Title: Intermittent Time Series Forecasting
Description: Functions for analysing and forecasting intermittent demand/slow moving items time series.
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes <n.kourentzes@lancaster.ac.uk>
Diff between tsintermittent versions 1.8 dated 2015-09-24 and 1.9 dated 2016-03-10
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/crost.R | 25 ++++++++++++++++++++----- R/crost.ma.R | 30 +++++++++++++++++++++++------- man/crost.Rd | 1 + man/crost.ma.Rd | 1 + 7 files changed, 59 insertions(+), 22 deletions(-)
More information about tsintermittent at CRAN
Permanent link
Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>
Diff between tablaxlsx versions 1.0.6 dated 2016-02-23 and 1.0.8 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/escribirTabla.R | 17 ++++++++++++++--- data/estilosDGE.rda |binary inst/img/logoJMR.png |binary 5 files changed, 22 insertions(+), 11 deletions(-)
Title: Sparse Bayesian Models for Regression, Subgroup Analysis, and
Panel Data
Description: Sparse modeling provides a mean selecting a small number of non-zero effects from a large possible number of candidate effects. This package includes a suite of methods for sparse modeling: estimation via EM or MCMC, approximate confidence intervals with nominal coverage, and diagnostic and summary plots. The method can implement sparse linear regression and sparse probit regression. Beyond regression analyses, applications include subgroup analysis, particularly for conjoint experiments, and panel data. Future versions will include extensions to models with truncated outcomes, propensity score, and instrumental variable analysis.
Author: Marc Ratkovic and Dustin Tingley
Maintainer: Marc Ratkovic <ratkovic@princeton.edu>
Diff between sparsereg versions 1.1 dated 2015-10-01 and 1.2 dated 2016-03-10
ChangeLog | 3 DESCRIPTION | 10 +- MD5 | 16 ++-- NAMESPACE | 3 R/cleandata.R | 35 ++++++++++ R/subgroup.R | 158 ++++++++++++++++++++++++++++++++++------------ R/utility.R | 6 + man/sparsereg-internal.Rd | 1 man/sparsereg.Rd | 32 +++++---- 9 files changed, 193 insertions(+), 71 deletions(-)
Title: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies <tdavies@maths.otago.ac.nz>
Diff between sparr versions 0.3-7 dated 2015-09-17 and 0.3-8 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/tolerance.R | 2 ++ R/zzz.R | 2 +- man/sparr-package.Rd | 4 ++-- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Read and Write 'SAS' 'XPORT' Files
Description: Functions for reading, listing
the contents of, and writing 'SAS' 'xport' format files.
The functions support reading and writing of either
individual data frames or sets of data frames. Further,
a mechanism has been provided for customizing how
variables of different data types are stored.
Author: Unless otherwise noted, the contents of this package were written by
Gregory R. Warnes <greg@warnes.net> and are provided under the
terms of the GNU General Public License, version 2.0 or later.
--
The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from
BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John
Muuss, Copyright (c) 2004-2007 United States Government as
represented by the U.S. Army Research Laboratory, and is utilized
and redistributed under the terms of the GNU Lesser General Public
License, version 2.1.
--
The files 'R/AFirst.lib.s', 'R/all.is.numeric.R',
'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R',
'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the
'Hmisc' package created by Frank E. Harrell, Jr.
<f.harrell@vanderbilt.edu>, and are utilized and redistributed under
the terms of the GNU General Public License, version 2.0 or later.
--
The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and
'src/foreign.h' are copied or adapted from the 'R' 'foreign' package
created by Douglas M. Bates <bates@stat.wisc.edu> and Saikat DebRoy
<saikat@stat.wisc.edu>, and are utilized and redistributed under the
terms of the GNU General Public License, version 2.0 or later.
--
The creation of this package was partially funded by Metrum Institute
<http://metruminstitute.org>.
Maintainer: Gabor Csardi <gcsardi@mango-solutions.com>
Diff between SASxport versions 1.5.2 dated 2016-02-15 and 1.5.3 dated 2016-03-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/read.xport.R | 2 +- man/read.xport.Rd | 6 ++++++ 5 files changed, 16 insertions(+), 8 deletions(-)
Title: Probability of Sharing Rare Variants among Relatives
Description: Computes estimates of the probability of related individuals sharing a rare variant.
Author: Alexandre Bureau, Ingo Ruczinski, Samuel G. Younkin
Maintainer: Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>
Diff between RVsharing versions 1.3.4 dated 2015-05-11 and 1.4.0 dated 2016-03-10
DESCRIPTION | 11 ++++---- MD5 | 68 +++++++++++++++++++++++++++++++++++++++++++++----- NAMESPACE | 3 +- R/RVgene.R |only R/extract_carriers.R |only R/ped2trio.R | 32 ++++++++++++++--------- R/pvalue_functions.R |only data/ex.ped.mat.RData |only inst |only man/GeneDropSim.fn.Rd | 6 ++-- man/RVgene.Rd |only man/RVsharing.Rd | 2 - man/ex.ped.mat.Rd |only man/get.psubset.Rd |only man/ped.list.Rd | 2 - 15 files changed, 95 insertions(+), 29 deletions(-)
Title: Friendly Regular Expressions
Description: A friendly interface for the construction of regular expressions.
Author: Kevin Ushey [aut],
Jim Hester [aut, cre],
Robert Krzyzanowski [aut]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between rex versions 1.0.1 dated 2015-04-27 and 1.1.1 dated 2016-03-10
rex-1.0.1/rex/inst/doc/stackoverflow.R |only rex-1.0.1/rex/inst/doc/stackoverflow.Rmd |only rex-1.0.1/rex/inst/doc/stackoverflow.html |only rex-1.0.1/rex/tests/testthat/test-zzz.R |only rex-1.0.1/rex/vignettes/stackoverflow.Rmd |only rex-1.1.1/rex/DESCRIPTION | 10 - rex-1.1.1/rex/LICENSE | 2 rex-1.1.1/rex/MD5 | 65 +++---- rex-1.1.1/rex/NAMESPACE | 2 rex-1.1.1/rex/NEWS.md |only rex-1.1.1/rex/R/match.R | 4 rex-1.1.1/rex/R/shortcuts.R | 23 ++ rex-1.1.1/rex/R/utils.R | 2 rex-1.1.1/rex/R/zzz.R | 6 rex-1.1.1/rex/build/vignette.rds |binary rex-1.1.1/rex/man/as.regex.Rd | 2 rex-1.1.1/rex/man/capture.Rd | 28 --- rex-1.1.1/rex/man/character_class.Rd | 23 -- rex-1.1.1/rex/man/character_class_escape.Rd | 2 rex-1.1.1/rex/man/counts.Rd | 25 -- rex-1.1.1/rex/man/escape.Rd | 2 rex-1.1.1/rex/man/group.Rd | 27 --- rex-1.1.1/rex/man/lookarounds.Rd | 24 -- rex-1.1.1/rex/man/not.Rd | 27 --- rex-1.1.1/rex/man/or.Rd | 27 --- rex-1.1.1/rex/man/pipe.Rd | 2 rex-1.1.1/rex/man/re_matches.Rd | 2 rex-1.1.1/rex/man/re_substitutes.Rd | 2 rex-1.1.1/rex/man/regex.Rd | 2 rex-1.1.1/rex/man/register_shortcuts.Rd | 2 rex-1.1.1/rex/man/rex.Rd | 27 --- rex-1.1.1/rex/man/rex_mode.Rd | 2 rex-1.1.1/rex/man/shortcuts.Rd | 245 +++++++++++++--------------- rex-1.1.1/rex/man/single_shortcuts.Rd | 40 ++-- rex-1.1.1/rex/man/wildcards.Rd | 23 -- rex-1.1.1/rex/vignettes/log_parsing.Rmd | 2 rex-1.1.1/rex/vignettes/stackoverflow.R |only 37 files changed, 270 insertions(+), 380 deletions(-)
Title: A Simple General Purpose N-Gram Tokenizer
Description: A simple n-gram (contiguous sequences of n items from a
given sequence of text) tokenizer to be used with the 'tm' package with no
'rJava'/'RWeka' dependency.
