Title: Reproducible Reports in Psychology
Description: Helper functions for producing reports in Psychology (Reproducible Research). Provides required formatted strings (APA style) for use in 'Knitr'/'Latex' integration within *.Rnw files.
Author: Ian G Mackenzie
Maintainer: Ian G Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between psychReport versions 1.1.0 dated 2020-06-18 and 1.1.1 dated 2020-09-18
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/anova.R | 11 +++++++---- R/utils.R | 13 ++++--------- man/aovRoundDigits.Rd | 3 +-- man/aovTidyTable.Rd | 1 + man/printAovMeans.Rd | 2 +- man/printTable.Rd | 4 ++-- tests/testthat/test-aovRoundDigits.R | 10 +++++----- tests/testthat/test-statStrAov.R | 2 +- 11 files changed, 37 insertions(+), 39 deletions(-)
Title: Charles's Utility Function using Formula
Description: Utility functions that provides wrapper to descriptive base functions
like cor, mean and table. It makes use of the formula interface to pass
variables to functions. It also provides operators to concatenate (%+%), to
repeat (%n%) and manage character vectors for nice display.
Author: Charles-Édouard Giguère
Maintainer: Charles-Édouard Giguère <ce.giguere@gmail.com>
Diff between CUFF versions 1.6 dated 2019-01-22 and 1.7 dated 2020-09-18
ChangeLog | 6 + DESCRIPTION | 10 +- MD5 | 16 +-- NAMESPACE | 9 + R/cf.R | 267 ++++++++++++++++++++++++++++++++-------------------------- R/clip.R | 70 +++++++-------- R/cross.R | 54 +++++++---- R/xyboth.R |only man/ftab.Rd | 5 - man/xyboth.Rd |only 10 files changed, 248 insertions(+), 189 deletions(-)
Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized
linear, and mixed models. Compute contrasts or linear functions of EMMs,
trends, and comparisons of slopes. Plots and other displays.
Least-squares means are discussed, and the term "estimated marginal means"
is suggested, in Searle, Speed, and Milliken (1980) Population marginal means
in the linear model: An alternative to least squares means, The American
Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph],
Paul Buerkner [ctb],
Maxime Herve [ctb],
Jonathon Love [ctb],
Hannes Riebl [ctb],
Henrik Singmann [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between emmeans versions 1.5.0 dated 2020-08-18 and 1.5.1 dated 2020-09-18
DESCRIPTION | 8 - MD5 | 74 ++++++++--------- NEWS.md | 19 ++++ R/0nly-internal.R | 9 +- R/emmGrid-methods.R | 7 + R/gam-support.R | 7 - R/interfacing.R | 21 +++- R/multinom-support.R | 15 +++ R/plot.emm.R | 5 - R/pwpp.R | 56 +++++++++++-- R/ref-grid.R | 5 - build/vignette.rds |binary inst/doc/FAQs.html | 8 - inst/doc/basics.html | 4 inst/doc/comparisons.html | 22 ++--- inst/doc/confidence-intervals.Rmd | 2 inst/doc/confidence-intervals.html | 13 +-- inst/doc/interactions.html | 14 +-- inst/doc/messy-data.R | 13 +++ inst/doc/messy-data.Rmd | 61 +++++++++++++- inst/doc/messy-data.html | 84 +++++++++++++++++++ inst/doc/models.html | 4 inst/doc/predictions.html | 4 inst/doc/sophisticated.html | 4 inst/doc/transformations.html | 4 inst/doc/utilities.html | 5 - inst/doc/vignette-topics.Rmd | 11 ++ inst/doc/vignette-topics.html | 19 +++- inst/doc/xplanations.Rmd | 157 ++++++++++++++++++++++--------------- inst/doc/xplanations.html | 35 +++++--- inst/doc/xtending.html | 8 - man/emm_options.Rd | 6 + man/pwpp.Rd | 26 +++++- man/update.emmGrid.Rd | 2 vignettes/confidence-intervals.Rmd | 2 vignettes/messy-data.Rmd | 61 +++++++++++++- vignettes/vignette-topics.Rmd | 11 ++ vignettes/xplanations.Rmd | 157 ++++++++++++++++++++++--------------- 38 files changed, 698 insertions(+), 265 deletions(-)
Title: Sampling from Truncated Multivariate Normal and t Distributions
Description: Efficient sampling of truncated multivariate (scale) mixtures of normals under linear inequality constraints is nontrivial due to the analytically intractable normalizing constant. Meanwhile, traditional methods may subject to numerical issues, especially when the dimension is high and dependence is strong. Algorithms proposed by Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> are adopted for overcoming difficulties in simulating truncated distributions. Efficient rejection sampling for simulating truncated univariate normal distribution is included in the package, which shows superiority in terms of acceptance rate and numerical stability compared to existing methods and R packages. An efficient function for sampling from truncated multivariate normal distribution subject to convex polytope restriction regions based on Gibbs sampler for conditional truncated univariate distribution is provided. By extending the sampling method, a function for sampling truncated multivariate Student's t distribution is also developed. Moreover, the proposed method and computation remain valid for high dimensional and strong dependence scenarios. Empirical results in Li and Ghosh (2015) <doi: 10.1080/15598608.2014.996690> illustrated the superior performance in terms of various criteria (e.g. mixing and integrated auto-correlation time).
Author: Ting Fung (Ralph) Ma [cre, aut],
Sujit K. Ghosh [aut],
Yifang Li [aut]
Maintainer: Ting Fung (Ralph) Ma <tingfung.ma@wisc.edu>
Diff between tmvmixnorm versions 1.1.0 dated 2020-05-19 and 1.1.1 dated 2020-09-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/rtmvn.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb],
Bastian Greshake Tzovaras [ctb],
Philippe Marchand [ctb],
Vinh Tran [ctb],
Maëlle Salmon [ctb],
Gaopeng Li [ctb],
Matthias Grenié [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.97 dated 2020-06-09 and 0.9.98 dated 2020-09-18
DESCRIPTION | 10 MD5 | 247 +++--- NEWS.md | 21 R/apg.R | 2 R/apg_lookup.R | 2 R/bold_search.R | 2 R/class2tree.R | 28 R/downstream-utils.R | 15 R/eubon.R | 2 R/eubon_capabilities.R | 2 R/eubon_children.R | 2 R/eubon_hierarchy.R | 2 R/gbif_name_usage.R | 2 R/genbank2uid.R | 2 R/get_boldid.R | 2 R/get_eolid.R | 2 R/get_gbifid.R | 2 R/get_nbnid.R | 2 R/get_pow.R | 9 R/get_tpsid.R | 2 R/get_uid.R | 4 R/gn_parse.R | 2 R/gni_parse.R | 2 R/gni_search.R | 4 R/gnr_datasources.R | 2 R/gnr_resolve.R | 4 R/ion.R | 2 R/itis_refs.R | 3 R/iucn_summary.R | 2 R/nbn_classification.R | 2 R/nbn_search.R | 4 R/nbn_synonyms.R | 2 R/onload.R | 1 R/pow_search.R | 2 R/scrapenames.r | 4 R/tax_name.R | 2 R/taxize-authentication.R | 2 R/taxize-package.R | 25 R/tnrs.R | 2 R/tol_resolve.R | 2 R/tp_dist.R | 2 R/tp_search.R | 2 R/tpl_get.r | 2 R/vascan_search.r | 2 R/worms_downstream.R | 16 README.md | 564 --------------- build/vignette.rds |binary data/rank_ref.RData |binary data/rank_ref_zoo.RData |only inst/CITATION | 9 inst/doc/case_study.Rmd | 2 inst/doc/case_study.html | 20 inst/doc/infotable.html | 20 inst/doc/name_cleaning.Rmd | 33 inst/doc/name_cleaning.html | 49 - inst/doc/taxize.Rmd | 36 - inst/doc/taxize.html | 59 + inst/ignore/rank_ref_script.R | 68 + man/apg.Rd | 2 man/apg_families.Rd | 2 man/apg_lookup.Rd | 2 man/apg_orders.Rd | 2 man/bold_search.Rd | 2 man/children.Rd | 2 man/class2tree.Rd | 2 man/eubon_capabilities.Rd | 2 man/eubon_children.Rd | 2 man/eubon_hierarchy.Rd | 2 man/eubon_search.Rd | 2 man/gbif_name_usage.Rd | 2 man/genbank2uid.Rd | 2 man/get_boldid.Rd | 2 man/get_eolid.Rd | 2 man/get_gbifid.Rd | 2 man/get_nbnid.Rd | 2 man/get_pow.Rd | 11 man/get_tpsid.Rd | 2 man/get_uid.Rd | 4 man/gn_parse.Rd | 2 man/gni_parse.Rd | 2 man/gni_search.Rd | 4 man/gnr_datasources.Rd | 2 man/gnr_resolve.Rd | 4 man/ion.Rd | 2 man/itis_downstream.Rd | 2 man/itis_hierarchy.Rd | 4 man/itis_native.Rd | 6 man/itis_refs.Rd | 3 man/iucn_summary.Rd | 2 man/nbn_classification.Rd | 2 man/nbn_search.Rd | 4 man/nbn_synonyms.Rd | 2 man/pow_search.Rd | 2 man/rank_ref.Rd | 7 man/rank_ref_zoo.Rd |only man/scrapenames.Rd | 4 man/tax_name.Rd | 2 man/taxize-authentication.Rd | 2 man/taxize-package.Rd | 2 man/theplantlist.Rd | 2 man/tnrs.Rd | 2 man/tol_resolve.Rd | 2 man/tp_dist.Rd | 2 man/tp_search.Rd | 2 man/tpl_get.Rd | 2 man/vascan_search.Rd | 2 man/worms_downstream.Rd | 10 tests/fixtures/fg_name_by_key.yml | 50 - tests/fixtures/get_uid_filtering_rank.yml | 245 ++---- tests/fixtures/get_uid_rank_modifiers.yml | 54 - tests/fixtures/get_wormsid.yml | 167 ++-- tests/fixtures/ipni_search_no_results.yml | 60 - tests/fixtures/synonyms_name_found_but_no_synonyms.yml | 603 +++++++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test-comm2sci.R | 7 tests/testthat/test-fungorum.R | 2 tests/testthat/test-get_uid.R | 16 tests/testthat/test-get_wormsid.R | 2 tests/testthat/test-ipni_search.R | 1 tests/testthat/test-synonyms.R | 2 vignettes/case_study.Rmd | 2 vignettes/margins.sty |only vignettes/name_cleaning.Rmd | 33 vignettes/name_cleaning.Rmd.og | 2 vignettes/taxize.Rmd | 36 - vignettes/taxize.Rmd.og | 13 126 files changed, 1225 insertions(+), 1520 deletions(-)
Title: Robust Non-Linear Regression using AIC Scores
Description: Non-linear least squares regression with the Levenberg-Marquardt algorithm using multiple starting values for increasing the chance that the minimum found is the global minimum.
Author: Daniel Padfield [aut, cre],
Granville Matheson [aut]
Maintainer: Daniel Padfield <d.padfield@exeter.ac.uk>
Diff between nls.multstart versions 1.1.0 dated 2020-06-03 and 1.2.0 dated 2020-09-18
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 4 + R/nls_multstart.R | 9 ++ README.md | 110 ++++++++++++++++----------------- inst/image/README-confint_plot-1.png |binary inst/image/README-plot_many_fits-1.png |binary inst/image/README-plot_one_fit-1.png |binary man/Chlorella_TRC.Rd | 6 + man/nls_multstart.Rd | 2 10 files changed, 86 insertions(+), 71 deletions(-)
Title: Input Output Analysis
Description: Calculates fundamental IO matrices (Leontief, Wassily W. (1951) <doi:10.1038/scientificamerican1051-15>); within period analysis via various rankings and coefficients (Sonis and Hewings (2006) <doi:10.1080/09535319200000013>, Blair and Miller (2009) <ISBN:978-0-521-73902-3>, Antras et al (2012) <doi:10.3386/w17819>, Hummels, Ishii, and Yi (2001) <doi:10.1016/S0022-1996(00)00093-3>); across period analysis with impact analysis (Dietzenbacher, van der Linden, and Steenge (2006) <doi:10.1080/09535319300000017>, Sonis, Hewings, and Guo (2006) <doi:10.1080/09535319600000002>); and a variety of table operators.
