Title: Probing, Plotting, and Interpreting Multilevel Interaction
Effects
Description: Provides a unified workflow for probing, plotting, and assessing
the robustness of cross-level interaction effects in two-level mixed-effects
models fitted with 'lme4' (Bates et al., 2015)
<doi:10.18637/jss.v067.i01>. Implements simple slopes analysis following
Aiken and West (1991, ISBN:9780761907121), Johnson-Neyman intervals
following Johnson and Fay (1950) <doi:10.1007/BF02288864> and Bauer
and Curran (2005) <doi:10.1207/s15327906mbr4003_5>, and grand- or
group-mean centering as described in Enders and Tofighi (2007)
<doi:10.1037/1082-989X.12.2.121>. Includes a slope variance decomposition
that separates fixed-effect uncertainty from random-slope variance
(tau11), a contour surface plot of predicted outcomes over the full
predictor-by-moderator space, and robustness diagnostics comprising
intraclass correlation coefficient shift analysis and
leave-one-cluster-out (LOCO) stability checks. Designed for researchers
in education, psychology, biostatistics, epide [...truncated...]
Author: Subir Hait [aut, cre]
Maintainer: Subir Hait <haitsubi@msu.edu>
Diff between mlmoderator versions 0.2.0 dated 2026-03-27 and 0.2.1 dated 2026-04-03
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Allocate Samples Among Strata
Description: Functions for the design process of survey sampling, with specific tools for multi-wave and multi-phase designs. Perform optimum allocation using Neyman (1934) <doi:10.2307/2342192> or Wright (2012) <doi:10.1080/00031305.2012.733679> allocation, split strata based on quantiles or values of known variables, randomly select samples from strata, allocate sampling waves iteratively, and organize a complex survey design. Also includes a Shiny application for observing the effects of different strata splits. A paper on this package was published in the Journal of Statistical Software <doi:10.18637/jss.v114.i10>.
Author: Jasper Yang [aut, cre],
Pamela Shaw [aut],
Bryan Shepherd [ctb],
Thomas Lumley [ctb],
Gustavo Amorim [rev]
Maintainer: Jasper Yang <jbyang@uw.edu>
Diff between optimall versions 1.3.1 dated 2026-01-28 and 1.4.0 dated 2026-04-03
DESCRIPTION | 6 MD5 | 23 - NEWS.md | 5 R/allocate_wave.R | 61 +++ R/optimum_allocation.R | 453 +++++++++++++------------- inst/doc/optimall-vignette.Rmd | 2 inst/doc/optimall-vignette.html | 19 - man/allocate_wave.Rd | 14 man/allocate_wright.Rd |only man/optimum_allocation.Rd | 29 + tests/testthat/test-allocate_wave.R | 296 ++++++++++++++++- tests/testthat/test-optimum_allocation.R | 528 +++++++++++++++++++++++++++++++ vignettes/optimall-vignette.Rmd | 2 13 files changed, 1174 insertions(+), 264 deletions(-)
Title: Fast Decoding of SYNOP (Surface Synoptic Observations)
Meteorological Messages
Description: Decode raw SYNOP (surface synoptic observations) messages into
data frames, extracting data from Sections 0, 1, and 3, including temperature,
dew point, pressure, wind, clouds, and precipitation. Available functions to
download SYNOP messages from Ogimet <https://www.ogimet.com/> if needed.
The decoding logic follows the specifications defined in the World Meteorological
Organization (2019) "Manual on Codes, Volume I.1 (WMO-No. 306)".
Author: Ezequiel Elias [aut, cre]
Maintainer: Ezequiel Elias <elezeru15@gmail.com>
Diff between synopR versions 0.2.2 dated 2026-03-18 and 1.0.0 dated 2026-04-03
synopR-0.2.2/synopR/inst/doc/guia-inicio-es.R |only synopR-0.2.2/synopR/inst/doc/guia-inicio-es.Rmd |only synopR-0.2.2/synopR/inst/doc/guia-inicio-es.html |only synopR-0.2.2/synopR/vignettes/guia-inicio-es.Rmd |only synopR-1.0.0/synopR/DESCRIPTION | 24 synopR-1.0.0/synopR/MD5 | 53 - synopR-1.0.0/synopR/NAMESPACE | 12 synopR-1.0.0/synopR/NEWS.md | 12 synopR-1.0.0/synopR/R/checks.R |only synopR-1.0.0/synopR/R/constants.R |only synopR-1.0.0/synopR/R/decoder.R | 506 ++++++---- synopR-1.0.0/synopR/R/globals.R | 1 synopR-1.0.0/synopR/R/ogimet.R |only synopR-1.0.0/synopR/R/utils.R | 606 ++++++++++--- synopR-1.0.0/synopR/README.md | 103 +- synopR-1.0.0/synopR/build/vignette.rds |binary synopR-1.0.0/synopR/inst/WORDLIST |only synopR-1.0.0/synopR/inst/doc/Code_Tables.R | 20 synopR-1.0.0/synopR/inst/doc/Code_Tables.Rmd | 20 synopR-1.0.0/synopR/inst/doc/Code_Tables.html | 20 synopR-1.0.0/synopR/inst/doc/Extracted_data_reference.R |only synopR-1.0.0/synopR/inst/doc/Extracted_data_reference.Rmd |only synopR-1.0.0/synopR/inst/doc/Extracted_data_reference.html |only synopR-1.0.0/synopR/inst/doc/getting-started-en.R | 50 - synopR-1.0.0/synopR/inst/doc/getting-started-en.Rmd | 113 -- synopR-1.0.0/synopR/inst/doc/getting-started-en.html | 578 ++++++++---- synopR-1.0.0/synopR/man/check_synop.Rd | 48 - synopR-1.0.0/synopR/man/direct_download_from_ogimet.Rd |only synopR-1.0.0/synopR/man/download_from_ogimet.Rd |only synopR-1.0.0/synopR/man/figures/benchmark_result.png |only synopR-1.0.0/synopR/man/parse_ogimet.Rd | 44 synopR-1.0.0/synopR/man/show_synop_data.Rd | 160 ++- synopR-1.0.0/synopR/vignettes/Code_Tables.Rmd | 20 synopR-1.0.0/synopR/vignettes/Extracted_data_reference.Rmd |only synopR-1.0.0/synopR/vignettes/getting-started-en.Rmd | 113 -- 35 files changed, 1562 insertions(+), 941 deletions(-)
Title: Regression, Inference, and General Data Analysis Tools in R
Description: A set of tools to streamline data analysis. Learning both R and introductory statistics at the same time can be challenging, and so we created 'rigr' to facilitate common data analysis tasks and enable learners to focus on statistical concepts. We provide easy-to-use interfaces for descriptive statistics, one- and two-sample inference, and regression analyses. 'rigr' output includes key information while omitting unnecessary details that can be confusing to beginners. Heteroscedasticity-robust ("sandwich") standard errors are returned by default, and multiple partial F-tests and tests for contrasts are easy to specify. A single regression function can fit both linear and generalized linear models, allowing students to more easily make connections between different classes of models.
Author: Amy D Willis [aut, cre] ,
Taylor Okonek [aut],
Charles J Wolock [aut],
Brian D Williamson [aut],
Scott S Emerson [aut],
Andrew J Spieker [aut],
Yiqun T Chen [aut],
Travis Y Hee Wai [ctb],
James P Hughes [ctb],
R Core Team [ctb],
Akhil S Bhel [ctb],
T [...truncated...]
Maintainer: Amy D Willis <adwillis@uw.edu>
Diff between rigr versions 1.0.8 dated 2025-09-02 and 1.0.9 dated 2026-04-03
DESCRIPTION | 10 ++-- MD5 | 27 ++++++------ R/descrip.R | 13 +++++ R/descrip_utils.R | 50 ++++++++++++++--------- R/regress.R | 40 +++++++++++++----- R/regress_diagnostics_TODO.R |only R/regress_utils.R | 1 README.md | 11 ++++- build/vignette.rds |binary inst/doc/descrip_intro.html | 63 +++++++++++++++-------------- inst/doc/one_and_two_sample_inference.html | 9 ++-- inst/doc/regress_intro.html | 9 ++-- tests/testthat/test_descrip.R | 13 +---- tests/testthat/test_regress.R | 8 +++ tests/testthat/test_wilcoxon.R | 30 ++++++------- 15 files changed, 174 insertions(+), 110 deletions(-)
Title: Calculate (Stratified) Percentiles
Description: Calculate (stratified) percentiles on a data.frame
Stratification will split the data.frame into subgroups and calculate percentiles for each independently.
Author: Dr J. Peter Amin Marquardt [aut, cre]
Maintainer: Dr J. Peter Amin Marquardt <peter@kmarquardt.de>
This is a re-admission after prior archival of version 0.2.2 dated 2021-04-08
Diff between percentiles versions 0.2.2 dated 2021-04-08 and 0.2.3 dated 2026-04-03
DESCRIPTION | 21 ++++++++++++------- MD5 | 14 ++++++------ NAMESPACE | 1 NEWS.md | 4 +-- R/Stratified_percentile_calculator.R | 9 +++----- R/calculate_percentiles.R | 8 ++----- man/Stratified_percentile_calculator_generator.Rd | 24 +++++++++++----------- man/calculate_percentiles.Rd | 5 ++++ 8 files changed, 47 insertions(+), 39 deletions(-)
Title: Regression Models and Utilities for Repeated Measures and Panel
Data
Description: Provides an object type and associated tools for storing and
wrangling panel data. Implements several methods for creating regression
models that take advantage of the unique aspects of
panel data. Among other capabilities, automates the "within-between"
(also known as "between-within" and "hybrid") panel regression specification
that combines the desirable aspects of both fixed effects and random effects
econometric models and fits them as multilevel models
(Allison, 2009 <doi:10.4135/9781412993869.d33>;
Bell & Jones, 2015 <doi:10.1017/psrm.2014.7>). These models can also be
estimated via generalized estimating equations
(GEE; McNeish, 2019 <doi:10.1080/00273171.2019.1602504>) and Bayesian
estimation is (optionally) supported via 'Stan'.
Supports estimation of asymmetric effects models via first differences
(Allison, 2019 <doi:10.1177/2378023119826441>) as well as a generalized
linear model extension thereof using GEE.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <jacob.long@sc.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2026-01-21
Diff between panelr versions 1.0.0 dated 2026-01-21 and 1.0.1 dated 2026-04-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ inst/doc/reshape.html | 4 ++-- inst/doc/wbm.html | 4 ++-- tests/testthat/test-utils.R | 18 +++++------------- 6 files changed, 25 insertions(+), 25 deletions(-)
Title: Interface Tools for 'LSD' Simulation Results Files
Description: Interfaces 'R' with 'LSD' simulation models. Reads object-oriented data in results files (.res[.gz]) produced by 'LSD' and creates appropriate multi-dimensional arrays in 'R'. Supports multiple core parallel threads of multi-file data reading for increased performance. Also provides functions to extract basic information and statistics from data files. 'LSD' (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre]
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
This is a re-admission after prior archival of version 1.2.2 dated 2024-07-29
Diff between LSDinterface versions 1.2.2 dated 2024-07-29 and 1.2.5 dated 2026-04-03
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- R/info.R | 35 +++++++++++++++++++++-------------- build/partial.rdb |binary man/info.distance.lsd.Rd | 13 ++++++++----- man/list.files.lsd.Rd | 3 +-- 6 files changed, 44 insertions(+), 35 deletions(-)
Title: Query Data in 'Microsoft Fabric'
Description: Query data hosted in 'Microsoft Fabric'. Provides helpers to open 'DBI'
connections to 'SQL' endpoints of 'Lakehouse' and 'Data Warehouse' items; submit
'Data Analysis Expressions' ('DAX') queries to semantic model datasets in 'Microsoft
Fabric' and 'Power BI'; read 'Delta Lake' tables stored in 'OneLake'
('Azure Data Lake Storage Gen2'); and execute 'Spark' code via the 'Livy API'.
Author: Luka Koning [aut, cre, cph],
Kennispunt Twente [fnd]
Maintainer: Luka Koning <koningluka@gmail.com>
Diff between fabricQueryR versions 0.2.0 dated 2025-09-15 and 0.2.1 dated 2026-04-03
DESCRIPTION | 12 MD5 | 22 - NEWS.md | 25 - R/fabric_livy.R | 60 ++ R/fabric_onelake_read_delta_table.R | 592 +++++++++++++++-------------- R/fabric_pbi_dax_query.R | 27 - R/fabric_sql_connect.R | 11 R/httr2_helpers.R | 20 R/inform.R | 14 man/fabricQueryR-package.Rd | 2 man/fabric_onelake_read_delta_table.Rd | 26 + tests/testthat/test-fabric_pbi_dax_query.R | 7 12 files changed, 467 insertions(+), 351 deletions(-)
Title: Efficient Sampling for Gaussian Linear Regression with Arbitrary
Priors
Description: Efficient sampling for Gaussian linear regression with arbitrary priors, Hahn, He and Lopes (2018) <doi:10.48550/arXiv.1806.05738>.
Author: Jingyu He [aut, cre],
P. Richard Hahn [aut],
Hedibert Lopes [aut],
Andrew Herren [ctb]
Maintainer: Jingyu He <jingyuhe@cityu.edu.hk>
This is a re-admission after prior archival of version 1.0.1 dated 2022-06-27
Diff between bayeslm versions 1.0.1 dated 2022-06-27 and 2.0 dated 2026-04-03
DESCRIPTION | 10 MD5 | 63 ++-- R/RcppExports.R | 1 R/bayeslm.R | 4 R/bayeslm.default.R | 155 +++++------ R/bayeslm.formula.R | 161 +++++------ R/plot.mcmc.R | 164 ++++++----- R/predict.bayeslm.fit.R | 48 +-- R/summary.bayesm.fit.R | 10 R/summary.mcmc.R | 199 +++++++------- README.md | 2 build/vignette.rds |binary inst/doc/bayeslm_demo.R | 2 inst/doc/bayeslm_demo.html | 581 ++++++++++++++++++++++++++++------------- inst/include/bayeslm.h | 60 ++-- man/hs_gibbs.Rd | 2 man/predict.bayeslm.fit.Rd | 2 man/summary.bayeslm.fit.Rd | 2 man/summary.mcmc.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 389 ++++++++++++++------------- src/asymmetric.cpp | 279 ++++++++++++++----- src/bayeslm.cpp | 277 ++++++++++++++----- src/blasso.cpp | 301 +++++++++++++++------ src/gibbs.cpp | 32 +- src/gibbs_2.cpp | 46 +-- src/horseshoe.cpp | 282 ++++++++++++++------ src/inverseLaplace.cpp | 273 +++++++++++++------ src/nonlocal.cpp | 287 ++++++++++++++------ src/ridge.cpp | 297 +++++++++++++++------ src/utilityFunctions.cpp | 630 ++++++++++++++++++++++++++++++++------------- tools |only 33 files changed, 2949 insertions(+), 1614 deletions(-)
More information about multipleITScontrol at CRAN
Permanent link
Title: Flexible Modeling of Count Data
Description: For Bayesian and classical inference and prediction with count-valued data,
Simultaneous Transformation and Rounding (STAR) Models provide a flexible, interpretable,
and easy-to-use approach. STAR models the observed count data using a rounded
continuous data model and incorporates a transformation for greater flexibility.
Implicitly, STAR formalizes the commonly-applied yet incoherent procedure of
(i) transforming count-valued data and subsequently
(ii) modeling the transformed data using Gaussian models.
STAR is well-defined for count-valued data, which is reflected in predictive accuracy,
and is designed to account for zero-inflation, bounded or censored data, and over- or underdispersion.
Importantly, STAR is easy to combine with existing MCMC or point estimation
methods for continuous data, which allows seamless adaptation of continuous data
models (such as linear regressions, additive models, BART, random forests,
and gradient boosting machines) for count-valued data. The package [...truncated...]
Author: Brian King [aut, cre],
Dan Kowal [aut]
Maintainer: Brian King <brianking387@gmail.com>
Diff between countSTAR versions 1.0.2 dated 2023-06-30 and 1.2.0 dated 2026-04-03
countSTAR-1.0.2/countSTAR/man/blm_star_bnpgibbs.Rd |only countSTAR-1.0.2/countSTAR/man/g_bnp.Rd |only countSTAR-1.2.0/countSTAR/DESCRIPTION | 20 countSTAR-1.2.0/countSTAR/MD5 | 174 countSTAR-1.2.0/countSTAR/NAMESPACE | 21 countSTAR-1.2.0/countSTAR/NEWS.md | 30 countSTAR-1.2.0/countSTAR/R/RcppExports.R | 466 - countSTAR-1.2.0/countSTAR/R/STAR_Bayesian.R | 3142 +++---- countSTAR-1.2.0/countSTAR/R/STAR_frequentist.R | 3479 +++---- countSTAR-1.2.0/countSTAR/R/data.R | 30 countSTAR-1.2.0/countSTAR/R/helper_functions.R | 1606 +-- countSTAR-1.2.0/countSTAR/R/internal_functions.R | 7449 +++++++++-------- countSTAR-1.2.0/countSTAR/R/warpDLM.R | 479 - countSTAR-1.2.0/countSTAR/README.md | 144 countSTAR-1.2.0/countSTAR/build/partial.rdb |binary countSTAR-1.2.0/countSTAR/build/vignette.rds |binary countSTAR-1.2.0/countSTAR/inst/doc/countSTAR.R | 250 countSTAR-1.2.0/countSTAR/inst/doc/countSTAR.Rmd | 639 - countSTAR-1.2.0/countSTAR/inst/doc/countSTAR.html | 1782 ++-- countSTAR-1.2.0/countSTAR/man/BrentMethod.Rd | 62 countSTAR-1.2.0/countSTAR/man/HPDregion.Rd |only countSTAR-1.2.0/countSTAR/man/a_j.Rd | 64 countSTAR-1.2.0/countSTAR/man/bam_star.Rd | 278 countSTAR-1.2.0/countSTAR/man/bart_star.Rd | 382 countSTAR-1.2.0/countSTAR/man/bart_star_ispline.Rd | 215 countSTAR-1.2.0/countSTAR/man/blm_star.Rd | 276 countSTAR-1.2.0/countSTAR/man/blm_star_exact.Rd | 195 countSTAR-1.2.0/countSTAR/man/blm_star_exact_bnp.Rd |only countSTAR-1.2.0/countSTAR/man/blm_star_gibbs_bnp.Rd |only countSTAR-1.2.0/countSTAR/man/computeTimeRemaining.Rd | 48 countSTAR-1.2.0/countSTAR/man/confint.lmstar.Rd | 86 countSTAR-1.2.0/countSTAR/man/credBands.Rd | 48 countSTAR-1.2.0/countSTAR/man/ergMean.Rd | 56 countSTAR-1.2.0/countSTAR/man/expectation2_gRcpp.Rd | 60 countSTAR-1.2.0/countSTAR/man/expectation_gRcpp.Rd | 60 countSTAR-1.2.0/countSTAR/man/expectation_identity.Rd | 60 countSTAR-1.2.0/countSTAR/man/expectation_log.Rd | 60 countSTAR-1.2.0/countSTAR/man/expectation_sqrt.Rd | 60 countSTAR-1.2.0/countSTAR/man/g_bc.Rd | 70 countSTAR-1.2.0/countSTAR/man/g_cdf.Rd | 96 countSTAR-1.2.0/countSTAR/man/g_inv.Rd |only countSTAR-1.2.0/countSTAR/man/g_inv_approx.Rd | 76 countSTAR-1.2.0/countSTAR/man/g_inv_bc.Rd | 64 countSTAR-1.2.0/countSTAR/man/gbm_star.Rd | 277 countSTAR-1.2.0/countSTAR/man/genEM_star.Rd | 282 countSTAR-1.2.0/countSTAR/man/genMCMC_star.Rd | 299 countSTAR-1.2.0/countSTAR/man/genMCMC_star_ispline.Rd | 221 countSTAR-1.2.0/countSTAR/man/getEffSize.Rd | 57 countSTAR-1.2.0/countSTAR/man/init_bam_orthog.Rd | 84 countSTAR-1.2.0/countSTAR/man/init_bam_thin.Rd | 84 countSTAR-1.2.0/countSTAR/man/init_lm_gprior.Rd | 94 countSTAR-1.2.0/countSTAR/man/init_lm_hs.Rd | 86 countSTAR-1.2.0/countSTAR/man/init_lm_ridge.Rd | 78 countSTAR-1.2.0/countSTAR/man/init_params_mean.Rd | 56 countSTAR-1.2.0/countSTAR/man/interval_gRcpp.Rd | 64 countSTAR-1.2.0/countSTAR/man/invlogit.Rd | 36 countSTAR-1.2.0/countSTAR/man/lm_star.Rd | 212 countSTAR-1.2.0/countSTAR/man/logLikePointRcpp.Rd | 58 countSTAR-1.2.0/countSTAR/man/logLikeRcpp.Rd | 58 countSTAR-1.2.0/countSTAR/man/logit.Rd | 36 countSTAR-1.2.0/countSTAR/man/plot_coef.Rd | 62 countSTAR-1.2.0/countSTAR/man/plot_fitted.Rd | 54 countSTAR-1.2.0/countSTAR/man/plot_pmf.Rd | 54 countSTAR-1.2.0/countSTAR/man/pmaxRcpp.Rd | 46 countSTAR-1.2.0/countSTAR/man/pminRcpp.Rd | 46 countSTAR-1.2.0/countSTAR/man/predict.lmstar.Rd | 134 countSTAR-1.2.0/countSTAR/man/pvals.Rd | 72 countSTAR-1.2.0/countSTAR/man/randomForest_star.Rd | 276 countSTAR-1.2.0/countSTAR/man/rdir.Rd |only countSTAR-1.2.0/countSTAR/man/roaches.Rd | 2 countSTAR-1.2.0/countSTAR/man/round_floor.Rd | 62 countSTAR-1.2.0/countSTAR/man/rtruncnormRcpp.Rd | 64 countSTAR-1.2.0/countSTAR/man/sampleFastGaussian.Rd | 52 countSTAR-1.2.0/countSTAR/man/sample_bam_orthog.Rd | 128 countSTAR-1.2.0/countSTAR/man/sample_bam_thin.Rd | 128 countSTAR-1.2.0/countSTAR/man/sample_lm_gprior.Rd | 109 countSTAR-1.2.0/countSTAR/man/sample_lm_hs.Rd | 94 countSTAR-1.2.0/countSTAR/man/sample_lm_ridge.Rd | 90 countSTAR-1.2.0/countSTAR/man/sample_params_mean.Rd | 62 countSTAR-1.2.0/countSTAR/man/simBaS.Rd | 58 countSTAR-1.2.0/countSTAR/man/simulate_nb_friedman.Rd | 116 countSTAR-1.2.0/countSTAR/man/simulate_nb_lm.Rd | 132 countSTAR-1.2.0/countSTAR/man/splineBasis.Rd | 62 countSTAR-1.2.0/countSTAR/man/spline_star.Rd | 255 countSTAR-1.2.0/countSTAR/man/spline_star_exact.Rd | 178 countSTAR-1.2.0/countSTAR/man/spline_star_gibbs_bnp.Rd |only countSTAR-1.2.0/countSTAR/man/truncnorm_mom.Rd | 54 countSTAR-1.2.0/countSTAR/man/uni.slice.Rd | 72 countSTAR-1.2.0/countSTAR/man/update_struct.Rd | 52 countSTAR-1.2.0/countSTAR/man/warpDLM.Rd | 128 countSTAR-1.2.0/countSTAR/vignettes/countSTAR.Rmd | 639 - countSTAR-1.2.0/countSTAR/vignettes/refs.bib | 131 92 files changed, 14257 insertions(+), 13264 deletions(-)
Title: Access and Analysis of Brazilian CNEFE Address Data
Description: Download, cache and read municipality-level address data from the
Cadastro Nacional de Enderecos para Fins Estatisticos (CNEFE) of the 2022
Brazilian Census, published by the Instituto Brasileiro de Geografia e
Estatistica (IBGE)
<https://ftp.ibge.gov.br/Cadastro_Nacional_de_Enderecos_para_Fins_Estatisticos/>.
