Title: Basic Robust Statistics
Description: "Essential" Robust Statistics. The goal is to provide
tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by Maronna, Martin and Yohai; Wiley 2006.
Author: Original code by many authors, notably
Peter Rousseeuw and Christophe Croux, see file 'Copyrights';
Valentin Todorov
Maintainer: Martin Maechler
Diff between robustbase versions 0.90-1 dated 2014-01-30 and 0.90-2 dated 2014-02-04
DESCRIPTION | 9 ++++---- MD5 | 46 +++++++++++++++++++++--------------------- R/lmrob.M.S.R | 6 ++--- R/lmrob.MM.R | 25 ++++++++++++---------- R/lmrob.R | 45 ++++++++++++++++++++++++++++++++++++++--- inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary man/M.psi.Rd | 1 man/adjbox.Rd | 2 - man/lmrob.Rd | 9 ++++++++ man/summary.lmrob.Rd | 19 +++++++++++++++++ tests/NAcoef.Rout.save | 7 +++--- tests/Rsquared.R |only tests/Rsquared.Rout.save |only tests/lmrob-data.Rout.save | 14 +++++++++--- tests/lmrob-methods.Rout.save | 10 +++++++-- tests/lmrob-psifns.Rout.save | 19 ++++++++++++----- tests/weights.Rout.save | 9 +++++--- vignettes/psi-GGW.pdf |binary vignettes/psi-Hampel.pdf |binary vignettes/psi-Huber.pdf |binary vignettes/psi-LQQ.pdf |binary vignettes/psi-Welsh.pdf |binary vignettes/psi-bisquare.pdf |binary vignettes/psi-optimal.pdf |binary 25 files changed, 160 insertions(+), 61 deletions(-)
Title: A collection of network data sets for the igraph package
Description: A small collection of various network data sets,
to use with the igraph package. They also work with the igraph0
package.
Author: Gabor Csardi
Maintainer: Gabor Csardi
Diff between igraphdata versions 0.1-1 dated 2013-01-07 and 0.2 dated 2014-02-04
DESCRIPTION | 21 +++++++++++---------- MD5 | 6 +++--- data/karate.rda |binary man/karate.Rd | 2 +- 4 files changed, 15 insertions(+), 14 deletions(-)
Title: An R package for the analysis of epidemiological data
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson
Maintainer: Mark Stevenson
Diff between epiR versions 0.9-56 dated 2014-01-27 and 0.9-57 dated 2014-02-04
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/epi.2by2.Rd | 6 +++++- 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Analyzes Differential Promoter Composition in CAGE data
Description: CAGExploreR implements an algorithm to calculate and evaluate the statistical significance of the uncertainty coefficient (a.k.a. Theil's U or the proportional entropy reduction). This statistic measures the strength of association between two nominal random variables. One specific application of this package is the detection of differential composition (differences in vectors of proportions) of genes subunits (e.g. promoters) across various biological conditions. The two nominal variables here are the biological conditions and the promoters within genes. The differential composition and the genomic location of these promoters can also be visualized using this package.
Author: Emmanuel Dimont
Maintainer: Emmanuel Dimont
Diff between CAGExploreR versions 1.0 dated 2014-01-28 and 1.0.1 dated 2014-02-04
DESCRIPTION | 6 MD5 | 14 R/diffcomp.R | 9 README.md | 24 inst/doc/CAGExploreR.R | 24 inst/doc/CAGExploreR.Rnw | 34 inst/doc/CAGExploreR.pdf | 2584 +++++++++++++++++++++++----------------------- vignettes/CAGExploreR.Rnw | 34 8 files changed, 1376 insertions(+), 1353 deletions(-)
Title: Goodness-of-fit functions for comparison of simulated and
observed hydrological time series
Description: S3 functions implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological models. Missing values in observed and/or simulated values can be removed before computations. Comments / questions / collaboration of any kind are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre]
Maintainer: Mauricio Zambrano Bigiarini
Diff between hydroGOF versions 0.3-7 dated 2013-06-03 and 0.3-8 dated 2014-02-04