Author: Chung-hong Chan <chainsawtiney@gmail.com>
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between ngramrr versions 0.1.1 dated 2015-04-06 and 0.2.0 dated 2016-03-10
DESCRIPTION | 17 ++++++++++------- MD5 | 12 ++++++++---- NAMESPACE | 5 ++++- R/dtm2.R |only R/ngramrr.R | 12 ++++++++---- README.md |only man/dtmwrappers.Rd |only man/ngramrr.Rd | 4 ++-- tests/testthat/test_charngram.R |only 9 files changed, 32 insertions(+), 18 deletions(-)
Title: Replicate and Analyse InterVA4
Description: Provides an R version of the InterVA4 software for
coding cause of death from verbal autopsies. It also provides simple
graphical representation of individual and population level statistics.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InterVA4 versions 1.7 dated 2016-03-03 and 1.7.1 dated 2016-03-10
DESCRIPTION | 8 +-- MD5 | 12 ++--- R/InterVA.plot.R | 105 ++++++++++++++++++++++++++++++++-------------- R/InterVA.summary.r | 12 +++-- man/CSMF.Rd | 8 +-- man/Population.summary.Rd | 6 +- man/summary.interVA.Rd | 5 +- 7 files changed, 104 insertions(+), 52 deletions(-)
Title: Probabilistic Verbal Autopsy Coding with InSilicoVA
Description: Computes individual causes of death and population cause-specific mortality fractions using the 'InSilicoVA' algorithm. It uses data derived from verbal autopsy (VA) interviews, in a format similar to the input of the widely used 'InterVA4' method. This package provides general model fitting and customization for 'InSilicoVA' algorithm and basic graphical visualization of the output.
Author: Zehang Li, Tyler McCormick, Sam Clark
Maintainer: Zehang Li <lizehang@uw.edu>
Diff between InSilicoVA versions 1.0 dated 2015-12-04 and 1.1 dated 2016-03-10
InSilicoVA-1.0/InSilicoVA/R/insilico_java.r |only InSilicoVA-1.0/InSilicoVA/R/insilico_java2.r |only InSilicoVA-1.0/InSilicoVA/R/insilico_java3.r |only InSilicoVA-1.0/InSilicoVA/man/insilico.dev.Rd |only InSilicoVA-1.1/InSilicoVA/DESCRIPTION | 10 InSilicoVA-1.1/InSilicoVA/MD5 | 61 ++-- InSilicoVA-1.1/InSilicoVA/NAMESPACE | 10 InSilicoVA-1.1/InSilicoVA/R/diag.r | 12 InSilicoVA-1.1/InSilicoVA/R/extct_prob.r |only InSilicoVA-1.1/InSilicoVA/R/get_indiv.r |only InSilicoVA-1.1/InSilicoVA/R/groupplot.r |only InSilicoVA-1.1/InSilicoVA/R/indivplot.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_core.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_standard.r |only InSilicoVA-1.1/InSilicoVA/R/insilico_train.r |only InSilicoVA-1.1/InSilicoVA/R/phy_debias.r | 14 - InSilicoVA-1.1/InSilicoVA/R/plot.r | 73 ++--- InSilicoVA-1.1/InSilicoVA/R/print_insilico.r | 4 InSilicoVA-1.1/InSilicoVA/R/print_insilico_summary.r | 86 +++--- InSilicoVA-1.1/InSilicoVA/R/report.r | 41 ++- InSilicoVA-1.1/InSilicoVA/R/zzz.R | 2 InSilicoVA-1.1/InSilicoVA/data/RandomPhysician.rda |binary InSilicoVA-1.1/InSilicoVA/data/RandomVA1.rda |binary InSilicoVA-1.1/InSilicoVA/data/RandomVA2.rda |binary InSilicoVA-1.1/InSilicoVA/data/SampleCategory.rda |binary InSilicoVA-1.1/InSilicoVA/data/condprobnum.rda |only InSilicoVA-1.1/InSilicoVA/inst/java/Insilico.jar |binary InSilicoVA-1.1/InSilicoVA/man/RandomVA1.Rd | 11 InSilicoVA-1.1/InSilicoVA/man/RandomVA2.rd | 7 InSilicoVA-1.1/InSilicoVA/man/condprobnum.Rd |only InSilicoVA-1.1/InSilicoVA/man/csmf.diag.Rd | 14 - InSilicoVA-1.1/InSilicoVA/man/extract.prob.Rd |only InSilicoVA-1.1/InSilicoVA/man/get.indiv.Rd |only InSilicoVA-1.1/InSilicoVA/man/indivplot.Rd |only InSilicoVA-1.1/InSilicoVA/man/insilico.Rd | 241 ++++++++++++------- InSilicoVA-1.1/InSilicoVA/man/insilico.fit.Rd |only InSilicoVA-1.1/InSilicoVA/man/insilico.train.Rd |only InSilicoVA-1.1/InSilicoVA/man/physician_debias.Rd | 4 InSilicoVA-1.1/InSilicoVA/man/plot.insilico.Rd | 71 ++--- InSilicoVA-1.1/InSilicoVA/man/stackplot.Rd |only InSilicoVA-1.1/InSilicoVA/man/summary.insilico.Rd | 14 - 41 files changed, 397 insertions(+), 278 deletions(-)
Title: Functions to Automate Downloading Geospatial Data Available from
Several Federated Data Sources
Description: Functions to automate downloading geospatial data available from
several federated data sources (mainly sources maintained by the US Federal
government). Currently, the package allows for retrieval of five datasets:
The National Elevation Dataset digital elevation models (1 and 1/3 arc-second;
USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic
(SSURGO) database from the National Cooperative Soil Survey (NCSS), which is
led by the Natural Resources Conservation Service (NRCS) under the USDA; the
Global Historical Climatology Network (GHCN), coordinated by National Climatic
Data Center at NOAA; and the International Tree Ring Data Bank. Additional
data sources are in the works, including global DEM resources (ETOPO1, ETOPO5,
ETOPO30, SRTM), global soils (HWSD), MODIS satellite data products, the National
Atlas (US), Natural Earth, PRISM, and WorldClim.
