Title: R Binder for the Yhat API
Description: Deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp <greg@yhathq.com>, Brandon Hopkins <dev@yhathq.com>
Maintainer: Greg Lamp <greg@yhathq.com>
Diff between yhatr versions 0.13.7 dated 2015-07-29 and 0.13.9 dated 2016-02-11
yhatr-0.13.7/yhatr/man/yhat.deploy.to.file.Rd |only yhatr-0.13.7/yhatr/man/yhat.deploy.with.scp.Rd |only yhatr-0.13.7/yhatr/man/yhat.scaffolding.Rd |only yhatr-0.13.7/yhatr/man/yhat.show_models.Rd |only yhatr-0.13.7/yhatr/man/yhat.test_predict.Rd |only yhatr-0.13.7/yhatr/man/yhat.transform_from_example.Rd |only yhatr-0.13.9/yhatr/DESCRIPTION | 13 yhatr-0.13.9/yhatr/MD5 | 44 - yhatr-0.13.9/yhatr/NAMESPACE | 14 yhatr-0.13.9/yhatr/NEWS | 10 yhatr-0.13.9/yhatr/R/yhatR.R | 472 ++++++------------ yhatr-0.13.9/yhatr/man/add.dependency.Rd |only yhatr-0.13.9/yhatr/man/capture.src.Rd | 5 yhatr-0.13.9/yhatr/man/check.dependencies.Rd | 3 yhatr-0.13.9/yhatr/man/check.image.size.Rd | 3 yhatr-0.13.9/yhatr/man/is.https.Rd | 3 yhatr-0.13.9/yhatr/man/set.model.require.Rd |only yhatr-0.13.9/yhatr/man/yhat.deploy.Rd | 7 yhatr-0.13.9/yhatr/man/yhat.get.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.library.Rd |only yhatr-0.13.9/yhatr/man/yhat.ls.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.post.Rd | 5 yhatr-0.13.9/yhatr/man/yhat.predict.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.predict_raw.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.spider.block.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.spider.func.Rd | 3 yhatr-0.13.9/yhatr/man/yhat.unload.Rd |only yhatr-0.13.9/yhatr/man/yhat.verify.Rd | 3 28 files changed, 252 insertions(+), 348 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided by this package to parse, compile, test, estimate, and analyze Stan models by accessing the header-only Stan library provided by the 'StanHeaders' package. The Stan project develops a probabilistic programming language that implements full Bayesian statistical inference via Markov Chain Monte Carlo, rough Bayesian inference via variational approximation, and (optionally penalized) maximum likelihood estimation via optimization. In all three cases, automatic differentiation is used to quickly and accurately evaluate gradients without burdening the user with the need to derive the partial derivatives.
Author: Jiqiang Guo [aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Joel de Guzman [cph] (Boost),
Eric Niebler [cph] (Boost),
Thomas Heller [cph] (Boost),
John Fletcher [cph] (Boost)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.9.0 dated 2016-01-05 and 2.9.0-3 dated 2016-02-11
DESCRIPTION | 8 ++-- MD5 | 38 +++++++++---------- R/expose_stan_functions.R | 19 +++++---- R/misc.R | 13 ++++++ R/plugin.R | 6 +++ R/rstan.R | 16 +++++--- R/rstan_package_skeleton.R | 13 ++++-- R/stan_plot_helpers.R | 6 ++- R/stanfit-class.R | 6 +-- R/stanmodel-class.R | 74 ++++++++++++++++++++++++++++--------- build/vignette.rds |binary inst/NEWS | 13 ++++++ inst/doc/rstan_vignette.R | 6 +-- inst/doc/rstan_vignette.Rnw | 6 +-- inst/doc/rstan_vignette.pdf |binary man/rstan.Rd | 4 +- man/stan.Rd | 4 +- man/stanmodel-method-optimizing.Rd | 8 ++-- man/stanmodel-method-vb.Rd | 9 ++++ vignettes/rstan_vignette.Rnw | 6 +-- 20 files changed, 172 insertions(+), 83 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional
data, sea-level time series, coastline and topographic data, etc. Provides
specialized functions for calculating seawater properties such as potential
temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces
graphical displays that conform to the conventions of the Oceanographic literature.
Author: Dan Kelley [aut, cre],
Clark Richards [aut],
Chantelle Layton [ctb, cph] (curl() coauthor),
British Geological Survey [ctb, cph] (magnetic-field fortran
subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 0.9-17 dated 2015-05-22 and 0.9-18 dated 2016-02-11
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| 32 oce-0.9-18/oce/man/read.netcdf.Rd |only oce-0.9-18/oce/man/read.oce.Rd | 2 oce-0.9-18/oce/man/read.odf.Rd | 39 oce-0.9-18/oce/man/read.rsk.Rd |only oce-0.9-18/oce/man/read.sealevel.Rd | 16 oce-0.9-18/oce/man/read.section.Rd | 55 oce-0.9-18/oce/man/read.topo.Rd | 15 oce-0.9-18/oce/man/rescale.Rd | 4 oce-0.9-18/oce/man/resizableLabel.Rd | 55 oce-0.9-18/oce/man/rsk-class.Rd |only oce-0.9-18/oce/man/rsk.Rd |only oce-0.9-18/oce/man/rskPatm.Rd |only oce-0.9-18/oce/man/rskToc.Rd |only oce-0.9-18/oce/man/runlm.Rd | 3 oce-0.9-18/oce/man/satellite-class.Rd |only oce-0.9-18/oce/man/section-class.Rd | 5 oce-0.9-18/oce/man/sectionAddStation.Rd | 2 oce-0.9-18/oce/man/sectionGrid.Rd | 2 oce-0.9-18/oce/man/sectionSort.Rd | 2 oce-0.9-18/oce/man/shiftLongitude.Rd |only oce-0.9-18/oce/man/standardizeLongitude.Rd |only oce-0.9-18/oce/man/sub-sub-adp-method.Rd |only oce-0.9-18/oce/man/sub-sub-adv-method.Rd |only oce-0.9-18/oce/man/sub-sub-amsr-method.Rd |only oce-0.9-18/oce/man/sub-sub-argo-method.Rd 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| 32 oce-0.9-18/oce/man/swSigma0.Rd | 4 oce-0.9-18/oce/man/swSigmaT.Rd | 17 oce-0.9-18/oce/man/swSigmaTheta.Rd | 5 oce-0.9-18/oce/man/swSoundAbsorption.Rd | 5 oce-0.9-18/oce/man/swSoundSpeed.Rd | 24 oce-0.9-18/oce/man/swSpecificHeat.Rd | 20 