Title: Conjugate gradient minimization of nonlinear functions with box
constraints
Diff between Rcgmin versions 2011-2.101 dated 2011-10-18 and 2012-8.08 dated 2012-08-08
Description: Conjugate gradient minimization of nonlinear functions
with box constraints incorporating Dai/Yuan update
Author: John C. Nash
Maintainer: John C. Nash
Rcgmin-2011-2.101/Rcgmin/R/optansout.R |only
Rcgmin-2011-2.101/Rcgmin/man/optansout.Rd |only
Rcgmin-2012-8.08/Rcgmin/DESCRIPTION | 7
Rcgmin-2012-8.08/Rcgmin/FLAGS |only
Rcgmin-2012-8.08/Rcgmin/MD5 | 27 -
Rcgmin-2012-8.08/Rcgmin/Makefile |only
Rcgmin-2012-8.08/Rcgmin/NAMESPACE | 3
Rcgmin-2012-8.08/Rcgmin/NEWS |only
Rcgmin-2012-8.08/Rcgmin/R/Rcgmin.R | 578 ++++------------------------
Rcgmin-2012-8.08/Rcgmin/R/Rcgminb.R |only
Rcgmin-2012-8.08/Rcgmin/R/Rcgminu.R |only
Rcgmin-2012-8.08/Rcgmin/demo/broydt_test.R | 128 +++---
Rcgmin-2012-8.08/Rcgmin/demo/cyq_test.R | 148 +++----
Rcgmin-2012-8.08/Rcgmin/demo/genrose_test.R | 145 +++----
Rcgmin-2012-8.08/Rcgmin/man/Rcgmin.Rd | 142 +++++-
Rcgmin-2012-8.08/Rcgmin/man/Rcgminb.Rd |only
Rcgmin-2012-8.08/Rcgmin/man/Rcgminu.Rd |only
17 files changed, 465 insertions(+), 713 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.1-8 dated 2012-05-02 and 0.1-9 dated 2012-08-08
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 10 ++---
MD5 | 32 ++++++++++++-----
NAMESPACE | 12 +++---
R/anc.ML.R | 2 -
R/drop.tip.simmap.R | 85 +++++++++++++++++++++++++++++++++++-----------
R/evolvcv.lite.R | 73 ++++++++++++++++++++++-----------------
R/export.as.xml.R |only
R/fancyTree.R |only
R/findMRCA.R | 15 +++++++-
R/pgls.Ives.R |only
R/phylomorphospace3d.R |only
R/rescaleSimmap.R |only
R/sim.corrs.R |only
man/anc.Bayes.Rd | 2 -
man/drop.tip.simmap.Rd | 11 ++---
man/export.as.xml.Rd |only
man/fancyTree.Rd |only
man/fastMRCA.Rd |only
man/gammatest.Rd | 2 -
man/multiC.Rd |only
man/pgls.Ives.Rd |only
man/phylomorphospace3d.Rd |only
man/rescaleSimmap.Rd |only
man/sim.corrs.Rd |only
24 files changed, 162 insertions(+), 82 deletions(-)
Title: Miscellaneous 3D Plots
Diff between misc3d versions 0.8-2 dated 2012-02-04 and 0.8-3 dated 2012-08-08
Description: A collection of miscellaneous 3d plots, including
isosurfaces.
Author: Dai Feng and Luke Tierney
Maintainer: Luke Tierney
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/image3d.R | 19 ++++++++++++-------
3 files changed, 17 insertions(+), 12 deletions(-)
Title: Automating Mplus Model Estimation and Interpretation
Diff between MplusAutomation versions 0.5-2 dated 2012-07-12 and 0.5-3 dated 2012-08-08
More information about MplusAutomation at CRAN
Description: The MplusAutomation package leverages the flexibility of
the R language to automate latent variable model estimation and
interpretation using Mplus, a powerful latent variable modeling
program developed by Muthen and Muthen (www.statmodel.com).
Specifically, MplusAutomation provides routines for creating
related groups of models, running batches of models, and
extracting and tabulating model parameters and fit statistics.
Author: Michael Hallquist
Maintainer: Michael Hallquist
DESCRIPTION | 8 +--
MD5 | 27 +++++------
NAMESPACE | 3 -
NEWS | 12 ++++-
R/extractSaveData.R | 18 ++++++-
R/graphModels.R | 85 ++++++++++++++++++++++++++++++++++++
R/parseOutput.R | 83 ++++++++++++++++++++++++++++++++---
R/runModels.R | 3 -
R/utilityFunctions.R | 29 +++++++++++-
inst/doc/Vignette.Rnw | 4 -
inst/doc/Vignette.pdf |binary
man/MplusAutomation-package.Rd | 4 -
man/mplus.traceplot.Rd |only
man/testBParamCompoundConstraint.Rd | 16 ++++--
man/testBParamConstraint.Rd | 13 +++--
15 files changed, 260 insertions(+), 45 deletions(-)
Permanent link
Title: Rcpp bindings for the Boost Date_Time library
Diff between RcppBDT versions 0.2.0 dated 2012-07-03 and 0.2.1 dated 2012-08-08
Description: This package provides R with access to Boost Date_Time
functionality by using Rcpp modules.
Currently only Date functionality is covered.