Author: R. Kyle Bocinsky [aut, cre], Dylan Beaudette [ctb], Scott Chamberlain [ctb]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Diff between FedData versions 2.0.7 dated 2016-03-02 and 2.0.8 dated 2016-03-10
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/FedDataTester.R | 3 ++- man/FedData-package.Rd | 4 ++-- 4 files changed, 13 insertions(+), 12 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin <davidbolin@gmail.com> and Finn Lindgren <finn.lindgren@gmail.com>
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.0.16 dated 2015-02-09 and 2.1.1 dated 2016-03-10
excursions-2.0.16/excursions/README.md |only excursions-2.1.1/excursions/DESCRIPTION | 13 excursions-2.1.1/excursions/MD5 | 53 - excursions-2.1.1/excursions/NAMESPACE | 32 excursions-2.1.1/excursions/R/contourmap.R | 37 - excursions-2.1.1/excursions/R/contourmap.inla.R | 2 excursions-2.1.1/excursions/R/contourutil.R | 210 +++++ excursions-2.1.1/excursions/R/excursions.R | 24 excursions-2.1.1/excursions/R/excursions.inla.R | 4 excursions-2.1.1/excursions/R/gaussint.R | 22 excursions-2.1.1/excursions/R/geometry.R | 357 ++++++---- excursions-2.1.1/excursions/R/inlautils.R | 15 excursions-2.1.1/excursions/R/interface.mc.R |only excursions-2.1.1/excursions/R/simconf.R | 43 - excursions-2.1.1/excursions/R/simconf.inla.R | 41 - excursions-2.1.1/excursions/R/simconf.mixture.R | 76 +- excursions-2.1.1/excursions/R/utils.R | 216 +++++- excursions-2.1.1/excursions/man/continuous.Rd | 12 excursions-2.1.1/excursions/man/contourmap.Rd | 3 excursions-2.1.1/excursions/man/contourmap.inla.Rd | 2 excursions-2.1.1/excursions/man/contourmap.mc.Rd |only excursions-2.1.1/excursions/man/excursions.mc.Rd |only excursions-2.1.1/excursions/man/simconf.inla.Rd | 2 excursions-2.1.1/excursions/man/simconf.mc.Rd |only excursions-2.1.1/excursions/man/simconf.mixture.Rd | 2 excursions-2.1.1/excursions/man/submesh.grid.Rd |only excursions-2.1.1/excursions/man/submesh.mesh.Rd |only excursions-2.1.1/excursions/src/CAMD/Source/Makefile | 2 excursions-2.1.1/excursions/src/SuiteSparse_config/Makefile | 2 excursions-2.1.1/excursions/tests/testthat/helper-data.R | 2 excursions-2.1.1/excursions/tests/testthat/test.integration.R | 18 31 files changed, 922 insertions(+), 268 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and manipulation
utilities.
Author: Lahti Leo [aut, cre],
Biecek Przemyslaw [aut],
Kainu Markus [aut],
Huovari Janne [aut]
Maintainer: Lahti Leo <louhos@googlegroups.com>
Diff between eurostat versions 1.2.13 dated 2016-01-19 and 1.2.21 dated 2016-03-10
DESCRIPTION | 12 MD5 | 43 +- NAMESPACE | 1 R/get_eurostat.R | 117 ++++-- R/get_eurostat_json.R |only R/get_eurostat_raw.R | 4 R/label_eurostat.R | 5 R/tidy_eurostat.R | 44 +- README.md | 12 inst/doc/eurostat_tutorial.R | 28 + inst/doc/eurostat_tutorial.Rmd | 71 ++- inst/doc/eurostat_tutorial.pdf |binary man/convert_time_col.Rd |only man/get_eurostat.Rd | 65 ++- man/get_eurostat_json.Rd |only man/get_eurostat_raw.Rd | 4 man/label_eurostat.Rd | 4 tests/testthat/test-all.R | 14 vignettes/2015-RJournal/lahti-huovari-kainu-biecek.tex | 8 vignettes/eurostat_tutorial.Rmd | 71 ++- vignettes/eurostat_tutorial.html | 326 ++++++++++++----- vignettes/fig/plotGallery-1.pdf |binary vignettes/fig/trains_plot-1.pdf |binary vignettes/fig/trains_plot-1.png |binary 24 files changed, 616 insertions(+), 213 deletions(-)
Title: Methods for Detection of Clusters in Hierarchical Clustering
Dendrograms
Description: Contains methods for detection of clusters in hierarchical clustering dendrograms.
Author: Peter Langfelder <Peter.Langfelder@gmail.com> and Bin Zhang <binzhang.ucla@gmail.com>,
with contributions from Steve Horvath <SHorvath@mednet.ucla.edu>
Maintainer: Peter Langfelder <Peter.Langfelder@gmail.com>
Diff between dynamicTreeCut versions 1.62 dated 2014-04-22 and 1.63-1 dated 2016-03-10
Changelog | 14 ++++++++++ DESCRIPTION | 12 ++++---- MD5 | 22 +++++++-------- NAMESPACE | 4 ++ R/treeCut.R | 58 ++++++++++++++++++++++++++++++++++-------- man/cutreeDynamic.Rd | 2 - man/cutreeDynamicTree.Rd | 2 - man/cutreeHybrid.Rd | 2 - man/dynamicTreeCut-package.Rd | 7 ++--- man/indentSpaces.Rd | 2 - man/merge2Clusters.Rd | 2 - man/printFlush.Rd | 2 - 12 files changed, 92 insertions(+), 37 deletions(-)
More information about dynamicTreeCut at CRAN
Permanent link
Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at
coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 0.1-0 dated 2015-10-14 and 1.2-1 dated 2016-03-10
downscale-0.1-0/downscale/R/ExtendRaster.R |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale30.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale32.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale33.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale34.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale35.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale36.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale38.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale40.pdf |only downscale-0.1-0/downscale/vignettes/Downscaling-downscale41.pdf |only downscale-1.2-1/downscale/DESCRIPTION | 18 - downscale-1.2-1/downscale/MD5 | 50 +- downscale-1.2-1/downscale/NEWS | 17 downscale-1.2-1/downscale/R/upgrain.R | 105 +++--- downscale-1.2-1/downscale/build/vignette.rds |binary downscale-1.2-1/downscale/inst/doc/Downscaling.Rnw | 173 +++++----- downscale-1.2-1/downscale/inst/doc/Downscaling.pdf |binary downscale-1.2-1/downscale/inst/doc/Upgraining.Rnw | 18 - downscale-1.2-1/downscale/inst/doc/Upgraining.pdf |binary downscale-1.2-1/downscale/man/upgrain.Rd | 5 downscale-1.2-1/downscale/vignettes/Downscaling-downscale30.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale32.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale33.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale34.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale36.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale38.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale40.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale41.png |binary downscale-1.2-1/downscale/vignettes/Downscaling-downscale42.png |binary downscale-1.2-1/downscale/vignettes/Downscaling.Rnw | 173 +++++----- downscale-1.2-1/downscale/vignettes/Upgraining.Rnw | 18 - 31 files changed, 319 insertions(+), 258 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang <michellang@gmail.com>,
