Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII, and a set of formatters for transforming values or sets of values into ASCII-ready display strings.
Author: Gabriel Becker [aut, cre],
Adrian Waddell [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between formatters versions 0.2.0 dated 2022-03-29 and 0.3.1 dated 2022-05-20
formatters-0.2.0/formatters/tests/tinytest |only formatters-0.3.1/formatters/DESCRIPTION | 14 ++-- formatters-0.3.1/formatters/MD5 | 29 ++++----- formatters-0.3.1/formatters/NAMESPACE | 2 formatters-0.3.1/formatters/NEWS.md | 15 ++++ formatters-0.3.1/formatters/R/format_value.R | 26 +++++--- formatters-0.3.1/formatters/R/generics.R | 29 +++++---- formatters-0.3.1/formatters/R/matrix_form.R | 25 ++++++-- formatters-0.3.1/formatters/R/tostring.R | 59 ++++++++++++++----- formatters-0.3.1/formatters/README.md | 11 +-- formatters-0.3.1/formatters/build/vignette.rds |binary formatters-0.3.1/formatters/inst/doc/formatters.html | 15 ++-- formatters-0.3.1/formatters/man/default_hsep.Rd |only formatters-0.3.1/formatters/man/matrix_form.Rd | 7 +- formatters-0.3.1/formatters/man/tostring.Rd | 4 - formatters-0.3.1/formatters/tests/run_tests.R | 5 - formatters-0.3.1/formatters/tests/testthat |only 17 files changed, 158 insertions(+), 83 deletions(-)
Title: Ecological Limit Function Model Generation, Analysis, and
Visualization using 'ggplot2' and Statistical Methods
Description: A toolset for generating Ecological Limit Function (ELF) models and evaluating potential species loss resulting from flow change, based on the "elfgen" framework. ELFs describe the relation between aquatic species richness (fish or benthic macroinvertebrates) and stream size characteristics (streamflow or drainage area). Journal publications are available outlining framework methodology (Kleiner et al. (2020) <doi:10.1111/1752-1688.12876>) and application (Rapp et al. (2020) <doi:10.1111/1752-1688.12877>).
Author: Joseph Kleiner [aut, cre]
Maintainer: Joseph Kleiner <joseph.d.kleiner@gmail.com>
Diff between elfgen versions 2.2.8 dated 2022-03-29 and 2.3.0 dated 2022-05-20
DESCRIPTION | 10 ++++---- MD5 | 30 ++++++++++++------------- NAMESPACE | 3 +- R/bkpt-pwit.R | 13 +++++++---- R/bkpt-ymax.R | 2 - R/elfchange.R | 2 - R/elfdata.R | 57 +++++++++++++------------------------------------ R/elfgen.R | 2 - R/richness-change.R | 2 - README.md | 7 ++++-- man/bkpt_pwit.Rd | 9 ++++++- man/bkpt_ymax.Rd | 2 - man/elfchange.Rd | 2 - man/elfdata.Rd | 2 - man/elfgen.Rd | 2 - man/richness_change.Rd | 2 - 16 files changed, 68 insertions(+), 79 deletions(-)
Title: Covariance Based Single-Cell Decomposition of Bulk Expression
Data
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For more detail, see Karimnezhad, A. (2022) <doi:10.1101/2022.05.13.491858>.
Author: Ali Karimnezhad [aut, cre, ctb]
Maintainer: Ali Karimnezhad <ali.karimnezhad@gmail.com>
Diff between CSCDRNA versions 1.0.1 dated 2022-05-17 and 1.0.2 dated 2022-05-20
CSCDRNA-1.0.1/CSCDRNA/R/sample_data.R |only CSCDRNA-1.0.1/CSCDRNA/data/sample_data.rda |only CSCDRNA-1.0.1/CSCDRNA/man/sample_data.Rd |only CSCDRNA-1.0.2/CSCDRNA/DESCRIPTION | 12 +++++------ CSCDRNA-1.0.2/CSCDRNA/MD5 | 13 ++++++------ CSCDRNA-1.0.2/CSCDRNA/R/CSCD.R | 30 ++++++++++++++++------------ CSCDRNA-1.0.2/CSCDRNA/R/example_data.R |only CSCDRNA-1.0.2/CSCDRNA/README.md |only CSCDRNA-1.0.2/CSCDRNA/data/example_data.rda |only CSCDRNA-1.0.2/CSCDRNA/man/CSCD.Rd | 18 ++++++++++------ CSCDRNA-1.0.2/CSCDRNA/man/example_data.Rd |only 11 files changed, 42 insertions(+), 31 deletions(-)
Title: Predict Information Cascade by Self-Exciting Point Process
Description: An implementation of self-exciting point process model for information cascades, which occurs when many people engage in the same acts after observing the actions of others (e.g. post resharings on Facebook or Twitter). It provides functions to estimate the infectiousness of an information cascade and predict its popularity given the observed history. See <http://snap.stanford.edu/seismic/> for more information and datasets.
Author: Hera He, Murat Erdogdu, Qingyuan Zhao
Maintainer: Qingyuan Zhao <qingyzhao@gmail.com>
Diff between seismic versions 1.0 dated 2015-06-05 and 1.1 dated 2022-05-20
DESCRIPTION | 11 +++--- MD5 | 18 +++++----- NAMESPACE | 3 + R/tweetfunctions.R | 79 +++++++++++++++++++++++----------------------- man/get.infectiousness.Rd | 13 +++++-- man/linear.kernel.Rd | 35 ++++++++++++++------ man/memory.pdf.Rd | 8 ++-- man/pred.cascade.Rd | 13 +++++-- man/seismic.Rd | 4 -- man/tweet.Rd | 8 +--- 10 files changed, 108 insertions(+), 84 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's Biostatistics: A Foundation for Analysis in the Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.1.2 dated 2022-05-13 and 0.1.3 dated 2022-05-20
DESCRIPTION | 13 - MD5 | 68 ++++----- NAMESPACE | 16 +- NEWS.md | 11 + R/DanielBiostatistics10th.R | 3 R/Gosset_Welch.R | 16 -- R/chp12.R | 12 - R/chp2.R | 1 R/chp3.R | 117 ++++++++++----- R/chp4.R | 3 R/chp5.6.7.R | 204 +++++++++++++++------------ inst/example/Chapter1.R | 4 inst/example/Chapter10.R | 8 - inst/example/Chapter11.R | 73 ++++----- inst/example/Chapter12.R | 18 +- inst/example/Chapter13.R |only inst/example/Chapter14.R | 22 +- inst/example/Chapter2.R | 36 +--- inst/example/Chapter3.R | 28 ++- inst/example/Chapter4.R | 10 - inst/example/Chapter5.6.7.R | 82 +++++----- inst/example/Chapter7.power.R | 22 +- inst/example/Chapter8.R | 64 ++++---- inst/example/Chapter9.R | 9 - inst/example/Exercises.R |only inst/example/LDS_chp6.R | 10 - inst/example/LDS_chp8.R | 52 +++--- inst/example/LargeData_Chapter2_NCBIRTH800.R | 60 +++---- man/Chapter01.Rd | 4 man/Chapter02.Rd | 36 +--- man/Chapter03.Rd | 59 +++++-- man/Chapter04.Rd | 10 - man/Chapter05to07.Rd | 169 +++++++++++----------- man/Chapter07_power.Rd | 22 +- man/Chapter12.Rd | 26 +-- man/Gosset_Welch.Rd | 15 - 36 files changed, 701 insertions(+), 602 deletions(-)
More information about DanielBiostatistics10th at CRAN
Permanent link
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, inv] ,
Brenton M. Wiernik [aut, cre] ,
Indrajeet Patil [aut] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Mark White [rev],
Maximilian M. Rabe [rev]
Maintainer: Brenton M. Wiernik <brenton@wiernik.org>
Diff between correlation versions 0.8.0 dated 2022-02-14 and 0.8.1 dated 2022-05-20
DESCRIPTION | 12 MD5 | 202 +-- NAMESPACE | 153 +- NEWS.md | 344 +++--- R/backports.R | 16 R/cor_lower.R |only R/cor_smooth.R | 306 ++--- R/cor_sort.R | 170 +-- R/cor_test.R | 626 +++++------ R/cor_test_bayes.R | 214 +-- R/cor_test_biserial.R | 150 +- R/cor_test_biweight.R | 82 - R/cor_test_blomqvist.R | 52 R/cor_test_distance.R | 286 ++--- R/cor_test_freq.R | 159 +- R/cor_test_gamma.R | 58 - R/cor_test_gaussian.R | 24 R/cor_test_hoeffding.R | 50 R/cor_test_percentage.R | 101 - R/cor_test_polychoric.R | 94 - R/cor_test_shepherd.R | 36 R/cor_test_somers.R | 46 R/cor_test_tetrachoric.R | 70 - R/cor_text.R | 168 +-- R/cor_to_ci.R | 178 +-- R/cor_to_cov.R | 120 +- R/cor_to_p.R | 97 - R/cor_to_pcor.R | 523 ++++----- R/cor_to_spcor.R | 44 R/correlation.R | 1287 +++++++++++------------ R/display.R | 170 +-- R/mahalanobis.R | 125 +- R/matrix_inverse.R | 108 - R/methods.easycorrelation.R | 423 +++---- R/methods_format.R | 392 +++---- R/methods_plot.R | 24 R/methods_print.R | 359 +++--- R/reexports.R | 38 R/utils.R | 68 - R/utils_clean_data.R | 22 R/utils_create_diagonal.R | 92 - R/utils_find_correlationtype.R | 132 +- R/utils_get_combinations.R | 80 - R/utils_get_matrix.R | 32 R/utils_remove_redundant.R | 130 +- R/visualisation_recipe.cor_test.R | 346 +++--- R/visualisation_recipe.easycormatrix.R | 549 ++++----- R/visualisation_recipe.easycorrelation.R | 92 - R/z_fisher.R | 56 - README.md | 693 ++++++------ build/vignette.rds |binary inst/CITATION | 28 inst/WORDLIST | 188 +-- inst/doc/multilevel.R | 104 - inst/doc/multilevel.Rmd | 268 ++-- inst/doc/multilevel.html | 752 ++++++++----- inst/doc/types.R | 218 +-- inst/doc/types.Rmd | 524 ++++----- inst/doc/types.html | 1017 +++++++++++------- man/cor_lower.Rd |only man/cor_smooth.Rd | 88 - man/cor_sort.Rd | 62 - man/cor_test.Rd | 543 ++++----- man/cor_text.Rd | 56 - man/cor_to_cov.Rd | 60 - man/cor_to_p.Rd | 136 +- man/cor_to_pcor.Rd | 113 +- man/correlation.Rd | 653 +++++------ man/display.easycormatrix.Rd | 158 +- man/distance_mahalanobis.Rd | 90 - man/is.cor.Rd | 34 man/isSquare.Rd | 34 man/matrix_inverse.Rd | 52 man/reexports.Rd | 48 man/visualisation_recipe.easycormatrix.Rd | 247 ++-- man/z_fisher.Rd | 56 - tests/spelling.R | 12 tests/testthat.R | 22 tests/testthat/_snaps/as.list.md | 512 ++++----- tests/testthat/_snaps/correlation.md | 76 - tests/testthat/_snaps/display_print_dataframe.md | 64 - tests/testthat/_snaps/display_print_matrix.md | 96 - tests/testthat/_snaps/methods.md | 102 - tests/testthat/_snaps/renaming.md | 96 - tests/testthat/_snaps/selecting_variables.md | 100 - tests/testthat/test-as.list.R | 46 tests/testthat/test-cor_multilevel.R | 84 - tests/testthat/test-cor_test.R | 388 +++--- tests/testthat/test-cor_test_na_present.R | 260 ++-- tests/testthat/test-cor_to_cov.R | 16 tests/testthat/test-cor_to_p.R | 16 tests/testthat/test-cor_to_pcor.R | 164 +- tests/testthat/test-correlation.R | 372 +++--- tests/testthat/test-display_print_dataframe.R | 82 - tests/testthat/test-display_print_matrix.R | 110 - tests/testthat/test-grouped_data2.R | 36 tests/testthat/test-methods.R | 28 tests/testthat/test-misc.R | 76 - tests/testthat/test-renaming.R | 40 tests/testthat/test-selecting_variables.R | 76 - vignettes/bibliography.bib | 316 ++--- vignettes/multilevel.Rmd | 268 ++-- vignettes/types.Rmd | 524 ++++----- 103 files changed, 9803 insertions(+), 9307 deletions(-)
Title: Tidy Dataframes and Expressions with Statistical Details
Description: Utilities for producing dataframes with rich details for the
most common types of statistical approaches and tests: parametric,
nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation
analyses, contingency table analyses, and meta-analyses. The
functions are pipe-friendly and provide a consistent syntax to work
with tidy data. These dataframes additionally contain expressions with
statistical details, and can be used in graphing packages. This
package also forms the statistical processing backend for
'ggstatsplot'.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.3.1 dated 2022-03-29 and 1.3.2 dated 2022-05-20
