Title: A Unified Framework for Input-Output Operations in R
Diff between io versions 0.1 dated 2014-06-06 and 0.2 dated 2014-12-11
Description: One function to read files. One function to write files. One
function to direct plots to screen or file. Automatic file format inference
and directory structure creation.
Author: David J. H. Shih
Maintainer: David J. H. Shih
io-0.1/io/R/qread-qwrite.R |only
io-0.2/io/DESCRIPTION | 29 +++----
io-0.2/io/MD5 | 75 ++++++++++++++-----
io-0.2/io/NAMESPACE | 20 ++++-
io-0.2/io/R/annotated.matrix.R | 6 +
io-0.2/io/R/compressed.R |only
io-0.2/io/R/data.frame.R | 4 -
io-0.2/io/R/gct.R |only
io-0.2/io/R/gmt.R |only
io-0.2/io/R/hdf5.R | 150 +++++++++++++++++++++++++++++++++++++--
io-0.2/io/R/ini.R |only
io-0.2/io/R/internal.R | 22 +++--
io-0.2/io/R/json.R | 4 -
io-0.2/io/R/list.R | 60 +--------------
io-0.2/io/R/matrix.R | 29 ++++++-
io-0.2/io/R/qdraw.R | 27 +++++--
io-0.2/io/R/qread.R |only
io-0.2/io/R/qwrite.R |only
io-0.2/io/R/seg.R |only
io-0.2/io/R/supported.R |only
io-0.2/io/R/symlink_simplified.R |only
io-0.2/io/R/xml.R | 4 -
io-0.2/io/R/yaml.R | 4 -
io-0.2/io/R/zzz.R | 10 ++
io-0.2/io/README.md | 80 +++++++++++++++++---
io-0.2/io/man/io.Rd | 2
io-0.2/io/man/io_supported.Rd | 4 -
io-0.2/io/man/list_files.Rd | 6 -
io-0.2/io/man/qdraw.Rd | 25 ++++--
io-0.2/io/man/qread.Rd | 16 ++--
io-0.2/io/man/qwrite.Rd | 20 +++--
io-0.2/io/tests |only
32 files changed, 425 insertions(+), 172 deletions(-)
Title: Actuarial functions
Diff between actuar versions 1.1-6 dated 2013-01-13 and 1.1-7 dated 2014-12-11
Description: Additional actuarial science functionality, mostly in the
fields of loss distributions, risk theory (including ruin theory),
simulation of compound hierarchical models and credibility theory.
The package also features 17 probability laws commonly used in
insurance, mostly heavy tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet
actuar-1.1-6/actuar/actuar-Ex.R |only
actuar-1.1-7/actuar/DESCRIPTION | 23 +-
actuar-1.1-7/actuar/MD5 | 60 +++--
actuar-1.1-7/actuar/R/CTE.R | 8
actuar-1.1-7/actuar/R/adjCoef.R | 26 +-
actuar-1.1-7/actuar/R/bstraub.R | 7
actuar-1.1-7/actuar/R/elev.R | 23 +-
actuar-1.1-7/actuar/R/hache.origin.R | 4
actuar-1.1-7/actuar/R/panjer.R | 2
actuar-1.1-7/actuar/build |only
actuar-1.1-7/actuar/inst/NEWS.Rd | 18 +
actuar-1.1-7/actuar/inst/doc/actuar.R |only
actuar-1.1-7/actuar/inst/doc/actuar.pdf |binary
actuar-1.1-7/actuar/inst/doc/coverage.R |only
actuar-1.1-7/actuar/inst/doc/coverage.pdf |binary
actuar-1.1-7/actuar/inst/doc/credibility.R |only
actuar-1.1-7/actuar/inst/doc/credibility.pdf |binary
actuar-1.1-7/actuar/inst/doc/lossdist.R |only
actuar-1.1-7/actuar/inst/doc/lossdist.pdf |binary
actuar-1.1-7/actuar/inst/doc/risk.R |only
actuar-1.1-7/actuar/inst/doc/risk.pdf |binary
actuar-1.1-7/actuar/inst/doc/simulation.R |only
actuar-1.1-7/actuar/inst/doc/simulation.pdf |binary
actuar-1.1-7/actuar/inst/po/en@quot |only
actuar-1.1-7/actuar/inst/po/fr/LC_MESSAGES/R-actuar.mo |binary
actuar-1.1-7/actuar/inst/po/fr/LC_MESSAGES/actuar.mo |binary
actuar-1.1-7/actuar/man/adjCoef.Rd | 6
actuar-1.1-7/actuar/man/aggregateDist.Rd | 4
actuar-1.1-7/actuar/man/cm.Rd | 20 -
actuar-1.1-7/actuar/man/ruin.Rd | 2
actuar-1.1-7/actuar/man/simul.Rd | 2
actuar-1.1-7/actuar/po/R-actuar.pot | 29 +-
actuar-1.1-7/actuar/po/R-fr.po | 186 +++++++----------
actuar-1.1-7/actuar/po/actuar.pot | 59 ++---
actuar-1.1-7/actuar/po/fr.po | 122 +++++------
35 files changed, 315 insertions(+), 286 deletions(-)
Title: Generation, reconstruction, simulation and analysis of
synchronous, asynchronous, and probabilistic Boolean networks
Diff between BoolNet versions 2.0.1 dated 2014-08-26 and 2.0.2 dated 2014-12-11
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
inst/NEWS.Rd | 9 +++++++++
inst/doc/BoolNet_package_vignette.pdf |binary
man/BoolNet-package.Rd | 4 ++--
man/reconstructNetwork.Rd | 2 +-
src/probabilistic_boolean_network.c | 9 +++++++--
7 files changed, 29 insertions(+), 15 deletions(-)
Title: Data Analysis for Drug Stability
Diff between stab versions 0.1.8 dated 2013-12-30 and 0.1.9 dated 2014-12-11
Description: Data analysis of drug stability for shelf-life estimation
based on ICH Q1E guideline with single-factor analysis for single-batch
or multiple-batch.
