Title: Response-surface analysis
Diff between rsm versions 2.02 dated 2013-02-10 and 2.03 dated 2013-02-21
Description: Provides functions to generate response-surface designs,
fit first- and second-order response-surface models, make
surface plots, obtain the path of steepest ascent, and do
canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
R/contour-lm.R | 6 +++---
inst/NEWS | 6 ++++++
4 files changed, 17 insertions(+), 10 deletions(-)
Title: Miscellaneous functions intended to improve the R coding
experience
Diff between Kmisc versions 0.3.0 dated 2013-01-22 and 0.4.0-1 dated 2013-02-21
Description: A collection of functions for common data reshaping
operations, as well as functions for table and plot generation
for R Markdown documents.
Author: Kevin Ushey
Maintainer: Kevin Ushey
Kmisc-0.3.0/Kmisc/inst/doc/example.Rmd |only
Kmisc-0.3.0/Kmisc/man/anatomy.Rd |only
Kmisc-0.4.0-1/Kmisc/DESCRIPTION | 19
Kmisc-0.4.0-1/Kmisc/MD5 | 112 ++-
Kmisc-0.4.0-1/Kmisc/NAMESPACE | 127 ++-
Kmisc-0.4.0-1/Kmisc/NEWS | 91 +-
Kmisc-0.4.0-1/Kmisc/R/RcppExports.R |only
Kmisc-0.4.0-1/Kmisc/R/Rcpp_gen_makevars.R | 8
Kmisc-0.4.0-1/Kmisc/R/anat.R | 28
Kmisc-0.4.0-1/Kmisc/R/bwplot2.R | 228 +++---
Kmisc-0.4.0-1/Kmisc/R/clean_doc.R | 62 -
Kmisc-0.4.0-1/Kmisc/R/grid.text2.R |only
Kmisc-0.4.0-1/Kmisc/R/html.R | 788 ++++++++++++------------
Kmisc-0.4.0-1/Kmisc/R/html_attach.R |only
Kmisc-0.4.0-1/Kmisc/R/html_prep.R | 261 +++----
Kmisc-0.4.0-1/Kmisc/R/in_interval.R | 2
Kmisc-0.4.0-1/Kmisc/R/is_sorted.R | 30
Kmisc-0.4.0-1/Kmisc/R/misc.R | 201 ++----
Kmisc-0.4.0-1/Kmisc/R/pMerge.R | 142 ++--
Kmisc-0.4.0-1/Kmisc/R/package_description.R | 12
Kmisc-0.4.0-1/Kmisc/R/pad.R |only
Kmisc-0.4.0-1/Kmisc/R/par.reset.R | 22
Kmisc-0.4.0-1/Kmisc/R/pp_plot.R |only
Kmisc-0.4.0-1/Kmisc/R/rcpp_apply_generator.R | 117 +++
Kmisc-0.4.0-1/Kmisc/R/regex.R |only
Kmisc-0.4.0-1/Kmisc/R/remove_char_digit.R |only
Kmisc-0.4.0-1/Kmisc/R/split_runs.R |only
Kmisc-0.4.0-1/Kmisc/R/stack_list.R |only
Kmisc-0.4.0-1/Kmisc/R/str_rev.R | 86 +-
Kmisc-0.4.0-1/Kmisc/R/update_date.R |only
Kmisc-0.4.0-1/Kmisc/Rplots.pdf |only
Kmisc-0.4.0-1/Kmisc/data/html.rda |binary
Kmisc-0.4.0-1/Kmisc/data/html.txt.gz |binary
Kmisc-0.4.0-1/Kmisc/inst/doc/Kmisc-intro.Rmd |only
Kmisc-0.4.0-1/Kmisc/inst/doc/Kmisc-intro.html |only
Kmisc-0.4.0-1/Kmisc/inst/doc/markdown.css | 575 ++++++++---------
Kmisc-0.4.0-1/Kmisc/inst/tests |only
Kmisc-0.4.0-1/Kmisc/man/Rcpp_gen_makevars.Rd | 6
Kmisc-0.4.0-1/Kmisc/man/anat.Rd | 5
Kmisc-0.4.0-1/Kmisc/man/attachHTML.Rd | 4
Kmisc-0.4.0-1/Kmisc/man/cat.cb.Rd | 2
Kmisc-0.4.0-1/Kmisc/man/char_to_factor.Rd | 10
Kmisc-0.4.0-1/Kmisc/man/factor_to_char.Rd | 12
Kmisc-0.4.0-1/Kmisc/man/fgrep.Rd |only
Kmisc-0.4.0-1/Kmisc/man/grid.text2.Rd |only
Kmisc-0.4.0-1/Kmisc/man/hImg.Rd | 4
Kmisc-0.4.0-1/Kmisc/man/html.Rd | 41 -
Kmisc-0.4.0-1/Kmisc/man/html_tags.Rd |only
