Title: Competing risks regression models with covariate-adjusted
censoring weight
Diff between wtcrsk versions 1.2 dated 2014-04-30 and 1.3 dated 2014-05-05
Description: Estimation and regression modeling of subdistribution functions for competing risks data with adjustment for covariate-dependent censoring, as described in He et al. (2013).
Author: Peng He
Maintainer: Peng He
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
man/wtcrsk-package.Rd | 4 ++--
src/p1.cc | 4 ++--
4 files changed, 11 insertions(+), 11 deletions(-)
Title: Structural Equation Models
Diff between sem versions 3.1-3 dated 2013-04-09 and 3.1-4 dated 2014-05-05
Description: This package contains functions for fitting general linear structural
equation models (with observed and unobserved variables) using the RAM approach,
and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre],
Zhenghua Nie [aut],
Jarrett Byrnes [aut],
Michael Culbertson [ctb],
Saikat DebRoy [ctb],
Michael Friendly [ctb],
Richard H. Jones [ctb],
Adam Kramer [ctb],
Georges Monette [ctb],
R-Core [ctb]
Maintainer: John Fox
sem-3.1-3/sem/data/Klein.txt.gz |only
sem-3.1-4/sem/DESCRIPTION | 58 ++-
sem-3.1-4/sem/MD5 | 34 +-
sem-3.1-4/sem/NAMESPACE | 5
sem-3.1-4/sem/NEWS | 20 +
sem-3.1-4/sem/R/multigroup.R | 415 +++++++++++++-------------
sem-3.1-4/sem/R/specifyModel.R | 232 +++++++-------
sem-3.1-4/sem/R/summary.methods.R | 6
sem-3.1-4/sem/R/tsls.R | 63 ++-
sem-3.1-4/sem/data/Bollen.rda |binary
sem-3.1-4/sem/data/CNES.rda |binary
sem-3.1-4/sem/data/Klein.txt.bz2 |only
sem-3.1-4/sem/data/Kmenta.txt.gz |binary
sem-3.1-4/sem/data/Tests.rda |binary
sem-3.1-4/sem/man/ML.methods.Rd | 24 +
sem-3.1-4/sem/man/sem.Rd | 52 +--
sem-3.1-4/sem/man/specifyModel.Rd | 17 -
sem-3.1-4/sem/man/standardizedCoefficients.Rd | 3
sem-3.1-4/sem/man/tsls.Rd | 5
19 files changed, 514 insertions(+), 420 deletions(-)
Title: Tools for ecological network analysis (ena) in R
Diff between enaR versions 2.5 dated 2013-11-08 and 2.6 dated 2014-05-05
Description: Functions for the analysis of ecological networks
Author: M.K. Lau, S.R. Borrett, D.E. Hines
Maintainer: Matthew K. Lau
enaR-2.5/enaR/inst |only
enaR-2.5/enaR/vignettes/ecology.bst |only
enaR-2.5/enaR/vignettes/enaR.Rnw |only
enaR-2.5/enaR/vignettes/srb.bib |only
enaR-2.5/enaR/vignettes/srbbib_abb.bib |only
enaR-2.5/enaR/vignettes/srbbib_long.bib |only
enaR-2.6/enaR/DESCRIPTION | 10 ++++----
enaR-2.6/enaR/MD5 | 37 ++++++++++++++------------------
enaR-2.6/enaR/NAMESPACE | 5 ++++
enaR-2.6/enaR/R/pack.R | 3 +-
enaR-2.6/enaR/R/read.enam.R | 4 +--
enaR-2.6/enaR/R/read.scor.R | 11 +++++----
enaR-2.6/enaR/R/read.wand.R | 6 ++---
enaR-2.6/enaR/data/bgcModels.rda |binary