Beyond data access, provides spatial aggregation of addresses, computation
of land-use mix indices, and dasymetric interpolation of census tract
variables using CNEFE dwelling points as ancillary data. Results can be
produced on 'H3' hexagonal grids or user-supplied polygons, and heavy
operations leverage a 'DuckDB' backend with extensions for fast,
in-process execution.
Author: Jorge Ubirajara Pedreira Junior [aut, cre, cph] ,
Bruno Mioto [aut],
Kaio Cunha Pedreira [ctb]
Maintainer: Jorge Ubirajara Pedreira Junior <jorge.ubirajara@ufba.br>
This is a re-admission after prior archival of version 0.2.3 dated 2026-03-06
Diff between cnefetools versions 0.2.3 dated 2026-03-06 and 0.2.5 dated 2026-04-03
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++--------------- R/cnefe_counts.R | 13 +++++++++-- R/compute_lumi.R | 13 +++++++++-- R/read_cnefe.R | 4 +-- R/tracts_to_h3.R | 29 +++++++++++++++++------- R/tracts_to_polygon.R | 20 +++++++++++++++-- R/utils-internal.R | 11 ++++----- README.md | 35 +++++++++++++++++++++++++++++- man/cnefe_counts.Rd | 5 ++-- man/compute_lumi.Rd | 5 ++-- man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/read_cnefe.Rd | 4 +-- man/tracts_to_h3.Rd | 3 +- man/tracts_to_polygon.Rd | 3 +- 18 files changed, 133 insertions(+), 52 deletions(-)
Title: Progression Models for Repeated Measures
Description: A progression model for repeated measures (PMRM)
is a continuous-time nonlinear mixed-effects model for
longitudinal clinical trials in progressive diseases.
Unlike mixed models for repeated measures (MMRMs),
which estimate treatment effects as linear combinations
of additive effects on the outcome scale,
PMRMs characterize treatment effects
in terms of the underlying disease trajectory.
This framing yields clinically interpretable quantities
such as average time saved
and percent reduction in decline due to treatment.
This package implements frequentist PMRMs by
Raket (2022) <doi:10.1002/sim.9581> using
'RTMB' by Kristensen (2016) <doi:10.18637/jss.v070.i05>.
Author: William Michael Landau [aut, cre] ,
Lars Lau Raket [aut] ,
Kasper Kristensen [aut] ,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between pmrm versions 0.0.3 dated 2026-03-12 and 0.0.4 dated 2026-04-03
DESCRIPTION | 6 MD5 | 60 ++--- NAMESPACE | 1 NEWS.md | 6 R/fitted.R | 3 R/pmrm_constants.R | 4 R/pmrm_data.R | 2 R/pmrm_estimates.R | 2 R/pmrm_initial.R | 75 ++++++ R/pmrm_marginals.R | 15 - R/pmrm_model.R | 3 R/pmrm_objective.R | 19 + R/pmrm_package.R | 3 R/print.R | 4 R/vcov.R | 2 inst/doc/usage.html | 8 inst/doc/validation.html | 4 man/fitted.pmrm_fit.Rd | 13 - man/pmrm_marginals.Rd | 17 + man/pmrm_model.Rd | 2 man/pmrm_model_decline_nonproportional.Rd | 2 man/pmrm_model_decline_proportional.Rd | 2 man/pmrm_model_slowing_nonproportional.Rd | 2 man/pmrm_model_slowing_proportional.Rd | 2 man/print.pmrm_fit.Rd | 3 tests/testthat/test-pmrm_estimates.R | 24 +- tests/testthat/test-pmrm_marginals.R | 178 +++++---------- tests/testthat/test-pmrm_model_decline_proportional.R | 3 tests/testthat/test-pmrm_model_slowing_nonproportional.R | 3 vignettes/validation/coverage.png |binary vignettes/validation/version.csv | 2 31 files changed, 256 insertions(+), 214 deletions(-)
Title: Spatial Phylogenetic Analysis
Description: Analyze spatial phylogenetic diversity patterns.
Use your data on an evolutionary tree and geographic distributions of the
terminal taxa to compute diversity and endemism metrics, test significance
with null model randomization, analyze community turnover and biotic
regionalization, and perform spatial conservation prioritizations. All
functions support quantitative community data in addition to binary data.
Author: Matthew Kling [aut, cre, cph]
Maintainer: Matthew Kling <mattkling@berkeley.edu>
Diff between phylospatial versions 1.2.1 dated 2025-12-23 and 1.3.0 dated 2026-04-03
phylospatial-1.2.1/phylospatial/man/build_tree_ranges_fast.Rd |only phylospatial-1.3.0/phylospatial/DESCRIPTION | 9 phylospatial-1.3.0/phylospatial/MD5 | 75 - phylospatial-1.3.0/phylospatial/NAMESPACE | 2 phylospatial-1.3.0/phylospatial/NEWS.md | 24 phylospatial-1.3.0/phylospatial/R/moss.R | 13 phylospatial-1.3.0/phylospatial/R/phylospatial-methods.R | 3 phylospatial-1.3.0/phylospatial/R/phylospatial.R | 66 + phylospatial-1.3.0/phylospatial/R/ps_canape.R | 17 phylospatial-1.3.0/phylospatial/R/ps_dissim.R | 123 ++- phylospatial-1.3.0/phylospatial/R/ps_diversity.R | 75 - phylospatial-1.3.0/phylospatial/R/ps_geodist.R |only phylospatial-1.3.0/phylospatial/R/ps_ordinate.R | 39 phylospatial-1.3.0/phylospatial/R/ps_prioritize.R | 159 +-- phylospatial-1.3.0/phylospatial/R/ps_quantize.R | 29 phylospatial-1.3.0/phylospatial/R/ps_rand.R | 29 phylospatial-1.3.0/phylospatial/R/ps_regions.R | 38 phylospatial-1.3.0/phylospatial/R/utils.R | 404 +++++----- phylospatial-1.3.0/phylospatial/inst/doc/alpha-diversity.html | 8 phylospatial-1.3.0/phylospatial/inst/doc/beta-diversity.html | 10 phylospatial-1.3.0/phylospatial/inst/doc/phylospatial-data.Rmd | 8 phylospatial-1.3.0/phylospatial/inst/doc/phylospatial-data.html | 70 + phylospatial-1.3.0/phylospatial/inst/doc/prioritization.R | 4 phylospatial-1.3.0/phylospatial/inst/doc/prioritization.Rmd | 6 phylospatial-1.3.0/phylospatial/inst/doc/prioritization.html | 16 phylospatial-1.3.0/phylospatial/man/clade_dist.Rd | 2 phylospatial-1.3.0/phylospatial/man/figures/README-example-1.png |binary phylospatial-1.3.0/phylospatial/man/phylospatial.Rd | 25 phylospatial-1.3.0/phylospatial/man/ps_dissim.Rd | 14 phylospatial-1.3.0/phylospatial/man/ps_expand.Rd |only phylospatial-1.3.0/phylospatial/man/ps_geodist.Rd |only phylospatial-1.3.0/phylospatial/man/ps_get_comm.Rd | 8 phylospatial-1.3.0/phylospatial/man/to_spatial.Rd | 7 phylospatial-1.3.0/phylospatial/tests/testthat/test-phylospatial.R | 11 phylospatial-1.3.0/phylospatial/tests/testthat/test-ps_dissim.R | 72 + phylospatial-1.3.0/phylospatial/tests/testthat/test-ps_diversity.R | 40 phylospatial-1.3.0/phylospatial/tests/testthat/test-ps_geodist.R |only phylospatial-1.3.0/phylospatial/tests/testthat/test-ps_prioritize.R | 2 phylospatial-1.3.0/phylospatial/tests/testthat/test-utils.R | 11 phylospatial-1.3.0/phylospatial/vignettes/phylospatial-data.Rmd | 8 phylospatial-1.3.0/phylospatial/vignettes/prioritization.Rmd | 6 41 files changed, 818 insertions(+), 615 deletions(-)
Title: An Analyzer of International Large Scale Assessments in
Education
Description: An easy way to analyze international large-scale assessments and surveys in education or any other dataset that includes replicated weights (Balanced Repeated Replication (BRR) weights, Jackknife replicate weights,...) while also allowing for analysis with multiply imputed variables (plausible values). It supports the estimation of univariate statistics (e.g. mean, variance, standard deviation, quantiles), frequencies, correlation, linear regression and any other model already implemented in R that takes a data frame and weights as parameters. It also includes options to prepare the results for publication, following the table formatting standards of the Organization for Economic Cooperation and Development (OECD).
Author: Rodolfo Ilizaliturri [aut, cre],
Francesco Avvisati [aut],
Francois Keslair [aut]
Maintainer: Rodolfo Ilizaliturri <rodolfo.ilizaliturri@oecd.org>
Diff between Rrepest versions 1.6.11 dated 2026-02-03 and 1.6.12 dated 2026-04-03
DESCRIPTION | 6 ++-- MD5 | 50 ++++++++++++++++++------------------- R/average.R | 20 +++++++------- R/coverage_pct.R | 16 +++++------ R/flags.R | 1 R/n_obs_x.R | 10 ++----- R/pv_rrepest_gen.R | 19 +++++++------- R/repest_auxiliaries.R | 2 - R/rrepest.R | 43 ++++++++++++++----------------- R/weighted_correlation.R | 2 - R/weighted_covariance.R | 2 - R/weighted_multivariate_corr_cov.R | 2 - R/weighted_sdev.R | 2 - R/weighted_variance.R | 2 - data/df_pisa18.rda |binary data/df_talis18.rda |binary man/Rrepest.Rd | 43 ++++++++++++++----------------- man/average_groups.Rd | 20 +++++++------- man/coverage_pct.Rd | 16 +++++------ man/format_data_repest.Rd | 2 - man/n_obs_x.Rd | 10 ++----- man/weighted.corr.Rd | 2 - man/weighted.corr.cov.n.Rd | 2 - man/weighted.cov.Rd | 2 - man/weighted.std.Rd | 2 - man/weighted.var.Rd | 2 - 26 files changed, 133 insertions(+), 145 deletions(-)
Title: Multicore Multivariable Isotonic Regression
Description: Provides functions for isotonic regression and classification
when there are multiple independent variables. The functions solve the
optimization problem using a projective Bayes approach with recursive
sequential update algorithms, and are useful for situations with a
relatively large number of covariates. Supports binary outcomes via a
Beta-Binomial conjugate model ('miso', 'PBclassifier') and continuous
outcomes via a Normal-Inverse-Chi-Squared conjugate model ('misoN').
Parallel computing wrappers ('mcmiso', 'mcPBclassifier', 'mcmisoN') are
provided that run the down-up and up-down algorithms simultaneously and
return whichever finishes first. The estimation method follows the
projective Bayes solution described in Cheung and Diaz (2023)
<doi:10.1093/jrsssb/qkad014>.
Author: Cheung Ken [aut, cre]
Maintainer: Cheung Ken <yc632@cumc.columbia.edu>
Diff between McMiso versions 0.1.2 dated 2025-11-21 and 0.2.0 dated 2026-04-03
DESCRIPTION | 28 - MD5 | 18 NAMESPACE | 9 NEWS.md |only R/fun.R | 1218 ++++++++++++++++++++++++++++++++++++++++++-------- man/PBclassifier.Rd | 56 +- man/boundary.Rd |only man/mcPBclassifier.Rd |only man/mcmiso.Rd |only man/mcmisoN.Rd |only man/miso.Rd | 48 + man/misoN.Rd |only man/predict.pbc.Rd | 37 + 13 files changed, 1194 insertions(+), 220 deletions(-)
Title: Collection of Correlation and Association Estimators
Description: Compute correlation, association, and agreement measures for
small to high-dimensional datasets through a consistent matrix-oriented
interface. Supports classical correlations (Pearson, Spearman, Kendall),
distance correlation, partial correlation with regularised estimators,
shrinkage correlation for p >= n settings, robust correlations including
biweight mid-correlation, percentage-bend, and skipped correlation,
latent-variable methods for binary and ordinal data, repeated-measures
correlation, and agreement analyses based on Bland-Altman methods and
Lin's concordance correlation coefficient, including repeated-measures
extensions. Implemented with optimized C++ backends using BLAS/OpenMP and
memory-aware symmetric updates, and returns standard R objects with
print/summary/plot methods plus optional Shiny viewers for matrix
inspection. Methods based on Ledoit and Wolf (2004)
<doi:10.1016/S0047-259X(03)00096-4>; high-dimensional shrinkage covariance
estimation <doi:10.2202 [...truncated...]
Author: Thiago de Paula Oliveira [aut, cre]
Maintainer: Thiago de Paula Oliveira <thiago.paula.oliveira@gmail.com>
Diff between matrixCorr versions 0.8.5 dated 2026-03-20 and 0.10.0 dated 2026-04-03
matrixCorr-0.10.0/matrixCorr/DESCRIPTION | 47 matrixCorr-0.10.0/matrixCorr/MD5 | 165 matrixCorr-0.10.0/matrixCorr/NAMESPACE | 78 matrixCorr-0.10.0/matrixCorr/R/RcppExports.R | 86 matrixCorr-0.10.0/matrixCorr/R/ba.R |only matrixCorr-0.10.0/matrixCorr/R/ba_rm.R |only matrixCorr-0.10.0/matrixCorr/R/bicor.R |only matrixCorr-0.10.0/matrixCorr/R/ccc_repeated.R | 431 +- matrixCorr-0.10.0/matrixCorr/R/concordance_corr.R | 276 - matrixCorr-0.10.0/matrixCorr/R/dcor.R |only matrixCorr-0.10.0/matrixCorr/R/deprecated.R |only matrixCorr-0.10.0/matrixCorr/R/display_utils.R |only matrixCorr-0.10.0/matrixCorr/R/kendall_corr.R | 746 ++-- matrixCorr-0.10.0/matrixCorr/R/latent_corr.R |only matrixCorr-0.10.0/matrixCorr/R/matrixCorr-package.R | 50 matrixCorr-0.10.0/matrixCorr/R/pbcor.R |only matrixCorr-0.10.0/matrixCorr/R/pcorr.R |only matrixCorr-0.10.0/matrixCorr/R/pearson_corr.R | 455 +- matrixCorr-0.10.0/matrixCorr/R/rmcorr.R |only matrixCorr-0.10.0/matrixCorr/R/schafer_corr.R | 182 - matrixCorr-0.10.0/matrixCorr/R/skipcor.R |only matrixCorr-0.10.0/matrixCorr/R/spearman_rho.R | 718 ++-- matrixCorr-0.10.0/matrixCorr/R/view_corr_shiny.R | 1079 ++++-- matrixCorr-0.10.0/matrixCorr/R/view_rmcorr_shiny.R |only matrixCorr-0.10.0/matrixCorr/R/wincor.R |only matrixCorr-0.10.0/matrixCorr/README.md | 436 ++ matrixCorr-0.10.0/matrixCorr/inst/app-www |only matrixCorr-0.10.0/matrixCorr/man/ba.Rd |only matrixCorr-0.10.0/matrixCorr/man/ba_rm.Rd |only matrixCorr-0.10.0/matrixCorr/man/bicor.Rd |only matrixCorr-0.10.0/matrixCorr/man/biserial.Rd |only matrixCorr-0.10.0/matrixCorr/man/ccc.Rd | 57 matrixCorr-0.10.0/matrixCorr/man/ccc_rm_reml.Rd |only matrixCorr-0.10.0/matrixCorr/man/ccc_rm_ustat.Rd |only matrixCorr-0.10.0/matrixCorr/man/dcor.Rd |only matrixCorr-0.10.0/matrixCorr/man/deprecated-matrixCorr.Rd |only matrixCorr-0.10.0/matrixCorr/man/dot-ba_rep_two_methods.Rd | 4 matrixCorr-0.10.0/matrixCorr/man/figures |only matrixCorr-0.10.0/matrixCorr/man/kendall_tau.Rd | 447 +- matrixCorr-0.10.0/matrixCorr/man/matrixCorr-internal.Rd | 20 matrixCorr-0.10.0/matrixCorr/man/matrixCorr-package.Rd |only matrixCorr-0.10.0/matrixCorr/man/pbcor.Rd |only matrixCorr-0.10.0/matrixCorr/man/pcorr.Rd |only matrixCorr-0.10.0/matrixCorr/man/pearson_corr.Rd | 115 matrixCorr-0.10.0/matrixCorr/man/polychoric.Rd |only matrixCorr-0.10.0/matrixCorr/man/polyserial.Rd |only matrixCorr-0.10.0/matrixCorr/man/print.matrixCorr_ccc.Rd | 23 matrixCorr-0.10.0/matrixCorr/man/print.summary_corr_matrix.Rd |only matrixCorr-0.10.0/matrixCorr/man/print.summary_latent_corr.Rd |only matrixCorr-0.10.0/matrixCorr/man/rmcorr.Rd |only matrixCorr-0.10.0/matrixCorr/man/rmcorr_matrix_methods.Rd |only matrixCorr-0.10.0/matrixCorr/man/rmcorr_methods.Rd |only matrixCorr-0.10.0/matrixCorr/man/schafer_corr.Rd | 72 matrixCorr-0.10.0/matrixCorr/man/skipped_corr.Rd |only matrixCorr-0.10.0/matrixCorr/man/spearman_rho.Rd | 478 +- matrixCorr-0.10.0/matrixCorr/man/summary.ccc_rm_reml.Rd |only matrixCorr-0.10.0/matrixCorr/man/tetrachoric.Rd |only matrixCorr-0.10.0/matrixCorr/man/view_corr_shiny.Rd | 5 matrixCorr-0.10.0/matrixCorr/man/view_rmcorr_shiny.Rd |only matrixCorr-0.10.0/matrixCorr/man/wincor.Rd |only matrixCorr-0.10.0/matrixCorr/src/RcppExports.cpp | 291 + matrixCorr-0.10.0/matrixCorr/src/biweight_mid_corr.cpp | 64 matrixCorr-0.10.0/matrixCorr/src/bland_altman.cpp | 10 matrixCorr-0.10.0/matrixCorr/src/bland_altman_repeated.cpp | 1761 +++++++--- matrixCorr-0.10.0/matrixCorr/src/ccc_repeated.cpp | 4 matrixCorr-0.10.0/matrixCorr/src/ccc_repeated_mixed_model.cpp | 52 matrixCorr-0.10.0/matrixCorr/src/distance_correlation.cpp | 4 matrixCorr-0.10.0/matrixCorr/src/kendall_corr.cpp | 611 +++ matrixCorr-0.10.0/matrixCorr/src/matrixCorr_detail.h | 453 ++ matrixCorr-0.10.0/matrixCorr/src/matrixCorr_omp.h |only matrixCorr-0.10.0/matrixCorr/src/partial_correlation.cpp | 180 - matrixCorr-0.10.0/matrixCorr/src/pearson.cpp | 195 + matrixCorr-0.10.0/matrixCorr/src/rmcorr.cpp |only matrixCorr-0.10.0/matrixCorr/src/robust_correlations.cpp |only matrixCorr-0.10.0/matrixCorr/src/spearman.cpp | 371 +- matrixCorr-0.10.0/matrixCorr/src/tetrachoric.cpp | 953 ++++- matrixCorr-0.10.0/matrixCorr/src/validate_corr_input.cpp | 1 matrixCorr-0.10.0/matrixCorr/tests/testthat/test_bicor.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_bland_altman.R | 105 matrixCorr-0.10.0/matrixCorr/tests/testthat/test_bland_altman_repeated.R | 632 +++ matrixCorr-0.10.0/matrixCorr/tests/testthat/test_ccc_repeated.R | 250 + matrixCorr-0.10.0/matrixCorr/tests/testthat/test_dcor.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_deprecated_api.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_display_methods.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_kendall.R | 732 +++- matrixCorr-0.10.0/matrixCorr/tests/testthat/test_latent_corr.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_pcorr.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_pearson_corr.R | 82 matrixCorr-0.10.0/matrixCorr/tests/testthat/test_rmcorr.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_robust_extra.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_schafer_corr.R | 234 + matrixCorr-0.10.0/matrixCorr/tests/testthat/test_spearman_rho.R | 185 + matrixCorr-0.10.0/matrixCorr/tests/testthat/test_summary_methods.R |only matrixCorr-0.10.0/matrixCorr/tests/testthat/test_view_corr_shiny.R | 154 matrixCorr-0.10.0/matrixCorr/tests/testthat/test_view_rmcorr_shiny.R |only matrixCorr-0.8.5/matrixCorr/R/biweight_mid_corr.R |only matrixCorr-0.8.5/matrixCorr/R/bland_altman.R |only matrixCorr-0.8.5/matrixCorr/R/bland_altman_repeated.R |only matrixCorr-0.8.5/matrixCorr/R/distance_corr.R |only matrixCorr-0.8.5/matrixCorr/R/partial_correlation.R |only matrixCorr-0.8.5/matrixCorr/man/biweight_mid_corr.Rd |only matrixCorr-0.8.5/matrixCorr/man/bland_altman.Rd |only matrixCorr-0.8.5/matrixCorr/man/bland_altman_repeated.Rd |only matrixCorr-0.8.5/matrixCorr/man/ccc_lmm_reml.Rd |only matrixCorr-0.8.5/matrixCorr/man/ccc_pairwise_u_stat.Rd |only matrixCorr-0.8.5/matrixCorr/man/distance_corr.Rd |only matrixCorr-0.8.5/matrixCorr/man/partial_correlation.Rd |only matrixCorr-0.8.5/matrixCorr/man/summary.ccc_lmm_reml.Rd |only matrixCorr-0.8.5/matrixCorr/tests/testthat/test_biweight_mid_corr.R |only matrixCorr-0.8.5/matrixCorr/tests/testthat/test_distance_corr.R |only matrixCorr-0.8.5/matrixCorr/tests/testthat/test_partial_correlation.R |only matrixCorr-0.8.5/matrixCorr/tests/testthat/tests_partial_correlation.R |only matrixCorr-0.8.5/matrixCorr/tests/testthat/tests_schafer_corr.R |only 113 files changed, 10194 insertions(+), 3100 deletions(-)
Title: Unified Interface for Machine Learning Models
Description: Provides a unified R6-based interface for various machine learning models with automatic interface detection, consistent cross-validation, model interpretations via numerical derivatives, and visualization. Supports both regression and classification tasks with any model function that follows R's standard modeling conventions (formula or matrix interface).
