Title: Lasso and Elastic-Net Regularized Generalized Linear Models
Diff between glmnet versions 2.0-1 dated 2015-04-08 and 2.0-2 dated 2015-04-11
Description: Extremely efficient procedures for fitting the entire lasso or elastic-net regularization path for linear regression, logistic and multinomial regression models, Poisson regression and the Cox model. Two recent additions are the multiple-response Gaussian, and the grouped multinomial. The algorithm uses cyclical coordinate descent in a path-wise fashion, as described in the paper linked to via the URL below.
Author: Jerome Friedman, Trevor Hastie, Noah Simon, Rob Tibshirani
Maintainer: Trevor Hastie
DESCRIPTION | 10 +-
MD5 | 12 +-
inst/doc/Coxnet.pdf |binary
inst/doc/glmnet_beta.R | 27 ++++--
inst/doc/glmnet_beta.Rmd | 18 +++-
inst/doc/glmnet_beta.html | 192 ++++++++++++++++++++++------------------------
vignettes/glmnet_beta.Rmd | 18 +++-
7 files changed, 155 insertions(+), 122 deletions(-)
Title: Explorer of World Population Prospects
Diff between wppExplorer versions 1.5-0 dated 2015-02-07 and 1.6-1 dated 2015-04-11
Description: A shiny interface for exploring data in the 'wpp2012' (or 2010, 2008) package.
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 6 ++++++
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
R/global.R | 10 ++++++----
R/wpp.R | 9 +++++++++
inst/explore/server.R | 25 ++++++++++++++-----------
inst/explore/ui.R | 12 ++++++++----
inst/explore/www/geochart.js | 34 ++++++++++++++++++++++++++++++++--
man/wpp.explore.Rd | 2 ++
man/wpp.indicator.Rd | 3 ++-
man/wppExplorer-package.Rd | 14 +++++++++-----
11 files changed, 103 insertions(+), 42 deletions(-)
Title: Simulating the Evolution of Biological Sequences
Diff between scrm versions 1.3-3 dated 2014-11-18 and 1.5.0-1 dated 2015-04-11
Description: A coalescent simulator that allows the rapid simulation of
biological sequences under neutral models of evolution. Different to
other coalescent based simulations, scrm has an optional approximation
parameter that allows for high accuracy while maintaining a linear run time
cost for long sequences. It is optimized for simulating massive data sets as
produced by Next-Generation Sequencing technologies for up to several thousand
sequences.
Author: Paul Staab [aut, cre, cph],
Zhu Sha [aut, cph],
Dirk Metzler [aut, cph, ths],
Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
DESCRIPTION | 15 -
MD5 | 115 +++----
NAMESPACE | 2
NEWS | 22 -
R/RcppExports.R | 26 -
R/scrm.R | 18 -
README.md | 11
build/vignette.rds |binary
inst/CITATION |only
inst/doc/scrm-Arguments.Rmd | 55 ++-
inst/doc/scrm-Arguments.html | 320 ++++++----------------
inst/doc/scrm-TreesForApe.Rmd | 2
inst/doc/scrm-TreesForApe.html | 261 +++--------------
man/scrm-package.Rd | 3
man/scrm.Rd | 3
src/Makevars | 2
src/Makevars.win | 2
src/RcppExports.cpp | 60 +---
src/r_random_generator.h | 18 -
src/scrm/contemporaries_container.h | 2
src/scrm/event.h | 2
src/scrm/forest.cc | 201 +++++++++----
src/scrm/forest.h | 12
src/scrm/macros.h | 21 +
src/scrm/model.cc | 111 ++++---
src/scrm/model.h | 34 +-
src/scrm/node.cc | 21 +
src/scrm/node.h | 32 +-
src/scrm/node_container.cc | 63 +++-
src/scrm/node_container.h | 45 ++-
src/scrm/param.cc | 111 +++++--
src/scrm/param.h | 39 ++
src/scrm/random/fastfunc.cc | 9