oce-0.9-18/oce/man/swSpice.Rd | 43 oce-0.9-18/oce/man/swTFreeze.Rd | 49 oce-0.9-18/oce/man/swTSrho.Rd | 23 oce-0.9-18/oce/man/swThermalConductivity.Rd | 42 oce-0.9-18/oce/man/swTheta.Rd | 16 oce-0.9-18/oce/man/swViscosity.Rd | 24 oce-0.9-18/oce/man/tidedata.Rd | 2 oce-0.9-18/oce/man/tidem.Rd | 155 - oce-0.9-18/oce/man/topoWorld.Rd | 25 oce-0.9-18/oce/man/useHeading.Rd | 29 oce-0.9-18/oce/man/velocityStatistics.Rd | 2 oce-0.9-18/oce/man/webtide.Rd | 19 oce-0.9-18/oce/po/R-de.po | 10 oce-0.9-18/oce/po/R-es.po | 18 oce-0.9-18/oce/po/R-fr.po | 10 oce-0.9-18/oce/po/R-oce.pot | 10 oce-0.9-18/oce/po/R-zh.po | 10 oce-0.9-18/oce/src/amsr.c |only oce-0.9-18/oce/src/bin.cpp | 56 oce-0.9-18/oce/src/binmap.c | 51 oce-0.9-18/oce/src/coastline.c |only oce-0.9-18/oce/src/geod.c | 463 ++- oce-0.9-18/oce/src/magdec.f | 158 - oce-0.9-18/oce/src/map.c | 2 oce-0.9-18/oce/tests/colormap.R | 2 oce-0.9-18/oce/tests/testthat |only oce-0.9-18/oce/tests/testthat.R |only oce-0.9-18/oce/tests/tide.R | 2 oce-0.9-18/oce/vignettes/ctd-object.png |only oce-0.9-18/oce/vignettes/oce.Rmd |only 507 files changed, 11906 insertions(+), 7914 deletions(-)
Title: '--omics' Data Analysis Toolbox
Description: A collection of functions to analyse '--omics' datasets such as DNA
methylation and gene expression profiles.
Author: Gianluca Campanella [aut, cre]
Maintainer: Gianluca Campanella <gianluca@campanella.org>
Diff between omics versions 0.1-3 dated 2016-01-27 and 0.1-4 dated 2016-02-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/mlm.R | 5 +++++ R/mlmer.R | 11 ++++++++--- R/private.R | 4 ++-- inst/NEWS.Rd | 7 +++++++ 7 files changed, 33 insertions(+), 15 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.1.3 dated 2016-01-20 and 1.2.0 dated 2016-02-11
geoknife-1.1.3/geoknife/R/gcontent.R |only geoknife-1.2.0/geoknife/DESCRIPTION | 13 - geoknife-1.2.0/geoknife/MD5 | 76 +++++----- geoknife-1.2.0/geoknife/NAMESPACE | 5 geoknife-1.2.0/geoknife/R/00-gconfig.R |only geoknife-1.2.0/geoknife/R/01-webdata-obj.R | 16 ++ geoknife-1.2.0/geoknife/R/04-webprocess-obj.R | 63 +++----- geoknife-1.2.0/geoknife/R/algorithmVersion-webprocess.R | 6 geoknife-1.2.0/geoknife/R/check.R | 7 geoknife-1.2.0/geoknife/R/download-geojob.R | 4 geoknife-1.2.0/geoknife/R/geoknife-generic.R | 7 geoknife-1.2.0/geoknife/R/geoknifeUtils.R |only geoknife-1.2.0/geoknife/R/initializeProcessInputs.R | 26 +-- geoknife-1.2.0/geoknife/R/parseTimeseries.R | 1 geoknife-1.2.0/geoknife/R/processInputsToXML.R | 4 geoknife-1.2.0/geoknife/R/query-webdata-times.R | 4 geoknife-1.2.0/geoknife/R/query-webdata.R | 4 geoknife-1.2.0/geoknife/R/query-webgeom.R | 2 geoknife-1.2.0/geoknife/R/query-webprocess.R | 2 geoknife-1.2.0/geoknife/R/setProcessInputs.R | 18 +- geoknife-1.2.0/geoknife/R/show-webprocess.R | 1 geoknife-1.2.0/geoknife/R/start-geojob.R | 4 geoknife-1.2.0/geoknife/R/values-webgeom.R | 3 geoknife-1.2.0/geoknife/R/waitUntilFinished.R | 2 geoknife-1.2.0/geoknife/README.md | 60 ++++--- geoknife-1.2.0/geoknife/build/vignette.rds |binary geoknife-1.2.0/geoknife/inst/doc/geoknife.R | 5 geoknife-1.2.0/geoknife/inst/doc/geoknife.Rmd | 7 geoknife-1.2.0/geoknife/inst/doc/geoknife.html | 55 ++----- geoknife-1.2.0/geoknife/inst/doc/plot_geotiff.R |only geoknife-1.2.0/geoknife/inst/doc/plot_geotiff.Rmd |only geoknife-1.2.0/geoknife/inst/doc/plot_geotiff.html |only geoknife-1.2.0/geoknife/man/gconfig.Rd |only geoknife-1.2.0/geoknife/man/gcontent.Rd | 2 geoknife-1.2.0/geoknife/man/waitUntilFinished.Rd | 2 geoknife-1.2.0/geoknife/man/webprocess-class.Rd | 2 geoknife-1.2.0/geoknife/tests/testthat/test-gconfig.R |only geoknife-1.2.0/geoknife/tests/testthat/test-geoknife_setters.R | 2 geoknife-1.2.0/geoknife/tests/testthat/test-setJobState.R | 19 +- geoknife-1.2.0/geoknife/tests/testthat/test-sleep_time.R |only geoknife-1.2.0/geoknife/tests/testthat/test-waitUntilFinished.R | 1 geoknife-1.2.0/geoknife/tests/testthat/test-webprocess_object.R | 39 +++-- geoknife-1.2.0/geoknife/vignettes/geoknife.Rmd | 7 geoknife-1.2.0/geoknife/vignettes/plot_geotiff.Rmd |only 44 files changed, 260 insertions(+), 209 deletions(-)
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI: 10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI: 10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biran@iastate.edu>
Diff between ssizeRNA versions 1.1.2 dated 2015-05-12 and 1.2.4 dated 2016-02-11
DESCRIPTION | 36 +++++++-- MD5 | 33 +++++--- NAMESPACE | 15 +++ R/check.power.R | 145 ++++++++++++++++++++----------------- R/sim.counts.R | 125 ++++++++++++++++++++------------ R/ssize.twoSampVaryDelta.R | 147 ++++++++++++++++++++++---------------- R/ssizeRNA_single.R | 127 +++++++++++++++++++-------------- R/ssizeRNA_vary.R | 161 ++++++++++++++++++++++++------------------ build |only data |only inst |only man/check.power.Rd | 104 +++++++++++++++------------ man/hammer.eset.Rd |only man/sim.counts.Rd | 72 +++++++++++------- man/ssize.twoSampVaryDelta.Rd | 82 ++++++++++++--------- man/ssizeRNA_single.Rd | 96 ++++++++++++++----------- man/ssizeRNA_vary.Rd | 115 +++++++++++++++++------------- vignettes |only 18 files changed, 756 insertions(+), 502 deletions(-)
Title: Download or Upload 'Socrata' Data Sets
Description: Provides easier interaction with
Socrata open data portals http://dev.socrata.com.