Boost header files are needed to build the package. Linking is optional
to provide supplementary date to/from strings conversion
functions.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/bdt.R | 4 +++-
inst/NEWS.Rd | 7 +++++++
5 files changed, 23 insertions(+), 9 deletions(-)
Title: An R client for the OGC Sensor Observation Service
Diff between sos4R versions 0.2-7 dated 2011-12-02 and 0.2-9 dated 2012-08-08
Description: sos4R is a client for Sensor Observation Services (SOS) as
specified by the Open Geospatial Consortium (OGC). It allows
users to retrieve metadata from SOS web services and to
interactively create requests for near real-time observation
data based on the available sensors, phenomena, observations et
cetera using thematic, temporal and spatial filtering.
Author: Daniel Nuest [cre, aut]
Maintainer: Daniel Nuest
sos4R-0.2-7/sos4R/inst/doc/err.response.RData |only
sos4R-0.2-7/sos4R/inst/doc/exceptionResponse.RData |only
sos4R-0.2-7/sos4R/inst/doc/mbari.RData |only
sos4R-0.2-7/sos4R/inst/doc/mbari2.RData |only
sos4R-0.2-7/sos4R/inst/doc/mbariObs1.xml |only
sos4R-0.2-7/sos4R/inst/doc/mbariObs2.xml |only
sos4R-0.2-7/sos4R/inst/doc/mySOS.RData |only
sos4R-0.2-7/sos4R/inst/doc/mySOS2.RData |only
sos4R-0.2-7/sos4R/inst/doc/mySOS2.disabled.RData |only
sos4R-0.2-7/sos4R/inst/doc/mySensor.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.oneWeek.filter.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.oneWeek.fois.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.oneWeek.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.sept09.bbox.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.sept09.xml |only
sos4R-0.2-7/sos4R/inst/doc/obs.temp.xml |only
sos4R-0.2-7/sos4R/inst/doc/obsId.xml |only
sos4R-0.2-7/sos4R/inst/doc/procs.descr.RData |only
sos4R-0.2-7/sos4R/sandbox/belgrade.R |only
sos4R-0.2-9/sos4R/DESCRIPTION | 35
sos4R-0.2-9/sos4R/MD5 | 91 +-
sos4R-0.2-9/sos4R/R/Defaults.R | 158 ++--
sos4R-0.2-9/sos4R/R/SML-methods-coercion.R | 11
sos4R-0.2-9/sos4R/R/SML-methods-util.R | 48 +
sos4R-0.2-9/sos4R/R/SML-methods.R | 16
sos4R-0.2-9/sos4R/R/SOS-methods-accessor.R | 1
sos4R-0.2-9/sos4R/R/SOS-methods-coercion.R | 3
sos4R-0.2-9/sos4R/R/SOS-methods-plotting.R | 9
sos4R-0.2-9/sos4R/R/SOS-methods-util.R | 49 -
sos4R-0.2-9/sos4R/R/SOS-methods.R | 3
sos4R-0.2-9/sos4R/demo/00Index | 1
sos4R-0.2-9/sos4R/demo/co-ops.R |only
sos4R-0.2-9/sos4R/demo/coastlab.R | 4
sos4R-0.2-9/sos4R/demo/eo2heaven.R | 17
sos4R-0.2-9/sos4R/demo/ioos.R | 24
sos4R-0.2-9/sos4R/demo/southesk.R | 800 ++++++++++-----------
sos4R-0.2-9/sos4R/demo/weathersos.R | 66 +
sos4R-0.2-9/sos4R/inst/NEWS | 18
sos4R-0.2-9/sos4R/inst/doc/sos4R.Rnw | 136 ++-
sos4R-0.2-9/sos4R/inst/doc/sos4R.pdf |binary
sos4R-0.2-9/sos4R/inst/doc/sos4r_cheat-sheet.pdf |binary
sos4R-0.2-9/sos4R/man/Defaults.Rd | 11
sos4R-0.2-9/sos4R/man/sos4R-package.Rd | 9
sos4R-0.2-9/sos4R/sandbox/loadSources.R | 82 +-
sos4R-0.2-9/sos4R/sandbox/mailinglist-support.R | 71 +
sos4R-0.2-9/sos4R/sandbox/testing-SOSs.R | 86 ++
sos4R-0.2-9/sos4R/sos4R-Ex.R | 6
sos4R-0.2-9/sos4R/vignettes |only
48 files changed, 1052 insertions(+), 703 deletions(-)
Title: Visualizing Hypothesis Tests in Multivariate Linear Models
Diff between heplots versions 0.9-12 dated 2012-05-17 and 1.0-0 dated 2012-08-08
Description: Provides HE plot functions for visualizing hypothesis
tests in multivariate linear models. They represents
sums-of-squares-and-products matrices for linear hypotheses and
for error using ellipses (in two dimensions) and ellipsoids (in
three dimensions).
Author: John Fox, Michael Friendly, and Georges Monette
Maintainer: Michael Friendly
heplots-0.9-12/heplots/.project |only
heplots-0.9-12/heplots/inst/doc/HE-examples.bib |only
heplots-0.9-12/heplots/inst/doc/fig |only
heplots-0.9-12/heplots/inst/doc/plastic1-HE3D.jpg |only
heplots-0.9-12/heplots/inst/doc/repeated.bib |only
heplots-0.9-12/heplots/inst/doc/rohwer-HE3D.png |only
heplots-0.9-12/heplots/inst/doc/skulls.jpg |only
heplots-1.0-0/heplots/DESCRIPTION | 8
heplots-1.0-0/heplots/MD5 | 67 --
heplots-1.0-0/heplots/NEWS | 7
heplots-1.0-0/heplots/data/Oslo.RData |only
heplots-1.0-0/heplots/demo/OBK.R | 4
heplots-1.0-0/heplots/inst/doc/HE-examples.Rnw | 567 +++++++++++++++++++++-
heplots-1.0-0/heplots/inst/doc/HE-examples.pdf |binary
heplots-1.0-0/heplots/inst/doc/repeated.pdf |binary
heplots-1.0-0/heplots/man/Oslo.Rd |only
heplots-1.0-0/heplots/man/heplot-package.Rd | 4
heplots-1.0-0/heplots/vignettes |only
18 files changed, 584 insertions(+), 73 deletions(-)
Title: Wildlife Sightability Modeling
Diff between SightabilityModel versions 1.0 dated 2012-05-12 and 1.1 dated 2012-08-08
More information about SightabilityModel at CRAN
Description: Uses logistic regression to model the probability of
detection as a function of covariates. This model is then used
with observational survey data to estimate population size,
while accounting for uncertain detection. See Steinhorst and
Samuel (1989).
