Title: Generalized Additive Models with Hyper Column
Description: An interactive HTML widget of the perspective plot for generalized additive models. An alternative solution of the function mgcv::vis.gam(). The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.
Author: Tingting Zhan [aut, cre] ,
Erjia Cui [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between hyper.gam versions 0.3.0 dated 2026-05-17 and 0.3.1 dated 2026-06-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/widget_gam.R | 22 +++++----------------- man/hyper.gam-package.Rd | 2 +- man/widget_gam.Rd | 11 ++++------- 5 files changed, 19 insertions(+), 34 deletions(-)
Title: Grouped Hyper Data Frame
Description: To aggregate a hyper data frame, defined in the package 'spatstat.geom', according to a grouping structure. To facilitate downstream analysis based on a "grouped" hyper data frame. The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between groupedHyperframe versions 0.4.1 dated 2026-05-19 and 0.4.2 dated 2026-06-13
groupedHyperframe-0.4.1/groupedHyperframe/R/Defunct.R |only groupedHyperframe-0.4.1/groupedHyperframe/R/aggregate_FUN.R |only groupedHyperframe-0.4.1/groupedHyperframe/man/aggregate_FUN.Rd |only groupedHyperframe-0.4.1/groupedHyperframe/man/defunct.Rd |only groupedHyperframe-0.4.2/groupedHyperframe/DESCRIPTION | 10 ++--- groupedHyperframe-0.4.2/groupedHyperframe/MD5 | 17 ++++------ groupedHyperframe-0.4.2/groupedHyperframe/NAMESPACE | 2 - groupedHyperframe-0.4.2/groupedHyperframe/R/aggregate.hyperframe.R | 16 ++++++--- groupedHyperframe-0.4.2/groupedHyperframe/R/int.R |only groupedHyperframe-0.4.2/groupedHyperframe/R/pppBy.R | 2 - groupedHyperframe-0.4.2/groupedHyperframe/man/aggregate.hyperframe.Rd | 11 ++++++ groupedHyperframe-0.4.2/groupedHyperframe/man/groupedHyperframe-package.Rd | 2 - 12 files changed, 36 insertions(+), 24 deletions(-)
More information about groupedHyperframe at CRAN
Permanent link
Title: Byte Pair Encoding Text Tokenization
Description: Unsupervised text tokenizer focused on computational efficiency. Wraps the 'YouTokenToMe' library <https://github.com/VKCOM/YouTokenToMe> which is an implementation of fast Byte Pair Encoding (BPE) <https://aclanthology.org/P16-1162/>.
Author: Jan Wijffels [aut, cre, cph] ,
BNOSAC [cph] ,
VK.com [cph],
Gregory Popovitch [ctb, cph] ,
The Abseil Authors [ctb, cph] ,
Ivan Belonogov [ctb, cph] )
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between tokenizers.bpe versions 0.1.5 dated 2026-05-20 and 0.1.6 dated 2026-06-13
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 4 src/parallel_hashmap/phmap.h | 279 +++++++++++++++---------------- src/parallel_hashmap/phmap_base.h | 323 ++++++++++++++++++------------------ src/parallel_hashmap/phmap_bits.h | 6 src/parallel_hashmap/phmap_config.h | 8 7 files changed, 328 insertions(+), 310 deletions(-)
More information about tokenizers.bpe at CRAN
Permanent link
Title: Triple-Difference Estimators
Description: Implements triple-difference (DDD) estimators for both average
treatment effects and event-study parameters. Methods include regression
adjustment, inverse-probability weighting, and doubly-robust estimators,
all of which rely on a conditional DDD parallel-trends assumption and
allow covariate adjustment across multiple pre- and post-treatment
periods. The methodology is detailed in Ortiz-Villavicencio and
Sant'Anna (2025) <doi:10.48550/arXiv.2505.09942>.
Author: Marcelo Ortiz-Villavicencio [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Marcelo Ortiz-Villavicencio <marcelo.ortiz@emory.edu>
Diff between triplediff versions 0.2.0 dated 2026-01-15 and 0.2.4 dated 2026-06-13
DESCRIPTION | 8 MD5 | 35 NEWS.md | 21 R/agg_ddd.R | 3 R/att_gt.R | 45 R/compute_aggregations.R | 65 - R/compute_nuisances.R | 224 ++- R/ddd.R | 12 R/mboot.R | 37 R/preprocess.R | 189 ++ README.md | 2 man/agg_ddd.Rd | 3 man/compute_se_agg.Rd | 7 man/ddd.Rd | 10 man/figures/README-unnamed-chunk-10-1.png |binary tests/testthat/test-aggte-clustervars-override.R |only tests/testthat/test-cluster-alignment-correctness.R |only tests/testthat/test-cluster-analytic.R |only tests/testthat/test-cluster-unbalanced-bootstrap.R |only tests/testthat/test-mboot-cluster.R |only tests/testthat/test-preprocess.R | 1295 +++++++++++++++++++- 21 files changed, 1804 insertions(+), 152 deletions(-)
Title: Switzerland's Data Series in One Place
Description: Download and import open Swiss economic time series from
'dataseries.org' <https://dataseries.org>, a comprehensive and
up-to-date collection of public data from Switzerland. Series are
retrieved through the public 'dataseries.org' API and imported as a
'data.frame' or 'ts' object.
Author: Christoph Sax [aut, cre],
Jannes Muenchow [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between dataseries versions 0.2.0 dated 2017-04-29 and 1.0.0 dated 2026-06-13
dataseries-0.2.0/dataseries/NEWS |only dataseries-0.2.0/dataseries/R/as_ts.R |only dataseries-0.2.0/dataseries/R/inventory.R |only dataseries-1.0.0/dataseries/DESCRIPTION | 34 +- dataseries-1.0.0/dataseries/MD5 | 28 + dataseries-1.0.0/dataseries/NAMESPACE | 7 dataseries-1.0.0/dataseries/NEWS.md |only dataseries-1.0.0/dataseries/R/api.R |only dataseries-1.0.0/dataseries/R/catalog.R |only dataseries-1.0.0/dataseries/R/dataseries-package.R |only dataseries-1.0.0/dataseries/R/ds.R | 258 +++++++++++------- dataseries-1.0.0/dataseries/R/utils.R |only dataseries-1.0.0/dataseries/README.md | 89 +++++- dataseries-1.0.0/dataseries/man/cache_ls.Rd |only dataseries-1.0.0/dataseries/man/dataseries-package.Rd |only dataseries-1.0.0/dataseries/man/ds.Rd | 79 +++-- dataseries-1.0.0/dataseries/man/ds_catalog.Rd |only dataseries-1.0.0/dataseries/man/ds_meta.Rd |only dataseries-1.0.0/dataseries/man/ds_search.Rd |only dataseries-1.0.0/dataseries/man/inventory.Rd | 27 - dataseries-1.0.0/dataseries/tests |only 21 files changed, 346 insertions(+), 176 deletions(-)
Title: Model Cumulative Growing Degree-Days for Pest Monitoring
Description: Pest monitoring is crucial, especially during the early season, to understand the distribution and the proliferation of the target pest. Raw count data from pest monitoring/traps can be coupled with environmental variables such as temperature, growing degree-day ('GDD') etc. to get useful insights about the pest phenology. This package pulls temperature data from the California Irrigation Management Information System ('CIMIS', <https://cimis.water.ca.gov>), the 'Daymet' application programming interface ('API', <https://daymet.ornl.gov>), or 'Open Meteo' ('API', <https://open-meteo.com/>) sequentially for a user-specified time period and calculates cumulative growing degree-days. Users provide pest development thresholds (lower and upper temperatures), pest of concern, and the geographic coordinates of the trap location to track emergence and phenology.
