Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.24 dated 2014-07-31 and 1.0.28 dated 2014-09-03
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus
DESCRIPTION | 11
MD5 | 19
NAMESPACE | 8
R/AllClasses.R | 43 +
R/adaBayes.R | 2
R/asymptotic_term_second.R | 2
R/asymptotic_term_third.R | 2
R/qmle.R | 1258 +++++++++++++++++++++++----------------------
R/yuima.sampling.R | 5
man/qmle.Rd | 4
man/yuima.CP.qmle-class.Rd |only
11 files changed, 724 insertions(+), 630 deletions(-)
Title: A dependency management system for projects and their R package
dependencies
Diff between packrat versions 0.4.1 dated 2014-09-02 and 0.4.1-1 dated 2014-09-03
Description: Packrat is a tool for managing the R packages your project depends
on in an isolated, portable, and reproducible way.
Author: Kevin Ushey, Jonathan McPherson, Joe Cheng, JJ Allaire
Maintainer: Kevin Ushey
packrat-0.4.1-1/packrat/DESCRIPTION | 6 ++--
packrat-0.4.1-1/packrat/MD5 | 47 +-----------------------------------
packrat-0.4.1-1/packrat/R/utils.R | 7 +++++
packrat-0.4.1/packrat/tests |only
4 files changed, 12 insertions(+), 48 deletions(-)
Title: Miscellaneous general purpose functions
Diff between NCmisc versions 1.1.2 dated 2014-09-01 and 1.1.3 dated 2014-09-03
Description: A set of handy functions. Includes: versatile one line progress bar, one
line function timer with detailed output, time delay function, text histogram, object
preview, CRAN package search, simpler package installer, Linux command install check,
a flexible Mode function, top function, simulation of correlated data, and more
Author: Nicholas Cooper
Maintainer: Nicholas Cooper
DESCRIPTION | 8 +--
MD5 | 14 ++---
R/NCmisc.R | 120 +++++++++++++++++++++++++++++++--------------
man/NCmisc-internal.Rd | 1
man/NCmisc-package.Rd | 4 -
man/check.linux.install.Rd | 11 ++--
man/file.split.Rd | 2
man/timeit.Rd | 2
8 files changed, 109 insertions(+), 53 deletions(-)
Title: Wraps libnabo, a fast K Nearest Neighbour library for low
dimensions
Diff between nabor versions 0.4.2 dated 2014-09-02 and 0.4.3 dated 2014-09-03
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 | 9 +++++----
MD5 | 6 +++---
NEWS | 4 ++++
src/kdtree_cpu.cpp | 2 +-
4 files changed, 13 insertions(+), 8 deletions(-)
Title: Multivariate normal mixture models and mixtures of generalized
linear mixed models including model based clustering
Diff between mixAK versions 3.6-1 dated 2014-08-06 and 3.8 dated 2014-09-03
Description: This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models.
Author: Arnošt Komárek
Maintainer: Arnošt Komárek
DESCRIPTION | 10 ++---
MD5 | 43 +++++++++++++----------
NAMESPACE | 10 +++++
NEWS | 9 ++++
R/GLMM_MCMCdata.R | 37 ++++++++++++++------
R/NMixCluster.GLMM_MCMC.R |only
R/NMixCluster.R |only
R/NMixCluster.default.R |only
R/plotProfiles.R | 32 ++++++++++-------
inst/CITATION | 71 ++++++++++++++-------------------------
inst/CITATION_includeMethodology |only
inst/doc/index.html | 38 +++++++++++---------
man/GLMMMCMC.Rd | 9 +++-
man/GLMMlongitDA.Rd | 2 -
man/NMixCluster.Rd |only
man/NMixMCMC.Rd | 18 ++++-----
man/NMixPredCDFMarg.Rd | 4 +-
man/NMixPredDensJoint2.Rd | 10 ++---
man/NMixPredDensMarg.Rd | 4 +-
man/PBC910.Rd | 7 +++
man/TandmobEmer.Rd | 2 -
man/plot.NMixPredCDFMarg.Rd | 2 -
man/plot.NMixPredDensJoint2.Rd | 2 -
man/plot.NMixPredDensMarg.Rd | 2 -
man/plotProfiles.Rd | 13 ++++---
25 files changed, 184 insertions(+), 141 deletions(-)
Title: jSonar Analytics Platform API for R
Diff between jSonarR versions 1.0 dated 2014-07-22 and 1.1 dated 2014-09-03
Description: This package enables users to access MongoDB by running queries
and returning their results in R data frames. Usually, data in MongoDB is
only available in the form of a JSON document. jSonarR uses data
processing and conversion capabilities in the jSonar Analytics Platform
and the JSON Studio Gateway (http://www.jsonstudio.com), to convert it to
a tabular format which is easy to use with existing R packages.