Author: John Wade [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: John Wade <jjpwade2@illinois.edu>
Diff between ioanalysis versions 0.3.3 dated 2020-07-06 and 0.3.4 dated 2020-09-18
ioanalysis-0.3.3/ioanalysis/R/disaggregate.R |only ioanalysis-0.3.3/ioanalysis/man/disaggregate.Rd |only ioanalysis-0.3.4/ioanalysis/DESCRIPTION | 6 +++--- ioanalysis-0.3.4/ioanalysis/MD5 | 12 +++++------- ioanalysis-0.3.4/ioanalysis/R/export.total.R | 2 +- ioanalysis-0.3.4/ioanalysis/R/import.total.R | 12 ++++++------ ioanalysis-0.3.4/ioanalysis/R/ras.R | 16 ++++++---------- ioanalysis-0.3.4/ioanalysis/man/ras.Rd | 5 ++--- 8 files changed, 23 insertions(+), 30 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.3.0 dated 2019-10-16 and 0.5.0 dated 2020-09-18
hutilscpp-0.3.0/hutilscpp/R/pminC.R |only hutilscpp-0.3.0/hutilscpp/man/do_pmaxC.Rd |only hutilscpp-0.3.0/hutilscpp/man/do_pmaxV.Rd |only hutilscpp-0.3.0/hutilscpp/man/do_pminC.Rd |only hutilscpp-0.3.0/hutilscpp/man/do_pminV.Rd |only hutilscpp-0.3.0/hutilscpp/man/pminC.Rd |only hutilscpp-0.3.0/hutilscpp/src/AnyWhich.cpp |only hutilscpp-0.3.0/hutilscpp/src/do_sum_dbl_par.cpp |only hutilscpp-0.3.0/hutilscpp/src/pmax0.cpp |only hutilscpp-0.3.0/hutilscpp/src/pmaxC.cpp |only hutilscpp-0.3.0/hutilscpp/src/pmaxV.cpp |only hutilscpp-0.3.0/hutilscpp/src/pminC.cpp |only hutilscpp-0.3.0/hutilscpp/src/pminV.cpp |only hutilscpp-0.3.0/hutilscpp/tests/testthat/test-cpp-AnyWhich.R |only hutilscpp-0.5.0/hutilscpp/DESCRIPTION | 12 hutilscpp-0.5.0/hutilscpp/MD5 | 199 - hutilscpp-0.5.0/hutilscpp/NAMESPACE | 28 hutilscpp-0.5.0/hutilscpp/NEWS.md | 326 +- hutilscpp-0.5.0/hutilscpp/R/R_xlen_t.R |only hutilscpp-0.5.0/hutilscpp/R/RcppExports.R | 371 +- hutilscpp-0.5.0/hutilscpp/R/anyOutside.R | 8 hutilscpp-0.5.0/hutilscpp/R/are_even.R | 135 hutilscpp-0.5.0/hutilscpp/R/as_integer_if_safe.R | 87 hutilscpp-0.5.0/hutilscpp/R/between.R |only hutilscpp-0.5.0/hutilscpp/R/count_logical.R |only hutilscpp-0.5.0/hutilscpp/R/decompose_expr.R |only hutilscpp-0.5.0/hutilscpp/R/divisible.R |only hutilscpp-0.5.0/hutilscpp/R/first_which.R |only hutilscpp-0.5.0/hutilscpp/R/helper.R | 2 hutilscpp-0.5.0/hutilscpp/R/hutilscpp-package.R | 7 hutilscpp-0.5.0/hutilscpp/R/is_constant.R | 136 hutilscpp-0.5.0/hutilscpp/R/is_sorted.R | 30 hutilscpp-0.5.0/hutilscpp/R/logical3s.R |only hutilscpp-0.5.0/hutilscpp/R/pmaxC.R | 581 ++-- hutilscpp-0.5.0/hutilscpp/R/pmax_pure_C.R | 17 hutilscpp-0.5.0/hutilscpp/R/range_rcpp.R | 172 - hutilscpp-0.5.0/hutilscpp/R/rev.R |only hutilscpp-0.5.0/hutilscpp/R/seqN_by.R | 12 hutilscpp-0.5.0/hutilscpp/R/sum3.R |only hutilscpp-0.5.0/hutilscpp/R/sum_isna.R | 112 hutilscpp-0.5.0/hutilscpp/R/utils-omp.R |only hutilscpp-0.5.0/hutilscpp/R/utils.R | 216 - hutilscpp-0.5.0/hutilscpp/R/which2_yr.R |only hutilscpp-0.5.0/hutilscpp/R/which3.R | 50 hutilscpp-0.5.0/hutilscpp/R/which_first.R | 895 +++--- hutilscpp-0.5.0/hutilscpp/R/which_firstNA.R |only hutilscpp-0.5.0/hutilscpp/R/which_isnt_integerish.R |only hutilscpp-0.5.0/hutilscpp/R/whichs.R |only hutilscpp-0.5.0/hutilscpp/R/xor2.R | 20 hutilscpp-0.5.0/hutilscpp/R/zzz.R | 7 hutilscpp-0.5.0/hutilscpp/man/anyOutside.Rd | 8 hutilscpp-0.5.0/hutilscpp/man/are_even.Rd | 21 hutilscpp-0.5.0/hutilscpp/man/count_logical.Rd |only hutilscpp-0.5.0/hutilscpp/man/cumsum_reset.Rd | 56 hutilscpp-0.5.0/hutilscpp/man/divisible.Rd |only hutilscpp-0.5.0/hutilscpp/man/is_constant.Rd | 15 hutilscpp-0.5.0/hutilscpp/man/logical3s.Rd |only hutilscpp-0.5.0/hutilscpp/man/match_nrst_haversine.Rd | 16 hutilscpp-0.5.0/hutilscpp/man/pmaxC.Rd | 122 hutilscpp-0.5.0/hutilscpp/man/poleInaccessibility.Rd | 21 hutilscpp-0.5.0/hutilscpp/man/range_rcpp.Rd | 8 hutilscpp-0.5.0/hutilscpp/man/sum_and3s.Rd |only hutilscpp-0.5.0/hutilscpp/man/sum_isna.Rd | 11 hutilscpp-0.5.0/hutilscpp/man/which3.Rd | 11 hutilscpp-0.5.0/hutilscpp/man/which_first.Rd | 49 hutilscpp-0.5.0/hutilscpp/man/which_firstNA.Rd |only hutilscpp-0.5.0/hutilscpp/man/whichs.Rd |only hutilscpp-0.5.0/hutilscpp/src/AnyCharMatch.cpp | 27 hutilscpp-0.5.0/hutilscpp/src/Makevars |only hutilscpp-0.5.0/hutilscpp/src/RcppExports.cpp | 1019 ++++--- hutilscpp-0.5.0/hutilscpp/src/allocate.cpp |only hutilscpp-0.5.0/hutilscpp/src/cpphutils.h | 48 hutilscpp-0.5.0/hutilscpp/src/do_and3s.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_divisible.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_even.cpp | 69 hutilscpp-0.5.0/hutilscpp/src/do_logical3s.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_op2M.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_or3s.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_range.cpp | 35 hutilscpp-0.5.0/hutilscpp/src/do_which_first.cpp | 682 +++- hutilscpp-0.5.0/hutilscpp/src/do_which_isnt_integerish.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_whichs.cpp |only hutilscpp-0.5.0/hutilscpp/src/do_xor2.cpp | 3 hutilscpp-0.5.0/hutilscpp/src/haversineDistance.cpp | 6 hutilscpp-0.5.0/hutilscpp/src/is_constant_x.cpp |only hutilscpp-0.5.0/hutilscpp/src/is_safe2int.cpp | 29 hutilscpp-0.5.0/hutilscpp/src/omp_diagnose.cpp |only hutilscpp-0.5.0/hutilscpp/src/pminmax.cpp |only hutilscpp-0.5.0/hutilscpp/src/ppmax.c | 29 hutilscpp-0.5.0/hutilscpp/src/sum_isna.cpp | 60 hutilscpp-0.5.0/hutilscpp/src/texParse.cpp | 240 + hutilscpp-0.5.0/hutilscpp/tests/testthat/test-000.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-allocate.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-and3.R | 66 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-and3s-coverage.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-and3s-nframes.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-and3s.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-are_even.R | 121 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-as_integer_if_safe.R | 94 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-between.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-check_omp.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-count_logical.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-cpp-haversine.R | 758 ++--- hutilscpp-0.5.0/hutilscpp/tests/testthat/test-divisible.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-do_duplicated_sorted.R | 20 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-do_par_in_hash.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-do_which_in.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-in.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-is_constant.R | 76 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-is_sorted.R | 96 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-or3s.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmax0.R | 372 +- hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmax3.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmaxC.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmaxV.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmax_friends.R | 402 +- hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmax_pure_c.R | 5 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmin.R | 25 hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmin0.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pmin3.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pminC.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-pminV.R |only hutilscpp-0.5.0/hutilscpp/tests/testthat/test-range-cpp.R | 197 - 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Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE)
biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>,
geometric adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method <doi:10.12702/1984-7033.v04n01a02>, power law residuals
(POLAR) statistics by Doring et al. (2015)
<doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for
computing biometrical analysis such as path analysis, canonical
correlation, partial correlation, clustering analysis, and tools for
inspecting, manipulating, summarizing and plotting typical
multi-environment trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.8.1 dated 2020-09-10 and 1.9.0 dated 2020-09-18
DESCRIPTION | 42 MD5 | 56 NAMESPACE | 12 NEWS.md | 12 R/acv.R |only R/clustering.R | 12 R/ge_acv.R |only R/ge_polar.R |only R/ge_stats.R | 72 R/get_model_data.R | 54 R/mantel_test.R |only R/mtsi.R | 39 R/pairs_mantel.R | 57 R/path_coeff.R | 16 R/select_pred.R |only R/split_factors.R | 2 R/utilities.R | 52 R/zzz.R | 14 build/metan.pdf |32003 +++++++++++++++++++++++----------------------- build/partial.rdb |binary inst/doc/metan_start.Rmd | 14 inst/doc/metan_start.html | 60 man/acv.Rd |only man/ge_acv.Rd |only man/ge_polar.Rd |only man/ge_stats.Rd | 63 man/get_model_data.Rd | 24 man/mantel_test.Rd |only man/mtsi.Rd | 4 man/pairs_mantel.Rd | 3 man/select_pred.Rd |only man/utils_rows_cols.Rd | 34 vignettes/metan_start.Rmd | 14 vignettes/metanref.bib | 34 34 files changed, 16975 insertions(+), 15718 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values.
Many times large experimental datasets need some additional filtering, adequate functions are provided.
Batch reading (or writing) of sets of files and combining data to arrays is supported, too.
Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrMisc versions 1.3.0 dated 2020-07-24 and 1.3.1 dated 2020-09-18
DESCRIPTION | 15 ++++++-- MD5 | 24 +++++++------ NAMESPACE | 2 - R/extrColsDeX.R | 8 ++-- R/htmlSpecCharConv.R | 29 ++++++++-------- R/presenceFilt.R | 41 +++++++++++----------- R/sumNAperGroup.R |only inst/doc/wrMiscVignette1.R | 7 ++- inst/doc/wrMiscVignette1.Rmd | 53 +++++++++++++++-------------- inst/doc/wrMiscVignette1.html | 75 +++++++++++++++++++++--------------------- man/htmlSpecCharConv.Rd | 10 +++-- man/presenceFilt.Rd | 19 ++++++++-- man/sumNAperGroup.Rd |only vignettes/wrMiscVignette1.Rmd | 53 +++++++++++++++-------------- 14 files changed, 186 insertions(+), 150 deletions(-)
Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides a set of methods for metabolomics
data analysis, including data loading in different formats,
pre-processing, metabolite identification, univariate and multivariate
data analysis, machine learning, feature selection and pathway analysis. Case studies
can be found on the website: <http://bio.di.uminho.pt/metabolomicspackage/index.html>.
This package suggests 'rcytoscapejs', a package not in mainstream repositories. If you need to install it,
use: devtools::install_github('cytoscape/r-cytoscape.js@v0.0.7').
Author: Christopher Costa <chrisbcl@hotmail.com> [aut],
Marcelo Maraschin <mtocsy@gmail.com> [aut],
Miguel Rocha <mrocha@di.uminho.pt> [aut, cre],
Sara Cardoso <saracardoso501@gmail.com> [aut],
Telma Afonso <telma.afonso94@gmail.com> [aut],
C. Beleites [cph],
Jie Hao [cph]
Maintainer: Miguel Rocha <mrocha@di.uminho.pt>
Diff between specmine versions 3.0.0 dated 2020-07-10 and 3.0.2 dated 2020-09-18
DESCRIPTION | 12 MD5 | 474 ++++---- NAMESPACE | 416 +++---- R/MAIT_metabolite_identification.R | 300 ++--- R/NMR_metabolite_identification.R | 1036 ++++++++--------- R/PATHWAY_ANALYSIS.R | 928 +++++++-------- R/clustering.R | 256 ++-- R/convert_chemospec.R | 30 R/convert_hyperspec.R | 56 R/data_integration.R | 64 - R/feature_selection.R | 100 - R/filter_dataset.R | 484 ++++---- R/filters_flat.R | 178 +-- R/get_metabolights_study.R | 300 ++--- R/graphics.R | 554 ++++----- R/init.R | 2 R/machinelearning.R | 486 ++++---- R/missing_values.R | 186 +-- R/ms_functions.R | 128 +- R/nmr_id_utils.R | 124 +- R/normalization.R | 378 +++--- R/pca.R | 930 +++++++-------- R/peak_alignment.R | 630 +++++----- R/peaklists.R | 424 +++---- R/preprocessing.R | 456 +++---- R/read.spc.modified.R | 1572 +++++++++++++-------------- R/read_NMR_spectra.R | 788 ++++++------- R/read_dx.R | 242 ++-- R/read_spc.R | 100 - R/reading_data.R | 106 - R/regression.R | 174 +- R/stats.R | 148 +- R/structure.R | 870 +++++++------- R/univariate.R | 962 ++++++++-------- R/utils.R | 36 inst/read_varian_spec_raw.py | 142 +- man/MAIT_identify_metabolites.Rd | 108 - man/absorbance_to_transmittance.Rd | 54 man/aggregate_samples.Rd | 86 - man/aov_all_vars.Rd | 94 - man/apply_by_group.Rd | 84 - man/apply_by_groups.Rd | 90 - man/apply_by_sample.Rd | 86 - man/apply_by_variable.Rd | 100 - man/background_correction.Rd | 68 - man/baseline_correction.Rd | 88 - man/boxplot_variables.Rd | 102 - man/boxplot_vars_factor.Rd | 124 +- man/cachexia.Rd | 56 man/check_dataset.Rd | 64 - man/clustering.Rd | 112 - man/compare_regions_by_sample.Rd | 96 - man/convert_chebi_to_kegg.Rd | 48 man/convert_from_chemospec.Rd | 68 - man/convert_from_hyperspec.Rd | 82 - man/convert_hmdb_to_kegg.Rd | 50 man/convert_keggpathway_2_reactiongraph.Rd | 38 man/convert_multiple_spcmnm_to_kegg.Rd | 44 man/convert_to_factor.Rd | 60 - man/convert_to_hyperspec.Rd | 54 man/correlation_test.Rd | 98 - man/correlations_dataset.Rd | 84 - man/correlations_test.Rd | 90 - man/count_missing_values.Rd | 62 - man/count_missing_values_per_sample.Rd | 70 - man/count_missing_values_per_variable.Rd | 70 - man/create_dataset.Rd | 144 +- man/create_pathway_with_reactions.Rd | 54 man/cubic_root_transform.Rd | 66 - man/data_correction.Rd | 74 - man/dataset_from_peaks.Rd | 88 - man/dendrogram_plot.Rd | 88 - man/dendrogram_plot_col.Rd | 112 - man/detect_nmr_peaks_from_dataset.Rd | 50 man/feature_selection.Rd | 128 +- man/filter_feature_selection.Rd | 98 - man/find_equal_samples.Rd | 64 - man/first_derivative.Rd | 54 man/flat_pattern_filter.Rd | 104 - man/fold_change.Rd | 100 - man/fold_change_var.Rd | 100 - man/get_MetabolitePath.Rd | 38 man/get_OrganismsCodes.Rd | 40 man/get_cpd_names.Rd | 52 man/get_data.Rd | 64 - man/get_data_as_df.Rd | 64 - man/get_data_value.Rd | 84 - man/get_data_values.Rd | 78 - man/get_files_list_assay.Rd | 54 man/get_metabPaths_org.Rd | 32 man/get_metabolights_study.Rd | 66 - man/get_metabolights_study_files_assay.Rd | 78 - man/get_metabolights_study_metadata_assay.Rd | 64 - man/get_metabolights_study_samples_files.Rd | 54 man/get_metadata.Rd | 62 - man/get_metadata_value.Rd | 76 - man/get_metadata_var.Rd | 70 - man/get_paths_with_cpds_org.Rd | 66 - man/get_peak_values.Rd | 70 - man/get_sample_names.Rd | 64 - man/get_samples_names_dx.Rd | 54 man/get_samples_names_spc.Rd | 54 man/get_type.Rd | 64 - man/get_value_label.Rd | 66 - man/get_x_label.Rd | 64 - man/get_x_values_as_num.Rd | 62 - man/get_x_values_as_text.Rd | 64 - man/group_peaks.Rd | 122 +- man/heatmap_correlations.Rd | 74 - man/hierarchical_clustering.Rd | 88 - man/impute_nas_knn.Rd | 76 - man/impute_nas_linapprox.Rd | 66 - man/impute_nas_mean.Rd | 64 - man/impute_nas_median.Rd | 64 - man/impute_nas_value.Rd | 72 - man/indexes_to_xvalue_interval.Rd | 68 - man/is_spectra.Rd | 62 - man/kmeans_clustering.Rd | 76 - man/kmeans_plot.Rd | 68 - man/kmeans_result_df.Rd | 66 - man/kruskalTest_dataset.Rd | 92 - man/ksTest_dataset.Rd | 92 - man/linreg_all_vars.Rd | 66 - man/linreg_coef_table.Rd | 68 - man/linreg_pvalue_table.Rd | 68 - man/linreg_rsquared.Rd | 68 - man/linregression_onevar.Rd | 72 - man/log_transform.Rd | 64 - man/low_level_fusion.Rd | 54 man/mean_centering.Rd | 54 man/merge_data_metadata.Rd | 90 - man/merge_datasets.Rd | 60 - man/metabolights_studies_list.Rd | 42 man/metadata_as_variables.Rd | 76 - man/missingvalues_imputation.Rd | 98 - man/msc_correction.Rd | 56 man/multiClassSummary.Rd | 66 - man/multifactor_aov_all_vars.Rd | 80 - man/multifactor_aov_pvalues_table.Rd | 84 - man/multifactor_aov_varexp_table.Rd | 84 - man/multiplot.Rd | 100 - man/nmr_identification.Rd | 158 +- man/normalize.Rd | 84 - man/normalize_samples.Rd | 84 - man/num_samples.Rd | 64 - man/num_x_values.Rd | 62 - man/offset_correction.Rd | 56 man/pathway_analysis.Rd | 92 - man/pca_analysis_dataset.Rd | 96 - man/pca_biplot.Rd | 102 - man/pca_biplot3D.Rd | 80 - man/pca_importance.Rd | 98 - man/pca_kmeans_plot2D.Rd | 124 +- man/pca_kmeans_plot3D.Rd | 108 - man/pca_pairs_kmeans_plot.Rd | 90 - man/pca_pairs_plot.Rd | 84 - man/pca_plot_3d.Rd | 102 - man/pca_robust.Rd | 104 - man/pca_scoresplot2D.Rd | 124 +- man/pca_scoresplot3D.Rd | 82 - man/pca_scoresplot3D_rgl.Rd | 96 - man/pca_screeplot.Rd | 112 - man/peaks_per_sample.Rd | 70 - man/peaks_per_samples.Rd | 64 - man/plot_anova.Rd | 88 - man/plot_fold_change.Rd | 92 - man/plot_kruskaltest.Rd | 76 - man/plot_kstest.Rd | 76 - man/plot_peaks.Rd | 108 - man/plot_regression_coefs_pvalues.Rd | 66 - man/plot_spectra.Rd | 114 - man/plot_spectra_simple.Rd | 102 - man/plot_ttests.Rd | 74 - man/plotvar_twofactor.Rd | 108 - man/predict_samples.Rd | 76 - man/propolis.Rd | 84 - man/propolisSampleList.Rd | 84 - man/read-spc.Rd | 144 +- man/read_Bruker_files.Rd | 86 - man/read_csvs_folder.Rd | 60 - man/read_data_csv.Rd | 80 - man/read_data_dx.Rd | 60 - man/read_data_spc.Rd | 60 - man/read_dataset_csv.Rd | 140 +- man/read_dataset_dx.Rd | 110 - man/read_dataset_spc.Rd | 114 - man/read_metadata.Rd | 74 - man/read_ms_spectra.Rd | 132 +- man/read_multiple_csvs.Rd | 66 - man/read_varian_spectra_raw.Rd | 98 - man/recursive_feature_elimination.Rd | 114 - man/remove_data.Rd | 104 - man/remove_data_variables.Rd | 80 - man/remove_metadata_variables.Rd | 70 - man/remove_peaks_interval.Rd | 76 - man/remove_peaks_interval_sample_list.Rd | 78 - man/remove_samples.Rd | 76 - man/remove_samples_by_na_metadata.Rd | 72 - man/remove_samples_by_nas.Rd | 76 - man/remove_variables_by_nas.Rd | 76 - man/remove_x_values_by_interval.Rd | 66 - man/replace_data_value.Rd | 92 - man/replace_metadata_value.Rd | 84 - man/savitzky_golay.Rd | 72 - man/scaling.Rd | 72 - man/scaling_samples.Rd | 72 - man/set_metadata.Rd | 76 - man/set_sample_names.Rd | 72 - man/set_value_label.Rd | 70 - man/set_x_label.Rd | 70 - man/set_x_values.Rd | 78 - man/shift_correction.Rd | 88 - man/smoothing_interpolation.Rd | 98 - man/snv_dataset.Rd | 54 man/spectra_options.Rd | 62 - man/stats_by_sample.Rd | 70 - man/stats_by_variable.Rd | 78 - man/subset_by_samples_and_xvalues.Rd | 102 - man/subset_metadata.Rd | 70 - man/subset_random_samples.Rd | 70 - man/subset_samples.Rd | 76 - man/subset_samples_by_metadata_values.Rd | 78 - man/subset_x_values.Rd | 76 - man/subset_x_values_by_interval.Rd | 74 - man/sum_dataset.Rd | 106 - man/summary_var_importance.Rd | 78 - man/tTests_dataset.Rd | 92 - man/train_and_predict.Rd | 132 +- man/train_classifier.Rd | 130 +- man/train_models_performance.Rd | 154 +- man/transform_data.Rd | 82 - man/transmittance_to_absorbance.Rd | 60 - man/values_per_peak.Rd | 64 - man/values_per_sample.Rd | 64 - man/variables_as_metadata.Rd | 76 - man/volcano_plot_fc_tt.Rd | 96 - man/x_values_to_indexes.Rd | 70 - man/xvalue_interval_to_indexes.Rd | 76 - 238 files changed, 15130 insertions(+), 15130 deletions(-)
Title: Sound Synthesis and Acoustic Analysis
Description: Performs parametric synthesis of sounds with harmonic and noise
components such as animal vocalizations or human voice. Also offers tools
for spectral analysis, audio segmentation, self-similarity matrices,
modulation spectra, morphing, etc., as well as interactive web apps for
manually corrected pitch tracking and formant measurement. Reference:
Anikin (2019) <doi:10.3758/s13428-018-1095-7>.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.8.0 dated 2020-08-11 and 1.8.1 dated 2020-09-18
DESCRIPTION |only MD5 |only NEWS |only R |only README.md | 17 +++------- build |only data/def_form.rda |binary data/defaults.rda |binary data/defaults_analyze.rda |binary data/permittedValues.rda |binary data/presets.rda |binary inst |only man/HzToSemitones.Rd |only man/addFormants.Rd |only man/addPitchCands.Rd | 3 + man/analyze.Rd | 49 ++++++++++++++++++----------- man/analyzeFolder.Rd | 16 ++++++--- man/analyzeFrame.Rd | 11 +++--- man/convert_sec_to_hms.Rd |only man/crossFade.Rd | 7 +--- man/def_form.Rd |only man/divideIntoSyllables.Rd |only man/estimateVTL.Rd | 8 ++++ man/evaluatePars.Rd |only man/fade.Rd | 48 ++++++++++------------------ man/fart.Rd |only man/figures |only man/filterMS.Rd |only man/filterSoundByMS.Rd | 67 +++++++++++++++++++++++++++++++++++++++- man/findGrad.Rd |only man/findVoicedSegments.Rd |only man/forcePerPath.Rd |only man/ftwindow_modif.Rd |only man/gaussian.w.Rd |only man/generateEpoch.Rd |only man/generateGC.Rd |only man/generateHarmonics.Rd | 13 ++++--- man/generateNoise.Rd |only man/generatePath.Rd |only man/getBandwidth.Rd |only man/getDiscreteContour.Rd |only man/getFormantDispersion.Rd | 4 ++ man/getGlottalCycles.Rd |only man/getIntegerRandomWalk.Rd |only man/getMelSpec.Rd |only man/getPitchSpec.Rd |only man/getRMS.Rd |only man/getRandomWalk.Rd |only man/getSmoothContour.Rd |only man/getSmoothSpectrum.Rd |only man/getSpectralEnvelope.Rd |only man/harmEnergy.Rd |only man/harmHeight_dif.Rd |only man/htmlPlots.Rd |only man/interpolate.Rd |only man/intplPitch.Rd |only man/lockToFormants.Rd |only man/matchLengths.Rd |only man/matchPars.Rd |only man/mergeSyllables.Rd |only man/modulationSpectrumFolder.Rd |only man/morphDF.Rd |only man/morphFormants.Rd |only man/normalizeFolder.Rd |only man/notesDict.Rd |only man/objectToString.Rd |only man/optimizePars.Rd |only man/osc.Rd |only man/osc_dB.Rd |only man/parabPeakInterpol.Rd |only man/pathfinder.Rd |only man/pathfinding_slow.Rd |only man/permittedValues.Rd |only man/pitchManual.Rd |only man/pitch_app.Rd |only man/reportCI.Rd |only man/reportTime.Rd |only man/rnorm_truncated.Rd |only man/schwa.Rd | 4 ++ man/segmentFolder.Rd |only man/segmentManual.Rd |only man/snake.Rd |only man/soundgen.Rd | 24 +++++++------- man/soundgen_app.Rd |only man/spectrogram.Rd |only man/ssm.Rd |only man/switchColorTheme.Rd |only man/transplantFormants.Rd |only man/updateAnalyze.Rd | 11 +++++- man/upsample.Rd |only man/validatePars.Rd |only man/wiggleAnchors.Rd |only man/wiggleGC.Rd |only man/wigglePars.Rd |only man/zeroOne.Rd | 4 +- vignettes |only 96 files changed, 191 insertions(+), 95 deletions(-)
Title: Finding Needles (=differentially Expressed Genes) in Haystacks
(=single Cell Data)
Description: Identification of differentially expressed genes (DEGs) is a key step in single-cell
transcriptomics data analysis. 'singleCellHaystack' predicts DEGs without relying on
clustering of cells into arbitrary clusters. Single-cell RNA-seq (scRNA-seq) data is
often processed to fewer dimensions using Principal Component Analysis (PCA) and
represented in 2-dimensional plots (e.g. t-SNE or UMAP plots). 'singleCellHaystack'
uses Kullback-Leibler divergence to find genes that are expressed in subsets of cells
that are non-randomly positioned in a these multi-dimensional spaces or 2D representations.
For the theoretical background of 'singleCellHaystack' we refer to
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>.
Author: Alexis Vandenbon [aut, cre] (<https://orcid.org/0000-0003-2180-5732>),
Diego Diez [aut] (<https://orcid.org/0000-0002-2325-4893>)
Maintainer: Alexis Vandenbon <alexis.vandenbon@gmail.com>
Diff between singleCellHaystack versions 0.3.2 dated 2020-07-01 and 0.3.3 dated 2020-09-18
singleCellHaystack-0.3.2/singleCellHaystack/vignettes/examples/a04_example_tsne2D_default.Rmd |only singleCellHaystack-0.3.2/singleCellHaystack/vignettes/examples/a05_example_tsne2D_advanced.Rmd |only singleCellHaystack-0.3.2/singleCellHaystack/vignettes/examples/a06_example_spatial_transcriptomics.Rmd |only singleCellHaystack-0.3.3/singleCellHaystack/DESCRIPTION | 14 - singleCellHaystack-0.3.3/singleCellHaystack/MD5 | 55 +++--- singleCellHaystack-0.3.3/singleCellHaystack/NAMESPACE | 6 singleCellHaystack-0.3.3/singleCellHaystack/R/haystack.R | 89 ++++++---- singleCellHaystack-0.3.3/singleCellHaystack/R/haystack_clustering.R | 10 + singleCellHaystack-0.3.3/singleCellHaystack/R/haystack_clustering_highD.R | 53 +++++ singleCellHaystack-0.3.3/singleCellHaystack/R/haystack_highD.R | 51 +++-- singleCellHaystack-0.3.3/singleCellHaystack/R/haystack_visualization.R | 44 ++++ singleCellHaystack-0.3.3/singleCellHaystack/R/s3.R | 28 ++- singleCellHaystack-0.3.3/singleCellHaystack/R/singleCellHaystack-package.R | 5 singleCellHaystack-0.3.3/singleCellHaystack/R/sparse.R |only singleCellHaystack-0.3.3/singleCellHaystack/build/vignette.rds |binary singleCellHaystack-0.3.3/singleCellHaystack/inst/CITATION |only singleCellHaystack-0.3.3/singleCellHaystack/inst/doc/a01_toy_example.html | 39 ++-- singleCellHaystack-0.3.3/singleCellHaystack/man/extract_row_dgRMatrix.Rd |only singleCellHaystack-0.3.3/singleCellHaystack/man/extract_row_lgRMatrix.Rd |only singleCellHaystack-0.3.3/singleCellHaystack/man/get_density.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/man/haystack.Rd | 15 + singleCellHaystack-0.3.3/singleCellHaystack/man/hclust_haystack.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/man/kmeans_haystack.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/man/plot_gene_haystack.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/man/plot_gene_set_haystack.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/man/singleCellHaystack-package.Rd | 2 singleCellHaystack-0.3.3/singleCellHaystack/tests/testthat/test-extract_row.R |only singleCellHaystack-0.3.3/singleCellHaystack/tests/testthat/test-haystack_sparse.R |only singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a02_example_highD_default.Rmd | 4 singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a03_example_highD_advanced.Rmd | 4 singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a04_example_spatial_transcriptomics.Rmd |only singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a05_moca_100k.Rmd |only singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a06_example_tsne2D_default.Rmd |only singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/a07_example_tsne2D_advanced.Rmd |only singleCellHaystack-0.3.3/singleCellHaystack/vignettes/examples/figure |only 35 files changed, 309 insertions(+), 120 deletions(-)
More information about singleCellHaystack at CRAN
Permanent link
Title: Estimation of the Structural Topic Model
Description: The Structural Topic Model (STM) allows researchers
to estimate topic models with document-level covariates.
The package also includes tools for model selection, visualization,
and estimation of topic-covariate regressions. Methods developed in
Roberts et. al. (2014) <doi:10.1111/ajps.12103> and
Roberts et. al. (2016) <doi:10.1080/01621459.2016.1141684>. Vignette
is Roberts et. al. (2019) <doi:10.18637/jss.v091.i02>.