hydroGOF-0.3-7/hydroGOF/WhatsNew.txt |only hydroGOF-0.3-8/hydroGOF/ChangeLog |only hydroGOF-0.3-8/hydroGOF/DESCRIPTION | 21 +--- hydroGOF-0.3-8/hydroGOF/MD5 | 72 ++++++++--------- hydroGOF-0.3-8/hydroGOF/NAMESPACE | 4 hydroGOF-0.3-8/hydroGOF/NEWS | 11 ++ hydroGOF-0.3-8/hydroGOF/R/KGE.R | 5 - hydroGOF-0.3-8/hydroGOF/R/ggof.R | 2 hydroGOF-0.3-8/hydroGOF/build |only hydroGOF-0.3-8/hydroGOF/inst/doc/hydroGOF_Vignette.pdf |binary hydroGOF-0.3-8/hydroGOF/man/KGE.Rd | 2 hydroGOF-0.3-8/hydroGOF/man/NSE.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/br2.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/cp.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/d.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/ggof.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/gof.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/hydroGOF-package.Rd | 18 ++-- hydroGOF-0.3-8/hydroGOF/man/mNSE.rd | 3 hydroGOF-0.3-8/hydroGOF/man/mae.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/md.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/me.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/mse.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/nrmse.Rd | 23 +++-- hydroGOF-0.3-8/hydroGOF/man/pbias.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/pbiasfdc.Rd | 5 - hydroGOF-0.3-8/hydroGOF/man/pfactor.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/plot2.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/plotbands.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/plotbandsonly.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/rNSE.rd | 3 hydroGOF-0.3-8/hydroGOF/man/rSD.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/rd.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/rfactor.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/rmse.Rd | 4 hydroGOF-0.3-8/hydroGOF/man/rsr.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/ssq.Rd | 3 hydroGOF-0.3-8/hydroGOF/man/valindex.Rd | 2 hydroGOF-0.3-8/hydroGOF/vignettes |only 39 files changed, 116 insertions(+), 119 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: This package implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
Diff between strum versions 0.1 dated 2013-11-05 and 0.2 dated 2014-02-04
ChangeLog |only DESCRIPTION | 18 +- MD5 | 23 +-- NAMESPACE | 4 R/00strumVirtualModel.R | 307 +++++++++++++++++++++++++++++++++++++++++ R/01strumSimModel.R | 14 + R/02strumModel.R | 13 + inst/doc/strum-example.pdf |binary inst/doc/strum-intro.pdf |binary man/strum-package.Rd | 4 man/strumModel-class.Rd | 3 man/strumSimModel-class.Rd | 3 man/strumVirtualModel-class.Rd | 4 13 files changed, 369 insertions(+), 24 deletions(-)
Title: Read and write of MAT files together with R-to-MATLAB
connectivity
Description: This package provides methods readMat() and writeMat() to read and write MAT files. It also makes it possible to communicate (evaluate code, send and retrieve objects etc.) with MATLAB v6 or higher running locally or on a remote host.
Author: Henrik Bengtsson [aut, cre, cph], Andy Jacobson [ctb] (Internal MAT v4 reader), Jason Riedy [ctb] (Support for reading compressed files (via 'Rcompression'), sparse matrices and UTF-encoded strings.)
Maintainer: Henrik Bengtsson
Diff between R.matlab versions 2.1.0 dated 2013-12-06 and 2.2.3 dated 2014-02-04
R.matlab-2.1.0/R.matlab/inst/NEWS |only R.matlab-2.2.3/R.matlab/DESCRIPTION | 12 - R.matlab-2.2.3/R.matlab/MD5 | 21 +- R.matlab-2.2.3/R.matlab/NAMESPACE | 3 R.matlab-2.2.3/R.matlab/NEWS |only R.matlab-2.2.3/R.matlab/R/999.package.R | 16 - R.matlab-2.2.3/R.matlab/R/Matlab.R | 98 +++++---- R.matlab-2.2.3/R.matlab/R/readMat.R | 101 +++++++++- R.matlab-2.2.3/R.matlab/inst/externals/MatlabServer.m | 31 ++- R.matlab-2.2.3/R.matlab/man/1._The_MATLAB_server_running_in_MATLAB.Rd | 31 ++- R.matlab-2.2.3/R.matlab/man/Matlab.Rd | 37 +-- R.matlab-2.2.3/R.matlab/man/R.matlab-package.Rd | 20 - R.matlab-2.2.3/R.matlab/tests/Matlab.R |only 13 files changed, 247 insertions(+), 123 deletions(-)
Title: Exact (Restricted) Likelihood Ratio tests for mixed and additive
models.