Kmisc-0.4.0-1/Kmisc/man/in_interval.Rd | 5
Kmisc-0.4.0-1/Kmisc/man/kAnova.Rd | 1
Kmisc-0.4.0-1/Kmisc/man/kLoad.Rd | 5
Kmisc-0.4.0-1/Kmisc/man/kMerge.Rd | 10
Kmisc-0.4.0-1/Kmisc/man/ngrep.Rd | 50 -
Kmisc-0.4.0-1/Kmisc/man/pad.Rd |only
Kmisc-0.4.0-1/Kmisc/man/pp_plot.Rd |only
Kmisc-0.4.0-1/Kmisc/man/print.kHTML.Rd | 2
Kmisc-0.4.0-1/Kmisc/man/rcpp_apply_generator.Rd | 71 ++
Kmisc-0.4.0-1/Kmisc/man/remove_chars.Rd |only
Kmisc-0.4.0-1/Kmisc/man/remove_digits.Rd |only
Kmisc-0.4.0-1/Kmisc/man/split_runs.Rd |only
Kmisc-0.4.0-1/Kmisc/man/stack_list.Rd | 56 +
Kmisc-0.4.0-1/Kmisc/man/str_split.Rd | 19
Kmisc-0.4.0-1/Kmisc/man/swap.Rd | 3
Kmisc-0.4.0-1/Kmisc/man/update_date.Rd |only
Kmisc-0.4.0-1/Kmisc/src/Makevars |only
Kmisc-0.4.0-1/Kmisc/src/Makevars.win |only
Kmisc-0.4.0-1/Kmisc/src/RcppExports.cpp |only
Kmisc-0.4.0-1/Kmisc/src/factor_to_char.c |only
Kmisc-0.4.0-1/Kmisc/src/in_interval.c | 4
Kmisc-0.4.0-1/Kmisc/src/split_runs.cpp |only
Kmisc-0.4.0-1/Kmisc/src/stack_list.cpp |only
71 files changed, 1694 insertions(+), 1527 deletions(-)
Title: SAP Netweaver RFC connector for R
Diff between RSAP versions 0.7 dated 2013-02-02 and 0.9 dated 2013-02-21
Description: The SAP Netweaver RFC connector for R
Author: Piers Harding
Maintainer: Piers Harding
RSAP-0.7/RSAP/.Rinstignore |only
RSAP-0.7/RSAP/sap.yml |only
RSAP-0.7/RSAP/tst.sh |only
RSAP-0.9/RSAP/ChangeLog | 11 +
RSAP-0.9/RSAP/DESCRIPTION | 19 +-
RSAP-0.9/RSAP/INSTALL | 47 +++++--
RSAP-0.9/RSAP/MD5 | 44 +++---
RSAP-0.9/RSAP/README | 15 +-
RSAP-0.9/RSAP/configure | 267 +++++++++++++++++++++++------------------
RSAP-0.9/RSAP/configure.ac | 52 ++++++-
RSAP-0.9/RSAP/configure.win | 15 ++
RSAP-0.9/RSAP/run_tests.R | 2
RSAP-0.9/RSAP/send.sh |only
RSAP-0.9/RSAP/src/Makevars.in | 15 --
RSAP-0.9/RSAP/src/Makevars.win | 10 -
RSAP-0.9/RSAP/src/config.h.in | 61 ---------
RSAP-0.9/RSAP/tests/1.R | 2
RSAP-0.9/RSAP/tests/2.R | 2
RSAP-0.9/RSAP/tests/3.R | 2
RSAP-0.9/RSAP/tests/4.R | 2
RSAP-0.9/RSAP/tests/5.R | 2
RSAP-0.9/RSAP/tests/6.R | 2
RSAP-0.9/RSAP/tests/7.R | 2
RSAP-0.9/RSAP/tests/8.R | 2
RSAP-0.9/RSAP/tests/9.R | 2
RSAP-0.9/RSAP/tests/sap.yml |only
26 files changed, 316 insertions(+), 260 deletions(-)
Title: An efficient swiss army knife for population genetic & genomic
analysis
Diff between PopGenome versions 1.2.2 dated 2013-02-21 and 1.2.3 dated 2013-02-21
Description: PopGenome is an R-package for Population Genetic & Genomic
Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer
PopGenome-1.2.2/PopGenome/src/tabix/bedidx.o |only
PopGenome-1.2.2/PopGenome/src/tabix/bgzf.o |only
PopGenome-1.2.2/PopGenome/src/tabix/index.o |only
PopGenome-1.2.2/PopGenome/src/tabix/knetfile.o |only