enaR-2.6/enaR/data/enaModelInfo.rda |only
enaR-2.6/enaR/data/enaModels.rda |only
enaR-2.6/enaR/data/oyster.rda |binary
enaR-2.6/enaR/data/troModels.rda |binary
enaR-2.6/enaR/man/TES.Rd | 3 +-
enaR-2.6/enaR/man/enaModelInfo.Rd |only
enaR-2.6/enaR/man/enaModels.Rd |only
enaR-2.6/enaR/man/enaR-package.Rd | 4 +--
enaR-2.6/enaR/man/pack.Rd | 9 +++++--
enaR-2.6/enaR/vignettes/enaR.pdf |only
24 files changed, 50 insertions(+), 42 deletions(-)
Title: Multivariate Dependence with Copulas
Diff between copula versions 0.999-8 dated 2014-02-04 and 0.999-9 dated 2014-05-05
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
copula-0.999-8/copula/do-now.org |only
copula-0.999-8/copula/feature-table.org |only
copula-0.999-9/copula/DESCRIPTION | 11 ++-
copula-0.999-9/copula/MD5 | 53 ++++++++----------
copula-0.999-9/copula/R/aux-acopula.R | 23 +++----
copula-0.999-9/copula/R/fgmCopula.R | 61 +++++++++++++++------
copula-0.999-9/copula/R/gofTests.R | 4 -
copula-0.999-9/copula/R/gofTrafos.R | 53 ++++++++++++++++--
copula-0.999-9/copula/R/graphics.R | 19 +++---
copula-0.999-9/copula/R/normalCopula.R | 35 ++++++++++++
copula-0.999-9/copula/TODO | 10 ++-
copula-0.999-9/copula/build/vignette.rds |binary
copula-0.999-9/copula/inst/doc/Frank-Rmpfr.pdf |binary
copula-0.999-9/copula/inst/doc/nacopula-pkg.pdf |binary
copula-0.999-9/copula/man/fitCopula.Rd | 2
copula-0.999-9/copula/man/gofTrafos.Rd | 18 ++++--
copula-0.999-9/copula/man/indepTest.Rd | 21 +++++--
copula-0.999-9/copula/man/qqplot2.Rd | 20 +++---
copula-0.999-9/copula/man/retstable.Rd | 8 ++
copula-0.999-9/copula/src/copula_int.h |only
copula-0.999-9/copula/src/ecIndepTest.c | 47 ++++++++++------
copula-0.999-9/copula/src/indepTest_utils.c | 16 ++---
copula-0.999-9/copula/src/indepTests.h | 2
copula-0.999-9/copula/src/multIndepTest.c | 26 ++++++--
copula-0.999-9/copula/src/multSerialIndepTest.c | 22 ++++++-
copula-0.999-9/copula/src/nacopula.h | 10 ---
copula-0.999-9/copula/src/serialIndepTest.c | 22 ++++++-
copula-0.999-9/copula/tests/tail-pcopula.R | 13 ++--
copula-0.999-9/copula/tests/tail-pcopula.Rout.save | 20 +++---
29 files changed, 349 insertions(+), 167 deletions(-)
Title: Polygon Clipping
Diff between polyclip versions 1.2-0 dated 2013-11-21 and 1.3-0 dated 2014-05-05
Description: R port of the Clipper library. Performs polygon clipping operations (intersection, union, set minus, set difference) for polygonal regions of arbitrary complexity, including holes. Also computes offset polygons (spatial buffer zones, morphological dilations, Minkowski dilations) for polygonal regions and polygonal lines.
Author: Angus Johnson. Ported to R by Adrian Baddeley and Brian Ripley.