Author: T. Moudiki [aut, cre]
Maintainer: T. Moudiki <thierry.moudiki@gmail.com>
Diff between unifiedml versions 0.2.0 dated 2026-01-10 and 0.2.1 dated 2026-04-03
unifiedml-0.2.0/unifiedml/R/RcppExports.R |only unifiedml-0.2.0/unifiedml/R/matrix-vs-formula-interface.R |only unifiedml-0.2.0/unifiedml/man/print.model_adapter.Rd |only unifiedml-0.2.0/unifiedml/man/rcpp_hello_world.Rd |only unifiedml-0.2.0/unifiedml/src |only unifiedml-0.2.0/unifiedml/vignettes/booster.html |only unifiedml-0.2.1/unifiedml/DESCRIPTION | 9 unifiedml-0.2.1/unifiedml/MD5 | 47 +- unifiedml-0.2.1/unifiedml/NAMESPACE | 7 unifiedml-0.2.1/unifiedml/NEWS.md | 7 unifiedml-0.2.1/unifiedml/R/cross_val_score.R |only unifiedml-0.2.1/unifiedml/R/interface_to_interface.R |only unifiedml-0.2.1/unifiedml/R/model.R | 214 ------------- unifiedml-0.2.1/unifiedml/README.md | 11 unifiedml-0.2.1/unifiedml/build/partial.rdb |binary unifiedml-0.2.1/unifiedml/build/vignette.rds |binary unifiedml-0.2.1/unifiedml/inst/doc/formula_vs_matrix.R | 2 unifiedml-0.2.1/unifiedml/inst/doc/formula_vs_matrix.Rmd | 7 unifiedml-0.2.1/unifiedml/inst/doc/formula_vs_matrix.html | 6 unifiedml-0.2.1/unifiedml/inst/doc/unifiedml-vignette.R | 39 ++ unifiedml-0.2.1/unifiedml/inst/doc/unifiedml-vignette.Rmd | 39 ++ unifiedml-0.2.1/unifiedml/inst/doc/unifiedml-vignette.html | 140 +++++++- unifiedml-0.2.1/unifiedml/man/Model.Rd | 4 unifiedml-0.2.1/unifiedml/man/cross_val_score.Rd | 2 unifiedml-0.2.1/unifiedml/man/formula_to_matrix.Rd | 37 +- unifiedml-0.2.1/unifiedml/man/matrix_to_formula.Rd | 51 ++- unifiedml-0.2.1/unifiedml/vignettes/formula_vs_matrix.Rmd | 7 unifiedml-0.2.1/unifiedml/vignettes/unifiedml-vignette.Rmd | 39 ++ 28 files changed, 348 insertions(+), 320 deletions(-)
More information about OdysseusSurvivalModule at CRAN
Permanent link
Title: Logic Forest
Description: Logic Forest is an ensemble machine learning method that identifies important and interpretable combinations of binary predictors using logic regression trees to model complex relationships with an outcome. Wolf, B.J., Slate, E.H., Hill, E.G. (2010) <doi:10.1093/bioinformatics/btq354>.
Author: Bethany Wolf [aut],
Melica Nikahd [ctb, cre],
Andrew Gothard [ctb],
Madison Hyer [ctb]
Maintainer: Melica Nikahd <melica.nikahd@osumc.edu>
Diff between LogicForest versions 2.1.3 dated 2026-02-13 and 2.1.4 dated 2026-04-03
DESCRIPTION | 6 MD5 | 8 R/pimp.import.R | 450 +++++++++++++++++++++++++++---------------------------- R/prime.imp.R | 137 ++++++++-------- man/prime.imp.Rd | 17 +- 5 files changed, 314 insertions(+), 304 deletions(-)
Title: Plotting Tool for Brain Atlases
Description: Provides a 'ggplot2' geom and position for visualizing brain
region data on cortical, subcortical, and white matter tract atlases.
Brain atlas geometries are stored as simple features ('sf'), enabling
seamless integration with the 'ggplot2' ecosystem including faceting,
custom scales, and themes. Mowinckel & Vidal-Piñeiro (2020)
<doi:10.1177/2515245920928009>.
Author: Athanasia Mo Mowinckel [aut, cre, cph] ,
Didac Vidal-Pineiro [aut, cph] ,
Ramiro Magno [aut] ,
Center for Lifespan Changes in Brain and Cognition, University of Oslo,
Norway [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg versions 2.0.0 dated 2026-02-19 and 2.1.0 dated 2026-04-03
DESCRIPTION | 22 ++++--- LICENSE | 2 MD5 | 39 ++++++------- NAMESPACE | 25 +++----- NEWS.md | 7 ++ R/adapt_scales.R | 101 +++++++++++++++++---------------- R/brain_join.R | 2 R/coord-funcs.R | 113 -------------------------------------- R/coords.R | 41 ------------- R/ggseg-package.R | 8 ++ R/scale-brain.R | 4 + README.md | 2 inst/WORDLIST | 21 +++---- inst/doc/external-data.html | 8 +- inst/doc/ggseg.html | 18 +++--- inst/doc/positioning-views.html | 6 +- man/ggseg.Rd | 9 ++- man/scale_brain2-deprecated.Rd | 3 + tests/testthat/Rplots.pdf |only tests/testthat/test-coord-funcs.R | 54 +----------------- tests/testthat/test-coords.R | 26 -------- 21 files changed, 154 insertions(+), 357 deletions(-)
Title: Cluster Analysis with Missing Values by Multiple Imputation
Description: Allows clustering of incomplete observations by addressing missing values using multiple imputation. For achieving this goal, the methodology consists in three steps, following Audigier and Niang 2022 <doi:10.1007/s11634-022-00519-1>. I) Missing data imputation using dedicated models. Four multiple imputation methods are proposed, two are based on joint modelling and two are fully sequential methods, as discussed in Audigier et al. (2021) <doi:10.48550/arXiv.2106.04424>. II) cluster analysis of imputed data sets. Six clustering methods are available (distances-based or model-based), but custom methods can also be easily used. III) Partition pooling. The set of partitions is aggregated using Non-negative Matrix Factorization based method. An associated instability measure is computed by bootstrap (see Fang, Y. and Wang, J., 2012 <doi:10.1016/j.csda.2011.09.003>). Among applications, this instability measure can be used to choose a number of clusters with missing value [...truncated...]
Author: Vincent Audigier [aut, cre] ,
Hang Joon Kim [ctb]
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between clusterMI versions 1.5 dated 2025-02-24 and 1.6 dated 2026-04-03
DESCRIPTION | 10 +++---- MD5 | 25 +++++++++-------- NAMESPACE | 1 R/ca.intern.R |only R/choosem.R | 19 ++++++++++--- R/choosenbclust.R | 20 +++++++++----- R/fastnmf.R | 14 +++++---- R/initfastnmf.intern.R | 65 +++++++++++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/clusterMI.pdf |binary man/choosem.Rd | 2 - man/choosenbclust.Rd | 2 - man/fastnmf.Rd | 6 ++-- man/initfastnmf.intern.Rd | 2 - 14 files changed, 106 insertions(+), 60 deletions(-)
Title: Spatial Parallel Computing by Hierarchical Data Partitioning
Description: Geospatial data computation is parallelized by grid, hierarchy,
or raster files. Based on 'future' (Bengtsson, 2024 <doi:10.32614/CRAN.package.future>)
and 'mirai' (Gao et al., 2025 <doi:10.32614/CRAN.package.mirai>) parallel back-ends,
'terra' (Hijmans et al., 2025 <doi:10.32614/CRAN.package.terra>) and
'sf' (Pebesma et al., 2024 <doi:10.32614/CRAN.package.sf>)
functions as well as convenience functions in the package can be distributed
over multiple threads. The simplest way of parallelizing generic geospatial
computation is to start from par_pad_*() functions to par_grid(),
par_hierarchy(), or par_multirasters() functions. Virtually any functions
accepting classes in 'terra' or 'sf' packages can be used in the three
parallelization functions. A common raster-vector overlay operation
is provided as a function extract_at(), which uses
'exactextractr' (Baston, 2023 <doi:10.32614/CRAN.package.exactextractr>), with
options for kernel weights for summarizing [...truncated...]
Author: Insang Song [aut, cre] ,
Kyle Messier [aut, ctb] ,
Alec L. Robitaille [rev] ,
Eric R. Scott [rev]
Maintainer: Insang Song <geoissong@gmail.com>
Diff between chopin versions 0.9.9 dated 2025-09-10 and 0.9.9-5 dated 2026-04-03
DESCRIPTION | 8 MD5 | 30 +-- NAMESPACE | 3 NEWS.md | 3 R/gridding.R | 10 + R/processing.R | 364 +++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/v01_start.html | 70 +++---- inst/doc/v03_par_pad_grid.html | 32 +-- man/extract_at.Rd | 4 man/kernelfunction.Rd | 4 man/par_make_h3.Rd | 2 man/summarize_aw.Rd | 4 man/summarize_pp.Rd |only man/summarize_sedc.Rd | 4 man/summarize_st.Rd |only 17 files changed, 463 insertions(+), 75 deletions(-)
Title: A Blazing Fast Implementation of Random Forest
Description: Yet another implementation of the Random Forest method by Breiman (2001) <doi:10.1023/A:1010933404324>, written in Rust and tailored towards stability, correctness, efficiency and scalability on modern multi-core machines.
Handles both classification and regression, as well as provides permutation feature importance via a novel, highly optimised algorithm.
Author: Miron Bartosz Kursa [aut, cre] ,
Krzysztof Piotr Piwonski [aut]
Maintainer: Miron Bartosz Kursa <m@mbq.me>
Diff between fru versions 0.0.4 dated 2026-03-21 and 0.0.5 dated 2026-04-03
fru-0.0.4/fru/src/fru/vendor.tar.xz |only fru-0.0.5/fru/DESCRIPTION | 6 +- fru-0.0.5/fru/MD5 | 19 +++---- fru-0.0.5/fru/inst/NEWS | 7 ++ fru-0.0.5/fru/src/fru/Cargo.lock | 4 - fru-0.0.5/fru/src/fru/src/attribute.rs | 1 fru-0.0.5/fru/src/fru/src/classification.rs | 42 ---------------- fru-0.0.5/fru/src/fru/src/classification/impurity.rs | 46 ++---------------- fru-0.0.5/fru/src/fru/src/lib.rs | 1 fru-0.0.5/fru/src/fru/src/regression.rs | 47 +------------------ fru-0.0.5/fru/src/fru/src/regression/impurity.rs | 47 ++----------------- 11 files changed, 37 insertions(+), 183 deletions(-)
Title: Statistics for International Large-Scale Assessments (ILSA)
Description: Calculates point estimates and standard errors using replicate weights and plausible values for International Large-Scale Assessments (ILSA), including: means, proportions, quantiles, correlations, singlelevel regressions, and multilevel regressions.
Author: Andres Christiansen [aut, cre] ,
Andres Strello [ctb]
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Diff between ILSAstats versions 0.4.4 dated 2026-03-13 and 0.4.5 dated 2026-04-03
DESCRIPTION | 11 MD5 | 118 ++++-- NAMESPACE | 11 NEWS.md | 12 R/WeMixPV.R | 16 R/argchecks.R | 4 R/autoILSA.R |only R/internal.R | 201 +++++++++++ R/leaguetable.R | 80 ++-- R/lmerPV.R | 22 - R/proflevels.R | 210 ++++++++++- R/proflevels.get.R | 35 - R/repcreate.R | 152 ++------ R/repglm.R | 12 R/replm.R | 14 R/repmean.R | 653 ++++++++++--------------------------- R/repmeanCI.R | 18 - R/repmeandif.R | 80 ++++ R/repmeanfast.R |only R/repmeanslow.R |only R/repprop.R | 346 ++++++------------- R/repquant.R | 61 ++- R/reprho.R | 34 + R/repse.R | 45 +- R/repsetup.R | 72 +++- README.md |only build |only data/ILSAinfo.RData |binary inst/doc |only inst/examples/repglm_example.R | 106 ------ inst/examples/repmeanCI_example.R | 8 inst/examples/repmean_example.R | 18 - inst/examples/repmeandif_example.R | 8 inst/examples/repquant_example.R | 7 man/WeMixPV.Rd | 13 man/autoILSA.Rd |only man/leaguetable.Rd | 11 man/lmerPV.Rd | 4 man/prepILSA.Rd | 7 man/proflevels.Rd | 16 man/proflevels.get.Rd | 7 man/repcreate.Rd | 18 - man/repglm.Rd | 163 ++------- man/repmean.Rd | 38 +- man/repmeanCI.Rd | 8 man/repmeandif.Rd | 11 man/repprop.Rd | 7 man/repquant.Rd | 11 man/repse.Rd | 9 man/repsetup.Rd | 24 + vignettes |only 51 files changed, 1379 insertions(+), 1322 deletions(-)
More information about seroreconstruct at CRAN
Permanent link
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.8.5 dated 2026-04-02 and 1.8.6 dated 2026-04-03
DESCRIPTION | 6 ++-- MD5 | 10 +++---- R/las_specifications.r | 48 +++++++++++++++++++++---------------- src/LASlib/lasreader_bin.cpp | 18 ++++++------- src/LASlib/laswaveform13writer.cpp | 4 +-- src/LASzip/mydefs.hpp | 2 - 6 files changed, 48 insertions(+), 40 deletions(-)
Title: High Dimensional Time Series Analysis Tools
Description: An implementation for high-dimensional time series analysis methods, including factor model for vector time series
proposed by Lam and Yao (2012) <doi:10.1214/12-AOS970> and Chang, Guo and Yao (2015)
<doi:10.1016/j.jeconom.2015.03.024>, martingale difference test proposed by
Chang, Jiang and Shao (2023) <doi:10.1016/j.jeconom.2022.09.001>, principal
component analysis for vector time series proposed by Chang, Guo and Yao (2018) <doi:10.1214/17-AOS1613>,
cointegration analysis proposed by Zhang, Robinson and Yao (2019)
<doi:10.1080/01621459.2018.1458620>, unit root test proposed by Chang, Cheng and Yao (2022)
<doi:10.1093/biomet/asab034>, white noise tests proposed by Chang, Yao and Zhou (2017)
<doi:10.1093/biomet/asw066> and Chang et al. (2026+), CP-decomposition for matrix time
series proposed by Chang et al. (2023) <doi:10.1093/jrsssb/qkac011> and
Chang et al. (2026+) <doi:10.48550/arXiv.2410.05634>, and statistical inference for
[...truncated...]
Author: Jinyuan Chang [aut],
Jing He [aut],
Chen Lin [aut, cre],
Qiwei Yao [aut]
Maintainer: Chen Lin <linchen@smail.swufe.edu.cn>
Diff between HDTSA versions 1.0.5-1 dated 2025-01-27 and 1.0.6 dated 2026-04-03
DESCRIPTION | 20 ++--- MD5 | 40 +++++------ R/CP_functions_unified.R | 6 - R/HDSreg.R | 10 +- R/HDTSA-package.R | 34 ++++----- R/RcppExports.R | 4 + R/Tools_SpecTest.R | 10 +- R/tools_wntest.R | 168 ++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary data/FamaFrench.rda |binary data/IPindices.rda |binary data/QWIdata.rda |binary man/CP_MTS.Rd | 6 - man/HDTSA-package.Rd | 32 +++----- man/SpecMulTest.Rd | 5 - man/SpecTest.Rd | 5 - man/WN_test.Rd | 48 +++++++++---- src/Makevars | 1 src/Makevars.win | 2 src/RcppExports.cpp | 17 ++++ src/WNtest.cpp | 45 ++++++++++++ 21 files changed, 293 insertions(+), 160 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like
objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] ,
Romain Francois [aut] ,
Lionel Henry [aut],
Kirill Mueller [aut] ,
Davis Vaughan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between dplyr versions 1.2.0 dated 2026-02-03 and 1.2.1 dated 2026-04-03
DESCRIPTION | 6 +- MD5 | 88 ++++++++++++++++----------------- NEWS.md | 4 + R/data-mask.R | 6 +- build/stage23.rdb |binary inst/doc/base.R | 17 +++--- inst/doc/base.Rmd | 18 ++++-- inst/doc/base.html | 97 ++++++++++++++++++------------------ inst/doc/colwise.R | 57 ++++++++++++++------- inst/doc/colwise.Rmd | 57 ++++++++++++++------- inst/doc/colwise.html | 101 ++++++++++++++++++++++---------------- inst/doc/dplyr.R | 6 +- inst/doc/dplyr.Rmd | 6 +- inst/doc/dplyr.html | 42 ++++++++------- inst/doc/grouping.R | 2 inst/doc/grouping.Rmd | 4 + inst/doc/grouping.html | 2 inst/doc/programming.R | 29 ++++++---- inst/doc/programming.Rmd | 29 ++++++---- inst/doc/programming.html | 101 +++++++++++++++++++------------------- inst/doc/rowwise.R | 26 ++++----- inst/doc/rowwise.Rmd | 26 ++++----- inst/doc/rowwise.html | 18 +++--- inst/doc/window-functions.R | 2 inst/doc/window-functions.Rmd | 2 inst/doc/window-functions.html | 2 src/chop.cpp | 99 +++++++++++++++++++++++++------------ src/dplyr.h | 41 ++++++++++----- src/filter.cpp | 14 ++++- src/imports.cpp | 10 +-- src/init.cpp | 9 +-- src/mask.cpp | 16 +++--- src/mutate.cpp | 9 +++ src/slice.cpp | 9 +++ src/summarise.cpp | 9 +++ src/utils.h | 36 ++++++++++++- tests/testthat/test-across.R | 12 +++- tests/testthat/test-count-tally.R | 18 +++++- vignettes/base.Rmd | 18 ++++-- vignettes/colwise.Rmd | 57 ++++++++++++++------- vignettes/dplyr.Rmd | 6 +- vignettes/grouping.Rmd | 4 + vignettes/programming.Rmd | 29 ++++++---- vignettes/rowwise.Rmd | 26 ++++----- vignettes/window-functions.Rmd | 2 45 files changed, 710 insertions(+), 462 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-01 1.6
2020-05-18 1.5.3
2019-07-22 1.5.2
2019-03-25 1.5.1
2019-02-14 1.5
2019-01-12 1.4
2018-10-14 1.2
2018-08-28 1.0
2018-07-27 0.9
2018-07-16 0.8
2018-05-06 0.7
2018-02-16 0.6
2017-12-07 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-06 3.10.1
2025-03-01 3.10.0
2024-05-29 3.9.4
2024-04-24 3.9.3
Title: Trust, but Verify
Description: Declarative template-based framework for verifying that objects
meet structural requirements, and auto-composing error messages when they do
not.
Author: Brodie Gaslam [aut, cre],
Paxdiablo [cph] ,
R Core Team [cph] ,
Michael Chirico [ctb]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between vetr versions 0.2.20 dated 2026-01-23 and 0.2.21 dated 2026-04-03
DESCRIPTION | 6 ++-- MD5 | 30 ++++++++++---------- NEWS.md | 5 +++ build/vignette.rds |binary inst/doc/alike.html | 12 ++++---- inst/doc/vetr.html | 10 +++--- src/alike.c | 22 ++++++--------- src/backports.c | 43 +++++++++++++++++++++++++++--- src/backports.h | 7 ++++ src/init.c | 12 +++++++- src/lang.c | 5 ++- src/parse.c | 4 ++ src/r-copied.c | 32 ++++++++++++---------- src/validate.h | 1 tests/unitizer/internal.R | 7 ++-- tests/unitizer/internal.unitizer/data.rds |binary 16 files changed, 129 insertions(+), 67 deletions(-)
Title: Bindings to 'Tree-Sitter'
Description: Provides bindings to 'Tree-sitter', an incremental parsing
system for programming tools. 'Tree-sitter' builds concrete syntax
trees for source files of any language, and can efficiently update
those syntax trees as the source file is edited. It also includes a
robust error recovery system that provides useful parse results even
in the presence of syntax errors.