Author: Hsin-ya Lee, Yung-jin Lee
Maintainer: Yung-jin Lee
DESCRIPTION | 12 ++++++------
MD5 | 12 ++++++------
NEWS | 6 ++++++
R/go.r | 8 +++++---
R/stab.setup.r | 20 ++++----------------
R/stab.version.r | 21 +++++++++++++++++----
R/zzz.R | 2 +-
7 files changed, 45 insertions(+), 36 deletions(-)
Title: Response Probability Functions
Diff between rpf versions 0.43 dated 2014-11-13 and 0.44 dated 2014-12-11
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb]
Maintainer: Joshua Pritikin
DESCRIPTION | 14 +--
MD5 | 151 ++++++++++++++++++++---------------------
NAMESPACE | 2
R/diagnose.R | 79 ++++++++++++++-------
R/fit.R |only
R/openmx.R | 10 ++
R/util.R | 55 +++++++++++++-
build/vignette.rds |binary
inst/doc/diagnostics.html | 42 +++++------
inst/doc/flexmirt-plots.html | 6 -
inst/tests/test-multinomial.R | 6 +
inst/tests/test-weightColumn.R | 4 +
man/ChenThissen1997.Rd | 2
man/EAPscores.Rd | 10 +-
man/LSAT6.Rd | 2
man/LSAT7.Rd | 2
man/SitemFit.Rd | 2
man/SitemFit1.Rd | 2
man/as.IFAgroup.Rd | 2
man/bestToOmit.Rd | 2
man/compressDataFrame.Rd | 2
man/crosstabTest.Rd | 2
man/expandDataFrame.Rd | 2
man/fromFactorLoading.Rd |only
man/itemOutcomeBySumScore.Rd | 2
man/kct.Rd | 2
man/logit.Rd | 2
man/multinomialFit.Rd | 26 +++++--
man/observedSumScore.Rd | 2
man/omitItems.Rd | 2
man/omitMostMissing.Rd | 2
man/orderCompletely.Rd | 2
man/ordinal.gamma.Rd | 2
man/ptw2011.gof.test.Rd | 2
man/read.flexmirt.Rd | 2
man/rpf.1dim-class.Rd | 2
man/rpf.1dim.drm-class.Rd | 2
man/rpf.1dim.fit.Rd | 6 -
man/rpf.1dim.graded-class.Rd | 2
man/rpf.1dim.grm-class.Rd | 2
man/rpf.1dim.moment.Rd | 2
man/rpf.1dim.residual.Rd | 2
man/rpf.1dim.stdresidual.Rd | 2
man/rpf.base-class.Rd | 2
man/rpf.dLL.Rd | 2
man/rpf.dTheta.Rd | 2
man/rpf.drm.Rd | 2
man/rpf.grm.Rd | 2
man/rpf.id_of.Rd | 2
man/rpf.info.Rd | 2
man/rpf.introduction.Rd | 2
man/rpf.logprob.Rd | 2
man/rpf.mcm.Rd | 2
man/rpf.mdim-class.Rd | 2
man/rpf.mdim.drm-class.Rd | 2
man/rpf.mdim.graded-class.Rd | 2
man/rpf.mdim.grm-class.Rd | 2
man/rpf.mdim.mcm-class.Rd | 2
man/rpf.mdim.nrm-class.Rd | 2
man/rpf.mean.info.Rd | 2
man/rpf.mean.info1.Rd | 2
man/rpf.modify.Rd | 2
man/rpf.nrm.Rd | 2
man/rpf.numParam.Rd | 2
man/rpf.numSpec.Rd | 2
man/rpf.ogive.Rd | 2
man/rpf.paramInfo.Rd | 2
man/rpf.prob.Rd | 2
man/rpf.rescale.Rd | 2
man/rpf.rparam.Rd | 2
man/rpf.sample.Rd | 2
man/science.Rd | 2
man/stripData.Rd | 4 -
man/sumScoreEAP.Rd | 2
man/sumScoreEAPTest.Rd | 2
man/tabulateRows.Rd | 2
man/toFactorLoading.Rd |only
man/write.flexmirt.Rd | 2
78 files changed, 320 insertions(+), 215 deletions(-)
Title: Geostatistical Modelling of Spatially Referenced Prevalence Data
Diff between PrevMap versions 1.1.2 dated 2014-12-09 and 1.1.3 dated 2014-12-11
Description: It provides functions for both likelihood-based
and Bayesian analysis of spatially referenced prevalence data. 'PrevMap' is
also an extension of the 'geoR' package which should be installed first
together with the 'maxLik', 'raster' and 'pdist' packages.