Maintainer: Adrian Baddeley
DESCRIPTION | 8
MD5 | 18
R/clipper.R | 124 -
configure | 4
configure.ac | 4
man/polylineoffset.Rd | 48
man/polyoffset.Rd | 24
src/clipper.cpp | 4777 +++++++++++++++++++++++++++++---------------------
src/clipper.h | 368 ++-
src/interface.cpp | 213 +-
10 files changed, 3292 insertions(+), 2296 deletions(-)
Title: Multivariate Normal and t Distributions
Diff between mvtnorm versions 0.9-99991 dated 2014-04-25 and 0.9-99992 dated 2014-05-05
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch,
Fabian Scheipl, Bjoern Bornkamp, Martin Maechler, Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 12 ++--
MD5 | 22 ++++----
NAMESPACE | 6 +-
R/mvnorm.R | 114 ++++++++++++++++++------------------------
R/mvt.R | 116 +++++++++++++++++++------------------------
inst/NEWS | 6 +-
inst/doc/MVT_Rnews.pdf |binary
man/Mvnorm.Rd | 31 +++++------
man/Mvt.Rd | 3 -
tests/bugfix-tests.R | 43 +++++++++++----
tests/bugfix-tests.Rout.save | 57 +++++++++++++++------
tests/rmvnorm.R | 22 ++++++++
12 files changed, 242 insertions(+), 190 deletions(-)
Title: Meta-Analysis Package for R
Diff between metafor versions 1.9-2 dated 2013-10-07 and 1.9-3 dated 2014-05-05
Description: The metafor package provides a comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects (conditional) logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer
Maintainer: Wolfgang Viechtbauer
metafor-1.9-2/metafor/man/baujat.rma.uni.Rd |only
metafor-1.9-2/metafor/man/blup.rma.uni.Rd |only
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metafor-1.9-2/metafor/man/radial.rma.Rd |only
metafor-1.9-2/metafor/man/ranktest.rma.Rd |only
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metafor-1.9-2/metafor/man/trimfill.rma.uni.Rd |only
metafor-1.9-2/metafor/man/weights.rma.uni.Rd |only
metafor-1.9-3/metafor/DESCRIPTION | 15
metafor-1.9-3/metafor/MD5 | 246
metafor-1.9-3/metafor/NAMESPACE | 10
metafor-1.9-3/metafor/NEWS | 202
metafor-1.9-3/metafor/R/metafor.R | 5817 ++++++++++-------
metafor-1.9-3/metafor/build |only
metafor-1.9-3/metafor/data/dat.bangertdrowns2004.rda |binary
metafor-1.9-3/metafor/data/dat.bcg.rda |binary
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metafor-1.9-3/metafor/data/dat.berkey1998.rda |binary
metafor-1.9-3/metafor/data/dat.bonett2010.rda |binary
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metafor-1.9-3/metafor/data/dat.collins1985a.rda |binary
metafor-1.9-3/metafor/data/dat.collins1985b.rda |binary
metafor-1.9-3/metafor/data/dat.curtis1998.rda |binary
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metafor-1.9-3/metafor/data/dat.nielweise2008.rda |binary
metafor-1.9-3/metafor/data/dat.normand1999.rda |binary
metafor-1.9-3/metafor/data/dat.pignon2000.rda |binary
metafor-1.9-3/metafor/data/dat.pritz1997.rda |binary
metafor-1.9-3/metafor/data/dat.raudenbush1985.rda |binary
metafor-1.9-3/metafor/data/dat.yusuf1985.rda |binary
metafor-1.9-3/metafor/inst/doc/metafor.Rnw |only
metafor-1.9-3/metafor/inst/doc/metafor_diagram.Rnw |only
metafor-1.9-3/metafor/inst/doc/metafor_diagram.pdf |binary
metafor-1.9-3/metafor/man/addpoly.Rd | 2
metafor-1.9-3/metafor/man/addpoly.default.Rd | 25
metafor-1.9-3/metafor/man/addpoly.rma.Rd | 34
metafor-1.9-3/metafor/man/anova.rma.uni.Rd | 18
metafor-1.9-3/metafor/man/baujat.Rd | 51
metafor-1.9-3/metafor/man/bldiag.Rd |only
metafor-1.9-3/metafor/man/blup.Rd | 71
metafor-1.9-3/metafor/man/coef.permutest.rma.uni.Rd | 6
metafor-1.9-3/metafor/man/coef.rma.Rd | 7
metafor-1.9-3/metafor/man/confint.rma.Rd |only
metafor-1.9-3/metafor/man/cumul.Rd | 69