Users can provide a 'Socrata' data set resource URL,
or a 'Socrata' Open Data API (SoDA) web query,
or a 'Socrata' "human-friendly" URL,
returns an R data frame. Converts dates to 'POSIX'
format and manages throttling by 'Socrata'.
Users can upload data to Socrata portals directly
from R.
Author: Hugh Devlin, Ph. D., Tom Schenk, Jr., and John Malc
Maintainer: "Tom Schenk Jr." <developers@cityofchicago.org>
Diff between RSocrata versions 1.6.2-10 dated 2015-07-13 and 1.7.0-14 dated 2016-02-11
DESCRIPTION | 20 +++--- MD5 | 23 ++++--- NAMESPACE | 4 + R/RSocrata.R | 134 +++++++++++++++++++++++++++++++++++++++++++--- README.md | 37 ++++++++++++ man/fieldName.Rd | 2 man/isFourByFour.Rd | 2 man/ls.socrata.Rd | 2 man/posixify.Rd | 2 man/read.socrata.Rd | 34 ++++++++--- man/validateUrl.Rd | 4 - man/write.socrata.Rd |only tests/testthat/test-all.R | 85 ++++++++++++++++++++++++++++- 13 files changed, 304 insertions(+), 45 deletions(-)
Title: Bayesian Analysis of Multivariate Counts Data in DNA
Metabarcoding and Ecology
Description: Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between MCMC.OTU versions 1.0.8 dated 2014-05-05 and 1.0.10 dated 2016-02-11
DESCRIPTION | 15 ++++++++------- MD5 | 10 +++++----- NAMESPACE | 9 ++++++++- R/mcmc.otu.R | 2 +- man/MCMC.OTU-package.Rd | 14 ++++++-------- man/mcmc.otu.Rd | 2 +- 6 files changed, 29 insertions(+), 23 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova <alku@dtu.dk>
Diff between lmerTest versions 2.0-29 dated 2015-07-16 and 2.0-30 dated 2016-02-11
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS |only R/utils.R | 8 ++++++-- tests/Examples/lmerTest-Ex.Rout.save | 8 ++++---- tests/envir.R | 9 +++++---- tests/packageExamplesExtra.Rout.save | 11 +++++------ tests/testKeep.Rout.save | 8 ++++---- tests/testRand.Rout.save | 8 ++++---- tests/testTVbo.Rout.save | 12 ++++++------ 10 files changed, 46 insertions(+), 41 deletions(-)
Title: Bayesian Nonparametric Latent-Class Capture-Recapture
Description: Bayesian population size estimation using non parametric latent-class models.
Author: Daniel Manrique-Vallier
Maintainer: Daniel Manrique-Vallier <dmanriqu@indiana.edu>
Diff between LCMCR versions 0.4 dated 2016-02-08 and 0.4.1 dated 2016-02-11
DESCRIPTION | 6 ++--- MD5 | 36 +++++++++++++++++------------------ R/Rcode.R | 2 + man/LCMCR-package.Rd | 4 +-- src/CData_DM.h | 6 ++--- src/NPLCM_CR_Basic_Freq.cpp | 16 +++++++++++---- src/NPLCM_CR_Basic_Freq.h | 14 ++++++------- src/R_Lcm_CR.cpp | 5 +--- src/daniel2/CChain.cpp | 4 +-- src/daniel2/CData.h | 7 ++++-- src/daniel2/CPar_Data_Type.h | 4 +-- src/daniel2/CParams_generic.h | 2 - src/daniel2/CVariable_Container.cpp | 24 ++++++++++++----------- src/daniel2/CVariable_Container.h | 14 ++++++------- src/daniel2/Model_Environ.h | 37 ++++++++++++++++++++++-------------- src/daniel2/R_Environ_Simple.cpp | 9 +++++--- src/daniel2/dan_array_utils.cpp | 23 ++++++++++++---------- src/daniel2/dan_array_utils.h | 4 +-- src/daniel2/dan_sys.h | 17 +++++++++++----- 19 files changed, 135 insertions(+), 99 deletions(-)
More information about customizedTraining at CRAN
Permanent link
Title: Correspondence Analysis Variants
Description: Provides six variants of two-way correspondence analysis (ca):
simple ca, singly ordered ca, doubly ordered ca, non-symmetrical ca,
singly ordered non symmetrical ca, and doubly ordered non symmetrical
ca.
