Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut],
Jacob van Etten [ctb],
Joe Cheng [ctb],
Matteo Mattiuzzi [ctb],
Michael Sumner [ctb],
Jonathan A. Greenberg [ctb],
Oscar Perpinan Lamigueiro [ctb],
Andrew Bevan [ctb],
Etienne B. Racine [ctb],
Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.4-20 dated 2015-09-08 and 2.4-30 dated 2015-12-10
raster-2.4-20/raster/R/VectorLayer.R |only raster-2.4-30/raster/ChangeLog | 11 + raster-2.4-30/raster/DESCRIPTION | 12 - raster-2.4-30/raster/MD5 | 162 ++++++++++---------- raster-2.4-30/raster/NAMESPACE | 4 raster-2.4-30/raster/R/GDALtransient.R | 2 raster-2.4-30/raster/R/aggregate_sp.R | 4 raster-2.4-30/raster/R/area.R | 2 raster-2.4-30/raster/R/bind.R | 12 - raster-2.4-30/raster/R/canProcessInMemory.R | 2 raster-2.4-30/raster/R/clamp.R | 2 raster-2.4-30/raster/R/click.R | 11 - raster-2.4-30/raster/R/colortable.R | 6 raster-2.4-30/raster/R/connection.R | 12 - raster-2.4-30/raster/R/coverPolygons.R | 4 raster-2.4-30/raster/R/crop.R | 5 raster-2.4-30/raster/R/cropSpatial.R | 4 raster-2.4-30/raster/R/destair.R | 2 raster-2.4-30/raster/R/erase.R | 2 raster-2.4-30/raster/R/extractLines.R | 4 raster-2.4-30/raster/R/extractPoints.R | 2 raster-2.4-30/raster/R/extractPoints_sp.R | 2 raster-2.4-30/raster/R/extractPolygons.R | 4 raster-2.4-30/raster/R/getData.R | 2 raster-2.4-30/raster/R/head.R | 4 raster-2.4-30/raster/R/intersect.R | 1 raster-2.4-30/raster/R/intersect_sp.R | 26 ++- raster-2.4-30/raster/R/kml.R | 2 raster-2.4-30/raster/R/mask.R | 2 raster-2.4-30/raster/R/naValue.R | 2 raster-2.4-30/raster/R/names.R | 4 raster-2.4-30/raster/R/netCDFread.R | 80 +--------- raster-2.4-30/raster/R/netCDFreadCells.R | 39 +--- raster-2.4-30/raster/R/netCDFtoRasterCD.R | 104 ++++--------- raster-2.4-30/raster/R/netCDFtoRasterGMT.R | 38 +--- raster-2.4-30/raster/R/netCDFtoStack.R | 14 - raster-2.4-30/raster/R/netCDFutil.R | 50 ------ raster-2.4-30/raster/R/netCDFwriteCD.R | 183 ++++++----------------- raster-2.4-30/raster/R/plotCT.R | 2 raster-2.4-30/raster/R/print.R | 14 - raster-2.4-30/raster/R/progressBar.R | 4 raster-2.4-30/raster/R/projectRaster.R | 2 raster-2.4-30/raster/R/raster.R | 1 raster-2.4-30/raster/R/rasterFromFile.R | 17 -- raster-2.4-30/raster/R/rasterFromGRASSascii.R |only raster-2.4-30/raster/R/rasterFromXYZ.R | 4 raster-2.4-30/raster/R/rasterOptions.R | 6 raster-2.4-30/raster/R/rasterizePolygons.R | 37 ++-- raster-2.4-30/raster/R/resample.R | 2 raster-2.4-30/raster/R/rotate.R | 5 raster-2.4-30/raster/R/select.R | 4 raster-2.4-30/raster/R/shift.R | 10 - raster-2.4-30/raster/R/shp.R | 4 raster-2.4-30/raster/R/simplifyPols.R | 2 raster-2.4-30/raster/R/stackQuick.R | 2 raster-2.4-30/raster/R/text.R | 4 raster-2.4-30/raster/R/tmpFile.R | 2 raster-2.4-30/raster/R/tmppath.R | 5 raster-2.4-30/raster/R/union_sp.R | 6 raster-2.4-30/raster/R/update.R | 43 ++--- raster-2.4-30/raster/R/writeAllGDAL.R | 2 raster-2.4-30/raster/R/writeRaster.R | 2 raster-2.4-30/raster/R/writeStartStopRaster.R | 2 raster-2.4-30/raster/R/xyValuesBuffer.R | 2 raster-2.4-30/raster/R/zoom.R | 2 raster-2.4-30/raster/R/zzz.R | 2 raster-2.4-30/raster/build/vignette.rds |binary raster-2.4-30/raster/inst/doc/Raster.pdf |binary raster-2.4-30/raster/inst/doc/functions.pdf |binary raster-2.4-30/raster/inst/doc/rasterfile.Rnw | 88 ++++++----- raster-2.4-30/raster/inst/doc/rasterfile.pdf |binary raster-2.4-30/raster/inst/external/countries.csv | 2 raster-2.4-30/raster/man/as.matrix.Rd | 12 + raster-2.4-30/raster/man/brick.Rd | 2 raster-2.4-30/raster/man/geom.Rd | 2 raster-2.4-30/raster/man/intersect.Rd | 4 raster-2.4-30/raster/man/mosaic.Rd | 9 + raster-2.4-30/raster/man/plot.Rd | 7 raster-2.4-30/raster/man/raster.Rd | 2 raster-2.4-30/raster/man/rowSums.Rd | 7 raster-2.4-30/raster/man/writeFormats.Rd | 2 raster-2.4-30/raster/man/writeRaster.Rd | 9 - raster-2.4-30/raster/vignettes/rasterfile.Rnw | 88 ++++++----- 83 files changed, 522 insertions(+), 722 deletions(-)
Title: IBM in-Database Analytics for R
Description: Functionality required to efficiently use R with
IBM DB2(C) for Linux, Unix and Windows as well as IBM dashDB(C).
Many basic and complex R operations are pushed down into the database, which removes
the main memory boundary of R and allows to make full use of parallel processing in
the underlying database.
Author: IBM Corporation
Maintainer: Michael Wurst <inza@de.ibm.com>
Diff between ibmdbR versions 1.42.2 dated 2015-08-06 and 1.47.1 dated 2015-12-10
DESCRIPTION | 9 MD5 | 39 +- NAMESPACE | 24 + R/coldef.R | 57 +++ R/connect.R | 14 R/connection.R | 25 - R/data.frame.R | 44 ++ R/lm.R | 730 +++++++++++++++++++++++++++------------------ R/model.management.R | 36 +- R/plot.idaLm.R |only R/sql.R | 136 +++++++- R/statistics.R | 71 ++-- R/tree.R |only R/update.R | 6 inst/doc/ibmdbR.pdf |binary man/ida.col.def.methods.Rd | 1 man/idaArule.Rd | 2 man/idaDropModel.Rd | 4 man/idaLm.Rd | 90 ++++- man/idaQuery.Rd | 3 man/idaTree.Rd |only man/showtables.Rd | 3 22 files changed, 879 insertions(+), 415 deletions(-)
Title: Provides Access to Git Repositories
Description: Interface to the 'libgit2' library, which is a pure C
implementation of the 'Git' core methods. Provides access to 'Git'
repositories to extract data and running some basic 'Git'
commands.