metafor-1.9-3/metafor/man/dat.bangertdrowns2004.Rd | 8
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metafor-1.9-3/metafor/man/dat.berkey1998.Rd | 20
metafor-1.9-3/metafor/man/dat.bonett2010.Rd | 2
metafor-1.9-3/metafor/man/dat.colditz1994.Rd | 6
metafor-1.9-3/metafor/man/dat.collins1985a.Rd | 17
metafor-1.9-3/metafor/man/dat.collins1985b.Rd | 16
metafor-1.9-3/metafor/man/dat.curtis1998.Rd | 7
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metafor-1.9-3/metafor/man/dat.hine1989.Rd | 4
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metafor-1.9-3/metafor/man/dat.pritz1997.Rd | 12
metafor-1.9-3/metafor/man/dat.raudenbush1985.Rd | 4
metafor-1.9-3/metafor/man/dat.yusuf1985.Rd | 2
metafor-1.9-3/metafor/man/escalc.Rd | 66
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metafor-1.9-3/metafor/man/figures/structs2.png |only
metafor-1.9-3/metafor/man/fitstats.Rd | 76
metafor-1.9-3/metafor/man/fitted.rma.Rd | 8
metafor-1.9-3/metafor/man/forest.Rd | 2
metafor-1.9-3/metafor/man/forest.cumul.rma.Rd | 22
metafor-1.9-3/metafor/man/forest.default.Rd | 17
metafor-1.9-3/metafor/man/forest.rma.Rd | 76
metafor-1.9-3/metafor/man/fsn.Rd | 13
metafor-1.9-3/metafor/man/funnel.Rd | 117
metafor-1.9-3/metafor/man/hc.Rd | 7
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metafor-1.9-3/metafor/man/influence.rma.uni.Rd | 26
metafor-1.9-3/metafor/man/labbe.Rd | 51
metafor-1.9-3/metafor/man/leave1out.Rd | 69
metafor-1.9-3/metafor/man/llplot.Rd | 2
metafor-1.9-3/metafor/man/metafor-package.Rd | 35
metafor-1.9-3/metafor/man/metafor.news.Rd | 2
metafor-1.9-3/metafor/man/permutest.Rd | 94
metafor-1.9-3/metafor/man/plot.infl.rma.uni.Rd | 8
metafor-1.9-3/metafor/man/plot.rma.Rd |only
metafor-1.9-3/metafor/man/predict.rma.Rd | 61
metafor-1.9-3/metafor/man/print.anova.rma.uni.Rd | 10
metafor-1.9-3/metafor/man/print.confint.rma.Rd | 6
metafor-1.9-3/metafor/man/print.escalc.Rd | 16
metafor-1.9-3/metafor/man/print.fsn.Rd | 6
metafor-1.9-3/metafor/man/print.hc.rma.uni.Rd | 8
metafor-1.9-3/metafor/man/print.list.rma.Rd | 9
metafor-1.9-3/metafor/man/print.permutest.rma.uni.Rd | 6
metafor-1.9-3/metafor/man/print.ranktest.rma.Rd | 6
metafor-1.9-3/metafor/man/print.regtest.rma.Rd | 8
metafor-1.9-3/metafor/man/print.rma.uni.Rd | 42
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metafor-1.9-3/metafor/man/radial.Rd | 52
metafor-1.9-3/metafor/man/ranktest.Rd | 39
metafor-1.9-3/metafor/man/regtest.Rd | 79
metafor-1.9-3/metafor/man/residuals.rma.Rd | 33
metafor-1.9-3/metafor/man/rma.glmm.Rd | 38
metafor-1.9-3/metafor/man/rma.mh.Rd | 12
metafor-1.9-3/metafor/man/rma.mv.Rd | 128
metafor-1.9-3/metafor/man/rma.peto.Rd | 10
metafor-1.9-3/metafor/man/rma.uni.Rd | 78
metafor-1.9-3/metafor/man/to.long.Rd | 4
metafor-1.9-3/metafor/man/to.table.Rd | 4
metafor-1.9-3/metafor/man/transf.Rd | 15
metafor-1.9-3/metafor/man/trimfill.Rd | 54
metafor-1.9-3/metafor/man/vcov.rma.Rd | 6
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147 files changed, 5197 insertions(+), 2934 deletions(-)
Title: Interface between R and the Google Chart Tools
Diff between googleVis versions 0.5.1 dated 2014-04-13 and 0.5.2 dated 2014-05-05
Description: The googleVis package provides an interface between R and the
Google Chart Tools API. It allows users to create web pages with
interactive charts based on R data frames, using the Google Chart Tools and
to display them either via the local R HTTP help server or within their own
sites, without uploading the data to Google. A modern browser with Internet
connection is required and for some charts Flash. Please visit the project