Author: jSonar Inc.
Maintainer: Dylan McCall
DESCRIPTION | 8 +-
MD5 | 26 ++++----
NAMESPACE | 5 +
R/exampleData.R |only
R/jSonarR.R | 3
R/new.SonarConnection.R | 44 +++++++++++++
R/sonarAgg.R | 6 +
R/sonarCSV.R | 144 ++++++++++++---------------------------------
R/sonarFind.R | 6 +
R/sonarJSON.R |only
man/jSonarR.Rd | 4 -
man/new.SonarConnection.Rd | 8 +-
man/sonarAgg.Rd | 12 ++-
man/sonarCSV.Rd |only
man/sonarFind.Rd | 12 ++-
man/sonarJSON.Rd |only
16 files changed, 143 insertions(+), 135 deletions(-)
Title: Gaussian Processes Modeling
Diff between GPfit versions 0.2-0 dated 2014-06-24 and 0.2-1 dated 2014-09-03
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld, Hugh Chipman, Pritam Ranjan
Maintainer: Hugh Chipman
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/corr_matrix.R | 3 +++
R/predict.GP.R | 9 ++++++++-
4 files changed, 18 insertions(+), 8 deletions(-)
Title: docopt, command-line interface specification language
Diff between docopt versions 0.1.1 dated 2014-06-10 and 0.3 dated 2014-09-03
Description: docopt lets you define a command-line interface by just giving it
a description in the specific format.
Author: Edwin de Jonge (edwindjonge@gmail.com)
Maintainer: Edwin de Jonge
docopt-0.1.1/docopt/inst/tests |only
docopt-0.3/docopt/DESCRIPTION | 14
docopt-0.3/docopt/LICENSE | 4
docopt-0.3/docopt/MD5 | 56
docopt-0.3/docopt/NAMESPACE | 8
docopt-0.3/docopt/NEWS |only
docopt-0.3/docopt/R/Pattern.R | 924 ++++-----
docopt-0.3/docopt/R/Tokens.R | 193 +
docopt-0.3/docopt/R/docopt.R | 29
docopt-0.3/docopt/R/parse.R | 546 ++---
docopt-0.3/docopt/R/pkg.R | 20
docopt-0.3/docopt/README.md | 152 -
docopt-0.3/docopt/inst/paper/Makefile | 24
docopt-0.3/docopt/inst/paper/beamer.tex |only
docopt-0.3/docopt/inst/paper/docopt.bib | 64
docopt-0.3/docopt/inst/paper/docopt.tex | 160 -
docopt-0.3/docopt/inst/paper/figures |only
docopt-0.3/docopt/inst/paper/test.R |only
docopt-0.3/docopt/inst/paper/user2014.html |only
docopt-0.3/docopt/inst/paper/user2014.md |only
docopt-0.3/docopt/inst/paper/user2014.pdf |only
docopt-0.3/docopt/inst/spec/README.md | 14
docopt-0.3/docopt/inst/spec/docopt.py | 1162 +++++------
docopt-0.3/docopt/inst/spec/generate_tests.R | 179 -
docopt-0.3/docopt/inst/spec/testcases.docopt | 1914 +++++++++----------
docopt-0.3/docopt/man/as.character-Pattern-method.Rd | 36
docopt-0.3/docopt/man/as.character-Tokens-method.Rd | 36
docopt-0.3/docopt/man/docopt-package.Rd | 26
docopt-0.3/docopt/man/docopt.Rd | 45
docopt-0.3/docopt/man/sub-Tokens-method.Rd | 95
docopt-0.3/docopt/man/subset-Tokens-method.Rd | 89
docopt-0.3/docopt/tests |only
32 files changed, 2920 insertions(+), 2870 deletions(-)
Title: Data Sets from Montgomery, Peck and Vining's Book
Diff between MPV versions 1.29 dated 2013-09-22 and 1.35 dated 2014-09-03
Description: Most of this package consists of data sets from the
textbook Introduction
to Linear Regression Analysis (3rd ed), by Montgomery et al.
