Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-14 0.1.2
2022-05-13 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-19 1.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-17 1.0.1
2022-04-15 1.0.0
2022-01-25 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-10 0.1.0
Title: OLS, Moderated, Logistic, and Count Regressions Made Simple
Description: Provides SPSS- and SAS-like output for least squares multiple regression,
logistic regression, and count variable regressions. Detailed output is also provided for
OLS moderated regression, interaction plots, and Johnson-Neyman
regions of significance. The output includes standardized
coefficients, partial and semi-partial correlations, collinearity diagnostics,
plots of residuals, and detailed information about simple slopes for interactions.
The output for some functions includes Bayes Factors and, if requested,
regression coefficients from Bayesian Markov Chain Monte Carlo analyses.
There are numerous options for model plots.
The REGIONS_OF_SIGNIFICANCE function also provides
Johnson-Neyman regions of significance and plots of interactions for both lm
and lme models.
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between SIMPLE.REGRESSION versions 0.1.9 dated 2024-07-14 and 0.2.1 dated 2025-01-11
DESCRIPTION | 35 ++- MD5 | 28 +-- NAMESPACE | 9 R/COUNT_REGRESSION.R | 359 +++++++++++++++++++++++++++++++-------- R/LOGISTIC_REGRESSION.R | 40 ++++ R/MODERATED_REGRESSION.R | 158 +++++++++++++++-- R/OLS_REGRESSION.R | 211 ++++++++++++++++++++-- R/PLOT_MODEL.R | 63 ++++-- R/utilities_boc.R | 144 ++++++++++++++- man/COUNT_REGRESSION.Rd | 63 ++++++ man/LOGISTIC_REGRESSION.Rd | 28 ++- man/MODERATED_REGRESSION.Rd | 33 +++ man/OLS_REGRESSION.Rd | 49 ++++- man/PLOT_MODEL.Rd | 11 - man/SIMPLE.REGRESSION-package.Rd | 6 15 files changed, 1043 insertions(+), 194 deletions(-)
More information about SIMPLE.REGRESSION at CRAN
Permanent link
Title: Estimate Orientation of an Inertial Measurement Unit
Description: Estimate the orientation of an inertial measurement unit
(IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a
complementary filter. 'imuf' takes an IMU's accelerometer and gyroscope
readings, time duration, its initial orientation, and a gain factor as
inputs, and returns an estimate of the IMU's final orientation.
Author: Felix Chan [aut, cre, cph],
Ricardo Cabello [cph]
Maintainer: Felix Chan <chanfelix@gmail.com>
Diff between imuf versions 0.4.0 dated 2024-12-08 and 0.5.0 dated 2025-01-11
DESCRIPTION | 21 ++++++++++++--------- LICENSE |only LICENSE.note |only MD5 | 29 +++++++++++++++++++++-------- NAMESPACE | 4 ++++ NEWS.md | 2 ++ R/animate_imu.R |only build/vignette.rds |binary inst/doc/animate_imu.R |only inst/doc/animate_imu.Rmd |only inst/doc/animate_imu.html |only inst/doc/imuf.Rmd | 2 +- inst/doc/imuf.html | 4 ++-- inst/htmlwidgets |only man/animate_imu-shiny.Rd |only man/animate_imu.Rd |only man/imuf-package.Rd | 5 +++++ tests/testthat/test-animate_imu.R |only vignettes/animate_imu.Rmd |only vignettes/imuf.Rmd | 2 +- 20 files changed, 48 insertions(+), 21 deletions(-)
Title: Effect Plots
Description: High-performance implementation of various effect plots
useful for regression and probabilistic classification tasks. The
package includes partial dependence plots (Friedman, 2021,
<doi:10.1214/aos/1013203451>), accumulated local effect plots and
M-plots (both from Apley and Zhu, 2016, <doi:10.1111/rssb.12377>), as
well as plots that describe the statistical associations between model
response and features. It supports visualizations with either
'ggplot2' or 'plotly', and is compatible with most models, including
'Tidymodels', models wrapped in 'DALEX' explainers, or models with
case weights.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between effectplots versions 0.2.0 dated 2024-12-11 and 0.2.1 dated 2025-01-11
DESCRIPTION | 9 ++-- MD5 | 14 +++--- NEWS.md | 11 +++++ R/feature_effects.R | 4 + R/plot.R | 40 ++++++++++++++++-- R/utils.R | 61 ++++++++++++++++++++++++++++ README.md | 2 tests/testthat/test-feature_effects.R | 72 ++++++++++++++++++++++++++++++++++ 8 files changed, 194 insertions(+), 19 deletions(-)
Title: Chinese Numerals Processing
Description: Chinese numerals processing in R, such as conversion between
Chinese numerals and Arabic numerals as well as detection and extraction of
Chinese numerals in character objects and string. This package supports
the casual scale naming system and the respective SI prefix systems used
in mainland China and Taiwan:
"The State Council's Order on the Unified Implementation of Legal Measurement Units in Our Country"
The State Council of the People's Republic of China (1984)
"Names, Definitions and Symbols of the Legal Units of Measurement and the Decimal Multiples and Submultiples"
Ministry of Economic Affairs (2019) <https://gazette.nat.gov.tw/egFront/detail.do?metaid=108965>.
Author: Elgar Teo [aut, cre]
Maintainer: Elgar Teo <elgarteo@connect.hku.hk>
Diff between cnum versions 0.1.4 dated 2025-01-11 and 0.1.5 dated 2025-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/num2c-utils.R | 2 +- R/num2c.R | 6 +++--- man/conversion.Rd | 6 +++--- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Distance and Travel Time Between Two Points from Google Maps
Description: Get distance and travel time between two points from Google Maps.
Four possible modes of transportation (bicycling, walking, driving and
public transportation).
Author: Rodrigo Azuero Melo [aut],
David Zarruk [aut],
Jindra Lacko [cre]
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between gmapsdistance versions 4.0.4 dated 2023-08-10 and 4.0.5 dated 2025-01-11
DESCRIPTION | 29 +- MD5 | 24 +- NEWS.md | 4 README.md | 16 + build/vignette.rds |binary inst/doc/vignette.Rmd | 312 ++++++++++++++++------------- inst/doc/vignette.html | 364 ++++++++++++++++++---------------- tests/testthat/test-1-sanity.R | 18 - tests/testthat/test-3-matrix.R | 4 tests/testthat/test-5-vignette.R | 8 tests/testthat/test-6-graceful-fail.R | 2 tests/testthat/test-7-arrival-time.R | 9 vignettes/vignette.Rmd | 312 ++++++++++++++++------------- 13 files changed, 618 insertions(+), 484 deletions(-)
Title: D-Vine Quantile Regression
Description: Implements D-vine quantile regression models with
parametric or nonparametric pair-copulas. See
Kraus and Czado (2017) <doi:10.1016/j.csda.2016.12.009> and
Schallhorn et al. (2017) <doi:10.48550/arXiv.1705.08310>.
