Title: Seawater Carbonate Chemistry
Diff between seacarb versions 3.0.4 dated 2015-01-05 and 3.0.5 dated 2015-01-12
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [ctb],
Bernard Gentili [ctb],
Andreas Hofmann [ctb],
Aurélien Proye [ctb],
Karline Soetaert [ctb],
James Rae [ctb]
Maintainer: Jean-Pierre Gattuso
ChangeLog | 7 +++++++
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/buffer.R | 53 ++++++++++++++++++++++++++++++++---------------------
R/carb.R | 2 +-
5 files changed, 49 insertions(+), 31 deletions(-)
Title: Random Forests for Survival, Regression and Classification
(RF-SRC)
Diff between randomForestSRC versions 1.5.5 dated 2014-08-26 and 1.6.0 dated 2015-01-12
More information about randomForestSRC at CRAN
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran
Maintainer: Udaya B. Kogalur
DESCRIPTION | 10
MD5 | 188 +++++++-------
R/data.utilities.R | 79 ++++--
R/factor.utilities.R | 2
R/find.interaction.R | 2
R/generic.impute.rfsrc.R | 15 -
R/generic.predict.rfsrc.R | 38 ++
R/impute.rfsrc.R | 63 +++-
R/max.subtree.R | 2
R/plot.competing.risk.R | 2
R/plot.rfsrc.R | 2
R/plot.survival.R | 2
R/plot.variable.R | 2
R/predict.rfsrc.R | 2
R/print.rfsrc.R | 10
R/rf2rfz.R | 2
R/rfsrc.R | 57 +++-
R/rfsrc.news.R | 2
R/rfsrcSyn.R | 2
R/stat.split.R | 2
R/utilities.R | 19 +
R/var.select.R | 6
R/vimp.R | 2
R/zzz.R | 2
configure.ac | 2
inst/NEWS | 19 +
inst/doc/rsf-Rnews.pdf |binary
man/find.interaction.Rd | 5
man/impute.Rd | 21 -
man/predict.rfsrc.Rd | 9
man/randomForestSRC_package.Rd | 5
man/rfsrc.Rd | 29 +-
man/var.select.Rd | 5
man/vimp.Rd | 5
src/bootstrap.c | 2
src/bootstrap.h | 2
src/classification.c | 64 +++-
src/classification.h | 13
src/dataParser.c | 2
src/dataParser.h | 2
src/entry.c | 29 +-
src/entry.h | 11
src/extern.h | 44 ++-
src/factor.h | 2
src/factorOps.c | 2
src/factorOps.h | 2
src/global.h | 19 +
src/importance.c | 133 +++++-----
src/importance.h | 32 +-
src/impute.c | 305 ++++++++++++-----------
src/impute.h | 2
src/node.h | 25 -
src/nodeOps.c | 463 -----------------------------------
src/nodeOps.h | 35 --
src/nrutil.c | 35 ++
src/nrutil.h | 37 +-
src/random.c | 2
src/random.h | 2
src/regression.c | 58 +++-
src/regression.h | 3
src/rfsrc.c | 293 +++++++++++-----------
src/rfsrc.h | 2
src/rfsrcUtil.c | 108 +++++++-
src/rfsrcUtil.h | 12
src/split.c | 18 +
src/split.h | 2
src/splitClas.c | 7
src/splitClas.h | 2
src/splitCustom.c |only
src/splitCustom.h |only
src/splitRegr.c | 7
src/splitRegr.h | 2
src/splitSurv.c | 12
src/splitSurv.h | 2
src/splitUspv.c | 535 +++++++++++++++++++++++++++++++++++------
src/splitUspv.h | 15 +
src/splitUtil.c | 17 -
src/splitUtil.h | 2
src/stack.c | 54 +++-
src/stack.h | 41 +--
src/stackOutput.c | 479 +++++++++++++++++++++++++++++++++++-
src/stackOutput.h | 29 ++
src/stackPreDefined.c | 30 +-
src/stackPreDefined.h | 2
src/survival.c | 473 +++++++++++++++++++-----------------
src/survival.h | 11
src/survivalE.c | 12
src/survivalE.h | 2
src/termOps.c |only
src/termOps.h |only
src/terminal.h | 28 +-
src/trace.c | 8
src/trace.h | 2
src/tree.c | 185 ++++++++------
src/tree.h | 18 -
src/treeUtil.c | 24 +
src/treeUtil.h | 11
97 files changed, 2686 insertions(+), 1698 deletions(-)
Permanent link
Title: Wraps libnabo, a fast K Nearest Neighbour library for low
dimensions
Diff between nabor versions 0.4.3 dated 2014-09-03 and 0.4.4 dated 2015-01-12
Description: An R wrapper for libnabo, an exact or approximate k nearest
neighbour library which is optimised for low dimensional spaces (e.g. 3D).
libnabo has speed and space advantages over the ANN library wrapped by
package RANN. nabor includes a knn function that is designed as a drop-in
replacement for RANN::nn2. In addition, objects which include the k-d tree
search structure can be returned to speed up repeated queries of the same
set of target points.
