Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-23 0.1.17
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-10 0.2.11
2020-07-27 0.2.10
2020-03-26 0.2.9
2020-03-22 0.2.8
2019-01-31 0.2.7
2018-02-28 0.2.6
2018-01-03 0.2.5
2017-11-20 0.2.4
2017-08-01 0.2.2
2017-06-08 0.2.1
2017-04-28 0.2.0
2017-04-11 0.1.4
2016-09-14 0.1.3
2016-07-07 0.1.1
2016-07-05 0.1.0
Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data,
with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French [aut, cre] (<https://orcid.org/0000-0002-9708-3353>),
Mohammad Meysami [ctb] (<https://orcid.org/0000-0002-3322-5244>)
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 1.4 dated 2021-02-06 and 1.4.2 dated 2021-02-12
smerc-1.4.2/smerc/DESCRIPTION | 6 +- smerc-1.4.2/smerc/MD5 | 11 ++- smerc-1.4.2/smerc/R/optimal_ubpop.R | 9 --- smerc-1.4.2/smerc/inst/doc/smerc_demo.html | 10 +-- smerc-1.4.2/smerc/inst/randomTests |only smerc-1.4.2/smerc/tests/testthat/test-optimal_ubpop.R | 54 ++++-------------- smerc-1.4/smerc/tests/testthat/test-seq_scan_test.R |only 7 files changed, 28 insertions(+), 62 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.2-1 dated 2021-02-05 and 1.2-2 dated 2021-02-12
DESCRIPTION | 8 ++-- MD5 | 12 +++--- R/sample.R | 4 +- build/partial.rdb |binary inst/NEWS.Rd | 10 +++++ tests/dpq-Ex.R | 2 - tests/dpq-Ex.Rout.save | 88 +++++++++++++++++++++++-------------------------- 7 files changed, 65 insertions(+), 59 deletions(-)
Title: Designs of Computer Experiments
Description: Space-Filling Designs and space-filling criteria (distance-based and uniformity-based), with emphasis to computer experiments; <doi:10.18637/jss.v065.i11>.
Author: Jessica Franco, Delphine Dupuy, Olivier Roustant,
Patrice Kiener, Guillaume Damblin and Bertrand Iooss.
Maintainer: Celine Helbert <Celine.Helbert@ec-lyon.fr>
Diff between DiceDesign versions 1.8-1 dated 2019-07-31 and 1.9 dated 2021-02-12
DESCRIPTION | 12 +- MD5 | 58 +++++++------- NAMESPACE | 46 ++++++++--- NEWS | 18 +--- R/discrepancyCriteria.R | 29 +++++-- R/faureprimeDesign.R |only R/fcts_optimalLHSDesigns.R | 30 ++++--- R/scaleDesign.R | 30 +++---- R/unscaleDesign.R | 20 ++-- R/wspDesign.R | 116 ++++++++++++++-------------- inst/CITATION | 4 man/DiceDesign-package.Rd | 14 ++- man/NOLHDRdesigns.Rd | 118 ++++++++++++++-------------- man/NOLHdesigns.Rd | 110 +++++++++++++------------- man/OA131.Rd | 74 +++++++++--------- man/OA131_scrambled.Rd | 64 +++++++-------- man/coverage.Rd | 78 +++++++++---------- man/discrepESE_LHS.Rd | 141 +++++++++++++++++----------------- man/discrepSA_LHS.Rd | 149 ++++++++++++++++++------------------ man/discrepancyCriteria.Rd | 140 +++++++++++++++++----------------- man/faureprimeDesign.Rd |only man/maximinESE_LHS.Rd | 141 +++++++++++++++++----------------- man/maximinSA_LHS.Rd | 151 ++++++++++++++++++------------------ man/mstCriteria.Rd | 96 +++++++++++------------ man/phiP.Rd | 2 man/rss2d.Rd | 154 ++++++++++++++++++------------------- man/rss3d.Rd | 184 ++++++++++++++++++++++----------------------- man/scaleDesign.Rd | 80 +++++++++---------- man/straussDesign.Rd | 176 +++++++++++++++++++++---------------------- man/unscaleDesign.Rd | 86 ++++++++++----------- man/wspDesign.Rd | 112 +++++++++++++-------------- 31 files changed, 1239 insertions(+), 1194 deletions(-)
Title: Estimate Univariate Gaussian or Student's t Mixture
Autoregressive Model
Description: Maximum likelihood estimation of univariate Gaussian Mixture Autoregressive (GMAR),
Student's t Mixture Autoregressive (StMAR), and Gaussian and Student's t Mixture Autoregressive (G-StMAR) models,
quantile residual tests, graphical diagnostics, forecast and simulate from GMAR, StMAR and G-StMAR processes.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2015) <doi:10.1111/jtsa.12108>,
Mika Meitz, Daniel Preve, Pentti Saikkonen (2018) <arXiv:1805.04010>,
Savi Virolainen (2020) <arXiv:2003.05221>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between uGMAR versions 3.2.6 dated 2020-12-17 and 3.3.0 dated 2021-02-12
uGMAR-3.2.6/uGMAR/man/changeRegime.Rd |only uGMAR-3.2.6/uGMAR/man/checkAndCorrectData.Rd |only uGMAR-3.2.6/uGMAR/man/checkConstraintMat.Rd |only uGMAR-3.2.6/uGMAR/man/checkPM.Rd |only uGMAR-3.2.6/uGMAR/man/extractRegime.Rd |only uGMAR-3.2.6/uGMAR/man/getOmega.Rd |only uGMAR-3.2.6/uGMAR/man/isStationary_int.Rd |only uGMAR-3.2.6/uGMAR/man/mixingWeights_int.Rd |only uGMAR-3.2.6/uGMAR/man/nParams.Rd |only uGMAR-3.2.6/uGMAR/man/parameterChecks.Rd |only uGMAR-3.2.6/uGMAR/man/quantileResiduals_int.Rd |only uGMAR-3.2.6/uGMAR/man/randomIndividual_int.Rd |only uGMAR-3.2.6/uGMAR/man/reformConstrainedPars.Rd |only uGMAR-3.2.6/uGMAR/man/reformParameters.Rd |only uGMAR-3.2.6/uGMAR/man/reformRestrictedPars.Rd |only uGMAR-3.2.6/uGMAR/man/removeAllConstraints.Rd |only uGMAR-3.2.6/uGMAR/man/sortComponents.Rd |only uGMAR-3.2.6/uGMAR/man/standardErrors.Rd |only uGMAR-3.2.6/uGMAR/man/uncondMoments.Rd |only uGMAR-3.2.6/uGMAR/man/uncondMoments_int.Rd |only uGMAR-3.3.0/uGMAR/DESCRIPTION | 10 uGMAR-3.3.0/uGMAR/MD5 | 228 +++--- uGMAR-3.3.0/uGMAR/NAMESPACE | 12 