Title: Genome Interval Arithmetic in R
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Author: Jay Hesselberth [aut, cre],
Kent Riemondy [aut]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.3.0 dated 2017-06-15 and 0.3.1 dated 2017-07-21
valr-0.3.0/valr/R/sorting.r |only valr-0.3.0/valr/inst/doc/interval-stats.R |only valr-0.3.0/valr/inst/doc/interval-stats.Rmd |only valr-0.3.0/valr/inst/doc/interval-stats.html |only valr-0.3.0/valr/man/sorting.Rd |only valr-0.3.0/valr/man/trbl_genome.Rd |only valr-0.3.0/valr/man/trbl_interval.Rd |only valr-0.3.0/valr/src/absdist.cpp |only valr-0.3.0/valr/src/reldist.cpp |only valr-0.3.0/valr/tests/testthat/test_reldist.R |only valr-0.3.0/valr/tests/testthat/test_utils.R |only valr-0.3.0/valr/vignettes/interval-stats.Rmd |only valr-0.3.1/valr/DESCRIPTION | 17 - valr-0.3.1/valr/MD5 | 245 +++++++-------- valr-0.3.1/valr/NAMESPACE | 8 valr-0.3.1/valr/NEWS.md | 22 + valr-0.3.1/valr/R/RcppExports.R | 34 -- valr-0.3.1/valr/R/bed12_to_exons.r | 9 valr-0.3.1/valr/R/bed_absdist.r | 40 -- valr-0.3.1/valr/R/bed_closest.r | 25 - valr-0.3.1/valr/R/bed_cluster.r | 29 - valr-0.3.1/valr/R/bed_complement.r | 32 - valr-0.3.1/valr/R/bed_coverage.R | 23 - valr-0.3.1/valr/R/bed_fisher.r | 42 -- valr-0.3.1/valr/R/bed_flank.r | 23 - valr-0.3.1/valr/R/bed_glyph.r | 30 - valr-0.3.1/valr/R/bed_intersect.r | 70 ++-- valr-0.3.1/valr/R/bed_jaccard.r | 35 +- valr-0.3.1/valr/R/bed_makewindows.r | 7 valr-0.3.1/valr/R/bed_map.r | 47 +- valr-0.3.1/valr/R/bed_merge.r | 27 + valr-0.3.1/valr/R/bed_projection.r | 65 +-- valr-0.3.1/valr/R/bed_random.r | 10 valr-0.3.1/valr/R/bed_reldist.r | 34 -- valr-0.3.1/valr/R/bed_shift.r | 26 - valr-0.3.1/valr/R/bed_shuffle.r | 25 - valr-0.3.1/valr/R/bed_slop.r | 24 - valr-0.3.1/valr/R/bed_sort.r |only valr-0.3.1/valr/R/bed_subtract.r | 33 +- valr-0.3.1/valr/R/bed_window.r | 10 valr-0.3.1/valr/R/db.r | 8 valr-0.3.1/valr/R/features.r | 42 ++ valr-0.3.1/valr/R/globals.r | 7 valr-0.3.1/valr/R/read_bed.r | 17 - valr-0.3.1/valr/R/read_genome.r | 8 valr-0.3.1/valr/R/read_vcf.r | 22 - valr-0.3.1/valr/R/spacing.r | 4 valr-0.3.1/valr/R/strands.r | 10 valr-0.3.1/valr/R/tbls.r | 126 ++++++- valr-0.3.1/valr/R/utils.r | 4 valr-0.3.1/valr/R/valr-package.r | 8 valr-0.3.1/valr/README.md | 48 +- valr-0.3.1/valr/build/vignette.rds |binary valr-0.3.1/valr/inst/CITATION | 18 - valr-0.3.1/valr/inst/doc/valr.R | 83 +---- valr-0.3.1/valr/inst/doc/valr.Rmd | 146 ++------ valr-0.3.1/valr/inst/doc/valr.html | 162 ++++----- valr-0.3.1/valr/inst/include/DataFrameBuilder.h |only valr-0.3.1/valr/inst/include/valr.h | 1 valr-0.3.1/valr/man/as.tbl_genome.Rd |only valr-0.3.1/valr/man/as.tbl_interval.Rd |only valr-0.3.1/valr/man/bed12_to_exons.Rd | 6 valr-0.3.1/valr/man/bed_absdist.Rd | 27 - valr-0.3.1/valr/man/bed_closest.Rd | 11 valr-0.3.1/valr/man/bed_cluster.Rd | 22 - valr-0.3.1/valr/man/bed_complement.Rd | 20 - valr-0.3.1/valr/man/bed_coverage.Rd | 13 valr-0.3.1/valr/man/bed_fisher.Rd | 26 - valr-0.3.1/valr/man/bed_flank.Rd | 7 valr-0.3.1/valr/man/bed_glyph.Rd | 2 valr-0.3.1/valr/man/bed_intersect.Rd | 53 +-- valr-0.3.1/valr/man/bed_jaccard.Rd | 27 - valr-0.3.1/valr/man/bed_makewindows.Rd | 5 valr-0.3.1/valr/man/bed_map.Rd | 25 - valr-0.3.1/valr/man/bed_projection.Rd | 39 -- valr-0.3.1/valr/man/bed_reldist.Rd | 14 valr-0.3.1/valr/man/bed_shift.Rd | 16 valr-0.3.1/valr/man/bed_shuffle.Rd | 5 valr-0.3.1/valr/man/bed_sort.Rd | 21 - valr-0.3.1/valr/man/bed_subtract.Rd | 24 - valr-0.3.1/valr/man/bound_intervals.Rd | 6 valr-0.3.1/valr/man/create_introns.Rd | 6 valr-0.3.1/valr/man/create_tss.Rd |only valr-0.3.1/valr/man/create_utrs3.Rd | 6 valr-0.3.1/valr/man/create_utrs5.Rd | 6 valr-0.3.1/valr/man/figures/README-intersect_glyph-1.png |only valr-0.3.1/valr/man/flip_strands.Rd | 6 valr-0.3.1/valr/man/interval_spacing.Rd | 5 valr-0.3.1/valr/man/tbl_genome.Rd | 13 valr-0.3.1/valr/man/tbl_interval.Rd | 17 - valr-0.3.1/valr/man/valr.Rd | 10 valr-0.3.1/valr/src/RcppExports.cpp | 59 +-- valr-0.3.1/valr/src/closest.cpp | 48 -- valr-0.3.1/valr/src/coverage.cpp | 41 -- valr-0.3.1/valr/src/dist.cpp |only valr-0.3.1/valr/src/init.c | 50 +-- valr-0.3.1/valr/src/intersect.cpp | 40 -- valr-0.3.1/valr/src/merge.cpp | 36 -- valr-0.3.1/valr/src/subtract.cpp | 22 - valr-0.3.1/valr/tests/testthat/helper-astyle.r | 2 valr-0.3.1/valr/tests/testthat/test-db.r | 16 valr-0.3.1/valr/tests/testthat/test-style.r | 3 valr-0.3.1/valr/tests/testthat/test_absdist.r | 26 - valr-0.3.1/valr/tests/testthat/test_bed12_to_exons.r | 8 valr-0.3.1/valr/tests/testthat/test_closest.r | 136 ++++---- valr-0.3.1/valr/tests/testthat/test_cluster.r | 28 - valr-0.3.1/valr/tests/testthat/test_complement.r | 8 valr-0.3.1/valr/tests/testthat/test_coverage.r | 126 +++---- valr-0.3.1/valr/tests/testthat/test_features.r | 23 + valr-0.3.1/valr/tests/testthat/test_fisher.r | 2 valr-0.3.1/valr/tests/testthat/test_flank.r | 7 valr-0.3.1/valr/tests/testthat/test_genome.r | 4 valr-0.3.1/valr/tests/testthat/test_glyph.r | 18 - valr-0.3.1/valr/tests/testthat/test_intersect.r | 38 +- valr-0.3.1/valr/tests/testthat/test_jaccard.r | 2 valr-0.3.1/valr/tests/testthat/test_makewindows.r | 39 +- valr-0.3.1/valr/tests/testthat/test_map.r | 45 +- valr-0.3.1/valr/tests/testthat/test_merge.r | 79 ++-- valr-0.3.1/valr/tests/testthat/test_projection.r | 4 valr-0.3.1/valr/tests/testthat/test_random.r | 8 valr-0.3.1/valr/tests/testthat/test_read_bed.r | 24 - valr-0.3.1/valr/tests/testthat/test_read_vcf.r | 15 valr-0.3.1/valr/tests/testthat/test_reldist.r |only valr-0.3.1/valr/tests/testthat/test_shift.r | 22 - valr-0.3.1/valr/tests/testthat/test_shuffle.r | 33 -- valr-0.3.1/valr/tests/testthat/test_slop.r | 6 valr-0.3.1/valr/tests/testthat/test_sort.r | 74 ++-- valr-0.3.1/valr/tests/testthat/test_spacing.r | 10 valr-0.3.1/valr/tests/testthat/test_strands.r | 16 valr-0.3.1/valr/tests/testthat/test_subtract.r | 8 valr-0.3.1/valr/tests/testthat/test_tbls.r | 78 +++- valr-0.3.1/valr/tests/testthat/test_utils.r |only valr-0.3.1/valr/tests/testthat/test_window.r | 16 valr-0.3.1/valr/vignettes/valr.Rmd | 146 ++------ 134 files changed, 1693 insertions(+), 1817 deletions(-)
Title: Analysis of Aerobiological Data
Description: Supports analysis of aerobiological data. Available features include determination of pollen season limits, replacement of outliers (Kasprzyk and Walanus (2014) <doi:10.1007/s10453-014-9332-8>), and calculation of growing degree days.
Author: Jakub Nowosad [aut, cre]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between pollen versions 0.52.00 dated 2017-04-17 and 0.53.00 dated 2017-07-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/outliers_replacer.R | 11 +++++------ build/vignette.rds |binary inst/doc/intro.html | 24 ++++++++++++------------ man/outliers_replacer.Rd | 4 ++-- 6 files changed, 27 insertions(+), 28 deletions(-)
Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov
models. These include processing of tracking data, fitting hidden Markov models
to movement data, visualization of data and fitted model, decoding of the state
process...
