Title: Programmatic Interface to 'Orthanc' DICOM Servers
Description: An R Interface to 'Orthanc' DICOM servers for medical imaging workflows.
'Orthanc' is a lightweight, open-source DICOM server that exposes a comprehensive
REST API for managing, querying, retrieving, and modifying DICOM resources
(<https://www.orthanc-server.com>). The goal of this package is to provide
comprehensive and user-friendly access to the 'Orthanc' REST API, designed to
align with idiomatic R workflows while preserving the structure and semantics
of DICOM resources.
Author: Matthew T. Warkentin [aut, cre, cph]
Maintainer: Matthew T. Warkentin <matthew.warkentin@ucalgary.ca>
Diff between orthanc versions 0.1.0 dated 2026-03-03 and 0.2.0 dated 2026-03-11
orthanc-0.1.0/orthanc/R/retrieve.R |only orthanc-0.1.0/orthanc/inst/Orthanc/Orthanc_endpoints_1_12_10.csv |only orthanc-0.1.0/orthanc/inst/Orthanc/Orthanc_roxygen_1_12_10.csv |only orthanc-0.1.0/orthanc/inst/Orthanc/get_Orthanc_endpoints.R |only orthanc-0.1.0/orthanc/inst/Orthanc/orthanc-openapi.json |only orthanc-0.2.0/orthanc/DESCRIPTION | 11 orthanc-0.2.0/orthanc/MD5 | 64 +- orthanc-0.2.0/orthanc/NAMESPACE | 4 orthanc-0.2.0/orthanc/NEWS.md | 68 ++ orthanc-0.2.0/orthanc/R/Instance.R | 275 ++++++++-- orthanc-0.2.0/orthanc/R/Job.R | 2 orthanc-0.2.0/orthanc/R/Modality.R | 2 orthanc-0.2.0/orthanc/R/Orthanc.R | 2 orthanc-0.2.0/orthanc/R/OrthancAsync.R | 9 orthanc-0.2.0/orthanc/R/Patient.R | 179 ++++-- orthanc-0.2.0/orthanc/R/Resource.R | 62 +- orthanc-0.2.0/orthanc/R/Series.R | 158 ++++- orthanc-0.2.0/orthanc/R/Study.R | 141 +++-- orthanc-0.2.0/orthanc/R/filtering.R | 91 ++- orthanc-0.2.0/orthanc/R/retrieve-dicom.R |only orthanc-0.2.0/orthanc/R/retrieve-others.R |only orthanc-0.2.0/orthanc/R/utils-checks.R | 38 + orthanc-0.2.0/orthanc/R/utils-other.R | 10 orthanc-0.2.0/orthanc/README.md | 17 orthanc-0.2.0/orthanc/inst/benchmark_downloads.R |only orthanc-0.2.0/orthanc/inst/paper/paper.pdf |only orthanc-0.2.0/orthanc/man/Instance.Rd | 152 ++++- orthanc-0.2.0/orthanc/man/Job.Rd | 18 orthanc-0.2.0/orthanc/man/Modality.Rd | 18 orthanc-0.2.0/orthanc/man/Orthanc.Rd | 2 orthanc-0.2.0/orthanc/man/OrthancAsync.Rd | 2 orthanc-0.2.0/orthanc/man/Patient.Rd | 82 ++ orthanc-0.2.0/orthanc/man/Resource.Rd | 20 orthanc-0.2.0/orthanc/man/Series.Rd | 96 ++- orthanc-0.2.0/orthanc/man/Study.Rd | 76 ++ orthanc-0.2.0/orthanc/man/find_and_filter_patients.Rd | 11 orthanc-0.2.0/orthanc/man/retrieve_and_write_nifti.Rd |only orthanc-0.2.0/orthanc/man/retrieve_and_write_patients.Rd | 15 38 files changed, 1236 insertions(+), 389 deletions(-)
Title: Basic Sequence Processing Tool for Biological Data
Description: Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
Author: Ambu Vijayan [aut, cre] ,
J. Sreekumar [aut]
Maintainer: Ambu Vijayan <ambuvjyn@gmail.com>
Diff between baseq versions 0.1.4 dated 2023-05-03 and 0.2.0 dated 2026-03-11
baseq-0.1.4/baseq/R/clean_DNA.R |only baseq-0.1.4/baseq/R/clean_DNA_sequence.R |only baseq-0.1.4/baseq/R/clean_RNA.R |only baseq-0.1.4/baseq/R/clean_RNA_sequence.R |only baseq-0.1.4/baseq/R/clean_sequence.R |only baseq-0.1.4/baseq/R/count_bases.R |only baseq-0.1.4/baseq/R/count_seq_pattern.R |only baseq-0.1.4/baseq/R/dna_to_protein.R |only baseq-0.1.4/baseq/R/dna_to_rna.R |only baseq-0.1.4/baseq/R/fastq_to_fasta.R |only baseq-0.1.4/baseq/R/gc_content.R |only baseq-0.1.4/baseq/R/gc_content_file.R |only baseq-0.1.4/baseq/R/read_fasta_df.R |only baseq-0.1.4/baseq/R/read_fasta_list.R |only baseq-0.1.4/baseq/R/read_fastq_df.R |only baseq-0.1.4/baseq/R/read_fastq_list.R |only baseq-0.1.4/baseq/R/reverse_complement.R |only baseq-0.1.4/baseq/R/rna_reverse_complement.R |only baseq-0.1.4/baseq/R/rna_to_dna.R |only baseq-0.1.4/baseq/R/rna_to_protein.R |only baseq-0.1.4/baseq/R/write_df_to_fasta.R |only baseq-0.1.4/baseq/R/write_df_to_fastq.R |only baseq-0.1.4/baseq/R/write_dna_to_rna.R |only baseq-0.1.4/baseq/R/write_list_to_fasta.R |only baseq-0.1.4/baseq/R/write_list_to_fastq.R |only baseq-0.1.4/baseq/R/write_rna_to_dna.R |only baseq-0.1.4/baseq/man/clean_DNA_file.Rd |only baseq-0.1.4/baseq/man/clean_DNA_sequence.Rd |only baseq-0.1.4/baseq/man/clean_RNA_file.Rd |only baseq-0.1.4/baseq/man/clean_RNA_sequence.Rd |only baseq-0.1.4/baseq/man/clean_sequence.Rd |only baseq-0.1.4/baseq/man/count_seq_pattern.Rd |only baseq-0.1.4/baseq/man/gc_content_file.Rd |only baseq-0.1.4/baseq/man/read.fasta_to_df.Rd |only baseq-0.1.4/baseq/man/read.fasta_to_list.Rd |only baseq-0.1.4/baseq/man/read.fastq_to_df.Rd |only baseq-0.1.4/baseq/man/read.fastq_to_list.Rd |only baseq-0.1.4/baseq/man/reverse_complement.Rd |only baseq-0.1.4/baseq/man/rna_reverse_complement.Rd |only baseq-0.1.4/baseq/man/write.df_to_fasta.Rd |only baseq-0.1.4/baseq/man/write.df_to_fastq.Rd |only baseq-0.1.4/baseq/man/write.dna_to_rna.Rd |only baseq-0.1.4/baseq/man/write.list_to_fasta.Rd |only baseq-0.1.4/baseq/man/write.list_to_fastq.Rd |only baseq-0.1.4/baseq/man/write.rna_to_dna.Rd |only baseq-0.2.0/baseq/DESCRIPTION | 21 +- baseq-0.2.0/baseq/MD5 | 124 +++++++------ baseq-0.2.0/baseq/NAMESPACE | 60 ++++-- baseq-0.2.0/baseq/NEWS.md | 24 +- baseq-0.2.0/baseq/R/analysis.R |only baseq-0.2.0/baseq/R/classes.R |only baseq-0.2.0/baseq/R/conversions.R |only baseq-0.2.0/baseq/R/data.R |only baseq-0.2.0/baseq/R/discovery.R |only baseq-0.2.0/baseq/R/io.R |only baseq-0.2.0/baseq/R/plots.R |only baseq-0.2.0/baseq/R/processing.R |only baseq-0.2.0/baseq/R/utils.R |only baseq-0.2.0/baseq/R/wetlab.R |only baseq-0.2.0/baseq/README.md | 205 ++++------------------ baseq-0.2.0/baseq/build |only baseq-0.2.0/baseq/data |only baseq-0.2.0/baseq/inst/doc |only baseq-0.2.0/baseq/man/as_Biostrings.Rd |only baseq-0.2.0/baseq/man/as_baseq_dna.Rd |only baseq-0.2.0/baseq/man/as_baseq_rna.Rd |only baseq-0.2.0/baseq/man/calculate_assembly_stats.Rd |only baseq-0.2.0/baseq/man/calculate_charge.Rd |only baseq-0.2.0/baseq/man/calculate_codon_usage.Rd |only baseq-0.2.0/baseq/man/calculate_identity.Rd |only baseq-0.2.0/baseq/man/calculate_mw.Rd |only baseq-0.2.0/baseq/man/calculate_pi.Rd |only baseq-0.2.0/baseq/man/calculate_tm.Rd |only baseq-0.2.0/baseq/man/clean_file.Rd |only baseq-0.2.0/baseq/man/clean_seq.Rd |only baseq-0.2.0/baseq/man/count_bases.Rd | 20 -- baseq-0.2.0/baseq/man/count_kmers.Rd |only baseq-0.2.0/baseq/man/count_pattern.Rd |only baseq-0.2.0/baseq/man/dna_to_protein.Rd | 36 --- baseq-0.2.0/baseq/man/dna_to_rna.Rd | 17 - baseq-0.2.0/baseq/man/fastq_to_fasta.Rd | 22 -- baseq-0.2.0/baseq/man/filter_fastq_quality.Rd |only baseq-0.2.0/baseq/man/find_cpg_islands.Rd |only baseq-0.2.0/baseq/man/find_longest_orf.Rd |only baseq-0.2.0/baseq/man/gc_content.Rd | 17 - baseq-0.2.0/baseq/man/get_genetic_code.Rd |only baseq-0.2.0/baseq/man/plot_aa_composition.Rd |only baseq-0.2.0/baseq/man/plot_dotplot.Rd |only baseq-0.2.0/baseq/man/plot_gc_skew.Rd |only baseq-0.2.0/baseq/man/plot_hydrophobicity.Rd |only baseq-0.2.0/baseq/man/read_seq.Rd |only baseq-0.2.0/baseq/man/rev_comp.Rd |only baseq-0.2.0/baseq/man/reverse_translate.Rd |only baseq-0.2.0/baseq/man/rna_to_dna.Rd | 17 - baseq-0.2.0/baseq/man/rna_to_protein.Rd | 36 --- baseq-0.2.0/baseq/man/sars_fragment.Rd |only baseq-0.2.0/baseq/man/search_motif.Rd |only baseq-0.2.0/baseq/man/shuffle_sequence.Rd |only baseq-0.2.0/baseq/man/simulate_digestion.Rd |only baseq-0.2.0/baseq/man/simulate_fasta.Rd |only baseq-0.2.0/baseq/man/simulate_fastq.Rd |only baseq-0.2.0/baseq/man/simulate_pcr.Rd |only baseq-0.2.0/baseq/man/simulate_sequence.Rd |only baseq-0.2.0/baseq/man/summarize_fasta.Rd |only baseq-0.2.0/baseq/man/translate.Rd |only baseq-0.2.0/baseq/man/write_seq.Rd |only baseq-0.2.0/baseq/tests |only baseq-0.2.0/baseq/vignettes |only 108 files changed, 231 insertions(+), 368 deletions(-)
Title: Framework for Tick Population and Infection Modeling
Description: Code to specify, run, and then visualize and analyze the results of
Ixodidae (hard-bodied ticks) population and infection dynamics models. Such
models exist in the literature, but the source code to run them is not
always available. 'IxPopDyMod' provides an easy way for these models to be
written and shared.
Author: Myles Stokowski [aut, cre],
David Allen [aut]
Maintainer: Myles Stokowski <mylesstokowski@gmail.com>
Diff between IxPopDyMod versions 0.3.0 dated 2023-10-23 and 0.4.0 dated 2026-03-11
DESCRIPTION | 22 +- MD5 | 24 +- NAMESPACE | 2 NEWS.md | 4 R/life_cycle.R | 16 - R/parameters.R | 2 R/predictors.R | 5 R/run.R | 288 ++++++++++++++++------------- R/transition.R | 6 build/partial.rdb |binary tests/testthat/_snaps/run.md | 422 ++++++++++++++++++------------------------- tests/testthat/helper.R | 2 tests/testthat/test-run.R | 19 - 13 files changed, 394 insertions(+), 418 deletions(-)
Title: Extra Twitter Bootstrap Components for Shiny
Description: Adds easy access to additional Twitter Bootstrap components to Shiny.
Author: Eric Bailey [aut],
Federico Marini [cre, ctb] ,
Jesse Koops [ctb]
Maintainer: Federico Marini <marinif@uni-mainz.de>
Diff between shinyBS versions 0.63.0 dated 2025-12-17 and 0.64.0 dated 2026-03-11
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- NEWS.md |only inst/www/shinyBS.js | 4 ++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Common Argument Checks for 'r-dcm' Packages
Description: Many packages in the 'r-dcm' family take similar arguments,
which are checked for expected structures and values. Rather than
duplicating code across several packages, commonly used check
functions are included here. This package can then be imported to
access the check functions in other packages.