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo <rosaria.lombardo@unina2.it>
Diff between CAvariants versions 3.0 dated 2015-09-11 and 3.1 dated 2016-02-11
CAvariants-3.0/CAvariants/R/cacorporateplus.R |only CAvariants-3.0/CAvariants/R/nsca.ellipse.R |only CAvariants-3.0/CAvariants/man/cacorporateplus-class.Rd |only CAvariants-3.0/CAvariants/man/nsca.ellipse.Rd |only CAvariants-3.1/CAvariants/DESCRIPTION | 6 CAvariants-3.1/CAvariants/MD5 | 88 ++--- CAvariants-3.1/CAvariants/NAMESPACE | 3 CAvariants-3.1/CAvariants/R/CAvariants.R | 104 ++++-- CAvariants-3.1/CAvariants/R/cabasic.R | 21 - CAvariants-3.1/CAvariants/R/cabasicresults.R | 4 CAvariants-3.1/CAvariants/R/caellipse.R | 129 ++++---- CAvariants-3.1/CAvariants/R/compsonetable.exe.R | 18 - CAvariants-3.1/CAvariants/R/compstable.exe.R | 57 ++- CAvariants-3.1/CAvariants/R/docabasic.R | 6 CAvariants-3.1/CAvariants/R/donscabasic.R | 15 CAvariants-3.1/CAvariants/R/nscabasic.R | 10 CAvariants-3.1/CAvariants/R/nscaellipse.R |only CAvariants-3.1/CAvariants/R/plot.CAvariants.R | 256 ++++++++--------- CAvariants-3.1/CAvariants/R/print.CAvariants.R | 212 ++++++++------ CAvariants-3.1/CAvariants/R/printwithaxes.R | 4 CAvariants-3.1/CAvariants/R/socabasic.R | 12 CAvariants-3.1/CAvariants/R/sonscabasic.R | 19 - CAvariants-3.1/CAvariants/R/summary.CAvariants.R | 93 +++--- CAvariants-3.1/CAvariants/data/asbestos.rda |binary CAvariants-3.1/CAvariants/data/shopdataM.rda |binary CAvariants-3.1/CAvariants/man/CAvariants.Rd | 13 CAvariants-3.1/CAvariants/man/angle.Rd | 5 CAvariants-3.1/CAvariants/man/asbestos.Rd | 2 CAvariants-3.1/CAvariants/man/cabasic.Rd | 2 CAvariants-3.1/CAvariants/man/cabasicresults-class.Rd | 12 CAvariants-3.1/CAvariants/man/caellipse.Rd | 172 +---------- CAvariants-3.1/CAvariants/man/compsonetable.exe.Rd | 2 CAvariants-3.1/CAvariants/man/compstable.exe.Rd | 2 CAvariants-3.1/CAvariants/man/docabasic.Rd | 2 CAvariants-3.1/CAvariants/man/donscabasic.Rd | 2 CAvariants-3.1/CAvariants/man/ellipse.Rd | 3 CAvariants-3.1/CAvariants/man/emerson.poly.Rd | 3 CAvariants-3.1/CAvariants/man/nscabasic.Rd | 2 CAvariants-3.1/CAvariants/man/nscaellipse.Rd |only CAvariants-3.1/CAvariants/man/plot.CAvariants.Rd | 20 - CAvariants-3.1/CAvariants/man/plotone.Rd | 2 CAvariants-3.1/CAvariants/man/print.CAvariants.Rd | 17 - CAvariants-3.1/CAvariants/man/printwithaxes.Rd | 5 CAvariants-3.1/CAvariants/man/shopdataM.Rd | 1 CAvariants-3.1/CAvariants/man/socabasic.Rd | 2 CAvariants-3.1/CAvariants/man/sonscabasic.Rd | 2 CAvariants-3.1/CAvariants/man/summary.CAvariants.Rd | 9 CAvariants-3.1/CAvariants/man/trendplot.Rd | 2 48 files changed, 657 insertions(+), 682 deletions(-)
Title: Pathway and Gene-Level Association Test
Description: Pathway and gene level association test using raw data or summary statistics.
Author: Han Zhang, Bill Wheeler, Kai Yu, Yifan Yang
Maintainer: Han Zhang <han.zhang2@nih.gov>
Diff between ARTP2 versions 0.9.21 dated 2016-02-11 and 0.9.22 dated 2016-02-11
ARTP2-0.9.21/ARTP2/R/pathway.rawData.R |only ARTP2-0.9.21/ARTP2/R/pathway.summaryData.R |only ARTP2-0.9.21/ARTP2/R/pathway.warm.start.R |only ARTP2-0.9.21/ARTP2/man/pathway.rawData.Rd |only ARTP2-0.9.21/ARTP2/man/pathway.summaryData.Rd |only ARTP2-0.9.21/ARTP2/man/pathway.warm.start.Rd |only ARTP2-0.9.22/ARTP2/DESCRIPTION | 12 ++++---- ARTP2-0.9.22/ARTP2/MD5 | 37 ++++++++++++------------- ARTP2-0.9.22/ARTP2/NAMESPACE | 5 +-- ARTP2-0.9.22/ARTP2/NEWS.md |only ARTP2-0.9.22/ARTP2/R/options.setup.R | 2 - ARTP2-0.9.22/ARTP2/R/rARTP.R |only ARTP2-0.9.22/ARTP2/R/sARTP.R |only ARTP2-0.9.22/ARTP2/R/validate.lambda.rawData.R | 2 - ARTP2-0.9.22/ARTP2/R/warm.start.R |only ARTP2-0.9.22/ARTP2/man/ARTP2-package.Rd | 12 ++++---- ARTP2-0.9.22/ARTP2/man/data.Rd | 2 - ARTP2-0.9.22/ARTP2/man/geno.Rd | 2 - ARTP2-0.9.22/ARTP2/man/options.Rd | 18 ++++++------ ARTP2-0.9.22/ARTP2/man/options.default.Rd | 2 - ARTP2-0.9.22/ARTP2/man/pathway.Rd | 2 - ARTP2-0.9.22/ARTP2/man/rARTP.Rd |only ARTP2-0.9.22/ARTP2/man/ref.geno.Rd | 4 +- ARTP2-0.9.22/ARTP2/man/sARTP.Rd |only ARTP2-0.9.22/ARTP2/man/subj.id.Rd | 2 - ARTP2-0.9.22/ARTP2/man/warm.start.Rd |only 26 files changed, 52 insertions(+), 50 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.1 dated 2016-01-05 and 1.0.2 dated 2016-02-11
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/entirelogprofilelikelihood.R | 6 ++---- 3 files changed, 8 insertions(+), 10 deletions(-)
Title: Reads, Annotates, and Normalizes Reverse Phase Protein Array
Data
Description: Reads in sample description and slide description files and
annotates the expression values taken from GenePix results files
(text file format used by many microarray scanner and software providers).
After normalization data can be visualized as boxplot, heatmap or dotplot.
Author: Heiko Mannsperger with contributions of Stephan Gade
Maintainer: Astrid Wachter <astrid.wachter@med.uni-goettingen.de>
Diff between RPPanalyzer versions 1.4.1 dated 2015-06-24 and 1.4.3 dated 2016-02-11
DESCRIPTION | 18 +++++++++--------- MD5 | 6 +++--- NAMESPACE | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary 4 files changed, 62 insertions(+), 13 deletions(-)
Title: Support Functions and Data for "Ecological Models and Data"
Description: Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).