Author: Margaret Roberts [aut],
Brandon Stewart [aut, cre],
Dustin Tingley [aut],
Kenneth Benoit [ctb]
Maintainer: Brandon Stewart <bms4@princeton.edu>
Diff between stm versions 1.3.5 dated 2019-12-17 and 1.3.6 dated 2020-09-18
stm-1.3.5/stm/data/datalist |only stm-1.3.5/stm/tests/testthat/Rplots.pdf |only stm-1.3.5/stm/tests/testthat/test-visualize.R |only stm-1.3.6/stm/DESCRIPTION | 18 +-- stm-1.3.6/stm/MD5 | 137 ++++++++++++-------------- stm-1.3.6/stm/R/asSTMCorpus.R | 4 stm-1.3.6/stm/R/estimateEffect.R | 12 +- stm-1.3.6/stm/R/exclusivity.R | 1 stm-1.3.6/stm/R/multiSTM.R | 22 ---- stm-1.3.6/stm/R/plot.STM.R | 2 stm-1.3.6/stm/R/plot.estimateEffect.R | 4 stm-1.3.6/stm/R/plot.searchK.R | 2 stm-1.3.6/stm/R/plotQuote.R | 2 stm-1.3.6/stm/R/searchK.R | 2 stm-1.3.6/stm/R/semanticCoherence.R | 1 stm-1.3.6/stm/R/spectral.R | 2 stm-1.3.6/stm/R/stm-package.R | 8 - stm-1.3.6/stm/R/stm.R | 5 stm-1.3.6/stm/R/textProcessor.R | 8 - stm-1.3.6/stm/R/toLDAvis.R | 4 stm-1.3.6/stm/R/topicCorr.R | 2 stm-1.3.6/stm/R/topicLasso.R | 2 stm-1.3.6/stm/build/vignette.rds |binary stm-1.3.6/stm/data/gadarian.RData |binary stm-1.3.6/stm/data/gadarianFit.RData |binary stm-1.3.6/stm/data/poliblog5k.RData |binary stm-1.3.6/stm/inst/NEWS.Rd | 8 + stm-1.3.6/stm/inst/doc/stmVignette.R | 3 stm-1.3.6/stm/inst/doc/stmVignette.Rnw | 2 stm-1.3.6/stm/inst/doc/stmVignette.pdf |binary stm-1.3.6/stm/man/asSTMCorpus.Rd | 2 stm-1.3.6/stm/man/calcfrex.Rd | 2 stm-1.3.6/stm/man/calclift.Rd | 2 stm-1.3.6/stm/man/cloud.Rd | 11 +- stm-1.3.6/stm/man/estimateEffect.Rd | 12 +- stm-1.3.6/stm/man/exclusivity.Rd | 3 stm-1.3.6/stm/man/findThoughts.Rd | 11 +- stm-1.3.6/stm/man/findTopic.Rd | 9 + stm-1.3.6/stm/man/fitNewDocuments.Rd | 23 +++- stm-1.3.6/stm/man/gadarian.Rd | 8 - stm-1.3.6/stm/man/make.heldout.Rd | 9 + stm-1.3.6/stm/man/makeDesignMatrix.Rd | 3 stm-1.3.6/stm/man/manyTopics.Rd | 23 +++- stm-1.3.6/stm/man/multiSTM.Rd | 27 ++--- stm-1.3.6/stm/man/optimizeDocument.Rd | 15 ++ stm-1.3.6/stm/man/permutationTest.Rd | 15 ++ stm-1.3.6/stm/man/plot.MultimodDiagnostic.Rd | 11 -- stm-1.3.6/stm/man/plot.STM.Rd | 28 +++-- stm-1.3.6/stm/man/plot.STMpermute.Rd | 3 stm-1.3.6/stm/man/plot.estimateEffect.Rd | 44 ++++++-- stm-1.3.6/stm/man/plot.searchK.Rd | 2 stm-1.3.6/stm/man/plot.topicCorr.Rd | 16 ++- stm-1.3.6/stm/man/plotModels.Rd | 12 +- stm-1.3.6/stm/man/plotQuote.Rd | 17 ++- stm-1.3.6/stm/man/plotTopicLoess.Rd | 12 +- stm-1.3.6/stm/man/poliblog5k.Rd | 8 - stm-1.3.6/stm/man/prepDocuments.Rd | 11 +- stm-1.3.6/stm/man/searchK.Rd | 17 ++- stm-1.3.6/stm/man/selectModel.Rd | 26 +++- stm-1.3.6/stm/man/semanticCoherence.Rd | 1 stm-1.3.6/stm/man/stm-package.Rd | 4 stm-1.3.6/stm/man/stm.Rd | 35 ++++-- stm-1.3.6/stm/man/summary.estimateEffect.Rd | 5 stm-1.3.6/stm/man/textProcessor.Rd | 31 ++++- stm-1.3.6/stm/man/thetaPosterior.Rd | 8 + stm-1.3.6/stm/man/toLDAvis.Rd | 17 ++- stm-1.3.6/stm/man/toLDAvisJson.Rd | 12 +- stm-1.3.6/stm/man/topicCorr.Rd | 3 stm-1.3.6/stm/man/topicLasso.Rd | 20 ++- stm-1.3.6/stm/man/topicQuality.Rd | 11 +- stm-1.3.6/stm/vignettes/stmVignette.Rnw | 2 71 files changed, 492 insertions(+), 290 deletions(-)
Title: In-depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Description: Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
Maintainer: Steve Rozen <steverozen@gmail.com>
Diff between ICAMS versions 2.1.2 dated 2020-04-21 and 2.2.3 dated 2020-09-18
ICAMS-2.1.2/ICAMS/data/datalist |only ICAMS-2.1.2/ICAMS/man/MakeDataFrameFromMutectVCF.Rd |only ICAMS-2.1.2/ICAMS/man/MakeDataFrameFromStrelkaSBSVCF.Rd |only ICAMS-2.1.2/ICAMS/tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.vcf |only ICAMS-2.1.2/ICAMS/tests/testthat/testdata/Mutect-GRCh37/Mutect1.GRCh37.vcf |only ICAMS-2.1.2/ICAMS/tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.vcf |only ICAMS-2.1.2/ICAMS/tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.vcf |only ICAMS-2.2.3/ICAMS/DESCRIPTION | 21 ICAMS-2.2.3/ICAMS/LICENSE |only ICAMS-2.2.3/ICAMS/MD5 | 316 + ICAMS-2.2.3/ICAMS/NAMESPACE | 3 ICAMS-2.2.3/ICAMS/R/ICAMS.R | 5 ICAMS-2.2.3/ICAMS/R/ID_functions.R | 388 +- ICAMS-2.2.3/ICAMS/R/VCF_to_catalog_functions.R | 1675 +++++++--- ICAMS-2.2.3/ICAMS/R/data.R | 8 ICAMS-2.2.3/ICAMS/R/other_catalog_formats.R | 64 ICAMS-2.2.3/ICAMS/R/plot.R | 105 ICAMS-2.2.3/ICAMS/R/read_write_catalog.R | 2 ICAMS-2.2.3/ICAMS/R/shiny_related_functions.R | 1204 ++++--- ICAMS-2.2.3/ICAMS/R/strandbias_functions.R | 24 ICAMS-2.2.3/ICAMS/R/sysdata.rda |binary ICAMS-2.2.3/ICAMS/R/test_functions.R | 2 ICAMS-2.2.3/ICAMS/R/utility_functions.R | 235 + ICAMS-2.2.3/ICAMS/README.md | 59 ICAMS-2.2.3/ICAMS/data/all.abundance.rda |binary ICAMS-2.2.3/ICAMS/data/catalog.row.order.rda |binary ICAMS-2.2.3/ICAMS/data/catalog.row.order.sp.rda |binary ICAMS-2.2.3/ICAMS/data/gene.expression.data.HepG2.rda |binary ICAMS-2.2.3/ICAMS/data/gene.expression.data.MCF10A.rda |binary ICAMS-2.2.3/ICAMS/data/trans.ranges.GRCh37.rda |binary ICAMS-2.2.3/ICAMS/data/trans.ranges.GRCh38.rda |binary ICAMS-2.2.3/ICAMS/data/trans.ranges.GRCm38.rda |binary ICAMS-2.2.3/ICAMS/inst/WORDLIST | 22 ICAMS-2.2.3/ICAMS/man/AddAndCheckDBSClassInVCF.Rd |only ICAMS-2.2.3/ICAMS/man/AddAndCheckSBSClassInVCF.Rd |only ICAMS-2.2.3/ICAMS/man/AddDBSClass.Rd |only ICAMS-2.2.3/ICAMS/man/AddRunInformation.Rd | 46 ICAMS-2.2.3/ICAMS/man/AddSBSClass.Rd |only ICAMS-2.2.3/ICAMS/man/AddSeqContext.Rd | 50 ICAMS-2.2.3/ICAMS/man/AddTranscript.Rd | 46 ICAMS-2.2.3/ICAMS/man/AnnotateDBSVCF.Rd | 98 ICAMS-2.2.3/ICAMS/man/AnnotateIDVCF.Rd | 119 ICAMS-2.2.3/ICAMS/man/AnnotateSBSVCF.Rd | 98 ICAMS-2.2.3/ICAMS/man/CalculateNumberOfSpace.Rd | 40 ICAMS-2.2.3/ICAMS/man/Canonicalize1Del.Rd | 108 ICAMS-2.2.3/ICAMS/man/Canonicalize1ID.Rd | 72 ICAMS-2.2.3/ICAMS/man/Canonicalize1INS.Rd | 54 ICAMS-2.2.3/ICAMS/man/CanonicalizeID.Rd | 54 ICAMS-2.2.3/ICAMS/man/CatalogRowOrder.Rd | 109 ICAMS-2.2.3/ICAMS/man/CheckAndFixChrNames.Rd | 62 ICAMS-2.2.3/ICAMS/man/CheckAndReturnDBSCatalogs.Rd |only ICAMS-2.2.3/ICAMS/man/CheckAndReturnDBSMatrix.Rd |only ICAMS-2.2.3/ICAMS/man/CheckAndReturnIDCatalog.Rd |only ICAMS-2.2.3/ICAMS/man/CheckAndReturnIDMatrix.Rd |only ICAMS-2.2.3/ICAMS/man/CheckAndReturnSBSCatalogs.Rd |only ICAMS-2.2.3/ICAMS/man/CheckAndReturnSBSMatrix.Rd |only ICAMS-2.2.3/ICAMS/man/CheckDBSClassInVCF.Rd |only ICAMS-2.2.3/ICAMS/man/CheckSBSClassInVCF.Rd |only ICAMS-2.2.3/ICAMS/man/CheckSeqContextInVCF.Rd | 52 ICAMS-2.2.3/ICAMS/man/CollapseCatalog.Rd | 96 ICAMS-2.2.3/ICAMS/man/ConvertICAMSCatalogToSigProSBS96.Rd |only ICAMS-2.2.3/ICAMS/man/CreateDinucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/CreateExomeStrandedRanges.Rd | 50 ICAMS-2.2.3/ICAMS/man/CreateOneColDBSMatrix.Rd | 63 ICAMS-2.2.3/ICAMS/man/CreateOneColIDMatrix.Rd | 80 ICAMS-2.2.3/ICAMS/man/CreateOneColSBSMatrix.Rd | 70 ICAMS-2.2.3/ICAMS/man/CreateOnePPMFromSBSVCF.Rd | 54 ICAMS-2.2.3/ICAMS/man/CreatePPMFromSBSVCFs.Rd | 50 ICAMS-2.2.3/ICAMS/man/CreatePentanucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/CreateStrandedDinucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/CreateStrandedTrinucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/CreateTetranucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/CreateTransRanges.Rd | 42 ICAMS-2.2.3/ICAMS/man/CreateTrinucAbundance.Rd | 40 ICAMS-2.2.3/ICAMS/man/FindDelMH.Rd | 313 - ICAMS-2.2.3/ICAMS/man/FindMaxRepeatDel.Rd | 165 ICAMS-2.2.3/ICAMS/man/FindMaxRepeatIns.Rd | 118 ICAMS-2.2.3/ICAMS/man/GeneExpressionData.Rd | 70 ICAMS-2.2.3/ICAMS/man/GetCustomKmerCounts.Rd | 64 ICAMS-2.2.3/ICAMS/man/GetGenomeKmerCounts.Rd | 52 ICAMS-2.2.3/ICAMS/man/GetMutationLoadsFromMutectVCFs.Rd | 66 ICAMS-2.2.3/ICAMS/man/GetMutationLoadsFromStrelkaIDVCFs.Rd | 68 ICAMS-2.2.3/ICAMS/man/GetMutationLoadsFromStrelkaSBSVCFs.Rd | 68 ICAMS-2.2.3/ICAMS/man/GetSequenceKmerCounts.Rd | 40 ICAMS-2.2.3/ICAMS/man/GetStrandedKmerCounts.Rd | 72 ICAMS-2.2.3/ICAMS/man/GetVAF.Rd | 83 ICAMS-2.2.3/ICAMS/man/ICAMS.Rd | 583 +-- ICAMS-2.2.3/ICAMS/man/InferAbundance.Rd | 58 ICAMS-2.2.3/ICAMS/man/MakeDataFrameFromVCF.Rd | 36 ICAMS-2.2.3/ICAMS/man/MakeVCFDBSdf.Rd | 48 ICAMS-2.2.3/ICAMS/man/MutectVCFFilesToCatalog.Rd | 243 - ICAMS-2.2.3/ICAMS/man/MutectVCFFilesToCatalogAndPlotToPdf.Rd | 262 - ICAMS-2.2.3/ICAMS/man/MutectVCFFilesToZipFile.Rd | 279 + ICAMS-2.2.3/ICAMS/man/NormalizeGenomeArg.Rd | 44 ICAMS-2.2.3/ICAMS/man/Plot96PartOfCompositeToPDF.Rd | 38 ICAMS-2.2.3/ICAMS/man/PlotCatalog.Rd | 163 ICAMS-2.2.3/ICAMS/man/PlotCatalogToPdf.Rd | 165 ICAMS-2.2.3/ICAMS/man/PlotPPM.Rd | 44 ICAMS-2.2.3/ICAMS/man/PlotPPMToPdf.Rd | 44 ICAMS-2.2.3/ICAMS/man/PlotTransBiasGeneExp.Rd | 176 - ICAMS-2.2.3/ICAMS/man/PlotTransBiasGeneExpToPdf.Rd | 182 - ICAMS-2.2.3/ICAMS/man/ReadAndSplitMutectVCFs.Rd | 118 ICAMS-2.2.3/ICAMS/man/ReadAndSplitStrelkaSBSVCFs.Rd | 103 ICAMS-2.2.3/ICAMS/man/ReadCatalog.Rd | 112 ICAMS-2.2.3/ICAMS/man/ReadDukeNUSCat192.Rd | 56 ICAMS-2.2.3/ICAMS/man/ReadMutectVCF.Rd | 64 ICAMS-2.2.3/ICAMS/man/ReadMutectVCFs.Rd | 68 ICAMS-2.2.3/ICAMS/man/ReadStapleGT96SBS.Rd | 2 ICAMS-2.2.3/ICAMS/man/ReadStrelkaIDVCF.Rd | 58 ICAMS-2.2.3/ICAMS/man/ReadStrelkaIDVCFs.Rd | 78 ICAMS-2.2.3/ICAMS/man/ReadStrelkaSBSVCF.Rd | 54 ICAMS-2.2.3/ICAMS/man/ReadStrelkaSBSVCFs.Rd | 56 ICAMS-2.2.3/ICAMS/man/ReadTranscriptRanges.Rd | 42 ICAMS-2.2.3/ICAMS/man/ReadVCF.Rd |only ICAMS-2.2.3/ICAMS/man/ReadVCFs.Rd |only ICAMS-2.2.3/ICAMS/man/RemoveRangesOnBothStrand.Rd | 40 ICAMS-2.2.3/ICAMS/man/RenameColumnsWithNameStrand.Rd | 32 ICAMS-2.2.3/ICAMS/man/RenameColumnsWithNameVAF.Rd | 32 ICAMS-2.2.3/ICAMS/man/Restaple96.Rd | 38 ICAMS-2.2.3/ICAMS/man/RevcDBS144.Rd | 44 ICAMS-2.2.3/ICAMS/man/RevcSBS96.Rd | 46 ICAMS-2.2.3/ICAMS/man/SplitListOfMutectVCFs.Rd | 79 ICAMS-2.2.3/ICAMS/man/SplitListOfStrelkaSBSVCFs.Rd | 83 ICAMS-2.2.3/ICAMS/man/SplitOneMutectVCF.Rd | 76 ICAMS-2.2.3/ICAMS/man/SplitStrelkaSBSVCF.Rd | 82 ICAMS-2.2.3/ICAMS/man/StandardChromName.Rd | 38 ICAMS-2.2.3/ICAMS/man/StandardChromNameNew.Rd |only ICAMS-2.2.3/ICAMS/man/StrelkaIDVCFFilesToCatalog.Rd | 164 ICAMS-2.2.3/ICAMS/man/StrelkaIDVCFFilesToCatalogAndPlotToPdf.Rd | 185 - ICAMS-2.2.3/ICAMS/man/StrelkaIDVCFFilesToZipFile.Rd | 204 - ICAMS-2.2.3/ICAMS/man/StrelkaSBSVCFFilesToCatalog.Rd | 190 - ICAMS-2.2.3/ICAMS/man/StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd | 206 - ICAMS-2.2.3/ICAMS/man/StrelkaSBSVCFFilesToZipFile.Rd | 226 - ICAMS-2.2.3/ICAMS/man/TestMakeCatalogFromStrelkaIDVCFs.Rd | 28 ICAMS-2.2.3/ICAMS/man/TestMakeCatalogFromStrelkaSBSVCFs.Rd | 28 ICAMS-2.2.3/ICAMS/man/TestPlotCatCOMPOSITE.Rd | 54 ICAMS-2.2.3/ICAMS/man/TransRownames.ID.PCAWG.SigPro.Rd | 34 ICAMS-2.2.3/ICAMS/man/TransRownames.ID.SigPro.PCAWG.Rd | 34 ICAMS-2.2.3/ICAMS/man/TranscriptRanges.Rd | 140 ICAMS-2.2.3/ICAMS/man/TransformCatalog.Rd | 249 - ICAMS-2.2.3/ICAMS/man/Unstaple96.Rd | 4 ICAMS-2.2.3/ICAMS/man/VCFsToDBSCatalogs.Rd | 161 ICAMS-2.2.3/ICAMS/man/VCFsToIDCatalogs.Rd | 146 ICAMS-2.2.3/ICAMS/man/VCFsToSBSCatalogs.Rd | 161 ICAMS-2.2.3/ICAMS/man/WriteCat.Rd | 54 ICAMS-2.2.3/ICAMS/man/WriteCatalog.Rd | 70 ICAMS-2.2.3/ICAMS/man/WriteCatalogIndelSigPro.Rd | 54 ICAMS-2.2.3/ICAMS/man/all.abundance.Rd | 78 ICAMS-2.2.3/ICAMS/man/as.catalog.Rd | 126 ICAMS-2.2.3/ICAMS/man/revc.Rd | 58 ICAMS-2.2.3/ICAMS/tests/testthat/test_0TransformCatalogDBS144.R | 2 ICAMS-2.2.3/ICAMS/tests/testthat/test_1TransformCatalog.R | 87 ICAMS-2.2.3/ICAMS/tests/testthat/test_1VCFFilesToZipFile.R | 4 ICAMS-2.2.3/ICAMS/tests/testthat/test_1strandbias_functions.R | 4 ICAMS-2.2.3/ICAMS/tests/testthat/test_AddSeqContext.R | 2 ICAMS-2.2.3/ICAMS/tests/testthat/test_AnnotateIDVCF.R | 2 ICAMS-2.2.3/ICAMS/tests/testthat/test_CanonicalizeDBS.R | 1 ICAMS-2.2.3/ICAMS/tests/testthat/test_ConvertICAMSCatalogToSigPro.R |only ICAMS-2.2.3/ICAMS/tests/testthat/test_ID_fns.R | 4 ICAMS-2.2.3/ICAMS/tests/testthat/test_ReadVCF.R | 130 ICAMS-2.2.3/ICAMS/tests/testthat/test_Read_and_Split_VCFs.R |only ICAMS-2.2.3/ICAMS/tests/testthat/test_SplitStrelkaVCF.R | 4 ICAMS-2.2.3/ICAMS/tests/testthat/test_cbind_catalogs.R | 9 ICAMS-2.2.3/ICAMS/tests/testthat/test_discarded_variants.R |only ICAMS-2.2.3/ICAMS/tests/testthat/test_extended_seq.context_functions.R | 4 ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s1.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s2.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Mutect-GRCh37/Mutect.GRCh37.s3.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s1.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka-ID-GRCh37/Strelka.ID.GRCh37.s3.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s1.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka-SBS-GRCh37/Strelka.SBS.GRCh37.s3.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka-mult-alt.vcf | 1322 +++---- ICAMS-2.2.3/ICAMS/tests/testthat/testdata/Strelka.mixed.GRCh37.vcf |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/regress.cat.sbs.96.one.column.csv |only ICAMS-2.2.3/ICAMS/tests/testthat/testdata/test_AddSeqContext.Rdata |binary ICAMS-2.2.3/ICAMS/tests/testthat/testdata/test_AnnotateIDVCF.Rdata |binary 177 files changed, 8730 insertions(+), 6330 deletions(-)
Title: Spacekime Analytics, Time Complexity and Inferential Uncertainty
Description: Provide the core functionality to transform longitudinal data to
complex-time (kime) data using analytic and numerical techniques, visualize the original
time-series and reconstructed kime-surfaces, perform model based (e.g., tensor-linear regression)
and model-free classification and clustering methods in the book Dinov, ID and Velev, MV. (2021)
"Data Science: Time Complexity, Inferential Uncertainty, and Spacekime Analytics", De Gruyter STEM Series,
ISBN 978-3-11-069780-3. <https://www.degruyter.com/view/title/576646>.
The package includes 18 core functions which can be separated into three groups.
1) draw longitudinal data, such as fMRI time-series, and forecast or transform the time-series data.
2) simulate real-valued time-series data, e.g., fMRI time-courses, detect the activated areas,
report the corresponding p-values, and visualize the p-values in the 3D brain space.
3) Laplace transform and kimesurface reconstructions of the fMRI data.
Author: Yongkai Qiu [aut],
Zhe Yin [aut],
Jinwen Cao [aut],
Yupeng Zhang [aut],
Yuyao Liu [aut],
Rongqian Zhang [aut],
Rouben Rostamian [ctb],
Ranjan Maitra [ctb],
Daniel Rowe [ctb],
Daniel Adrian [ctb] (gLRT method for complex-valued fMRI statistics),
Yunjie Guo [aut, cre],
Ivo Dinov [aut]
Maintainer: Yunjie Guo <jerryguo@umich.edu>
Diff between TCIU versions 1.0.0 dated 2020-08-27 and 1.1.0 dated 2020-09-18
TCIU-1.0.0/TCIU/src/complex_Sig=gen.c |only TCIU-1.0.0/TCIU/src/complex_Sig=gen.h |only TCIU-1.0.0/TCIU/src/complex_Sig=sig2I.c |only TCIU-1.0.0/TCIU/src/complex_Sig=sig2I.h |only TCIU-1.1.0/TCIU/DESCRIPTION | 15 ++++++---- TCIU-1.1.0/TCIU/MD5 | 15 +++++----- TCIU-1.1.0/TCIU/inst/doc/tciu-LT-kimesurface.html | 16 +++++------ TCIU-1.1.0/TCIU/inst/doc/tciu-fMRI-analytics.html | 32 +++++++++++----------- TCIU-1.1.0/TCIU/src/complex_Sig_gen.c |only TCIU-1.1.0/TCIU/src/complex_Sig_gen.h |only TCIU-1.1.0/TCIU/src/complex_Sig_sig2I.c |only TCIU-1.1.0/TCIU/src/complex_Sig_sig2I.h |only TCIU-1.1.0/TCIU/src/registerDynamicSymbol.c |only 13 files changed, 41 insertions(+), 37 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.4.2 dated 2020-06-27 and 1.4.3 dated 2020-09-18
DESCRIPTION | 6 ++--- MD5 | 35 ++++++++++++++++++---------------- NEWS | 3 ++ R/hash.R | 2 - R/init.R |only R/rand.R | 2 - inst/doc/bignum.html | 30 ++++++++++++++--------------- inst/doc/crypto_hashing.R | 5 +++- inst/doc/crypto_hashing.Rmd | 9 +++++--- inst/doc/crypto_hashing.html | 15 ++++++++------ inst/doc/keys.html | 44 +++++++++++++++++++++---------------------- inst/doc/secure_rng.Rmd | 4 +-- inst/doc/secure_rng.html | 24 +++++++++++------------ man/hash.Rd | 2 - man/rand_bytes.Rd | 2 - src/bcrypt/bcrypt_pbkdf.c | 5 +--- tests/engine.R |only tests/engine.Rout.save |only vignettes/crypto_hashing.Rmd | 9 +++++--- vignettes/secure_rng.Rmd | 4 +-- 20 files changed, 109 insertions(+), 92 deletions(-)
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to 'stats::lowess' function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting "Venn" diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y plot so they don't overlap ('space').
Author: Gregory R. Warnes [aut],
Ben Bolker [aut],
Lodewijk Bonebakker [aut],
Robert Gentleman [aut],
Wolfgang Huber [aut],
Andy Liaw [aut],
Thomas Lumley [aut],
Martin Maechler [aut],
Arni Magnusson [aut],
Steffen Moeller [aut],
Marc Schwartz [aut],
Bill Venables [aut],
Tal Galili [ctb, cre]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between gplots versions 3.0.4 dated 2020-07-05 and 3.1.0 dated 2020-09-18
DESCRIPTION | 10 ++++---- MD5 | 41 ++++++++++++++++++++---------------- NAMESPACE | 9 +++++-- NEWS | 10 +++++++- NEWS.md | 10 +++++++- R/nobs.R |only R/reorder.R |only R/zzz.R | 1 README.md |only inst/doc/venn.R | 2 - inst/doc/venn.Rnw | 2 - inst/doc/venn.pdf |binary man/balloonplot.Rd | 2 - man/ci2d.Rd | 2 - man/ooplot.Rd | 1 man/reorder.Rd |only man/textplot.Rd | 2 - tests/heatmap2Test.R | 3 -- tests/heatmap2Test.Rout.save | 10 -------- tests/heatmap_to_heatmap.2_test.R | 2 - tests/plotmeans_nobars.R | 2 - tests/test.reorder.factor.R |only tests/test_plottingDeepDendrogram.R | 2 - vignettes/venn.Rnw | 2 - 24 files changed, 65 insertions(+), 48 deletions(-)
More information about CovidMutations at CRAN
Permanent link
More information about tradestatistics at CRAN
Permanent link
Title: Compile and Preview Snippets of 'LaTeX'
Description: Compile snippets of 'LaTeX' directly into images
from the R console to view in the 'RStudio' viewer pane, Shiny apps
and 'RMarkdown' documents.
Author: Jonathan Sidi [aut, cre],
Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between texPreview versions 1.4.4 dated 2020-02-16 and 1.4.6 dated 2020-09-18
DESCRIPTION | 20 - LICENSE |only MD5 | 89 ++++---- NAMESPACE | 1 R/get_texpackages.R | 19 - R/tex_check.R | 17 + R/utils.R | 4 README.md | 17 + build/texPreview.pdf |binary build/vignette.rds |binary inst/doc/classes.R | 14 - inst/doc/classes.html | 60 ++++- inst/doc/engine.R | 6 inst/doc/engine.Rmd | 6 inst/doc/engine.html | 138 +++++++------ inst/doc/kable.R | 14 - inst/doc/kable.html | 74 ++++--- inst/doc/rmarkdown.R | 8 inst/doc/rmarkdown.Rmd | 2 inst/doc/rmarkdown.html | 58 ++++- inst/doc/slickr.R | 14 - inst/doc/slickr.Rmd | 6 inst/doc/slickr.html | 88 ++++++-- inst/doc/tests_and_coverage.R | 2 inst/doc/tests_and_coverage.Rmd | 132 +++++++----- inst/doc/tests_and_coverage.html | 407 +++++++++++++++++++++++++++++++-------- inst/doc/tex_packages.R | 8 inst/doc/tex_packages.Rmd | 2 inst/doc/tex_packages.html | 54 +++-- inst/doc/tikz.R | 16 - inst/doc/tikz.html | 54 +++-- man/BuildUsepackage.Rd | 2 man/getTexPackages.Rd | 2 man/get_texpackages.Rd | 3 man/texPreview.Rd | 2 man/tex_opts.Rd | 6 man/tex_preview.Rd | 2 tests/README.md | 68 +++--- tests/testthat/test-rmd.R | 4 tests/testthat/test-tex.R | 7 tests/testthat/test-utilities.R | 8 vignettes/engine.Rmd | 6 vignettes/rmarkdown.Rmd | 2 vignettes/slickr.Rmd | 6 vignettes/tests_and_coverage.Rmd | 132 +++++++----- vignettes/tex_packages.Rmd | 2 46 files changed, 1046 insertions(+), 536 deletions(-)
Title: Spatial Survey Design and Analysis
Description: These functions provide procedures for selecting sites for spatial
surveys using spatially balanced algorithms applied to discrete points,
linear networks, or polygons. The probability survey designs available
include independent random samples, stratified random samples, and unequal
probability random samples (categorical or probability proportional to
size). Design-based estimation based on the results from surveys is
available for estimating totals, means, quantiles, CDFs, and linear models.