Author: John Fieberg
Maintainer: John Fieberg
SightabilityModel-1.0/SightabilityModel/INDEX |only
SightabilityModel-1.1/SightabilityModel/DESCRIPTION | 8
SightabilityModel-1.1/SightabilityModel/MD5 | 55 +-
SightabilityModel-1.1/SightabilityModel/NAMESPACE | 5
SightabilityModel-1.1/SightabilityModel/R/SS.est.R | 197 ++++----
SightabilityModel-1.1/SightabilityModel/R/Sight.Est.R | 201 ++++----
SightabilityModel-1.1/SightabilityModel/R/Wong.est.R | 246 ++++------
SightabilityModel-1.1/SightabilityModel/R/covtheta.R | 60 +-
SightabilityModel-1.1/SightabilityModel/R/print.sightest.R | 76 +--
SightabilityModel-1.1/SightabilityModel/R/summary.sightest.R | 38 -
SightabilityModel-1.1/SightabilityModel/R/vardiff.R | 96 +--
SightabilityModel-1.1/SightabilityModel/R/varlog.lam.R | 95 +--
SightabilityModel-1.1/SightabilityModel/data/gdat.rda |binary
SightabilityModel-1.1/SightabilityModel/inst |only
SightabilityModel-1.1/SightabilityModel/man/SS.est.Rd | 6
SightabilityModel-1.1/SightabilityModel/man/Sight.Est.Rd | 109 ++--
SightabilityModel-1.1/SightabilityModel/man/SightabilityModel-package.Rd | 14
SightabilityModel-1.1/SightabilityModel/man/Wong.est.Rd | 5
SightabilityModel-1.1/SightabilityModel/man/covtheta.Rd | 32 -
SightabilityModel-1.1/SightabilityModel/man/exp.m.Rd | 4
SightabilityModel-1.1/SightabilityModel/man/g.fit.Rd | 2
SightabilityModel-1.1/SightabilityModel/man/gdat.Rd | 6
SightabilityModel-1.1/SightabilityModel/man/obs.m.Rd | 6
SightabilityModel-1.1/SightabilityModel/man/print.sightest.Rd | 8
SightabilityModel-1.1/SightabilityModel/man/sampinfo.m.Rd | 5
SightabilityModel-1.1/SightabilityModel/man/summary.sightest.Rd | 6
SightabilityModel-1.1/SightabilityModel/man/vardiff.Rd | 27 -
SightabilityModel-1.1/SightabilityModel/man/varlog.lam.Rd | 24
28 files changed, 659 insertions(+), 672 deletions(-)
Permanent link
Title: Functions for plotting graphical shapes, colors
Diff between shape versions 1.3.4 dated 2011-08-11 and 1.4.0 dated 2012-08-08
Description: Functions for plotting graphical shapes such as ellipses,
circles, cylinders, arrows, ...
Author: Karline Soetaert
Maintainer: Karline Soetaert
shape-1.3.4/shape/inst/doc/jss.bst |only
shape-1.3.4/shape/inst/doc/jss.cls |only
shape-1.4.0/shape/DESCRIPTION | 19 +++------
shape-1.4.0/shape/MD5 | 62 ++++++++++++++----------------
shape-1.4.0/shape/R/Arrows.R | 6 +-
shape-1.4.0/shape/R/drapecol.R | 5 +-
shape-1.4.0/shape/demo/colorshapes.r | 4 -
shape-1.4.0/shape/inst/doc/shape.Rnw | 12 ++---
shape-1.4.0/shape/inst/doc/shape.pdf |binary
shape-1.4.0/shape/man/A4.Rd | 4 -
shape-1.4.0/shape/man/Arrowhead.Rd | 2
shape-1.4.0/shape/man/Arrows.Rd | 8 +--
shape-1.4.0/shape/man/colorlegend.Rd | 2
shape-1.4.0/shape/man/cylindersegment.Rd | 2
shape-1.4.0/shape/man/drapecol.Rd | 6 +-
shape-1.4.0/shape/man/emptyplot.Rd | 2
shape-1.4.0/shape/man/femmecol.Rd | 2
shape-1.4.0/shape/man/filledcircle.Rd | 2
shape-1.4.0/shape/man/filledcylinder.Rd | 2
shape-1.4.0/shape/man/filledellipse.Rd | 2
shape-1.4.0/shape/man/filledmultigonal.Rd | 2
shape-1.4.0/shape/man/filledrectangle.Rd | 2
shape-1.4.0/shape/man/filledshape.Rd | 2
shape-1.4.0/shape/man/getellipse.Rd | 2
shape-1.4.0/shape/man/greycol.Rd | 2
shape-1.4.0/shape/man/intpalette.Rd | 2
shape-1.4.0/shape/man/plotcircle.Rd | 2
shape-1.4.0/shape/man/plotellipse.Rd | 2
shape-1.4.0/shape/man/rotatexy.Rd | 2
shape-1.4.0/shape/man/roundrect.Rd | 2
shape-1.4.0/shape/man/shadepalette.Rd | 2
shape-1.4.0/shape/man/textflag.Rd | 2
shape-1.4.0/shape/man/writelabel.Rd | 2
33 files changed, 81 insertions(+), 87 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Diff between Rmpi versions 0.5-9 dated 2010-11-30 and 0.6-0 dated 2012-08-08
Description: Rmpi provides an interface (wrapper) to MPI APIs. It also
provides interactive R slave environment.