Author: Emanuele Giorgi, Peter J. Diggle
Maintainer: Emanuele Giorgi
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/foo.R | 16 ++++++++--------
3 files changed, 14 insertions(+), 14 deletions(-)
Title: Groupwise statistics, LSmeans, linear contrasts, utilities
Diff between doBy versions 4.5-12 dated 2014-11-13 and 4.5-13 dated 2014-12-11
Description: doBy originally contained facilities to 'do' something to data stratified 'by' some variables. doBy contains a
variety of utilities including:
1) Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 9 +++-
DESCRIPTION | 9 ++--
MD5 | 20 +++++-----
R/LSmeans.R | 1
R/linest.R | 6 +--
R/linestGet.R | 93 +++++++++++++++++++++++++++++++-----------------
R/linestMatrix.R | 29 +++++++++++++--
build/vignette.rds |binary
inst/doc/LSmeans.pdf |binary
inst/doc/doBy.pdf |binary
man/LSmeans.Rd | 97 +++++++++++++++++++++++++++++++++++++++------------
11 files changed, 185 insertions(+), 79 deletions(-)
Title: Extended Inference for Lasso and Elastic-Net Regularized Cox and
Generalized Linear Models
Diff between c060 versions 0.2-3 dated 2014-01-22 and 0.2-4 dated 2014-12-11
Description: c060 provides additional functions to perform stability selection, model validation and parameter tuning for glmnet models
Author: Martin Sill, Thomas Hielscher, Manuela Zucknick, Natalia Becker.
Maintainer: Martin Sill
DESCRIPTION | 12 +--
MD5 | 38 +++++-----
inst |only
man/EPSGO.Rd | 7 +
man/PLL.coxnet.Rd | 4 +
man/Plot.coef.glmnet.Rd | 8 +-
man/Plot.peperr.curves.Rd | 5 +
man/aggregation.auc.Rd | 46 ++++++------
man/balancedFolds.Rd | 97 +++++++++++++------------
man/coef.intsearch.Rd | 4 +
man/complexity.glmnet.Rd | 98 +++++++++++++-------------
man/fit.glmnet.Rd | 96 +++++++++++++------------
man/plot.stabpath.Rd | 6 +
man/plot.summary.int.Rd | 69 +++++++++---------
man/predictProb.coxnet.Rd | 4 -
man/predictProb.glmnet.Rd | 4 -
man/stabpath.Rd | 5 +
man/stabsel.Rd | 5 +
man/summary.intsearch.Rd | 15 ++--
man/tune.glmnet.interval.Rd | 165 ++++++++++++++++++++++----------------------
20 files changed, 369 insertions(+), 319 deletions(-)
Title: Fitting Separable Nonlinear Models in Spectroscopy and
Microscopy
Diff between TIMP versions 1.12.0 dated 2014-12-02 and 1.12.1 dated 2014-12-11
Description: TIMP is a problem-solving environment (PSE) for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments, and has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey P. Laptenok, David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg
TIMP-1.12.0/TIMP/R/initModelClassTest.R |only
TIMP-1.12.1/TIMP/DESCRIPTION | 13 ++++++++-----
TIMP-1.12.1/TIMP/MD5 | 18 +++++++++---------
TIMP-1.12.1/TIMP/NEWS |only
TIMP-1.12.1/TIMP/R/getCoh.R | 4 ++--
TIMP-1.12.1/TIMP/data/denS4.rda |binary
TIMP-1.12.1/TIMP/data/denS5.rda |binary
TIMP-1.12.1/TIMP/data/donorAcceptorTagged.rda |binary
TIMP-1.12.1/TIMP/data/donorTagged.rda |binary
TIMP-1.12.1/TIMP/data/mea_IRF.rda |binary
TIMP-1.12.1/TIMP/data/target.rda |binary
11 files changed, 19 insertions(+), 16 deletions(-)
Title: R Interface to the Protocol Buffers API
Diff between RProtoBuf versions 0.4.1 dated 2014-03-25 and 0.4.2 dated 2014-12-11
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal RPC protocols and file formats. Additional
documentation is available in the arXiv.org preprint "RProtoBuf:
Efficient Cross-Language Data Serialization in R" by Eddelbuettel,
Stokely, and Ooms (2014) http://arxiv.org/abs/1401.7372
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel
ChangeLog | 112 ++++++++++++++++++++++++++++++++-
DESCRIPTION | 8 +-
MD5 | 65 ++++++++++---------
NAMESPACE | 2
R/00classes.R | 76 +++++++++++++++++++---
R/aslist.R | 3
R/rexp_obj.R | 54 +++++++--------
R/serialize.R | 8 +-
R/wrapper_ZeroCopyInputStream.R | 4 -
README.md |only
build/vignette.rds |binary
inst/NEWS.Rd | 27 +++++++
inst/doc/RProtoBuf-intro.Rnw | 12 +--
inst/doc/RProtoBuf-intro.pdf |binary
inst/doc/RProtoBuf-quickref.pdf |binary
inst/doc/RProtoBuf-unitTests.pdf |binary
inst/proto/rexp.proto | 14 +++-
inst/unitTests/runit.FieldDescriptor.R | 87 ++++++++++++++-----------
inst/unitTests/runit.descriptors.R |only
inst/unitTests/runit.enums.R | 4 +
inst/unitTests/runit.golden.message.R | 26 +++----
inst/unitTests/runit.int64.R | 8 +-
inst/unitTests/runit.serialize_pb.R | 20 +++++
man/Descriptor-class.Rd | 6 +
man/EnumDescriptor-class.Rd | 5 +
man/Message-class.Rd | 5 +
man/P.Rd | 2
man/aslist.Rd | 8 +-
src/Makevars.win | 33 ++++-----
src/S4_classes.h | 8 +-
src/wrapper_Descriptor.cpp | 29 ++++++++
src/wrapper_EnumDescriptor.cpp | 30 +++++---
tests/runUnitTests.R | 8 ++
tools |only
vignettes/RProtoBuf-intro.Rnw | 12 +--
35 files changed, 478 insertions(+), 198 deletions(-)
Title: Reversible Jump MCMC for the analysis of CGH arrays.