Author: W. Jake Thompson [aut, cre] ,
University of Kansas [cph],
Institute of Education Sciences [fnd],
Accessible Teaching, Learning, and Assessment Systems [fnd]
Maintainer: W. Jake Thompson <wjakethompson@gmail.com>
Diff between rdcmchecks versions 0.1.0 dated 2025-09-15 and 0.1.1 dated 2026-03-11
DESCRIPTION | 10 ++-- MD5 | 19 ++++--- NAMESPACE | 1 NEWS.md | 8 +++ R/check-data.R | 6 +- R/check-missing.R |only R/utils.R |only inst/WORDLIST | 4 - man/check_missing.Rd |only man/rdcmchecks-package.Rd | 2 tests/testthat/test-check-data.R | 89 ++++++++++++++++++++++++++++++++++++ tests/testthat/test-check-missing.R |only tests/testthat/test-utils.R |only 13 files changed, 122 insertions(+), 17 deletions(-)
Title: Product-Limit Estimation for Censored Event History Analysis
Description: Fast and user friendly implementation of nonparametric estimators
for censored event history (survival) analysis. Kaplan-Meier and
Aalen-Johansen method.
Author: Thomas A. Gerds [aut, cre]
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>
Diff between prodlim versions 2025.04.28 dated 2025-04-28 and 2026.03.11 dated 2026-03-11
DESCRIPTION | 10 MD5 | 34 +- NAMESPACE | 2 R/EventHistory.frame.R | 76 ++-- R/GeomProdlim.R |only R/StatProdlim.R |only R/geom_prodlim.R |only R/ggprodlim.R | 704 +++++++++++++++++++++++++++++++++--------- R/model.design.R | 14 R/parseFormula.R |only R/parseSpecialNames.R | 1 R/predict.prodlim.R | 1 R/prodlim-package.R | 7 R/stat_prodlim.R |only R/strip.terms.R | 4 README.md |only man/EventHistory.frame.Rd | 11 man/geom_prodlim.Rd |only man/ggprodlim.Rd | 160 ++++++--- man/model.design.Rd | 3 man/parseFormula.Rd |only tests/testthat/test-prodlim.R | 46 -- 22 files changed, 766 insertions(+), 307 deletions(-)
Title: Seasonal Adjustment with TRAMO-SEATS in 'JDemetra+' 3.x
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to options and
outputs of 'TRAMO-SEATS' (Time series Regression with ARIMA noise,
Missing values and Outliers - Signal Extraction in ARIMA Time Series),
including 'TRAMO' modelling (ARIMA model with outlier detection and
trading days adjustment). ARIMA = AutoRegressive Integrated Moving Average.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3tramoseats versions 3.6.0 dated 2026-01-27 and 3.7.1 dated 2026-03-11
rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.6.0.jar |only rjd3tramoseats-3.6.0/rjd3tramoseats/man/java_version.Rd |only rjd3tramoseats-3.7.1/rjd3tramoseats/DESCRIPTION | 10 - rjd3tramoseats-3.7.1/rjd3tramoseats/MD5 | 53 ++++------ rjd3tramoseats-3.7.1/rjd3tramoseats/NAMESPACE | 11 +- rjd3tramoseats-3.7.1/rjd3tramoseats/NEWS.md | 6 + rjd3tramoseats-3.7.1/rjd3tramoseats/R/revisions.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/seats.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/seats_spec.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramo_outliers.R | 3 rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramoseats.R | 12 +- rjd3tramoseats-3.7.1/rjd3tramoseats/R/tramoseats_spec.R | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/R/zzz.R | 30 +---- rjd3tramoseats-3.7.1/rjd3tramoseats/README.md | 24 +--- rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-api-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-core-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-protobuf-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/inst/java/jdplus-tramoseats-base-r-3.7.1.jar |only rjd3tramoseats-3.7.1/rjd3tramoseats/man/refresh.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/seats_decompose.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/set_seats.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/terror.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo_forecast.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramo_outliers.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_dictionary.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_revisions.Rd | 2 rjd3tramoseats-3.7.1/rjd3tramoseats/man/tramoseats_spec.Rd | 2 32 files changed, 82 insertions(+), 97 deletions(-)
More information about rjd3tramoseats at CRAN
Permanent link
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.1.2 dated 2026-02-05 and 2.2.0 dated 2026-03-11
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Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.3-3 dated 2025-01-10 and 1.3-5 dated 2026-03-11
mvtnorm-1.3-3/mvtnorm/inst/litdb.bib |only mvtnorm-1.3-3/mvtnorm/vignettes/litdb.bib |only mvtnorm-1.3-5/mvtnorm/DESCRIPTION | 17 mvtnorm-1.3-5/mvtnorm/MD5 | 59 mvtnorm-1.3-5/mvtnorm/NAMESPACE | 6 mvtnorm-1.3-5/mvtnorm/R/interface.R | 93 mvtnorm-1.3-5/mvtnorm/R/lpmvnorm.R | 4 mvtnorm-1.3-5/mvtnorm/R/ltMatrices.R | 35 mvtnorm-1.3-5/mvtnorm/build/partial.rdb |binary mvtnorm-1.3-5/mvtnorm/build/vignette.rds |binary mvtnorm-1.3-5/mvtnorm/inst/NEWS.Rd | 31 mvtnorm-1.3-5/mvtnorm/inst/REFERENCES.bib |only mvtnorm-1.3-5/mvtnorm/inst/doc/MVT_Rnews.Rnw | 8 mvtnorm-1.3-5/mvtnorm/inst/doc/MVT_Rnews.pdf |binary mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.R | 545 +++- mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.Rnw | 1985 +++++++++++------- mvtnorm-1.3-5/mvtnorm/inst/doc/lmvnorm_src.pdf |binary mvtnorm-1.3-5/mvtnorm/man/Mvt.Rd | 26 mvtnorm-1.3-5/mvtnorm/man/algorithms.Rd | 38 mvtnorm-1.3-5/mvtnorm/man/interface.Rd | 9 mvtnorm-1.3-5/mvtnorm/man/lpRR.Rd | 19 mvtnorm-1.3-5/mvtnorm/man/lpmvnorm.Rd | 18 mvtnorm-1.3-5/mvtnorm/man/ltMatrices.Rd | 10 mvtnorm-1.3-5/mvtnorm/man/mvtnorm-package.Rd | 6 mvtnorm-1.3-5/mvtnorm/man/pmvnorm.Rd | 40 mvtnorm-1.3-5/mvtnorm/man/pmvt.Rd | 44 mvtnorm-1.3-5/mvtnorm/man/qmvnorm.Rd | 9 mvtnorm-1.3-5/mvtnorm/man/qmvt.Rd | 22 mvtnorm-1.3-5/mvtnorm/tests/slpmvnorm.R | 87 mvtnorm-1.3-5/mvtnorm/vignettes/MVT_Rnews.Rnw | 8 mvtnorm-1.3-5/mvtnorm/vignettes/lmvnorm_src.Rnw | 1985 +++++++++++------- mvtnorm-1.3-5/mvtnorm/vignettes/lmvnorm_src.Rout.save | 577 +++-- 32 files changed, 3630 insertions(+), 2051 deletions(-)
Title: Estimate the Effective Reproductive Number with Trend Filtering
Description: Use trend filtering, a type of regularized nonparametric
regression, to estimate the instantaneous reproduction number, also
called Rt. This value roughly says how many new infections will result
from each new infection today. Values larger than 1 indicate that an
epidemic is growing while those less than 1 indicate decline. For more
details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024)
<doi:10.1371/journal.pcbi.1012324>.
Author: Daniel J. McDonald [aut, cre, cph],
Jiaping Liu [aut],
Zhenglun Cai [ctb]
Maintainer: Daniel J. McDonald <daniel@stat.ubc.ca>
Diff between rtestim versions 1.0.1 dated 2025-10-24 and 1.0.2 dated 2026-03-11
rtestim-1.0.1/rtestim/inst/doc/delay-distributions.R |only rtestim-1.0.1/rtestim/inst/doc/delay-distributions.Rmd |only rtestim-1.0.1/rtestim/inst/doc/delay-distributions.html |only rtestim-1.0.1/rtestim/vignettes/backer.csv |only rtestim-1.0.1/rtestim/vignettes/delay-distns-byvar.rds |only rtestim-1.0.1/rtestim/vignettes/delay-distributions.Rmd |only rtestim-1.0.1/rtestim/vignettes/duotang-counts.rds |only rtestim-1.0.1/rtestim/vignettes/xu-etal-DATA_RAW.xlsx |only rtestim-1.0.2/rtestim/DESCRIPTION | 9 +++--- rtestim-1.0.2/rtestim/MD5 | 22 +++++----------- rtestim-1.0.2/rtestim/NEWS.md | 6 ++++ rtestim-1.0.2/rtestim/build/partial.rdb |binary rtestim-1.0.2/rtestim/build/vignette.rds |binary rtestim-1.0.2/rtestim/inst/doc/rtestim.html | 5 ++- rtestim-1.0.2/rtestim/man/figures/README-full-fit-1.png |binary rtestim-1.0.2/rtestim/src/RcppExports.cpp | 4 +- 16 files changed, 23 insertions(+), 23 deletions(-)
Title: Inference on Predicted Data
Description: Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2025) <doi:10.1093/bioinformatics/btaf055>.
Author: Stephen Salerno [aut, cre, cph] ,
Jiacheng Miao [aut],
Awan Afiaz [aut],
Kentaro Hoffman [aut],
Jesse Gronsbell [aut],
Jianhui Gao [aut],
David Cheng [aut],
Anna Neufeld [aut],
Qiongshi Lu [aut],
Tyler H McCormick [aut],
Jeffrey T Leek [aut]
Maintainer: Stephen Salerno <ssalerno@fredhutch.org>
Diff between ipd versions 0.4.0 dated 2026-03-06 and 0.4.1 dated 2026-03-11
DESCRIPTION | 10 ++-- MD5 | 12 ++--- NAMESPACE | 1 NEWS.md | 123 +++++++++++++++++++++++++++--------------------------- R/ipd-package.R | 2 README.md | 6 +- inst/doc/ipd.html | 45 +++++++++---------- 7 files changed, 98 insertions(+), 101 deletions(-)
Title: Bayesian Analyses for One- and Two-Sample Inference and
Regression Methods
Description: Perform fundamental analyses using Bayesian parametric and non-parametric inference (regression, anova, 1 and 2 sample inference, non-parametric tests, etc.). (Practically) no Markov chain Monte Carlo (MCMC) is used; all exact finite sample inference is completed via closed form solutions or else through posterior sampling automated to ensure precision in interval estimate bounds. Diagnostic plots for model assessment, and key inferential quantities (point and interval estimates, probability of direction, region of practical equivalence, and Bayes factors) and model visualizations are provided. Bayes factors are computed either by the Savage Dickey ratio given in Dickey (1971) <doi:10.1214/aoms/1177693507> or by Chib's method as given in xxx. Interpretations are from Kass and Raftery (1995) <doi:10.1080/01621459.1995.10476572>. ROPE bounds are based on discussions in Kruschke (2018) <doi:10.1177/2515245918771304>. Methods for determining the number of posterior samp [...truncated...]
Author: Daniel K. Sewell [aut, cre, cph] ,
Alan Arakkal [aut]
Maintainer: Daniel K. Sewell <daniel-sewell@uiowa.edu>
Diff between bayesics versions 2.1.0 dated 2026-02-20 and 2.1.1 dated 2026-03-11
DESCRIPTION | 6 MD5 | 14 - NAMESPACE | 384 ++++++++++++++++++++++----------------------- NEWS.md | 6 R/frac_bayes_factors.R | 3 R/lm_b.R | 20 +- man/lm_b.Rd | 8 tests/testthat/test-lm_b.R | 73 ++++++++ 8 files changed, 303 insertions(+), 211 deletions(-)
Title: A Deep Dynamic Experimental Self-Organizing Neural Network
Framework
Description: Provides a fully native R deep learning framework for
constructing, training, evaluating, and inspecting Deep Dynamic Ensemble
Self Organizing Neural Networks at research scale. The core engine is an
object oriented R6 class-based implementation with explicit control over
layer layout, dimensional flow, forward propagation, back propagation, and
transparent optimizer state updates. The framework does not rely on external
deep learning back ends, enabling direct inspection of model state,
reproducible numerical behavior, and fine grained architectural control
without requiring compiled dependencies or graphics processing unit specific
run times. Users can define dimension agnostic single layer or deep
multi-layer networks without hard coded architecture limits, with per layer
configuration vectors for activation functions, derivatives, dropout
behavior, and initialization strategies automatically aligned to network
depth through controlled replication or truncation. Reproducible workflo [...truncated...]