Bernd Bischl <bernd_bischl@gmx.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 1.7.2 dated 2016-02-25 and 1.7.3 dated 2016-03-10
DESCRIPTION | 18 ++-- MD5 | 141 +++++++++++++++++----------------- NAMESPACE | 7 + R/asInteger.r | 10 -- R/assert.r | 16 +-- R/checkAtomic.r | 2 R/checkCharacter.r | 4 R/checkDataFrame.r | 2 R/checkDataTable.r | 2 R/checkDate.r |only R/checkDirectory.r | 13 +-- R/checkFactor.r | 5 - R/checkFile.r | 29 +++++- R/checkFunction.r | 2 R/checkList.r | 4 R/checkOS.r | 12 +- R/checkPathForOutput.r | 15 +-- R/checkString.r | 2 R/coalesce.r | 2 R/helper.r | 6 - R/makeAssertion.r | 11 +- R/makeExpectation.r | 2 R/makeTest.r | 5 - R/qassert.r | 8 - R/qassertr.r | 8 - R/zzz.r | 1 inst/NEWS.md | 8 + inst/doc/checkmate.html | 76 +++++++++--------- man/asInteger.Rd | 13 +-- man/assert.Rd | 10 +- man/checkAccess.Rd | 10 +- man/checkArray.Rd | 10 +- man/checkAtomic.Rd | 22 +---- man/checkAtomicVector.Rd | 10 +- man/checkCharacter.Rd | 10 +- man/checkChoice.Rd | 10 +- man/checkClass.Rd | 10 +- man/checkComplex.Rd | 10 +- man/checkCount.Rd | 10 +- man/checkDataFrame.Rd | 10 +- man/checkDataTable.Rd | 10 +- man/checkDate.Rd |only man/checkDirectory.Rd | 10 +- man/checkEnvironment.Rd | 12 +- man/checkFactor.Rd | 10 +- man/checkFile.Rd | 23 +++-- man/checkFlag.Rd | 10 +- man/checkFunction.Rd | 10 +- man/checkInt.Rd | 10 +- man/checkInteger.Rd | 10 +- man/checkIntegerish.Rd | 10 +- man/checkList.Rd | 10 +- man/checkLogical.Rd | 10 +- man/checkMatrix.Rd | 10 +- man/checkNamed.Rd | 10 +- man/checkNames.Rd | 10 +- man/checkNull.Rd | 10 +- man/checkNumber.Rd | 10 +- man/checkNumeric.Rd | 12 +- man/checkOS.Rd | 6 - man/checkPathForOutput.Rd | 10 +- man/checkScalar.Rd | 10 +- man/checkScalarNA.Rd | 10 +- man/checkSetEqual.Rd | 10 +- man/checkString.Rd | 10 +- man/checkSubset.Rd | 10 +- man/checkVector.Rd | 10 +- man/makeAssertion.Rd | 9 +- man/qassert.Rd | 8 - man/qassertr.Rd | 8 - tests/testthat/test_checkDate.r |only tests/testthat/test_checkFilesystem.r | 6 + tests/testthat/test_checkOS.r | 20 ++++ 73 files changed, 462 insertions(+), 408 deletions(-)
Title: Cognitive Diagnosis Modeling
Description:
Functions for cognitive diagnosis modeling
and multidimensional item response modeling for
dichotomous and polytomous data. This package
enables the estimation of the DINA and DINO model,
the multiple group (polytomous) GDINA model,
the multiple choice DINA model, the general diagnostic
model (GDM), the multidimensional linear compensatory
item response model and the structured latent class
model (SLCA).
Author:
Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 4.7-0 dated 2016-01-30 and 4.8-0 dated 2016-03-10
DESCRIPTION | 8 +- MD5 | 96 +++++++++++++++++----------------- NAMESPACE | 3 + R/itemfit.sx2.R | 6 ++ R/numerical_Hessian.R |only R/osink.R |only R/print.din.R | 10 ++- R/print.gdina.R | 10 ++- R/print.gdm.R | 12 ++-- R/print.mcdina.R | 10 ++- R/print.slca.R | 10 ++- R/print.summary.din.R | 4 + R/summary.din.R | 8 +- R/summary.gdina.R | 13 +++- R/summary.gdm.R | 9 ++- R/summary.mcdina.R | 8 ++ R/summary.slca.R | 10 ++- data/data.Students.rda |binary data/data.cdm01.rda |binary data/data.cdm02.rda |binary data/data.dcm.rda |binary data/data.dtmr.rda |binary data/data.ecpe.rda |binary data/data.fraction1.rda |binary data/data.fraction2.rda |binary data/data.hr.rda |binary data/data.jang.rda |binary data/data.melab.rda |binary data/data.mg.rda |binary data/data.pgdina.rda |binary data/data.sda6.rda |binary data/data.timss03.G8.su.rda |binary data/data.timss07.G4.lee.rda |binary data/data.timss11.G4.AUT.part.rda |binary data/data.timss11.G4.AUT.rda |binary data/fraction.subtraction.data.rda |binary data/fraction.subtraction.qmatrix.rda |binary data/sim.dina.rda |binary data/sim.dino.rda |binary data/sim.qmatrix.rda |binary inst/NEWS | 23 +++++++- man/CDM-package.Rd | 84 +++++++++++++++-------------- man/din.Rd | 3 + man/din.deterministic.Rd | 2 man/gdina.Rd | 6 +- man/gdm.Rd | 4 + man/mcdina.Rd | 6 +- man/numerical_Hessian.Rd |only man/osink.Rd |only man/slca.Rd | 4 + man/summary.din.Rd | 5 + 51 files changed, 225 insertions(+), 129 deletions(-)
Title: Stochastic Model for Analysis of Longitudinal Data
Description: Utilities to estimate parameters of stochastic process and modeling survival trajectories
and time-to-event outcomes observed from longitudinal studies.
Miscellaneous function for data preparation is also provided.
For more information, see: "Stochastic model for analysis of longitudinal data on aging
and mortality" by Yashin A. et al, 2007, Mathematical Biosciences, 208(2), 538-551
<DOI:10.1016/j.mbs.2006.11.006>.
Author: I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.0 dated 2016-02-08 and 1.1.2 dated 2016-03-10
DESCRIPTION | 10 +- MD5 | 45 ++++----- NAMESPACE | 3 R/prepare_data.R | 3 R/simdata_cont.R | 109 ++++++++++++++++++++-- R/simdata_discr.R | 38 ++++--- R/spm.R | 109 +++++++++++++--------- R/spm_continuous.R | 192 ++++++++++++++++++++++++-------------- R/spm_discrete.R | 30 +++--- R/spm_projection.R |only R/spm_time-dependent.R | 20 ++-- README.md | 21 ++-- man/optimize.Rd | 6 - man/simdata_cont.Rd | 8 - man/simdata_cont2.Rd |only man/simdata_discr.Rd | 6 - man/spm.Rd | 27 ++++- man/spm_continuous.Rd | 22 ++-- man/spm_discrete.Rd | 8 - man/spm_projection.Rd |only man/spm_time_dep.Rd | 10 +- src/simdataND.cpp | 1 src/spm_integral_MD.cpp | 201 +++++++++++++++++++++++++++++++++++++++- vignettes/stpm-vignette.Rmd | 30 ++---- vignettes/stpm-vignette.html | 212 ++++++++++++++++++++++--------------------- 25 files changed, 757 insertions(+), 354 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multi-type/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Tuomas Rajala;
Dominic Schuhmacher;
and
Rasmus Waagepetersen.