Diff between RJaCGH versions 2.0.2 dated 2011-10-10 and 2.0.3 dated 2014-12-11
Description: Bayesian analysis of CGH microarrays fitting Hidden Markov
Chain models. The selection of the number of states is made via
their posterior probability computed by Reversible Jump Markov
Chain Monte Carlo Methods. Also returns probabilistic common
regions for gains/losses.
Author: Oscar Rueda
Maintainer: Oscar Rueda
RJaCGH-2.0.2/RJaCGH/README |only
RJaCGH-2.0.2/RJaCGH/README.RJaCGH |only
RJaCGH-2.0.2/RJaCGH/README.zlib |only
RJaCGH-2.0.2/RJaCGH/README.zlib.in.RJaCGH |only
RJaCGH-2.0.2/RJaCGH/src/adler32.c |only
RJaCGH-2.0.2/RJaCGH/src/compress.c |only
RJaCGH-2.0.2/RJaCGH/src/crc32.c |only
RJaCGH-2.0.2/RJaCGH/src/crc32.h |only
RJaCGH-2.0.2/RJaCGH/src/deflate.c |only
RJaCGH-2.0.2/RJaCGH/src/deflate.h |only
RJaCGH-2.0.2/RJaCGH/src/gzio.c |only
RJaCGH-2.0.2/RJaCGH/src/infback.c |only
RJaCGH-2.0.2/RJaCGH/src/inffast.c |only
RJaCGH-2.0.2/RJaCGH/src/inffast.h |only
RJaCGH-2.0.2/RJaCGH/src/inffixed.h |only
RJaCGH-2.0.2/RJaCGH/src/inflate.c |only
RJaCGH-2.0.2/RJaCGH/src/inflate.h |only
RJaCGH-2.0.2/RJaCGH/src/inftrees.c |only
RJaCGH-2.0.2/RJaCGH/src/inftrees.h |only
RJaCGH-2.0.2/RJaCGH/src/trees.c |only
RJaCGH-2.0.2/RJaCGH/src/trees.h |only
RJaCGH-2.0.2/RJaCGH/src/uncompr.c |only
RJaCGH-2.0.2/RJaCGH/src/zconf.h |only
RJaCGH-2.0.2/RJaCGH/src/zconf.in.h |only
RJaCGH-2.0.2/RJaCGH/src/zlib.h |only
RJaCGH-2.0.2/RJaCGH/src/zutil.c |only
RJaCGH-2.0.2/RJaCGH/src/zutil.h |only
RJaCGH-2.0.3/RJaCGH/DESCRIPTION | 8 ++++--
RJaCGH-2.0.3/RJaCGH/MD5 | 37 ++++--------------------------
RJaCGH-2.0.3/RJaCGH/R/RJaCGH.R | 4 +--
RJaCGH-2.0.3/RJaCGH/man/plot.RJaCGH.Rd | 10 ++++----
RJaCGH-2.0.3/RJaCGH/src/Makevars |only
RJaCGH-2.0.3/RJaCGH/src/Makevars.win |only
RJaCGH-2.0.3/RJaCGH/src/nnhl.c | 6 ++++
34 files changed, 24 insertions(+), 41 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution based on
Exponential-Family Random Graph Models
Diff between tergm versions 3.1.4 dated 2014-01-22 and 3.2.3 dated 2014-12-11
Description: An integrated set of extensions to the `ergm` package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). "tergm" is a part of the "statnet" suite of packages for network analysis.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky
DESCRIPTION | 22 ++--
LICENSE | 2
MD5 | 153 ++++++++++++++++---------------
NAMESPACE | 2
R/InitConstraint.R | 2
R/InitErgmTerm.duration.R | 15 ++-
R/InitMHP.DynMLE.R | 2
R/InitMHP.DynMLE.blockdiag.R | 2
R/InitMHP.DynMoME.R | 7 +
R/coef.stergm.R | 2
R/combine.networks.R | 2
R/control.logLik.stergm.R | 2
R/control.simulate.stergm.R | 2
R/control.stergm.R | 4
R/ergm.godfather.R | 13 +-
R/gof.stergm.R | 2
R/impute.network.list.R | 85 +++++++++++++++++
R/is.lasttoggle.R |only
R/logLik.stergm.R | 2
R/mcmc.diagnostics.stergm.R | 2
R/print.stergm.R | 2
R/simulate.stergm.R | 61 +++++++++---
R/stergm.CMLE.R | 2
R/stergm.EGMME.GD.R | 21 +++-
R/stergm.EGMME.R | 33 +++++-
R/stergm.EGMME.SA.R | 49 +++++++--
R/stergm.EGMME.initialfit.R | 7 -
R/stergm.R | 20 ++--
R/stergm.getMCMCsample.R | 21 ++--
R/stergm.utils.R | 82 ++++++++--------
R/summary.statistics.networkDynamic.R | 24 +++-
R/summary.stergm.R | 2
R/zzz.R | 5 -
build |only
inst/NEWS.Rd | 100 +++++++++++++++++++-
inst/doc |only
man/coef.stergm.Rd | 2
man/control.simulate.stergm.Rd | 2
man/control.stergm.Rd | 19 ++-
man/ergm-constraints.Rd | 2
man/ergm-terms.Rd | 5 -
man/gof.stergm.Rd | 2
man/impute.network.list.Rd | 2
