Title: Soil Database Interface
Diff between soilDB versions 0.8-1 dated 2012-08-27 and 0.8-3 dated 2012-10-10
Description: A collection of functions for reading data from USDA-NCSS
soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 11 ++++++-----
MD5 | 18 +++++++++---------
NEWS | 4 ++++
R/fetchNASIS.R | 3 ++-
R/fetchPedonPC.R | 4 +++-
R/get_site_data_from_NASIS_db.R | 2 +-
R/get_site_data_from_pedon_db.R | 2 +-
data/gopheridge.rda |binary
man/SDA_query.Rd | 10 +++++++++-
man/soilDB-package.Rd | 4 +++-
10 files changed, 38 insertions(+), 20 deletions(-)
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 1.2-7 dated 2012-08-27 and 1.3 dated 2012-10-10
Description: A collection of algorithms related to modeling of soil
resources, soil classification, soil profile aggregation, and
visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 13 ++-
MD5 | 42 ++++++------
NAMESPACE | 4 -
NEWS | 18 +++++
R/SoilProfileCollection-coercion.R | 2
R/SoilProfileCollection-methods.R | 110 ++++++++++++++++++++++++++++++--
R/SoilProfileCollection-slice-methods.R | 7 +-
R/SoilProfileCollection-spatial.R | 2
R/f.noise.R | 91 +++++++++++++-------------
R/prepanel.depth_function.R | 45 ++++---------
R/setters.R | 11 ++-
R/test_hz_logic.R | 6 +
TODO | 1
data/amarillo.rda |only
man/SPC-plotting.Rd | 1
man/SoilProfileCollection-class.Rd | 44 ++++++++++++
man/amarillo.Rd |only
man/aqp-package.Rd | 8 +-
man/ca630.Rd | 51 +++++++++-----
man/profileApply-methods.Rd | 32 ---------
man/sp1.Rd | 6 -
man/sp2.Rd | 40 ++++++-----
man/sp4.Rd | 108 ++++++++++++++++++++++++++++---
23 files changed, 438 insertions(+), 204 deletions(-)
Title: Models for Data from Unmarked Animals
Diff between unmarked versions 0.9-8 dated 2012-06-25 and 0.9-9 dated 2012-10-10
Description: Unmarked fits hierarchical models of animal abundance and
occurrence to data collected using survey methods such as point
counts, site occupancy sampling, distance sampling, removal
sampling, and double observer sampling. Parameters governing
the state and observation processes can be modeled as functions
of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc
Kery
Maintainer: Richard Chandler
unmarked-0.9-8/unmarked/vignettes/auto |only
unmarked-0.9-9/unmarked/DESCRIPTION | 13
unmarked-0.9-9/unmarked/MD5 | 82 +-
unmarked-0.9-9/unmarked/NAMESPACE | 13
unmarked-0.9-9/unmarked/R/boot.R | 7
unmarked-0.9-9/unmarked/R/getDesign.R | 167 ++++
unmarked-0.9-9/unmarked/R/gpcount.R |only
unmarked-0.9-9/unmarked/R/occuFP.R |only
unmarked-0.9-9/unmarked/R/pcountOpen.R | 2
unmarked-0.9-9/unmarked/R/ranef.R | 93 ++
unmarked-0.9-9/unmarked/R/unmarkedFit.R | 367 +++++++++-
unmarked-0.9-9/unmarked/R/unmarkedFitList.R | 6
unmarked-0.9-9/unmarked/R/unmarkedFrame.R | 181 +++-
unmarked-0.9-9/unmarked/inst/doc/cap-recap.pdf |binary
unmarked-0.9-9/unmarked/inst/doc/colext.pdf |binary
unmarked-0.9-9/unmarked/inst/doc/distsamp.pdf |binary
unmarked-0.9-9/unmarked/inst/doc/spp-dist.pdf |binary
unmarked-0.9-9/unmarked/inst/doc/unmarked.pdf |binary
unmarked-0.9-9/unmarked/inst/unitTests/runit.gpcount.R |only
unmarked-0.9-9/unmarked/inst/unitTests/runit.ranef.R | 28
unmarked-0.9-9/unmarked/inst/unitTests/runit.unmarkedMultFrame.R | 80 ++
unmarked-0.9-9/unmarked/inst/unitTests/sim.colext.R | 120 +++
unmarked-0.9-9/unmarked/inst/unitTests/sim.gmultmix.R | 57 +
unmarked-0.9-9/unmarked/inst/unitTests/sim.gpcount.R |only
unmarked-0.9-9/unmarked/man/extract-methods.Rd | 3
unmarked-0.9-9/unmarked/man/fitted-methods.Rd | 1
unmarked-0.9-9/unmarked/man/gdistsamp.Rd | 3
unmarked-0.9-9/unmarked/man/getB-methods.Rd |only
unmarked-0.9-9/unmarked/man/getFP-methods.Rd |only
unmarked-0.9-9/unmarked/man/getP-methods.Rd | 6
unmarked-0.9-9/unmarked/man/gmultmix.Rd | 28
unmarked-0.9-9/unmarked/man/gpcount.Rd |only
unmarked-0.9-9/unmarked/man/nonparboot-methods.Rd | 4
unmarked-0.9-9/unmarked/man/occuFP.Rd |only
unmarked-0.9-9/unmarked/man/pcountOpen.Rd | 3
unmarked-0.9-9/unmarked/man/predict-methods.Rd | 1
unmarked-0.9-9/unmarked/man/ranef-methods.Rd | 14
unmarked-0.9-9/unmarked/man/simulate-methods.Rd | 2
unmarked-0.9-9/unmarked/man/unmarked-package.Rd | 23
unmarked-0.9-9/unmarked/man/unmarkedFit-class.Rd | 6