Author: Stephane Mangenat (for libnabo), Gregory Jefferis
Maintainer: Gregory Jefferis
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NAMESPACE | 2 +-
NEWS | 4 ++++
R/WKNNClasses.R | 14 ++++++++------
man/WKNN-class.Rd | 14 ++++++++------
man/kcpoints.Rd | 2 +-
man/knn.Rd | 2 +-
man/nabor-package.Rd | 2 +-
src/Makevars | 2 +-
10 files changed, 38 insertions(+), 30 deletions(-)
Title: Functions for Plotting HPO Terms
Diff between hpoPlot versions 1.0 dated 2014-05-10 and 2.0 dated 2015-01-12
Description: Collection of functions for manipulating sets of HPO terms and plotting them with a various options
Author: Daniel Greene
Maintainer: Daniel Greene
hpoPlot-1.0/hpoPlot/R/hpoPlotCode.R |only
hpoPlot-1.0/hpoPlot/data/hpo.rda |only
hpoPlot-1.0/hpoPlot/man/border.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/colouring.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/get.cohort.information.Rd |only
hpoPlot-1.0/hpoPlot/man/get.term.patient.matrix.Rd |only
hpoPlot-1.0/hpoPlot/man/hpo.graph.Rd |only
hpoPlot-1.0/hpoPlot/man/labelling.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/remove.duplicate.term.sets.Rd |only
hpoPlot-1.0/hpoPlot/man/size.functions.Rd |only
hpoPlot-1.0/hpoPlot/man/suggest.aspect.ratio.width.to.height.Rd |only
hpoPlot-2.0/hpoPlot/DESCRIPTION | 17 +
hpoPlot-2.0/hpoPlot/MD5 | 91 +++++++---
hpoPlot-2.0/hpoPlot/NAMESPACE | 53 +++++
hpoPlot-2.0/hpoPlot/R/data.R |only
hpoPlot-2.0/hpoPlot/R/graphs.R |only
hpoPlot-2.0/hpoPlot/R/sets.R |only
hpoPlot-2.0/hpoPlot/R/utils.R |only
hpoPlot-2.0/hpoPlot/build |only
hpoPlot-2.0/hpoPlot/data/datalist |only
hpoPlot-2.0/hpoPlot/data/hpo.terms.RData |only
hpoPlot-2.0/hpoPlot/data/mpo.terms.RData |only
hpoPlot-2.0/hpoPlot/data/mpo.to.hpo.RData |only
hpoPlot-2.0/hpoPlot/inst |only
hpoPlot-2.0/hpoPlot/man/apply.term.filters.Rd |only
hpoPlot-2.0/hpoPlot/man/calibrate.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/clean.terms.Rd | 34 +--
hpoPlot-2.0/hpoPlot/man/exclude.branch.Rd |only
hpoPlot-2.0/hpoPlot/man/get.ancestors.Rd | 38 +---
hpoPlot-2.0/hpoPlot/man/get.case.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.case.based.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.case.term.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.code.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.descendants.Rd | 44 ++--
hpoPlot-2.0/hpoPlot/man/get.frequency.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.frequency.based.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.frequency.based.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.full.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.grey.borders.Rd |only
hpoPlot-2.0/hpoPlot/man/get.hpo.graph.Rd |only
hpoPlot-2.0/hpoPlot/man/get.hpo.terms.Rd | 35 ---
hpoPlot-2.0/hpoPlot/man/get.informative.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.mpo.to.hpo.Rd |only
hpoPlot-2.0/hpoPlot/man/get.no.borders.Rd |only
hpoPlot-2.0/hpoPlot/man/get.node.friendly.long.names.Rd | 42 +---
hpoPlot-2.0/hpoPlot/man/get.ontology.Rd |only
hpoPlot-2.0/hpoPlot/man/get.pop.frequency.based.colours.Rd |only
hpoPlot-2.0/hpoPlot/man/get.shortened.names.Rd |only
hpoPlot-2.0/hpoPlot/man/get.significance.based.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.simple.node.labels.Rd |only
hpoPlot-2.0/hpoPlot/man/get.standard.sizes.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.adjacency.matrix.Rd | 49 +----
hpoPlot-2.0/hpoPlot/man/get.term.descendancy.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.frequencies.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.info.content.Rd |only
hpoPlot-2.0/hpoPlot/man/get.term.pseudo.adjacency.matrix.Rd |only
hpoPlot-2.0/hpoPlot/man/get.white.nodes.Rd |only
hpoPlot-2.0/hpoPlot/man/hpo.plot.Rd |only
hpoPlot-2.0/hpoPlot/man/hpo.terms.Rd | 20 --
hpoPlot-2.0/hpoPlot/man/hpoPlot-package.Rd | 56 +-----
hpoPlot-2.0/hpoPlot/man/intersection.with.branches.Rd |only
hpoPlot-2.0/hpoPlot/man/mpo.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/mpo.to.hpo.Rd |only
hpoPlot-2.0/hpoPlot/man/n.most.frequent.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/p.values.for.occurrence.of.term.in.group.Rd |only
hpoPlot-2.0/hpoPlot/man/prune.branch.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.links.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.non.pa.terms.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.terms.with.less.than.n.occurrences.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.uninformative.for.plot.Rd |only
hpoPlot-2.0/hpoPlot/man/remove.uninformative.terms.Rd | 42 +---
hpoPlot-2.0/hpoPlot/man/setDimNames.Rd | 32 +--
hpoPlot-2.0/hpoPlot/man/simpleCap.Rd |only
hpoPlot-2.0/hpoPlot/man/swap.out.alt.ids.Rd | 36 +--
hpoPlot-2.0/hpoPlot/man/term.set.list.from.character.Rd | 41 +---
hpoPlot-2.0/hpoPlot/vignettes |only
76 files changed, 279 insertions(+), 351 deletions(-)
Title: Loading System Fonts into R
Diff between sysfonts versions 0.3 dated 2014-12-21 and 0.4 dated 2015-01-12
Description: This package uses FreeType to load system fonts
and Google Fonts (https://www.google.com/fonts) into R.