Author: See AUTHORS file.
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between git2r versions 0.12.1 dated 2015-12-05 and 0.13.1 dated 2015-12-10
git2r-0.12.1/git2r/src/libgit2/idxmap.h |only git2r-0.12.1/git2r/src/libgit2/stransport_stream.c |only git2r-0.12.1/git2r/src/libgit2/transaction.h |only git2r-0.13.1/git2r/DESCRIPTION | 6 git2r-0.13.1/git2r/MD5 | 216 ++-- git2r-0.13.1/git2r/NEWS | 19 git2r-0.13.1/git2r/R/libgit2.r | 2 git2r-0.13.1/git2r/configure | 140 +- git2r-0.13.1/git2r/configure.ac | 146 +- git2r-0.13.1/git2r/src/Makevars.in | 63 - git2r-0.13.1/git2r/src/Makevars.win | 60 - git2r-0.13.1/git2r/src/git2r_config.c | 83 - git2r-0.13.1/git2r/src/git2r_remote.c | 2 git2r-0.13.1/git2r/src/libgit2/attr_file.c | 6 git2r-0.13.1/git2r/src/libgit2/attrcache.c | 5 git2r-0.13.1/git2r/src/libgit2/blame.c | 2 git2r-0.13.1/git2r/src/libgit2/blame_git.c | 34 git2r-0.13.1/git2r/src/libgit2/blame_git.h | 2 git2r-0.13.1/git2r/src/libgit2/checkout.c | 59 - git2r-0.13.1/git2r/src/libgit2/commit.c | 35 git2r-0.13.1/git2r/src/libgit2/commit_list.c | 8 git2r-0.13.1/git2r/src/libgit2/commit_list.h | 3 git2r-0.13.1/git2r/src/libgit2/common.h | 9 git2r-0.13.1/git2r/src/libgit2/config.c | 46 git2r-0.13.1/git2r/src/libgit2/config.h | 16 git2r-0.13.1/git2r/src/libgit2/config_file.c | 151 --- git2r-0.13.1/git2r/src/libgit2/config_file.h | 10 git2r-0.13.1/git2r/src/libgit2/curl_stream.c | 1 git2r-0.13.1/git2r/src/libgit2/diff.c | 123 -- git2r-0.13.1/git2r/src/libgit2/diff_driver.c | 13 git2r-0.13.1/git2r/src/libgit2/diff_file.c | 25 git2r-0.13.1/git2r/src/libgit2/diff_patch.c | 4 git2r-0.13.1/git2r/src/libgit2/diff_print.c | 2 git2r-0.13.1/git2r/src/libgit2/diff_tform.c | 6 git2r-0.13.1/git2r/src/libgit2/diff_xdiff.c | 7 git2r-0.13.1/git2r/src/libgit2/diff_xdiff.h | 5 git2r-0.13.1/git2r/src/libgit2/filebuf.c | 84 - git2r-0.13.1/git2r/src/libgit2/fileops.c | 308 ++---- git2r-0.13.1/git2r/src/libgit2/fileops.h | 20 git2r-0.13.1/git2r/src/libgit2/ignore.c | 16 git2r-0.13.1/git2r/src/libgit2/include/git2/common.h | 14 git2r-0.13.1/git2r/src/libgit2/include/git2/config.h | 48 git2r-0.13.1/git2r/src/libgit2/include/git2/cred_helpers.h | 2 git2r-0.13.1/git2r/src/libgit2/include/git2/diff.h | 37 git2r-0.13.1/git2r/src/libgit2/include/git2/errors.h | 1 git2r-0.13.1/git2r/src/libgit2/include/git2/index.h | 39 git2r-0.13.1/git2r/src/libgit2/include/git2/merge.h | 12 git2r-0.13.1/git2r/src/libgit2/include/git2/remote.h | 13 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/config.h | 14 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/odb_backend.h | 4 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/refdb_backend.h | 4 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/stream.h | 13 git2r-0.13.1/git2r/src/libgit2/include/git2/sys/transport.h | 28 git2r-0.13.1/git2r/src/libgit2/include/git2/transport.h | 11 git2r-0.13.1/git2r/src/libgit2/index.c | 428 +------- git2r-0.13.1/git2r/src/libgit2/index.h | 2 git2r-0.13.1/git2r/src/libgit2/iterator.c | 500 ++-------- git2r-0.13.1/git2r/src/libgit2/iterator.h | 48 git2r-0.13.1/git2r/src/libgit2/merge.c | 381 ++----- git2r-0.13.1/git2r/src/libgit2/merge_file.c | 98 - git2r-0.13.1/git2r/src/libgit2/merge_file.h |only git2r-0.13.1/git2r/src/libgit2/notes.c | 2 git2r-0.13.1/git2r/src/libgit2/odb.c | 246 +--- git2r-0.13.1/git2r/src/libgit2/odb_loose.c | 4 git2r-0.13.1/git2r/src/libgit2/odb_mempack.c | 8 git2r-0.13.1/git2r/src/libgit2/odb_pack.c | 82 + git2r-0.13.1/git2r/src/libgit2/oidmap.h | 2 git2r-0.13.1/git2r/src/libgit2/openssl_stream.c | 7 git2r-0.13.1/git2r/src/libgit2/pack-objects.c | 3 git2r-0.13.1/git2r/src/libgit2/path.c | 23 git2r-0.13.1/git2r/src/libgit2/path.h | 8 git2r-0.13.1/git2r/src/libgit2/pathspec.c | 36 git2r-0.13.1/git2r/src/libgit2/pool.c | 241 +++- git2r-0.13.1/git2r/src/libgit2/pool.h | 54 - git2r-0.13.1/git2r/src/libgit2/push.c | 3 git2r-0.13.1/git2r/src/libgit2/push.h | 1 git2r-0.13.1/git2r/src/libgit2/refdb.c | 8 git2r-0.13.1/git2r/src/libgit2/refdb_fs.c | 16 git2r-0.13.1/git2r/src/libgit2/remote.c | 46 git2r-0.13.1/git2r/src/libgit2/repository.c | 55 - git2r-0.13.1/git2r/src/libgit2/revwalk.c | 6 git2r-0.13.1/git2r/src/libgit2/signature.c | 18 git2r-0.13.1/git2r/src/libgit2/sortedcache.c | 5 git2r-0.13.1/git2r/src/libgit2/stash.c | 29 git2r-0.13.1/git2r/src/libgit2/stream.h | 3 git2r-0.13.1/git2r/src/libgit2/submodule.c | 406 +++----- git2r-0.13.1/git2r/src/libgit2/sysdir.c | 19 git2r-0.13.1/git2r/src/libgit2/sysdir.h | 14 git2r-0.13.1/git2r/src/libgit2/tls_stream.c | 13 git2r-0.13.1/git2r/src/libgit2/transaction.c | 44 git2r-0.13.1/git2r/src/libgit2/transports/cred.c | 8 git2r-0.13.1/git2r/src/libgit2/transports/git.c | 11 git2r-0.13.1/git2r/src/libgit2/transports/http.c | 16 git2r-0.13.1/git2r/src/libgit2/transports/smart.c | 95 - git2r-0.13.1/git2r/src/libgit2/transports/smart.h | 1 