Some additional data sets and functions useful in an
undergraduate regression course are included.
Author: W.J. Braun
Maintainer: W.J. Braun
DESCRIPTION | 8 ++++----
MD5 | 10 +++++++---
R/GFplot.R |only
R/GRegplot.R |only
data/pathoeg.rda |binary
man/GFplot.Rd |only
man/GRegplot.Rd |only
man/Uplot.Rd | 4 ++--
8 files changed, 13 insertions(+), 9 deletions(-)
Title: Local Approximate Gaussian Process Regression
Diff between laGP versions 1.1 dated 2014-03-20 and 1.1-1 dated 2014-09-03
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
ChangeLog | 14 ++
DESCRIPTION | 14 +-
MD5 | 44 ++++----
NAMESPACE | 8 +
R/auglag.R | 10 +
R/gp.R | 52 ++++++----
R/laGP.R | 56 +++++++----
R/parallel.R | 11 +-
man/aGP.Rd | 79 ++++++++++-----
man/alcGP.Rd | 25 +++-
man/darg.Rd | 3
man/laGP.Rd | 120 +++++++++++++++--------
man/mleGP.Rd | 9 -
man/newGP.Rd | 7 -
man/optim.auglag.Rd | 63 +++++++++---
man/predGP.Rd | 6 -
src/covar.c | 2
src/gp.c | 264 +++++++++++++++++++++++++++++++---------------------
src/gp.h | 4
src/laGP.c | 100 +++++++++++++++----
src/laGP.h | 22 ++--
src/matrix.c | 32 ++++--
src/matrix.h | 1
23 files changed, 624 insertions(+), 322 deletions(-)
Title: Tools for analysing forensic genetic DNA data
Diff between DNAtools versions 0.1-8 dated 2013-12-06 and 0.1-21 dated 2014-09-03
Description: Computationally efficient tools for comparing all pairs of profiles in a DNA database. The expectation and covariance of the summary statistic
is implemented for fast computing. Routines for estimating proportions of close related individuals are available. The use of wildcards (also
called F-designation) is implemented. Dedicated functions ease plotting the results.