Author: Thomas Nagler [aut, cre],
Dani Kraus [ctb]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between vinereg versions 0.10.0 dated 2024-02-09 and 0.11.0 dated 2025-01-11
DESCRIPTION | 12 +++---- MD5 | 42 +++++++++++++-------------- NEWS.md | 13 +++++++- R/RcppExports.R | 4 +- R/cpit.R | 12 +++---- R/generics.R | 4 +- R/predict.vinereg.R | 14 ++------- R/tools.R | 25 +++++++++++----- R/vinereg.R | 16 +++++----- README.md | 26 ++++++++-------- build/vignette.rds |binary inst/doc/abalone-example.html | 45 +++++++++++++++-------------- inst/doc/bike-rental.html | 48 +++++++++++++++---------------- man/cll.Rd | 4 +- man/cpdf.Rd | 4 +- man/cpit.Rd | 4 +- man/figures/README-unnamed-chunk-1-1.png |binary man/plot_effects.Rd | 4 +- man/predict.vinereg.Rd | 14 ++------- man/vinereg.Rd | 4 +- src/RcppExports.cpp | 10 +++--- src/vinereg.cpp | 26 +++++++--------- 22 files changed, 171 insertions(+), 160 deletions(-)
Title: Replacements for Base String Functions Powered by 'stringi'
Description: English is the native language for only 5% of the World population.
Also, only 17% of us can understand this text. Moreover, the Latin alphabet
is the main one for merely 36% of the total.
The early computer era, now a very long time ago, was dominated by the US.
Due to the proliferation of the internet, smartphones, social media, and
other technologies and communication platforms, this is no longer the case.
This package replaces base R string functions (such as grep(),
tolower(), sprintf(), and strptime()) with ones that fully
support the Unicode standards related to natural language and
date-time processing. It also fixes some long-standing inconsistencies,
and introduces some new, useful features.
Thanks to 'ICU' (International Components for Unicode) and 'stringi',
they are fast, reliable, and portable across different platforms.
Author: Marek Gagolewski [aut, cre, cph]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringx versions 0.2.8 dated 2024-04-09 and 0.2.9 dated 2025-01-11
DESCRIPTION | 10 +++--- MD5 | 60 ++++++++++++++++++++-------------------- NEWS | 9 ++++++ R/ISOdatetime.R | 2 - R/about_stringx.R | 4 +- R/chartr.R | 2 - R/common.R | 2 - R/constants.R | 2 - R/gregexpr.R | 2 - R/gregextr.R | 2 - R/grepl.R | 2 - R/gsub.R | 2 - R/nchar.R | 2 - R/paste.R | 2 - R/sort.R | 2 - R/sprintf.R | 2 - R/startswith.R | 2 - R/strcoll.R | 2 - R/strptime.R | 14 ++++++--- R/strrep.R | 2 - R/strsplit.R | 2 - R/strtrim.R | 2 - R/strwrap.R | 2 - R/substr.R | 2 - R/trimws.R | 2 - inst/realtest/ISOdatetime-all.R | 3 +- inst/realtest/strptime-all.R | 12 ++++++-- man/about_stringx.Rd | 3 +- man/chartr.Rd | 1 man/constants.Rd | 1 tests/realtest.R | 2 - 31 files changed, 92 insertions(+), 67 deletions(-)
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R, enabling
interactive analysis and visualization of genome-scale data. Riemondy
et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut] ,
Kent Riemondy [aut, cre] ,
RNA Bioscience Initiative [fnd, cph]
Maintainer: Kent Riemondy <kent.riemondy@gmail.com>
Diff between valr versions 0.8.2 dated 2024-08-30 and 0.8.3 dated 2025-01-11
DESCRIPTION | 12 ++--- MD5 | 24 ++++++----- NAMESPACE | 2 NEWS.md | 47 +++++++++++++--------- R/read_bed.r | 69 ++++++++++++++------------------- R/valr-package.r | 1 README.md | 2 inst/doc/valr.html | 4 - man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/read_bigwig.Rd | 25 ++++------- man/read_gtf.Rd | 4 + tests/testthat/test_read_bed.r | 7 +-- 15 files changed, 101 insertions(+), 96 deletions(-)
Title: Read/Write, Analyze, and Visualize 'BIOM' Data
Description: A toolkit for working with Biological Observation Matrix ('BIOM') files.
Read/write all 'BIOM' formats. Compute rarefaction, alpha diversity, and
beta diversity (including 'UniFrac'). Summarize counts by taxonomic level.
Subset based on metadata. Generate visualizations and statistical analyses.
CPU intensive operations are coded in C++ for speed.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between rbiom versions 1.0.3 dated 2021-11-05 and 2.0.7 dated 2025-01-11
rbiom-1.0.3/rbiom/NEWS.md |only rbiom-1.0.3/rbiom/R/accessors.r |only rbiom-1.0.3/rbiom/R/alpha.div.r |only rbiom-1.0.3/rbiom/R/beta.div.r |only rbiom-1.0.3/rbiom/R/imports.r |only rbiom-1.0.3/rbiom/R/print.r |only rbiom-1.0.3/rbiom/R/rbiom.r |only rbiom-1.0.3/rbiom/R/read.biom.r |only rbiom-1.0.3/rbiom/R/read.fasta.r |only rbiom-1.0.3/rbiom/R/read.tree.r |only rbiom-1.0.3/rbiom/R/select.r |only rbiom-1.0.3/rbiom/R/subset.r |only rbiom-1.0.3/rbiom/R/subtree.r |only rbiom-1.0.3/rbiom/R/taxa.rollup.r |only rbiom-1.0.3/rbiom/R/tips.r |only rbiom-1.0.3/rbiom/R/unifrac.r |only rbiom-1.0.3/rbiom/R/write.biom.r |only rbiom-1.0.3/rbiom/R/write.fasta.r |only rbiom-1.0.3/rbiom/R/write.tree.r |only rbiom-1.0.3/rbiom/R/write.xlsx.r |only rbiom-1.0.3/rbiom/man/alpha.div.Rd |only rbiom-1.0.3/rbiom/man/beta.div.Rd |only rbiom-1.0.3/rbiom/man/counts.Rd |only rbiom-1.0.3/rbiom/man/info.Rd |only rbiom-1.0.3/rbiom/man/metadata.Rd |only rbiom-1.0.3/rbiom/man/nsamples.Rd |only rbiom-1.0.3/rbiom/man/ntaxa.Rd |only rbiom-1.0.3/rbiom/man/phylogeny.Rd |only rbiom-1.0.3/rbiom/man/pipe.Rd |only rbiom-1.0.3/rbiom/man/print.Rd |only rbiom-1.0.3/rbiom/man/rbiom.Rd |only rbiom-1.0.3/rbiom/man/read.biom.Rd |only rbiom-1.0.3/rbiom/man/read.fasta.Rd |only rbiom-1.0.3/rbiom/man/read.tree.Rd |only rbiom-1.0.3/rbiom/man/sample.names.Rd |only rbiom-1.0.3/rbiom/man/select.Rd |only rbiom-1.0.3/rbiom/man/sequences.Rd |only rbiom-1.0.3/rbiom/man/subtree.Rd |only rbiom-1.0.3/rbiom/man/taxa.names.Rd |only rbiom-1.0.3/rbiom/man/taxa.ranks.Rd |only rbiom-1.0.3/rbiom/man/taxa.rollup.Rd |only rbiom-1.0.3/rbiom/man/taxonomy.Rd |only rbiom-1.0.3/rbiom/man/tips.Rd |only rbiom-1.0.3/rbiom/man/unifrac.Rd |only