Title: Binary Expansion Testing
Description: Nonparametric detection of nonuniformity and dependence with Binary Expansion Testing (BET). See Kai Zhang (2019) BET on Independence, Journal of the American Statistical Association, 114:528, 1620-1637, <DOI:10.1080/01621459.2018.1537921>, Kai Zhang, Wan Zhang, Zhigen Zhao, Wen Zhou. (2023). BEAUTY Powered BEAST, <doi:10.48550/arXiv.2103.00674> and Wan Zhang, Zhigen Zhao, Michael Baiocchi, Yao Li, Kai Zhang. (2023) SorBET: A Fast and Powerful Algorithm to Test Dependence of Variables, Techinical report.
Author: Wan Zhang [aut, cre],
Zhigen Zhao [aut],
Michael Baiocchi [aut],
Kai Zhang [aut]
Maintainer: Wan Zhang <wanz63@live.unc.edu>
Diff between BET versions 0.5.3 dated 2023-12-20 and 0.5.4 dated 2024-09-08
BET-0.5.3/BET/man/BEAST_null.Rd |only BET-0.5.4/BET/DESCRIPTION | 8 - BET-0.5.4/BET/MD5 | 19 +- BET-0.5.4/BET/NAMESPACE | 1 BET-0.5.4/BET/R/RcppExports.R | 4 BET-0.5.4/BET/R/plot.R | 99 +++++++-------- BET-0.5.4/BET/build/partial.rdb |binary BET-0.5.4/BET/man/BET_package.Rd | 1 BET-0.5.4/BET/man/Beast.Rd | 156 +++++++++++------------ BET-0.5.4/BET/src/BET3.cpp | 249 +++++++++++++++++++------------------- BET-0.5.4/BET/src/RcppExports.cpp | 22 --- 11 files changed, 263 insertions(+), 296 deletions(-)
Title: Modified Generalized Estimating Equations for Binary Outcome
Description: Analyze small-sample clustered or longitudinal data with binary
outcome using modified generalized estimating equations (GEE) with
bias-adjusted covariance estimator. The package provides any combination of
three GEE methods and 12 covariance estimators.
Author: Ryota Ishii [aut, cre],
Tomohiro Ohigashi [ctb],
Kazushi Maruo [ctb],
Masahiko Gosho [ctb]
Maintainer: Ryota Ishii <r.ishii0808@gmail.com>
Diff between geessbin versions 0.1.2 dated 2023-07-08 and 1.0.0 dated 2024-09-08
DESCRIPTION | 15 +++++++-------- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/geessbin.R | 16 ++++++++-------- R/geessbin_all.R |only R/wheeze.R | 14 +++++++++----- build/partial.rdb |binary man/geessbin.Rd | 12 ++++++------ man/geessbin_all.Rd |only man/wheeze.Rd | 14 +++++++++----- 11 files changed, 55 insertions(+), 40 deletions(-)
Title: Marginal Structural Models with Latent Class Growth Analysis of
Treatment Trajectories
Description: Implements marginal structural models combined with a latent class growth analysis framework for assessing the causal effect of treatment trajectories. Based on the approach described in "Marginal Structural Models with Latent Class Growth Analysis of Treatment Trajectories" Diop, A., Sirois, C., Guertin, J.R., Schnitzer, M.E., Candas, B., Cossette, B., Poirier, P., Brophy, J., Mésidor, M., Blais, C. and Hamel, D., (2023) <doi:10.1177/09622802231202384>.
Author: Awa Diop [aut, cre],
Denis Talbot [aut]
Maintainer: Awa Diop <awa.diop.2@ulaval.ca>
Diff between trajmsm versions 0.1.0 dated 2024-02-14 and 0.1.1 dated 2024-09-08
DESCRIPTION | 10 +++--- MD5 | 38 ++++++++++++------------ NAMESPACE | 1 R/build_traj.R | 2 - R/ipw.R | 1 R/pltmle.R | 74 +++++++++++++++++++++++++++++++++++++----------- R/split_data.R | 2 - R/trajhrmsm_gform.R | 6 +-- R/trajhrmsm_ipw.R | 6 +-- R/trajhrmsm_pltmle.R | 10 +++--- R/trajmsm_gform.R | 2 - R/trajmsm_ipw.R | 40 ++++++++++++------------- R/trajmsm_pltmle.R | 22 ++++++++------ man/pltmle.Rd | 7 +++- man/trajhrmsm_gform.Rd | 6 +-- man/trajhrmsm_ipw.Rd | 4 +- man/trajhrmsm_pltmle.Rd | 6 +-- man/trajmsm_gform.Rd | 2 - man/trajmsm_ipw.Rd | 2 - man/trajmsm_pltmle.Rd | 25 +++++++++------- 20 files changed, 159 insertions(+), 107 deletions(-)
Title: A Lightweight Version of R Markdown
Description: Render R Markdown to Markdown (without using 'knitr'), and Markdown
to lightweight HTML/LaTeX documents with the 'commonmark' package (instead
of 'Pandoc'). Some missing Markdown features in 'commonmark' are also
supported, such as raw HTML/LaTeX blocks, LaTeX math, superscripts,
subscripts, footnotes, element attributes, and appendices,
but not all 'Pandoc' Markdown features are (or will be) supported. With
additional JavaScript and CSS, you can also create HTML slides and articles.
This package can be viewed as a trimmed-down version of R Markdown and
'knitr'. It does not aim at rich Markdown features or a large variety of
output formats (the primary formats are HTML and LaTeX). Book and website
projects of multiple input documents are also supported.
Author: Yihui Xie [aut, cre]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between litedown versions 0.1 dated 2024-08-20 and 0.2 dated 2024-09-08
DESCRIPTION | 17 ++--- MD5 | 39 ++++++----- NAMESPACE | 1 NEWS.md | 13 +++ R/fuse.R | 65 +++++++++++-------- R/mark.R | 7 +- R/package.R | 29 ++++---- R/preview.R | 5 + R/site.R | 11 +-- R/utils.R | 133 ++++++++++++++++++++++++++-------------- R/zzz.R |only README.md | 8 ++ build/vignette.rds |binary inst/doc/markdown-examples.html | 10 +-- inst/doc/markdown-output.html | 10 +-- inst/doc/slides.html | 26 +++---- inst/resources/default.css | 5 - inst/resources/litedown.html | 2 inst/resources/server.css | 8 +- inst/resources/server.js | 27 ++++++-- tests/tests.Rout.save | 2 21 files changed, 253 insertions(+), 165 deletions(-)
Title: Label Data Frames, Variables, and Values
Description: Create and use data frame labels for data frame objects (frame labels), their columns (name labels), and individual values of a column (value labels). Value labels include one-to-one and many-to-one labels for nominal and ordinal variables, as well as numerical range-based value labels for continuous variables. Convert value-labeled variables so each value is replaced by its corresponding value label. Add values-converted-to-labels columns to a value-labeled data frame while preserving parent columns. Filter and subset a value-labeled data frame using labels, while returning results in terms of values. Overlay labels in place of values in common R commands to increase interpretability. Generate tables of value frequencies, with categories expressed as raw values or as labels. Access data frames that show value-to-label mappings for easy reference.