statsExpressions-1.3.1/statsExpressions/tests/testthat/_snaps/tidy_model_expressions_F.md |only statsExpressions-1.3.1/statsExpressions/tests/testthat/_snaps/windows |only statsExpressions-1.3.1/statsExpressions/tests/testthat/test-grouped_dataframes.R |only statsExpressions-1.3.1/statsExpressions/tests/testthat/test-tidy_model_expressions_F.R |only statsExpressions-1.3.2/statsExpressions/DESCRIPTION | 17 statsExpressions-1.3.2/statsExpressions/MD5 | 179 +-- statsExpressions-1.3.2/statsExpressions/NAMESPACE | 2 statsExpressions-1.3.2/statsExpressions/NEWS.md | 20 statsExpressions-1.3.2/statsExpressions/R/add_expression_col.R | 33 statsExpressions-1.3.2/statsExpressions/R/centrality_description.R | 20 statsExpressions-1.3.2/statsExpressions/R/contingency_table.R | 438 +++---- statsExpressions-1.3.2/statsExpressions/R/corr_test.R | 14 statsExpressions-1.3.2/statsExpressions/R/global_vars.R | 78 - statsExpressions-1.3.2/statsExpressions/R/helpers_easystats.R | 1 statsExpressions-1.3.2/statsExpressions/R/long_to_wide_converter.R | 44 statsExpressions-1.3.2/statsExpressions/R/meta_analysis.R | 13 statsExpressions-1.3.2/statsExpressions/R/one_sample_test.R | 16 statsExpressions-1.3.2/statsExpressions/R/oneway_anova.R | 25 statsExpressions-1.3.2/statsExpressions/R/pairwise_comparisons.R |only statsExpressions-1.3.2/statsExpressions/R/switch_functions.R | 209 +-- statsExpressions-1.3.2/statsExpressions/R/tidy_model_expressions.R | 161 +- statsExpressions-1.3.2/statsExpressions/R/two_sample_test.R | 13 statsExpressions-1.3.2/statsExpressions/README.md | 182 +-- statsExpressions-1.3.2/statsExpressions/build/vignette.rds |binary statsExpressions-1.3.2/statsExpressions/inst/WORDLIST | 5 statsExpressions-1.3.2/statsExpressions/inst/doc/statsExpressions.html | 52 statsExpressions-1.3.2/statsExpressions/inst/doc/stats_details.Rmd | 8 statsExpressions-1.3.2/statsExpressions/inst/doc/stats_details.html | 69 - statsExpressions-1.3.2/statsExpressions/man/add_expression_col.Rd | 4 statsExpressions-1.3.2/statsExpressions/man/centrality_description.Rd | 16 statsExpressions-1.3.2/statsExpressions/man/contingency_table.Rd | 15 statsExpressions-1.3.2/statsExpressions/man/corr_test.Rd | 11 statsExpressions-1.3.2/statsExpressions/man/figures/README-anova_parametric2-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-anova_rob1-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-centrality-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-corr-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-custom_expr-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-gof-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-metaanalysis-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_one-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_two-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/README-t_two_paired1-1.png |binary statsExpressions-1.3.2/statsExpressions/man/figures/card.png |binary statsExpressions-1.3.2/statsExpressions/man/long_to_wide_converter.Rd | 28 statsExpressions-1.3.2/statsExpressions/man/meta_analysis.Rd | 10 statsExpressions-1.3.2/statsExpressions/man/one_sample_test.Rd | 11 statsExpressions-1.3.2/statsExpressions/man/oneway_anova.Rd | 28 statsExpressions-1.3.2/statsExpressions/man/p_adjust_text.Rd |only statsExpressions-1.3.2/statsExpressions/man/pairwise_comparisons.Rd |only statsExpressions-1.3.2/statsExpressions/man/reexports.Rd | 2 statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/functionality.Rmd | 13 statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/pairwise_comparisons.Rmd |only statsExpressions-1.3.2/statsExpressions/man/rmd-fragments/return.Rmd | 4 statsExpressions-1.3.2/statsExpressions/man/tidy_model_expressions.Rd | 6 statsExpressions-1.3.2/statsExpressions/man/two_sample_test.Rd | 28 statsExpressions-1.3.2/statsExpressions/tests/spelling.R | 12 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/centrality_description.md | 298 +++-- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/contingency_table.md | 105 + statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/corr_test.md | 168 ++- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/long_to_wide_converter.md | 192 +-- statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/meta_random_parametric.md | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/meta_random_robust.md | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/one_sample.md | 69 - statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/one_two_sample_dataframes.md | 56 - statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_bayes.md |only statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_nonparametric.md | 36 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_parametric.md | 40 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/oneway_anova_robust.md | 26 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/pairwise_comparisons.md |only statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/tidy_model_expressions.md | 147 ++ statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_bayes.md | 20 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_nonparametric.md | 17 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_parametric.md | 34 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/two_sample_robust.md | 32 statsExpressions-1.3.2/statsExpressions/tests/testthat/_snaps/z_meta_random_bayes.md | 17 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-centrality_description.R | 29 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-contingency_table.R | 554 ++++------ statsExpressions-1.3.2/statsExpressions/tests/testthat/test-corr_test.R | 167 +-- statsExpressions-1.3.2/statsExpressions/tests/testthat/test-long_to_wide_converter.R | 21 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-meta_random_parametric.R | 4 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-meta_random_robust.R | 4 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-one_sample.R | 24 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-one_two_sample_dataframes.R | 10 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_bayes.R | 50 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_nonparametric.R | 91 - statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_parametric.R | 18 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-oneway_anova_robust.R | 18 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-pairwise_comparisons.R |only statsExpressions-1.3.2/statsExpressions/tests/testthat/test-tidy_model_expressions.R | 190 ++- statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_bayes.R | 15 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_nonparametric.R | 8 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_parametric.R | 16 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-two_sample_robust.R | 16 statsExpressions-1.3.2/statsExpressions/tests/testthat/test-z_meta_random_bayes.R | 10 statsExpressions-1.3.2/statsExpressions/vignettes/stats_details.Rmd | 8 statsExpressions-1.3.2/statsExpressions/vignettes/web_only/dataframe_outputs.Rmd | 127 ++ 96 files changed, 2501 insertions(+), 1939 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Nonparametric Methods for Generating High Quality Comparative
Effectiveness Evidence
Description: Implements novel nonparametric approaches to address
biases and confounding when comparing treatments or exposures in
observational studies of outcomes. While designed and appropriate for use
in studies involving medicine and the life sciences, the package can be
used in other situations involving outcomes with multiple confounders.
The package implements a family of methods for non-parametric bias correction
when comparing treatments in observational studies, including survival
analysis settings, where competing risks and/or censoring may be present.
The approach extends to bias-corrected personalized predictions of treatment
outcome differences, and analysis of heterogeneity of treatment effect-sizes
across patient subgroups. For further details, please see:
Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
An R Package for Comparative Safety and Effectiveness Research.
Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
Author: Nicolas R. Lauve [aut] ,
Stuart J. Nelson [aut] ,
S. Stanley Young [aut] ,
Robert L. Obenchain [aut] ,
Melania Pintilie [ctb],
Martin Kutz [ctb],
Christophe G. Lambert [aut, cre]
Maintainer: Christophe G. Lambert <cglambert@unm.edu>
Diff between LocalControl versions 1.1.2.2 dated 2020-11-26 and 1.1.3 dated 2022-05-20
LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.R |only LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.Rnw |only LocalControl-1.1.2.2/LocalControl/inst/doc/LocalControl-jss-2018.pdf |only LocalControl-1.1.2.2/LocalControl/vignettes/LocalControl-jss-2018.Rnw |only LocalControl-1.1.3/LocalControl/DESCRIPTION | 10 +- LocalControl-1.1.3/LocalControl/MD5 | 22 ++-- LocalControl-1.1.3/LocalControl/NEWS.md | 8 + LocalControl-1.1.3/LocalControl/R/clusteringLC.R | 2 LocalControl-1.1.3/LocalControl/R/localControl.R | 2 LocalControl-1.1.3/LocalControl/build/vignette.rds |binary LocalControl-1.1.3/LocalControl/inst/CITATION | 48 ++++------ LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.R |only LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.Rnw |only LocalControl-1.1.3/LocalControl/inst/doc/LocalControl-jss-2020.pdf |only LocalControl-1.1.3/LocalControl/src/RcppExports.cpp | 5 + LocalControl-1.1.3/LocalControl/vignettes/LocalControl-jss-2020.Rnw |only 16 files changed, 51 insertions(+), 46 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations and (3) calculating confidence intervals and the associated
actual coverage for binomial proportions. Each is given in greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif,
weibull) corresponding to a user-given complete or right-censored dataset and level of
significance. The crplot() algorithm plots more points in areas of greater curvature to
ensure a smooth appearance throughout the confidence region boundary. An alternative
heuristic plots a specified number of points at roughly uniform intervals along its boundary.
Both heuristics build upon the radial profile log-likelihood ratio technique for plotting
confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>, and
are detailed in a publication by Weld (2019) <doi:10.1080/00031305.2018.1564696>.
(2) Performs confidence region coverage simulations for a random sample drawn from a user-
specified parametric population distribution, or for a user-specified dataset and point of
interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion
with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the
actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the
binomial proportion using an ensemble of constituent confidence intervals with
binomTestEnsemble(). Calculates confidence interval bounds for the binomial proportion using
a complete enumeration of all possible transitions from one actual coverage acceptance curve
to another which minimizes the root mean square error for n <= 15 and follows the transitions
for well-known confidence intervals for n > 15 using binomTestMSE().
Author: Christopher Weld [aut, cre] ,
Hayeon Park [aut],
Kexin Feng [aut],
Heather Sasinowska [aut],
Lawrence Leemis [aut],
Andrew Loh [ctb],
Yuan Chang [ctb],
Brock Crook [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>
Diff between conf versions 1.7.0 dated 2020-08-24 and 1.7.1 dated 2022-05-20
DESCRIPTION | 13 MD5 | 22 NAMESPACE | 15 R/STAR_package_functions.R |only R/coversim.R | 66 - R/crplot.R | 1688 +++++++++++++++++++++--------------------- inst/CITATION | 2 inst/doc/coversim.html | 22 inst/doc/crplot.html | 32 inst/doc/crplot_advanced.html | 28 man/dinvgauss.Rd |only man/dllogis.Rd |only man/gammaMLE.Rd |only man/invgaussMLE.Rd |only man/llogisMLE.Rd |only 15 files changed, 959 insertions(+), 929 deletions(-)
Title: Interactive Model Exploration using 'GGobi'
Description: Exploratory model analysis with <http://ggobi.org>.
Fit and graphical explore ensembles of linear models.
Author: Hadley Wickham <h.wickham@gmail.com>
Maintainer: Hadley Wickham <h.wickham@gmail.com>
Diff between meifly versions 0.3 dated 2014-04-23 and 0.3.1 dated 2022-05-20
meifly-0.3.1/meifly/DESCRIPTION | 22 ++++++------ meifly-0.3.1/meifly/MD5 | 32 +++++++++--------- meifly-0.3.1/meifly/NAMESPACE | 2 - meifly-0.3.1/meifly/NEWS.md |only meifly-0.3.1/meifly/R/generate.r | 30 ++++++++--------- meifly-0.3.1/meifly/R/summarise.r | 33 +++++++++---------- meifly-0.3.1/meifly/man/coef.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/findmodels.Rd | 4 +- meifly-0.3.1/meifly/man/fitall.Rd | 4 +- meifly-0.3.1/meifly/man/fitbest.Rd | 4 +- meifly-0.3.1/meifly/man/lmboot.Rd | 4 +- meifly-0.3.1/meifly/man/meifly.Rd | 4 +- meifly-0.3.1/meifly/man/new_ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/residuals.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.resid_ensemble.Rd | 4 +- meifly-0.3.1/meifly/man/summary.variable_ensemble.Rd | 4 +- meifly-0.3/meifly/NEWS |only 18 files changed, 82 insertions(+), 81 deletions(-)
Title: Fundamental Clustering Problems Suite
Description: Over sixty clustering algorithms are provided in this package with consistent input and output, which enables the user to try out algorithms swiftly. Additionally, 26 statistical approaches for the estimation of the number of clusters as well as the mirrored density plot (MD-plot) of clusterability are implemented. The packages is published in Thrun, M.C., Stier Q.: "Fundamental Clustering Algorithms Suite" (2021), SoftwareX, <DOI:10.1016/j.softx.2020.100642>. Moreover, the fundamental clustering problems suite (FCPS) offers a variety of clustering challenges any algorithm should handle when facing real world data, see Thrun, M.C., Ultsch A.: "Clustering Benchmark Datasets Exploiting the Fundamental Clustering Problems" (2020), Data in Brief, <DOI:10.1016/j.dib.2020.105501>.