Author: Davis Vaughan [aut, cre],
Posit Software, PBC [cph, fnd],
Tree-sitter authors [cph]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between treesitter versions 0.3.1 dated 2026-01-13 and 0.3.2 dated 2026-04-03
DESCRIPTION | 8 - MD5 | 147 +++++++++++----------- NEWS.md | 4 man/TreeCursor.Rd | 2 man/is_language.Rd | 2 man/is_node.Rd | 2 man/is_parser.Rd | 2 man/is_query.Rd | 2 man/is_tree.Rd | 2 man/language_field_count.Rd | 2 man/language_field_id_for_name.Rd | 2 man/language_field_name_for_id.Rd | 2 man/language_name.Rd | 2 man/language_next_state.Rd | 2 man/language_state_count.Rd | 2 man/language_symbol_count.Rd | 2 man/language_symbol_for_name.Rd | 2 man/language_symbol_name.Rd | 2 man/node-child-by-field.Rd | 2 man/node-child-count.Rd | 2 man/node-child.Rd | 2 man/node-children.Rd | 2 man/node-descendant.Rd | 2 man/node-field-name-for-child.Rd | 2 man/node-first-child-byte.Rd | 2 man/node-grammar.Rd | 2 man/node-location.Rd | 2 man/node-metadata.Rd | 2 man/node-parse-state.Rd | 2 man/node-sibling.Rd | 2 man/node_descendant_count.Rd | 2 man/node_language.Rd | 2 man/node_parent.Rd | 2 man/node_raw_s_expression.Rd | 2 man/node_show_s_expression.Rd | 2 man/node_symbol.Rd | 2 man/node_text.Rd | 2 man/node_type.Rd | 2 man/node_walk.Rd | 2 man/parser-adjustments.Rd | 2 man/parser-parse.Rd | 2 man/parser.Rd | 2 man/query-accessors.Rd | 2 man/query-matches-and-captures.Rd | 2 man/query.Rd | 2 man/text_parse.Rd | 2 man/tree-accessors.Rd | 2 man/tree_root_node.Rd | 2 man/tree_root_node_with_offset.Rd | 2 man/tree_walk.Rd | 2 src/node.c | 8 - src/query-matches.c | 6 src/rlang/attrib.c | 125 +++--------------- src/rlang/attrib.h | 68 ++++------ src/rlang/cnd.c | 2 src/rlang/debug.c | 2 src/rlang/decl/env-binding-decl.h |only src/rlang/decl/env-decl.h | 7 - src/rlang/decl/walk-decl.h | 2 src/rlang/dots-info.c |only src/rlang/dots-info.h |only src/rlang/dyn-array.c | 15 -- src/rlang/env-binding.c | 251 ++++++++++++++++++++++++++++++++++---- src/rlang/env-binding.h | 50 ++++++- src/rlang/env.c | 122 ++++++++++-------- src/rlang/env.h | 90 ------------- src/rlang/eval.c | 48 +++---- src/rlang/formula.c | 6 src/rlang/globals.c | 1 src/rlang/globals.h | 1 src/rlang/obj.c | 5 src/rlang/obj.h | 8 - src/rlang/rlang-types.h | 71 ++++++++++ src/rlang/rlang.c | 1 src/rlang/rlang.h | 2 src/rlang/walk.c | 28 ++-- 76 files changed, 652 insertions(+), 520 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut] ,
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.13 dated 2025-09-26 and 2.9.1 dated 2026-04-03
soilDB-2.8.13/soilDB/data/gopheridge.rda |only soilDB-2.8.13/soilDB/data/loafercreek.rda |only soilDB-2.8.13/soilDB/data/mineralKing.rda |only soilDB-2.8.13/soilDB/tests/testthat/test-fetchSDA_component.R |only soilDB-2.8.13/soilDB/tests/testthat/test-multi-row-simplification.R |only soilDB-2.9.1/soilDB/DESCRIPTION | 18 soilDB-2.9.1/soilDB/MD5 | 563 +- soilDB-2.9.1/soilDB/NAMESPACE | 436 - soilDB-2.9.1/soilDB/NEWS.md | 1882 +++---- soilDB-2.9.1/soilDB/R/AAAA.R | 205 soilDB-2.9.1/soilDB/R/ISSR800.R | 492 - soilDB-2.9.1/soilDB/R/KSSL_VG_model.R | 242 soilDB-2.9.1/soilDB/R/OSDquery.R | 305 - soilDB-2.9.1/soilDB/R/ROSETTA.R | 514 + soilDB-2.9.1/soilDB/R/SDA-spatial.R | 1096 ++-- soilDB-2.9.1/soilDB/R/SDA_query.R | 694 +- soilDB-2.9.1/soilDB/R/SDA_utils.R | 66 soilDB-2.9.1/soilDB/R/SSURGO_spatial_query.R | 169 soilDB-2.9.1/soilDB/R/STR.R | 694 +- soilDB-2.9.1/soilDB/R/SoilDataViewer.R | 260 soilDB-2.9.1/soilDB/R/WCS-utils.R | 1472 ++--- soilDB-2.9.1/soilDB/R/aqp_data.R | 96 soilDB-2.9.1/soilDB/R/createSSURGO.R | 1224 ++-- soilDB-2.9.1/soilDB/R/createStaticNASIS.R | 372 - soilDB-2.9.1/soilDB/R/database-sources.R | 34 soilDB-2.9.1/soilDB/R/dbQueryNASIS.R | 168 soilDB-2.9.1/soilDB/R/estimateColorMixture.R | 174 soilDB-2.9.1/soilDB/R/fetchEDIT_tools.R | 320 - soilDB-2.9.1/soilDB/R/fetchHWSD.R | 240 soilDB-2.9.1/soilDB/R/fetchHenry.R | 902 +-- soilDB-2.9.1/soilDB/R/fetchKSSL.R | 898 +-- soilDB-2.9.1/soilDB/R/fetchLDM.R | 766 +- soilDB-2.9.1/soilDB/R/fetchNASIS.R | 277 - soilDB-2.9.1/soilDB/R/fetchNASISLabData.R | 148 soilDB-2.9.1/soilDB/R/fetchNASISWebReport.R | 767 +- soilDB-2.9.1/soilDB/R/fetchNASIS_components.R | 402 - soilDB-2.9.1/soilDB/R/fetchNASIS_pedons.R | 689 +- soilDB-2.9.1/soilDB/R/fetchNASIS_report.R | 852 +-- soilDB-2.9.1/soilDB/R/fetchNOAA.R | 262 soilDB-2.9.1/soilDB/R/fetchOSD.R | 944 +-- soilDB-2.9.1/soilDB/R/fetchPedonPC.R | 242 soilDB-2.9.1/soilDB/R/fetchRaCA.R | 402 - soilDB-2.9.1/soilDB/R/fetchSCAN.R | 1197 ++-- soilDB-2.9.1/soilDB/R/fetchSDA_spatial.R | 776 +- soilDB-2.9.1/soilDB/R/fetchSOLUS.R | 730 +- soilDB-2.9.1/soilDB/R/fetchSRI.R | 362 - soilDB-2.9.1/soilDB/R/fetchSoilGrids.R | 937 +-- soilDB-2.9.1/soilDB/R/fetchVegdata.R | 203 soilDB-2.9.1/soilDB/R/filter_KSSL.R | 88 soilDB-2.9.1/soilDB/R/getHzErrorsNASIS.R | 92 soilDB-2.9.1/soilDB/R/getHzErrorsPedonPC.R | 48 soilDB-2.9.1/soilDB/R/get_NASIS_table_key_by_name.R | 126 soilDB-2.9.1/soilDB/R/get_NASIS_table_name_by_purpose.R | 478 - soilDB-2.9.1/soilDB/R/get_OSD.R | 473 - soilDB-2.9.1/soilDB/R/get_RMF_from_NASIS_db.R | 136 soilDB-2.9.1/soilDB/R/get_SDA_NASIS_keys.R | 156 soilDB-2.9.1/soilDB/R/get_SDA_coecoclass.R | 641 +- soilDB-2.9.1/soilDB/R/get_SDA_cosurfmorph.R | 372 - soilDB-2.9.1/soilDB/R/get_SDA_hydric.R | 264 soilDB-2.9.1/soilDB/R/get_SDA_interpretation.R | 2042 +++---- soilDB-2.9.1/soilDB/R/get_SDA_metrics.R | 124 soilDB-2.9.1/soilDB/R/get_SDA_muaggatt.R | 100 soilDB-2.9.1/soilDB/R/get_SDA_pmgroupname.R | 434 - soilDB-2.9.1/soilDB/R/get_SDA_property.R | 1538 ++--- soilDB-2.9.1/soilDB/R/get_SSURGO_utils.R | 720 +- soilDB-2.9.1/soilDB/R/get_colors_from_NASIS_db.R | 286 - soilDB-2.9.1/soilDB/R/get_colors_from_pedon_db.R | 202 soilDB-2.9.1/soilDB/R/get_component_data_from_NASIS_db.R | 1418 ++--- soilDB-2.9.1/soilDB/R/get_component_from_GDB.R | 1552 ++--- soilDB-2.9.1/soilDB/R/get_component_from_SDA.R | 2096 +++---- soilDB-2.9.1/soilDB/R/get_concentrations_from_NASIS_db.R | 107 soilDB-2.9.1/soilDB/R/get_cosoilmoist_from_NASIS.R | 146 soilDB-2.9.1/soilDB/R/get_cosoilmoist_from_NASISWebReport.R | 98 soilDB-2.9.1/soilDB/R/get_cosoilmoist_from_SDA.R | 99 soilDB-2.9.1/soilDB/R/get_ecosite_history_from_NASIS_db.R | 92 soilDB-2.9.1/soilDB/R/get_extended_data_from_NASIS_db.R | 699 +- soilDB-2.9.1/soilDB/R/get_extended_data_from_pedon_db.R | 286 - soilDB-2.9.1/soilDB/R/get_hz_data_from_NASIS_db.R | 157 soilDB-2.9.1/soilDB/R/get_hz_data_from_pedon_db.R | 168 soilDB-2.9.1/soilDB/R/get_lablayer_data_from_NASIS_db.R | 122 soilDB-2.9.1/soilDB/R/get_labpedon_data_from_NASIS_db.R | 78 soilDB-2.9.1/soilDB/R/get_mapunit_from_NASIS.R | 388 - soilDB-2.9.1/soilDB/R/get_phfmp_from_NASIS_db.R | 65 soilDB-2.9.1/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 277 - soilDB-2.9.1/soilDB/R/get_phroots_from_NASIS_db.R | 102 soilDB-2.9.1/soilDB/R/get_project_from_NASIS.R | 198 soilDB-2.9.1/soilDB/R/get_site_data_from_NASIS_db.R | 545 -- soilDB-2.9.1/soilDB/R/get_site_data_from_pedon_db.R | 190 soilDB-2.9.1/soilDB/R/get_soilseries_from_NASIS.R | 253 soilDB-2.9.1/soilDB/R/get_text_notes_from_NASIS_db.R | 368 - soilDB-2.9.1/soilDB/R/get_veg_data_from_NASIS_db.R | 145 soilDB-2.9.1/soilDB/R/get_veg_from_AK_Site.R | 88 soilDB-2.9.1/soilDB/R/get_veg_from_MT_veg_db.R | 84 soilDB-2.9.1/soilDB/R/get_veg_from_NPS_PLOTS_db.R | 78 soilDB-2.9.1/soilDB/R/get_veg_other_from_MT_veg_db.R | 84 soilDB-2.9.1/soilDB/R/get_veg_species_from_MT_veg_db.R | 80 soilDB-2.9.1/soilDB/R/get_vegplot_data_from_NASIS_db.R | 1246 ++-- soilDB-2.9.1/soilDB/R/mukey-WCS.R | 534 + soilDB-2.9.1/soilDB/R/openNASISchannel.R | 188 soilDB-2.9.1/soilDB/R/parseWebReport.R | 246 soilDB-2.9.1/soilDB/R/seriesExtent.R | 308 - soilDB-2.9.1/soilDB/R/siblings.R | 272 - soilDB-2.9.1/soilDB/R/simplifyArtifactData.R | 298 - soilDB-2.9.1/soilDB/R/simplifyColorData.R | 366 - soilDB-2.9.1/soilDB/R/simplifyFragmentData.R | 526 - soilDB-2.9.1/soilDB/R/soilColorWCS.R | 418 - soilDB-2.9.1/soilDB/R/soilDB-package.R | 325 - soilDB-2.9.1/soilDB/R/soilDB_user_dir.R | 127 soilDB-2.9.1/soilDB/R/taxaExtent.R | 681 +- soilDB-2.9.1/soilDB/R/uncode.R | 813 +-- soilDB-2.9.1/soilDB/R/utils.R | 2676 +++++----- soilDB-2.9.1/soilDB/R/waterDayYear.R | 110 soilDB-2.9.1/soilDB/build/partial.rdb |binary soilDB-2.9.1/soilDB/build/vignette.rds |binary soilDB-2.9.1/soilDB/data/gopheridge.R |only soilDB-2.9.1/soilDB/data/loafercreek.R |only soilDB-2.9.1/soilDB/data/mineralKing.R |only soilDB-2.9.1/soilDB/inst/CITATION | 36 soilDB-2.9.1/soilDB/inst/WORDLIST | 1570 ++--- soilDB-2.9.1/soilDB/inst/doc/dominant-es.R | 288 - soilDB-2.9.1/soilDB/inst/doc/dominant-es.Rmd | 578 +- soilDB-2.9.1/soilDB/inst/doc/dominant-es.html | 1325 ++-- soilDB-2.9.1/soilDB/inst/doc/fetchNASIS.R | 521 - soilDB-2.9.1/soilDB/inst/doc/fetchNASIS.Rmd | 555 +- soilDB-2.9.1/soilDB/inst/doc/fetchNASIS.html | 2538 ++++++++- soilDB-2.9.1/soilDB/inst/doc/local-ssurgo.R | 290 - soilDB-2.9.1/soilDB/inst/doc/local-ssurgo.Rmd | 612 +- soilDB-2.9.1/soilDB/inst/doc/local-ssurgo.html | 1357 ++--- soilDB-2.9.1/soilDB/inst/doc/sda.R |only soilDB-2.9.1/soilDB/inst/doc/sda.Rmd |only soilDB-2.9.1/soilDB/inst/doc/sda.html |only soilDB-2.9.1/soilDB/inst/doc/soilweb-data-functions.R |only soilDB-2.9.1/soilDB/inst/doc/soilweb-data-functions.Rmd |only soilDB-2.9.1/soilDB/inst/doc/soilweb-data-functions.html |only soilDB-2.9.1/soilDB/inst/doc/wcs-ssurgo.R | 1202 ++-- soilDB-2.9.1/soilDB/inst/doc/wcs-ssurgo.Rmd | 1708 +++--- soilDB-2.9.1/soilDB/inst/doc/wcs-ssurgo.html | 2429 ++++----- soilDB-2.9.1/soilDB/inst/extdata |only soilDB-2.9.1/soilDB/man/ISSR800.wcs.Rd | 108 soilDB-2.9.1/soilDB/man/KSSL_VG_model.Rd | 122 soilDB-2.9.1/soilDB/man/NASISChoiceList.Rd | 120 soilDB-2.9.1/soilDB/man/NASISDomainsAsFactor.Rd | 44 soilDB-2.9.1/soilDB/man/NASISLocalDatabase.Rd | 36 soilDB-2.9.1/soilDB/man/OSDquery.Rd | 228 soilDB-2.9.1/soilDB/man/ROSETTA.Rd | 205 soilDB-2.9.1/soilDB/man/SCAN_SNOTEL_metadata.Rd | 28 soilDB-2.9.1/soilDB/man/SDA_query.Rd | 165 soilDB-2.9.1/soilDB/man/SDA_spatialQuery.Rd | 472 - soilDB-2.9.1/soilDB/man/STRplot.Rd | 88 soilDB-2.9.1/soilDB/man/SoilWeb_spatial_query.Rd | 110 soilDB-2.9.1/soilDB/man/WCS_details.Rd | 42 soilDB-2.9.1/soilDB/man/createSSURGO.Rd | 182 soilDB-2.9.1/soilDB/man/createStaticNASIS.Rd | 84 soilDB-2.9.1/soilDB/man/dbConnectNASIS.Rd | 44 soilDB-2.9.1/soilDB/man/dbQueryNASIS.Rd | 46 soilDB-2.9.1/soilDB/man/downloadSSURGO.Rd | 156 soilDB-2.9.1/soilDB/man/estimateColorMixture.Rd | 54 soilDB-2.9.1/soilDB/man/fetchGDB.Rd | 192 soilDB-2.9.1/soilDB/man/fetchHWSD.Rd | 138 soilDB-2.9.1/soilDB/man/fetchHenry.Rd | 198 soilDB-2.9.1/soilDB/man/fetchKSSL.Rd | 262 soilDB-2.9.1/soilDB/man/fetchLDM.Rd | 176 soilDB-2.9.1/soilDB/man/fetchNASIS.Rd | 249 soilDB-2.9.1/soilDB/man/fetchNASISLabData.Rd | 58 soilDB-2.9.1/soilDB/man/fetchNASISWebReport.Rd | 221 soilDB-2.9.1/soilDB/man/fetchOSD.Rd | 249 soilDB-2.9.1/soilDB/man/fetchPedonPC.Rd | 78 soilDB-2.9.1/soilDB/man/fetchRaCA.Rd | 118 soilDB-2.9.1/soilDB/man/fetchSCAN.Rd | 250 soilDB-2.9.1/soilDB/man/fetchSDA.Rd | 245 soilDB-2.9.1/soilDB/man/fetchSDA_spatial.Rd | 182 soilDB-2.9.1/soilDB/man/fetchSOLUS.Rd | 280 - soilDB-2.9.1/soilDB/man/fetchSRI.Rd | 70 soilDB-2.9.1/soilDB/man/fetchSoilGrids.Rd | 370 - soilDB-2.9.1/soilDB/man/fetchVegdata.Rd | 258 soilDB-2.9.1/soilDB/man/filter_geochem.Rd | 68 soilDB-2.9.1/soilDB/man/format_SQL_in_statement.Rd | 46 soilDB-2.9.1/soilDB/man/getHzErrorsNASIS.Rd | 50 soilDB-2.9.1/soilDB/man/get_EDIT_ecoclass_by_geoUnit.Rd | 52 soilDB-2.9.1/soilDB/man/get_NASIS_metadata.Rd | 90 soilDB-2.9.1/soilDB/man/get_NASIS_table_key_by_name.Rd | 60 soilDB-2.9.1/soilDB/man/get_NASIS_table_metadata.Rd | 92 soilDB-2.9.1/soilDB/man/get_NASIS_table_name_by_purpose.Rd | 82 soilDB-2.9.1/soilDB/man/get_NOAA_GHCND.Rd | 76 soilDB-2.9.1/soilDB/man/get_NOAA_stations_nearXY.Rd | 72 soilDB-2.9.1/soilDB/man/get_OSD.Rd | 94 soilDB-2.9.1/soilDB/man/get_RMF_from_NASIS_db.Rd | 46 soilDB-2.9.1/soilDB/man/get_SDA_NASIS_key.Rd | 118 soilDB-2.9.1/soilDB/man/get_SDA_coecoclass.Rd | 173 soilDB-2.9.1/soilDB/man/get_SDA_cosurfmorph.Rd | 170 soilDB-2.9.1/soilDB/man/get_SDA_hydric.Rd | 114 soilDB-2.9.1/soilDB/man/get_SDA_interpretation.Rd | 1428 ++--- soilDB-2.9.1/soilDB/man/get_SDA_metrics.Rd | 62 soilDB-2.9.1/soilDB/man/get_SDA_muaggatt.Rd | 68 soilDB-2.9.1/soilDB/man/get_SDA_pmgroupname.Rd | 98 soilDB-2.9.1/soilDB/man/get_SDA_property.Rd | 310 - soilDB-2.9.1/soilDB/man/get_SDV_legend_elements.Rd | 56 soilDB-2.9.1/soilDB/man/get_SRI.Rd | 158 soilDB-2.9.1/soilDB/man/get_SRI_layers.Rd | 58 soilDB-2.9.1/soilDB/man/get_colors_from_NASIS_db.Rd | 78 soilDB-2.9.1/soilDB/man/get_colors_from_pedon_db.Rd | 50 soilDB-2.9.1/soilDB/man/get_comonth_from_NASIS_db.Rd | 96 soilDB-2.9.1/soilDB/man/get_component_data_from_NASIS_db.Rd | 196 soilDB-2.9.1/soilDB/man/get_cosoilmoist_from_NASIS.Rd | 115 soilDB-2.9.1/soilDB/man/get_ecosite_history_from_NASIS_db.Rd | 62 soilDB-2.9.1/soilDB/man/get_extended_data_from_NASIS_db.Rd | 101 soilDB-2.9.1/soilDB/man/get_extended_data_from_pedon_db.Rd | 50 soilDB-2.9.1/soilDB/man/get_hz_data_from_NASIS_db.Rd | 71 soilDB-2.9.1/soilDB/man/get_hz_data_from_pedon_db.Rd | 58 soilDB-2.9.1/soilDB/man/get_lablayer_data_from_NASIS_db.Rd | 64 soilDB-2.9.1/soilDB/man/get_labpedon_data_from_NASIS_db.Rd | 64 soilDB-2.9.1/soilDB/man/get_mapunit_from_NASIS.Rd | 95 soilDB-2.9.1/soilDB/man/get_phroots_from_NASIS_db.Rd | 38 soilDB-2.9.1/soilDB/man/get_project_from_NASIS.Rd | 50 soilDB-2.9.1/soilDB/man/get_site_data_from_NASIS_db.Rd | 117 soilDB-2.9.1/soilDB/man/get_site_data_from_pedon_db.Rd | 50 soilDB-2.9.1/soilDB/man/get_soilDB_env.Rd | 52 soilDB-2.9.1/soilDB/man/get_soilseries_from_NASIS.Rd | 99 soilDB-2.9.1/soilDB/man/get_text_notes_from_NASIS_db.Rd | 110 soilDB-2.9.1/soilDB/man/get_veg_data_from_NASIS_db.Rd | 66 soilDB-2.9.1/soilDB/man/get_veg_from_AK_Site.Rd | 50 soilDB-2.9.1/soilDB/man/get_veg_from_MT_veg_db.Rd | 52 soilDB-2.9.1/soilDB/man/get_veg_from_NPS_PLOTS_db.Rd | 54 soilDB-2.9.1/soilDB/man/get_veg_other_from_MT_veg_db.Rd | 52 soilDB-2.9.1/soilDB/man/get_veg_species_from_MT_veg_db.Rd | 52 soilDB-2.9.1/soilDB/man/loafercreek.Rd | 162 soilDB-2.9.1/soilDB/man/local_NASIS_defined.Rd | 64 soilDB-2.9.1/soilDB/man/make_EDIT_service_URL.Rd | 184 soilDB-2.9.1/soilDB/man/metadata.Rd | 52 soilDB-2.9.1/soilDB/man/mukey.wcs.Rd | 150 soilDB-2.9.1/soilDB/man/parseWebReport.Rd | 66 soilDB-2.9.1/soilDB/man/processSDA_WKT.Rd | 76 soilDB-2.9.1/soilDB/man/seriesExtent.Rd | 130 soilDB-2.9.1/soilDB/man/siblings.Rd | 124 soilDB-2.9.1/soilDB/man/simplifyColorData.Rd | 102 soilDB-2.9.1/soilDB/man/simplifyFragmentData.Rd | 138 soilDB-2.9.1/soilDB/man/soilColor.wcs.Rd | 108 soilDB-2.9.1/soilDB/man/soilDB-package.Rd | 42 soilDB-2.9.1/soilDB/man/soilDB_user_dir.Rd | 124 soilDB-2.9.1/soilDB/man/taxaExtent.Rd | 480 - soilDB-2.9.1/soilDB/man/uncode.Rd | 147 soilDB-2.9.1/soilDB/man/waterDayYear.Rd | 74 soilDB-2.9.1/soilDB/tests/testthat.R | 12 soilDB-2.9.1/soilDB/tests/testthat/test-ISSR800.R | 193 soilDB-2.9.1/soilDB/tests/testthat/test-OSDquery.R | 85 soilDB-2.9.1/soilDB/tests/testthat/test-ROSETTA.R | 335 - soilDB-2.9.1/soilDB/tests/testthat/test-SDA_query.R | 642 +- soilDB-2.9.1/soilDB/tests/testthat/test-SoilDataViewer.R | 58 soilDB-2.9.1/soilDB/tests/testthat/test-aqp_data.R | 38 soilDB-2.9.1/soilDB/tests/testthat/test-dbQueryNASIS.R | 64 soilDB-2.9.1/soilDB/tests/testthat/test-estimateColorMixture.R | 94 soilDB-2.9.1/soilDB/tests/testthat/test-estimateSTR.R | 86 soilDB-2.9.1/soilDB/tests/testthat/test-fetchEDIT_tools.R | 92 soilDB-2.9.1/soilDB/tests/testthat/test-fetchHenry.R | 412 - soilDB-2.9.1/soilDB/tests/testthat/test-fetchKSSL.R | 400 - soilDB-2.9.1/soilDB/tests/testthat/test-fetchLDM.R | 132 soilDB-2.9.1/soilDB/tests/testthat/test-fetchNASIS.R | 310 - soilDB-2.9.1/soilDB/tests/testthat/test-fetchNASISLabData.R | 94 soilDB-2.9.1/soilDB/tests/testthat/test-fetchNASISWebReport.R | 198 soilDB-2.9.1/soilDB/tests/testthat/test-fetchOSD.R | 286 - soilDB-2.9.1/soilDB/tests/testthat/test-fetchSCAN.R | 154 soilDB-2.9.1/soilDB/tests/testthat/test-fetchSDA.R |only soilDB-2.9.1/soilDB/tests/testthat/test-fetchSDA_spatial.R | 184 soilDB-2.9.1/soilDB/tests/testthat/test-fetchSOLUS.R | 206 soilDB-2.9.1/soilDB/tests/testthat/test-fetchSRI.R | 92 soilDB-2.9.1/soilDB/tests/testthat/test-fetchSoilGrids.R | 87 soilDB-2.9.1/soilDB/tests/testthat/test-get_OSD.R | 126 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_coecoclass.R | 121 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_cosurfmorph.R | 65 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_hydric.R | 66 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_interpretation.R | 184 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_muaggatt.R | 30 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_pmgroupname.R | 59 soilDB-2.9.1/soilDB/tests/testthat/test-get_SDA_property.R | 656 +- soilDB-2.9.1/soilDB/tests/testthat/test-get_SSURGO_utils.R | 30 soilDB-2.9.1/soilDB/tests/testthat/test-mukey-WCS.R | 87 soilDB-2.9.1/soilDB/tests/testthat/test-seriesExtent.R | 50 soilDB-2.9.1/soilDB/tests/testthat/test-siblings.R | 124 soilDB-2.9.1/soilDB/tests/testthat/test-simplifyArtifactData.R | 388 - soilDB-2.9.1/soilDB/tests/testthat/test-simplifyColorData.R | 326 - soilDB-2.9.1/soilDB/tests/testthat/test-simplifyFragmentData.R | 980 +-- soilDB-2.9.1/soilDB/tests/testthat/test-soilDBdata.R | 190 soilDB-2.9.1/soilDB/tests/testthat/test-taxaExtent.R |only soilDB-2.9.1/soilDB/tests/testthat/test-uncode.R | 110 soilDB-2.9.1/soilDB/tests/testthat/test-waterDayYear.R | 216 soilDB-2.9.1/soilDB/vignettes/dominant-es.Rmd | 578 +- soilDB-2.9.1/soilDB/vignettes/fetchNASIS.Rmd | 555 +- soilDB-2.9.1/soilDB/vignettes/local-ssurgo.Rmd | 612 +- soilDB-2.9.1/soilDB/vignettes/sda.Rmd |only soilDB-2.9.1/soilDB/vignettes/soilweb-data-functions.Rmd |only soilDB-2.9.1/soilDB/vignettes/wcs-ssurgo.Rmd | 1708 +++--- 291 files changed, 46480 insertions(+), 44787 deletions(-)
Title: Functionalities for the 'INLA' Package
Description: Contain code to work with a C struct, in short
cgeneric, to define a Gaussian Markov random (GMRF) model.