git2r-0.13.1/git2r/src/libgit2/transports/smart_pkt.c | 11 git2r-0.13.1/git2r/src/libgit2/transports/smart_protocol.c | 2 git2r-0.13.1/git2r/src/libgit2/transports/ssh.c | 4 git2r-0.13.1/git2r/src/libgit2/transports/winhttp.c | 18 git2r-0.13.1/git2r/src/libgit2/unix/posix.h | 15 git2r-0.13.1/git2r/src/libgit2/util.c | 26 git2r-0.13.1/git2r/src/libgit2/win32/findfile.c | 10 git2r-0.13.1/git2r/src/libgit2/win32/findfile.h | 1 git2r-0.13.1/git2r/src/libgit2/win32/path_w32.c | 23 git2r-0.13.1/git2r/src/libgit2/win32/posix_w32.c | 11 git2r-0.13.1/git2r/src/libgit2/win32/w32_util.c | 34 git2r-0.13.1/git2r/src/libgit2/win32/w32_util.h | 16 git2r-0.13.1/git2r/src/libgit2/xdiff/xdiff.h | 8 git2r-0.13.1/git2r/src/libgit2/xdiff/xdiffi.c | 12 git2r-0.13.1/git2r/src/libgit2/xdiff/xhistogram.c | 6 git2r-0.13.1/git2r/src/libgit2/xdiff/xmerge.c | 142 -- 111 files changed, 1774 insertions(+), 3532 deletions(-)
Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions
such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>
Diff between forestmodel versions 0.3.3 dated 2015-11-26 and 0.4.0 dated 2015-12-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ R/forest_breaks.R | 4 ++++ R/forest_model.R | 42 +++++++++++++++++++++++++----------------- R/panel_forest_plot.R | 9 ++++++++- man/forest_breaks.Rd | 3 ++- 7 files changed, 54 insertions(+), 29 deletions(-)
Title: Ranking-Based Variable Selection
Description: Implements the Ranking-Based Variable Selection
algorithm for variable selection in high-dimensional data.
Author: Rafal Baranowski, Patrick Breheny, Isaac Turner
Maintainer: Rafal Baranowski <r.baranowski@lse.ac.uk>
Diff between rbvs versions 1.0 dated 2015-12-08 and 1.0.1 dated 2015-12-10
DESCRIPTION | 6 - MD5 | 10 - src/Makevars | 1 src/rankings.c | 2 src/rbvs.c | 55 +++++++++- src/sort_r.h | 308 ++++++++++++++++++++++++++++++++++++++++++--------------- 6 files changed, 291 insertions(+), 91 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 0.6 dated 2015-09-21 and 1.0 dated 2015-12-10
DESCRIPTION | 22 ++++++-- MD5 | 92 +++++++++++++++++------------------ NAMESPACE | 3 - R/kde.R | 4 - R/plot.R | 16 +++--- R/provenance.R | 95 +++++++++++++++++++++++++++++++++---- man/CLR.Rd | 2 man/KDE.Rd | 2 man/KDEs.Rd | 7 +- man/KS.diss.Rd | 2 man/MDS.Rd | 2 man/Namib.Rd | 2 man/PCA.Rd | 2 man/SH.diss.Rd | 2 man/amalgamate.Rd | 2 man/as.acomp.Rd | 4 - man/as.compositional.Rd | 4 - man/as.data.frame.compositional.Rd | 2 man/botev.Rd | 2 man/bray.diss.Rd | 2 man/densities.Rd | 2 man/diss.Rd | 2 man/endmembers.Rd | 2 man/get.f.Rd | 2 man/get.n.Rd | 4 - man/get.p.Rd | 2 man/indscal.Rd | 2 man/minsorting.Rd | 2 man/plot.GPA.Rd | 2 man/plot.INDSCAL.Rd | 2 man/plot.KDE.Rd | 2 man/plot.MDS.Rd | 2 man/plot.PCA.Rd | 2 man/plot.compositional.Rd | 2 man/plot.distributional.Rd | 2 man/plot.minsorting.Rd | 2 man/plot.ternary.Rd | 2 man/procrustes.Rd | 16 +++--- man/provenance.Rd | 2 man/read.compositional.Rd | 2 man/read.densities.Rd | 2 man/read.distributional.Rd | 2 man/restore.Rd | 2 man/subset.compositional.Rd | 2 man/subset.distributional.Rd | 2 man/summaryplot.Rd | 2 man/ternary.Rd | 2 47 files changed, 213 insertions(+), 126 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 1.99.14 dated 2015-07-09 and 2.0.0 dated 2015-12-10
phangorn-1.99.14/phangorn/TODO |only phangorn-2.0.0/phangorn/DESCRIPTION | 24 phangorn-2.0.0/phangorn/MD5 | 131 - phangorn-2.0.0/phangorn/NAMESPACE | 32 phangorn-2.0.0/phangorn/NEWS | 36 phangorn-2.0.0/phangorn/R/Densi.R | 28 phangorn-2.0.0/phangorn/R/SH.R |only phangorn-2.0.0/phangorn/R/bootstrap.R |only phangorn-2.0.0/phangorn/R/clanistic.R | 8 phangorn-2.0.0/phangorn/R/dist.p.R | 2 phangorn-2.0.0/phangorn/R/distSeq.R | 98 + phangorn-2.0.0/phangorn/R/distTree.R | 4 phangorn-2.0.0/phangorn/R/fitch.R | 8 phangorn-2.0.0/phangorn/R/hadamard.R | 8 phangorn-2.0.0/phangorn/R/modelTest.R | 59 phangorn-2.0.0/phangorn/R/networx.R | 261 +- phangorn-2.0.0/phangorn/R/parsimony.R | 20 phangorn-2.0.0/phangorn/R/phyDat.R | 73 phangorn-2.0.0/phangorn/R/phylo.R | 1491 +++++++--------- phangorn-2.0.0/phangorn/R/sankoff.R | 6 phangorn-2.0.0/phangorn/R/simSeq.R | 6 phangorn-2.0.0/phangorn/R/treeManipulation.R | 27 phangorn-2.0.0/phangorn/R/treedist.R | 6 phangorn-2.0.0/phangorn/README.md | 1 phangorn-2.0.0/phangorn/build/vignette.rds |binary phangorn-2.0.0/phangorn/inst/doc/Ancestral.R | 15 phangorn-2.0.0/phangorn/inst/doc/Ancestral.Rnw | 1 phangorn-2.0.0/phangorn/inst/doc/Ancestral.pdf |binary phangorn-2.0.0/phangorn/inst/doc/Networx.R | 9 phangorn-2.0.0/phangorn/inst/doc/Networx.Rmd | 9 phangorn-2.0.0/phangorn/inst/doc/Networx.html | 38 phangorn-2.0.0/phangorn/inst/doc/Trees.R | 155 + phangorn-2.0.0/phangorn/inst/doc/Trees.Rnw | 142 - phangorn-2.0.0/phangorn/inst/doc/Trees.pdf |binary phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.R | 19 phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.Rnw | 7 