Author: Mathew William Armitage Fok [aut, cre]
Maintainer: Mathew William Armitage Fok <quiksilver67213@yahoo.com>
Diff between DDESONN versions 7.1.9 dated 2026-03-03 and 7.1.11 dated 2026-03-11
DDESONN-7.1.11/DDESONN/DESCRIPTION | 6 DDESONN-7.1.11/DDESONN/MD5 | 31 - DDESONN-7.1.11/DDESONN/README.md | 60 ++- DDESONN-7.1.11/DDESONN/build/partial.rdb |only DDESONN-7.1.11/DDESONN/build/vignette.rds |binary DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.R |only DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.Rmd |only DDESONN-7.1.11/DDESONN/inst/doc/DDESONNvsKeras_1000Seeds.html |only DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.R | 2 DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.Rmd | 2 DDESONN-7.1.11/DDESONN/inst/doc/logs_main-change-movement_ensemble_runs_scenarioD.html | 184 +++++----- DDESONN-7.1.11/DDESONN/inst/doc/plot-controls_scenario1-2_single-run_scenarioA.html | 24 - DDESONN-7.1.11/DDESONN/man/DDESONN-package.Rd | 2 DDESONN-7.1.11/DDESONN/man/ddesonn_artifacts_root.Rd | 6 DDESONN-7.1.11/DDESONN/man/ddesonn_plots_dir.Rd |only DDESONN-7.1.11/DDESONN/vignettes/DDESONNvsKeras_1000Seeds.Rmd |only DDESONN-7.1.11/DDESONN/vignettes/logs_main-change-movement_ensemble_runs_scenarioD.Rmd | 2 DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.R |only DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.Rmd |only DDESONN-7.1.9/DDESONN/inst/doc/DDESONNvKeras_1000Seeds.html |only DDESONN-7.1.9/DDESONN/man/DDESONN_plots_dir.Rd |only DDESONN-7.1.9/DDESONN/vignettes/DDESONNvKeras_1000Seeds.Rmd |only 22 files changed, 184 insertions(+), 135 deletions(-)
Title: Connectome Predictive Modelling in R
Description: Connectome Predictive Modelling (CPM) (Shen et al. (2017)
<doi:10.1038/nprot.2016.178>) is a method to predict individual
differences in behaviour from brain functional connectivity. 'cpmr'
provides a simple yet efficient implementation of this method.
Author: Liang Zhang [aut, cre]
Maintainer: Liang Zhang <psychelzh@outlook.com>
Diff between cpmr versions 0.1.0 dated 2024-10-06 and 0.1.1 dated 2026-03-11
cpmr-0.1.0/cpmr/tests/testthat/test-check_names.R |only cpmr-0.1.1/cpmr/DESCRIPTION | 8 cpmr-0.1.1/cpmr/LICENSE | 4 cpmr-0.1.1/cpmr/MD5 | 34 cpmr-0.1.1/cpmr/NAMESPACE | 1 cpmr-0.1.1/cpmr/NEWS.md | 131 + cpmr-0.1.1/cpmr/R/constants.R | 4 cpmr-0.1.1/cpmr/R/cpm.R | 671 ++++----- cpmr-0.1.1/cpmr/R/cpmr-package.R | 1 cpmr-0.1.1/cpmr/R/summary.R | 144 +- cpmr-0.1.1/cpmr/R/tidy.R | 3 cpmr-0.1.1/cpmr/R/utils.R |only cpmr-0.1.1/cpmr/build/partial.rdb |binary cpmr-0.1.1/cpmr/man/cpm.Rd | 6 cpmr-0.1.1/cpmr/tests/testthat.R | 24 cpmr-0.1.1/cpmr/tests/testthat/_snaps/cpm.md | 1362 ++++++++++---------- cpmr-0.1.1/cpmr/tests/testthat/_snaps/tidy.md | 294 ++-- cpmr-0.1.1/cpmr/tests/testthat/test-cpm-internals.R |only cpmr-0.1.1/cpmr/tests/testthat/test-cpm.R | 309 ++-- cpmr-0.1.1/cpmr/tests/testthat/test-utils.R |only 20 files changed, 1510 insertions(+), 1486 deletions(-)
Title: Proteomics Data Analysis Functions
Description: Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data.
Fasta-formatted proteomes (eg from UniProt Consortium <doi:10.1093/nar/gky1049>) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted.
Initial results from multiple software for protein (and peptide) quantitation can be imported (to a common format):
MaxQuant (Tyanova et al 2016 <doi:10.1038/nprot.2016.136>), Dia-NN (Demichev et al 2020 <doi:10.1038/s41592-019-0638-x>),
Fragpipe (da Veiga et al 2020 <doi:10.1038/s41592-020-0912-y>), ionbot (Degroeve et al 2021 <doi:10.1101/2021.07.02.450686>),
MassChroq (Valot et al 2011 <doi:10.1002/pmic.201100120>),
OpenMS (Strauss et al 2021 <doi:10.1038/nmeth.3959>), ProteomeDiscoverer (Orsburn 2021 <doi:10.3390/proteomes9010015>),
Proline (Bouyssie et a [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrProteo versions 1.13.3 dated 2025-08-22 and 2.0.0.2 dated 2026-03-11
wrProteo-1.13.3/wrProteo/R/readProtDiscovPeptides.R |only wrProteo-1.13.3/wrProteo/man/readProtDiscovPeptides.Rd |only wrProteo-2.0.0.2/wrProteo/DESCRIPTION | 12 wrProteo-2.0.0.2/wrProteo/MD5 | 129 wrProteo-2.0.0.2/wrProteo/NAMESPACE | 2 wrProteo-2.0.0.2/wrProteo/R/combineMultFilterNAimput.R | 102 wrProteo-2.0.0.2/wrProteo/R/corColumnOrder.R | 2 wrProteo-2.0.0.2/wrProteo/R/exportSdrfDraft.R | 2 wrProteo-2.0.0.2/wrProteo/R/extractTestingResults.R | 83 wrProteo-2.0.0.2/wrProteo/R/fuseProteomicsProjects.R | 4 wrProteo-2.0.0.2/wrProteo/R/getUPS1acc.R | 47 wrProteo-2.0.0.2/wrProteo/R/matrixNAinspect.R | 18 wrProteo-2.0.0.2/wrProteo/R/matrixNAneighbourImpute.R | 32 wrProteo-2.0.0.2/wrProteo/R/readAlphaPeptFile.R | 11 wrProteo-2.0.0.2/wrProteo/R/readDiaNNFile.R | 13 wrProteo-2.0.0.2/wrProteo/R/readDiaNNPeptides.R | 11 wrProteo-2.0.0.2/wrProteo/R/readFasta2.R | 320 - wrProteo-2.0.0.2/wrProteo/R/readFragpipeFile.R | 8 wrProteo-2.0.0.2/wrProteo/R/readIonbotPeptides.R | 20 wrProteo-2.0.0.2/wrProteo/R/readMassChroQFile.R | 19 wrProteo-2.0.0.2/wrProteo/R/readMaxQuantFile.R | 46 wrProteo-2.0.0.2/wrProteo/R/readMaxQuantPeptides.R | 19 wrProteo-2.0.0.2/wrProteo/R/readOpenMSFile.R | 18 wrProteo-2.0.0.2/wrProteo/R/readProlineFile.R | 36 wrProteo-2.0.0.2/wrProteo/R/readProteomeDiscovererFile.R | 171 wrProteo-2.0.0.2/wrProteo/R/readProteomeDiscovererPeptides.R | 33 wrProteo-2.0.0.2/wrProteo/R/readSampleMetaData.R | 741 +- wrProteo-2.0.0.2/wrProteo/R/readSdrf.R | 23 wrProteo-2.0.0.2/wrProteo/R/readWombatNormFile.R | 11 wrProteo-2.0.0.2/wrProteo/R/removeSampleInList.R | 115 wrProteo-2.0.0.2/wrProteo/R/replMissingProtNames.R | 14 wrProteo-2.0.0.2/wrProteo/R/summarizeForROC.R | 2 wrProteo-2.0.0.2/wrProteo/R/testRobustToNAimputation.R | 346 + wrProteo-2.0.0.2/wrProteo/R/writeFasta2.R | 64 wrProteo-2.0.0.2/wrProteo/build/vignette.rds |binary wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.R | 52 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.Rmd | 93 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignette1.html | 769 ++ wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.R | 35 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.Rmd | 42 wrProteo-2.0.0.2/wrProteo/inst/doc/wrProteoVignetteUPS1.html | 2566 +++++----- wrProteo-2.0.0.2/wrProteo/inst/extdata/conta1.fasta.gz |binary wrProteo-2.0.0.2/wrProteo/man/combineMultFilterNAimput.Rd | 23 wrProteo-2.0.0.2/wrProteo/man/corColumnOrder.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/dot-checkSetupGroups.Rd | 3 wrProteo-2.0.0.2/wrProteo/man/dot-commonSpecies.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/dot-parseFastaHeader.Rd |only wrProteo-2.0.0.2/wrProteo/man/exportSdrfDraft.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/extractTestingResults.Rd | 16 wrProteo-2.0.0.2/wrProteo/man/matrixNAinspect.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/matrixNAneighbourImpute.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readFasta2.Rd | 21 wrProteo-2.0.0.2/wrProteo/man/readIonbotPeptides.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readMaxQuantFile.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readMaxQuantPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readProlineFile.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readProtDiscovererPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readProteomeDiscovererFile.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/readProteomeDiscovererPeptides.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/readSampleMetaData.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/removeSampleInList.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/replMissingProtNames.Rd | 4 wrProteo-2.0.0.2/wrProteo/man/summarizeForROC.Rd | 2 wrProteo-2.0.0.2/wrProteo/man/testRobustToNAimputation.Rd | 54 wrProteo-2.0.0.2/wrProteo/man/writeFasta2.Rd | 26 wrProteo-2.0.0.2/wrProteo/vignettes/wrProteoVignette1.Rmd | 93 wrProteo-2.0.0.2/wrProteo/vignettes/wrProteoVignetteUPS1.Rmd | 42 67 files changed, 3786 insertions(+), 2569 deletions(-)
Title: Wearable Accelerometer Data File Readers
Description: Reads data collected from wearable acceleratometers as used in sleep and physical activity research. Currently supports file formats: binary data from 'GENEActiv' <https://activinsights.com/>, .bin-format from GENEA devices (not for sale), and .cwa-format from 'Axivity' <https://axivity.com>. Further, it has functions for reading text files with epoch level aggregates from 'Actical', 'Fitbit', 'Actiwatch', 'ActiGraph', and 'PhilipsHealthBand'. Primarily designed to complement R package GGIR <https://CRAN.R-project.org/package=GGIR>.
Author: Vincent T van Hees [aut, cre],
Patrick Bos [aut] ,
Lena Kushleyeva [ctb],
Jing Hua Zhao [ctb],
Evgeny Mirkes [ctb],
Dan Jackson [ctb],
Jairo H Migueles [ctb],
Medical Research Council UK [cph, fnd],
Accelting [cph, fnd]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIRread versions 1.0.7 dated 2025-11-26 and 1.0.8 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 8 ++++++-- R/readActiwatchCount.R | 2 +- README.md | 2 +- man/GGIRread-package.Rd | 4 ++-- man/readParmayMatrix.Rd | 2 +- tests/testthat/test_readActiwatchCount.R | 8 +++++--- 8 files changed, 27 insertions(+), 21 deletions(-)
Title: Various Blocking Methods for Entity Resolution
Description: The goal of 'blocking' is to provide blocking methods for record linkage and deduplication using approximate nearest neighbour (ANN) algorithms and graph techniques. It supports multiple ANN implementations via 'rnndescent', 'RcppHNSW', 'RcppAnnoy', and 'mlpack' packages, and provides integration with the 'reclin2' package. The package generates shingles from character strings and similarity vectors for record comparison, and includes evaluation metrics for assessing blocking performance including false positive rate (FPR) and false negative rate (FNR) estimates. For details see: Papadakis et al. (2020) <doi:10.1145/3377455>, Steorts et al. (2014) <doi:10.1007/978-3-319-11257-2_20>, Dasylva and Goussanou (2021) <https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X202100200002>, Dasylva and Goussanou (2022) <doi:10.1007/s42081-022-00153-3>.
Author: Maciej Beresewicz [aut, cre] ,
Adam Struzik [aut, ctr]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between blocking versions 1.0.1 dated 2025-06-18 and 1.0.2 dated 2026-03-11
DESCRIPTION | 8 +- MD5 | 58 +++++++++--------- NAMESPACE | 2 NEWS.md | 10 ++- R/blocking.R | 57 ++++++++++-------- R/est_block_error.R | 127 ++++++++++++++++++++++++++++++++++------- R/methods.R | 26 +++++++- build/partial.rdb |binary build/vignette.rds |binary data/RLdata500.rda |binary data/census.rda |binary data/cis.rda |binary data/foreigners.rda |binary inst/doc/v1-deduplication.R | 8 ++ inst/doc/v1-deduplication.Rmd | 15 +++- inst/doc/v1-deduplication.html | 18 +++-- inst/doc/v2-reclin.R | 3 inst/doc/v2-reclin.Rmd | 3 inst/doc/v2-reclin.html | 15 ++-- inst/doc/v3-integration.R | 4 + inst/doc/v3-integration.Rmd | 4 + inst/doc/v3-integration.html | 14 ++-- inst/tinytest/test_annoy.R | 2 inst/tinytest/test_hnsw.R | 2 inst/tinytest/test_mlpack.R | 2 man/blocking.Rd | 9 +- man/est_block_error.Rd | 71 +++++++++++++++++++--- vignettes/v1-deduplication.Rmd | 15 +++- vignettes/v2-reclin.Rmd | 3 vignettes/v3-integration.Rmd | 4 + 30 files changed, 351 insertions(+), 129 deletions(-)
Title: Accrual Plots and Predictions for Clinical Trials
Description: Tracking accrual in clinical trials is important for trial success.
If accrual is too slow, the trial will take too long and be too expensive. If
accrual is much faster than expected, time sensitive tasks such as the writing
of statistical analysis plans might need to be rushed. 'accrualPlot' provides
functions to aid the tracking of accrual and predict when a trial will reach
it's intended sample size.