unmarked-0.9-9/unmarked/man/unmarkedFrame-class.Rd | 54 -
unmarked-0.9-9/unmarked/man/unmarkedFrame.Rd | 101 +-
unmarked-0.9-9/unmarked/man/unmarkedFrameOccuFP.Rd |only
unmarked-0.9-9/unmarked/man/unmarkedMultFrame.Rd | 12
unmarked-0.9-9/unmarked/src/nll_distsamp.cpp | 32
unmarked-0.9-9/unmarked/src/nll_gpcount.cpp |only
unmarked-0.9-9/unmarked/src/nll_gpcount.h |only
unmarked-0.9-9/unmarked/src/nll_pcountOpen.cpp | 4
48 files changed, 1277 insertions(+), 236 deletions(-)
Title: Significance analysis of sequencing data based on a Poisson log
linear model
Diff between PoissonSeq versions 1.1.1 dated 2012-10-09 and 1.1.2 dated 2012-10-10
Description: This package implements a method for normalization,
testing, and false discovery rate estimation for RNA-sequencing
data. The description of the method is in Li J, Witten DM,
Johnstone I, Tibshirani R (2012). Normalization, testing, and
false discovery rate estimation for RNA-sequencing data.
Biostatistics 13(3): 523-38. We estimate the sequencing depths
of experiments using a new method based on Poisson
goodness-of-fit statistic, calculate a score statistic on the
basis of a Poisson log-linear model, and then estimate the
false discovery rate using a modified version of permutation
plug-in method. A more detailed instruction as well as sample
data is available at
http://www.stanford.edu/~junli07/research.html. In this
version, we changed the way of calculating log foldchange for
two-class data. The FDR estimation part remains unchanged.
Author: Jun Li
Maintainer: Jun Li
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/ps_other.R | 10 ++++++----
3 files changed, 13 insertions(+), 11 deletions(-)
Title: Spatio-Temporal Model Estimation
Diff between SpatioTemporal versions 1.1.1 dated 2012-08-28 and 1.1.2 dated 2012-10-10
More information about SpatioTemporal at CRAN
Description: Utilities that estimate, predict and cross-validate the
spatio-temporal model developed for MESA Air.
Author: Johan Lindstrom, Adam Szpiro, Paul D. Sampson, Silas Bergen,
Assaf P. Oron
Maintainer: Johan Lindstrom
SpatioTemporal-1.1.1/SpatioTemporal/vignettes/ST_intro.dvi |only
SpatioTemporal-1.1.2/SpatioTemporal/DESCRIPTION | 8
SpatioTemporal-1.1.2/SpatioTemporal/MD5 | 131
SpatioTemporal-1.1.2/SpatioTemporal/NAMESPACE | 334
SpatioTemporal-1.1.2/SpatioTemporal/R/CV_aux.R | 1028 +-
SpatioTemporal-1.1.2/SpatioTemporal/R/CV_estimate.R | 790 -
SpatioTemporal-1.1.2/SpatioTemporal/R/CV_predict.R | 1212 +-
SpatioTemporal-1.1.2/SpatioTemporal/R/MCMC.R | 630 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STdata.R | 1052 +-
SpatioTemporal-1.1.2/SpatioTemporal/R/STdata_processing.R | 586 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel.R | 772 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_combine.R | 318
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_estimate.R | 834 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_predict.R | 1813 ++--
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_processing.R | 482 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_setup.R | 524 -
SpatioTemporal-1.1.2/SpatioTemporal/R/STmodel_simulate.R | 402
SpatioTemporal-1.1.2/SpatioTemporal/R/SpatioTemporal-data.R | 632 -
SpatioTemporal-1.1.2/SpatioTemporal/R/SpatioTemporal-package.R | 281
SpatioTemporal-1.1.2/SpatioTemporal/R/block_matrices.R | 160
SpatioTemporal-1.1.2/SpatioTemporal/R/c_F_mult.R | 462 -
SpatioTemporal-1.1.2/SpatioTemporal/R/c_cov_matrices.R | 532 -
SpatioTemporal-1.1.2/SpatioTemporal/R/c_lin_alg.R | 410
SpatioTemporal-1.1.2/SpatioTemporal/R/deprecated.R | 776 -
SpatioTemporal-1.1.2/SpatioTemporal/R/internal.R | 752 -
SpatioTemporal-1.1.2/SpatioTemporal/R/loglikeST.R | 720 -
SpatioTemporal-1.1.2/SpatioTemporal/R/loglikeST_aux.R | 520 -
SpatioTemporal-1.1.2/SpatioTemporal/R/loglikeST_derivatives.R | 322
SpatioTemporal-1.1.2/SpatioTemporal/R/temporal_SVD_incomplete_data.R | 857 +-
SpatioTemporal-1.1.2/SpatioTemporal/R/utils.R | 740 -
SpatioTemporal-1.1.2/SpatioTemporal/VERSIONS | 752 -
SpatioTemporal-1.1.2/SpatioTemporal/data/MCMC.mesa.model.RData |binary
SpatioTemporal-1.1.2/SpatioTemporal/data/datalist | 14