It is supposed to support other packages like R2SWF
and showtext.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu
DESCRIPTION | 10 +++----
MD5 | 10 +++----
NEWS | 11 ++++++++
R/google.R | 56 +++++++++++++++++++++++---------------------
man/font.add.google.Rd | 11 +++++++-
man/font.families.google.Rd | 2 -
6 files changed, 61 insertions(+), 39 deletions(-)
Title: Stability Selection with Error Control
Diff between stabs versions 0.5-0 dated 2014-12-09 and 0.5-1 dated 2015-01-12
Description: Resampling procedures to assess the stability of selected variables
with additional finite sample error control for high-dimensional variable
selection procedures such as Lasso or boosting
Author: Benjamin Hofner [aut, cre],
Torsten Hothorn [aut]
Maintainer: Benjamin Hofner
ChangeLog | 37 ++++++++++++++++++++++++++++++++--
DESCRIPTION | 8 +++----
MD5 | 10 ++++-----
R/fitfuns.R | 8 +++----
inst/CITATION | 63 ++++++++++++++++++++++++++++------------------------------
inst/NEWS.Rd | 13 +++++++++++
6 files changed, 91 insertions(+), 48 deletions(-)
Title: Detection of structure from multilocus genetic data.
Diff between Geneland versions 4.0.4 dated 2014-03-24 and 4.0.5 dated 2015-01-12
Description: Stochastic simulation and MCMC inference of structure from genetic data.
Author: Gilles Guillot, Filipe Santos, Arnaud Estoup
Maintainer: Gilles Guillot
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
inst/CITATION | 9 ++++++---
3 files changed, 12 insertions(+), 9 deletions(-)
Title: Boosting Methods for GAMLSS
Diff between gamboostLSS versions 1.1-2 dated 2014-06-26 and 1.1-3 dated 2015-01-12
Description: Boosting models for fitting generalized additive models for
location, shape and scale (GAMLSS) to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner
gamboostLSS-1.1-2/gamboostLSS/NEWS |only
gamboostLSS-1.1-2/gamboostLSS/inst/CHANGES |only
gamboostLSS-1.1-3/gamboostLSS/ChangeLog | 930 ++++++++++++---------
gamboostLSS-1.1-3/gamboostLSS/DESCRIPTION | 10
gamboostLSS-1.1-3/gamboostLSS/MD5 | 29
gamboostLSS-1.1-3/gamboostLSS/NAMESPACE | 1
gamboostLSS-1.1-3/gamboostLSS/R/as.families.R | 50 -
gamboostLSS-1.1-3/gamboostLSS/R/families.R | 12
gamboostLSS-1.1-3/gamboostLSS/R/helpers.R | 21
gamboostLSS-1.1-3/gamboostLSS/R/methods.R | 21
gamboostLSS-1.1-3/gamboostLSS/data/india.RData |binary
gamboostLSS-1.1-3/gamboostLSS/data/india.bnd.RData |binary
gamboostLSS-1.1-3/gamboostLSS/inst/CITATION | 7
gamboostLSS-1.1-3/gamboostLSS/inst/NEWS.Rd |only
gamboostLSS-1.1-3/gamboostLSS/man/as.families.Rd | 6
gamboostLSS-1.1-3/gamboostLSS/man/india.Rd | 7
gamboostLSS-1.1-3/gamboostLSS/man/methods.Rd | 10
17 files changed, 632 insertions(+), 472 deletions(-)
Title: Ecological models and data (book support)
Diff between emdbook versions 1.3.6 dated 2014-11-25 and 1.3.7 dated 2015-01-12
Description: Auxiliary functions and data sets for _Ecological Models and Data_, a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0)
Author: Ben Bolker
Maintainer: Ben Bolker
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 23 +++++++++++++++--------
inst/NEWS.Rd | 5 +++++
4 files changed, 27 insertions(+), 15 deletions(-)
Title: Multivariate Adaptive Regression Splines
Diff between earth versions 4.1.0 dated 2014-12-17 and 4.2.0 dated 2015-01-12
Description: Build regression models using the techniques in Friedman's
papers "Fast MARS" and "Multivariate Adaptive Regression
Splines". (The term "MARS" is trademarked and thus not used in
the name of the package.)