phangorn-2.0.0/phangorn/inst/doc/phangorn-specials.pdf |binary phangorn-2.0.0/phangorn/inst/extdata/trees |only phangorn-2.0.0/phangorn/man/Ancestors.Rd | 2 phangorn-2.0.0/phangorn/man/addConfidences.Rd |only phangorn-2.0.0/phangorn/man/allTrees.Rd | 60 phangorn-2.0.0/phangorn/man/ancestral.pml.Rd | 2 phangorn-2.0.0/phangorn/man/as.splits.Rd | 10 phangorn-2.0.0/phangorn/man/bootstrap.pml.Rd | 11 phangorn-2.0.0/phangorn/man/consensusNet.Rd | 5 phangorn-2.0.0/phangorn/man/cophenetic.networx.Rd |only phangorn-2.0.0/phangorn/man/delta.score.Rd |only phangorn-2.0.0/phangorn/man/dfactorial.Rd | 56 phangorn-2.0.0/phangorn/man/dist.hamming.Rd | 19 phangorn-2.0.0/phangorn/man/dist.p.Rd | 2 phangorn-2.0.0/phangorn/man/distanceHadamard.Rd | 4 phangorn-2.0.0/phangorn/man/midpoint.Rd | 3 phangorn-2.0.0/phangorn/man/modelTest.Rd | 24 phangorn-2.0.0/phangorn/man/neighborNet.Rd | 2 phangorn-2.0.0/phangorn/man/nni.Rd | 2 phangorn-2.0.0/phangorn/man/phangorn-package.Rd | 83 phangorn-2.0.0/phangorn/man/phyDat.Rd | 13 phangorn-2.0.0/phangorn/man/plot.networx.Rd | 6 phangorn-2.0.0/phangorn/man/pml.Rd | 19 phangorn-2.0.0/phangorn/man/simSeq.Rd | 2 phangorn-2.0.0/phangorn/man/superTree.Rd | 2 phangorn-2.0.0/phangorn/man/treedist.Rd | 1 phangorn-2.0.0/phangorn/tests/testthat/test_distances.R |only phangorn-2.0.0/phangorn/tests/testthat/test_pml.R |only phangorn-2.0.0/phangorn/vignettes/Ancestral.Rnw | 1 phangorn-2.0.0/phangorn/vignettes/Networx.Rmd | 9 phangorn-2.0.0/phangorn/vignettes/Trees.RData |binary phangorn-2.0.0/phangorn/vignettes/Trees.Rnw | 142 - phangorn-2.0.0/phangorn/vignettes/phangorn-specials.Rnw | 7 phangorn-2.0.0/phangorn/vignettes/phangorn.bib | 205 ++ 70 files changed, 1991 insertions(+), 1425 deletions(-)
Title: Parametric Bootstrap and Kenward-Roger-Based Methods for Mixed
Model Comparison
Diff between pbkrtest versions 0.4-2 dated 2014-11-13 and 0.4-3 dated 2015-12-10
Description: Test in mixed effects models.
Attention is on mixed effects models as implemented in the
lme4 package.
The package implements a parametric bootstrap test and a Kenward-Roger
modification of F-tests for linear mixed effects models and a parametric bootstrap
test for generalized linear mixed models.
Author: Ulrich Halekoh
Maintainer: Søren Højsgaard
pbkrtest-0.4-2/pbkrtest/R/KR-vcovAdj2-prev.R |only
pbkrtest-0.4-3/pbkrtest/ChangeLog | 10
pbkrtest-0.4-3/pbkrtest/DESCRIPTION | 24
pbkrtest-0.4-3/pbkrtest/MD5 | 49 -
pbkrtest-0.4-3/pbkrtest/NAMESPACE | 74 ++
pbkrtest-0.4-3/pbkrtest/R/KR-Sigma-G.R | 174 ++---
pbkrtest-0.4-3/pbkrtest/R/KR-Sigma-G2.R | 6
pbkrtest-0.4-3/pbkrtest/R/KR-init-modcomp.R | 104 +--
pbkrtest-0.4-3/pbkrtest/R/KR-linearAlgebra.R | 12
pbkrtest-0.4-3/pbkrtest/R/KR-modcomp.R | 8
pbkrtest-0.4-3/pbkrtest/R/KR-utils.R | 23
pbkrtest-0.4-3/pbkrtest/R/KR-vcovAdj.R | 407 ++++++++-----
pbkrtest-0.4-3/pbkrtest/R/PB-modcomp.R | 37 -
pbkrtest-0.4-3/pbkrtest/R/PB-refdist.R | 26
pbkrtest-0.4-3/pbkrtest/R/PB-utils.R | 2
pbkrtest-0.4-3/pbkrtest/R/modelCoercion.R | 5
pbkrtest-0.4-3/pbkrtest/build/vignette.rds |binary
pbkrtest-0.4-3/pbkrtest/data/beets.txt.gz |binary
pbkrtest-0.4-3/pbkrtest/data/budworm.txt.gz |binary
pbkrtest-0.4-3/pbkrtest/inst/doc/pbkrtest-introduction.R | 304 ++++-----
pbkrtest-0.4-3/pbkrtest/inst/doc/pbkrtest-introduction.pdf |binary
pbkrtest-0.4-3/pbkrtest/man/KRmodcomp.Rd | 13
pbkrtest-0.4-3/pbkrtest/man/PBmodcomp.Rd | 62 +
pbkrtest-0.4-3/pbkrtest/man/PBrefdist.Rd | 11
pbkrtest-0.4-3/pbkrtest/man/pbkrtest-internal.Rd | 7
pbkrtest-0.4-3/pbkrtest/man/vcovAdj.Rd | 4
26 files changed, 845 insertions(+), 517 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits and imputed cross-validation. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included; uses Maarloes Maathius's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.8 dated 2015-10-27 and 1.3.1 dated 2015-12-10
DESCRIPTION | 10 MD5 | 54 +++- NAMESPACE | 10 NEWS | 11 R/Utilities.R | 139 +++++++++++- R/icenReg_CV.R |only R/referenceClasses.R | 7 R/user_functions.R | 331 ++++++++++++++++++++++++----- build |only inst |only man/abs_inv.Rd |only man/diag_baseline.Rd | 2 man/getFitEsts.Rd | 32 +- man/ic_par.Rd | 2 man/ic_sp.Rd | 2 man/icenReg_cv.Rd |only man/imputeCens.Rd |only man/predict.icenReg_fit.Rd |only src/icenReg.cpp | 1 src/icenReg_files/basicUtilities.cpp | 81 +++++++ src/icenReg_files/ic_par.cpp | 71 ++++++ src/icenReg_files/ic_par.h | 10 src/icenReg_files/ic_sp_ch.cpp | 90 ++++++- src/icenReg_files/ic_sp_ch.h | 24 +- src/icenReg_files/ic_sp_gradDescent.cpp | 124 +--------- src/icenReg_files/regressionTransforms.cpp |only src/icenReg_files/regressionTransforms.h |only vignettes |only 28 files changed, 774 insertions(+), 227 deletions(-)
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, including classical ones (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M). Relies on spatstat for some core calculation.