Author: Santosh Bhandari [aut, cre],
Lalit Kharel [aut],
Mahesh Ghimire [aut]
Maintainer: Santosh Bhandari <santoshbhandari4556@gmail.com>
Diff between TrackTrap versions 0.1.0 dated 2026-05-20 and 1.0.0 dated 2026-06-13
TrackTrap-0.1.0/TrackTrap/man/plot_phenology_trend.Rd |only TrackTrap-1.0.0/TrackTrap/DESCRIPTION | 26 - TrackTrap-1.0.0/TrackTrap/LICENSE | 2 TrackTrap-1.0.0/TrackTrap/MD5 | 27 - TrackTrap-1.0.0/TrackTrap/NAMESPACE | 8 TrackTrap-1.0.0/TrackTrap/NEWS.md |only TrackTrap-1.0.0/TrackTrap/R/TrackTrap-package.R |only TrackTrap-1.0.0/TrackTrap/R/data.R | 1 TrackTrap-1.0.0/TrackTrap/R/globals.R |only TrackTrap-1.0.0/TrackTrap/R/phenology.R | 350 +++++++++++------- TrackTrap-1.0.0/TrackTrap/R/utils-pipe.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.R |only TrackTrap-1.0.0/TrackTrap/data/pest_thresholds.rda |binary TrackTrap-1.0.0/TrackTrap/man/calc_pest_phenology.Rd | 84 +--- TrackTrap-1.0.0/TrackTrap/man/fetch_open_meteo.Rd |only TrackTrap-1.0.0/TrackTrap/man/pest_thresholds.Rd | 48 +- TrackTrap-1.0.0/TrackTrap/man/pipe.Rd |only TrackTrap-1.0.0/TrackTrap/man/plot_trap_phenology.Rd |only TrackTrap-1.0.0/TrackTrap/tests |only 19 files changed, 333 insertions(+), 213 deletions(-)
Title: Geographically-Conscious Taxonomic Assignment for Metabarcoding
Description: A bioinformatics pipeline for performing taxonomic
assignment of DNA metabarcoding sequence data while considering
geographic location. A detailed tutorial is available at
<https://urodelan.github.io/LocaTT_Tutorial/>.
A manuscript describing these methods is in preparation.
Author: Kenen B Goodwin [aut, cre] ,
Christopher Cousins [ctb],
Taal Levi [ctb],
Tiffany S Garcia [ths]
Maintainer: Kenen B Goodwin <urodelan@gmail.com>
Diff between LocaTT versions 1.2.0 dated 2026-03-27 and 1.3.0 dated 2026-06-13
DESCRIPTION | 9 ++--- MD5 | 55 +++++++++++++++++++++++++++++-- NAMESPACE | 20 +++++++++++ R/cor2cov.R |only R/dcopula.R |only R/ddirmult.R |only R/dissimilarity.R |only R/diversity.R |only R/djsdm.R |only R/dmWAIC.R |only R/dmpredict.R |only R/dmreg.R |only R/dmvlogis.R |only R/mlWAIC.R |only R/mlcoef.R |only R/mlcor.R |only R/mlformat.R |only R/mlpredict.R |only R/mlreg.R |only R/normalize.R |only R/richness.R |only R/softmax.R |only R/waic.R |only inst/CITATION | 4 +- inst/extdata/example_mvlogistic_data.rds |only inst/extdata/example_regression_data.rds |only inst/intdata |only man/cor2cov.Rd |only man/dcopula.Rd |only man/ddirmult.Rd |only man/dissimilarity.Rd |only man/diversity.Rd |only man/djsdm.Rd |only man/dmWAIC.Rd |only man/dmpredict.Rd |only man/dmreg.Rd |only man/dmvlogis.Rd |only man/mlWAIC.Rd |only man/mlcoef.Rd |only man/mlcor.Rd |only man/mlformat.Rd |only man/mlpredict.Rd |only man/mlreg.Rd |only man/normalize.Rd |only man/richness.Rd |only man/softmax.Rd |only man/waic.Rd |only 47 files changed, 79 insertions(+), 9 deletions(-)
Title: Creating and Significance Testing Language Features for
Visualisation
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
Author: Leon Ackermann [aut] ,
Zhuojun Gu [aut] ,
Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between topics versions 0.70 dated 2026-02-16 and 1.0 dated 2026-06-13
DESCRIPTION | 6 MD5 | 38 - NAMESPACE | 1 NEWS.md | 21 R/0_globals.R | 3 R/2_1_1_topicsModel_Pred.R | 89 ++- R/2_2_topicsGrams.R | 6 R/4_1_topicsPlot.R | 234 +++++++- README.md | 13 inst/doc/extended_installation_guide.Rmd | 3 inst/doc/extended_installation_guide.html | 2 man/topicsModel.Rd | 12 man/topicsPlot.Rd | 30 - man/topicsPlotOverview.Rd | 53 + tests/testthat/_snaps/1_6_topicsPlot/2-ngram-negative.svg | 44 - tests/testthat/_snaps/1_6_topicsPlot/3-ngram-positive.svg | 66 +- tests/testthat/_snaps/1_6_topicsPlot/topics-overview-plot.svg | 108 +-- tests/testthat/_snaps/1_6_topicsPlot/topics2-overview-plot.svg | 272 +++++----- tests/testthat/test_1_6_topicsPlot.R | 29 - vignettes/extended_installation_guide.Rmd | 3 20 files changed, 687 insertions(+), 346 deletions(-)
Title: Genome-Wide Nucleic Acid Melting Temperature Profiling and
Multi-Omics Integration
Description: Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Corrections are supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as [...truncated...]