rbiom-1.0.3/rbiom/man/write.biom.Rd |only rbiom-1.0.3/rbiom/man/write.fasta.Rd |only rbiom-1.0.3/rbiom/man/write.tree.Rd |only rbiom-1.0.3/rbiom/man/write.xlsx.Rd |only rbiom-1.0.3/rbiom/src/Makevars.win |only rbiom-1.0.3/rbiom/src/par_beta_div.cpp |only rbiom-1.0.3/rbiom/src/par_unifrac.cpp |only rbiom-1.0.3/rbiom/tests/testthat.R |only rbiom-1.0.3/rbiom/tests/testthat/outputs/alpha.div.rds |only rbiom-1.0.3/rbiom/tests/testthat/outputs/beta.div.rds |only rbiom-1.0.3/rbiom/tests/testthat/outputs/taxa.rollup.rds |only rbiom-1.0.3/rbiom/tests/testthat/test_accessors.r |only rbiom-1.0.3/rbiom/tests/testthat/test_calculations.r |only rbiom-1.0.3/rbiom/tests/testthat/test_distance.r |only rbiom-1.0.3/rbiom/tests/testthat/test_file_io.r |only rbiom-1.0.3/rbiom/tests/testthat/test_subsetting.r |only rbiom-1.0.3/rbiom/tests/testthat/test_tree.r |only rbiom-2.0.7/rbiom/DESCRIPTION | 63 +- rbiom-2.0.7/rbiom/LICENSE |only rbiom-2.0.7/rbiom/MD5 | 279 +++++++++---- rbiom-2.0.7/rbiom/NAMESPACE | 245 +++++++++-- rbiom-2.0.7/rbiom/R/RcppExports.R | 38 + rbiom-2.0.7/rbiom/R/adiv_table.r |only rbiom-2.0.7/rbiom/R/apcoa.r |only rbiom-2.0.7/rbiom/R/as_rbiom.r |only rbiom-2.0.7/rbiom/R/bdiv_heatmap.r |only rbiom-2.0.7/rbiom/R/bdiv_ord_plot.r |only rbiom-2.0.7/rbiom/R/bdiv_ord_table.r |only rbiom-2.0.7/rbiom/R/bdiv_table.r |only rbiom-2.0.7/rbiom/R/biom_merge.r |only rbiom-2.0.7/rbiom/R/biom_ply.r |only rbiom-2.0.7/rbiom/R/boxplot.r |only rbiom-2.0.7/rbiom/R/boxplot_build.r |only rbiom-2.0.7/rbiom/R/boxplot_stats.r |only rbiom-2.0.7/rbiom/R/cache.r |only rbiom-2.0.7/rbiom/R/clustering.r |only rbiom-2.0.7/rbiom/R/convert.r |only rbiom-2.0.7/rbiom/R/corrplot.r |only rbiom-2.0.7/rbiom/R/corrplot_build.r |only rbiom-2.0.7/rbiom/R/corrplot_stats.r |only rbiom-2.0.7/rbiom/R/data.r |only rbiom-2.0.7/rbiom/R/distmat_ord_table.r |only rbiom-2.0.7/rbiom/R/distmat_stats.r |only rbiom-2.0.7/rbiom/R/documentation.r |only rbiom-2.0.7/rbiom/R/embed.r |only rbiom-2.0.7/rbiom/R/geom_dendro.r |only rbiom-2.0.7/rbiom/R/import_table.r |only rbiom-2.0.7/rbiom/R/plot_build.r |only rbiom-2.0.7/rbiom/R/plot_facets.r |only rbiom-2.0.7/rbiom/R/plot_heatmap.r |only rbiom-2.0.7/rbiom/R/plot_layers.r |only rbiom-2.0.7/rbiom/R/plot_palettes.r |only rbiom-2.0.7/rbiom/R/provenance.r |only rbiom-2.0.7/rbiom/R/rare_multiplot.r |only rbiom-2.0.7/rbiom/R/rare_stacked.r |only rbiom-2.0.7/rbiom/R/rarefy.r | 299 +++++++++----- rbiom-2.0.7/rbiom/R/rbiom-deprecated.r |only rbiom-2.0.7/rbiom/R/rbiom-package.R |only rbiom-2.0.7/rbiom/R/rbiom_objects.r |only rbiom-2.0.7/rbiom/R/read_biom.r |only rbiom-2.0.7/rbiom/R/read_fasta.r |only rbiom-2.0.7/rbiom/R/read_tree.r |only rbiom-2.0.7/rbiom/R/reexport.r |only rbiom-2.0.7/rbiom/R/s3_methods.r |only rbiom-2.0.7/rbiom/R/speed_ups.r |only rbiom-2.0.7/rbiom/R/stats_common.r |only rbiom-2.0.7/rbiom/R/stats_emmeans.r |only rbiom-2.0.7/rbiom/R/stats_table.r |only rbiom-2.0.7/rbiom/R/stats_wilcox.r |only rbiom-2.0.7/rbiom/R/taxa_heatmap.r |only rbiom-2.0.7/rbiom/R/taxa_map.r |only rbiom-2.0.7/rbiom/R/taxa_stacked.r |only rbiom-2.0.7/rbiom/R/taxa_table.r |only rbiom-2.0.7/rbiom/R/tree_plot.r |only rbiom-2.0.7/rbiom/R/utils.r |only rbiom-2.0.7/rbiom/R/validate.r |only rbiom-2.0.7/rbiom/R/write_biom.r |only rbiom-2.0.7/rbiom/R/write_xlsx.r |only rbiom-2.0.7/rbiom/R/zzz.r |only rbiom-2.0.7/rbiom/README.md | 105 +++- rbiom-2.0.7/rbiom/build |only rbiom-2.0.7/rbiom/data |only rbiom-2.0.7/rbiom/exec |only rbiom-2.0.7/rbiom/inst/extdata/babies.bz2 |only rbiom-2.0.7/rbiom/inst/extdata/gems.bz2 |only rbiom-2.0.7/rbiom/inst/extdata/hmp50.bz2 |binary rbiom-2.0.7/rbiom/man/adiv_boxplot.Rd |only rbiom-2.0.7/rbiom/man/adiv_corrplot.Rd |only rbiom-2.0.7/rbiom/man/adiv_matrix.Rd |only rbiom-2.0.7/rbiom/man/adiv_stats.Rd |only rbiom-2.0.7/rbiom/man/adiv_table.Rd |only rbiom-2.0.7/rbiom/man/as.list.rbiom.Rd |only rbiom-2.0.7/rbiom/man/as.matrix.rbiom.Rd |only rbiom-2.0.7/rbiom/man/as_rbiom.Rd |only rbiom-2.0.7/rbiom/man/babies.Rd |only rbiom-2.0.7/rbiom/man/bdiv_boxplot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_clusters.Rd |only rbiom-2.0.7/rbiom/man/bdiv_corrplot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_heatmap.Rd |only rbiom-2.0.7/rbiom/man/bdiv_ord_plot.Rd |only rbiom-2.0.7/rbiom/man/bdiv_ord_table.Rd |only 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|only rbiom-2.0.7/rbiom/man/modify_metadata.Rd |only rbiom-2.0.7/rbiom/man/plot_heatmap.Rd |only rbiom-2.0.7/rbiom/man/pull.rbiom.Rd |only rbiom-2.0.7/rbiom/man/rare_corrplot.Rd |only rbiom-2.0.7/rbiom/man/rare_multiplot.Rd |only rbiom-2.0.7/rbiom/man/rare_stacked.Rd |only rbiom-2.0.7/rbiom/man/rarefy.Rd | 110 +++-- rbiom-2.0.7/rbiom/man/rarefy_cols.Rd |only rbiom-2.0.7/rbiom/man/rbiom-deprecated.Rd |only rbiom-2.0.7/rbiom/man/rbiom-package.Rd |only rbiom-2.0.7/rbiom/man/rbiom_objects.Rd |only rbiom-2.0.7/rbiom/man/read_biom.Rd |only rbiom-2.0.7/rbiom/man/read_fasta.Rd |only rbiom-2.0.7/rbiom/man/read_tree.Rd |only rbiom-2.0.7/rbiom/man/reexports.Rd |only rbiom-2.0.7/rbiom/man/sample_sums.Rd |only rbiom-2.0.7/rbiom/man/slice_metadata.Rd |only rbiom-2.0.7/rbiom/man/speed.Rd |only rbiom-2.0.7/rbiom/man/stats_boxplot.Rd |only rbiom-2.0.7/rbiom/man/stats_corrplot.Rd |only rbiom-2.0.7/rbiom/man/stats_table.Rd |only rbiom-2.0.7/rbiom/man/subset.Rd | 124 ++++- rbiom-2.0.7/rbiom/man/taxa_boxplot.Rd |only rbiom-2.0.7/rbiom/man/taxa_clusters.Rd |only rbiom-2.0.7/rbiom/man/taxa_corrplot.Rd |only rbiom-2.0.7/rbiom/man/taxa_heatmap.Rd |only rbiom-2.0.7/rbiom/man/taxa_map.Rd |only rbiom-2.0.7/rbiom/man/taxa_matrix.Rd |only rbiom-2.0.7/rbiom/man/taxa_stacked.Rd |only rbiom-2.0.7/rbiom/man/taxa_stats.Rd |only rbiom-2.0.7/rbiom/man/taxa_sums.Rd |only rbiom-2.0.7/rbiom/man/tree_subset.Rd |only rbiom-2.0.7/rbiom/man/with.Rd |only rbiom-2.0.7/rbiom/man/write_biom.Rd |only rbiom-2.0.7/rbiom/src/Makevars |only rbiom-2.0.7/rbiom/src/RcppExports.cpp | 145 ++++++ rbiom-2.0.7/rbiom/src/parallel_beta_div.cpp |only rbiom-2.0.7/rbiom/src/parallel_unifrac.cpp |only rbiom-2.0.7/rbiom/src/rcpp_alpha_div.cpp | 7 rbiom-2.0.7/rbiom/src/rcpp_rarefy.cpp | 12 rbiom-2.0.7/rbiom/src/rcpp_treeIO.cpp | 5 rbiom-2.0.7/rbiom/tests/testthat.r |only rbiom-2.0.7/rbiom/tests/testthat/_test-accessors.r |only rbiom-2.0.7/rbiom/tests/testthat/_test-adiv_boxplot.