Author: Stephen Milborrow. Derived from mda:mars by Trevor Hastie and
Rob Tibshirani. Uses Alan Miller's Fortran utilities
with Thomas Lumley's leaps wrapper.
Maintainer: Stephen Milborrow
earth-4.1.0/earth/man/print.evimp.Rd |only
earth-4.2.0/earth/DESCRIPTION | 8
earth-4.2.0/earth/MD5 | 122
earth-4.2.0/earth/NAMESPACE | 3
earth-4.2.0/earth/NEWS | 48
earth-4.2.0/earth/R/earth.R | 478
earth-4.2.0/earth/R/earth.cv.R | 23
earth-4.2.0/earth/R/earth.cv.lib.R | 2
earth-4.2.0/earth/R/earth.glm.R | 3
earth-4.2.0/earth/R/earth.methods.R |only
earth-4.2.0/earth/R/earth.regress.R | 14
earth-4.2.0/earth/R/earthlib.R | 172
earth-4.2.0/earth/R/evimp.R | 2
earth-4.2.0/earth/R/format.earth.R | 6
earth-4.2.0/earth/R/mars.to.earth.R | 14
earth-4.2.0/earth/R/model.matrix.earth.R | 4
earth-4.2.0/earth/R/plot.earth.R | 100
earth-4.2.0/earth/R/plot.model.selection.R | 33
earth-4.2.0/earth/R/plotd.R | 2
earth-4.2.0/earth/R/plotmor.R | 786 -
earth-4.2.0/earth/R/predict.earth.R | 10
earth-4.2.0/earth/R/print.earth.R | 39
earth-4.2.0/earth/R/residuals.earth.R |only
earth-4.2.0/earth/R/varmod.R | 621 -
earth-4.2.0/earth/inst/doc/earth-notes.pdf |binary
earth-4.2.0/earth/inst/doc/earth-varmod.pdf |binary
earth-4.2.0/earth/inst/slowtests/earth.times.R | 4
earth-4.2.0/earth/inst/slowtests/make.bat | 17
earth-4.2.0/earth/inst/slowtests/test.big.R | 6
earth-4.2.0/earth/inst/slowtests/test.big.Rout.save | 45
earth-4.2.0/earth/inst/slowtests/test.big.bat | 12
earth-4.2.0/earth/inst/slowtests/test.cv.R | 4
earth-4.2.0/earth/inst/slowtests/test.cv.Rout.save | 1438 +-
earth-4.2.0/earth/inst/slowtests/test.earthc.c | 129
earth-4.2.0/earth/inst/slowtests/test.earthc.out.save | 4408 +++++---
earth-4.2.0/earth/inst/slowtests/test.earthmain.out.save | 35
earth-4.2.0/earth/inst/slowtests/test.full.R | 449
earth-4.2.0/earth/inst/slowtests/test.full.Rout.save | 7654 ++++++---------
earth-4.2.0/earth/inst/slowtests/test.glm.R | 102
earth-4.2.0/earth/inst/slowtests/test.glm.Rout.save | 5808 ++++++-----
earth-4.2.0/earth/inst/slowtests/test.mods.R |only
earth-4.2.0/earth/inst/slowtests/test.mods.Rout.save |only
earth-4.2.0/earth/inst/slowtests/test.mods.bat |only
earth-4.2.0/earth/inst/slowtests/test.plotd.Rout.save | 16
earth-4.2.0/earth/inst/slowtests/test.varmod.R | 141
earth-4.2.0/earth/inst/slowtests/test.varmod.Rout.save | 2714 ++---
earth-4.2.0/earth/inst/slowtests/test.weights.R | 45
earth-4.2.0/earth/inst/slowtests/test.weights.Rout.save | 133
earth-4.2.0/earth/man/earth.Rd | 280
earth-4.2.0/earth/man/mars.to.earth.Rd | 23
earth-4.2.0/earth/man/model.matrix.earth.Rd | 35
earth-4.2.0/earth/man/plot.earth.Rd | 160
earth-4.2.0/earth/man/plot.earth.models.Rd | 8
earth-4.2.0/earth/man/plot.evimp.Rd | 2
earth-4.2.0/earth/man/plot.varmod.Rd | 6
earth-4.2.0/earth/man/predict.earth.Rd | 6
earth-4.2.0/earth/man/predict.varmod.Rd | 15
earth-4.2.0/earth/man/residuals.earth.Rd | 15
earth-4.2.0/earth/man/update.earth.Rd | 8
earth-4.2.0/earth/man/varmod.Rd | 47
earth-4.2.0/earth/src/allowed.c | 2
earth-4.2.0/earth/src/allowed.h | 2
earth-4.2.0/earth/src/earth.c | 554 -
earth-4.2.0/earth/src/earth.h | 6
earth-4.2.0/earth/tests/test.earth.Rout.save | 16
65 files changed, 14169 insertions(+), 12666 deletions(-)
Title: Copy Numbers of Genes in prokaryotes
Diff between CNOGpro versions 1.0 dated 2014-07-09 and 1.1 dated 2015-01-12
Description: Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms.