Author: Torben Tvedebrink
Maintainer: Torben Tvedebrink
DNAtools-0.1-21/DNAtools/DESCRIPTION | 17
DNAtools-0.1-21/DNAtools/MD5 | 69 -
DNAtools-0.1-21/DNAtools/NAMESPACE | 2
DNAtools-0.1-21/DNAtools/R/RcppExports.R |only
DNAtools-0.1-21/DNAtools/R/dbcompare.R | 158 +-
DNAtools-0.1-21/DNAtools/R/induceRare.R |only
DNAtools-0.1-21/DNAtools/R/numberOfAlleles.R | 8
DNAtools-0.1-21/DNAtools/R/prob.R |only
DNAtools-0.1-21/DNAtools/R/rareallele.R |only
DNAtools-0.1-21/DNAtools/R/rarity.R | 148 +-
DNAtools-0.1-21/DNAtools/R/score.R |only
DNAtools-0.1-21/DNAtools/build/vignette.rds |binary
DNAtools-0.1-21/DNAtools/inst/doc/DNAtools.Rnw | 65
DNAtools-0.1-21/DNAtools/inst/doc/DNAtools.pdf |binary
DNAtools-0.1-21/DNAtools/man/DNAtools-package.Rd | 9
DNAtools-0.1-21/DNAtools/man/dbcollapse.Rd |only
DNAtools-0.1-21/DNAtools/man/dbcompare.Rd |only
DNAtools-0.1-21/DNAtools/man/dbsimulate.Rd |only
DNAtools-0.1-21/DNAtools/man/estimatePD.Rd | 6
DNAtools-0.1-21/DNAtools/man/noa.Rd |only
DNAtools-0.1-21/DNAtools/man/noaTabs.Rd | 3
DNAtools-0.1-21/DNAtools/man/pContrib.Rd | 20
DNAtools-0.1-21/DNAtools/man/pContrib.locus.Rd | 17
DNAtools-0.1-21/DNAtools/man/plot.dbOptim.Rd | 2
DNAtools-0.1-21/DNAtools/man/plot.dbcompare.Rd | 2
DNAtools-0.1-21/DNAtools/man/print.dbOptim.Rd | 4
DNAtools-0.1-21/DNAtools/man/print.dbcompare.Rd | 2
DNAtools-0.1-21/DNAtools/man/rarity.Rd |only
DNAtools-0.1-21/DNAtools/man/rarityVar.Rd |only
DNAtools-0.1-21/DNAtools/man/rcpp_hello_world.Rd |only
DNAtools-0.1-21/DNAtools/man/relatedness.Rd |only
DNAtools-0.1-21/DNAtools/src/DNTRare.cpp |only
DNAtools-0.1-21/DNAtools/src/DNTRare.h |only
DNAtools-0.1-21/DNAtools/src/RcppExports.cpp |only
DNAtools-0.1-21/DNAtools/src/mcompare.cpp | 1451 +++++++++-------------
DNAtools-0.1-21/DNAtools/src/prob.cpp |only
DNAtools-0.1-21/DNAtools/src/profile.cpp |only
DNAtools-0.1-21/DNAtools/src/profile.h |only
DNAtools-0.1-21/DNAtools/src/rcpp_hello_world.cpp |only
DNAtools-0.1-21/DNAtools/vignettes/DNAtools.Rnw | 65
DNAtools-0.1-21/DNAtools/vignettes/DNAtools.tex |only
DNAtools-0.1-21/DNAtools/vignettes/Makefile |only
DNAtools-0.1-8/DNAtools/R/olddbcompare.R |only
DNAtools-0.1-8/DNAtools/R/rarityJunk.R |only
DNAtools-0.1-8/DNAtools/man/dbCollapse.Rd |only
DNAtools-0.1-8/DNAtools/man/dbCompare.Rd |only
DNAtools-0.1-8/DNAtools/man/dbExpect.Rd |only
DNAtools-0.1-8/DNAtools/man/dbSimulate.Rd |only
DNAtools-0.1-8/DNAtools/man/dbVariance.Rd |only
DNAtools-0.1-8/DNAtools/man/optim.relatedness.Rd |only
DNAtools-0.1-8/DNAtools/man/pNoA.Rd |only
51 files changed, 1009 insertions(+), 1039 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL detection using
mixed models
Diff between wgaim versions 1.4-0 dated 2013-05-07 and 1.4-3 dated 2014-09-03
Description: This package integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor
Maintainer: Julian Taylor
wgaim-1.4-0/wgaim/R/wgaim6.R |only
wgaim-1.4-0/wgaim/inst/doc/wgaim.R |only
wgaim-1.4-0/wgaim/inst/doc/wgaim.Rnw |only
wgaim-1.4-3/wgaim/DESCRIPTION | 16 ++++++----------
wgaim-1.4-3/wgaim/MD5 | 32 +++++++++++++++-----------------
wgaim-1.4-3/wgaim/NAMESPACE | 5 +++++