Author: Junhui Li [cre, aut] ,
Lihua Julie Zhu [aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between TmCalculator versions 1.0.5 dated 2026-06-04 and 1.0.6 dated 2026-06-13
TmCalculator-1.0.5/TmCalculator/R/plot_circos_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_karyotype_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_linear_genome.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_genome_tracks.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_heatmap.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_interactive.R |only TmCalculator-1.0.5/TmCalculator/R/plot_tm_linear.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.R |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.Rmd |only TmCalculator-1.0.5/TmCalculator/inst/doc/TmCalculator.html |only TmCalculator-1.0.5/TmCalculator/man/plot_circos_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_karyotype_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_linear_genome.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_genome_tracks.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_heatmap.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_interactive.Rd |only TmCalculator-1.0.5/TmCalculator/man/plot_tm_linear.Rd |only TmCalculator-1.0.5/TmCalculator/vignettes/TmCalculator.Rmd |only TmCalculator-1.0.6/TmCalculator/DESCRIPTION | 26 TmCalculator-1.0.6/TmCalculator/MD5 | 58 TmCalculator-1.0.6/TmCalculator/NAMESPACE | 105 - TmCalculator-1.0.6/TmCalculator/R/coor_to_genomic_ranges.R | 3 TmCalculator-1.0.6/TmCalculator/R/ecoli_rep_hotspots.R | 50 TmCalculator-1.0.6/TmCalculator/R/integrate_granges.R | 8 TmCalculator-1.0.6/TmCalculator/R/make_genomiccoord.R | 5 TmCalculator-1.0.6/TmCalculator/R/plot_genome_track.R |only TmCalculator-1.0.6/TmCalculator/R/plot_tm.R |only TmCalculator-1.0.6/TmCalculator/R/to_genomic_ranges.R | 4 TmCalculator-1.0.6/TmCalculator/build/vignette.rds |binary TmCalculator-1.0.6/TmCalculator/data/ecoli_rep_hotspots.rda |binary TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.R | 469 +++-- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.Rmd | 406 ++--- TmCalculator-1.0.6/TmCalculator/inst/doc/genome_wide_tm_ecoli.html | 782 +++++----- TmCalculator-1.0.6/TmCalculator/inst/scripts |only TmCalculator-1.0.6/TmCalculator/inst/vignette-source |only TmCalculator-1.0.6/TmCalculator/man/TmCalculator-package.Rd | 2 TmCalculator-1.0.6/TmCalculator/man/ecoli_rep_hotspots.Rd | 49 TmCalculator-1.0.6/TmCalculator/man/integrate_granges.Rd | 8 TmCalculator-1.0.6/TmCalculator/man/plot_genome_track.Rd |only TmCalculator-1.0.6/TmCalculator/man/plot_tm.Rd |only TmCalculator-1.0.6/TmCalculator/vignettes/genome_wide_tm_ecoli.Rmd | 406 ++--- 41 files changed, 1267 insertions(+), 1114 deletions(-)
Title: Tidy Intensive Longitudinal Data Analysis
Description: A reproducible, tidyverse-style framework for intensive longitudinal
data analysis in R, with built-in methodological safeguards, provenance
tracking, and reporting tools. Encodes time structure, enforces
within-between decomposition, provides spacing-aware lags, and integrates
diagnostics and visualization. Use ild_prepare(), ild_center(), ild_lag(),
and related functions for a unified pipeline from raw EMA/diary data to
interpretable models.
Author: Alex Litovchenko [aut, cre]
Maintainer: Alex Litovchenko <al4877@columbia.edu>
This is a re-admission after prior archival of version 0.4.0 dated 2026-04-17
Diff between tidyILD versions 0.4.0 dated 2026-04-17 and 0.4.1 dated 2026-06-13
DESCRIPTION | 28 +++-- LICENSE | 2 MD5 | 54 +++++----- NEWS.md | 16 +++ R/ild_prepare.R | 59 +++++++++++ R/ild_prepare_wide.R |only README.md | 2 inst/CITATION | 4 inst/doc/benchmark-simulation-recovery.html | 8 - inst/doc/brms-dynamics-recipes.html | 4 inst/doc/ctsem-continuous-time-dynamics.html | 4 inst/doc/ild-analysis-report.html | 4 inst/doc/ild-decomposition-and-spacing.html | 4 inst/doc/ild-glossary-and-quickstart.R | 17 +++ inst/doc/ild-glossary-and-quickstart.Rmd | 29 +++++ inst/doc/ild-glossary-and-quickstart.html | 133 ++++++++++++++++++++++++++- inst/doc/ild-provenance.html | 34 +++--- inst/doc/ild-specialist-backends.html | 8 - inst/doc/kfas-choosing-backend.html | 4 inst/doc/kfas-irregular-timing-spacing.html | 4 inst/doc/kfas-state-space-modeling.html | 4 inst/doc/temporal-dynamics-model-choice.html | 8 - inst/doc/tidyILD-workflow.html | 4 inst/doc/tsibble-interoperability.html | 4 man/ild_prepare.Rd | 29 +++++ tests/testthat/helper-contract-fixtures.R | 15 ++- tests/testthat/test-heterogeneity-lmer.R | 17 ++- tests/testthat/test-ild_prepare_wide.R |only vignettes/ild-glossary-and-quickstart.Rmd | 29 +++++ 29 files changed, 429 insertions(+), 99 deletions(-)
Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.8.1 dated 2026-02-16 and 1.9 dated 2026-06-13
DESCRIPTION | 6 ++--- MD5 | 42 ++++++++++++++++++----------------- NAMESPACE | 4 +++ NEWS.md | 6 +++++ R/0_0_text_install.R | 11 +++++---- R/4_4_textWordPrediction.R |only R/7_1_textTopics.R | 31 +++++++++++++++++++++++-- R/7_2_textTopicsAnalysis.R | 16 +++++++++++++ README.md | 7 +++++ inst/doc/LBAM.html | 4 +-- inst/doc/ext_install_guide.Rmd | 2 - inst/doc/ext_install_guide.html | 2 - inst/doc/huggingface_in_r.R | 2 - inst/doc/huggingface_in_r.Rmd | 2 - inst/doc/huggingface_in_r.html | 3 -- inst/python/bert_topic.py | 2 + man/textTopics.Rd | 41 ++++++++++++++++++++++++++++++++-- man/textTopicsWordcloud.Rd | 11 ++++++++- man/textWordPrediction.Rd |only tests/testthat/test_6_textFineTune.R | 2 - tests/testthat/test_7_textTopics.R | 2 - vignettes/ext_install_guide.Rmd | 2 - vignettes/huggingface_in_r.Rmd | 2 - 23 files changed, 154 insertions(+), 46 deletions(-)
Title: Panel VAR Models with Interactive Fixed Effects
Description: Implements the estimator of Tugan (2021) <doi:10.1093/ectj/utaa021>
for panel vector autoregression (VAR) models with interactive fixed effects.
Provides joint estimation of VAR coefficients, latent common factors, and
factor loadings via an iterative algorithm that alternates between principal
component estimation of the factors and least squares estimation of the VAR
coefficients, following the approach of Bai (2009) <doi:10.3982/ECTA6135>.
Supports
impulse response functions under recursive (Cholesky) identification,
parametric confidence bands from the joint asymptotic distribution of the
estimator (Theorem 2.3), and a classical residual bootstrap for robustness
checks.
Author: Binzhi Chen [aut, cre]
Maintainer: Binzhi Chen <Binzhi.Chen9@gmail.com>
Diff between pvarife versions 0.1.1 dated 2026-06-11 and 0.1.2 dated 2026-06-13
DESCRIPTION | 9 +- MD5 | 33 ++++---- R/asymptotic.R | 53 ++++++++++-- R/confidence_bands.R | 143 ++++++++++++++++++++++++----------- R/estimate_pvarife.R | 32 +++++-- R/initial_step.R | 9 ++ R/irf.R | 15 ++- R/simulate.R | 18 ++-- R/utils.R | 7 + man/asymptotic_var.Rd | 18 +++- man/bootstrap_irf_bands.Rd | 38 +++++++-- man/irf_bands.Rd | 15 +++ man/pvarife.Rd | 12 ++ tests/testthat/test-asymptotic.R | 26 ++++++ tests/testthat/test-estimate.R | 18 ++++ tests/testthat/test-generalization.R |only tests/testthat/test-irf.R | 28 ++++++ tests/testthat/test-simulate.R | 18 ++++ 18 files changed, 381 insertions(+), 111 deletions(-)
Title: Diagnostic Tools for Data Frame Joins
Description: Provides diagnostic tools for understanding and debugging data frame
joins. Analyzes key columns before joining to detect duplicates, mismatches,
encoding issues, and other common problems. Explains unexpected row count
changes and provides safe join wrappers with cardinality enforcement. Concepts
and diagnostics build on tidy data principles as described in 'Wickham' (2014)
<doi:10.18637/jss.v059.i10>.