uGMAR-3.3.0/uGMAR/NEWS.md | 22 uGMAR-3.3.0/uGMAR/R/GSMARconstructor.R | 120 +-- uGMAR-3.3.0/uGMAR/R/MAINest.R | 155 ++-- uGMAR-3.3.0/uGMAR/R/WaldAndLR.R | 14 uGMAR-3.3.0/uGMAR/R/argumentChecks.R | 99 +- uGMAR-3.3.0/uGMAR/R/data.R | 12 uGMAR-3.3.0/uGMAR/R/deprecatedFunctions.R |only uGMAR-3.3.0/uGMAR/R/diagnosticPlot.R | 133 +-- uGMAR-3.3.0/uGMAR/R/geneticAlgorithm.R | 363 ++++------ uGMAR-3.3.0/uGMAR/R/getOmega.R | 14 uGMAR-3.3.0/uGMAR/R/loglikelihood.R | 148 +--- uGMAR-3.3.0/uGMAR/R/misc3methods.R | 1 uGMAR-3.3.0/uGMAR/R/morePlots.R | 41 - uGMAR-3.3.0/uGMAR/R/numericalDifferentiation.R | 34 uGMAR-3.3.0/uGMAR/R/parameterReforms.R | 51 - uGMAR-3.3.0/uGMAR/R/pickAndChangeParams.R | 84 +- uGMAR-3.3.0/uGMAR/R/plotMethods.R | 21 uGMAR-3.3.0/uGMAR/R/predictMethod.R | 79 +- uGMAR-3.3.0/uGMAR/R/printMethods.R | 31 uGMAR-3.3.0/uGMAR/R/quantileResidualTests.R | 85 +- uGMAR-3.3.0/uGMAR/R/quantileResiduals.R | 43 - uGMAR-3.3.0/uGMAR/R/simulateGSMAR.R | 86 +- uGMAR-3.3.0/uGMAR/R/standardErrors.R | 4 uGMAR-3.3.0/uGMAR/R/uGMAR.R | 25 uGMAR-3.3.0/uGMAR/R/uncondMoments.R | 27 uGMAR-3.3.0/uGMAR/README.md | 29 uGMAR-3.3.0/uGMAR/data/M10Y1Y.rda |only uGMAR-3.3.0/uGMAR/inst/doc/intro-to-uGMAR.Rmd | 2 uGMAR-3.3.0/uGMAR/inst/doc/intro-to-uGMAR.html | 16 uGMAR-3.3.0/uGMAR/man/GAfit.Rd | 21 uGMAR-3.3.0/uGMAR/man/GSMAR.Rd | 36 uGMAR-3.3.0/uGMAR/man/LR_test.Rd | 8 uGMAR-3.3.0/uGMAR/man/M10Y1Y.Rd |only uGMAR-3.3.0/uGMAR/man/Wald_test.Rd | 4 uGMAR-3.3.0/uGMAR/man/add_data.Rd | 14 uGMAR-3.3.0/uGMAR/man/alt_gsmar.Rd | 17 uGMAR-3.3.0/uGMAR/man/calc_gradient.Rd | 34 uGMAR-3.3.0/uGMAR/man/change_parametrization.Rd | 2 uGMAR-3.3.0/uGMAR/man/change_regime.Rd |only uGMAR-3.3.0/uGMAR/man/check_and_correct_data.Rd |only uGMAR-3.3.0/uGMAR/man/check_constraint_mat.Rd |only uGMAR-3.3.0/uGMAR/man/check_pM.Rd |only uGMAR-3.3.0/uGMAR/man/check_params_length.Rd | 2 uGMAR-3.3.0/uGMAR/man/condMoments.Rd | 39 - uGMAR-3.3.0/uGMAR/man/cond_moment_plot.Rd |only uGMAR-3.3.0/uGMAR/man/cond_moments.Rd |only uGMAR-3.3.0/uGMAR/man/condmomentPlot.Rd | 30 uGMAR-3.3.0/uGMAR/man/diagnosticPlot.Rd | 50 - uGMAR-3.3.0/uGMAR/man/diagnostic_plot.Rd |only uGMAR-3.3.0/uGMAR/man/extract_regime.Rd |only uGMAR-3.3.0/uGMAR/man/fitGSMAR.Rd | 107 +- uGMAR-3.3.0/uGMAR/man/get_ar_roots.Rd | 2 uGMAR-3.3.0/uGMAR/man/get_regime_autocovs.Rd | 4 uGMAR-3.3.0/uGMAR/man/get_regime_means.Rd | 6 uGMAR-3.3.0/uGMAR/man/get_regime_vars.Rd | 4 uGMAR-3.3.0/uGMAR/man/get_test_Omega.Rd |only uGMAR-3.3.0/uGMAR/man/get_varying_h.Rd | 2 uGMAR-3.3.0/uGMAR/man/isStationary.Rd | 45 - uGMAR-3.3.0/uGMAR/man/is_stationary.Rd |only uGMAR-3.3.0/uGMAR/man/is_stationary_int.Rd |only uGMAR-3.3.0/uGMAR/man/iterate_more.Rd | 11 uGMAR-3.3.0/uGMAR/man/loglikelihood.Rd | 37 - uGMAR-3.3.0/uGMAR/man/loglikelihood_int.Rd | 2 uGMAR-3.3.0/uGMAR/man/mixingWeights.Rd | 30 uGMAR-3.3.0/uGMAR/man/mixing_weights.Rd |only uGMAR-3.3.0/uGMAR/man/mixing_weights_int.Rd |only uGMAR-3.3.0/uGMAR/man/n_params.Rd |only uGMAR-3.3.0/uGMAR/man/parameter_checks.Rd |only uGMAR-3.3.0/uGMAR/man/pick_alphas.Rd | 2 uGMAR-3.3.0/uGMAR/man/pick_dfs.Rd | 2 uGMAR-3.3.0/uGMAR/man/pick_pars.Rd | 2 uGMAR-3.3.0/uGMAR/man/pick_phi0.Rd | 2 uGMAR-3.3.0/uGMAR/man/plot.gsmarpred.Rd | 9 uGMAR-3.3.0/uGMAR/man/predict.gsmar.Rd | 71 + uGMAR-3.3.0/uGMAR/man/print.gsmarpred.Rd | 10 uGMAR-3.3.0/uGMAR/man/print.gsmarsum.Rd | 9 uGMAR-3.3.0/uGMAR/man/profile_logliks.Rd | 27 uGMAR-3.3.0/uGMAR/man/quantileResidualPlot.Rd | 36 uGMAR-3.3.0/uGMAR/man/quantileResidualTests.Rd | 86 -- uGMAR-3.3.0/uGMAR/man/quantileResiduals.Rd | 29 uGMAR-3.3.0/uGMAR/man/quantile_residual_plot.Rd |only uGMAR-3.3.0/uGMAR/man/quantile_residual_tests.Rd |only uGMAR-3.3.0/uGMAR/man/quantile_residuals.Rd |only uGMAR-3.3.0/uGMAR/man/quantile_residuals_int.Rd |only uGMAR-3.3.0/uGMAR/man/randomIndividual.Rd | 120 --- uGMAR-3.3.0/uGMAR/man/random_ind.Rd |only uGMAR-3.3.0/uGMAR/man/random_ind_int.Rd |only uGMAR-3.3.0/uGMAR/man/random_regime.Rd | 8 uGMAR-3.3.0/uGMAR/man/reform_constrained_pars.Rd |only uGMAR-3.3.0/uGMAR/man/reform_parameters.Rd |only uGMAR-3.3.0/uGMAR/man/reform_restricted_pars.Rd |only uGMAR-3.3.0/uGMAR/man/remove_all_constraints.Rd |only uGMAR-3.3.0/uGMAR/man/simulateGSMAR.Rd | 72 - uGMAR-3.3.0/uGMAR/man/sort_components.Rd |only uGMAR-3.3.0/uGMAR/man/standard_errors.Rd |only uGMAR-3.3.0/uGMAR/man/stmar_to_gstmar.Rd | 12 uGMAR-3.3.0/uGMAR/man/stmarpars_to_gstmar.Rd | 10 uGMAR-3.3.0/uGMAR/man/swap_parametrization.Rd | 15 uGMAR-3.3.0/uGMAR/man/uGMAR.Rd | 9 uGMAR-3.3.0/uGMAR/man/uncond_moments.Rd |only uGMAR-3.3.0/uGMAR/man/uncond_moments_int.Rd |only uGMAR-3.3.0/uGMAR/man/warn_dfs.Rd | 20 uGMAR-3.3.0/uGMAR/tests/testthat/test_GAfunctions.R | 227 +++--- uGMAR-3.3.0/uGMAR/tests/testthat/test_MAINest.R | 2 uGMAR-3.3.0/uGMAR/tests/testthat/test_argumentChecks.R | 106 +- uGMAR-3.3.0/uGMAR/tests/testthat/test_checkStatIdent.R | 74 +- uGMAR-3.3.0/uGMAR/tests/testthat/test_getOmega.R | 78 +- uGMAR-3.3.0/uGMAR/tests/testthat/test_gsmarConstructor.R | 2 uGMAR-3.3.0/uGMAR/tests/testthat/test_loglikelihood.R | 250 +++--- uGMAR-3.3.0/uGMAR/tests/testthat/test_parameterReforms.R | 122 +-- uGMAR-3.3.0/uGMAR/tests/testthat/test_pickAndChangeParams.R | 134 ++- uGMAR-3.3.0/uGMAR/tests/testthat/test_predictMethod.R | 22 uGMAR-3.3.0/uGMAR/tests/testthat/test_quantileResidualTests.R | 18 uGMAR-3.3.0/uGMAR/tests/testthat/test_quantileResiduals.R | 60 - uGMAR-3.3.0/uGMAR/tests/testthat/test_simulateGSMAR.R | 144 +-- uGMAR-3.3.0/uGMAR/tests/testthat/test_standardErrors.R | 8 uGMAR-3.3.0/uGMAR/tests/testthat/test_uncondMoments.R | 18 uGMAR-3.3.0/uGMAR/vignettes/intro-to-uGMAR.Rmd | 2 141 files changed, 2016 insertions(+), 2298 deletions(-)