Author: Michael Thrun [aut, cre, cph] ,
Peter Nahrgang [ctr, ctb],
Felix Pape [ctr, ctb],
Vasyl Pihur [ctb],
Guy Brock [ctb],
Susmita Datta [ctb],
Somnath Datta [ctb],
Luis Winckelmann [com],
Alfred Ultsch [dtc, ctb],
Quirin Stier [ctb, rev]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between FCPS versions 1.3.0 dated 2021-07-07 and 1.3.1 dated 2022-05-20
DESCRIPTION | 12 MD5 | 68 NAMESPACE | 199 - R/ClusterAccuracy.R | 204 - R/ClusterChallenge.R | 393 +- R/ClusterCount.R | 3 R/ClusterDaviesBouldinIndex.R | 12 R/ClusterDunnIndex.R | 125 R/ClusterEqualWeighting.R | 91 R/ClusterMCC.R |only R/ClusterNoEstimation.R | 662 ++-- R/ClusterNormalize.R |only R/ClusterRedefine.R |only R/ClusterRenameDescendingSize.R | 18 R/ClusterUpsamplingMinority.R |only R/ModelBasedVarSelClustering.R | 176 - R/NetworkClustering.R |only R/SparseClustering.R | 168 - README.md | 17 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FCPS.R | 208 - inst/doc/FCPS.Rmd | 332 +- inst/doc/FCPS.html | 4928 ++++++++++++++++++------------------- man/ClusterAccuracy.Rd | 136 - man/ClusterDaviesBouldinIndex.Rd | 4 man/ClusterDunnIndex.Rd | 143 - man/ClusterEqualWeighting.Rd | 4 man/ClusterMCC.Rd |only man/ClusterNoEstimation.Rd | 303 +- man/ClusterNormalize.Rd |only man/ClusterRedefine.Rd |only man/ClusterRenameDescendingSize.Rd | 27 man/ClusterUpsamplingMinority.Rd |only man/DivisiveAnalysisClustering.Rd | 104 man/FCPS-package.Rd | 1 man/MoGclustering.Rd | 156 - man/NetworkClustering.Rd |only man/SparseClustering.Rd | 147 - vignettes/FCPS.Rmd | 332 +- 40 files changed, 4598 insertions(+), 4375 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-20 0.7.0
2022-02-18 0.6.0
2021-07-27 0.5.0
2021-04-30 0.4.1
Title: Tools for Information-Based Feature Selection and Scoring
Description: A toolbox of fast, native and parallel implementations of various information-based importance criteria estimators and feature selection filters based on them, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <https://www.jmlr.org/papers/v13/brown12a.html>.
Contains, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <https://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre]
Maintainer: Miron B. Kursa <m@mbq.me>
Diff between praznik versions 10.0.0 dated 2021-11-09 and 11.0.0 dated 2022-05-20
DESCRIPTION | 13 +++++++------ MD5 | 32 ++++++++++++++++---------------- R/praznik.R | 2 +- R/transforms.R | 4 ++-- inst/CITATION | 16 ++++++++++++++++ inst/NEWS | 3 +++ man/kInverse.Rd | 2 +- man/kTransform.Rd | 2 +- man/praznik-package.Rd | 2 +- src/trips.h | 2 +- tests/testthat/test-engine.R | 2 -- tests/testthat/test-input.R | 2 -- tests/testthat/test-madelon.R | 2 -- tests/testthat/test-matrix.R | 2 -- tests/testthat/test-native-pure.R | 2 -- tests/testthat/test-tools.R | 2 -- tests/testthat/test-transform.R | 2 -- 17 files changed, 49 insertions(+), 43 deletions(-)
Title: User-Friendly R Package for Supervised Machine Learning
Pipelines
Description: An interface to build machine learning models for
classification and regression problems. 'mikropml' implements the ML
pipeline described by Topçuoğlu et al. (2020)
<doi:10.1128/mBio.00434-20> with reasonable default options for data
preprocessing, hyperparameter tuning, cross-validation, testing, model
evaluation, and interpretation steps. See the website
<https://www.schlosslab.org/mikropml/> for more information,
documentation, and examples.
Author: Beguem Topcuoğlu [aut] ,
Zena Lapp [aut] ,
Kelly Sovacool [aut, cre] ,
Evan Snitkin [aut] ,
Jenna Wiens [aut] ,
Patrick Schloss [aut] ,
Nick Lesniak [ctb] ,
Courtney Armour [ctb] ,
Sarah Lucas [ctb]
Maintainer: Kelly Sovacool <sovacool@umich.edu>
Diff between mikropml versions 1.2.2 dated 2022-02-03 and 1.3.0 dated 2022-05-20
DESCRIPTION | 12 MD5 | 84 ++-- NAMESPACE | 2 NEWS.md | 7 R/checks.R | 2 R/compare_models.R |only R/cross_val.R | 1 R/data.R | 10 R/feature_importance.R | 61 ++- R/utils.R | 6 build/partial.rdb |binary build/vignette.rds |binary data/otu_mini_bin.rda |binary data/otu_mini_bin_results_glmnet.rda |binary data/otu_mini_bin_results_rf.rda |binary data/otu_mini_bin_results_rpart2.rda |binary data/otu_mini_bin_results_svmRadial.rda |binary data/otu_mini_bin_results_xgbTree.rda |binary data/otu_mini_cont_results_glmnet.rda |binary data/otu_mini_cont_results_nocv.rda |binary data/otu_mini_cv.rda |binary data/otu_mini_multi.rda |binary data/otu_mini_multi_group.rda |binary data/otu_mini_multi_results_glmnet.rda |binary data/otu_small.rda |binary inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 605 ++++++++++++++++++++++++++----- inst/doc/paper.Rmd | 2 inst/doc/paper.html | 497 ++++++++++++++++++++++--- man/compare_models.Rd |only man/get_feature_importance.Rd | 61 ++- man/otu_mini_bin_results_glmnet.Rd | 4 man/otu_mini_bin_results_rf.Rd | 4 man/otu_mini_bin_results_rpart2.Rd | 4 man/otu_mini_bin_results_svmRadial.Rd | 4 man/otu_mini_bin_results_xgbTree.Rd | 4 man/permute_p_value.Rd |only man/reexports.Rd | 2 tests/testthat/test-compare_models.R |only tests/testthat/test-cross_val.R | 26 - tests/testthat/test-feature_importance.R | 20 - tests/testthat/test-run_ml.R | 5 tests/testthat/test-utils.R | 5 vignettes/introduction.Rmd | 4 vignettes/paper.Rmd | 2 45 files changed, 1161 insertions(+), 277 deletions(-)
Title: Threshold Regression that Fits the (Randomized Drift) Inverse
Gaussian Distribution to Survival Data
Description: Fits the (randomized drift) inverse Gaussian distribution to survival data. The model is described in Aalen OO, Borgan O, Gjessing HK. Survival and Event History Analysis. A Process Point of View. Springer, 2008. It is based on describing time to event as the barrier hitting time of a Wiener process, where drift towards the barrier has been randomized with a Gaussian distribution. The model allows covariates to influence starting values of the Wiener process and/or average drift towards a barrier, with a user-defined choice of link functions.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between invGauss versions 1.1 dated 2014-03-28 and 1.2 dated 2022-05-20
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 3 ++- R/predict.invGauss.R | 7 +++++-- man/d.oropha.rec.Rd | 2 +- 5 files changed, 20 insertions(+), 16 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 3.4.0 dated 2022-04-26 and 3.5.0 dated 2022-05-20
DESCRIPTION | 12 +- MD5 | 83 ++++++++++--------- NAMESPACE | 1 NEWS.md | 5 + R/delete_trailing_blank_lines.R |only R/test_helpers.R | 7 - R/view.R | 9 +- inst/NEWS.rd | 7 + inst/files/blanks.txt |only inst/runit_tests/runit-delete_trailing_blank_lines.R |only inst/runit_tests/runit-delete_trailing_whitespace.R |only inst/source/R/delete_trailing_blank_lines.R |only inst/source/R/test_helpers.R | 7 - inst/source/R/view.R | 9 +- inst/source/man/clipboard_path.Rd | 1 inst/source/man/delete_trailing_blank_lines.Rd |only inst/source/man/delete_trailing_whitespace.Rd | 1 inst/source/man/develop_test.Rd | 1 inst/source/man/file_copy.Rd | 1 inst/source/man/file_modified_last.Rd | 1 inst/source/man/file_save.Rd | 1 inst/source/man/find_files.Rd | 1 inst/source/man/get_mtime.Rd | 1 inst/source/man/get_unique_string.Rd | 1 inst/source/man/is_files_current.Rd | 1 inst/source/man/is_path.Rd | 1 inst/source/man/paths.Rd | 1 inst/source/man/search_files.Rd | 1 inst/source/man/split_code_file.Rd | 1 inst/source/man/touch.Rd | 1 man/clipboard_path.Rd | 1 man/delete_trailing_blank_lines.Rd |only man/delete_trailing_whitespace.Rd | 1 man/develop_test.Rd | 1 man/file_copy.Rd | 1 man/file_modified_last.Rd | 1 man/file_save.Rd | 1 man/find_files.Rd | 1 man/get_mtime.Rd | 1 man/get_unique_string.Rd | 1 man/is_files_current.Rd | 1 man/is_path.Rd | 1 man/paths.Rd | 1 man/search_files.Rd | 1 man/split_code_file.Rd | 1 man/touch.Rd | 1 46 files changed, 112 insertions(+), 58 deletions(-)
Title: Unbinned Weighted Histogram Analysis Method (UWHAM)
Description: A method for estimating log-normalizing constants (or free
energies) and expectations from multiple distributions (such as
multiple generalized ensembles).
Author: Zhiqiang Tan and Emilio Gallicchio
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>
Diff between UWHAM versions 1.0 dated 2013-01-26 and 1.1 dated 2022-05-20
DESCRIPTION | 14 ++++++++------ MD5 | 5 +++-- NAMESPACE | 2 ++ NEWS.md |only 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 2.5.1 dated 2022-01-26 and 2.6.0 dated 2022-05-20
DESCRIPTION | 8 - MD5 | 83 ++++++------- NAMESPACE | 1 NEWS.md | 12 + R/Connection.R | 113 ++++++++++------- R/Driver.R | 49 +++++++ R/File_Parser.R | 4 R/Options.R | 20 ++- R/Result.R | 38 ++--- R/View.R | 70 ++++++---- R/athena_low_api.R | 68 ++++++---- R/dplyr_integration.R | 6 R/fetch_utils.R | 10 - R/table.R | 10 - R/utils.R | 185 ++++++++++++++++++----------- R/zzz.R | 4 README.md | 1 build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 22 +-- inst/doc/aws_athena_unload.Rmd | 9 - inst/doc/aws_athena_unload.html | 13 +- inst/doc/aws_s3_backend.html | 9 - inst/doc/changing_backend_file_parser.Rmd | 2 inst/doc/changing_backend_file_parser.html | 3 inst/doc/convert_and_save_cost.html | 1 inst/doc/getting_started.Rmd | 2 inst/doc/getting_started.html | 25 ++- inst/doc/how_to_retry.Rmd | 2 inst/doc/how_to_retry.html | 7 - man/RAthena_options.Rd | 5 man/dbClearResult.Rd | 3 man/dbConnect-AthenaDriver-method.Rd | 49 +++++++ man/dbGetQuery.Rd | 4 man/db_compute.Rd | 6 man/install_boto.Rd | 4 tests/testthat/test-endpoint-override.R |only tests/testthat/test-keyboard-interrupt.R | 8 - tests/testthat/test-metadata.R | 44 ++++++ tests/testthat/test-view.R | 2 vignettes/aws_athena_unload.Rmd | 9 - vignettes/changing_backend_file_parser.Rmd | 2 vignettes/getting_started.Rmd | 2 vignettes/how_to_retry.Rmd | 2 43 files changed, 592 insertions(+), 325 deletions(-)
Title: Ridge-Type Penalized Estimation of a Potpourri of Models
Description: The name of the package is derived from the French, 'pour' ridge, and provides functionality for ridge-type estimation of a potpourri of models. Currently, this estimation concerns that of various Gaussian graphical models from different study designs. Among others it considers the regular Gaussian graphical model and a mixture of such models. The porridge-package implements the estimation of the former either from i) data with replicated observations by penalized loglikelihood maximization using the regular ridge penalty on the parameters (van Wieringen, Chen, 2021) or ii) from non-replicated data by means of either a ridge estimator with multiple shrinkage targets (as presented in van Wieringen et al. 2020, <doi:10.1016/j.jmva.2020.104621>) or the generalized ridge estimator that allows for both the inclusion of quantitative and qualitative prior information on the precision matrix via element-wise penalization and shrinkage (van Wieringen, 2019, <doi:10.1080/10618600.2019.1604374>). Additionally, the porridge-package facilitates the ridge penalized estimation of a mixture of Gaussian graphical models (Aflakparast et al., 2018). On another note, the package also includes functionality for ridge-type estimation of the generalized linear model (as presented in van Wieringen, Binder, 2022, <doi:10.1080/10618600.2022.2035231>).