Author: Gilles Colling [aut, cre, cph]
Maintainer: Gilles Colling <gilles.colling051@gmail.com>
Diff between joinspy versions 0.8.2 dated 2026-06-12 and 0.8.3 dated 2026-06-13
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 14 R/backends.R | 10 R/join_explain.R | 19 README.md | 2 inst/doc/backends.R | 128 ++ inst/doc/backends.Rmd | 954 ++++++++++++++------ inst/doc/backends.html | 635 ++++++++++--- inst/doc/common-issues.R | 180 +++ inst/doc/common-issues.Rmd | 512 +++++++++-- inst/doc/common-issues.html | 1645 ++++++++++++++++++++++++----------- inst/doc/production.R | 155 +++ inst/doc/production.Rmd | 1306 +++++++++++++++++++--------- inst/doc/production.html | 1206 ++++++++++++++++++-------- inst/doc/quickstart.R | 182 +++ inst/doc/quickstart.Rmd | 1317 +++++++++++++++++----------- inst/doc/quickstart.html | 1748 ++++++++++++++++++++++++++++---------- inst/doc/why-keys-dont-match.R | 67 + inst/doc/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- inst/doc/why-keys-dont-match.html | 785 +++++++++++++---- tests/testthat/Rplots.pdf |binary vignettes/backends.Rmd | 954 ++++++++++++++------ vignettes/common-issues.Rmd | 512 +++++++++-- vignettes/production.Rmd | 1306 +++++++++++++++++++--------- vignettes/quickstart.Rmd | 1317 +++++++++++++++++----------- vignettes/why-keys-dont-match.Rmd | 1069 +++++++++++++++-------- 27 files changed, 12128 insertions(+), 5022 deletions(-)
Title: Visually Exploring Random Forests
Description: Graphic elements for exploring Random Forests using the
'randomForest' or 'randomForestSRC' package for survival, regression
and classification forests and 'ggplot2' package plotting. Implements
visualisations of the methods described in Breiman (2001)
<doi:10.1023/A:1010933404324> and Ishwaran, Kogalur, Blackstone, and
Lauer (2008) <doi:10.1214/08-AOAS169>.
Author: John Ehrlinger [aut, cre]
Maintainer: John Ehrlinger <john.ehrlinger@gmail.com>
Diff between ggRandomForests versions 3.1.0 dated 2026-06-11 and 3.1.2 dated 2026-06-13
DESCRIPTION | 8 +- MD5 | 32 +++++----- NEWS.md | 40 ++++++++++++ inst/doc/ggRandomForests-regression.html | 34 +++++----- inst/doc/ggRandomForests-survival.html | 40 ++++++------ inst/doc/ggRandomForests.html | 4 - inst/doc/varpro.R | 81 +++++++++++++++++++------ inst/doc/varpro.html | 97 ++++++++++++++++++++++--------- inst/doc/varpro.qmd | 81 +++++++++++++++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/helper-varpro-fixtures.R | 6 + tests/testthat/test_gg_isopro.R | 9 ++ tests/testthat/test_gg_udependent.R | 3 tests/testthat/test_gg_varpro.R | 2 vignettes/precompute_varpro.R | 95 +++++++++++++++++++++++++----- vignettes/varpro.qmd | 81 +++++++++++++++++++------ vignettes/varpro_precomputed.rds |binary 17 files changed, 454 insertions(+), 159 deletions(-)
More information about ggRandomForests at CRAN
Permanent link
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption [...truncated...]
Author: Brantly Callaway [aut, cre],
Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between did versions 2.3.0 dated 2025-12-13 and 2.5.0 dated 2026-06-13
did-2.3.0/did/vignettes/TWFE_cache |only did-2.5.0/did/DESCRIPTION | 21 did-2.5.0/did/MD5 | 208 +-- did-2.5.0/did/NAMESPACE | 30 did-2.5.0/did/NEWS.md | 132 + did-2.5.0/did/R/AGGTEobj.R | 8 did-2.5.0/did/R/DIDparams.R | 2 did-2.5.0/did/R/DIDparams2.R | 4 did-2.5.0/did/R/MP.R | 16 did-2.5.0/did/R/aggte.R | 24 did-2.5.0/did/R/att_gt.R | 473 +++++-- did-2.5.0/did/R/compute.aggte.R | 221 ++- did-2.5.0/did/R/compute.att_gt.R | 1067 ++++++++++++---- did-2.5.0/did/R/compute.att_gt2.R | 708 ++++++++-- did-2.5.0/did/R/conditional_did_pretest.R | 224 ++- did-2.5.0/did/R/data.R | 11 did-2.5.0/did/R/ggdid.R | 32 did-2.5.0/did/R/gplot.R | 14 did-2.5.0/did/R/imports.R | 15 did-2.5.0/did/R/mboot.R | 137 +- did-2.5.0/did/R/pre_process_did.R | 298 +++- did-2.5.0/did/R/pre_process_did2.R | 393 +++-- did-2.5.0/did/R/process_attgt.R | 21 did-2.5.0/did/R/simulate_data.R | 15 did-2.5.0/did/R/tidy.R | 130 + did-2.5.0/did/R/utility_functions.R | 116 + did-2.5.0/did/README.md | 56 did-2.5.0/did/build/partial.rdb |binary did-2.5.0/did/build/vignette.rds |binary did-2.5.0/did/inst/CITATION | 2 did-2.5.0/did/inst/doc/TWFE.R | 10 did-2.5.0/did/inst/doc/TWFE.Rmd | 34 did-2.5.0/did/inst/doc/TWFE.html | 59 did-2.5.0/did/inst/doc/did-basics.R | 7 did-2.5.0/did/inst/doc/did-basics.Rmd | 13 did-2.5.0/did/inst/doc/did-basics.html | 82 - did-2.5.0/did/inst/doc/extensions.html | 6 did-2.5.0/did/inst/doc/multi-period-did.Rmd | 2 did-2.5.0/did/inst/doc/multi-period-did.html | 11 did-2.5.0/did/inst/doc/pre-testing.R | 8 did-2.5.0/did/inst/doc/pre-testing.Rmd | 12 did-2.5.0/did/inst/doc/pre-testing.html | 34 did-2.5.0/did/man/AGGTEobj.Rd | 2 did-2.5.0/did/man/DIDparams.Rd | 110 + did-2.5.0/did/man/MP.Rd | 8 did-2.5.0/did/man/aggte.Rd | 24 did-2.5.0/did/man/att_gt.Rd | 150 +- did-2.5.0/did/man/compute.aggte.Rd | 14 did-2.5.0/did/man/compute.att_gt2.Rd | 4 did-2.5.0/did/man/conditional_did_pretest.Rd | 64 did-2.5.0/did/man/did-package.Rd | 3 did-2.5.0/did/man/figures/README-unnamed-chunk-12-1.png |binary did-2.5.0/did/man/figures/README-unnamed-chunk-9-1.png |binary did-2.5.0/did/man/ggdid.AGGTEobj.Rd | 2 did-2.5.0/did/man/ggdid.MP.Rd | 2 did-2.5.0/did/man/ggdid.Rd | 19 did-2.5.0/did/man/mboot.Rd | 9 did-2.5.0/did/man/mpdta.Rd | 11 did-2.5.0/did/man/nobs.AGGTEobj.Rd |only did-2.5.0/did/man/nobs.MP.Rd |only did-2.5.0/did/man/pre_process_did.Rd | 112 + did-2.5.0/did/man/pre_process_did2.Rd | 112 + did-2.5.0/did/man/reexports.Rd | 2 did-2.5.0/did/man/test.mboot.Rd | 8 did-2.5.0/did/man/tidy.AGGTEobj.Rd | 35 did-2.5.0/did/man/tidy.MP.Rd | 25 did-2.5.0/did/man/trimmer.Rd | 4 did-2.5.0/did/tests |only did-2.5.0/did/vignettes/TWFE.Rmd | 34 did-2.5.0/did/vignettes/did-basics.Rmd | 13 did-2.5.0/did/vignettes/multi-period-did.Rmd | 2 did-2.5.0/did/vignettes/pre-testing.Rmd | 12 72 files changed, 4021 insertions(+), 1416 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-12 0.1.0
Title: Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding
Description: Methods for analyzing DNA methylation data via Most Recurrent Methylation Patterns (MRMPs). Supports cell-type annotation, spatial deconvolution, unsupervised clustering, and cancer cell-of-origin inference. Includes C-backed summaries for YAME “.cg/.cm” files (overlap counts, log2 odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS deconvolution, and plotting utilities. Scales to large spatial and single-cell methylomes and is robust to extreme sparsity.