Author: Theo Michelot, Roland Langrock, Toby Patterson, Brett McClintock, Eric Rexstad (ctb)
Maintainer: Theo Michelot <tmichelot1@sheffield.ac.uk>
Diff between moveHMM versions 1.4 dated 2017-04-06 and 1.5 dated 2017-07-21
DESCRIPTION | 12 +- MD5 | 62 ++++++------ NAMESPACE | 3 R/fitHMM.R | 4 R/plotSat.R | 9 + R/plot_moveData.R | 22 ++-- R/plot_moveHMM.R | 12 +- R/prepData.R | 21 +++- R/turnAngle.R | 26 +++-- build/vignette.rds |binary inst/doc/moveHMM-guide.Rnw | 6 - inst/doc/moveHMM-guide.pdf |binary man/prepData.Rd | 6 - man/turnAngle.Rd | 8 + tests/testthat/test_CI.R | 18 +-- tests/testthat/test_allProbs.R | 42 ++++---- tests/testthat/test_densities.R | 62 ++++++------ tests/testthat/test_fitHMM.R | 186 ++++++++++++++++++------------------ tests/testthat/test_logAlpha.R | 14 +- tests/testthat/test_moveData.R | 30 ++--- tests/testthat/test_moveHMM.R | 54 +++++----- tests/testthat/test_n2w.R | 36 +++--- tests/testthat/test_nLogLike.R | 94 +++++++++--------- tests/testthat/test_parDef.R | 32 +++--- tests/testthat/test_prepData.R | 48 ++++----- tests/testthat/test_simData.R | 92 ++++++++--------- tests/testthat/test_stateProbs.R | 10 - tests/testthat/test_trMatrix_rcpp.R | 28 ++--- tests/testthat/test_turnAngle.R | 14 +- tests/testthat/test_viterbi.R | 4 tests/testthat/test_w2n.R | 60 +++++------ vignettes/moveHMM-guide.Rnw | 6 - 32 files changed, 532 insertions(+), 489 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [cre, aut],
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 2.7 dated 2017-06-26 and 2.8.1 dated 2017-07-21
DESCRIPTION | 6 +-- MD5 | 58 +++++++++++++++++++------------------ NAMESPACE | 1 NEWS | 16 ++++++++++ R/fetch.R | 6 +-- R/handle.R | 1 R/multi.R | 6 ++- R/proxy.R | 5 +++ build/vignette.rds |binary inst/doc/intro.html | 58 ++++++++++++++++++------------------- man/multi.Rd | 5 ++- src/Makevars.win | 28 ++++++++++++----- src/curl-common.h | 3 + src/curl.c | 10 +++--- src/download.c | 5 +-- src/fetch.c | 12 +++---- src/form.c | 12 +++++-- src/handle.c | 33 +++++++++++++++++++-- src/ieproxy.c | 12 +++++++ src/init.c | 2 + src/multi.c | 13 +++++--- src/nslookup.c | 15 ++++++++- src/utils.c | 15 ++++++++- src/version.c | 11 +++++-- src/winidn.c |only tests/testthat/helper-version.R | 2 - tests/testthat/test-certificates.R | 7 ++++ tests/testthat/test-idn.R |only tests/testthat/test-nonblocking.R | 1 tests/testthat/test-post.R | 56 ++++++++++++++++++++++++++++------- tools/winlibs.R | 4 +- 31 files changed, 287 insertions(+), 116 deletions(-)
Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by
Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data.
Functions include methods for searching by sequences by taxonomic names,
ids, collectors, and institutions; as well as a function for searching
for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between bold versions 0.4.0 dated 2017-01-06 and 0.5.0 dated 2017-07-21
DESCRIPTION | 24 +++--- MD5 | 70 +++++++++-------- NAMESPACE | 15 --- NEWS.md | 28 +++++++ R/bold-package.R | 28 +++---- R/bold_filter.R | 28 +++---- R/bold_identify.R | 25 +++--- R/bold_identify_parents.R | 62 ++++++++------- R/bold_seq.R | 14 +-- R/bold_seqspec.R | 70 +++++++++-------- R/bold_specimens.R | 27 +++--- R/bold_stats.R |only R/bold_tax_id.R | 20 ++--- R/bold_tax_name.R | 31 ++++--- R/bold_trace.R | 41 +++++----- R/zzz.R | 35 ++++---- README.md | 131 +++++++++++++++++++------------- build/vignette.rds |binary inst/doc/bold_vignette.Rmd | 140 ++++++++++++++--------------------- inst/doc/bold_vignette.html | 140 ++++++++++++++--------------------- man/bold-package.Rd | 17 ++-- man/bold_filter.Rd | 17 ++-- man/bold_identify.Rd | 11 +- man/bold_identify_parents.Rd | 27 +++--- man/bold_seq.Rd | 49 ++++++------ man/bold_seqspec.Rd | 74 ++++++++++-------- man/bold_specimens.Rd | 57 +++++++------- man/bold_stats.Rd |only man/bold_tax_id.Rd | 18 ++-- man/bold_tax_name.Rd | 20 ++--- man/bold_trace.Rd | 42 +++++----- man/sequences.Rd | 1 tests/testthat/test-bold_identify.R | 2 tests/testthat/test-bold_seq.R | 8 +- tests/testthat/test-bold_seqspec.R | 6 - tests/testthat/test-bold_specimens.R | 12 +-- vignettes/bold_vignette.Rmd | 140 ++++++++++++++--------------------- 37 files changed, 718 insertions(+), 712 deletions(-)
Title: Download, Manipulate, and Present American Community Survey and
Decennial Data from the US Census
Description: Provides a general toolkit for downloading, managing,
analyzing, and presenting data from the U.S. Census
(<https://www.census.gov/data/developers/data-sets.html>), including
SF1 (Decennial short-form), SF3 (Decennial long-form), and the
American Community Survey (ACS). Confidence intervals provided with
ACS data are converted to standard errors to be bundled with
estimates in complex acs objects. Package provides new methods to
conduct standard operations on acs objects and present/plot data in
statistically appropriate ways.
Author: Ezra Haber Glenn [aut, cre]
Maintainer: Ezra Haber Glenn <eglenn@mit.edu>
Diff between acs versions 2.1.0 dated 2017-07-03 and 2.1.1 dated 2017-07-21
DESCRIPTION | 23 ++++++++++++----------- MD5 | 12 ++++++------ NAMESPACE | 2 +- R/acs.R | 9 ++++----- README.md | 24 +++++++++++++++++------- man/acs-package.Rd | 2 +- man/acs.lookup.Rd | 3 ++- 7 files changed, 43 insertions(+), 32 deletions(-)
Title: Spatial Regression Models for Large Datasets using Nearest
Neighbor Gaussian Processes
Description: Fits Gaussian univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, Cook, Morton, Andersen, and Banerjee (2017) <arXiv:1702.00434v2>.
Author: Andrew Finley [aut, cre],
Abhirup Datta [aut],
Sudipto Banerjee [aut],
Alexander Mckim [ctb]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spNNGP versions 0.1.0 dated 2017-07-16 and 0.1.1 dated 2017-07-21
DESCRIPTION | 12 ++-- MD5 | 26 ++++----- R/spConjNNGP.R | 74 +++++++++++++++------------- R/spNNGP.R | 14 +++-- R/spPredict.R | 10 +-- man/spConjNNGP.Rd | 134 +++++++++++++++++++++++++++++++++++++-------------- man/spNNGP.Rd | 95 ++++++++++++++++++++++++------------ man/spPredict.Rd | 4 - src/cNNGP.cpp | 39 ++++++++------ src/rNNGP.cpp | 4 - src/rNNGPPredict.cpp | 12 ++-- src/sNNGP.cpp | 8 ++- src/sNNGPPredict.cpp | 4 - src/util.cpp | 4 - 14 files changed, 283 insertions(+), 157 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(<https://api.omniture.com/admin/1.4/rest/>).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.12 dated 2017-04-07 and 1.4.13 dated 2017-07-21