Author: Hao Yu
Maintainer: Hao Yu
Rmpi-0.5-9/Rmpi/man/mpi.init.sprng.Rd |only
Rmpi-0.6-0/Rmpi/DESCRIPTION | 12
Rmpi-0.6-0/Rmpi/INDEX | 2
Rmpi-0.6-0/Rmpi/MD5 |only
Rmpi-0.6-0/Rmpi/NAMESPACE |only
Rmpi-0.6-0/Rmpi/R/Rcoll.R | 8
Rmpi-0.6-0/Rmpi/R/Rcomm.R | 7
Rmpi-0.6-0/Rmpi/R/Rng.R | 85
Rmpi-0.6-0/Rmpi/R/Rparutilities.R | 50
Rmpi-0.6-0/Rmpi/README | 3
Rmpi-0.6-0/Rmpi/configure | 4193 ++++++++++++++-----------------
Rmpi-0.6-0/Rmpi/configure.ac | 9
Rmpi-0.6-0/Rmpi/demo/00Index | 4
Rmpi-0.6-0/Rmpi/demo/simPI.R | 1
Rmpi-0.6-0/Rmpi/man/mpi.comm.spawn.Rd | 5
Rmpi-0.6-0/Rmpi/man/mpi.gather.Robj.Rd | 9
Rmpi-0.6-0/Rmpi/man/mpi.parSim.Rd | 6
Rmpi-0.6-0/Rmpi/man/mpi.remote.exec.Rd | 3
Rmpi-0.6-0/Rmpi/man/mpi.setup.rng.Rd | 24
Rmpi-0.6-0/Rmpi/man/mpi.spawn.Rslaves.Rd | 5
Rmpi-0.6-0/Rmpi/src/Rmpi.c | 15
21 files changed, 2031 insertions(+), 2410 deletions(-)
Title: Johnson Transformation
Diff between Johnson versions 1.2 dated 2012-03-24 and 1.3 dated 2012-08-08
Description: RE.Johnson perform the Johnson Transformation for achieve
normality.
Author: Edgar Santos Fernandez
Maintainer: Edgar Santos Fernandez
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/RE.ADT.R | 25 ++++++++++++-------------
R/RE.Johnson.R | 6 ++++++
man/Johnson-package.Rd | 20 ++++++++++----------
man/RE.ADT.Rd | 12 ++++++------
man/RE.Johnson.Rd | 12 ++++++------
7 files changed, 50 insertions(+), 45 deletions(-)
Title: "A practical guide to ecological modelling - using R as a
simulation platform"
Diff between ecolMod versions 1.2.3 dated 2011-03-23 and 1.2.4 dated 2012-08-08
Description: Figures, data sets and examples from the book "A practical
guide to ecological modelling - using R as a simulation
platform" by Karline Soetaert and Peter MJ Herman (2009).
Springer. All figures from chapter x can be generated by
"demo(chapx)", where x = 1 to 11. The R-scripts of the model
examples discussed in the book are in subdirectory "examples",
ordered per chapter. Solutions to model projects are in the
same subdirectories.
Author: Karline Soetaert
Maintainer: Karline Soetaert
ecolMod-1.2.3/ecolMod/inst/doc/examples |only
ecolMod-1.2.4/ecolMod/DESCRIPTION | 22 ++++++--------
ecolMod-1.2.4/ecolMod/MD5 |only
ecolMod-1.2.4/ecolMod/demo/chap1.r | 2 -
ecolMod-1.2.4/ecolMod/demo/chap11.r | 6 ++--
ecolMod-1.2.4/ecolMod/demo/chap2.r | 28 +++++++++---------
ecolMod-1.2.4/ecolMod/demo/chap4.r | 4 +-
ecolMod-1.2.4/ecolMod/demo/chap5.r | 8 ++---
ecolMod-1.2.4/ecolMod/demo/chap6.r | 36 ++++++++++++------------
ecolMod-1.2.4/ecolMod/demo/chap7.r | 2 -
ecolMod-1.2.4/ecolMod/demo/chap8.r | 6 ++--
ecolMod-1.2.4/ecolMod/inst/doc/StabilityFig.pdf |binary
ecolMod-1.2.4/ecolMod/inst/doc/ecolMod.Rnw | 12 +++-----
ecolMod-1.2.4/ecolMod/inst/doc/ecolMod.pdf |binary
ecolMod-1.2.4/ecolMod/inst/examples |only
ecolMod-1.2.4/ecolMod/man/OMEXDIAsteady.Rd | 2 -
ecolMod-1.2.4/ecolMod/man/SCOC.Rd | 2 -
ecolMod-1.2.4/ecolMod/man/Zoogrowth.Rd | 2 -
ecolMod-1.2.4/ecolMod/man/deepCmin.Rd | 2 -
ecolMod-1.2.4/ecolMod/man/dilution.Rd | 2 -
ecolMod-1.2.4/ecolMod/man/pricefit.Rd | 2 -
21 files changed, 67 insertions(+), 71 deletions(-)
Title: OCI based Oracle database interface for R
Diff between ROracle versions 1.1-3 dated 2012-07-21 and 1.1-4 dated 2012-08-08
Description: Oracle database interface (DBI) driver for R. This is a
DBI-compliant Oracle driver based on the OCI.