Author: Ben Bolker
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between emdbook versions 1.3.8 dated 2015-05-01 and 1.3.9 dated 2016-02-11
emdbook-1.3.8/emdbook/NEWS |only emdbook-1.3.9/emdbook/DESCRIPTION | 12 ++++++------ emdbook-1.3.9/emdbook/MD5 | 13 ++++++------- emdbook-1.3.9/emdbook/NAMESPACE | 9 ++++++++- emdbook-1.3.9/emdbook/R/utils3d.R | 18 +++++++++++++++--- emdbook-1.3.9/emdbook/inst/NEWS.Rd | 9 +++++++++ emdbook-1.3.9/emdbook/man/contour3d.Rd | 2 ++ emdbook-1.3.9/emdbook/man/curve3d.Rd | 4 ++++ 8 files changed, 50 insertions(+), 17 deletions(-)
Title: Asymptotic Covariance Matrices of Some BSS Mixing and Unmixing
Matrix Estimates
Description: Functions to compute the asymptotic covariance matrices of mixing and unmixing matrix estimates of the following blind source separation (BSS) methods: symmetric and squared symmetric FastICA, regular and adaptive deflation-based FastICA, FOBI, JADE, AMUSE and deflation-based and symmetric SOBI. Also functions to estimate these covariances based on data are available.
Author: Jari Miettinen, Klaus Nordhausen, Hannu Oja, Sara Taskinen
Maintainer: Jari Miettinen <jari.p.miettinen@jyu.fi>
Diff between BSSasymp versions 1.1-1 dated 2015-08-17 and 1.1-2 dated 2016-02-11
DESCRIPTION | 8 +- MD5 | 24 +++++--- NAMESPACE | 2 R/FastICA_ascov2.R |only R/SOBI_ascov.R | 16 ++--- R/aSOBI.R |only R/eSOBI.R |only R/eSOBI_lags.R |only R/internals.R |only inst/ChangeLog | 17 ++++- man/ASCOV_SOBI.Rd | 16 ++++- man/ASCOV_SOBI_est.Rd | 20 ++++-- man/BSSasymp-package.Rd | 4 - man/aSOBI.Rd |only man/eSOBI.Rd |only man/eSOBI_lags.Rd |only src/SOBIasc.cpp | 138 +++++++++++++++++++++++++++++++++++++++++------- 17 files changed, 189 insertions(+), 56 deletions(-)
Title: Markov Beta and Gamma Processes for Modeling Hazard Rates
Description: Computes the hazard rate estimate as described by Nieto-Barajas and Walker (2002) and Nieto-Barajas (2003).
Author: L. E. Nieto-Barajas and J. A. Garcia Bueno
Maintainer: Jose Antonio Garcia Bueno <joseagbueno@gmail.com>
Diff between BGPhazard versions 1.2.2 dated 2015-03-17 and 1.2.3 dated 2016-02-11
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NAMESPACE | 5 +++++ build/vignette.rds |binary inst/doc/BGPhazard.pdf |binary man/BGPhazard-package.Rd | 4 ++-- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R.
This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker <bolker@mcmaster.ca>, R Development Core Team
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.17 dated 2014-05-27 and 1.0.18 dated 2016-02-11
DESCRIPTION | 14 +++--- MD5 | 32 +++++++------- NAMESPACE | 10 +++- R/mle.R | 4 - R/slice.R | 53 ++++++++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++ inst/doc/mle2.R | 109 +++++++----------------------------------------- inst/doc/mle2.Rnw | 2 inst/doc/mle2.pdf |binary inst/doc/quasi.R | 11 ---- inst/doc/quasi.pdf |binary man/mle2.Rd | 3 - man/slice.Rd | 7 ++- tests/grtest1.R | 2 tests/grtest1.Rout.save | 14 +++--- vignettes/mle2.Rnw | 2 17 files changed, 103 insertions(+), 166 deletions(-)
Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Author: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>.
Maintainer: Marc J. Mazerolle <marc.mazerolle@sbf.ulaval.ca>
Diff between AICcmodavg versions 2.0-3 dated 2015-01-16 and 2.0-4 dated 2016-02-11
AICcmodavg-2.0-3/AICcmodavg/R/AICcmodavg-deprecated.R |only AICcmodavg-2.0-3/AICcmodavg/R/Custom.functions.r |only AICcmodavg-2.0-3/AICcmodavg/R/boot.wt.r |only AICcmodavg-2.0-3/AICcmodavg/R/dictab.r |only AICcmodavg-2.0-3/AICcmodavg/R/extractCN.r |only AICcmodavg-2.0-3/AICcmodavg/R/modavgEffect.r |only AICcmodavg-2.0-3/AICcmodavg/R/xtable.r |only AICcmodavg-2.0-3/AICcmodavg/man/AICcmodavg-deprecated.Rd |only AICcmodavg-2.0-4/AICcmodavg/DESCRIPTION | 20 AICcmodavg-2.0-4/AICcmodavg/MD5 | 96 AICcmodavg-2.0-4/AICcmodavg/NAMESPACE | 123 AICcmodavg-2.0-4/AICcmodavg/R/AICc.R | 90 AICcmodavg-2.0-4/AICcmodavg/R/AICcmodavg-defunct.R |only AICcmodavg-2.0-4/AICcmodavg/R/Custom.functions.R |only AICcmodavg-2.0-4/AICcmodavg/R/Nmix.gof.test.R | 2 AICcmodavg-2.0-4/AICcmodavg/R/aictab.R | 174 AICcmodavg-2.0-4/AICcmodavg/R/boot.wt.R |only AICcmodavg-2.0-4/AICcmodavg/R/c_hat.R | 163 AICcmodavg-2.0-4/AICcmodavg/R/countDist.R |only AICcmodavg-2.0-4/AICcmodavg/R/countHist.R |only AICcmodavg-2.0-4/AICcmodavg/R/covDiag.R |only AICcmodavg-2.0-4/AICcmodavg/R/detHist.R |only AICcmodavg-2.0-4/AICcmodavg/R/dictab.R |only AICcmodavg-2.0-4/AICcmodavg/R/evidence.R | 2 AICcmodavg-2.0-4/AICcmodavg/R/extractCN.R |only AICcmodavg-2.0-4/AICcmodavg/R/importance.R | 6 AICcmodavg-2.0-4/AICcmodavg/R/mb.gof.test.R | 111 AICcmodavg-2.0-4/AICcmodavg/R/modavg.R | 31 AICcmodavg-2.0-4/AICcmodavg/R/modavgEffect.R |only AICcmodavg-2.0-4/AICcmodavg/R/modavgPred.R | 3688 +++++++++++---- AICcmodavg-2.0-4/AICcmodavg/R/modavgShrink.R | 136 AICcmodavg-2.0-4/AICcmodavg/R/multComp.R | 23 AICcmodavg-2.0-4/AICcmodavg/R/xtable.R |only AICcmodavg-2.0-4/AICcmodavg/data/fat.rda |only AICcmodavg-2.0-4/AICcmodavg/data/gpa.rda |only AICcmodavg-2.0-4/AICcmodavg/inst/NEWS | 46 AICcmodavg-2.0-4/AICcmodavg/man/AICc.Rd | 55 AICcmodavg-2.0-4/AICcmodavg/man/AICcCustom.Rd | 15 AICcmodavg-2.0-4/AICcmodavg/man/AICcmodavg-defunct.