Author: Robert Hartman [aut, cre],
The MITRE Corporation [cph]
Maintainer: Robert Hartman <rohartman@gmail.com>
Diff between labelr versions 0.1.8 dated 2024-08-27 and 0.1.9 dated 2024-09-08
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 3 R/smerge.R | 18 - R/tabl.R | 2 inst/doc/labelr-special-topics.R | 561 ------------------------------------ inst/doc/labelr-special-topics.Rmd | 1 inst/doc/labelr-special-topics.html | 2 vignettes/labelr-special-topics.Rmd | 1 9 files changed, 30 insertions(+), 580 deletions(-)
Title: Rmetrics - Nonlinear and Chaotic Time Series Modelling
Description: Provides a collection of functions for testing various aspects of
univariate time series including independence and neglected
nonlinearities. Further provides functions to investigate the chaotic
behavior of time series processes and to simulate different types of chaotic
time series maps.
Author: Diethelm Wuertz [aut],
Tobias Setz [aut],
Yohan Chalabi [aut],
Paul Smith [cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between fNonlinear versions 4021.81 dated 2022-10-26 and 4041.82 dated 2024-09-08
ChangeLog | 6 +++++- DESCRIPTION | 31 ++++++++++++++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 6 ++---- src/BDSTest.c | 20 ++++++++++---------- 5 files changed, 43 insertions(+), 28 deletions(-)
Title: Comprehensive Single-Cell Annotation and Transcriptomic Analysis
Toolkit
Description: Provides a comprehensive toolkit for single-cell annotation with the 'CellMarker2.0' database <http://bio-bigdata.hrbmu.edu.cn/CellMarker/>. Streamlines biological label assignment in single-cell RNA-seq data and facilitates transcriptomic analysis, including preparation of TCGA<https://portal.gdc.cancer.gov/> and GEO<https://www.ncbi.nlm.nih.gov/geo/> datasets, differential expression analysis and visualization of enrichment analysis results. Additional utility functions support various bioinformatics workflows.
Author: Wei Cui [aut, cre, cph]
Maintainer: Wei Cui <m2c.w@outlook.com>
Diff between easybio versions 1.0 dated 2024-09-05 and 1.0.1 dated 2024-09-08
DESCRIPTION | 6 - MD5 | 29 ++-- NEWS.md |only R/uniprot.R | 41 +++---- README.md | 2 build/vignette.rds |binary inst/doc/example-bulk-rna-seq-workflow.R | 3 inst/doc/example-bulk-rna-seq-workflow.Rmd | 38 ++---- inst/doc/example-bulk-rna-seq-workflow.html | 157 +++++++++++++-------------- inst/doc/example-single-cell-annotation.R | 4 inst/doc/example-single-cell-annotation.Rmd | 33 +++-- inst/doc/example-single-cell-annotation.html | 55 ++++----- inst/example-single-cell.R | 7 + man/uniprot_id_map.Rd | 1 vignettes/example-bulk-rna-seq-workflow.Rmd | 38 ++---- vignettes/example-single-cell-annotation.Rmd | 33 +++-- 16 files changed, 229 insertions(+), 218 deletions(-)
Title: Functions for Declared Missing Values
Description: A zero dependency package containing functions to declare labels
and missing values, coupled with associated functions to create (weighted)
tables of frequencies and various other summary measures.
Some of the base functions have been rewritten to make use of the specific
information about the missing values, most importantly to distinguish
between empty NA and declared NA values.
Some functions have similar functionality with the corresponding ones from
packages "haven" and "labelled". The aim is to ensure as much compatibility
as possible with these packages, while offering an alternative in the
objects of class "declared".
Author: Adrian Dusa [aut, cre, cph] ,
Daniel Antal [ctb]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.24 dated 2023-12-07 and 0.25 dated 2024-09-08
declared-0.24/declared/inst/doc |only declared-0.25/declared/DESCRIPTION | 6 declared-0.25/declared/MD5 | 39 +-- declared-0.25/declared/NAMESPACE | 2 declared-0.25/declared/R/as.declared.R | 15 - declared-0.25/declared/R/class_methods.R | 211 +++++++++++++-------- declared-0.25/declared/R/declared_package.R | 7 declared-0.25/declared/R/drop_undeclare.R | 18 + declared-0.25/declared/R/haven.R | 20 - declared-0.25/declared/R/internals.R | 69 ++++-- declared-0.25/declared/R/onLoad.R | 31 ++- declared-0.25/declared/R/pillar.R | 2 declared-0.25/declared/R/vctrs.R | 47 ++++ declared-0.25/declared/inst/ChangeLog | 12 - declared-0.25/declared/man/declared_package.Rd | 7 declared-0.25/declared/src/declared.c | 41 ++-- declared-0.25/declared/src/registerDynamicSymbol.c | 12 + 17 files changed, 348 insertions(+), 191 deletions(-)
Title: R-Based Visualization Techniques for Task-Based Applications
Description: Performance analysis workflow that combines the power of the R
language (and the tidyverse realm) and many auxiliary tools to
provide a consistent, flexible, extensible, fast, and versatile
framework for the performance analysis of task-based applications
that run on top of the StarPU runtime (with its MPI (Message
Passing Interface) layer for multi-node support). Its goal is to
provide a fruitful prototypical environment to conduct performance
analysis hypothesis-checking for task-based applications that run
on heterogeneous (multi-GPU, multi-core) multi-node HPC
(High-performance computing) platforms.
Author: Lucas Mello Schnorr [aut, ths]
,
Vinicius Garcia Pinto [aut] ,
Lucas Leandro Nesi [aut, cre] ,
Marcelo Cogo Miletto [aut] ,
Guilherme Alles [ctb],
Arnaud Legrand [ctb],
Luka Stanisic [ctb],
Remy Drouilhet [ctb]
Maintainer: Lucas Leandro Nesi <lucas.nesi@inf.ufrgs.br>
Diff between starvz versions 0.8.0 dated 2024-02-23 and 0.8.2 dated 2024-09-08
DESCRIPTION | 23 +++++++++++------------ MD5 | 8 ++++---- R/phase1.R | 2 +- R/phase2_states_chart.R | 3 +-- inst/tools/fxt2paje.sh | 13 ++++++++++--- 5 files changed, 27 insertions(+), 22 deletions(-)
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman
filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in
BLAS and LAPACK. Due to the speed of the filter, the fitting of
high-dimensional linear state space models to large datasets
becomes possible. This package also contains a plot function
for the visualization of the state vector and graphical
diagnostics of the residuals.