SpatioTemporal-1.1.2/SpatioTemporal/data/est.mesa.model.RData |binary
SpatioTemporal-1.1.2/SpatioTemporal/inst/doc/ST_intro.Rnw | 1088 +-
SpatioTemporal-1.1.2/SpatioTemporal/inst/doc/ST_intro.pdf |binary
SpatioTemporal-1.1.2/SpatioTemporal/inst/doc/Tutorial.Rnw | 4256 +++++-----
SpatioTemporal-1.1.2/SpatioTemporal/inst/doc/Tutorial.pdf |binary
SpatioTemporal-1.1.2/SpatioTemporal/man/MCMC.STmodel.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/SVDsmooth.Rd | 6
SpatioTemporal-1.1.2/SpatioTemporal/man/SpatioTemporal-package.Rd | 23
SpatioTemporal-1.1.2/SpatioTemporal/man/c.STmodel.Rd | 14
SpatioTemporal-1.1.2/SpatioTemporal/man/createDataMatrix.Rd | 4
SpatioTemporal-1.1.2/SpatioTemporal/man/createSTdata.Rd | 10
SpatioTemporal-1.1.2/SpatioTemporal/man/createSTmodel.Rd | 10
SpatioTemporal-1.1.2/SpatioTemporal/man/detrendSTdata.Rd | 5
SpatioTemporal-1.1.2/SpatioTemporal/man/estimate.STmodel.Rd | 6
SpatioTemporal-1.1.2/SpatioTemporal/man/estimateCV.STmodel.Rd | 5
SpatioTemporal-1.1.2/SpatioTemporal/man/plot.STdata.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/plot.SVDcv.Rd | 6
SpatioTemporal-1.1.2/SpatioTemporal/man/predict.STmodel.Rd | 6
SpatioTemporal-1.1.2/SpatioTemporal/man/print.STmodel.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/print.SVDcv.Rd | 6
SpatioTemporal-1.1.2/SpatioTemporal/man/print.summary.STmodel.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/removeSTcovarMean.Rd | 5
SpatioTemporal-1.1.2/SpatioTemporal/man/simulate.STmodel.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/summary.STmodel.Rd | 8
SpatioTemporal-1.1.2/SpatioTemporal/man/updateSTdataTrend.Rd | 5
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/AppMCMC.tex | 202
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/AppRcode.tex | 1170 +-
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/AppST.tex | 396
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/AppSim.tex | 382
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/AppUnobs.tex | 502 -
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/ST_intro.Rnw | 1088 +-
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/Tutorial.Rnw | 4256 +++++-----
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/tutorial.bib | 248
SpatioTemporal-1.1.2/SpatioTemporal/vignettes/tutorial.sty | 166
67 files changed, 16431 insertions(+), 16328 deletions(-)
Permanent link
Title: Regularization paths for SCAD- and MCP-penalized regression
models
Diff between ncvreg versions 2.3-2 dated 2011-05-16 and 2.4-0 dated 2012-10-10
Description: Efficient algorithms for fitting regularization paths for
linear or logistic regression models penalized by MCP or SCAD,
with optional additional L2 penalty ("Mnet").
Author: Patrick Breheny
Maintainer: Patrick Breheny
ncvreg-2.3-2/ncvreg/R/setupXYL.R |only
ncvreg-2.4-0/ncvreg/DESCRIPTION | 10 -
ncvreg-2.4-0/ncvreg/MD5 |only
ncvreg-2.4-0/ncvreg/NAMESPACE | 2
ncvreg-2.4-0/ncvreg/NEWS | 19 ++-
ncvreg-2.4-0/ncvreg/R/convexMin.R | 89 +++++++-------
ncvreg-2.4-0/ncvreg/R/cv.ncvreg.R | 111 ++++++-----------
ncvreg-2.4-0/ncvreg/R/logLik.R |only
ncvreg-2.4-0/ncvreg/R/loss.R | 15 +-
ncvreg-2.4-0/ncvreg/R/ncvreg.R | 151 ++++++++++++-----------
ncvreg-2.4-0/ncvreg/R/plot.cv.ncvreg.R | 41 +++---
ncvreg-2.4-0/ncvreg/R/plot.ncvreg.R | 67 +++++-----
ncvreg-2.4-0/ncvreg/R/predict.R | 21 ++-
ncvreg-2.4-0/ncvreg/R/setupLambda.R | 44 +++---
ncvreg-2.4-0/ncvreg/R/standardize.R |only
ncvreg-2.4-0/ncvreg/inst/tests |only
ncvreg-2.4-0/ncvreg/man/cv.ncvreg.Rd | 48 ++-----
ncvreg-2.4-0/ncvreg/man/heart.Rd | 37 ++---
ncvreg-2.4-0/ncvreg/man/ncvreg-internal.Rd | 2
ncvreg-2.4-0/ncvreg/man/ncvreg.Rd | 21 ++-
ncvreg-2.4-0/ncvreg/man/predict.Rd | 13 +-
ncvreg-2.4-0/ncvreg/man/prostate.Rd | 39 ++----
ncvreg-2.4-0/ncvreg/src/ncvreg.c | 183 ++++++++++++++++-------------
ncvreg-2.4-0/ncvreg/tests |only
24 files changed, 472 insertions(+), 441 deletions(-)
Title: R functions for Generalized Simulated Annealing
Diff between GenSA versions 1.0.3 dated 2012-04-27 and 1.1.0 dated 2012-10-10
Description: This package searches for global minimum of a very complex
non-linear objective function with a very large number of
optima.
