Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.11.0 dated 2020-06-26 and 0.12.0 dated 2020-08-28
renv-0.11.0/renv/tests/testthat/test-diagnostics.R |only renv-0.12.0/renv/DESCRIPTION | 14 - renv-0.12.0/renv/MD5 | 138 +++++++------- renv-0.12.0/renv/NEWS.md | 36 +++ renv-0.12.0/renv/R/activate.R | 18 + renv-0.12.0/renv/R/archive.R | 3 renv-0.12.0/renv/R/cache.R | 19 + renv-0.12.0/renv/R/config-defaults.R | 2 renv-0.12.0/renv/R/difftime.R |only renv-0.12.0/renv/R/equip-macos.R | 2 renv-0.12.0/renv/R/http.R | 8 renv-0.12.0/renv/R/hydrate.R | 35 +-- renv-0.12.0/renv/R/imbue.R | 9 renv-0.12.0/renv/R/install.R | 83 +++++++- renv-0.12.0/renv/R/l10n.R |only renv-0.12.0/renv/R/load.R | 52 +++-- renv-0.12.0/renv/R/lockfile-diff.R | 3 renv-0.12.0/renv/R/packages.R | 5 renv-0.12.0/renv/R/patch.R | 26 ++ renv-0.12.0/renv/R/paths.R | 8 renv-0.12.0/renv/R/project.R | 50 ++--- renv-0.12.0/renv/R/record.R | 10 + renv-0.12.0/renv/R/regexps.R |only renv-0.12.0/renv/R/remotes.R | 30 +++ renv-0.12.0/renv/R/remove.R | 1 renv-0.12.0/renv/R/repos.R | 2 renv-0.12.0/renv/R/restart.R | 2 renv-0.12.0/renv/R/restore.R | 2 renv-0.12.0/renv/R/retrieve.R | 110 ++++++++--- renv-0.12.0/renv/R/rspm.R | 2 renv-0.12.0/renv/R/rstudio.R | 15 + renv-0.12.0/renv/R/run.R | 4 renv-0.12.0/renv/R/snapshot-auto.R |only renv-0.12.0/renv/R/snapshot.R | 48 ---- renv-0.12.0/renv/R/test.R |only renv-0.12.0/renv/R/tests.R | 75 ++++++- renv-0.12.0/renv/R/testthat-reporter.R |only renv-0.12.0/renv/R/upgrade.R | 20 +- renv-0.12.0/renv/R/zzz.R | 1 renv-0.12.0/renv/README.md | 2 renv-0.12.0/renv/build/vignette.rds |binary renv-0.12.0/renv/inst/config.yml | 2 renv-0.12.0/renv/inst/doc/collaborating.Rmd | 80 ++++---- renv-0.12.0/renv/inst/doc/collaborating.html | 22 +- renv-0.12.0/renv/inst/doc/docker.Rmd | 2 renv-0.12.0/renv/inst/doc/docker.html | 10 - renv-0.12.0/renv/inst/doc/faq.Rmd | 54 +++++ renv-0.12.0/renv/inst/doc/faq.html | 35 ++- renv-0.12.0/renv/inst/doc/local-sources.html | 2 renv-0.12.0/renv/inst/doc/lockfile.html | 2 renv-0.12.0/renv/inst/doc/mran.html | 10 - renv-0.12.0/renv/inst/doc/renv.html | 42 ++-- renv-0.12.0/renv/inst/resources/WELCOME | 2 renv-0.12.0/renv/man/config.Rd | 2 renv-0.12.0/renv/man/imbue.Rd | 4 renv-0.12.0/renv/man/install.Rd | 37 +++ renv-0.12.0/renv/man/renv-package.Rd | 2 renv-0.12.0/renv/man/snapshot.Rd | 7 renv-0.12.0/renv/tests/testthat.R | 4 renv-0.12.0/renv/tests/testthat/helper-aaa.R | 8 renv-0.12.0/renv/tests/testthat/test-activate.R | 2 renv-0.12.0/renv/tests/testthat/test-archive.R | 2 renv-0.12.0/renv/tests/testthat/test-available-packages.R | 8 renv-0.12.0/renv/tests/testthat/test-files.R | 2 renv-0.12.0/renv/tests/testthat/test-install.R | 15 + renv-0.12.0/renv/tests/testthat/test-parse.R | 2 renv-0.12.0/renv/tests/testthat/test-paths.R | 6 renv-0.12.0/renv/tests/testthat/test-profiles.R | 2 renv-0.12.0/renv/tests/testthat/test-remotes.R | 2 renv-0.12.0/renv/vignettes/collaborating.Rmd | 80 ++++---- renv-0.12.0/renv/vignettes/configuration.R |only renv-0.12.0/renv/vignettes/configuration.html |only renv-0.12.0/renv/vignettes/configuration.md |only renv-0.12.0/renv/vignettes/docker.Rmd | 2 renv-0.12.0/renv/vignettes/faq.Rmd | 54 +++++ 75 files changed, 948 insertions(+), 391 deletions(-)
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.9.3 dated 2020-05-26 and 0.9.4 dated 2020-08-28
DESCRIPTION | 6 MD5 | 14 - build/vignette.rds |binary inst/NEWS | 3 inst/doc/HTML.html | 528 +++++++++++++++++++++++++++++++-------------- inst/doc/knitrTables.pdf |binary inst/doc/tables.pdf |binary vignettes/tables.Rout.save | 10 8 files changed, 384 insertions(+), 177 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 3.8 dated 2020-06-29 and 4.0 dated 2020-08-28
DESCRIPTION | 12 - MD5 | 21 +- NEWS | 8 + R/emf.R | 9 - configure | 33 ++++ configure.ac | 25 +++ man/emf.Rd | 31 ++-- src/devEMF.cpp | 144 ++++++++++++++---- src/emf+.h | 198 +++++++++++++++++++------ src/emf.h | 21 -- src/fontembed.h |only src/fontmetrics.h | 414 ++++++++++++++++++++++++++++++++++++++++++++++-------- 12 files changed, 721 insertions(+), 195 deletions(-)
Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: The goal for of the 'SwimmeR' package is to provide means of acquiring, and then analyzing, data from swimming (and diving) competitions. To that end 'SwimmeR' allows results to be read in from .html sources, like 'Hy-Tek' real time results pages, '.pdf' files, and now (on a development basis) '.hy3' files. Once read in, 'SwimmeR' can convert swimming times (performances) between the computationally useful format of seconds reported to the '100ths' place (e.g. 95.37), and the conventional reporting format (1:35.37) used in the swimming community. 'SwimmeR' can also score meets in a variety of formats with user defined point values, convert times between courses ('LCM', 'SCM', 'SCY') and draw single elimination brackets, as well as providing a suite of tools for working cleaning swimming data. This is a developmental package, not yet mature.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between SwimmeR versions 0.3.1 dated 2020-07-11 and 0.4.1 dated 2020-08-28
SwimmeR-0.3.1/SwimmeR/R/test_sets.R |only SwimmeR-0.3.1/SwimmeR/inst/extdata/df_test.csv |only SwimmeR-0.3.1/SwimmeR/tests/testthat/Texas-Florida-Indiana.pdf |only SwimmeR-0.4.1/SwimmeR/DESCRIPTION | 15 SwimmeR-0.4.1/SwimmeR/LICENSE | 4 SwimmeR-0.4.1/SwimmeR/MD5 | 114 SwimmeR-0.4.1/SwimmeR/NAMESPACE | 109 SwimmeR-0.4.1/SwimmeR/NEWS.md | 47 SwimmeR-0.4.1/SwimmeR/R/Course_Convert.R | 182 SwimmeR-0.4.1/SwimmeR/R/Course_Convert_DF.R | 208 SwimmeR-0.4.1/SwimmeR/R/King200Breast.R | 28 SwimmeR-0.4.1/SwimmeR/R/Read_Results.R | 116 SwimmeR-0.4.1/SwimmeR/R/SwimR.R | 12 SwimmeR-0.4.1/SwimmeR/R/Swim_Parse.R | 2586 +++++----- SwimmeR-0.4.1/SwimmeR/R/add_row_numbers.R |only SwimmeR-0.4.1/SwimmeR/R/dive_place.R |only SwimmeR-0.4.1/SwimmeR/R/draw_bracket.R | 632 +- SwimmeR-0.4.1/SwimmeR/R/event_parse.R |only SwimmeR-0.4.1/SwimmeR/R/fold.R | 60 SwimmeR-0.4.1/SwimmeR/R/get_mode.R | 92 SwimmeR-0.4.1/SwimmeR/R/globals.R | 73 SwimmeR-0.4.1/SwimmeR/R/hy3_places.R |only SwimmeR-0.4.1/SwimmeR/R/hy3_times.R |only SwimmeR-0.4.1/SwimmeR/R/interleave_results.R |only SwimmeR-0.4.1/SwimmeR/R/mmss_format.R | 52 SwimmeR-0.4.1/SwimmeR/R/not_in.R |only SwimmeR-0.4.1/SwimmeR/R/parse_hy3.R |only SwimmeR-0.4.1/SwimmeR/R/relay_aggregate.R | 18 SwimmeR-0.4.1/SwimmeR/R/results_score.R |only SwimmeR-0.4.1/SwimmeR/R/sec_format.R | 56 SwimmeR-0.4.1/SwimmeR/R/sec_format_helper.R | 56 SwimmeR-0.4.1/SwimmeR/R/swim_place.R |only SwimmeR-0.4.1/SwimmeR/R/tie_rescore.R |only SwimmeR-0.4.1/SwimmeR/R/utils-pipe.R | 22 SwimmeR-0.4.1/SwimmeR/README.md | 226 SwimmeR-0.4.1/SwimmeR/build/vignette.rds |binary SwimmeR-0.4.1/SwimmeR/inst/doc/SwimmeR.R | 191 SwimmeR-0.4.1/SwimmeR/inst/doc/SwimmeR.Rmd | 336 - SwimmeR-0.4.1/SwimmeR/inst/doc/SwimmeR.html | 1029 ++- SwimmeR-0.4.1/SwimmeR/inst/extdata/2020_NI_Champs_Qualifier_UNAC.hy3 |only SwimmeR-0.4.1/SwimmeR/inst/extdata/BigTen_WSWIM_2018.pdf |only SwimmeR-0.4.1/SwimmeR/inst/extdata/Meet-Results-Nassau-County-Championships-09Feb2011-002.hy3 |only SwimmeR-0.4.1/SwimmeR/inst/extdata/Swim_Parse_Testing.R | 2264 ++++---- SwimmeR-0.4.1/SwimmeR/inst/extdata/TX_OH_Results.csv |only SwimmeR-0.4.1/SwimmeR/inst/extdata/df_standard.csv |only SwimmeR-0.4.1/SwimmeR/inst/extdata/larger_Swim_Parse_test.R | 104 SwimmeR-0.4.1/SwimmeR/man/King200Breast.Rd | 38 SwimmeR-0.4.1/SwimmeR/man/Read_Results.Rd | 64 SwimmeR-0.4.1/SwimmeR/man/Swim_Parse.Rd | 104 SwimmeR-0.4.1/SwimmeR/man/SwimmeR.Rd | 29 SwimmeR-0.4.1/SwimmeR/man/add_row_numbers.Rd |only SwimmeR-0.4.1/SwimmeR/man/dive_place.Rd |only SwimmeR-0.4.1/SwimmeR/man/event_parse.Rd |only SwimmeR-0.4.1/SwimmeR/man/get_mode.Rd | 82 SwimmeR-0.4.1/SwimmeR/man/grapes-notin-grapes.Rd |only SwimmeR-0.4.1/SwimmeR/man/hy3_places.Rd |only SwimmeR-0.4.1/SwimmeR/man/hy3_times.Rd |only SwimmeR-0.4.1/SwimmeR/man/interleave_results.Rd |only SwimmeR-0.4.1/SwimmeR/man/mmss_format.Rd | 60 SwimmeR-0.4.1/SwimmeR/man/parse_hy3.Rd |only SwimmeR-0.4.1/SwimmeR/man/results_score.Rd |only SwimmeR-0.4.1/SwimmeR/man/sec_format.Rd | 62 SwimmeR-0.4.1/SwimmeR/man/sec_format_helper.Rd | 34 SwimmeR-0.4.1/SwimmeR/man/swim_place.Rd |only SwimmeR-0.4.1/SwimmeR/man/tie_rescore.Rd |only SwimmeR-0.4.1/SwimmeR/tests/testthat.R | 8 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-Course_Convert.R | 6 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-Course_Convert_DF.R | 22 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-Read_Results_works.R | 38 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-Swim_Parse_works.R | 251 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-get_mode.R | 20 SwimmeR-0.4.1/SwimmeR/tests/testthat/test-hy3_parse_works.R |only SwimmeR-0.4.1/SwimmeR/tests/testthat/test-results_score_works.R |only SwimmeR-0.4.1/SwimmeR/vignettes/SwimmeR.Rmd | 336 - 74 files changed, 5139 insertions(+), 4647 deletions(-)
Title: Creating Flexible, Reproducible 'PDF' Reports
Description: A tool which allows users the ability to intuitively create
flexible, reproducible portable document format reports comprised of
aesthetically pleasing tables, images, plots and/or text.
Author: Calvin Floyd [aut, cre, cph]
Maintainer: Calvin Floyd <calvin.michael.floyd@gmail.com>
Diff between grobblR versions 0.1.0 dated 2020-06-25 and 0.1.1 dated 2020-08-28
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NEWS.md | 8 ++++++++ R/alter.R | 2 +- README.md | 9 +++++---- build/vignette.rds |binary inst/doc/grob_layout.html | 20 ++++++++++++++++++-- inst/doc/grob_matrix.html | 20 ++++++++++++++++++-- inst/doc/grobblR.Rmd | 5 ++--- inst/doc/grobblR.html | 25 ++++++++++++++++++++----- tests/testthat/test_grob_matrix.R | 36 ++++++++++++++++++++++++++++++------ vignettes/grobblR.Rmd | 5 ++--- 12 files changed, 119 insertions(+), 41 deletions(-)
Title: Heteroskedasticity Diagnostics for Linear Regression Models
Description: Implements numerous methods for detecting heteroskedasticity
(sometimes called heteroscedasticity) in the classical linear regression
model. These include a test based on Anscombe (1961)
<https://projecteuclid.org/ euclid.bsmsp/1200512155>, Ramsey's (1969)
BAMSET Test <doi:10.1111/j.2517-6161.1969.tb00796.x>, the tests of Bickel
(1978) <doi:10.1214/aos/1176344124>, Breusch and Pagan (1979)
<doi:10.2307/1911963> with and without the modification
proposed by Koenker (1981) <doi:10.1016/0304-4076(81)90062-2>, Carapeto and
Holt (2003) <doi:10.1080/0266476022000018475>, Cook and Weisberg (1983)
<doi:10.1093/biomet/70.1.1> (including their graphical methods), Diblasi
and Bowman (1997) <doi:10.1016/S0167-7152(96)00115-0>, Dufour, Khalaf,
Bernard, and Genest (2004) <doi:10.1016/j.jeconom.2003.10.024>, Evans and
King (1985) <doi:10.1016/0304-4076(85)90085-5> and Evans and King (1988)
<doi:10.1016/0304-4076(88)90006-1>, Glejser (1969)
<doi:10.1080/01621459.1969.10500976> as formulated by
Mittelhammer, Judge and Miller (2000, ISBN: 0-521-62394-4), Godfrey and
Orme (1999) <doi:10.1080/07474939908800438>, Goldfeld and Quandt
(1965) <doi:10.1080/01621459.1965.10480811>, Harvey (1976)
<doi:10.2307/1913974>, Honda (1989)
<doi:10.1111/j.2517-6161.1989.tb01749.x>, Horn (1981)
<doi:10.1080/03610928108828074>, Li and Yao (2019)
<doi:10.1016/j.ecosta.2018.01.001> with and without the modification of
Bai, Pan, and Yin (2016) <doi:10.1007/s11749-017-0575-x>, Rackauskas and
Zuokas (2007) <doi:10.1007/s10986-007-0018-6>, Simonoff and Tsai (1994)
<doi:10.2307/2986026> with and without the modification of Ferrari,
Cysneiros, and Cribari-Neto (2004) <doi:10.1016/S0378-3758(03)00210-6>,
Szroeter (1978) <doi:10.2307/1913831>, Verbyla (1993)
<doi:10.1111/j.2517-6161.1993.tb01918.x>, White (1980)
<doi:10.2307/1912934>, Wilcox and Keselman (2006)
<doi:10.1080/10629360500107923>, and Zhou, Song, and Thompson (2015)
<doi:10.1002/cjs.11252>. Besides these heteroskedasticity tests, there are
supporting functions that compute the BLUS residuals of Theil (1965)
<doi:10.1080/01621459.1965.10480851>, the conditional two-sided p-values of
Kulinskaya (2008) <arXiv:0810.2124v1>, and probabilities for the
nonparametric trend statistic of Lehmann (1975, ISBN: 0-816-24996-1).