Description: Rapid, simulation-based exact (restricted) likelihood ratio tests
for testing the presence of variance components/nonparametric terms for
models fit with nlme::lme(),lme4::lmer(), mgcv::gamm() and SemiPar:spm()
Author: Fabian Scheipl, Ben Bolker
Maintainer: Fabian Scheipl
Diff between RLRsim versions 2.1-2 dated 2014-02-03 and 2.1-3 dated 2014-02-04
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 3 ++- R/LRTSim.R | 1 + R/RLRTSim.R | 1 + 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
Diff between psych versions 1.4.2 dated 2014-02-03 and 1.4.2.3 dated 2014-02-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/print.psych.fa.R | 8 ++++---- inst/CITATION | 4 ++-- inst/NEWS.Rd | 9 +++++++++ inst/doc/overview.pdf |binary inst/doc/psych_for_sem.pdf |binary 7 files changed, 25 insertions(+), 16 deletions(-)
Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre],
Mark S. Handcock [aut],
Susan M. Shortreed [ctb],
Jeremy Tantrum [ctb],
Peter D. Hoff [ctb]
Maintainer: Pavel N. Krivitsky
Diff between latentnet versions 2.4.6 dated 2013-11-28 and 2.5.0 dated 2014-02-04
ChangeLog | 14 ++ DESCRIPTION | 14 +- MD5 | 26 ++--- NAMESPACE | 3 R/InitErgmm.fixed.R | 213 ++++++++++++++++++++++++++++++++------------- R/InitErgmm.latent.R | 8 - R/ergmm.get.model.R | 65 ++++++++++--- R/gof.ergmm.R | 1 R/mcmc.diagnostics.ergmm.R | 11 -- R/print.ergmm.model.R | 5 - R/summary.ergmm.R | 7 + man/ergmm.Rd | 10 +- man/summary.ergmm.Rd | 16 ++- man/terms.ergmm.Rd | 155 +++++++++++++++++++++++++++----- 14 files changed, 407 insertions(+), 141 deletions(-)
Title: Plot a model's response while varying the values of the
predictors.
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
Diff between plotmo versions 1.3-2 dated 2012-05-01 and 1.3-3 dated 2014-02-04
plotmo-1.3-2/plotmo/src |only plotmo-1.3-3/plotmo/DESCRIPTION | 9 ++--- plotmo-1.3-3/plotmo/MD5 | 42 ++++++++++++------------ plotmo-1.3-3/plotmo/NEWS | 6 ++- plotmo-1.3-3/plotmo/R/plotmo.R | 2 + plotmo-1.3-3/plotmo/inst |only plotmo-1.3-3/plotmo/man/plotmo.Rd | 26 ++++++++++---- plotmo-1.3-3/plotmo/tests/test.plotmo.R | 2 - plotmo-1.3-3/plotmo/tests/test.plotmo.Rout.save | 2 - 9 files changed, 53 insertions(+), 36 deletions(-)
Title: Observed-Score Linking and Equating
Description: The equate package contains methods for
observed-score linking and equating under the single-
group, equivalent-groups, and nonequivalent-groups
designs. Equating types include identity, mean, linear,
general linear, equipercentile, circle-arc, and
composites of these. Equating methods include synthetic,
nominal weights, Tucker, Levine observed score, Levine
true score, Braun/Holland, frequency estimation, and
chained equating. Plotting and summary methods, and
methods for univariate and bivariate presmoothing are
also provided.
Author: Anthony Albano
Maintainer: Anthony Albano
Diff between equate versions 2.0-0 dated 2014-01-07 and 2.0-1 dated 2014-02-04
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 24 +++++++++++++++++++++++- R/circlearc.R | 1 + R/equate.R | 8 ++++---- R/equipercentile.R | 44 +++++++++++++++++++++++--------------------- R/freqtab.R | 6 ++++-- R/linear.R | 3 +++ man/equate-package.rd | 4 ++-- 9 files changed, 72 insertions(+), 42 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Description: Fit latent (hidden) Markov models on mixed categorical and continuous (time series)
data, otherwise known as dependent mixture models
Author: Ingmar Visser
Maintainer: Ingmar Visser
Diff between depmixS4 versions 1.3-1 dated 2013-12-11 and 1.3-2 dated 2014-02-04
DESCRIPTION | 10 +++--- MD5 | 23 ++++++++------- NEWS | 71 ++++++++++++++++++++++++++----------------------- build |only data/balance.rda |binary data/sp500.rda |binary data/speed.rda |binary inst/doc/depmixS4.R | 48 ++++++++++++++++----------------- inst/doc/depmixS4.Rnw | 24 ++++++++-------- inst/doc/depmixS4.pdf |binary man/responses.Rd | 2 - vignettes/depmixS4.Rnw | 24 ++++++++-------- vignettes/depmixS4.bib | 24 ++++++++-------- 13 files changed, 119 insertions(+), 107 deletions(-)
Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme
value and some more copula families. Methods for density, distribution,
random number generation, bivariate dependence measures, perspective and
contour plots. Fitting copula models including variance estimates.
Independence and serial (univariate and multivariate) independence tests,
and other copula related tests. Empirical copula and multivariate CDF.