wgaim-1.4-3/wgaim/R/wgaim7.R |only
wgaim-1.4-3/wgaim/inst/NEWS.Rd | 19 ++++++++++++-------
wgaim-1.4-3/wgaim/inst/doc/RxKExample.R | 21 ++++++++++++---------
wgaim-1.4-3/wgaim/inst/doc/SxTExample.R | 12 ++++++------
wgaim-1.4-3/wgaim/inst/doc/wgaim.pdf |binary
wgaim-1.4-3/wgaim/man/genoCxR.Rd | 4 ++--
wgaim-1.4-3/wgaim/man/genoRxK.Rd | 4 ++--
wgaim-1.4-3/wgaim/man/genoSxT.Rd | 4 ++--
wgaim-1.4-3/wgaim/man/phenoCxR.Rd | 6 +++---
wgaim-1.4-3/wgaim/man/phenoRxK.Rd | 6 +++---
wgaim-1.4-3/wgaim/man/phenoSxT.Rd | 6 +++---
wgaim-1.4-3/wgaim/man/wgaim-internal.Rd | 6 ++++--
wgaim-1.4-3/wgaim/man/wgaim.asreml.Rd | 24 ++++++++++++++----------
19 files changed, 89 insertions(+), 76 deletions(-)
Title: Updated Classification Methods using Unlabeled Data
Diff between upclass versions 1.0 dated 2012-09-20 and 2.0 dated 2014-09-03
Description: This package contains a collection of functions which
implement data classification. It uses unlabeled data to obtain
parameter estimates of models. The functions can be implemented
over a number of models with the best model selected and
displayed.
Author: Niamh Russell, Laura Cribbin, Thomas Brendan Murphy
Maintainer: Niamh Russell
upclass-1.0/upclass/LICENSE.txt |only
upclass-1.0/upclass/inst/doc/manual.Rnw |only
upclass-1.0/upclass/inst/doc/manual.pdf |only
upclass-2.0/upclass/DESCRIPTION | 22 ++++-----
upclass-2.0/upclass/MD5 | 50 +++++++++++---------
upclass-2.0/upclass/NAMESPACE | 2
upclass-2.0/upclass/R/noupclassify.R | 6 +-
upclass-2.0/upclass/R/noupclassifymodel.R | 19 +++----
upclass-2.0/upclass/R/plot.upclassfit.R | 26 +++++-----
upclass-2.0/upclass/R/print.upclassfit.R | 46 +++++-------------
upclass-2.0/upclass/R/summary.upclassfit.R | 50 ++++++--------------
upclass-2.0/upclass/R/upclassify.R | 6 +-
upclass-2.0/upclass/R/upclassifymodel.R | 22 ++++-----
upclass-2.0/upclass/build |only
upclass-2.0/upclass/inst/doc/upclass.R |only
upclass-2.0/upclass/inst/doc/upclass.Rnw |only
upclass-2.0/upclass/inst/doc/upclass.pdf |only
upclass-2.0/upclass/man/Aitken.Rd | 7 +-
upclass-2.0/upclass/man/noupclassify.Rd | 53 ++++++++++++++++-----
upclass-2.0/upclass/man/noupclassifymodel.Rd | 17 +++----
upclass-2.0/upclass/man/plot.upclassfit.Rd | 8 +--
upclass-2.0/upclass/man/print.upclassfit.Rd | 21 ++------
upclass-2.0/upclass/man/summary.upclassfit.Rd | 29 ++++-------
upclass-2.0/upclass/man/upclass-package.Rd | 6 +-
upclass-2.0/upclass/man/upclassify.Rd | 63 +++++++++++++++++++-------
upclass-2.0/upclass/man/upclassifymodel.Rd | 25 +++++-----
upclass-2.0/upclass/vignettes |only
27 files changed, 249 insertions(+), 229 deletions(-)
Title: Functions for calculating tolerance intervals
Diff between tolerance versions 0.5.3 dated 2013-10-11 and 1.0.0 dated 2014-09-03
Description: Tolerance limits provide the limits between which we can expect to find a specified proportion of a sampled population with a given level of confidence. This package provides functions for estimating tolerance limits for various distributions. Plotting is also available for tolerance limits of continuous random variables.