Author: Hongxiang Fu [aut, cre] ,
Wanding Zhou [cph, fnd],
The SAMtools/HTSlib authors [ctb, cph] ,
Attractive Chaos [ctb, cph] )
Maintainer: Hongxiang Fu <fhx@seas.upenn.edu>
Diff between MethScope versions 1.0.1 dated 2026-02-26 and 1.0.2 dated 2026-06-13
DESCRIPTION | 11 ++++++----- MD5 | 33 ++++++++++++++++++++------------- NAMESPACE | 2 ++ R/ModelTraining.R | 28 +++++++++++++++++++--------- R/PredictCellType.R | 38 +++++++++++++++++++++++++++++--------- R/PretrainedModels.R |only R/sysdata.rda |binary README.md | 4 +++- inst/doc/MethScope-Tutorial.R | 3 ++- inst/doc/MethScope-Tutorial.Rmd | 5 +++-- inst/doc/MethScope-Tutorial.html | 8 ++++---- inst/extdata/models |only inst/extdata/toy.cm |binary man/Input_training.Rd | 2 +- man/Liu2021_MouseBrain_P1000.Rd |only man/PredictCellType.Rd | 3 ++- man/Zhou2025_HumanAtlas_P1000.Rd |only tests/testthat |only tests/testthat.R |only vignettes/MethScope-Tutorial.Rmd | 5 +++-- 20 files changed, 94 insertions(+), 48 deletions(-)
Title: Bayesian Estimation of Dynamic VAR Models using STAN
Description: Bayesian estimation of multilevel Vector Autoregression (VAR) models
using Stan. Supports Gaussian, Binary, and Ordinal (adjacent category) outcome
variables with random effects and customizable priors.
Author: Florian Metwaly [aut, cre, cph]
Maintainer: Florian Metwaly <f.j.metwaly@uva.nl>
Diff between bvarnet versions 1.0.0 dated 2026-05-27 and 1.0.1 dated 2026-06-13
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NEWS.md | 3 +++ R/bvar.R | 2 ++ R/zzz.R |only README.md | 21 ++++++++++++++++++--- inst/CITATION | 2 +- 7 files changed, 33 insertions(+), 12 deletions(-)
Title: Computes Diversity Indices for Archaeological Data
Description: Companion package of Arnaud Barat, Andreu Sansó, Maite Arilla-Osuna, Ruth Blasco, Iñaki Pérez-Fernández, Gabriel Cifuentes-Alcobenda, Rubén Llorente, Daniel Vivar-Ríos, Ella Assaf, Ran Barkai, Avi Gopher, & Jordi Rosell-Ardèvol (2026) <doi:10.1007/s10816-026-09802-3>. It computes Diversity Indices, decomposes several of them and computes bootstrap confidence intervals.
Author: Andreu Sanso [aut, cre],
Arnaud Barat [aut],
Jordi Rosell [aut]
Maintainer: Andreu Sanso <andreu.sanso@uib.eu>
Diff between diversityArch versions 0.3.0 dated 2026-05-04 and 0.4.0 dated 2026-06-13
DESCRIPTION | 12 +++---- MD5 | 72 +++++++++++++++++++++---------------------- NEWS.md | 11 ++++++ R/all_indices.R | 87 ++++++++++++++++++++++++++++++++-------------------- R/bs.R | 6 +-- R/bs_dec.R | 10 ++--- R/bs_frag.R | 4 +- R/check_x.R | 11 +----- R/dec_equit.R | 4 +- R/dec_shannon.R | 7 +--- R/dominance.R | 4 +- R/equitability.R | 4 +- R/evenness.R | 4 +- R/margalef.R | 4 +- R/menhinick.R | 4 +- R/shannon.R | 4 +- R/shannon_frag.R | 2 - R/simpson_D.R | 4 +- R/simpson_E.R | 4 +- man/Qesem_f.Rd | 9 ++--- man/Qesem_s.Rd | 9 ++--- man/all_indices.Rd | 8 ++-- man/bs.Rd | 4 +- man/bs_dec.Rd | 4 +- man/bs_frag.Rd | 4 +- man/check_x.Rd | 5 -- man/dec_equit.Rd | 4 +- man/dec_shannon.Rd | 4 +- man/dominance.Rd | 4 +- man/equitability.Rd | 4 +- man/evenness.Rd | 4 +- man/margalef.Rd | 4 +- man/menhinick.Rd | 4 +- man/shannon.Rd | 4 +- man/shannon_frag.Rd | 2 - man/simpson_D.Rd | 4 +- man/simpson_E.Rd | 4 +- 37 files changed, 183 insertions(+), 160 deletions(-)
Title: Canonical Correlation Analysis via Reduced Rank Regression
Description: Canonical correlation analysis (CCA) via reduced-rank regression with support for regularization and cross-validation. Several methods for estimating CCA in high-dimensional settings are implemented. The first set of methods, cca_rrr() (and variants: cca_group_rrr() and cca_graph_rrr()), assumes that one dataset is high-dimensional and the other is low-dimensional, while the second, ecca() (for Efficient CCA) assumes that both datasets are high-dimensional. For both methods, standard l1 regularization as well as group-lasso regularization are available. cca_graph_rrr further supports total variation regularization when there is a known graph structure among the variables of the high-dimensional dataset. In this case, the loadings of the canonical directions of the high-dimensional dataset are assumed to be smooth on the graph. For more details see Donnat and Tuzhilina (2024) <doi:10.48550/arXiv.2405.19539> and Wu, Tuzhilina and Donnat (2025) <doi:10.48550/arXiv.2507.11160> [...truncated...]