Goodness-of-fit tests for copulas based on multipliers, the parametric
bootstrap with several transformation options.
Merged former package 'nacopula' for nested Archimedean copulas: Efficient
sampling algorithms, various estimators, goodness-of-fit tests and related
tools and special functions.
Author: Marius Hofert
Maintainer: Martin Maechler
Diff between copula versions 0.999-7 dated 2013-05-21 and 0.999-8 dated 2014-02-04
DESCRIPTION | 53 +- MD5 | 154 +++--- NAMESPACE | 15 R/acR.R | 18 R/amhCopula.R | 33 - R/archmCopula.R | 10 R/asymExplicitCopula.R | 12 R/aux-acopula.R | 11 R/claytonCopula.R | 29 - R/cop_objects.R | 67 +- R/derCdfPdf.R | 30 - R/device.R |only R/empcop.R | 111 ++-- R/estimation.R | 12 R/fgmCopula.R | 20 R/fitCopula.R | 93 ++- R/frankCopula.R | 31 - R/galambosCopula.R | 4 R/ggraph-tools.R | 23 R/graphics.R | 59 +- R/gumbelCopula.R | 30 - R/indepCopula.R | 20 R/joeCopula.R | 13 R/pairsRosenblatt.R | 32 - R/rstable1.R | 23 R/special-func.R | 10 R/tawnCopula.R | 4 R/tevCopula.R | 4 R/wrapper.R | 8 TODO | 28 + build |only demo/G_ak.R | 2 demo/dDiag-plots.R | 4 demo/dnac-demo.R | 2 demo/gof_graph.R | 80 +-- demo/gof_radial.R | 1010 ++++++++++++++++++++++++------------------- demo/logL-vis.R | 24 - demo/polyGJ.R | 2 demo/retstable.R | 4 inst/Rsource/AC-Liouville.R | 229 ++++++--- inst/Rsource/MO.R |only inst/Rsource/dnac.R | 8 inst/doc/Frank-Rmpfr.pdf |binary inst/doc/nacopula-pkg.pdf |binary man/Copula.Rd | 4 man/Mvdc.Rd | 24 - man/absdpsiMC.Rd | 11 man/acR.Rd | 5 man/archmCopula.Rd | 32 + man/assocMeasures.Rd | 24 - man/copula-package.Rd | 2 man/dDiag.Rd | 9 man/device.Rd |only man/dnacopula.Rd | 11 man/ellipCopula.Rd | 2 man/emde.Rd | 13 man/emle.Rd | 16 man/empcop.Rd | 61 +- man/enacopula.Rd | 15 man/estim-misc.Rd | 15 man/evTestA.Rd | 6 man/evTestC.Rd | 6 man/evTestK.Rd | 12 man/fitCopula.Rd | 11 man/fitMvdc.Rd | 4 man/gnacopula.Rd | 2 man/gofTrafos.Rd | 6 man/indepCopula-class.Rd | 12 man/initOpt.Rd | 2 man/pairsRosenblatt.Rd | 12 man/pobs.Rd | 12 man/qqplot2.Rd | 30 + man/setTheta.Rd | 2 tests/Stirling-etc.R | 8 tests/copula-play.R | 4 tests/estim-ex.R | 4 tests/fitting-ex.R | 54 +- tests/nac-experi.R | 18 tests/tail-pcopula.R | 26 - tests/tail-pcopula.Rout.save | 35 - 80 files changed, 1689 insertions(+), 1143 deletions(-)
Title: Variational Bayesian mixture models
Description: Variational algorithms and methods for fitting mixture
models. Main functions are varbayes, vbcomp, vbconstr, mppca,
mmppca and gmmkmsock.
Author: Pierrick Bruneau
Maintainer: Pierrick Bruneau
Diff between VBmix versions 0.2.13 dated 2013-06-25 and 0.2.16 dated 2014-02-04
VBmix-0.2.13/VBmix/socket |only VBmix-0.2.16/VBmix/DESCRIPTION | 16 ++++++++-------- VBmix-0.2.16/VBmix/MD5 | 32 ++++++++++++++++---------------- VBmix-0.2.16/VBmix/R/RGBtoLab.R | 8 ++++---- VBmix-0.2.16/VBmix/R/Rutils.R | 14 +++++++------- VBmix-0.2.16/VBmix/R/classicEM.R | 4 ++-- VBmix-0.2.16/VBmix/R/displayScatter.R | 20 ++++++++++++++------ VBmix-0.2.16/VBmix/R/interfaces.R | 2 +- VBmix-0.2.16/VBmix/data/VBmix.RData |binary VBmix-0.2.16/VBmix/inst |only VBmix-0.2.16/VBmix/man/displayNnet.Rd | 4 ++-- VBmix-0.2.16/VBmix/man/displaySVM.Rd | 2 +- VBmix-0.2.16/VBmix/src/mppca.cpp | 6 ++++-- VBmix-0.2.16/VBmix/src/utils.c | 1 + VBmix-0.2.16/VBmix/src/varbayes.c | 8 ++++---- VBmix-0.2.16/VBmix/src/vbconstr.c | 5 +++++ 16 files changed, 69 insertions(+), 53 deletions(-)
Title: Differential Evolution Optimization in pure R
Description: An implementation of the jDE variant of the Differential Evolution
stochastic algorithm for global optimization of nonlinear programming problems.