Title: Split Generalized Linear Models
Description: Functions to compute split generalized linear models. The approach fits
generalized linear models that split the covariates into groups. The
optimal split of the variables into groups and the regularized estimation
of the coefficients are performed by minimizing an objective function
that encourages sparsity within each group and diversity among them.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>,
Stefan Van Aelst <stefan.vanaelst@kuleuven.be>,
Ruben Zamar <ruben@stat.ubc.ca>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Diff between SplitGLM versions 1.0.0 dated 2021-02-09 and 1.0.1 dated 2021-02-12
DESCRIPTION | 12 +++++------ MD5 | 6 ++--- NEWS | 3 ++ tests/testthat/test_cv_function.R | 40 +++++++++++++++++++------------------- 4 files changed, 33 insertions(+), 28 deletions(-)
Title: 'Rcpp' Bindings for the 'simdjson' Header-Only Library for
'JSON' Parsing
Description: The 'JSON' format is ubiquitous for data interchange, and the
'simdjson' library written by Daniel Lemire (and many contributors) provides
a high-performance parser for these files which by relying on parallel 'SIMD'
instruction manages to parse these files as faster than disk speed. See the
<arXiv:1902.08318> paper for more details about 'simdjson'. This package
parses 'JSON' from string, file, or remote URLs under a variety of settings.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSimdJson versions 0.1.3 dated 2020-11-02 and 0.1.4 dated 2021-02-12
ChangeLog | 52 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 14 ++++----- MD5 | 24 +++++++-------- R/fload.R | 20 +++++++++++-- R/fparse.R | 21 ++++++++++++- R/utils.R | 12 ++++--- README.md | 10 +----- build/partial.rdb |binary inst/NEWS.Rd | 16 ++++++++-- inst/tinytest/test_compressed_files.R | 5 +-- inst/tinytest/test_issues.R | 46 +++++++++++++++++++++++++++--- man/fparse.Rd | 17 +++++++++-- man/simdjson-utilities.Rd | 4 +- 13 files changed, 192 insertions(+), 49 deletions(-)
Title: Analysis of Basketball Data
Description: Collection of tools to work with basketball data. Functions available are related to friendly
web scraping and visualization. Data were obtained from <https://www.euroleague.net/>,
<https://www.eurocupbasketball.com/> and <http://www.acb.com>, following the instructions
of their respectives robots.txt files, when available. Tools for visualization include a population pyramid, 2D plots,
circular plots of players' percentiles, plots of players' monthly/yearly stats,
team heatmaps, team shooting plots, team four factors plots, cross-tables with the results of regular season games
and maps of nationalities. Please see Vinue (2020) <doi:10.1089/big.2018.0124>.
Author: Guillermo Vinue
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between BAwiR versions 1.2.4 dated 2020-05-11 and 1.2.5 dated 2021-02-12
DESCRIPTION | 14 +++++------ MD5 | 48 ++++++++++++++++++++--------------------- NEWS | 5 ++++ R/do_add_adv_stats.R | 2 - R/do_four_factors_df.R | 2 - R/get_bubble_plot.R | 5 ++-- R/get_four_factors_plot.R | 7 ++++- R/get_heatmap_bb.R | 5 ++-- R/get_similar_players.R | 11 ++++++--- R/get_similar_teams.R | 10 +++++--- R/scraping_games_acb.R | 2 - R/scraping_games_euro.R | 6 ++--- R/scraping_rosters_euro.R | 2 - inst/doc/BAwiR.html | 4 +-- man/do_add_adv_stats.Rd | 2 - man/do_four_factors_df.Rd | 2 - man/eurocup_games_1718.Rd | 2 - man/eurocup_players_1718.Rd | 2 - man/euroleague_games_1718.Rd | 2 - man/euroleague_players_1718.Rd | 2 - man/get_bubble_plot.Rd | 2 - man/get_heatmap_bb.Rd | 2 - man/scraping_games_acb.Rd | 2 - man/scraping_games_euro.Rd | 6 ++--- man/scraping_rosters_euro.Rd | 2 - 25 files changed, 84 insertions(+), 65 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-11 0.1.1
Title: Linkage Disequilibrium Shrinkage Estimation for Polyploids
Description: Estimate haplotypic or composite pairwise linkage disequilibrium
(LD) in polyploids, using either genotypes or genotype likelihoods.
Support is provided to estimate the popular measures of LD: the LD
coefficient D, the standardized LD coefficient D', and the Pearson
correlation coefficient r. All estimates are returned with corresponding
standard errors. These estimates and standard errors can then be used
for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(),
sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods
are available in Gerard (2021a) <doi:10.1111/1755-0998.13349>
and Gerard (2021b) <doi:10.1101/2021.02.08.430270>.