Author: Ola Brynildsrud, Lars-Gustav Snipen
Maintainer: Ola Brynildsrud
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/CNOGpro.R | 3 +++
R/getreadcounts.R | 1 +
R/readGenBank.R | 1 +
man/CNOGpro-package.Rd | 4 ++--
6 files changed, 16 insertions(+), 11 deletions(-)
Title: Analysis of Factorial Experiments
Diff between afex versions 0.12-135 dated 2014-11-03 and 0.13-145 dated 2015-01-12
Description: Provides convenience functions for analyzing factorial experiments
using ANOVA or mixed models. ez.glm(), aov.car(), and aov4() allow
convenient specification of between, within (i.e., repeated-measures),
or mixed between-within (i.e., split-plot) ANOVAs for data in long
format (i.e., one observation per row), potentially aggregating multiple
observations per individual and cell of the design. mixed() fits a mixed
model using lme4::lmer() and computes p-values for all effects using either
Kenward-Roger approximation for degrees of freedom (LMM only), parametric
bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex
uses type 3 sums of squares as default (imitating commercial statistical
software). compare.2.vectors() compares two vectors using a variety of tests
(t, Wilcoxon, and permutation).
Author: Henrik Singmann [aut, cre],
Ben Bolker [aut],
Jake Westfall [aut],
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb]
Maintainer: Henrik Singmann
DESCRIPTION | 48 ++++++++++++++++---------------
MD5 | 32 ++++++++++----------
NAMESPACE | 1
NEWS | 30 +++++++++++++++++++
R/afex-package.R | 8 ++---
R/aov.car.R | 32 +++++++++-----------
R/ems.R |only
R/nice.anova.R | 5 +--
data/md_12.1.rda |binary
data/md_15.1.rda |binary
data/md_16.1.rda |binary
data/md_16.4.rda |binary
data/obk.long.rda |binary
man/afex-package.Rd | 8 ++---
man/aov.car.Rd | 24 +++++++--------
man/ems.Rd |only
tests/testthat/test-aov.car-bugs.R | 18 +++++++++++
tests/testthat/test-aov.car-structural.R | 16 ++++++++++
18 files changed, 144 insertions(+), 78 deletions(-)
Title: Rcpp Integration for GNU GSL Vectors and Matrices
Diff between RcppGSL versions 0.2.2 dated 2014-05-31 and 0.2.3 dated 2015-01-12
Description: Rcpp integration for GNU GSL vectors and matrices
The GNU Scientific Library (GSL) is a collection of numerical routines for
scientific computing. It is particularly useful for C and C++ programs as it
provides a standard C interface to a wide range of mathematical routines
such as special functions, permutations, combinations, fast fourier
transforms, eigensystems, random numbers, quadrature, random distributions,
quasi-random sequences, Monte Carlo integration, N-tuples, differential
equations, simulated annealing, numerical differentiation, interpolation,
series acceleration, Chebyshev approximations, root-finding, discrete
Hankel transforms physical constants, basis splines and wavelets. There
are over 1000 functions in total with an extensive test suite.
The RcppGSL package provides an easy-to-use interface between GSL data
structures and R using concepts from Rcpp which is itself a package that
eases the interfaces between R and C++.
This package also serves as a prime example of how to build a package
that uses Rcpp to connect to another third-party library. The autoconf
script, inline plugin and example package can all be used as a stanza to
write a similar package against another library.