Author: Denis Mukhin, David A. James and Jake Luciani
Maintainer: Denis Mukhin
DESCRIPTION | 8 ++---
INSTALL | 14 ++++-----
MD5 | 12 ++++----
NEWS | 4 ++
src/rodbi.c | 90 +++++++++++++++++++++++++++++++++++++++++++++++++++++-------
src/rooci.c | 3 +-
src/rooci.h | 2 -
7 files changed, 104 insertions(+), 29 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 1.0-0 dated 2012-02-27 and 1.0-2 dated 2012-08-08
Description: A package for probability propagation in graphical
independence networks, also known as probabilistic expert
systems or Bayesian networks.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRain-1.0-0/gRain/.Rbuildindex.3356 |only
gRain-1.0-0/gRain/inst/doc |only
gRain-1.0-0/gRain/vignettes |only
gRain-1.0-2/gRain/ChangeLog | 26 +
gRain-1.0-2/gRain/DESCRIPTION | 12
gRain-1.0-2/gRain/MD5 | 50 +-
gRain-1.0-2/gRain/R/compile-grain.R | 83 ++--
gRain-1.0-2/gRain/R/compileCPT.R | 107 ++++--
gRain-1.0-2/gRain/R/grain-main.R | 18 -
gRain-1.0-2/gRain/R/propagate.R | 4
gRain-1.0-2/gRain/R/summary.R | 2
gRain-1.0-2/gRain/gRain-Ex.R | 507 +++++++++++++++---------------
gRain-1.0-2/gRain/man/andtable.Rd | 2
gRain-1.0-2/gRain/man/compile.grain.Rd | 2
gRain-1.0-2/gRain/man/compileCPT.Rd | 9
gRain-1.0-2/gRain/man/cptable.Rd | 2
gRain-1.0-2/gRain/man/extractCPT.Rd | 2
gRain-1.0-2/gRain/man/gRain-package.Rd | 4
gRain-1.0-2/gRain/man/grain.Rd | 52 +--
gRain-1.0-2/gRain/man/loadSaveHuginNet.Rd | 2
gRain-1.0-2/gRain/man/predict.Rd | 2
gRain-1.0-2/gRain/man/propagate.grain.Rd | 2
gRain-1.0-2/gRain/man/querygrain.Rd | 2
gRain-1.0-2/gRain/man/repeatPattern.Rd | 4
gRain-1.0-2/gRain/man/simulate.Rd | 2
25 files changed, 474 insertions(+), 422 deletions(-)
Title: Identification of dichotomous differential item functioning
(DIF) using Angoff's Delta Plot method
Diff between deltaPlotR versions 1.0 dated 2012-06-01 and 1.1 dated 2012-08-08
Description: The deltaPlotR package proposes an implementation of
Angoff's Delta Plot method to detect dichotomous DIF. Several
detection thresholds are included, either from multivariate
normality assumption or by prior determination. Item
purification is supported.
Author: David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France)
Maintainer: David Magis
DESCRIPTION | 16 ++++++++--------
MD5 | 10 +++++-----
NEWS | 13 ++++++-------
inst/CITATION | 4 ++--
inst/doc/deltaPlotR-manual.pdf |binary
man/deltaPlot.Rd | 3 +--
6 files changed, 22 insertions(+), 24 deletions(-)
Title: AquaEnv - an integrated development toolbox for aquatic chemical
model generation
Diff between AquaEnv versions 1.0-2 dated 2011-04-06 and 1.0-3 dated 2012-08-08
Description: AquaEnv is an integrated development toolbox for aquatic
chemical model generation focused on (ocean) acidification and
CO2 air-water exchange. It contains all elements necessary to
model the pH, the related CO2 air-water exchange, as well as
aquatic acid-base chemistry in general for an arbitrary marine,
estuarine or freshwater system. Also chemical batches can be
modelled. Next to the routines necessary to calculate desired
information, AquaEnv also contains a suite of tools to
visualize this information. Furthermore, AquaEnv can not only
be used to build dynamic models of aquatic systems, but it can
also serve as a simple desktop tool for the experimental
aquatic chemist to generate and visualize all possible derived
information from a set of measurements with one single easy to
use R function. Additionally, the sensitivity of the system to
variations in the input variables can be visualized. The
corresponding publication in Aquatic Geochemistry can be found
at http://www.springerlink.com/content/l4747417w0k50463/
Author: Andreas F. Hofmann, Karline Soetaert, Filip J.R. Meysman
Maintainer: Andreas F. Hofmann
AquaEnv-1.0-2/AquaEnv/inst/doc/AquaEnv-ConstantsAndFormulae.tex |only
AquaEnv-1.0-2/AquaEnv/inst/doc/AquaEnv-PrivateFunctions.tex |only
AquaEnv-1.0-2/AquaEnv/inst/doc/AquaEnv.bib |only
AquaEnv-1.0-2/AquaEnv/inst/doc/AquaEnv.rnw |only
AquaEnv-1.0-2/AquaEnv/inst/doc/Makefile |only
AquaEnv-1.0-2/AquaEnv/inst/doc/jss.bst |only
AquaEnv-1.0-2/AquaEnv/inst/doc/jss.cls |only
AquaEnv-1.0-3/AquaEnv/DESCRIPTION | 21 ++++------
AquaEnv-1.0-3/AquaEnv/MD5 |only
AquaEnv-1.0-3/AquaEnv/data/sample_dickson1981.rda |binary
AquaEnv-1.0-3/AquaEnv/data/sample_dickson2007.rda |binary
AquaEnv-1.0-3/AquaEnv/inst/doc/AquaEnv-ConstantsAndFormulae.pdf |binary
AquaEnv-1.0-3/AquaEnv/inst/doc/AquaEnv-PrivateFunctions.pdf |binary
AquaEnv-1.0-3/AquaEnv/inst/doc/AquaEnv.pdf |binary
AquaEnv-1.0-3/AquaEnv/man/as.data.frame.aquaenv.Rd | 2
AquaEnv-1.0-3/AquaEnv/man/c.aquaenv.Rd | 2
AquaEnv-1.0-3/AquaEnv/man/length.aquaenv.Rd | 2
AquaEnv-1.0-3/AquaEnv/man/merge.aquaenv.Rd | 2
18 files changed, 13 insertions(+), 16 deletions(-)
Title: The sparr package: SPAtial Relative Risk
Diff between sparr versions 0.3-1 dated 2011-12-13 and 0.3-2 dated 2012-08-08
Description: Provides functions to estimate kernel-smoothed relative
risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: T.M.D.