The analyses rely on package survey for most results. Variance estimation
options include a local neighborhood variance estimator that is appropriate
for spatially-balanced survey designs. A reference for the survey design
portion of the package is: D. L. Stevens, Jr. and A. R. Olsen (2004),
"Spatially-balanced sampling of natural resources.", Journal of the American
Statistical Association 99(465): 262-278, <DOI:10.1198/016214504000000250>.
Additional helpful references for this package are A. R. Olsen, T. M.
Kincaid, and Q. Payton (2012) and T. M. Kincaid and A. R. Olsen (2012), both
of which are chapters in the book "Design and Analysis of Long-Term
Ecological Monitoring Studies" (R. A. Gitzen, J. J. Millspaugh, A. B.
Cooper, and D. S. Licht (eds.), Cambridge University Press, New York,
<Online ISBN:9781139022422>).
Author: Tom Kincaid [aut],
Tony Olsen [aut],
Marc Weber [aut, cre],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Marc Weber <Weber.Marc@epa.gov>
Diff between spsurvey versions 4.1.3 dated 2020-06-18 and 4.1.4 dated 2020-09-18
spsurvey-4.1.3/spsurvey/tests/testthat/ButteCreek.dbf |only spsurvey-4.1.3/spsurvey/tests/testthat/ButteCreek.prj |only spsurvey-4.1.3/spsurvey/tests/testthat/ButteCreek.shp |only spsurvey-4.1.3/spsurvey/tests/testthat/ButteCreek.shx |only spsurvey-4.1.3/spsurvey/tests/testthat/NHDPoint.dbf |only spsurvey-4.1.3/spsurvey/tests/testthat/NHDPoint.prj |only spsurvey-4.1.3/spsurvey/tests/testthat/NHDPoint.shp |only spsurvey-4.1.3/spsurvey/tests/testthat/NHDPoint.shx |only spsurvey-4.1.3/spsurvey/tests/testthat/reg1_lakes.dbf |only spsurvey-4.1.3/spsurvey/tests/testthat/reg1_lakes.prj |only spsurvey-4.1.3/spsurvey/tests/testthat/reg1_lakes.shp |only spsurvey-4.1.3/spsurvey/tests/testthat/reg1_lakes.shx |only spsurvey-4.1.4/spsurvey/DESCRIPTION | 8 spsurvey-4.1.4/spsurvey/MD5 | 42 +-- spsurvey-4.1.4/spsurvey/NEWS.md | 8 spsurvey-4.1.4/spsurvey/R/ranho.R | 2 spsurvey-4.1.4/spsurvey/build/vignette.rds |binary spsurvey-4.1.4/spsurvey/inst/doc/Area_Analysis.html | 30 ++ spsurvey-4.1.4/spsurvey/inst/doc/Area_Design.html | 132 ++++++----- spsurvey-4.1.4/spsurvey/inst/doc/CDF_Analysis.html | 20 + spsurvey-4.1.4/spsurvey/inst/doc/CDF_Deconvolution.html | 20 + spsurvey-4.1.4/spsurvey/inst/doc/CHANGES.pdf |binary spsurvey-4.1.4/spsurvey/inst/doc/Change_Analysis.html | 20 + spsurvey-4.1.4/spsurvey/inst/doc/Finite_Analysis.html | 20 + spsurvey-4.1.4/spsurvey/inst/doc/Finite_Design.html | 147 +++++++------ spsurvey-4.1.4/spsurvey/inst/doc/Linear_Analysis.html | 20 + spsurvey-4.1.4/spsurvey/inst/doc/Linear_Design.html | 180 ++++++++-------- spsurvey-4.1.4/spsurvey/inst/doc/Risk_Analysis.html | 20 + 28 files changed, 415 insertions(+), 254 deletions(-)
Title: Semi-Automatic Analysis of Sound Correspondences
Description: A set of tools that can be used in computer-aided analysis of
sound correspondences between languages, plus several helper functions.
Analytic functions range from purely qualitative analysis, through
statistic methods yielding qualitative results, to an entirely
quantitative approach.
Author: Kamil Stachowski [aut, cre]
Maintainer: Kamil Stachowski <kamil.stachowski@gmail.com>
Diff between soundcorrs versions 0.2.0 dated 2020-09-01 and 0.3.0 dated 2020-09-18
soundcorrs-0.2.0/soundcorrs/R/data.R |only soundcorrs-0.2.0/soundcorrs/data |only soundcorrs-0.2.0/soundcorrs/man/sampleSoundCorrsData.abc.Rd |only soundcorrs-0.2.0/soundcorrs/man/sampleSoundCorrsData.capitals.Rd |only soundcorrs-0.2.0/soundcorrs/man/sampleSoundCorrsData.ie.Rd |only soundcorrs-0.3.0/soundcorrs/DESCRIPTION | 10 soundcorrs-0.3.0/soundcorrs/MD5 | 143 soundcorrs-0.3.0/soundcorrs/NAMESPACE | 8 soundcorrs-0.3.0/soundcorrs/NEWS | 20 soundcorrs-0.3.0/soundcorrs/R/helpers.R |only soundcorrs-0.3.0/soundcorrs/R/soundchange.R |only soundcorrs-0.3.0/soundcorrs/R/soundcorrs.R | 1282 ------- soundcorrs-0.3.0/soundcorrs/R/transcription.R |only soundcorrs-0.3.0/soundcorrs/R/z-obsolete.R |only soundcorrs-0.3.0/soundcorrs/R/zzz.R |only soundcorrs-0.3.0/soundcorrs/build/vignette.rds |binary soundcorrs-0.3.0/soundcorrs/inst/doc/soundcorrs.R | 117 soundcorrs-0.3.0/soundcorrs/inst/doc/soundcorrs.Rmd | 150 soundcorrs-0.3.0/soundcorrs/inst/doc/soundcorrs.html | 1741 +++++----- soundcorrs-0.3.0/soundcorrs/inst/extdata/change-dl2l.R |only soundcorrs-0.3.0/soundcorrs/inst/extdata/change-palatalization.R |only soundcorrs-0.3.0/soundcorrs/inst/extdata/change-rhotacism.R |only soundcorrs-0.3.0/soundcorrs/inst/extdata/data-abc.tsv | 2 soundcorrs-0.3.0/soundcorrs/inst/extdata/trans-common.tsv | 3 soundcorrs-0.3.0/soundcorrs/man/addSeparators.Rd | 5 soundcorrs-0.3.0/soundcorrs/man/allCooccs.Rd | 7 soundcorrs-0.3.0/soundcorrs/man/allPairs.Rd | 13 soundcorrs-0.3.0/soundcorrs/man/applyChanges.Rd |only soundcorrs-0.3.0/soundcorrs/man/binTable.Rd | 5 soundcorrs-0.3.0/soundcorrs/man/cbind.soundcorrs.Rd | 7 soundcorrs-0.3.0/soundcorrs/man/char2value.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/checkCount.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/checkUnit.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/collapse.Rd | 5 soundcorrs-0.3.0/soundcorrs/man/coocc.Rd | 7 soundcorrs-0.3.0/soundcorrs/man/expandMeta.Rd | 23 soundcorrs-0.3.0/soundcorrs/man/findExamples.Rd | 36 soundcorrs-0.3.0/soundcorrs/man/findPairs.Rd | 14 soundcorrs-0.3.0/soundcorrs/man/findSegments.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/fitTable.Rd | 24 soundcorrs-0.3.0/soundcorrs/man/formatter.html.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/formatter.latex.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/formatter.none.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/grapes-.-grapes.Rd | 4 soundcorrs-0.3.0/soundcorrs/man/grapes-hasPrefix-grapes.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/grapes-hasSuffix-grapes.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/grapes-nin-grapes.Rd | 4 soundcorrs-0.3.0/soundcorrs/man/lapplyTest.Rd | 10 soundcorrs-0.3.0/soundcorrs/man/list.depth.Rd | 5 soundcorrs-0.3.0/soundcorrs/man/list.transpose.Rd | 5 soundcorrs-0.3.0/soundcorrs/man/loadSampleDataset.Rd |only soundcorrs-0.3.0/soundcorrs/man/long2wide.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/merge.soundcorrs.Rd | 3 soundcorrs-0.3.0/soundcorrs/man/multiFit.Rd | 22 soundcorrs-0.3.0/soundcorrs/man/ngrams.Rd | 7 soundcorrs-0.3.0/soundcorrs/man/ngrams.scOne.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/print.df.findExamples.Rd | 10 soundcorrs-0.3.0/soundcorrs/man/print.list.applyChanges.Rd |only soundcorrs-0.3.0/soundcorrs/man/print.scOne.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/print.soundchange.Rd |only soundcorrs-0.3.0/soundcorrs/man/print.soundcorrs.Rd | 13 soundcorrs-0.3.0/soundcorrs/man/print.transcription.Rd | 12 soundcorrs-0.3.0/soundcorrs/man/print.tree.applyChanges.Rd |only soundcorrs-0.3.0/soundcorrs/man/read.scOne.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/read.soundcorrs.Rd | 13 soundcorrs-0.3.0/soundcorrs/man/read.transcription.Rd | 16 soundcorrs-0.3.0/soundcorrs/man/revChar.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/scOne.Rd | 2 soundcorrs-0.3.0/soundcorrs/man/soundchange.Rd |only soundcorrs-0.3.0/soundcorrs/man/soundcorrs.Rd | 22 soundcorrs-0.3.0/soundcorrs/man/subset.soundcorrs.Rd | 8 soundcorrs-0.3.0/soundcorrs/man/summary.list.lapplyTest.Rd | 10 soundcorrs-0.3.0/soundcorrs/man/summary.list.multiFit.Rd | 22 soundcorrs-0.3.0/soundcorrs/man/summary.soundcorrs.Rd | 11 soundcorrs-0.3.0/soundcorrs/man/tabAbs2Rel.Rd | 7 soundcorrs-0.3.0/soundcorrs/man/transcription.Rd | 30 soundcorrs-0.3.0/soundcorrs/man/vec2df.hist.Rd | 12 soundcorrs-0.3.0/soundcorrs/man/vec2df.id.Rd | 12 soundcorrs-0.3.0/soundcorrs/man/vec2df.rank.Rd | 12 soundcorrs-0.3.0/soundcorrs/man/wide2long.Rd | 8 soundcorrs-0.3.0/soundcorrs/vignettes/soundcorrs.Rmd | 150 81 files changed, 1855 insertions(+), 2273 deletions(-)
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.0.0 dated 2020-06-15 and 5.1.0 dated 2020-09-18
huxtable-5.0.0/huxtable/tests/testthat/fontspec-test.log |only huxtable-5.0.0/huxtable/tests/testthat/huxreg.log |only huxtable-5.0.0/huxtable/tests/testthat/huxtable.aux |only huxtable-5.0.0/huxtable/tests/testthat/huxtable.log |only huxtable-5.0.0/huxtable/tests/testthat/table-tester-2.log |only huxtable-5.0.0/huxtable/tests/testthat/temp-artefacts/huxreg.log |only huxtable-5.0.0/huxtable/tests/testthat/temp-artefacts/huxreg.tex |only huxtable-5.0.0/huxtable/tests/testthat/temp-artefacts/huxtable.tex |only huxtable-5.1.0/huxtable/DESCRIPTION | 25 huxtable-5.1.0/huxtable/MD5 | 152 ++-- huxtable-5.1.0/huxtable/NEWS.md | 55 + huxtable-5.1.0/huxtable/R/Workbook.R | 51 + huxtable-5.1.0/huxtable/R/aaa-utils.R | 10 huxtable-5.1.0/huxtable/R/bind-insert-internal.R | 5 huxtable-5.1.0/huxtable/R/bind-insert.R | 15 huxtable-5.1.0/huxtable/R/brdr.R | 2 huxtable-5.1.0/huxtable/R/clean-contents.R | 24 huxtable-5.1.0/huxtable/R/dplyr.R | 2 huxtable-5.1.0/huxtable/R/flextable.R | 11 huxtable-5.1.0/huxtable/R/huxreg.R | 117 ++- huxtable-5.1.0/huxtable/R/latex-dependencies.R | 5 huxtable-5.1.0/huxtable/R/markdown.R | 310 ++++++++-- huxtable-5.1.0/huxtable/R/merge.R | 7 huxtable-5.1.0/huxtable/R/misc.R | 5 huxtable-5.1.0/huxtable/R/package-docs.R | 30 huxtable-5.1.0/huxtable/R/properties-cell.R | 27 huxtable-5.1.0/huxtable/R/properties-table.R | 4 huxtable-5.1.0/huxtable/R/quick-functions.R | 2 huxtable-5.1.0/huxtable/R/restack-split.R | 4 huxtable-5.1.0/huxtable/R/screen.R | 27 huxtable-5.1.0/huxtable/R/style-cells.R | 4 huxtable-5.1.0/huxtable/R/subset-extract.R | 6 huxtable-5.1.0/huxtable/R/zzz.R | 10 huxtable-5.1.0/huxtable/build/vignette.rds |binary huxtable-5.1.0/huxtable/inst/doc/design-principles.Rmd | 4 huxtable-5.1.0/huxtable/inst/doc/design-principles.html | 6 huxtable-5.1.0/huxtable/inst/doc/huxreg.html | 17 huxtable-5.1.0/huxtable/inst/doc/huxtable.R | 2 huxtable-5.1.0/huxtable/inst/doc/huxtable.Rmd | 2 huxtable-5.1.0/huxtable/inst/doc/huxtable.html | 26 huxtable-5.1.0/huxtable/inst/doc/themes.html | 6 huxtable-5.1.0/huxtable/man/as_Workbook.Rd | 12 huxtable-5.1.0/huxtable/man/brdr_thickness.Rd | 4 huxtable-5.1.0/huxtable/man/dplyr-verbs.Rd | 6 huxtable-5.1.0/huxtable/man/huxreg.Rd | 9 huxtable-5.1.0/huxtable/man/huxtable-FAQ.Rd | 19 huxtable-5.1.0/huxtable/man/huxtable-news.Rd | 210 +----- huxtable-5.1.0/huxtable/man/huxtable-options.Rd | 2 huxtable-5.1.0/huxtable/man/knit_print.data.frame.Rd | 2 huxtable-5.1.0/huxtable/man/knit_print.huxtable.Rd | 2 huxtable-5.1.0/huxtable/man/label.Rd | 2 huxtable-5.1.0/huxtable/man/markdown.Rd | 25 huxtable-5.1.0/huxtable/man/number_format.Rd | 5 huxtable-5.1.0/huxtable/man/position.Rd | 2 huxtable-5.1.0/huxtable/man/print.huxtable.Rd | 2 huxtable-5.1.0/huxtable/man/quick-output.Rd | 2 huxtable-5.1.0/huxtable/man/report_latex_dependencies.Rd | 2 huxtable-5.1.0/huxtable/man/restack-across-down.Rd | 2 huxtable-5.1.0/huxtable/man/split-across-down.Rd | 2 huxtable-5.1.0/huxtable/tests/testthat/bones.png |only huxtable-5.1.0/huxtable/tests/testthat/huxtable-output.pdf |only huxtable-5.1.0/huxtable/tests/testthat/table-tester-2.Rmd | 4 huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.docx |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.html |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.pdf |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.pptx |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.rtf |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.tex |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/long-minus-test.xlsx |only huxtable-5.1.0/huxtable/tests/testthat/temp-artefacts/table-tester-2.tex | 5 huxtable-5.1.0/huxtable/tests/testthat/test-attributes.R | 79 -- huxtable-5.1.0/huxtable/tests/testthat/test-dplyr.R | 1 huxtable-5.1.0/huxtable/tests/testthat/test-huxreg.R | 23 huxtable-5.1.0/huxtable/tests/testthat/test-manipulation-helpers.R | 13 huxtable-5.1.0/huxtable/tests/testthat/test-map-interface.R | 2 huxtable-5.1.0/huxtable/tests/testthat/test-markdown.R |only huxtable-5.1.0/huxtable/tests/testthat/test-merge.R | 15 huxtable-5.1.0/huxtable/tests/testthat/test-number-formatting.R |only huxtable-5.1.0/huxtable/tests/testthat/test-object-manipulation.R | 8 huxtable-5.1.0/huxtable/tests/testthat/test-openxlsx.R | 7 huxtable-5.1.0/huxtable/tests/testthat/test-print.R | 8 huxtable-5.1.0/huxtable/tests/testthat/test-style.R | 8 huxtable-5.1.0/huxtable/tests/testthat/test-themes.R | 3 huxtable-5.1.0/huxtable/tests/testthat/test-yy-end-to-end.R | 46 + huxtable-5.1.0/huxtable/tests/testthat/themes.log |only huxtable-5.1.0/huxtable/vignettes/design-principles.Rmd | 4 huxtable-5.1.0/huxtable/vignettes/huxtable.Rmd | 2 87 files changed, 955 insertions(+), 556 deletions(-)
Title: Search and Retrieve Data from Eurostat Database
Description: Eurostat is the statistical office of the European Union and provides high quality statistics for Europe.
Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/data/database>).
The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX <https://sdmx.org>) Web Services
(<https://ec.europa.eu/eurostat/web/sdmx-web-services/about-this-service>) to search and download data from
the Eurostat database using the SDMX standard.
Author: Mátyás Mészáros [aut, cre]
Maintainer: Mátyás Mészáros <matyas.meszaros@ec.europa.eu>
Diff between restatapi versions 0.8.6 dated 2020-05-29 and 0.8.10 dated 2020-09-18
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/create_filter_table.R | 25 ++++++++++++++++--------- R/get_eurostat_data.R | 37 +++++++++++++++++++------------------ R/get_eurostat_raw.R | 8 ++++---- R/load_cfg.R | 2 +- README.md | 26 +++++++++++++++++--------- tests/testthat/test-all.R | 22 +++++++++++++++------- 8 files changed, 84 insertions(+), 60 deletions(-)
Title: Learning Causal or Non-Causal Graphical Models Using Information
Theory
Description: We report an information-theoretic method which learns a large
class of causal or non-causal graphical models from purely observational
data, while including the effects of unobserved latent variables, commonly
found in many datasets. Starting from a complete graph, the method
iteratively removes dispensable edges, by uncovering significant information
contributions from indirect paths, and assesses edge-specific confidences
from randomization of available data. The remaining edges are then oriented
based on the signature of causality in observational data. This approach can
be applied on a wide range of datasets and provide new biological insights
on regulatory networks from single cell expression data, genomic alterations
during tumor development and co-evolving residues in protein structures.
For more information you can refer to:
Cabeli et al. PLoS Comp. Bio. 2020 <doi:10.1371/journal.pcbi.1007866>,
Verny et al. PLoS Comp. Bio. 2017 <doi:10.1371/journal.pcbi.1005662>.
Author: Vincent Cabeli [aut, cre],
Honghao Li [aut],
Marcel Ribeiro Dantas [aut],
Nadir Sella [aut],
Louis Verny [aut],
Severine Affeldt [aut],
Hervé Isambert [aut]
Maintainer: Vincent Cabeli <vincent.cabeli@curie.fr>
Diff between miic versions 1.5.0 dated 2020-09-11 and 1.5.1 dated 2020-09-18
miic-1.5.0/miic/src/compute_ens_information.cpp |only miic-1.5.0/miic/src/compute_ens_information.h |only miic-1.5.0/miic/src/compute_info.cpp |only miic-1.5.0/miic/src/compute_info.h |only miic-1.5.0/miic/src/info_cnt.cpp |only miic-1.5.0/miic/src/info_cnt.h |only miic-1.5.0/miic/src/orientation_probability.cpp |only miic-1.5.0/miic/src/orientation_probability.h |only miic-1.5.0/miic/src/reconstruct.h |only miic-1.5.0/miic/src/skeleton_initialization.cpp |only miic-1.5.0/miic/src/skeleton_iteration.cpp |only miic-1.5.1/miic/DESCRIPTION | 6 miic-1.5.1/miic/MD5 | 71 - miic-1.5.1/miic/R/discretizeMDL.R | 4 miic-1.5.1/miic/R/miic.R | 38 miic-1.5.1/miic/R/miic.export.R | 26 miic-1.5.1/miic/R/miic.reconstruct.R | 14 miic-1.5.1/miic/R/parseResults.R | 13 miic-1.5.1/miic/man/miic.Rd | 38 miic-1.5.1/miic/man/miic.export.Rd | 3 miic-1.5.1/miic/src/biconnected_component.cpp |only miic-1.5.1/miic/src/biconnected_component.h |only miic-1.5.1/miic/src/computation_cache.cpp | 16 miic-1.5.1/miic/src/computation_cache.h | 164 +++ miic-1.5.1/miic/src/computation_continuous.cpp |only miic-1.5.1/miic/src/computation_continuous.h |only miic-1.5.1/miic/src/computation_discrete.cpp |only miic-1.5.1/miic/src/computation_discrete.h |only miic-1.5.1/miic/src/confidence_cut.cpp | 140 +-- miic-1.5.1/miic/src/cycle_tracker.cpp |only miic-1.5.1/miic/src/cycle_tracker.h |only miic-1.5.1/miic/src/environment.cpp | 53 - miic-1.5.1/miic/src/environment.h | 39 miic-1.5.1/miic/src/get_information.cpp |only miic-1.5.1/miic/src/get_information.h |only miic-1.5.1/miic/src/linear_allocator.cpp |only miic-1.5.1/miic/src/linear_allocator.h |only miic-1.5.1/miic/src/mdl_discretize.cpp | 19 miic-1.5.1/miic/src/mdl_pair_discretize.cpp | 136 +-- miic-1.5.1/miic/src/mutual_information.cpp | 702 ++++------------ miic-1.5.1/miic/src/mutual_information.h | 152 ++- miic-1.5.1/miic/src/orientation.cpp |only miic-1.5.1/miic/src/orientation.h |only miic-1.5.1/miic/src/proba_orientation.cpp | 5 miic-1.5.1/miic/src/reconstruct.cpp | 167 +-- miic-1.5.1/miic/src/skeleton.cpp |only miic-1.5.1/miic/src/skeleton.h |only miic-1.5.1/miic/src/structure.h | 232 +++-- miic-1.5.1/miic/src/utilities.cpp | 1009 +++++++++--------------- miic-1.5.1/miic/src/utilities.h | 112 +- 50 files changed, 1363 insertions(+), 1796 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autosuggest addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) request intermodal routes using the 'Intermodal Routing' API;
(6) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre] (<https://orcid.org/0000-0003-2020-2366>),
Daniel Possenriede [ctb] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.4.1 dated 2020-08-24 and 0.5.0 dated 2020-09-18
hereR-0.4.1/hereR/R/autocomplete.R |only hereR-0.4.1/hereR/man/autocomplete.Rd |only hereR-0.4.1/hereR/man/set_proxy.Rd |only hereR-0.4.1/hereR/tests/testthat/test-autocomplete.R |only hereR-0.5.0/hereR/DESCRIPTION | 15 hereR-0.5.0/hereR/MD5 | 98 +++-- hereR-0.5.0/hereR/NAMESPACE | 2 hereR-0.5.0/hereR/NEWS.md | 15 hereR-0.5.0/hereR/R/authentication.R | 42 -- hereR-0.5.0/hereR/R/autosuggest.R |only hereR-0.5.0/hereR/R/checks.R | 34 -- hereR-0.5.0/hereR/R/connection.R | 264 ++++++---------- hereR-0.5.0/hereR/R/defunct.R | 78 ++++ hereR-0.5.0/hereR/R/geocode.R | 155 +++++---- hereR-0.5.0/hereR/R/hereR-package.R | 1 hereR-0.5.0/hereR/R/intermodal_route.R | 1 hereR-0.5.0/hereR/R/isoline.R | 8 hereR-0.5.0/hereR/R/reverse_geocode.R | 166 +++++----- hereR-0.5.0/hereR/R/route.R | 1 hereR-0.5.0/hereR/R/station.R | 94 +++-- hereR-0.5.0/hereR/R/sysdata.rda |binary hereR-0.5.0/hereR/R/utils.R | 36 +- hereR-0.5.0/hereR/R/weather.R | 4 hereR-0.5.0/hereR/README.md | 18 - hereR-0.5.0/hereR/inst/doc/authentication.R | 6 hereR-0.5.0/hereR/inst/doc/authentication.Rmd | 25 - hereR-0.5.0/hereR/inst/doc/authentication.html | 18 - hereR-0.5.0/hereR/inst/doc/geocoder.R | 34 -- hereR-0.5.0/hereR/inst/doc/geocoder.Rmd | 48 +- hereR-0.5.0/hereR/inst/doc/geocoder.html | 78 ++-- hereR-0.5.0/hereR/inst/doc/intermodal.html | 28 - hereR-0.5.0/hereR/inst/doc/routing.html | 90 ++--- hereR-0.5.0/hereR/inst/doc/transit.Rmd | 6 hereR-0.5.0/hereR/inst/doc/transit.html | 215 +++++++++---- hereR-0.5.0/hereR/inst/doc/weather.html | 171 +++++----- hereR-0.5.0/hereR/man/autocomplete-defunct.Rd |only hereR-0.5.0/hereR/man/autosuggest.Rd |only hereR-0.5.0/hereR/man/connection.Rd | 7 hereR-0.5.0/hereR/man/geocode.Rd | 23 - hereR-0.5.0/hereR/man/hereR-defunct.Rd | 16 hereR-0.5.0/hereR/man/hereR-package.Rd | 4 hereR-0.5.0/hereR/man/reverse_geocode.Rd | 26 - hereR-0.5.0/hereR/man/set_proxy-defunct.Rd |only hereR-0.5.0/hereR/man/station.Rd | 6 hereR-0.5.0/hereR/man/unset_proxy-defunct.Rd |only hereR-0.5.0/hereR/man/unset_proxy.Rd | 15 hereR-0.5.0/hereR/tests/testthat/test-authentication.R | 16 hereR-0.5.0/hereR/tests/testthat/test-autosuggest.R |only hereR-0.5.0/hereR/tests/testthat/test-connection.R | 3 hereR-0.5.0/hereR/tests/testthat/test-defunct.R | 8 hereR-0.5.0/hereR/tests/testthat/test-geocode.R | 23 - hereR-0.5.0/hereR/tests/testthat/test-reverse_geocode.R | 24 - hereR-0.5.0/hereR/vignettes/authentication.Rmd | 25 - hereR-0.5.0/hereR/vignettes/geocoder.Rmd | 48 +- hereR-0.5.0/hereR/vignettes/transit.Rmd | 6 55 files changed, 1075 insertions(+), 926 deletions(-)
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 0.2-35 dated 2020-09-05 and 0.2-357 dated 2020-09-18
ChangeLog | 6 +++ DESCRIPTION | 8 ++-- MD5 | 75 ++++++++++++++++++++++++------------------ NAMESPACE | 18 +++++++--- R/commutation.R | 8 ++-- R/lu.R |only R/sherman_morrison.R | 5 +- R/symmetrizer.R |only R/utils.R | 2 - inst/CITATION | 4 +- inst/include/fastmatrix.h | 18 +++++++--- inst/include/fastmatrix_API.h | 74 ++++++++++++++++++++++++++++++++++++++--- man/array.mult.Rd | 10 ++--- man/bracket.prod.Rd | 8 ++-- man/comm.info.Rd | 4 +- man/comm.prod.Rd | 12 +++--- man/commutation.Rd | 6 +-- man/dupl.cross.Rd | 6 +-- man/dupl.info.Rd | 2 - man/dupl.prod.Rd | 12 +++--- man/duplication.Rd | 4 +- man/equilibrate.Rd | 2 - man/hadamard.prod.Rd | 2 - man/lu-methods.Rd |only man/lu.Rd |only man/lu2inv.Rd |only man/matrix.inner.Rd | 2 - man/matrix.norm.Rd | 4 +- man/minkowski.Rd | 8 ++-- man/power.method.Rd | 2 - man/sherman.morrison.Rd | 14 +++---- man/sweep.operator.Rd | 2 - man/symm.info.Rd |only man/symm.prod.Rd |only man/symmetrizer.Rd |only man/vec.Rd | 2 - man/vech.Rd | 2 - src/R_init_fastmatrix.c | 70 ++++++++++++++++++++++----------------- src/blas_3.c |only src/fastmatrix.h | 26 ++++++++++++-- src/lu.c |only src/pivot.f |only src/stats.c | 73 +++++++++++++++++++++++++++++++++++++++- src/symmetrizer.c |only src/symmetrizer_mat.f |only 45 files changed, 347 insertions(+), 144 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between devtools versions 2.3.1 dated 2020-07-21 and 2.3.2 dated 2020-09-18
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 22 +++++++++++----------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/lint.R | 2 +- R/usethis.R | 21 ++++++--------------- R/utils.R | 2 +- README.md | 32 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/dependencies.html | 4 ++-- man/check.Rd | 13 +++++-------- man/lint.Rd | 2 +- 12 files changed, 61 insertions(+), 70 deletions(-)
Title: Bayesian Inference of Vector Autoregressive Models
Description: Assists in the set-up of algorithms for Bayesian inference of vector autoregressive (VAR) models. Functions for posterior simulation, forecasting, impulse response analysis and forecast error variance decomposition are largely based on the introductory texts of Chan, Koop, Poirier and Tobias (2019, ISBN: 9781108437493), Koop and Korobilis (2010) <doi:10.1561/0800000013> and Luetkepohl (2006, ISBN: 9783540262398).