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- NEWS | 5 +++ R/RSiteCatalyst.R | 4 +- R/SCAuth.R | 25 +++++++++-------- man/RSiteCatalyst.Rd | 4 +- tests/testthat/test-queuedatawarehouse.R | 44 +++++++++++++++---------------- 7 files changed, 55 insertions(+), 47 deletions(-)
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 2.0 dated 2017-06-08 and 2.0.2 dated 2017-07-21
RSDA-2.0.2/RSDA/DESCRIPTION | 13 RSDA-2.0.2/RSDA/MD5 | 230 ++++++------- RSDA-2.0.2/RSDA/NAMESPACE | 8 RSDA-2.0.2/RSDA/R/RSDA.R | 7 RSDA-2.0.2/RSDA/R/SDS.to.RSDA.R | 204 +++++------ RSDA-2.0.2/RSDA/R/SODAS.to.RSDA.R | 58 +-- RSDA-2.0.2/RSDA/R/centers.interval.R | 5 RSDA-2.0.2/RSDA/R/cfa.CVPRealz.R | 8 RSDA-2.0.2/RSDA/R/cfa.Czz.R | 10 RSDA-2.0.2/RSDA/R/cfa.MatrixZ.R | 10 RSDA-2.0.2/RSDA/R/cfa.minmax.R | 14 RSDA-2.0.2/RSDA/R/cfa.scatterplot.R | 30 - RSDA-2.0.2/RSDA/R/cfa.totals.R | 17 RSDA-2.0.2/RSDA/R/change.coord.j.r | 4 RSDA-2.0.2/RSDA/R/classic.to.sym.R | 118 +++--- RSDA-2.0.2/RSDA/R/cor.sym.data.table.R | 25 - RSDA-2.0.2/RSDA/R/cov.sym.data.table.R | 28 - RSDA-2.0.2/RSDA/R/data.R | 34 + RSDA-2.0.2/RSDA/R/data.frame.to.RSDA.inteval.table.j.r | 6 RSDA-2.0.2/RSDA/R/data.frame.to.sym.inteval.j.r | 6 RSDA-2.0.2/RSDA/R/deter.coefficient.R | 6 RSDA-2.0.2/RSDA/R/dist.R |only RSDA-2.0.2/RSDA/R/dist.interval.R | 280 ++++++++------- RSDA-2.0.2/RSDA/R/dist.modal.R |only RSDA-2.0.2/RSDA/R/dist.set.R | 169 +++++---- RSDA-2.0.2/RSDA/R/downarrow.matrix.R | 11 RSDA-2.0.2/RSDA/R/generate.sym.table.R | 39 -- RSDA-2.0.2/RSDA/R/interscal.B.R | 4 RSDA-2.0.2/RSDA/R/interscal.R | 12 RSDA-2.0.2/RSDA/R/interscal.delta.R | 3 RSDA-2.0.2/RSDA/R/interval.dist.R | 19 - RSDA-2.0.2/RSDA/R/interval.dist.tobj.R | 4 RSDA-2.0.2/RSDA/R/interval.histogram.plot.R | 100 ++--- RSDA-2.0.2/RSDA/R/mean.sym.data.table.R | 11 RSDA-2.0.2/RSDA/R/median.sym.data.table.R | 14 RSDA-2.0.2/RSDA/R/meta.to.RSDA.j.r | 4 RSDA-2.0.2/RSDA/R/newSobject.R | 12 RSDA-2.0.2/RSDA/R/optim.pca.distance.j.r | 3 RSDA-2.0.2/RSDA/R/optim.pca.variance.j.r | 3 RSDA-2.0.2/RSDA/R/predictsym.glm.R | 25 - RSDA-2.0.2/RSDA/R/predictsym.lm.R | 22 - RSDA-2.0.2/RSDA/R/process.continue.variable.R | 3 RSDA-2.0.2/RSDA/R/process.continuum.variable.R | 6 RSDA-2.0.2/RSDA/R/process.histogram.variable.R | 44 +- RSDA-2.0.2/RSDA/R/process.inter.cont.variable.R | 11 RSDA-2.0.2/RSDA/R/process.interval.variable.R | 7 RSDA-2.0.2/RSDA/R/process.modal.variable.R | 42 +- RSDA-2.0.2/RSDA/R/process.mult.nominal.modif.variable.R | 20 - RSDA-2.0.2/RSDA/R/process.mult.nominal.variable.R | 17 RSDA-2.0.2/RSDA/R/process.nominal.variable.R | 14 RSDA-2.0.2/RSDA/R/process.set.variable.R | 15 RSDA-2.0.2/RSDA/R/read.sym.table.R | 14 RSDA-2.0.2/RSDA/R/scatter.sym.j.r | 4 RSDA-2.0.2/RSDA/R/sd.sym.data.table.R | 24 - RSDA-2.0.2/RSDA/R/sym.cfa.R | 29 - RSDA-2.0.2/RSDA/R/sym.circle.plot.R | 15 RSDA-2.0.2/RSDA/R/sym.cor.R | 19 - RSDA-2.0.2/RSDA/R/sym.cov.R | 30 - RSDA-2.0.2/RSDA/R/sym.data.table.to.sym.var.R | 3 RSDA-2.0.2/RSDA/R/sym.glm.R | 31 - RSDA-2.0.2/RSDA/R/sym.hclust.R | 5 RSDA-2.0.2/RSDA/R/sym.histogram.pca.R | 4 RSDA-2.0.2/RSDA/R/sym.interval.pc.2.j.r | 4 RSDA-2.0.2/RSDA/R/sym.interval.pc.R | 45 -- RSDA-2.0.2/RSDA/R/sym.interval.pc.limits.R | 7 RSDA-2.0.2/RSDA/R/sym.interval.pca.R | 283 +++++++--------- RSDA-2.0.2/RSDA/R/sym.kmeans.R | 9 RSDA-2.0.2/RSDA/R/sym.lm.R | 15 RSDA-2.0.2/RSDA/R/sym.lm.bi.R | 42 -- RSDA-2.0.2/RSDA/R/sym.mds.R | 4 RSDA-2.0.2/RSDA/R/sym.mean.R | 15 RSDA-2.0.2/RSDA/R/sym.median.R | 14 RSDA-2.0.2/RSDA/R/sym.normalize.R | 11 RSDA-2.0.2/RSDA/R/sym.obj.R | 6 RSDA-2.0.2/RSDA/R/sym.radar.plot.R | 181 +++++----- RSDA-2.0.2/RSDA/R/sym.scatterplot.R | 22 - RSDA-2.0.2/RSDA/R/sym.scatterplot.ggplot.R | 24 - RSDA-2.0.2/RSDA/R/sym.scatterplot3d.R | 58 +-- RSDA-2.0.2/RSDA/R/sym.sd.R | 26 - RSDA-2.0.2/RSDA/R/sym.variance.R | 24 - RSDA-2.0.2/RSDA/R/var.sym.data.table.R | 17 RSDA-2.0.2/RSDA/R/variance.princ.curve.R | 5 RSDA-2.0.2/RSDA/R/vertex.interval.R | 10 RSDA-2.0.2/RSDA/R/write.sym.table.R | 7 RSDA-2.0.2/RSDA/data/StudentsGrades.rda |binary RSDA-2.0.2/RSDA/data/VeterinaryData.rda |binary RSDA-2.0.2/RSDA/data/abalone.rda |binary RSDA-2.0.2/RSDA/data/example1.rda |binary RSDA-2.0.2/RSDA/data/example2.rda |binary RSDA-2.0.2/RSDA/data/example3.rda |binary RSDA-2.0.2/RSDA/data/example4.rda |binary RSDA-2.0.2/RSDA/data/example5.rda |binary RSDA-2.0.2/RSDA/data/example6.rda |binary RSDA-2.0.2/RSDA/data/lynne1.rda |binary RSDA-2.0.2/RSDA/data/lynne2.rda |binary RSDA-2.0.2/RSDA/data/oils.rda |binary RSDA-2.0.2/RSDA/data/sodasXML.rda |binary RSDA-2.0.2/RSDA/data/table7.rda |binary RSDA-2.0.2/RSDA/man/RSDA.Rd | 4 RSDA-2.0.2/RSDA/man/USCrime.Rd | 4 RSDA-2.0.2/RSDA/man/classic.to.sym.Rd | 2 RSDA-2.0.2/RSDA/man/cont.distance.Rd |only RSDA-2.0.2/RSDA/man/cor.Rd | 4 RSDA-2.0.2/RSDA/man/cov.Rd | 4 RSDA-2.0.2/RSDA/man/dist.Rd |only RSDA-2.0.2/RSDA/man/dist.mod.Rd |only RSDA-2.0.2/RSDA/man/dist.modal.Rd |only RSDA-2.0.2/RSDA/man/ex1_db2so.Rd | 2 RSDA-2.0.2/RSDA/man/example1.Rd | 4 RSDA-2.0.2/RSDA/man/example5.Rd | 12 RSDA-2.0.2/RSDA/man/example7.Rd | 12 RSDA-2.0.2/RSDA/man/hist.distance.Rd |only RSDA-2.0.2/RSDA/man/interval.distance.Rd |only RSDA-2.0.2/RSDA/man/modal.distance.Rd |only RSDA-2.0.2/RSDA/man/pander.sym.data.table.Rd |only RSDA-2.0.2/RSDA/man/process.histogram.variable.Rd | 2 RSDA-2.0.2/RSDA/man/select.dist.Rd |only RSDA-2.0.2/RSDA/man/set.distance.Rd |only RSDA-2.0.2/RSDA/man/sym.dist.interval.Rd |only RSDA-2.0.2/RSDA/man/sym.dist.set.Rd |only RSDA-2.0.2/RSDA/man/sym.interval.pca.Rd | 4 RSDA-2.0.2/RSDA/man/var.Rd | 4 RSDA-2.0/RSDA/man/dist.interval.Rd |only RSDA-2.0/RSDA/man/dist.set.Rd |only 124 files changed, 1359 insertions(+), 1461 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt and Changliang Zou
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.8.1 dated 2017-05-15 and 1.8.2 dated 2017-07-21