Author: David Luethi [aut],
Philipp Erb [aut],
Simon Otziger [aut],
Daniel McDonald [aut],
Paul Smith [aut, cre]
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between FKF versions 0.2.5 dated 2024-01-30 and 0.2.6 dated 2024-09-08
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------- NEWS.md | 6 +++++ README.md | 2 - build/vignette.rds |binary inst/doc/FKF.html | 20 +++++++++--------- man/plot.fks.Rd | 2 - src/fkflib.c | 56 ++++++++++++++++++++++++++--------------------------- 8 files changed, 57 insertions(+), 51 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'. References: Patil (2021) <doi:10.21105/joss.03236>.
Author: Indrajeet Patil [cre, aut, cph]
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 1.5.5 dated 2024-07-05 and 1.6.0 dated 2024-09-08
statsExpressions-1.5.5/statsExpressions/data/movies_wide.rdata |only statsExpressions-1.5.5/statsExpressions/inst/doc/stats_details.R |only statsExpressions-1.5.5/statsExpressions/inst/doc/stats_details.Rmd |only statsExpressions-1.5.5/statsExpressions/inst/doc/stats_details.html |only statsExpressions-1.5.5/statsExpressions/man/movies_wide.Rd |only statsExpressions-1.5.5/statsExpressions/vignettes/stats_details.Rmd |only statsExpressions-1.6.0/statsExpressions/DESCRIPTION | 27 statsExpressions-1.6.0/statsExpressions/MD5 | 124 -- statsExpressions-1.6.0/statsExpressions/NEWS.md | 9 statsExpressions-1.6.0/statsExpressions/R/add-expression-col.R | 358 ++--- statsExpressions-1.6.0/statsExpressions/R/centrality-description.R | 154 +- statsExpressions-1.6.0/statsExpressions/R/contingency-table.R | 304 ++-- statsExpressions-1.6.0/statsExpressions/R/corr-test.R | 114 - statsExpressions-1.6.0/statsExpressions/R/data.R | 210 +-- statsExpressions-1.6.0/statsExpressions/R/globals.R | 78 - statsExpressions-1.6.0/statsExpressions/R/helpers-easystats.R | 132 +- statsExpressions-1.6.0/statsExpressions/R/long-to-wide-converter.R | 190 +-- statsExpressions-1.6.0/statsExpressions/R/meta-analysis.R | 193 +-- statsExpressions-1.6.0/statsExpressions/R/one-sample-test.R | 206 +-- statsExpressions-1.6.0/statsExpressions/R/oneway-anova.R | 574 ++++----- statsExpressions-1.6.0/statsExpressions/R/pairwise-comparisons.R | 616 +++++----- statsExpressions-1.6.0/statsExpressions/R/statsExpressions-package.R | 60 statsExpressions-1.6.0/statsExpressions/R/tidy-model-expressions.R | 239 +-- statsExpressions-1.6.0/statsExpressions/R/two-sample-test.R | 272 ++-- statsExpressions-1.6.0/statsExpressions/README.md | 11 statsExpressions-1.6.0/statsExpressions/build/vignette.rds |binary statsExpressions-1.6.0/statsExpressions/inst/WORDLIST | 2 statsExpressions-1.6.0/statsExpressions/inst/doc/statsExpressions.R | 2 statsExpressions-1.6.0/statsExpressions/inst/doc/statsExpressions.Rmd | 2 statsExpressions-1.6.0/statsExpressions/inst/doc/statsExpressions.html | 98 - statsExpressions-1.6.0/statsExpressions/man/add_expression_col.Rd | 4 statsExpressions-1.6.0/statsExpressions/man/bugs_long.Rd | 9 statsExpressions-1.6.0/statsExpressions/man/centrality_description.Rd | 2 statsExpressions-1.6.0/statsExpressions/man/contingency_table.Rd | 12 statsExpressions-1.6.0/statsExpressions/man/corr_test.Rd | 4 statsExpressions-1.6.0/statsExpressions/man/figures/README-anova_parametric2-1.png |binary statsExpressions-1.6.0/statsExpressions/man/figures/README-anova_rob1-1.png |binary statsExpressions-1.6.0/statsExpressions/man/iris_long.Rd | 2 statsExpressions-1.6.0/statsExpressions/man/long_to_wide_converter.Rd | 2 statsExpressions-1.6.0/statsExpressions/man/meta_analysis.Rd | 15 statsExpressions-1.6.0/statsExpressions/man/movies_long.Rd | 14 statsExpressions-1.6.0/statsExpressions/man/one_sample_test.Rd | 4 statsExpressions-1.6.0/statsExpressions/man/oneway_anova.Rd | 10 statsExpressions-1.6.0/statsExpressions/man/pairwise_comparisons.Rd | 8 statsExpressions-1.6.0/statsExpressions/man/statsExpressions-package.Rd | 2 statsExpressions-1.6.0/statsExpressions/man/tidy_model_expressions.Rd | 8 statsExpressions-1.6.0/statsExpressions/man/two_sample_test.Rd | 8 statsExpressions-1.6.0/statsExpressions/tests/testthat.R | 1 statsExpressions-1.6.0/statsExpressions/tests/testthat/_snaps/centrality-description.md | 176 -- statsExpressions-1.6.0/statsExpressions/tests/testthat/_snaps/meta-random-parametric.md | 8 statsExpressions-1.6.0/statsExpressions/tests/testthat/_snaps/one-sample.md | 327 ++++- statsExpressions-1.6.0/statsExpressions/tests/testthat/test-centrality-description.R | 15 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-meta-random-bayes.R | 1 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-meta-random-parametric.R | 4 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-one-sample.R | 174 -- statsExpressions-1.6.0/statsExpressions/tests/testthat/test-one-two-sample-dataframes.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-oneway-anova-bayes.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-oneway-anova-nonparametric.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-oneway-anova-parametric.R | 15 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-two-sample-bayes.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-two-sample-nonparametric.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-two-sample-parametric.R | 2 statsExpressions-1.6.0/statsExpressions/tests/testthat/test-two-sample-robust.R | 2 statsExpressions-1.6.0/statsExpressions/vignettes/setup.R | 32 statsExpressions-1.6.0/statsExpressions/vignettes/statsExpressions.Rmd | 2 statsExpressions-1.6.0/statsExpressions/vignettes/stats_reporting_format.png |only statsExpressions-1.6.0/statsExpressions/vignettes/web_only/stats_details.md |only 67 files changed, 2419 insertions(+), 2429 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Informative Nonparametric Bootstrap Test with Pooled Resampling
Description: Sample sizes are often small due to hard to reach target populations,
rare target events, time constraints, limited budgets, or ethical considerations.