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/AICcmodavg-package.Rd | 89 AICcmodavg-2.0-4/AICcmodavg/man/aictab.Rd | 80 AICcmodavg-2.0-4/AICcmodavg/man/aictabCustom.Rd | 13 AICcmodavg-2.0-4/AICcmodavg/man/bullfrog.Rd | 8 AICcmodavg-2.0-4/AICcmodavg/man/c_hat.Rd | 62 AICcmodavg-2.0-4/AICcmodavg/man/confset.Rd | 39 AICcmodavg-2.0-4/AICcmodavg/man/countDist.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/countHist.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/covDiag.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/detHist.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/fam.link.mer.Rd | 2 AICcmodavg-2.0-4/AICcmodavg/man/fat.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/gpa.Rd |only AICcmodavg-2.0-4/AICcmodavg/man/importance.Rd | 41 AICcmodavg-2.0-4/AICcmodavg/man/mb.gof.test.Rd | 10 AICcmodavg-2.0-4/AICcmodavg/man/modavg.Rd | 121 AICcmodavg-2.0-4/AICcmodavg/man/modavgCustom.Rd | 19 AICcmodavg-2.0-4/AICcmodavg/man/modavgEffect.Rd | 98 AICcmodavg-2.0-4/AICcmodavg/man/modavgPred.Rd | 128 AICcmodavg-2.0-4/AICcmodavg/man/modavgShrink.Rd | 21 AICcmodavg-2.0-4/AICcmodavg/man/multComp.Rd | 48 AICcmodavg-2.0-4/AICcmodavg/man/newt.Rd | 7 AICcmodavg-2.0-4/AICcmodavg/man/tortoise.Rd | 21 AICcmodavg-2.0-4/AICcmodavg/man/xtable.Rd | 86 63 files changed, 4409 insertions(+), 1265 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.3.3-2 dated 2014-03-07 and 0.4 dated 2016-02-11
DESCRIPTION | 15 ++-- LICENSE | 14 +++- MD5 | 44 +++++++++---- NAMESPACE | 23 ++++++- R/extmat.R | 147 +++++++++++++++++++++++++++++++++++++++++---- R/propack_svd.R | 7 +- R/trlan.R | 44 ++++++++++++- inst/COPYRIGHTS |only man/eigen.Rd |only man/extmat-class.Rd |only man/extmat.Rd | 15 ++++ man/svd.Rd | 8 +- src/Makevars | 8 +- src/extmat.c | 128 ++++++++++++++++++++------------------- src/trlan/trlan.h | 11 +++ src/trlan/trlan_R.c | 16 ++-- src/trlan/trlcore.c | 12 +-- src/trlan/trlmap.c | 41 ++++++++++++ src/trlan/zdaxpy.c |only src/trlan/zdgemm.c |only src/trlan/zdgemv.c |only src/trlan/ztrl_comm_i.h |only src/trlan/ztrl_comm_none.c |only src/trlan/ztrlan.c |only src/trlan/ztrlan.h |only src/trlan/ztrlan_R.c |only src/trlan/ztrlan_i.h |only src/trlan/ztrlaux.c |only src/trlan/ztrlaux_i.h |only src/trlan/ztrlcore.c |only src/trlan/ztrlcore_i.h |only 31 files changed, 413 insertions(+), 120 deletions(-)
Title: Modelling Space Time AutoRegressive Moving Average (STARMA)
Processes
Description: Statistical functions to identify, estimate and diagnose a Space-Time AutoRegressive Moving Average (STARMA) model.
Author: Felix Cheysson
Maintainer: Felix Cheysson <felix@cheysson.fr>
Diff between starma versions 1.2 dated 2015-11-12 and 1.3 dated 2016-02-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 2 +- man/starma-package.Rd | 6 +++--- src/starma.cpp | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Data Transformation and Labelled Data Utility Functions
Description: Collection of miscellaneous utility functions (especially intended
for people coming from other statistical software packages like 'SPSS', and/
or who are new to R), supporting following common tasks: 1) Reading and writing
data between R and other statistical software packages like 'SPSS', 'SAS' or
'Stata' and working with labelled data; this includes easy ways to get and set
label attributes, to convert labelled vectors into factors (and vice versa),
or to deal with multiple declared missing values etc. 2) Data transformation
tasks like recoding, dichotomizing or grouping variables, setting and replacing
missing values. 3) Convenient functions to perform frequently used statistical
tests, or to calculate various commonly used statistical coefficients.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjmisc versions 1.4 dated 2016-01-13 and 1.5 dated 2016-02-11
DESCRIPTION | 13 - MD5 | 55 ++--- NAMESPACE | 277 ++++++++++++++------------ NEWS | 14 + NEWS.md |only R/S3-methods.R | 101 +++++---- R/converge_ok.R | 3 R/get_labels.R | 522 ++++++++++++++++++++++++-------------------------- R/group_str.R | 3 R/helpfunctions.R | 50 ---- R/mean_n.R | 167 +++++++-------- R/mwu.R | 6 R/pseudo_r2.R | 5 R/read_write.R | 4 R/se.R | 1 R/set_na.R | 488 +++++++++++++++++++++++----------------------- R/std_b.R | 43 +++- R/str_pos.R | 1 R/to_dummy.R | 224 ++++++++++----------- R/to_long.R |only R/word_wrap.R | 129 ++++++------ README.md | 97 ++++----- man/efc.Rd | 68 +++--- man/get_labels.Rd | 4 man/is_empty.Rd | 102 ++++----- man/mean_n.Rd | 5 man/sjmisc-package.Rd | 4 man/std_beta.Rd | 14 + man/to_dummy.Rd | 96 ++++----- man/to_long.Rd |only 30 files changed, 1265 insertions(+), 1231 deletions(-)
Title: R Interface to X-13-ARIMA-SEATS
Description: Easy-to-use interface to X-13-ARIMA-SEATS, the
seasonal adjustment software by the US Census Bureau. It offers full
access to almost all options and outputs of X-13, including X-11 and SEATS,
automatic ARIMA model search, outlier detection and support for user
defined holiday variables, such as Chinese New Year or Indian Diwali. It
also includes a Shiny-based graphical user interface. Seasonal uses the
X-13 binaries from the 'x13binary' package.