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_calculations.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_distance.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_file_io.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_subsetting.r |only rbiom-2.0.7/rbiom/tests/testthat/_test_tree.r |only rbiom-2.0.7/rbiom/tests/testthat/helper.r |only rbiom-2.0.7/rbiom/tests/testthat/outputs/adiv_table.rds |only rbiom-2.0.7/rbiom/tests/testthat/outputs/bdiv_dist.rds |only rbiom-2.0.7/rbiom/tests/testthat/outputs/subset_ex2.rds |binary rbiom-2.0.7/rbiom/tests/testthat/outputs/taxa_rollup.rds |only rbiom-2.0.7/rbiom/tests/testthat/test-adiv_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-as_rbiom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_ord_plot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-bdiv_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-biom_merge.r |only rbiom-2.0.7/rbiom/tests/testthat/test-biom_ply.r |only rbiom-2.0.7/rbiom/tests/testthat/test-boxplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-boxplot_build.r |only rbiom-2.0.7/rbiom/tests/testthat/test-cache.r |only rbiom-2.0.7/rbiom/tests/testthat/test-clustering.r |only rbiom-2.0.7/rbiom/tests/testthat/test-convert.r |only rbiom-2.0.7/rbiom/tests/testthat/test-corrplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-distmat_ord_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-distmat_stats.r |only rbiom-2.0.7/rbiom/tests/testthat/test-embed.r |only rbiom-2.0.7/rbiom/tests/testthat/test-import_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-plot_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-plot_palettes.r |only rbiom-2.0.7/rbiom/tests/testthat/test-provenance.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rare_multiplot.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rare_stacked.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rarefy.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rbiom-deprecated.r |only rbiom-2.0.7/rbiom/tests/testthat/test-rbiom_objects.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_biom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_fasta.r |only rbiom-2.0.7/rbiom/tests/testthat/test-read_tree.r |only rbiom-2.0.7/rbiom/tests/testthat/test-s3_methods.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_emmeans.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-stats_wilcox.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_heatmap.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_map.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_stacked.r |only rbiom-2.0.7/rbiom/tests/testthat/test-taxa_table.r |only rbiom-2.0.7/rbiom/tests/testthat/test-utils.r |only rbiom-2.0.7/rbiom/tests/testthat/test-validate.r |only rbiom-2.0.7/rbiom/tests/testthat/test-write_biom.r |only rbiom-2.0.7/rbiom/tests/testthat/test-write_xlsx.r |only 260 files changed, 1050 insertions(+), 382 deletions(-)
Title: Linear Mixed-Effects Models using 'Eigen' and S4
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut, cre] ,
Steven Walker [aut] ,
Rune Haubo Bojesen Christensen [ctb]
,
Henrik Singmann [ctb] ,
Bin Dai [ctb],
Fabian Scheipl [ctb] ,
Gabor Grothendieck [ctb],
Peter Green [ctb] ,
John Fox [c [...truncated...]
Maintainer: Ben Bolker <bbolker+lme4@gmail.com>
Diff between lme4 versions 1.1-35.5 dated 2024-07-03 and 1.1-36 dated 2025-01-11
DESCRIPTION | 9 MD5 | 47 ++--- NAMESPACE | 17 + R/lmer.R | 40 ++++ R/predict.R | 36 +-- R/utilities.R | 263 ---------------------------- inst/NEWS.Rd | 29 ++- inst/doc/PLSvGLS.pdf |binary inst/doc/Theory.pdf |binary inst/doc/lmer.R | 124 ++++++------- inst/doc/lmer.pdf |binary inst/doc/lmerperf.R | 4 inst/doc/lmerperf.html | 4 man/lmer.Rd | 3 man/merMod-class.Rd | 36 --- man/vcov.merMod.Rd |only tests/simulate.R | 12 - tests/testthat/test-glmFamily.R | 17 + tests/testthat/test-glmer.R | 5 tests/testthat/test-glmernbref.R | 3 tests/testthat/test-glmmFail.R | 3 tests/testthat/test-lmer.R | 16 + tests/testthat/test-methods.R | 25 +- tests/testthat/test-resids.R | 8 tests/testthat/test-summary_testlevel_1.rda |binary 25 files changed, 251 insertions(+), 450 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.9.1 dated 2024-09-07 and 2.9.2 dated 2025-01-11
DESCRIPTION | 8 MD5 | 46 NEWS.md | 505 ++--- R/cluster_stats.R | 548 +++--- R/tree_distance_utilities.R | 2 build/partial.rdb |binary inst/apa-old-doi-prefix.csl | 2306 +++++++++++++++++--------- inst/doc/Generalized-RF.html | 34 inst/doc/Robinson-Foulds.html | 32 inst/doc/Using-TreeDist.html | 12 inst/doc/compare-treesets.html | 14 inst/doc/different-leaves.html | 8 inst/doc/information.html | 8 inst/doc/landscapes.html | 1955 +++++++++++++++++++++- inst/doc/treespace.html | 20 inst/doc/using-distances.html | 22 src/ints.h | 2 src/nni_distance.cpp | 151 - src/spr.cpp | 33 src/tree_distances.cpp | 48 tests/testthat/test-tree_distance.R | 1 tests/testthat/test-tree_distance_nni.R | 366 ++-- tests/testthat/test-tree_distance_spr.R | 331 +-- tests/testthat/test-tree_distance_utilities.R | 26 24 files changed, 4682 insertions(+), 1796 deletions(-)
Title: Classical Age-Depth Modelling of Cores from Deposits
Description: Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010) <doi:10.1016/j.quageo.2010.01.002>.