Author: Lukas Buetikofer [cre, aut],
Alan G. Haynes [aut]
Maintainer: Lukas Buetikofer <lukas.buetikofer@unibe.ch>
Diff between accrualPlot versions 1.0.7 dated 2022-08-16 and 1.0.10 dated 2026-03-11
accrualPlot-1.0.10/accrualPlot/DESCRIPTION | 20 accrualPlot-1.0.10/accrualPlot/MD5 | 72 - accrualPlot-1.0.10/accrualPlot/NEWS.md | 15 accrualPlot-1.0.10/accrualPlot/R/accrual_create_df.R | 10 accrualPlot-1.0.10/accrualPlot/R/gg_accrual_plots.R | 6 accrualPlot-1.0.10/accrualPlot/build/vignette.rds |binary accrualPlot-1.0.10/accrualPlot/inst/doc/accrualPlot.R | 16 accrualPlot-1.0.10/accrualPlot/inst/doc/accrualPlot.html | 597 +++++----- accrualPlot-1.0.10/accrualPlot/man/accrual_create_df.Rd | 2 accrualPlot-1.0.10/accrualPlot/man/accrual_plot_abs.Rd | 2 accrualPlot-1.0.10/accrualPlot/man/accrual_plot_predict.Rd | 2 accrualPlot-1.0.10/accrualPlot/tests/testthat/Rplots.pdf |only accrualPlot-1.0.10/accrualPlot/tests/testthat/_snaps |only accrualPlot-1.0.10/accrualPlot/tests/testthat/test-accrual_plots.R | 4 accrualPlot-1.0.7/accrualPlot/tests/figs |only 15 files changed, 411 insertions(+), 335 deletions(-)
Title: Calculate High Resolution Water Balance of Starch Potatoes
Description: Calculates the water balance of starch potatoes from Normalized Distance Vegetation Index (NDVI) images, German Weather Service (DWD) reference evapotranspiration, German Weather Service RADOLAN precipitation data and irrigation information. For more details see Piernicke et al. (2025) <doi:10.3390/rs17183227>.
Author: Thomas Piernicke [aut, cre]
Maintainer: Thomas Piernicke <thomasp@gfz.de>
Diff between WaterBalanceR versions 0.1.19 dated 2025-12-19 and 0.1.20 dated 2026-03-11
DESCRIPTION | 8 +- MD5 | 15 ++- NEWS.md | 9 ++ R/calcWB.R | 20 ++--- README.md | 122 ++++++++++++++------------------ inst/CITATION | 2 inst/UserGuide.md |only inst/doc/WaterBalanceR_DataSources.html | 4 - inst/doc/WaterBalanceR_Workflow.html | 6 - 9 files changed, 94 insertions(+), 92 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] ,
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Inaki Ucar [aut] ,
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 1.0-0 dated 2025-10-09 and 1.0-1 dated 2026-03-11
units-1.0-0/units/tests/testthat/_snaps/plot/ggplot2-range.svg |only units-1.0-1/units/DESCRIPTION | 8 units-1.0-1/units/MD5 | 50 +-- units-1.0-1/units/NEWS.md | 16 + units-1.0-1/units/R/RcppExports.R | 8 units-1.0-1/units/R/mixed.R | 1 units-1.0-1/units/R/summaries.R | 12 units-1.0-1/units/R/udunits.R | 6 units-1.0-1/units/build/vignette.rds |binary units-1.0-1/units/configure | 134 ++++++++ units-1.0-1/units/configure.ac | 34 ++ units-1.0-1/units/inst/doc/measurement_units_in_R.Rmd | 2 units-1.0-1/units/inst/doc/measurement_units_in_R.html | 2 units-1.0-1/units/inst/doc/units.Rmd | 4 units-1.0-1/units/inst/doc/units.html | 104 +++--- units-1.0-1/units/src/RcppExports.cpp | 73 ++-- units-1.0-1/units/src/udunits.cpp | 150 +++------- units-1.0-1/units/src/units_types.h |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-0.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-1.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-2.svg |only units-1.0-1/units/tests/testthat/_snaps/plot/ggplot2-range-3.svg |only units-1.0-1/units/tests/testthat/test_conversion.R | 2 units-1.0-1/units/tests/testthat/test_mixed.R | 4 units-1.0-1/units/tests/testthat/test_plot.R | 8 units-1.0-1/units/tests/testthat/test_summaries.R | 5 units-1.0-1/units/tests/testthat/test_udunits.R | 1 units-1.0-1/units/vignettes/measurement_units_in_R.Rmd | 2 units-1.0-1/units/vignettes/units.Rmd | 4 29 files changed, 385 insertions(+), 245 deletions(-)
Title: Sumerian Cuneiform Text Analysis
Description: Provides functions for converting transliterated Sumerian texts to sign names and cuneiform characters,
creating and querying dictionaries, analyzing the structure of
Sumerian words, and creating translations. Includes a built-in dictionary and supports both
forward lookup (Sumerian to English) and reverse lookup (English to
Sumerian).
Author: Robin Wellmann [aut, cre]
Maintainer: Robin Wellmann <ro.wellmann@gmail.com>
Diff between sumer versions 1.2.0 dated 2026-02-28 and 1.3.0 dated 2026-03-11
DESCRIPTION | 7 - MD5 | 54 +++++---- NAMESPACE | 6 + R/add_brackets.R |only R/apply_translation_rules.R |only R/as.cuneiform.R | 6 - R/as.sign_name.R | 4 R/compose_skeleton_entry.R |only R/eval_operator.R |only R/extract_skeleton_entries.R | 14 ++ R/grammatical_structure.R |only R/guess_substr_info.R | 2 R/info.R | 2 R/look_up.R | 2 R/mark_ngrams.R | 2 R/mark_skeleton_entries.R | 33 +++++- R/ngram_frequencies.R | 4 R/plot_sign_grammar.R | 2 R/sign_grammar.R | 4 R/skeleton.R | 163 ++++++++++++++---------------- R/standardize_signs.R | 10 + R/translate.R | 140 +++++++++++++++++++------ inst/doc/getting-started.html | 48 ++++---- inst/doc/translating-texts.html | 2 inst/extdata/enki_and_the_world_order.txt | 2 man/add_brackets.Rd |only man/apply_translation_rules.Rd |only man/compose_skeleton_entry.Rd |only man/eval_operator.Rd |only man/extract_skeleton_entries.Rd | 90 ++++++++-------- man/grammatical_structure.Rd |only man/mark_skeleton_entries.Rd | 102 +++++++++--------- man/translate.Rd | 36 ++++-- 33 files changed, 428 insertions(+), 307 deletions(-)
Title: Seasonal Adjustment with 'X-13' in 'JDemetra+' 3.x
Description: R Interface to 'JDemetra+' 3.x
(<https://github.com/jdemetra>) time series analysis software. It
offers full access to options and outputs of 'X-13', including Reg-ARIMA
modelling (automatic AutoRegressive Integrated Moving Average (ARIMA) model
with outlier detection and trading days adjustment) and X-11 decomposition.
Author: Jean Palate [aut],
Alain Quartier-la-Tente [aut] ,
Tanguy Barthelemy [aut, cre, art],
Anna Smyk [aut]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between rjd3x13 versions 3.6.0 dated 2026-01-27 and 3.7.1 dated 2026-03-11
rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-api-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-core-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-protobuf-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/inst/java/jdplus-x13-base-r-3.6.0.jar |only rjd3x13-3.6.0/rjd3x13/man/java_version.Rd |only rjd3x13-3.7.1/rjd3x13/DESCRIPTION | 14 +- rjd3x13-3.7.1/rjd3x13/MD5 | 49 ++++------ rjd3x13-3.7.1/rjd3x13/NAMESPACE | 7 - rjd3x13-3.7.1/rjd3x13/NEWS.md | 6 + rjd3x13-3.7.1/rjd3x13/R/regarima_outliers.R | 2 rjd3x13-3.7.1/rjd3x13/R/revisions.R | 2 rjd3x13-3.7.1/rjd3x13/R/set_x11_spec.R | 2 rjd3x13-3.7.1/rjd3x13/R/utils.R | 1 rjd3x13-3.7.1/rjd3x13/R/x13.R | 10 +- rjd3x13-3.7.1/rjd3x13/R/x13_spec.R | 2 rjd3x13-3.7.1/rjd3x13/R/zzz.R | 26 +---- rjd3x13-3.7.1/rjd3x13/README.md | 28 +---- rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-api-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-core-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-protobuf-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/inst/java/jdplus-x13-base-r-3.7.1.jar |only rjd3x13-3.7.1/rjd3x13/man/refresh.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/regarima.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/regarima_outliers.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x11.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x11_spec.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_dictionary.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_revisions.Rd | 2 rjd3x13-3.7.1/rjd3x13/man/x13_spec.Rd | 2 30 files changed, 69 insertions(+), 98 deletions(-)
Title: Interface to 'JDemetra+' 3.x Time Series Analysis Software
Description: Interface to 'JDemetra+' 3.x (<https://github.com/jdemetra>)
time series analysis software. It offers full access to txt, csv, xml
and spreadsheets files which are meant to be read by 'JDemetra+'
Graphical User Interface.
Author: Jean Palate [aut],
Alessandro Piovani [aut, cre],
Tanguy Barthelemy [ctb, art]
Maintainer: Alessandro Piovani <alessandro.piovani@istat.it>
Diff between rjd3providers versions 3.6.0 dated 2026-02-20 and 3.7.1 dated 2026-03-11
rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-text-base-api-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-text-base-r-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.6.0.jar |only rjd3providers-3.6.0/rjd3providers/man/java_version.Rd |only rjd3providers-3.7.1/rjd3providers/DESCRIPTION | 10 rjd3providers-3.7.1/rjd3providers/MD5 | 91 - rjd3providers-3.7.1/rjd3providers/NAMESPACE | 4 rjd3providers-3.7.1/rjd3providers/NEWS.md | 9 rjd3providers-3.7.1/rjd3providers/R/deprecated.R | 344 ++-- rjd3providers-3.7.1/rjd3providers/R/jd3spreadsheet.R | 676 ++++---- rjd3providers-3.7.1/rjd3providers/R/jd3txt.R | 780 +++++----- rjd3providers-3.7.1/rjd3providers/R/jd3xml.R | 522 +++--- rjd3providers-3.7.1/rjd3providers/R/providers.R | 120 - rjd3providers-3.7.1/rjd3providers/R/zzz.R | 70 rjd3providers-3.7.1/rjd3providers/README.md | 2 rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-spreadsheet-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-api-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-text-base-r-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-tsp-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/inst/java/jdplus-toolkit-base-xml-3.7.1.jar |only rjd3providers-3.7.1/rjd3providers/man/dot-obs_format.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-obs_gathering.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-spreadsheet_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-txt_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/dot-xml_moniker.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_spreadsheet_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_txt_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/set_xml_paths.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/spreadsheet_series.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/txt_series.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_change_file.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_content.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_data.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_id_to_properties.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_name.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_properties_to_id.Rd | 2 rjd3providers-3.7.1/rjd3providers/man/xml_series.Rd | 2 53 files changed, 1330 insertions(+), 1356 deletions(-)
Title: Wrangle Large Simulation Studies
Description: An 'R6' class to set up, run, monitor, collate, and debug large simulation studies comprising many small independent replications and treatment configurations. Parallel processing, reproducibility, fault- and error-tolerance, and ability to resume an interrupted or timed-out simulation study are built in.
Author: Pavel N. Krivitsky [aut, cre]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
This is a re-admission after prior archival of version 0.1.0 dated 2025-09-22
Diff between piecemeal versions 0.1.0 dated 2025-09-22 and 0.2.0 dated 2026-03-11
DESCRIPTION | 15 MD5 | 28 - NAMESPACE | 10 NEWS |only NEWS.md | 21 + R/Piecemeal.R | 192 ++++++++--- R/consolidate.R |only R/piecemeal-package.R | 2 build/stage23.rdb |only inst/doc/piecemeal.R | 4 inst/doc/piecemeal.Rmd | 2 inst/doc/piecemeal.html | 617 +++++++++++++++++++----------------- man/Piecemeal.Rd | 18 + man/piecemeal-package.Rd | 7 tests/testthat/test-consolidation.R |only tests/testthat/test-vignette.R | 6 vignettes/piecemeal.Rmd | 2 17 files changed, 561 insertions(+), 363 deletions(-)
Title: Simulation for Factorial Designs
Description: Create datasets with factorial structure through simulation by specifying variable parameters. Extended documentation at <https://www.scienceverse.org/faux/>. Described in DeBruine (2020) <doi:10.5281/zenodo.2669586>.
Author: Lisa DeBruine [aut, cre, cph] ,
Anna Krystalli [ctb] ,
Andrew Heiss [ctb]
Maintainer: Lisa DeBruine <debruine@gmail.com>
This is a re-admission after prior archival of version 1.2.3 dated 2025-10-01
Diff between faux versions 1.2.3 dated 2025-10-01 and 1.2.4 dated 2026-03-11
DESCRIPTION | 12 +++++------ MD5 | 51 +++++++++++++++++++++++------------------------ NEWS.md | 4 ++- R/check_design.R | 2 - R/codebook.R | 2 - R/faceratings.R | 4 +-- R/plot_design.R | 2 - R/rnorm_multi.R | 2 - R/sim_design.R | 2 - R/sim_df.R | 2 - R/sim_mixed_cc.R | 2 - R/zzz.R | 2 - README.md | 4 +-- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 - inst/doc/sim_design.html | 40 +++++++++++++++++++----------------- man/check_design.Rd | 2 - man/codebook.Rd | 2 - man/faceratings.Rd | 2 - man/faux.Rd | 2 - man/fr4.Rd | 2 - man/plot_design.Rd | 2 - man/rnorm_multi.Rd | 2 - man/sim_design.Rd | 2 - man/sim_df.Rd | 2 - man/sim_mixed_cc.Rd | 2 - 27 files changed, 79 insertions(+), 74 deletions(-)
Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal
Predictions
Description: Set of generalised tools for the flexible computation of climate
related indicators defined by the user. Each method represents a specific
mathematical approach which is combined with the possibility to select an
arbitrary time period to define the indicator. This enables a wide range of
possibilities to tailor the most suitable indicator for each particular climate
service application (agriculture, food security, energy, water management, health...).