Author: Sylvain Gubian, Yang Xiang, Brian Suomela, Julia Hoeng, PMP SA.
Maintainer: Sylvain Gubian
DESCRIPTION | 8
MD5 | 18
NEWS | 13
R/GenSA.R | 4
man/GenSA.Rd | 31
src/Caller.cpp | 12
src/Engine.cpp | 59
src/Engine.h | 7
src/Utils.cpp | 3623 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
src/Utils.h | 127 +
10 files changed, 3852 insertions(+), 50 deletions(-)
Title: sybil - Efficient Constrained Based Modelling in R
Diff between sybil versions 1.1.1 dated 2012-10-08 and 1.1.2 dated 2012-10-10
Description: The package sybil is a Systems Biology Library for R,
implementing algorithms for constraint based analyses of
metabolic networks (e.g. flux-balance analysis (FBA),
minimization of metabolic adjustment (MOMA), regulatory on/off
minimization (ROOM), robustness analysis and flux variability
analysis).
Author: Gabriel Gelius-Dietrich [aut, cre], C. Jonathan Fritzemeier
[ctb], Rajen Piernikarczyk [ctb], Marc Andre Daxer [ctb],
Benjamin Braasch [ctb], Abdelmoneim Desouki [ctb]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 17 +--
MD5 | 220 +++++++++++++++++++--------------------
R/addAlgorithm.R | 4
R/addExchReact.R | 4
R/addReact.R | 4
R/addSolver.R | 4
R/blockedReact.R | 7 -
R/bracket_pairs.R | 4
R/ceilValues.R | 4
R/changeBounds.R | 4
R/changeGPR.R | 4
R/changeObjFunc.R | 4
R/checkAlgorithm.R | 4
R/checkDefaultMethod.R | 7 -
R/checkOptSol.R | 4
R/checkReactId.R | 4
R/check_brackets.R | 4
R/checksolClass.R | 4
R/createReactionString.R | 4
R/deadEndMetabolite.R | 4
R/doInRound.R | 4
R/doubleFluxDel.R | 4
R/doubleGeneDel.R | 4
R/doubleReact.R | 4
R/findExchReact.R | 4
R/floorValues.R | 4
R/fluxDistributionClass.R | 4
R/fluxVar.R | 6 -
R/geneDel.R | 6 -
R/geneDeletion.R | 4
R/generateWT.R | 4
R/generics.R | 4
R/getsybilenv.R | 4
R/mod2irrev.R | 4
R/modelorg2ExPA.R | 4
R/modelorg2text.R | 4
R/modelorg2tsv.R | 4
R/modelorgClass.R | 4
R/modelorg_irrevClass.R | 4
R/multiDel.R | 4
R/oneFluxDel.R | 4
R/oneGeneDel.R | 4
R/onlyChangeGPR.R | 4
R/onlyCheckGPR.R | 4
R/optObjClass.R | 4
R/optObj_basicfunc.R | 4
R/optObj_clpAPIClass.R | 6 -
R/optObj_cplexAPIClass.R | 6 -
R/optObj_glpkAPIClass.R | 6 -
R/optObj_lpSolveAPIClass.R | 4
R/optObj_lpSolveAPIcompat.R | 4
R/optObj_pointer.R | 4
R/optimizer.R | 6 -
R/optsolClass.R | 22 +++
R/optsol_blockedReactClass.R | 4
R/optsol_fluxVarClass.R | 4
R/optsol_fluxdelClass.R | 19 ---
R/optsol_genedelClass.R | 4
R/optsol_optimizeProbClass.R | 4
R/optsol_robAnaClass.R | 4
R/optsol_simpleFBAClass.R |only
R/parseBoolean.R | 4
R/ppProcClass.R | 4
R/ppProcessing.R | 4
R/prepProbObj.R | 4
R/prepareSubSysMatrix.R | 4
R/printLogComment.R | 4
R/printNamedList.R | 4
R/printObjFunc.R | 4
R/progress.R | 4
R/promptSysBiolAlg.R | 4
R/reactIdClass.R | 4
R/readTEXTmod.R | 4
R/readTSVmod.R | 4
R/reassignFwBwMatch.R | 4
R/rmReact.R | 4
R/robAna.R | 4
R/settings.R | 4
R/simpleFBA.R | 4
R/singletonMetabolite.R | 4
R/sybilErrorClass.R | 4
R/sybilLogClass.R | 4
R/sybilStack.R | 4
R/sysBiolAlgClass.R | 4
R/sysBiolAlg_fbaClass.R | 4
R/sysBiolAlg_fvClass.R | 4
R/sysBiolAlg_lmomaClass.R | 4
R/sysBiolAlg_momaClass.R | 4
R/sysBiolAlg_mtfClass.R | 4
R/sysBiolAlg_roomClass.R | 4
R/validmodelorg.R | 4
R/validoptsol.R | 4
R/validreactId.R | 4
R/validsysBiolAlg.R | 4
R/ypd.R | 4
R/zzz.R | 4
inst/NEWS.Rd | 12 ++
inst/doc/sybil.pdf |binary
man/optObj-class.Rd | 2
man/optimizeProb-methods.Rd | 6 -
man/optsol-class.Rd | 14 ++
man/optsol_blockedReact-class.Rd | 3
man/optsol_fluxVar-class.Rd | 3
man/optsol_fluxdel-class.Rd | 14 --
man/optsol_genedel-class.Rd | 3