PopGenome-1.2.2/PopGenome/src/tabix/kstring.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/readdnapp.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whop_r_dataframe.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_codemat.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_filtering.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_main.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_read.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_region.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_rsupport.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_samples.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_tools.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whopgen_vcf.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whoptbi_Rifc.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whoptbi_info.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whoptbi_main.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whoptbi_read.o |only
PopGenome-1.2.2/PopGenome/src/whopgenome/whoptbi_region.o |only
PopGenome-1.2.2/PopGenome/src/zlib/adler32.o |only
PopGenome-1.2.2/PopGenome/src/zlib/compress.o |only
PopGenome-1.2.2/PopGenome/src/zlib/crc32.o |only
PopGenome-1.2.2/PopGenome/src/zlib/deflate.o |only
PopGenome-1.2.2/PopGenome/src/zlib/gzclose.o |only
PopGenome-1.2.2/PopGenome/src/zlib/gzlib.o |only
PopGenome-1.2.2/PopGenome/src/zlib/gzread.o |only
PopGenome-1.2.2/PopGenome/src/zlib/gzwrite.o |only
PopGenome-1.2.2/PopGenome/src/zlib/infback.o |only
PopGenome-1.2.2/PopGenome/src/zlib/inffast.o |only
PopGenome-1.2.2/PopGenome/src/zlib/inflate.o |only
PopGenome-1.2.2/PopGenome/src/zlib/inftrees.o |only
PopGenome-1.2.2/PopGenome/src/zlib/trees.o |only
PopGenome-1.2.2/PopGenome/src/zlib/uncompr.o |only
PopGenome-1.2.2/PopGenome/src/zlib/zutil.o |only
PopGenome-1.2.3/PopGenome/DESCRIPTION | 6 -
PopGenome-1.2.3/PopGenome/MD5 | 44 +----------
PopGenome-1.2.3/PopGenome/NEWS | 6 +
PopGenome-1.2.3/PopGenome/R/readData.R | 15 ++-
PopGenome-1.2.3/PopGenome/R/readVCF.R | 8 +-
41 files changed, 26 insertions(+), 53 deletions(-)
Title: A set of datasets used in my classes or in the book ,,Modele
liniowe i mieszane w R, wraz z przykladami w analizie danych''
Diff between PBImisc versions 0.997 dated 2013-01-18 and 0.998 dated 2013-02-21
Description: A set of datasets prepared as a support for my classes or
the book ,,Modele liniowe i mieszane w R, wraz z przykladami w
analizie danych''
Author: Przemyslaw Biecek
Maintainer: Przemyslaw Biecek
DESCRIPTION | 7 ++++---
MD5 | 11 +++++++++--
data/corn.rda |only
data/datalist |only
data/musculus.rda |only
man/PBImisc-package.Rd | 6 +++---
man/corn.Rd |only
man/musculus.Rd |only
other |only
9 files changed, 16 insertions(+), 8 deletions(-)
Title: Miscellaneous functions intended to improve the R coding
experience
Diff between Kmisc versions 0.3.0 dated 2013-01-22 and 0.4.0 dated 2013-02-21
Description: A collection of functions for common data reshaping
operations, as well as functions for table and plot generation
for R Markdown documents.