sparr-0.3-1/sparr/NEWS |only
sparr-0.3-2/sparr/DESCRIPTION | 11 -
sparr-0.3-2/sparr/MD5 | 17 +-
sparr-0.3-2/sparr/R/LSCV.density.R | 2
sparr-0.3-2/sparr/R/LSCV.risk.R | 2
sparr-0.3-2/sparr/R/bivariate.density.R | 33 ++--
sparr-0.3-2/sparr/R/zzz.R | 2
sparr-0.3-2/sparr/man/risk.Rd | 241 ++++++++++++++++----------------
sparr-0.3-2/sparr/man/sparr-package.Rd | 10 -
sparr-0.3-2/sparr/man/tolerance.Rd | 224 ++++++++++++++---------------
10 files changed, 273 insertions(+), 269 deletions(-)
Title: Response Probability Functions
Diff between rpf versions 0.2 dated 2012-08-06 and 0.3 dated 2012-08-08
Description: The purpose of this package is to factor out logic and
math common to Item Response Theory fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for
more specialized IRT packages to build upon. A version 1.0 will
offer optimized, low-level functions to map parameters to
response probabilities for a wide variety of dichotomous and
polytomous item models.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb]
Maintainer: Joshua Pritikin
rpf-0.2/rpf/TODO |only
rpf-0.2/rpf/man/rpf.drm-class.Rd |only
rpf-0.2/rpf/man/rpf.gpcm-class.Rd |only
rpf-0.2/rpf/man/rpf.paramDim.Rd |only
rpf-0.3/rpf/DESCRIPTION | 10 -
rpf-0.3/rpf/MD5 | 48 ++++--
rpf-0.3/rpf/NAMESPACE | 11 +
rpf-0.3/rpf/R/classes.R | 229 ++++++++++++++++++++++-----------
rpf-0.3/rpf/R/drm.R | 127 ++++++++++++++----
rpf-0.3/rpf/R/gpcm.R | 113 ++++++++++++----
rpf-0.3/rpf/R/mcm.R |only
rpf-0.3/rpf/R/nrm.R |only
rpf-0.3/rpf/man/rpf.1dim.drm-class.Rd |only
rpf-0.3/rpf/man/rpf.1dim.gpcm-class.Rd |only
rpf-0.3/rpf/man/rpf.drm.Rd | 14 +-
rpf-0.3/rpf/man/rpf.getLocation.Rd | 8 -
rpf-0.3/rpf/man/rpf.gpcm.Rd | 11 +
rpf-0.3/rpf/man/rpf.introduction.Rd | 15 +-
rpf-0.3/rpf/man/rpf.logLik.Rd | 8 -
rpf-0.3/rpf/man/rpf.mcm.Rd |only
rpf-0.3/rpf/man/rpf.mdim.drm-class.Rd |only
rpf-0.3/rpf/man/rpf.mdim.gpcm-class.Rd |only
rpf-0.3/rpf/man/rpf.mdim.mcm-class.Rd |only
rpf-0.3/rpf/man/rpf.mdim.nrm-class.Rd |only
rpf-0.3/rpf/man/rpf.nrm.Rd |only
rpf-0.3/rpf/man/rpf.prob.Rd | 19 +-
rpf-0.3/rpf/man/rpf.prob.wrapper1.Rd |only
rpf-0.3/rpf/man/rpf.prob.wrapper2.Rd |only
rpf-0.3/rpf/man/rpf.rparam.Rd | 8 -
rpf-0.3/rpf/man/rpf.sample.Rd | 2
rpf-0.3/rpf/man/rpf.setLocation.Rd | 8 -
rpf-0.3/rpf/man/rpf.startingParam.Rd | 8 -
rpf-0.3/rpf/tests/plink.R | 47 ++++++
33 files changed, 499 insertions(+), 187 deletions(-)
Title: Parametric Time Warping
Diff between ptw versions 1.0-3 dated 2012-07-26 and 1.0-4 dated 2012-08-08
Description: Parametric Time Warping aligns patterns, i.e. it aims to
put corresponding features at the same locations. The algorithm
searches for an optimal polynomial describing the warping. It
is possible to align one sample to a reference, several samples
to the same reference, or several samples to several
references. One can choose between calculating individual
warpings, or one global warping for a set of samples and one
reference. Two optimization criteria are implemented: RMS (Root
Mean Square error) and WCC (Weighted Cross Correlation).