Author: Christoph Sax
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between seasonal versions 1.2.0 dated 2016-01-28 and 1.2.1 dated 2016-02-11
DESCRIPTION | 8 ++--- MD5 | 16 +++++------ NEWS | 71 +++++++++++++++++---------------------------------- R/checkX13.R | 5 +-- R/seas.R | 5 +++ R/startup.R | 11 +++++++ README.md | 11 +++---- inst/doc/seas.pdf |binary vignettes/README.tex | 27 ++++++++++++------- 9 files changed, 76 insertions(+), 78 deletions(-)
Title: Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Description: A method for obtain nonparametric estimates of regression models
with or without factor-by-curve interactions using local polynomial
kernel smoothers. Additionally, a parametric model (allometric model)
can be estimated.
Author: Marta Sestelo [aut, cre],
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between npregfast versions 1.0.1 dated 2015-11-16 and 1.2.0 dated 2016-02-11
npregfast-1.0.1/npregfast/src/norm.c |only npregfast-1.2.0/npregfast/DESCRIPTION | 10 npregfast-1.2.0/npregfast/MD5 | 38 +- npregfast-1.2.0/npregfast/NAMESPACE | 3 npregfast-1.2.0/npregfast/NEWS | 5 npregfast-1.2.0/npregfast/R/allotest.R | 7 npregfast-1.2.0/npregfast/R/frfast.R | 9 npregfast-1.2.0/npregfast/R/globaltest.R | 7 npregfast-1.2.0/npregfast/R/localtest.R | 8 npregfast-1.2.0/npregfast/R/npregfast-package.R | 7 npregfast-1.2.0/npregfast/R/plot.frfast.R | 304 +++++++++--------- npregfast-1.2.0/npregfast/R/plotdiff.R | 385 +++++++++++++++++------- npregfast-1.2.0/npregfast/R/predict.frfast.R | 6 npregfast-1.2.0/npregfast/R/runExample.R |only npregfast-1.2.0/npregfast/README.md |only npregfast-1.2.0/npregfast/inst |only npregfast-1.2.0/npregfast/man/npregfast.Rd | 7 npregfast-1.2.0/npregfast/man/plot.frfast.Rd | 36 +- npregfast-1.2.0/npregfast/man/plotdiff.Rd | 32 - npregfast-1.2.0/npregfast/man/runExample.Rd |only npregfast-1.2.0/npregfast/src/program2.f90 | 62 ++- 21 files changed, 574 insertions(+), 352 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-22 0.1.1
2014-03-09 0.1
Title: Taxonomic Standardization of Plant Species Names
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using 'The Plant List' website (www.theplantlist.org).
Author: Luis Cayuela, Jari Oksanen
Maintainer: Luis Cayuela <luis.cayuela@urjc.es>
Diff between Taxonstand versions 1.7 dated 2014-12-15 and 1.8 dated 2016-02-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/TPLck.R | 2 +- man/TPL.Rd | 20 ++++++++++++-------- man/TPLck.Rd | 5 +++-- 6 files changed, 26 insertions(+), 20 deletions(-)
Title: Capture the Genes and Variants Related to a Genetic Disease from
Public Databases
Description: Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, http://human-phenotype-ontology.github.io/about.html), Orphanet (http://www.orpha.net/consor/cgi-bin/index.php), OMIM (Online Mendelian Inheritance in Man, http://www.omim.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), and Uniprot (Universal Protein Resource, http://www.uniprot.org) and Pubmed. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Uniprot focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the Uniprot are manually curated from UniProtKB/Swiss-Prot.
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu@gmail.com>
Diff between VarfromPDB versions 1.1.0 dated 2015-12-21 and 2.0.5 dated 2016-02-11
DESCRIPTION | 15 +++++++++------ MD5 | 17 ++++++++++++----- NAMESPACE | 24 +++++++++++++++++++++++- R/extract_pubmed.R |only R/genes_add_pubmed.R |only R/sysdata.rda |only data |only inst/doc/VarfromPDB.pdf |binary man/aa.Rd |only man/extract_omim.Rd | 2 +- man/extract_pubmed.Rd |only man/genes_add_pubmed.Rd |only man/genes_compile.Rd | 26 +++++++++++++------------- 13 files changed, 58 insertions(+), 26 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigenfunctions by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data.