This package is intended for sub-seasonal, seasonal and decadal climate
predictions, but its methods are also applicable to other time-scales,
provided the dimensional structure of the input is maintained. Additionally,
the outputs of the functions in this package are compatible with 'CSTools'.
This package is described in Pérez-Zanón et al. (2023)
<doi:10.1016/j.cliser.2023.100393> and was developed in the context of the
H2020 projects MED-GOLD (776467) and S2S4E (776787) projects, as well as the
Horizon Europe project MEDEWSA (101 [...truncated...]
Author: Nuria Perez-Zanon [aut] ,
Chou Chihchung [aut],
Llorenc Lledo [aut],
Victoria Agudetse [ctb, cre],
Eva Rifa [ctb],
Gonzalez-Reviriego Nube [ctb],
Marcos Rauel [ctb],
Palma Lluis [ctb],
An-Chi Ho [ctb],
Javier Corvillo [ctb],
Alberto Bojaly [ctb],
Thee [...truncated...]
Maintainer: Victoria Agudetse <victoria.agudetse@bsc.es>
Diff between CSIndicators versions 1.1.3 dated 2025-11-24 and 1.2.0 dated 2026-03-11
DESCRIPTION | 32 +++++++++++--------- MD5 | 37 ++++++++++++++++++------ NAMESPACE | 10 ++++++ NEWS.md | 19 ++++++++++++ R/AccumulationExceedingThreshold.R | 17 +++++++---- R/DayLength.R |only R/HeatIndex.R |only R/MaxSpellTimeExceedingThreshold.R |only R/MultiVarExceedingThreshold.R |only R/Threshold.R | 11 +++++-- build/vignette.rds |binary inst/doc/AgriculturalIndicators.html | 2 - inst/doc/EnergyIndicators.html | 2 - inst/doc/HeatIndexIndicator.Rmd |only inst/doc/HeatIndexIndicator.html |only man/CST_DayLength.Rd |only man/CST_HeatIndex.Rd |only man/CST_MaxSpellTimeExceedingThreshold.Rd |only man/CST_MultiVarExceedingThreshold.Rd |only man/DayLength.Rd |only man/HeatIndex.Rd |only man/MaxSpellTimeExceedingThreshold.Rd |only man/MultiVarExceedingThreshold.Rd |only vignettes/Figures/HI_ANO_OBS.png |only vignettes/Figures/HI_BIAS.png |only vignettes/Figures/HI_TimeSpellThreshold_exp.png |only vignettes/Figures/HI_TimeSpellThreshold_obs.png |only vignettes/Figures/Spatial_rh.png |only vignettes/Figures/Spatial_temp.png |only vignettes/HeatIndexIndicator.Rmd |only 30 files changed, 98 insertions(+), 32 deletions(-)
Title: Cyclomatic Complexity of R Code
Description: Cyclomatic complexity is a software metric (measurement),
used to indicate the complexity of a program. It is a quantitative
measure of the number of linearly independent paths through a
program's source code. It was developed by Thomas J. McCabe, Sr. in
1976.
Author: Gabor Csardi [aut, cre]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between cyclocomp versions 1.1.1 dated 2023-08-30 and 1.1.2 dated 2026-03-11
DESCRIPTION | 22 ++++++----- MD5 | 50 +++++++++++++------------ NEWS.md | 4 ++ R/cyclocomp.R | 5 +- R/flowgraph.R | 37 ++++++------------ R/package_dir.R | 25 +++++++----- R/post-process.R | 10 ++--- R/utils.R | 2 - README.md | 2 + man/cyclocomp.Rd | 6 +-- man/cyclocomp_package.Rd | 4 +- man/cyclocomp_package_dir.Rd | 8 ++-- tests/testthat.R | 8 ++++ tests/testthat/_snaps |only tests/testthat/test-andor.R | 15 +++---- tests/testthat/test-break.R | 28 +++++++++----- tests/testthat/test-calls.R | 5 -- tests/testthat/test-cyclocomp-package.R | 3 - tests/testthat/test-cyclocomp_q.R | 41 +++++++++++++++----- tests/testthat/test-formatting.R |only tests/testthat/test-function.R | 4 -- tests/testthat/test-if.R | 63 +++++++++++++++++++++----------- tests/testthat/test-next.R | 49 +++++++++++++++++++----- tests/testthat/test-repeat.R | 6 --- tests/testthat/test-return.R | 9 ++-- tests/testthat/test-seq.R | 29 +++++++++----- tests/testthat/test-stress.R | 4 -- 27 files changed, 255 insertions(+), 184 deletions(-)
Title: Fits Psychometric Functions for Multiple Groups
Description: Quickly fits and plots psychometric functions (normal, logistic,
Weibull or any or any function defined by the user) for multiple groups.
Author: Linares Daniel [aut, cre],
L<U+00F3>pez-Moliner Joan [aut]
Maintainer: Linares Daniel <danilinares@gmail.com>
Diff between quickpsy versions 0.1.5.1 dated 2019-10-02 and 0.1.5.2 dated 2026-03-11
DESCRIPTION | 10 +++--- MD5 | 63 +++++++++++++++++++++---------------------- R/curvesbootstrap.R | 4 +- R/devianceboot.R | 13 ++++---- R/deviancep.R | 3 +- R/fitpsy.R | 6 ++-- R/logliksboot.R | 26 ++++++++++------- R/logliksbootsaturated.R | 4 +- R/one_parcomparisons.R | 4 +- R/one_thresholdcomparisons.R | 4 +- R/parbootstrap.R | 4 +- R/parci.R | 3 +- R/parcomparisons.R | 3 +- R/quickreadfiles.R | 4 +- R/thresholds.R | 1 R/thresholdsbootstrap.R | 4 +- R/thresholdsci.R | 2 - inst/CITATION | 8 ++--- man/dot-.Rd |only man/fitpsy.Rd | 21 ++++++++++++-- man/one_parameters.Rd | 16 +++++++++- man/parameters.Rd | 16 +++++++++- man/parn.Rd | 4 ++ man/plotcurves.Rd | 13 +++++++- man/plotcurves_.Rd | 14 +++++++-- man/plotpar.Rd | 12 ++++++-- man/plotpar_.Rd | 12 ++++++-- man/plotthresholds.Rd | 13 +++++++- man/plotthresholds_.Rd | 14 +++++++-- man/qpdat.Rd | 4 ++ man/quickpsy.Rd | 27 +++++++++++++++--- man/quickpsy_.Rd | 27 +++++++++++++++--- man/thresholds.Rd | 3 -- 33 files changed, 249 insertions(+), 113 deletions(-)
Title: A Simple Way to Specify Symmetric, Block Diagonal Matrices
Description: Provides a simple mechanism to specify a symmetric block
diagonal matrices (often used for covariance matrices). This is based
on the domain specific language implemented in 'nlmixr2' but expanded
to create matrices in R generally instead of specifying parts of
matrices to estimate. It has expanded to include some matrix manipulation
functions that are generally useful for 'rxode2' and 'nlmixr2'.
Author: Matthew L. Fidler [aut, cre] ,
Mauricio Vargas Sepulveda [ctb] ,
Bill Denney [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between lotri versions 1.0.2 dated 2025-08-29 and 1.0.3 dated 2026-03-11
DESCRIPTION | 18 + MD5 | 12 - NEWS.md | 4 build/vignette.rds |binary inst/doc/lotri-motivation.html | 410 +++++++++++++++++++++-------------------- src/nearPD.cpp | 4 src/rcm.cpp | 12 - 7 files changed, 240 insertions(+), 220 deletions(-)
Title: Merge and Download International Large-Scale Assessments (ILSA)
Data
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), and others.
Author: Andres Christiansen [aut, cre] ,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAmerge versions 1.3.8 dated 2025-04-10 and 1.4.0 dated 2026-03-11
DESCRIPTION | 12 - MD5 | 52 +++--- NEWS.md | 11 + R/ILSAdownload.R | 4 R/ILSAmerge.R | 2 R/ILSAready.R | 4 R/ILSArename.R | 2 R/availableILSA.R | 17 +- R/justload.R | 2 R/sysdata.rda |binary build/vignette.rds |binary inst/doc/Download.R | 14 - inst/doc/Download.html | 51 +++--- inst/doc/IdentifyILSAfiles.html | 16 - inst/doc/Load.html | 102 ++++++------ inst/doc/Merge.R | 6 inst/doc/Merge.html | 174 ++++++++++----------- inst/doc/Onestep.html | 124 +++++++-------- inst/doc/Rename.html | 28 +-- inst/extdata/ilsainfo/ILSAcou.csv | 202 ++++++++++++------------ inst/extdata/ilsainfo/ILSAlinks.csv | 2 inst/extdata/ilsainfo/ILSApops.csv | 296 ++++++++++++++++++------------------ man/ILSAdownload.Rd | 2 man/ILSAmerge.Rd | 2 man/ILSAready.Rd | 6 man/ILSArename.Rd | 2 man/justload.Rd | 2 27 files changed, 581 insertions(+), 554 deletions(-)
Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation, the graphical lasso,
or the TIGER (tuning-insensitive graph estimation and
regression) method, and the first two can be further
accelerated by the lossy screening rule preselecting the
neighborhood of each variable by correlation thresholding. We
target on high-dimensional data analysis usually d >> n, and
the computation is memory-optimized using the sparse matrix
output. We also provide a computationally efficient approach,
correlation thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stab [...truncated...]
Author: Haoming Jiang [aut],
Xinyu Fei [aut],
Han Liu [aut],
Kathryn Roeder [aut],
John Lafferty [aut],
Larry Wasserman [aut],
Xingguo Li [aut],
Tuo Zhao [aut, cre]
Maintainer: Tuo Zhao <tourzhao@gatech.edu>
Diff between huge versions 1.4 dated 2026-02-19 and 1.5 dated 2026-03-11
huge-1.4/huge/inst/doc/vignette.Rnw |only huge-1.4/huge/inst/doc/vignette.pdf |only huge-1.4/huge/vignettes/huge.pdf |only huge-1.4/huge/vignettes/vignette.Rnw |only huge-1.5/huge/DESCRIPTION | 30 +- huge-1.5/huge/MD5 | 80 ++++-- huge-1.5/huge/NAMESPACE | 4 huge-1.5/huge/NEWS.md |only huge-1.5/huge/R/RcppExports.R | 13 - huge-1.5/huge/R/huge-internal.R |only huge-1.5/huge/R/huge-package.R | 27 -- huge-1.5/huge/R/huge.R | 77 +----- huge-1.5/huge/R/huge.ct.R | 28 -- huge-1.5/huge/R/huge.generator.R | 60 +---- huge-1.5/huge/R/huge.glasso.R | 18 - huge-1.5/huge/R/huge.mb.R | 40 --- huge-1.5/huge/R/huge.npn.R | 17 - huge-1.5/huge/R/huge.plot.R | 12 - huge-1.5/huge/R/huge.roc.R | 15 - huge-1.5/huge/R/huge.select.R | 24 -- huge-1.5/huge/R/huge.tiger.R | 40 --- huge-1.5/huge/build/vignette.rds |binary huge-1.5/huge/configure | 18 - huge-1.5/huge/configure.ac | 2 huge-1.5/huge/inst/doc/huge-content.pdf |only huge-1.5/huge/inst/doc/huge.Rnw |only huge-1.5/huge/inst/doc/huge.pdf |only huge-1.5/huge/man/huge-package.Rd | 26 -- huge-1.5/huge/man/huge.Rd | 4 huge-1.5/huge/man/huge.select.Rd | 4 huge-1.5/huge/src/Makevars.in | 2 huge-1.5/huge/src/Makevars.win | 2 huge-1.5/huge/src/RIC.cpp | 42 --- huge-1.5/huge/src/RcppExports.cpp | 22 + huge-1.5/huge/src/SFGen.cpp | 61 +---- huge-1.5/huge/src/SPMBgraph.cpp | 344 +++-------------------------- huge-1.5/huge/src/SPMBgraphsqrt.cpp | 313 +++----------------------- huge-1.5/huge/src/huge |only huge-1.5/huge/src/huge_core.cpp |only huge-1.5/huge/src/hugeglasso.cpp | 363 ++++--------------------------- huge-1.5/huge/tests/testthat |only huge-1.5/huge/tests/testthat.R |only huge-1.5/huge/vignettes/huge-content.pdf |only huge-1.5/huge/vignettes/huge.Rnw |only 44 files changed, 351 insertions(+), 1337 deletions(-)
Title: Applied Statistical Time Series Analysis
Description: Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <DOI:10.1007/978-3-031-70584-7>, and Time Series: A Data Analysis Approach Using R (2nd ed). Chapman-Hall, 2026, <https://www.routledge.com/Time-Series-A-Data-Analysis-Approach-Using-R/Shumway-Stoffer/p/book/9781041031642>. Most scripts are designed to require minimal input to produce aesthetically pleasing output for ease of use in live demonstrations and course work.