Author: Romain Francois and Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 18 +++++++++++++++-
DESCRIPTION | 44 ++++++++++++++++++++---------------------
MD5 | 26 ++++++++++++------------
README.md | 10 +++------
build/vignette.rds |binary
configure | 22 ++++++++------------
configure.ac | 26 ++----------------------
inst/NEWS.Rd | 11 ++++++++++
inst/doc/RcppGSL-intro.R | 8 +++----
inst/doc/RcppGSL-intro.Rnw | 25 ++++++++++-------------
inst/doc/RcppGSL-intro.pdf |binary
inst/doc/RcppGSL-unitTests.pdf |binary
src/Makevars.in | 3 --
vignettes/RcppGSL-intro.Rnw | 25 ++++++++++-------------
14 files changed, 106 insertions(+), 112 deletions(-)
Title: Community Ecology Package
Diff between vegan versions 2.2-0 dated 2014-11-17 and 2.2-1 dated 2015-01-12
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen
vegan-2.2-0/vegan/README.md |only
vegan-2.2-1/vegan/DESCRIPTION | 8
vegan-2.2-1/vegan/MD5 | 137 +++++-----
vegan-2.2-1/vegan/NAMESPACE | 7
vegan-2.2-1/vegan/R/adonis.R | 2
vegan-2.2-1/vegan/R/alias.cca.R | 2
vegan-2.2-1/vegan/R/anosim.R | 9
vegan-2.2-1/vegan/R/as.hclust.spantree.R | 4
vegan-2.2-1/vegan/R/as.mlm.R | 7
vegan-2.2-1/vegan/R/bioenv.default.R | 3
vegan-2.2-1/vegan/R/biplot.rda.R | 11
vegan-2.2-1/vegan/R/coef.cca.R | 10
vegan-2.2-1/vegan/R/coef.rda.R | 6
vegan-2.2-1/vegan/R/cophenetic.spantree.R | 6
vegan-2.2-1/vegan/R/estaccumR.R | 38 ++
vegan-2.2-1/vegan/R/estimateR.default.R | 31 +-
vegan-2.2-1/vegan/R/fitted.capscale.R | 2
vegan-2.2-1/vegan/R/fitted.cca.R | 2
vegan-2.2-1/vegan/R/fitted.rda.R | 2
vegan-2.2-1/vegan/R/intersetcor.R | 2
vegan-2.2-1/vegan/R/lines.spantree.R | 7
vegan-2.2-1/vegan/R/linestack.R | 36 +-
vegan-2.2-1/vegan/R/mantel.R | 2
vegan-2.2-1/vegan/R/mantel.partial.R | 2
vegan-2.2-1/vegan/R/metaMDSiter.R | 2
vegan-2.2-1/vegan/R/mrpp.R | 2
vegan-2.2-1/vegan/R/oecosimu.R | 2
vegan-2.2-1/vegan/R/ordiareatest.R | 2
vegan-2.2-1/vegan/R/orditkplot.R | 275 ++++++++++----------
vegan-2.2-1/vegan/R/permutest.betadisper.R | 5
vegan-2.2-1/vegan/R/permutest.cca.R | 2
vegan-2.2-1/vegan/R/plot.spantree.R | 17 -
vegan-2.2-1/vegan/R/poolaccum.R | 14 -
vegan-2.2-1/vegan/R/print.mantel.correlog.R | 2
vegan-2.2-1/vegan/R/renyiaccum.R | 6
vegan-2.2-1/vegan/R/simper.R | 44 +--
vegan-2.2-1/vegan/R/spantree.R | 4
vegan-2.2-1/vegan/R/specaccum.R | 12
vegan-2.2-1/vegan/R/specpool.R | 2
vegan-2.2-1/vegan/R/tolerance.cca.R | 6
vegan-2.2-1/vegan/R/tsallisaccum.R | 10
vegan-2.2-1/vegan/R/vegandocs.R | 2
vegan-2.2-1/vegan/R/vif.cca.R | 2
vegan-2.2-1/vegan/inst/ChangeLog | 11
vegan-2.2-1/vegan/inst/NEWS.Rd | 66 ++++
vegan-2.2-1/vegan/inst/doc/FAQ-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/NEWS.html | 82 ++++++
vegan-2.2-1/vegan/inst/doc/decision-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/diversity-vegan.R | 50 +--
vegan-2.2-1/vegan/inst/doc/diversity-vegan.Rnw | 245 +++++++++++-------
vegan-2.2-1/vegan/inst/doc/diversity-vegan.pdf |binary
vegan-2.2-1/vegan/inst/doc/intro-vegan.pdf |binary
vegan-2.2-1/vegan/man/betadisper.Rd | 8
vegan-2.2-1/vegan/man/isomap.Rd | 19 -
vegan-2.2-1/vegan/man/kendall.global.Rd | 2
vegan-2.2-1/vegan/man/linestack.Rd | 31 +-
vegan-2.2-1/vegan/man/monoMDS.Rd | 2
vegan-2.2-1/vegan/man/pcnm.Rd | 2
vegan-2.2-1/vegan/man/renyi.Rd | 6
vegan-2.2-1/vegan/man/specaccum.Rd | 7
vegan-2.2-1/vegan/man/specpool.Rd | 11
vegan-2.2-1/vegan/man/tsallis.Rd | 8
vegan-2.2-1/vegan/man/vegandocs.Rd | 5
vegan-2.2-1/vegan/vignettes/FAQ-vegan.pdf |binary
vegan-2.2-1/vegan/vignettes/NEWS.html | 82 ++++++
vegan-2.2-1/vegan/vignettes/decision-vegan.tex | 18 -
vegan-2.2-1/vegan/vignettes/diversity-vegan.Rnw | 245 +++++++++++-------
vegan-2.2-1/vegan/vignettes/diversity-vegan.tex | 321 ++++++++++++++----------
vegan-2.2-1/vegan/vignettes/intro-vegan.tex | 57 +---
vegan-2.2-1/vegan/vignettes/vegan.bib | 20 +
70 files changed, 1302 insertions(+), 743 deletions(-)
Title: Numerical Calibration of Proxy-Climate Relationships
Diff between treeclim versions 1.0.7 dated 2014-08-08 and 1.0.9 dated 2015-01-12
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang
DESCRIPTION | 10 +++++-----
MD5 | 11 ++++++-----
R/dcc.R | 2 +-
R/init_boot_data.R | 4 ++++
inst/CITATION |only
inst/Changelog | 23 +++++++++++++++++++----
man/dcc.Rd | 2 +-
7 files changed, 36 insertions(+), 16 deletions(-)
Title: Simulation of Event Histories for Multi-state Models
Diff between simMSM versions 1.0.1 dated 2014-03-28 and 1.1.2 dated 2015-01-12
Description: Simulation of event histories with possibly non-linear baseline hazard rate functions, non-linear (time-varying) covariate effect functions using inversion sampling on the cumulative all-cause hazard rate functions.