Author: Kevin Ushey
Maintainer: Kevin Ushey
Kmisc |only
1 file changed
Title: The Fisher-EM algorithm
Diff between FisherEM versions 1.3.1 dated 2013-02-20 and 1.3.2 dated 2013-02-21
Description: The FisherEM package provides an efficient algorithm for
the unsupervised classification of high-dimensional data. This
FisherEM algorithm models and clusters the data in a
discriminative and low-dimensional latent subspace. It also
provides a low-dimensional representation of the clustered
data.
Author: Charles Bouveyron and Camille Brunet
Maintainer: Camille Brunet
DESCRIPTION | 6 +++---
MD5 | 4 ++--
NAMESPACE | 1 -
3 files changed, 5 insertions(+), 6 deletions(-)
Title: Comparing correlations
Diff between cocor versions 0.01-1 dated 2012-11-30 and 0.01-2 dated 2013-02-21
Description: This package provides functions to compare two
correlations based on either dependent or independent groups.
Author: Birk Diedenhofen
Maintainer: Birk Diedenhofen
ChangeLog | 4
DESCRIPTION | 9
MD5 | 26 -
R/cocor-package.R | 4
R/cocor.dep.groups.nonoverlap.r | 141 ++++-----
R/cocor.dep.groups.overlap.r | 262 ++++++++---------
R/cocor.indep.groups.r | 43 +-
R/helper.r | 4
inst/CITATION | 8
inst/rkward/rkwarddev.cocor.plugin.script.R | 2
man/cocor-package.Rd | 4
man/cocor.dep.groups.nonoverlap.Rd | 231 ++++++---------
man/cocor.dep.groups.overlap.Rd | 420 +++++++++++-----------------
man/cocor.indep.groups.Rd | 62 ++--
14 files changed, 550 insertions(+), 670 deletions(-)
Title: Computation of Bayes factors for simple designs
Diff between BayesFactor versions 0.9.0 dated 2013-01-17 and 0.9.1 dated 2013-02-21
Description: The BayesFactor package is a suite of functions for
computing various Bayes factors for simple designs, including
the one- and two-sample designs, one-way designs, general ANOVA
designs, and linear regression.