man/optsol_optimizeProb-class.Rd | 3
man/optsol_robAna-class.Rd | 3
man/optsol_simpleFBA-class.Rd |only
man/simpleFBA.Rd | 6 -
man/sysBiolAlg.Rd | 2
vignettes/optObj-class.pdf |binary
vignettes/optsol-class.pdf |binary
112 files changed, 378 insertions(+), 353 deletions(-)
Title: Serialize R objects to JSON, JavaScript Object Notation
Diff between RJSONIO versions 1.0-0 dated 2012-09-30 and 1.0-1 dated 2012-10-10
Description: This is a package that allows conversion to and from data
in Javascript object notation (JSON) format. This allows R
objects to be inserted into Javascript/ECMAScript/ActionScript
code and allows R programmers to read and convert JSON content
to R objects. This is an alternative to rjson package. That
version was too slow for converting large R objects to JSON and
is not extensible, but a very useful prototype. It is fast for
parsing. This package uses methods, vectorized operations and
C code and callbacks to R functions for deserializing JSON
objects to R. Verison 0.4 of this package uses a new native
parser, implements the transformation code in C and allocates
memory efficiently (rather than concatenating because of event
driven parsing). The result is a significantly faster parsing
of large JSON documents.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
DESCRIPTION | 6 ++--
MD5 | 11 ++++----
R/json.R | 65 +++++++++++++++++++++++++++++++++----------------
Web/index.html | 2 -
man/toJSON.Rd | 4 +--
tests/containers.R |only
tests/scalarCollapse.R | 2 -
7 files changed, 58 insertions(+), 32 deletions(-)
Title: Phylogenetic analysis in R
Diff between phangorn versions 1.6-4 dated 2012-08-02 and 1.6-5 dated 2012-10-10
Description: Phylogenetic analysis in R (Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
Distance methods & Hadamard conjugation)
Author: Klaus Schliep, Emmanuel Paradis
Maintainer: Klaus Schliep
DESCRIPTION | 9 -
MD5 | 16 +--
NEWS | 14 ++
R/phylo.R | 213 +++++++++++++++++++++++++++++++++--------
inst/doc/Trees.pdf |binary
inst/doc/phangorn-specials.pdf |binary
man/dist.hamming.Rd | 2
man/parsimony.Rd | 8 -
src/phangorn.c | 101 ++++++++++++++-----
9 files changed, 282 insertions(+), 81 deletions(-)
Title: Functional Data Analysis
Diff between fda versions 2.2.8 dated 2012-05-15 and 2.3.1 dated 2012-10-10
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer. They were
ported from earlier versions in Matlab and S-PLUS. An
introduction appears in Ramsay, J. O., Hooker, Giles, and
Graves, Spencer (2009) Functional Data Analysis with R and
Matlab (Springer). The package includes data sets and script
files working many examples including all but one of the 76
figures in this latter book. As of this release, the R-Project
is no longer distributing the Matlab versions of the functional
data analysis functions and sample analyses through the CRAN
distribution system. This is due to the pressure placed on
storage required in the many CRAN sites by the rapidly
increasing number of R packages, of which the fda package is
one. The three of us involved in this package have agreed to
help out this situation by switching to distributing the Matlab
functions and analyses through Jim Ramsay's ftp site at McGill
University. To obtain these Matlab files, go to this site
using an ftp utility:
http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There
you find a set of .zip files containing the functions and
sample analyses, as well as two .txt files giving instructions
for installation and some additional information.