Two statistical methods with promising performance in small samples are the
nonparametric bootstrap test with pooled resampling method, which is the
focus of Dwivedi, Mallawaarachchi, and Alvarado (2017) <doi:10.1002/sim.7263>,
and informative hypothesis testing, which is implemented in the 'restriktor'
package. The 'npboottprmFBar' package uses the nonparametric bootstrap test
with pooled resampling method to implement informative hypothesis testing.
The bootFbar() function can be used to analyze data with this method and the
persimon() function can be used to conduct performance simulations on type-one
error and statistical power.
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between npboottprmFBar versions 0.1.1 dated 2024-02-22 and 0.2.0 dated 2024-09-08
DESCRIPTION | 10 +++---- MD5 | 16 +++++++---- NAMESPACE | 1 R/persimon.R | 5 ++- R/persimon_app.R |only R/persimon_app_helpers.R |only README.md | 8 ++--- man/appendInputParams.Rd |only man/getUIParams.Rd |only man/persimon_app.Rd |only man/runSimulation.Rd |only tests/testthat/test-persimon.R | 58 ++++++++++++++++++++--------------------- 12 files changed, 53 insertions(+), 45 deletions(-)
More information about npboottprmFBar at CRAN
Permanent link
Title: Likelihood Ratio Tests and Confidence Intervals
Description: A collection of hypothesis tests and confidence intervals based on the likelihood ratio
<https://en.wikipedia.org/wiki/Likelihood-ratio_test>.
Author: Greg McMahan [aut, cre]
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between LRTesteR versions 1.2.0 dated 2024-08-21 and 1.2.1 dated 2024-09-08
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Spatial Data Science Complementary Features
Description: Wrapping and supplementing commonly used functions in the R ecosystem related
to spatial data science, while serving as a basis for other packages maintained
by Wenbo Lv.
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between sdsfun versions 0.1.0 dated 2024-08-30 and 0.1.1 dated 2024-09-08
DESCRIPTION | 17 +- MD5 | 20 +-- NEWS.md | 7 + R/pipe.R | 24 +-- R/sf_helpers.R | 166 ++++++++++++------------- R/spdep_helpers.R | 231 ++++++++++++++++++------------------ README.md | 17 +- man/figures/logo.png |binary man/spdep_contiguity_swm.Rd | 2 man/spdep_distance_swm.Rd | 17 +- tests/testthat/test-spdep_helpers.R | 123 ++++++++++--------- 11 files changed, 323 insertions(+), 301 deletions(-)
Title: Geographically Optimal Similarity
Description: Understanding spatial association is essential for spatial
statistical inference, including factor exploration and spatial prediction.
Geographically optimal similarity (GOS) model is an effective method
for spatial prediction, as described in Yongze Song (2022)
<doi:10.1007/s11004-022-10036-8>. GOS was developed based on
the geographical similarity principle, as described in Axing Zhu (2018)
<doi:10.1080/19475683.2018.1534890>. GOS has advantages in
more accurate spatial prediction using fewer samples and
critically reduced prediction uncertainty.
Author: Yongze Song [aut, cph] ,
Wenbo Lv [aut, cre]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between geosimilarity versions 3.1 dated 2024-08-29 and 3.2 dated 2024-09-08
DESCRIPTION | 8 ++++---- MD5 | 23 ++++++++++++----------- NAMESPACE | 1 + NEWS.md | 8 ++++++++ R/gos.R | 3 +-- R/gos_bestkappa.R | 3 +-- R/utils.R | 33 +++++++++++++++++++++++++++++++++ R/zzz.R | 2 +- man/gos.Rd | 3 +-- man/gos_bestkappa.Rd | 3 +-- man/removeoutlier.Rd |only tests/testthat/test-gos.R | 2 +- tests/testthat/test-gos_bestkappa.R | 2 +- 13 files changed, 65 insertions(+), 26 deletions(-)
Title: Standardize Dates in Different Formats or with Missing Data
Description: There are many different formats dates are commonly
represented with: the order of day, month, or year can differ,
different separators ("-", "/", or whitespace) can be used, months can
be numerical, names, or abbreviations and year given as two digits or
four. 'datefixR' takes dates in all these different formats and
converts them to R's built-in date class. If 'datefixR' cannot
standardize a date, such as because it is too malformed, then the user
is told which date cannot be standardized and the corresponding ID for
the row. 'datefixR' also allows the imputation of missing days and
months with user-controlled behavior.
Author: Nathan Constantine-Cooke [aut, cre]
,
Jonathan Kitt [ctb, trl],
Antonio J. Perez-Luque [ctb, trl]
,
Daniel Possenriede [ctb, trl] ,
Michal Lauer [ctb, trl],
Kaique dos S. Alves [rev] ,
Al-Ahmadgaid B. Asaad [rev] ,
Anatoly Tsyplenkov [ctb, trl] ,
Chi [...truncated...]
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>
Diff between datefixR versions 1.6.1 dated 2023-12-11 and 1.7.0 dated 2024-09-08
DESCRIPTION | 32 +++++++++++--------- MD5 | 32 +++++++++++--------- NEWS.md | 5 +++ R/months.R | 18 +++++++---- R/shinyapp.R | 6 +++ README.md | 18 ++++++----- build/vignette.rds |binary inst/WORDLIST | 48 +++++++++++++++--------------- inst/doc/datefixR.html | 28 ++--------------- inst/po/en@quot/LC_MESSAGES/R-datefixR.mo |binary inst/po/en@quot/LC_MESSAGES/datefixR.mo |binary inst/po/id |only man/datefixR.Rd | 3 + po/R-datefixR.pot | 4 +- po/R-id.po |only po/datefixR.pot | 4 +- po/id.po |only tests/testthat/test_fix_date_df.R | 17 ++++++++++ 18 files changed, 120 insertions(+), 95 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehr [...truncated...]
Author: Thorsten Pohlert [aut, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.9.10 dated 2023-12-10 and 1.9.12 dated 2024-09-08
DESCRIPTION | 10 - MD5 | 72 ++++---- NAMESPACE | 9 - R/adKSampleTest.R | 312 ++++++++++++++++++-------------------- R/chackoTest.R | 2 R/kwManyOneConoverTest.R | 4 R/kwManyOneDunnTest.R | 9 - R/kwManyOneNdwTest.R | 4 R/manyOneUTest.R | 4 R/medianAllPairsTest.R |only R/medianTest.R |only R/print.PMCMR.R | 3 R/sysdata.rda |binary R/williamsTest.R | 2 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary data/Pentosan.rda |binary data/algae.rda |binary data/qPCR.rda |binary data/reviewers.rda |binary data/trout.rda |binary inst/NEWS.Rd | 23 ++ inst/doc/QuickReferenceGuide.html | 4 man/adKSampleTest.Rd | 7 man/bwsKSampleTest.Rd | 7 man/chackoTest.Rd | 2 man/kruskalTest.Rd | 7 man/kwAllPairsConoverTest.Rd | 4 man/kwAllPairsDunnTest.Rd | 4 man/kwAllPairsNemenyiTest.Rd | 4 man/kwManyOneConoverTest.Rd | 2 man/kwManyOneDunnTest.Rd | 7 man/kwManyOneNdwTest.Rd | 2 man/manyOneUTest.Rd | 2 man/medianAllPairsTest.Rd |only man/medianTest.Rd |only man/williamsTest.Rd | 2 src/init.c | 4 39 files changed, 290 insertions(+), 224 deletions(-)
Title: Spatio-Temporal Bayesian Modelling
Description: Fits, spatially predicts and temporally forecasts large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models for spatio-temporal big-n problems. Bakar and Sahu (2015) <doi:10.18637/jss.v063.i15>.