Author: Eric Marcon, Gabriel Lang, Stephane Traissac, Florence Puech
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between dbmss versions 2.2.3 dated 2015-10-01 and 2.2-4 dated 2015-12-10
DESCRIPTION | 12 - MD5 | 36 ++-- NAMESPACE | 1 NEWS | 10 + R/Kdhat.R | 24 +- R/Mhat.R | 12 - R/RcppExports.R | 20 +- R/m_hat.R | 46 +++-- build/vignette.rds |binary inst/doc/dbmss.Rnw | 2 inst/doc/dbmss.pdf |binary man/Rcpp.Rd | 46 ++++- man/dbmss-package.Rd | 20 +- src/CountNbd.cpp | 409 ++++++++++++++++++++++++++++++--------------------- src/Makevars | 29 --- src/Makevars.win | 8 src/RcppExports.cpp | 81 +++++----- vignettes/dbmss.Rnw | 2 vignettes/dbmss.bib | 41 +++-- 19 files changed, 472 insertions(+), 327 deletions(-)
Title: Helper Functions for Structural Equation Modelling in OpenMx
Description: Helper functions for making, running, and reporting SEM
and twin models in OpenMx.
If you are just starting, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.0.0 dated 2015-10-27 and 1.1.0 dated 2015-12-10
umx-1.0.0/umx/man/umxStandardizeACE.Rd |only umx-1.0.0/umx/man/umx_APA_CI.Rd |only umx-1.0.0/umx/man/umx_check_multi_core.Rd |only umx-1.0.0/umx/man/umx_get_CI_as_APA_string.Rd |only umx-1.1.0/umx/DESCRIPTION | 9 umx-1.1.0/umx/MD5 | 332 +++---- umx-1.1.0/umx/NAMESPACE | 18 umx-1.1.0/umx/NEWS | 20 umx-1.1.0/umx/R/build_run_modify.r | 727 ++++++++++++--- umx-1.1.0/umx/R/datasets.R |only umx-1.1.0/umx/R/fit_and_reporting.r | 736 ++++++++-------- umx-1.1.0/umx/R/hermine_original_twinHetMulAceCon.R |only umx-1.1.0/umx/R/misc_and_utility.r | 640 ++++++++----- umx-1.1.0/umx/R/umxCF_SexLim.R |only umx-1.1.0/umx/R/xmu.r | 6 umx-1.1.0/umx/data |only umx-1.1.0/umx/inst/CITATION | 2 umx-1.1.0/umx/man/RMSEA.MxModel.Rd | 27 umx-1.1.0/umx/man/RMSEA.Rd | 27 umx-1.1.0/umx/man/RMSEA.summary.mxmodel.Rd | 27 umx-1.1.0/umx/man/confint.MxModel.Rd | 39 umx-1.1.0/umx/man/dl_from_dropbox.Rd | 8 umx-1.1.0/umx/man/extractAIC.MxModel.Rd | 31 umx-1.1.0/umx/man/figures/ACE.png |only umx-1.1.0/umx/man/figures/CP.png |only umx-1.1.0/umx/man/figures/GxE.png |only umx-1.1.0/umx/man/figures/IP.png |only umx-1.1.0/umx/man/figures/umx_help_figures.graffle |binary umx-1.1.0/umx/man/logLik.Rd | 35 umx-1.1.0/umx/man/plot.MxModel.Rd | 36 umx-1.1.0/umx/man/qm.Rd | 14 umx-1.1.0/umx/man/reliability.Rd | 10 umx-1.1.0/umx/man/residuals.MxModel.Rd | 31 umx-1.1.0/umx/man/summaryAPA.Rd |only umx-1.1.0/umx/man/umx-deprecated.Rd | 2 umx-1.1.0/umx/man/umx.Rd | 152 +-- umx-1.1.0/umx/man/umxACE.Rd | 80 + umx-1.1.0/umx/man/umxACESexLim.Rd |only umx-1.1.0/umx/man/umxAdd1.Rd | 14 umx-1.1.0/umx/man/umxCF_SexLim.Rd |only umx-1.1.0/umx/man/umxCI.Rd | 34 umx-1.1.0/umx/man/umxCI_boot.Rd | 33 umx-1.1.0/umx/man/umxCP.Rd | 66 + umx-1.1.0/umx/man/umxCompare.Rd | 57 - umx-1.1.0/umx/man/umxCov2cor.Rd | 8 umx-1.1.0/umx/man/umxCovData.Rd | 28 umx-1.1.0/umx/man/umxDiagnose.Rd | 23 umx-1.1.0/umx/man/umxDrop1.Rd | 18 umx-1.1.0/umx/man/umxEFA.Rd | 6 umx-1.1.0/umx/man/umxEquate.Rd | 35 umx-1.1.0/umx/man/umxEval.Rd | 51 - umx-1.1.0/umx/man/umxExpCov.Rd | 44 umx-1.1.0/umx/man/umxExpMeans.Rd | 32 umx-1.1.0/umx/man/umxFactor.Rd |only umx-1.1.0/umx/man/umxFitIndices.Rd | 32 umx-1.1.0/umx/man/umxFixAll.Rd | 16 umx-1.1.0/umx/man/umxGetParameters.Rd | 20 umx-1.1.0/umx/man/umxGxE.Rd | 39 umx-1.1.0/umx/man/umxGxE_window.Rd | 40 umx-1.1.0/umx/man/umxHetCor.Rd | 29 umx-1.1.0/umx/man/umxIP.Rd | 36 umx-1.1.0/umx/man/umxJiggle.Rd | 35 umx-1.1.0/umx/man/umxLabel.Rd | 25 umx-1.1.0/umx/man/umxLatent.Rd | 40 umx-1.1.0/umx/man/umxMI.Rd | 20 umx-1.1.0/umx/man/umxPadAndPruneForDefVars.Rd | 25 umx-1.1.0/umx/man/umxPath.Rd | 44 umx-1.1.0/umx/man/umxPlotACE.Rd | 28 umx-1.1.0/umx/man/umxPlotCP.Rd | 12 umx-1.1.0/umx/man/umxPlotGxE.Rd | 12 umx-1.1.0/umx/man/umxPlotIP.Rd | 4 umx-1.1.0/umx/man/umxRAM.Rd | 44 umx-1.1.0/umx/man/umxReRun.Rd | 25 umx-1.1.0/umx/man/umxReduce.Rd | 10 umx-1.1.0/umx/man/umxRun.Rd | 25 umx-1.1.0/umx/man/umxSetParameters.Rd | 40 umx-1.1.0/umx/man/umxStandardizeModel.Rd | 31 umx-1.1.0/umx/man/umxSummary.MxModel.Rd | 63 - umx-1.1.0/umx/man/umxSummary.Rd | 4 umx-1.1.0/umx/man/umxSummaryACE.Rd | 15 umx-1.1.0/umx/man/umxSummaryCP.Rd | 20 umx-1.1.0/umx/man/umxSummaryGxE.Rd | 25 umx-1.1.0/umx/man/umxSummaryIP.Rd | 14 umx-1.1.0/umx/man/umxThresholdMatrix.Rd | 60 - umx-1.1.0/umx/man/umxUnexplainedCausalNexus.Rd | 13 umx-1.1.0/umx/man/umxValues.Rd | 35 umx-1.1.0/umx/man/umx_APA_model_CI.Rd |only