Author: Eduardo L. T. Conceicao and Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao
Diff between DEoptimR versions 1.0-0 dated 2014-01-27 and 1.0-1 dated 2014-02-04
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/JDEoptim.R | 2 +- tests/JDEoptim-tst.R | 6 ++++-- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: SNPs enrichment analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal)
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil
Diff between snpEnrichment versions 1.2-3 dated 2013-09-27 and 1.4-0 dated 2014-02-04
snpEnrichment-1.2-3/snpEnrichment/data/datalist |only snpEnrichment-1.2-3/snpEnrichment/data/toyEnrichmentM1.RData |only snpEnrichment-1.2-3/snpEnrichment/data/toyEnrichmentM2.RData |only snpEnrichment-1.2-3/snpEnrichment/man/summary-methods.Rd |only snpEnrichment-1.2-3/snpEnrichment/man/toyEnrichmentM1-dataset.Rd |only snpEnrichment-1.2-3/snpEnrichment/man/toyEnrichmentM2-dataset.Rd |only snpEnrichment-1.4-0/snpEnrichment/ChangeLog | 86 snpEnrichment-1.4-0/snpEnrichment/DESCRIPTION | 9 snpEnrichment-1.4-0/snpEnrichment/MD5 | 183 snpEnrichment-1.4-0/snpEnrichment/NAMESPACE | 4 snpEnrichment-1.4-0/snpEnrichment/R/Global.R | 640 snpEnrichment-1.4-0/snpEnrichment/R/SNP.R | 116 snpEnrichment-1.4-0/snpEnrichment/R/chromosome.R | 210 snpEnrichment-1.4-0/snpEnrichment/R/enrichment.R | 998 snpEnrichment-1.4-0/snpEnrichment/data/toyEnrichment.RData |only snpEnrichment-1.4-0/snpEnrichment/inst/extdata/Exclude/toyExclude.txt | 398 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom1-toyList.txt | 201 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom10-toyList.txt | 140 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom11-toyList.txt | 156 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom12-toyList.txt | 134 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom13-toyList.txt | 99 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom14-toyList.txt | 85 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom15-toyList.txt | 68 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom16-toyList.txt | 78 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom17-toyList.txt | 59 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom18-toyList.txt | 73 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom19-toyList.txt | 48 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom2-toyList.txt | 221 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom20-toyList.txt | 61 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom21-toyList.txt | 30 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom22-toyList.txt | 37 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom3-toyList.txt | 196 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom4-toyList.txt | 173 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom5-toyList.txt | 180 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom6-toyList.txt | 167 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom7-toyList.txt | 147 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom8-toyList.txt | 172 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/List/Chrom9-toyList.txt | 141 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/Signal/toySignal.txt |20001 ++++------ snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom1-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom1-toy.bim | 1515 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom10-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom10-toy.bim | 1081 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom11-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom11-toy.bim | 1027 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom12-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom12-toy.bim | 974 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom13-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom13-toy.bim | 802 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom14-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom14-toy.bim | 658 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom15-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom15-toy.bim | 559 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom16-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom16-toy.bim | 559 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom17-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom17-toy.bim | 462 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom18-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom18-toy.bim | 599 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom19-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom19-toy.bim | 299 