Author: David Gerard [aut, cre] (<https://orcid.org/0000-0001-9450-5023>)
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between ldsep versions 1.1.0 dated 2020-11-14 and 2.0.1 dated 2021-02-12
DESCRIPTION | 14 MD5 | 75 + NAMESPACE | 4 NEWS.md | 12 R/RcppExports.R | 61 + R/data.R | 79 +- R/fast.R |only R/generics.R | 400 +++++----- R/ldgeno.R | 1394 ++++++++++++++++++------------------ R/ldsep-package.R | 4 R/multild.R | 883 +++++++++++----------- R/sliding_window.R | 2 README.md | 93 +- build/partial.rdb |only build/vignette.rds |binary data/glike.rda |only data/gp.rda |only inst/CITATION | 51 - inst/doc/fast.R |only inst/doc/fast.Rmd |only inst/doc/fast.html |only inst/doc/vcf.Rmd | 526 ++++++------- inst/doc/vcf.html | 502 +++--------- man/gl_to_gp.Rd |only man/glike.Rd |only man/gp.Rd |only man/ldest.Rd | 27 man/ldfast.Rd |only man/ldsep-package.Rd | 2 man/mldest.Rd | 13 man/pvcalc.Rd |only man/sldest.Rd | 2 man/uit.Rd | 4 src/RcppExports.cpp | 93 ++ src/derivatives.cpp | 4 src/postmom.cpp |only tests/testthat/test-cube.R | 3 tests/testthat/test-derivatives.R | 16 tests/testthat/test-em_vs_grad.R | 1 tests/testthat/test-hessian.R | 5 tests/testthat/test-lp.R | 1 tests/testthat/test-pbnorm.R | 1 tests/testthat/test-posteriormean.R |only tests/testthat/test-problem_data.R | 1 vignettes/fast.Rmd |only vignettes/vcf.Rmd | 526 ++++++------- 46 files changed, 2467 insertions(+), 2332 deletions(-)
Title: Single-Index Models with a Surface-Link
Description: An implementation of a single-index regression for optimizing individualized dose rules from an observational study. To model interaction effects between baseline covariates and a treatment variable defined on a continuum, we employ two-dimensional penalized spline regression on an index-treatment domain, where the index is defined as a linear combination of the covariates (a single-index). An unspecified main effect for the covariates is allowed, which can also be modeled through a parametric model. A unique contribution of this work is in the parsimonious single-index parametrization specifically defined for the interaction effect term. We refer to Park, Petkova, Tarpey, and Ogden (2020) <doi:10.1111/biom.13320> (for the case of a discrete treatment) and Park, Petkova, Tarpey, and Ogden (2021) "A single-index model with a surface-link for optimizing individualized dose rules" <arXiv:2006.00267v2> for detail of the method. The model can take a member of the exponential family as a response variable and can also take an ordinal categorical response. The main function of this package is simsl().
Author: Hyung Park, Eva Petkova, Thaddeus Tarpey, R. Todd Ogden
Maintainer: Hyung Park <parkh15@nyu.edu>
Diff between simsl versions 0.2.0 dated 2021-02-08 and 0.2.1 dated 2021-02-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/simsl.main.R | 28 +++++++++------------------- man/simsl.Rd | 28 +++++++++------------------- 4 files changed, 24 insertions(+), 44 deletions(-)
Title: Build Resumes with R
Description: Using a CSV, LaTeX and R to easily build attractive resumes.
Author: Jared Lander [aut, cre]
Maintainer: Jared Lander <packages@jaredlander.com>
Diff between resumer versions 0.0.4 dated 2021-01-10 and 0.0.5 dated 2021-02-12
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 9 +++++---- NEWS.md | 14 +++++++++++--- README.md | 4 ++++ inst/rmarkdown/templates/resumer/resources/resume.cls |only 6 files changed, 24 insertions(+), 11 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.7.3 dated 2020-09-19 and 2.7.4 dated 2021-02-12
HEMDAG-2.7.3/HEMDAG/inst/HEMDAG_2.7.3.pdf |only HEMDAG-2.7.4/HEMDAG/DESCRIPTION | 8 HEMDAG-2.7.4/HEMDAG/MD5 | 71 +++--- HEMDAG-2.7.4/HEMDAG/NEWS.md | 8 HEMDAG-2.7.4/HEMDAG/R/gpav.R | 36 +-- HEMDAG-2.7.4/HEMDAG/R/graph.utility.R | 16 - HEMDAG-2.7.4/HEMDAG/R/htd.dag.R | 22 +- HEMDAG-2.7.4/HEMDAG/R/norm.fun.R | 4 HEMDAG-2.7.4/HEMDAG/R/obozinski.methods.R | 20 - HEMDAG-2.7.4/HEMDAG/R/perf.meas.R | 148 +++++--------- HEMDAG-2.7.4/HEMDAG/R/tpr.dag.R | 170 +++++++--------- HEMDAG-2.7.4/HEMDAG/build |only HEMDAG-2.7.4/HEMDAG/inst/HEMDAG_2.7.4.pdf |only HEMDAG-2.7.4/HEMDAG/man/HEMDAG-package.Rd | 2 HEMDAG-2.7.4/HEMDAG/man/auprc.Rd | 4 HEMDAG-2.7.4/HEMDAG/man/auroc.Rd | 4 HEMDAG-2.7.4/HEMDAG/man/check.dag.integrity.Rd | 2 HEMDAG-2.7.4/HEMDAG/man/find.best.f.Rd | 37 +-- HEMDAG-2.7.4/HEMDAG/man/fmax.Rd | 38 +-- HEMDAG-2.7.4/HEMDAG/man/gpav.Rd | 18 - HEMDAG-2.7.4/HEMDAG/man/gpav.holdout.Rd | 10 HEMDAG-2.7.4/HEMDAG/man/gpav.parallel.Rd | 2 HEMDAG-2.7.4/HEMDAG/man/gpav.vanilla.Rd | 10 HEMDAG-2.7.4/HEMDAG/man/hierarchical.checkers.Rd | 14 - HEMDAG-2.7.4/HEMDAG/man/htd.Rd | 14 - HEMDAG-2.7.4/HEMDAG/man/htd.holdout.Rd | 6 HEMDAG-2.7.4/HEMDAG/man/htd.vanilla.Rd | 6 HEMDAG-2.7.4/HEMDAG/man/multilabel.F.measure.Rd | 26 +- HEMDAG-2.7.4/HEMDAG/man/obozinski.heuristic.methods.Rd | 12 - HEMDAG-2.7.4/HEMDAG/man/obozinski.holdout.Rd | 6 HEMDAG-2.7.4/HEMDAG/man/obozinski.methods.Rd | 6 HEMDAG-2.7.4/HEMDAG/man/pxr.Rd | 4 HEMDAG-2.7.4/HEMDAG/man/scores.normalization.Rd | 4 HEMDAG-2.7.4/HEMDAG/man/tpr.dag.Rd | 38 +-- HEMDAG-2.7.4/HEMDAG/man/tpr.dag.cv.Rd | 32 +-- HEMDAG-2.7.4/HEMDAG/man/tpr.dag.holdout.Rd | 30 +- HEMDAG-2.7.4/HEMDAG/tests/testthat/test.perf.meas.R | 65 +++++- HEMDAG-2.7.4/HEMDAG/tests/testthat/test.tpr.dag.R | 179 ++++++++--------- 38 files changed, 529 insertions(+), 543 deletions(-)
Title: Models for the 'nflfastR' Package
Description: A data package that hosts all models for the
'nflfastR' package.
Author: Sebastian Carl [cre, aut],
Ben Baldwin [aut]
Maintainer: Sebastian Carl <mrcaseb@gmail.com>
Diff between fastrmodels versions 1.0.0 dated 2021-02-11 and 1.0.1 dated 2021-02-12
DESCRIPTION | 8 +-- LICENSE | 4 - MD5 | 30 +++++++------- NAMESPACE | 4 - NEWS.md | 4 + R/data.R | 96 ++++++++++++++++++++++----------------------- R/fastrmodels-package.R | 16 +++---- README.md | 82 +++++++++++++++++++------------------- man/cp_model.Rd | 40 +++++++++--------- man/ep_model.Rd | 40 +++++++++--------- man/fastrmodels-package.Rd | 58 +++++++++++++-------------- man/fg_model.Rd | 40 +++++++++--------- man/wp_model.Rd | 40 +++++++++--------- man/wp_model_spread.Rd | 40 +++++++++--------- man/xpass_model.Rd | 40 +++++++++--------- man/xyac_model.Rd | 40 +++++++++--------- 16 files changed, 294 insertions(+), 288 deletions(-)
Title: Automatic Unobserved Components Models
Description: Comprehensive analysis and forecasting
of univariate time series using automatic
unobserved components models and algorithms.
Harvey, AC (1989) <doi:10.1017/CBO9781107049994>.
Pedregal, DJ and Young PC (2002) <doi:10.1002/9780470996430>.
Durbin J and Koopman SJ (2012) <doi:10.1093/acprof:oso/9780199641178.001.0001>.