Author: Richard D. Morey, Jeffrey N. Rouder
Maintainer: Richard D. Morey
BayesFactor-0.9.0/BayesFactor/inst/doc/Makefile |only
BayesFactor-0.9.1/BayesFactor/DESCRIPTION | 12 -
BayesFactor-0.9.1/BayesFactor/MD5 | 22 +-
BayesFactor-0.9.1/BayesFactor/R/anovaBF.R | 7
BayesFactor-0.9.1/BayesFactor/R/gaussApproxAOV.R |only
BayesFactor-0.9.1/BayesFactor/R/nWayAOV.R | 42 +++-
BayesFactor-0.9.1/BayesFactor/inst/SVN_VERSION | 2
BayesFactor-0.9.1/BayesFactor/inst/doc/index.Rmd | 13 +
BayesFactor-0.9.1/BayesFactor/inst/doc/index.html | 202 ++++++++++------------
BayesFactor-0.9.1/BayesFactor/man/anovaBF.Rd | 5
BayesFactor-0.9.1/BayesFactor/man/nWayAOV.Rd | 20 +-
BayesFactor-0.9.1/BayesFactor/src/BFPCL.h | 5
BayesFactor-0.9.1/BayesFactor/src/nWayAOV.c | 117 +++++++++++-
13 files changed, 303 insertions(+), 144 deletions(-)
Title: Visualization of regression models
Diff between visreg versions 1.2-0 dated 2013-01-20 and 1.2-1 dated 2013-02-21
Description: Provides convenient interface for constructing plots to
visualize the fit of regression models arising from a wide
variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
DESCRIPTION | 9 ++++----
MD5 | 18 ++++++++--------
NEWS | 6 +++++
R/Response.R | 12 ++++++++--
R/Terms.R | 11 +++++++--
R/visreg.R | 5 +---
R/visregLatticePlot.R | 2 +
tests/visreg-glm.R | 56 +++++++++++++++++++++++++-------------------------
tests/visreg-lm.R | 2 -
tests/visreg-mlm.R | 2 -
10 files changed, 71 insertions(+), 52 deletions(-)
Title: Simulating Phylogenetic Trees under a General Model
Diff between TreeSimGM versions 1.0 dated 2013-02-14 and 1.1 dated 2013-02-21
Description: The package is a flexible simulation tool for phylogenetic
trees under a general model. It is possible to assume any
probability distribution for the waiting time until speciation
and extinction independently. Thus, TreeSimGM allows to
simulate stochastic phylogenetic trees using any probability
distribution and parameters for speciation and extinction. The
speciation modes have all binary splits and are: (i) symmetric,
where for every speciation event new waiting times until
speciation and extinction are drawn for both daughter lineages;
and (ii) asymmetric, where a speciation event results in one
species with new waiting times, and another that carries the
extinction time and age of its ancestor. Those two modes were
inspired by allopatric and peripatric speciation
respectively.Both models (symmetric and asymmetric) were
created and implemented so that different processes
(distributions) for speciation and extinction could be
independently and explicitly specified. It is also possible to
have an implicit extinction process by setting the extinction
rate to zero.
Author: Oskar Hagen, Tanja Stadler
Maintainer: Oskar Hagen
DESCRIPTION | 7 ++++---
MD5 | 16 ++++++++--------
R/mytree.asymmetric.age.R | 3 ++-
R/mytree.asymmetric.taxa.R | 3 ++-
R/mytree.symmetric.age.R | 3 ++-
R/mytree.symmetric.taxa.R | 3 ++-
man/TreeSimGM-package.Rd | 6 ++++--
man/sim.age.Rd | 2 ++
man/sim.taxa.Rd | 6 ++++--
9 files changed, 30 insertions(+), 19 deletions(-)
Title: Fitting Hansen Models to Investigate Convergent Evolution
Diff between surface versions 0.2 dated 2013-01-04 and 0.3 dated 2013-02-21
Description: SURFACE is a data-driven phylogenetic comparative method
for fitting stabilizing selection models to continuous trait
data, building on the ouch package. The main functions fit a
series of Hansen models using stepwise AIC, then identifies
cases of convergent evolution where multiple lineages have
shifted to the same evolutionary regime.