umx-1.1.0/umx/man/umx_APA_pval.Rd | 43 umx-1.1.0/umx/man/umx_RAM_ordinal_objective.Rd | 7 umx-1.1.0/umx/man/umx_add_variances.Rd | 42 umx-1.1.0/umx/man/umx_aggregate.Rd | 16 umx-1.1.0/umx/man/umx_apply.Rd | 40 umx-1.1.0/umx/man/umx_as_numeric.Rd | 26 umx-1.1.0/umx/man/umx_check.Rd | 46 - umx-1.1.0/umx/man/umx_check_OS.Rd | 45 umx-1.1.0/umx/man/umx_check_model.Rd | 51 - umx-1.1.0/umx/man/umx_check_names.Rd | 23 umx-1.1.0/umx/man/umx_check_parallel.Rd |only umx-1.1.0/umx/man/umx_cont_2_ordinal.Rd | 26 umx-1.1.0/umx/man/umx_cor.Rd | 17 umx-1.1.0/umx/man/umx_cov2raw.Rd | 28 umx-1.1.0/umx/man/umx_cov_diag.Rd | 4 umx-1.1.0/umx/man/umx_default_option.Rd | 44 umx-1.1.0/umx/man/umx_drop_ok.Rd | 25 umx-1.1.0/umx/man/umx_explode.Rd | 17 umx-1.1.0/umx/man/umx_fake_data.Rd | 16 umx-1.1.0/umx/man/umx_find_object.Rd | 14 umx-1.1.0/umx/man/umx_fix_first_loadings.Rd | 19 umx-1.1.0/umx/man/umx_fix_latents.Rd | 20 umx-1.1.0/umx/man/umx_fun_mean_sd.Rd |only umx-1.1.0/umx/man/umx_get_bracket_addresses.Rd | 44 umx-1.1.0/umx/man/umx_get_checkpoint.Rd | 43 umx-1.1.0/umx/man/umx_get_cores.Rd | 39 umx-1.1.0/umx/man/umx_get_optimizer.Rd | 36 umx-1.1.0/umx/man/umx_grep.Rd | 26 umx-1.1.0/umx/man/umx_has_CIs.Rd | 51 - umx-1.1.0/umx/man/umx_has_been_run.Rd | 50 - umx-1.1.0/umx/man/umx_has_means.Rd | 51 - umx-1.1.0/umx/man/umx_has_square_brackets.Rd | 45 umx-1.1.0/umx/man/umx_is_MxMatrix.Rd | 45 umx-1.1.0/umx/man/umx_is_MxModel.Rd | 45 umx-1.1.0/umx/man/umx_is_RAM.Rd | 51 - umx-1.1.0/umx/man/umx_is_cov.Rd | 45 umx-1.1.0/umx/man/umx_is_endogenous.Rd | 45 umx-1.1.0/umx/man/umx_is_exogenous.Rd | 47 - umx-1.1.0/umx/man/umx_is_ordered.Rd | 48 - umx-1.1.0/umx/man/umx_lower2full.Rd | 39 umx-1.1.0/umx/man/umx_make_bin_cont_pair_data.Rd | 26 umx-1.1.0/umx/man/umx_means.Rd | 8 umx-1.1.0/umx/man/umx_merge_CIs.Rd | 26 umx-1.1.0/umx/man/umx_move_file.Rd | 8 umx-1.1.0/umx/man/umx_msg.Rd | 18 umx-1.1.0/umx/man/umx_names.Rd | 14 umx-1.1.0/umx/man/umx_object_as_str.Rd | 38 umx-1.1.0/umx/man/umx_open.Rd | 9 umx-1.1.0/umx/man/umx_paste_names.Rd | 28 umx-1.1.0/umx/man/umx_pb_note.Rd | 14 umx-1.1.0/umx/man/umx_print.Rd | 30 umx-1.1.0/umx/man/umx_read_lower.Rd | 28 umx-1.1.0/umx/man/umx_rename.Rd | 14 umx-1.1.0/umx/man/umx_rename_file.Rd | 8 umx-1.1.0/umx/man/umx_reorder.Rd | 46 - umx-1.1.0/umx/man/umx_residualize.Rd | 70 - umx-1.1.0/umx/man/umx_rot.Rd | 11 umx-1.1.0/umx/man/umx_round.Rd | 28 umx-1.1.0/umx/man/umx_scale.Rd | 29 umx-1.1.0/umx/man/umx_scale_wide_twin_data.Rd | 28 umx-1.1.0/umx/man/umx_set_checkpoint.Rd | 40 umx-1.1.0/umx/man/umx_set_cores.Rd | 40 umx-1.1.0/umx/man/umx_set_optimizer.Rd | 37 umx-1.1.0/umx/man/umx_show.Rd | 18 umx-1.1.0/umx/man/umx_standardize_ACE.Rd |only umx-1.1.0/umx/man/umx_standardize_CP.Rd |only umx-1.1.0/umx/man/umx_standardize_IP.Rd | 41 umx-1.1.0/umx/man/umx_string_to_algebra.Rd | 38 umx-1.1.0/umx/man/umx_swap_a_block.Rd | 28 umx-1.1.0/umx/man/umx_time.Rd | 18 umx-1.1.0/umx/man/umx_trim.Rd | 11 umx-1.1.0/umx/man/us_skinfold_data.Rd |only umx-1.1.0/umx/man/xmuHasSquareBrackets.Rd | 22 umx-1.1.0/umx/man/xmuLabel_MATRIX_Model.Rd | 32 umx-1.1.0/umx/man/xmuLabel_Matrix.Rd | 22 umx-1.1.0/umx/man/xmuLabel_RAM_Model.Rd | 22 umx-1.1.0/umx/man/xmuMI.Rd | 24 umx-1.1.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 22 umx-1.1.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 22 umx-1.1.0/umx/man/xmuMakeThresholdsMatrices.Rd | 4 umx-1.1.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 22 umx-1.1.0/umx/man/xmuMaxLevels.Rd | 24 umx-1.1.0/umx/man/xmuMinLevels.Rd | 24 umx-1.1.0/umx/man/xmuPropagateLabels.Rd | 28 umx-1.1.0/umx/man/xmu_dot_make_paths.Rd | 22 umx-1.1.0/umx/man/xmu_dot_make_residuals.Rd | 22 umx-1.1.0/umx/man/xmu_start_value_list.Rd | 22 umx-1.1.0/umx/tests/testthat/test_DoF.r |only umx-1.1.0/umx/tests/testthat/test_umxLabel.r |only umx-1.1.0/umx/tests/testthat/test_umx_APA_pval.r |only umx-1.1.0/umx/tests/testthat/test_umx_has_means.r | 16 umx-1.1.0/umx/tests/testthat/test_umx_is_RAM.r |only umx-1.1.0/umx/tests/testthat/test_umx_is_cov.r |only umx-1.1.0/umx/tests/testthat/test_umx_rename.r |only 181 files changed, 3452 insertions(+), 3308 deletions(-)
Title: Bi-Directional Interface Between R and Scala with Callbacks
Description: The Scala interpreter is embedded in R and callbacks to R from the embedded interpreter are supported. Conversely, the R interpreter is embedded in Scala. Scala versions 2.10 and 2.11 are supported.