Author: Claire Donnat [aut, cre] ,
Elena Tuzhilina [aut] ,
Zixuan Wu [aut]
Maintainer: Claire Donnat <cdonnat@uchicago.edu>
This is a re-admission after prior archival of version 0.1.1 dated 2026-04-29
Diff between ccar3 versions 0.1.1 dated 2026-04-29 and 0.1.2 dated 2026-06-13
DESCRIPTION | 10 ++--- MD5 | 25 ++++++------- R/ecca.r | 1 R/graph_reduced_rank_regression.R | 1 R/group_reduced_rank_regression.R | 15 +++++++ R/reduced_rank_regression.R | 11 +++++ R/utils.R | 62 ++++++++++++++++++++++++++++++++- tests/testthat/helper-cran.R |only tests/testthat/test-cca_graph_rrr_cv.R | 2 + tests/testthat/test-cca_group_rrr.R | 2 - tests/testthat/test-cca_group_rrr_cv.R | 1 tests/testthat/test-cca_rrr.R | 2 - tests/testthat/test-cca_rrr_cv.R | 4 +- tests/testthat/test-ecca.R | 2 - 14 files changed, 114 insertions(+), 24 deletions(-)
Title: Bayesian Exposure-Response Analysis Tools
Description: Suite of tools that facilitate
exposure-response analysis using Bayesian methods. The package
provides a streamlined workflow for fitting types of models that are
commonly used in exposure-response analysis - linear and Emax for continuous
endpoints, logistic linear and logistic Emax for binary endpoints, as well
as performing simulation and visualization. Learn more about the workflow
at <https://genentech.github.io/BayesERbook/>.
Author: Kenta Yoshida [aut, cre] ,
Francois Mercier [aut] ,
Danielle Navarro [aut] ,
Genentech, Inc. [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between BayesERtools versions 0.2.5 dated 2026-04-23 and 0.2.6 dated 2026-06-13
DESCRIPTION | 10 MD5 | 157 +- NAMESPACE | 212 +-- NEWS.md | 128 +- R/BayesERtools-package.R | 12 R/build_spec_coveff.R | 842 ++++++------- R/coveff.R | 903 +++++++------- R/dev_ermod_emax.R | 688 +++++------ R/dev_ermod_lin.R | 1658 +++++++++++++-------------- R/ermod-class.R | 730 ++++++------ R/ermod-methods.R | 750 ++++++------ R/ersim-class.R | 152 +- R/ersim-methods.R | 220 +-- R/eval_ermod.R | 278 ++-- R/loo_kfold.R | 496 ++++---- R/p_direction.R | 164 +- R/plot_ermod.R | 1940 ++++++++++++++++---------------- R/plot_ermod_exp_cov_sel.R | 346 ++--- R/s3_generics.R | 108 - R/sim_ermod.R | 967 ++++++++------- R/utils-draws.R |only R/yyy.R | 356 ++--- README.md | 448 +++---- build/vignette.rds |binary inst/doc/overview_of_the_package.R | 120 - inst/doc/overview_of_the_package.Rmd | 266 ++-- inst/doc/overview_of_the_package.html | 1566 ++++++++++++------------- man/BayesERtools-package.Rd | 72 - man/as_draws.Rd | 104 - man/build_spec_coveff.Rd | 172 +- man/calc_ersim_med_qi.Rd | 40 man/combine_er_components.Rd | 90 - man/d_sim_binom_cov.Rd | 116 - man/d_sim_emax.Rd | 78 - man/d_sim_lin.Rd | 70 - man/d_sim_placebo.Rd | 84 - man/dev_ermod_bin.Rd | 172 +- man/dev_ermod_bin_cov_functions.Rd | 180 +- man/dev_ermod_bin_cov_sel.Rd | 236 +-- man/dev_ermod_bin_exp_sel.Rd | 164 +- man/dev_ermod_emax.Rd | 256 ++-- man/dev_ermod_emax_exp_sel.Rd | 214 +-- man/edit_spec_coveff.Rd | 210 +-- man/ermod_cov_sel_method.Rd | 50 man/ermod_exp_sel_method.Rd | 50 man/ermod_method.Rd | 84 - man/ersim_method.Rd | 56 man/eval_ermod.Rd | 146 +- man/extract_coef_exp_ci.Rd | 54 man/extract_ermod.Rd | 104 - man/extract_ersim.Rd | 104 - man/extract_method.Rd | 104 - man/figures/logo_svg.svg | 1870 +++++++++++++++--------------- man/kfold.Rd | 126 +- man/loo.Rd | 56 man/p_direction.Rd | 146 +- man/plot_cov_sel.Rd | 102 - man/plot_coveff.Rd | 154 +- man/plot_er.Rd | 346 ++--- man/plot_er_exp_sel.Rd | 74 - man/plot_er_gof.Rd | 280 ++-- man/print_coveff.Rd | 150 +- man/prior_summary.Rd | 44 man/sim_coveff.Rd | 142 +- man/sim_er.Rd | 172 +- man/sim_er_new_exp.Rd | 226 +-- man/sim_er_new_exp_marg.Rd | 224 +-- tests/testthat.R | 24 tests/testthat/test-build_spec_coveff.R | 166 +- tests/testthat/test-coveff.R | 346 ++--- tests/testthat/test-dev_ermod_emax.R | 456 +++---- tests/testthat/test-dev_ermod_lin.R | 930 +++++++-------- tests/testthat/test-ermod-methods.R | 298 ++-- tests/testthat/test-eval_ermod.R | 268 ++-- tests/testthat/test-loo_kfold.R | 289 ++-- tests/testthat/test-p_direction.R | 104 - tests/testthat/test-plot_ermod.R | 672 +++++------ tests/testthat/test-sim_ermod.R | 374 +++--- vignettes/data/supported_models.csv | 16 vignettes/overview_of_the_package.Rmd | 266 ++-- 80 files changed, 12438 insertions(+), 12410 deletions(-)
Title: Emax Model Analysis with 'Stan'
Description: Perform sigmoidal Emax model fit using 'Stan' in a formula notation, without writing 'Stan' model code.
Author: Kenta Yoshida [aut, cre] ,
Danielle Navarro [aut] ,
Trustees of Columbia University [cph]
Maintainer: Kenta Yoshida <yoshida.kenta.6@gmail.com>
Diff between rstanemax versions 0.1.9 dated 2025-02-17 and 0.1.10 dated 2026-06-13
rstanemax-0.1.10/rstanemax/DESCRIPTION | 16 - rstanemax-0.1.10/rstanemax/MD5 | 19 - rstanemax-0.1.10/rstanemax/NEWS.md | 7 rstanemax-0.1.10/rstanemax/R/posterior_predict.R | 4 rstanemax-0.1.10/rstanemax/build/vignette.rds |binary rstanemax-0.1.10/rstanemax/inst/doc/emaxmodel.html | 117 +++++----- rstanemax-0.1.10/rstanemax/man/posterior_predict.Rd | 4 rstanemax-0.1.10/rstanemax/src/stanExports_emax.cc | 34 +- rstanemax-0.1.10/rstanemax/src/stanExports_emax_binary.cc | 34 +- rstanemax-0.1.10/rstanemax/tests/testthat/test-posterior_integration.R |only rstanemax-0.1.9/rstanemax/src/Makevars.win |only rstanemax-0.1.9/rstanemax/tests/testthat/test-tidybayes_integration.R |only 12 files changed, 121 insertions(+), 114 deletions(-)
Title: A Lightweight Interface Between 'igraph' and 'ggplot2' Graphics
Description: An interface to integrate 'igraph' and 'ggplot2' graphics within
a normalized coordinate system. 'RGraphSpace' extends 'ggplot2' with
graph-aware geometries optimized for large networks. The 'GraphSpace' class
integrates directly with 'ggplot2' through specialized 'geoms' and lazy
resolution of node attributes, supporting customization of aesthetics and
visual styles. These 'geoms' use a dual-anchor normalization approach to
align layers, particularly useful for analyses in which network elements
must be spatially aligned with reference maps and images.