Author: Jan Gerretzen
Maintainer: Tom Bloemberg
COPYRIGHT.approx |only
DESCRIPTION | 12 ++++++------
MD5 | 8 +++++---
R/interpol.R | 2 +-
man/interpol.Rd | 10 +++++++++-
src/approx.c |only
6 files changed, 21 insertions(+), 11 deletions(-)
Title: Gaussian Copula Marginal Regression
Diff between gcmr versions 0.3 dated 2012-03-29 and 0.4 dated 2012-08-08
Description: likelihood inference in Gaussian copula marginal
regression models
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin
gcmr-0.3/gcmr/data/.Rhistory |only
gcmr-0.3/gcmr/man/hausman.Rd |only
gcmr-0.4/gcmr/DESCRIPTION | 9 -
gcmr-0.4/gcmr/MD5 | 23 +-
gcmr-0.4/gcmr/NAMESPACE | 7
gcmr-0.4/gcmr/R/cormat.R | 75 +++++---
gcmr-0.4/gcmr/R/gcmr.R | 34 +++-
gcmr-0.4/gcmr/R/marginals.R | 304 +++++++++++++++++++++++-------------
gcmr-0.4/gcmr/man/cluster.cormat.Rd | 7
gcmr-0.4/gcmr/man/gcmr.Rd | 4
gcmr-0.4/gcmr/man/gs.marg.Rd | 30 ++-
gcmr-0.4/gcmr/man/profile.gcmr.Rd | 8
gcmr-0.4/gcmr/man/residuals.gcmr.Rd | 2
gcmr-0.4/gcmr/man/se.Rd | 2
14 files changed, 316 insertions(+), 189 deletions(-)
Title: Coupled dipole approximation
Diff between cda versions 1.1.3 dated 2012-03-05 and 1.2 dated 2012-08-08
Description: Given a set of ellipsoidal nanoparticles (positions and
sizes), calculates the polarizability tensor for the dipoles
associated with each particle, and solves the coupled-dipole
equations by direct inversion of the interaction matrix.
Retardation is included in the interaction.
Author: baptiste Auguie
Maintainer: baptiste Auguie
cda-1.1.3/cda/man/array-module.Rd |only
cda-1.1.3/cda/man/cd-module.Rd |only
cda-1.1.3/cda/man/cda-module.Rd |only
cda-1.1.3/cda/man/linear-module.Rd |only
cda-1.1.3/cda/vignettes/axes.pov |only
cda-1.1.3/cda/vignettes/dimer-rgl.png |only
cda-1.1.3/cda/vignettes/euler.pov |only
cda-1.1.3/cda/vignettes/helix-rgl.png |only
cda-1.1.3/cda/vignettes/introduction-diffractive_chain.pdf |only
cda-1.1.3/cda/vignettes/introduction-dimer_cd.pdf |only
cda-1.1.3/cda/vignettes/introduction-dimer_linear.pdf |only
cda-1.1.3/cda/vignettes/introduction-helix_cd.pdf |only
cda-1.1.3/cda/vignettes/introduction-lattice_sum.pdf |only
cda-1.1.3/cda/vignettes/pos-dimer.pov |only
cda-1.1.3/cda/vignettes/pos-helix-ell.pov |only
cda-1.1.3/cda/vignettes/pos-helix.pov |only
cda-1.1.3/cda/vignettes/template-dimer.png |only
cda-1.1.3/cda/vignettes/template-dimer.pov |only
cda-1.1.3/cda/vignettes/template-helix-ell.png |only
cda-1.1.3/cda/vignettes/template-helix-ell.pov |only
cda-1.1.3/cda/vignettes/template-helix.png |only
cda-1.1.3/cda/vignettes/template-helix.pov |only
cda-1.2/cda/.Rinstignore | 3
cda-1.2/cda/DESCRIPTION | 6
cda-1.2/cda/MD5 | 121 +++++--------
cda-1.2/cda/NAMESPACE | 30 +++
cda-1.2/cda/NEWS | 12 +
cda-1.2/cda/R/array.factor.R | 2
cda-1.2/cda/R/cd.r | 12 -
cda-1.2/cda/R/cda-package.r | 89 +++++++++
cda-1.2/cda/R/epsilon.r | 4
cda-1.2/cda/R/linear.r | 62 ++++++
cda-1.2/cda/R/polarizability.R | 8
cda-1.2/cda/R/positions.R | 22 ++
cda-1.2/cda/R/povray.r | 4
cda-1.2/cda/R/rgl.r | 4
cda-1.2/cda/R/themes.r | 48 +----
cda-1.2/cda/demo/00Index | 1
cda-1.2/cda/demo/dimer_cd.r | 99 ++++++++++
cda-1.2/cda/demo/timing_dispersion.r |only
cda-1.2/cda/inst/doc/CD-theory.pdf |binary
cda-1.2/cda/inst/doc/introduction-cda.pdf |binary
cda-1.2/cda/inst/tests/cda_dispersion.r |only
cda-1.2/cda/man/G0.Rd | 25 +-
cda-1.2/cda/man/La.Rd | 5
cda-1.2/cda/man/alpha_kuwata.Rd | 7
cda-1.2/cda/man/array.Rd |only
cda-1.2/cda/man/cd.Rd |only
cda-1.2/cda/man/cda-package.Rd | 2
cda-1.2/cda/man/cda.Rd |only
cda-1.2/cda/man/circular_dichroism_spectrum.Rd | 3
cda-1.2/cda/man/clust.equalangles.Rd | 10 +
cda-1.2/cda/man/clust.equalsizes.Rd | 10 +
cda-1.2/cda/man/curve.povray.Rd | 3
cda-1.2/cda/man/dispersion_spectrum.Rd |only
cda-1.2/cda/man/epsAg.Rd | 3