Author: David B. Dahl [aut, cre],
Scala developers [ctb] (see http://scala-lang.org/)
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 1.0.6 dated 2015-05-15 and 1.0.8 dated 2015-12-10
rscala-1.0.6/rscala/inst/java/rscala_2.10-1.0.6.jar |only rscala-1.0.6/rscala/inst/java/rscala_2.11-1.0.6.jar |only rscala-1.0.6/rscala/java/rscala_2.10-1.0.6-sources.jar |only rscala-1.0.6/rscala/java/rscala_2.11-1.0.6-sources.jar |only rscala-1.0.8/rscala/DESCRIPTION | 8 +++---- rscala-1.0.8/rscala/MD5 | 18 ++++++++--------- rscala-1.0.8/rscala/NEWS | 9 ++++++++ rscala-1.0.8/rscala/R/scalaInterpreter.R | 9 +++++++- rscala-1.0.8/rscala/inst/doc/readme.html | 5 +--- rscala-1.0.8/rscala/inst/java/rscala_2.10-1.0.8.jar |only rscala-1.0.8/rscala/inst/java/rscala_2.11-1.0.8.jar |only rscala-1.0.8/rscala/java/rscala_2.10-1.0.8-sources.jar |only rscala-1.0.8/rscala/java/rscala_2.11-1.0.8-sources.jar |only rscala-1.0.8/rscala/man/strintrpl.Rd | 4 +-- 14 files changed, 34 insertions(+), 19 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.5-00 dated 2015-09-25 and 0.5-10 dated 2015-12-10
phytools-0.5-00/phytools/README.md |only phytools-0.5-10/phytools/DESCRIPTION | 8 phytools-0.5-10/phytools/MD5 | 65 +++--- phytools-0.5-10/phytools/NAMESPACE | 187 +++++++++---------- phytools-0.5-10/phytools/R/add.species.to.genus.R | 20 ++ phytools-0.5-10/phytools/R/anc.ML.R | 12 - phytools-0.5-10/phytools/R/contMap.R | 43 +++- phytools-0.5-10/phytools/R/cophylo.R | 78 +++++++ phytools-0.5-10/phytools/R/densityMap.R | 30 ++- phytools-0.5-10/phytools/R/fastAnc.R | 27 ++ phytools-0.5-10/phytools/R/fitMk.R | 19 + phytools-0.5-10/phytools/R/make.simmap.R | 39 ++- phytools-0.5-10/phytools/R/mrp.supertree.R | 39 ++- phytools-0.5-10/phytools/R/optim.phylo.ls.R | 106 ++-------- phytools-0.5-10/phytools/R/phylo.to.map.R | 140 ++++++++++---- phytools-0.5-10/phytools/R/plotSimmap.R | 32 +-- phytools-0.5-10/phytools/R/plotTree.wBars.R | 11 - phytools-0.5-10/phytools/R/rerootingMethod.R | 2 phytools-0.5-10/phytools/R/utilities.R | 177 +++++++++++++++-- phytools-0.5-10/phytools/man/add.species.to.genus.Rd | 14 - phytools-0.5-10/phytools/man/bind.tip.Rd | 7 phytools-0.5-10/phytools/man/collapse.to.star.Rd | 2 phytools-0.5-10/phytools/man/contMap.Rd | 4 phytools-0.5-10/phytools/man/cophylo.Rd | 2 phytools-0.5-10/phytools/man/densityMap.Rd | 2 phytools-0.5-10/phytools/man/edgeProbs.Rd |only phytools-0.5-10/phytools/man/fastAnc.Rd | 3 phytools-0.5-10/phytools/man/fastMRCA.Rd | 4 phytools-0.5-10/phytools/man/mrp.supertree.Rd | 7 phytools-0.5-10/phytools/man/nodelabels.cophylo.Rd |only phytools-0.5-10/phytools/man/pbtree.Rd | 4 phytools-0.5-10/phytools/man/plotSimmap.Rd | 2 phytools-0.5-10/phytools/man/plotTree.wBars.Rd | 4 phytools-0.5-10/phytools/man/reroot.Rd | 4 phytools-0.5-10/phytools/man/write.simmap.Rd | 10 - 35 files changed, 720 insertions(+), 384 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty. Supported
models include cumulative logit, probit, cauchit, and complementary log-log.
The algorithm uses Fisher Scoring with Coordinate Descent updates.
Author: Mike Wurm [aut, cre]
Maintainer: Mike Wurm <wurm@wisc.edu>
Diff between ordinalNet versions 1.3 dated 2015-11-30 and 1.4 dated 2015-12-10
DESCRIPTION | 16 ++++---- MD5 | 17 ++++---- NAMESPACE | 2 - R/ordinalNet.R | 4 +- man/coef.ordinalNetFit.Rd | 2 - man/ordinalNet.Rd | 2 - man/predict.ordinalNetFit.Rd | 2 - man/print.ordinalNetFit.Rd | 2 - tests/testdata.rda |only tests/testthat/test-ordinalNet.R | 78 ++++++++++++++++----------------------- 10 files changed, 56 insertions(+), 69 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com> [aut, cre],
Hironobu Takahashi [cph],
Hajime Baba [cph],
Takatsugu Nokubi [cph]
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.6.1 dated 2015-06-26 and 0.6.3 dated 2015-12-10
ChangeLog | 9 +++++++++ DESCRIPTION | 13 ++++++++----- MD5 | 18 +++++++++--------- NAMESPACE | 6 +++++- R/zen2han.R | 7 ++++--- R/zzz.R | 4 +--- man/Nippon-package.Rd | 4 ++-- man/zen2han.Rd | 4 ++-- src/kakasi/Makefile.in | 4 ++-- src/kakasi/Makefile.win | 4 ++-- 10 files changed, 44 insertions(+), 29 deletions(-)
Title: Import, Plot and Analyze Bathymetric and Topographic Data
Description: Import xyz data from the NOAA, GEBCO and other sources, plot xyz data to prepare publication-ready figures, analyze xyz data to extract transects, get depth / altitude based on geographical coordinates, or calculate z-constrained least-cost paths.