Author: Derek S. Young [aut, cre]
Maintainer: Derek S. Young
DESCRIPTION | 12 ++--
MD5 | 31 ++++++------
NEWS | 14 +++++
R/hypertolint.R | 57 ++++++++++++-----------
R/interpextrap.R |only
R/neghyper.R | 114 +++++++++++++++++++++++-----------------------
R/neghypertolint.R | 34 +++++++------
R/nonpartolint.R | 11 ++++
man/accsamp.Rd | 2
man/exptolint.Rd | 2
man/hypertolint.Rd | 9 ++-
man/negbintolint.Rd | 2
man/neghypertolint.Rd | 7 ++
man/nonpartolint.Rd | 18 ++++---
man/plottol.Rd | 2
man/tolerance-internal.Rd | 15 ++++--
man/tolerance.package.Rd | 6 +-
17 files changed, 194 insertions(+), 142 deletions(-)
Title: Functions for a variety of stylometric analyses
Diff between stylo versions 0.5.7 dated 2014-08-13 and 0.5.8 dated 2014-09-03
Description: A number of functions, supplemented by GUI, to perform various
analyses in the field of computational stylistics, authorship
attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder
stylo-0.5.7/stylo/R/culling.R |only
stylo-0.5.7/stylo/man/culling.Rd |only
stylo-0.5.8/stylo/DESCRIPTION | 8
stylo-0.5.8/stylo/MD5 | 64 ++--
stylo-0.5.8/stylo/NAMESPACE | 16 -
stylo-0.5.8/stylo/NEWS | 13
stylo-0.5.8/stylo/R/assign.plot.colors.R | 23 +
stylo-0.5.8/stylo/R/classify.R | 390 +++----------------------
stylo-0.5.8/stylo/R/load.corpus.and.parse.R | 1
stylo-0.5.8/stylo/R/make.samples.R | 8
stylo-0.5.8/stylo/R/oppose.R | 2
stylo-0.5.8/stylo/R/perform.culling.R |only
stylo-0.5.8/stylo/R/perform.delta.R |only
stylo-0.5.8/stylo/R/perform.knn.R |only
stylo-0.5.8/stylo/R/perform.naivebayes.R |only
stylo-0.5.8/stylo/R/perform.nsc.R |only
stylo-0.5.8/stylo/R/perform.svm.R |only
stylo-0.5.8/stylo/R/rolling.classify.r |only
stylo-0.5.8/stylo/R/rolling.delta.R | 4
stylo-0.5.8/stylo/R/stylo.R | 10
stylo-0.5.8/stylo/R/zeta.chisquare.R | 8
stylo-0.5.8/stylo/R/zzz.R |only
stylo-0.5.8/stylo/man/assign.plot.colors.Rd | 3
stylo-0.5.8/stylo/man/classify.Rd | 4
stylo-0.5.8/stylo/man/delete.stop.words.Rd | 2
stylo-0.5.8/stylo/man/gui.classify.Rd | 2
stylo-0.5.8/stylo/man/gui.oppose.Rd | 2
stylo-0.5.8/stylo/man/gui.stylo.Rd | 2
stylo-0.5.8/stylo/man/load.corpus.and.parse.Rd | 4
stylo-0.5.8/stylo/man/make.samples.Rd | 4
stylo-0.5.8/stylo/man/perform.culling.Rd |only
stylo-0.5.8/stylo/man/perform.delta.Rd |only
stylo-0.5.8/stylo/man/perform.knn.Rd |only
stylo-0.5.8/stylo/man/perform.naivebayes.Rd |only
stylo-0.5.8/stylo/man/perform.nsc.Rd |only
stylo-0.5.8/stylo/man/perform.svm.Rd |only
stylo-0.5.8/stylo/man/rolling.classify.Rd |only
stylo-0.5.8/stylo/man/rolling.delta.Rd | 7
stylo-0.5.8/stylo/man/stylo.Rd | 15
stylo-0.5.8/stylo/man/txt.to.words.Rd | 6
stylo-0.5.8/stylo/man/zeta.chisquare.Rd |only
stylo-0.5.8/stylo/man/zeta.craig.Rd |only
stylo-0.5.8/stylo/man/zeta.eder.Rd |only
43 files changed, 191 insertions(+), 407 deletions(-)
Title: A Fast Parameter Estimation Method for Evolutionary Biology
Diff between jaatha versions 2.5.1 dated 2014-08-14 and 2.6 dated 2014-09-03
Description: Jaatha is a composite likelihood method for inferring evolutionary
parameters using genetic data. Given a model of the evolutionary history of
two biological populations as well as SNP data from multiple individuals
from each population, it estimates model parameters like the time of
separation of both species.