cda-1.2/cda/man/epsAu.Rd | 3
cda-1.2/cda/man/helix.Rd | 11 +
cda-1.2/cda/man/helix.zt.Rd | 11 +
cda-1.2/cda/man/linear.Rd |only
cda-1.2/cda/man/linear_extinction_spectrum.Rd | 4
cda-1.2/cda/man/make.invalpha.Rd | 5
cda-1.2/cda/man/makeDimerCluster.Rd | 10 +
cda-1.2/cda/man/makeDimerDihedral.Rd | 10 +
cda-1.2/cda/man/makeHelixCluster.Rd | 12 +
cda-1.2/cda/man/makeHelixCluster.zt.Rd | 10 +
cda-1.2/cda/man/makeRodChain.Rd | 10 +
cda-1.2/cda/man/makeSpheresCluster.Rd | 10 +
cda-1.2/cda/man/particles.povray.Rd | 3
cda-1.2/cda/man/polarizability.ellipsoid.Rd | 4
cda-1.2/cda/man/rgl.ellipsoid.Rd | 3
cda-1.2/cda/man/rgl.ellipsoids.Rd | 3
cda-1.2/cda/man/theme_minimal.Rd | 2
cda-1.2/cda/src/internals.cpp |only
cda-1.2/cda/src/internals.h |only
cda-1.2/cda/src/linear.cpp | 110 +++++++++++
cda-1.2/cda/src/linear.h | 2
cda-1.2/cda/vignettes/introduction-cda.Rnw | 2
78 files changed, 688 insertions(+), 132 deletions(-)
Title: A collection of functions for estimating centrographic
statistics and computational geometries for spatial point
patterns
Diff between aspace versions 3.0 dated 2011-03-31 and 3.1 dated 2012-08-08
Description: A collection of functions for computing centrographic
statistics (e.g., standard distance, standard deviation
ellipse, standard deviation box) for observations taken at
point locations. Separate plotting functions have been
developed for each measure. Users interested in writing results
to ESRI shapefiles can do so by using results from aspace
functions as inputs to the convert.to.shapefile and
write.shapefile functions in the shapefiles library. The aspace
library was originally conceived to aid in the analysis of
spatial patterns of travel behaviour (see Buliung and Remmel,
2008). Major changes in the current version include (1) removal
of dependencies on several external libraries (e.g., gpclib,
maptools, sp), (2) the separation of plotting and estimation
capabilities, (3) reduction in the number of functions, and (4)
expansion of analytical capabilities with additional functions
for descriptive analysis and visualization (e.g., standard
deviation box, centre of minimum distance, central feature).
Author: Randy Bui, Ron N. Buliung, Tarmo K. Remmel
Maintainer: Ron N. Buliung
DESCRIPTION | 10 +++++-----
MD5 |only
R/calc_sde.R | 4 ++--
data/activities.rda |binary
data/centre.rda |binary
data/wts.rda |binary
man/calc_box.Rd | 2 ++
man/calc_sdd.Rd | 2 ++
man/calc_sde.Rd | 2 ++
man/centre.Rd | 2 ++
man/plot_box.Rd | 6 +++++-
man/plot_centres.Rd | 5 ++++-
man/plot_sdd.Rd | 5 ++++-
man/plot_sde.Rd | 5 ++++-
14 files changed, 32 insertions(+), 11 deletions(-)
Title: SpatialTools
Diff between SpatialTools versions 0.4.1 dated 2012-05-25 and 0.4.2 dated 2012-08-08
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
SpatialTools-0.4.1/SpatialTools/man/condnorm.par.Rd |only
SpatialTools-0.4.1/SpatialTools/man/rcondsim.Rd |only
SpatialTools-0.4.2/SpatialTools/DESCRIPTION | 8 -
SpatialTools-0.4.2/SpatialTools/MD5 | 30 ++---
SpatialTools-0.4.2/SpatialTools/NAMESPACE | 4
SpatialTools-0.4.2/SpatialTools/NEWS | 2
SpatialTools-0.4.2/SpatialTools/R/arg_check.R | 66 -----------
SpatialTools-0.4.2/SpatialTools/R/cov.R | 16 +-
SpatialTools-0.4.2/SpatialTools/R/generate_norm.R | 51 --------
SpatialTools-0.4.2/SpatialTools/R/krige_tools.R | 21 +--
SpatialTools-0.4.2/SpatialTools/R/old_code.R | 52 ++++++++
SpatialTools-0.4.2/SpatialTools/R/preamble.R | 2
SpatialTools-0.4.2/SpatialTools/man/krige.ok.Rd | 15 --
SpatialTools-0.4.2/SpatialTools/man/krige.sk.Rd | 6 -
SpatialTools-0.4.2/SpatialTools/man/krige.uk.Rd | 14 --
SpatialTools-0.4.2/SpatialTools/src/krige.cpp | 120 ++------------------
SpatialTools-0.4.2/SpatialTools/src/krige.h | 6 -
17 files changed, 122 insertions(+), 291 deletions(-)