Author: Wen-Ting Wang and Hsin-Cheng Huang
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.1.0.0 dated 2015-11-01 and 1.1.1.0 dated 2016-02-11
SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal4.Rd |only SpatPCA-1.1.0.0/SpatPCA/man/SpatPCAinternal5.Rd |only SpatPCA-1.1.0.0/SpatPCA/man/covfn.Rd |only SpatPCA-1.1.1.0/SpatPCA/DESCRIPTION | 8 SpatPCA-1.1.1.0/SpatPCA/MD5 | 25 SpatPCA-1.1.1.0/SpatPCA/NAMESPACE | 1 SpatPCA-1.1.1.0/SpatPCA/R/RcppExports.R | 12 SpatPCA-1.1.1.0/SpatPCA/R/SpatPCA.R | 213 ++----- SpatPCA-1.1.1.0/SpatPCA/man/SpatPCA-package.Rd | 6 SpatPCA-1.1.1.0/SpatPCA/man/SpatPCAinternal1.Rd | 7 SpatPCA-1.1.1.0/SpatPCA/man/SpatPCAinternal2.Rd | 7 SpatPCA-1.1.1.0/SpatPCA/man/SpatPCAinternal3.Rd | 4 SpatPCA-1.1.1.0/SpatPCA/man/spatpca.Rd | 50 + SpatPCA-1.1.1.0/SpatPCA/src/RcppExports.cpp | 43 - SpatPCA-1.1.1.0/SpatPCA/src/rcpp_SpatPCA.cpp | 644 +++++++++++++++++------- 15 files changed, 602 insertions(+), 418 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.8.0 dated 2015-12-14 and 1.8.2 dated 2016-02-11
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/build.dist.struct.R | 1 + R/rcbalance-internal.R | 1 - R/rcbalance.R | 3 ++- man/rcbalance-package.Rd | 14 ++++++++------ man/rcbalance.Rd | 4 +--- tests/testthat/test-exclude_treated.R | 14 ++++++++++++++ 8 files changed, 38 insertions(+), 23 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return coda mcmc objects that can then be summarized
using the coda package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.3-3 dated 2013-05-01 and 1.3-4 dated 2016-02-11
MCMCpack-1.3-3/MCMCpack/HISTORY |only MCMCpack-1.3-3/MCMCpack/R/MCMCintervention.R |only MCMCpack-1.3-3/MCMCpack/man/MCMCintervention.Rd |only MCMCpack-1.3-3/MCMCpack/man/plotIntervention.Rd |only MCMCpack-1.3-3/MCMCpack/src/MCMCintervention.cc |only MCMCpack-1.3-3/MCMCpack/src/Makevars |only MCMCpack-1.3-4/MCMCpack/DESCRIPTION | 26 ++-- MCMCpack-1.3-4/MCMCpack/MD5 | 114 +++++++++---------- MCMCpack-1.3-4/MCMCpack/NAMESPACE | 24 ++-- MCMCpack-1.3-4/MCMCpack/R/BayesFactors.R | 11 + MCMCpack-1.3-4/MCMCpack/R/MCMCdynamicIRT1d-b.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCdynamicIRT1d.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCirt1d.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCirtHier1d.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCirtKdRob.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCmetrop1R.R | 15 +- MCMCpack-1.3-4/MCMCpack/R/MCMCmixfactanal.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCordfactanal.R | 2 MCMCpack-1.3-4/MCMCpack/R/MCMCprobit.R | 2 MCMCpack-1.3-4/MCMCpack/R/testpanelSubjectBreak.R | 2 MCMCpack-1.3-4/MCMCpack/cleanup | 2 MCMCpack-1.3-4/MCMCpack/man/HMMpanelFE.Rd | 18 +-- MCMCpack-1.3-4/MCMCpack/man/HMMpanelRE.Rd | 6 - MCMCpack-1.3-4/MCMCpack/man/MCMCSVDreg.Rd | 8 - MCMCpack-1.3-4/MCMCpack/man/MCMCbinaryChange.Rd | 24 ++-- MCMCpack-1.3-4/MCMCpack/man/MCMCdynamicEI.Rd | 13 +- MCMCpack-1.3-4/MCMCpack/man/MCMCfactanal.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMChierEI.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMChlogit.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMChpoisson.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMChregress.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCirt1d.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCirtHier1d.Rd | 16 +- MCMCpack-1.3-4/MCMCpack/man/MCMCirtKd.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCirtKdHet.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCirtKdRob.Rd | 11 + MCMCpack-1.3-4/MCMCpack/man/MCMClogit.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCmetrop1R.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCmixfactanal.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCmnl.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCoprobit.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCoprobitChange.Rd | 15 +- MCMCpack-1.3-4/MCMCpack/man/MCMCordfactanal.Rd | 7 - MCMCpack-1.3-4/MCMCpack/man/MCMCpoisson.Rd | 8 - MCMCpack-1.3-4/MCMCpack/man/MCMCpoissonChange.Rd | 4 MCMCpack-1.3-4/MCMCpack/man/MCMCprobit.Rd | 8 - MCMCpack-1.3-4/MCMCpack/man/MCMCprobitChange.Rd | 2 MCMCpack-1.3-4/MCMCpack/man/MCMCquantreg.Rd | 8 - MCMCpack-1.3-4/MCMCpack/man/MCMCregress.Rd | 10 + MCMCpack-1.3-4/MCMCpack/man/MCMCregressChange.Rd | 23 ++- MCMCpack-1.3-4/MCMCpack/man/MCMCtobit.Rd | 9 - MCMCpack-1.3-4/MCMCpack/man/PErisk.Rd | 4 MCMCpack-1.3-4/MCMCpack/man/Rehnquist.Rd | 2 MCMCpack-1.3-4/MCMCpack/man/SSVSquantreg.Rd | 10 + MCMCpack-1.3-4/MCMCpack/man/Senate.Rd | 2 MCMCpack-1.3-4/MCMCpack/man/SupremeCourt.Rd | 2 MCMCpack-1.3-4/MCMCpack/man/plotChangepoint.Rd | 2 MCMCpack-1.3-4/MCMCpack/man/plotState.Rd | 5 MCMCpack-1.3-4/MCMCpack/man/testpanelGroupBreak.Rd | 6 - MCMCpack-1.3-4/MCMCpack/man/testpanelSubjectBreak.Rd | 11 - MCMCpack-1.3-4/MCMCpack/src/MCMCregressChange.cc | 4 61 files changed, 288 insertions(+), 251 deletions(-)
Title: Extensible Package for Parallel, Batch Training of Base Learners
for Ensemble Modeling
Description: Extensible S4 classes and methods for batch training of regression and classification algorithms such as Random Forest, Gradient Boosting Machine, Neural Network, Support Vector Machines, K-Nearest Neighbors, Penalized Regression (L1/L2), and Bayesian Additive Regression Trees. These algorithms constitute a set of 'base learners', which can subsequently be combined together to form ensemble predictions. This package provides cross-validation wrappers to allow for downstream application of ensemble integration techniques, including best-error selection. All base learner estimation objects are retained, allowing for repeated prediction calls without the need for re-training. For large problems, an option is provided to save estimation objects to disk, along with prediction methods that utilize these objects. This allows users to train and predict with large ensembles of base learners without being constrained by system RAM.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.mahani@sentrana.com>
Diff between EnsembleBase versions 1.0.0 dated 2016-01-18 and 1.0.1 dated 2016-02-11
ChangeLog | 25 ++++++++++++++----------- DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/regression_bart.R | 2 +- R/regression_gbm.R | 2 +- R/regression_knn.R | 2 +- R/regression_nnet.R | 2 +- R/regression_penreg.R | 2 +- R/regression_rf.R | 2 +- R/regression_svm.R | 2 +- 10 files changed, 34 insertions(+), 31 deletions(-)