web site for more information and examples.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann
DESCRIPTION | 8
MD5 | 55 -
NEWS | 14
R/gvis.R | 10
R/gvisCoreCharts.R | 30
README.md | 5
THANKS | 5
build/googleVis.pdf |binary
build/vignette.rds |binary
demo/googleVis.R | 55 -
inst/doc/Using_Roles_via_googleVis.Rmd | 12
inst/doc/Using_Roles_via_googleVis.html | 211 ++--
inst/doc/Using_Trendlines_with_googleVis.Rmd | 3
inst/doc/Using_Trendlines_with_googleVis.html | 122 +-
inst/doc/Using_googleVis_with_knitr.html | 115 +-
inst/doc/googleVis.pdf |binary
inst/doc/googleVis_examples.R | 6
inst/doc/googleVis_examples.Rmd | 14
inst/doc/googleVis_examples.html | 1312 ++++++++++++++++----------
man/createGoogleGadget.Rd | 2
man/googleVis-package.Rd | 6
man/gvisLineChart.Rd | 11
man/gvisScatterChart.Rd | 19
vignettes/Using_Roles_via_googleVis.Rmd | 12
vignettes/Using_Trendlines_with_googleVis.Rmd | 3
vignettes/googleVis.Rmd |only
vignettes/googleVis.bib | 6
vignettes/googleVis.html |only
vignettes/googleVis.md |only
vignettes/googleVis_examples.Rmd | 14
30 files changed, 1262 insertions(+), 788 deletions(-)
Title: Semi-parametric estimators of truncated regression models
Diff between truncSP versions 1.2.1 dated 2013-11-20 and 1.2.2 dated 2014-05-05
Description: Semi-parametric estimation of truncated linear regression models
Author: Anita Lindmark and Maria Karlsson, Department of Statistics, Umea University
Maintainer: Anita Lindmark
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
inst |only
man/lt.Rd | 5 +++--
man/qme.Rd | 3 ++-
man/stls.Rd | 3 ++-
man/truncSP-package.Rd | 7 ++++---
7 files changed, 21 insertions(+), 16 deletions(-)
Title: Companion Package to the Book “R: Einführung durch angewandte
Statistik”
Diff between REdaS versions 0.9.0 dated 2014-04-23 and 0.9.1 dated 2014-05-05
Description: This package provides functions used in the second edition of “R: Einführung durch angewandte Statistik”.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DESCRIPTION | 11 ++++---
MD5 | 16 +++++------
R/densbox.R | 74 +++++++++++++++++++++++++++++++--------------------
build/partial.rdb |binary
man/KMO.Rd | 6 ++--
man/REdaS-package.Rd | 6 ++--
man/densbox.Rd | 18 ++++++++++--
man/freqCI.Rd | 2 -
man/odds_ratios.Rd | 2 -
9 files changed, 82 insertions(+), 53 deletions(-)
Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.10 dated 2014-04-22 and 1.0.21 dated 2014-05-05
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano Maria Iacus
DESCRIPTION | 10 +--
MD5 | 28 +++++-----
NAMESPACE | 3 +
NEWS | 4 +
R/CPoint.R | 3 +
R/CarmaNoise.R | 2
R/cce.R | 5 +
R/lasso.R | 146 +++++++++++++++++++++++++-------------------------------
R/llag.R | 9 ++-
R/qmle.R | 26 +++++-----
R/yuima.R | 147 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-
R/yuima.data.R | 3 -
data |only
man/MWK151.Rd |only
man/mmfrac.Rd | 2
man/qmle.Rd | 1
16 files changed, 271 insertions(+), 118 deletions(-)
Title: SSD for R to analyze single system data
Diff between SSDforR versions 1.4.3 dated 2014-04-03 and 1.4.4 dated 2014-05-05
Description: Package to visually and statistically analyze single system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler School of Social Work
Maintainer: Charles Auerbach
DESCRIPTION | 6 +++---
MD5 | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.4.200.0 dated 2014-04-07 and 0.4.300.0 dated 2014-05-05
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to combine
several operations into one, and to reduce (or eliminate) the need for
temporaries. This is accomplished through recursive templates and template
meta-programming.