Author: K. Shuvo Bakar [aut, cre] ,
Sujit K. Sahu [ctb]
Maintainer: K. Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTimer versions 3.3.2 dated 2022-10-26 and 3.3.3 dated 2024-09-08
DESCRIPTION | 26 +++- MD5 | 28 ++-- R/spTfnc.R | 70 +++++------ inst/CITATION | 45 +------ inst/ChangeLog | 7 + man/predict.spT.Rd | 89 -------------- man/spT.Gibbs.Rd | 84 ------------- src/gibbs_ar.c | 334 ----------------------------------------------------- src/gibbs_gp.c | 302 ----------------------------------------------- src/gibbs_gpp.c | 323 --------------------------------------------------- src/main_ar.h | 12 - src/main_gp.h | 245 +------------------------------------- src/main_gpp.h | 18 -- src/mathematics.c | 18 +- src/spTimer_init.c | 6 15 files changed, 111 insertions(+), 1496 deletions(-)
Title: Tools for Social Network Analysis
Description: A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.
Author: Carter T. Butts [aut, cre, cph]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between sna versions 2.7-2 dated 2023-12-06 and 2.8 dated 2024-09-08
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/randomgraph.R | 41 +++++++++++++++++++++++++++++++---------- man/gplot.Rd | 2 +- man/rgbn.Rd | 49 ++++++++++++++++++++++++++++++++++--------------- src/Rinit.c | 4 ++-- src/layout.c | 18 +++++++++--------- src/paths.c | 26 +++++++++++++------------- src/randomgraph.c | 46 ++++++++++++++++++++++++++++++++++++---------- src/randomgraph.h | 4 ++-- src/utils.c | 5 +++-- 12 files changed, 153 insertions(+), 79 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian M [...truncated...]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 1.4.0 dated 2024-09-04 and 1.4.1 dated 2024-09-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 9 +++++++++ inst/WORDLIST | 2 ++ inst/doc/matrixStats-methods.html | 2 +- src/rowSums2_lowlevel_template.h | 14 +++++++++++--- 6 files changed, 31 insertions(+), 12 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani [aut],
S.Ramachandran [aut],
Ab Rauf Shah [aut],
S. Ramachandran [cre]
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.20 dated 2024-04-08 and 1.0.21 dated 2024-09-08
DESCRIPTION | 29 +++++++++++++++++++++++------ MD5 | 16 +++++++++------- NAMESPACE | 1 + R/pubtator3_function.R |only data/GeneToEntrez.rda |binary data/HGNC2UniprotID.rda |binary data/HGNCdata.rda |binary data/common_words_new.rda |binary man/pubtator3_function.Rd |only man/pubtator_function.Rd | 4 ++-- 10 files changed, 35 insertions(+), 15 deletions(-)
Title: Creating and Working with Pedigrees and Marker Data
Description: A comprehensive collection of tools for creating,
manipulating and visualising pedigrees and genetic marker data.
Pedigrees can be read from text files or created on the fly with
built-in functions. A range of utilities enable modifications like
adding or removing individuals, breaking loops, and merging pedigrees.
An online tool for creating pedigrees interactively, based on
'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>.
'pedtools' is the hub of the 'pedsuite', a collection of packages for
pedigree analysis. A detailed presentation of the 'pedsuite' is given
in the book 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedtools versions 2.7.0 dated 2024-06-28 and 2.7.1 dated 2024-09-08
DESCRIPTION | 8 +- MD5 | 23 +++--- NAMESPACE | 1 NEWS.md | 11 +++ R/marker_utils.R | 38 +++++++++++ R/ped_basic.R | 18 +++-- R/ped_plot.R | 15 +++- R/plot_methods.R | 16 +--- inst/doc/pedtools.html | 168 ++++++++++++++++++++++++------------------------- man/ped_basic.Rd | 15 +++- man/plotPedList.Rd | 4 + man/plotmethods.Rd | 15 +--- man/swapGenotypes.Rd |only 13 files changed, 197 insertions(+), 135 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.8 dated 2024-07-07 and 1.9 dated 2024-09-08
openxlsx2-1.8/openxlsx2/vignettes/img/worksheet_styling.jpg |only openxlsx2-1.9/openxlsx2/DESCRIPTION | 10 openxlsx2-1.9/openxlsx2/MD5 | 95 - openxlsx2-1.9/openxlsx2/NAMESPACE | 3 openxlsx2-1.9/openxlsx2/NEWS.md | 23 openxlsx2-1.9/openxlsx2/R/class-workbook-wrappers.R | 45 openxlsx2-1.9/openxlsx2/R/class-workbook.R | 43 openxlsx2-1.9/openxlsx2/R/class-worksheet.R | 12 openxlsx2-1.9/openxlsx2/R/converters.R | 7 openxlsx2-1.9/openxlsx2/R/helper-functions.R | 10 openxlsx2-1.9/openxlsx2/R/openxlsx2-package.R | 11 openxlsx2-1.9/openxlsx2/R/read.R | 49 openxlsx2-1.9/openxlsx2/R/utils.R | 457 +++-- openxlsx2-1.9/openxlsx2/R/wb_functions.R | 4 openxlsx2-1.9/openxlsx2/R/wb_load.R | 16 openxlsx2-1.9/openxlsx2/R/write.R | 91 - openxlsx2-1.9/openxlsx2/README.md | 4 openxlsx2-1.9/openxlsx2/inst/doc/conditional-formatting.R | 36 openxlsx2-1.9/openxlsx2/inst/doc/conditional-formatting.Rmd | 4 openxlsx2-1.9/openxlsx2/inst/doc/conditional-formatting.html | 26 openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2.html | 184 +- openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_charts_manual.R | 39 openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_charts_manual.Rmd | 5 openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_charts_manual.html | 218 +- openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_formulas_manual.html | 220 +- openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_style_manual.R | 18 openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_style_manual.Rmd | 24 openxlsx2-1.9/openxlsx2/inst/doc/openxlsx2_style_manual.html | 817 ++++------ openxlsx2-1.9/openxlsx2/man/openxlsx2-package.Rd | 2 openxlsx2-1.9/openxlsx2/man/openxlsx2_options.Rd | 1 openxlsx2-1.9/openxlsx2/man/wbWorkbook.Rd | 9 openxlsx2-1.9/openxlsx2/man/wb_add_formula.Rd | 8 openxlsx2-1.9/openxlsx2/man/wb_set_header_footer.Rd | 6 openxlsx2-1.9/openxlsx2/man/wb_to_df.Rd | 5 