Homoskedasticity refers to the assumption of constant variance that is
imposed on the model errors (disturbances); heteroskedasticity is the
violation of this assumption.
Author: Thomas Farrar [aut, cre] (<https://orcid.org/0000-0003-0744-6972>),
University of the Western Cape [cph]
Maintainer: Thomas Farrar <tjfarrar@alumni.uwaterloo.ca>
Diff between skedastic versions 1.0.0 dated 2020-08-11 and 1.0.1 dated 2020-08-28
DESCRIPTION | 25 ++++++++++++------------- MD5 | 14 +++++++------- R/myutils.R | 5 ----- R/simonoff_tsai.R | 2 +- R/verbyla.R | 10 +++------- build/partial.rdb |binary man/simonoff_tsai.Rd | 2 +- tests/testthat/test-pRQF.R | 21 +++++++++++---------- 8 files changed, 35 insertions(+), 44 deletions(-)
Title: Bayesian Network Learning with the PCHC Algorithm
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing. It is a new hybrid algorithm that used PC to construct the skeleton of the BN and then utilizes the Hill-Climbing greedy search. The relevant paper has been submitted and is currently in revision.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between pchc versions 0.1 dated 2020-07-06 and 0.2 dated 2020-08-28
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 6 +++--- R/bnplot.R |only R/chi2test.R |only R/g2test.R |only R/g2test_perm.R |only R/pchc.R | 14 +++++++------- R/pcor.R | 5 ++++- R/rbn.R |only man/bnplot.Rd |only man/cat.tests.Rd | 5 ++--- man/cortest.Rd | 10 +++++----- man/g2test.Rd |only man/pchc-package.Rd | 4 ++-- man/pchc.Rd | 35 ++++++++++++++--------------------- man/pchc.skel.Rd | 20 +++++--------------- man/pcor.Rd | 6 ++---- man/rbn.Rd |only 19 files changed, 67 insertions(+), 76 deletions(-)
Title: Tests of Independence and Analysis of Dependence Between Point
Processes in Time
Description: It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence, and functions for generating and analysing different types of dependence.
Author: Ana C. Cebrian
Maintainer: Ana C. Cebrian <acebrian@unizar.es>
Diff between IndTestPP versions 1.0 dated 2016-08-01 and 3.0 dated 2020-08-28
IndTestPP-1.0/IndTestPP/R/CPSPPOTevents.fun.R |only IndTestPP-1.0/IndTestPP/R/CPSPpoints.fun.R |only IndTestPP-1.0/IndTestPP/R/ComplPos.fun.R |only IndTestPP-1.0/IndTestPP/R/CondTest.fun.R |only IndTestPP-1.0/IndTestPP/R/DepMarkedNHPP.fun.R |only IndTestPP-1.0/IndTestPP/R/DepNHCPSP.fun.R |only IndTestPP-1.0/IndTestPP/R/DepNHNeyScot.fun.R |only IndTestPP-1.0/IndTestPP/R/DepNHPPqueue.fun.R |only IndTestPP-1.0/IndTestPP/R/DistObs.fun.R |only IndTestPP-1.0/IndTestPP/R/DistShift.fun.R |only IndTestPP-1.0/IndTestPP/R/DistSim.fun.R |only IndTestPP-1.0/IndTestPP/R/DistSimfix.fun.R |only IndTestPP-1.0/IndTestPP/R/DutilleulPlot.fun.R |only IndTestPP-1.0/IndTestPP/R/GenSons.fun.R |only IndTestPP-1.0/IndTestPP/R/IndNHNeyScot.fun.R |only IndTestPP-1.0/IndTestPP/R/IndNHPP.fun.R |only IndTestPP-1.0/IndTestPP/R/IndTestPP-internal.R |only IndTestPP-1.0/IndTestPP/R/NHD.fun.R |only IndTestPP-1.0/IndTestPP/R/NHF.fun.R |only IndTestPP-1.0/IndTestPP/R/NHJ.fun.R |only IndTestPP-1.0/IndTestPP/R/NHK.fun.R |only IndTestPP-1.0/IndTestPP/R/SpecGap.fun.R |only IndTestPP-1.0/IndTestPP/R/TestIndLS.fun.R |only IndTestPP-1.0/IndTestPP/R/TestIndNH.fun.R |only IndTestPP-1.0/IndTestPP/R/calcdist.fun.R |only IndTestPP-1.0/IndTestPP/R/depchi.fun.R |only IndTestPP-1.0/IndTestPP/R/genbiPos.fun.R |only IndTestPP-1.0/IndTestPP/R/gentriPos.fun.R |only IndTestPP-1.0/IndTestPP/R/miKS.fun.R |only IndTestPP-1.0/IndTestPP/R/mirank.fun.R |only IndTestPP-1.0/IndTestPP/R/nearestdist.fun.R |only IndTestPP-1.0/IndTestPP/R/pdist.fun.R |only IndTestPP-1.0/IndTestPP/R/simHPc.fun.R |only IndTestPP-1.0/IndTestPP/R/simNHPc.fun.R |only IndTestPP-1.0/IndTestPP/R/uniongentri.fun.R |only IndTestPP-1.0/IndTestPP/data/BarTxTn.rda |only IndTestPP-1.0/IndTestPP/man/BarTxTn.Rd |only IndTestPP-1.0/IndTestPP/man/CPSPPOTevents.fun.Rd |only IndTestPP-1.0/IndTestPP/man/CPSPpoints.fun.Rd |only IndTestPP-1.0/IndTestPP/man/ComplPos.fun.Rd |only IndTestPP-1.0/IndTestPP/man/CondTest.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DepMarkedNHPP.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DepNHCPSP.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DepNHNeyScot.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DepNHPPqueue.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DistObs.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DistShift.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DistSim.fun.Rd |only IndTestPP-1.0/IndTestPP/man/DutilleulPlot.fun.Rd |only IndTestPP-1.0/IndTestPP/man/IndNHNeyScot.fun.Rd |only IndTestPP-1.0/IndTestPP/man/IndNHPP.fun.Rd |only IndTestPP-1.0/IndTestPP/man/NHD.fun.Rd |only IndTestPP-1.0/IndTestPP/man/NHF.fun.Rd |only IndTestPP-1.0/IndTestPP/man/NHJ.fun.Rd |only IndTestPP-1.0/IndTestPP/man/NHK.fun.Rd |only IndTestPP-1.0/IndTestPP/man/SpecGap.fun.Rd |only IndTestPP-1.0/IndTestPP/man/TestIndLS.fun.Rd |only IndTestPP-1.0/IndTestPP/man/TestIndNH.fun.Rd |only IndTestPP-1.0/IndTestPP/man/depchi.fun.Rd |only IndTestPP-1.0/IndTestPP/man/nearestdist.fun.Rd |only IndTestPP-1.0/IndTestPP/man/simHPc.fun.Rd |only IndTestPP-1.0/IndTestPP/man/simNHPc.fun.Rd |only IndTestPP-1.0/IndTestPP/man/uniongentri.fun.Rd |only IndTestPP-3.0/IndTestPP/DESCRIPTION | 18 +- IndTestPP-3.0/IndTestPP/MD5 | 179 +++++++++++++---------- IndTestPP-3.0/IndTestPP/NAMESPACE | 6 IndTestPP-3.0/IndTestPP/R/BinPer.R |only IndTestPP-3.0/IndTestPP/R/CPSPPOTevents.R |only IndTestPP-3.0/IndTestPP/R/CPSPpoints.R |only IndTestPP-3.0/IndTestPP/R/ComplPos.R |only IndTestPP-3.0/IndTestPP/R/CondTest.R |only IndTestPP-3.0/IndTestPP/R/CountingCor.R |only IndTestPP-3.0/IndTestPP/R/DepCPSPKenv.R |only IndTestPP-3.0/IndTestPP/R/DepCPSPNHK.R |only IndTestPP-3.0/IndTestPP/R/DepNHCPSP.R |only IndTestPP-3.0/IndTestPP/R/DepNHNeyScot.R |only IndTestPP-3.0/IndTestPP/R/DepNHPPMarked.R |only IndTestPP-3.0/IndTestPP/R/DepNHPPqueue.R |only IndTestPP-3.0/IndTestPP/R/DepNHPPqueue1.R |only IndTestPP-3.0/IndTestPP/R/DepNHPPqueueI.R |only IndTestPP-3.0/IndTestPP/R/DepqueueKenv.R |only IndTestPP-3.0/IndTestPP/R/DepqueueNHK.R |only IndTestPP-3.0/IndTestPP/R/DistObs.R |only IndTestPP-3.0/IndTestPP/R/DistShift.R |only IndTestPP-3.0/IndTestPP/R/DistSim.R |only IndTestPP-3.0/IndTestPP/R/DistSimfix.R |only IndTestPP-3.0/IndTestPP/R/DutilleulPlot.R |only IndTestPP-3.0/IndTestPP/R/GenSons.R |only IndTestPP-3.0/IndTestPP/R/IndNHNeyScot.R |only IndTestPP-3.0/IndTestPP/R/IndNHPP.R |only IndTestPP-3.0/IndTestPP/R/IntMPP.R |only IndTestPP-3.0/IndTestPP/R/Jenv.R | 3 IndTestPP-3.0/IndTestPP/R/Kenv.R | 7 IndTestPP-3.0/IndTestPP/R/NHD.R |only IndTestPP-3.0/IndTestPP/R/NHF.R |only IndTestPP-3.0/IndTestPP/R/NHJ.R |only IndTestPP-3.0/IndTestPP/R/NHK.R |only IndTestPP-3.0/IndTestPP/R/NHKaux.R | 8 - IndTestPP-3.0/IndTestPP/R/NHKaux2.R | 4 IndTestPP-3.0/IndTestPP/R/NHKaux3.R | 34 ++-- IndTestPP-3.0/IndTestPP/R/NumI.R |only IndTestPP-3.0/IndTestPP/R/PlotICPSP.R |only IndTestPP-3.0/IndTestPP/R/PlotMCPSP.R |only IndTestPP-3.0/IndTestPP/R/PlotMargP.R |only IndTestPP-3.0/IndTestPP/R/PsimNHPc.R |only IndTestPP-3.0/IndTestPP/R/SpecGap.R |only IndTestPP-3.0/IndTestPP/R/TestIndLS.R |only IndTestPP-3.0/IndTestPP/R/TestIndNH.R |only IndTestPP-3.0/IndTestPP/R/TranM.R |only IndTestPP-3.0/IndTestPP/R/calcNmu.R | 14 - IndTestPP-3.0/IndTestPP/R/calcdist.R |only IndTestPP-3.0/IndTestPP/R/countP.R |only IndTestPP-3.0/IndTestPP/R/depchi.R |only IndTestPP-3.0/IndTestPP/R/firstt.R |only IndTestPP-3.0/IndTestPP/R/fn2.R | 2 IndTestPP-3.0/IndTestPP/R/fn2B.R | 2 IndTestPP-3.0/IndTestPP/R/fn2fix.R | 2 IndTestPP-3.0/IndTestPP/R/fn3.R | 4 IndTestPP-3.0/IndTestPP/R/funMPPGen.R |only IndTestPP-3.0/IndTestPP/R/genbiPos.R |only IndTestPP-3.0/IndTestPP/R/gentriPos.R |only IndTestPP-3.0/IndTestPP/R/marca.R |only IndTestPP-3.0/IndTestPP/R/miKS.R |only IndTestPP-3.0/IndTestPP/R/mirank.R |only IndTestPP-3.0/IndTestPP/R/nearestdist.R |only IndTestPP-3.0/IndTestPP/R/pdist.R |only IndTestPP-3.0/IndTestPP/R/simHPc.R |only IndTestPP-3.0/IndTestPP/R/simNHPc.R |only IndTestPP-3.0/IndTestPP/R/uniongentri.R |only IndTestPP-3.0/IndTestPP/data/TxBHZ.RData |only IndTestPP-3.0/IndTestPP/man/BinPer.Rd |only IndTestPP-3.0/IndTestPP/man/CPSPPOTevents.Rd |only IndTestPP-3.0/IndTestPP/man/CPSPpoints.Rd |only IndTestPP-3.0/IndTestPP/man/ComplPos.Rd |only IndTestPP-3.0/IndTestPP/man/CondTest.Rd |only IndTestPP-3.0/IndTestPP/man/CountingCor.Rd |only IndTestPP-3.0/IndTestPP/man/DepCPSPNHK.Rd |only IndTestPP-3.0/IndTestPP/man/DepNHCPSP.Rd |only IndTestPP-3.0/IndTestPP/man/DepNHNeyScot.Rd |only IndTestPP-3.0/IndTestPP/man/DepNHPPMarked.Rd |only IndTestPP-3.0/IndTestPP/man/DepNHPPqueue.Rd |only IndTestPP-3.0/IndTestPP/man/DepqueueNHK.Rd |only IndTestPP-3.0/IndTestPP/man/DistObs.Rd |only IndTestPP-3.0/IndTestPP/man/DistShift.Rd |only IndTestPP-3.0/IndTestPP/man/DistSim.Rd |only IndTestPP-3.0/IndTestPP/man/DutilleulPlot.Rd |only IndTestPP-3.0/IndTestPP/man/IndNHNeyScot.Rd |only IndTestPP-3.0/IndTestPP/man/IndNHPP.Rd |only IndTestPP-3.0/IndTestPP/man/IndTestPP-package.Rd | 16 +- IndTestPP-3.0/IndTestPP/man/IntMPP.Rd |only IndTestPP-3.0/IndTestPP/man/NHD.Rd |only IndTestPP-3.0/IndTestPP/man/NHF.Rd |only IndTestPP-3.0/IndTestPP/man/NHJ.Rd |only IndTestPP-3.0/IndTestPP/man/NHK.Rd |only IndTestPP-3.0/IndTestPP/man/PlotICPSP.Rd |only IndTestPP-3.0/IndTestPP/man/PlotMCPSP.Rd |only IndTestPP-3.0/IndTestPP/man/PlotMargP.Rd |only IndTestPP-3.0/IndTestPP/man/SpecGap.Rd |only IndTestPP-3.0/IndTestPP/man/TestIndLS.Rd |only IndTestPP-3.0/IndTestPP/man/TestIndNH.Rd |only IndTestPP-3.0/IndTestPP/man/TranM.Rd |only IndTestPP-3.0/IndTestPP/man/TxBHZ.Rd |only IndTestPP-3.0/IndTestPP/man/depchi.Rd |only IndTestPP-3.0/IndTestPP/man/nearestdist.Rd |only IndTestPP-3.0/IndTestPP/man/simHPc.Rd |only IndTestPP-3.0/IndTestPP/man/simNHPc.Rd |only IndTestPP-3.0/IndTestPP/man/uniongentri.Rd |only 167 files changed, 170 insertions(+), 129 deletions(-)
Title: Analyze Two Choice Reaction Time Data with the D*M Method
Description: A collection of functions to estimate parameters of a diffusion model via a D*M analysis. Build in models are: the Ratcliff diffusion model, the RWiener diffusion model, and Linear Ballistic Accumulator models. Custom models functions can be specified as long as they have a density function.