Author: Wessel N. van Wieringen [aut, cre]
,
Mehran Aflakparast [ctb]
Maintainer: Wessel N. van Wieringen <w.vanwieringen@vumc.nl>
Diff between porridge versions 0.3.0 dated 2022-01-08 and 0.3.1 dated 2022-05-20
DESCRIPTION | 23 ++++++----- MD5 | 30 +++++++------- R/ridgeGGMmixtureAndCo.R | 18 ++++---- R/ridgePgenAndCo.R | 75 +++++++++++++++++++------------------ R/ridgePmultitTandCo.R | 10 ++-- R/ridgePrepAndCo.R | 34 ++++++++-------- inst/CITATION | 19 +++++++++ inst/NEWS.Rd | 12 +++++ man/genRidgePenaltyMat.Rd | 5 +- man/makeFoldsGLMcv.Rd | 8 +-- man/optPenaltyGLM.kCVauto.Rd | 2 man/optPenaltyGLMmultiT.kCVauto.Rd | 2 man/porridge-package.Rd | 25 +++--------- man/ridgeGLM.Rd | 2 src/RcppExports.cpp | 6 ++ src/ridgeGGMmix.h | 29 ++++++++------ 16 files changed, 169 insertions(+), 131 deletions(-)
Title: Improved Methods for Causal Inference and Missing Data Problems
Description: Improved methods based on inverse probability weighting
and outcome regression for causal inference and missing data
problems.
Author: Zhiqiang Tan and Heng Shu
Maintainer: Zhiqiang Tan <ztan@stat.rutgers.edu>
Diff between iWeigReg versions 1.0 dated 2013-02-25 and 1.1 dated 2022-05-20
DESCRIPTION | 12 ++++++------ MD5 | 9 ++++++--- NAMESPACE | 1 + NEWS.md |only build |only inst/doc/vig.R |only inst/doc/vig.pdf |binary 7 files changed, 13 insertions(+), 9 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [ctb]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.1.1 dated 2022-01-09 and 0.2.0 dated 2022-05-20
DESCRIPTION | 8 MD5 | 34 +- NAMESPACE | 26 - NEWS.md | 18 + R/data.R | 16 - R/frscore.R | 74 +++-- R/frscored_cna.R | 505 ++++++++++++++++++------------------- README.md | 14 - inst/WORDLIST | 54 +-- man/d.error.Rd | 36 +- man/frscore.Rd | 208 +++++++-------- man/frscored_cna.Rd | 15 - man/rean_cna.Rd | 124 ++++----- tests/spelling.R | 6 tests/testthat.R | 10 tests/testthat/_snaps |only tests/testthat/test_frscore.R | 143 +++++----- tests/testthat/test_frscored_cna.R | 41 +-- 18 files changed, 695 insertions(+), 637 deletions(-)
Title: Brings Seurat to the Tidyverse
Description: It creates an invisible layer that allow to see the 'Seurat' object
as tibble and interact seamlessly with the tidyverse.
Author: Stefano Mangiola [aut, cre],
Maria Doyle [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyseurat versions 0.5.1 dated 2022-02-03 and 0.5.3 dated 2022-05-20
DESCRIPTION | 12 MD5 | 28 - NAMESPACE | 9 R/pillar_utilities.R |only R/print_method.R | 519 +++++++----------------- R/tidyr_methods.R | 8 R/utilities.R | 775 ++++++++++++++++++------------------ README.md | 100 ---- build/tidyseurat.pdf |binary inst/doc/introduction.R | 195 ++++----- inst/doc/introduction.html | 174 ++------ man/figures/pc_plot-1.png |binary man/figures/plot2-1.png |binary man/figures/unnamed-chunk-12-1.png |binary man/fragments/intro.Rmd | 789 ++++++++++++++++++------------------- man/tbl_format_header-methods.Rd |only 16 files changed, 1150 insertions(+), 1459 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.3 dated 2021-03-05 and 1.0.4 dated 2022-05-20
tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.R |only tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.Rmd |only tidyquant-1.0.3/tidyquant/inst/doc/TQ06-excel-in-r.html |only tidyquant-1.0.3/tidyquant/vignettes/TQ06-excel-in-r.Rmd |only tidyquant-1.0.3/tidyquant/vignettes/r-for-excel-users.jpg |only tidyquant-1.0.4/tidyquant/DESCRIPTION | 13 tidyquant-1.0.4/tidyquant/LICENSE | 4 tidyquant-1.0.4/tidyquant/MD5 | 205 tidyquant-1.0.4/tidyquant/NAMESPACE | 400 - tidyquant-1.0.4/tidyquant/NEWS.md | 530 +- tidyquant-1.0.4/tidyquant/R/api-alphavantager.R | 58 tidyquant-1.0.4/tidyquant/R/api-quandl.R | 124 tidyquant-1.0.4/tidyquant/R/api-tiingo.R | 66 tidyquant-1.0.4/tidyquant/R/data.R | 38 tidyquant-1.0.4/tidyquant/R/deprecated.R | 78 tidyquant-1.0.4/tidyquant/R/excel-date-functions.R | 1216 ++-- tidyquant-1.0.4/tidyquant/R/excel-financial-math-functions.R | 380 - tidyquant-1.0.4/tidyquant/R/excel-if-functions.R | 422 - tidyquant-1.0.4/tidyquant/R/excel-pivot-table.R | 540 +- tidyquant-1.0.4/tidyquant/R/excel-ref-functions.R | 130 tidyquant-1.0.4/tidyquant/R/excel-stat-mutation-functions.R | 382 - tidyquant-1.0.4/tidyquant/R/excel-stat-summary-functions.R | 472 - tidyquant-1.0.4/tidyquant/R/ggplot-coord_date.R | 162 tidyquant-1.0.4/tidyquant/R/ggplot-geom_bbands.R | 670 +- tidyquant-1.0.4/tidyquant/R/ggplot-geom_chart.R | 470 - tidyquant-1.0.4/tidyquant/R/ggplot-geom_ma.R | 492 - tidyquant-1.0.4/tidyquant/R/ggplot-scale_manual.R | 298 - tidyquant-1.0.4/tidyquant/R/ggplot-theme_tq.R | 292 - tidyquant-1.0.4/tidyquant/R/global_vars.R | 296 - tidyquant-1.0.4/tidyquant/R/tidyquant.R | 82 tidyquant-1.0.4/tidyquant/R/tq_get.R | 2576 +++++----- tidyquant-1.0.4/tidyquant/R/tq_mutate.R | 827 +-- tidyquant-1.0.4/tidyquant/R/tq_performance.R | 634 +- tidyquant-1.0.4/tidyquant/R/tq_portfolio.R | 898 +-- tidyquant-1.0.4/tidyquant/R/tq_stock_list.R | 648 +- tidyquant-1.0.4/tidyquant/R/tq_transmute.R | 804 +-- tidyquant-1.0.4/tidyquant/R/utils-dates.R | 58 tidyquant-1.0.4/tidyquant/R/utils-downloaders.R | 168 tidyquant-1.0.4/tidyquant/R/utils-formatting.R | 98 tidyquant-1.0.4/tidyquant/R/utils-pipe.R | 22 tidyquant-1.0.4/tidyquant/R/utils-validation.R | 28 tidyquant-1.0.4/tidyquant/R/zzz.R | 68 tidyquant-1.0.4/tidyquant/README.md | 341 - tidyquant-1.0.4/tidyquant/build/vignette.rds |binary tidyquant-1.0.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.R | 66 tidyquant-1.0.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.Rmd | 244 tidyquant-1.0.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.html | 289 - tidyquant-1.0.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.R | 328 - tidyquant-1.0.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 838 +-- tidyquant-1.0.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.html | 1235 ++-- tidyquant-1.0.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.R | 606 +- tidyquant-1.0.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.Rmd | 1110 ++-- tidyquant-1.0.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.html | 1694 +++--- tidyquant-1.0.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.R | 294 - tidyquant-1.0.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 648 +- tidyquant-1.0.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 1129 ++-- tidyquant-1.0.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.R | 560 +- tidyquant-1.0.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.Rmd | 962 +-- tidyquant-1.0.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.html | 1151 ++-- tidyquant-1.0.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.R | 708 +- tidyquant-1.0.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 1400 ++--- tidyquant-1.0.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.html | 2245 ++++---- tidyquant-1.0.4/tidyquant/man/FANG.Rd | 62 tidyquant-1.0.4/tidyquant/man/av_api_key.Rd | 60 tidyquant-1.0.4/tidyquant/man/coord_x_date.Rd | 142 tidyquant-1.0.4/tidyquant/man/deprecated.Rd | 90 tidyquant-1.0.4/tidyquant/man/excel_date_functions.Rd | 744 +- tidyquant-1.0.4/tidyquant/man/excel_financial_math_functions.Rd | 216 tidyquant-1.0.4/tidyquant/man/excel_if_functions.Rd | 276 - tidyquant-1.0.4/tidyquant/man/excel_pivot_table.Rd | 170 tidyquant-1.0.4/tidyquant/man/excel_ref_functions.Rd | 124 tidyquant-1.0.4/tidyquant/man/excel_stat_mutation_functions.Rd | 246 tidyquant-1.0.4/tidyquant/man/excel_stat_summary_functions.Rd | 260 - tidyquant-1.0.4/tidyquant/man/geom_bbands.Rd | 418 - tidyquant-1.0.4/tidyquant/man/geom_chart.Rd | 296 - tidyquant-1.0.4/tidyquant/man/geom_ma.Rd | 346 - tidyquant-1.0.4/tidyquant/man/palette_tq.Rd | 46 tidyquant-1.0.4/tidyquant/man/pipe.Rd | 24 tidyquant-1.0.4/tidyquant/man/quandl_api_key.Rd | 58 tidyquant-1.0.4/tidyquant/man/quandl_search.Rd | 70 tidyquant-1.0.4/tidyquant/man/scale_manual.Rd | 124 tidyquant-1.0.4/tidyquant/man/theme_tq.Rd | 100 tidyquant-1.0.4/tidyquant/man/tidyquant.Rd | 62 tidyquant-1.0.4/tidyquant/man/tiingo_api_key.Rd | 60 tidyquant-1.0.4/tidyquant/man/tq_get.Rd | 362 - tidyquant-1.0.4/tidyquant/man/tq_index.Rd | 140 tidyquant-1.0.4/tidyquant/man/tq_mutate.Rd | 347 - tidyquant-1.0.4/tidyquant/man/tq_performance.Rd | 208 tidyquant-1.0.4/tidyquant/man/tq_portfolio.Rd | 302 - tidyquant-1.0.4/tidyquant/tests/testthat.R | 14 tidyquant-1.0.4/tidyquant/tests/testthat/test-excel-pivot_table.R | 84 tidyquant-1.0.4/tidyquant/tests/testthat/test-index-tq_index.R | 92 tidyquant-1.0.4/tidyquant/tests/testthat/test-index_tq_exchange.R | 76 tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_get_economic_data.R | 72 tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_get_stock_prices.R | 80 tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_mutate.R | 396 - tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_performance.R | 114 tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_portfolio.R | 152 tidyquant-1.0.4/tidyquant/tests/testthat/test-tq_transmute.R | 380 - tidyquant-1.0.4/tidyquant/vignettes/TQ00-introduction-to-tidyquant.Rmd | 244 tidyquant-1.0.4/tidyquant/vignettes/TQ01-core-functions-in-tidyquant.Rmd | 838 +-- tidyquant-1.0.4/tidyquant/vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 1110 ++-- tidyquant-1.0.4/tidyquant/vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 648 +- tidyquant-1.0.4/tidyquant/vignettes/TQ04-charting-with-tidyquant.Rmd | 962 +-- tidyquant-1.0.4/tidyquant/vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 1400 ++--- tidyquant-1.0.4/tidyquant/vignettes/temp |only 106 files changed, 21269 insertions(+), 21243 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 2.5.1 dated 2022-01-26 and 2.6.0 dated 2022-05-20
DESCRIPTION | 8 +-- MD5 | 55 ++++++++++---------- NAMESPACE | 1 NEWS.md | 6 ++ R/Connection.R | 76 +++++++++++++++++++---------- R/Driver.R | 35 ++++++++++++- R/File_Parser.R | 4 - R/Options.R | 19 +++++-- R/Result.R | 8 +-- R/dplyr_integration.R | 2 R/utils.R | 30 +++++++++++ README.md | 1 build/vignette.rds |binary inst/doc/aws_athena_query_caching.html | 22 ++++---- inst/doc/aws_athena_unload.html | 5 + inst/doc/aws_s3_backend.html | 1 inst/doc/changing_backend_file_parser.Rmd | 2 inst/doc/changing_backend_file_parser.html | 3 - inst/doc/convert_and_save_cost.html | 1 inst/doc/getting_started.html | 21 ++++---- inst/doc/how_to_retry.html | 5 + man/dbClearResult.Rd | 4 + man/dbConnect-AthenaDriver-method.Rd | 35 ++++++++++++- man/dbGetQuery.Rd | 4 + man/db_compute.Rd | 6 -- man/noctua_options.Rd | 5 + tests/testthat/test-endpoint-override.R |only tests/testthat/test-metadata.R | 50 +++++++++++++++++-- vignettes/changing_backend_file_parser.Rmd | 2 29 files changed, 301 insertions(+), 110 deletions(-)
Title: Demand Analysis with the Almost Ideal Demand System (AIDS)
Description: Functions and tools
for analysing consumer demand
with the Almost Ideal Demand System (AIDS)
suggested by Deaton and Muellbauer (1980).