Rfast-1.8.1/Rfast/R/sourceRfiles.R |only Rfast-1.8.1/Rfast/man/iag.mle.Rd |only Rfast-1.8.1/Rfast/man/score.negbinregs.Rd |only Rfast-1.8.1/Rfast/man/score.weibregs.Rd |only Rfast-1.8.1/Rfast/man/sourceRfiles.Rd |only Rfast-1.8.1/Rfast/man/weibull.mle.Rd |only Rfast-1.8.1/Rfast/src/addfunctionstoexport.cpp |only Rfast-1.8.1/Rfast/src/colTabulate.cpp |only Rfast-1.8.1/Rfast/src/colmaxs.cpp |only Rfast-1.8.1/Rfast/src/colmeans.cpp |only Rfast-1.8.1/Rfast/src/colmeds.cpp |only Rfast-1.8.1/Rfast/src/colmins.cpp |only Rfast-1.8.1/Rfast/src/colnth.cpp |only Rfast-1.8.1/Rfast/src/colshuffle.cpp |only Rfast-1.8.1/Rfast/src/colsums.cpp |only Rfast-1.8.1/Rfast/src/cova.cpp |only Rfast-1.8.1/Rfast/src/functions_to_export.cpp |only Rfast-1.8.1/Rfast/src/functions_to_export.h |only Rfast-1.8.1/Rfast/src/rowMaxs.cpp |only Rfast-1.8.1/Rfast/src/rowMins.cpp |only Rfast-1.8.1/Rfast/src/rowTabulate.cpp |only Rfast-1.8.1/Rfast/src/rowmeans.cpp |only Rfast-1.8.1/Rfast/src/rowmeds.cpp |only Rfast-1.8.1/Rfast/src/rownth.cpp |only Rfast-1.8.1/Rfast/src/rowrange.cpp |only Rfast-1.8.1/Rfast/src/rowshuffle.cpp |only Rfast-1.8.1/Rfast/src/rowsums.cpp |only Rfast-1.8.2/Rfast/DESCRIPTION | 8 Rfast-1.8.2/Rfast/MD5 | 402 +++++++++++++++++++------ Rfast-1.8.2/Rfast/NAMESPACE | 4 Rfast-1.8.2/Rfast/R/AddToNamespace.R | 2 Rfast-1.8.2/Rfast/R/Diag.fill.R |only Rfast-1.8.2/Rfast/R/Diag.matrix.R |only Rfast-1.8.2/Rfast/R/Norm.R |only Rfast-1.8.2/Rfast/R/Pmax.R |only Rfast-1.8.2/Rfast/R/Pmin.R |only Rfast-1.8.2/Rfast/R/Table.R |only Rfast-1.8.2/Rfast/R/XopY.sum.R |only Rfast-1.8.2/Rfast/R/acg.mle.R | 2 Rfast-1.8.2/Rfast/R/allttests.R |only Rfast-1.8.2/Rfast/R/betaprime.mle.R |only Rfast-1.8.2/Rfast/R/bic.corfsreg.R |only Rfast-1.8.2/Rfast/R/binom.mle.R |only Rfast-1.8.2/Rfast/R/borel.mle.R |only Rfast-1.8.2/Rfast/R/btmprobs.R |only Rfast-1.8.2/Rfast/R/cauchy.mle.R |only Rfast-1.8.2/Rfast/R/checkAliases.R |only Rfast-1.8.2/Rfast/R/checkExamples.R |only Rfast-1.8.2/Rfast/R/checkNamespace.R |only Rfast-1.8.2/Rfast/R/chisq.mle.R |only Rfast-1.8.2/Rfast/R/cholesky.R |only Rfast-1.8.2/Rfast/R/colAny.R |only Rfast-1.8.2/Rfast/R/colFalse.R |only Rfast-1.8.2/Rfast/R/colMads.R | 6 Rfast-1.8.2/Rfast/R/colMaxs.R | 4 Rfast-1.8.2/Rfast/R/colMedians.R | 2 Rfast-1.8.2/Rfast/R/colMins.R | 4 Rfast-1.8.2/Rfast/R/colOrder.R |only Rfast-1.8.2/Rfast/R/colTabulate.R | 2 Rfast-1.8.2/Rfast/R/colTrue.R |only Rfast-1.8.2/Rfast/R/colTrueFalse.R |only Rfast-1.8.2/Rfast/R/colaucs.R |only Rfast-1.8.2/Rfast/R/coldiffs.R |only Rfast-1.8.2/Rfast/R/colgeom.mle.R |only Rfast-1.8.2/Rfast/R/colmeans.R | 2 Rfast-1.8.2/Rfast/R/colnth.R | 2 Rfast-1.8.2/Rfast/R/colpois.tests.R |only Rfast-1.8.2/Rfast/R/colpoisdisp.tests.R |only Rfast-1.8.2/Rfast/R/colpoisson.mle.R |only Rfast-1.8.2/Rfast/R/colprods.R |only Rfast-1.8.2/Rfast/R/colrow.zero.R |only Rfast-1.8.2/Rfast/R/colsums.R | 2 Rfast-1.8.2/Rfast/R/comb_n.R | 9 Rfast-1.8.2/Rfast/R/cor.fsreg.R | 53 ++- Rfast-1.8.2/Rfast/R/count_value.R | 6 Rfast-1.8.2/Rfast/R/cova.R | 6 Rfast-1.8.2/Rfast/R/ct.mle.R |only Rfast-1.8.2/Rfast/R/dmvnorm.R |only Rfast-1.8.2/Rfast/R/dmvt.R |only Rfast-1.8.2/Rfast/R/edist.R |only Rfast-1.8.2/Rfast/R/eel.test1.R |only Rfast-1.8.2/Rfast/R/eel.test2.R |only Rfast-1.8.2/Rfast/R/el.test1.R |only Rfast-1.8.2/Rfast/R/expmle.R |only Rfast-1.8.2/Rfast/R/floyd.R | 1 Rfast-1.8.2/Rfast/R/foldnorm.mle.R |only Rfast-1.8.2/Rfast/R/g2tests.R |only Rfast-1.8.2/Rfast/R/g2tests_perm.R |only Rfast-1.8.2/Rfast/R/gammamle.R |only Rfast-1.8.2/Rfast/R/gaussian.nb.R |only Rfast-1.8.2/Rfast/R/gaussiannb.pred.R |only Rfast-1.8.2/Rfast/R/geom.anova.R |only Rfast-1.8.2/Rfast/R/geom.anovas.R |only Rfast-1.8.2/Rfast/R/geom.mle.R |only Rfast-1.8.2/Rfast/R/gumbel.mle.R |only Rfast-1.8.2/Rfast/R/halfnorm.mle.R |only Rfast-1.8.2/Rfast/R/hash2list.R |only Rfast-1.8.2/Rfast/R/hd.eigen.R |only Rfast-1.8.2/Rfast/R/hsecant01.mle.R |only Rfast-1.8.2/Rfast/R/iag.mle.R | 88 ++--- Rfast-1.8.2/Rfast/R/ibeta.mle.R |only Rfast-1.8.2/Rfast/R/invdir.mle.R |only Rfast-1.8.2/Rfast/R/invgauss.mle.R |only Rfast-1.8.2/Rfast/R/knn.R |only Rfast-1.8.2/Rfast/R/laplace.mle.R |only Rfast-1.8.2/Rfast/R/lindley.mle.R |only Rfast-1.8.2/Rfast/R/logcauchy.mle.R |only Rfast-1.8.2/Rfast/R/logistic.cat1.R |only Rfast-1.8.2/Rfast/R/logistic.mle.R |only Rfast-1.8.2/Rfast/R/logitnorm.mle.R |only Rfast-1.8.2/Rfast/R/loglogistic.mle.R |only Rfast-1.8.2/Rfast/R/lognorm.mle.R |only Rfast-1.8.2/Rfast/R/logseries.mle.R |only Rfast-1.8.2/Rfast/R/lomax.mle.R |only Rfast-1.8.2/Rfast/R/lower_tri.R |only Rfast-1.8.2/Rfast/R/matrix.sum.R |only Rfast-1.8.2/Rfast/R/maxboltz.mle.R |only Rfast-1.8.2/Rfast/R/mediandir.R |only Rfast-1.8.2/Rfast/R/multinom.mle.R |only Rfast-1.8.2/Rfast/R/multinom.nb.R |only Rfast-1.8.2/Rfast/R/multinomnb.pred.R |only Rfast-1.8.2/Rfast/R/multivmf.mle.R |only Rfast-1.8.2/Rfast/R/mvnorm.mle.R |only Rfast-1.8.2/Rfast/R/normal.mle.R |only Rfast-1.8.2/Rfast/R/normlog.mle.R |only Rfast-1.8.2/Rfast/R/odds.R |only Rfast-1.8.2/Rfast/R/odds.ratio.R |only Rfast-1.8.2/Rfast/R/ordinal.mle.R |only Rfast-1.8.2/Rfast/R/pareto.mle.R |only Rfast-1.8.2/Rfast/R/pc.skel.R |only Rfast-1.8.2/Rfast/R/pois.test.R |only Rfast-1.8.2/Rfast/R/poisdisp.test.R |only Rfast-1.8.2/Rfast/R/poisson.anova.R |only Rfast-1.8.2/Rfast/R/poisson.anovas.R |only Rfast-1.8.2/Rfast/R/poisson.cat1.R |only Rfast-1.8.2/Rfast/R/poisson.mle.R |only Rfast-1.8.2/Rfast/R/poisson.nb.R |only Rfast-1.8.2/Rfast/R/poissonnb.pred.R |only Rfast-1.8.2/Rfast/R/prop.reg.R | 8 Rfast-1.8.2/Rfast/R/qpois.reg.R |only Rfast-1.8.2/Rfast/R/rayleigh.mle.R |only Rfast-1.8.2/Rfast/R/read.examples.R |only Rfast-1.8.2/Rfast/R/rep_col.R |only Rfast-1.8.2/Rfast/R/rint.mle.R |only Rfast-1.8.2/Rfast/R/rmdp.R | 11 Rfast-1.8.2/Rfast/R/rowAny.R |only Rfast-1.8.2/Rfast/R/rowFalse.R |only Rfast-1.8.2/Rfast/R/rowMads.R |only Rfast-1.8.2/Rfast/R/rowMaxs.R | 5 Rfast-1.8.2/Rfast/R/rowMedians.R | 2 Rfast-1.8.2/Rfast/R/rowMins.R | 5 Rfast-1.8.2/Rfast/R/rowOrder.R |only Rfast-1.8.2/Rfast/R/rowTabulate.R | 2 Rfast-1.8.2/Rfast/R/rowTrue.R |only Rfast-1.8.2/Rfast/R/rowTrueFalse.R |only Rfast-1.8.2/Rfast/R/rowmeans.R | 2 Rfast-1.8.2/Rfast/R/rownth.R | 2 Rfast-1.8.2/Rfast/R/rowprods.R |only Rfast-1.8.2/Rfast/R/rowrange.R | 6 Rfast-1.8.2/Rfast/R/rowsums.R | 2 Rfast-1.8.2/Rfast/R/score.expregs.R |only Rfast-1.8.2/Rfast/R/score.gammaregs.R |only Rfast-1.8.2/Rfast/R/score.geomregs.R |only Rfast-1.8.2/Rfast/R/score.invgaussregs.R |only Rfast-1.8.2/Rfast/R/score.ztpregs.R |only Rfast-1.8.2/Rfast/R/sourceR.R |only Rfast-1.8.2/Rfast/R/sourceRd.R |only Rfast-1.8.2/Rfast/R/spml.mle.R |only Rfast-1.8.2/Rfast/R/spml.reg.R |only Rfast-1.8.2/Rfast/R/tmle.R |only Rfast-1.8.2/Rfast/R/tobit.mle.R |only Rfast-1.8.2/Rfast/R/total.dist.R |only Rfast-1.8.2/Rfast/R/total.dista.R |only Rfast-1.8.2/Rfast/R/ttest1.R |only Rfast-1.8.2/Rfast/R/ttests.pairs.R |only Rfast-1.8.2/Rfast/R/upper_tri.R |only Rfast-1.8.2/Rfast/R/vm.mle.R | 6 Rfast-1.8.2/Rfast/R/weibull.mle.R | 2 Rfast-1.8.2/Rfast/R/wigner.mle.R |only Rfast-1.8.2/Rfast/man/AddToNamespace.Rd | 2 Rfast-1.8.2/Rfast/man/Diag.fill.Rd |only Rfast-1.8.2/Rfast/man/Norm.Rd |only Rfast-1.8.2/Rfast/man/Order.Rd | 2 Rfast-1.8.2/Rfast/man/Pmax.Rd |only Rfast-1.8.2/Rfast/man/Rfast-package.Rd | 12 Rfast-1.8.2/Rfast/man/Round.Rd | 4 Rfast-1.8.2/Rfast/man/Table.Rd |only Rfast-1.8.2/Rfast/man/XopY.sum.Rd |only Rfast-1.8.2/Rfast/man/acg.mle.Rd | 46 ++ Rfast-1.8.2/Rfast/man/allttests.Rd |only Rfast-1.8.2/Rfast/man/beta.mle.Rd | 80 ++++ Rfast-1.8.2/Rfast/man/bic.corfsreg.Rd |only Rfast-1.8.2/Rfast/man/btmprobs.Rd |only Rfast-1.8.2/Rfast/man/checkNamespace.Rd |only Rfast-1.8.2/Rfast/man/cholesky.Rd |only Rfast-1.8.2/Rfast/man/colAny.Rd |only Rfast-1.8.2/Rfast/man/colMads.Rd | 2 Rfast-1.8.2/Rfast/man/colOrder.Rd |only Rfast-1.8.2/Rfast/man/colTrue.Rd |only Rfast-1.8.2/Rfast/man/colaucs.Rd |only Rfast-1.8.2/Rfast/man/coldiffs.Rd |only Rfast-1.8.2/Rfast/man/colpoisdisp.tests.Rd |only Rfast-1.8.2/Rfast/man/colprods.Rd |only Rfast-1.8.2/Rfast/man/colrint.regbx.Rd | 3 Rfast-1.8.2/Rfast/man/colrow.zero.Rd |only Rfast-1.8.2/Rfast/man/cor.fsreg.Rd | 7 Rfast-1.8.2/Rfast/man/count_value.Rd | 18 - Rfast-1.8.2/Rfast/man/cova.Rd | 16 Rfast-1.8.2/Rfast/man/dista.Rd | 7 Rfast-1.8.2/Rfast/man/dmvnorm.Rd |only Rfast-1.8.2/Rfast/man/edist.Rd |only Rfast-1.8.2/Rfast/man/eel.test1.Rd |only Rfast-1.8.2/Rfast/man/eel.test2.Rd |only Rfast-1.8.2/Rfast/man/floyd.Rd | 15 Rfast-1.8.2/Rfast/man/fs.reg.Rd | 4 Rfast-1.8.2/Rfast/man/g2Test.Rd | 3 Rfast-1.8.2/Rfast/man/g2Test_univariate.Rd | 14 Rfast-1.8.2/Rfast/man/g2tests.Rd |only Rfast-1.8.2/Rfast/man/gammamle.Rd |only Rfast-1.8.2/Rfast/man/gaussian.nb.Rd |only Rfast-1.8.2/Rfast/man/gaussiannb.pred.Rd |only Rfast-1.8.2/Rfast/man/group.sum.Rd | 1 Rfast-1.8.2/Rfast/man/hash2list.Rd |only Rfast-1.8.2/Rfast/man/hd.eigen.Rd |only Rfast-1.8.2/Rfast/man/invdir.mle.Rd |only Rfast-1.8.2/Rfast/man/knn.Rd |only Rfast-1.8.2/Rfast/man/logistic.cat1.Rd |only Rfast-1.8.2/Rfast/man/lower_tri.Rd |only Rfast-1.8.2/Rfast/man/matrix.sum.Rd |only Rfast-1.8.2/Rfast/man/mediandir.Rd |only Rfast-1.8.2/Rfast/man/multinom.mle.Rd |only Rfast-1.8.2/Rfast/man/mvnorm.mle.Rd |only Rfast-1.8.2/Rfast/man/normal.mle.Rd |only Rfast-1.8.2/Rfast/man/odds.Rd |only Rfast-1.8.2/Rfast/man/odds.ratio.Rd |only Rfast-1.8.2/Rfast/man/ordinal.mle.Rd |only Rfast-1.8.2/Rfast/man/pc.skel.Rd |only Rfast-1.8.2/Rfast/man/poisdisp.test.Rd |only Rfast-1.8.2/Rfast/man/poisson.anova.Rd |only Rfast-1.8.2/Rfast/man/poisson.anovas.Rd |only Rfast-1.8.2/Rfast/man/prop.reg.Rd | 6 Rfast-1.8.2/Rfast/man/qpois.reg.Rd |only Rfast-1.8.2/Rfast/man/read.directory.Rd | 35 +- Rfast-1.8.2/Rfast/man/rep_col.Rd |only Rfast-1.8.2/Rfast/man/rm.lines.Rd | 55 ++- Rfast-1.8.2/Rfast/man/rowTrue.Rd |only Rfast-1.8.2/Rfast/man/score.betaregs.Rd | 68 ++-- Rfast-1.8.2/Rfast/man/score.glms.Rd | 7 Rfast-1.8.2/Rfast/man/sourceR.Rd |only Rfast-1.8.2/Rfast/man/spml.reg.Rd |only Rfast-1.8.2/Rfast/man/tobit.mle.Rd |only Rfast-1.8.2/Rfast/man/total.dist.Rd |only Rfast-1.8.2/Rfast/man/ttest1.Rd |only Rfast-1.8.2/Rfast/man/varcomps.mom.Rd | 5 Rfast-1.8.2/Rfast/man/vm.mle.Rd | 24 + Rfast-1.8.2/Rfast/man/zip.mle.Rd | 37 +- Rfast-1.8.2/Rfast/src/Diag_fill.cpp |only Rfast-1.8.2/Rfast/src/Diag_matrix.cpp |only Rfast-1.8.2/Rfast/src/Norm.cpp |only Rfast-1.8.2/Rfast/src/Table.cpp |only Rfast-1.8.2/Rfast/src/add_to_namespace.cpp |only Rfast-1.8.2/Rfast/src/all__functions.cpp | 71 ++++ Rfast-1.8.2/Rfast/src/binarysearch.cpp | 2 Rfast-1.8.2/Rfast/src/calc_k_nn.cpp |only Rfast-1.8.2/Rfast/src/calc_k_nn.h |only Rfast-1.8.2/Rfast/src/calc_pc_skel.cpp |only Rfast-1.8.2/Rfast/src/calc_pc_skel.h |only Rfast-1.8.2/Rfast/src/check_aliases.cpp |only Rfast-1.8.2/Rfast/src/check_namespace.cpp |only Rfast-1.8.2/Rfast/src/cholesky.cpp |only Rfast-1.8.2/Rfast/src/col_any.cpp |only Rfast-1.8.2/Rfast/src/col_diffs.cpp |only Rfast-1.8.2/Rfast/src/col_false.cpp |only Rfast-1.8.2/Rfast/src/col_mads.cpp |only Rfast-1.8.2/Rfast/src/col_max.cpp |only Rfast-1.8.2/Rfast/src/col_means.cpp |only Rfast-1.8.2/Rfast/src/col_meds.cpp |only Rfast-1.8.2/Rfast/src/col_min.cpp |only Rfast-1.8.2/Rfast/src/col_nth.cpp |only Rfast-1.8.2/Rfast/src/col_order.cpp |only Rfast-1.8.2/Rfast/src/col_prods.cpp |only Rfast-1.8.2/Rfast/src/col_row_zero.cpp |only Rfast-1.8.2/Rfast/src/col_shuffle.cpp |only Rfast-1.8.2/Rfast/src/col_sums.cpp |only Rfast-1.8.2/Rfast/src/col_tabulate.cpp |only Rfast-1.8.2/Rfast/src/col_true.cpp |only Rfast-1.8.2/Rfast/src/col_true_false.cpp |only Rfast-1.8.2/Rfast/src/comb_n.cpp | 12 Rfast-1.8.2/Rfast/src/count_value.cpp | 23 + Rfast-1.8.2/Rfast/src/cts.cpp |only Rfast-1.8.2/Rfast/src/cts.h |only Rfast-1.8.2/Rfast/src/edist.cpp |only Rfast-1.8.2/Rfast/src/gsquare_ex.cpp | 29 + Rfast-1.8.2/Rfast/src/hash2list.cpp |only Rfast-1.8.2/Rfast/src/init.c | 173 ++++++++-- Rfast-1.8.2/Rfast/src/k_nn.cpp |only Rfast-1.8.2/Rfast/src/logistic_only.cpp | 71 ++-- Rfast-1.8.2/Rfast/src/lower_tri.cpp |only Rfast-1.8.2/Rfast/src/matrix_sum.cpp |only Rfast-1.8.2/Rfast/src/mn.cpp | 72 ++++ Rfast-1.8.2/Rfast/src/mn.h | 11 Rfast-1.8.2/Rfast/src/odds_helper.cpp |only Rfast-1.8.2/Rfast/src/pc_skel.cpp |only Rfast-1.8.2/Rfast/src/pmax.cpp |only Rfast-1.8.2/Rfast/src/pmin.cpp |only Rfast-1.8.2/Rfast/src/poisson_only.cpp | 4 Rfast-1.8.2/Rfast/src/qpois_reg.cpp |only Rfast-1.8.2/Rfast/src/read_examples.cpp |only Rfast-1.8.2/Rfast/src/rep_col.cpp | 31 + Rfast-1.8.2/Rfast/src/row_any.cpp |only Rfast-1.8.2/Rfast/src/row_false.cpp |only Rfast-1.8.2/Rfast/src/row_len_sort_un_int.cpp |only Rfast-1.8.2/Rfast/src/row_mads.cpp |only Rfast-1.8.2/Rfast/src/row_max.cpp |only Rfast-1.8.2/Rfast/src/row_means.cpp |only Rfast-1.8.2/Rfast/src/row_meds.cpp |only Rfast-1.8.2/Rfast/src/row_min.cpp |only Rfast-1.8.2/Rfast/src/row_min_max.cpp | 27 - Rfast-1.8.2/Rfast/src/row_nth.cpp |only Rfast-1.8.2/Rfast/src/row_order.cpp |only Rfast-1.8.2/Rfast/src/row_prods.cpp |only Rfast-1.8.2/Rfast/src/row_shuffle.cpp |only Rfast-1.8.2/Rfast/src/row_sums.cpp |only Rfast-1.8.2/Rfast/src/row_tabulate.cpp |only Rfast-1.8.2/Rfast/src/row_true.cpp |only Rfast-1.8.2/Rfast/src/row_true_false.cpp |only Rfast-1.8.2/Rfast/src/spat_med.cpp | 4 Rfast-1.8.2/Rfast/src/spml_mle.cpp |only Rfast-1.8.2/Rfast/src/sum_x_op_x.cpp |only Rfast-1.8.2/Rfast/src/sum_x_op_y.cpp |only Rfast-1.8.2/Rfast/src/system_files.cpp |only Rfast-1.8.2/Rfast/src/system_files.h |only Rfast-1.8.2/Rfast/src/total_dist.cpp |only Rfast-1.8.2/Rfast/src/total_dista.cpp |only Rfast-1.8.2/Rfast/src/upper_triangle.cpp |only 335 files changed, 1229 insertions(+), 432 deletions(-)
Title: A Rules Engine Based on 'Drools'
Description: An interface for using the popular Java based Drools, which is a Business Rule Management System (See <https://www.drools.org> for more information). This package allows you to run a set of rules written in DRL format on the data using the Drools engine. Credits to Mu Sigma for their continued support throughout the development of the package.