Author: David Stoffer [aut, cre],
Nicky Poison [ctb, mus, spy]
Maintainer: David Stoffer <stoffer@pitt.edu>
Diff between astsa versions 2.4 dated 2025-12-15 and 2.5 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NEWS.md |only R/EM.R | 12 ++++++------ R/sarima.R | 6 +++--- build/partial.rdb |binary man/astsa-package.Rd | 4 ++-- 7 files changed, 21 insertions(+), 20 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>
Diff between tidyILD versions 0.2.0 dated 2026-03-05 and 0.3.0 dated 2026-03-11
DESCRIPTION | 32 ++++++----- MD5 | 80 +++++++++++++++++++--------- NAMESPACE | 13 ++++ NEWS.md | 49 +++++++++++++++-- R/ild-class.R | 8 ++ R/ild_align.R | 7 ++ R/ild_center.R | 10 +++ R/ild_compare_pipelines.R |only R/ild_crosslag.R | 13 ++++ R/ild_diagnostics.R | 5 + R/ild_ipw_refit.R |only R/ild_ipw_weights.R |only R/ild_lag.R | 9 ++- R/ild_lme.R | 13 ++++ R/ild_methods.R |only R/ild_missing_model.R |only R/ild_model_tidiers.R | 77 +++++++++++++++++++------- R/ild_power.R | 10 +++ R/ild_prepare.R | 11 +++ R/ild_provenance.R |only R/ild_robust_se.R |only R/ild_tvem.R |only R/ild_tvem_plot.R |only R/package.R | 31 +++++++--- README.md | 7 +- build/vignette.rds |binary inst/doc/ild-analysis-report.R | 11 +++ inst/doc/ild-analysis-report.Rmd | 19 ++++++ inst/doc/ild-analysis-report.html | 80 ++++++++++++++++++---------- inst/doc/ild-decomposition-and-spacing.html | 4 - inst/doc/ild-glossary-and-quickstart.html | 4 - inst/doc/ild-provenance.R |only inst/doc/ild-provenance.Rmd |only inst/doc/ild-provenance.html |only inst/doc/tidyILD-workflow.html | 4 - man/ild_compare_pipelines.Rd |only man/ild_export_provenance.Rd |only man/ild_history.Rd |only man/ild_ipw_refit.Rd |only man/ild_ipw_weights.Rd |only man/ild_methods.Rd |only man/ild_missing_model.Rd |only man/ild_provenance.Rd |only man/ild_report.Rd |only man/ild_robust_se.Rd |only man/ild_tvem.Rd |only man/ild_tvem_plot.Rd |only man/tidyILD-package.Rd | 31 +++++++--- man/tidy_ild_model.Rd | 26 ++++++++- tests/testthat/test-ild_methods.R |only tests/testthat/test-ild_missing_model_ipw.R |only tests/testthat/test-ild_provenance.R |only tests/testthat/test-ild_robust_se.R |only tests/testthat/test-ild_tvem.R |only vignettes/ild-analysis-report.Rmd | 19 ++++++ vignettes/ild-provenance.Rmd |only 56 files changed, 444 insertions(+), 129 deletions(-)
Title: Interactive Tabular Matrix Problems via Pseudoinverse Estimation
Description: Provides an interactive wrapper for the 'tmpinv()' function from
the 'rtmpinv' package with options extending its functionality to pre-
and post-estimation processing and streamlined incorporation of prior cell
information. The Tabular Matrix Problems via Pseudoinverse Estimation
(TMPinv) is a two-stage estimation method that reformulates structured
table-based systems - such as allocation problems, transaction matrices,
and input-output tables - as structured least-squares problems. Based
on the Convex Least Squares Programming (CLSP) framework, TMPinv solves
systems with row and column constraints, block structure, and optionally
reduced dimensionality by (1) constructing a canonical constraint form
and applying a pseudoinverse-based projection, followed by (2) a
convex-programming refinement stage to improve fit, coherence, and
regularization (e.g., via Lasso, Ridge, or Elastic Net).
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rtmpinvi versions 0.1.0 dated 2026-02-25 and 0.2.0 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 3 ++- NEWS.md |only 3 files changed, 6 insertions(+), 5 deletions(-)
Title: Low-Level R to Java Interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek [aut, cre, cph]
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between rJava versions 1.0-14 dated 2026-01-20 and 1.0-15 dated 2026-03-11
rJava-1.0-14/rJava/jri |only rJava-1.0-15/rJava/DESCRIPTION | 6 rJava-1.0-15/rJava/MD5 | 276 +- rJava-1.0-15/rJava/NEWS | 6 rJava-1.0-15/rJava/configure | 3365 +++++++++++++++--------------- rJava-1.0-15/rJava/configure.ac | 2 rJava-1.0-15/rJava/inst/jri/JRIEngine.jar |binary rJava-1.0-15/rJava/inst/jri/REngine.jar |binary rJava-1.0-15/rJava/src/Makevars.in | 10 rJava-1.0-15/rJava/src/config.h.in | 19 rJava-1.0-15/rJava/src/java/Makefile | 5 rJava-1.0-15/rJava/src/jri |only rJava-1.0-15/rJava/src/rJava.h | 2 13 files changed, 1945 insertions(+), 1746 deletions(-)
Title: Create Randomization Lists
Description: Randomization lists are an integral component of randomized clinical trials. 'randotools' provides tools to easily create such lists.
Author: Alan G Haynes [aut, cre]
Maintainer: Alan G Haynes <alan.haynes@unibe.ch>
Diff between randotools versions 0.2.4 dated 2025-12-03 and 0.2.6 dated 2026-03-11
DESCRIPTION | 12 +++--- MD5 | 10 ++--- NEWS.md | 80 +++++++++++++++++++++++++--------------------- README.md | 14 ++++---- man/figures/imbseq-1.png |binary man/figures/imbtest-1.png |binary 6 files changed, 63 insertions(+), 53 deletions(-)
Title: Precision Based Sample Size Calculation
Description: Bland (2009) <doi:10.1136/bmj.b3985> recommended to
base study sizes on the width of the confidence interval rather the power of
a statistical test. The goal of 'presize' is to provide functions for such
precision based sample size calculations. For a given sample size, the
functions will return the precision (width of the confidence interval), and
vice versa.
Author: Armando Lenz [aut],
Alan G. Haynes [cre, aut],
Andreas Limacher [aut],
Odile Stalder [ctb],
Marie Roumet [ctb]
Maintainer: Alan G. Haynes <alan.haynes@unibe.ch>
Diff between presize versions 0.3.9 dated 2025-11-18 and 0.3.11 dated 2026-03-11
DESCRIPTION | 12 ++-- MD5 | 8 +- NEWS.md | 4 + inst/doc/presize.html | 131 ++++++++++++++++++++++++------------------------- man/presize-package.Rd | 6 +- 5 files changed, 83 insertions(+), 78 deletions(-)
Title: 'PLINK' 2 Binary (.pgen) Reader
Description: A thin wrapper over 'PLINK' 2's core libraries which provides an R
interface for reading .pgen files. A minimal .pvar loader is also
included. Chang et al. (2015) <doi:10.1186/s13742-015-0047-8>.
Author: Christopher Chang [aut, cre],
Eric Biggers [ctb, cph] ,
Yann Collet [ctb] ,
Meta Platforms, Inc. [cph] ,
Evan Nemerson [ctb, cph] ,
Przemyslaw Skibinski [ctb] ,
Nick Terrell [ctb]
Maintainer: Christopher Chang <chrchang@alumni.caltech.edu>
This is a re-admission after prior archival of version 0.5.4 dated 2026-01-17
Diff between pgenlibr versions 0.5.4 dated 2026-01-17 and 0.5.5 dated 2026-03-11
pgenlibr-0.5.4/pgenlibr/inst/include/include/SFMT.c |only pgenlibr-0.5.4/pgenlibr/inst/include/include/SFMT.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/pgenlib_write.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/pgenlib_write.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_bitmap.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_bitmap.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_fmath.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_fmath.h |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_stats.cc |only pgenlibr-0.5.4/pgenlibr/inst/include/include/plink2_stats.h |only pgenlibr-0.5.5/pgenlibr/DESCRIPTION | 14 - pgenlibr-0.5.5/pgenlibr/MD5 | 32 +- pgenlibr-0.5.5/pgenlibr/configure | 18 - pgenlibr-0.5.5/pgenlibr/configure.ac | 2 pgenlibr-0.5.5/pgenlibr/inst/include/include/pgenlib_read.h | 1 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_base.cc | 10 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_base.h | 40 +++ pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_float.cc |only pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_float.h |only pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_string.cc | 8 pgenlibr-0.5.5/pgenlibr/inst/include/include/plink2_string.h | 113 ---------- pgenlibr-0.5.5/pgenlibr/src/Makevars.in | 2 pgenlibr-0.5.5/pgenlibr/src/Makevars.win | 2 23 files changed, 92 insertions(+), 150 deletions(-)
Title: Visualizing Panel Data
Description: Visualizes panel data. It has three main functionalities: (1) it plots the treatment status and missing values in a panel dataset; (2) it visualizes the temporal dynamics of a main variable of interest; (3) it depicts the bivariate relationships between a treatment variable and an outcome variable either by unit or in aggregate. For details, see <doi:10.18637/jss.v107.i07>.
Author: Hongyu Mou [aut],
Licheng Liu [aut],
Yiqing Xu [aut, cre]
Maintainer: Yiqing Xu <yiqingxu@stanford.edu>
Diff between panelView versions 1.1.18 dated 2024-06-17 and 1.2.0 dated 2026-03-11
DESCRIPTION | 14 MD5 | 11 R/panelView.R | 1771 ----------------------------------------------------- R/plot-bivariate.R |only R/plot-outcome.R |only R/plot-treat.R |only R/zzz.r | 2 tests |only 8 files changed, 37 insertions(+), 1761 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: NNS (Nonlinear Nonparametric Statistics) leverages partial moments – the fundamental elements of variance that asymptotically approximate the area under f(x) – to provide a robust foundation for nonlinear analysis while maintaining linear equivalences. NNS delivers a comprehensive suite of advanced statistical techniques, including: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.open.source@gmail.com>
Diff between NNS versions 11.6.4 dated 2026-01-10 and 11.6.5 dated 2026-03-11
DESCRIPTION | 8 MD5 | 85 ++-- R/ANOVA.R | 92 ++--- R/Boost.R | 43 +- R/FSD.R | 17 R/NNS_meboot.R | 8 R/Normalization.R | 3 R/Partial_Moments.R | 80 ++++ R/RcppExports.R | 50 -- R/SSD.R | 49 +- R/Stack.R | 7 R/TSD.R | 49 +- R/Uni_SD_Routines.R | 90 +++-- README.md | 6 build/vignette.rds |binary inst/doc/NNSvignette_Clustering_and_Regression.R | 18 - inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 18 - inst/doc/NNSvignette_Clustering_and_Regression.html | 18 - inst/doc/NNSvignette_Normalization_and_Rescaling.R |only inst/doc/NNSvignette_Normalization_and_Rescaling.Rmd |only inst/doc/NNSvignette_Normalization_and_Rescaling.html |only inst/doc/NNSvignette_Overview.R | 32 + inst/doc/NNSvignette_Overview.Rmd | 135 +++++-- inst/doc/NNSvignette_Overview.html | 311 ++++++++++-------- inst/doc/NNSvignette_Partial_Moments.Rmd | 6 inst/doc/NNSvignette_Partial_Moments.html | 8 inst/doc/NNSvignette_Sampling.R | 4 inst/doc/NNSvignette_Sampling.Rmd | 4 inst/doc/NNSvignette_Sampling.html | 4 man/Co.LPM.Rd | 9 man/Co.UPM.Rd | 9 man/PM.matrix.Rd | 24 + src/RcppExports.cpp | 26 - src/internal_functions.cpp | 39 +- src/nns_rcpp.cpp |only src/partial_moments.cpp | 86 ++-- src/partial_moments.h | 8 src/partial_moments_rcpp.cpp | 66 --- src/partial_moments_rcpp.h | 6 tests/testthat/Rplots.pdf |binary tests/testthat/test_Partial_Moments.R | 14 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 18 - vignettes/NNSvignette_Normalization_and_Rescaling.Rmd |only vignettes/NNSvignette_Overview.Rmd | 135 +++++-- vignettes/NNSvignette_Partial_Moments.Rmd | 6 vignettes/NNSvignette_Sampling.Rmd | 4 46 files changed, 952 insertions(+), 643 deletions(-)
Title: Examples from Multilevel Modelling Software Review
Description: Data and examples from a multilevel modelling software review
as well as other well-known data sets from the multilevel modelling
literature.