Author: Travis Ingram
Maintainer: Travis Ingram
surface-0.2/surface/man/SURFACE-package.Rd |only
surface-0.3/surface/DESCRIPTION | 18 +++--
surface-0.3/surface/MD5 | 66 ++++++++++-----------
surface-0.3/surface/NAMESPACE | 7 --
surface-0.3/surface/R/addRegime.R | 6 -
surface-0.3/surface/R/collapseRegimes.R | 11 +--
surface-0.3/surface/R/convertTreeData.R | 3
surface-0.3/surface/R/pmcSurface.R | 3
surface-0.3/surface/R/runSurface.R | 8 +-
surface-0.3/surface/R/surfaceAICMultiPlot.R |only
surface-0.3/surface/R/surfaceAICPlot.R | 48 +++++++++++++--
surface-0.3/surface/R/surfaceForward.R | 4 -
surface-0.3/surface/R/surfaceSimulate.R | 46 ++++++++++----
surface-0.3/surface/R/surfaceSummary.R | 22 +++++--
surface-0.3/surface/R/surfaceTraitPlot.R | 42 ++++++++++++-
surface-0.3/surface/R/surfaceTreePlot.R | 6 -
surface-0.3/surface/inst/doc/surface_tutorial.Rnw | 19 ++----
surface-0.3/surface/inst/doc/surface_tutorial.pdf |binary
surface-0.3/surface/man/convertTreeData.Rd | 12 +--
surface-0.3/surface/man/getAIC.Rd | 13 +---
surface-0.3/surface/man/getBranchTimes.Rd | 4 -
surface-0.3/surface/man/ouchDescendants.Rd | 8 +-
surface-0.3/surface/man/pmcSurface.Rd | 10 +--
surface-0.3/surface/man/propRegMatch.Rd | 4 -
surface-0.3/surface/man/repaint.Rd | 4 -
surface-0.3/surface/man/runSurface.Rd | 18 ++---
surface-0.3/surface/man/startingModel.Rd | 9 +-
surface-0.3/surface/man/surface-package.Rd |only
surface-0.3/surface/man/surfaceAICPlot.Rd |only
surface-0.3/surface/man/surfaceBackward.Rd | 8 +-
surface-0.3/surface/man/surfaceDemo.Rd | 6 -
surface-0.3/surface/man/surfaceForward.Rd | 14 ++--
surface-0.3/surface/man/surfaceSimulate.Rd | 17 +++--
surface-0.3/surface/man/surfaceSummary.Rd | 30 ++++++---
surface-0.3/surface/man/surfaceTreePlot.Rd | 47 ++++++++------
surface-0.3/surface/vignettes/surface_tutorial.Rnw | 19 ++----
36 files changed, 327 insertions(+), 205 deletions(-)
Title: An efficient swiss army knife for population genetic & genomic
analysis
Diff between PopGenome versions 1.2.1 dated 2012-12-27 and 1.2.2 dated 2013-02-21
Description: PopGenome is an R-package for Population Genetic & Genomic
Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer
DESCRIPTION | 13 +-
MD5 | 151 ++++++++++++++--------------
NAMESPACE | 1
NEWS | 37 ++++++
R/GENOME.R | 172 ++++++++++++++++++++++++++------
R/PopGenread.R | 17 +++
R/SNPFST.R | 4
R/calc_diversities.R |only
R/calc_hwhafsth_FAST.R | 58 +++++-----
R/calc_phi_st.R |only
R/diversity.stats.R |only
R/get_data.R | 33 ++++--
R/get_gff_info.R | 27 ++++-
R/parse_HapMap.R | 39 +++++--
R/parse_gff.R | 19 ++-
R/readData.R | 45 +++++---
R/readSNP.R | 110 +++++++++++++-------
R/readVCF.R | 19 ++-
R/readVCFchunk.R |only
R/readVCFchunkHap.R |only
R/region.as.fasta.R | 71 ++++++++++++-
R/sliding.window.transform.fast.R | 65 +++++++++---
R/snn.R | 2
R/splitting.data.R | 96 ++++++++++-------
inst/doc/Integration_of_new_Methods.pdf |binary
inst/doc/PopGenome_Vignette.pdf |binary
man/F_ST.stats-methods.Rd | 7 -
man/F_ST.stats.2-methods.Rd | 26 ++++
man/GENOME-class.Rd | 4
man/PopGenome.Rd | 3
man/diversity.stats-methods.Rd |only
man/get_gff_info.Rd | 4
man/readData.Rd | 8 -
man/readSNP.Rd | 15 +-
man/readVCF.Rd | 7 -
man/region.as.fasta.Rd | 4
man/set.populations-methods.Rd | 3