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <bvartools@outlook.com>
Diff between bvartools versions 0.0.3 dated 2020-07-23 and 0.1.0 dated 2020-09-18
bvartools-0.0.3/bvartools/R/thin.R |only bvartools-0.0.3/bvartools/man/thin.Rd |only bvartools-0.1.0/bvartools/DESCRIPTION | 23 bvartools-0.1.0/bvartools/MD5 | 163 +-- bvartools-0.1.0/bvartools/NAMESPACE | 11 bvartools-0.1.0/bvartools/NEWS.md | 14 bvartools-0.1.0/bvartools/R/RcppExports.R | 156 +-- bvartools-0.1.0/bvartools/R/add_priors.R |only bvartools-0.1.0/bvartools/R/bvar.R | 181 ++- bvartools-0.1.0/bvartools/R/bvarpost.R |only bvartools-0.1.0/bvartools/R/bvartools.R | 14 bvartools-0.1.0/bvartools/R/bvec.R | 330 +++++- bvartools-0.1.0/bvartools/R/bvec_to_bvar.R | 306 +++--- bvartools-0.1.0/bvartools/R/bvecpost.R |only bvartools-0.1.0/bvartools/R/data.R | 4 bvartools-0.1.0/bvartools/R/draw_posterior.R |only bvartools-0.1.0/bvartools/R/fevd.R | 175 +-- bvartools-0.1.0/bvartools/R/gen_var.R | 209 +++- bvartools-0.1.0/bvartools/R/gen_vec.R | 259 +++-- bvartools-0.1.0/bvartools/R/inclusion_prior.R | 69 - bvartools-0.1.0/bvartools/R/irf.R | 139 +- bvartools-0.1.0/bvartools/R/minnesota_prior.R | 88 + bvartools-0.1.0/bvartools/R/plot.bvarfevd.R | 74 - bvartools-0.1.0/bvartools/R/plot.bvarirf.R | 71 - bvartools-0.1.0/bvartools/R/plot.bvarprd.R | 75 - bvartools-0.1.0/bvartools/R/predict.bvar.R | 177 +-- bvartools-0.1.0/bvartools/R/print.summary.bvar.R | 35 bvartools-0.1.0/bvartools/R/print.summary.bvec.R | 31 bvartools-0.1.0/bvartools/R/ssvs_prior.R | 32 bvartools-0.1.0/bvartools/R/summary.bvar.R | 160 ++- bvartools-0.1.0/bvartools/R/summary.bvarlist.R |only bvartools-0.1.0/bvartools/R/summary.bvec.R | 206 ++-- bvartools-0.1.0/bvartools/R/thin_posterior.R |only bvartools-0.1.0/bvartools/R/thin_posterior.bvar.R |only bvartools-0.1.0/bvartools/R/thin_posterior.bvarlist.R |only bvartools-0.1.0/bvartools/R/thin_posterior.bvec.R |only bvartools-0.1.0/bvartools/build/vignette.rds |binary bvartools-0.1.0/bvartools/inst/doc/bvartools.R | 162 +-- bvartools-0.1.0/bvartools/inst/doc/bvartools.Rmd | 288 +++-- bvartools-0.1.0/bvartools/inst/doc/bvartools.html | 480 ++++++--- bvartools-0.1.0/bvartools/inst/doc/bvec.R | 110 +- bvartools-0.1.0/bvartools/inst/doc/bvec.Rmd | 159 +-- bvartools-0.1.0/bvartools/inst/doc/bvec.html | 533 ++++++---- bvartools-0.1.0/bvartools/inst/doc/model-comparison.R |only bvartools-0.1.0/bvartools/inst/doc/model-comparison.Rmd |only bvartools-0.1.0/bvartools/inst/doc/model-comparison.html |only bvartools-0.1.0/bvartools/inst/doc/ssvs.R | 85 - bvartools-0.1.0/bvartools/inst/doc/ssvs.Rmd | 132 +- bvartools-0.1.0/bvartools/inst/doc/ssvs.html | 756 +++++++-------- bvartools-0.1.0/bvartools/man/add_priors.Rd |only bvartools-0.1.0/bvartools/man/bvar.Rd | 196 +-- bvartools-0.1.0/bvartools/man/bvarpost.Rd |only bvartools-0.1.0/bvartools/man/bvartools.Rd | 11 bvartools-0.1.0/bvartools/man/bvec.Rd | 161 ++- bvartools-0.1.0/bvartools/man/bvec_to_bvar.Rd | 52 - bvartools-0.1.0/bvartools/man/bvecpost.Rd |only bvartools-0.1.0/bvartools/man/bvs.Rd | 20 bvartools-0.1.0/bvartools/man/draw_posterior.Rd |only bvartools-0.1.0/bvartools/man/e1.Rd | 2 bvartools-0.1.0/bvartools/man/e6.Rd | 2 bvartools-0.1.0/bvartools/man/fevd.Rd | 148 -- bvartools-0.1.0/bvartools/man/gen_var.Rd | 62 - bvartools-0.1.0/bvartools/man/gen_vec.Rd | 54 - bvartools-0.1.0/bvartools/man/inclusion_prior.Rd | 3 bvartools-0.1.0/bvartools/man/irf.Rd | 155 --- bvartools-0.1.0/bvartools/man/kalman_dk.Rd | 24 bvartools-0.1.0/bvartools/man/loglik_normal.Rd | 6 bvartools-0.1.0/bvartools/man/minnesota_prior.Rd | 6 bvartools-0.1.0/bvartools/man/plot.bvarprd.Rd | 71 - bvartools-0.1.0/bvartools/man/post_coint_kls.Rd | 17 bvartools-0.1.0/bvartools/man/post_coint_kls_sur.Rd | 21 bvartools-0.1.0/bvartools/man/post_normal.Rd | 15 bvartools-0.1.0/bvartools/man/post_normal_sur.Rd | 16 bvartools-0.1.0/bvartools/man/ssvs.Rd | 27 bvartools-0.1.0/bvartools/man/summary.bvarlist.Rd |only bvartools-0.1.0/bvartools/man/thin_posterior.Rd |only bvartools-0.1.0/bvartools/man/thin_posterior.bvar.Rd |only bvartools-0.1.0/bvartools/man/thin_posterior.bvarlist.Rd |only bvartools-0.1.0/bvartools/man/thin_posterior.bvec.Rd |only bvartools-0.1.0/bvartools/src/RcppExports.cpp | 39 bvartools-0.1.0/bvartools/src/bvaralg.cpp |only bvartools-0.1.0/bvartools/src/bvecalg.cpp |only bvartools-0.1.0/bvartools/src/bvs.cpp | 22 bvartools-0.1.0/bvartools/src/ir.cpp | 45 bvartools-0.1.0/bvartools/src/kalman_dk.cpp | 24 bvartools-0.1.0/bvartools/src/loglik_normal.cpp | 6 bvartools-0.1.0/bvartools/src/post_coint_kls.cpp | 17 bvartools-0.1.0/bvartools/src/post_coint_kls_sur.cpp | 21 bvartools-0.1.0/bvartools/src/post_normal.cpp | 24 bvartools-0.1.0/bvartools/src/post_normal_sur.cpp | 16 bvartools-0.1.0/bvartools/src/svss.cpp | 27 bvartools-0.1.0/bvartools/src/vardecomp.cpp |only bvartools-0.1.0/bvartools/vignettes/bvartools.Rmd | 288 +++-- bvartools-0.1.0/bvartools/vignettes/bvec.Rmd | 159 +-- bvartools-0.1.0/bvartools/vignettes/model-comparison.Rmd |only bvartools-0.1.0/bvartools/vignettes/ssvs.Rmd | 132 +- 96 files changed, 4264 insertions(+), 3332 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, and ANOVA. Some packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.1.4 dated 2020-06-04 and 0.2.0 dated 2020-09-18
sasLM-0.1.4/sasLM/inst/doc/Validation-Report-GLM-2006042258.pdf |only sasLM-0.2.0/sasLM/DESCRIPTION | 6 sasLM-0.2.0/sasLM/MD5 | 22 +- sasLM-0.2.0/sasLM/R/SS.R | 2 sasLM-0.2.0/sasLM/R/T3MS.R |only sasLM-0.2.0/sasLM/R/T3test.R |only sasLM-0.2.0/sasLM/R/e3.R | 75 +++++++--- sasLM-0.2.0/sasLM/R/satt.R |only sasLM-0.2.0/sasLM/inst/NEWS.Rd | 11 + sasLM-0.2.0/sasLM/inst/doc/Validation-Report-GLM-2009181133.pdf |only sasLM-0.2.0/sasLM/inst/doc/sasLM-manual.pdf |binary sasLM-0.2.0/sasLM/man/T3MS.Rd |only sasLM-0.2.0/sasLM/man/T3test.Rd |only sasLM-0.2.0/sasLM/man/lfit.Rd | 3 sasLM-0.2.0/sasLM/man/satt.Rd |only sasLM-0.2.0/sasLM/tests/Test.R | 18 +- 16 files changed, 97 insertions(+), 40 deletions(-)
Title: Functions for University of Auckland Course STATS 201/208 Data
Analysis
Description: A set of functions used in teaching STATS 201/208 Data Analysis at
the University of Auckland. The functions are designed to make parts of R more
accessible to a large undergraduate population who are mostly not statistics
majors.
Author: Andrew Balemi, Dineika Chandra, James Curran, Brant Deppa, Mike Forster,
Brendan McArdle, Ben Stevenson, Chris Wild
Maintainer: James Curran <j.curran@auckland.ac.nz>
Diff between s20x versions 3.1-28 dated 2019-05-23 and 3.1-29 dated 2020-09-18
DESCRIPTION | 10 +-- MD5 | 120 +++++++++++++++++++++++------------------------ NAMESPACE | 1 R/estimateContrasts.R | 10 ++- R/estimateContrasts1.R | 4 - R/estimateContrasts2.R | 4 - R/multipleComp.R | 13 ++++- R/predictGLM.R |only R/summary2way.R | 65 ++++++++++++++++++------- man/airpass.df.Rd | 4 + man/apples.df.Rd | 6 +- man/arousal.df.Rd | 6 +- man/beer.df.Rd | 4 + man/body.df.Rd | 6 +- man/books.df.Rd | 6 +- man/bursary.df.Rd | 6 +- man/butterfat.df.Rd | 6 +- man/camplake.df.Rd | 6 +- man/chalk.df.Rd | 6 +- man/computer.df.Rd | 6 +- man/cooks20x.Rd | 13 +++-- man/course.df.Rd | 6 +- man/course2way.df.Rd | 6 +- man/diamonds.df.Rd | 6 +- man/eovcheck.Rd | 17 ++++-- man/estimateContrasts.Rd | 13 ++++- man/fire.df.Rd | 6 +- man/freq1way.Rd | 11 +++- man/fruitfly.df.Rd | 6 +- man/house.df.Rd | 6 +- man/interactionPlots.Rd | 53 ++++++++++++++++---- man/lakemary.df.Rd | 6 +- man/larain.df.Rd | 4 + man/mazda.df.Rd | 6 +- man/mening.df.Rd | 6 +- man/modcheck.Rd | 24 +++++---- man/mozart.df.Rd | 6 +- man/multipleComp.Rd | 10 +++ man/nail.df.Rd | 6 +- man/normcheck.Rd | 40 +++++++++++---- man/onewayPlot.Rd | 32 +++++++++--- man/oysters.df.Rd | 6 +- man/peru.df.Rd | 6 +- man/predict20x.Rd | 3 - man/predictCount.Rd | 3 - man/predictGLM.Rd |only man/rain.df.Rd | 6 +- man/rowdistr.Rd | 9 ++- man/s0x.Rd | 1 man/seeds.df.Rd | 6 +- man/sheep.df.Rd | 6 +- man/skulls.df.Rd | 6 +- man/soyabean.df.Rd | 6 +- man/summary1way.Rd | 12 +++- man/summary2way.Rd | 22 +++++++- man/summaryStats.Rd | 12 +++- man/teach.df.Rd | 6 +- man/technitron.df.Rd | 6 +- man/thyroid.df.Rd | 6 +- man/toothpaste.df.Rd | 6 +- man/trendscatter.Rd | 14 +++-- man/zoo.df.Rd | 6 +- 62 files changed, 489 insertions(+), 231 deletions(-)
Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable
way to store tables from databases. This package provides convenient
functions for exporting tables from relational database connections
into compressed text files and streaming those text files back into
a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Richard FitzJohn [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between arkdb versions 0.0.5 dated 2018-10-31 and 0.0.6 dated 2020-09-18
DESCRIPTION | 14 - MD5 | 62 ++++-- NAMESPACE | 10 - NEWS.md | 16 + R/ark.R | 4 R/assert.R | 12 - R/bulk_importers.R |only R/local_db.R |only R/process_chunks.R |only R/streamable_table.R | 39 +++- R/unark.R | 102 +++------- R/utils.R |only README.md | 72 +++---- build/vignette.rds |binary inst/WORDLIST | 27 +- inst/doc/arkdb.R | 38 ++-- inst/doc/arkdb.Rmd | 12 - inst/doc/arkdb.html | 354 +++++++++++++++++++++----------------- inst/examples/monetdblite.R |only inst/extdata |only man/ark.Rd | 14 + man/arkdb-package.Rd | 2 man/figures |only man/local_db.Rd |only man/local_db_disconnect.Rd |only man/process_chunks.Rd |only man/streamable_readr_csv.Rd | 2 man/streamable_readr_tsv.Rd | 2 man/streamable_vroom.Rd |only man/unark.Rd | 21 +- tests/testthat.R | 1 tests/testthat/setup-test_db.R |only tests/testthat/teardown-test_db.R |only tests/testthat/test-arkdb.R | 37 +-- tests/testthat/test-bulk-import.R |only tests/testthat/test-errors.R | 20 +- tests/testthat/test-local_db.R |only tests/testthat/test-streamable.R | 11 - vignettes/arkdb.Rmd | 12 - 39 files changed, 489 insertions(+), 395 deletions(-)