Author: J. O. Ramsay
Maintainer: J. O. Ramsay
fda-2.2.8/fda/inst/Matlab/fdaM |only
fda-2.2.8/fda/inst/scripts/CSTR |only
fda-2.2.8/fda/inst/scripts/fdarm-ch01.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch03.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch04.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch05.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch06.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch07.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch08.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch09.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch10.m |only
fda-2.2.8/fda/inst/scripts/fdarm-ch11.m |only
fda-2.3.1/fda/DESCRIPTION | 31 -
fda-2.3.1/fda/MD5 | 674 +++-----------------------
fda-2.3.1/fda/R/CRAN.R |only
fda-2.3.1/fda/R/Data2fd.R | 5
fda-2.3.1/fda/R/as.POSIXct1970.R |only
fda-2.3.1/fda/R/basisfd.R | 4
fda-2.3.1/fda/R/bsplinepen.R | 124 ++--
fda-2.3.1/fda/R/create.bspline.basis.R | 231 ++++-----
fda-2.3.1/fda/R/create.bspline.irregular.R |only
fda-2.3.1/fda/R/create.monomial.basis.R | 151 +++--
fda-2.3.1/fda/R/eval.basis.R | 117 ++--
fda-2.3.1/fda/R/eval.fd.R | 144 +++--
fda-2.3.1/fda/R/eval.penalty.R | 2
fda-2.3.1/fda/R/exponentiate.fd.R |only
fda-2.3.1/fda/R/fRegress.CV.R | 49 +
fda-2.3.1/fda/R/fRegress.R | 49 +
fda-2.3.1/fda/R/fd.R | 315 +-----------
fda-2.3.1/fda/R/fdPar.R | 6
fda-2.3.1/fda/R/getbasismatrix.R | 134 ++---
fda-2.3.1/fda/R/landmarkreg.R | 2
fda-2.3.1/fda/R/matplot.R |only
fda-2.3.1/fda/R/monomialpen.R | 69 +-
fda-2.3.1/fda/R/pda.fd.R | 275 +++++-----
fda-2.3.1/fda/R/plot.basisfd.R | 47 +
fda-2.3.1/fda/R/plot.fd.R | 19
fda-2.3.1/fda/R/readHMD.R |only
fda-2.3.1/fda/R/smooth.basis.R | 710 ++--------------------------
fda-2.3.1/fda/R/smooth.basis1.R |only
fda-2.3.1/fda/R/vec2Lfd.R | 31 -
fda-2.3.1/fda/data/CanadianWeather.rda |binary
fda-2.3.1/fda/data/MontrealTemp.rda |binary
fda-2.3.1/fda/data/ReginaPrecip.rda |binary
fda-2.3.1/fda/data/StatSciChinese.rda |binary
fda-2.3.1/fda/data/daily.rda |binary
fda-2.3.1/fda/data/dateAccessories.rda |binary
fda-2.3.1/fda/data/gait.rda |binary
fda-2.3.1/fda/data/growth.rda |binary
fda-2.3.1/fda/data/handwrit.rda |binary
fda-2.3.1/fda/data/infantGrowth.rda |binary
fda-2.3.1/fda/data/landmark.reg.expData.rda |binary
fda-2.3.1/fda/data/lip.rda |binary
fda-2.3.1/fda/data/melanoma.rda |binary
fda-2.3.1/fda/data/nondurables.rda |binary
fda-2.3.1/fda/data/onechild.rda |binary
fda-2.3.1/fda/data/pinch.rda |binary
fda-2.3.1/fda/data/pinchraw.rda |binary
fda-2.3.1/fda/data/refinery.rda |binary
fda-2.3.1/fda/data/seabird.rda |binary
fda-2.3.1/fda/demo/00Index | 43 -
fda-2.3.1/fda/demo/create.test.R | 27 -
fda-2.3.1/fda/demo/fdarm.R |only
fda-2.3.1/fda/demo/gait.R | 11
fda-2.3.1/fda/demo/handwrit.R | 175 ++----
fda-2.3.1/fda/inst/Matlab/README |only
fda-2.3.1/fda/inst/README.txt |only
fda-2.3.1/fda/inst/doc/FDAfuns.pdf |binary
fda-2.3.1/fda/inst/scripts/fdarm-ch07.R | 8
fda-2.3.1/fda/inst/scripts/fdarm-ch09.R | 17
fda-2.3.1/fda/inst/scripts/fdarm-ch10.R | 181 +++----
fda-2.3.1/fda/inst/scripts/fdarm-ch11.R | 76 ++
fda-2.3.1/fda/man/CRAN.Rd |only
fda-2.3.1/fda/man/Data2fd.Rd | 25
fda-2.3.1/fda/man/Fperm.fd.Rd | 12
fda-2.3.1/fda/man/arithmetic.fd.Rd | 47 +
fda-2.3.1/fda/man/as.POSIXct1970.Rd |only
fda-2.3.1/fda/man/basisfd.product.Rd | 9
fda-2.3.1/fda/man/bsplinepen.Rd | 16
fda-2.3.1/fda/man/create.bspline.basis.Rd | 97 +++
fda-2.3.1/fda/man/create.monomial.basis.Rd | 14
fda-2.3.1/fda/man/eigen.pda.rd | 15
fda-2.3.1/fda/man/eval.basis.Rd | 33 +
fda-2.3.1/fda/man/eval.fd.Rd | 22
fda-2.3.1/fda/man/eval.monfd.Rd | 9
fda-2.3.1/fda/man/exponentiate.fd.Rd |only
fda-2.3.1/fda/man/fRegress.CV.Rd | 9
fda-2.3.1/fda/man/fRegress.stderr.Rd | 8
fda-2.3.1/fda/man/fd.Rd | 11
fda-2.3.1/fda/man/fdPar.Rd | 5
fda-2.3.1/fda/man/fda-internal.Rd | 2
fda-2.3.1/fda/man/getbasismatrix.Rd | 46 +
fda-2.3.1/fda/man/knots.fd.Rd | 28 -
fda-2.3.1/fda/man/landmarkreg.Rd | 17
fda-2.3.1/fda/man/matplot.Rd |only
fda-2.3.1/fda/man/monomialpen.Rd | 28 -
fda-2.3.1/fda/man/norder.Rd | 33 -
fda-2.3.1/fda/man/odesolv.Rd | 24
fda-2.3.1/fda/man/phaseplanePlot.Rd | 2
fda-2.3.1/fda/man/plot.basisfd.Rd | 17
fda-2.3.1/fda/man/plot.fd.Rd | 21
fda-2.3.1/fda/man/plot.pca.fd.Rd | 29 -
fda-2.3.1/fda/man/plot.pda.fd.rd | 11
fda-2.3.1/fda/man/plotreg.fd.rd | 2
fda-2.3.1/fda/man/readHMD.Rd |only
fda-2.3.1/fda/man/register.fd.Rd | 18
fda-2.3.1/fda/man/smooth.basis.Rd | 105 ++--
fda-2.3.1/fda/man/smooth.monotone.Rd | 10
fda-2.3.1/fda/man/vec2Lfd.Rd | 12
109 files changed, 1907 insertions(+), 2557 deletions(-)
Title: Plot rpart models. An enhanced version of plot.rpart.