Author: Don van den Bergh, Stijn Verdonck, Francis Tuerlinckx
Maintainer: Don van den Bergh <donvdbergh@hotmail.com>
Diff between DstarM versions 0.3.0 dated 2018-05-18 and 0.4.0 dated 2020-08-28
DESCRIPTION | 9 MD5 | 112 +- NAMESPACE | 72 - NEWS.md |only R/Densities.R | 325 ++++--- R/Distances.R | 154 +-- R/DstarMcoef.R | 8 R/DstarMmethods.R | 308 +++---- R/DstarMmethodsDeprecated.R | 260 +++--- R/RcppExports.R | 142 +-- R/byParticipant.R | 220 ++--- R/calcIC.R | 540 ++++++------- R/chisqFit.R | 286 +++---- R/estCdf.R | 84 +- R/estDensities.R |only R/estDstarM.R | 1504 ++++++++++++++++++------------------- R/estND.R | 782 +++++++++---------- R/estObserved.R | 380 ++++----- R/estQdf.R | 94 +- R/getOptim.R | 34 R/getPdfs.R | 118 +- R/getSter.R | 48 - R/getTer.R | 134 +-- R/normalize.R | 74 - R/obsQuantiles.R | 102 +- R/plotObserved.R | 426 +++++----- R/rtDescriptives.R | 148 +-- R/rtHist.R | 124 +-- R/simData.R | 238 +++-- R/testFun.R | 100 +- R/utilities.R | 502 ++++++------ README.md |only man/Density.Rd |only man/Voss.density.Rd | 148 +-- man/chisq.Rd | 136 +-- man/chisqFit.Rd | 114 +- man/estCdf.Rd | 80 - man/estDstarM.Rd | 336 ++++---- man/estND.Rd | 198 ++-- man/estObserved.Rd | 151 +-- man/estQdf.Rd | 78 - man/getPdfs.Rd | 70 - man/getSter.Rd | 42 - man/getTer.Rd | 56 - man/normalize.Rd | 66 - man/obsQuantiles.Rd | 70 - man/plotObserved.Rd | 179 ++-- man/rtDescriptives.Rd | 86 +- man/rtHist.Rd | 81 - man/simData.Rd | 113 +- man/testFun.Rd | 70 - man/upgradeDstarM.Rd | 34 src/cppFunctions.cpp | 39 tests/testthat.R | 8 tests/testthat/helper-tolerance.R | 18 tests/testthat/test-CdfQdf.R | 104 +- tests/testthat/test-getpdfs.R | 39 tests/testthat/test-obsquantiles.R | 46 - tests/testthat/test-simulate.R | 435 +++++----- 59 files changed, 5132 insertions(+), 4993 deletions(-)
Title: Bayesian Variable Selection in High Dimensional Settings using
Nonlocal Priors
Description: Variable/Feature selection in high or ultra-high dimensional
settings has gained a lot of attention recently specially in cancer genomic
studies. This package provides a Bayesian approach to tackle this problem,
where it exploits mixture of point masses at zero and nonlocal priors to
improve the performance of variable selection and coefficient estimation.
product moment (pMOM) and product inverse moment (piMOM) nonlocal priors
are implemented and can be used for the analyses. This package performs
variable selection for binary response and survival time response datasets
which are widely used in biostatistic and bioinformatics community.
Benefiting from parallel computing ability, it reports necessary outcomes
of Bayesian variable selection such as Highest Posterior Probability Model
(HPPM), Median Probability Model (MPM) and posterior inclusion probability
for each of the covariates in the model. The option to use Bayesian Model
Averaging (BMA) is also part of this package that can be exploited for
predictive power measurements in real datasets.
Author: Amir Nikooienejad [aut, cre], Valen E. Johnson [ths]
Maintainer: Amir Nikooienejad <amir.nikooienejad@gmail.com>
Diff between BVSNLP versions 1.1.8 dated 2019-06-12 and 1.1.9 dated 2020-08-28
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/CoefEst.R | 6 +++--- R/ModProb.R | 6 +++--- R/RcppExports.R | 22 +++++++++++----------- R/bvs.R | 25 +++++++++++++++---------- R/predBMA.R | 6 +++--- man/CoefEst.Rd | 17 ++++++++++++----- man/HyperSelect.Rd | 11 +++++++++-- man/ModProb.Rd | 19 ++++++++++++++----- man/bvs.Rd | 47 +++++++++++++++++++++++++++++++++-------------- man/logreg_bvs.Rd | 16 ++++++++++++++-- man/predBMA.Rd | 21 ++++++++++++++++----- src/RcppExports.cpp | 42 +++++++++++++++++++++++++++++++----------- 14 files changed, 182 insertions(+), 92 deletions(-)
Title: Estimating Regional Trends of a Prevalence from a DHS and
Similar Surveys
Description: Spatial estimation of a prevalence surface
or a relative risks surface, using data from a Demographic and Health
Survey (DHS) or an analog survey, see Larmarange et al. (2011)
<doi:10.4000/cybergeo.24606>.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>)
Maintainer: Joseph Larmarange <joseph.larmarange@ird.fr>
Diff between prevR versions 3.4.0 dated 2019-05-06 and 3.4.1 dated 2020-08-28
prevR-3.4.0/prevR/data/datalist |only prevR-3.4.1/prevR/DESCRIPTION | 13 prevR-3.4.1/prevR/MD5 | 131 ++++----- prevR-3.4.1/prevR/NEWS.md | 7 prevR-3.4.1/prevR/R/NA.outside.SpatialPolygons.prevR.r | 10 prevR-3.4.1/prevR/R/Noptim.r | 6 prevR-3.4.1/prevR/R/as.SpatialGrid.prevR.r | 11 prevR-3.4.1/prevR/R/as.data.frame.prevR.r | 8 prevR-3.4.1/prevR/R/as.prevR.r | 29 -- prevR-3.4.1/prevR/R/changeproj.prevR.r | 10 prevR-3.4.1/prevR/R/colors.prevR.r | 22 - prevR-3.4.1/prevR/R/create.boundary.prevR.r | 20 - prevR-3.4.1/prevR/R/direct.label_prevR.r | 6 prevR-3.4.1/prevR/R/export.prevR.r | 17 - prevR-3.4.1/prevR/R/import.dhs.prevR.r | 16 - prevR-3.4.1/prevR/R/is.prevR.r | 8 prevR-3.4.1/prevR/R/kde.prevR.r | 24 - prevR-3.4.1/prevR/R/krige.prevR.r | 44 +-- prevR-3.4.1/prevR/R/plot.prevR.r | 13 prevR-3.4.1/prevR/R/point.in.SpatialPolygons.prevR.r | 6 prevR-3.4.1/prevR/R/prevR-package.r | 75 ++--- prevR-3.4.1/prevR/R/print.prevR.r | 8 prevR-3.4.1/prevR/R/quick.prevR.r | 17 - prevR-3.4.1/prevR/R/rings.prevR.r | 10 prevR-3.4.1/prevR/R/setClass.prevR.r | 15 - prevR-3.4.1/prevR/R/show.prevR.r | 10 prevR-3.4.1/prevR/R/summary.prevR.r | 10 prevR-3.4.1/prevR/R/theme_prevR.r | 2 prevR-3.4.1/prevR/R/xyz2dataframe.prevR.r | 4 prevR-3.4.1/prevR/build/vignette.rds |binary prevR-3.4.1/prevR/data/TMWorldBorders.rda |binary prevR-3.4.1/prevR/data/fdhs.rda |binary prevR-3.4.1/prevR/demo/prevR.r | 6 prevR-3.4.1/prevR/inst/CITATION | 4 prevR-3.4.1/prevR/inst/doc/intro_prevR.R | 20 - prevR-3.4.1/prevR/inst/doc/intro_prevR.Rmd | 2 prevR-3.4.1/prevR/inst/doc/intro_prevR.html | 246 ++++++++--------- prevR-3.4.1/prevR/man/NA.outside.SpatialPolygons.Rd | 12 prevR-3.4.1/prevR/man/Noptim.Rd | 8 prevR-3.4.1/prevR/man/TMWorldBorders.Rd | 38 +- prevR-3.4.1/prevR/man/as.SpatialGrid.Rd | 25 - prevR-3.4.1/prevR/man/as.data.frame.prevR.Rd | 17 - prevR-3.4.1/prevR/man/as.prevR.Rd | 54 +-- prevR-3.4.1/prevR/man/changeproj-prevR-method.Rd | 17 - prevR-3.4.1/prevR/man/create.boundary.Rd | 27 + prevR-3.4.1/prevR/man/direct.label_prevR.Rd | 6 prevR-3.4.1/prevR/man/export-prevR-method.Rd | 68 ++-- prevR-3.4.1/prevR/man/fdhs.Rd | 14 prevR-3.4.1/prevR/man/import.dhs.Rd | 24 - prevR-3.4.1/prevR/man/is.prevR.Rd | 20 - prevR-3.4.1/prevR/man/kde-prevR-method.Rd | 100 +++--- prevR-3.4.1/prevR/man/krige-ANY-prevR-method.Rd | 113 ++++--- prevR-3.4.1/prevR/man/plot-prevR-missing-method.Rd | 39 +- prevR-3.4.1/prevR/man/point.in.SpatialPolygons.Rd | 10 prevR-3.4.1/prevR/man/prevR-class.Rd | 101 +++--- prevR-3.4.1/prevR/man/prevR-package.Rd | 119 ++++---- prevR-3.4.1/prevR/man/prevR.colors.Rd | 35 +- prevR-3.4.1/prevR/man/print-prevR-method.Rd | 9 prevR-3.4.1/prevR/man/quick.prevR.Rd | 38 +- prevR-3.4.1/prevR/man/rings-prevR-method.Rd | 68 ++-- prevR-3.4.1/prevR/man/show-prevR-method.Rd | 9 prevR-3.4.1/prevR/man/summary-prevR-method.Rd | 12 prevR-3.4.1/prevR/man/theme_prevR.Rd | 3 prevR-3.4.1/prevR/man/xyz2dataframe.Rd | 12 prevR-3.4.1/prevR/po/R-fr.po | 4 prevR-3.4.1/prevR/po/R-prevR.pot | 2 prevR-3.4.1/prevR/vignettes/intro_prevR.Rmd | 2 67 files changed, 937 insertions(+), 899 deletions(-)
Title: Nested and Crossed Block Designs for Factorial and Unstructured
Treatment Sets
Description: Constructs D-optimal or near D-optimal treatment and block designs for linear
treatment models with crossed or nested block factors. The treatment design can be any
arbitrary linear model defined by a treatment model formula and the block design can be
any feasible combination of crossed or nested block factors. The block design factors
are optimized sequentially and the levels of each successive block factor are optimized
within the levels of each preceding block factor. Crossed block designs with non-singular
interaction effects are optimized using a weighting scheme that allows for differential
weighting of first and second-order block effects. Outputs include a table showing the
allocation of treatments to blocks and tables showing the achieved D-efficiency factors
for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 4.3 dated 2020-07-09 and 4.4 dated 2020-08-28
DESCRIPTION | 8 - MD5 | 10 - R/blocks.r | 2 R/design.r | 249 +++++++++++++++++++------------------------ inst/doc/design_Vignette.pdf |binary man/design.Rd | 33 ++--- 6 files changed, 137 insertions(+), 165 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Neal Richardson [aut, cre],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 1.0.0 dated 2020-07-25 and 1.0.1 dated 2020-08-28
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 13 ++++++++++++- R/dataset.R | 1 + R/parquet.R | 5 +++-- configure | 1 + inst/doc/install.Rmd | 2 ++ inst/doc/install.html | 2 ++ man/arrow-package.Rd | 2 +- man/write_parquet.Rd | 3 ++- src/arrow_exports.h | 12 ++++++------ tests/testthat/test-dataset.R | 27 +++++++++++++++++++++++++++ tests/testthat/test-parquet.R | 14 ++++++++++++++ tools/linuxlibs.R | 33 ++++++++++++++++++++++++--------- vignettes/install.Rmd | 2 ++ 15 files changed, 115 insertions(+), 38 deletions(-)
Title: Technical Trading Rules
Description: A collection of over 50 technical indicators for creating technical trading rules. The package also provides fast implementations of common rolling-window functions, and several volatility calculations.
Author: Joshua Ulrich
Maintainer: Joshua Ulrich <josh.m.ulrich@gmail.com>
Diff between TTR versions 0.24.0 dated 2020-08-10 and 0.24.1 dated 2020-08-28
CHANGES | 37 ++++++++++ DESCRIPTION | 6 - MD5 | 104 +++++++++++++++--------------- R/ADX.R | 2 R/ATR.R | 2 R/CCI.R | 2 R/CLV.R | 2 R/CMF.R | 2 R/DPO.R | 2 R/MACD.R | 4 - R/MFI.R | 9 ++ R/MovingAverages.R | 9 -- R/OBV.R | 2 R/RSI.R | 9 +- R/SAR.R | 2 R/TRIX.R | 2 R/TTR-package.R | 2 R/WPR.R | 2 R/ZigZag.R | 2 R/aroon.R | 2 R/bollingerBands.R | 4 - R/chaikinAD.R | 2 R/stochastics.R | 6 - R/ultimateOscillator.R | 2 inst/unitTests/runit.TTR.MovingAverages.R | 9 ++ inst/unitTests/runit.TTR.Oscillators.R | 23 ++++++ inst/unitTests/runit.TTR.Volume.R | 15 ++++ inst/unitTests/runit.TTR.runFun.R | 4 + man/ADX.Rd | 2 man/ATR.Rd | 2 man/CCI.Rd | 2 man/CLV.Rd | 2 man/CMF.Rd | 2 man/DPO.Rd | 2 man/MACD.Rd | 4 - man/MFI.Rd | 2 man/OBV.Rd | 2 man/RSI.Rd | 7 -- man/SAR.Rd | 2 man/TRIX.Rd | 2 man/TTR.Rd | 2 man/WPR.Rd | 2 man/ZigZag.Rd | 2 man/aroon.Rd | 2 man/bollingerBands.Rd | 4 - man/chaikinAD.Rd | 2 man/stochastics.Rd | 2 man/ultimateOscillator.Rd | 2 src/adjRatios.c | 6 - src/aroon.c | 4 - src/moving_averages.c | 63 +++++++++--------- src/sar.c | 4 - src/wilderSum.c | 4 - 53 files changed, 243 insertions(+), 156 deletions(-)
Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Calculates the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 1.1.1 dated 2020-07-10 and 1.2.0 dated 2020-08-28
DESCRIPTION | 8 MD5 | 76 +++---- NEWS.md | 20 +- R/TreeDist-package.R | 4 R/lap.R | 10 + R/median.R | 4 R/tree_distance.R | 9 R/tree_distance_info.R | 33 ++- R/tree_distance_mmsi.R | 12 - R/tree_distance_nye.R | 22 +- R/tree_distance_rf.R | 20 +- R/tree_distance_utilities.R | 36 +-- build/partial.rdb |binary inst/CITATION | 4 inst/doc/Generalized-RF.html | 4 inst/doc/Robinson-Foulds.html | 4 inst/doc/Using-TreeDist.html | 10 - inst/doc/information.Rmd | 2 inst/doc/information.html | 6 inst/doc/using-distances.Rmd | 2 inst/doc/using-distances.html | 14 - man/CompareAll.Rd | 2 man/LAPJV.Rd | 10 + man/NyeSimilarity.Rd | 7 man/TreeDist-package.Rd | 4 man/TreeDistance.Rd | 13 + src/ints.h | 1 src/lap.cpp | 111 +++++------ src/nni_distance.cpp | 97 +++++---- src/tree_distance_functions.cpp | 74 +++++-- src/tree_distances.cpp | 102 ++++++---- src/tree_distances.h | 24 +- tests/testthat/test-lap.R | 255 ++++++++++++++++++++++++++ tests/testthat/test-real-data.R |only tests/testthat/test-tree_distance.R | 41 ++-- tests/testthat/test-tree_distance_nni.R | 22 +- tests/testthat/test-tree_distance_utilities.R | 40 ++-- tests/testthat/test-tree_shape.R |only vignettes/information.Rmd | 2 vignettes/using-distances.Rmd | 2 40 files changed, 778 insertions(+), 329 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <https://cyclestreets.net/>;
calculation of route segment attributes such as bearing and aggregate flow;
and 'travel watershed' analysis.
See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb],
Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.7.0 dated 2020-08-27 and 0.7.1 dated 2020-08-28
DESCRIPTION | 8 +++--- MD5 | 44 ++++++++++++++++++------------------ NEWS.md | 4 +++ R/SpatialLinesNetwork.R | 8 ++++-- R/geo_projected.R | 9 ++++--- R/overline.R | 47 +++++++++++++++------------------------ R/toptail.R | 23 +++++++++---------- inst/doc/stplanr-od.R | 6 +--- inst/doc/stplanr-od.Rmd | 13 ++++------ inst/doc/stplanr-od.html | 9 +++---- inst/doc/stplanr-route-nets.Rmd | 2 - inst/doc/stplanr-route-nets.html | 2 - inst/doc/stplanr.R | 9 +++++-- inst/doc/stplanr.Rmd | 13 ++++++++-- inst/doc/stplanr.html | 6 ++-- man/SpatialLinesNetwork.Rd | 3 ++ man/geo_buffer.Rd | 9 ++++--- man/geo_toptail.Rd | 23 +++++++++---------- man/gsection.Rd | 21 +++++++++++------ man/overline.Rd | 26 ++++----------------- vignettes/stplanr-od.Rmd | 13 ++++------ vignettes/stplanr-route-nets.Rmd | 2 - vignettes/stplanr.Rmd | 13 ++++++++-- 23 files changed, 162 insertions(+), 151 deletions(-)
Title: Data Mining Classification and Regression Methods
Description: Facilitates the use of data mining algorithms in classification and regression (including time series forecasting) tasks by presenting a short and coherent set of functions. Versions: 1.4.6 / 1.4.5 / 1.4.4 new automated machine learning (AutoML) and ensembles, via improved fit(), mining() and mparheuristic() functions, and new categorical preprocessing, via improved delevels() function; 1.4.3 new metrics (e.g., macro precision, explained variance), new "lssvm" model and improved mparheuristic() function; 1.4.2 new "NMAE" metric, "xgboost" and "cv.glmnet" models (16 classification and 18 regression models); 1.4.1 new tutorial and more robust version; 1.4 - new classification and regression models, with a total of 14 classification and 15 regression methods, including: Decision Trees, Neural Networks, Support Vector Machines, Random Forests, Bagging and Boosting; 1.3 and 1.3.1 - new classification and regression metrics; 1.2 - new input importance methods via improved Importance() function; 1.0 - first version.