The cgeneric contain code to specify GMRF elements such as
the graph and the precision matrix, and also the initial and
prior for its parameters, useful for model inference.
It can be accessed from a C program and is the recommended
way to implement new GMRF models in the 'INLA' package
(<https://www.r-inla.org>).
The 'INLAtools' implement functions to evaluate
each one of the model specifications from R.
The implemented functionalities leverage the use
of 'cgeneric' models and provide a way to debug
the code as well to work with the prior for the
model parameters and to sample from it.
The `generic0` can be used to implement intrinsic models with the
scaling as proposed in
Sørbye & Rue (2014) <doi:10.1016/j.spasta.2013.06.004>,
and the required contraints.
A very useful functionality is the Kronecker product method
that creates a new model from multiple cgeneric mo [...truncated...]
Author: Elias Teixeira Krainski [cre, aut, cph] ,
Finn Lindgren [aut] ,
Haavard Rue’ [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAtools versions 0.1.0 dated 2026-03-29 and 0.1.1 dated 2026-04-03
DESCRIPTION | 14 ++++++---- MD5 | 18 ++++++------- NAMESPACE | 1 R/cgeneric.R | 27 ++++++++++---------- R/cgeneric_generic0.R | 67 ++++++++++++++++++++++++-------------------------- R/kronecker.R | 21 ++++++++++----- R/rgeneric.R | 7 +++++ R/rgeneric_utils.R | 67 +++++++++++++++++++++++++++----------------------- man/cgeneric-class.Rd | 8 +++-- man/rgeneric_get.Rd | 8 +++++ 10 files changed, 136 insertions(+), 102 deletions(-)
Title: Download and Process Brazilian Education Data from INEP
Description: Download and process public education data from INEP (Instituto
Nacional de Estudos e Pesquisas Educacionais Anísio Teixeira). Provides
functions to access microdata from the School Census (Censo Escolar),
ENEM (Exame Nacional do Ensino Médio), SAEB (Sistema de Avaliação da
Educação Básica), Higher Education Census (Censo da Educação Superior),
ENADE (Exame Nacional de Desempenho dos Estudantes),
ENCCEJA (Exame Nacional para Certificação de Competências de Jovens e Adultos),
IDD (Indicador de Diferença entre os Desempenhos Observado e Esperado),
CPC (Conceito Preliminar de Curso),
IGC (Índice Geral de Cursos),
CAPES graduate education data,
FUNDEB (Fundo de Manutencao e Desenvolvimento da Educacao Basica),
IDEB (Índice de Desenvolvimento da Educação Básica),
and other educational datasets. Returns data in
tidy format ready for analysis. Data source: INEP Open Data Portal
<https://www.gov.br/inep/pt-br/acesso-a-informacao/dados-abertos>.
Author: Sidney da Silva Pereira Bissoli [aut, cre]
Maintainer: Sidney da Silva Pereira Bissoli <sbissoli76@gmail.com>
Diff between educabR versions 0.1.3 dated 2026-03-05 and 0.9.0 dated 2026-04-03
educabR-0.1.3/educabR/inst/doc/introducao-educabr.R |only educabR-0.1.3/educabR/inst/doc/introducao-educabr.Rmd |only educabR-0.1.3/educabR/inst/doc/introducao-educabr.html |only educabR-0.1.3/educabR/vignettes/introducao-educabr.Rmd |only educabR-0.9.0/educabR/DESCRIPTION | 23 educabR-0.9.0/educabR/MD5 | 137 - educabR-0.9.0/educabR/NAMESPACE | 16 educabR-0.9.0/educabR/NEWS.md | 243 +- educabR-0.9.0/educabR/R/educabR-package.R | 45 educabR-0.9.0/educabR/R/get-capes.R |only educabR-0.9.0/educabR/R/get-censo-escolar.R | 536 ++-- educabR-0.9.0/educabR/R/get-censo-superior.R |only educabR-0.9.0/educabR/R/get-cpc.R |only educabR-0.9.0/educabR/R/get-enade.R |only educabR-0.9.0/educabR/R/get-encceja.R |only educabR-0.9.0/educabR/R/get-enem-escola.R |only educabR-0.9.0/educabR/R/get-enem.R | 641 +++-- educabR-0.9.0/educabR/R/get-fundeb.R |only educabR-0.9.0/educabR/R/get-idd.R |only educabR-0.9.0/educabR/R/get-ideb.R | 626 +++-- educabR-0.9.0/educabR/R/get-igc.R |only educabR-0.9.0/educabR/R/get-saeb.R |only educabR-0.9.0/educabR/R/utils-cache.R | 436 ++-- educabR-0.9.0/educabR/R/utils-download.R | 1082 ++++++---- educabR-0.9.0/educabR/R/utils-validation.R |only educabR-0.9.0/educabR/README.md | 140 + educabR-0.9.0/educabR/build/vignette.rds |binary educabR-0.9.0/educabR/inst/doc/basic-education-assessments.R |only educabR-0.9.0/educabR/inst/doc/basic-education-assessments.Rmd |only educabR-0.9.0/educabR/inst/doc/basic-education-assessments.html |only educabR-0.9.0/educabR/inst/doc/education-funding.R |only educabR-0.9.0/educabR/inst/doc/education-funding.Rmd |only educabR-0.9.0/educabR/inst/doc/education-funding.html |only educabR-0.9.0/educabR/inst/doc/getting-started.R |only educabR-0.9.0/educabR/inst/doc/getting-started.Rmd |only educabR-0.9.0/educabR/inst/doc/getting-started.html |only educabR-0.9.0/educabR/inst/doc/higher-education.R |only educabR-0.9.0/educabR/inst/doc/higher-education.Rmd |only educabR-0.9.0/educabR/inst/doc/higher-education.html |only educabR-0.9.0/educabR/man/available_years.Rd | 10 educabR-0.9.0/educabR/man/build_fundeb_url.Rd |only educabR-0.9.0/educabR/man/build_saeb_zip_filename.Rd |only educabR-0.9.0/educabR/man/clean_dash_values.Rd |only educabR-0.9.0/educabR/man/clean_ideb_values.Rd |only educabR-0.9.0/educabR/man/clear_cache.Rd | 61 educabR-0.9.0/educabR/man/convert_faixa_columns.Rd |only educabR-0.9.0/educabR/man/detect_delim.Rd |only educabR-0.9.0/educabR/man/discover_capes_url.Rd |only educabR-0.9.0/educabR/man/educabR-package.Rd | 61 educabR-0.9.0/educabR/man/enem_summary.Rd | 69 educabR-0.9.0/educabR/man/extract_archive.Rd |only educabR-0.9.0/educabR/man/fetch_fundeb_enrollment.Rd |only educabR-0.9.0/educabR/man/find_censo_superior_file.Rd |only educabR-0.9.0/educabR/man/find_enade_file.Rd |only educabR-0.9.0/educabR/man/find_encceja_file.Rd |only educabR-0.9.0/educabR/man/find_enem_escola_file.Rd |only educabR-0.9.0/educabR/man/find_enem_file.Rd | 4 educabR-0.9.0/educabR/man/find_idd_file.Rd |only educabR-0.9.0/educabR/man/find_saeb_file.Rd |only educabR-0.9.0/educabR/man/get_cache_dir.Rd | 41 educabR-0.9.0/educabR/man/get_capes.Rd |only educabR-0.9.0/educabR/man/get_censo_escolar.Rd | 119 - educabR-0.9.0/educabR/man/get_censo_superior.Rd |only educabR-0.9.0/educabR/man/get_cpc.Rd |only educabR-0.9.0/educabR/man/get_enade.Rd |only educabR-0.9.0/educabR/man/get_encceja.Rd |only educabR-0.9.0/educabR/man/get_enem.Rd | 146 - educabR-0.9.0/educabR/man/get_enem_escola.Rd |only educabR-0.9.0/educabR/man/get_enem_itens.Rd | 65 educabR-0.9.0/educabR/man/get_fundeb_distribution.Rd |only educabR-0.9.0/educabR/man/get_fundeb_enrollment.Rd |only educabR-0.9.0/educabR/man/get_idd.Rd |only educabR-0.9.0/educabR/man/get_ideb.Rd | 150 - educabR-0.9.0/educabR/man/get_ideb_series.Rd | 90 educabR-0.9.0/educabR/man/get_igc.Rd |only educabR-0.9.0/educabR/man/get_saeb.Rd |only educabR-0.9.0/educabR/man/list_cache.Rd | 51 educabR-0.9.0/educabR/man/list_censo_files.Rd | 49 educabR-0.9.0/educabR/man/list_censo_superior_files.Rd |only educabR-0.9.0/educabR/man/list_ideb_available.Rd | 40 educabR-0.9.0/educabR/man/parse_sas_dates.Rd |only educabR-0.9.0/educabR/man/read_excel_safe.Rd |only educabR-0.9.0/educabR/man/set_cache_dir.Rd | 63 educabR-0.9.0/educabR/man/validate_data.Rd |only educabR-0.9.0/educabR/tests/testthat/setup.R |only educabR-0.9.0/educabR/tests/testthat/test-capes.R |only educabR-0.9.0/educabR/tests/testthat/test-censo-superior.R |only educabR-0.9.0/educabR/tests/testthat/test-coverage-gaps.R |only educabR-0.9.0/educabR/tests/testthat/test-cpc.R |only educabR-0.9.0/educabR/tests/testthat/test-enade.R |only educabR-0.9.0/educabR/tests/testthat/test-encceja.R |only educabR-0.9.0/educabR/tests/testthat/test-enem-escola.R |only educabR-0.9.0/educabR/tests/testthat/test-enem-summary.R |only educabR-0.9.0/educabR/tests/testthat/test-file-finders.R |only educabR-0.9.0/educabR/tests/testthat/test-fundeb.R |only educabR-0.9.0/educabR/tests/testthat/test-get-censo-escolar.R |only educabR-0.9.0/educabR/tests/testthat/test-get-enem.R |only educabR-0.9.0/educabR/tests/testthat/test-get-ideb.R |only educabR-0.9.0/educabR/tests/testthat/test-get-pipelines-excel.R |only educabR-0.9.0/educabR/tests/testthat/test-get-pipelines.R |only educabR-0.9.0/educabR/tests/testthat/test-idd.R |only educabR-0.9.0/educabR/tests/testthat/test-igc.R |only educabR-0.9.0/educabR/tests/testthat/test-saeb.R |only educabR-0.9.0/educabR/tests/testthat/test-utils-cache.R | 430 +++ educabR-0.9.0/educabR/tests/testthat/test-utils-download.R | 657 +++++- educabR-0.9.0/educabR/tests/testthat/test-utils-validation.R |only educabR-0.9.0/educabR/vignettes/basic-education-assessments.Rmd |only educabR-0.9.0/educabR/vignettes/education-funding.Rmd |only educabR-0.9.0/educabR/vignettes/getting-started.Rmd |only educabR-0.9.0/educabR/vignettes/higher-education.Rmd |only 110 files changed, 4043 insertions(+), 1988 deletions(-)
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] ,
Michael Sumner [ctb] ,
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb],
Krzysztof Dyba [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.7-1 dated 2026-02-13 and 0.7-2 dated 2026-04-03
DESCRIPTION | 6 - MD5 | 149 ++++++++++++++++++++++---------------------- NAMESPACE | 2 NEWS.md | 10 ++ R/aggregate.R | 2 R/dimensions.R | 3 R/extract.R | 2 R/ops.R | 2 R/proxy.R | 25 ++++--- R/sample.R | 18 ++--- R/sf.R | 1 R/subset.R | 8 ++ R/tidyverse.R | 6 - R/warp.R | 2 build/vignette.rds |binary inst/doc/stars1.html | 4 - inst/doc/stars2.R | 24 +++---- inst/doc/stars2.Rmd | 24 +++---- inst/doc/stars2.html | 42 +++++------- inst/doc/stars3.R | 14 ++-- inst/doc/stars3.Rmd | 14 ++-- inst/doc/stars3.html | 14 ++-- inst/doc/stars5.R | 10 +- inst/doc/stars5.Rmd | 10 +- inst/doc/stars5.html | 10 +- inst/doc/stars6.R | 38 +++++------ inst/doc/stars6.Rmd | 38 +++++------ inst/doc/stars6.html | 28 ++++---- man/aggregate.stars.Rd | 2 man/dplyr.Rd | 4 - man/geom_stars.Rd | 2 man/st_apply.Rd | 2 man/st_dimensions.Rd | 2 man/st_extract.Rd | 2 man/st_normalize.Rd |only man/st_warp.Rd | 2 man/stars_subset.Rd | 6 - tests/aggregate.Rout.save | 6 - tests/align.Rout.save | 4 - tests/area.Rout.save | 4 - tests/crop.Rout.save | 4 - tests/curvilinear.Rout.save | 4 - tests/datasets.Rout.save | 4 - tests/dimensions.R | 4 - tests/dimensions.Rout.save | 8 +- tests/downsample.Rout.save | 4 - tests/ee.Rout.save | 4 - tests/extract.Rout.save | 4 - tests/gridtypes.Rout.save | 4 - tests/mdim.Rout.save | 4 - tests/nc.R | 8 -- tests/nc.Rout.save | 33 +-------- tests/plot.Rout.save | 4 - tests/predict.Rout.save | 8 -- tests/proxy.Rout.save | 20 ----- tests/raster.Rout.save | 4 - tests/rasterize.Rout.save | 4 - tests/rectilinear.Rout.save | 4 - tests/redimension.Rout.save | 4 - tests/sf.Rout.save | 4 - tests/sp.Rout.save | 4 - tests/spacetime.Rout.save | 4 - tests/spatstat.Rout.save | 4 - tests/stars.R | 4 - tests/stars.Rout.save | 8 +- tests/subset.R | 7 ++ tests/subset.Rout.save | 20 +++++ tests/tidy.R | 12 +-- tests/tidy.Rout.save | 16 ++-- tests/transform.Rout.save | 6 - tests/warp.Rout.save | 4 - tests/write.Rout.save | 4 - vignettes/stars2.Rmd | 24 +++---- vignettes/stars3.Rmd | 14 ++-- vignettes/stars5.Rmd | 10 +- vignettes/stars6.Rmd | 38 +++++------ 76 files changed, 428 insertions(+), 430 deletions(-)
Title: Utilities for the Open Geospatial Consortium 'GeoPackage' Format
Description: Build Open Geospatial Consortium 'GeoPackage' files (<https://www.geopackage.org/>). 'GDAL' utilities for reading and writing spatial data are provided by the 'terra' package. Additional 'GeoPackage' and 'SQLite' features for attributes and tabular data are implemented with the 'RSQLite' package.
Author: Andrew Brown [aut, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between gpkg versions 0.0.12 dated 2025-03-16 and 0.0.14 dated 2026-04-03
DESCRIPTION | 13 +- MD5 | 45 +++---- NAMESPACE | 1 NEWS.md | 12 + R/gpkg-attributes.R | 5 R/gpkg-class.R | 2 R/gpkg-contents.R | 65 +++++++--- R/gpkg-io.R | 99 +++++++++++++--- R/gpkg-sqlite.R | 36 ++++- R/gpkg-table.R | 6 R/gpkg-util.R | 93 +++++++++++++++ README.md | 98 +++++++--------- build/vignette.rds |binary inst/doc/intro.R | 8 - inst/doc/intro.Rmd | 10 - inst/doc/intro.html | 275 ++++++++++++++++++++++----------------------- inst/tinytest/test_gpkg.R | 207 +++++++++++++++++++++++++++++---- man/gpkg-attributes.Rd | 5 man/gpkg-package.Rd | 2 man/gpkg_bbox.Rd | 2 man/gpkg_default_nodata.Rd |only man/gpkg_table.Rd | 8 - man/gpkg_write.Rd | 51 ++++++-- vignettes/intro.Rmd | 10 - 24 files changed, 721 insertions(+), 332 deletions(-)
Title: Brain Atlas Data Structures for the 'ggseg' Ecosystem
Description: Provides the 'ggseg_atlas' S3 class used across the 'ggseg'
ecosystem for 2D and 3D brain visualisation. Ships three bundled atlases
('Desikan-Killiany', 'FreeSurfer' 'aseg', 'TRACULA') and functions for
querying, subsetting, renaming, and enriching atlas objects. Also includes
readers for 'FreeSurfer' statistics files.
Author: Athanasia Mo Mowinckel [aut, cre] ,
Center for Lifespan Changes in Brain and Cognition , University
of Oslo [cph]
Maintainer: Athanasia Mo Mowinckel <a.m.mowinckel@psykologi.uio.no>
Diff between ggseg.formats versions 0.0.1 dated 2026-02-18 and 0.0.2 dated 2026-04-03
DESCRIPTION | 23 +++--- LICENSE | 2 MD5 | 55 +++++++------- NAMESPACE | 4 + NEWS.md |only R/atlas-utils.R | 70 +++++++++++++++--- R/atlases.R | 9 +- R/brain-mesh.R | 21 +++++ R/ggseg_atlas.R | 14 ++- R/ggseg_atlas_data.R | 80 +++++++++++++++++++++ R/read_freesurfer.R | 13 --- R/sysdata.rda |binary R/validation.R | 12 ++- README.md | 2 man/aseg.Rd | 3 man/dk.Rd | 3 man/get_cerebellar_mesh.Rd |only man/ggseg.Rd | 5 + man/ggseg_atlas.Rd | 4 - man/ggseg_data_cerebellar.Rd |only man/is_ggseg_atlas.Rd | 3 man/read_atlas_files.Rd | 5 - man/read_freesurfer_stats.Rd | 4 - man/read_freesurfer_table.Rd | 4 - man/tracula.Rd | 3 tests/testthat/_snaps/ggseg_atlas_data.md | 26 +++++++ tests/testthat/test-atlas-utils.R | 95 +++++++++++++++++++++++++ tests/testthat/test-brain-mesh.R | 18 ++++ tests/testthat/test-ggseg_atlas.R | 111 ++++++++++++++++++++++++++++++ tests/testthat/test-ggseg_atlas_data.R | 91 ++++++++++++++++++++++++ 30 files changed, 597 insertions(+), 83 deletions(-)
Title: Connect to an OMOP Common Data Model
Description: Provides tools for working with observational health data in the
Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax.
Common data model database table references are stored in a single compound object along with metadata.
Author: Adam Black [aut, cre] ,
Artem Gorbachev [aut],
Edward Burn [aut],
Marti Catala Sabate [aut],
Ioanna Nika [aut]
Maintainer: Adam Black <ablack3@gmail.com>
Diff between CDMConnector versions 2.5.0 dated 2026-03-08 and 2.5.1 dated 2026-04-03
CDMConnector-2.5.0/CDMConnector/R/circe.R |only CDMConnector-2.5.0/CDMConnector/R/dag_cache.R |only CDMConnector-2.5.0/CDMConnector/R/execution_graph.R |only CDMConnector-2.5.0/CDMConnector/R/optimizer.R |only CDMConnector-2.5.0/CDMConnector/R/sqlrender.R |only CDMConnector-2.5.0/CDMConnector/R/translate_lightweight.R |only CDMConnector-2.5.0/CDMConnector/inst/csv/replacementPatterns.csv |only CDMConnector-2.5.0/CDMConnector/inst/csv/supportedDialects.csv |only CDMConnector-2.5.0/CDMConnector/inst/doc/a07_batch-optimization.R |only CDMConnector-2.5.0/CDMConnector/inst/doc/a07_batch-optimization.Rmd |only CDMConnector-2.5.0/CDMConnector/inst/doc/a07_batch-optimization.html |only CDMConnector-2.5.0/CDMConnector/inst/doc/a08_dag-caching.R |only CDMConnector-2.5.0/CDMConnector/inst/doc/a08_dag-caching.Rmd |only CDMConnector-2.5.0/CDMConnector/inst/doc/a08_dag-caching.html |only CDMConnector-2.5.0/CDMConnector/man/generateCohortSet2.Rd |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-circe-builders-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-circe-domains.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-circe-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-dag_cache-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-dag_cache.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-execution_graph-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-generateCohortSet2-db.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-generateCohortSet2-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-generateCohortSet2-postgres.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-optimizer-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-optimizer.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-sqlrender-extra.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-sqlrender.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-translate-lightweight.R |only CDMConnector-2.5.0/CDMConnector/tests/testthat/test-translate_lightweight-extra.R |only CDMConnector-2.5.0/CDMConnector/vignettes/a07_batch-optimization.Rmd |only CDMConnector-2.5.0/CDMConnector/vignettes/a08_dag-caching.Rmd |only CDMConnector-2.5.1/CDMConnector/DESCRIPTION | 6 CDMConnector-2.5.1/CDMConnector/MD5 | 75 ++------ CDMConnector-2.5.1/CDMConnector/NAMESPACE | 6 CDMConnector-2.5.1/CDMConnector/NEWS.md | 5 CDMConnector-2.5.1/CDMConnector/R/Eunomia.R | 8 CDMConnector-2.5.1/CDMConnector/R/cdm.R | 18 ++ CDMConnector-2.5.1/CDMConnector/R/cdmFromCohortSet.R | 3 CDMConnector-2.5.1/CDMConnector/R/cdmSubset.R | 2 CDMConnector-2.5.1/CDMConnector/R/cdmTrimVocabulary.R |only CDMConnector-2.5.1/CDMConnector/R/cohortTransformations.R |only CDMConnector-2.5.1/CDMConnector/R/dbSource.R | 53 ++++-- CDMConnector-2.5.1/CDMConnector/R/generateCohortSet.R | 2 CDMConnector-2.5.1/CDMConnector/R/generateConceptCohortSet.R | 2 CDMConnector-2.5.1/CDMConnector/R/utils.R | 38 ++++ CDMConnector-2.5.1/CDMConnector/build/vignette.rds |binary CDMConnector-2.5.1/CDMConnector/inst/doc/a01_getting-started.html | 58 +++--- CDMConnector-2.5.1/CDMConnector/inst/doc/a02_cohorts.html | 84 +++++----- CDMConnector-2.5.1/CDMConnector/inst/doc/a03_dbplyr.html | 4 CDMConnector-2.5.1/CDMConnector/inst/doc/a06_using_cdm_attributes.html | 4 CDMConnector-2.5.1/CDMConnector/man/cdmTrimVocabulary.Rd |only CDMConnector-2.5.1/CDMConnector/tests/testthat/_problems |only CDMConnector-2.5.1/CDMConnector/tests/testthat/test-03-db-generateCohortSet.R | 11 - CDMConnector-2.5.1/CDMConnector/tests/testthat/test-cdmTrimVocabulary.R |only CDMConnector-2.5.1/CDMConnector/tests/testthat/test-cohort-transformations-extra.R |only CDMConnector-2.5.1/CDMConnector/tests/testthat/test-misc-extra.R | 59 ------- CDMConnector-2.5.1/CDMConnector/tests/testthat/testthat-problems.rds |only 58 files changed, 219 insertions(+), 219 deletions(-)
Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this
package. The backports are conditionally exported in order to let R resolve
the function name to either the implemented backport, or the respective base
version, if available. Package developers can make use of new functions or
arguments by selectively importing specific backports to
support older installations.