Author: Diego J. Pedregal [aut, cre] (<https://orcid.org/0000-0003-4958-0969>)
Maintainer: Diego J. Pedregal <Diego.Pedregal@uclm.es>
Diff between UComp versions 2.1.1 dated 2021-02-02 and 2.1.2 dated 2021-02-12
DESCRIPTION | 10 +++++--- MD5 | 19 +++++++++++----- NAMESPACE | 4 ++- R/RcppExports.R | 14 ++++++------ R/data.R | 64 +++++++++++++++++++++++++++++++++----------------------- build |only data/airpas.rda |binary data/sales.rda |only inst |only man/airpas.Rd | 5 ---- man/sales.Rd |only vignettes |only 12 files changed, 68 insertions(+), 48 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-02-11 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-03 1.1.19
2020-11-10 1.1.18
2020-07-07 1.1.16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-28 1.0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-27 1.1.25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-17 0.1.1
2020-05-25 0.1.0
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary
data. See Abrams et al., 2021, <doi:10.1093/bioinformatics/btab037>.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 0.99.0 dated 2021-01-10 and 1.0.0 dated 2021-02-12
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- inst/doc/mercVis.html | 6 +++--- inst/doc/mercator.html | 4 ++-- 4 files changed, 14 insertions(+), 13 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-53 dated 2020-09-09 and 7.3-53.1 dated 2021-02-12
DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++--------------- build |only inst/CITATION | 2 +- inst/po/de/LC_MESSAGES/R-MASS.mo |binary inst/po/en@quot/LC_MESSAGES/R-MASS.mo |binary inst/po/fr/LC_MESSAGES/R-MASS.mo |binary inst/po/it/LC_MESSAGES/R-MASS.mo |binary inst/po/ko/LC_MESSAGES/R-MASS.mo |binary inst/po/pl/LC_MESSAGES/R-MASS.mo |binary man/Cars93.Rd | 2 +- po/R-MASS.pot | 10 ++++++++-- po/R-de.po | 8 +++++++- po/R-fr.po | 8 +++++++- po/R-it.po | 8 +++++++- po/R-ko.po | 8 +++++++- po/R-pl.po | 8 +++++++- 17 files changed, 66 insertions(+), 29 deletions(-)
Title: High-Throughput Screening for Plate Based Essays
Description: Can be used to carry out extraction, normalization, quality control (QC), candidate hits identification and visualization for plate based assays, in drug discovery. The package methods were applied in H. W. Choi et al. "Identification of Novel Mast Cell Activators Using Cell-Based High-Throughput Screening", SLAS Discovery 24(6), 2019. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.
Author: Ivo D. Shterev [aut, cre],
Cliburn Chan [aut],
Gregory D. Sempowski [aut]
Maintainer: Ivo D. Shterev <i.shterev@gmail.com>
Diff between highSCREEN versions 0.3 dated 2018-08-22 and 0.4 dated 2021-02-12
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/highSCREENmanual.R | 18 +++++++++--------- inst/doc/highSCREENmanual.pdf |binary man/highSCREEN-package.Rd | 4 ++-- 7 files changed, 24 insertions(+), 24 deletions(-)
Title: Fill Missing Values in Satellite Data
Description: Tools to fill missing values in satellite data and to develop new
gap-fill algorithms. The methods are tailored to data (images) observed
at equally-spaced points in time. The package is illustrated with MODIS
NDVI data.
Author: Florian Gerber [aut, cre] (<https://orcid.org/0000-0001-8545-5263>)
Maintainer: Florian Gerber <flora.fauna.gerber@gmail.com>
Diff between gapfill versions 0.9.6 dated 2018-04-06 and 0.9.6-1 dated 2021-02-12
DESCRIPTION | 21 ++++++++++++--------- MD5 | 33 +++++++++++++++++---------------- NEWS | 7 +++++++ R/gapfill.R | 34 +++++++++++++++++----------------- README.md | 16 ++++++++-------- build |only man/Array2Matrix.Rd | 2 +- man/ArrayAround.Rd | 10 +++++++--- man/EstimateQuantile.Rd | 4 ++-- man/Extend.Rd | 4 ++-- man/Gapfill.Rd | 19 ++++++++++++++----- man/Image.Rd | 20 +++++++++++++++----- man/Index.Rd | 3 +-- man/Score.Rd | 4 ++-- man/Subset-Predict.Rd | 16 +++++++++++----- man/Validate.Rd | 10 +++++++--- man/gapfill-package.Rd | 4 ++-- man/ndvi.Rd | 6 ++++-- 18 files changed, 129 insertions(+), 84 deletions(-)
Title: Models and Equations for Human Comfort Research
Description: Calculation of various common and less common comfort indices such as predicted mean vote or the two node model. Converts physical variables such as relative to absolute humidity and evaluates the performance of comfort indices.
Author: Marcel Schweiker [aut, cre] (<https://orcid.org/0000-0003-3906-4688>),
Sophia Mueller [aut],
Michael Kleber [ctr],
Boris Kingma [ctr] (<https://orcid.org/0000-0001-5961-0215>),
Masanori Shukuya [ctr] (<https://orcid.org/0000-0003-2777-4375>),
Shaomi Rahman [ctr],
Shoaib Sarwar [ctr]
Maintainer: Marcel Schweiker <mschweiker@ukaachen.de>
Diff between comf versions 0.1.9 dated 2019-04-08 and 0.1.10 dated 2021-02-12
comf-0.1.10/comf/DESCRIPTION | 24 comf-0.1.10/comf/MD5 | 175 +++- comf-0.1.10/comf/NAMESPACE | 58 + comf-0.1.10/comf/NEWS | 9 comf-0.1.10/comf/R/ComfortIndices.r | 731 +++++++++--------- comf-0.1.10/comf/R/calc2Node.r |only comf-0.1.10/comf/R/calcAComf.R |only comf-0.1.10/comf/R/calcAD.R |only comf-0.1.10/comf/R/calcATHBpmv.r |only comf-0.1.10/comf/R/calcATHBpts.R |only comf-0.1.10/comf/R/calcATHBset.R |only comf-0.1.10/comf/R/calcAvgAcc.R |only comf-0.1.10/comf/R/calcBias.R |only comf-0.1.10/comf/R/calcCE.R |only comf-0.1.10/comf/R/calcCOEFF.R |only comf-0.1.10/comf/R/calcComfInd.R |only comf-0.1.10/comf/R/calcDisc.r |only comf-0.1.10/comf/R/calcET.r |only comf-0.1.10/comf/R/calcHbExSteady.r |only comf-0.1.10/comf/R/calcHbExUnsteady.R |only comf-0.1.10/comf/R/calcHumidity.R |only comf-0.1.10/comf/R/calcIREQ.R |only comf-0.1.10/comf/R/calcIso7933.R |only comf-0.1.10/comf/R/calcPD.r |only comf-0.1.10/comf/R/calcPMV.R |only comf-0.1.10/comf/R/calcPMVGagge.r |only comf-0.1.10/comf/R/calcPMVPPD.R |only comf-0.1.10/comf/R/calcPMVStar.r |only comf-0.1.10/comf/R/calcPMVadj.R |only comf-0.1.10/comf/R/calcPPD.R |only comf-0.1.10/comf/R/calcPS.r |only comf-0.1.10/comf/R/calcPTS.r |only comf-0.1.10/comf/R/calcPtsa.r |only comf-0.1.10/comf/R/calcPtse.r |only comf-0.1.10/comf/R/calcRT.R |only comf-0.1.10/comf/R/calcSET.r |only comf-0.1.10/comf/R/calcSkinWettedness.r |only comf-0.1.10/comf/R/calcSolarGain.r |only comf-0.1.10/comf/R/calcTNZPDF.R |only comf-0.1.10/comf/R/calcTPRTSV.r |only comf-0.1.10/comf/R/calcTSens.r |only comf-0.1.10/comf/R/calcTWC.R |only comf-0.1.10/comf/R/calcTroin.R |only comf-0.1.10/comf/R/calcUTCI.r |only comf-0.1.10/comf/R/calcVTG.R |only comf-0.1.10/comf/R/calcaPMV.R |only comf-0.1.10/comf/R/calcdTNZ.r |only comf-0.1.10/comf/R/calcePMV.R |only comf-0.1.10/comf/R/createCond.R |only comf-0.1.10/comf/R/cutTSV.r |only comf-0.1.10/comf/R/dfASHRAETableG11.R | 6 comf-0.1.10/comf/R/dfField.R | 4 comf-0.1.10/comf/R/dfISO7730AppE.R | 4 comf-0.1.10/comf/R/dfISO7730TableD1.R | 4 comf-0.1.10/comf/R/dfISO7933AppF.R | 4 comf-0.1.10/comf/R/dfSolarGainValues.R |only comf-0.1.10/comf/R/dfUtcivalues.R |only comf-0.1.10/comf/R/dfVariables.R |only comf-0.1.10/comf/R/fctHelp.r | 1003 ++++++++++++++++--------- comf-0.1.10/comf/R/validator.r |only comf-0.1.10/comf/build/vignette.rds |binary comf-0.1.10/comf/data/dfSolarGainValues.RData |only comf-0.1.10/comf/data/dfUTCIValues.RData |only comf-0.1.10/comf/data/dfVariables.RData |only comf-0.1.10/comf/inst/doc/R_packages-comf.ltx | 4 comf-0.1.10/comf/inst/doc/R_packages-comf.pdf |binary comf-0.1.10/comf/man/calc2Node.Rd | 262 ++---- comf-0.1.10/comf/man/calcAD.Rd |only comf-0.1.10/comf/man/calcATHBpmv.Rd |only comf-0.1.10/comf/man/calcATHBpts.Rd |only comf-0.1.10/comf/man/calcATHBset.Rd |only comf-0.1.10/comf/man/calcAvgAcc.Rd | 98 +- comf-0.1.10/comf/man/calcBias.Rd | 117 +- comf-0.1.10/comf/man/calcCE.Rd |only comf-0.1.10/comf/man/calcComfInd.Rd | 229 ++--- comf-0.1.10/comf/man/calcDisc.Rd |only comf-0.1.10/comf/man/calcET.Rd |only comf-0.1.10/comf/man/calcHbExSteady.Rd | 295 +++---- comf-0.1.10/comf/man/calcHbExUnsteady.Rd | 290 +++---- comf-0.1.10/comf/man/calcIREQ.Rd |only comf-0.1.10/comf/man/calcIso7933.Rd |only comf-0.1.10/comf/man/calcMixR.Rd |only comf-0.1.10/comf/man/calcPD.Rd |only comf-0.1.10/comf/man/calcPMV.Rd |only comf-0.1.10/comf/man/calcPMVGagge.Rd |only comf-0.1.10/comf/man/calcPMVPPD.Rd | 136 +-- comf-0.1.10/comf/man/calcPMVStar.Rd |only comf-0.1.10/comf/man/calcPMVadj.Rd | 151 +-- comf-0.1.10/comf/man/calcPPD.Rd |only comf-0.1.10/comf/man/calcPS.Rd |only comf-0.1.10/comf/man/calcPTS.Rd |only comf-0.1.10/comf/man/calcPtsa.Rd |only comf-0.1.10/comf/man/calcPtse.Rd |only comf-0.1.10/comf/man/calcRT.Rd |only comf-0.1.10/comf/man/calcSET.Rd |only comf-0.1.10/comf/man/calcSkinWettedness.Rd |only comf-0.1.10/comf/man/calcSolarGain.Rd |only comf-0.1.10/comf/man/calcTNZPDF.Rd | 294 +++---- comf-0.1.10/comf/man/calcTPRTSV.Rd | 88 +- comf-0.1.10/comf/man/calcTSens.Rd |only comf-0.1.10/comf/man/calcTWC.Rd |only comf-0.1.10/comf/man/calcTroin.Rd | 106 +- comf-0.1.10/comf/man/calcUTCI.Rd |only comf-0.1.10/comf/man/calcVTG.Rd |only comf-0.1.10/comf/man/calcaPMV.Rd |only comf-0.1.10/comf/man/calcdTNZ.Rd | 190 ++-- comf-0.1.10/comf/man/calcePMV.Rd |only comf-0.1.10/comf/man/calcepCoeff.Rd |only comf-0.1.10/comf/man/calctAdapt15251.Rd |only comf-0.1.10/comf/man/comf-internal.Rd | 20 comf-0.1.10/comf/man/comf-package.Rd | 8 comf-0.1.10/comf/man/createCond.Rd | 155 +-- comf-0.1.10/comf/man/cutTSV.Rd | 68 - comf-0.1.10/comf/man/dfASHRAETableG11.Rd | 89 -- comf-0.1.10/comf/man/dfField.Rd | 69 - comf-0.1.10/comf/man/dfISO7730AppE.Rd | 73 - comf-0.1.10/comf/man/dfISO7730TableD1.Rd | 84 -- comf-0.1.10/comf/man/dfISO7933AppF.Rd | 91 +- comf-0.1.10/comf/man/dfSolarGainValues.Rd |only comf-0.1.10/comf/man/dfUTCIValues.Rd |only comf-0.1.10/comf/man/dfVariables.Rd |only comf-0.1.10/comf/vignettes/R_packages-comf.ltx | 4 comf-0.1.9/comf/R/fct2Node.r |only comf-0.1.9/comf/R/fctATHB.r |only comf-0.1.9/comf/R/fctCalcISO7933.R |only comf-0.1.9/comf/R/fctHBxStSt.r |only comf-0.1.9/comf/R/fctHBxUnSt.r |only comf-0.1.9/comf/R/fctMRT.R |only comf-0.1.9/comf/R/fctOther.r |only comf-0.1.9/comf/R/fctPMVPPD.r |only comf-0.1.9/comf/R/fctSimpleMRT.r |only comf-0.1.9/comf/R/fctTNZPDF.r |only comf-0.1.9/comf/R/fctdTNZ.r |only comf-0.1.9/comf/README.md |only comf-0.1.9/comf/man/calcATHB.Rd |only comf-0.1.9/comf/man/calcCOEFF.Rd |only comf-0.1.9/comf/man/calcHumidity.Rd |only comf-0.1.9/comf/man/calcISO7933.Rd |only comf-0.1.9/comf/man/calcMRT.Rd |only comf-0.1.9/comf/man/calcPTSadj.Rd |only comf-0.1.9/comf/man/calcTAdapt.Rd |only 141 files changed, 2592 insertions(+), 2351 deletions(-)
Title: Election Vote Counting
Description: Counting election votes and determining election results by different methods, including
the single transferable vote or ranked choice, approval, score, plurality, condorcet and two-round runoff methods (Raftery et al. (2021) <arXiv:2102.05801>).
Author: Hana Sevcikova, Bernard Silverman, Adrian Raftery
Maintainer: Hana Sevcikova<hanas@uw.edu>
Diff between vote versions 2.1-0 dated 2021-01-06 and 2.2-0 dated 2021-02-12
ChangeLog | 9 +++++ DESCRIPTION | 11 +++--- MD5 | 14 ++++---- NAMESPACE | 3 + R/check_votes.R | 10 ++++++ R/stv.R | 85 ++++++++++++++++++++++++++++++++++++++++++---------- man/stv.Rd | 24 +++++++++++++- man/vote-package.Rd | 6 +++ 8 files changed, 130 insertions(+), 32 deletions(-)
Title: PHATE - Potential of Heat-Diffusion for Affinity-Based
Transition Embedding
Description: PHATE is a tool for visualizing high dimensional single-cell data
with natural progressions or trajectories. PHATE uses a novel conceptual framework
for learning and visualizing the manifold inherent to biological systems in which
smooth transitions mark the progressions of cells from one state to another.