Author: Paulo Cortez [aut, cre]
Maintainer: Paulo Cortez <pcortez@dsi.uminho.pt>
Diff between rminer versions 1.4.5 dated 2020-04-14 and 1.4.6 dated 2020-08-28
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/estimate.R | 33 ++++++++++++++++++++++++++++----- R/plots.R | 8 +++++--- man/CasesSeries.Rd | 2 +- man/Importance.Rd | 18 +++++++++++++++++- man/crossvaldata.Rd | 5 ++++- man/delevels.Rd | 2 +- man/fit.Rd | 4 ++-- man/holdout.Rd | 22 ++++++++++++++++++++-- man/imputation.Rd | 2 +- man/lforecast.Rd | 2 +- man/mgraph.Rd | 2 +- man/mining.Rd | 4 ++-- man/mmetric.Rd | 4 ++-- man/mparheuristic.Rd | 2 +- man/rminer-internal.Rd | 1 + man/savemining.Rd | 2 +- man/vecplot.Rd | 2 +- 19 files changed, 112 insertions(+), 49 deletions(-)
Title: Probabilistic Supervised Learning for 'mlr3'
Description: Provides extensions for probabilistic supervised
learning for 'mlr3'. This includes extending the regression task to
probabilistic and interval regression, adding a survival task, and
other specialized models, predictions, and measures.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Nurul Ain Toha [ctb],
Andreas Bender [ctb] (<https://orcid.org/0000-0001-5628-8611>)
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between mlr3proba versions 0.2.0 dated 2020-07-25 and 0.2.1 dated 2020-08-28
mlr3proba-0.2.0/mlr3proba/R/LearnerProbreg.R |only mlr3proba-0.2.0/mlr3proba/R/LearnerProbregGaussian.R |only mlr3proba-0.2.0/mlr3proba/R/PipeOpProbRegr.R |only mlr3proba-0.2.0/mlr3proba/R/PredictionProbreg.R |only mlr3proba-0.2.0/mlr3proba/R/PredictionRegr.R |only mlr3proba-0.2.0/mlr3proba/R/TaskDens_faithful.R |only mlr3proba-0.2.0/mlr3proba/R/TaskDens_precip.R |only mlr3proba-0.2.0/mlr3proba/R/TaskProbreg.R |only mlr3proba-0.2.0/mlr3proba/R/TaskSurv_lung.R |only mlr3proba-0.2.0/mlr3proba/R/TaskSurv_rats.R |only mlr3proba-0.2.0/mlr3proba/R/TaskSurv_unemployment.R |only mlr3proba-0.2.0/mlr3proba/R/crank_compositor.R |only mlr3proba-0.2.0/mlr3proba/R/distr_compositor.R |only mlr3proba-0.2.0/mlr3proba/R/probregr_compose.R |only mlr3proba-0.2.0/mlr3proba/R/surv_average.R |only mlr3proba-0.2.0/mlr3proba/man/PredictionRegr.Rd |only mlr3proba-0.2.0/mlr3proba/man/crankcompositor.Rd |only mlr3proba-0.2.0/mlr3proba/man/distrcompositor.Rd |only mlr3proba-0.2.0/mlr3proba/man/probregr_compose.Rd |only mlr3proba-0.2.0/mlr3proba/man/surv_averager.Rd |only mlr3proba-0.2.1/mlr3proba/DESCRIPTION | 58 +-- mlr3proba-0.2.1/mlr3proba/MD5 | 133 ++++---- mlr3proba-0.2.1/mlr3proba/NAMESPACE | 16 mlr3proba-0.2.1/mlr3proba/NEWS.md | 13 mlr3proba-0.2.1/mlr3proba/R/LearnerDensKDE.R | 2 mlr3proba-0.2.1/mlr3proba/R/LearnerRegrGaussian.R |only mlr3proba-0.2.1/mlr3proba/R/LearnerSurvCoxPH.R | 4 mlr3proba-0.2.1/mlr3proba/R/LearnerSurvKaplan.R | 2 mlr3proba-0.2.1/mlr3proba/R/MeasureSurvCindex.R | 4 mlr3proba-0.2.1/mlr3proba/R/PipeOpCrankCompositor.R | 161 +++------- mlr3proba-0.2.1/mlr3proba/R/PipeOpDistrCompositor.R | 146 +-------- mlr3proba-0.2.1/mlr3proba/R/PipeOpPredRegrSurv.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpPredSurvRegr.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpPredTransformer.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpProbregrCompositor.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpSurvAvg.R | 48 +- mlr3proba-0.2.1/mlr3proba/R/PipeOpTaskRegrSurv.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpTaskSurvRegr.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpTaskTransformer.R |only mlr3proba-0.2.1/mlr3proba/R/PipeOpTransformer.R |only mlr3proba-0.2.1/mlr3proba/R/PredictionSurv.R | 33 +- mlr3proba-0.2.1/mlr3proba/R/TaskDens_X.R |only mlr3proba-0.2.1/mlr3proba/R/TaskSurv_X.R |only mlr3proba-0.2.1/mlr3proba/R/data.R |only mlr3proba-0.2.1/mlr3proba/R/pipelines.R |only mlr3proba-0.2.1/mlr3proba/R/zzz.R | 32 + mlr3proba-0.2.1/mlr3proba/README.md | 12 mlr3proba-0.2.1/mlr3proba/build/partial.rdb |binary mlr3proba-0.2.1/mlr3proba/data |only mlr3proba-0.2.1/mlr3proba/inst/doc/density.html | 31 - mlr3proba-0.2.1/mlr3proba/inst/references.bib | 53 +++ mlr3proba-0.2.1/mlr3proba/inst/testthat/helper_expectations.R | 6 mlr3proba-0.2.1/mlr3proba/man/PipeOpCrankCompositor.Rd | 84 ----- mlr3proba-0.2.1/mlr3proba/man/PipeOpDistrCompositor.Rd | 84 ----- mlr3proba-0.2.1/mlr3proba/man/PipeOpPredTransformer.Rd |only mlr3proba-0.2.1/mlr3proba/man/PipeOpProbregrCompositor.Rd | 125 +------ mlr3proba-0.2.1/mlr3proba/man/PipeOpTaskTransformer.Rd |only mlr3proba-0.2.1/mlr3proba/man/PipeOpTransformer.Rd |only mlr3proba-0.2.1/mlr3proba/man/PredictionDens.Rd | 1 mlr3proba-0.2.1/mlr3proba/man/PredictionSurv.Rd | 3 mlr3proba-0.2.1/mlr3proba/man/actg.Rd |only mlr3proba-0.2.1/mlr3proba/man/gbcs.Rd |only mlr3proba-0.2.1/mlr3proba/man/grace.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_crankcompositor.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_distrcompositor.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_probregrcompositor.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_survaverager.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_survbagging.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_graphs_survtoregr.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_measures_surv.cindex.Rd | 4 mlr3proba-0.2.1/mlr3proba/man/mlr_pipeops_survavg.Rd | 29 - mlr3proba-0.2.1/mlr3proba/man/mlr_pipeops_trafopred_regrsurv.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_pipeops_trafopred_survregr.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_pipeops_trafotask_regrsurv.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_pipeops_trafotask_survregr.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_actg.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_faithful.Rd | 2 mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_gbcs.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_grace.Rd |only mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_lung.Rd | 2 mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_precip.Rd | 2 mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_rats.Rd | 2 mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_unemployment.Rd | 2 mlr3proba-0.2.1/mlr3proba/man/mlr_tasks_whas.Rd |only mlr3proba-0.2.1/mlr3proba/man/whas.Rd |only mlr3proba-0.2.1/mlr3proba/tests/testthat/Rplots.pdf |binary mlr3proba-0.2.1/mlr3proba/tests/testthat/helper.R | 6 mlr3proba-0.2.1/mlr3proba/tests/testthat/helper_pipeops.R | 4 mlr3proba-0.2.1/mlr3proba/tests/testthat/test_pipelines.R |only mlr3proba-0.2.1/mlr3proba/tests/testthat/test_pipeop_crankcompositor.R | 54 ++- mlr3proba-0.2.1/mlr3proba/tests/testthat/test_pipeop_distrcompositor.R | 16 mlr3proba-0.2.1/mlr3proba/tests/testthat/test_pipeop_probregrcompositor.R | 21 - mlr3proba-0.2.1/mlr3proba/tests/testthat/test_pipeop_survavg.R | 25 - mlr3proba-0.2.1/mlr3proba/tests/testthat/test_register.R | 3 94 files changed, 498 insertions(+), 725 deletions(-)
Title: Collection of Scripts for Interface Between 'Cornerstone' and
'R'
Description: Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'.
The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>)
is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster.
The engineers incorporate intensified hands-on statistics into their projects.
They benefit from an intuitive and uniquely designed graphical Workmap concept: you design
experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon,
immediately, interactively, and without any programming.
While 'Cornerstone's' interface to the statistical programming language 'R' has been available
since version 6.0, the latest interface with 'R' is even much more efficient.
'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the
standard 'Cornerstone' GUI.
Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R'
routines, immediately and without the need to deal with programming code.
Additionally, your 'R' programming team develops corresponding 'R' packages detached from
'Cornerstone' in their favorite 'R' environment.
Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel
(<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).
Author: Gerrith Djaja [aut, cre],
Dirk Surmann [aut] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Gerrith Djaja <gerrith.djaja@camline.com>
Diff between CornerstoneR versions 2.0.1 dated 2020-06-02 and 2.0.2 dated 2020-08-28
DESCRIPTION | 29 - MD5 | 50 +- NEWS.md | 4 R/data.R | 2 build/vignette.rds |binary inst/doc/fitFunction.html | 489 +++++++++++++---------- inst/doc/matchNearestNeighbor.html | 337 ++++++++++----- inst/doc/mosaicPlot.html | 277 ++++++++----- inst/doc/randomForest.html | 510 ++++++++++++++---------- inst/doc/redirectDataset.html | 311 +++++++++----- inst/doc/reshape.html | 784 ++++++++++++++++++++----------------- inst/doc/showVersions.html | 219 +++++++--- man/CornerstoneR-package.Rd | 17 man/LocalInterface.Rd | 178 ++++---- man/fitFunction.Rd | 248 +++++------ man/matchNearestNeighbor.Rd | 114 ++--- man/mosaicPlot.Rd | 106 ++--- man/randomForest.Rd | 220 +++++----- man/randomForestPredict.Rd | 108 ++--- man/redirectDataset.Rd | 130 +++--- man/reshapeLong.Rd | 136 +++--- man/reshapeTranspose.Rd | 118 ++--- man/reshapeWide.Rd | 150 +++---- man/rundata.Rd | 36 - man/showVersions.Rd | 58 +- man/titanic.Rd | 2 26 files changed, 2631 insertions(+), 2002 deletions(-)
Title: A S3 Class for Vectors of 64bit Integers
Description: Package 'bit64' provides serializable S3 atomic 64bit (signed) integers.
These are useful for handling database keys and exact counting in +-2^63.
WARNING: do not use them as replacement for 32bit integers, integer64 are not
supported for subscripting by R-core and they have different semantics when
combined with double, e.g. integer64 + double => integer64.
Class integer64 can be used in vectors, matrices, arrays and data.frames.
Methods are available for coercion from and to logicals, integers, doubles,
characters and factors as well as many elementwise and summary functions.
Many fast algorithmic operations such as 'match' and 'order' support inter-
active data exploration and manipulation and optionally leverage caching.
Author: Jens Oehlschlägel [aut, cre], Leonardo Silvestri [ctb]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit64 versions 4.0.2 dated 2020-07-30 and 4.0.4 dated 2020-08-28
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS | 24 +++++++++++++++++++++++- R/hash64.R | 6 +++--- R/integer64.R | 10 +++++----- R/sort64.R | 2 +- man/bit64-package.rd | 4 ++-- man/hashmap.rd | 2 +- man/ramsort.integer64.rd | 2 +- src/Makevars |only src/init.c | 2 +- src/integer64.c | 16 +++++++++++----- 12 files changed, 63 insertions(+), 34 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen, Valeria Vitelli, Marta Crispino, Qinghua Liu
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 0.4.4 dated 2020-08-07 and 0.5.0 dated 2020-08-28
DESCRIPTION | 14 +- MD5 | 20 +-- NEWS.md | 4 R/compute_consensus.R | 117 +++++++++++++------ build/partial.rdb |binary inst/REFERENCES.bib | 2 inst/examples/compute_consensus_example.R | 24 ++++ man/compute_consensus.Rd | 43 ++++++- man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary tests/testthat/test_compute_consensus.R | 177 +++++++++++++++++++++++++++++- 11 files changed, 340 insertions(+), 61 deletions(-)
Title: Hydrology and Climate Forecasting
Description: Focuses on data processing and visualization in hydrology and
climate forecasting. Main function includes data extraction, data downscaling,
data resampling, gap filler of precipitation, bias correction of forecasting
data, flexible time series plot, and spatial map generation. It is a good pre-
processing and post-processing tool for hydrological and hydraulic modellers.
Author: Yuanchao Xu [aut, cre]
Maintainer: Yuanchao Xu <xuyuanchao37@gmail.com>
Diff between hyfo versions 1.4.2 dated 2020-04-04 and 1.4.3 dated 2020-08-28
DESCRIPTION | 10 +++--- MD5 | 70 +++++++++++++++++++++--------------------- NEWS | 8 ++++ R/ncdf.R | 5 ++- README.md | 4 +- build/vignette.rds |binary data/testCat.rda |binary inst/doc/hyfo.Rmd | 4 +- inst/doc/hyfo.html | 2 - man/applyBiasFactor.Rd | 9 +++-- man/biasCorrect.Rd | 46 +++++++-------------------- man/collectData.Rd | 3 + man/collectData_txt_anarbe.Rd | 7 +--- man/downscaleNcdf.Rd | 5 +-- man/extractPeriod.Rd | 31 ++++-------------- man/getAnnual.Rd | 7 +++- man/getBiasFactor.Rd | 42 +++++++------------------ man/getEnsem_comb.Rd | 12 +------ man/getFrcEnsem.Rd | 14 +------- man/getHisEnsem.Rd | 13 +------ man/getMeanPreci.Rd | 13 +------ man/getNcdfVar.Rd | 2 - man/getPreciBar.Rd | 52 +++++++------------------------ man/getPreciBar_comb.Rd | 13 +------ man/getSpatialMap.Rd | 2 - man/getSpatialMap_comb.Rd | 13 +------ man/getSpatialMap_mat.Rd | 17 ++-------- man/loadNcdf.Rd | 2 - man/plotTS.Rd | 15 +-------- man/plotTS_comb.Rd | 12 +------ man/resample.Rd | 1 man/testCat.Rd | 6 +-- man/testdl.Rd | 6 +-- man/tgridData.Rd | 6 +-- man/writeNcdf.Rd | 17 ++++------ vignettes/hyfo.Rmd | 4 +- 36 files changed, 164 insertions(+), 309 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.2.0 dated 2020-08-24 and 1.2.1 dated 2020-08-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/intro-to-gmvarkit.html | 4 ++-- tests/testthat/test_waldAndLR.R | 4 ++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
Description: A programmatic interface to various 'SNP' 'datasets'
on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database
(<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions
are included for searching for 'NCBI'. For 'OpenSNP', functions are included
for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations,
and bulk downloads of data by user.