Author: Paul R. Staab, Lisha Mathew and Dirk Metzler
Maintainer: Paul R. Staab
jaatha-2.5.1/jaatha/R/Block.R |only
jaatha-2.5.1/jaatha/R/DemographicModel.R |only
jaatha-2.5.1/jaatha/R/Jaatha.R |only
jaatha-2.5.1/jaatha/inst/integrationTests |only
jaatha-2.5.1/jaatha/inst/unitTests |only
jaatha-2.5.1/jaatha/man/setLogging.Rd |only
jaatha-2.5.1/jaatha/tests/doRUnit.R |only
jaatha-2.6/jaatha/DESCRIPTION | 16 +-
jaatha-2.6/jaatha/MD5 | 116 ++++++++++----------
jaatha-2.6/jaatha/NAMESPACE | 2
jaatha-2.6/jaatha/NEWS | 20 +++
jaatha-2.6/jaatha/R/RcppExports.R | 12 +-
jaatha-2.6/jaatha/R/block.R |only
jaatha-2.6/jaatha/R/confidence_intervals.R | 98 +++++++++++-----
jaatha-2.6/jaatha/R/demographic_model.R |only
jaatha-2.6/jaatha/R/fit_glm.R | 1
jaatha-2.6/jaatha/R/helper_functions.R | 53 ---------
jaatha-2.6/jaatha/R/initial_search.R | 5
jaatha-2.6/jaatha/R/jaatha.R |only
jaatha-2.6/jaatha/R/parallelization.R | 36 +++---
jaatha-2.6/jaatha/R/refined_search.R | 72 +-----------
jaatha-2.6/jaatha/R/sim_program_ms.R | 7 -
jaatha-2.6/jaatha/R/sim_program_msms.R | 10 -
jaatha-2.6/jaatha/R/sim_program_seqgen.R | 31 +++--
jaatha-2.6/jaatha/README | 10 -
jaatha-2.6/jaatha/man/Jaatha.confidenceIntervals.Rd | 20 ++-
jaatha-2.6/jaatha/man/Jaatha.getCIsFromLogs.Rd |only
jaatha-2.6/jaatha/man/dm.addSummaryStatistic.Rd |only
jaatha-2.6/jaatha/man/dm.getLociLength.Rd | 2
jaatha-2.6/jaatha/man/dm.getLociNumber.Rd | 5
jaatha-2.6/jaatha/man/setCores.Rd |only
jaatha-2.6/jaatha/src/RcppExports.cpp | 41 ++++++-
jaatha-2.6/jaatha/src/parse_output.cpp | 104 ++++++++++-------
jaatha-2.6/jaatha/src/parse_trees.cpp |only
jaatha-2.6/jaatha/src/sum_stat_polym_classes.cpp |only
jaatha-2.6/jaatha/tests/integration |only
jaatha-2.6/jaatha/tests/testsetup |only
jaatha-2.6/jaatha/tests/testthat |only
jaatha-2.6/jaatha/tests/testthat.R |only
39 files changed, 345 insertions(+), 316 deletions(-)
Title: Fast and versatile argument checks
Diff between checkmate versions 1.3 dated 2014-08-15 and 1.4 dated 2014-09-03
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang
Maintainer: Michel Lang
DESCRIPTION | 6
MD5 | 81 +++++------
NEWS | 8 +
R/checkAccess.r | 21 +-
R/checkVector.r | 2
man/checkAccess.Rd | 3
man/checkDirectory.Rd | 3
man/checkFile.Rd | 3
src/checks.c | 231 ++++++++++++++++++--------------
src/cmessages.c | 6
src/cmessages.h | 4
tests/testthat/helper.r |only
tests/testthat/test_checkArray.r | 7
tests/testthat/test_checkAtomic.r | 6
tests/testthat/test_checkAtomicVector.r | 8 -
tests/testthat/test_checkCharacter.r | 6
tests/testthat/test_checkChoice.R | 6