openxlsx2-1.9/openxlsx2/src/xlsb_funs.h | 7 openxlsx2-1.9/openxlsx2/tests/testthat/helper.R | 7 openxlsx2-1.9/openxlsx2/tests/testthat/test-class-worksheet.R | 21 openxlsx2-1.9/openxlsx2/tests/testthat/test-cloneWorksheet.R | 5 openxlsx2-1.9/openxlsx2/tests/testthat/test-converters.R | 11 openxlsx2-1.9/openxlsx2/tests/testthat/test-formulas.R | 46 openxlsx2-1.9/openxlsx2/tests/testthat/test-named_regions.R | 10 openxlsx2-1.9/openxlsx2/tests/testthat/test-read_from_created_wb.R | 54 openxlsx2-1.9/openxlsx2/tests/testthat/test-read_sources.R | 8 openxlsx2-1.9/openxlsx2/tests/testthat/test-read_xlsb.R | 19 openxlsx2-1.9/openxlsx2/tests/testthat/test-utils.R | 123 + openxlsx2-1.9/openxlsx2/tests/testthat/test-wb_functions.R | 75 openxlsx2-1.9/openxlsx2/vignettes/conditional-formatting.Rmd | 4 openxlsx2-1.9/openxlsx2/vignettes/openxlsx2_charts_manual.Rmd | 5 openxlsx2-1.9/openxlsx2/vignettes/openxlsx2_style_manual.Rmd | 24 49 files changed, 1785 insertions(+), 1136 deletions(-)
Title: Multi-State Markov and Hidden Markov Models in Continuous Time
Description: Functions for fitting continuous-time Markov and hidden
Markov multi-state models to longitudinal data. Designed for
processes observed at arbitrary times in continuous time (panel data)
but some other observation schemes are supported. Both Markov
transition rates and the hidden Markov output process can be modelled
in terms of covariates, which may be constant or piecewise-constant
in time.
Author: Christopher Jackson [aut, cre]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between msm versions 1.7.1 dated 2023-11-23 and 1.8 dated 2024-09-08
DESCRIPTION | 12 MD5 | 112 +- NAMESPACE | 15 NEWS.md | 23 R/MatrixExp.R | 4 R/constants.R | 6 R/efpt.R |only R/hmm-dists.R | 2 R/hmodel2list.R |only R/msm-package.R | 2 R/msm.R | 101 + R/optim.R | 3 R/outputs.R | 2008 -------------------------------------- R/pearson.R | 5 R/phase.R | 5 R/plot.R |only R/ppass.R |only R/prevalence.R |only R/print.R |only R/scoreresid.R |only R/simul.R | 12 R/summary.R |only R/tidy.R |only R/tnorm.R | 3 R/totlos.R |only R/utils.R | 1 R/viterbi.R |only build/vignette.rds |binary inst/doc/msm-manual.Rnw |only inst/doc/msm-manual.pdf |binary man/MatrixExp.Rd | 4 man/efpt.msm.Rd | 2 man/hmm-dists.Rd | 2 man/hmodel2list.Rd |only man/msm-package.Rd | 1 man/msm.Rd | 10 man/msm.form.qoutput.Rd | 98 - man/pearson.msm.Rd | 2 man/plot.msm.Rd | 156 +- man/plot.prevalence.msm.Rd | 240 ++-- man/plotprog.msm.Rd | 138 +- man/pmatrix.piecewise.msm.Rd | 2 man/ppass.msm.Rd | 40 man/prevalence.msm.Rd | 414 +++---- man/print.msm.Rd | 122 +- man/printold.msm.Rd | 56 - man/scoreresid.msm.Rd | 2 man/summary.msm.Rd | 86 - man/surface.msm.Rd | 182 +-- man/tidy.msm.Rd |only man/tidy.msm.est.Rd |only man/tidy.msm.estbystate.Rd |only man/tidy.msm.prevalence.Rd |only man/tnorm.Rd | 3 man/totlos.msm.Rd | 2 man/twophase.Rd | 2 man/viterbi.msm.Rd | 4 src/analyticp.c | 6 src/lik.c | 209 +-- src/pijt.c | 100 - tests/testthat/test_hmodel2list.R |only tests/testthat/test_models.r | 34 tests/testthat/test_models_hmm.r | 32 tests/testthat/test_pearson.R | 12 tests/testthat/test_ppass.R |only tests/testthat/test_simul.R |only tests/testthat/test_tidy.R |only tests/testthat/test_weights.R |only 68 files changed, 1283 insertions(+), 2992 deletions(-)
Title: Routines for L1 Estimation
Description: L1 estimation for linear regression using Barrodale and Roberts' method
<doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
Estimation of mean and covariance matrix using the multivariate Laplace distribution,
density, distribution function, quantile function and random number generation
for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
Implementation of Naik and Plungpongpun <doi:10.1007/0-8176-4487-3_7> for the
Generalized spatial median estimator is included.
Author: Felipe Osorio [aut, cre] ,
Tymoteusz Wolodzko [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between L1pack versions 0.41-245 dated 2024-04-23 and 0.50 dated 2024-09-08
L1pack-0.41-245/L1pack/src/l1_BR.f |only L1pack-0.41-245/L1pack/src/wilson-hilferty.c |only L1pack-0.50/L1pack/ChangeLog | 4 ++ L1pack-0.50/L1pack/DESCRIPTION | 10 +++--- L1pack-0.50/L1pack/MD5 | 39 +++++++++++++------------ L1pack-0.50/L1pack/NAMESPACE | 3 + L1pack-0.50/L1pack/R/lad.R | 8 ++--- L1pack-0.50/L1pack/R/spatial.median.R |only L1pack-0.50/L1pack/inst/CITATION | 4 +- L1pack-0.50/L1pack/man/LaplaceFit.Rd | 4 +- L1pack-0.50/L1pack/man/lad.Rd | 6 +++ L1pack-0.50/L1pack/man/spatial.median.Rd |only L1pack-0.50/L1pack/src/CALGO478.f |only L1pack-0.50/L1pack/src/RNG.c | 6 +-- L1pack-0.50/L1pack/src/R_init_L1pack.c | 4 ++ L1pack-0.50/L1pack/src/base.h | 5 ++- L1pack-0.50/L1pack/src/distn.c | 8 ++--- L1pack-0.50/L1pack/src/interface.c | 42 ++++++++++++++++++++++++++- L1pack-0.50/L1pack/src/interface.h | 10 +++++- L1pack-0.50/L1pack/src/lad_EM.c | 20 ++++++------ L1pack-0.50/L1pack/src/lad_LP.c | 8 ++--- L1pack-0.50/L1pack/src/laplace_fitter.c | 12 +++---- L1pack-0.50/L1pack/src/spatial_median.c |only L1pack-0.50/L1pack/src/wilson_hilferty.c |only 24 files changed, 132 insertions(+), 61 deletions(-)
Title: Isoscape Computation and Inference of Spatial Origins using
Mixed Models
Description: Building isoscapes using mixed models and inferring the geographic
origin of samples based on their isotopic ratios. This package is essentially a
simplified interface to several other packages which implements a new
statistical framework based on mixed models. It uses 'spaMM' for fitting and
predicting isoscapes, and assigning an organism's origin depending on its
isotopic ratio. 'IsoriX' also relies heavily on the package 'rasterVis' for
plotting the maps produced with 'terra' using 'lattice'.