To see how PHATE can be applied to single-cell RNA-seq datasets from hematopoietic
stem cells, human embryonic stem cells, and bone marrow samples, check out our publication in Nature Biotechnology
at <doi:10.1038/s41587-019-0336-3>.
Author: Krishnan Srinivasan [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between phateR versions 1.0.4 dated 2020-05-22 and 1.0.7 dated 2021-02-12
phateR-1.0.4/phateR/data/datalist |only phateR-1.0.4/phateR/inst/examples/bonemarrow_tutorial.nb.html |only phateR-1.0.7/phateR/DESCRIPTION | 8 +-- phateR-1.0.7/phateR/MD5 | 20 ++++----- phateR-1.0.7/phateR/R/cluster.R | 9 +--- phateR-1.0.7/phateR/R/phate.R | 15 ++++++ phateR-1.0.7/phateR/R/utils.R | 6 +- phateR-1.0.7/phateR/README.md | 4 + phateR-1.0.7/phateR/inst/CITATION | 22 +++++----- phateR-1.0.7/phateR/man/phate.Rd | 6 ++ phateR-1.0.7/phateR/man/tree.data.Rd | 6 +- phateR-1.0.7/phateR/man/tree.data.small.Rd | 6 +- 12 files changed, 64 insertions(+), 38 deletions(-)
Title: Simulate Genotypes from the BN-PSD Admixture Model
Description: The Pritchard-Stephens-Donnelly (PSD) admixture model has k intermediate subpopulations from which n individuals draw their alleles dictated by their individual-specific admixture proportions. The BN-PSD model additionally imposes the Balding-Nichols (BN) allele frequency model to the intermediate populations, which therefore evolved independently from a common ancestral population T with subpopulation-specific FST (Wright's fixation index) parameters. The BN-PSD model can be used to yield complex population structures. Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>),
John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between bnpsd versions 1.2.1 dated 2020-01-10 and 1.2.3 dated 2021-02-12
DESCRIPTION | 10 MD5 | 74 ++-- NEWS.md | 21 + R/admix_prop_1d_circular.R | 62 +-- R/admix_prop_1d_linear.R | 54 +-- R/admix_prop_indep_subpops.R | 30 - R/bias_coeff_admix_fit.R | 27 + R/bnpsd.R | 2 R/coanc_admix.R | 11 R/coanc_to_kinship.R | 14 R/draw_all_admix.R | 96 +++-- R/draw_genotypes_admix.R | 30 + R/draw_p_anc.R | 12 R/draw_p_subpops.R | 24 - R/fixed_loci.R | 20 - R/fst_admix.R | 13 R/make_p_ind_admix.R | 14 R/rescale_coanc_subpops.R | 14 README.md | 5 build/vignette.rds |binary inst/doc/bnpsd.Rmd | 6 inst/doc/bnpsd.html | 674 +++++++++++++++++++++------------------- man/admix_prop_1d_circular.Rd | 50 +- man/admix_prop_1d_linear.Rd | 44 +- man/admix_prop_indep_subpops.Rd | 12 man/bnpsd.Rd | 2 man/coanc_admix.Rd | 11 man/coanc_to_kinship.Rd | 14 man/draw_all_admix.Rd | 42 +- man/draw_genotypes_admix.Rd | 20 - man/draw_p_anc.Rd | 12 man/draw_p_subpops.Rd | 24 - man/fixed_loci.Rd | 20 - man/fst_admix.Rd | 13 man/make_p_ind_admix.Rd | 14 tests/testthat/test_bnpsd.R | 67 +++ vignettes/bnpsd.Rmd | 6 vignettes/bnpsd.bib | 27 - 38 files changed, 878 insertions(+), 713 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-30 0.1.3
2019-10-09 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-27 5.1.1
2020-09-18 5.1.0
2020-06-15 5.0.0
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds
of correlations, such as partial correlations, Bayesian correlations,
multilevel correlations, polychoric correlations, biweight
correlations, distance correlations and more. Part of the 'easystats'
ecosystem.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between correlation versions 0.5.0 dated 2020-12-02 and 0.6.0 dated 2021-02-12
correlation-0.5.0/correlation/R/utils_bootstrapping.R |only correlation-0.5.0/correlation/R/utils_reorder_matrix.R |only correlation-0.6.0/correlation/DESCRIPTION | 82 - correlation-0.6.0/correlation/MD5 | 118 - correlation-0.6.0/correlation/NAMESPACE | 15 correlation-0.6.0/correlation/NEWS.md | 20 correlation-0.6.0/correlation/R/backports.R |only correlation-0.6.0/correlation/R/cor_test.R | 141 + correlation-0.6.0/correlation/R/cor_test_bayes.R | 63 correlation-0.6.0/correlation/R/cor_test_biserial.R | 3 correlation-0.6.0/correlation/R/cor_test_biweight.R | 2 correlation-0.6.0/correlation/R/cor_test_blomqvist.R | 2 correlation-0.6.0/correlation/R/cor_test_distance.R | 9 correlation-0.6.0/correlation/R/cor_test_freq.R | 8 correlation-0.6.0/correlation/R/cor_test_gamma.R | 2 correlation-0.6.0/correlation/R/cor_test_hoeffding.R | 2 correlation-0.6.0/correlation/R/cor_test_percentage.R | 2 correlation-0.6.0/correlation/R/cor_test_polychoric.R | 2 correlation-0.6.0/correlation/R/cor_test_somers.R | 2 correlation-0.6.0/correlation/R/cor_test_tetrachoric.R | 2 correlation-0.6.0/correlation/R/cor_to_ci.R | 6 correlation-0.6.0/correlation/R/cor_to_cov.R | 3 correlation-0.6.0/correlation/R/cor_to_p.R | 4 correlation-0.6.0/correlation/R/cor_to_pcor.R | 62 correlation-0.6.0/correlation/R/cor_to_spcor.R | 33 correlation-0.6.0/correlation/R/correlation.R | 390 +++-- correlation-0.6.0/correlation/R/display.R | 8 correlation-0.6.0/correlation/R/print.easycormatrix.R | 46 correlation-0.6.0/correlation/R/print.easycorrelation.R |only correlation-0.6.0/correlation/R/print_md.R | 89 + correlation-0.6.0/correlation/R/utils_create_diagonal.R | 9 correlation-0.6.0/correlation/R/utils_get_combinations.R | 7 correlation-0.6.0/correlation/R/winsorize.R | 27 correlation-0.6.0/correlation/README.md | 217 +-- correlation-0.6.0/correlation/build/vignette.rds |binary correlation-0.6.0/correlation/inst/WORDLIST | 3 correlation-0.6.0/correlation/inst/doc/multilevel.html | 636 -------- correlation-0.6.0/correlation/inst/doc/types.html | 710 ---------- correlation-0.6.0/correlation/man/cor_test.Rd | 262 ++- correlation-0.6.0/correlation/man/cor_to_cov.Rd | 58 correlation-0.6.0/correlation/man/cor_to_p.Rd | 31 correlation-0.6.0/correlation/man/cor_to_pcor.Rd | 105 - correlation-0.6.0/correlation/man/correlation.Rd | 278 +++ correlation-0.6.0/correlation/man/distance_mahalanobis.Rd | 6 correlation-0.6.0/correlation/man/figures/README-12-1.png |only correlation-0.6.0/correlation/man/figures/README-7-1.png |only correlation-0.6.0/correlation/man/figures/unnamed-chunk-12-1.png |binary correlation-0.6.0/correlation/man/figures/unnamed-chunk-7-1.png |binary correlation-0.6.0/correlation/man/reexports.Rd | 3 correlation-0.6.0/correlation/man/winsorize.Rd | 11 correlation-0.6.0/correlation/tests/testthat/_snaps |only correlation-0.6.0/correlation/tests/testthat/test-cor_multilevel.R | 76 - correlation-0.6.0/correlation/tests/testthat/test-cor_test.R | 142 +- correlation-0.6.0/correlation/tests/testthat/test-cor_test_na_present.R |only correlation-0.6.0/correlation/tests/testthat/test-cor_to_cov.R |only correlation-0.6.0/correlation/tests/testthat/test-cor_to_p.R |only correlation-0.6.0/correlation/tests/testthat/test-cor_to_pcor.R | 24 correlation-0.6.0/correlation/tests/testthat/test-correlation.R | 80 - correlation-0.6.0/correlation/tests/testthat/test-display_print_dataframe.R |only correlation-0.6.0/correlation/tests/testthat/test-display_print_matrix.R |only correlation-0.6.0/correlation/tests/testthat/test-grouped_data2.R |only correlation-0.6.0/correlation/tests/testthat/test-methods.R |only correlation-0.6.0/correlation/tests/testthat/test-misc.R | 28 correlation-0.6.0/correlation/tests/testthat/test-winsorization.R |only correlation-0.6.0/correlation/vignettes/multilevel_files/figure-gfm/unnamed-chunk-3-1.png |binary correlation-0.6.0/correlation/vignettes/multilevel_files/figure-gfm/unnamed-chunk-5-1.png |binary correlation-0.6.0/correlation/vignettes/types_files/figure-gfm/unnamed-chunk-4-1.png |binary 67 files changed, 1731 insertions(+), 2098 deletions(-)
Title: Bootstrap Functions (Originally by Angelo Canty for S)