Author: Julia Gustavsen [aut, cre] (<https://orcid.org/0000-0002-4764-4802>),
Sina Rüeger [aut] (<https://orcid.org/0000-0003-2848-9242>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Kevin Ushey [aut],
Hao Zhu [aut]
Maintainer: Julia Gustavsen <j.gustavsen@gmail.com>
Diff between rsnps versions 0.3.0 dated 2018-09-20 and 0.4.0 dated 2020-08-28
rsnps-0.3.0/rsnps/R/NCBI_snp_query.R |only rsnps-0.3.0/rsnps/R/NCBI_snp_query2.R |only rsnps-0.3.0/rsnps/R/ncbi_snp_summary.R |only rsnps-0.3.0/rsnps/inst/doc/rsnps_vignette.Rmd |only rsnps-0.3.0/rsnps/inst/doc/rsnps_vignette.html |only rsnps-0.3.0/rsnps/man/ncbi_snp_query2.Rd |only rsnps-0.3.0/rsnps/man/ncbi_snp_summary.Rd |only rsnps-0.3.0/rsnps/tests/testthat/test-NCBI_snp_query.R |only rsnps-0.3.0/rsnps/tests/testthat/test-NCBI_snp_query2.R |only rsnps-0.3.0/rsnps/vignettes/rsnps_vignette.Rmd |only rsnps-0.4.0/rsnps/DESCRIPTION | 42 ++-- rsnps-0.4.0/rsnps/LICENSE | 4 rsnps-0.4.0/rsnps/MD5 | 74 +++---- rsnps-0.4.0/rsnps/NAMESPACE | 10 rsnps-0.4.0/rsnps/NEWS.md | 31 ++- rsnps-0.4.0/rsnps/R/allphenotypes.R | 2 rsnps-0.4.0/rsnps/R/annotations.R | 4 rsnps-0.4.0/rsnps/R/deprecated-defunct.R | 23 ++ rsnps-0.4.0/rsnps/R/fetch_genotypes.R | 4 rsnps-0.4.0/rsnps/R/ncbi_snp_api.R |only rsnps-0.4.0/rsnps/R/rsnps-package.R | 11 - rsnps-0.4.0/rsnps/R/utils.R | 3 rsnps-0.4.0/rsnps/README.md | 165 ++++++++-------- rsnps-0.4.0/rsnps/build/vignette.rds |binary rsnps-0.4.0/rsnps/inst/doc/rsnps.Rmd |only rsnps-0.4.0/rsnps/inst/doc/rsnps.html |only rsnps-0.4.0/rsnps/man/NCBI_snp_query-defunct.Rd | 12 + rsnps-0.4.0/rsnps/man/allgensnp.Rd | 14 - rsnps-0.4.0/rsnps/man/allphenotypes.Rd | 16 - rsnps-0.4.0/rsnps/man/annotations.Rd | 26 +- rsnps-0.4.0/rsnps/man/download_users.Rd | 14 - rsnps-0.4.0/rsnps/man/fetch_genotypes.Rd | 16 - rsnps-0.4.0/rsnps/man/genotypes.Rd | 15 - rsnps-0.4.0/rsnps/man/get_frequency.Rd |only rsnps-0.4.0/rsnps/man/get_gene_names.Rd |only rsnps-0.4.0/rsnps/man/get_placements.Rd |only rsnps-0.4.0/rsnps/man/ncbi_snp_query.Rd | 79 +++---- rsnps-0.4.0/rsnps/man/phenotypes.Rd | 14 - rsnps-0.4.0/rsnps/man/phenotypes_byid.Rd | 21 +- rsnps-0.4.0/rsnps/man/rsnps-defunct.Rd | 4 rsnps-0.4.0/rsnps/man/rsnps-package.Rd | 10 rsnps-0.4.0/rsnps/man/rsnpsCache.Rd | 4 rsnps-0.4.0/rsnps/man/split_to_df.Rd | 3 rsnps-0.4.0/rsnps/man/users.Rd | 14 - rsnps-0.4.0/rsnps/tests/testthat/test-allphenotypes.R | 10 rsnps-0.4.0/rsnps/tests/testthat/test-ncbi_snp_api.R |only rsnps-0.4.0/rsnps/vignettes/rsnps.Rmd |only 47 files changed, 378 insertions(+), 267 deletions(-)
Title: Gathering Bibliographic Records from 'Digital Science
Dimensions' Using 'DSL' API
Description: A set of tools to extract bibliographic content from 'Digital Science Dimensions' using 'DSL' API <https://www.dimensions.ai/dimensions-apis/>.
Author: Massimo Aria [aut, cre] (<https://orcid.org/0000-0002-8517-9411>)
Maintainer: Massimo Aria <massimo.aria@gmail.com>
Diff between dimensionsR versions 0.0.1 dated 2020-03-20 and 0.0.2 dated 2020-08-28
DESCRIPTION | 8 MD5 | 31 NAMESPACE | 3 NEWS |only R/altmetric.R |only R/dsApi2df.R | 1281 ++++++++++++++++++++--------------------- R/dsApiRequest.R | 228 +++---- R/dsAuth.R | 126 ++-- R/dsQueryBuild.R | 302 +++++---- build/vignette.rds |binary inst/doc/A_Brief_Example.R | 6 inst/doc/A_Brief_Example.Rmd | 849 ++++++++++++++------------- inst/doc/A_Brief_Example.html | 1310 +++++++++++++++++++++--------------------- man/altmetric.Rd |only man/dsApiRequest.Rd | 15 man/dsAuth.Rd | 9 man/dsQueryBuild.Rd | 10 vignettes/A_Brief_Example.Rmd | 849 ++++++++++++++------------- 18 files changed, 2617 insertions(+), 2410 deletions(-)
Title: R Interface to COVID-19 Data Hub
Description: Download COVID-19 data across governmental sources at national, regional, and city level, as described in Guidotti and Ardia (2020) <doi:10.21105/joss.02376>. Includes policy measures by 'Oxford COVID-19 Government Response Tracker' <https://www.bsg.ox.ac.uk/research/research-projects/coronavirus-government-response-tracker>. Provides a seamless integration with 'World Bank Open Data' <https://data.worldbank.org/>, 'Google Mobility Reports' <https://www.google.com/covid19/mobility/>, 'Apple Mobility Reports' <https://covid19.apple.com/mobility>.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>),
David Ardia [ctb] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between COVID19 versions 2.2.0 dated 2020-07-13 and 2.3.0 dated 2020-08-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/covid19.R | 19 ++++++++++--------- R/utils.R | 14 +++++++++----- R/wb.R | 14 ++++++++++++-- README.md | 6 +++--- build/partial.rdb |binary man/covid19.Rd | 19 ++++++++++--------- 8 files changed, 55 insertions(+), 39 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-25 1.0
Title: Wrapper of Python Library 'shap'
Description: Provides SHAP explanations of machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the Interpretable Machine Learning, there are more and more new ideas for explaining black-box models. One of the best known method for local explanations is SHapley Additive exPlanations (SHAP) introduced by Lundberg, S., et al., (2016) <arXiv:1705.07874> The SHAP method is used to calculate influences of variables on the particular observation. This method is based on Shapley values, a technique used in game theory. The R package 'shapper' is a port of the Python library 'shap'.
Author: Szymon Maksymiuk [aut, cre],
Alicja Gosiewska [aut],
Przemyslaw Biecek [aut],
Mateusz Staniak [ctb],
Michal Burdukiewicz [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between shapper versions 0.1.2 dated 2019-08-02 and 0.1.3 dated 2020-08-28
DESCRIPTION | 12 ++++----- MD5 | 31 ++++++++++++------------ NAMESPACE | 4 +-- NEWS.md | 8 +++++- R/individual_variable_effect.R | 2 - R/plot_individual_variable_effect.R | 27 +++++++++++---------- R/theme_drwhy.R | 41 --------------------------------- build/vignette.rds |binary inst/doc/shapper_classification.R | 20 ++++++++-------- inst/doc/shapper_classification.Rmd | 2 - inst/doc/shapper_classification.html | 2 - inst/doc/shapper_regression.R | 18 +++++++------- man/figures |only man/individual_variable_effect.Rd | 26 +++++++++++++++----- man/plot.individual_variable_effect.Rd | 22 ++++++++++++----- man/theme_drwhy.Rd | 8 ------ vignettes/shapper_classification.Rmd | 2 - 17 files changed, 104 insertions(+), 121 deletions(-)
Title: Core Utilities for Developing and Running Spatially Explicit
Discrete Event Models
Description: Provides the core framework for a discrete event system (DES) to
implement a complete data-to-decisions, reproducible workflow.
The core DES components facilitate modularity, and easily enable the user
to include additional functionality by running user-built modules.
Includes conditional scheduling, restart after interruption, packaging of
reusable modules, tools for developing arbitrary automated workflows,
automated interweaving of modules of different temporal resolution,
and tools for visualizing and understanding the DES project.
Author: Alex M Chubaty [aut, cre] (<https://orcid.org/0000-0001-7146-8135>),
Eliot J B McIntire [aut] (<https://orcid.org/0000-0002-6914-8316>),
Yong Luo [ctb],
Steve Cumming [ctb],
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES.core versions 1.0.1 dated 2020-05-15 and 1.0.2 dated 2020-08-28
DESCRIPTION | 43 +-- MD5 | 199 ++++++++--------- NAMESPACE | 14 - NEWS.md | 21 + R/cache.R | 135 ++++++++--- R/checkpoint.R | 4 R/code-checking.R | 20 - R/copy.R | 63 +---- R/debugging.R |only R/downloadData.R | 42 +-- R/load.R | 12 - R/memory.R | 50 ++-- R/misc-methods.R | 29 +- R/modActiveBinding.R | 10 R/module-define.R | 56 +++- R/module-dependencies-class.R | 2 R/module-repository.R | 6 R/module-template.R | 12 - R/moduleMetadata.R | 35 ++- R/options.R | 8 R/plotting-diagrams.R | 2 R/plotting.R | 40 +-- R/progress.R | 4 R/project-template.R | 6 R/restart.R | 8 R/save.R | 1 R/simList-accessors.R | 34 ++ R/simList-class.R | 6 R/simulation-parseModule.R | 73 +++--- R/simulation-simInit.R | 75 +++--- R/simulation-spades.R | 171 ++++++++------ R/spades-core-package.R | 38 +-- R/times.R | 1 R/zzz.R | 3 README.md | 14 - build/vignette.rds |binary inst/WORDLIST | 17 - inst/doc/i-introduction.Rmd | 6 inst/doc/i-introduction.html | 30 +- inst/doc/ii-modules.R | 2 inst/doc/ii-modules.Rmd | 16 - inst/doc/ii-modules.html | 37 +-- inst/doc/iii-cache.R | 5 inst/doc/iii-cache.Rmd | 16 - inst/doc/iii-cache.html | 338 +++++++++++++++-------------- inst/doc/iv-advanced.Rmd | 25 -- inst/doc/iv-advanced.html | 31 +- inst/sampleModules/fireSpread/fireSpread.R | 3 inst/templates/module.Rmd.template | 8 man/Plot.Rd | 20 - man/SpaDES.core-package.Rd | 36 +-- man/addChangedAttr.Rd | 4 man/addTagsToOutput.Rd | 4 man/cacheMessage.Rd | 4 man/checkCacheRepo.Rd | 4 man/checkpoint.Rd | 2 man/classFilter.Rd | 4 man/defineModule.Rd | 6 man/doEvent.Rd | 2 man/eventDiagram.Rd | 2 man/getModuleVersion.Rd | 4 man/moduleDeps-class.Rd | 2 man/moduleParamsInputsOuputs.Rd | 5 man/paddedFloatToChar.Rd | 9 man/parseElems.Rd | 6 man/preDigestByClass.Rd | 4 man/prepareOutput.Rd | 4 man/remoteFileSize.Rd | 9 man/scheduleConditionalEvent.Rd | 2 man/scheduleEvent.Rd | 2 man/setPaths.Rd | 2 man/simInit.Rd | 55 ++-- man/simInitAnd.Rd | 18 - man/simList-accessors-metadata.Rd | 22 + man/simList-class.Rd | 2 man/spades.Rd | 44 +-- man/spadesOptions.Rd | 4 man/tagsByClass.Rd | 4 man/writeEventInfo.Rd |only man/writeRNGInfo.Rd |only tests/testthat/helper-initTests.R | 24 +- tests/testthat/test-Copy.R | 1 tests/testthat/test-cache.R | 73 +++--- tests/testthat/test-checkpoint.R | 19 - tests/testthat/test-downloadData.R | 19 - tests/testthat/test-downloadModule.R | 67 ++--- tests/testthat/test-load.R | 42 +-- tests/testthat/test-memory.R | 4 tests/testthat/test-misc.R | 5 tests/testthat/test-mod.R | 54 ++-- tests/testthat/test-module-deps-methods.R | 17 + tests/testthat/test-objectSynonyms.R | 10 tests/testthat/test-save.R | 14 - tests/testthat/test-simList.R | 11 tests/testthat/test-simulation.R | 148 +++++++----- tests/testthat/test-timeunits.R | 10 tests/testthat/test-userSuppliedObjs.R | 38 ++- vignettes/bibliography.bib | 9 vignettes/i-introduction.Rmd | 6 vignettes/ii-modules.Rmd | 16 - vignettes/iii-cache.Rmd | 16 - vignettes/iv-advanced.Rmd | 25 -- 102 files changed, 1478 insertions(+), 1207 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized maximum likelihood estimators for precision matrices and supporting functions to employ these estimators in a graphical modeling setting. For details see van Wieringen & Peeters (2016) <doi:10.1016/j.csda.2016.05.012> and associated publications.