Additional contributions
by M. Adepeju;
Q.W. Ang;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
R. Corria Ainslie;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
E. Mudrak;
G.M. Nair;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud,
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.44-1 dated 2015-12-29 and 1.45-0 dated 2016-03-10
DESCRIPTION | 16 MD5 | 757 ++++++++++++++++++++++--------------------- NAMESPACE | 106 +++++- NEWS | 337 +++++++++++++++++++ R/Fest.R | 16 R/Hest.R | 5 R/Iest.R | 2 R/Jinhom.R | 4 R/Kest.R | 57 +-- R/Tstat.R | 4 R/addvar.R | 4 R/allstats.R | 6 R/alltypes.R | 6 R/anova.mppm.R | 28 + R/anova.ppm.R | 6 R/areainter.R | 16 R/as.im.R | 5 R/badgey.R | 6 R/bermantest.R | 14 R/blur.R | 4 R/boundingbox.R | 8 R/breakpts.R | 29 + R/bw.optim.R | 10 R/cdftest.R | 16 R/clickppp.R | 21 - R/close3Dpairs.R | 74 +++- R/closepairs.R | 197 +++++++++-- R/clusterset.R | 6 R/colourtables.R | 14 R/compileK.R | 4 R/concom.R | 6 R/density.lpp.R | 16 R/density.ppp.R | 6 R/detpointprocfamilyfun.R | 1 R/diagnoseppm.R | 26 + R/dist2dpath.R | 19 - R/distcdf.R | 4 R/distfunlpp.R | 2 R/dppm.R | 37 +- R/dppmclass.R | 2 R/dummify.R | 4 R/edgeRipley.R | 2 R/edgeTrans.R | 40 +- R/effectfun.R | 6 R/envelope.R | 31 + R/envelope3.R | 9 R/envelopelpp.R | 14 R/eval.fasp.R | 4 R/eval.fv.R | 12 R/eval.im.R | 12 R/evalcovar.R | 4 R/ewcdf.R | 4 R/factors.R | 2 R/fasp.R | 6 R/fii.R | 4 R/fiksel.R | 4 R/fitted.ppm.R | 51 ++ R/fryplot.R | 4 R/funxy.R | 46 ++ R/fv.R | 26 + R/geyer.R | 66 ++- R/hackglmm.R | 6 R/hexagons.R | 6 R/hierhard.R | 4 R/hierpair.family.R | 4 R/hierstrauss.R | 4 R/hierstrhard.R | 4 R/hybrid.R | 6 R/hybrid.family.R | 6 R/hyperframe.R | 18 - R/hypersub.R | 8 R/idw.R | 3 R/images.R | 21 - R/indices.R |only R/infline.R | 4 R/interactions.R | 42 +- R/ippm.R | 6 R/kppm.R | 40 +- R/laslett.R |only R/layered.R | 10 R/lennard.R | 4 R/leverage.R | 211 ++++++++---- R/linalg.R | 28 + R/linfun.R | 31 + R/linim.R | 21 - R/linnet.R | 111 +++++- R/linnetsurgery.R |only R/lintess.R |only R/localpcf.R | 4 R/logistic.R | 2 R/lpp.R | 129 ++++--- R/lppm.R | 46 +- R/lurking.R | 11 R/markcorr.R | 10 R/marks.R | 23 - R/measures.R | 16 R/mincontrast.R | 12 R/morisita.R | 4 R/mpl.R | 184 ++++++---- R/mppm.R | 51 ++ R/multihard.R | 4 R/multistrauss.R | 2 R/multistrhard.R | 4 R/nnclean.R | 8 R/nndist.R | 6 R/nndistlpp.R | 20 - R/nnmap.R | 4 R/objsurf.R | 10 R/options.R | 5 R/pairs.im.R | 14 R/pairsat.family.R | 17 R/pairwise.family.R | 6 R/parres.R | 4 R/pcf.R | 80 +++- R/pcfinhom.R | 35 + R/penttinen.R | 4 R/persp.im.R | 4 R/pixellate.R | 6 R/plot.anylist.R | 10 R/plot.fasp.R | 4 R/plot.fv.R | 16 R/plot.im.R | 10 R/plot.mppm.R | 8 R/plot.owin.R | 24 - R/plot.plotppm.R | 8 R/plot.ppp.R | 28 - R/pool.R | 5 R/pp3.R | 4 R/ppm.R | 17 R/ppmclass.R | 19 - R/ppp.R | 4 R/ppx.R | 20 - R/predict.ppm.R | 57 ++- R/profilepl.R | 42 +- R/progress.R | 4 R/psp.R | 12 R/psp2pix.R | 4 R/pspcross.R | 24 + R/qqplotppm.R | 419 ++++++++++++----------- R/quadclass.R | 18 - R/quadratcount.R | 8 R/quadrattest.R | 16 R/quadscheme.R | 6 R/quantess.R | 4 R/random.R | 8 R/reduceformula.R | 3 R/replace.ppp.R | 2 R/resid4plot.R | 10 R/residppm.R | 29 - R/rho2hat.R | 13 R/rhohat.R | 6 R/rmh.default.R | 6 R/rmh.ppm.R | 6 R/rmhcontrol.R | 8 R/rmhexpand.R | 4 R/rmhmodel.R | 6 R/rmhmodel.ppm.R | 15 R/rmhstart.R | 6 R/rshift.R | 6 R/satpiece.R | 4 R/scanstat.R | 7 R/sigtrace.R | 2 R/slrm.R | 24 - R/smooth.ppp.R | 20 - R/smoothfun.R | 4 R/softcore.R | 4 R/sparse3Darray.R |only R/sparsecommon.R |only R/sparselinalg.R |only R/split.ppx.R | 4 R/strauss.R | 13 R/strausshard.R | 4 R/subfits.R | 791 ++++++++++++++++++++++++--------------------- R/subset.R | 18 - R/summary.mppm.R | 4 R/summary.ppm.R | 8 R/superimpose.R | 46 +- R/symbolmap.R | 60 ++- R/tess.R | 14 R/texture.R | 27 - R/triplets.R | 4 R/unique.ppp.R | 2 R/unnormdensity.R | 16 R/update.ppm.R | 11 R/util.R | 89 ++--- R/varblock.R | 26 - R/vcov.mppm.R | 49 ++ R/vcov.ppm.R | 100 +++-- R/versions.R | 7 R/window.R | 11 R/wingeom.R | 42 +- R/xypolygon.R | 4 R/zclustermodel.R | 2 demo/spatstat.R | 3 inst/CITATION | 40 +- inst/doc/datasets.R | 129 +++---- inst/doc/datasets.Rnw | 1 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/replicated.R | 142 ++++---- inst/doc/replicated.Rnw | 18 - inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 8 inst/doc/updates.Rnw | 293 +++++++++++++++- inst/doc/updates.pdf |binary man/Emark.Rd | 2 man/Extract.fasp.Rd | 10 man/Extract.layered.Rd | 5 man/Extract.linnet.Rd | 35 + man/Extract.lpp.Rd | 30 + man/Extract.msr.Rd | 6 man/Extract.ppp.Rd | 41 +- man/Extract.splitppp.Rd | 2 man/Fest.Rd | 2 man/Gcross.Rd | 4 man/Gdot.Rd | 2 man/Gest.Rd | 2 man/Geyer.Rd | 20 - man/Gmulti.Rd | 17 man/Jcross.Rd | 18 - man/Jdot.Rd | 10 man/Jest.Rd | 2 man/Jmulti.Rd | 17 man/Kcross.Rd | 2 man/Kcross.inhom.Rd | 29 - man/Kdot.Rd | 14 man/Kdot.inhom.Rd | 21 - man/Kest.fft.Rd | 3 man/Kinhom.Rd | 7 man/Kmark.Rd | 2 man/Kmulti.Rd | 21 - man/Kmulti.inhom.Rd | 6 man/Lcross.inhom.Rd | 18 - man/Ldot.inhom.Rd | 21 - man/Poisson.Rd | 31 - man/Smooth.msr.Rd | 6 man/anova.lppm.Rd | 6 man/ants.Rd | 2 man/applynbd.Rd | 39 +- man/as.im.Rd | 2 man/as.linfun.Rd |only man/as.lpp.Rd | 5 man/bdist.points.Rd | 2 man/clarkevans.Rd | 2 man/closepairs.Rd | 28 + man/closepairs.pp3.Rd | 21 - man/coef.mppm.Rd | 36 +- man/complement.owin.Rd | 4 man/connected.linnet.Rd |only man/connected.ppp.Rd | 2 man/convexhull.Rd | 2 man/crossing.psp.Rd | 22 + man/cut.ppp.Rd | 23 - man/deletebranch.Rd | 24 - man/density.lpp.Rd | 9 man/diagnose.ppm.Rd | 12 man/dirichletWeights.Rd | 2 man/discretise.Rd | 8 man/distfun.Rd | 24 - man/distfun.lpp.Rd | 21 - man/divide.linnet.Rd |only man/dppm.Rd | 15 man/dummy.ppm.Rd | 2 man/edge.Ripley.Rd | 2 man/edge.Trans.Rd | 14 man/eem.Rd | 2 man/envelope.Rd | 24 + man/envelope.lpp.Rd | 8 man/envelope.pp3.Rd | 6 man/eval.linim.Rd | 14 man/fitted.ppm.Rd | 6 man/fixef.mppm.Rd | 16 man/funxy.Rd | 21 - man/harmonic.Rd | 27 - man/harmonise.fv.Rd | 2 man/humberside.Rd | 2 man/idw.Rd | 9 man/im.Rd | 23 + man/influence.ppm.Rd | 4 man/insertVertices.Rd |only man/laslett.Rd |only man/leverage.ppm.Rd | 4 man/lineardisc.Rd | 12 man/linim.Rd | 5 man/linnet.Rd | 17 man/lintess.Rd |only man/lpp.Rd | 18 - man/lppm.Rd | 5 man/markconnect.Rd | 2 man/markcorr.Rd | 4 man/marks.Rd | 15 man/marks.psp.Rd | 13 man/markstat.Rd | 21 - man/methods.linfun.Rd | 9 man/methods.linim.Rd | 16 man/methods.linnet.Rd | 44 +- man/methods.lpp.Rd | 2 man/methods.lppm.Rd | 2 man/methods.objsurf.Rd | 3 man/mppm.Rd | 52 ++ man/nbfires.Rd | 444 ++++++++++++------------- man/nncorr.Rd | 2 man/nndist.lpp.Rd | 2 man/nnwhich.lpp.Rd | 2 man/nvertices.Rd |only man/osteo.Rd | 2 man/overlap.owin.Rd | 2 man/owin.Rd | 8 man/owin.object.Rd | 24 - man/pairdist.lpp.Rd | 2 man/pcf.Rd | 17 man/pcf.fv.Rd | 15 man/pcf.ppp.Rd | 34 + man/pcfinhom.Rd | 27 + man/periodify.Rd | 2 man/plot.laslett.Rd |only man/plot.linim.Rd | 10 man/plot.linnet.Rd | 3 man/plot.lpp.Rd | 8 man/plot.lppm.Rd | 6 man/plot.msr.Rd | 6 man/plot.ppp.Rd | 31 + man/plot.psp.Rd | 4 man/ppp.Rd | 2 man/ppp.object.Rd | 2 man/pppdist.Rd | 444 ++++++++++++------------- man/pppmatching.Rd | 2 man/predict.lppm.Rd | 4 man/predict.mppm.Rd | 2 man/print.owin.Rd | 2 man/psp.Rd | 5 man/quad.object.Rd | 4 man/quad.ppm.Rd | 7 man/quadrat.test.Rd | 2 man/quadratcount.Rd | 2 man/quadrats.Rd | 2 man/quadscheme.Rd | 8 man/quadscheme.logi.Rd | 5 man/ranef.mppm.Rd | 17 man/reload.or.compute.Rd | 2 man/requireversion.Rd |only man/rescale.owin.Rd | 2 man/residuals.ppm.Rd | 11 man/rmh.default.Rd | 8 man/rmhcontrol.Rd | 2 man/rthin.Rd | 2 man/run.simplepanel.Rd | 57 +++ man/scan.test.Rd | 6 man/selfcut.psp.Rd | 10 man/simplepanel.Rd | 9 man/simplify.owin.Rd | 13 man/spatstat-internal.Rd | 150 +++++++- man/spatstat-package.Rd | 93 +++-- man/split.ppp.Rd | 26 - man/subfits.Rd | 24 - man/subset.ppp.Rd | 29 + man/summary.owin.Rd | 2 man/summary.ppm.Rd | 13 man/summary.ppp.Rd | 19 - man/superimpose.Rd | 4 man/symbolmap.Rd | 21 - man/texturemap.Rd | 18 - man/textureplot.Rd | 16 man/thinNetwork.Rd |only man/transect.im.Rd | 2 man/treebranchlabels.Rd | 16 man/treeprune.Rd | 32 + man/unmark.Rd | 6 man/vcov.ppm.Rd | 9 src/PerfectPenttinen.h | 4 src/bdrymask.c | 4 src/close3pair.c | 3 src/closefuns.h | 373 ++++++++++++++++++++- src/closepair.c | 1 src/knngrid.h | 4 src/linSnncross.h | 9 src/linequad.c | 24 - src/linknnd.c | 11 src/linvknndist.c | 12 src/methas.c | 2 src/sparselinalg.c |only src/spasumsymout.h |only src/whist.c | 4 tests/alltests.R | 390 ++++++++++++++++++---- vignettes/datasets.Rnw | 1 vignettes/packagesizes.txt | 1 vignettes/replicated.Rnw | 18 - vignettes/updates.Rnw | 293 +++++++++++++++- 389 files changed, 6955 insertions(+), 3646 deletions(-)
Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal
Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide
Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.3 dated 2016-02-18 and 1.3.1 dated 2016-03-10
idm-1.3.1/idm/DESCRIPTION | 8 idm-1.3.1/idm/MD5 | 17 - idm-1.3.1/idm/NAMESPACE | 2 idm-1.3.1/idm/R/i_pca.r | 466 ++++++++++++++++++++-------------------- idm-1.3.1/idm/R/update.i_pca.R | 3 idm-1.3.1/idm/man/i_pca.Rd | 2 idm-1.3.1/idm/man/idm.Rd | 62 ++--- idm-1.3.1/idm/man/plot.i_pca.Rd | 3 idm-1.3.1/idm/man/tweet.Rd | 58 ++-- idm-1.3/idm/man/transform_z.Rd |only 10 files changed, 311 insertions(+), 310 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Provides implementations of functions which have been introduced in
R since version 3.0.0. The backports are conditionally exported which
results in R resolving the function names to the version shipped with R (if
available) and uses the implemented backports as fallback. This way package
developers can make use of the new functions without worrying about the
minimum required R version.
