Title: Basic Robust Statistics
Diff between robustbase versions 0.90-1 dated 2014-01-30 and 0.90-2 dated 2014-02-04
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
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
Diff between igraphdata versions 0.1-1 dated 2013-01-07 and 0.2 dated 2014-02-04
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
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
Diff between epiR versions 0.9-56 dated 2014-01-27 and 0.9-57 dated 2014-02-04
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
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/epi.2by2.Rd | 6 +++++-
3 files changed, 11 insertions(+), 7 deletions(-)
Title: Analyzes Differential Promoter Composition in CAGE data
Diff between CAGExploreR versions 1.0 dated 2014-01-28 and 1.0.1 dated 2014-02-04
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
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
Diff between hydroGOF versions 0.3-7 dated 2013-06-03 and 0.3-8 dated 2014-02-04
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
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
Diff between strum versions 0.1 dated 2013-11-05 and 0.2 dated 2014-02-04
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
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
Diff between R.matlab versions 2.1.0 dated 2013-12-06 and 2.2.3 dated 2014-02-04
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
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.
Diff between RLRsim versions 2.1-2 dated 2014-02-03 and 2.1-3 dated 2014-02-04
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
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
Diff between psych versions 1.4.2 dated 2014-02-03 and 1.4.2.3 dated 2014-02-04
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
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
Diff between latentnet versions 2.4.6 dated 2013-11-28 and 2.5.0 dated 2014-02-04
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
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.
Diff between plotmo versions 1.3-2 dated 2012-05-01 and 1.3-3 dated 2014-02-04
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
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
Diff between equate versions 2.0-0 dated 2014-01-07 and 2.0-1 dated 2014-02-04
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
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
Diff between depmixS4 versions 1.3-1 dated 2013-12-11 and 1.3-2 dated 2014-02-04
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
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
Diff between copula versions 0.999-7 dated 2013-05-21 and 0.999-8 dated 2014-02-04
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
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
Diff between VBmix versions 0.2.13 dated 2013-06-25 and 0.2.16 dated 2014-02-04
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
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
Diff between DEoptimR versions 1.0-0 dated 2014-01-27 and 1.0-1 dated 2014-02-04
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
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/JDEoptim.R | 2 +-
tests/JDEoptim-tst.R | 6 ++++--
4 files changed, 14 insertions(+), 12 deletions(-)
Title: SNPs enrichment analysis
Diff between snpEnrichment versions 1.2-3 dated 2013-09-27 and 1.4-0 dated 2014-02-04
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
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
Diff between rbison versions 0.2.4 dated 2013-12-02 and 0.3.0 dated 2014-02-04
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
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
Diff between pumilioR versions 1.1 dated 2014-01-02 and 1.2 dated 2014-02-04
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
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
Diff between pdc versions 0.3 dated 2012-05-21 and 0.4 dated 2014-02-04
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
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
Diff between paleotree versions 1.9 dated 2014-01-03 and 2.0 dated 2014-02-04