Author: Michel Lang [cre, aut] ,
Duncan Murdoch [aut],
R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between backports versions 1.5.0 dated 2024-05-23 and 1.5.1 dated 2026-04-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ src/dotsElt.c | 24 ++++++++++++++++-------- src/dotsLength.c | 16 ++++++++++++---- src/dotsNames.c | 48 +++++++++++++++++++++++++++--------------------- 6 files changed, 69 insertions(+), 43 deletions(-)
Title: Comprehensive Unit Root and Stationarity Tests
Description: A unified framework for unit root and stationarity testing
including quantile ADF tests (Koenker and Xiao, 2004)
<doi:10.1198/016214504000001114>, GARCH-based unit root tests with
endogenous structural breaks (Narayan and Liu, 2015)
<doi:10.1016/j.eneco.2014.11.021>, and comprehensive Dickey-Fuller,
Phillips-Perron, KPSS, ERS/DF-GLS, Zivot-Andrews, and
Kobayashi-McAleer tests with an Elder-Kennedy decision strategy
(Elder and Kennedy, 2001) <doi:10.1080/00220480109595179>.
Author: Muhammad Abdullah Alkhalaf [aut, cre, cph]
Maintainer: Muhammad Abdullah Alkhalaf <muhammedalkhalaf@gmail.com>
Diff between unitrootests versions 1.0.0 dated 2026-03-27 and 1.1.0 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 55 +++++++++++++++++++++++++++---------------------------- R/garchur_main.R | 1 + R/qadf_main.R | 48 +++++++----------------------------------------- R/qadf_methods.R | 6 +----- R/urstat_main.R | 4 ++++ 7 files changed, 50 insertions(+), 84 deletions(-)
Title: A Fast and Light Package to Compute Polygenic Risk Scores
Description: Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".
Author: Guillermo Reales [aut, cre] ,
Chris Wallace [aut] ,
Olly Burren [ctb]
Maintainer: Guillermo Reales <grealesm@gmail.com>
This is a re-admission after prior archival of version 2.3.1 dated 2025-02-19
Diff between RapidoPGS versions 2.3.1 dated 2025-02-19 and 2.3.2 dated 2026-04-02
DESCRIPTION | 21 MD5 | 64 - NAMESPACE | 56 NEWS.md | 219 ++- R/data.R | 152 +- R/globals.R | 2 R/rapfunc.R | 1798 ++++++++++++++++---------------- README.md | 142 +- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 38 inst/doc/Computing_RapidoPGSmulti.R | 60 - inst/doc/Computing_RapidoPGSmulti.Rmd | 708 ++++++------ inst/doc/Computing_RapidoPGSmulti.html | 1476 +++++++++++++------------- inst/doc/Computing_RapidoPGSsingle.R | 102 - inst/doc/Computing_RapidoPGSsingle.Rmd | 356 +++--- inst/doc/Computing_RapidoPGSsingle.html | 1251 +++++++++++----------- man/EUR_ld.blocks19.Rd | 52 man/EUR_ld.blocks38.Rd | 54 man/create_1000G.Rd | 98 - man/find_file_in_ftp.Rd | 52 man/gwascat.download.Rd | 60 - man/logsum.Rd | 42 man/michailidou19.Rd | 64 - man/michailidou38.Rd | 64 - man/rapidopgs_multi.Rd | 248 ++-- man/rapidopgs_single.Rd | 214 +-- man/sd.prior.est.Rd | 84 - man/sdY.est.Rd | 60 - man/wakefield_pp.Rd | 60 - man/wakefield_pp_quant.Rd | 68 - vignettes/Computing_RapidoPGSmulti.Rmd | 708 ++++++------ vignettes/Computing_RapidoPGSsingle.Rmd | 356 +++--- 33 files changed, 4369 insertions(+), 4360 deletions(-)
Title: Approximate Bayesian Latent Variable Analysis
Description: Implements approximate Bayesian inference for Structural
Equation Models (SEM) using a custom adaptation of the Integrated
Nested Laplace Approximation (Rue et al., 2009)
<doi:10.1111/j.1467-9868.2008.00700.x> as described in Jamil and Rue
(2026a) <doi:10.48550/arXiv.2603.25690>. Provides a computationally
efficient alternative to Markov Chain Monte Carlo (MCMC) for Bayesian
estimation, allowing users to fit latent variable models using the
'lavaan' syntax. See also the companion paper on implementation and
workflows, Jamil and Rue (2026b) <doi:10.48550/arXiv.2604.00671>.
Author: Haziq Jamil [aut, cre, cph] ,
Havard Rue [ctb] ,
Alvin Bong [ctb]
Maintainer: Haziq Jamil <haziq.jamil@gmail.com>
Diff between INLAvaan versions 0.2.3 dated 2026-01-28 and 0.2.4 dated 2026-04-02
INLAvaan-0.2.3/INLAvaan/R/zzz_OLD_log-likelihood-and-grad.R |only INLAvaan-0.2.3/INLAvaan/R/zzz_OLD_log-prior-and-grad.R |only INLAvaan-0.2.3/INLAvaan/inst/examples/heywood.R |only INLAvaan-0.2.3/INLAvaan/man/fitMeasures.Rd |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-ecmerkle.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-mismatch.R |only INLAvaan-0.2.3/INLAvaan/tests/testthat/test-variance_estimation.R |only INLAvaan-0.2.3/INLAvaan/vignettes/glycemic-table.png |only INLAvaan-0.2.4/INLAvaan/DESCRIPTION | 23 INLAvaan-0.2.4/INLAvaan/MD5 | 189 - INLAvaan-0.2.4/INLAvaan/NAMESPACE | 59 INLAvaan-0.2.4/INLAvaan/NEWS.md | 35 INLAvaan-0.2.4/INLAvaan/R/INLAvaan-class.R | 26 INLAvaan-0.2.4/INLAvaan/R/INLAvaan-package.R | 48 INLAvaan-0.2.4/INLAvaan/R/compare.R | 217 + INLAvaan-0.2.4/INLAvaan/R/create_lav_from_inlavaan_internal.R | 5 INLAvaan-0.2.4/INLAvaan/R/globals.R |only INLAvaan-0.2.4/INLAvaan/R/inlavaan.R | 481 +-- INLAvaan-0.2.4/INLAvaan/R/lavaan-unexported.R | 12 INLAvaan-0.2.4/INLAvaan/R/log-likelihood-and-grad.R | 8 INLAvaan-0.2.4/INLAvaan/R/log-prior-and-grad.R | 98 INLAvaan-0.2.4/INLAvaan/R/method-diagnostics.R |only INLAvaan-0.2.4/INLAvaan/R/method-fitmeasures.R | 502 +++ INLAvaan-0.2.4/INLAvaan/R/method-others.R |only INLAvaan-0.2.4/INLAvaan/R/method-plot.R | 271 + INLAvaan-0.2.4/INLAvaan/R/method-predict.R | 1224 +++++++- INLAvaan-0.2.4/INLAvaan/R/method-sampling.R |only INLAvaan-0.2.4/INLAvaan/R/method-show.R | 2 INLAvaan-0.2.4/INLAvaan/R/method-simulate.R |only INLAvaan-0.2.4/INLAvaan/R/method-summary.R | 77 INLAvaan-0.2.4/INLAvaan/R/method-timing.R |only INLAvaan-0.2.4/INLAvaan/R/method-vcov.R | 50 INLAvaan-0.2.4/INLAvaan/R/norta.R |only INLAvaan-0.2.4/INLAvaan/R/pars_to_x.R | 4 INLAvaan-0.2.4/INLAvaan/R/partable.R | 4 INLAvaan-0.2.4/INLAvaan/R/posterior-marginals.R | 64 INLAvaan-0.2.4/INLAvaan/R/posterior-sampling.R | 408 +- INLAvaan-0.2.4/INLAvaan/R/priors_for.R |only INLAvaan-0.2.4/INLAvaan/R/qsnorm_fast.R | 114 INLAvaan-0.2.4/INLAvaan/R/rgeneric.R | 8 INLAvaan-0.2.4/INLAvaan/R/skew-normal.R | 19 INLAvaan-0.2.4/INLAvaan/R/sobol.R |only INLAvaan-0.2.4/INLAvaan/R/standardisedsolution.R | 16 INLAvaan-0.2.4/INLAvaan/R/sysdata.rda |only INLAvaan-0.2.4/INLAvaan/R/utils-compare_mcmc.R | 623 +++- INLAvaan-0.2.4/INLAvaan/R/utils-inlavaan.R |only INLAvaan-0.2.4/INLAvaan/R/utils-optim.R |only INLAvaan-0.2.4/INLAvaan/R/utils-visual_debug.R | 213 + INLAvaan-0.2.4/INLAvaan/R/utils.R | 175 - INLAvaan-0.2.4/INLAvaan/R/zzz.R | 26 INLAvaan-0.2.4/INLAvaan/README.md | 180 - INLAvaan-0.2.4/INLAvaan/demo |only INLAvaan-0.2.4/INLAvaan/inst/CITATION |only INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.R | 21 INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.html | 369 +- INLAvaan-0.2.4/INLAvaan/inst/doc/INLAvaan.qmd | 56 INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.R | 2 INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.html | 1470 +++++++--- INLAvaan-0.2.4/INLAvaan/inst/doc/mediation.qmd | 2 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-model_comparison.R | 8 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-sampling.R |only INLAvaan-0.2.4/INLAvaan/inst/examples/ex-simulate.R |only INLAvaan-0.2.4/INLAvaan/inst/examples/ex-skewnorm-fit.R | 49 INLAvaan-0.2.4/INLAvaan/inst/examples/ex-stdsoln.R | 12 INLAvaan-0.2.4/INLAvaan/inst/validation-tests |only INLAvaan-0.2.4/INLAvaan/man/INLAvaan-class.Rd | 69 INLAvaan-0.2.4/INLAvaan/man/INLAvaan-package.Rd | 14 INLAvaan-0.2.4/INLAvaan/man/acfa.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/agrowth.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/asem.Rd | 70 INLAvaan-0.2.4/INLAvaan/man/bfit_indices.Rd |only INLAvaan-0.2.4/INLAvaan/man/compare.Rd | 57 INLAvaan-0.2.4/INLAvaan/man/diagnostics.Rd |only INLAvaan-0.2.4/INLAvaan/man/figures/README-fig-compare-poldem-1.png |binary INLAvaan-0.2.4/INLAvaan/man/fit_skew_normal.Rd | 49 INLAvaan-0.2.4/INLAvaan/man/fitmeasures.Rd |only INLAvaan-0.2.4/INLAvaan/man/get_inlavaan_internal.Rd |only INLAvaan-0.2.4/INLAvaan/man/inlavaan.Rd | 64 INLAvaan-0.2.4/INLAvaan/man/plot.Rd |only INLAvaan-0.2.4/INLAvaan/man/predict.Rd |only INLAvaan-0.2.4/INLAvaan/man/priors_for.Rd |only INLAvaan-0.2.4/INLAvaan/man/qsnorm_fast.Rd | 7 INLAvaan-0.2.4/INLAvaan/man/sampling.Rd |only INLAvaan-0.2.4/INLAvaan/man/simulate.Rd |only INLAvaan-0.2.4/INLAvaan/man/standardisedsolution.Rd | 15 INLAvaan-0.2.4/INLAvaan/man/timing.Rd |only INLAvaan-0.2.4/INLAvaan/man/vcov.Rd |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-binary.R | 25 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-cfa.R | 24 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-compare.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-diagnostics.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-equality_constraints.R | 48 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-fast_jacobian.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-fitmeasures.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-growth.R | 74 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-loglik.R | 2 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-multilevel.R | 117 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-mvn_loglik.R | 2 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-norta.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-plot.R | 42 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-predict.R | 121 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-priors.R | 108 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-priors_for.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-qsnorm_fast.R | 26 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sampling.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sem.R | 65 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-simulate.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-sobol.R |only INLAvaan-0.2.4/INLAvaan/tests/testthat/test-standardised_solution.R | 29 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-utils.R | 37 INLAvaan-0.2.4/INLAvaan/tests/testthat/test-vcov.R |only INLAvaan-0.2.4/INLAvaan/vignettes/INLAvaan.qmd | 56 INLAvaan-0.2.4/INLAvaan/vignettes/mediation.qmd | 2 INLAvaan-0.2.4/INLAvaan/vignettes/refs.bib | 42 114 files changed, 6133 insertions(+), 2342 deletions(-)
Title: Bayesian Quantile Regression Models for Complex Survey Data
Analysis
Description: Provides Bayesian quantile regression models for complex survey data
under informative sampling using survey-weighted estimators. Both single- and
multiple-output models are supported. To accelerate computation, all algorithms
are implemented in 'C++' using 'Rcpp', 'RcppArmadillo', and 'RcppEigen', and
are called from 'R'. See Nascimento and Gonçalves (2024) <doi:10.1093/jssam/smae015>
and Nascimento and Gonçalves (2025, in press) <https://academic.oup.com/jssam>.
Author: Tomas Rodriguez Taborda [aut, cre],
Johnatan Cardona Jimenez [aut],
Marcus L. Nascimento [aut],
Kelly Cristina Mota Goncalves [aut]
Maintainer: Tomas Rodriguez Taborda <torodriguezt@unal.edu.co>
Diff between bayesQRsurvey versions 0.2.0 dated 2026-03-27 and 0.2.1 dated 2026-04-02
DESCRIPTION | 8 +- MD5 | 19 +++--- NEWS.md | 25 ++++++++- R/bqr.svy.R | 2 R/mo.bqr.svy.R | 2 R/plot_quantile.R | 150 ++++++++++++++++++++++++++++++++---------------------- build |only data/Anthro.rda |binary man/Anthro.Rd | 2 man/bqr.svy.Rd | 2 man/mo.bqr.svy.Rd | 2 11 files changed, 133 insertions(+), 79 deletions(-)
Title: 'LiDAR' Terrain Analysis and Change Detection from Above
Description: Terrain change detection, cut and fill volume estimation,
terrain profiling, flood inundation analysis, slope and aspect
computation, hillshade generation, contour extraction, reclamation
monitoring, erosion analysis, and engineering export (LandXML, STL)
from 'LiDAR' (Light Detection and Ranging) point clouds and digital
elevation models ('DEMs'). Applications include surface mine
reclamation monitoring, sediment pond capacity tracking, highwall
safety classification, and erosion channel detection. Built on 'lidR'
for point cloud I/O and 'terra' for raster operations. Includes
access utilities for 'KyFromAbove' cloud-native elevation data on
Amazon Web Services ('AWS') <https://kyfromabove.ky.gov/>. Methods
for terrain change detection and volume estimation follow Li and
others (2005) <doi:10.1016/j.geomorph.2004.10.007>.
Author: Chris Lyons [aut, cre]
Maintainer: Chris Lyons <chris.lyons@ky.gov>
Diff between aboveR versions 0.1.0 dated 2026-03-19 and 1.0.0 dated 2026-04-02
DESCRIPTION | 32 - MD5 | 75 ++- NAMESPACE | 79 ++- NEWS.md |only R/export.R |only R/flood.R |only R/highwall.R | 228 +++++++--- R/kfa_counties.R |only R/kfa_read.R | 374 ++++++++--------- R/kfa_stac.R | 72 ++- R/kfa_tiles.R | 260 +++++------ R/security.R |only R/terrain.R |only R/utils.R | 346 +++++++-------- R/visualize.R | 90 ++-- README.md | 197 ++++----- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST |only inst/doc/getting-started.R | 114 ++--- inst/doc/getting-started.html | 890 ++++++++++++++++++++--------------------- man/aboveR-package.Rd | 50 +- man/bench_detection.Rd |only man/change_colors.Rd |only man/contour_lines.Rd |only man/export_landxml.Rd |only man/export_stl.Rd |only man/flood_colors.Rd |only man/flood_depth.Rd |only man/flood_inundation.Rd |only man/has_s3_access.Rd | 40 - man/height_above_drainage.Rd |only man/hillshade.Rd |only man/kfa_county_bbox.Rd |only man/kfa_find_tiles.Rd | 94 ++-- man/kfa_list_counties.Rd |only man/kfa_read_dem.Rd | 70 +-- man/kfa_read_ortho.Rd | 64 +- man/kfa_read_pointcloud.Rd | 60 +- man/kfa_stac_search.Rd | 62 +- man/kfa_tile_index.Rd | 58 +- man/slope_aspect.Rd |only man/terrain_colors.Rd |only man/zonal_stats.Rd |only tests/testthat/test-counties.R |only tests/testthat/test-export.R |only tests/testthat/test-exports.R | 75 ++- tests/testthat/test-flood.R |only tests/testthat/test-highwall.R | 69 +-- tests/testthat/test-kfa.R | 2 tests/testthat/test-security.R |only tests/testthat/test-terrain.R |only 52 files changed, 1823 insertions(+), 1578 deletions(-)
Title: Using Relative Abundance Data to Estimate of Multiplicative
Differences in Mean Absolute Abundance
Description: A differential abundance method for the analysis of microbiome data. 'radEmu' estimates fold-differences in the abundance of taxa across samples relative to "typical" fold-differences. Notably, it does not require pseudocounts, nor choosing a denominator taxon. For more details, see Clausen et al. (2026) <doi:10.1093/biomet/asag009>.
Author: David Clausen [aut],
Amy D Willis [aut, cre] ,
Sarah Teichman [aut]
Maintainer: Amy D Willis <adwillis@uw.edu>
Diff between radEmu versions 2.3.1.0 dated 2026-03-26 and 2.3.2.0 dated 2026-04-02
DESCRIPTION | 6 - MD5 | 30 +++--- README.md | 8 + inst/doc/intro_radEmu.html | 4 inst/doc/intro_radEmu_with_phyloseq.html | 4 inst/doc/intro_radEmu_with_tse.html | 4 inst/doc/parallel_radEmu.html | 4 inst/doc/quick_start.html | 4 inst/doc/radEmu_clustered_data.html | 4 inst/doc/radEmu_with_reference_taxon.html | 4 tests/testthat/test-X_cup_from_X.R | 3 tests/testthat/test-emuFit_micro.R | 123 +------------------------- tests/testthat/test-emuFit_micro_penalized.R | 3 tests/testthat/test-fit_null_discrete.R | 2 tests/testthat/test-get_G_for_augmentations.R | 2 tests/testthat/test-macro_fisher_null.R | 97 -------------------- 16 files changed, 52 insertions(+), 250 deletions(-)
Title: Standardization-Based Effect Estimation with Optional Prior
Covariance Adjustment
Description: The Prognostic Regression Offsets with Propagation of
ERrors (for Treatment Effect Estimation) package facilitates
direct adjustment for experiments and observational studies that
is compatible with a range of study designs and covariance
adjustment strategies. It uses explicit specification of clusters,
blocks and treatment allocations to furnish probability of
assignment-based weights targeting any of several average
treatment effect parameters, and for standard error calculations
reflecting these design parameters. For covariance adjustment of
its Hajek and (one-way) fixed effects estimates, it enables
offsetting the outcome against predictions from a dedicated
covariance model, with standard error calculations propagating
error as appropriate from the covariance model.
Author: Josh Errickson [cre, aut],
Josh Wasserman [aut],
Mark Fredrickson [ctb],
Adam Sales [ctb],
Xinhe Wang [ctb],
Ben Hansen [aut]
Maintainer: Josh Errickson <jerrick@umich.edu>
Diff between propertee versions 1.0.4 dated 2026-01-23 and 1.0.5 dated 2026-04-02
DESCRIPTION | 6 MD5 | 34 ++-- NEWS.md | 9 + R/SandwichLayerVariance.R | 136 +++++++++------- R/teeMod.R | 230 ++++++++++++++++------------ R/weights_internal.R | 3 build/partial.rdb |binary build/vignette.rds |binary inst/doc/RDD.html | 4 inst/doc/intro-to-propertee.html | 4 inst/doc/non-binary-treatment.html | 4 man/bread.teeMod.Rd | 4 man/dot-align_and_extend_estfuns.Rd | 15 + man/dot-check_df_moderator_estimates.Rd | 1 man/estfun.teeMod.Rd | 10 - man/sandwich_elements_calc.Rd | 6 tests/testthat/test.SandwichLayerVariance.R | 62 ++++++- tests/testthat/test.teeMod.R | 192 +++++++++++++++++++++-- 18 files changed, 511 insertions(+), 209 deletions(-)
Title: Adaptive Sample Size Simulator
Description: A simulations-first sample size determination package that aims at making sample size formulae obsolete for most easily computable statistical experiments ; the main envisioned use case is clinical trials. The proposed clinical trial must be written by the user in the form of a function that takes as argument a sample size and returns a boolean (for whether or not the trial is a success). The 'adsasi' functions will then use it to find the correct sample size empirically. The unavoidable mis-specification is obviated by trying sample size values close to the right value, the latter being understood as the value that gives the probability of success the user wants (usually 80 or 90% in biostatistics, corresponding to 20 or 10% type II error).
Author: Skerdi Haviari [aut, cre]
Maintainer: Skerdi Haviari <skerdi.haviari@aphp.fr>
Diff between adsasi versions 0.9.0.1 dated 2026-02-01 and 0.9.0.2 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/adsasi_0d.r | 24 ++++++++++++------------ R/adsasi_1d.r | 52 ++++++++++++++++++++++++++-------------------------- man/adsasi_0d.Rd | 2 +- man/adsasi_1d.Rd | 4 ++-- 6 files changed, 49 insertions(+), 49 deletions(-)
Title: Stationary Subspace Analysis
Description: Stationary subspace analysis (SSA) is a blind source separation (BSS) variant where stationary components are separated from non-stationary components. Several SSA methods for multivariate time series are provided here (Flumian et al. (2024) <doi:10.1016/j.cam.2023.115379>; Hara et al. (2010) <doi:10.1007/978-3-642-17537-4_52>) along with functions to simulate time series with time-varying variance and autocovariance (Patilea and Raissi(2014) <doi:10.1080/01621459.2014.884504>).