Author: Michel Lang <michellang@gmail.com>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.0.0 dated 2016-02-19 and 1.0.1 dated 2016-03-10
DESCRIPTION | 10 +++++----- MD5 | 9 ++++++--- NAMESPACE | 3 +++ NEWS.md | 8 ++++++-- R/file.x.r |only man/file.size.Rd |only tests/testthat/test_file.x.r |only 7 files changed, 20 insertions(+), 10 deletions(-)
Title: Applications of Empirical Dynamic Modeling from Time Series
Description: Contains C++ compiled objects that use time delay embedding to perform state-space reconstruction and nonlinear forecasting and an R interface to those objects using 'Rcpp'. It supports both the simplex projection method from Sugihara & May (1990) <DOI:10.1038/344734a0> and the S-map algorithm in Sugihara (1994) <DOI:10.1098/rsta.1994.0106>. In addition, this package implements convergent cross mapping as described by Sugihara et al. (2012) <DOI:10.1126/science.1227079>.
Author: Hao Ye, Adam Clark, Ethan Deyle
Maintainer: Hao Ye <hye@ucsd.edu>
Diff between rEDM versions 0.4.5 dated 2016-03-07 and 0.4.7 dated 2016-03-10
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- inst/doc/rEDM_tutorial.html | 14 +++++++------- inst/tests/Rplots.pdf |only inst/tests/test_lnlp.R | 2 ++ src/block_lnlp.cpp | 7 +++++-- src/block_lnlp.h | 2 +- src/lnlp.cpp | 4 +++- src/lnlp.h | 2 +- src/xmap.cpp | 5 ++++- src/xmap.h | 2 +- 11 files changed, 38 insertions(+), 27 deletions(-)
Title: Spatial Analysis and Modelling
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization and statistical
exploratory tools.
Author: Jeffrey S. Evans [aut, cre],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 0.1-3 dated 2015-10-29 and 0.1-4 dated 2016-03-10
DESCRIPTION | 10 +-- MD5 | 141 +++++++++++++++++++++++++-------------------- NAMESPACE | 12 +++ R/DAYMET_tiles-data.R |only R/breeding.density.R | 3 R/daymet.point.R |only R/daymet.tiles.R |only R/download.hansen.R | 2 R/download.prism.R | 5 - R/effect.size.R |only R/logistic.regression.R | 31 ++++++--- R/plot.effect.size.R |only R/plot.loess.boot.R | 2 R/print.effect.size.R |only R/pseudo.absence.R | 29 ++++----- R/sample.annulus.R |only R/sample.line.R | 4 - R/se.news.R |only R/sp.na.omit.R | 66 +++++++++++---------- R/spatialEcoNews.R |only R/summary.effect.size.R |only R/tri.R | 2 R/zzz.R |only data/DAYMET_tiles.rda |only inst/CITATION | 4 - inst/NEWS | 15 +++- man/DAYMET_tiles.Rd |only man/ants.Rd | 2 man/bearing.distance.Rd | 7 -- man/breeding.density.Rd | 21 +----- man/concordance.Rd | 21 +----- man/conf.interval.Rd | 5 - man/correlogram.Rd | 20 ++---- man/csi.Rd | 14 +--- man/daymet.point.Rd |only man/daymet.tiles.Rd |only man/dispersion.Rd | 12 --- man/download.daymet.Rd | 32 +++------- man/download.hansen.Rd | 15 +--- man/download.prism.Rd | 24 ++----- man/effect.size.Rd |only man/gaussian.kernel.Rd | 3 man/group.pdf.Rd | 8 -- man/hexagons.Rd | 5 - man/idw.smoothing.Rd | 11 --- man/insert.values.Rd | 6 - man/kl.divergence.Rd | 8 -- man/land.metrics.Rd | 18 +---- man/local.min.max.Rd | 12 +-- man/loess.boot.Rd | 32 +++------- man/loess.ci.Rd | 15 +--- man/logistic.regression.Rd | 48 +++++++-------- man/moments.Rd | 35 +++++------ man/nni.Rd | 9 -- man/o.ring.Rd | 12 --- man/optimal.k.Rd | 7 -- man/outliers.Rd | 7 -- man/parea.sample.Rd | 8 -- man/plot.effect.size.Rd |only man/plot.loess.boot.Rd | 9 -- man/point.in.poly.Rd | 4 - man/pp.subsample.Rd | 24 +------ man/print.effect.size.Rd |only man/pseudo.absence.Rd | 55 ++++++----------- man/pu.Rd | 5 - man/raster.entropy.Rd | 11 --- man/raster.vol.Rd | 6 - man/sample.annulus.Rd |only man/sample.line.Rd | 10 --- man/sample.poly.Rd | 6 - man/se.news.Rd |only man/separability.Rd | 36 +++-------- man/shannons.Rd | 10 --- man/similarity.Rd | 12 --- man/sp.na.omit.Rd | 43 ++++++------- man/stratified.random.Rd | 8 -- man/summary.effect.size.Rd |only man/tpi.Rd | 7 -- man/trend.line.Rd | 3 man/tri.Rd | 9 -- man/wt.centroid.Rd | 11 --- man/zonal.stats.Rd | 11 --- 82 files changed, 408 insertions(+), 615 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains also functions scABEL.ad() and sampleN.scABEL.ad() to iteratively
adjust alpha in order to maintain the consumer risk in ABEL studies
and adapt the sample size for the loss in power.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-3 dated 2016-01-15 and 1.3-4 dated 2016-03-10