man/logLik.stergm.Rd | 2
man/mcmc.diagnostics.stergm.Rd | 2
man/print.stergm.Rd | 2
man/simulate.stergm.Rd | 25 +++--
man/stergm.Rd | 44 +++++---
man/summary.statistics.networkDynamic.Rd | 18 ++-
man/tergm-internal.Rd | 4
man/tergm-package.Rd | 2
man/tergm.godfather.Rd | 4
src/DynSA.c | 5 -
src/DynSA.h | 2
src/MCMCDyn.c | 8 +
src/MCMCDyn.h | 2
src/MHproposals_DynMLE.c | 11 +-
src/MHproposals_DynMLE.h | 2
src/MHproposals_DynMLE_block.c | 8 +
src/MHproposals_DynMLE_block.h | 2
src/MHproposals_DynMoME.c | 76 +++++++++++++--
src/MHproposals_DynMoME.h | 7 -
src/changestats_duration.c | 2
src/changestats_duration.h | 2
src/godfather.c | 5 -
src/godfather.h | 2
src/include_stubs.c | 2
tests/degree.mean.age.R | 2
tests/dynamic_EGMME.R | 2
tests/dynamic_EGMME.simple.R | 9 +
tests/dynamic_MLE.R | 2
tests/dynamic_MLE_2.R | 2
tests/dynamic_MLE_blockdiag.R | 2
tests/examples.R | 9 +
tests/sim_gf_sum.R | 3
tests/simulate_networkDynamic.R | 98 +++++++++++++++++++
tests/tergm_offset_tests.R |only
tests/tergm_parallel.R |only
vignettes |only
79 files changed, 852 insertions(+), 302 deletions(-)
Title: R interface to Geochemical Modeling Software
Diff between phreeqc versions 1.0-8877 dated 2014-07-29 and 1.0-9102 dated 2014-12-11
Description: PHREEQC (Version 3) is a geochemical modeling program developed
by the US Geological Survey that is designed to perform a wide variety
of aqueous geochemical calculations, including speciation,
batch-reaction, one-dimensional reactive-transport, and inverse
geochemical calculations.
Author: S.R. Charlton, D.L. Parkhurst, and C.A.J. Appelo, with contributions
from D. Gillespie for Chipmunk BASIC and S.D. Cohen, A.C. Hindmarsh,
R. Serban, D. Shumaker, and A.G. Taylor for CVODE/SUNDIALS
Maintainer: S.R. Charlton
DESCRIPTION | 18 +-
MD5 | 226 ++++++++++++++++++------------------
NAMESPACE | 2
R/phreeqc.R | 6
data/databases.rda |binary
data/examples.rda |binary
man/Amm.dat.Rd | 18 +-
man/ex1.Rd | 32 ++---
man/ex10.Rd | 44 +++----
man/ex11.Rd | 42 +++---
man/ex12.Rd | 58 ++++-----
man/ex13.Rd | 41 +++---
man/ex14.Rd | 51 ++++----
man/ex15.Rd | 46 +++----
man/ex15.dat.Rd | 15 +-
man/ex16.Rd | 52 ++++----
man/ex17.Rd | 51 ++++----
man/ex18.Rd | 71 ++++++-----
man/ex19.Rd | 37 +++--
man/ex2.Rd | 28 ++--
man/ex20.Rd | 56 ++++----
man/ex21.Rd | 51 ++++----
man/ex22.Rd | 45 +++----
man/ex3.Rd | 50 ++++---
man/ex4.Rd | 53 ++++----
man/ex5.Rd | 40 +++---
man/ex6.Rd | 35 ++---
man/ex7.Rd | 60 +++++----
man/ex8.Rd | 37 +++--
man/ex9.Rd | 61 +++++----
man/iso.dat.Rd | 17 +-
man/llnl.dat.Rd | 16 +-
man/minteq.dat.Rd | 13 --
man/minteq.v4.dat.Rd | 13 --
man/phrAccumulateLine.Rd | 11 -
man/phrClearAccumulatedLines.Rd | 10 -
man/phrGetAccumulatedLines.Rd | 5
man/phrGetComponentList.Rd | 4
man/phrGetDumpFileName.Rd | 16 +-
man/phrGetDumpFileOn.Rd | 11 -
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man/phrGetDumpStringsOn.Rd | 11 -
man/phrGetErrorFileName.Rd | 17 +-
man/phrGetErrorFileOn.Rd | 11 -
man/phrGetErrorStrings.Rd | 31 ++--
man/phrGetErrorStringsOn.Rd | 11 -
man/phrGetLogFileName.Rd | 14 +-
man/phrGetLogFileOn.Rd | 11 -
man/phrGetLogStrings.Rd | 11 -
man/phrGetLogStringsOn.Rd | 11 -
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man/phrGetOutputFileOn.Rd | 11 -
man/phrGetOutputStrings.Rd | 11 -
man/phrGetOutputStringsOn.Rd | 11 -
man/phrGetSelectedOutput.Rd | 29 ++--
man/phrGetSelectedOutputFileName.Rd | 14 +-
man/phrGetWarningStrings.Rd | 13 +-