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
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
Diff between neldermead versions 1.0-7 dated 2012-01-04 and 1.0-8 dated 2014-02-04
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
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 -
neldermead-1.0-8/neldermead/R/costf.transposex.R | 2
neldermead-1.0-8/neldermead/R/fmin.gridsearch.R | 2
neldermead-1.0-8/neldermead/R/fminbnd.R |only
neldermead-1.0-8/neldermead/R/fminbnd.function.R |only
neldermead-1.0-8/neldermead/R/fminbnd.outputfun.R |only
neldermead-1.0-8/neldermead/R/fminsearch.R | 113 ++--
neldermead-1.0-8/neldermead/R/fminsearch.function.R | 2
neldermead-1.0-8/neldermead/R/fminsearch.outputfun.R | 2
neldermead-1.0-8/neldermead/R/is.R |only
neldermead-1.0-8/neldermead/R/neldermead.R |only
neldermead-1.0-8/neldermead/R/neldermead.algo.R | 2
neldermead-1.0-8/neldermead/R/neldermead.autorestart.R | 2
neldermead-1.0-8/neldermead/R/neldermead.box.R | 21
neldermead-1.0-8/neldermead/R/neldermead.cget.R | 6
neldermead-1.0-8/neldermead/R/neldermead.configure.R | 259 ++++++----
neldermead-1.0-8/neldermead/R/neldermead.costf.R | 2
neldermead-1.0-8/neldermead/R/neldermead.destroy.R | 2
neldermead-1.0-8/neldermead/R/neldermead.fixed.R | 27 -
neldermead-1.0-8/neldermead/R/neldermead.function.R | 2
neldermead-1.0-8/neldermead/R/neldermead.get.R | 2
neldermead-1.0-8/neldermead/R/neldermead.interpolate.R | 2
neldermead-1.0-8/neldermead/R/neldermead.isrkelley.R | 2
neldermead-1.0-8/neldermead/R/neldermead.isroneill.R | 6
neldermead-1.0-8/neldermead/R/neldermead.istorestart.R | 2
neldermead-1.0-8/neldermead/R/neldermead.log.R | 2
neldermead-1.0-8/neldermead/R/neldermead.outputcmd.R | 6
neldermead-1.0-8/neldermead/R/neldermead.restart.R | 2
neldermead-1.0-8/neldermead/R/neldermead.scaletocenter.R | 2
neldermead-1.0-8/neldermead/R/neldermead.scaletox0.R | 2
neldermead-1.0-8/neldermead/R/neldermead.search.R | 3
neldermead-1.0-8/neldermead/R/neldermead.startup.R | 15
neldermead-1.0-8/neldermead/R/neldermead.storehistory.R | 12
neldermead-1.0-8/neldermead/R/neldermead.termination.R | 20
neldermead-1.0-8/neldermead/R/neldermead.termstartup.R | 2
neldermead-1.0-8/neldermead/R/neldermead.updatesimp.R | 18
neldermead-1.0-8/neldermead/R/neldermead.variable.R | 52 +-
neldermead-1.0-8/neldermead/R/optimget.R | 7
neldermead-1.0-8/neldermead/R/optimset.R | 59 --
neldermead-1.0-8/neldermead/R/optimset.method.R | 21
neldermead-1.0-8/neldermead/R/print.neldermead.R |only
neldermead-1.0-8/neldermead/R/scaleinconstraints.R | 2
neldermead-1.0-8/neldermead/R/summary.neldermead.R |only
neldermead-1.0-8/neldermead/build |only
neldermead-1.0-8/neldermead/inst/doc/neldermead_manual.R |only
neldermead-1.0-8/neldermead/inst/doc/neldermead_manual.Rnw |only
neldermead-1.0-8/neldermead/inst/doc/neldermead_manual.pdf |only
neldermead-1.0-8/neldermead/man/fminbnd.Rd |only
neldermead-1.0-8/neldermead/man/fminbnd.function.Rd |only
neldermead-1.0-8/neldermead/man/fminbnd.outputfun.Rd |only
neldermead-1.0-8/neldermead/man/fminsearch.Rd | 13
neldermead-1.0-8/neldermead/man/fminsearch.function.Rd | 8
neldermead-1.0-8/neldermead/man/fminsearch.outputfun.Rd | 24
neldermead-1.0-8/neldermead/man/neldermead-package.Rd | 15
neldermead-1.0-8/neldermead/man/neldermead.Rd |only
neldermead-1.0-8/neldermead/man/neldermead.algo.Rd | 3
neldermead-1.0-8/neldermead/man/neldermead.configure.Rd | 4
neldermead-1.0-8/neldermead/man/neldermead.search.Rd | 2
neldermead-1.0-8/neldermead/man/optimset.Rd | 76 +-
neldermead-1.0-8/neldermead/vignettes |only
94 files changed, 580 insertions(+), 472 deletions(-)
Title: Derivative-free optimization algorithms by quadratic
approximation
Diff between minqa versions 1.2.2 dated 2013-12-19 and 1.2.3 dated 2014-02-04
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
ChangeLog | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
NAMESPACE | 3 +--
4 files changed, 11 insertions(+), 9 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Diff between C50 versions 0.1.0-15 dated 2013-05-27 and 0.1.0-16 dated 2014-02-04
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
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(-)