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom2-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom2-toy.bim | 1731 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom20-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom20-toy.bim | 492 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom21-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom21-toy.bim | 274 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom22-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom22-toy.bim | 257 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom3-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom3-toy.bim | 1386 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom4-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom4-toy.bim | 1277 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom5-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom5-toy.bim | 1332 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom6-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom6-toy.bim | 1387 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom7-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom7-toy.bim | 1124 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom8-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom8-toy.bim | 1170 snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom9-toy.bed |binary snpEnrichment-1.4-0/snpEnrichment/inst/extdata/snpInfo/Chrom9-toy.bim | 958 snpEnrichment-1.4-0/snpEnrichment/man/Chromosome-class.Rd | 2 snpEnrichment-1.4-0/snpEnrichment/man/EnrichSNP-class.Rd | 4 snpEnrichment-1.4-0/snpEnrichment/man/Enrichment-class.Rd | 17 snpEnrichment-1.4-0/snpEnrichment/man/compareEnrichment.Rd | 29 snpEnrichment-1.4-0/snpEnrichment/man/excludeSNP-methods.Rd | 6 snpEnrichment-1.4-0/snpEnrichment/man/initFiles.Rd | 17 snpEnrichment-1.4-0/snpEnrichment/man/plot-methods.Rd | 15 snpEnrichment-1.4-0/snpEnrichment/man/print-methods.Rd |only snpEnrichment-1.4-0/snpEnrichment/man/reSample-methods.Rd | 20 snpEnrichment-1.4-0/snpEnrichment/man/readEnrichment.Rd | 12 snpEnrichment-1.4-0/snpEnrichment/man/snpEnrichment-internal.Rd | 5 snpEnrichment-1.4-0/snpEnrichment/man/snpEnrichment-package.Rd | 33 snpEnrichment-1.4-0/snpEnrichment/man/toyEnrichment-dataset.Rd |only snpEnrichment-1.4-0/snpEnrichment/man/writeLD.Rd | 15 97 files changed, 22811 insertions(+), 22598 deletions(-)
Title: R interface to the USGS BISON API
Description: This package is an R interface to the USGS BISON API, a database
for species occurrence data on the web. Data comes from species in the
United States, from participating data providers. This package focuses on
getting the data from BISON - but does provide a function to help visualize
data quickly.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
Diff between rbison versions 0.2.4 dated 2013-12-02 and 0.3.0 dated 2014-02-04
rbison-0.2.4/rbison/R/bison_data.r |only rbison-0.2.4/rbison/man/bison_data.Rd |only rbison-0.2.4/rbison/tests/testthat/test-bison_data.R |only rbison-0.2.4/rbison/vignettes/rbison_vignette.pdf |only rbison-0.3.0/rbison/DESCRIPTION | 13 rbison-0.3.0/rbison/MD5 | 65 +-- rbison-0.3.0/rbison/NAMESPACE | 6 rbison-0.3.0/rbison/NEWS | 17 rbison-0.3.0/rbison/R/bison.r | 147 ++++++- rbison-0.3.0/rbison/R/bison_providers.r |only rbison-0.3.0/rbison/R/bison_solr.r | 199 ++++++++-- rbison-0.3.0/rbison/R/bison_tax.r | 45 -- rbison-0.3.0/rbison/R/bisonmap.r | 13 rbison-0.3.0/rbison/R/rbison-package.r | 27 + rbison-0.3.0/rbison/R/startup.r |only rbison-0.3.0/rbison/R/zzz.r | 34 - rbison-0.3.0/rbison/README.md | 89 +++- rbison-0.3.0/rbison/build |only rbison-0.3.0/rbison/data/fips.rda |binary rbison-0.3.0/rbison/inst |only rbison-0.3.0/rbison/man/all_states.Rd | 3 rbison-0.3.0/rbison/man/bison.Rd | 74 ++- rbison-0.3.0/rbison/man/bison_map_maker.Rd | 4 rbison-0.3.0/rbison/man/bison_providers.Rd |only rbison-0.3.0/rbison/man/bison_solr.Rd | 142 ++++--- rbison-0.3.0/rbison/man/bison_tax.Rd | 56 +- rbison-0.3.0/rbison/man/bisonmap.Rd | 17 rbison-0.3.0/rbison/man/blanktheme.Rd | 4 rbison-0.3.0/rbison/man/fips.Rd | 3 rbison-0.3.0/rbison/man/is.bison.Rd | 4 rbison-0.3.0/rbison/man/is.bison_solr.Rd | 4 rbison-0.3.0/rbison/man/rbison-package.Rd |only rbison-0.3.0/rbison/tests/testthat/test-bison.R | 14 rbison-0.3.0/rbison/tests/testthat/test-bison_solr.R | 33 - rbison-0.3.0/rbison/tests/testthat/test-bison_tax.R | 18 rbison-0.3.0/rbison/vignettes/rbison_vignette.Rmd | 353 ++++++++++++++++++ rbison-0.3.0/rbison/vignettes/rbison_vignette.html | 364 ++++++++++++++++++- rbison-0.3.0/rbison/vignettes/rbison_vignette.md |only 38 files changed, 1370 insertions(+), 378 deletions(-)
Title: Pumilio in R
Description: R package to query and get data out of a Pumilio sound archive system (http://ljvillanueva.github.io/pumilio/).