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [ctb] ,
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between clam versions 2.6.1 dated 2024-09-25 and 2.6.2 dated 2025-01-11
clam-2.6.1/clam/man/calib.t.Rd |only clam-2.6.1/clam/vignettes/clam_runs |only clam-2.6.2/clam/DESCRIPTION | 11 ++- clam-2.6.2/clam/MD5 | 55 ++++++------------ clam-2.6.2/clam/NAMESPACE | 3 - clam-2.6.2/clam/NEWS.md | 5 + clam-2.6.2/clam/R/calibrate.R | 104 ----------------------------------- clam-2.6.2/clam/R/clam-package.R | 2 clam-2.6.2/clam/R/clam.R | 15 +++-- clam-2.6.2/clam/R/plots.R | 5 + clam-2.6.2/clam/R/postanalysis.R | 21 +++++-- clam-2.6.2/clam/R/readwrite.R | 68 +++++++++++++--------- clam-2.6.2/clam/build/partial.rdb |binary clam-2.6.2/clam/build/vignette.rds |binary clam-2.6.2/clam/inst/doc/clam.R | 14 +++- clam-2.6.2/clam/inst/doc/clam.Rmd | 10 ++- clam-2.6.2/clam/inst/doc/clam.html | 29 +++++---- clam-2.6.2/clam/man/add.dates.Rd | 5 + clam-2.6.2/clam/man/clam.Rd | 7 +- clam-2.6.2/clam/man/deptime.age.Rd | 5 + clam-2.6.2/clam/man/deptime.depth.Rd | 5 + clam-2.6.2/clam/man/plot_proxies.Rd | 9 ++- clam-2.6.2/clam/vignettes/clam.Rmd | 10 ++- 23 files changed, 164 insertions(+), 219 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray,
Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.3.4 dated 2024-02-16 and 1.3.5 dated 2025-01-11
mets-1.3.4/mets/inst/doc/binreg-TRS.rmd |only mets-1.3.4/mets/src/init.c |only mets-1.3.4/mets/vignettes/binreg-TRS.rmd |only mets-1.3.5/mets/DESCRIPTION | 14 mets-1.3.5/mets/MD5 | 232 + mets-1.3.5/mets/NAMESPACE | 36 mets-1.3.5/mets/NEWS.md | 11 mets-1.3.5/mets/R/Event.Split.R | 127 mets-1.3.5/mets/R/RcppExports.R | 16 mets-1.3.5/mets/R/WA-estimands.R |only mets-1.3.5/mets/R/binomial.regression.R | 1282 ++++++---- mets-1.3.5/mets/R/binregTSR.R | 91 mets-1.3.5/mets/R/casewise.R | 3 mets-1.3.5/mets/R/cifreg.R | 141 - mets-1.3.5/mets/R/claytonakes.R | 17 mets-1.3.5/mets/R/clusterindex-reshape.R | 6 mets-1.3.5/mets/R/daggregate.R | 2 mets-1.3.5/mets/R/event.r | 90 mets-1.3.5/mets/R/fastapprox.R | 13 mets-1.3.5/mets/R/gof-phreg.R | 40 mets-1.3.5/mets/R/ipw.R | 44 mets-1.3.5/mets/R/kmplot.R |only mets-1.3.5/mets/R/mets-package.R | 48 mets-1.3.5/mets/R/normal0.R | 42 mets-1.3.5/mets/R/phreg.R | 1133 ++------ mets-1.3.5/mets/R/phreg_rct.R |only mets-1.3.5/mets/R/pmvn.R | 42 mets-1.3.5/mets/R/recreg.R | 411 ++- mets-1.3.5/mets/R/recurrent.marginal.R | 473 +++ mets-1.3.5/mets/R/restricted.mean.R | 193 - mets-1.3.5/mets/R/riskRegression.R |only mets-1.3.5/mets/R/sim-pc-hazard.R | 659 +++-- mets-1.3.5/mets/R/wild-phreg.R | 10 mets-1.3.5/mets/build/partial.rdb |only mets-1.3.5/mets/build/vignette.rds |binary mets-1.3.5/mets/data/ACTG175.rda |only mets-1.3.5/mets/data/calgb8923.rda |only mets-1.3.5/mets/data/hfaction_cpx12.rda |only mets-1.3.5/mets/inst/doc/basic-dutils.html | 42 mets-1.3.5/mets/inst/doc/binomial-family.html | 42 mets-1.3.5/mets/inst/doc/binomial-twin.html | 118 mets-1.3.5/mets/inst/doc/binreg-TRS.R | 15 mets-1.3.5/mets/inst/doc/binreg-TRS.Rmd |only mets-1.3.5/mets/inst/doc/binreg-TRS.html | 592 ++-- mets-1.3.5/mets/inst/doc/binreg-ate.R | 4 mets-1.3.5/mets/inst/doc/binreg-ate.Rmd | 4 mets-1.3.5/mets/inst/doc/binreg-ate.html | 191 - mets-1.3.5/mets/inst/doc/binreg.Rmd | 7 mets-1.3.5/mets/inst/doc/binreg.html | 94 mets-1.3.5/mets/inst/doc/cifreg.R | 3 mets-1.3.5/mets/inst/doc/cifreg.Rmd | 8 mets-1.3.5/mets/inst/doc/cifreg.html | 472 +-- mets-1.3.5/mets/inst/doc/cooking-survival-data.R |only mets-1.3.5/mets/inst/doc/cooking-survival-data.Rmd |only mets-1.3.5/mets/inst/doc/cooking-survival-data.html |only mets-1.3.5/mets/inst/doc/glm-utility.html | 45 mets-1.3.5/mets/inst/doc/haplo-discrete-ttp.html | 43 mets-1.3.5/mets/inst/doc/interval-discrete-survival.R | 25 mets-1.3.5/mets/inst/doc/interval-discrete-survival.Rmd | 25 mets-1.3.5/mets/inst/doc/interval-discrete-survival.html | 152 - mets-1.3.5/mets/inst/doc/marginal-cox.html | 49 mets-1.3.5/mets/inst/doc/mediation-survival.R | 20 mets-1.3.5/mets/inst/doc/mediation-survival.html | 135 - mets-1.3.5/mets/inst/doc/phreg_rct.R |only mets-1.3.5/mets/inst/doc/phreg_rct.Rmd |only mets-1.3.5/mets/inst/doc/phreg_rct.html |only mets-1.3.5/mets/inst/doc/quantitative-twin.R | 8 mets-1.3.5/mets/inst/doc/quantitative-twin.html | 11 mets-1.3.5/mets/inst/doc/recurrent-events.R | 172 - mets-1.3.5/mets/inst/doc/recurrent-events.Rmd | 46 mets-1.3.5/mets/inst/doc/recurrent-events.html | 991 ++++--- mets-1.3.5/mets/inst/doc/rmst-ate.R | 12 mets-1.3.5/mets/inst/doc/rmst-ate.Rmd | 12 mets-1.3.5/mets/inst/doc/rmst-ate.html | 396 +-- mets-1.3.5/mets/inst/doc/survival-ate.R | 10 mets-1.3.5/mets/inst/doc/survival-ate.Rmd | 15 mets-1.3.5/mets/inst/doc/survival-ate.html | 400 +-- mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.R | 277 +- mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.Rmd | 13 mets-1.3.5/mets/inst/doc/time-to-event-family-studies-arev.html | 283 -- mets-1.3.5/mets/inst/doc/twostage-survival.html | 58 mets-1.3.5/mets/inst/doc/while-alive.R |only mets-1.3.5/mets/inst/doc/while-alive.Rmd |only mets-1.3.5/mets/inst/doc/while-alive.html |only mets-1.3.5/mets/inst/include/mets_RcppExports.h | 29 mets-1.3.5/mets/man/ACTG175.Rd |only mets-1.3.5/mets/man/ClaytonOakes.Rd | 16 mets-1.3.5/mets/man/Event.Rd |only mets-1.3.5/mets/man/WA_recurrent.Rd |only mets-1.3.5/mets/man/aalenMets.Rd | 4 mets-1.3.5/mets/man/basehazplot.phreg.Rd | 2 mets-1.3.5/mets/man/binreg.Rd | 29 mets-1.3.5/mets/man/binregATE.Rd | 19 mets-1.3.5/mets/man/binregTSR.Rd | 3 mets-1.3.5/mets/man/calgb8923.Rd |only mets-1.3.5/mets/man/cifreg.Rd | 4 