This library is useful if C++ has been decided as the language of choice
(due to speed and/or integration capabilities), rather than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++ integration.
Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL version 2
or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 25 ++
DESCRIPTION | 8
MD5 | 51 ++--
configure | 28 +-
inst/NEWS.Rd | 19 +
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/RcppArmadilloAs.h | 86 +++++---
inst/include/RcppArmadilloConfig.h | 8
inst/include/armadillo | 7
inst/include/armadillo_bits/arma_version.hpp | 4
inst/include/armadillo_bits/compiler_setup.hpp | 8
inst/include/armadillo_bits/config.hpp | 9
inst/include/armadillo_bits/diskio_meat.hpp | 120 +++++------
inst/include/armadillo_bits/fn_find.hpp | 125 +++++++++++
inst/include/armadillo_bits/fn_misc.hpp | 51 ++++
inst/include/armadillo_bits/fn_reshape.hpp | 24 +-
inst/include/armadillo_bits/glue_times_bones.hpp | 4
inst/include/armadillo_bits/glue_times_meat.hpp | 132 ++++--------
inst/include/armadillo_bits/hdf5_bones.hpp |only
inst/include/armadillo_bits/hdf5_misc.hpp | 206 +++++++++----------
inst/include/armadillo_bits/op_find_bones.hpp | 34 +++
inst/include/armadillo_bits/op_find_meat.hpp | 244 +++++++++++++++++++++--
inst/include/armadillo_bits/op_reshape_bones.hpp | 19 +
inst/include/armadillo_bits/op_reshape_meat.hpp | 169 ++++++++++++++-
inst/unitTests/cpp/armadillo.cpp | 23 ++
inst/unitTests/runit.RcppArmadillo.R | 16 +
27 files changed, 1041 insertions(+), 379 deletions(-)
Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.3-93 dated 2014-03-03 and 0.4-05 dated 2014-05-05
Description: phytools provides various functions for phylogenetic analysis,
mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 8 -
MD5 | 29 ++-
NAMESPACE | 23 +--
R/contMap.R | 12 +
R/densityMap.R | 14 +
R/evol.rate.mcmc.R | 22 --
R/ltt95.R | 84 ++++++++---
R/paintSubTree.R | 160 ++++++++++++---------
R/roundPhylogram.R |only
R/utilities.R | 359 +++++++++++++++++++++++++++++++++---------------
man/cladelabels.Rd |only
man/fastMRCA.Rd | 12 -
man/ltt95.Rd | 7
man/map.to.singleton.Rd | 7
man/nodeHeights.Rd | 11 -
man/paintSubTree.Rd | 5
man/roundPhylogram.Rd |only
17 files changed, 484 insertions(+), 269 deletions(-)
Title: A Replacement and Extension of the optim() Function
Diff between optimx versions 2013.8.6 dated 2013-08-09 and 2014.5.4 dated 2014-05-05
Description: Provides a replacement and extension of the optim()
function to unify and streamline optimization capabilities in R
for smooth, possibly box constrained functions of several or
many parameters. This is the CRAN version of the package.