Author: Markus Matilainen [cre, aut] ,
Lea Flumian [aut],
Klaus Nordhausen [aut] ,
Sara Taskinen [aut]
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between ssaBSS versions 0.1.1 dated 2022-12-01 and 0.1.2 dated 2026-04-02
DESCRIPTION | 21 +++++++++++---------- MD5 | 16 ++++++++-------- NAMESPACE | 4 +++- inst/ChangeLog | 5 +++++ man/SSAcomb.Rd | 2 +- man/SSAcor.Rd | 2 +- man/SSAsave.Rd | 2 +- man/SSAsir.Rd | 2 +- man/ssaBSS-package.Rd | 20 ++++++++++---------- 9 files changed, 41 insertions(+), 33 deletions(-)
Title: Fast and Effortless Calibration of Agent-Based Models using
Machine Learning
Description: Provides tools and pre-trained Machine Learning [ML] models for
calibration of Agent-Based Models [ABMs] built with the R package
'epiworldR'. Implements methods described in Najafzadehkhoei, Vega Yon,
Modenesi, and Meyer (2025) <doi:10.48550/arXiv.2509.07013>. Users can
automatically calibrate ABMs in seconds with pre-trained ML models,
effectively focusing on simulation rather than calibration. Bridges a gap
by allowing public health practitioners to run their own ABMs without the
advanced technical expertise often required by calibration.
Author: Sima Najafzadehkhoei [aut, cre] ,
George Vega Yon [aut] ,
Jake Wagoner [aut],
Bernardo Modenesi [aut],
Centers for Disease Control and Prevention [fnd]
Maintainer: Sima Najafzadehkhoei <sima.njf@utah.edu>
Diff between epiworldRcalibrate versions 0.1.2 dated 2026-02-18 and 0.1.4 dated 2026-04-02
epiworldRcalibrate-0.1.2/epiworldRcalibrate/man/dot-find_python.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/DESCRIPTION | 12 epiworldRcalibrate-0.1.4/epiworldRcalibrate/MD5 | 21 epiworldRcalibrate-0.1.4/epiworldRcalibrate/NAMESPACE | 1 epiworldRcalibrate-0.1.4/epiworldRcalibrate/R/calibrate_sir.R | 615 ++++------ epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.bib |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.html |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/inst/paper.md | 329 +++-- epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/check_python_setup.Rd | 5 epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-required_python_modules.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-required_python_packages.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-resolve_python_target.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/dot-verify_python_imports.Rd |only epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/epiworldRcalibrate-package.Rd | 1 epiworldRcalibrate-0.1.4/epiworldRcalibrate/man/setup_python_deps.Rd | 22 15 files changed, 520 insertions(+), 486 deletions(-)
More information about epiworldRcalibrate at CRAN
Permanent link
Title: Sensitivity Analysis with 'mrgsolve'
Description: Perform sensitivity analysis on ordinary differential equation
based models, including ad-hoc graphical analyses based on structured
sequences of parameters as well as local sensitivity analysis. Functions
are provided for creating inputs, simulating scenarios and plotting outputs.
Author: Kyle Baron [aut, cre]
Maintainer: Kyle Baron <kylebtwin@imap.cc>
Diff between mrgsim.sa versions 0.2.0 dated 2023-12-08 and 0.3.0 dated 2026-04-02
DESCRIPTION | 15 +- MD5 | 82 ++++++------- NAMESPACE | 5 NEWS.md | 26 ++++ R/AAA.R | 39 +++--- R/lsa.R | 43 ++++--- R/parseq.R | 23 +-- R/sens.R | 2 R/sens_each.R | 6 R/sens_grid.R | 1 R/sens_plot.R | 183 ++++++++++++++++++++++++++---- R/sens_run.R | 4 R/seq.R | 31 ++--- R/utils.R | 17 ++ build/vignette.rds |binary inst/doc/mrgsim.sa.R | 27 ++-- inst/doc/mrgsim.sa.Rmd | 31 +++-- inst/doc/mrgsim.sa.html | 36 +++-- man/as.data.frame.sens_each.Rd | 2 man/denest.Rd | 2 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/lsa.Rd | 8 - man/mrgsim.sa.Rd | 10 + man/parseq_cv.Rd | 4 man/parseq_fct.Rd | 2 man/parseq_range.Rd | 2 man/plot.lsa.Rd | 10 + man/select_par.Rd | 4 man/sens_fun.Rd | 2 man/sens_plot.Rd | 55 ++++++++- man/sens_run.Rd | 4 man/seq_cv.Rd | 2 man/seq_fct.Rd | 2 tests/testthat/test-lsa.R | 15 ++ tests/testthat/test-sens-plot.R | 158 +++++++++++++++++++++++++ tests/testthat/test-sens_grid.R | 15 ++ vignettes/mrgsim.sa.Rmd | 31 +++-- 42 files changed, 704 insertions(+), 195 deletions(-)
Title: Fit Difference-in-Differences Models with Staggered
Interventions
Description: Fits linear difference-in-differences models in scenarios where
intervention roll-outs are staggered over time. The package implements a
version of an approach proposed by Sun and Abraham (2021)
<doi:10.1016/j.jeconom.2020.09.006> to estimate cohort- and
time-since-treatment specific difference-in-differences parameters, and it
provides convenience functions both for specifying the model and for
flexibly aggregating coefficients to answer a variety of research questions.
Author: Kyle Hart [aut, cre, cph] ,
Stephan Lindner [aut]
Maintainer: Kyle Hart <hartky@ohsu.edu>
Diff between staggR versions 0.1.1 dated 2026-01-14 and 0.2.0 dated 2026-04-02
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++++--------- NAMESPACE | 2 + NEWS.md | 5 ++++ R/detrend.R |only R/detrend_factor.R |only R/pick_time_refs.R | 6 +++++ R/sdid.R | 36 ++++++++++++++++++++++++++--------- inst/doc/staggR.R | 37 ++++++++++++++++++++++++++++++++---- inst/doc/staggR.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++----- inst/doc/staggR.html | 51 +++++++++++++++++++++++++++++++++++++++++++++----- man/detrend.Rd |only man/detrend_factor.Rd |only vignettes/staggR.Rmd | 46 ++++++++++++++++++++++++++++++++++++++++----- 14 files changed, 217 insertions(+), 40 deletions(-)
Title: A Calculator for Single-Case Effect Sizes
Description: Provides R functions for calculating basic effect size indices for
single-case designs, including several non-overlap measures and parametric
effect size measures, and for estimating the gradual effects model developed
by Swan and Pustejovsky (2018) <DOI:10.1080/00273171.2018.1466681>.
Standard errors and confidence intervals (based on the assumption that the outcome
measurements are mutually independent) are provided for the subset of effect sizes
indices with known sampling distributions.
Author: James E. Pustejovsky [aut, cre],
Man Chen [aut],
Daniel M. Swan [aut],
Paulina Grekov [ctb],
Amy Cai [ctb]
Maintainer: James E. Pustejovsky <jepusto@gmail.com>
Diff between SingleCaseES versions 0.7.3 dated 2024-09-07 and 0.7.4 dated 2026-04-02
DESCRIPTION | 22 MD5 | 18 NEWS.md | 4 R/calculate-effect-sizes.R | 22 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Effect-size-definitions.html | 23 inst/doc/Using-SingleCaseES.R | 18 inst/doc/Using-SingleCaseES.html | 858 ++++++++------------------- tests/testthat/test-SCD-effect-sizes.R | 1037 ++++++++++++++++----------------- 10 files changed, 841 insertions(+), 1161 deletions(-)
Title: Core File Structures and Workflows for 'RAVE'
Description: Defines storage standard for Read, process, and analyze
intracranial electroencephalography and deep-brain stimulation in 'RAVE',
a reproducible framework for analysis and visualization of iEEG
by Magnotti, Wang, and Beauchamp, (2020,
<doi:10.1016/j.neuroimage.2020.117341>).
Supports brain imaging data structure (BIDS)
<https://bids.neuroimaging.io> and native file structure to
ingest signals from 'Matlab' data files, hierarchical data format 5 (HDF5),
European data format (EDF), BrainVision core data format (BVCDF), or
BlackRock Microsystem (NEV/NSx); process images in
Neuroimaging informatics technology initiative (NIfTI) and
'FreeSurfer' formats, providing brain imaging normalization to template
brain, facilitating 'threeBrain' package for comprehensive electrode
localization via 'YAEL' (your advanced electrode localizer) by Wang,
Magnotti, Zhang, and Beauchamp
(2023, <doi:10.1523/ENEURO.0328-23.2023>).
Author: Zhengjia Wang [aut, cre] ,
Xiang Zhang [aut],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravecore versions 0.1.0 dated 2025-09-23 and 0.1.1 dated 2026-04-02
DESCRIPTION | 10 MD5 | 259 +++++---- NAMESPACE | 4 NEWS.md | 44 + R/aaa-cmd.R | 27 - R/aaa-common.R | 29 - R/aaa-constants.R | 6 R/class002-project.R | 114 ++-- R/class003-subject-internal.R | 176 +++--- R/class004-epoch.R | 60 +- R/class005-subject.R | 308 +++++------ R/class006-rawsubject.R | 246 ++++----- R/class007-abstract_electrode.R | 142 ++--- R/class008-LFP_electrode.R | 264 +++++----- R/class008-LFP_reference.R | 254 ++++----- R/class009-Auxiliary_channel.R | 134 ++--- R/class010-Spike_channel.R | 142 ++--- R/class011-YAEL_process.R | 163 +++--- R/class012-rave_brain.R | 50 + R/class100-base_repository.R | 96 ++- R/class101-epoched_repository.R | 64 +- R/class102-epoched_rawvoltage.R | 18 R/class103-epoched_voltage.R | 16 R/class104-epoched_time-frequency.R | 22 R/class111-recording_blocks_repository.R | 28 - R/class112-recording_blocks_rawvoltage.R | 30 - R/class112-recording_blocks_voltage.R | 28 - R/class113-recording_blocks_coefs.R | 18 R/cmd-tools.R | 72 +- R/import-brainvision.R | 36 - R/import-edf.R | 42 - R/import-h5_matlab_per_block.R | 36 - R/import-h5_matlab_per_channel.R | 38 - R/import-nev.R | 50 - R/internal.R | 53 +- R/legacy-convert_backwards.R | 18 R/math-baseline_power.R | 50 - R/math-collapse_arrays.R | 60 +- R/utils-ants.R | 8 R/utils-bezier.R | 50 + R/utils-csv.R | 81 +-- R/utils-fs.R | 124 ++-- R/utils-matlab.R | 34 - R/utils-nifti2svg.R | 40 - R/utils-openneuro.R | 23 R/utils-operators.R | 7 R/utils-package.R | 8 R/utils-snapshot.R |only R/utils-spikeinterface.R |only R/utils-string.R | 22 R/utils-sys.R | 10 R/utils-tables.R | 64 +- R/validator-brainvision.R | 28 - R/validator-edf.R | 32 - R/validator-h5_matlab_per_block.R | 30 - R/validator-h5_matlab_per_channel.R | 66 +- R/validator-nev.R | 32 - R/validator-subject.R | 418 ++++++++-------- R/validator-time_windows.R | 18 R/visualization-plotly_signals.R | 146 ++--- R/visualization-voltage_repository.R | 160 +++--- R/workflow-ANTs_ct_mri_coregistration.R | 38 - R/workflow-afni_3dallineate.R | 18 R/workflow-archive-subject.R | 158 +++--- R/workflow-compose_channel.R | 74 +- R/workflow-dcm2niix.R | 38 - R/workflow-freesurfer_recon_all.R | 46 - R/workflow-fsl_flirt.R | 17 R/workflow-generate_reference.R | 20 R/workflow-import_electrode_coordinates.R | 20 R/workflow-niftyreg.R | 10 R/workflow-nipy_coreg.R | 14 R/workflow-template_mapping.R | 96 +-- R/workflow-volumetric_atlases.R |only R/workflow-wavelet.R | 76 +- R/workflow-yael_preprocess.R | 96 ++- R/zzz.R |only build/partial.rdb |binary inst/WORDLIST | 7 inst/ravecorepy |only inst/reports |only inst/shell-templates/rave-ants-coregistration.R | 8 inst/shell-templates/rave-ants-mri-to-template.R | 2 inst/shell-templates/rave-nifty-coregistration.R | 6 inst/shell-templates/rave-nipy-coregistration.R | 12 inst/shell-templates/yael-preprocess.R | 39 - man/RAVESubjectBaseRepository.Rd | 13 man/RAVESubjectEpochPhaseRepository.Rd | 1 man/RAVESubjectEpochPowerRepository.Rd | 1 man/RAVESubjectEpochRawVoltageRepository.Rd | 3 man/RAVESubjectEpochRepository.Rd | 3 man/RAVESubjectEpochTimeFreqBaseRepository.Rd | 3 man/RAVESubjectEpochTimeFreqCoefRepository.Rd | 1 man/RAVESubjectEpochVoltageRepository.Rd | 3 man/RAVESubjectRecordingBlockPhaseRepository.Rd | 3 man/RAVESubjectRecordingBlockPowerRepository.Rd | 3 man/RAVESubjectRecordingBlockRawVoltageRepository.Rd | 1 man/RAVESubjectRecordingBlockRepository.Rd | 3 man/RAVESubjectRecordingBlockTimeFreqBaseRepository.Rd | 1 man/RAVESubjectRecordingBlockTimeFreqCoefRepository.Rd | 3 man/RAVESubjectRecordingBlockVoltageRepository.Rd | 1 man/YAELProcess.Rd | 17 man/cmd_run_yael_preprocess.Rd | 7 man/generate_atlases_from_template.Rd |only man/get_available_morph_to_template.Rd |only man/prepare_subject_bare.Rd | 2 man/prepare_subject_with_epochs.Rd | 2 man/rave_brain.Rd | 2 man/snapshot_project.Rd |only man/transform_point_to_template.Rd | 2 tests/testthat/test-class008-LFP_electrode.R | 4 tests/testthat/test-class008-LFP_reference.R | 10 tests/testthat/test-class009-Auxiliary_channel.R | 4 tests/testthat/test-class011-YAEL_process.R | 2 tests/testthat/test-class100-base_repository.R | 28 - tests/testthat/test-class101-epoched_repository.R | 52 - tests/testthat/test-class103-epoched_voltage.R | 82 +-- tests/testthat/test-class104-epoched_time-frequency.R | 80 +-- tests/testthat/test-class112-recording_blocks_voltage.R | 70 +- tests/testthat/test-math-collapse_arrays.R | 18 120 files changed, 3095 insertions(+), 2733 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS
Optimization
Description: Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the
'Scilab' optimization documentation located at
<https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Bill Denney [ctb] ,
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukha [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.1-12 dated 2024-09-17 and 6.0.1-13 dated 2026-04-02
DESCRIPTION | 16 +++++++----- MD5 | 27 ++++++++++----------- NEWS.md | 10 +++++++ R/n1qn1.R | 2 - README.md | 3 ++ man/n1qn1.Rd | 2 - src/RcppExpMod.cpp | 22 ++++++++++++----- src/ajour.c | 24 +++++++++--------- src/calmaj.c | 2 - src/n1qn1_all.c | 46 ++++++++++++++++++------------------ src/proj.c | 2 - src/satur.c | 10 +++---- tests/testthat.R | 8 ++++++ tests/testthat/test-banana.R | 1 tests/testthat/test-memory-safety.R |only 15 files changed, 105 insertions(+), 70 deletions(-)
Title: Joint Model of Heterogeneous Repeated Measures and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data in the presence of heterogeneous within-subject variability, proposed by Li and colleagues (2023) <doi:10.48550/arXiv.2506.12741>.
The proposed method models the within-subject variability of the biomarker and associates it with the risk of the competing risks event. The time-to-event data is modeled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates.
The longitudinal outcome is modeled using a mixed-effects location and scale model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm. This is the final release of the 'JMH' package. Active development has been moved to the 'FastJM' package, which provides improved functionality and ongoing support. Users are strongly encouraged to transition to 'FastJM'.
Author: Shanpeng Li [aut, cre],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between JMH versions 1.0.3 dated 2024-02-20 and 1.0.4 dated 2026-04-02
JMH-1.0.3/JMH/R/bootsfit.R |only JMH-1.0.3/JMH/R/bootsfitMESA.R |only JMH-1.0.3/JMH/R/bootsfitRI.R |only JMH-1.0.3/JMH/R/bootsfitRISF.R |only JMH-1.0.3/JMH/R/bootsfitRISF_Brier.R |only JMH-1.0.3/JMH/R/bootsfitRISF_MAEQ.R |only JMH-1.0.3/JMH/R/bootsfitRI_Brier.R |only JMH-1.0.3/JMH/R/bootsfitRI_MAEQ.R |only JMH-1.0.3/JMH/R/bootsfitRI_MAEQ2.R |only JMH-1.0.3/JMH/R/bootsfitRIhomo.R |only JMH-1.0.3/JMH/R/bootsfitSF.R |only JMH-1.0.3/JMH/R/simJMMESA.R |only JMH-1.0.3/JMH/R/simJMdata.R |only JMH-1.0.3/JMH/R/simJMdataRI.R |only JMH-1.0.3/JMH/R/simJMdataRISF.R |only JMH-1.0.3/JMH/R/simJMdataRIhomo.R |only JMH-1.0.3/JMH/R/simJMdataSF.R |only JMH-1.0.3/JMH/R/simfit.R |only JMH-1.0.3/JMH/R/simfitMESA.R |only JMH-1.0.3/JMH/R/simfitRI.R |only JMH-1.0.3/JMH/R/simfitRISF.R |only JMH-1.0.3/JMH/R/simfitRISF_DPBrier.R |only JMH-1.0.3/JMH/R/simfitRISF_DPMAEQ.R |only JMH-1.0.3/JMH/R/simfitRI_DPBrier.R |only JMH-1.0.3/JMH/R/simfitRI_DPMAEQ.R |only JMH-1.0.3/JMH/R/simfitRIhomo.R |only JMH-1.0.3/JMH/R/simfitSF.R |only JMH-1.0.3/JMH/man/summary.AUCJMMLSM.Rd |only JMH-1.0.3/JMH/man/summary.MAEQJMMLSM.Rd |only JMH-1.0.3/JMH/man/summary.PEJMMLSM.Rd |only JMH-1.0.4/JMH/DESCRIPTION | 25 ++--- JMH-1.0.4/JMH/MD5 | 113 +++++++++-------------- JMH-1.0.4/JMH/NAMESPACE | 10 +- JMH-1.0.4/JMH/R/AUCJMMLSM.R | 111 ++++++++++++++++------- JMH-1.0.4/JMH/R/CindexCR.R |only JMH-1.0.4/JMH/R/ConcordanceJMMLSM.R |only JMH-1.0.4/JMH/R/GetBayes.R |only JMH-1.0.4/JMH/R/GetGHmatrix.R | 111 +++-------------------- JMH-1.0.4/JMH/R/Getinit.R | 2 JMH-1.0.4/JMH/R/JMH.R | 7 - JMH-1.0.4/JMH/R/JMMLSM.R | 10 +- JMH-1.0.4/JMH/R/MAEQJMMLSM.R | 26 ++++- JMH-1.0.4/JMH/R/PEJMMLSM.R | 40 +++++++- JMH-1.0.4/JMH/R/RcppExports.R | 12 ++ JMH-1.0.4/JMH/R/logLik.R | 4 JMH-1.0.4/JMH/R/logLikCR.R | 4 JMH-1.0.4/JMH/R/print.JMMLSM.R | 28 ++++- JMH-1.0.4/JMH/R/sortdata.R | 6 - JMH-1.0.4/JMH/R/summary.AUCJMMLSM.R | 24 +++-- JMH-1.0.4/JMH/R/summary.ConcordanceJMMLSM.R |only JMH-1.0.4/JMH/R/summary.JMMLSM.R | 10 ++ JMH-1.0.4/JMH/R/summary.MAEQJMMLSM.R | 5 - JMH-1.0.4/JMH/R/summary.PEJMMLSM.R | 4 JMH-1.0.4/JMH/R/survfitJMMLSM.R | 46 ++++++++- JMH-1.0.4/JMH/R/timeROC.R |only JMH-1.0.4/JMH/R/vcov.JMMLSM.R | 88 ++++++++++-------- JMH-1.0.4/JMH/README.md | 35 +++++-- JMH-1.0.4/JMH/inst |only JMH-1.0.4/JMH/man/AUCJMMLSM.Rd | 30 +++++- JMH-1.0.4/JMH/man/ConcordanceJMMLSM.Rd |only JMH-1.0.4/JMH/man/JMMLSM.Rd | 6 + JMH-1.0.4/JMH/man/MAEQJMMLSM.Rd | 11 ++ JMH-1.0.4/JMH/man/PEJMMLSM.Rd | 17 +++ JMH-1.0.4/JMH/man/summary.Rd |only JMH-1.0.4/JMH/man/survfitJMMLSM.Rd | 11 ++ JMH-1.0.4/JMH/src/RcppExports.cpp | 84 +++++++++++++++++ JMH-1.0.4/JMH/src/basics.cpp | 134 ++++++++++++++++++++++++++++ JMH-1.0.4/JMH/src/basics.h | 18 +++ JMH-1.0.4/JMH/src/getCov.cpp | 8 + JMH-1.0.4/JMH/src/getCovSF.cpp | 8 + JMH-1.0.4/JMH/src/getEC.cpp | 16 ++- JMH-1.0.4/JMH/src/getECIFall.cpp |only JMH-1.0.4/JMH/src/getECSF.cpp | 15 +-- JMH-1.0.4/JMH/src/getECSFad.cpp | 12 +- JMH-1.0.4/JMH/src/getECad.cpp | 23 ++-- JMH-1.0.4/JMH/src/getMC.cpp | 26 +++-- JMH-1.0.4/JMH/src/getMCSF.cpp | 18 ++- 77 files changed, 809 insertions(+), 349 deletions(-)
Title: Pre-Processing of 'GENEActiv' Data
Description: Analytics to read in and segment raw 'GENEActiv' accelerometer data into epochs and events.
For more details on the 'GENEActiv' device, see <https://activinsights.com/resources/geneactiv-support-1-2/>.