Author: Alexandre Courtiol [aut, cre] ,
Francois Rousset [aut] ,
Marie-Sophie Rohwaeder [aut],
Stephanie Kramer-Schadt [aut]
Maintainer: Alexandre Courtiol <alexandre.courtiol@gmail.com>
Diff between IsoriX versions 0.9.2 dated 2023-11-14 and 0.9.3 dated 2024-09-08
DESCRIPTION | 8 MD5 | 117 +++++++------- NAMESPACE | 9 - NEWS.md | 106 ++++++++---- R/IsoriX-datasets.R | 320 ++++++++++++++++++++++----------------- R/IsoriX-package.R | 47 ++--- R/calibfit.R | 36 +++- R/create_aliens.R | 12 - R/getelev.R | 36 ++-- R/isofind.R | 36 +++- R/isofit.R | 26 +-- R/isoscape.R | 38 ++-- R/options.R | 25 ++- R/plots.R | 55 +++--- R/prepcipitate.R | 15 - R/prepraster.R | 12 - R/prepsources.R | 36 +++- R/reexport.R | 12 + R/serialize.R | 6 R/zzz.R | 13 - data/AssignDataBat.rda |binary data/AssignDataBat2.rda |binary data/AssignDataBat2Rev.rda |only data/AssignDataBatRev.rda |only data/CalibDataBat.rda |binary data/CalibDataBat2.rda |binary data/CalibDataBat2Rev.rda |only data/CalibDataBatRev.rda |only inst/WORDLIST | 26 +-- man/AssignDataAlien.Rd | 13 - man/AssignDataBat.Rd | 37 ++-- man/AssignDataBat2.Rd | 35 ++-- man/CalibDataAlien.Rd | 25 +-- man/CalibDataBat.Rd | 57 ++++-- man/CalibDataBat2.Rd | 55 ++++-- man/CountryBorders.Rd | 2 man/ElevRasterDE.Rd | 2 man/GNIPDataDE.Rd | 30 +-- man/GNIPDataEUagg.Rd | 28 +-- man/IsoriX-package.Rd | 53 +++--- man/OceanMask.Rd | 2 man/PrecipBrickDE.Rd | 8 man/calibfit.Rd | 24 +- man/create_aliens.Rd | 8 man/downloadfile.Rd | 8 man/getelev.Rd | 16 - man/getprecip.Rd | 10 - man/isofind.Rd | 21 +- man/isofit.Rd | 20 +- man/isomultifit.Rd | 6 man/isomultiscape.Rd | 22 +- man/isopalette2.Rd | 17 +- man/isoscape.Rd | 20 +- man/options.Rd | 21 ++ man/plots.Rd | 37 ++-- man/prepcipitate.Rd | 15 - man/prepraster.Rd | 12 - man/prepsources.Rd | 10 - man/reexports.Rd | 8 man/serialize.Rd | 6 tests/testthat/test_duplicates.R |only tests/testthat/test_options.R | 2 62 files changed, 936 insertions(+), 685 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'pedsuite' collection of packages for pedigree analysis.
A detailed presentation of the 'ped suite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'Shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 2.1.0 dated 2024-08-16 and 2.1.1 dated 2024-09-08
DESCRIPTION | 10 ++++---- MD5 | 14 ++++++------ NEWS.md | 14 ++++++++++++ R/haploDraw.R | 20 ++++++++++------- README.md | 2 - inst/shiny/R/builtin-peds.R | 39 +++++++++++++++++++++------------- inst/shiny/R/plot-functions.R | 7 +++--- inst/shiny/app.R | 48 +++++++++++++++++++++++------------------- 8 files changed, 95 insertions(+), 59 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-01 1.1.0
Title: Linking R with the Open-Source 'SAGA-GIS' Software
Description: Provides an R scripting interface to the open-source 'SAGA-GIS'
(System for Automated Geoscientific Analyses Geographical Information
System) software. 'Rsagacmd' dynamically generates R functions for every
'SAGA-GIS' geoprocessing tool based on the user's currently installed
'SAGA-GIS' version. These functions are contained within an S3 object
and are accessed as a named list of libraries and tools. This structure
facilitates an easier scripting experience by organizing the large number
of 'SAGA-GIS' geoprocessing tools (>700) by their respective library.
Interactive scripting can fully take advantage of code autocompletion tools
(e.g. in 'RStudio'), allowing for each tools syntax to be quickly
recognized. Furthermore, the most common types of spatial data (via the
'terra', 'sp', and 'sf' packages) along with non-spatial data are
automatically passed from R to the 'SAGA-GIS' command line tool for
geoprocessing operations, and the results are loaded as the appropriate R
object. Outp [...truncated...]