mets-1.3.5/mets/man/daggregate.Rd | 2 mets-1.3.5/mets/man/evalTerminal.Rd |only mets-1.3.5/mets/man/event.split.Rd |only mets-1.3.5/mets/man/hfaction_cpx12.Rd |only mets-1.3.5/mets/man/ipw2.Rd | 44 mets-1.3.5/mets/man/mets-package.Rd | 23 mets-1.3.5/mets/man/phreg_IPTW.Rd | 9 mets-1.3.5/mets/man/phreg_rct.Rd | 18 mets-1.3.5/mets/man/predictRisk.phreg.Rd |only mets-1.3.5/mets/man/rchaz.Rd | 7 mets-1.3.5/mets/man/rcrisk.Rd | 18 mets-1.3.5/mets/man/recreg.Rd | 13 mets-1.3.5/mets/man/resmean.phreg.Rd | 1 mets-1.3.5/mets/man/resmeanATE.Rd | 18 mets-1.3.5/mets/man/resmeanIPCW.Rd | 80 mets-1.3.5/mets/man/sim.cause.cox.Rd | 30 mets-1.3.5/mets/man/sim.cox.Rd | 39 mets-1.3.5/mets/man/simRecurrentII.Rd | 14 mets-1.3.5/mets/man/survivalG.Rd | 4 mets-1.3.5/mets/src/RcppExports.cpp | 216 + mets-1.3.5/mets/src/fastcox.cpp | 15 mets-1.3.5/mets/src/mvn.cpp | 309 -- mets-1.3.5/mets/src/sim-tools.cpp | 13 mets-1.3.5/mets/tests/testthat/test_binreg.R |only mets-1.3.5/mets/tests/testthat/test_iid.R | 2 mets-1.3.5/mets/tests/testthat/test_mvn.R |only mets-1.3.5/mets/tests/testthat/test_rmst.R |only mets-1.3.5/mets/vignettes/binreg-TRS.Rmd |only mets-1.3.5/mets/vignettes/binreg-ate.Rmd | 4 mets-1.3.5/mets/vignettes/binreg.Rmd | 7 mets-1.3.5/mets/vignettes/cifreg.Rmd | 8 mets-1.3.5/mets/vignettes/cooking-survival-data.Rmd |only mets-1.3.5/mets/vignettes/interval-discrete-survival.Rmd | 25 mets-1.3.5/mets/vignettes/phreg_rct.Rmd |only mets-1.3.5/mets/vignettes/recurrent-events.Rmd | 46 mets-1.3.5/mets/vignettes/rmst-ate.Rmd | 12 mets-1.3.5/mets/vignettes/survival-ate.Rmd | 15 mets-1.3.5/mets/vignettes/time-to-event-family-studies-arev.Rmd | 13 mets-1.3.5/mets/vignettes/while-alive.Rmd |only 135 files changed, 6257 insertions(+), 4820 deletions(-)
Title: Fake Web Apps for HTTP Testing
Description: Create a web app that makes it easier to test web clients
without using the internet. It includes a web app framework with path
matching, parameters and templates. Can parse various 'HTTP' request
bodies. Can send 'JSON' data or files from the disk. Includes a web
app that implements the 'httpbin.org' web service.
Author: Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd],
Civetweb contributors [ctb] ,
Redoc contributors [ctb] ,
L. Peter Deutsch [ctb] ,
Martin Purschke [ctb] ,
Aladdin Enterprises [cph] ,
Maelle Salmon [ctb]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between webfakes versions 1.3.1 dated 2024-04-25 and 1.3.2 dated 2025-01-11
DESCRIPTION | 8 MD5 | 41 NEWS.md | 5 R/app-process.R | 5 R/mw-cgi.R | 4 R/server.R | 10 README.md | 6 man/mw_cgi.Rd | 4 man/server_opts.Rd | 8 src/Makevars | 1 src/Makevars.win | 1 src/civetweb.c | 9092 ++++++++++++++++++++--------------- src/civetweb.h | 540 +- src/handle_form.h | 74 src/http2.h |only src/match.h |only src/md5.h | 19 src/mod_mbedtls.h |only src/response.h |only src/sha1.h |only src/sort.h |only src/timer.h |only tests/testthat.R | 2 tests/testthat/_snaps/app-process.md |only tests/testthat/test-app-process.R | 19 tests/testthat/test-decode-url.R |only 26 files changed, 5952 insertions(+), 3887 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.3.0 dated 2024-10-23 and 1.4.0 dated 2025-01-11
REDCapR-1.3.0/REDCapR/inst/test-data/projects/super-wide-3/generate-dictionary.R |only REDCapR-1.4.0/REDCapR/DESCRIPTION | 11 REDCapR-1.4.0/REDCapR/MD5 | 121 REDCapR-1.4.0/REDCapR/NAMESPACE | 1 REDCapR-1.4.0/REDCapR/NEWS.md | 794 ++-- REDCapR-1.4.0/REDCapR/R/REDCapR-package.R | 4 REDCapR-1.4.0/REDCapR/R/helpers-testing.R | 32 REDCapR-1.4.0/REDCapR/R/redcap-file-repo-list.R |only REDCapR-1.4.0/REDCapR/R/sanitize-token.R | 3 REDCapR-1.4.0/REDCapR/R/skippers.R | 12 REDCapR-1.4.0/REDCapR/README.md | 6 REDCapR-1.4.0/REDCapR/build/vignette.rds |binary REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.R | 126 REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 10 REDCapR-1.4.0/REDCapR/inst/doc/BasicREDCapROperations.html | 257 - REDCapR-1.4.0/REDCapR/inst/doc/SecurityDatabase.Rmd | 1 REDCapR-1.4.0/REDCapR/inst/doc/SecurityDatabase.html | 2 REDCapR-1.4.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 8 REDCapR-1.4.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 10 REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.R | 220 - REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 7 REDCapR-1.4.0/REDCapR/inst/doc/advanced-redcapr-operations.html | 377 -- REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.R | 169 - REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.Rmd | 1 REDCapR-1.4.0/REDCapR/inst/doc/longitudinal-and-repeating.html | 1297 -------- REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.R | 161 REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.Rmd | 3 REDCapR-1.4.0/REDCapR/inst/doc/workflow-read.html | 1615 ---------- REDCapR-1.4.0/REDCapR/inst/doc/workflow-write.Rmd | 15 REDCapR-1.4.0/REDCapR/inst/doc/workflow-write.html | 53 REDCapR-1.4.0/REDCapR/inst/misc/coph.credentials |only REDCapR-1.4.0/REDCapR/inst/misc/dev-2.credentials | 1 REDCapR-1.4.0/REDCapR/inst/misc/example.credentials | 1 REDCapR-1.4.0/REDCapR/inst/misc/plugin-redirection.yml | 8 REDCapR-1.4.0/REDCapR/inst/misc/project-redirection.yml | 36 REDCapR-1.4.0/REDCapR/inst/test-data/projects/README.md | 11 REDCapR-1.4.0/REDCapR/inst/test-data/projects/arm-multiple-delete/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/arm-single-delete/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/blank-for-gray-status/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/dag-write/README.md | 7 REDCapR-1.4.0/REDCapR/inst/test-data/projects/dag/README.md | 7 