Description: Functions and datasets for bootstrapping from the
book "Bootstrap Methods and Their Application" by A. C. Davison and
D. V. Hinkley (1997, CUP), originally written by Angelo Canty for S.
Author: Angelo Canty [aut],
Brian Ripley [aut, trl, cre] (author of parallel support)
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between boot versions 1.3-26 dated 2021-01-25 and 1.3-27 dated 2021-02-12
ChangeLog | 17 +++ DESCRIPTION | 8 - MD5 | 25 +++-- R/bootfuns.q | 3 inst/po/de/LC_MESSAGES/R-boot.mo |binary inst/po/en@quot/LC_MESSAGES/R-boot.mo |binary inst/po/fr/LC_MESSAGES/R-boot.mo |binary inst/po/it/LC_MESSAGES/R-boot.mo |binary inst/po/ko/LC_MESSAGES/R-boot.mo |binary inst/po/pl/LC_MESSAGES/R-boot.mo |binary inst/po/ru/LC_MESSAGES/R-boot.mo |binary po/R-boot.pot | 4 po/R-fr.po | 146 +++++++++++++++------------------- tests/parallel-censboot.R |only 14 files changed, 104 insertions(+), 99 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-27 0.1.4
2020-04-01 0.1.3
Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also
given. Set partitions and now compositions are included.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>),
Paul Egeler [ctb] (<https://orcid.org/0000-0001-6948-9498>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.9-22 dated 2019-10-21 and 1.10-1 dated 2021-02-12
partitions-1.10-1/partitions/DESCRIPTION | 23 +- partitions-1.10-1/partitions/MD5 | 48 ++-- partitions-1.10-1/partitions/NAMESPACE | 1 partitions-1.10-1/partitions/R/partitions.R | 46 ++-- partitions-1.10-1/partitions/README.md | 26 -- partitions-1.10-1/partitions/build/partitions.pdf |only partitions-1.10-1/partitions/build/vignette.rds |binary partitions-1.10-1/partitions/inst/doc/partitionspaper.pdf |binary partitions-1.10-1/partitions/inst/doc/scrabble.Rnw | 2 partitions-1.10-1/partitions/inst/doc/scrabble.pdf |binary partitions-1.10-1/partitions/inst/doc/setpartitions.pdf |binary partitions-1.10-1/partitions/inst/restrictedpartitionsgeneratingfunction.Rmd |only partitions-1.10-1/partitions/man/bin.Rd | 5 partitions-1.10-1/partitions/man/conjugate.Rd | 33 +- partitions-1.10-1/partitions/man/parts.Rd | 90 +++++++ partitions-1.10-1/partitions/man/perms.Rd | 5 partitions-1.10-1/partitions/man/setparts.Rd | 16 - partitions-1.10-1/partitions/src/partitions.c | 115 ++++++---- partitions-1.10-1/partitions/src/partitions_init.c | 6 partitions-1.10-1/partitions/src/permutations.c | 2 partitions-1.10-1/partitions/tests/testthat/test_aaa.R | 86 +++++-- partitions-1.10-1/partitions/tests/testthat/test_aab.R | 36 +-- partitions-1.10-1/partitions/vignettes/partitions.bib | 8 partitions-1.10-1/partitions/vignettes/scrabble.Rnw | 2 partitions-1.9-22/partitions/inst/doc/restrictedpartitionsgeneratingfunction.R |only partitions-1.9-22/partitions/inst/doc/restrictedpartitionsgeneratingfunction.Rnw |only partitions-1.9-22/partitions/inst/doc/restrictedpartitionsgeneratingfunction.pdf |only partitions-1.9-22/partitions/vignettes/restrictedpartitionsgeneratingfunction.Rnw |only 28 files changed, 356 insertions(+), 194 deletions(-)
Title: Optimal Capital Allocations
Description: Computes optimal capital allocations based on some standard principles such as Haircut, Overbeck type II and the Covariance Allocation Principle. It also provides some shortcuts for obtaining the Value at Risk and the Expectation Shortfall, using both the normal and the t-student distribution, see Urbina and Guillén (2014)<doi:10.1016/j.eswa.2014.05.017> and Urbina (2013)<http://hdl.handle.net/2099.1/19443>.
Author: Jilber Urbina
Maintainer: Jilber Urbina <jurbina@cipadla.com>
Diff between OCA versions 0.3 dated 2021-01-27 and 0.4 dated 2021-02-12
OCA-0.3/OCA/man/OCA-package.Rd |only OCA-0.4/OCA/DESCRIPTION | 9 +- OCA-0.4/OCA/MD5 | 29 ++++---- OCA-0.4/OCA/NAMESPACE | 16 ++++ OCA-0.4/OCA/R/ES.R | 126 +++++++++++++++++++++++++++++-------- OCA-0.4/OCA/R/Overbeck2.R | 75 +++++++++++++++++++--- OCA-0.4/OCA/R/Risk.R | 70 +++++++++++++++++--- OCA-0.4/OCA/R/VaR.R | 74 ++++++++++++++++++--- OCA-0.4/OCA/R/cap.R | 46 +++++++++++++ OCA-0.4/OCA/R/hap.R | 76 +++++++++++++++++++--- OCA-0.4/OCA/man/ES.Rd | 138 ++++++++++++++++------------------------- OCA-0.4/OCA/man/Overbeck2.Rd | 99 +++++++++++++---------------- OCA-0.4/OCA/man/Risk.Rd | 116 ++++++++++++++-------------------- OCA-0.4/OCA/man/VaR.Rd | 101 +++++++++++++----------------- OCA-0.4/OCA/man/cap.Rd | 75 ++++++++-------------- OCA-0.4/OCA/man/hap.Rd | 93 +++++++++++---------------- 16 files changed, 697 insertions(+), 446 deletions(-)