Author: Ashwin Raaghav [cre, aut],
Zubin Dowlaty [aut],
Arushi Khattri [aut]
Maintainer: Ashwin Raaghav <Ashwin.Raaghav@mu-sigma.com>
Diff between Rdrools versions 1.0.1 dated 2017-06-19 and 1.0.2 dated 2017-07-21
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 10 +++++----- R/Rdrools.R | 12 ++++++------ inst/java/drools-1.0.2.jar |only man/Rdrools-package.Rd | 8 ++++---- man/rules.Rd | 2 +- man/rulesSession.Rd | 10 +++++----- man/runRules.Rd | 4 ++-- 9 files changed, 37 insertions(+), 36 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.7.4 dated 2017-07-10 and 0.7.5 dated 2017-07-21
DESCRIPTION | 6 +++--- MD5 | 20 +++++++++++--------- NAMESPACE | 5 +++++ R/init.R | 3 ++- R/superset.R | 4 +++- R/util.R | 37 +++++++++++++++++++++++++++++++++++++ inst/doc/parameter-table.html | 4 ++-- man/locf.Rd |only man/maxWidths.Rd | 9 --------- man/maxWidths.list.Rd |only man/superset.Rd | 3 +++ man/superset.numeric.Rd | 3 +++ 12 files changed, 69 insertions(+), 25 deletions(-)
Title: Create a Mini Version of CRAN Containing Only Selected Packages
Description: Makes it possible to create an internally consistent
repository consisting of selected packages from CRAN-like repositories.
The user specifies a set of desired packages, and 'miniCRAN' recursively
reads the dependency tree for these packages, then downloads only this
subset. The user can then install packages from this repository directly,
rather than from CRAN. This is useful in production settings, e.g. server
behind a firewall, or remote locations with slow broadband access.
Author: Microsoft Corporation [cph],
Andrie de Vries [aut, cre],
Alex Chubaty [ctb]
Maintainer: Andrie de
Vries <adevries@microsoft.com>
Diff between miniCRAN versions 0.2.7 dated 2016-08-21 and 0.2.9 dated 2017-07-21
miniCRAN-0.2.7/miniCRAN/R/testSuiteFunctions.R |only miniCRAN-0.2.7/miniCRAN/R/testthat_helpers.R |only miniCRAN-0.2.7/miniCRAN/tests/testthat/test-3b-makeRepo-from-localCRAN.R |only miniCRAN-0.2.7/miniCRAN/tests/testthat/test-4-updateRepo.R |only miniCRAN-0.2.9/miniCRAN/DESCRIPTION | 25 miniCRAN-0.2.9/miniCRAN/MD5 | 105 ++-- miniCRAN-0.2.9/miniCRAN/NAMESPACE | 8 miniCRAN-0.2.9/miniCRAN/NEWS | 77 +-- miniCRAN-0.2.9/miniCRAN/R/addPackages.R | 252 ++++++++-- miniCRAN-0.2.9/miniCRAN/R/getCranDescription.R | 45 + miniCRAN-0.2.9/miniCRAN/R/github-functions.R | 54 +- miniCRAN-0.2.9/miniCRAN/R/helpers.R | 28 - miniCRAN-0.2.9/miniCRAN/R/makeDepGraph.R | 60 +- miniCRAN-0.2.9/miniCRAN/R/makeRepo.R | 72 +- miniCRAN-0.2.9/miniCRAN/R/minicran-package.R | 63 +- miniCRAN-0.2.9/miniCRAN/R/pkgDep.R | 105 ++-- miniCRAN-0.2.9/miniCRAN/R/plot.pkgDepGraph.R | 11 miniCRAN-0.2.9/miniCRAN/R/updatePackages.R | 76 +-- miniCRAN-0.2.9/miniCRAN/build/vignette.rds |binary miniCRAN-0.2.9/miniCRAN/inst/doc/miniCRAN-dependency-graph.R | 10 miniCRAN-0.2.9/miniCRAN/inst/doc/miniCRAN-dependency-graph.html | 38 - miniCRAN-0.2.9/miniCRAN/inst/doc/miniCRAN-dependency-graph.rmd | 11 miniCRAN-0.2.9/miniCRAN/inst/doc/miniCRAN-introduction.html | 21 miniCRAN-0.2.9/miniCRAN/inst/doc/miniCRAN-non-CRAN-repos.html | 21 miniCRAN-0.2.9/miniCRAN/inst/examples/example_addPackageListingGithub.R | 10 miniCRAN-0.2.9/miniCRAN/inst/examples/example_checkVersions.R | 26 - miniCRAN-0.2.9/miniCRAN/inst/examples/example_makeDepGraph.R | 6 miniCRAN-0.2.9/miniCRAN/inst/examples/example_makeRepo.R | 12 miniCRAN-0.2.9/miniCRAN/inst/examples/example_pkgDep.R | 2 miniCRAN-0.2.9/miniCRAN/inst/examples/example_plot.pkgDepGraph.R | 11 miniCRAN-0.2.9/miniCRAN/inst/examples/example_updatePackages.R | 26 - miniCRAN-0.2.9/miniCRAN/man/addLocalPackage.Rd |only miniCRAN-0.2.9/miniCRAN/man/addOldPackage.Rd | 35 - miniCRAN-0.2.9/miniCRAN/man/addPackage.Rd | 35 - miniCRAN-0.2.9/miniCRAN/man/addPackageListingGithub.Rd | 15 miniCRAN-0.2.9/miniCRAN/man/basePkgs.Rd | 5 miniCRAN-0.2.9/miniCRAN/man/checkVersions.Rd | 31 - miniCRAN-0.2.9/miniCRAN/man/cranJuly2014.Rd | 3 miniCRAN-0.2.9/miniCRAN/man/getCranDescription.Rd | 5 miniCRAN-0.2.9/miniCRAN/man/listFiles.Rd |only miniCRAN-0.2.9/miniCRAN/man/makeDepGraph.Rd | 17 miniCRAN-0.2.9/miniCRAN/man/makeLibrary.Rd | 3 miniCRAN-0.2.9/miniCRAN/man/makeRepo.Rd | 78 +-- miniCRAN-0.2.9/miniCRAN/man/miniCRAN-package.Rd | 44 - miniCRAN-0.2.9/miniCRAN/man/pkgAvail.Rd | 15 miniCRAN-0.2.9/miniCRAN/man/pkgDep.Rd | 17 miniCRAN-0.2.9/miniCRAN/man/plot.pkgDepGraph.Rd | 20 miniCRAN-0.2.9/miniCRAN/man/repoBinPath.Rd | 5 miniCRAN-0.2.9/miniCRAN/man/repoPrefix.Rd | 63 +- miniCRAN-0.2.9/miniCRAN/man/twodigitRversion.Rd | 3 miniCRAN-0.2.9/miniCRAN/man/updatePackages.Rd | 57 +- miniCRAN-0.2.9/miniCRAN/tests/testthat/helpers.R |only miniCRAN-0.2.9/miniCRAN/tests/testthat/test-2-makeDepGraph.R | 58 -- miniCRAN-0.2.9/miniCRAN/tests/testthat/test-3-makeRepo.R | 30 - miniCRAN-0.2.9/miniCRAN/tests/testthat/test-4-makeRepo-from-localCRAN.R |only miniCRAN-0.2.9/miniCRAN/tests/testthat/test-5-updateRepo.R |only miniCRAN-0.2.9/miniCRAN/tests/testthat/test-6-getCranDescription.R |only miniCRAN-0.2.9/miniCRAN/tests/testthat/test-7-addGithubPackage.R |only miniCRAN-0.2.9/miniCRAN/vignettes/miniCRAN-dependency-graph.rmd | 11 59 files changed, 980 insertions(+), 745 deletions(-)
Title: Fuzzy Stationary Probabilities from a Sequence of Observations
of an Unknown Markov Chain
Description: An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain,
from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley
in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package 'FuzzyNumbers' is used to represent the output probabilities.
Author: Author: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Maintainer: Pablo J. Villacorta <pjvi@decsai.ugr.es>
Diff between FuzzyStatProb versions 2.0.2 dated 2016-07-30 and 2.0.3 dated 2017-07-21
FuzzyStatProb-2.0.2/FuzzyStatProb/inst/CITATION |only FuzzyStatProb-2.0.3/FuzzyStatProb/DESCRIPTION | 9 FuzzyStatProb-2.0.3/FuzzyStatProb/MD5 | 7 FuzzyStatProb-2.0.3/FuzzyStatProb/build/vignette.rds |binary FuzzyStatProb-2.0.3/FuzzyStatProb/man/fuzzyStationaryProb.Rd | 106 +++++------ 5 files changed, 59 insertions(+), 63 deletions(-)
Title: Meta-Analysis of Studies with Non Statistically-Significant
Unreported Effects
Description: Revisited version of MetaNSUE, a novel meta-analytic method that allows an unbiased inclusion of studies with Non Statistically-Significant Unreported Effects (NSUEs). Briefly, the method first calculates the interval where the unreported effects (e.g. t-values) should be according to the threshold of statistical significance used in each study. Afterwards, maximum likelihood techniques are used to impute the expected effect size of each study with NSUEs, accounting for between-study heterogeneity and potential covariates. Multiple imputations of the NSUEs are then randomly created based on the expected value, variance and statistical significance bounds. Finally, a restricted-maximum likelihood random-effects meta-analysis is separately conducted for each set of imputations, and estimations from these meta-analyses are pooled. Please read the reference in 'metansue' for details of the procedure.
Author: Joaquim Radua
Maintainer: Joaquim Radua <jradua@fidmag.com>
Diff between metansue versions 1.2 dated 2016-09-01 and 2.0 dated 2017-07-21
metansue-1.2/metansue/man/forest.meta.nsue.Rd |only metansue-1.2/metansue/man/funnel.meta.nsue.Rd |only metansue-1.2/metansue/man/leave1out.nsue.Rd |only metansue-1.2/metansue/man/linearHypothesis.Rd |only metansue-1.2/metansue/man/linearHypothesis.meta.nsue.Rd |only metansue-1.2/metansue/man/meta.nsue.Rd |only metansue-1.2/metansue/man/metabias.meta.nsue.Rd |only metansue-1.2/metansue/man/metalm.Rd |only metansue-1.2/metansue/man/metalm.meta.nsue.Rd |only metansue-2.0/metansue/DESCRIPTION | 11 metansue-2.0/metansue/MD5 | 51 metansue-2.0/metansue/NAMESPACE | 29 metansue-2.0/metansue/NEWS | 52 metansue-2.0/metansue/R/source.R | 1894 +++++++--------- metansue-2.0/metansue/build |only metansue-2.0/metansue/inst/CITATION | 3 metansue-2.0/metansue/inst/doc |only metansue-2.0/metansue/man/forest.Rd | 29 metansue-2.0/metansue/man/funnel.Rd | 34 metansue-2.0/metansue/man/leave1out.Rd | 48 metansue-2.0/metansue/man/meta.Rd | 73 metansue-2.0/metansue/man/metabias.Rd | 54 metansue-2.0/metansue/man/smc_from_t.Rd | 61 metansue-2.0/metansue/vignettes |only 24 files changed, 1237 insertions(+), 1102 deletions(-)
Title: Bayesian Inference for Marketing/Micro-Econometrics
Description: Covers many important models used
in marketing and micro-econometrics applications.