Author: Douglas Bates [aut] ,
Martin Maechler [aut] ,
Ben Bolker [aut] ,
Anna Ly [cre]
Maintainer: Anna Ly <annahuynh.ly@utoronto.ca>
Diff between mlmRev versions 1.0-8 dated 2020-04-05 and 1.0-9 dated 2026-03-11
DESCRIPTION | 30 - MD5 | 40 - build/vignette.rds |binary inst/doc/MlmSoftRev.Rnw | 1292 +++++++++++++++++++++++------------------------ inst/doc/MlmSoftRev.pdf |binary inst/doc/StarData.Rnw | 612 +++++++++++----------- inst/doc/StarData.pdf |binary man/Chem97.Rd | 2 man/Contraception.Rd | 7 man/Exam.Rd | 2 man/Gcsemv.Rd | 2 man/Mmmec.Rd | 2 man/ScotsSec.Rd | 2 man/Socatt.Rd | 2 man/guImmun.Rd | 118 ++-- man/guPrenat.Rd | 108 +-- man/s3bbx.Rd | 71 +- man/s3bby.Rd | 61 +- man/star.Rd | 126 ++-- vignettes/MlmSoftRev.Rnw | 1292 +++++++++++++++++++++++------------------------ vignettes/StarData.Rnw | 612 +++++++++++----------- 21 files changed, 2198 insertions(+), 2183 deletions(-)
Title: LUCID with Multiple Omics Data
Description: Implements Latent Unknown Clusters By Integrating Multi-omics Data
(LUCID; Peng (2019) <doi:10.1093/bioinformatics/btz667>) for integrative
clustering with exposures, multi-omics data, and health outcomes.
Supports three integration strategies: early, parallel, and serial.
Provides model fitting and tuning, lasso-type regularization for exposure
and omics feature selection, handling of missing data, including both
sporadic and complete-case patterns, prediction, and g-computation for
estimating causal effects of exposures, bootstrap inference for
uncertainty estimation, and S3 summary and plot methods. For the
multi-omics integration framework, see Jia (2024)
<https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf>.
For the missing-data imputation mechanism, see Jia (2024)
<doi:10.1093/bioadv/vbae123>.
Author: Qiran Jia [aut, cre] ,
Yinqi Zhao [aut] ,
David Conti [ths] ,
Jesse Goodrich [ctb]
Maintainer: Qiran Jia <qiranjia@usc.edu>
Diff between LUCIDus versions 3.0.3 dated 2024-09-23 and 3.1.0 dated 2026-03-11
LUCIDus-3.0.3/LUCIDus/man/summary.early_lucid.Rd |only LUCIDus-3.1.0/LUCIDus/DESCRIPTION | 33 LUCIDus-3.1.0/LUCIDus/MD5 | 140 - LUCIDus-3.1.0/LUCIDus/NAMESPACE | 11 LUCIDus-3.1.0/LUCIDus/R/00_stability_preload.R |only LUCIDus-3.1.0/LUCIDus/R/EM_all.R | 537 ++-- LUCIDus-3.1.0/LUCIDus/R/boot_lucid.R | 1017 +++++++ LUCIDus-3.1.0/LUCIDus/R/early_estep.R | 303 +- LUCIDus-3.1.0/LUCIDus/R/em.R | 1314 ++++------ LUCIDus-3.1.0/LUCIDus/R/lucid.R | 154 - LUCIDus-3.1.0/LUCIDus/R/missing.R | 521 +++ LUCIDus-3.1.0/LUCIDus/R/missing_utils.R |only LUCIDus-3.1.0/LUCIDus/R/parallel_estep.R | 88 LUCIDus-3.1.0/LUCIDus/R/parallel_mstep.R | 572 ++-- LUCIDus-3.1.0/LUCIDus/R/pred_lucid.R | 159 - LUCIDus-3.1.0/LUCIDus/R/predict_lucid_all.R | 113 LUCIDus-3.1.0/LUCIDus/R/stability_utils.R |only LUCIDus-3.1.0/LUCIDus/R/summary.R | 1205 +++++++-- LUCIDus-3.1.0/LUCIDus/R/tune_lucid.R | 473 +-- LUCIDus-3.1.0/LUCIDus/R/utility.R | 70 LUCIDus-3.1.0/LUCIDus/R/utils.R |only LUCIDus-3.1.0/LUCIDus/inst |only LUCIDus-3.1.0/LUCIDus/man/Istep_Z.Rd | 19 LUCIDus-3.1.0/LUCIDus/man/analyze_missing_pattern.Rd |only LUCIDus-3.1.0/LUCIDus/man/boot_lucid.Rd | 59 LUCIDus-3.1.0/LUCIDus/man/check_and_stabilize_sigma.Rd |only LUCIDus-3.1.0/LUCIDus/man/check_convergence.Rd |only LUCIDus-3.1.0/LUCIDus/man/check_imputation_quality.Rd |only LUCIDus-3.1.0/LUCIDus/man/check_na.Rd | 17 LUCIDus-3.1.0/LUCIDus/man/estimate_lucid.Rd | 31 LUCIDus-3.1.0/LUCIDus/man/fill_data.Rd | 10 LUCIDus-3.1.0/LUCIDus/man/gen_ci.Rd | 2 LUCIDus-3.1.0/LUCIDus/man/lucid.Rd | 92 LUCIDus-3.1.0/LUCIDus/man/predict_lucid.Rd | 57 LUCIDus-3.1.0/LUCIDus/man/print.sumlucid_early.Rd | 15 LUCIDus-3.1.0/LUCIDus/man/print.sumlucid_parallel.Rd | 6 LUCIDus-3.1.0/LUCIDus/man/safe_impute.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_log_sum_exp.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_normalize.Rd |only LUCIDus-3.1.0/LUCIDus/man/safe_solve.Rd |only LUCIDus-3.1.0/LUCIDus/man/summarize_missing_stats.Rd |only LUCIDus-3.1.0/LUCIDus/man/summary.lucid_parallel.Rd | 7 LUCIDus-3.1.0/LUCIDus/man/summary_lucid.Rd |only LUCIDus-3.1.0/LUCIDus/man/tune_lucid.Rd | 108 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-Serial-binary-missing.R | 49 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-Serial-binary-summary.R | 30 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-Serial-normal-missing.R | 18 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-boot-lucid-early.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-boot-lucid-parallel.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-boot-lucid-serial.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-early-robustness.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-em-restart-guard.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-extreme-edge-cases.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-gcomp-early-parallel-contract.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-gcomp-serial-normal-5-layers.R | 44 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-binary-1-layer.R | 52 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-binary-3-layers.R | 20 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-binary-5-layers.R | 24 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-normal-1-layer.R | 39 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-normal-3-layers.R | 20 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-lucid-normal-5-layers.R | 4 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-missing-binary-1-layer.R | 44 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-missing-binary-5-layers.R | 21 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-missing-normal-1-layers.R | 45 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-missing-normal-3-layers.R | 15 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-parallel-p0-regressions.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-parallel-p1-plumbing.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-parallel-robustness-extra.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-parallel-selection-impute.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-parallel-tuning-penalty-grid.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-predict-binary-1-layer.R | 10 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-predict-binary-5-layers.R | 41 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-predict-serial-binary-5-layers.R | 16 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-predict-serial-normal-5-layers.R | 12 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-predict_normal_1_layer.R | 4 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-rho-g-exposure-only-consistency.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-serial-6stage-parallel-smoke.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-serial-fit-missing-robustness.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-serial-summary-context-labels.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-summart-binary-5-layers.R | 72 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-summary-missing-profile.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-summary-normal-5-layers.R | 62 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-tune-Serial-binary.R | 169 - LUCIDus-3.1.0/LUCIDus/tests/testthat/test-tune-Serial-normal.R | 138 - LUCIDus-3.1.0/LUCIDus/tests/testthat/test-tune-binary-2-layers.R | 96 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-tune-normal-2-layers.R | 85 LUCIDus-3.1.0/LUCIDus/tests/testthat/test-tune-penalty-fail-guard.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-verbose-fit-logging.R |only LUCIDus-3.1.0/LUCIDus/tests/testthat/test-workhorse-p0-p1-regressions.R |only 89 files changed, 5426 insertions(+), 2837 deletions(-)
Title: Indices of Effect Size
Description: Provide utilities to work with indices of effect size for a wide
variety of models and hypothesis tests (see list of supported models using
the function 'insight::supported_models()'), allowing computation of and
conversion between indices such as Cohen's d, r, odds, etc.
References: Ben-Shachar et al. (2020) <doi:10.21105/joss.02815>.
Author: Mattan S. Ben-Shachar [aut, cre] ,
Dominique Makowski [aut] ,
Daniel Luedecke [aut] ,
Indrajeet Patil [aut] ,
Brenton M. Wiernik [aut] ,
Remi Theriault [aut] ,
Ken Kelley [ctb],
David Stanley [ctb],
Aaron Caldwell [ctb] ,
Jessica Burnett [rev] ,
Johan [...truncated...]
Maintainer: Mattan S. Ben-Shachar <mattansb@msbstats.info>
Diff between effectsize versions 1.0.1 dated 2025-05-27 and 1.0.2 dated 2026-03-11
effectsize-1.0.1/effectsize/man/convert_chisq.Rd |only effectsize-1.0.2/effectsize/DESCRIPTION | 12 effectsize-1.0.2/effectsize/MD5 | 253 - effectsize-1.0.2/effectsize/NAMESPACE | 31 effectsize-1.0.2/effectsize/NEWS.md | 18 effectsize-1.0.2/effectsize/R/cohens_d.R | 723 +-- effectsize-1.0.2/effectsize/R/cohens_g.R | 242 - effectsize-1.0.2/effectsize/R/common_language.R | 1079 ++--- effectsize-1.0.2/effectsize/R/convert_between_anova.R | 143 effectsize-1.0.2/effectsize/R/convert_between_common_language.R | 633 +- effectsize-1.0.2/effectsize/R/convert_between_d_to_r.R | 327 - effectsize-1.0.2/effectsize/R/convert_between_odds_to_probs.R | 191 effectsize-1.0.2/effectsize/R/convert_between_riskchange.R | 704 ++- effectsize-1.0.2/effectsize/R/convert_between_riskchange_ro_probs.R |only effectsize-1.0.2/effectsize/R/convert_between_xtabcorr.R | 246 - effectsize-1.0.2/effectsize/R/convert_stat_chisq.R | 867 ++-- effectsize-1.0.2/effectsize/R/convert_stat_to_anova.R | 689 +-- effectsize-1.0.2/effectsize/R/convert_stat_to_d.R | 222 - effectsize-1.0.2/effectsize/R/convert_stat_to_r.R | 357 - effectsize-1.0.2/effectsize/R/datasets.R | 32 effectsize-1.0.2/effectsize/R/docs_extra.R | 357 - effectsize-1.0.2/effectsize/R/effectsize-package.R | 62 effectsize-1.0.2/effectsize/R/effectsize.BFBayesFactor.R | 70 effectsize-1.0.2/effectsize/R/effectsize.R | 337 - effectsize-1.0.2/effectsize/R/effectsize.data_tabulate.R |only effectsize-1.0.2/effectsize/R/effectsize.htest.R | 129 effectsize-1.0.2/effectsize/R/equivalence_test.R | 301 - effectsize-1.0.2/effectsize/R/eta_squared-main.R | 2153 +++++----- effectsize-1.0.2/effectsize/R/eta_squared-methods.R | 1018 ++-- effectsize-1.0.2/effectsize/R/eta_squared_posterior.R | 313 - effectsize-1.0.2/effectsize/R/format_standardize.R | 142 effectsize-1.0.2/effectsize/R/interpret.R | 562 +- effectsize-1.0.2/effectsize/R/interpret_bf.R | 203 effectsize-1.0.2/effectsize/R/interpret_cfa_fit.R | 613 +- effectsize-1.0.2/effectsize/R/interpret_cohens_d.R | 29 effectsize-1.0.2/effectsize/R/interpret_cohens_g.R | 95 effectsize-1.0.2/effectsize/R/interpret_direction.R | 42 effectsize-1.0.2/effectsize/R/interpret_ess_rhat.R | 142 effectsize-1.0.2/effectsize/R/interpret_icc.R | 76 effectsize-1.0.2/effectsize/R/interpret_kendalls_w.R | 78 effectsize-1.0.2/effectsize/R/interpret_oddsratio.R | 108 effectsize-1.0.2/effectsize/R/interpret_omega_squared.R | 130 effectsize-1.0.2/effectsize/R/interpret_p.R | 96 effectsize-1.0.2/effectsize/R/interpret_pd.R | 98 effectsize-1.0.2/effectsize/R/interpret_r.R | 262 - 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More information about easyRaschBayes at CRAN
Permanent link
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include:
a) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) Paine J.P., Preston S.P., Tsagris M. and Wood A.T.A. (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872 [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Zehao Yu [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Panagiotis Papastamoulis [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 7.3 dated 2025-10-22 and 7.4 dated 2026-03-11
DESCRIPTION | 9 +++++---- MD5 | 17 ++++++++++------- R/gcpc.means.test.R |only R/gcpc.mle.R | 37 ++++++++++++++++++++----------------- R/gcpc.reg.R | 25 ++++++++++++------------- R/ggvm.mle.R | 11 ++++++----- R/wraplaplace.mle.R |only man/Directional-package.Rd | 4 ++-- man/gcpc.means.test.Rd |only man/spml.mle.Rd | 14 ++++++-------- man/spml.reg.Rd | 5 +---- 11 files changed, 62 insertions(+), 60 deletions(-)
Title: Versatile Curation of Table Metadata
Description: A YAML-based
mechanism for working with table metadata. Supports
compact syntax for creating, modifying, viewing, exporting,
importing, displaying, and plotting metadata coded as column
attributes. The 'yamlet' dialect is valid 'YAML' with
defaults and conventions chosen to improve readability.
See ?yamlet, ?decorate, ?modify, ?io_csv, and ?ggplot.decorated.