REDCapR-1.4.0/REDCapR/inst/test-data/projects/file-repo |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/simple/README.md |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/simple/project-old.xml |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/super-wide-3/README.md | 15 REDCapR-1.4.0/REDCapR/inst/test-data/projects/super-wide-3/generate-project.R |only REDCapR-1.4.0/REDCapR/inst/test-data/projects/survey/README.md | 2 REDCapR-1.4.0/REDCapR/inst/test-data/specific-redcapr/file-repo-list-oneshot |only REDCapR-1.4.0/REDCapR/inst/test-data/specific-redcapr/project-info-read/all-test-projects.R | 117 REDCapR-1.4.0/REDCapR/man/REDCapR-package.Rd | 4 REDCapR-1.4.0/REDCapR/man/redcap_file_repo_list_oneshot.Rd |only REDCapR-1.4.0/REDCapR/man/sanitize_token.Rd | 3 REDCapR-1.4.0/REDCapR/tests/test-all.R | 7 REDCapR-1.4.0/REDCapR/tests/testthat/test-event-instruments.R | 12 REDCapR-1.4.0/REDCapR/tests/testthat/test-file-repo-list-oneshot.R |only REDCapR-1.4.0/REDCapR/tests/testthat/test-instruments-metadata.R | 11 REDCapR-1.4.0/REDCapR/tests/testthat/test-instruments.R | 6 REDCapR-1.4.0/REDCapR/tests/testthat/test-read-batch-longitudinal.R | 4 REDCapR-1.4.0/REDCapR/tests/testthat/test-read-batch-plumbing.R | 8 REDCapR-1.4.0/REDCapR/vignettes/BasicREDCapROperations.Rmd | 10 REDCapR-1.4.0/REDCapR/vignettes/SecurityDatabase.Rmd | 1 REDCapR-1.4.0/REDCapR/vignettes/TroubleshootingApiCalls.Rmd | 8 REDCapR-1.4.0/REDCapR/vignettes/advanced-redcapr-operations.Rmd | 7 REDCapR-1.4.0/REDCapR/vignettes/longitudinal-and-repeating.Rmd | 1 REDCapR-1.4.0/REDCapR/vignettes/workflow-read.Rmd | 3 REDCapR-1.4.0/REDCapR/vignettes/workflow-write.Rmd | 15 66 files changed, 1319 insertions(+), 4302 deletions(-)
Title: The Iterated Score Regression-Based Estimation
Description: We use the ISR to handle with PCA-based missing data with high correlation, and the DISR to handle with distributed PCA-based missing data. The philosophy of the package is described in Guo G. (2024) <doi:10.1080/03610918.2022.2091779>.
Author: Guangbao Guo [aut, cre] ,
Haoyue Song [aut],
Lixing Zhu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between ISR versions 2022.4.22 dated 2022-04-22 and 2025-01-10 dated 2025-01-11
DESCRIPTION | 27 +++++++++++---------- LICENSE | 2 - MD5 | 34 +++++++++++++-------------- NAMESPACE | 23 +++++++++--------- R/DISR.R | 40 ++++++++++++++++++-------------- R/ISR.R | 31 +++++++++++++++---------- R/MMLPCA.R | 29 +++++++++++++---------- R/MNIPALS.R | 27 +++++++++++++-------- R/MRPCA.R | 28 +++++++++++++--------- R/Mean.R | 26 +++++++++++++-------- R/SR.R | 27 +++++++++++++-------- man/DISR.Rd | 70 +++++++++++++++++++++++++++++++-------------------------- man/ISR.Rd | 68 ++++++++++++++++++++++++++++++------------------------- man/MMLPCA.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/MNIPALS.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/MRPCA.Rd | 68 ++++++++++++++++++++++++++++++------------------------- man/Mean.Rd | 67 ++++++++++++++++++++++++++++++------------------------ man/SR.Rd | 66 +++++++++++++++++++++++++++++------------------------ 18 files changed, 430 insertions(+), 337 deletions(-)
Title: Datetimes with Optional UTC Offsets and/or Heterogeneous Time
Zones
Description: Supports import/export for a number of datetime string standards
and R datetime classes often including
lossless re-export of
any original reduced precision including 'ISO 8601' <https://en.wikipedia.org/wiki/ISO_8601> and
'pdfmark' <https://opensource.adobe.com/dc-acrobat-sdk-docs/library/pdfmark/> datetime strings.
Supports local/global datetimes with optional UTC offsets and/or (possibly heterogeneous) time zones
with up to nanosecond precision.
Author: Trevor L. Davis [aut, cre]
Maintainer: Trevor L. Davis <trevor.l.davis@gmail.com>
Diff between datetimeoffset versions 0.3.1 dated 2023-05-11 and 0.4.1 dated 2025-01-11
DESCRIPTION | 22 - LICENSE | 4 MD5 | 44 +-- NAMESPACE | 17 + NEWS.md | 19 + R/as_datetimeoffset.r | 4 R/format.r | 52 ++- R/from-datetimeoffset.r | 48 +-- R/getset.r | 8 R/hooks.r | 8 R/precision.r | 5 R/timezone.r | 2 README.md | 3 build/vignette.rds |binary inst/doc/datetimeoffset.html | 434 ++++++++++++++++++++++-------- man/format.Rd | 7 man/from_datetimeoffset.Rd | 30 ++ man/getters.Rd | 3 tests/testthat/test-as_datetimeoffset.r | 21 + tests/testthat/test-format.r | 50 +++ tests/testthat/test-from-datetimeoffset.r | 4 tests/testthat/test-getset-clock.r | 2 tests/testthat/test-leap-seconds.r | 2 23 files changed, 577 insertions(+), 212 deletions(-)
More information about datetimeoffset at CRAN
Permanent link
Title: 'CDsampling': Constraint Sampling in Paid Research Studies
Description: In the context of paid research studies and clinical trials, budget considerations and patient sampling from available populations are subject to inherent constraints. We introduce the 'CDsampling' package, which integrates optimal design theories within the framework of constrained sampling. This package offers the possibility to find both D-optimal approximate and exact allocations for samplings with or without constraints. Additionally, it provides functions to find constrained uniform sampling as a robust sampling strategy with limited model information. Our package offers functions for the computation of the Fisher information matrix under generalized linear models (including regular linear regression model) and multinomial logistic models.To demonstrate the applications, we also provide a simulated dataset and a real dataset embedded in the package. Yifei Huang, Liping Tong, and Jie Yang (2025)<doi:10.5705/ss.202022.0414>.