src/scrm/random/fastfunc.h | 28 -
src/scrm/random/random_generator.cc | 2
src/scrm/random/random_generator.h | 2
src/scrm/summary_statistics/frequency_spectrum.cc | 2
src/scrm/summary_statistics/frequency_spectrum.h | 2
src/scrm/summary_statistics/newick_tree.cc | 19 -
src/scrm/summary_statistics/newick_tree.h | 27 -
src/scrm/summary_statistics/oriented_forest.cc | 2
src/scrm/summary_statistics/oriented_forest.h | 2
src/scrm/summary_statistics/seg_sites.cc | 2
src/scrm/summary_statistics/seg_sites.h | 2
src/scrm/summary_statistics/summary_statistic.h | 2
src/scrm/summary_statistics/tmrca.cc | 2
src/scrm/summary_statistics/tmrca.h | 2
src/scrm/time_interval.cc | 2
src/scrm/time_interval.h | 2
src/scrm/tree_point.cc | 2
src/scrm/tree_point.h | 2
src/scrmr.cpp | 88 +++---
src/test_exports.cpp | 4
tests/testthat.R | 2
tests/testthat/test-r_random-generator.R | 8
tests/testthat/test-scrm.R | 86 ++++-
tests/testthat/test-summary-statistics.R | 54 +--
vignettes/scrm-Arguments.Rmd | 55 ++-
vignettes/scrm-TreesForApe.Rmd | 2
59 files changed, 1084 insertions(+), 957 deletions(-)
Title: Geographic Data Analysis and Modeling
Diff between raster versions 2.3-33 dated 2015-03-14 and 2.3-40 dated 2015-04-11
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],
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
ChangeLog | 13
DESCRIPTION | 13
MD5 | 78 ++---
NAMESPACE | 2
R/GDALtransient.R | 30 +
R/area.R | 9
R/arith_sp.R | 12
R/as.data.frame.R | 40 +-
R/boxplot.R | 2
R/brick.R | 14
R/factor.R | 4
R/hdrPRJ.R | 2
R/hdrRaster.R | 83 ++---
R/intersect_sp.R | 39 ++
R/kml.R | 2
R/overlay.R | 8
R/rasterFromRasterFile.R | 86 ++---
R/rasterizeLines.R | 62 +++
R/rasterizePolygons.R | 4
R/shp.R | 2
R/speasy.R |only
R/spplot.R | 12
R/which.max.R | 2
R/writeAllGDAL.R | 3
R/writeRaster.R | 14
R/writeStartStopRaster.R | 11
build/vignette.rds |binary
inst/doc/Raster.R | 732 +++++++++++++++++++++++------------------------
inst/doc/Raster.pdf |binary
inst/doc/functions.R | 686 ++++++++++++++++++++++----------------------
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/Arith-methods.Rd | 4
man/as.data.frame.Rd | 6
man/autocor.Rd | 2
man/extract.Rd | 5
man/intersect.Rd | 5
man/rasterFromXYZ.Rd | 10
man/rasterize.Rd | 14
man/spEasy.Rd |only
man/spplot.Rd | 11
41 files changed, 1108 insertions(+), 914 deletions(-)
Title: Evaluation of Diversity in Nucleotide Libraries
Diff between peptider versions 0.1.7 dated 2015-02-03 and 0.2 dated 2015-04-11
Description: Evaluation of diversity in peptide libraries, including NNN, NNB,
NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined.
Metrics for evaluation include expected coverage, relative efficiency, and
the functional diversity of the library. Peptide-level inclusion
probabilities are computable for both the native and custom encoding
schemes.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare
DESCRIPTION | 35 +++++++++++++++++++++++------------
MD5 | 4 ++--
R/peptider.r | 6 +++---
3 files changed, 28 insertions(+), 17 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.3-11 dated 2014-09-09 and 1.3-13 dated 2015-04-11
Description: Spherical trigonometry for geographic applications. That is, compute distances and related measures for angular (longitude/latitude) locations.