Author: Sysbiolab Team [aut],
Flavio Kessler [ctb],
Jonathan Back [ctb],
Lana Querne [ctb],
Victor Apolonio [ctb],
Vinicius Chagas [ctb],
Mauro Castro [cre]
Maintainer: Mauro Castro <mauro.a.castro@gmail.com>
Diff between RGraphSpace versions 1.3.0 dated 2026-05-22 and 1.4.0 dated 2026-06-13
RGraphSpace-1.3.0/RGraphSpace/R/inject-nodespace.R |only RGraphSpace-1.4.0/RGraphSpace/DESCRIPTION | 35 - RGraphSpace-1.4.0/RGraphSpace/MD5 | 73 +- RGraphSpace-1.4.0/RGraphSpace/NAMESPACE | 26 RGraphSpace-1.4.0/RGraphSpace/R/annotation-gspace.R |only RGraphSpace-1.4.0/RGraphSpace/R/geom-edgespace.R | 263 ++++--- RGraphSpace-1.4.0/RGraphSpace/R/geom-graphspace.R | 34 RGraphSpace-1.4.0/RGraphSpace/R/geom-nodespace.R | 165 +++- RGraphSpace-1.4.0/RGraphSpace/R/gspace-checks.R | 15 RGraphSpace-1.4.0/RGraphSpace/R/gspace-classes.R | 104 ++ RGraphSpace-1.4.0/RGraphSpace/R/gspace-coercion.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-constructor.R | 18 RGraphSpace-1.4.0/RGraphSpace/R/gspace-features.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-generics.R | 42 + RGraphSpace-1.4.0/RGraphSpace/R/gspace-ggplot-constructor.R |only RGraphSpace-1.4.0/RGraphSpace/R/gspace-methods.R | 261 +++++-- RGraphSpace-1.4.0/RGraphSpace/R/gspace-normalize.R | 349 +++++----- RGraphSpace-1.4.0/RGraphSpace/R/gspace-supplements.R | 2 RGraphSpace-1.4.0/RGraphSpace/R/gspace-themes.R | 173 ++-- RGraphSpace-1.4.0/RGraphSpace/data/gtoy1.RData |binary RGraphSpace-1.4.0/RGraphSpace/inst/NEWS.Rd | 7 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.R | 10 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/inst/doc/RGraphSpace.html | 52 - RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-accessors.Rd | 90 +- RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-class.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/GraphSpace-methods.Rd | 15 RGraphSpace-1.4.0/RGraphSpace/man/RGraphSpace-package.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/annotation_gspace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/as.GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/geom_edgespace.Rd | 28 RGraphSpace-1.4.0/RGraphSpace/man/geom_graphspace.Rd | 17 RGraphSpace-1.4.0/RGraphSpace/man/geom_nodespace.Rd | 26 RGraphSpace-1.4.0/RGraphSpace/man/getGraphSpace-methods.Rd | 4 RGraphSpace-1.4.0/RGraphSpace/man/ggplot-GraphSpace.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/gs_features-utils.Rd |only RGraphSpace-1.4.0/RGraphSpace/man/inject_nodespace.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/normalizeGraphSpace-methods.Rd | 65 + RGraphSpace-1.4.0/RGraphSpace/man/plotGraphSpace-methods.Rd | 2 RGraphSpace-1.4.0/RGraphSpace/man/theme_gspace.Rd | 42 - RGraphSpace-1.4.0/RGraphSpace/vignettes/RGraphSpace.Rmd | 12 RGraphSpace-1.4.0/RGraphSpace/vignettes/bibliography.bib | 33 42 files changed, 1300 insertions(+), 696 deletions(-)
Title: Biological Analysis and Visualization of Weather Radar Data
Description: Extract, visualize and summarize aerial movements of birds and
insects from weather radar data. See Dokter, A. M. et al. (2018)
"bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028>
for a software paper describing package and methodologies.
Author: Adriaan M. Dokter [aut, cre] ,
Peter Desmet [aut] ,
Bart Kranstauber [aut] ,
Cecilia Nilsson [aut] ,
Alexander Tedeschi [aut] ,
Stijn Van Hoey [aut] ,
Bart Hoekstra [ctb] ,
Pieter Huybrechts [ctb] ,
Hidde Leijnse [ctb] ,
Nicolas Noe [ctb] ,
Raphael N [...truncated...]
Maintainer: Adriaan M. Dokter <biorad@cornell.edu>
Diff between bioRad versions 0.11.0 dated 2025-08-29 and 0.12.0 dated 2026-06-13
DESCRIPTION | 14 MD5 | 135 ++--- NAMESPACE | 6 NEWS.md | 45 + R/add_param.R |only R/apply_mistnet.R | 6 R/beam.R | 63 +- R/bioRad-deprecated.R | 4 R/calculate_vp.R | 132 ++++- R/clean_mixture.R | 6 R/color_scale.R | 22 R/dbz_eta.R | 2 R/filter_precip.R | 39 + R/integrate_to_ppi.R | 130 ++++ R/project_as_ppi.R | 7 R/read_pvolfile.R | 12 R/s3.R | 2 R/scan_convert.R | 12 R/select.R | 4 R/sunrise_sunset.R | 52 - R/utils.R | 72 ++ R/validate_vpts.R | 18 R/vpts.R | 2 README.md | 24 build/partial.rdb |binary build/vignette.rds |binary inst/doc/bioRad.Rmd | 2 inst/doc/bioRad.html | 7 inst/doc/rad_aero_22.R | 868 ++++++++++++++++----------------- inst/doc/rad_aero_22.Rmd | 2 inst/doc/rad_aero_22.html | 7 inst/doc/range_correction.html | 41 - man/add_expected_eta_to_scan.Rd | 11 man/add_param.Rd |only man/apply_mistnet.Rd | 4 man/beam_distance.Rd | 14 man/beam_height.Rd | 14 man/beam_profile.Rd | 26 man/beam_profile_overlap.Rd | 26 man/beam_range.Rd | 14 man/beam_width.Rd | 38 - man/bioRad-package.Rd | 1 man/calculate_vp.Rd | 82 ++- man/check_night.Rd | 2 man/clean_mixture.Rd | 4 man/composite_ppi.Rd | 8 man/doy_noy.Rd | 2 man/figures/README-plot_ppi-1.png |binary man/filter_precip.Rd | 10 man/gaussian_beam_profile.Rd | 26 man/integrate_to_ppi.Rd | 63 +- man/is.nan.data.frame.Rd | 20 man/map.Rd | 2 man/min_package_version.Rd |only man/plot.vp.Rd | 2 man/plot.vpi.Rd | 4 man/project_as_ppi.Rd | 4 man/read_pvolfile.Rd | 3 man/scan_to_raster.Rd | 10 man/sunrise_sunset.Rd | 49 - man/tidyverse.Rd | 3 tests/testthat/test-add_param.R |only tests/testthat/test-apply_mistnet.R | 2 tests/testthat/test-beam.R | 31 - tests/testthat/test-filter_precip.R |only tests/testthat/test-integrate_to_ppi.R | 122 ++++ tests/testthat/test-project_as_ppi.R | 11 tests/testthat/test-s3.R | 10 tests/testthat/test-scan_convert.R | 9 vignettes/bioRad.Rmd | 2 vignettes/rad_aero_22.Rmd | 2 71 files changed, 1465 insertions(+), 902 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.10.0 dated 2026-04-08 and 1.10.1 dated 2026-06-13