The package includes:
Bayes Regression (univariate or multivariate dep var),
Bayes Seemingly Unrelated Regression (SUR),
Binary and Ordinal Probit,
Multinomial Logit (MNL) and Multinomial Probit (MNP),
Multivariate Probit,
Negative Binomial (Poisson) Regression,
Multivariate Mixtures of Normals (including clustering),
Dirichlet Process Prior Density Estimation with normal base,
Hierarchical Linear Models with normal prior and covariates,
Hierarchical Linear Models with a mixture of normals prior and covariates,
Hierarchical Multinomial Logits with a mixture of normals prior
and covariates,
Hierarchical Multinomial Logits with a Dirichlet Process prior and covariates,
Hierarchical Negative Binomial Regression Models,
Bayesian analysis of choice-based conjoint data,
Bayesian treatment of linear instrumental variables models,
Analysis of Multivariate Ordinal survey data with scale
usage heterogeneity (as in Rossi et al, JASA (01)),
Bayesian Analysis of Aggregate Random Coefficient Logit Models as in BLP (see
Jiang, Manchanda, Rossi 2009)
For further reference, consult our book, Bayesian Statistics and
Marketing by Rossi, Allenby and McCulloch (Wiley 2005) and Bayesian Non- and Semi-Parametric
Methods and Applications (Princeton U Press 2014).
Author: Peter Rossi <perossichi@gmail.com>
Maintainer: Peter Rossi <perossichi@gmail.com>
Diff between bayesm versions 3.1-0 dated 2017-06-25 and 3.1-0.1 dated 2017-07-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/rhierMnlRwMixture_rcpp_loop.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between igraph versions 1.1.1 dated 2017-07-16 and 1.1.2 dated 2017-07-21
DESCRIPTION | 7 +++---- MD5 | 16 ++++++++-------- inst/NEWS.md | 7 +++++++ src/attributes.c | 4 ++++ src/bliss/utils.hh | 1 + src/second.f | 2 +- tests/testthat/test_graphNEL.R | 3 ++- tests/testthat/test_layout.fr.R | 2 ++ tests/testthat/test_sir.R | 2 ++ 9 files changed, 30 insertions(+), 14 deletions(-)
Title: Spatial Implementation of Bayesian Networks and Mapping
Description: Allows spatial implementation of Bayesian networks and mapping in geographical space. It makes maps of expected value (or most likely state) given known and unknown conditions, maps of uncertainty measured as coefficient of variation or Shannon index (entropy), maps of probability associated to any states of any node of the network. Some additional features are provided as well: parallel processing options, data discretization routines and function wrappers designed for users with minimal knowledge of the R language. Outputs can be exported to any common GIS format. Development was funded by the European Union FP7 (2007-2013), under project ROBIN (<http://robinproject.info>).
Author: Dario Masante [aut, cre]
Maintainer: Dario Masante <dario.masante@gmail.com>
Diff between bnspatial versions 1.0.1 dated 2016-12-14 and 1.0.2 dated 2017-07-21
bnspatial-1.0.1/bnspatial/man/ConwyLU.Rd |only bnspatial-1.0.1/bnspatial/man/ConwySlope.Rd |only bnspatial-1.0.1/bnspatial/man/ConwyStatus.Rd |only bnspatial-1.0.1/bnspatial/man/LUclasses.Rd |only bnspatial-1.0.1/bnspatial/man/LandUseChange.Rd |only bnspatial-1.0.1/bnspatial/man/evidence.Rd |only bnspatial-1.0.2/bnspatial/DESCRIPTION | 15 ++--- bnspatial-1.0.2/bnspatial/MD5 | 64 +++++++++------------- bnspatial-1.0.2/bnspatial/NEWS.md | 10 +++ bnspatial-1.0.2/bnspatial/R/Conwy-data.R | 53 ++---------------- bnspatial-1.0.2/bnspatial/R/aoi.R | 8 +- bnspatial-1.0.2/bnspatial/R/bnspatial.R | 2 bnspatial-1.0.2/bnspatial/R/dataDiscretize.R | 2 bnspatial-1.0.2/bnspatial/R/extractByMask.R | 2 bnspatial-1.0.2/bnspatial/R/linkNode.R | 7 +- bnspatial-1.0.2/bnspatial/R/loadNetwork.R | 2 bnspatial-1.0.2/bnspatial/R/mapTarget.R | 2 bnspatial-1.0.2/bnspatial/R/queryNet.R | 2 bnspatial-1.0.2/bnspatial/R/setClasses.R | 8 +- bnspatial-1.0.2/bnspatial/build/vignette.rds |binary bnspatial-1.0.2/bnspatial/data/ConwyData.RData |binary bnspatial-1.0.2/bnspatial/inst/COPYRIGHTS | 2 bnspatial-1.0.2/bnspatial/inst/doc/bnspatial.R | 4 + bnspatial-1.0.2/bnspatial/inst/doc/bnspatial.Rmd | 10 ++- bnspatial-1.0.2/bnspatial/inst/doc/bnspatial.html | 54 +++++++++--------- bnspatial-1.0.2/bnspatial/man/ConwyData.Rd | 5 + bnspatial-1.0.2/bnspatial/man/aoi.Rd | 3 - bnspatial-1.0.2/bnspatial/man/bnspatial.Rd | 5 + bnspatial-1.0.2/bnspatial/man/dataDiscretize.Rd | 6 +- bnspatial-1.0.2/bnspatial/man/extractByMask.Rd | 3 - bnspatial-1.0.2/bnspatial/man/linkNode.Rd | 13 ++-- bnspatial-1.0.2/bnspatial/man/loadNetwork.Rd | 3 - bnspatial-1.0.2/bnspatial/man/mapTarget.Rd | 3 - bnspatial-1.0.2/bnspatial/man/queryNet.Rd | 6 +- bnspatial-1.0.2/bnspatial/man/setClasses.Rd | 8 +- bnspatial-1.0.2/bnspatial/vignettes/bnspatial.Rmd | 10 ++- 36 files changed, 155 insertions(+), 157 deletions(-)
Title: The Impact of Items
Description: Implement a multivariate analysis of the impact of items to identify a bias in the questionnaire validation of Likert-type scale variables. The items requires considering a null value (category doesn't have tendency). Offering frequency, importance and impact of the items.
Author: Nery Sofia Huerta-Pacheco
Maintainer: Nery Sofia Huerta-Pacheco <nehuerta@uv.mx>
Diff between IMPACT versions 0.1.0 dated 2016-06-20 and 0.1.1 dated 2017-07-21
DESCRIPTION | 12 +++++----- MD5 | 8 +++--- NAMESPACE | 8 ++++-- R/IMPACT.R | 69 +++++++++++++++++++++++++++++++++++++++------------------- man/IMPACT.Rd | 29 +++++++++++++++--------- 5 files changed, 80 insertions(+), 46 deletions(-)
Title: Methods for Statistical Disclosure Control in Tabular Data
Description: Methods for statistical disclosure control in
tabular data such as primary and secondary cell suppression are covered in
this package.
Author: Bernhard Meindl
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between sdcTable versions 0.22.6 dated 2017-05-18 and 0.22.7 dated 2017-07-21
DESCRIPTION | 8 - MD5 | 27 ++-- NAMESPACE | 1 R/RcppExports.R | 8 - R/classes_tauBatch.r | 33 ++++- R/createArgusInput.R | 61 ++++++++-- R/runArgusBatchFile.R | 82 +++++++++----- R/tauBatch_helpers.R | 275 +++++++++++++++++++++++++++++++++++------------ inst/doc/sdcTable.pdf |binary man/argusVersion.Rd |only man/createArgusInput.Rd | 34 ++++- man/runArgusBatchFile.Rd | 19 ++- src/RcppExports.cpp | 8 - src/init.c | 18 +-- src/suppMultDimTable.cpp | 54 ++++----- 15 files changed, 450 insertions(+), 178 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.3.8 dated 2016-11-26 and 3.4.3 dated 2017-07-21
DESCRIPTION | 26 +++--- MD5 | 32 ++++--- R/formula.R | 58 +++++++++++++ R/rcdk.R | 3 R/smiles.R | 147 +++++++++++++++++++++++++++------- R/visual.R | 77 +++++++++++++++-- build/vignette.rds |binary inst/cont/rcdk.jar |binary inst/doc/rcdk.R | 4 inst/doc/rcdk.Rnw | 4 inst/doc/rcdk.pdf |binary inst/unitTests/runit.smiles.R | 2 man/compare.isotope.pattern.Rd |only man/get.isotope.pattern.generator.Rd |only man/get.isotope.pattern.similarity.Rd |only man/getsmiles.Rd | 22 ++--- man/smiles.flavors.Rd |only man/viewmol2d.Rd | 36 ++++++-- vignettes/rcdk.Rnw | 4 19 files changed, 320 insertions(+), 95 deletions(-)
Title: Maximal Information-Based Nonparametric Exploration for Variable
Analysis
Description: Wrapper for 'minepy' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation of
'minepy' can be found at <http://minepy.readthedocs.io/en/latest>.