Author: Luis J. Villanueva-Rivera
Maintainer: Luis J. Villanueva-Rivera
Diff between pumilioR versions 1.1 dated 2014-01-02 and 1.2 dated 2014-02-04
pumilioR-1.1/pumilioR/R/getVersion.R |only pumilioR-1.1/pumilioR/man/getVersion.Rd |only pumilioR-1.2/pumilioR/.Rinstignore |only pumilioR-1.2/pumilioR/DESCRIPTION | 15 +++++++---- pumilioR-1.2/pumilioR/MD5 | 33 +++++++++++++++----------- pumilioR-1.2/pumilioR/NAMESPACE | 4 +-- pumilioR-1.2/pumilioR/NEWS |only pumilioR-1.2/pumilioR/R/checkVersion.R |only pumilioR-1.2/pumilioR/R/getCollections.R | 22 +++++++++++------ pumilioR-1.2/pumilioR/R/getFile.R | 16 ++++++++---- pumilioR-1.2/pumilioR/R/getSites.R | 25 +++++++++++-------- pumilioR-1.2/pumilioR/R/getSounds.R | 21 +++++++++++----- pumilioR-1.2/pumilioR/build |only pumilioR-1.2/pumilioR/inst |only pumilioR-1.2/pumilioR/man/checkVersion.Rd |only pumilioR-1.2/pumilioR/man/getCollections.Rd | 13 +++++++--- pumilioR-1.2/pumilioR/man/getFile.Rd | 6 +++- pumilioR-1.2/pumilioR/man/getSites.Rd | 14 +++++++---- pumilioR-1.2/pumilioR/man/getSounds.Rd | 15 +++++++---- pumilioR-1.2/pumilioR/man/pumilioR.package.Rd | 8 +++--- pumilioR-1.2/pumilioR/vignettes |only 21 files changed, 122 insertions(+), 70 deletions(-)
Title: Permutation Distribution Clustering
Description: Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
Author: Andreas M. Brandmaier
Maintainer: Andreas M. Brandmaier
Diff between pdc versions 0.3 dated 2012-05-21 and 0.4 dated 2014-02-04
pdc-0.3/pdc/man/symmetric.alpha.divergence.Rd |only pdc-0.3/pdc/src/factorial.h |only pdc-0.4/pdc/ChangeLog | 6 +++++ pdc-0.4/pdc/DESCRIPTION | 17 +++++--------- pdc-0.4/pdc/MD5 | 31 ++++++++++++++++---------- pdc-0.4/pdc/NAMESPACE | 7 +++++ pdc-0.4/pdc/R/codebook.R | 9 +++++-- pdc-0.4/pdc/R/convert.image.R |only pdc-0.4/pdc/R/hellinger.distance.R |only pdc-0.4/pdc/R/pdclust.R | 1 pdc-0.4/pdc/R/plot.mine.R | 6 ++--- pdc-0.4/pdc/R/squared.hellinger.distance.R |only pdc-0.4/pdc/R/symmetric.alpha.divergence.R | 4 +-- pdc-0.4/pdc/R/trace.image.R |only pdc-0.4/pdc/data |only pdc-0.4/pdc/man/codebook.Rd | 4 ++- pdc-0.4/pdc/man/complex.shapes.Rd |only pdc-0.4/pdc/man/distance.Rd |only pdc-0.4/pdc/man/pdc-package.Rd | 1 pdc-0.4/pdc/man/star.shapes.Rd |only pdc-0.4/pdc/man/trace.image.Rd |only pdc-0.4/pdc/src/fast_codebook0.c |only 22 files changed, 55 insertions(+), 31 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst
Diff between paleotree versions 1.9 dated 2014-01-03 and 2.0 dated 2014-02-04
CHANGELOG | 15 ++ DESCRIPTION | 8 - MD5 | 50 +++++---- NAMESPACE | 3 R/DiversityCurves.R | 2 R/cal3TimePaleoPhy.R | 138 +++++++++++++++++++-------- R/compareTimescaling.R | 3 R/constrainParPaleo.R | 7 - R/dateNodes.R |only R/degradeTree.R | 68 ++++++++++++- R/durationFreq.R | 44 +++++++- R/footeValues.R | 67 +++++++------ R/inverseSurv.R |only R/modelMethods.R | 20 ++- R/perCapitaRates.R | 25 +++- R/plotTraitgram.R | 7 + R/timePaleoPhy.R | 216 ++++++++++++++++++++++++++++++------------ man/cal3TimePaleoPhy.Rd | 118 +++++++++++++++-------- man/compareTimescaling.Rd | 3 man/constrainParPaleo.Rd | 10 - man/dateNodes.Rd |only man/degradeTree.Rd | 43 +++++++- man/durationFreq.Rd | 38 ++++++- man/footeValues.Rd | 83 +++++++++------- man/inverseSurv.Rd |only man/modelMethods.Rd | 21 ++-- man/perCapitaRates.Rd | 19 ++- man/timePaleoPhy.Rd | 232 +++++++++++++++++++++++++++++----------------- 28 files changed, 862 insertions(+), 378 deletions(-)
Title: R port of the Scilab neldermead module
Description: Provides several direct search optimization algorithms based on the
simplex method. The provided algorithms are direct search algorithms, i.e.