Diff between rpart.plot versions 1.3-0 dated 2012-08-18 and 1.4-0 dated 2012-10-10
Description: Plot rpart models. Extends plot.rpart and text.rpart in
the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 6
MD5 | 30
NEWS | 11
R/layout.R | 7
R/mvpart.labs.R |only
R/my.rpartco.R |only
R/my.rpconvert.R |only
R/my.snip.rpart.R |only
R/node.labs.R | 139
R/prp.R | 12
R/snip.R | 10
inst/doc/prp.pdf |binary
man/prp.Rd | 11
man/rpart.plot.Rd | 8
src/tests/code.in.rpart.report.with.prp.R | 86
src/tests/test.prp.R | 104
src/tests/test.prp.Rout.save | 278
src/tests/test.prp.save.ps |18487 ++++++++++++++++++------------
18 files changed, 11449 insertions(+), 7740 deletions(-)
Title: GAMLSS Utilities.
Diff between gamlss.util versions 4.1-1 dated 2012-02-15 and 4.2-0 dated 2012-10-10
Description: Extra utilities for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.util-4.1-1/gamlss.util/R/freeKnots-14-07-10.R |only
gamlss.util-4.1-1/gamlss.util/man/fitFixBP.Rd |only
gamlss.util-4.2-0/gamlss.util/DESCRIPTION | 11
gamlss.util-4.2-0/gamlss.util/MD5 | 19
gamlss.util-4.2-0/gamlss.util/NAMESPACE | 40
gamlss.util-4.2-0/gamlss.util/R/PenRegQ.R |only
gamlss.util-4.2-0/gamlss.util/R/centiles-ts.R |only
gamlss.util-4.2-0/gamlss.util/R/createLags.R |only
gamlss.util-4.2-0/gamlss.util/R/garmaFit.R |only
gamlss.util-4.2-0/gamlss.util/R/lagPlot.R |only
gamlss.util-4.2-0/gamlss.util/R/pbq.R |only
gamlss.util-4.2-0/gamlss.util/R/penReg.R | 829 +++++++++++--------
gamlss.util-4.2-0/gamlss.util/man/centiles.ts.Rd |only
gamlss.util-4.2-0/gamlss.util/man/garmaFit.Rd |only
gamlss.util-4.2-0/gamlss.util/man/lagPlot.Rd |only
gamlss.util-4.2-0/gamlss.util/man/penReg.Rd | 271 +++---
16 files changed, 689 insertions(+), 481 deletions(-)
Title: GAMLSS Additive.
Diff between gamlss.add versions 4.2-0 dated 2012-09-29 and 4.2-1 dated 2012-10-10
Description: Extra additive terms for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/ga.Rd | 19 ++++++++++++-------
3 files changed, 18 insertions(+), 13 deletions(-)
Title: Analysis of categorical-variable datasets with missing values
Diff between cat versions 0.0-6.3 dated 2011-11-04 and 0.0-6.4 dated 2012-10-10
Description: Analysis of categorical-variable with missing values
Author: Ported to R by Ted Harding and Fernando Tusell. Original by
Joseph L. Schafer
Maintainer: Fernando Tusell
DESCRIPTION | 12 ++++++------
MD5 | 7 ++++---
NAMESPACE |only
data/belt.rda |binary
data/older.rda |binary
5 files changed, 10 insertions(+), 9 deletions(-)
Title: classes and methods for spatial data
Diff between sp versions 1.0-0 dated 2012-09-30 and 1.0-1 dated 2012-10-10
Description: A package that provides classes and methods for spatial
data. The classes document where the spatial location
information resides, for 2D or 3D data. Utility functions are
provided, e.g. for plotting data as maps, spatial selection, as
well as methods for retrieving coordinates, for subsetting,
print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut]
Maintainer: Edzer Pebesma
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
R/CRS-methods.R | 14 ++++++++------
R/SpatialGridDataFrame-methods.R | 6 +++---
R/SpatialLines-methods.R | 4 ++--
R/SpatialLinesDataFrame-methods.R | 3 ++-
R/SpatialPolygonsDataFrame-methods.R | 3 ++-
R/over.R | 2 +-
R/spplot.R | 3 ++-
R/spsample.R | 2 +-
inst/doc/intro_sp.pdf |binary
inst/doc/over.pdf |binary
man/over.Rd | 21 ++++++++++++++-------
13 files changed, 51 insertions(+), 39 deletions(-)
Title: cMonkey integrated biclustering algorithm
Diff between cMonkey versions 4.8.5 dated 2011-05-31 and 4.9.2 dated 2012-10-10
Description: cMonkey integrated biclustering algorithm for learning
co-regulated gene modules