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide
Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman
[ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi <michele.filosi@unitn.it>
Diff between minerva versions 1.4.5 dated 2016-03-14 and 1.4.7 dated 2017-07-21
DESCRIPTION | 33 - MD5 | 24 - NAMESPACE | 2 NEWS | 4 R/mine.R | 66 +-- README.md | 35 + man/mine.Rd | 12 man/minerva-package.Rd | 9 src/mine.c | 973 +++++++++++++++++++++++++------------------------ src/mine.h | 150 +++++-- src/mine_interface.c | 10 src/minerva_init.c |only tests/testspellman0.R | 3 tests/testthat |only 14 files changed, 747 insertions(+), 574 deletions(-)
Title: Masked User Input
Description: A micro-package for reading "passwords", i.e. reading
user input with masking, so that the input is not displayed as it
is typed. Currently we have support for 'RStudio', the command line
(every OS), and any platform where 'tcltk' is present.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
Gabor Csardi [ctb] (Improved terminal detection),
Rich FitzJohn [ctb]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between getPass versions 0.2-1 dated 2017-07-18 and 0.2-2 dated 2017-07-21
ChangeLog | 5 ++++- DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 2 +- inst/doc/getPass.pdf |binary tests/readline_masked.r | 11 ++--------- 6 files changed, 15 insertions(+), 19 deletions(-)
Title: Extract-Transform-Load Framework for Medium Data
Description: A framework for loading medium-sized data from
the Internet to a local or remote relational database management system.
This package itself does not do much more than provide a toy example and set up
the method structure. Packages that depend on this package will facilitate the
construction and maintenance of their respective databases.
Author: Ben Baumer [aut, cre],
Carson Sievert [ctb]
Maintainer: Ben Baumer <ben.baumer@gmail.com>
Diff between etl versions 0.3.5 dated 2016-11-29 and 0.3.6 dated 2017-07-21
DESCRIPTION | 15 ++++---- MD5 | 40 ++++++++++++----------- NAMESPACE | 7 ++-- NEWS.md | 10 +++++ R/dbRunScript.R | 14 +++----- R/etl.R | 10 ++--- R/etl_extract.R | 38 +++++++++++++++++++++ R/etl_load.R | 52 +++++++++++++++++++++++------ R/utils.R | 66 ++++++++++++++++++++++---------------- README.md | 34 ++++++++----------- man/dbRunScript.Rd | 11 ++---- man/dbWipe.Rd | 5 +- man/db_type.Rd |only man/etl.Rd | 13 +++---- man/etl_create.Rd | 8 ++-- man/etl_init.Rd | 1 man/match_files_by_year_months.Rd | 5 +- man/smart_download.Rd | 15 ++++++-- man/smart_upload.Rd |only man/src_mysql_cnf.Rd | 1 man/valid_year_month.Rd | 1 tests/testthat/test-etl.R | 62 ++++++++++++++++++++--------------- 22 files changed, 252 insertions(+), 156 deletions(-)
Title: Statistical Patterns in Genomic Sequences
Description: A collection of statistical hypothesis tests and other
techniques for identifying certain spatial relationships/phenomena in
DNA sequences. In particular, it provides tests and graphical methods for determining
whether or not DNA sequences comply with Chargaff's second parity rule
or exhibit purine-pyrimidine parity. In addition, there are functions for
efficiently simulating discrete state space Markov chains and testing
arbitrary symbolic sequences of symbols for the presence of first-order
Markovianness.
Also, it has functions for counting words/k-mers (and cylinder patterns) in
arbitrary symbolic sequences. Functions which take a DNA sequence as input
can handle sequences stored as SeqFastadna objects from the 'seqinr' package.
Author: Andrew Hart [aut, cre], Servet Martínez [aut], Universidad de Chile [cph], INRIA-Chile [cph]
Maintainer: Andrew Hart <ahart@dim.uchile.cl>
Diff between spgs versions 1.0 dated 2015-03-28 and 1.0-1 dated 2017-07-21
spgs-1.0-1/spgs/DESCRIPTION | 9 spgs-1.0-1/spgs/MD5 | 96 spgs-1.0-1/spgs/NAMESPACE | 4 spgs-1.0-1/spgs/R/MarkovChains.R | 5 spgs-1.0-1/spgs/R/agct.test.R | 9 spgs-1.0-1/spgs/R/auxtests.R | 8 spgs-1.0-1/spgs/R/chargaff1.test.R | 8 spgs-1.0-1/spgs/R/chargaff2.test.R | 18 spgs-1.0-1/spgs/R/counting.R | 25 spgs-1.0-1/spgs/cleanup | 4 spgs-1.0-1/spgs/configure | 3940 ++++++++++++----------------- spgs-1.0-1/spgs/configure.ac | 48 spgs-1.0-1/spgs/inst |only spgs-1.0-1/spgs/man/ag.test.Rd | 36 spgs-1.0-1/spgs/man/agct.test.Rd | 36 spgs-1.0-1/spgs/man/array2vector.Rd | 36 spgs-1.0-1/spgs/man/chargaff.gibbs.test.Rd | 36 spgs-1.0-1/spgs/man/chargaff0.test.Rd | 36 spgs-1.0-1/spgs/man/chargaff1.test.Rd | 36 spgs-1.0-1/spgs/man/chargaff2.test.Rd | 36 spgs-1.0-1/spgs/man/chisq.unif.test.Rd | 36 spgs-1.0-1/spgs/man/complement.Rd | 36 spgs-1.0-1/spgs/man/cylinder.counts.Rd | 36 spgs-1.0-1/spgs/man/diffsign.test.Rd | 36 spgs-1.0-1/spgs/man/diid.disturbance.Rd | 38 spgs-1.0-1/spgs/man/diid.test.Rd | 39 spgs-1.0-1/spgs/man/disambiguate.Rd | 36 spgs-1.0-1/spgs/man/estimateMarkovChain.Rd | 36 spgs-1.0-1/spgs/man/ks.unif.test.Rd | 36 spgs-1.0-1/spgs/man/lb.test.Rd | 36 spgs-1.0-1/spgs/man/markov.disturbance.Rd | 36 spgs-1.0-1/spgs/man/markov.test.Rd | 39 spgs-1.0-1/spgs/man/nanoarchaeum.Rd | 36 spgs-1.0-1/spgs/man/pair.counts.Rd | 36 spgs-1.0-1/spgs/man/pieris.Rd | 36 spgs-1.0-1/spgs/man/quadruple.counts.Rd | 36 spgs-1.0-1/spgs/man/rcspr2mat.Rd | 36 spgs-1.0-1/spgs/man/reverseComplement.Rd | 36 spgs-1.0-1/spgs/man/rstochmat.Rd | 36 spgs-1.0-1/spgs/man/rstochvec.Rd | 36 spgs-1.0-1/spgs/man/simulateMarkovChain.Rd | 36 spgs-1.0-1/spgs/man/spgs-package.Rd | 36 spgs-1.0-1/spgs/man/triple.counts.Rd | 36 spgs-1.0-1/spgs/man/turningpoint.test.Rd | 36 spgs-1.0-1/spgs/src/Makevars.in | 3 spgs-1.0-1/spgs/src/Makevars.win | 3 spgs-1.0-1/spgs/src/spgs-win.def |only spgs-1.0-1/spgs/src/spgs.c | 26 spgs-1.0-1/spgs/src/spgs.h | 97 spgs-1.0/spgs/src/sharedef.h |only 50 files changed, 2427 insertions(+), 3000 deletions(-)
Title: Generalized Random Forests (Beta)
Description: A pluggable package for forest-based statistical estimation and inference.
GRF currently provides methods for non-parametric least-squares regression,
quantile regression, and treatment effect estimation (optionally using instrumental
variables). This package is currently in beta, and we expect to make continual
improvements to its performance and usability.
Author: Julie Tibshirani [aut, cre],
Susan Athey [aut],
Stefan Wager [aut],
Marvin Wright [ctb],
all contributors to the included version of Eigen [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>
Diff between grf versions 0.9.2 dated 2017-07-04 and 0.9.3 dated 2017-07-21
DESCRIPTION | 6 MD5 | 78 +++--- R/RcppExports.R | 52 ++-- R/analysis_tools.R | 27 ++ R/average_effect.R | 20 + R/causal_forest.R | 62 ++++- R/custom_forest.R | 37 ++- R/instrumental_forest.R | 31 +- R/print.R | 2 R/quantile_forest.R | 46 +++ R/regression_forest.R | 61 ++++- man/causal_forest.Rd | 27 ++ man/custom_forest.Rd | 13 + man/estimate_average_effect.Rd | 21 + man/get_tree.Rd | 12 + man/instrumental_forest.Rd | 7 man/predict.causal_forest.Rd | 21 + man/predict.custom_forest.Rd | 13 + man/predict.quantile_forest.Rd | 18 + man/predict.regression_forest.Rd | 22 + man/quantile_forest.Rd | 19 + man/regression_forest.Rd | 29 ++ man/split_frequencies.Rd | 15 + src/CustomForestBindings.cpp | 9 src/InstrumentalForestBindings.cpp | 35 +- src/QuantileForestBindings.cpp | 9 src/RcppExports.cpp | 120 ++++------ src/RcppUtilities.cpp | 6 src/RcppUtilities.h | 1 src/RegressionForestBindings.cpp | 20 - src/src/commons/Data.cpp | 50 ---- src/src/commons/Data.h | 44 --- src/src/forest/ForestPredictor.cpp | 4 src/src/forest/ForestTrainer.cpp | 64 ++--- src/src/forest/ForestTrainer.h | 5 src/src/forest/ForestTrainers.cpp | 36 +++ src/src/forest/ForestTrainers.h | 13 + src/src/splitting/RegularizedRegressionSplittingRule.cpp |only src/src/splitting/RegularizedRegressionSplittingRule.h |only src/src/splitting/factory/RegularizedRegressionSplittingRuleFactory.cpp |only src/src/splitting/factory/RegularizedRegressionSplittingRuleFactory.h |only tests/testthat/test_causal_forest.R | 4 42 files changed, 712 insertions(+), 347 deletions(-)
Title: Perform Spatial Error Estimation and Variable Importance in
Parallel
Description: Implements spatial error estimation and
permutation-based variable importance measures for predictive models using
spatial cross-validation and spatial block bootstrap.
Author: Alexander Brenning [aut, cre],
Patrick Schratz [aut],
Tobias Herrmann [aut]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between sperrorest versions 2.0.0 dated 2017-06-13 and 2.0.1 dated 2017-07-21
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++++------ NEWS | 6 ++++++ NEWS.md | 5 +++++ R/processing.R | 4 ++++ README.md | 2 +- build/vignette.rds |binary inst/testfiles/sptune_input.rda |only inst/testfiles/svm_cv_err_input.rda |only inst/testfiles/svm_cv_err_input.rda_3 |only inst/testfiles/svm_cv_err_input_2.rda |only inst/testfiles/svm_cv_err_input_3.rda |only 12 files changed, 31 insertions(+), 11 deletions(-)