algorithms which do not use the derivative of the cost function. They are
based on the update of a simplex. The following algorithms are available: the
fixed shape simplex method of Spendley, Hext and Himsworth (unconstrained
optimization with a fixed shape simplex), the variable shape simplex method of
Nelder and Mead (unconstrained optimization with a variable shape simplex
made), and Box's complex method (constrained optimization with a variable
shape simplex).
Author: Sebastien Bihorel, Michael Baudin (author of the original
module)
Maintainer: Sebastien Bihorel
Diff between neldermead versions 1.0-7 dated 2012-01-04 and 1.0-8 dated 2014-02-04
neldermead-1.0-7/neldermead/R/neldermead.new.R |only neldermead-1.0-7/neldermead/inst/doc/Rd2latex.sh |only neldermead-1.0-7/neldermead/inst/doc/costf.transposex.tex |only neldermead-1.0-7/neldermead/inst/doc/fmin.gridsearch.tex |only neldermead-1.0-7/neldermead/inst/doc/fminsearch.function.tex |only neldermead-1.0-7/neldermead/inst/doc/fminsearch.outputfun.tex |only neldermead-1.0-7/neldermead/inst/doc/fminsearch.pdf |only neldermead-1.0-7/neldermead/inst/doc/fminsearch.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead-package.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.Rnw |only neldermead-1.0-7/neldermead/inst/doc/neldermead.algo.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.bib |only neldermead-1.0-7/neldermead/inst/doc/neldermead.configure.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.destroy.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.function.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.get.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.new.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.pdf |only neldermead-1.0-7/neldermead/inst/doc/neldermead.restart.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.search.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermead.startup.tex |only neldermead-1.0-7/neldermead/inst/doc/neldermeadalgo1.pdf |only neldermead-1.0-7/neldermead/inst/doc/neldermeadalgo2.pdf |only neldermead-1.0-7/neldermead/inst/doc/neldermeadalgo3.pdf |only neldermead-1.0-7/neldermead/inst/doc/neldermeadsearch1.pdf |only neldermead-1.0-7/neldermead/inst/doc/neldermeadsearch2.pdf |only neldermead-1.0-7/neldermead/inst/doc/optimget.tex |only neldermead-1.0-7/neldermead/inst/doc/optimset.method.tex |only neldermead-1.0-7/neldermead/inst/doc/optimset.tex |only neldermead-1.0-7/neldermead/man/neldermead.new.Rd |only neldermead-1.0-8/neldermead/Changelog | 13 neldermead-1.0-8/neldermead/DESCRIPTION | 11 neldermead-1.0-8/neldermead/MD5 | 168 +++--- neldermead-1.0-8/neldermead/NAMESPACE |only neldermead-1.0-8/neldermead/R/boxlinesearch.R | 32 - 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Title: Derivative-free optimization algorithms by quadratic
approximation
Description: Derivative-free optimization by quadratic approximation
based on an interface to Fortran implementations by M. J. D.
Powell.
Author: Douglas Bates, Katharine M. Mullen, John C. Nash, Ravi Varadhan
Maintainer: Katharine M. Mullen
Diff between minqa versions 1.2.2 dated 2013-12-19 and 1.2.3 dated 2014-02-04
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 3 +-- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition
Author: Max Kuhn, Steve Weston, Nathan Coulter. C code for C5.0 by R. Quinlan
Maintainer: Max Kuhn
Diff between C50 versions 0.1.0-15 dated 2013-05-27 and 0.1.0-16 dated 2014-02-04
DESCRIPTION | 14 ++++++-------- MD5 | 10 +++++----- R/C5.0.R | 6 +++--- R/makeDataFile.R | 3 ++- R/makeNamesFile.R | 30 ++++++++++++------------------ man/C5.0.Rd | 3 +-- 6 files changed, 29 insertions(+), 37 deletions(-)