Author: John C Nash [aut, cre], Ravi Varadhan [aut], Gabor Grothendieck [ctb]
Maintainer: John C Nash
DESCRIPTION | 12 ++++++------
MD5 | 12 ++++++------
NAMESPACE | 3 ++-
NEWS | 15 ++++++++++++++-
R/optimx.check.R | 7 ++++---
R/optimx.run.R | 44 ++++++++++++++++++++++++++++++++++----------
R/optimx.setup.R | 17 ++++++++++++-----
7 files changed, 78 insertions(+), 32 deletions(-)
Title: Functions for nonlinear least squares solutions
Diff between nlmrt versions 2013-8.10 dated 2013-08-11 and 2013-9.24 dated 2014-05-05
Description: nlmrt provides tools for working with nonlinear least squares problems
using a calling structure similar to, but much simpler than, that of the nls()
function. Moreover, where nls() specifically does NOT deal with small or zero
residual problems, nlmrt is quite happy to solve them. It also attempts to be
more robust in finding solutions, thereby avoiding 'singular gradient' messages
that arise in the Gauss-Newton method within nls(). The Marquardt-Nash approach
in nlmrt generally works more reliably to get a solution, though this may be
one of a set of possibilities, and may also be statistically unsatisfactory.
Added print and summary as of August 28, 2012.
Author: John C. Nash [aut, cre]
Maintainer: John C. Nash
DESCRIPTION | 8 -
MD5 | 34 ++++----
NAMESPACE | 22 +++++
NEWS | 29 ++++++-
R/nlfb.R | 18 +++-
R/nlmrt.R | 176 ++++++++++++++++---------------------------
R/nlxb.R | 21 +++--
build |only
inst/dev-codes/nlfb.R.130709 |only
inst/dev-codes/nlxb.R.130710 |only
inst/dev-codes/nlxbreloff.R |only
inst/dev-codes/summary.pg.R |only
inst/doc/nlmrt-vignette.R | 2
inst/doc/nlmrt-vignette.Rnw | 2
man/coef.nlmrt.Rd |only
man/nlfb.Rd | 15 ++-
man/nlmrt-package.Rd | 14 +--
man/nlxb.Rd | 14 +++
man/print.nlmrt.Rd | 6 -
man/summary.nlmrt.Rd | 17 ++--
vignettes/nlmrt-vignette.Rnw | 2
21 files changed, 222 insertions(+), 158 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-32 dated 2014-04-27 and 7.3-33 dated 2014-05-05
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/lqs.R | 9 ++++++---
inst/NEWS | 3 ++-
man/npr1.Rd | 7 +++++--
man/rlm.Rd | 4 ++--
tests/rlm.R | 6 ++++++
7 files changed, 32 insertions(+), 19 deletions(-)
Title: Learning graphical models with hubs
Diff between hglasso versions 1.0 dated 2014-03-29 and 1.1 dated 2014-05-05
Description: Implements the hub graphical lasso and hub covariance graph proposal by Tan, KM., London, P., Mohan, K., Lee, S-I., Fazel, M., and Witten, D. (2014). Learning graphical models with hubs. arXiv.org/pdf/1402.7349.pdf.
Author: Kean Ming Tan
Maintainer: Kean Ming Tan
DESCRIPTION | 10 ++---
MD5 | 34 ++++++++++-------
NAMESPACE | 6 ++-
R/Functions.R | 96 +++++++++++++++++++++++++++++++++++++++++++++++++
R/HubNetwork.R | 7 +++
R/binaryMCMC.R |only
R/hbn.R |only
R/image.hbn.R |only
R/plot.hbn.R |only
R/print.hbn.R |only
R/print.hcov.R | 2 -
R/print.hglasso.R | 2 -
R/summary.hbn.R |only
R/summary.hcov.R | 2 -
R/summary.hglasso.R | 2 -
man/HubNetwork.Rd | 9 +++-
man/binaryMCMC.Rd |only
man/hbn.Rd |only
man/hglasso-package.Rd | 21 +++++++---
man/image.hglasso.Rd | 10 +++--
man/plot.hglasso.Rd | 8 ++--
man/summary.hglasso.Rd | 12 +++---
22 files changed, 175 insertions(+), 46 deletions(-)