man/phrLoadDatabase.Rd | 6
man/phrLoadDatabaseString.Rd | 8 -
man/phrRunAccumulated.Rd | 24 ++-
man/phrRunFile.Rd | 5
man/phrRunString.Rd | 17 +-
man/phrSetDumpFileName.Rd | 18 +-
man/phrSetDumpFileOn.Rd | 19 +--
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man/phrSetErrorStringsOn.Rd | 24 ++-
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man/phrSetLogFileOn.Rd | 23 +--
man/phrSetLogStringsOn.Rd | 21 +--
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man/phreeqc.dat.Rd | 16 +-
man/pitzer.dat.Rd | 16 +-
man/sit.dat.Rd | 16 +-
man/wateq4f.dat.Rd | 14 +-
src/CSelectedOutput.cpp | 1
src/IPhreeqc.cpp | 8 +
src/IPhreeqc.h | 2
src/IPhreeqcLib.cpp | 4
src/IPhreeqchpp.h | 2
src/phreeqcpp/GasPhase.cpp | 10 +
src/phreeqcpp/PBasic.cpp | 77 +++++++++---
src/phreeqcpp/PBasic.h | 3
src/phreeqcpp/PHRQ_io.cpp | 5
src/phreeqcpp/Parser.cpp | 24 ++-
src/phreeqcpp/Phreeqc.cpp | 2
src/phreeqcpp/Phreeqc.h | 10 +
src/phreeqcpp/ReadClass.cpp | 45 +++----
src/phreeqcpp/Solution.cpp | 8 +
src/phreeqcpp/System.cpp | 2
src/phreeqcpp/UserPunch.cpp | 8 -
src/phreeqcpp/basicsubs.cpp | 31 ++++
src/phreeqcpp/cl1.cpp | 54 --------
src/phreeqcpp/gases.cpp | 18 +-
src/phreeqcpp/inverse.cpp | 12 +
src/phreeqcpp/isotopes.cpp | 67 ++++++----
src/phreeqcpp/mainsubs.cpp | 9 -
src/phreeqcpp/parse.cpp | 13 +-
src/phreeqcpp/phqalloc.cpp | 5
src/phreeqcpp/prep.cpp | 40 ++++--
src/phreeqcpp/print.cpp | 3
src/phreeqcpp/read.cpp | 100 ++++++++++++---
src/phreeqcpp/sit.cpp | 3
src/phreeqcpp/spread.cpp | 52 ++++++--
src/phreeqcpp/step.cpp | 55 ++++----
src/phreeqcpp/structures.cpp | 91 ++++++++++++--
src/phreeqcpp/tidy.cpp | 2
src/phreeqcpp/utilities.cpp | 10 +
114 files changed, 1617 insertions(+), 1279 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Diff between ergm versions 3.1.3 dated 2014-07-19 and 3.2.3 dated 2014-12-11
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb]
Maintainer: Pavel N. Krivitsky
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ergm-3.2.3/ergm/src/changestats.c | 1079 +++++++++-------
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ergm-3.2.3/ergm/src/wtedgetree.c | 111 -
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ergm-3.2.3/ergm/tests/nodrop.R | 6
ergm-3.2.3/ergm/tests/off |only
ergm-3.2.3/ergm/tests/parallel.R | 59
ergm-3.2.3/ergm/tests/runtime_diags.R | 6
ergm-3.2.3/ergm/tests/stocapprox.R |only
ergm-3.2.3/ergm/tests/target_offset.R |only
ergm-3.2.3/ergm/tests/termTests.b12factor.R |only
ergm-3.2.3/ergm/tests/termTests.b12nodematch.R |only
ergm-3.2.3/ergm/tests/termTests.bipartite.R | 80 +
ergm-3.2.3/ergm/tests/termTests.directed.R | 69 +
ergm-3.2.3/ergm/tests/termTests.undirected.R | 114 +
ergm-3.2.3/ergm/tests/testgmonkmiss.R | 9
ergm-3.2.3/ergm/tests/testnet3u.RData |only
ergm-3.2.3/ergm/tests/testrank3d.RData |only
ergm-3.2.3/ergm/tests/utils_tests.R |only
ergm-3.2.3/ergm/tests/valued_sim.R | 58
ergm-3.2.3/ergm/tests/valued_terms.R | 1
ergm-3.2.3/ergm/vignettes |only
263 files changed, 4491 insertions(+), 2441 deletions(-)
Title: R Client for Various CrossRef APIs
Diff between rcrossref versions 0.2.0 dated 2014-11-29 and 0.2.1 dated 2014-12-11
Description: R client for various CrossRef APIs, including metadata search
with their old and search APIs, get citations in various formats
(including bibtex, citeproc-json, rdf-xml, etc.), convert DOIs to PMIDs,
and vice versa, get citations for DOIs, and get links to full text of
articles when available.