Author: Eric Pante, Benoit Simon-Bouhet, and Jean-Olivier Irisson
Maintainer: Eric Pante <pante.eric@gmail.com>
Diff between marmap versions 0.9.4 dated 2015-12-01 and 0.9.5 dated 2015-12-10
DESCRIPTION | 8 +++--- MD5 | 45 +++++++++++++++++++----------------- NAMESPACE | 4 ++- R/combine.buffers.R | 55 +++++++++++++++++++++++++++++---------------- R/create.buffer.R | 22 +++++++++++++----- R/get.area.R | 4 ++- R/plot.bathy.R | 2 - R/plot.buffer.R |only R/print.buffer.R |only build/vignette.rds |binary data/aleutians.rda |binary data/celt.rda |binary data/florida.rda |binary data/hawaii.rda |binary data/hawaii.sites.rda |binary data/irregular.rda |binary data/metallo.rda |binary data/nw.atlantic.coast.rda |binary data/nw.atlantic.rda |binary man/combine.buffers.Rd | 22 +++++++++--------- man/create.buffer.Rd | 16 +++++++------ man/marmap.Rd | 4 +-- man/outline.buffer.Rd | 27 ++++++++++++++-------- man/plot.buffer.Rd |only man/plotArea.Rd | 2 - 25 files changed, 128 insertions(+), 83 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors, and for
the comparison of predictive errors between models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 0.1.3 dated 2015-09-18 and 0.1.4 dated 2015-12-10
loo-0.1.3/loo/R/misc.R |only loo-0.1.4/loo/DESCRIPTION | 21 ++-- loo-0.1.4/loo/MD5 | 53 ++++++------ loo-0.1.4/loo/NAMESPACE | 2 loo-0.1.4/loo/R/compare.R | 59 ++++++------- loo-0.1.4/loo/R/extract_log_lik.R | 20 +--- loo-0.1.4/loo/R/gpdfit.R | 5 - loo-0.1.4/loo/R/helpers.R | 86 ++++++++++++++++---- loo-0.1.4/loo/R/loo.R | 54 +++++------- loo-0.1.4/loo/R/loo_package.R | 17 --- loo-0.1.4/loo/R/print.R | 46 ++++++---- loo-0.1.4/loo/R/psislw.R | 52 ++++++------ loo-0.1.4/loo/R/waic.R | 17 +-- loo-0.1.4/loo/R/zzz.R | 3 loo-0.1.4/loo/man/compare.Rd | 47 +++++----- loo-0.1.4/loo/man/extract_log_lik.Rd | 11 -- loo-0.1.4/loo/man/gpdfit.Rd | 6 - loo-0.1.4/loo/man/loo-package.Rd | 19 +--- loo-0.1.4/loo/man/loo.Rd | 48 +++++------ loo-0.1.4/loo/man/nlist.Rd | 6 - loo-0.1.4/loo/man/print.loo.Rd | 43 +++++----- loo-0.1.4/loo/man/psislw.Rd | 28 +++--- loo-0.1.4/loo/man/waic.Rd | 14 +-- loo-0.1.4/loo/tests/testthat/test_compare.R |only loo-0.1.4/loo/tests/testthat/test_extract_log_lik.R |only loo-0.1.4/loo/tests/testthat/test_gpdfit.R | 12 +- loo-0.1.4/loo/tests/testthat/test_helpers.R | 68 ++++++--------- loo-0.1.4/loo/tests/testthat/test_loo_and_waic.R | 36 ++++---- loo-0.1.4/loo/tests/testthat/test_print_plot.R |only loo-0.1.4/loo/tests/testthat/test_psislw.R |only 30 files changed, 397 insertions(+), 376 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut],
Manuel Oviedo de la Fuente [aut, cre],
Pedro Galeano [ctb],
Alicia Nieto [ctb],
Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente <manuel.oviedo@usc.es>
Diff between fda.usc versions 1.2.1 dated 2014-12-01 and 1.2.2 dated 2015-12-10
DESCRIPTION | 9 MD5 | 154 ++++---- NAMESPACE | 38 + NEWS | 15 R/GCV.S.R | 2 R/Ginv.R |only R/classif.DD.r | 426 +++++++++++++++++++--- R/classif.gkam.R | 2 R/classif.glm.R | 2 R/classif.np.ldata.R |only R/classif.np.r | 290 +++++++-------- R/classif.univariate.R | 7 R/depth.FM.r | 2 R/depth.mode.r | 243 ++++++------ R/depth.multivariate.R | 19 R/dfv.test.R | 2 R/fda.usc.internal.R | 1 R/flm.Ftest.R | 2 R/flm.test.R | 2 R/fregre.PPC.PPLS.R | 610 ++++++++++++++++--------------- R/fregre.basis.cv.R | 44 -- R/fregre.basis.fr.r | 142 ++++--- R/fregre.gkam.r | 3 R/fregre.glm.R | 2 R/fregre.lm.r | 4 R/fregre.np.cv.r | 2 R/kmeans.centers.update.R | 2 R/metric.dist.R | 85 +++- R/plot.fdata.R | 4 R/plot.lfdata.R |only R/predict.classif.R | 744 +++++++++++++++++++-------------------- R/predict.classif.npp.R |only R/predict.fregre.fr.r | 8 R/quantile.outliers.trim.r | 2 R/subset.lfdata.R |only man/DepthFunctional.Rd | 24 - man/DepthFunctionalIntegrate.Rd | 36 - man/Descriptive.Rd | 3 man/GCV.S.Rd | 3 man/Outliers.fdata.Rd | 5 man/PCvM.statistic.Rd | 138 +++---- man/anova.RPm.Rd | 4 man/classif.DD.Rd | 15 man/classif.depth.Rd | 3 man/classif.gkam.Rd | 5 man/create.fdata.basis.Rd | 6 man/dcor.test.rd | 6 man/dev.S.Rd | 9 man/dfv.test.Rd | 218 +++++------ man/fda.usc-package.Rd | 8 man/fdata.Rd | 5 man/fdata.bootstrap.Rd | 4 man/fdata2fd.Rd | 3 man/fdata2pls.Rd | 6 man/flm.Ftest.Rd | 172 ++++----- man/flm.test.Rd | 436 +++++++++++----------- man/fregre.bootstrap.Rd | 5 man/fregre.gkam.Rd | 7 man/fregre.glm.Rd | 3 man/fregre.lm.Rd | 3 man/fregre.np.cv.Rd | 3 man/fregre.pc.Rd | 3 man/fregre.plm.Rd | 3 man/influence.quan.Rd | 4 man/metric.dist.Rd | 2 man/metric.kl.Rd | 3 man/min.basis.Rd | 3 man/min.np.Rd | 3 man/order.fdata.Rd | 2 man/poblenou.Rd | 2 man/predict.fregre.fd.Rd | 5 man/predict.fregre.functional.Rd | 2 man/predict.fregre.scalar.Rd | 8 man/rproc2fdata.Rd | 8 man/rwild.Rd | 3 man/semimetric.NPFDA.Rd | 3 man/subset.fdata.Rd |only man/summary.fregre.fd.Rd | 6 man/tecator.Rd | 5 src/Adot.f90 | 96 ++--- src/PCvM_statistic.f90 | 18 81 files changed, 2345 insertions(+), 1832 deletions(-)