tests/testthat/test_checkClass.r | 5
tests/testthat/test_checkComplex.r | 8 -
tests/testthat/test_checkCount.r | 6
tests/testthat/test_checkDataFrame.r | 36 ++++
tests/testthat/test_checkEnvironment.r | 8 -
tests/testthat/test_checkFactor.r | 8 -
tests/testthat/test_checkFilesystem.r | 26 ++-
tests/testthat/test_checkFlag.r | 6
tests/testthat/test_checkFunction.r | 6
tests/testthat/test_checkInt.r | 6
tests/testthat/test_checkInteger.r | 6
tests/testthat/test_checkIntegerish.r | 7
tests/testthat/test_checkList.r | 9 -
tests/testthat/test_checkLogical.r | 8 -
tests/testthat/test_checkMatrix.r | 8 -
tests/testthat/test_checkNamed.r | 11 -
tests/testthat/test_checkNull.r | 5
tests/testthat/test_checkNumber.r | 6
tests/testthat/test_checkNumeric.r | 8 -
tests/testthat/test_checkScalar.r | 6
tests/testthat/test_checkScalarNA.r | 1
tests/testthat/test_checkSetEqual.r | 6
tests/testthat/test_checkString.r | 6
tests/testthat/test_checkSubset.r | 6
tests/testthat/test_checkVector.r | 7
42 files changed, 403 insertions(+), 213 deletions(-)
Title: Calculate Predicted Means for Linear Models
Diff between predictmeans versions 0.97 dated 2014-07-03 and 0.98 dated 2014-09-03
Description: This package provides functions to diagnose
and make inferences from various linear models, such as those obtained from 'aov',
'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted
means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo
DESCRIPTION | 6 -
MD5 | 31 +++++-----
NAMESPACE | 2
R/CookD.R | 4 -
R/Kmatrix.R | 10 +--
R/PMplot.R | 12 ++-
R/contrastmeans.R | 1
R/covariatemeans.R | 65 +++++++++++----------
R/misc.R | 134 ++++++++++++++++++++++++++++++++++++++++++++
R/model.parm.functs.R | 4 -
R/predictmeans.R | 75 +++++++++++++-----------
R/rsplot.gls.R | 2
inst |only
man/Kmatrix.Rd | 2
man/covariatemeans.Rd | 15 +++-
man/predictmeans-package.Rd | 2
man/predictmeans.Rd | 15 +++-
17 files changed, 273 insertions(+), 107 deletions(-)
Title: Fitting l2-regularized logit choice models via generalized
gradient descent
Diff between logitchoice versions 0.9.3 dated 2014-08-26 and 0.9.4 dated 2014-09-03
Description: Fits linear discrete logit choice models with l2 regularization. To handle reasonably sized datasets, we employ an accelerated version of generalized gradient descent.
Author: Michael Lim
Maintainer: Michael Lim
DESCRIPTION | 8 +--
MD5 | 9 ++--
R/logitchoice.r | 9 +---
man/logitchoice.Rd | 2
src/mle.c | 115 +++--------------------------------------------------
src/mle_r.c |only
6 files changed, 21 insertions(+), 122 deletions(-)