PowerTOST-1.3-3/PowerTOST/R/power_scABEL2.R |only PowerTOST-1.3-4/PowerTOST/DESCRIPTION | 8 +-- PowerTOST-1.3-4/PowerTOST/MD5 | 50 ++++++++++---------- PowerTOST-1.3-4/PowerTOST/NEWS | 7 ++ PowerTOST-1.3-4/PowerTOST/R/SampleSize_HVNTID.R | 10 ++-- PowerTOST-1.3-4/PowerTOST/R/exppower.R | 3 - PowerTOST-1.3-4/PowerTOST/R/power2.R |only PowerTOST-1.3-4/PowerTOST/R/power_RSABE.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_RSABE_NTID.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_RSABE_pure.R | 1 PowerTOST-1.3-4/PowerTOST/R/power_TOST_sim.R | 5 +- PowerTOST-1.3-4/PowerTOST/R/power_scABEL.R | 29 ++++++----- PowerTOST-1.3-4/PowerTOST/R/power_scABEL_2.R |only PowerTOST-1.3-4/PowerTOST/R/power_scABEL_lo.R |only PowerTOST-1.3-4/PowerTOST/R/power_scABEL_pure.R | 6 ++ PowerTOST-1.3-4/PowerTOST/R/sampleN.scABEL.ad.R | 25 +++++----- PowerTOST-1.3-4/PowerTOST/R/samplesize_RSABE.R | 10 ++-- PowerTOST-1.3-4/PowerTOST/R/samplesize_RSABE_NTID.R | 11 ++-- PowerTOST-1.3-4/PowerTOST/R/samplesize_scABEL.R | 14 ++--- PowerTOST-1.3-4/PowerTOST/R/scABEL.ad.R | 5 +- PowerTOST-1.3-4/PowerTOST/man/power.HVNTID.Rd | 2 PowerTOST-1.3-4/PowerTOST/man/power.NTIDFDA.Rd | 4 + PowerTOST-1.3-4/PowerTOST/man/sampleN.HVNTID.Rd | 17 ++++-- PowerTOST-1.3-4/PowerTOST/man/sampleN.NTIDFDA.Rd | 13 ++++- PowerTOST-1.3-4/PowerTOST/man/sampleN.RSABE.Rd | 10 +++- PowerTOST-1.3-4/PowerTOST/man/sampleN.scABEL.Rd | 13 +++-- PowerTOST-1.3-4/PowerTOST/man/sampleN.scABEL.ad.Rd | 5 +- PowerTOST-1.3-4/PowerTOST/man/scABEL.ad.Rd | 9 ++- 28 files changed, 162 insertions(+), 97 deletions(-)
Title: Non-Negative Lasso and Elastic Net Penalized Generalized Linear
Models
Description: Estimates of coefficients of lasso penalized linear regression and generalized linear models subject to non-negativity constraints on the parameters using multiplicative iterative algorithm. Entire regularization path for a sequence of lambda values can be obtained. Functions are available for creating plots of regularization path, cross validation and estimating coefficients at a given lambda value. There is also provision for obtaining standard error of coefficient estimates.
Author: Baidya Nath Mandal <mandal.stat@gmail.com> and Jun Ma <jun.ma@mq.edu.au>
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Diff between nnlasso versions 0.2 dated 2015-04-10 and 0.3 dated 2016-03-10
DESCRIPTION | 14 +++++------ MD5 | 46 ++++++++++++++++++------------------- NAMESPACE | 2 + R/nnlasso.r | 50 ++++++++++++++++++++--------------------- man/bars.Rd | 2 - man/coef.nnlasso.Rd | 3 +- man/cv.nnlasso.Rd | 12 ++++----- man/cv.nnlasso.binomial.Rd | 5 ++-- man/cv.nnlasso.normal.Rd | 5 ++-- man/cv.nnlasso.poisson.Rd | 5 ++-- man/fold.Rd | 2 - man/kfold.Rd | 2 - man/msefun.binomial.Rd | 2 - man/msefun.normal.Rd | 2 - man/msefun.poisson.Rd | 2 - man/nnlasso.Rd | 16 ++++++++++++- man/nnlasso.binomial.Rd | 4 ++- man/nnlasso.binomial.lambda.Rd | 4 +-- man/nnlasso.normal.Rd | 3 +- man/nnlasso.normal.lambda.Rd | 2 - man/nnlasso.poisson.Rd | 4 ++- man/nnlasso.poisson.lambda.Rd | 2 - man/plot.nnlasso.Rd | 5 +++- man/predict.nnlasso.Rd | 5 +++- 24 files changed, 115 insertions(+), 84 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.22-1 dated 2016-02-07 and 2.23 dated 2016-03-10
DESCRIPTION | 16 - MD5 | 49 +++-- NAMESPACE | 28 ++- R/glht-support.R | 26 ++- R/helpers.R | 8 R/lsmeans.R | 16 + R/rbind.R | 11 - R/ref.grid.R | 98 ++++++++--- R/summary.R | 123 +++++++++----- R/transformations.R |only R/xtable-method.R |only inst/NEWS | 24 ++ inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 228 +++++++++++++++++---------- inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 361 ++++++++++++++++++++++++++++++-------------- man/contrast.Rd | 10 - man/glht.Rd | 14 + man/lsmeans.Rd | 14 - man/make.tran.Rd |only man/models.Rd | 2 man/ref.grid.Rd | 7 man/summary.Rd | 41 +++- man/update.Rd | 22 +- tests/tests1.Rout.save | 26 ++- vignettes/lsmeans.bib | 40 +++- vignettes/using-lsmeans.rnw | 361 ++++++++++++++++++++++++++++++-------------- 27 files changed, 1024 insertions(+), 501 deletions(-)
Title: Epistasis Test in Meta-Analysis
Description: Traditional meta-regression based method has been developed for using meta-analysis data, but it faced the challenge of inconsistent estimates. This package purpose a new statistical method to detect epistasis using incomplete information summary, and have proven it not only successfully let consistency of evidence, but also increase the power compared with traditional method (Detailed tutorial is shown in website <http://rpubs.com/chinlin/ETMA>).
Author: Chin Lin
Maintainer: Chin Lin <xup6fup@gmail.com>
Diff between etma versions 1.0-6 dated 2015-10-01 and 1.0-8 dated 2016-03-10
DESCRIPTION | 18 ++++++++++-------- MD5 | 13 +++++++++---- build/partial.rdb |binary build/vignette.rds |only inst |only man/ETMA.Rd | 5 +++-- man/etma-package.Rd | 1 + vignettes |only 8 files changed, 23 insertions(+), 14 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Package DoE.base creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Additionally, it provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 0.27-1 dated 2015-08-21 and 0.28 dated 2016-03-10
DESCRIPTION | 8 - MD5 | 26 +++-- NAMESPACE | 11 +- R/SCFTs.R | 45 ++++++++-- R/cross.design.R | 4 R/expansive.replace.R |only R/paramtowide.R | 2 R/show.oas.R | 6 + R/sysdata.rda |binary inst/NEWS | 21 ++++ man/GRind.Rd | 16 ++- man/arrays.Rd | 209 +++++++++++++++++++++++++++++++++-------------- man/expansive.replace.Rd |only man/oacat.Rd | 75 +++++++++++++--- man/show.oas.Rd | 10 +- 15 files changed, 324 insertions(+), 109 deletions(-)