Author: Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between micEconAids versions 0.6-18 dated 2017-03-16 and 0.6-20 dated 2022-05-20
DESCRIPTION | 8 ++--- MD5 | 34 +++++++++++----------- NEWS | 10 +++++- R/aidsCalc.R | 57 ++++++++++++++++++++++++++++++-------- R/aidsElas.R | 44 ++++++++++++++++++++++++----- R/aidsElasJacobian.R | 32 +++++++++++++++++++-- R/aidsEst.R | 9 ++++++ R/aidsPx.R | 8 ++--- R/aidsUtility.R | 2 - R/aidsUtilityDeriv.R | 2 - R/elas.aidsEst.R | 1 R/lrtest.aidsEst.R | 8 ++--- build/vignette.rds |binary inst/doc/micEconAids_vignette.R | 1 inst/doc/micEconAids_vignette.pdf |binary man/aidsCalc.Rd | 4 ++ man/aidsElas.Rd | 29 ++----------------- man/aidsEst.Rd | 1 18 files changed, 167 insertions(+), 83 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in `mrgsolve`, typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format.
Author: Felicien Le Louedec [aut, cre]
,
Kyle T Baron [ctb]
Maintainer: Felicien Le Louedec <lelouedec.felicien@iuct-oncopole.fr>
Diff between mapbayr versions 0.6.0 dated 2022-02-18 and 0.7.0 dated 2022-05-20
mapbayr-0.6.0/mapbayr/inst/models |only mapbayr-0.6.0/mapbayr/inst/nm001/data_to_fit001.csv |only mapbayr-0.6.0/mapbayr/inst/nm001/mrg_001.cpp |only mapbayr-0.6.0/mapbayr/man/add_covariates.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/adm_lines.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/derivatives.Rd |only mapbayr-0.6.0/mapbayr/man/get_cov.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_data.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_data.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/man/get_eta.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_param.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/get_phi.mapbayests.Rd |only mapbayr-0.6.0/mapbayr/man/mbrlib.Rd |only mapbayr-0.6.0/mapbayr/man/obs_lines.mrgmod.Rd |only mapbayr-0.6.0/mapbayr/tests/testthat/test-derivatives.R |only mapbayr-0.6.0/mapbayr/tests/testthat/test-oneindividual.R |only mapbayr-0.7.0/mapbayr/DESCRIPTION | 13 mapbayr-0.7.0/mapbayr/MD5 | 153 +- mapbayr-0.7.0/mapbayr/NAMESPACE | 5 mapbayr-0.7.0/mapbayr/NEWS.md | 32 mapbayr-0.7.0/mapbayr/R/data.R | 7 mapbayr-0.7.0/mapbayr/R/exmodel.R |only mapbayr-0.7.0/mapbayr/R/get.R | 473 +++--- mapbayr-0.7.0/mapbayr/R/mapbayest.R | 35 mapbayr-0.7.0/mapbayr/R/mapbayest_check_and_preprocess.R | 87 - mapbayr-0.7.0/mapbayr/R/mapbayest_ofv_computation.R | 129 + mapbayr-0.7.0/mapbayr/R/mapbayest_optimization.R | 56 mapbayr-0.7.0/mapbayr/R/mapbayests.R | 720 +++++----- mapbayr-0.7.0/mapbayr/R/mrgmod.R | 43 mapbayr-0.7.0/mapbayr/R/read_mrgsolve_model.R | 195 -- mapbayr-0.7.0/mapbayr/R/use_posterior.R | 23 mapbayr-0.7.0/mapbayr/R/vs_nonmem.R | 196 +- mapbayr-0.7.0/mapbayr/R/zzz_utils.R | 21 mapbayr-0.7.0/mapbayr/README.md | 24 mapbayr-0.7.0/mapbayr/data/est001.rda |binary mapbayr-0.7.0/mapbayr/inst/WORDLIST | 129 - mapbayr-0.7.0/mapbayr/inst/exmodel |only mapbayr-0.7.0/mapbayr/inst/nm001/run001.phi | 13 mapbayr-0.7.0/mapbayr/man/adm_0_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/adm_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/augment.mapbayests.Rd | 116 - mapbayr-0.7.0/mapbayr/man/check_mapbayr_model.Rd | 4 mapbayr-0.7.0/mapbayr/man/compute_ofv.Rd | 33 mapbayr-0.7.0/mapbayr/man/data_helpers.Rd | 33 mapbayr-0.7.0/mapbayr/man/est001.Rd | 12 mapbayr-0.7.0/mapbayr/man/exmodel_exdata.Rd |only mapbayr-0.7.0/mapbayr/man/get_x.Rd | 50 mapbayr-0.7.0/mapbayr/man/h.Rd |only mapbayr-0.7.0/mapbayr/man/hist.mapbayests.Rd | 5 mapbayr-0.7.0/mapbayr/man/mapbayest.Rd | 5 mapbayr-0.7.0/mapbayr/man/obs_cmt.Rd | 43 mapbayr-0.7.0/mapbayr/man/plot.mapbayests.Rd | 5 mapbayr-0.7.0/mapbayr/man/preprocess.ofv.Rd | 29 mapbayr-0.7.0/mapbayr/man/qparam.Rd |only mapbayr-0.7.0/mapbayr/man/use_posterior.Rd | 9 mapbayr-0.7.0/mapbayr/man/vs_nonmem.Rd | 134 - mapbayr-0.7.0/mapbayr/tests/testthat.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-adm_lines.R | 32 mapbayr-0.7.0/mapbayr/tests/testthat/test-annotated.R | 54 mapbayr-0.7.0/mapbayr/tests/testthat/test-augment.R | 69 mapbayr-0.7.0/mapbayr/tests/testthat/test-compute_ofv.R | 87 - mapbayr-0.7.0/mapbayr/tests/testthat/test-covariance.R | 81 - mapbayr-0.7.0/mapbayr/tests/testthat/test-evid_egal_2.R | 19 mapbayr-0.7.0/mapbayr/tests/testthat/test-exmodels.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-get_data.R | 27 mapbayr-0.7.0/mapbayr/tests/testthat/test-get_eta.R | 91 - mapbayr-0.7.0/mapbayr/tests/testthat/test-get_param.R | 107 - mapbayr-0.7.0/mapbayr/tests/testthat/test-get_phi.R | 30 mapbayr-0.7.0/mapbayr/tests/testthat/test-hist.R | 33 mapbayr-0.7.0/mapbayr/tests/testthat/test-mbrest.R | 11 mapbayr-0.7.0/mapbayr/tests/testthat/test-mdv_egal_0.R | 110 - mapbayr-0.7.0/mapbayr/tests/testthat/test-methods.R | 28 mapbayr-0.7.0/mapbayr/tests/testthat/test-multi-ID.R | 86 - mapbayr-0.7.0/mapbayr/tests/testthat/test-newini2.R | 45 mapbayr-0.7.0/mapbayr/tests/testthat/test-no_data.R | 24 mapbayr-0.7.0/mapbayr/tests/testthat/test-output.R | 137 - mapbayr-0.7.0/mapbayr/tests/testthat/test-plot.R | 13 mapbayr-0.7.0/mapbayr/tests/testthat/test-progress.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-qparam.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-read_mrgsolve_model.R | 129 + mapbayr-0.7.0/mapbayr/tests/testthat/test-rename_as_eta.R |only mapbayr-0.7.0/mapbayr/tests/testthat/test-reset-conditions.R | 28 mapbayr-0.7.0/mapbayr/tests/testthat/test-use_posterior.R | 204 -- mapbayr-0.7.0/mapbayr/tests/testthat/test-valid_dataset.R | 40 mapbayr-0.7.0/mapbayr/tests/testthat/test-verbose.R | 24 mapbayr-0.7.0/mapbayr/tests/testthat/test-vs_nonmem.R | 37 86 files changed, 2101 insertions(+), 2363 deletions(-)
Title: Estimation of Time Varying Reproduction Numbers and Restored
Incidence Curves Using Variational Techniques
Description: Estimation, by inverting a renewal equation,
of time-varying reproduction numbers and restored incidence curves with
festive days and weekly biases corrected as described in
Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and
Alvarez et al. (2022) <doi:10.3390/biology11040540>.
Author: Luis Alvarez [aut, cre] ,
Jean-David Morel [ctb] ,
Jean-Michel Morel [ctb]
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>
Diff between EpiInvert versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2022-05-20
EpiInvert-0.1.0/EpiInvert/build |only EpiInvert-0.1.0/EpiInvert/inst |only EpiInvert-0.1.0/EpiInvert/vignettes |only EpiInvert-0.1.1/EpiInvert/DESCRIPTION | 11 +- EpiInvert-0.1.1/EpiInvert/MD5 | 30 ++---- EpiInvert-0.1.1/EpiInvert/NEWS.md | 12 ++ EpiInvert-0.1.1/EpiInvert/R/EpiInvert.R | 49 +++++----- EpiInvert-0.1.1/EpiInvert/R/data.R | 11 +- EpiInvert-0.1.1/EpiInvert/R/plot.R | 8 - EpiInvert-0.1.1/EpiInvert/README.md | 75 +++------------- EpiInvert-0.1.1/EpiInvert/man/EpiInvert.Rd | 57 ++++++------ EpiInvert-0.1.1/EpiInvert/man/EpiInvert_plot.Rd | 8 - EpiInvert-0.1.1/EpiInvert/man/figures/README-fig1-1.png |binary EpiInvert-0.1.1/EpiInvert/man/incidence.Rd | 14 +- 14 files changed, 126 insertions(+), 149 deletions(-)
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 2.1.1 dated 2021-09-27 and 2.1.2 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/DJac.R | 2 +- R/FunImbalance.R |only R/PADDis.R | 2 ++ build/partial.rdb |binary man/FunImbalance.Rd |only man/betaUniqueness.Rd | 2 +- 8 files changed, 15 insertions(+), 11 deletions(-)
Title: Read, Validate, Analyze, and Map GTFS Feeds
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <https://gtfs.org/>.