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans
DESCRIPTION | 12 ++++++------
MD5 | 20 ++++++++++----------
R/distRhumb.R | 2 +-
R/distVincentyEllipsoid.R | 2 +-
R/gcIntersectBearing.R | 2 +-
R/gcMaxLat.R | 2 +-
R/geomedian.R | 3 ++-
R/span.R | 18 +++++++++---------
build/vignette.rds |binary
inst/doc/geosphere.pdf |binary
man/centroid.Rd | 4 ----
11 files changed, 31 insertions(+), 34 deletions(-)
Title: Frequency Distribution Tables, Histograms and Polygons
Diff between fdth versions 1.1-8 dated 2013-11-22 and 1.2-1 dated 2015-04-11
Description: Perform frequency distribution tables, associated histograms
and polygons from vector, data.frame and matrix objects for
numerical and categorical variables.
Author: José Cláudio Faria, Enio G. Jelihovschi and Ivan B. Allaman
Maintainer: José Cláudio Faria
fdth-1.1-8/fdth/man/make.fdt.format.classes.Rd |only
fdth-1.1-8/fdth/man/make.fdt.multiple.Rd |only
fdth-1.1-8/fdth/man/make.fdt.simple.Rd |only
fdth-1.2-1/fdth/ChangeLog | 18 +
fdth-1.2-1/fdth/DESCRIPTION | 19 -
fdth-1.2-1/fdth/INDEX | 30 ++-
fdth-1.2-1/fdth/MD5 | 113 +++++++----
fdth-1.2-1/fdth/NAMESPACE | 40 ++++
fdth-1.2-1/fdth/R/fdt.R | 2
fdth-1.2-1/fdth/R/fdt.data.frame.R | 24 +-
fdth-1.2-1/fdth/R/fdt.default.R | 34 ++-
fdth-1.2-1/fdth/R/fdt.matrix.R | 10 -
fdth-1.2-1/fdth/R/fdt_cat.R |only
fdth-1.2-1/fdth/R/fdt_cat.data.frame.R |only
fdth-1.2-1/fdth/R/fdt_cat.default.R |only
fdth-1.2-1/fdth/R/fdt_cat.matrix.R |only
fdth-1.2-1/fdth/R/latex.fdt.R | 11 -
fdth-1.2-1/fdth/R/latex.fdt_cat.R |only
fdth-1.2-1/fdth/R/latex.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/make.fdt.R |only
fdth-1.2-1/fdth/R/make.fdt.format.classes.R | 1
fdth-1.2-1/fdth/R/make.fdt.multiple.R | 3
fdth-1.2-1/fdth/R/make.fdt.simple.R | 30 +--
fdth-1.2-1/fdth/R/make.fdt_cat.R |only
fdth-1.2-1/fdth/R/make.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/make.fdt_cat.simple.R |only
fdth-1.2-1/fdth/R/mean.fdt.R |only
fdth-1.2-1/fdth/R/mean.fdt.multiple.R |only
fdth-1.2-1/fdth/R/median.fdt.R |only
fdth-1.2-1/fdth/R/median.fdt.multiple.R |only
fdth-1.2-1/fdth/R/mfv.R |only
fdth-1.2-1/fdth/R/mfv.default.R |only
fdth-1.2-1/fdth/R/mfv.fdt.R |only
fdth-1.2-1/fdth/R/mfv.fdt.multiple.R |only
fdth-1.2-1/fdth/R/mfv.fdt_cat.R |only
fdth-1.2-1/fdth/R/mfv.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/plot.fdt.default.R | 247 ++++++++++++++++---------
fdth-1.2-1/fdth/R/plot.fdt.multiple.R | 27 +-
fdth-1.2-1/fdth/R/plot.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/plot.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/print.fdt.default.R | 5
fdth-1.2-1/fdth/R/print.fdt.multiple.R | 8
fdth-1.2-1/fdth/R/print.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/print.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/quantile.fdt.R |only