Author: Yifei Huang [aut, cre],
Liping Tong [aut],
Jie Yang [aut]
Maintainer: Yifei Huang <yhuan39@uic.edu>
Diff between CDsampling versions 0.1.3 dated 2025-01-07 and 0.1.4 dated 2025-01-11
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/Intro_to_CDsampling.R | 2 +- inst/doc/Intro_to_CDsampling.Rmd | 2 +- inst/doc/Intro_to_CDsampling.html | 36 ++++++++++++++++++------------------ vignettes/Intro_to_CDsampling.Rmd | 2 +- 6 files changed, 29 insertions(+), 29 deletions(-)
Title: Visualizing the Elements Within Bio-Sequences
Description: Visualizing the types and distribution of elements within
bio-sequences. At the same time, We have developed a geom layer,
geom_rrect(), that can generate rounded rectangles. No external references
are used in the development of this package.
Author: Shiqi Zhao [aut, cre, cph]
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Diff between BioVizSeq versions 1.0.0 dated 2024-12-22 and 1.0.1 dated 2025-01-11
BioVizSeq-1.0.0/BioVizSeq/man/get_motif_location.Rd |only BioVizSeq-1.0.0/BioVizSeq/man/motif_seq.Rd |only BioVizSeq-1.0.1/BioVizSeq/DESCRIPTION | 8 +- BioVizSeq-1.0.1/BioVizSeq/MD5 | 35 +++++----- BioVizSeq-1.0.1/BioVizSeq/NAMESPACE | 5 - BioVizSeq-1.0.1/BioVizSeq/NEWS.md | 5 + BioVizSeq-1.0.1/BioVizSeq/R/combi_plot.R | 29 ++++++-- BioVizSeq-1.0.1/BioVizSeq/R/meme_plot.R | 18 ++--- BioVizSeq-1.0.1/BioVizSeq/README.md | 3 BioVizSeq-1.0.1/BioVizSeq/inst/extdata/ID_rename.csv |only BioVizSeq-1.0.1/BioVizSeq/inst/extdata/idpro2.gff3 |only BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/app.R | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/global.R | 1 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/aboutpage.R |only BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_advplot.R | 38 +++++++++-- BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_gff.R | 13 +++ BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/script/mod_meme.R | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/www/css/custom.css | 2 BioVizSeq-1.0.1/BioVizSeq/inst/shinyapp/www/html/README.html | 4 - BioVizSeq-1.0.1/BioVizSeq/man/combi_p.Rd | 6 + BioVizSeq-1.0.1/BioVizSeq/man/meme_seq.Rd |only BioVizSeq-1.0.1/BioVizSeq/man/meme_to_loc.Rd |only 22 files changed, 123 insertions(+), 48 deletions(-)
Title: Species Distribution Modelling
Description: An extensible framework for developing species distribution
models using individual and community-based approaches, generate ensembles of
models, evaluate the models, and predict species potential distributions in
space and time. For more information, please check the following paper:
Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.
Author: Babak Naimi [aut, cre] ,
Miguel B. Araujo [aut]
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between sdm versions 1.2-46 dated 2024-07-17 and 1.2-55 dated 2025-01-11
DESCRIPTION | 21 +++- MD5 | 32 ++++--- NAMESPACE | 2 R/aoa.R |only R/ensemble.R | 9 +- R/evaluates.R | 140 ++++++++++++++++++++++++++++++- R/nicheSimilarity.R | 207 +++++++++++++++++++++++++++++++++++++++------- R/pa.R | 32 +++++-- R/predict.R | 10 +- R/sdmData.R | 8 + R/show.R | 35 +++++++ R/threshold.R |only build/vignette.rds |binary inst/methods/sdm/maxNet.R | 4 man/aoa.Rd |only man/evaluates.Rd | 4 man/nicheSimilarity.Rd | 7 + man/pa.Rd | 1 man/threshold.Rd |only 19 files changed, 434 insertions(+), 78 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival, Including Copula-Based Analyses for
Dependent Censoring
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al (2019)<DOI:10.1016/j.cmpb.2018.10.020>.
Algorithms for generating correlated gene expressions are also available.
Estimation of survival functions via copula-graphic (CG) estimators is also implemented, which is useful for
sensitivity analyses under dependent censoring (Yeh et al 2023 Biomedicines) <DOI:10.3390/biomedicines11030797> and
factorial survival analyses (Emura et al 2024 Stat Methods Med Res) <DOI:10.1177/09622802231215805>.
Author: Takeshi Emura [aut, cre],
Hsuan-Yu Chen [aut],
Shigeyuki Matsui [aut],
Yi-Hau Chen [aut]
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.31 dated 2024-10-05 and 3.32 dated 2025-01-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/surv.factorial.R | 4 ++-- man/CG.Clayton.Rd | 4 ++-- man/CG.Frank.Rd | 4 ++-- man/CG.Gumbel.Rd | 4 ++-- man/compound.Cox-package.Rd | 4 ++-- 7 files changed, 20 insertions(+), 20 deletions(-)
Title: Chinese Numerals Processing
Description: Chinese numerals processing in R, such as conversion between
Chinese numerals and Arabic numerals as well as detection and extraction of
Chinese numerals in character objects and string. This package supports
the casual scale naming system and the respective SI prefix systems used
in mainland China and Taiwan:
"The State Council's Order on the Unified Implementation of Legal Measurement Units in Our Country"
The State Council of the People's Republic of China (1984)
"Names, Definitions and Symbols of the Legal Units of Measurement and the Decimal Multiples and Submultiples"
Ministry of Economic Affairs (2019) <https://gazette.nat.gov.tw/egFront/detail.do?metaid=108965>.
Author: Elgar Teo [aut, cre]
Maintainer: Elgar Teo <elgarteo@connect.hku.hk>
Diff between cnum versions 0.1.3 dated 2021-01-11 and 0.1.4 dated 2025-01-11
DESCRIPTION | 14 ++++++-------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/cnum-tools.R | 7 +++---- R/conversion.R | 27 +++++++++++++-------------- R/data-utils.R | 5 +++-- R/num2c-utils.R | 2 +- R/num2c.R | 4 ++-- man/conversion.Rd | 37 ++++++++++++++++++------------------- man/tools.Rd | 35 +++++++++++++++++------------------ src/RcppExports.cpp | 5 +++++ 11 files changed, 82 insertions(+), 78 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery [aut],
Jennifer Hoeting [aut],
Chris Volinsky [aut],
Ian Painter [aut],
Ka Yee Yeung [aut],
Hana Sevcikova [cre]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.19 dated 2024-10-18 and 3.18.20 dated 2025-01-11
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/iBMA.glm.R | 5 +++-- R/iBMA.surv.R | 5 +++-- 5 files changed, 17 insertions(+), 12 deletions(-)