9-3/diversitree/configure | 20
diversitree-0.9-3/diversitree/configure.ac | 19
diversitree-0.9-3/diversitree/man/argnames.Rd | 6
diversitree-0.9-3/diversitree/man/asr.Rd | 2
diversitree-0.9-3/diversitree/man/combine.Rd |only
diversitree-0.9-3/diversitree/man/constrain.Rd | 41 +
diversitree-0.9-3/diversitree/man/diversitree-deprecated.Rd | 10
diversitree-0.9-3/diversitree/man/make.bd.Rd | 23
diversitree-0.9-3/diversitree/man/make.bd.split.Rd | 11
diversitree-0.9-3/diversitree/man/make.bd.t.Rd | 3
diversitree-0.9-3/diversitree/man/make.bisse.Rd | 7
diversitree-0.9-3/diversitree/man/make.bisse.split.Rd | 18
diversitree-0.9-3/diversitree/man/make.bisse.td.Rd | 5
diversitree-0.9-3/diversitree/man/make.bisseness.Rd | 3
diversitree-0.9-3/diversitree/man/make.bm.Rd | 23
diversitree-0.9-3/diversitree/man/make.clade.tree.Rd | 4
diversitree-0.9-3/diversitree/man/make.classe.Rd | 21
diversitree-0.9-3/diversitree/man/make.geosse.Rd | 39 -
diversitree-0.9-3/diversitree/man/make.geosse.split.Rd | 3
diversitree-0.9-3/diversitree/man/make.mkn.Rd | 5
diversitree-0.9-3/diversitree/man/make.mkn.deriv.Rd | 9
diversitree-0.9-3/diversitree/man/make.musse.Rd | 5
diversitree-0.9-3/diversitree/man/make.musse.multitrait.Rd | 5
diversitree-0.9-3/diversitree/man/make.musse.split.Rd | 5
diversitree-0.9-3/diversitree/man/make.musse.td.Rd | 3
diversitree-0.9-3/diversitree/man/make.quasse.Rd | 10
diversitree-0.9-3/diversitree/man/make.quasse.split.Rd | 10
diversitree-0.9-3/diversitree/man/mcmc.Rd | 4
diversitree-0.9-3/diversitree/man/profiles.plot.Rd | 19
diversitree-0.9-3/diversitree/man/set.defaults.Rd |only
diversitree-0.9-3/diversitree/man/sim.character.Rd | 3
diversitree-0.9-3/diversitree/man/simulate.Rd | 29
diversitree-0.9-3/diversitree/man/time.Rd | 9
diversitree-0.9-3/diversitree/man/trait.plot.Rd | 12
diversitree-0.9-3/diversitree/src/continuous.c |only
diversitree-0.9-3/diversitree/src/continuous.h |only
diversitree-0.9-3/diversitree/src/cvodes_all_branches.c | 18
diversitree-0.9-3/diversitree/src/cvodes_all_branches.h | 1
diversitree-0.9-3/diversitree/src/cvodes_asr_marginal.c | 2
diversitree-0.9-3/diversitree/src/mkn.c | 14
diversitree-0.9-3/diversitree/src/util.c | 101 ++
diversitree-0.9-3/diversitree/src/util.h | 1
122 files changed, 3780 insertions(+), 4905 deletions(-)
Title: Dive analysis and calibration
Diff between diveMove versions 1.3.3 dated 2012-04-05 and 1.3.4 dated 2012-05-08
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 | 37 +++++++++++++++++++++++++++++++++++++
DESCRIPTION | 6 +++---
MD5 | 38 +++++++++++++++++++-------------------
NEWS | 14 ++++++++++++++
R/AllMethod.R | 8 ++++----
R/calibrate.R | 4 ++--
R/diveStats.R | 21 +++++++++++++--------
R/oneDiveStats.R | 4 ++--
R/plotTDR.R | 4 ++--
R/stampDive.R | 16 ++++++++--------
inst/doc/diveMove.Rnw | 6 +++---
inst/doc/diveMove.pdf |binary
man/bout-misc.Rd | 4 ++--
man/bouts2MLE.Rd | 4 ++--
man/bouts2NLS.Rd | 4 ++--
man/calibrateDepth.Rd | 7 ++++---
man/diveMove-internal.Rd | 11 ++++++-----
man/diveMove-package.Rd | 4 ++--
man/diveStats.Rd | 8 ++++----
man/plotZOC-methods.Rd | 2 +-
20 files changed, 130 insertions(+), 72 deletions(-)
Title: The bee swarm plot, an alternative to stripchart
Diff between beeswarm versions 0.1.1 dated 2011-08-04 and 0.1.5 dated 2012-05-08
Description: The bee swarm plot is a one-dimensional scatter plot like
"stripchart", but with closely-packed, non-overlapping points.
Author: Aron Eklund
Maintainer: Aron Eklund
DESCRIPTION | 8 ++---
MD5 |only
NAMESPACE |only
NEWS | 85 +++++++++++++++++---------------------------------------
R/beeswarm.R | 62 ++++++++++++++++++++++++++--------------
R/bxplot.R |only
R/zzz.R |only
man/beeswarm.Rd | 58 +++++++++++++++++++++++++-------------
man/bxplot.Rd |only
man/swarmx.Rd | 6 +--
10 files changed, 112 insertions(+), 107 deletions(-)
Title: Block, assign, and diagnose potential interference in randomized
experiments
Diff between blockTools versions 0.5-3 dated 2011-03-05 and 0.5-4 dated 2012-05-08
Description: Blocks units into experimental blocks, with one unit per
treatment condition, by creating a measure of multivariate
distance between all possible pairs of units. Maximum,
minimum, or an allowable range of differences between units on
one variable can be set. Randomly assign units to treatment
conditions. Diagnose potential interference between units
assigned to different treatment conditions. Write outputs to
.tex and .csv files.
Author: Ryan T. Moore
Maintainer: Ryan T. Moore
CHANGELOG | 4 ++++
DESCRIPTION | 8 ++++----
LICENSE | 2 +-
MD5 |only
R/outCSV.R | 10 ++++++++--
R/outTeX.R | 24 ++++++++++++++++++------
demo/outCSV.R | 2 ++
demo/outTeX.R | 3 +++
man/blockTools-package.Rd | 4 ++--
man/outCSV.Rd | 15 ++++++++++-----
man/outTeX.Rd | 31 ++++++++++++++++++++++++-------
11 files changed, 76 insertions(+), 27 deletions(-)