Author: Holger Reulen
Maintainer: Holger Reulen
simMSM-1.0.1/simMSM/R/f.for.uniroot.R |only
simMSM-1.0.1/simMSM/R/sim.event.histories.R |only
simMSM-1.0.1/simMSM/R/sim.exit.R |only
simMSM-1.0.1/simMSM/R/sim.single.history.R |only
simMSM-1.0.1/simMSM/R/sim.to.R |only
simMSM-1.0.1/simMSM/inst |only
simMSM-1.0.1/simMSM/man/f.for.uniroot.Rd |only
simMSM-1.0.1/simMSM/man/sim.event.histories.Rd |only
simMSM-1.0.1/simMSM/man/sim.exit.Rd |only
simMSM-1.0.1/simMSM/man/sim.single.history.Rd |only
simMSM-1.0.1/simMSM/man/sim.to.Rd |only
simMSM-1.1.2/simMSM/DESCRIPTION | 13 +--
simMSM-1.1.2/simMSM/MD5 | 45 ++++++-----
simMSM-1.1.2/simMSM/R/allcausehr.R | 15 +--
simMSM-1.1.2/simMSM/R/cumallcausehr.R | 9 +-
simMSM-1.1.2/simMSM/R/hr.R | 6 -
simMSM-1.1.2/simMSM/R/meancentering.R |only
simMSM-1.1.2/simMSM/R/simCR.R |only
simMSM-1.1.2/simMSM/R/simEBMT.R |only
simMSM-1.1.2/simMSM/R/simeventhistories.R |only
simMSM-1.1.2/simMSM/R/simexit.R |only
simMSM-1.1.2/simMSM/R/simexitinner.R |only
simMSM-1.1.2/simMSM/R/simsinglehistory.R |only
simMSM-1.1.2/simMSM/R/simto.R |only
simMSM-1.1.2/simMSM/R/unirootf.R |only
simMSM-1.1.2/simMSM/man/allcausehr.Rd | 12 +--
simMSM-1.1.2/simMSM/man/cumallcausehr.Rd | 14 +--
simMSM-1.1.2/simMSM/man/hr.Rd | 13 ++-
simMSM-1.1.2/simMSM/man/meancentering.Rd |only
simMSM-1.1.2/simMSM/man/simCR.Rd |only
simMSM-1.1.2/simMSM/man/simEBMT.Rd |only
simMSM-1.1.2/simMSM/man/simMSM-package.Rd | 96 +------------------------
simMSM-1.1.2/simMSM/man/simeventhistories.Rd |only
simMSM-1.1.2/simMSM/man/simexit.Rd |only
simMSM-1.1.2/simMSM/man/simexitinner.Rd |only
simMSM-1.1.2/simMSM/man/simsinglehistory.Rd |only
simMSM-1.1.2/simMSM/man/simto.Rd |only
simMSM-1.1.2/simMSM/man/unirootf.Rd |only
38 files changed, 75 insertions(+), 148 deletions(-)
Title: Estimating Regularized Multi-state Models Using L1 Penalties
Diff between penMSM versions 0.97 dated 2014-07-02 and 0.99 dated 2015-01-12
Description: Structured fusion Lasso penalized estimation of multi-state models with the penalty applied to absolute effects and absolute effect differences (i.e., effects on transition-type specific hazard rates).