Author: Carel F.W. Peeters [cre, aut], Anders Ellern Bilgrau [aut], Wessel N. van Wieringen [aut]
Maintainer: Carel F.W. Peeters <cf.peeters@vumc.nl>
Diff between rags2ridges versions 2.2.2 dated 2019-12-17 and 2.2.3 dated 2020-08-28
DESCRIPTION | 11 - MD5 | 38 ++-- R/rags2ridges.R | 312 ++++++++++++++++++++++++--------------- README.md | 37 ++-- inst/CITATION | 52 +++--- inst/NEWS.Rd | 24 +++ man/ADdata.Rd | 2 man/CNplot.Rd | 2 man/GGMpathStats.Rd | 31 ++- man/default.penalty.Rd | 6 man/fused.test.Rd | 6 man/getKEGGPathway.Rd | 2 man/is.Xlist.Rd | 6 man/kegg.target.Rd | 2 man/optPenalty.fused.Rd | 6 man/plot.ptest.Rd | 6 man/print.optPenaltyFusedGrid.Rd | 6 man/print.ptest.Rd | 6 man/rags2ridges-package.Rd | 16 +- man/ridgeP.fused.Rd | 6 20 files changed, 345 insertions(+), 232 deletions(-)
Title: Validation of Local and Remote Data Tables
Description: Validate data in data frames, 'tibble' objects, and in database
tables (e.g., 'PostgreSQL' and 'MySQL'). Validation pipelines can be made
using easily-readable, consecutive validation steps. Upon execution of the
validation plan, several reporting options are available. User-defined
thresholds for failure rates allow for the determination of appropriate
reporting actions.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between pointblank versions 0.5.1 dated 2020-08-27 and 0.5.2 dated 2020-08-28
pointblank-0.5.1/pointblank/tests/testthat/test-mysql-2.R |only pointblank-0.5.1/pointblank/tests/testthat/test-mysql.R |only pointblank-0.5.2/pointblank/DESCRIPTION | 6 +-- pointblank-0.5.2/pointblank/MD5 | 14 ++++---- pointblank-0.5.2/pointblank/NEWS.md | 6 +++ pointblank-0.5.2/pointblank/R/get_agent_report.R | 24 ++++++++++++-- pointblank-0.5.2/pointblank/R/interrogate.R | 5 +- pointblank-0.5.2/pointblank/README.md | 2 - pointblank-0.5.2/pointblank/tests/testthat/mysql-2.R |only pointblank-0.5.2/pointblank/tests/testthat/mysql.R |only 10 files changed, 40 insertions(+), 17 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Ben Goodrich [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph],
Juan Palacios [cph],
Jiang Yang [cph],
Gael Guennebaud [cph],
Jitse Niesen [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.17.4 dated 2020-06-07 and 2.18.1 dated 2020-08-28
OpenMx-2.17.4/OpenMx/inst/models/passing/NelderMead--bothConstraintTypes.R |only OpenMx-2.18.1/OpenMx/DESCRIPTION | 13 OpenMx-2.18.1/OpenMx/MD5 | 266 +++-- OpenMx-2.18.1/OpenMx/NAMESPACE | 3 OpenMx-2.18.1/OpenMx/NEWS.md | 89 + OpenMx-2.18.1/OpenMx/R/DefinitionVars.R | 3 OpenMx-2.18.1/OpenMx/R/MxAutoStart.R | 1 OpenMx-2.18.1/OpenMx/R/MxCompute.R | 21 OpenMx-2.18.1/OpenMx/R/MxCycleDetection.R | 5 OpenMx-2.18.1/OpenMx/R/MxEval.R | 6 OpenMx-2.18.1/OpenMx/R/MxExpectationGREML.R | 8 OpenMx-2.18.1/OpenMx/R/MxExpectationLISREL.R | 100 +- OpenMx-2.18.1/OpenMx/R/MxExpectationNormal.R | 304 ++++-- OpenMx-2.18.1/OpenMx/R/MxExpectationRAM.R | 118 +- OpenMx-2.18.1/OpenMx/R/MxExpectationStateSpace.R | 41 OpenMx-2.18.1/OpenMx/R/MxFactorScores.R | 26 OpenMx-2.18.1/OpenMx/R/MxFitFunction.R | 4 OpenMx-2.18.1/OpenMx/R/MxLISRELModel.R | 54 - OpenMx-2.18.1/OpenMx/R/MxMI.R | 1 OpenMx-2.18.1/OpenMx/R/MxModel.R | 17 OpenMx-2.18.1/OpenMx/R/MxModelFunctions.R | 29 OpenMx-2.18.1/OpenMx/R/MxModelParameters.R | 2 OpenMx-2.18.1/OpenMx/R/MxNamespace.R | 10 OpenMx-2.18.1/OpenMx/R/MxOptions.R | 10 OpenMx-2.18.1/OpenMx/R/MxPPML.R | 357 +++---- OpenMx-2.18.1/OpenMx/R/MxPredict.R |only OpenMx-2.18.1/OpenMx/R/MxRAMModel.R | 230 ++-- OpenMx-2.18.1/OpenMx/R/MxRename.R | 4 OpenMx-2.18.1/OpenMx/R/MxRestore.R | 5 OpenMx-2.18.1/OpenMx/R/MxRun.R | 15 OpenMx-2.18.1/OpenMx/R/MxSE.R | 7 OpenMx-2.18.1/OpenMx/R/MxSaturatedModel.R | 3 OpenMx-2.18.1/OpenMx/R/MxSummary.R | 8 OpenMx-2.18.1/OpenMx/R/MxThreshold.R | 346 ++++++- OpenMx-2.18.1/OpenMx/R/MxTryHard.R | 15 OpenMx-2.18.1/OpenMx/R/MxUnitTesting.R | 8 OpenMx-2.18.1/OpenMx/R/MxVersion.R | 2 OpenMx-2.18.1/OpenMx/R/omxGetNPSOL.R | 7 OpenMx-2.18.1/OpenMx/R/omxReadGRMBin.R | 2 OpenMx-2.18.1/OpenMx/R/sysdata.rda |binary OpenMx-2.18.1/OpenMx/R/zzz.R | 14 OpenMx-2.18.1/OpenMx/README.md | 12 OpenMx-2.18.1/OpenMx/build |only OpenMx-2.18.1/OpenMx/configure | 26 OpenMx-2.18.1/OpenMx/inst/CITATION | 2 OpenMx-2.18.1/OpenMx/inst/WORDLIST | 29 OpenMx-2.18.1/OpenMx/inst/models/nightly/DefinitionIloo.R | 6 OpenMx-2.18.1/OpenMx/inst/models/nightly/NelderMeadUnitTesting.R | 62 - OpenMx-2.18.1/OpenMx/inst/models/nightly/Power2.R | 35 OpenMx-2.18.1/OpenMx/inst/models/nightly/RampartDimnames.R |only OpenMx-2.18.1/OpenMx/inst/models/nightly/SkippedRows.R | 8 OpenMx-2.18.1/OpenMx/inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R | 9 OpenMx-2.18.1/OpenMx/inst/models/passing/FourAAAA.R | 2 OpenMx-2.18.1/OpenMx/inst/models/passing/InvalidWLS.R | 6 OpenMx-2.18.1/OpenMx/inst/models/passing/JointFIMLTest.R | 5 OpenMx-2.18.1/OpenMx/inst/models/passing/SimpleConfidenceIntervals.R | 101 +- OpenMx-2.18.1/OpenMx/inst/models/passing/jointFactorWls.R | 7 OpenMx-2.18.1/OpenMx/inst/models/passing/univACEP.R | 23 OpenMx-2.18.1/OpenMx/inst/models/passing/vcov.R | 7 OpenMx-2.18.1/OpenMx/man/DiscreteBase-class.Rd |only OpenMx-2.18.1/OpenMx/man/figures |only OpenMx-2.18.1/OpenMx/man/imxGenericModelBuilder.Rd | 3 OpenMx-2.18.1/OpenMx/man/imxGetNumThreads.Rd | 10 OpenMx-2.18.1/OpenMx/man/imxModelBuilder.Rd | 3 OpenMx-2.18.1/OpenMx/man/mxBootstrapStdizeRAMpaths.Rd | 41 OpenMx-2.18.1/OpenMx/man/mxComputeEM.Rd | 4 OpenMx-2.18.1/OpenMx/man/mxComputeLoadData.Rd | 7 OpenMx-2.18.1/OpenMx/man/mxComputeTryCatch.Rd | 4 OpenMx-2.18.1/OpenMx/man/mxData.Rd | 6 OpenMx-2.18.1/OpenMx/man/mxEval.Rd | 2 OpenMx-2.18.1/OpenMx/man/mxExpectationLISREL.Rd | 7 OpenMx-2.18.1/OpenMx/man/mxExpectationNormal.Rd | 25 OpenMx-2.18.1/OpenMx/man/mxExpectationRAM.Rd | 4 OpenMx-2.18.1/OpenMx/man/mxExpectationStateSpace.Rd | 7 OpenMx-2.18.1/OpenMx/man/mxExpectationStateSpaceContinuousTime.Rd | 11 OpenMx-2.18.1/OpenMx/man/mxMarginalNegativeBinomial.Rd |only OpenMx-2.18.1/OpenMx/man/mxMarginalPoisson.Rd |only OpenMx-2.18.1/OpenMx/man/mxModel.Rd | 2 OpenMx-2.18.1/OpenMx/man/mxOption.Rd | 2 OpenMx-2.18.1/OpenMx/man/mxPearsonSelCov.Rd | 1 OpenMx-2.18.1/OpenMx/man/mxThreshold.Rd | 3 OpenMx-2.18.1/OpenMx/man/omxCheckError.Rd | 9 OpenMx-2.18.1/OpenMx/man/omxGetRAMDepth.Rd | 2 OpenMx-2.18.1/OpenMx/man/omxReadGRMBin.Rd | 2 OpenMx-2.18.1/OpenMx/man/omxSetParameters.Rd | 2 OpenMx-2.18.1/OpenMx/man/predict.MxModel.Rd |only OpenMx-2.18.1/OpenMx/src/Compute.cpp | 202 ++-- OpenMx-2.18.1/OpenMx/src/Compute.h | 2 OpenMx-2.18.1/OpenMx/src/ComputeGD.cpp | 22 OpenMx-2.18.1/OpenMx/src/EnableWarnings.h | 2 OpenMx-2.18.1/OpenMx/src/LoadDataAPI.h | 39 OpenMx-2.18.1/OpenMx/src/Makevars.in | 5 OpenMx-2.18.1/OpenMx/src/MarkovExpectation.cpp | 15 OpenMx-2.18.1/OpenMx/src/RAMInternal.h | 23 OpenMx-2.18.1/OpenMx/src/ba81quad.cpp | 8 OpenMx-2.18.1/OpenMx/src/ba81quad.h | 15 OpenMx-2.18.1/OpenMx/src/finiteDifferences.h | 45 OpenMx-2.18.1/OpenMx/src/glue.cpp | 10 OpenMx-2.18.1/OpenMx/src/omxData.cpp | 346 ++++--- OpenMx-2.18.1/OpenMx/src/omxData.h | 89 + OpenMx-2.18.1/OpenMx/src/omxExpectation.cpp | 474 ++++++---- OpenMx-2.18.1/OpenMx/src/omxExpectation.h | 142 ++ OpenMx-2.18.1/OpenMx/src/omxExpectationBA81.cpp | 158 +-- OpenMx-2.18.1/OpenMx/src/omxExpectationBA81.h | 7 OpenMx-2.18.1/OpenMx/src/omxFIMLFitFunction.cpp | 84 + OpenMx-2.18.1/OpenMx/src/omxFIMLFitFunction.h | 33 OpenMx-2.18.1/OpenMx/src/omxFitFunctionBA81.cpp | 5 OpenMx-2.18.1/OpenMx/src/omxGREMLExpectation.cpp | 81 + OpenMx-2.18.1/OpenMx/src/omxGREMLExpectation.h | 26 OpenMx-2.18.1/OpenMx/src/omxLISRELExpectation.cpp | 196 ++-- OpenMx-2.18.1/OpenMx/src/omxMatrix.cpp | 22 OpenMx-2.18.1/OpenMx/src/omxMatrix.h | 2 OpenMx-2.18.1/OpenMx/src/omxNormalExpectation.cpp | 23 OpenMx-2.18.1/OpenMx/src/omxRAMExpectation.cpp | 104 +- OpenMx-2.18.1/OpenMx/src/omxSadmvnWrapper.h | 58 - OpenMx-2.18.1/OpenMx/src/omxState.cpp | 17 OpenMx-2.18.1/OpenMx/src/omxState.h | 9 OpenMx-2.18.1/OpenMx/src/omxStateSpaceExpectation.cpp | 285 +++--- OpenMx-2.18.1/OpenMx/src/omxWLSFitFunction.cpp | 155 +-- OpenMx-2.18.1/OpenMx/src/polynomial.h | 2 OpenMx-2.18.1/OpenMx/tests/testthat/test-LatentAR-190605.R | 35 OpenMx-2.18.1/OpenMx/tests/testthat/test-MatrixErrorDetection.R | 5 OpenMx-2.18.1/OpenMx/tests/testthat/test-NelderMead--bothConstraintTypes.R |only OpenMx-2.18.1/OpenMx/tests/testthat/test-defvar.R | 11 OpenMx-2.18.1/OpenMx/tests/testthat/test-discrete.R |only OpenMx-2.18.1/OpenMx/tests/testthat/test-loadDataByCol.R | 42 OpenMx-2.18.1/OpenMx/tests/testthat/test-loadDataByRow.R | 25 OpenMx-2.18.1/OpenMx/tests/testthat/test-omp.R |only OpenMx-2.18.1/OpenMx/tests/testthat/test-simplestCI.R | 2 OpenMx-2.18.1/OpenMx/tests/testthat/test-wls-binary.R | 2 OpenMx-2.18.1/OpenMx/tools/covr.R | 3 OpenMx-2.18.1/OpenMx/tools/splitLog |only OpenMx-2.18.1/OpenMx/tools/travis |only 133 files changed, 3345 insertions(+), 2137 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.4 dated 2020-08-01 and 0.0.5 dated 2020-08-28
gausscov-0.0.4/gausscov/data/abcq.rda |only gausscov-0.0.4/gausscov/data/dent.rda |only gausscov-0.0.4/gausscov/man/abcq.Rd |only gausscov-0.0.4/gausscov/man/dent.Rd |only gausscov-0.0.5/gausscov/DESCRIPTION | 10 +-- gausscov-0.0.5/gausscov/MD5 | 56 +++++++++++---------- gausscov-0.0.5/gausscov/R/decomp.R | 1 gausscov-0.0.5/gausscov/R/f1st.R | 30 +++++++---- gausscov-0.0.5/gausscov/R/f2st.R | 7 +- gausscov-0.0.5/gausscov/R/fgeninter.R | 2 gausscov-0.0.5/gausscov/R/fgr1st.R | 27 ++++++++-- gausscov-0.0.5/gausscov/R/fgr2st.R | 17 ++++++ gausscov-0.0.5/gausscov/R/fmch.R | 18 +++--- gausscov-0.0.5/gausscov/R/fpval.R | 42 ++++++++++------ gausscov-0.0.5/gausscov/R/frmch.R | 30 ++++++----- gausscov-0.0.5/gausscov/R/frobregp.R | 31 ++++++----- gausscov-0.0.5/gausscov/R/frst.R | 81 ++++++++++++++++++------------- gausscov-0.0.5/gausscov/R/fselect.R | 27 +++++----- gausscov-0.0.5/gausscov/data/abcql.rda |only gausscov-0.0.5/gausscov/data/dentx.rda |only gausscov-0.0.5/gausscov/data/denty.rda |only gausscov-0.0.5/gausscov/man/abcql.Rd |only gausscov-0.0.5/gausscov/man/dentx.Rd |only gausscov-0.0.5/gausscov/man/denty.Rd |only gausscov-0.0.5/gausscov/man/f1st.Rd | 4 - gausscov-0.0.5/gausscov/man/fgeninter.Rd | 2 gausscov-0.0.5/gausscov/man/fgr1st.Rd | 4 + gausscov-0.0.5/gausscov/man/fgr2st.Rd | 4 + gausscov-0.0.5/gausscov/man/fmch.Rd | 2 gausscov-0.0.5/gausscov/man/fpval.Rd | 7 +- gausscov-0.0.5/gausscov/man/frmch.Rd | 10 ++- gausscov-0.0.5/gausscov/man/frst.Rd | 8 +-- gausscov-0.0.5/gausscov/man/fselect.Rd | 5 + gausscov-0.0.5/gausscov/src/gaucov.f | 56 ++++++++++----------- 34 files changed, 287 insertions(+), 194 deletions(-)
Title: Easy Michaelis-Menten Enzyme Kinetics
Description: Serves as a platform for published fluorometric enzyme assay
protocols. 'ezmmek' calibrates, calculates, and plots enzyme activities as they
relate to the transformation of synthetic substrates. At present, 'ezmmek'
implements two common protocols found in the literature, and is modular to accommodate
additional protocols. Here, these protocols are referred to as the In-Sample
Calibration (Hoppe, 1983; <doi:10.3354/meps011299>) and In-Buffer Calibration (German et al., 2011; <doi:10.1016/j.soilbio.2011.03.017>).
protocols. By containing multiple protocols, 'ezmmek' aims to stimulate
discussion about how to best optimize fluorometric enzyme assays. A standardized
approach would make studies more comparable and reproducible.