fdth-1.2-1/fdth/R/quantile.fdt.multiple.R |only
fdth-1.2-1/fdth/R/sd.R |only
fdth-1.2-1/fdth/R/sd.default.R |only
fdth-1.2-1/fdth/R/sd.fdt.R |only
fdth-1.2-1/fdth/R/sd.fdt.multiple.R |only
fdth-1.2-1/fdth/R/summary.fdt.default.R | 6
fdth-1.2-1/fdth/R/summary.fdt.multiple.R | 6
fdth-1.2-1/fdth/R/summary.fdt_cat.default.R |only
fdth-1.2-1/fdth/R/summary.fdt_cat.multiple.R |only
fdth-1.2-1/fdth/R/var.R |only
fdth-1.2-1/fdth/R/var.default.R |only
fdth-1.2-1/fdth/R/var.fdt.R |only
fdth-1.2-1/fdth/R/var.fdt.multiple.R |only
fdth-1.2-1/fdth/README.md |only
fdth-1.2-1/fdth/build/vignette.rds |binary
fdth-1.2-1/fdth/inst/CITATION | 10 -
fdth-1.2-1/fdth/inst/COPYRIGHTS | 2
fdth-1.2-1/fdth/inst/doc/latex_fdt.R | 32 +++
fdth-1.2-1/fdth/inst/doc/latex_fdt.Rnw | 36 +++
fdth-1.2-1/fdth/man/fdt.Rd | 184 ++++++++----------
fdth-1.2-1/fdth/man/fdt_cat.Rd |only
fdth-1.2-1/fdth/man/fdth-internal.Rd |only
fdth-1.2-1/fdth/man/fdth-package.Rd | 217 ++++++++++-----------
fdth-1.2-1/fdth/man/latex.fdt.Rd | 102 ++++++++--
fdth-1.2-1/fdth/man/make.fdt.Rd |only
fdth-1.2-1/fdth/man/mean.fdt.Rd |only
fdth-1.2-1/fdth/man/median.fdt.Rd |only
fdth-1.2-1/fdth/man/mfv.Rd |only
fdth-1.2-1/fdth/man/plot.Rd | 207 ++++++++++++++++----
fdth-1.2-1/fdth/man/print.Rd | 63 ++++--
fdth-1.2-1/fdth/man/print.latex.fdt.Rd | 19 +
fdth-1.2-1/fdth/man/quantile.fdt.Rd |only
fdth-1.2-1/fdth/man/sd.Rd |only
fdth-1.2-1/fdth/man/summary.Rd | 44 +++-
fdth-1.2-1/fdth/man/summary.latex.fdt.Rd | 24 +-
fdth-1.2-1/fdth/man/var.Rd |only
fdth-1.2-1/fdth/vignettes/latex_fdt.Rnw | 36 +++
82 files changed, 1083 insertions(+), 527 deletions(-)
Title: Estimate Number of Latent Factors and Factor Matrix for Factor
Analysis
Diff between esaBcv versions 1.0.1 dated 2015-04-07 and 1.1.1 dated 2015-04-11
Description: These functions estimate the latent factors of a given matrix, no matter it is high-dimensional or not. It tries to first estimate the number of factors using bi-cross-validation and then estimate the latent factor matrix and the noise variances. For more information about the method, see Art B. Owen and Jingshu Wang 2015 archived article on factor model (http://arxiv.org/abs/1503.03515).
Author: Art B. Owen [aut],
Jingshu Wang [aut, cre]
Maintainer: Jingshu Wang
esaBcv-1.0.1/esaBcv/man/PseudoInv.Rd |only
esaBcv-1.1.1/esaBcv/DESCRIPTION | 8 -
esaBcv-1.1.1/esaBcv/MD5 | 17 +--
esaBcv-1.1.1/esaBcv/R/ESA_BCV.R | 158 ++++++++++++++++--------------
esaBcv-1.1.1/esaBcv/R/esaBcv-package.R | 2
esaBcv-1.1.1/esaBcv/R/simdat.R | 2
esaBcv-1.1.1/esaBcv/man/ESA.Rd | 18 +--
esaBcv-1.1.1/esaBcv/man/EsaBcv.Rd | 20 +--
esaBcv-1.1.1/esaBcv/man/esaBcv_package.Rd | 2
esaBcv-1.1.1/esaBcv/man/simdat.Rd | 2
10 files changed, 119 insertions(+), 110 deletions(-)