Author: Carl Boettiger [aut],
Ted Hart [aut],
Scott Chamberlain [aut, cre],
Karthik Ram [aut]
Maintainer: Scott Chamberlain
rcrossref-0.2.0/rcrossref/man/cr_citation.Rd |only
rcrossref-0.2.1/rcrossref/DESCRIPTION | 8 -
rcrossref-0.2.1/rcrossref/MD5 | 71 +++++----
rcrossref-0.2.1/rcrossref/NEWS | 9 +
rcrossref-0.2.1/rcrossref/R/cr_agency.r | 6
rcrossref-0.2.1/rcrossref/R/cr_citation.r | 7
rcrossref-0.2.1/rcrossref/R/cr_citation_count.r | 2
rcrossref-0.2.1/rcrossref/R/cr_cn.r | 6
rcrossref-0.2.1/rcrossref/R/cr_fundref.r | 8 -
rcrossref-0.2.1/rcrossref/R/cr_journals.r | 8 -
rcrossref-0.2.1/rcrossref/R/cr_licenses.R | 6
rcrossref-0.2.1/rcrossref/R/cr_members.r | 6
rcrossref-0.2.1/rcrossref/R/cr_prefixes.r | 6
rcrossref-0.2.1/rcrossref/R/cr_r.r | 2
rcrossref-0.2.1/rcrossref/R/cr_search.r | 5
rcrossref-0.2.1/rcrossref/R/cr_search_free.r | 7
rcrossref-0.2.1/rcrossref/R/cr_works.R | 7
rcrossref-0.2.1/rcrossref/R/pmid2doi.R | 13 +
rcrossref-0.2.1/rcrossref/R/rcrossref-package.R | 14 +
rcrossref-0.2.1/rcrossref/build/vignette.rds |binary
rcrossref-0.2.1/rcrossref/inst/doc/crossref_filters.html | 97 +++++--------
rcrossref-0.2.1/rcrossref/inst/doc/crossref_vignette.html | 100 ++++++--------
rcrossref-0.2.1/rcrossref/inst/ignore/cr_full.R | 16 +-
rcrossref-0.2.1/rcrossref/man/cr_agency.Rd | 3
rcrossref-0.2.1/rcrossref/man/cr_citation-deprecated.Rd |only
rcrossref-0.2.1/rcrossref/man/cr_citation_count.Rd | 2
rcrossref-0.2.1/rcrossref/man/cr_cn.Rd | 3
rcrossref-0.2.1/rcrossref/man/cr_fundref.Rd | 5
rcrossref-0.2.1/rcrossref/man/cr_journals.Rd | 5
rcrossref-0.2.1/rcrossref/man/cr_licenses.Rd | 3
rcrossref-0.2.1/rcrossref/man/cr_members.Rd | 3
rcrossref-0.2.1/rcrossref/man/cr_prefixes.Rd | 3
rcrossref-0.2.1/rcrossref/man/cr_r.Rd | 2
rcrossref-0.2.1/rcrossref/man/cr_search.Rd | 2
rcrossref-0.2.1/rcrossref/man/cr_search_free.Rd | 2
rcrossref-0.2.1/rcrossref/man/cr_works.Rd | 4
rcrossref-0.2.1/rcrossref/man/pmid2doi.Rd | 10 +
rcrossref-0.2.1/rcrossref/man/rcrossref-deprecated.Rd |only
38 files changed, 265 insertions(+), 186 deletions(-)
Title: Command line option parser.
Diff between optparse versions 1.2.0 dated 2014-04-04 and 1.3.0 dated 2014-12-11
Description: A command line parser inspired by Python's 'optparse' library to
be used with Rscript to write "#!" shebang scripts that accept short and
long flag/options.
Author: Trevor L Davis. Some documentation and examples ported from Allen Day's
getopt package. Some documentation from the optparse Python module by the
Python Software Foundation. Contributions from Steve Lianoglou, Jim
Nikelski, Kirill Müller, and Peter Humburg.
Maintainer: Trevor L Davis
DESCRIPTION | 9 +--
MD5 | 30 +++++-----
NAMESPACE | 5 +
NEWS | 6 ++
R/optparse.R | 57 ++++++++++++++++++-
build/vignette.rds |binary
exec/example.R | 1
inst/COPYRIGHTS | 5 +
inst/doc/optparse.R | 16 -----
inst/doc/optparse.pdf |binary
man/OptionParser-class.Rd |only
man/OptionParser.Rd | 68 ++++++++++-------------
man/OptionParserOption-class.Rd |only
man/add_make_option.Rd | 117 ++++++++++++++++++----------------------
man/optparse-package.Rd | 60 +++++++++-----------
man/parse_args.Rd | 83 +++++++++++++---------------
man/print_help.Rd | 24 ++++----
17 files changed, 252 insertions(+), 229 deletions(-)
Title: Analysis of the 'Elements of Metacommunity Structure'
Diff between metacom versions 1.3 dated 2013-11-13 and 1.4.2 dated 2014-12-11
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002
Author: person("Tad", "Dallas", role = c("aut", "cre"),
email = "tdallas@uga.edu")
Maintainer: Tad Dallas
metacom-1.3/metacom/README.md |only
metacom-1.4.2/metacom/DESCRIPTION | 19 +-
metacom-1.4.2/metacom/MD5 | 41 ++---
metacom-1.4.2/metacom/NAMESPACE | 2
metacom-1.4.2/metacom/R/BoundaryClump.R | 40 ++---
metacom-1.4.2/metacom/R/Coherence.R | 6
metacom-1.4.2/metacom/R/IdentifyStructure.R |only
metacom-1.4.2/metacom/R/Imagine.R | 8 -
metacom-1.4.2/metacom/R/Metacommunity.R | 180 ++++++++++++-------------
metacom-1.4.2/metacom/R/NullMaker.R | 80 ++++++-----
metacom-1.4.2/metacom/R/OrderMatrix.R | 13 +
metacom-1.4.2/metacom/R/Turnover.R | 12 -
metacom-1.4.2/metacom/data/TestMatrices.rda |binary
metacom-1.4.2/metacom/man/BoundaryClump.Rd | 8 -
metacom-1.4.2/metacom/man/Coherence.Rd | 15 +-