Author: David J Reiss, Institute for Systems Biology
Maintainer: David J Reiss
DESCRIPTION | 17
MD5 |only
R/cMonkey.pkg.R | 1833 +++++++++++++++++++++++++++++++------------------
man/cMonkey-package.Rd | 13
4 files changed, 1179 insertions(+), 684 deletions(-)
Title: Aster Models
Diff between aster versions 0.7-8 dated 2012-03-18 and 0.8-19 dated 2012-10-10
Description: functions and datasets for Aster modeling (forest graph
exponential family conditional or unconditional canonical
statistic models for life history analysis)
Author: Charles J. Geyer
Maintainer: Charles J. Geyer
aster-0.7-8/aster/COPYING |only
aster-0.8-19/aster/CHANGES | 75 ++++++++++++++++++++
aster-0.8-19/aster/DESCRIPTION | 9 +-
aster-0.8-19/aster/MD5 | 96 +++++++++++++++++---------
aster-0.8-19/aster/NAMESPACE | 16 ++++
aster-0.8-19/aster/R/aster.R | 2
aster-0.8-19/aster/R/is.zero.R |only
aster-0.8-19/aster/R/newpickle.R |only
aster-0.8-19/aster/R/penmlogl.R |only
aster-0.8-19/aster/R/pickle.R |only
aster-0.8-19/aster/R/pickle3.R |only
aster-0.8-19/aster/R/quickle.R |only
aster-0.8-19/aster/R/reaster.R |only
aster-0.8-19/aster/R/transform.R |only
aster-0.8-19/aster/data/aphid.rda |binary
aster-0.8-19/aster/data/chamae3.rda |only
aster-0.8-19/aster/data/oats.rda |only
aster-0.8-19/aster/data/radish.rda |only
aster-0.8-19/aster/inst/doc/Makefile | 4 -
aster-0.8-19/aster/inst/doc/design.pdf |binary
aster-0.8-19/aster/inst/doc/ktp.pdf |binary
aster-0.8-19/aster/inst/doc/re.Rnw |only
aster-0.8-19/aster/inst/doc/re.pdf |only
aster-0.8-19/aster/inst/doc/trunc.pdf |binary
aster-0.8-19/aster/inst/doc/tutor.pdf |binary
aster-0.8-19/aster/man/anova.aster.Rd | 11 +-
aster-0.8-19/aster/man/aphid.Rd | 7 +
aster-0.8-19/aster/man/aster.Rd | 13 +--
aster-0.8-19/aster/man/chamae.Rd | 13 ++-
aster-0.8-19/aster/man/chamae2.Rd | 12 ++-
aster-0.8-19/aster/man/chamae3.Rd |only
aster-0.8-19/aster/man/echin2.Rd | 8 ++
aster-0.8-19/aster/man/newpickle.Rd |only
aster-0.8-19/aster/man/oats.Rd |only
aster-0.8-19/aster/man/penmlogl.Rd |only
aster-0.8-19/aster/man/pickle.Rd |only
aster-0.8-19/aster/man/predict.aster.Rd | 14 ++-
aster-0.8-19/aster/man/quickle.Rd |only
aster-0.8-19/aster/man/radish.Rd |only
aster-0.8-19/aster/man/reaster.Rd |only
aster-0.8-19/aster/man/summary.reaster.Rd |only
aster-0.8-19/aster/man/transform.Rd |only
aster-0.8-19/aster/src/astfam.c | 24 ++++++
aster-0.8-19/aster/tests/aster.R | 4 -
aster-0.8-19/aster/tests/aster.Rout.save | 16 ++--
aster-0.8-19/aster/tests/cache.R |only
aster-0.8-19/aster/tests/cache.Rout.save |only
aster-0.8-19/aster/tests/gradmat.Rout.save | 34 +++++----
aster-0.8-19/aster/tests/ktnb.Rout.save | 65 ++++++++---------
aster-0.8-19/aster/tests/ktp.R | 2
aster-0.8-19/aster/tests/ktp.Rout.save | 30 ++++----
aster-0.8-19/aster/tests/mlogl-cond.R | 3
aster-0.8-19/aster/tests/mlogl-cond.Rout.save | 43 ++++++-----
aster-0.8-19/aster/tests/mlogl-unco.R | 7 +
aster-0.8-19/aster/tests/mlogl-unco.Rout.save | 72 ++++++++++---------
aster-0.8-19/aster/tests/newpickle.R |only
aster-0.8-19/aster/tests/newpickle.Rout.save |only
aster-0.8-19/aster/tests/penmlogl.R |only
aster-0.8-19/aster/tests/penmlogl.Rout.save |only
aster-0.8-19/aster/tests/pickle.R |only
aster-0.8-19/aster/tests/pickle.Rout.save |only
aster-0.8-19/aster/tests/predict.Rout.save | 34 +++++----
aster-0.8-19/aster/tests/quickle.R |only
aster-0.8-19/aster/tests/quickle.Rout.save |only
aster-0.8-19/aster/tests/reaster.R |only
aster-0.8-19/aster/tests/reaster.Rout.save |only
aster-0.8-19/aster/tests/reaster1.R |only
aster-0.8-19/aster/tests/reaster1.Rout.save |only
68 files changed, 412 insertions(+), 202 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-03 1.1-3
2011-04-05 1.1-2
2010-04-03 1.1.0
2009-01-23 1.0.0