Author: Christopher Cook [aut, cre],
Andrew Steen [aut]
Maintainer: Christopher Cook <ccook62@vols.utk.edu>
Diff between ezmmek versions 0.2.1 dated 2019-12-20 and 0.2.4 dated 2020-08-28
ezmmek-0.2.1/ezmmek/R/d_sat.R |only ezmmek-0.2.1/ezmmek/R/d_sat_n.R |only ezmmek-0.2.1/ezmmek/R/d_std.R |only ezmmek-0.2.1/ezmmek/R/ezmmek-package.R |only ezmmek-0.2.1/ezmmek/R/p_sat_curve.R |only ezmmek-0.2.1/ezmmek/R/p_sat_raw.R |only ezmmek-0.2.1/ezmmek/R/p_std_curve.R |only ezmmek-0.2.1/ezmmek/data |only ezmmek-0.2.1/ezmmek/man/d_sat.Rd |only ezmmek-0.2.1/ezmmek/man/d_sat_n.Rd |only ezmmek-0.2.1/ezmmek/man/d_std.Rd |only ezmmek-0.2.1/ezmmek/man/ezmmek-package.Rd |only ezmmek-0.2.1/ezmmek/man/p_sat_curve.Rd |only ezmmek-0.2.1/ezmmek/man/p_sat_raw.Rd |only ezmmek-0.2.1/ezmmek/man/p_std_curve.Rd |only ezmmek-0.2.1/ezmmek/tests/testthat/test_p_sat_curve.R |only ezmmek-0.2.1/ezmmek/tests/testthat/test_p_sat_raw.R |only ezmmek-0.2.1/ezmmek/tests/testthat/test_p_std_curve.R |only ezmmek-0.2.4/ezmmek/DESCRIPTION | 40 +++-- ezmmek-0.2.4/ezmmek/MD5 | 74 ++++++---- ezmmek-0.2.4/ezmmek/NAMESPACE | 11 + ezmmek-0.2.4/ezmmek/R/ezmmek_calc_mm_fit.R |only ezmmek-0.2.4/ezmmek/R/ezmmek_calc_std_lm_buffer.R |only ezmmek-0.2.4/ezmmek/R/ezmmek_calc_std_lm_homo.R |only ezmmek-0.2.4/ezmmek/R/ezmmek_calc_std_lm_homo_buf.R |only ezmmek-0.2.4/ezmmek/R/ezmmek_calibrate_activities.R |only ezmmek-0.2.4/ezmmek/R/ezmmek_std_lm.R |only ezmmek-0.2.4/ezmmek/R/globals.R | 58 +++++-- ezmmek-0.2.4/ezmmek/R/new_ezmmek_act_calibrate.R |only ezmmek-0.2.4/ezmmek/R/new_ezmmek_act_group.R |only ezmmek-0.2.4/ezmmek/R/new_ezmmek_sat_fit.R |only ezmmek-0.2.4/ezmmek/R/new_ezmmek_std_group.R |only ezmmek-0.2.4/ezmmek/R/plot_new_ezmmek_act_group.R |only ezmmek-0.2.4/ezmmek/R/plot_new_ezmmek_calibrate.R |only ezmmek-0.2.4/ezmmek/R/plot_new_ezmmek_sat_fit.R |only ezmmek-0.2.4/ezmmek/R/plot_new_ezmmek_std_group.R |only ezmmek-0.2.4/ezmmek/build |only ezmmek-0.2.4/ezmmek/inst |only ezmmek-0.2.4/ezmmek/man/ezmmek_calc_mm_fit.Rd |only ezmmek-0.2.4/ezmmek/man/ezmmek_calc_std_lm_buffer.Rd |only ezmmek-0.2.4/ezmmek/man/ezmmek_calc_std_lm_homo.Rd |only ezmmek-0.2.4/ezmmek/man/ezmmek_calc_std_lm_homo_buffer.Rd |only ezmmek-0.2.4/ezmmek/man/ezmmek_calibrate_activities.Rd |only ezmmek-0.2.4/ezmmek/man/ezmmek_std_lm.Rd |only ezmmek-0.2.4/ezmmek/man/new_ezmmek_act_calibrate.Rd |only ezmmek-0.2.4/ezmmek/man/new_ezmmek_act_group.Rd |only ezmmek-0.2.4/ezmmek/man/new_ezmmek_sat_fit.Rd |only ezmmek-0.2.4/ezmmek/man/new_ezmmek_std_group.Rd |only ezmmek-0.2.4/ezmmek/man/plot.new_ezmmek_act_group.Rd |only ezmmek-0.2.4/ezmmek/man/plot.new_ezmmek_calibrate.Rd |only ezmmek-0.2.4/ezmmek/man/plot.new_ezmmek_sat_fit.Rd |only ezmmek-0.2.4/ezmmek/man/plot.new_ezmmek_std_group.Rd |only ezmmek-0.2.4/ezmmek/tests/testthat/test_data |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_act_calibrate_ibc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_act_calibrate_isc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_act_group_ibc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_act_group_isc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_sat_fit_isc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_sat_fit_isc_dirty.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_std_ibc_clean.R |only ezmmek-0.2.4/ezmmek/tests/testthat/test_new_ezmmek_std_isc_clean.R |only ezmmek-0.2.4/ezmmek/vignettes |only 62 files changed, 127 insertions(+), 56 deletions(-)
Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building
simulation program 'EnergyPlus'(<https://energyplus.net>), which
enables programmatic navigation, modification of 'EnergyPlus' models
and makes it less painful to do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuan.jia@bears-berkeley.sg>
Diff between eplusr versions 0.12.0 dated 2020-02-20 and 0.13.0 dated 2020-08-28
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Title: Analysis of Niche Evolution using Niche and Distribution Models
Description: Description: Tools for constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Author: Dan Warren [aut, cre] (<https://orcid.org/0000-0002-8747-2451>),
Nick Matzke [ctb],
Marcel Cardillo [ctb],
John Baumgartner [ctb],
Linda Beaumont [ctb],
Nicholas Huron [ctb],
Marianna Simoes [ctb],
Teresa Iglesias [ctb],
Russell Dinnage [aut] (<https://orcid.org/0000-0003-0846-2819>)
Maintainer: Dan Warren <dan.l.warren@gmail.com>
Diff between ENMTools versions 1.0 dated 2020-07-29 and 1.0.1 dated 2020-08-28
DESCRIPTION | 12 +-- MD5 | 107 +++++++++++++++------------- NAMESPACE | 42 +---------- NEWS.md |only R/background.test.R | 87 ++++++++++++++--------- R/check.bg.R | 25 ++++-- R/clamp.env.R |only R/enmtools.aoc.R | 19 +++-- R/enmtools.bc.R | 70 ++++++++++++++++-- R/enmtools.calibrate.R | 2 R/enmtools.dm.R | 72 ++++++++++++++++--- R/enmtools.ecospat.bg.R | 9 +- R/enmtools.ecospat.id.R | 9 +- R/enmtools.gam.R | 61 ++++++++++++++-- R/enmtools.glm.R | 60 +++++++++++++-- R/enmtools.hypervolume.R | 9 +- R/enmtools.maxent.R | 65 ++++++++++++++--- R/enmtools.ppmlasso.R | 63 ++++++++++++++-- R/enmtools.rf.R | 61 ++++++++++++++-- R/enmtools.rf.ranger.R | 66 ++++++++++++++--- R/enmtools.vip.R |only R/env.evaluate.R | 7 + R/env.overlap.R | 9 +- R/identity.test.R | 86 ++++++++++++++-------- R/interactive.plot.R |only R/interactive.plot.enmtools.model.R | 6 - R/moses.list.R | 9 +- R/package.depends.R | 8 +- R/rangebreak.blob.R | 80 +++++++++++++-------- R/rangebreak.linear.R | 81 +++++++++++++-------- R/rangebreak.ribbon.R | 136 ++++++++++++++++++++---------------- R/threespace.plot.R | 2 R/zzz.R | 2 man/background.test.Rd | 6 + man/check.bg.Rd | 10 ++ man/clamp.env.Rd |only man/enmtools.aoc.Rd | 8 +- man/enmtools.bc.Rd | 6 + man/enmtools.dm.Rd | 6 + man/enmtools.ecospat.bg.Rd | 3 man/enmtools.ecospat.id.Rd | 5 + man/enmtools.gam.Rd | 6 + man/enmtools.glm.Rd | 6 + man/enmtools.hypervolume.Rd | 6 + man/enmtools.maxent.Rd | 6 + man/enmtools.ppmlasso.Rd | 6 + man/enmtools.rf.Rd | 6 + man/enmtools.rf.ranger.Rd | 8 +- man/enmtools.vip.Rd |only man/env.evaluate.Rd | 5 + man/env.overlap.Rd | 7 + man/identity.test.Rd | 6 + man/interactive.plot.Rd |only man/moses.list.Rd | 3 man/rangebreak.blob.Rd | 6 + man/rangebreak.linear.Rd | 6 + man/rangebreak.ribbon.Rd | 6 + tests/testthat/test_ENMTools.R | 2 58 files changed, 1002 insertions(+), 392 deletions(-)
Title: Some EM-Type Estimation Methods for the Heckman Selection Model
Description: Some EM-type algorithms to estimate parameters for the well-known Heckman selection model are provided in the package. Such algorithms are as follow: ECM(Expectation/Conditional Maximization), ECM(NR)(the Newton-Raphson method is adapted to the ECM) and ECME(Expectation/Conditional Maximization Either). Since the algorithms are based on the EM algorithm, they also have EM's main advantages, namely, stability and ease of implementation. Further details and explanations of the algorithms can be found in Zhao et al. (2020) <doi: 10.1016/j.csda.2020.106930>.
Author: Kexuan Yang <717260446@qq.com>, Sang Kyu Lee <leesa111@msu.edu>, Jun Zhao <zhaojun2021@hotmail.com>, and Hyoung-Moon Kim <hmk966a@gmail.com >
Maintainer: Sang Kyu Lee <leesa111@msu.edu>
Diff between EMSS versions 1.0.1 dated 2020-05-31 and 1.0.2 dated 2020-08-28
DESCRIPTION | 12 MD5 | 10 R/EMSS.R | 1942 ++++++++++++++++++++++++++-------------------------- man/EMSS.Rd | 10 man/Smoke.Rd | 6 man/summary.EMSS.Rd | 3 6 files changed, 999 insertions(+), 984 deletions(-)
Title: Estimation of Parameter-Dependent Network Centrality Measures
Description: Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018) and Battaglini, Patacchini, and Leone Sciabolazza (2020). For additional details, see the vignette.
Author: Marco Battaglini [aut] (<https://orcid.org/0000-0001-9690-0721>),
Valerio Leone Sciabolazza [aut, cre]
(<https://orcid.org/0000-0003-2537-3084>),
Eleonora Patacchini [aut] (<https://orcid.org/0000-0002-3510-2969>),
Sida Peng [aut] (<https://orcid.org/0000-0002-2151-0523>)
Maintainer: Valerio Leone Sciabolazza <valerio.leonesciabolazza@uniparthenope.it>
Diff between econet versions 0.1.81 dated 2018-11-08 and 0.1.91 dated 2020-08-28
DESCRIPTION | 13 MD5 | 66 - NAMESPACE | 6 R/boot.R | 80 + R/dep_mat.R | 5 R/globals.R | 4 R/horse_race.R | 4 R/ll_party_split_btw.R |only R/ll_party_split_with.R |only R/ll_party_split_with_btw.R |only R/mle_party_split_btw.R |only R/mle_party_split_with.R |only R/mle_party_split_with_btw.R |only R/mle_prepare_data.R | 127 ++ R/net_dep.R | 72 + R/nls_prepare_data.R | 60 + R/par_dep.R | 5 R/par_dep_mat.R | 5 R/parameter_dependent_centrality.R | 23 R/party_connection_split.R |only R/prepare_data.R | 1 R/quantify.R | 5 R/time_party_connection_split.R |only build/vignette.rds |binary inst/doc/econet.pdf |binary man/G_alumni_111.Rd | 4 man/G_cosponsor_111.Rd | 4 man/G_model_A_test.Rd | 4 man/a_G_alumni_111.Rd | 4 man/a_db_alumni.Rd | 6 man/boot.Rd | 28 man/db_alumni_test.Rd | 6 man/db_cosponsor.Rd | 6 man/horse_race.Rd | 32 man/net_dep.Rd | 53 - man/quantify.Rd | 2 vignettes/econet.tex | 1676 +++++++++++++++++++++---------------- vignettes/econet_refs.bib | 1115 ++++++++++++++++-------- 38 files changed, 2229 insertions(+), 1187 deletions(-)
Title: Dynamic Models for Survival Data
Description: Time-varying coefficient models for interval censored and
right censored survival data including
1) Bayesian Cox model with time-independent, time-varying or
dynamic coefficients for right censored and interval censored data studied by
Sinha et al. (1999) <doi:10.1111/j.0006-341X.1999.00585.x> and
Wang et al. (2013) <doi:10.1007/s10985-013-9246-8>,
2) Spline based time-varying coefficient Cox model for right censored data
proposed by Perperoglou et al. (2006) <doi:10.1016/j.cmpb.2005.11.006>, and
3) Transformation model with time-varying coefficients for right censored data
using estimating equations proposed by
Peng and Huang (2007) <doi:10.1093/biomet/asm058>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Ming-Hui Chen [aut],
Xiaojing Wang [aut],
Jun Yan [aut] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between dynsurv versions 0.3-7 dated 2019-08-27 and 0.4-1 dated 2020-08-28
ChangeLog | 25 +++ DESCRIPTION | 22 +-- MD5 | 57 ++++---- NAMESPACE | 16 +- R/bayesCox.R | 337 ++++++++++++++++++++++---------------------------- R/bayesCoxMcmc.R |only R/coef.R | 136 ++++++++++---------- R/data.R | 30 +--- R/dynsurv-package.R | 58 ++++---- R/jump.R | 111 +++++++--------- R/misc.R |only R/otherExports.R | 24 +-- R/plot.R | 56 +++----- R/print.R | 62 +++------ R/splineCox.R | 46 +++--- R/survCurv.R | 144 ++++++++------------- R/tvTran.R | 24 +-- inst/CITATION | 25 +-- inst/examples |only man/bayesCox.Rd | 108 ++++++++-------- man/bayesCoxMcmc.Rd |only man/bcos.Rd | 8 - man/coef.bayesCox.Rd | 1 man/coef.splineCox.Rd | 1 man/dynsurv.Rd | 1 man/is.bayesCox.Rd |only man/jump.Rd | 1 man/nu.Rd | 1 man/plotSurv.Rd | 12 + man/survCurve.Rd | 29 ++-- man/survDiff.Rd | 9 - man/tooth.Rd | 8 - 32 files changed, 642 insertions(+), 710 deletions(-)
Title: Multivariate Function Visualization and Smooth Multiband Color
Interpolation
Description: Combined contour/heatmap plots, 3d bar/surface plots, isosurface plots, triangular plots and 2d/3d vector fields. Builds on the colorspace package (Zeileis, A., et al. (2019) <arxiv.org/abs/1903.06490>), by supporting smooth multiband color interpolation, in sRGB, HSV and HCL color spaces. The default color functions for heatmaps, use HCL (Zeileis, A., et al. (2009) <doi:10.1016/j.csda.2008.11.033>) and support near-uniform perception.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between barsurf versions 0.5.0 dated 2020-05-04 and 0.6.1 dated 2020-08-28