bbotk-1.10.0/bbotk/inst |only bbotk-1.10.0/bbotk/src/is_dominated.c |only bbotk-1.10.1/bbotk/DESCRIPTION | 10 bbotk-1.10.1/bbotk/MD5 | 173 ++-- bbotk-1.10.1/bbotk/NAMESPACE | 4 bbotk-1.10.1/bbotk/NEWS.md | 7 bbotk-1.10.1/bbotk/R/OptimInstanceAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerAsync.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchFocusSearch.R | 16 bbotk-1.10.1/bbotk/R/OptimizerBatchIrace.R | 2 bbotk-1.10.1/bbotk/R/OptimizerBatchNLoptr.R | 4 bbotk-1.10.1/bbotk/R/TerminatorStagnationHypervolume.R | 10 bbotk-1.10.1/bbotk/R/helper.R | 6 bbotk-1.10.1/bbotk/R/zzz.R | 2 bbotk-1.10.1/bbotk/build/partial.rdb |binary bbotk-1.10.1/bbotk/man/Archive.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/ArchiveAsync.Rd | 403 +++++----- bbotk-1.10.1/bbotk/man/ArchiveAsyncFrozen.Rd | 313 +++---- bbotk-1.10.1/bbotk/man/ArchiveBatch.Rd | 247 +++--- bbotk-1.10.1/bbotk/man/CallbackAsync.Rd | 79 - bbotk-1.10.1/bbotk/man/CallbackBatch.Rd | 71 - bbotk-1.10.1/bbotk/man/Codomain.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ContextAsync.Rd | 119 +- bbotk-1.10.1/bbotk/man/ContextBatch.Rd | 113 +- bbotk-1.10.1/bbotk/man/EvalInstance.Rd | 185 ++-- bbotk-1.10.1/bbotk/man/Objective.Rd | 307 +++---- bbotk-1.10.1/bbotk/man/ObjectiveRFun.Rd | 145 +-- bbotk-1.10.1/bbotk/man/ObjectiveRFunDt.Rd | 187 ++-- bbotk-1.10.1/bbotk/man/ObjectiveRFunMany.Rd | 162 ++-- bbotk-1.10.1/bbotk/man/ObjectiveTestFunction.Rd | 121 +-- bbotk-1.10.1/bbotk/man/OptimInstance.Rd | 202 ++--- bbotk-1.10.1/bbotk/man/OptimInstanceAsync.Rd | 170 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncMultiCrit.Rd | 154 +-- bbotk-1.10.1/bbotk/man/OptimInstanceAsyncSingleCrit.Rd | 153 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatch.Rd | 199 ++-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchMultiCrit.Rd | 152 +-- bbotk-1.10.1/bbotk/man/OptimInstanceBatchSingleCrit.Rd | 140 +-- bbotk-1.10.1/bbotk/man/OptimInstanceMultiCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/OptimInstanceSingleCrit.Rd | 103 +- bbotk-1.10.1/bbotk/man/Optimizer.Rd | 193 ++-- bbotk-1.10.1/bbotk/man/OptimizerAsync.Rd | 91 +- bbotk-1.10.1/bbotk/man/OptimizerBatch.Rd | 88 +- bbotk-1.10.1/bbotk/man/Progressor.Rd | 116 +- bbotk-1.10.1/bbotk/man/Terminator.Rd | 261 +++--- bbotk-1.10.1/bbotk/man/bb_optimize.Rd | 3 bbotk-1.10.1/bbotk/man/bbotk-package.Rd | 1 bbotk-1.10.1/bbotk/man/bbotk_reflections.Rd | 1 bbotk-1.10.1/bbotk/man/branin.Rd | 3 bbotk-1.10.1/bbotk/man/is_dominated.Rd | 5 bbotk-1.10.1/bbotk/man/local_search.Rd | 10 bbotk-1.10.1/bbotk/man/mlr_optimizers.Rd | 5 bbotk-1.10.1/bbotk/man/mlr_optimizers_async_design_points.Rd | 98 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_grid_search.Rd | 101 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_async_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_chain.Rd | 88 +- bbotk-1.10.1/bbotk/man/mlr_optimizers_cmaes.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_design_points.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_focus_search.Rd | 70 - bbotk-1.10.1/bbotk/man/mlr_optimizers_gensa.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_grid_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_irace.Rd | 71 - bbotk-1.10.1/bbotk/man/mlr_optimizers_local_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_optimizers_nloptr.Rd | 69 - bbotk-1.10.1/bbotk/man/mlr_optimizers_random_search.Rd | 66 - bbotk-1.10.1/bbotk/man/mlr_terminators.Rd | 4 bbotk-1.10.1/bbotk/man/mlr_terminators_clock_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_combo.Rd | 220 ++--- bbotk-1.10.1/bbotk/man/mlr_terminators_evals.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_none.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_perf_reached.Rd | 105 +- bbotk-1.10.1/bbotk/man/mlr_terminators_run_time.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_batch.Rd | 102 +- bbotk-1.10.1/bbotk/man/mlr_terminators_stagnation_hypervolume.Rd | 107 +- bbotk-1.10.1/bbotk/man/mlr_test_functions.Rd | 2 bbotk-1.10.1/bbotk/man/reexports.Rd | 2 bbotk-1.10.1/bbotk/man/shrink_ps.Rd | 8 bbotk-1.10.1/bbotk/src/init.c | 4 bbotk-1.10.1/bbotk/src/local_search.c | 2 bbotk-1.10.1/bbotk/tests/testthat/helper.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_Objective.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_OptimInstanceBatchMultiCrit.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchFocusSearch.R | 12 bbotk-1.10.1/bbotk/tests/testthat/test_OptimizerBatchLocalSearch.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationBatch.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_TerminatorStagnationHypervolume.R | 4 bbotk-1.10.1/bbotk/tests/testthat/test_c_functions.R | 2 bbotk-1.10.1/bbotk/tests/testthat/test_helper.R |only bbotk-1.10.1/bbotk/tests/testthat/test_nds_selection.R | 20 89 files changed, 3704 insertions(+), 3561 deletions(-)
Title: Develop Hybridization Probes
Description: Hybridization probes for target sequences can be made based on melting temperature value calculated by R package 'TmCalculator' <https://CRAN.R-project.org/package=TmCalculator> and methods extended from Beliveau, B. J.,(2018) <doi:10.1073/pnas.1714530115>, and those hybridization probes can be used to capture specific target regions in fluorescence in situ hybridization and next generation sequence experiments.
Author: Junhui Li [cre, aut]
Maintainer: Junhui Li <ljh.biostat@gmail.com>
Diff between ProbeDeveloper versions 1.1.1 dated 2026-03-23 and 1.1.2 dated 2026-06-13
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- R/ProbeMake.R | 8 ++++---- README.md |only 4 files changed, 12 insertions(+), 11 deletions(-)
More information about ProbeDeveloper at CRAN
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