src/Makevars.win | 8 -
src/ap_pop_C.c | 4
src/combnsum2_C.c |only
src/combnsum_C.c |only
src/makeBial.c | 132 ++++++++++++++++++------
src/makeBialMatrix.c | 144 ++++++++++++++++++++++----
src/my_match_C.c | 42 +++++++
src/my_unique_C.c |only
src/tabix/bedidx.o |binary
src/tabix/bgzf.o |binary
src/tabix/index.o |binary
src/tabix/knetfile.o |binary
src/tabix/kstring.o |binary
src/whopgenome/readdnapp.o |binary
src/whopgenome/whop_r_dataframe.o |binary
src/whopgenome/whopgen_codemat.o |binary
src/whopgenome/whopgen_filtering.o |binary
src/whopgenome/whopgen_main.o |binary
src/whopgenome/whopgen_read.o |binary
src/whopgenome/whopgen_region.o |binary
src/whopgenome/whopgen_rsupport.o |binary
src/whopgenome/whopgen_samples.o |binary
src/whopgenome/whopgen_tools.o |binary
src/whopgenome/whopgen_vcf.o |binary
src/whopgenome/whoptbi_Rifc.o |binary
src/whopgenome/whoptbi_info.o |binary
src/whopgenome/whoptbi_main.o |binary
src/whopgenome/whoptbi_read.o |binary
src/whopgenome/whoptbi_region.o |binary
src/zlib/adler32.o |binary
src/zlib/compress.o |binary
src/zlib/crc32.o |binary
src/zlib/deflate.o |binary
src/zlib/gzclose.o |binary
src/zlib/gzlib.o |binary
src/zlib/gzread.o |binary
src/zlib/gzwrite.o |binary
src/zlib/infback.o |binary
src/zlib/inffast.o |binary
src/zlib/inflate.o |binary
src/zlib/inftrees.o |binary
src/zlib/trees.o |binary
src/zlib/uncompr.o |binary
src/zlib/zutil.o |binary
81 files changed, 1033 insertions(+), 357 deletions(-)
Title: Japanese utility functions and data
Diff between Nippon versions 0.4 dated 2013-01-24 and 0.4.2 dated 2013-02-21
Description: This package provides some Japanese utility functions and
data, which may be useful for Japanese R users.
Author: Susumu Tanimura
Maintainer: Susumu Tanimura
Nippon-0.4.2/Nippon/ChangeLog | 21 ++++++++++++---
Nippon-0.4.2/Nippon/DESCRIPTION | 10 +++----
Nippon-0.4.2/Nippon/MD5 | 38 ++++++++++++++--------------
Nippon-0.4.2/Nippon/Nippon-Ex.R | 19 ++++++++++++++
Nippon-0.4.2/Nippon/R/jholiday.R |only
Nippon-0.4.2/Nippon/R/kakasi.R | 4 +-
Nippon-0.4.2/Nippon/R/sysdata.rda |binary
Nippon-0.4.2/Nippon/TODO | 3 +-
Nippon-0.4.2/Nippon/data/jiscolors.rda |binary
Nippon-0.4.2/Nippon/data/month.name.jp.rda |binary
Nippon-0.4.2/Nippon/man/Nippon-internal.Rd | 23 ++++++++++++++++
Nippon-0.4.2/Nippon/man/jholiday.Rd |only
Nippon-0.4.2/Nippon/man/romanization.Rd | 14 ++++------
Nippon-0.4.2/Nippon/src/Makevars.orig |only
Nippon-0.4.2/Nippon/src/Makevars.win | 2 -
Nippon-0.4.2/Nippon/src/kakasi/Makefile.in | 4 +-
Nippon-0.4.2/Nippon/src/kakasi/Makefile.win | 3 +-
Nippon-0.4.2/Nippon/src/kakasi/libdict.c | 9 +++++-
Nippon-0.4.2/Nippon/src/kakasi/libg2.c | 6 ++--
Nippon-0.4.2/Nippon/src/kakasi/libkakasi.c | 5 +--
Nippon-0.4.2/Nippon/src/kakasi/libkanjiio.c | 11 ++++----
Nippon-0.4/Nippon/configure.win |only
22 files changed, 116 insertions(+), 56 deletions(-)
Title: Full feature implementation of hash/associated
arrays/dictionaries
Diff between hash versions 2.2.5 dated 2013-01-31 and 2.2.6 dated 2013-02-21
Description: This package implements a data structure similar to hashes
in Perl and dictionaries in Python but with a purposefully R
flavor. For objects of appreciable size, access using hashes
outperforms native named lists and vectors.