Author: Steven Pawley [aut, cre]
Maintainer: Steven Pawley <dr.stevenpawley@gmail.com>
Diff between Rsagacmd versions 0.4.2 dated 2023-10-16 and 0.4.3 dated 2024-09-08
Rsagacmd-0.4.2/Rsagacmd/NEWS.md |only Rsagacmd-0.4.3/Rsagacmd/DESCRIPTION | 14 Rsagacmd-0.4.3/Rsagacmd/MD5 | 163 - Rsagacmd-0.4.3/Rsagacmd/NAMESPACE | 74 Rsagacmd-0.4.3/Rsagacmd/R/Rsagacmd-package.R | 190 - Rsagacmd-0.4.3/Rsagacmd/R/data-formats.R | 88 Rsagacmd-0.4.3/Rsagacmd/R/file-extensions.R | 202 - Rsagacmd-0.4.3/Rsagacmd/R/io-read.R | 304 +- Rsagacmd-0.4.3/Rsagacmd/R/io-save.R | 392 +-- Rsagacmd-0.4.3/Rsagacmd/R/man.R | 76 Rsagacmd-0.4.3/Rsagacmd/R/parameters.R | 794 +++--- Rsagacmd-0.4.3/Rsagacmd/R/read-srtm.R | 44 Rsagacmd-0.4.3/Rsagacmd/R/run-cmd.R | 116 Rsagacmd-0.4.3/Rsagacmd/R/saga-gis.R | 1172 +++++----- Rsagacmd-0.4.3/Rsagacmd/R/saga-version.R | 39 Rsagacmd-0.4.3/Rsagacmd/R/search-saga.R | 201 - Rsagacmd-0.4.3/Rsagacmd/R/search-tools.R | 108 Rsagacmd-0.4.3/Rsagacmd/R/tempfiles.R | 156 - Rsagacmd-0.4.3/Rsagacmd/R/tidy.R | 410 +-- Rsagacmd-0.4.3/Rsagacmd/R/tool-execute.R | 300 +- Rsagacmd-0.4.3/Rsagacmd/R/tool-function.R | 68 Rsagacmd-0.4.3/Rsagacmd/R/tool-object.R | 164 - Rsagacmd-0.4.3/Rsagacmd/R/tool-overrides.R | 144 - Rsagacmd-0.4.3/Rsagacmd/R/utils.R | 190 - Rsagacmd-0.4.3/Rsagacmd/README.md | 563 ++-- Rsagacmd-0.4.3/Rsagacmd/man/Rsagacmd.Rd | 236 +- Rsagacmd-0.4.3/Rsagacmd/man/check_output_format.Rd | 54 Rsagacmd-0.4.3/Rsagacmd/man/convert_sagaext_r.Rd | 42 Rsagacmd-0.4.3/Rsagacmd/man/create_alias.Rd | 42 Rsagacmd-0.4.3/Rsagacmd/man/create_function.Rd | 46 Rsagacmd-0.4.3/Rsagacmd/man/create_tool.Rd | 68 Rsagacmd-0.4.3/Rsagacmd/man/create_tool_overrides.Rd | 44 Rsagacmd-0.4.3/Rsagacmd/man/drop_parameters.Rd | 36 Rsagacmd-0.4.3/Rsagacmd/man/extract_tool.Rd | 36 Rsagacmd-0.4.3/Rsagacmd/man/figures |only Rsagacmd-0.4.3/Rsagacmd/man/mrvbf_threshold.Rd | 56 Rsagacmd-0.4.3/Rsagacmd/man/parameter.Rd | 64 Rsagacmd-0.4.3/Rsagacmd/man/parameters.Rd | 42 Rsagacmd-0.4.3/Rsagacmd/man/parse_options.Rd | 40 Rsagacmd-0.4.3/Rsagacmd/man/print.saga_tool.Rd | 60 Rsagacmd-0.4.3/Rsagacmd/man/read_grid.Rd | 44 Rsagacmd-0.4.3/Rsagacmd/man/read_grid_list.Rd | 44 Rsagacmd-0.4.3/Rsagacmd/man/read_output.Rd | 58 Rsagacmd-0.4.3/Rsagacmd/man/read_shapes.Rd | 44 Rsagacmd-0.4.3/Rsagacmd/man/read_srtm.Rd | 56 Rsagacmd-0.4.3/Rsagacmd/man/read_table.Rd | 40 Rsagacmd-0.4.3/Rsagacmd/man/reexports.Rd | 32 Rsagacmd-0.4.3/Rsagacmd/man/run_cmd.Rd | 60 Rsagacmd-0.4.3/Rsagacmd/man/saga_configure.Rd | 88 Rsagacmd-0.4.3/Rsagacmd/man/saga_docs.Rd | 46 Rsagacmd-0.4.3/Rsagacmd/man/saga_env.Rd | 80 Rsagacmd-0.4.3/Rsagacmd/man/saga_execute.Rd | 84 Rsagacmd-0.4.3/Rsagacmd/man/saga_gis.Rd | 264 +- Rsagacmd-0.4.3/Rsagacmd/man/saga_remove_tmpfiles.Rd | 62 Rsagacmd-0.4.3/Rsagacmd/man/saga_show_tmpfiles.Rd | 58 Rsagacmd-0.4.3/Rsagacmd/man/saga_version.Rd | 36 Rsagacmd-0.4.3/Rsagacmd/man/save_object.Rd | 46 Rsagacmd-0.4.3/Rsagacmd/man/search_saga.Rd | 64 Rsagacmd-0.4.3/Rsagacmd/man/search_tools.Rd | 58 Rsagacmd-0.4.3/Rsagacmd/man/show_raster_formats.Rd | 38 Rsagacmd-0.4.3/Rsagacmd/man/show_vector_formats.Rd | 38 Rsagacmd-0.4.3/Rsagacmd/man/summarize_tool_params.Rd | 42 Rsagacmd-0.4.3/Rsagacmd/man/tidy.saga.Rd | 62 Rsagacmd-0.4.3/Rsagacmd/man/tidy.saga_library.Rd | 62 Rsagacmd-0.4.3/Rsagacmd/man/tidy.saga_tool.Rd | 64 Rsagacmd-0.4.3/Rsagacmd/man/tile_geoprocessor.Rd | 86 Rsagacmd-0.4.3/Rsagacmd/man/update_parameter_file.Rd | 54 Rsagacmd-0.4.3/Rsagacmd/man/update_parameters_file.Rd | 52 Rsagacmd-0.4.3/Rsagacmd/man/update_parameters_tempfiles.Rd | 52 Rsagacmd-0.4.3/Rsagacmd/tests/testthat.R | 8 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-backends-raster.R | 188 - Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-backends-vector.R | 58 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-data-formats.R | 160 - Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-noninteractive.R | 28 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-outputs-grid-lists.R | 82 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-saga-environment.R | 204 - Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-search-tools.R | 18 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-tempfiles.R | 80 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-tidy.R | 64 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-tool-overrides.R | 138 - Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-tools.R | 124 - Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-utils.R | 40 Rsagacmd-0.4.3/Rsagacmd/tests/testthat/test-versions.R | 354 +-- 83 files changed, 5104 insertions(+), 5094 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-15 dated 2023-09-05 and 0.2-16 dated 2024-09-08
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- src/M_emgroup.c | 2 +- src/dlmvnorm.c | 4 ++-- src/emgroup.c | 2 +- src/init_other.c | 2 +- src/it_init_EM.c | 2 +- src/mb_em_EM.c | 2 +- src/mb_rand_EM.c | 2 +- src/rand_EM.c | 2 +- src/ss_M_rand_EM.c | 2 +- src/ss_init_other.c | 2 +- src/ss_mb_em_EM.c | 2 +- src/ss_mb_rand_EM.c | 2 +- src/ss_rand_EM.c | 2 +- 16 files changed, 36 insertions(+), 33 deletions(-)