Author: Flavio Poletti [aut, cre],
Daniel Herszenhut [aut] ,
Mark Padgham [aut],
Tom Buckley [aut],
Danton Noriega-Goodwin [aut],
Angela Li [ctb],
Elaine McVey [ctb],
Charles Hans Thompson [ctb],
Michael Sumner [ctb],
Patrick Hausmann [ctb],
Bob Rudis [ctb], [...truncated...]
Maintainer: Flavio Poletti <flavio.poletti@hotmail.ch>
Diff between tidytransit versions 1.3.0 dated 2022-01-31 and 1.3.1 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/raptor.R | 7 +++---- inst/doc/frequency.html | 5 +++-- inst/doc/introduction.html | 21 +++++++++++---------- inst/doc/servicepatterns.html | 5 +++-- inst/doc/timetable.html | 1 + 7 files changed, 31 insertions(+), 28 deletions(-)
Title: Permutation Tests for Time Series Data
Description: Helps you determine the analysis window to use when analyzing densely-sampled
time-series data, such as EEG data, using permutation testing (Maris & Oostenveld, 2007)
<doi:10.1016/j.jneumeth.2007.03.024>. These permutation tests can help identify the timepoints
where significance of an effect begins and ends, and the results can be plotted in various
types of heatmap for reporting. Mixed-effects models are supported using an implementation of
the approach by Lee & Braun (2012) <doi:10.1111/j.1541-0420.2011.01675.x>.
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between permutes versions 2.3.2 dated 2021-12-16 and 2.4 dated 2022-05-20
DESCRIPTION | 12 ++--- MD5 | 20 ++++---- NAMESPACE | 2 R/buildmer.R | 107 ++++++++++++++++++++++++++++++++------------- R/discoverability.R | 41 ++++++++++++----- R/lmPerm.R | 2 build/vignette.rds |binary inst/doc/buildmer.pdf |binary inst/doc/permutes.pdf |binary man/clusterperm.glmmTMB.Rd |only man/perm.glmmTMB.Rd |only man/permu.test.Rd | 4 - 12 files changed, 129 insertions(+), 59 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in "Gjessing HK and Lie RT. Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Annals of Human Genetics (2006) 70, pp. 382-396".
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] ,
Julia Romanowska [ctb] ,
Oivind Skare [ctb]
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.2.3 dated 2020-09-07 and 7.3.0 dated 2022-05-20
DESCRIPTION | 14 - MD5 | 93 ++++---- R/coef.haptable.hapSlide.R | 20 + R/f.create.snp.names.R | 6 R/f.get.which.gen.el.names.R | 5 R/genDataGetPart.R | 8 R/genDataRead.R | 3 R/getDyads_or_Triads.R | 59 ++++- R/haplinStrat0.R | 2 R/plot.haplinSlide.R | 17 + R/showPheno.R | 4 build/vignette.rds |binary inst/CITATION | 1 inst/doc/A_Haplin_intro_installation.html | 92 +++++--- inst/doc/B_Reading_data.html | 268 ++++++++++++++--------- inst/doc/C_Running_Haplin.html | 343 ++++++++++++++++++------------ inst/doc/D_Running_Haplin_on_cluster.html | 145 ++++++++---- inst/doc/E_hapRelEff.html | 305 +++++++++++++++++++------- inst/extdata/qc_all.map |only inst/extdata/qc_all_ok_gen.RData |only inst/extdata/qc_all_ok_gen.ffData |only man/cbindFiles.Rd | 2 man/convertPed.Rd | 2 man/gxe.Rd | 2 man/hapPower.Rd | 4 man/hapPowerAsymp.Rd | 2 man/hapRelEff.Rd | 2 man/hapRun.Rd | 4 man/hapSim.Rd | 6 man/haplin.Rd | 2 man/haplinSlide.Rd | 2 man/haplinStrat.Rd | 2 man/haptable.Rd | 14 - man/lineByLine.Rd | 2 man/output.Rd | 2 man/pQQ.Rd | 2 man/pedToHaplin.Rd | 2 man/plot.haplin.Rd | 7 man/plot.haptable.Rd | 5 man/print.haplin.Rd | 2 man/print.summary.haplin.Rd | 2 man/rbindFiles.Rd | 2 man/snpPos.Rd | 2 man/snpPower.Rd | 2 man/snpSampleSize.Rd | 2 man/suest.Rd | 2 man/summary.haplin.Rd | 2 man/toDataFrame.Rd | 2 vignettes/Styrke_artikkel_rmd.bib | 2 49 files changed, 953 insertions(+), 516 deletions(-)
Title: Transfer Function and ARIMA Models
Description: Building customized transfer function and ARIMA models with multiple operators and parameter restrictions. Functions for model identification, model estimation (exact or conditional maximum likelihood), model diagnostic checking, automatic outlier detection, calendar effects, forecasting and seasonal adjustment. See Bell and Hillmer (1983) <doi:10.1080/01621459.1983.10478005>, Box, Jenkins, Reinsel and Ljung <ISBN:978-1-118-67502-1>, Box, Pierce and Newbold (1987) <doi:10.1080/01621459.1987.10478430>, Box and Tiao (1975) <doi:10.1080/01621459.1975.10480264>, Chen and Liu (1993) <doi:10.1080/01621459.1993.10594321>.
Author: Jose L. Gallego [aut, cre]
Maintainer: Jose L. Gallego <jose.gallego@unican.es>
Diff between tfarima versions 0.3.1 dated 2022-05-06 and 0.3.2 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ R/tf.R | 1 + R/tfm.R | 16 +++++++++------- R/um.R | 16 +++++++++++++--- inst/doc/tfarima.pdf |binary man/ucomp.Rd | 2 +- src/decomp.cpp | 38 ++++++++++++++++++-------------------- 9 files changed, 56 insertions(+), 43 deletions(-)
Title: Gaussian Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Gaussian finite mixture models fitted via EM algorithm for
model-based clustering, classification, and density estimation,
including Bayesian regularization, dimension reduction for
visualisation, and resampling-based inference.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut] ,
Luca Scrucca [aut, cre] ,
Thomas Brendan Murphy [ctb] ,
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclust versions 5.4.9 dated 2021-12-17 and 5.4.10 dated 2022-05-20
DESCRIPTION | 8 - MD5 | 72 ++++++++-------- NEWS.md | 7 + R/bootstrap.R | 4 R/densityMclust.R | 8 - R/graphics.R | 5 - R/mclustda.R | 12 +- R/mclustdr.R | 25 ++--- R/mclustssc.R | 4 R/options.R | 4 R/zzz.R | 19 +++- build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/EuroUnemployment.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/doc/mclust.html | 141 ++++++++++++++++++++------------ man/Baudry_etal_2010_JCGS_examples.Rd | 2 man/Mclust.Rd | 9 +- man/MclustBootstrap.Rd | 2 man/MclustDRsubsel.Rd | 18 ++-- man/cdfMclust.Rd | 6 - man/densityMclust.Rd | 2 man/densityMclust.diagnostic.Rd | 2 man/diabetes.Rd | 4 man/mclust-package.Rd | 5 - man/plot.densityMclust.Rd | 6 - man/predict.densityMclust.Rd | 4 man/summary.Mclust.Rd | 4 man/summary.MclustBootstrap.Rd | 2 man/thyroid.Rd | 4 man/wdbc.Rd | 4 37 files changed, 222 insertions(+), 161 deletions(-)
Title: Flux Estimation with Static Chamber Data
Description: Statistical analysis of static chamber concentration data for trace gas flux estimation.
Author: Asger R. Pedersen <asger@clin.au.dk>
Maintainer: Asger R. Pedersen <asger@clin.au.dk>
Diff between HMR versions 1.0.1 dated 2020-05-20 and 1.0.2 dated 2022-05-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/HMR.fit1.R | 4 ++-- R/HMR.read.R | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-)
Title: The Free Algebra
Description: The free algebra in R; multivariate polynomials with non-commuting indeterminates.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between freealg versions 1.0-6 dated 2022-04-10 and 1.0-7 dated 2022-05-20
DESCRIPTION | 6 +++--- MD5 | 38 ++++++++++++++++++++++---------------- R/dot.R | 2 +- R/free.R | 14 ++++++++++++-- R/freeops.R | 12 +++--------- README.md | 19 ++++++++++--------- build/freealg.pdf |binary build/partial.rdb |binary build/vignette.rds |binary inst/doc/adjoint.pdf |binary inst/doc/freealg.R |only inst/doc/freealg.Rmd |only inst/doc/freealg.html |only man/Ops.freealg.Rd | 16 +++++++++++++--- man/accessor.Rd | 9 +++++++-- man/deriv.Rd | 2 +- man/dot.Rd | 21 ++++++++++++++++----- man/grade.Rd | 11 +++++++++-- man/nterms.Rd |only src/RcppExports.cpp | 5 +++++ tests/testthat/test_aaa.R | 3 +-- tests/testthat/test_aaf.R |only vignettes/freealg.Rmd |only 23 files changed, 103 insertions(+), 55 deletions(-)
Title: Graphical User Interface for Data Quality Assessment
Description: A graphical user interface (GUI) to the functions implemented in the R package 'DQAstats'.
Author: Lorenz A. Kapsner [cre, aut] ,
Jonathan M. Mang [aut] ,
MIRACUM - Medical Informatics in Research and Care in University
Medicine [fnd],
Universitaetsklinikum Erlangen [cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@uk-erlangen.de>
Diff between DQAgui versions 0.1.8 dated 2022-02-21 and 0.2.0 dated 2022-05-20
DESCRIPTION | 18 MD5 | 33 R/app_utils.R | 1498 +++++++++-------- R/custom_buttons.R | 234 +- R/dot_helper.R |only R/launch_app.R | 187 +- R/moduleAtempPlausibility.R | 238 +- R/moduleConfig.R | 3415 ++++++++++++++++++++--------------------- R/moduleDashboard.R | 1311 ++++++++------- R/moduleDescriptive.R | 926 +++++------ README.md | 41 inst/application/server.R | 756 ++++----- inst/application/ui.R | 281 +-- man/dot_helper.Rd |only man/launch_app.Rd | 6 tests/testthat.R | 2 tests/testthat/_snaps |only tests/testthat/apps |only tests/testthat/test-lints.R | 50 tests/testthat/test-shinyapp.R |only 20 files changed, 4522 insertions(+), 4474 deletions(-)
Title: R Individual Specialization
Description: Functions to calculate several ecological indices of individual
and population niche width (Araujo's E, clustering and pairwise similarity
among individuals, IS, Petraitis' W, and Roughgarden's WIC/TNW) to assess
individual specialization based on data of resource use. Resource use can
be quantified by counts of categories, measures of mass or length, or
proportions. Monte Carlo resampling procedures are available for hypothesis
testing against multinomial null models.
Details are provided in Zaccarelli et al. (2013) <doi:10.1111/2041-210X.12079>
and associated references.
Author: Dr. Nicola Zaccarelli [aut, cre],
Giorgio Mancinelli [aut],
Dan Bolnick [ctb]
Maintainer: Dr. Nicola Zaccarelli <nicola.zaccarelli@gmail.com>
Diff between RInSp versions 1.2.4 dated 2020-02-11 and 1.2.5 dated 2022-05-20
DESCRIPTION | 12 +++++++----- MD5 | 6 +++--- inst/citation | 2 +- man/RInSp-package.Rd | 8 +++++--- 4 files changed, 16 insertions(+), 12 deletions(-)
Title: A Tidy Implementation of Heatmap
Description: This is a tidy implementation for heatmap. At the
moment it is based on the (great) package 'ComplexHeatmap'. The goal
of this package is to interface a tidy data frame with this powerful
tool. Some of the advantages are: Row and/or columns colour
annotations are easy to integrate just specifying one parameter
(column names). Custom grouping of rows is easy to specify providing
a grouped tbl. For example: df %>% group_by(...). Labels size
adjusted by row and column total number. Default use of Brewer and
Viridis palettes.