Author: Christopher Brown
Maintainer: Christopher Brown
hash-2.2.5/hash/ChangeLog |only
hash-2.2.6/hash/DESCRIPTION | 10 ++--
hash-2.2.6/hash/MD5 | 14 +++---
hash-2.2.6/hash/NEWS |only
hash-2.2.6/hash/R/Class-hash.R | 8 +--
hash-2.2.6/hash/TODO | 2
hash-2.2.6/hash/man/hash-package.Rd | 4 -
hash-2.2.6/hash/tests/accessors.R | 79 ++++++++++++++++++++++++++++--------
hash-2.2.6/hash/tests/clear.R | 12 ++++-
9 files changed, 92 insertions(+), 37 deletions(-)
Title: Functional time series analysis
Diff between ftsa versions 3.6 dated 2012-10-24 and 3.7 dated 2013-02-21
Description: Functions for functional time series
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Shang H.
CHANGELOG.txt | 6 +++-
DESCRIPTION | 11 ++++----
MD5 | 10 +++----
R/forecast.ftsm.R | 2 -
R/forecast.ftsm2.R | 67 ++++++++++++++++++-----------------------------------
inst/doc/ftsa.pdf |binary
6 files changed, 41 insertions(+), 55 deletions(-)
Title: Density surface modelling of distance sampling data
Diff between dsm versions 2.0 dated 2012-11-24 and 2.0.1 dated 2013-02-21
Description: This library implements density surface modelling of line
transect data, based on the methods of Hedley et al. (2004).
Some recent developments in the literature have also be
incorporated. Outputs are point and interval estimates of
population abundance and density. Please note that this
version of dsm WILL NOT work with the Windows package DISTANCE.
For a version that works with DISTANCE, please go to
https://github.com/lenthomas/dsm-distance-6.1. Hedley, S.L.
and S.T. Buckland. 2004. "Spatial distance sampling methods"
pp 48-70 in Advanced Distance Sampling, Buckland, S.T. et al.
(eds). Oxford University Press.
Author: David L. Miller, Eric Rexstad, Louise Burt, Mark V. Bravington,
Sharon Hedley.
Maintainer: David L. Miller
DESCRIPTION | 18 +++++++++++-------
MD5 | 20 ++++++++++----------
R/dsm.R | 46 ++++++++++++++++++++++++++--------------------
R/make.data.R | 18 ++++++++++--------
R/plot.dsm.var.R | 3 ---
R/predict.dsm.R | 17 ++++++++++-------
R/print.dsm.R | 5 +++++
R/print.dsm.var.R | 46 ++++++++++++++++++++++++----------------------
R/summary.dsm.var.R | 16 ++++++++++------
man/dsm.Rd | 17 +++++++++++++++--
man/predict.dsm.Rd | 2 +-
11 files changed, 122 insertions(+), 86 deletions(-)
Title: C5.0 Decision Trees and Rule-Based Models
Diff between C50 versions 0.1.0-013 dated 2012-10-19 and 0.1.0-14 dated 2013-02-21
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
C50-0.1.0-013/C50/inst |only
C50-0.1.0-14/C50/DESCRIPTION | 9 +++--
C50-0.1.0-14/C50/MD5 | 31 ++++---------------
C50-0.1.0-14/C50/R/C5.0.R | 5 +--
C50-0.1.0-14/C50/R/formatAttributes.R | 7 +++-
C50-0.1.0-14/C50/R/makeNamesFile.R | 3 +
C50-0.1.0-14/C50/configure.win | 1
C50-0.1.0-14/C50/data/churn.RData |binary
C50-0.1.0-14/C50/src/strbuf.c | 53 ++++++++++++++++++++++++++--------
9 files changed, 65 insertions(+), 44 deletions(-)