barsurf-0.5.0/barsurf/R/color.r |only barsurf-0.5.0/barsurf/R/litmus_2.r |only barsurf-0.5.0/barsurf/R/other.r |only barsurf-0.5.0/barsurf/man/01_scalar_fields_discretely-spaced.Rd |only barsurf-0.5.0/barsurf/man/02_scalar_fields_continuously-spaced_.Rd |only barsurf-0.5.0/barsurf/man/03_plot_contour_3d.Rd |only barsurf-0.5.0/barsurf/man/04_plot_cfield_3d.Rd |only barsurf-0.5.0/barsurf/man/05_vector_fields.Rd |only barsurf-0.5.0/barsurf/man/06_color_themes.Rd |only barsurf-0.5.0/barsurf/man/07_barface_objects.Rd |only barsurf-0.5.0/barsurf/man/08_litmus_objects.Rd |only barsurf-0.5.0/barsurf/man/09_multi-litmus_objects.Rd |only barsurf-0.5.0/barsurf/man/10_supporting_methods.Rd |only barsurf-0.5.0/barsurf/man/11_other_supporting_functions_1.Rd |only barsurf-0.5.0/barsurf/man/12_other_supporting_functions_2.Rd |only barsurf-0.5.0/barsurf/man/13_other_supporting_functions_3.Rd |only barsurf-0.5.0/barsurf/man/14_sample_functions.Rd |only barsurf-0.5.0/barsurf/man/15_fitting_litmus_objects_to_data.Rd |only barsurf-0.5.0/barsurf/man/16_deprecated.Rd |only barsurf-0.6.1/barsurf/DESCRIPTION | 16 barsurf-0.6.1/barsurf/MD5 | 71 - barsurf-0.6.1/barsurf/NAMESPACE | 2 barsurf-0.6.1/barsurf/R/bs.r |only barsurf-0.6.1/barsurf/R/colfs.r |only barsurf-0.6.1/barsurf/R/colfs2.r |only barsurf-0.6.1/barsurf/R/colvs.r |only barsurf-0.6.1/barsurf/R/global.r |only barsurf-0.6.1/barsurf/R/init.r | 23 barsurf-0.6.1/barsurf/R/litmus.r | 62 - barsurf-0.6.1/barsurf/R/plot2d.r | 453 ++------ barsurf-0.6.1/barsurf/R/plot3d.r | 317 ++--- barsurf-0.6.1/barsurf/R/plot3v.r | 452 +++----- barsurf-0.6.1/barsurf/R/plotf.r |only barsurf-0.6.1/barsurf/R/plotvec.r |only barsurf-0.6.1/barsurf/R/projection.r | 84 - barsurf-0.6.1/barsurf/R/val_iso.r |only barsurf-0.6.1/barsurf/R/val_xy.r |only barsurf-0.6.1/barsurf/build/vignette.rds |binary barsurf-0.6.1/barsurf/inst/doc/barsurf.R | 316 +---- barsurf-0.6.1/barsurf/inst/doc/barsurf.Rnw | 536 +++------- barsurf-0.6.1/barsurf/inst/doc/barsurf.pdf |binary barsurf-0.6.1/barsurf/man/11_main_plotting_functions.Rd |only barsurf-0.6.1/barsurf/man/12_functional_versions.Rd |only barsurf-0.6.1/barsurf/man/21_global_options.Rd |only barsurf-0.6.1/barsurf/man/22_standardized_palette_interface.Rd |only barsurf-0.6.1/barsurf/man/31_litmus_objects.Rd |only barsurf-0.6.1/barsurf/man/32_multi-litmus_objects.Rd |only barsurf-0.6.1/barsurf/man/33_litmus-fitting_functions.Rd |only barsurf-0.6.1/barsurf/man/41_print_and_plot_methods.Rd |only barsurf-0.6.1/barsurf/man/51_simple_color_palettes.Rd |only barsurf-0.6.1/barsurf/man/52_predefined_litmus_objects.Rd |only barsurf-0.6.1/barsurf/man/53_predefined_litmus-fitting_functions.Rd |only barsurf-0.6.1/barsurf/man/54_color_sequence_functions.Rd |only barsurf-0.6.1/barsurf/man/61_check_xy_relationship.Rd |only barsurf-0.6.1/barsurf/man/62_matrix_plot_margins.Rd |only barsurf-0.6.1/barsurf/man/63_color_conversion.Rd |only barsurf-0.6.1/barsurf/man/71_deprecated.Rd |only barsurf-0.6.1/barsurf/man/81_sample_functions.Rd |only barsurf-0.6.1/barsurf/vignettes/barsurf.Rnw | 536 +++------- 59 files changed, 1029 insertions(+), 1839 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Vilmantas Gegzna [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.6-2 dated 2020-01-22 and 2.7-0 dated 2020-08-28
Rcmdr-2.6-2/Rcmdr/build |only Rcmdr-2.6-2/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.R |only Rcmdr-2.6-2/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.Rnw |only Rcmdr-2.7-0/Rcmdr/DESCRIPTION | 16 Rcmdr-2.7-0/Rcmdr/MD5 | 137 Rcmdr-2.7-0/Rcmdr/NAMESPACE | 12 Rcmdr-2.7-0/Rcmdr/NEWS | 1284 - Rcmdr-2.7-0/Rcmdr/R/cluster.R | 4 Rcmdr-2.7-0/Rcmdr/R/commander.R | 3080 +- Rcmdr-2.7-0/Rcmdr/R/data-menu.R | 563 Rcmdr-2.7-0/Rcmdr/R/file-menu.R | 2171 - Rcmdr-2.7-0/Rcmdr/R/globals.R | 121 Rcmdr-2.7-0/Rcmdr/R/graphs-menu.R | 6026 ++--- Rcmdr-2.7-0/Rcmdr/R/model-menu.R | 2901 +- Rcmdr-2.7-0/Rcmdr/R/statistics-means-menu.R | 1328 - Rcmdr-2.7-0/Rcmdr/R/statistics-nonparametric-menu.R | 18 Rcmdr-2.7-0/Rcmdr/R/statistics-proportions-menu.R | 304 Rcmdr-2.7-0/Rcmdr/R/statistics-summaries-menu.R | 1321 - Rcmdr-2.7-0/Rcmdr/R/statistics-tables-menu.R | 3 Rcmdr-2.7-0/Rcmdr/R/statistics-variances-menu.R | 38 Rcmdr-2.7-0/Rcmdr/R/utilities.R | 7835 +++---- Rcmdr-2.7-0/Rcmdr/inst/CHANGES | 1962 - Rcmdr-2.7-0/Rcmdr/inst/CITATION | 76 Rcmdr-2.7-0/Rcmdr/inst/doc/Commander-ru.pdf |binary Rcmdr-2.7-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr-ja.pdf |binary Rcmdr-2.7-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary Rcmdr-2.7-0/Rcmdr/inst/etc/Rcmdr-RMarkdown-Template.Rmd | 30 Rcmdr-2.7-0/Rcmdr/inst/etc/Rcmdr-menus.txt | 18 Rcmdr-2.7-0/Rcmdr/inst/etc/linux/Rcmdr.svg | 2 Rcmdr-2.7-0/Rcmdr/inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/el/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/eu/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/gl/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/hu/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/id/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/it/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/ko/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/pt_BR/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/ro/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/inst/po/zh_CN/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.7-0/Rcmdr/man/AuxiliarySoftware.Rd | 92 Rcmdr-2.7-0/Rcmdr/man/CFA.Rd | 4 Rcmdr-2.7-0/Rcmdr/man/Commander.Rd | 7 Rcmdr-2.7-0/Rcmdr/man/Plugins.Rd | 80 Rcmdr-2.7-0/Rcmdr/man/Rcmdr-package.Rd | 138 Rcmdr-2.7-0/Rcmdr/man/Rcmdr.Utilities.Rd | 1307 - Rcmdr-2.7-0/Rcmdr/man/RcmdrEditor.Rd | 60 Rcmdr-2.7-0/Rcmdr/man/RecodeDialog.Rd | 106 Rcmdr-2.7-0/Rcmdr/man/RepeatedMeasuresDialogs.Rd |only Rcmdr-2.7-0/Rcmdr/man/ReshapeDatasetDialogs.Rd |only Rcmdr-2.7-0/Rcmdr/man/Scatter3DDialog.Rd | 4 Rcmdr-2.7-0/Rcmdr/po/R-Rcmdr.pot |10597 ++++----- Rcmdr-2.7-0/Rcmdr/po/R-ca.po | 2 Rcmdr-2.7-0/Rcmdr/po/R-es.po | 335 Rcmdr-2.7-0/Rcmdr/po/R-eu.po |11060 +++++----- Rcmdr-2.7-0/Rcmdr/po/R-fr.po | 479 Rcmdr-2.7-0/Rcmdr/po/R-gl.po | 4 Rcmdr-2.7-0/Rcmdr/po/R-hu.po | 485 Rcmdr-2.7-0/Rcmdr/po/R-id.po | 364 Rcmdr-2.7-0/Rcmdr/po/R-it.po | 2 Rcmdr-2.7-0/Rcmdr/po/R-ja.po | 752 Rcmdr-2.7-0/Rcmdr/po/R-ko.po | 500 Rcmdr-2.7-0/Rcmdr/po/R-ru.po | 234 Rcmdr-2.7-0/Rcmdr/po/R-sl.po |10889 +++++---- Rcmdr-2.7-0/Rcmdr/vignettes/Getting-Started-with-the-Rcmdr.Rnw | 259 Rcmdr-2.7-0/Rcmdr/vignettes/Rcmdr-Manual.bib | 204 72 files changed, 35389 insertions(+), 31825 deletions(-)
Title: Convenient Functions for Ensemble Time Series Forecasts
Description: Convenient functions for ensemble forecasts in R combining
approaches from the 'forecast' package. Forecasts generated from auto.arima(), ets(),
thetaf(), nnetar(), stlm(), tbats(), and snaive() can be combined with equal weights, weights
based on in-sample errors (introduced by Bates & Granger (1969) <doi:10.1057/jors.1969.103>),
or cross-validated weights. Cross validation for time series data with user-supplied models
and forecasting functions is also supported to evaluate model accuracy.
Author: David Shaub [aut, cre],
Peter Ellis [aut]
Maintainer: David Shaub <davidshaub@gmx.com>
Diff between forecastHybrid versions 5.0.18 dated 2020-04-02 and 5.0.19 dated 2020-08-28
DESCRIPTION | 10 - MD5 | 61 +++---- R/cvts.R | 236 +++++++++++++++++------------ R/forecast.hybridModel.R | 114 ++++++-------- R/generics.R | 197 +++++++++++++----------- R/helper.R | 131 ++++++++-------- R/hybridModel.R | 168 ++++++++++---------- R/theta.R | 83 +++++----- R/thiefModel.R | 22 +- inst/NEWS.md | 7 inst/doc/forecastHybrid.html | 108 ++++++------- man/accuracy.cvts.Rd | 6 man/checkCVArguments.Rd |only man/cvts.Rd | 80 ++++++--- man/forecast.hybridModel.Rd | 42 ++--- man/forecast.thetam.Rd | 3 man/hybridModel.Rd | 74 +++++---- man/plot.thetam.Rd | 10 - man/plotFitted.Rd |only man/plotModelObjects.Rd |only man/thetam.Rd | 13 - man/tsCombine.Rd | 14 - tests/testthat.R | 2 tests/testthat/test-accuracy.R | 2 tests/testthat/test-cvts.R | 79 +++++---- tests/testthat/test-cvts_examples.R | 5 tests/testthat/test-forecast.hybridModel.R | 59 +++---- tests/testthat/test-generics.R | 16 + tests/testthat/test-helpers.R | 2 tests/testthat/test-hybridModel.R | 21 +- tests/testthat/test-levels.R | 1 tests/testthat/test-theta.R | 23 +- tests/testthat/test-thiefModel.R | 4 33 files changed, 870 insertions(+), 723 deletions(-)
More information about forecastHybrid at CRAN
Permanent link
Title: Fast Computation of some Matrices Useful in Statistics
Description: Small set of functions to fast computation of some matrices and operations
useful in statistics.
Author: Felipe Osorio [aut, cre] (<https://orcid.org/0000-0002-4675-5201>),
Alonso Ogueda [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between fastmatrix versions 0.2 dated 2020-08-14 and 0.2-3 dated 2020-08-28
fastmatrix-0.2-3/fastmatrix/ChangeLog |only fastmatrix-0.2-3/fastmatrix/DESCRIPTION | 6 fastmatrix-0.2-3/fastmatrix/MD5 | 74 +++++-- fastmatrix-0.2-3/fastmatrix/NAMESPACE | 5 fastmatrix-0.2-3/fastmatrix/R/array.R |only fastmatrix-0.2-3/fastmatrix/R/commutation.R |only fastmatrix-0.2-3/fastmatrix/R/duplication.R | 8 fastmatrix-0.2-3/fastmatrix/R/equilibrate.R |only fastmatrix-0.2-3/fastmatrix/R/hadamard.R |only fastmatrix-0.2-3/fastmatrix/R/norms.R |only fastmatrix-0.2-3/fastmatrix/R/power_method.R |only fastmatrix-0.2-3/fastmatrix/R/sherman_morrison.R |only fastmatrix-0.2-3/fastmatrix/R/sweep.R |only fastmatrix-0.2-3/fastmatrix/R/utils.R | 53 ++--- fastmatrix-0.2-3/fastmatrix/inst/CITATION | 4 fastmatrix-0.2-3/fastmatrix/man/array.mult.Rd |only fastmatrix-0.2-3/fastmatrix/man/bracket.prod.Rd |only fastmatrix-0.2-3/fastmatrix/man/comm.info.Rd |only fastmatrix-0.2-3/fastmatrix/man/comm.prod.Rd |only fastmatrix-0.2-3/fastmatrix/man/commutation.Rd |only fastmatrix-0.2-3/fastmatrix/man/dupl.cross.Rd | 6 fastmatrix-0.2-3/fastmatrix/man/dupl.info.Rd | 3 fastmatrix-0.2-3/fastmatrix/man/dupl.prod.Rd | 15 - fastmatrix-0.2-3/fastmatrix/man/duplication.Rd | 17 - fastmatrix-0.2-3/fastmatrix/man/equilibrate.Rd |only fastmatrix-0.2-3/fastmatrix/man/hadamard.prod.Rd | 2 fastmatrix-0.2-3/fastmatrix/man/matrix.inner.Rd |only fastmatrix-0.2-3/fastmatrix/man/matrix.norm.Rd |only fastmatrix-0.2-3/fastmatrix/man/minkowski.Rd |only fastmatrix-0.2-3/fastmatrix/man/power.method.Rd |only fastmatrix-0.2-3/fastmatrix/man/sherman.morrison.Rd |only fastmatrix-0.2-3/fastmatrix/man/sweep.operator.Rd |only fastmatrix-0.2-3/fastmatrix/src/array.f |only fastmatrix-0.2-3/fastmatrix/src/array.h |only fastmatrix-0.2-3/fastmatrix/src/commutation.f |only fastmatrix-0.2-3/fastmatrix/src/commutation.h |only fastmatrix-0.2-3/fastmatrix/src/duplication.c | 19 + fastmatrix-0.2-3/fastmatrix/src/duplication.h | 1 fastmatrix-0.2-3/fastmatrix/src/init.c | 43 +++- fastmatrix-0.2-3/fastmatrix/src/matrix.c | 18 + fastmatrix-0.2-3/fastmatrix/src/matrix.h | 6 fastmatrix-0.2-3/fastmatrix/src/norms.c |only fastmatrix-0.2-3/fastmatrix/src/norms.h |only fastmatrix-0.2-3/fastmatrix/src/norms_extra.f |only fastmatrix-0.2-3/fastmatrix/src/power_method.c |only fastmatrix-0.2-3/fastmatrix/src/power_method.h |only fastmatrix-0.2-3/fastmatrix/src/sherman_morrison.c |only fastmatrix-0.2-3/fastmatrix/src/sherman_morrison.h |only fastmatrix-0.2-3/fastmatrix/src/sweep.f |only fastmatrix-0.2-3/fastmatrix/src/sweep_operator.c |only fastmatrix-0.2-3/fastmatrix/src/sweep_operator.h |only fastmatrix-0.2-3/fastmatrix/src/utils.f | 205 ++++++++++++++++---- fastmatrix-0.2-3/fastmatrix/src/utils.h | 7 fastmatrix-0.2-3/fastmatrix/src/vector.c |only fastmatrix-0.2-3/fastmatrix/src/vector.h |only fastmatrix-0.2/fastmatrix/R/matrix.R |only fastmatrix-0.2/fastmatrix/src/specmat.c |only fastmatrix-0.2/fastmatrix/src/specmat.h |only 58 files changed, 349 insertions(+), 143 deletions(-)
Title: Dissimilarity-Based Functions for Ecological Analysis
Description: Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.
Author: Sarah Goslee [aut, cre],
Dean Urban [aut]
Maintainer: Sarah Goslee <Sarah.Goslee@usda.gov>
Diff between ecodist versions 2.0.5 dated 2020-04-07 and 2.0.7 dated 2020-08-28
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/MRM.R | 2 +- R/mantel.R | 2 +- R/xmantel.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary man/MRM.Rd | 2 +- man/mantel.Rd | 2 +- man/xmantel.Rd | 2 +- 10 files changed, 20 insertions(+), 20 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.1.0 dated 2020-07-09 and 1.1.1 dated 2020-08-28
DESCRIPTION | 16 +++++------ MD5 | 14 ++++----- NEWS.md | 9 ++++++ R/kaplan.R | 22 ++++++++++++--- R/timeroc.R | 70 ++++++++++++++++++++++++++++--------------------- inst/doc/jsmodule.html | 4 +- man/timeROChelper.Rd | 5 ++- man/timerocModule.Rd | 12 +++++++- 8 files changed, 99 insertions(+), 53 deletions(-)
Title: Connect to Your 'IBM Acoustic' Data
Description: Authentication can be the most difficult part about
working with a new API. 'ibmAcousticR' facilitates making a
connection to the 'IBM Acoustic' email campaign management API
and executing various queries. The 'IBM Acoustic' API
documentation is available at
<https://developer.ibm.com/customer-engagement/docs/>. This
package is not supported by 'IBM'.
Author: Chris Umphlett [aut, cre],
Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between ibmAcousticR versions 0.1.2 dated 2020-06-03 and 0.2.1 dated 2020-08-28
DESCRIPTION | 32 ++++++++++++++++++------------ MD5 | 24 ++++++++++++++-------- NAMESPACE | 5 ++++ R/acoustic_auth.R | 14 ++++++++++--- R/get_all_contacts.R | 40 +++++++++++++++++++++++++------------- R/get_contact_list.R |only R/get_job_status.R | 16 +++++++++++---- R/get_programs.R |only R/utils.R | 46 ++++++++++++++++++++++++++++++++++++++++---- README.md | 15 +++++++++----- man/check_for_faulty_xml.Rd |only man/get_all_contacts.Rd | 13 ++++++++---- man/get_contact_list.Rd |only man/get_job_id.Rd | 4 ++- man/get_programs.Rd |only man/stop_quietly.Rd |only 16 files changed, 153 insertions(+), 56 deletions(-)
Title: Subgroup Specific Optimal Dose Assignment
Description: Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.
Author: Andrew Chapple
Maintainer: Andrew Chapple <achapp@lsuhsc.edu>
Diff between SubTite versions 3.0.2 dated 2020-07-02 and 4.0.0 dated 2020-08-28
SubTite-3.0.2/SubTite/README.md |only SubTite-4.0.0/SubTite/DESCRIPTION | 8 SubTite-4.0.0/SubTite/MD5 | 19 SubTite-4.0.0/SubTite/NAMESPACE | 1 SubTite-4.0.0/SubTite/R/GetSubTite.R | 648 +++++++++++++++++++---------- SubTite-4.0.0/SubTite/R/Print_SubTite.R |only SubTite-4.0.0/SubTite/man/GetSubTite.Rd | 95 ++-- SubTite-4.0.0/SubTite/man/MCMC.Rd | 24 - SubTite-4.0.0/SubTite/man/MCMCSIM.Rd | 24 - SubTite-4.0.0/SubTite/man/Print_SubTite.Rd |only SubTite-4.0.0/SubTite/man/SimTrial.Rd | 27 + SubTite-4.0.0/SubTite/man/SimTrial1.Rd | 28 + 12 files changed, 590 insertions(+), 284 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-10 1.2.2
2019-12-11 1.2.1
2019-08-20 1.2
2019-02-14 1.1
2019-01-10 1.0