Author: Stefano Mangiola [aut, cre],
Anthony Papenfuss [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidyHeatmap versions 1.6.0 dated 2022-01-28 and 1.8.1 dated 2022-05-20
DESCRIPTION | 6 MD5 | 75 NAMESPACE | 156 R/functions.R | 14 R/methods.R | 2442 +++++++------- R/utilities.R | 26 README.md | 1004 +++--- build/tidyHeatmap.pdf |binary inst/NEWS.rd |only inst/doc/introduction.R | 80 inst/doc/introduction.html | 668 ++-- man/add_bar-method.Rd | 4 man/add_line-method.Rd | 4 man/add_point-method.Rd | 4 man/add_tile-method.Rd | 4 man/as_ComplexHeatmap-method.Rd |only man/fragments/figures/unnamed-chunk-16-1.png |binary man/fragments/figures/unnamed-chunk-17-1.png |binary man/fragments/figures/unnamed-chunk-18-1.png |binary man/fragments/figures/unnamed-chunk-19-1.png |binary man/fragments/figures/unnamed-chunk-20-1.png |binary man/fragments/figures/unnamed-chunk-21-1.png |binary man/fragments/figures/unnamed-chunk-22-1.png |binary man/fragments/figures/unnamed-chunk-23-1.png |binary man/fragments/figures/unnamed-chunk-24-1.png |binary man/fragments/figures/unnamed-chunk-25-1.png |binary man/fragments/figures/unnamed-chunk-26-1.png |binary man/fragments/figures/unnamed-chunk-27-1.png |only man/fragments/figures/unnamed-chunk-28-1.png |only man/fragments/figures/unnamed-chunk-29-1.png |only man/fragments/intro.Rmd | 94 man/heatmap-method.Rd | 38 man/input_heatmap.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/tests/multi-type.svg | 2669 +++++++--------- tests/testthat/_snaps/tests/plus-operator.svg |only tests/testthat/_snaps/tests/scale-both.svg | 1834 +++++----- tests/testthat/_snaps/tests/scale-column.svg | 1834 +++++----- tests/testthat/_snaps/tests/scale-none.svg | 1834 +++++----- tests/testthat/_snaps/tests/scale-row.svg | 1838 +++++------ tests/testthat/_snaps/tests/tile-colorramp2-palette.svg |only tests/testthat/tests.R | 155 42 files changed, 7648 insertions(+), 7139 deletions(-)
Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate
time-dependent true/false positive rates and AUC curves from a
set of censored survival data.
Author: Sergej Potapov, Werner Adler and Matthias Schmid.
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between survAUC versions 1.1-0 dated 2022-05-18 and 1.1-1 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/IntegratedAUC.R | 9 +++++---- man/IntegratedAUC.Rd | 17 +++++++++++++++++ src/Makevars | 1 - src/R_init_survAUC.c | 6 +++--- src/survAUC_UNO.c | 10 ++++------ src/survAUC_UNO.h | 5 ++--- src/surv_measures.c | 6 +++--- 11 files changed, 54 insertions(+), 34 deletions(-)
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 1.0.0 dated 2021-07-28 and 1.0.1 dated 2022-05-20
DESCRIPTION | 8 MD5 | 158 NAMESPACE | 226 NEWS.md | 949 R/args_validation.R | 1464 - R/cleartmp.R | 94 R/ctable.R | 970 - R/define_keywords.R | 546 R/descr.R | 1204 - R/dfSummary.R | 3178 +-- R/examens.R | 56 R/exams.R | 54 R/freq.R | 1194 - R/helpers.R | 296 R/label.R | 280 R/parse_args.R | 1296 - R/print.list.R | 98 R/print.stby.R | 96 R/print.summarytools.R | 4924 ++--- R/st_css.R | 146 R/st_options.R | 788 R/stby.R | 138 R/summarytools.R | 68 R/tabagisme.R | 68 R/tb.R | 338 R/tobacco.R | 62 R/use_custom_lang.R | 168 R/view.R | 910 R/what.is.R | 262 R/zzz.R | 200 build/vignette.rds |binary inst/doc/introduction.R | 598 inst/doc/introduction.Rmd | 2506 +- inst/doc/introduction.html | 6944 ++++--- inst/doc/rmarkdown.R | 170 inst/doc/rmarkdown.Rmd | 1032 - inst/doc/rmarkdown.html | 4655 ++-- inst/includes/favicon.html | 2 inst/includes/fig-valign.tex | 28 inst/includes/language_template.csv | 157 inst/includes/scripts/bootstrap.min.js | 12 inst/includes/scripts/jquery-3.4.0.slim.min.js | 4 inst/includes/stylesheets/bootstrap-grid.css | 7438 +++---- inst/includes/stylesheets/bootstrap-grid.min.css | 14 inst/includes/stylesheets/bootstrap-reboot.css | 662 inst/includes/stylesheets/bootstrap-reboot.min.css | 16 inst/includes/stylesheets/bootstrap.css |20076 ++++++++++----------- inst/includes/stylesheets/bootstrap.min.css | 14 inst/includes/stylesheets/summarytools-global.css | 14 inst/includes/stylesheets/summarytools.css | 348 man/cleartmp.Rd | 62 man/ctable.Rd | 316 man/define_keywords.Rd | 250 man/descr.Rd | 276 man/dfSummary.Rd | 474 man/examens.Rd | 70 man/exams.Rd | 68 man/format_number.Rd | 58 man/freq.Rd | 328 man/label.Rd | 76 man/parse_args.Rd | 110 man/print.list.Rd | 154 man/print.stby.Rd | 146 man/print.summarytools.Rd | 316 man/st_css.Rd | 90 man/st_options.Rd | 536 man/stby.Rd | 76 man/summarytools-package.Rd | 104 man/tabagisme.Rd | 82 man/tb.Rd | 92 man/tobacco.Rd | 76 man/unlabel.Rd | 42 man/use_custom_lang.Rd | 48 man/view.Rd | 198 man/what.is.Rd | 114 vignettes/assets/exclamation-diamond.svg | 6 vignettes/assets/lightbulb.svg | 4 vignettes/assets/vignette.css | 426 vignettes/introduction.Rmd | 2506 +- vignettes/rmarkdown.Rmd | 1032 - 80 files changed, 37239 insertions(+), 35826 deletions(-)
Title: Wildlife Sightability Modeling
Description: Uses logistic regression to model the probability of detection as a function of covariates.
This model is then used with observational survey data to estimate population size, while
accounting for uncertain detection. See Steinhorst and Samuel (1989).
Author: Fieberg John [aut],
Schwarz Carl James [aut, cre]
Maintainer: Schwarz Carl James <cschwarz.stat.sfu.ca@gmail.com>
Diff between SightabilityModel versions 1.4.2 dated 2021-10-06 and 1.5 dated 2022-05-20
SightabilityModel-1.4.2/SightabilityModel/R/MoosePopR.r |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/MoosePopR-SightabilityPopR-Demo.R |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/MoosePopR-SightabilityPopR-Demo.Rmd |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/MoosePopR-SightabilityPopR-Demo.html |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/RatioEstimator.pdf |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/RatioEstimator.pdf.asis |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/SightabilityModel.R |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/SightabilityModel.Rnw |only SightabilityModel-1.4.2/SightabilityModel/inst/doc/SightabilityModel.pdf |only SightabilityModel-1.4.2/SightabilityModel/vignettes/MoosePopR-SightabilityPopR-Demo.Rmd |only SightabilityModel-1.4.2/SightabilityModel/vignettes/RatioEstimator.pdf.asis |only SightabilityModel-1.4.2/SightabilityModel/vignettes/SightabilityModel.Rnw |only SightabilityModel-1.5/SightabilityModel/DESCRIPTION | 19 +- SightabilityModel-1.5/SightabilityModel/MD5 | 62 +++++---- SightabilityModel-1.5/SightabilityModel/NAMESPACE | 10 + SightabilityModel-1.5/SightabilityModel/NEWS.md | 17 ++ SightabilityModel-1.5/SightabilityModel/R/MoosePopR.R |only SightabilityModel-1.5/SightabilityModel/R/MoosePopR_DomStrat.R |only SightabilityModel-1.5/SightabilityModel/R/MoosePopR_DomStrat_bootrep.R |only SightabilityModel-1.5/SightabilityModel/R/SightabilityPopR.R | 67 ++++++++-- SightabilityModel-1.5/SightabilityModel/R/SightabilityPopR_DomStrat.R |only SightabilityModel-1.5/SightabilityModel/R/check.sightability.model.args.R |only SightabilityModel-1.5/SightabilityModel/R/compute.SCF.R |only SightabilityModel-1.5/SightabilityModel/R/compute.detect.prob.R |only SightabilityModel-1.5/SightabilityModel/R/data.R | 2 SightabilityModel-1.5/SightabilityModel/README.md | 7 - SightabilityModel-1.5/SightabilityModel/build/vignette.rds |binary SightabilityModel-1.5/SightabilityModel/inst/doc/a-SightabilityModel.R |only SightabilityModel-1.5/SightabilityModel/inst/doc/a-SightabilityModel.Rnw |only SightabilityModel-1.5/SightabilityModel/inst/doc/a-SightabilityModel.pdf |only SightabilityModel-1.5/SightabilityModel/inst/doc/b-RatioEstimator.pdf |only SightabilityModel-1.5/SightabilityModel/inst/doc/b-RatioEstimator.pdf.asis |only SightabilityModel-1.5/SightabilityModel/inst/doc/d-DomainStratification-method-of-Heard-2008.html |only SightabilityModel-1.5/SightabilityModel/inst/doc/d-DomainStratification-method-of-Heard-2008.html.asis |only SightabilityModel-1.5/SightabilityModel/inst/extdata/ExampleDomainStratification.xlsx |only SightabilityModel-1.5/SightabilityModel/inst/extdata/SampleMooseSurveyData.xlsx |binary SightabilityModel-1.5/SightabilityModel/man/MoosePopR.Rd | 13 - SightabilityModel-1.5/SightabilityModel/man/MoosePopR_DomStrat.Rd |only SightabilityModel-1.5/SightabilityModel/man/MoosePopR_DomStrat_bootrep.Rd |only SightabilityModel-1.5/SightabilityModel/man/SightabilityPopR.Rd | 9 - SightabilityModel-1.5/SightabilityModel/man/SightabilityPopR_DomStrat.Rd |only SightabilityModel-1.5/SightabilityModel/man/check.sightability.model.args.Rd |only SightabilityModel-1.5/SightabilityModel/man/compute.SCF.Rd |only SightabilityModel-1.5/SightabilityModel/man/compute.detect.prob.Rd |only SightabilityModel-1.5/SightabilityModel/man/g.fit.Rd | 2 SightabilityModel-1.5/SightabilityModel/vignettes/a-Diagonal-model.html |only SightabilityModel-1.5/SightabilityModel/vignettes/a-SightabilityModel.Rnw |only SightabilityModel-1.5/SightabilityModel/vignettes/b-RatioEstimator.pdf.asis |only SightabilityModel-1.5/SightabilityModel/vignettes/c-MoosePopR-SightabilityPopR-Demo.Rmd |only SightabilityModel-1.5/SightabilityModel/vignettes/c-MoosePopR-SightabilityPopR-Demo.html |only SightabilityModel-1.5/SightabilityModel/vignettes/d-DomainStratification-method-of-Heard-2008.Rmd |only SightabilityModel-1.5/SightabilityModel/vignettes/d-DomainStratification-method-of-Heard-2008.html.asis |only 52 files changed, 146 insertions(+), 62 deletions(-)
More information about SightabilityModel at CRAN
Permanent link
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
<https://pj.freefaculty.org/guides/>. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette 'rockchalk' offers a
fairly comprehensive overview. The vignette 'Rstyle' has advice
about coding in R. The package title 'rockchalk' refers to our
school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre],
Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.151 dated 2022-02-13 and 1.8.152 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/outreg.R | 4 ++-- build/vignette.rds |binary data/cheating.RData |binary data/religioncrime.RData |binary inst/doc/Rchaeology.pdf |binary inst/doc/Rstyle.pdf |binary inst/doc/outreg.pdf |binary inst/doc/rockchalk.pdf |binary man/outreg.Rd | 2 +- man/outreg2HTML.Rd | 2 +- 12 files changed, 19 insertions(+), 19 deletions(-)
Title: Pre-Commit Hooks
Description: Useful git hooks for R building on top of the multi-language
framework 'pre-commit' for hook management. This package provides git
hooks for common tasks like formatting files with 'styler' or spell
checking as well as wrapper functions to access the 'pre-commit'
executable.