Author: Tim Bergsma [aut, cre]
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between yamlet versions 1.3.3 dated 2026-03-06 and 1.3.4 dated 2026-03-11
DESCRIPTION | 6 MD5 | 25 +-- R/as_categorical.R | 17 +- R/decorate.R | 2 inst/doc/aesthetics.html | 6 inst/doc/scripted-html.html | 4 inst/doc/scripted-pdf.pdf |binary inst/doc/yamlet-introduction.html | 4 man/as_categorical.decorated.Rd | 4 man/undecorate.default.Rd | 2 tests/testthat/137.rds |only tests/testthat/test-yamlet.R | 78 +++++++++- vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-4-1.pdf |binary vignettes/scripted-pdf_files/figure-latex/unnamed-chunk-5-1.pdf |binary 14 files changed, 120 insertions(+), 28 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph] ,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph] ,
Andrea Manica [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 1.0.0 dated 2026-01-23 and 1.1.0 dated 2026-03-11
tidyterra-1.0.0/tidyterra/inst/doc/tidyterra.Rmd |only tidyterra-1.0.0/tidyterra/inst/doc/welcome.Rmd |only tidyterra-1.0.0/tidyterra/vignettes/aggregate-1.png |only tidyterra-1.0.0/tidyterra/vignettes/aggregate-2.png |only tidyterra-1.0.0/tidyterra/vignettes/contourfilled-1.png |only tidyterra-1.0.0/tidyterra/vignettes/contourlines-1.png |only tidyterra-1.0.0/tidyterra/vignettes/faceted-1.png |only tidyterra-1.0.0/tidyterra/vignettes/hypso-1.png |only tidyterra-1.0.0/tidyterra/vignettes/lux_ggplot-1.png |only tidyterra-1.0.0/tidyterra/vignettes/rgb-1.png |only tidyterra-1.0.0/tidyterra/vignettes/spatraster-example1-1.png |only tidyterra-1.0.0/tidyterra/vignettes/spatraster-example2-1.png |only tidyterra-1.0.0/tidyterra/vignettes/tidyterra.Rmd |only tidyterra-1.0.0/tidyterra/vignettes/welcome.Rmd |only tidyterra-1.1.0/tidyterra/DESCRIPTION | 21 tidyterra-1.1.0/tidyterra/MD5 | 336 +-- tidyterra-1.1.0/tidyterra/NAMESPACE | 7 tidyterra-1.1.0/tidyterra/NEWS.md | 48 tidyterra-1.1.0/tidyterra/R/arrange-SpatVector.R | 19 tidyterra-1.1.0/tidyterra/R/as-coordinates.R | 2 tidyterra-1.1.0/tidyterra/R/as-spatraster.R | 8 tidyterra-1.1.0/tidyterra/R/as-spatvector.R | 11 tidyterra-1.1.0/tidyterra/R/as-tibble-Spat.R | 42 tidyterra-1.1.0/tidyterra/R/autoplot-Spat.R | 12 tidyterra-1.1.0/tidyterra/R/bind-cols-SpatVector.R | 11 tidyterra-1.1.0/tidyterra/R/bind-rows-SpatVector.R | 23 tidyterra-1.1.0/tidyterra/R/compare-spatrasters.R | 10 tidyterra-1.1.0/tidyterra/R/count-tally-SpatVector.R | 124 + tidyterra-1.1.0/tidyterra/R/data.R | 14 tidyterra-1.1.0/tidyterra/R/distinct-SpatVector.R | 258 +- tidyterra-1.1.0/tidyterra/R/drop-na-Spat.R | 10 tidyterra-1.1.0/tidyterra/R/fill-SpatVector.R | 8 tidyterra-1.1.0/tidyterra/R/filter-Spat.R | 69 tidyterra-1.1.0/tidyterra/R/fortify-Spat.R | 24 tidyterra-1.1.0/tidyterra/R/geom-spat-contour-fill.R | 623 +++--- tidyterra-1.1.0/tidyterra/R/geom-spat-contour-text.R | 18 tidyterra-1.1.0/tidyterra/R/geom-spat-contour.R | 58 tidyterra-1.1.0/tidyterra/R/geom-spatraster-rgb.R | 10 tidyterra-1.1.0/tidyterra/R/geom-spatraster.R | 16 tidyterra-1.1.0/tidyterra/R/geom-spatvector.R | 3 tidyterra-1.1.0/tidyterra/R/glance-Spat.R | 1 tidyterra-1.1.0/tidyterra/R/glimpse-Spat.R | 912 ++++------ tidyterra-1.1.0/tidyterra/R/group-by-SpatVector.R | 3 tidyterra-1.1.0/tidyterra/R/group-data-SpatVector.R | 4 tidyterra-1.1.0/tidyterra/R/grouped-SpatVector.R | 1 tidyterra-1.1.0/tidyterra/R/is-regular-grid.R | 1 tidyterra-1.1.0/tidyterra/R/join-SpatVector.R | 733 +++----- tidyterra-1.1.0/tidyterra/R/mutate-Spat.R | 159 - 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Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel [aut, cre] ,
David Ardia [aut] ,
Katharine Mullen [aut] ,
Brian Peterson [aut] ,
Joshua Ulrich [aut] ,
Kris Boudt [ctb] ,
Rainer Storn [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.8 dated 2025-02-18 and 0.1.9 dated 2026-03-11
ChangeLog | 49 ++++++++++++++++ DESCRIPTION | 11 +-- MD5 | 32 +++++----- R/RcppExports.R | 4 + README.md | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/RcppDE.Rnw | 12 +-- inst/doc/RcppDE.pdf |binary man/DEoptim-methods.Rd | 38 ++++++------ man/DEoptim.Rd | 114 ++++++++++++++++++------------------- man/DEoptim.control.Rd | 63 ++++++++++---------- src/Makevars | 4 - src/RcppExports.cpp | 11 +++ src/armadilloVersion.cpp |only src/evaluate.h | 4 - vignettes/RcppDE.Rnw | 12 +-- vignettes/RcppDE.bib | 142 +++++++++++++++++++++++++++++++++-------------- 18 files changed, 311 insertions(+), 187 deletions(-)
Title: Faster K-Medoids Clustering Algorithms: FastPAM, FastCLARA,
FastCLARANS
Description: R wrappers of C++ implementation of Faster K-Medoids clustering algorithms (FastPAM, FastCLARA and FastCLARANS) proposed in Erich Schubert, Peter J. Rousseeuw 2019 <doi:10.1007/978-3-030-32047-8_16>.
Author: Xun Li [aut, cre]
Maintainer: Xun Li <lixun910@gmail.com>
Diff between fastkmedoids versions 1.4 dated 2026-02-25 and 1.5 dated 2026-03-11
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Title: Programmatic Access to County Health Rankings & Roadmaps Data
Description: Provides a simple interface to pull County Health Rankings & Roadmaps (CHR&R) county-level health data and metadata directly from 'Zenodo' <doi:10.5281/zenodo.18157681>.
Users can retrieve data for CHR&R release years 2010 through 2025.
CHR&R data support research and decision-making to promote health equity
and policies that help all communities thrive.
Author: Hannah Olson-Williams [aut, cre]
Maintainer: Hannah Olson-Williams <hannaheow@gmail.com>
Diff between countyhealthR versions 0.1.3 dated 2026-02-25 and 0.1.5 dated 2026-03-11
DESCRIPTION | 14 +++++------- MD5 | 10 ++++---- R/zenodo_helpers.R | 47 +++++++++++++++++++++++++++--------------- inst/doc/getting_started.Rmd | 4 ++- inst/doc/getting_started.html | 10 ++++++++ vignettes/getting_started.Rmd | 4 ++- 6 files changed, 58 insertions(+), 31 deletions(-)
Title: Estimating Aboveground Biomass and Its Uncertainty in Tropical
Forests
Description: Contains functions for estimating above-ground biomass/carbon and its uncertainty in tropical forests. These functions allow to (1) retrieve and correct taxonomy, (2) estimate wood density and its uncertainty, (3) build height-diameter models, (4) manage tree and plot coordinates, (5) estimate above-ground biomass/carbon at stand level with associated uncertainty. To cite ‘BIOMASS’, please use citation(‘BIOMASS’). For more information, see Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.
Author: Dominique Lamonica [aut, cre],
Maxime Rejou-Mechain [aut, dtc],
Arthur Bailly [aut],
Guillaume Cornu [aut] ,
John Godlee [ctb],
Fabian Fischer [ctb],
Jerome Chave [ctb],
Arthur Pere [aut],
Ariane Tanguy [aut],
Camille Piponiot [aut],
Bruno Herault [a [...truncated...]
Maintainer: Dominique Lamonica <dominique.lamonica@ird.fr>
Diff between BIOMASS versions 2.2.4-1 dated 2025-10-10 and 2.2.7 dated 2026-03-11
BIOMASS-2.2.4-1/BIOMASS/tests/testthat/_snaps |only BIOMASS-2.2.7/BIOMASS/DESCRIPTION | 42 BIOMASS-2.2.7/BIOMASS/MD5 | 119 +- BIOMASS-2.2.7/BIOMASS/NAMESPACE | 5 BIOMASS-2.2.7/BIOMASS/NEWS | 16 BIOMASS-2.2.7/BIOMASS/R/AGBmonteCarlo.R | 114 +- BIOMASS-2.2.7/BIOMASS/R/cacheManager.R | 4 BIOMASS-2.2.7/BIOMASS/R/check_plot_coord.R | 291 +++-- BIOMASS-2.2.7/BIOMASS/R/data_documentation.R | 8 BIOMASS-2.2.7/BIOMASS/R/divide_plot.R | 239 ++-- BIOMASS-2.2.7/BIOMASS/R/globals.R | 7 BIOMASS-2.2.7/BIOMASS/R/loglogFunction.R | 65 - BIOMASS-2.2.7/BIOMASS/R/michaelisFunction.R | 133 +- BIOMASS-2.2.7/BIOMASS/R/modelHD.R | 227 ++-- BIOMASS-2.2.7/BIOMASS/R/predictHeight.R | 202 ++- BIOMASS-2.2.7/BIOMASS/R/retrieveH.R | 34 BIOMASS-2.2.7/BIOMASS/R/subplot_summary.R | 557 +++++++--- BIOMASS-2.2.7/BIOMASS/R/summaryByPlot.R | 4 BIOMASS-2.2.7/BIOMASS/R/weibullFunction.R | 146 +- BIOMASS-2.2.7/BIOMASS/R/zzz.R | 5 BIOMASS-2.2.7/BIOMASS/README.md | 6 BIOMASS-2.2.7/BIOMASS/build/partial.rdb |binary BIOMASS-2.2.7/BIOMASS/build/vignette.rds |binary BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_BIOMASS.R | 45 BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_BIOMASS.Rmd | 89 + BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_BIOMASS.html | 153 ++ BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_spatialized_trees_and_forest_stand_metrics.R | 69 - BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_spatialized_trees_and_forest_stand_metrics.Rmd | 123 +- BIOMASS-2.2.7/BIOMASS/inst/doc/Vignette_spatialized_trees_and_forest_stand_metrics.html | 467 +++++--- BIOMASS-2.2.7/BIOMASS/man/AGBmonteCarlo.Rd | 6 BIOMASS-2.2.7/BIOMASS/man/BIOMASS-package.Rd | 8 BIOMASS-2.2.7/BIOMASS/man/HDmethods.Rd | 63 - BIOMASS-2.2.7/BIOMASS/man/check_plot_coord.Rd | 13 BIOMASS-2.2.7/BIOMASS/man/divide_plot.Rd | 56 - BIOMASS-2.2.7/BIOMASS/man/figures/logo.png |binary BIOMASS-2.2.7/BIOMASS/man/figures/predictHeight_help.pdf |only BIOMASS-2.2.7/BIOMASS/man/modelHD.Rd | 73 + BIOMASS-2.2.7/BIOMASS/man/predictHeight.Rd | 12 BIOMASS-2.2.7/BIOMASS/man/subplot_summary.Rd | 83 + BIOMASS-2.2.7/BIOMASS/man/summaryByPlot.Rd | 4 BIOMASS-2.2.7/BIOMASS/tests/testdata |only BIOMASS-2.2.7/BIOMASS/tests/testthat/test-AGBmonteCarlo.R | 6 BIOMASS-2.2.7/BIOMASS/tests/testthat/test-check_coord_plot.R | 102 + BIOMASS-2.2.7/BIOMASS/tests/testthat/test-correctTaxo.R | 120 +- BIOMASS-2.2.7/BIOMASS/tests/testthat/test-dividePlot.R | 156 ++ BIOMASS-2.2.7/BIOMASS/tests/testthat/test-modelHD.R | 35 BIOMASS-2.2.7/BIOMASS/tests/testthat/test-predictHeight.R |only BIOMASS-2.2.7/BIOMASS/tests/testthat/test-small_function.R | 94 - BIOMASS-2.2.7/BIOMASS/tests/testthat/test-subplot_summary.R | 244 +++- BIOMASS-2.2.7/BIOMASS/tests/testthat/test-summaryByPlot.R | 2 BIOMASS-2.2.7/BIOMASS/vignettes/Vignette_BIOMASS.Rmd | 89 + BIOMASS-2.2.7/BIOMASS/vignettes/Vignette_spatialized_trees_and_forest_stand_metrics.Rmd | 123 +- BIOMASS-2.2.7/BIOMASS/vignettes/img/weibull_plot.png |only BIOMASS-2.2.7/BIOMASS/vignettes/img/weibull_plot_2.png |only BIOMASS-2.2.7/BIOMASS/vignettes/saved_data/error_prop.rds |only BIOMASS-2.2.7/BIOMASS/vignettes/saved_data/generate_data_for_predictmap_vignette.R |only 56 files changed, 3047 insertions(+), 1412 deletions(-)