Author: Holger Reulen
Maintainer: Holger Reulen
DESCRIPTION | 17 ++++---
MD5 | 46 ++++++++++++-------
NAMESPACE | 4 +
R/RcppExports.R |only
R/buildrisksets.R | 40 ++++++++++------
R/dapproxpenalty.R | 7 +-
R/dpenaltyfunction.R | 4 -
R/fisherinfo.R | 19 ++++----
R/fisherinfoP.R |only
R/llP.R |only
R/lpl.R | 4 -
R/penMSM.R | 113 +++++++++++++++++++++++++++++++++++-------------
R/penaltymatrix.R | 14 ++---
R/plmatrix.R | 16 +++---
R/sF.R |only
R/scorevector.R | 16 ++----
R/scorevectorP.R |only
man/buildrisksets.Rd | 3 -
man/dapproxpenalty.Rd | 10 +---
man/dpenaltyfunction.Rd | 6 +-
man/fishercpp.Rd |only
man/fisherinfoP.Rd |only
man/llP.Rd |only
man/penMSM.Rd | 37 ++++++++++++---
man/penaltymatrix.Rd | 6 +-
man/plmatrix.Rd | 8 +--
man/sF.Rd |only
man/scorevectorP.Rd |only
src |only
29 files changed, 234 insertions(+), 136 deletions(-)
Title: Embedded JavaScript Engine
Diff between V8 versions 0.3 dated 2014-12-21 and 0.4 dated 2015-01-12
Description: V8 is Google's open source, high performance JavaScript engine. It
is written in C++ and implements ECMAScript as specified in ECMA-262, 5th
edition.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 16 +++++++------
LICENSE | 4 +--
MD5 | 26 ++++++++++++++-------
NAMESPACE | 3 +-
R/RcppExports.R | 4 +--
R/V8.R | 64 +++++++++++++++++++++++++++++++++++++++-------------
build |only
inst/doc |only
man/new_context.Rd | 31 ++++++++++++++++++++-----
src/RcppExports.cpp | 7 +++--
src/V8.cpp | 42 ++++++++++++++++++++++++++++++++--
vignettes |only
12 files changed, 151 insertions(+), 46 deletions(-)
Title: Soundscape ecology
Diff between soundecology versions 1.1.1 dated 2014-04-14 and 1.2 dated 2015-01-12
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera
DESCRIPTION | 12 +--
MD5 | 22 +++---
NAMESPACE | 2
NEWS | 6 +
R/multiple_sounds.R | 63 +++++++++++++++++--
R/sound_raster.R | 2
build/vignette.rds |binary
inst/doc/changeADI.R | 2
inst/doc/changeADI.html | 142 +++++++++++++++++++++++++-------------------
inst/doc/intro.html | 122 ++++++++++++++++++++++---------------
man/multiple_sounds.Rd | 6 +
man/soundecology.package.Rd | 4 -
12 files changed, 240 insertions(+), 143 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design For MTA
Diff between dfmta versions 1.0-3 dated 2014-11-20 and 1.1-0 dated 2015-01-12
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization".
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere
dfmta-1.0-3/dfmta/man/mta_next.Rd |only
dfmta-1.0-3/dfmta/man/mta_sim.Rd |only
dfmta-1.0-3/dfmta/src/Makevars |only
dfmta-1.1-0/dfmta/DESCRIPTION | 13
dfmta-1.1-0/dfmta/MD5 | 36
dfmta-1.1-0/dfmta/NAMESPACE | 4
dfmta-1.1-0/dfmta/R/dfmta.R | 238 ++--
dfmta-1.1-0/dfmta/cleanup |only
dfmta-1.1-0/dfmta/configure |only
dfmta-1.1-0/dfmta/configure.ac |only
dfmta-1.1-0/dfmta/man/dfmta-package.Rd | 6
dfmta-1.1-0/dfmta/man/mtaBin_next.Rd |only
dfmta-1.1-0/dfmta/man/mtaBin_sim.Rd |only
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.bernoulli.hpp | 10
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.discrete.hpp | 12
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.exponential.censored.hpp | 6
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/distributions/mcmc.exponential.hpp | 6
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.jump.hpp | 4
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.math.hpp | 176 +--
dfmta-1.1-0/dfmta/src/CppBugs/cppbugs/mcmc.rng.hpp | 24
dfmta-1.1-0/dfmta/src/Makevars.in |only
dfmta-1.1-0/dfmta/src/Makevars.win | 2
dfmta-1.1-0/dfmta/src/dfmta.cpp | 533 ++++------
dfmta-1.1-0/dfmta/tools |only
24 files changed, 553 insertions(+), 517 deletions(-)
Title: Robust Variance Meta-regression
Diff between robumeta versions 1.4 dated 2014-12-09 and 1.5 dated 2015-01-12
Description: Functions for conducting robust variance estimation (RVE) meta-regression using both large and small sample RVE estimators under various weighting schemes. These methods are distribution free and provide valid point estimates, standard errors and hypothesis tests even when the degree and structure of dependence between effect sizes is unknown. Also included are functions for conducting sensitivity analyses under correlated effects weighting and producing RVE-based forest plots.
Author: Zachary Fisher and Elizabeth Tipton.
Maintainer: Zachary Fisher
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/robumeta.R | 37 ++++++++++++++++++++++++++-----------
3 files changed, 31 insertions(+), 16 deletions(-)