metacom-1.4.2/metacom/man/IdentifyStructure.Rd |only
metacom-1.4.2/metacom/man/Imagine.Rd | 19 ++
metacom-1.4.2/metacom/man/Metacommunity.Rd | 19 ++
metacom-1.4.2/metacom/man/NullMaker.Rd | 31 +++-
metacom-1.4.2/metacom/man/OrderMatrix.Rd | 7
metacom-1.4.2/metacom/man/TestMatrices.Rd | 8 -
metacom-1.4.2/metacom/man/Turnover.Rd | 16 +-
metacom-1.4.2/metacom/man/metacom-package.Rd | 8 -
23 files changed, 308 insertions(+), 224 deletions(-)
Title: R Client for the Enigma API
Diff between enigma versions 0.1.0 dated 2014-10-16 and 0.1.1 dated 2014-12-11
Description: Enigma (https://enigma.io) holds many public datasets from
governments, companies, universities, and organizations. Enigma provides an
API for data, metadata, and statistics on each of the datasets. enigma is
an R client to interact with the Enigma API, including getting the data
and metadata for datasets in Enigma, as well as collecting statistics on
datasets. In addition, you can download a gzipped csv file of a dataset
if you want the whole dataset. An API key from Enigma is required to use
enigma.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
DESCRIPTION | 13 +++++++----
MD5 | 32 +++++++++++++++++-----------
NEWS | 12 +++++++++-
R/enigma_data.r | 56 ++++++++++++++++++++++++-------------------------
R/enigma_fetch.r | 16 +++++++-------
R/enigma_metadata.r | 12 +++++-----
R/enigma_stats.r | 10 ++++----
R/rate_limit.R | 14 ++++++------
build |only
inst/doc |only
inst/vign |only
man/enigma_data.Rd | 2 -
man/enigma_fetch.Rd | 2 -
man/enigma_metadata.Rd | 2 -
man/enigma_stats.Rd | 2 -
man/rate_limit.Rd | 2 -
vignettes |only
17 files changed, 98 insertions(+), 77 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Diff between choroplethr versions 2.1.0 dated 2014-12-03 and 2.1.1 dated 2014-12-11
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. choroplethr simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. Please see the vignettes for more details.
Author: Ari Lamstein
Maintainer: Ari Lamstein
choroplethr-2.1.0/choroplethr/inst/doc/d-zip-choropleth.R |only
choroplethr-2.1.0/choroplethr/inst/doc/d-zip-choropleth.Rmd |only
choroplethr-2.1.0/choroplethr/inst/doc/d-zip-choropleth.html |only
choroplethr-2.1.1/choroplethr/DESCRIPTION | 6
choroplethr-2.1.1/choroplethr/MD5 | 65 ++++------
choroplethr-2.1.1/choroplethr/NEWS | 5
choroplethr-2.1.1/choroplethr/R/choroplethr_wdi.R | 2
choroplethr-2.1.1/choroplethr/README.md | 1
choroplethr-2.1.1/choroplethr/build/vignette.rds |binary
choroplethr-2.1.1/choroplethr/inst/doc/a-introduction.html | 2
choroplethr-2.1.1/choroplethr/inst/doc/b-state-choropleth.R | 2
choroplethr-2.1.1/choroplethr/inst/doc/b-state-choropleth.Rmd | 9 +
choroplethr-2.1.1/choroplethr/inst/doc/b-state-choropleth.html | 17 ++
choroplethr-2.1.1/choroplethr/inst/doc/c-county-choropleth.R | 2
choroplethr-2.1.1/choroplethr/inst/doc/c-county-choropleth.Rmd | 9 +
choroplethr-2.1.1/choroplethr/inst/doc/c-county-choropleth.html | 17 ++
choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.R | 2
choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.Rmd | 7 -
choroplethr-2.1.1/choroplethr/inst/doc/d-zip-map.html | 15 +-
choroplethr-2.1.1/choroplethr/inst/doc/e-country-choropleth.html | 6
choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.Rmd | 2
choroplethr-2.1.1/choroplethr/inst/doc/f-mapping-us-census-data.html | 2
choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.Rmd | 2
choroplethr-2.1.1/choroplethr/inst/doc/g-world-bank-data.html | 8 -
choroplethr-2.1.1/choroplethr/inst/doc/i-creating-your-own-maps.html | 16 +-
choroplethr-2.1.1/choroplethr/man/Admin1Choropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/CountryChoropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/CountyChoropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/CountyZoomChoropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/StateChoropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/USAChoropleth.Rd | 2
choroplethr-2.1.1/choroplethr/man/ZipMap.Rd | 2
choroplethr-2.1.1/choroplethr/man/choroplethr_wdi.Rd | 2
choroplethr-2.1.1/choroplethr/vignettes/f-mapping-us-census-data.Rmd | 2
choroplethr-2.1.1/choroplethr/vignettes/g-world-bank-data.Rmd | 2
35 files changed, 132 insertions(+), 85 deletions(-)