Author: Lorenz Walthert
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between precommit versions 0.2.1 dated 2021-12-14 and 0.3.0 dated 2022-05-20
precommit-0.2.1/precommit/inst/hooks/exported/codemeta-description-updated |only precommit-0.3.0/precommit/DESCRIPTION | 20 precommit-0.3.0/precommit/MD5 | 135 +- precommit-0.3.0/precommit/NAMESPACE | 1 precommit-0.3.0/precommit/NEWS.md | 528 +++++----- precommit-0.3.0/precommit/R/cache.R | 1 precommit-0.3.0/precommit/R/install.R | 2 precommit-0.3.0/precommit/R/precommit-package.R | 6 precommit-0.3.0/precommit/R/purl.R |only precommit-0.3.0/precommit/R/release.R | 20 precommit-0.3.0/precommit/R/roxygen2.R | 3 precommit-0.3.0/precommit/R/setup.R | 97 + precommit-0.3.0/precommit/R/testing.R | 73 - precommit-0.3.0/precommit/R/utils.R | 11 precommit-0.3.0/precommit/R/zzz.R | 1 precommit-0.3.0/precommit/README.md | 150 -- precommit-0.3.0/precommit/build/vignette.rds |binary precommit-0.3.0/precommit/inst/doc/FAQ.Rmd | 103 + precommit-0.3.0/precommit/inst/doc/FAQ.html | 272 ++++- precommit-0.3.0/precommit/inst/doc/available-hooks.Rmd | 303 +++-- precommit-0.3.0/precommit/inst/doc/available-hooks.html | 374 ++++++- precommit-0.3.0/precommit/inst/doc/ci.Rmd | 172 +-- precommit-0.3.0/precommit/inst/doc/ci.html | 284 ++++- precommit-0.3.0/precommit/inst/doc/hook-order.Rmd | 27 precommit-0.3.0/precommit/inst/doc/hook-order.html | 204 +++ precommit-0.3.0/precommit/inst/doc/precommit.R |only precommit-0.3.0/precommit/inst/doc/precommit.Rmd |only precommit-0.3.0/precommit/inst/doc/precommit.html |only precommit-0.3.0/precommit/inst/doc/testing.Rmd | 84 - precommit-0.3.0/precommit/inst/doc/testing.html | 242 ++++ precommit-0.3.0/precommit/inst/doc/why-use-hooks.Rmd | 94 + precommit-0.3.0/precommit/inst/doc/why-use-hooks.html | 259 ++++ precommit-0.3.0/precommit/inst/hooks/exported/codemeta-description-updated.R |only precommit-0.3.0/precommit/inst/hooks/exported/deps-in-desc.R | 6 precommit-0.3.0/precommit/inst/hooks/exported/no-debug-statement.R |only precommit-0.3.0/precommit/inst/hooks/exported/parsable-R.R | 7 precommit-0.3.0/precommit/inst/hooks/exported/readme-rmd-rendered.R | 4 precommit-0.3.0/precommit/inst/hooks/exported/roxygenize.R | 7 precommit-0.3.0/precommit/inst/hooks/exported/spell-check.R | 8 precommit-0.3.0/precommit/inst/hooks/exported/style-files.R | 13 precommit-0.3.0/precommit/inst/pre-commit-config-pkg.yaml | 8 precommit-0.3.0/precommit/inst/pre-commit-config-proj.yaml | 6 precommit-0.3.0/precommit/inst/pre-commit-hooks.yaml | 11 precommit-0.3.0/precommit/man/diff_requires_run_roxygenize.Rd | 2 precommit-0.3.0/precommit/man/dirs_R.cache.Rd | 2 precommit-0.3.0/precommit/man/figures/pre-commit-meme.jpeg |only precommit-0.3.0/precommit/man/hook_state_assert.Rd | 4 precommit-0.3.0/precommit/man/local_test_setup.Rd | 4 precommit-0.3.0/precommit/man/may_require_permanent_cache.Rd | 2 precommit-0.3.0/precommit/man/precommit-package.Rd | 6 precommit-0.3.0/precommit/man/robust_purl.Rd |only precommit-0.3.0/precommit/man/roxygen_assert_additional_dependencies.Rd | 2 precommit-0.3.0/precommit/man/roxygenize_with_cache.Rd | 2 precommit-0.3.0/precommit/man/run_test.Rd | 21 precommit-0.3.0/precommit/man/run_test_impl.Rd | 15 precommit-0.3.0/precommit/man/use_precommit.Rd | 4 precommit-0.3.0/precommit/tests/testthat/in/codemeta.json |only precommit-0.3.0/precommit/tests/testthat/in/flie-true.Rd |only precommit-0.3.0/precommit/tests/testthat/in/flie.Rd |only precommit-0.3.0/precommit/tests/testthat/in/no-debug-statement-fail.R |only precommit-0.3.0/precommit/tests/testthat/in/no-debug-statement-success.R |only precommit-0.3.0/precommit/tests/testthat/in/parsable-R-success.Rmd | 26 precommit-0.3.0/precommit/tests/testthat/in/style-files-ignore-fail.R |only precommit-0.3.0/precommit/tests/testthat/in/style-files-ignore-success.R |only precommit-0.3.0/precommit/tests/testthat/in/style-files-success.R | 3 precommit-0.3.0/precommit/tests/testthat/reference-objects/pre-commit-config.yaml | 1 precommit-0.3.0/precommit/tests/testthat/test-conda.R | 14 precommit-0.3.0/precommit/tests/testthat/test-hook-roxygenize.R | 13 precommit-0.3.0/precommit/tests/testthat/test-hooks.R | 328 ++++-- precommit-0.3.0/precommit/tests/testthat/test-setup.R | 30 precommit-0.3.0/precommit/vignettes/FAQ.Rmd | 103 + precommit-0.3.0/precommit/vignettes/available-hooks.Rmd | 303 +++-- precommit-0.3.0/precommit/vignettes/ci.Rmd | 172 +-- precommit-0.3.0/precommit/vignettes/hook-order.Rmd | 27 precommit-0.3.0/precommit/vignettes/precommit.Rmd |only precommit-0.3.0/precommit/vignettes/testing.Rmd | 84 - precommit-0.3.0/precommit/vignettes/why-use-hooks.Rmd | 94 + 77 files changed, 3354 insertions(+), 1444 deletions(-)
Title: Facilitating Estimation of the Intraclass Correlation
Coefficient
Description: Assist in the estimation of the Intraclass Correlation Coefficient
(ICC) from variance components of a one-way analysis of variance and also
estimate the number of individuals or groups necessary to obtain an ICC
estimate with a desired confidence interval width.
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between ICC versions 2.3.0 dated 2015-06-17 and 2.4.0 dated 2022-05-20
ICC-2.3.0/ICC/man/ICCbare.Rd |only ICC-2.3.0/ICC/man/ICCbareF.Rd |only ICC-2.4.0/ICC/DESCRIPTION | 18 ++++-- ICC-2.4.0/ICC/MD5 | 28 +++++----- ICC-2.4.0/ICC/NAMESPACE | 22 ++++++-- ICC-2.4.0/ICC/NEWS.md |only ICC-2.4.0/ICC/R/ICC.R |only ICC-2.4.0/ICC/R/ICCbare.R | 3 + ICC-2.4.0/ICC/R/ICCbareF.R | 3 + ICC-2.4.0/ICC/R/ICCest.R | 69 ++++++++++++++++++++++++++ ICC-2.4.0/ICC/R/Nest.R | 51 +++++++++++++++++++ ICC-2.4.0/ICC/R/effort.R | 48 ++++++++++++++++++ ICC-2.4.0/ICC/README.md | 5 + ICC-2.4.0/ICC/man/ICC-package.Rd | 30 ++++++----- ICC-2.4.0/ICC/man/ICCest.Rd | 101 ++++++++++++++++++++++++++++----------- ICC-2.4.0/ICC/man/Nest.Rd | 92 +++++++++++++++++++++++++---------- ICC-2.4.0/ICC/man/effort.Rd | 88 +++++++++++++++++++++------------ 17 files changed, 432 insertions(+), 126 deletions(-)
Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.2-1 dated 2022-05-18 and 0.2-2 dated 2022-05-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary configure | 2 +- configure.ac | 2 +- man/hgwrr-package.Rd | 8 +++++++- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.6.4 dated 2022-03-10 and 0.6.5 dated 2022-05-20
DESCRIPTION | 8 MD5 | 66 NEWS.md | 19 R/api_get.R | 30 R/coords.R | 2 R/filters.R | 10 R/finbif_occurrence.R | 28 R/finbif_occurrence_load.R | 306 +- R/finbif_records.R | 5 R/sysdata.rda |binary R/utils.R | 58 R/variables.R | 8 README.md | 6 build/vignette.rds |binary data/finland_map.rda |binary inst/NEWS.Rd | 20 inst/doc/finbif.html | 20 inst/doc/v02_occurrence_data.html | 17 inst/doc/v03_selecting_variables.html | 22 inst/doc/v04_metadata.html | 10 inst/doc/v05_filtering.html | 21 inst/doc/v06_plotting.html | 20 man/figures/plot-finland-1.png |binary man/filters.Rd | 10 man/finbif-package.Rd | 4 man/finbif_occurrence_load.Rd | 6 man/to_dwc.Rd | 6 man/variables.Rd | 8 tests/testthat/_snaps/local-finbif_occurrence_load.md | 82 tests/testthat/laji-data-pap.tsv | 1334 +++++++++ tests/testthat/laji-data.tsv | 2406 ++++++++---------- tests/testthat/test-local-finbif_coords.R | 4 tests/testthat/test-local-finbif_occurrence_load.R | 26 tests/testthat/test-zzz-finbif.R | 3 34 files changed, 2861 insertions(+), 1704 deletions(-)
Title: Explore Classification Models in High Dimensions
Description: Given $p$-dimensional training data containing $d$ groups
(the design space), a classification algorithm (classifier) predicts
which group new data belongs to. Generally the input to these
algorithms is high dimensional, and the boundaries between groups will
be high dimensional and perhaps curvilinear or multi-faceted. This
package implements methods for understanding the division of space
between the groups.
Author: Hadley Wickham <h.wickham@gmail.com>
Maintainer: Hadley Wickham <h.wickham@gmail.com>
Diff between classifly versions 0.4 dated 2014-04-23 and 0.4.1 dated 2022-05-20
classifly-0.4.1/classifly/DESCRIPTION | 32 ++++---- classifly-0.4.1/classifly/MD5 | 36 +++++----- classifly-0.4.1/classifly/NAMESPACE | 2 classifly-0.4.1/classifly/NEWS.md |only classifly-0.4.1/classifly/R/data.r | 4 - classifly-0.4.1/classifly/R/explore.r | 13 --- classifly-0.4.1/classifly/R/knn.r | 2 classifly-0.4.1/classifly/R/rescaler.R | 4 - classifly-0.4.1/classifly/man/advantage.Rd | 4 - classifly-0.4.1/classifly/man/classifly.Rd | 15 +++- classifly-0.4.1/classifly/man/classify.Rd | 4 - classifly-0.4.1/classifly/man/explore.Rd | 7 - classifly-0.4.1/classifly/man/generate_classification_data.Rd | 4 - classifly-0.4.1/classifly/man/generate_data.Rd | 4 - classifly-0.4.1/classifly/man/knnf.Rd | 4 - classifly-0.4.1/classifly/man/olives.Rd | 8 +- classifly-0.4.1/classifly/man/posterior.Rd | 4 - classifly-0.4.1/classifly/man/simvar.Rd | 4 - classifly-0.4.1/classifly/man/variables.Rd | 4 - classifly-0.4/classifly/NEWS |only 20 files changed, 76 insertions(+), 79 deletions(-)
Title: Censored Mixed-Effects Models with Different Correlation
Structures
Description: Left, right or interval censored mixed-effects linear model with autoregressive errors of order p or DEC correlation structure using the type-EM algorithm. The error distribution can be Normal or t-Student. It provides the parameter estimates, the standard errors and prediction of future observations (available only for the normal case). Olivari et all (2021) <doi:10.1080/10543406.2020.1852246>.
Author: Rommy C. Olivari, Kelin Zhong, Aldo M. Garay and Victor H. Lachos
Maintainer: Rommy C. Olivari <rco1@de.ufpe.br>
Diff between ARpLMEC versions 2.3 dated 2022-04-27 and 2.4 dated 2022-05-20
DESCRIPTION | 15 - MD5 | 22 +- NAMESPACE | 7 R/ARpMMEC.est.R | 280 +++++++++++++------------ R/ARpMMEC.sim.R | 64 +++-- R/EMCensArpN.R | 578 +++++++++++++++++++++++++++++------------------------ R/EMCensArpT.R | 348 ++++++++++++++++++------------- R/FunGeral.R | 319 +++++++++++++++++++---------- R/MMsimu.R | 176 +++++++++------- build/partial.rdb |binary man/ARpMMEC.est.Rd | 8 man/ARpMMEC.sim.Rd | 12 - 12 files changed, 1056 insertions(+), 773 deletions(-)