Author: Joss Langford [aut],
Ian Long [aut],
Jia Ying Chua [aut, cre],
Activinsights Ltd [cph]
Maintainer: Jia Ying Chua <jiayingc@activinsights.com>
Diff between GENEAcore versions 1.1.2 dated 2025-11-21 and 1.2.0 dated 2026-04-02
GENEAcore-1.1.2/GENEAcore/inst/extdata/100650Hz_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/1008667Hz.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/20Hz_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/667Hz.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/GENEAcore_Data_Dictionary_21Nov2025.pdf |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Incomplete_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Multi_page_reset_config_time.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Not_a_GENEActiv_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Not_contiguous.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/One_page_bin_file.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/One_page_reset_config_time.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Short_header.bin |only GENEAcore-1.1.2/GENEAcore/inst/extdata/Zero_data_pages.bin |only GENEAcore-1.2.0/GENEAcore/DESCRIPTION | 11 GENEAcore-1.2.0/GENEAcore/MD5 | 169 + GENEAcore-1.2.0/GENEAcore/NAMESPACE | 27 GENEAcore-1.2.0/GENEAcore/NEWS.md | 26 GENEAcore-1.2.0/GENEAcore/R/MPI_calibrate.R | 12 GENEAcore-1.2.0/GENEAcore/R/MPI_create.R | 169 + GENEAcore-1.2.0/GENEAcore/R/MPI_detect.R | 387 +-- GENEAcore-1.2.0/GENEAcore/R/aggregate_periods.R | 9 GENEAcore-1.2.0/GENEAcore/R/apply_measures.R | 3 GENEAcore-1.2.0/GENEAcore/R/coel_json_builder.R |only GENEAcore-1.2.0/GENEAcore/R/coel_json_create.R |only GENEAcore-1.2.0/GENEAcore/R/daily_measures.R |only GENEAcore-1.2.0/GENEAcore/R/geneabout.R |only GENEAcore-1.2.0/GENEAcore/R/geneabout_functions.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore.R | 324 --- GENEAcore-1.2.0/GENEAcore/R/geneacore_part1.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part2.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part3.R |only GENEAcore-1.2.0/GENEAcore/R/geneacore_part4.R |only GENEAcore-1.2.0/GENEAcore/R/math.R |only GENEAcore-1.2.0/GENEAcore/R/sample_binfile.R | 346 +-- GENEAcore-1.2.0/GENEAcore/R/step_counter.R | 64 GENEAcore-1.2.0/GENEAcore/R/utils.R | 576 ++++- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.R | 532 +++-- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.Rmd | 646 ++++-- GENEAcore-1.2.0/GENEAcore/inst/doc/GENEAcore.html | 685 +++++- GENEAcore-1.2.0/GENEAcore/inst/doc/breaking-changes.html | 1 GENEAcore-1.2.0/GENEAcore/inst/extdata/GENEAcore_Data_Dictionary_2Apr26.pdf |only GENEAcore-1.2.0/GENEAcore/inst/extdata/behavioural-bout-model-v1.0-to-coel-model-v2.0.csv |only GENEAcore-1.2.0/GENEAcore/inst/extdata/geneabout_functions.png |only GENEAcore-1.2.0/GENEAcore/inst/extdata/geneacore_functions.png |binary GENEAcore-1.2.0/GENEAcore/inst/extdata/math_example_13Mar26.R |only GENEAcore-1.2.0/GENEAcore/inst/extdata/rest-activity-model-v1.0-to-coel-model-v2.0.csv |only GENEAcore-1.2.0/GENEAcore/man/MPI_summary.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/MPI_toJSON.Rd |only GENEAcore-1.2.0/GENEAcore/man/aggregate_periods.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/apply_all.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/apply_calibration.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/binfile_summary.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/bouts_decision_tree.Rd |only GENEAcore-1.2.0/GENEAcore/man/calc_autocalparams.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/calculate_daily_activity_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/calculate_daily_sleep_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/check_MPI.Rd | 48 GENEAcore-1.2.0/GENEAcore/man/create_MPI.Rd | 2 GENEAcore-1.2.0/GENEAcore/man/create_coel_atoms_json.Rd |only GENEAcore-1.2.0/GENEAcore/man/create_event_mapping.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/create_summary.Rd | 10 GENEAcore-1.2.0/GENEAcore/man/cx_percentile.Rd |only GENEAcore-1.2.0/GENEAcore/man/detect_nonmovement.Rd | 26 GENEAcore-1.2.0/GENEAcore/man/detect_transitions.Rd | 32 GENEAcore-1.2.0/GENEAcore/man/expected_last_timestamp.Rd |only GENEAcore-1.2.0/GENEAcore/man/find_rest_intervals.Rd |only GENEAcore-1.2.0/GENEAcore/man/folder_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/fx_count.Rd |only GENEAcore-1.2.0/GENEAcore/man/geneabout.Rd |only GENEAcore-1.2.0/GENEAcore/man/geneacore.Rd | 80 GENEAcore-1.2.0/GENEAcore/man/geneacore_part1.Rd |only GENEAcore-1.2.0/GENEAcore/man/geneacore_part2.Rd |only GENEAcore-1.2.0/GENEAcore/man/geneacore_part3.Rd |only GENEAcore-1.2.0/GENEAcore/man/geneacore_part4.Rd |only GENEAcore-1.2.0/GENEAcore/man/get_UniqueBinFileIdentifier.Rd | 2 GENEAcore-1.2.0/GENEAcore/man/get_UniqueBinFileIdentifier.dir.Rd | 1 GENEAcore-1.2.0/GENEAcore/man/get_UniqueBinFileIdentifier.filepath.Rd | 3 GENEAcore-1.2.0/GENEAcore/man/get_UniqueBinFileIdentifier.vector.Rd | 3 GENEAcore-1.2.0/GENEAcore/man/get_cut_times.Rd | 2 GENEAcore-1.2.0/GENEAcore/man/get_events.Rd |only GENEAcore-1.2.0/GENEAcore/man/identifier_mapping.Rd |only GENEAcore-1.2.0/GENEAcore/man/mx_lx_window.Rd |only GENEAcore-1.2.0/GENEAcore/man/nonwear_rest_coverage.Rd |only GENEAcore-1.2.0/GENEAcore/man/remove_short_transitions.Rd | 7 GENEAcore-1.2.0/GENEAcore/man/sample_binfile.Rd | 8 GENEAcore-1.2.0/GENEAcore/man/single_file_measures.Rd |only GENEAcore-1.2.0/GENEAcore/man/step_counter.Rd | 4 GENEAcore-1.2.0/GENEAcore/man/valid_day_nonwear.Rd |only GENEAcore-1.2.0/GENEAcore/man/weighted_mean.Rd |only GENEAcore-1.2.0/GENEAcore/man/weighted_sum.Rd |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-MPI_create.R | 664 +++--- GENEAcore-1.2.0/GENEAcore/tests/testthat/test-MPI_detect.R | 131 - GENEAcore-1.2.0/GENEAcore/tests/testthat/test-apply_measures.R | 132 - GENEAcore-1.2.0/GENEAcore/tests/testthat/test-coel_json_create.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-daily_measures.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-geneabout_functions.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-geneacore.R | 381 +++ GENEAcore-1.2.0/GENEAcore/tests/testthat/test-math.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test-sample_binfile.R | 264 +- GENEAcore-1.2.0/GENEAcore/tests/testthat/test-step_counter.R | 95 GENEAcore-1.2.0/GENEAcore/tests/testthat/test-utils.R |only GENEAcore-1.2.0/GENEAcore/tests/testthat/test_aggregate_periods.R | 1026 +++++----- GENEAcore-1.2.0/GENEAcore/tests/testthat/testdata |only GENEAcore-1.2.0/GENEAcore/vignettes/GENEAcore.Rmd | 646 ++++-- 104 files changed, 4623 insertions(+), 2950 deletions(-)
Title: Check Text Files Content at a Glance
Description: Tools to help text files importation. It can return the
number of lines; print the first and last lines; convert encoding;
guess delimiters and file encoding. Operations are made without
reading the entire file before starting, resulting in good
performances with large files. This package provides an alternative to
a simple use of the 'head', 'tail', 'wc' and 'iconv' programs that are
not always available on machine where R is installed.
Author: David Gohel [aut, cre]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between fpeek versions 0.2.0 dated 2026-02-09 and 0.2.1 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/peek-guess-delim.R | 6 ++++-- 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Extracting and Visualizing Bayesian Graphical Models
Description: Fit and visualize the results of a Bayesian analysis of networks commonly found in psychology.
The package supports cross-sectional network models fitted using the packages 'BDgraph', 'bgms' and 'BGGM',
as well as network comparison tests fitted using the packages 'bgms' and 'BBGM'.
The package provides the parameter estimates, posterior inclusion probabilities, inclusion Bayes factor, and the
posterior density of the parameters. In addition, for 'BDgraph' and 'bgms' it allows to assess the posterior
structure space. Furthermore, the package comes with an extensive suite for visualizing results.
Author: Karoline Huth [aut, cre] ,
Sara Keetelaar [ctb],
Nikola Sekulovski [ctb],
Gali Geller [ctb]
Maintainer: Karoline Huth <k.huth@uva.nl>
Diff between easybgm versions 0.3.1 dated 2025-12-08 and 0.4.0 dated 2026-04-02
DESCRIPTION | 10 MD5 | 65 ++--- NAMESPACE | 2 R/AuxiliaryFunctions.R | 69 +++--- R/bgm_plot_class.R | 81 ++++--- R/easybgm.R | 27 +- R/easybgm_compare.R | 15 - R/functions.bdgraph.R | 77 +++--- R/functions.bggm.R | 9 R/functions.bgms.R | 86 ++++--- R/functions.bgmscompare.R | 144 ++++++++---- R/plottingfunctions.bgmCompare.R | 254 +++++++++++++++++----- R/plottingfunctions.bgms.R | 145 +++++++++++-- R/plottingfunctions.easybgm.R | 220 +++++++++++++++---- R/summary.easybgm.R | 76 +++++- R/summary.easybgm_compare.R | 139 +++++++++--- README.md | 135 ++++++++---- man/HDI.Rd | 4 man/centrality.Rd | 4 man/complexity_probs.Rd | 2 man/easybgm.Rd | 13 - man/easybgm_compare.Rd | 10 man/edgeevidence.Rd | 23 +- man/network.Rd | 17 + man/prior_sensitivity.Rd | 19 + man/readme_plots/easybgm_sticker.svg |only man/readme_plots/plot_edgeevidence.png |binary man/readme_plots/plot_network.png |binary man/structure.Rd | 4 man/structure_probs.Rd | 2 man/summary.easybgm.Rd | 15 + man/summary.easybgm_compare.Rd | 14 + tests/testthat/Rplots.pdf |binary tests/testthat/test-easybgm.R | 367 +++++++++++++++++---------------- 34 files changed, 1391 insertions(+), 657 deletions(-)
Title: Preprocessing and Feature Engineering Steps for Modeling
Description: A recipe prepares your data for modeling. We provide an
extensible framework for pipeable sequences of feature engineering
steps provides preprocessing tools to be applied to data. Statistical
parameters for the steps can be estimated from an initial data set and
then applied to other data sets. The resulting processed output can
then be used as inputs for statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
Emil Hvitfeldt [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Max Kuhn <max@posit.co>
Diff between recipes versions 1.3.1 dated 2025-05-21 and 1.3.2 dated 2026-04-02
recipes-1.3.1/recipes/tests/testthat/_snaps/R4.2 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.3 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.4 |only recipes-1.3.1/recipes/tests/testthat/_snaps/R4.5 |only recipes-1.3.2/recipes/DESCRIPTION | 18 recipes-1.3.2/recipes/MD5 | 249 +-- recipes-1.3.2/recipes/NEWS.md | 6 recipes-1.3.2/recipes/R/corr.R | 10 recipes-1.3.2/recipes/R/dummy.R | 4 recipes-1.3.2/recipes/R/impute_linear.R | 2 recipes-1.3.2/recipes/R/impute_mean.R | 4 recipes-1.3.2/recipes/R/impute_mode.R | 3 recipes-1.3.2/recipes/R/isomap.R | 26 recipes-1.3.2/recipes/R/misc.R | 7 recipes-1.3.2/recipes/R/newvalues.R | 4 recipes-1.3.2/recipes/R/nnmf.R | 15 recipes-1.3.2/recipes/R/pls.R | 4 recipes-1.3.2/recipes/R/select.R | 2 recipes-1.3.2/recipes/build/partial.rdb |binary recipes-1.3.2/recipes/build/vignette.rds |binary recipes-1.3.2/recipes/inst/doc/Dummies.html | 5 recipes-1.3.2/recipes/inst/doc/Roles.html | 5 recipes-1.3.2/recipes/inst/doc/Selecting_Variables.html | 5 recipes-1.3.2/recipes/inst/doc/Skipping.html | 5 recipes-1.3.2/recipes/inst/doc/recipes.html | 5 recipes-1.3.2/recipes/man/bake.Rd | 2 recipes-1.3.2/recipes/man/check_class.Rd | 2 recipes-1.3.2/recipes/man/check_cols.Rd | 2 recipes-1.3.2/recipes/man/check_missing.Rd | 2 recipes-1.3.2/recipes/man/check_new_values.Rd | 2 recipes-1.3.2/recipes/man/discretize.Rd | 2 recipes-1.3.2/recipes/man/get_data_types.Rd | 2 recipes-1.3.2/recipes/man/has_role.Rd | 6 recipes-1.3.2/recipes/man/prep.Rd | 2 recipes-1.3.2/recipes/man/recipe.Rd | 2 recipes-1.3.2/recipes/man/recipes.Rd | 2 recipes-1.3.2/recipes/man/recipes_argument_select.Rd | 2 recipes-1.3.2/recipes/man/recipes_eval_select.Rd | 2 recipes-1.3.2/recipes/man/rmd/num_comp.Rmd | 2 recipes-1.3.2/recipes/man/rmd/tunable-args.Rmd | 2 recipes-1.3.2/recipes/man/roles.Rd | 2 recipes-1.3.2/recipes/man/step_YeoJohnson.Rd | 2 recipes-1.3.2/recipes/man/step_bin2factor.Rd | 2 recipes-1.3.2/recipes/man/step_bs.Rd | 2 recipes-1.3.2/recipes/man/step_center.Rd | 2 recipes-1.3.2/recipes/man/step_classdist.Rd | 2 recipes-1.3.2/recipes/man/step_classdist_shrunken.Rd | 2 recipes-1.3.2/recipes/man/step_corr.Rd | 8 recipes-1.3.2/recipes/man/step_count.Rd | 2 recipes-1.3.2/recipes/man/step_depth.Rd | 2 recipes-1.3.2/recipes/man/step_discretize.Rd | 2 recipes-1.3.2/recipes/man/step_dummy.Rd | 2 recipes-1.3.2/recipes/man/step_dummy_extract.Rd | 2 recipes-1.3.2/recipes/man/step_dummy_multi_choice.Rd | 2 recipes-1.3.2/recipes/man/step_factor2string.Rd | 2 recipes-1.3.2/recipes/man/step_filter_missing.Rd | 4 recipes-1.3.2/recipes/man/step_geodist.Rd | 2 recipes-1.3.2/recipes/man/step_harmonic.Rd | 4 recipes-1.3.2/recipes/man/step_ica.Rd | 6 recipes-1.3.2/recipes/man/step_impute_bag.Rd | 4 recipes-1.3.2/recipes/man/step_impute_knn.Rd | 4 recipes-1.3.2/recipes/man/step_impute_linear.Rd | 4 recipes-1.3.2/recipes/man/step_impute_lower.Rd | 2 recipes-1.3.2/recipes/man/step_impute_mean.Rd | 4 recipes-1.3.2/recipes/man/step_impute_median.Rd | 2 recipes-1.3.2/recipes/man/step_impute_mode.Rd | 2 recipes-1.3.2/recipes/man/step_indicate_na.Rd | 2 recipes-1.3.2/recipes/man/step_integer.Rd | 2 recipes-1.3.2/recipes/man/step_interact.Rd | 2 recipes-1.3.2/recipes/man/step_intercept.Rd | 2 recipes-1.3.2/recipes/man/step_invlogit.Rd | 2 recipes-1.3.2/recipes/man/step_isomap.Rd | 6 recipes-1.3.2/recipes/man/step_kpca.Rd | 4 recipes-1.3.2/recipes/man/step_kpca_poly.Rd | 4 recipes-1.3.2/recipes/man/step_kpca_rbf.Rd | 4 recipes-1.3.2/recipes/man/step_lincomb.Rd | 2 recipes-1.3.2/recipes/man/step_nnmf.Rd | 17 recipes-1.3.2/recipes/man/step_nnmf_sparse.Rd | 4 recipes-1.3.2/recipes/man/step_normalize.Rd | 2 recipes-1.3.2/recipes/man/step_novel.Rd | 2 recipes-1.3.2/recipes/man/step_ns.Rd | 4 recipes-1.3.2/recipes/man/step_num2factor.Rd | 2 recipes-1.3.2/recipes/man/step_nzv.Rd | 2 recipes-1.3.2/recipes/man/step_other.Rd | 4 recipes-1.3.2/recipes/man/step_pca.Rd | 2 recipes-1.3.2/recipes/man/step_percentile.Rd | 2 recipes-1.3.2/recipes/man/step_pls.Rd | 4 recipes-1.3.2/recipes/man/step_poly.Rd | 4 recipes-1.3.2/recipes/man/step_poly_bernstein.Rd | 4 recipes-1.3.2/recipes/man/step_profile.Rd | 2 recipes-1.3.2/recipes/man/step_range.Rd | 2 recipes-1.3.2/recipes/man/step_ratio.Rd | 2 recipes-1.3.2/recipes/man/step_regex.Rd | 2 recipes-1.3.2/recipes/man/step_relevel.Rd | 2 recipes-1.3.2/recipes/man/step_relu.Rd | 2 recipes-1.3.2/recipes/man/step_rm.Rd | 2 recipes-1.3.2/recipes/man/step_scale.Rd | 2 recipes-1.3.2/recipes/man/step_spatialsign.Rd | 2 recipes-1.3.2/recipes/man/step_spline_b.Rd | 2 recipes-1.3.2/recipes/man/step_spline_convex.Rd | 2 recipes-1.3.2/recipes/man/step_spline_monotone.Rd | 2 recipes-1.3.2/recipes/man/step_spline_natural.Rd | 4 recipes-1.3.2/recipes/man/step_spline_nonnegative.Rd | 2 recipes-1.3.2/recipes/man/step_string2factor.Rd | 2 recipes-1.3.2/recipes/man/step_unknown.Rd | 2 recipes-1.3.2/recipes/man/step_window.Rd | 2 recipes-1.3.2/recipes/man/step_zv.Rd | 2 recipes-1.3.2/recipes/man/tidy.recipe.Rd | 2 recipes-1.3.2/recipes/man/update.step.Rd | 2 recipes-1.3.2/recipes/tests/testthat/_snaps/discretize.md | 12 recipes-1.3.2/recipes/tests/testthat/_snaps/isomap.md | 35 recipes-1.3.2/recipes/tests/testthat/_snaps/nnmf.md |only recipes-1.3.2/recipes/tests/testthat/_snaps/select.md | 2 recipes-1.3.2/recipes/tests/testthat/_snaps/selections.md | 10 recipes-1.3.2/recipes/tests/testthat/test-colcheck.R | 6 recipes-1.3.2/recipes/tests/testthat/test-date.R | 4 recipes-1.3.2/recipes/tests/testthat/test-discretize.R | 11 recipes-1.3.2/recipes/tests/testthat/test-dummy_extract.R | 20 recipes-1.3.2/recipes/tests/testthat/test-dummy_multi_choice.R | 55 recipes-1.3.2/recipes/tests/testthat/test-impute_knn.R | 39 recipes-1.3.2/recipes/tests/testthat/test-isomap.R | 73 recipes-1.3.2/recipes/tests/testthat/test-kpca_poly.R | 8 recipes-1.3.2/recipes/tests/testthat/test-nnmf.R |only recipes-1.3.2/recipes/tests/testthat/test-pls.R | 106 - recipes-1.3.2/recipes/tests/testthat/test-selections.R | 4 recipes-1.3.2/recipes/tests/testthat/test-term_info.R | 801 ++-------- 126 files changed, 694 insertions(+), 1104 deletions(-)
Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre],
Peter Steiner [aut],
Wai Wong [aut]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 2.3-0 dated 2026-02-28 and 2.3-1 dated 2026-04-02
Changelog | 174 +-- DESCRIPTION | 15 MD5 | 28 NAMESPACE | 1 R/kmassess.R | 47 R/kmsassess.R | 7 R/kmsurmiserelation.R | 5 build/partial.rdb |binary build/vignette.rds |binary inst/doc/kstMatrix.R | 48 - inst/doc/kstMatrix.Rmd | 505 +++++----- inst/doc/kstMatrix.html | 2240 ++++++----------------------------------------- man/kmassess.Rd | 10 man/kmsurmiserelation.Rd | 5 vignettes/kstMatrix.Rmd | 505 +++++----- 15 files changed, 1001 insertions(+), 2589 deletions(-)
Title: General-Purpose Unconstrained Non-Linear Optimization
Description: An algorithm for general-purpose unconstrained non-linear optimization.
The algorithm is of quasi-Newton type with BFGS updating of the inverse
Hessian and soft line search with a trust region type monitoring of the
input to the line search algorithm. The interface of 'ucminf' is
designed for easy interchange with 'optim'.
Author: K Herve Dakpo [ctb, cre],
Hans Bruun Nielsen [aut],
Stig Bousgaard Mortensen [aut]
Maintainer: K Herve Dakpo <k-herve.dakpo@inrae.fr>
Diff between ucminf versions 1.2.2 dated 2024-06-24 and 1.2.3 dated 2026-04-02
DESCRIPTION | 8 MD5 | 14 - NEWS.md | 50 +++-- R/ucminf.R | 512 ++++++++++++++++++++++++++++---------------------------- README.md | 202 +++++++++++----------- man/ucminf.Rd | 330 ++++++++++++++++++------------------ src/init.c | 3 src/interface.c | 150 +++++++++------- 8 files changed, 649 insertions(+), 620 deletions(-)
Title: Blind Source Separation and Supervised Dimension Reduction for
Time Series
Description: Different estimators are provided to solve the blind source separation problem for multivariate time series with stochastic volatility and supervised dimension reduction problem for multivariate time series. Different functions based on AMUSE and SOBI are also provided for estimating the dimension of the white noise subspace. The package is fully described in Nordhausen, Matilainen, Miettinen, Virta and Taskinen (2021) <doi:10.18637/jss.v098.i15>.
Author: Markus Matilainen [cre, aut] ,
Christophe Croux [aut],
Jari Miettinen [aut] ,
Klaus Nordhausen [aut] ,
Hannu Oja [aut],
Sara Taskinen [aut] ,
Joni Virta [aut]
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>
Diff between tsBSS versions 1.0.0 dated 2021-07-10 and 1.0.1 dated 2026-04-02
DESCRIPTION | 24 +++++++++++++----------- MD5 | 14 +++++++------- NAMESPACE | 4 +++- inst/ChangeLog | 4 ++++ man/WeeklyReturnsData.Rd | 2 +- man/tsBSS-package.Rd | 28 ++++++++++++++-------------- src/Makevars | 2 +- src/Makevars.win | 2 +- 8 files changed, 44 insertions(+), 36 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.4.0 dated 2026-03-17 and 2.5.0 dated 2026-04-02
GitStats-2.4.0/GitStats/R/gitstats_functions.R |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.R |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.Rmd |only GitStats-2.4.0/GitStats/inst/doc/get_repos_with_code.html |only GitStats-2.4.0/GitStats/vignettes/get_repos_with_code.Rmd |only GitStats-2.5.0/GitStats/DESCRIPTION | 14 GitStats-2.5.0/GitStats/MD5 | 122 +- GitStats-2.5.0/GitStats/NAMESPACE | 11 GitStats-2.5.0/GitStats/NEWS.md | 16 GitStats-2.5.0/GitStats/R/EngineGraphQL.R | 13 GitStats-2.5.0/GitStats/R/EngineGraphQLGitHub.R | 118 -- GitStats-2.5.0/GitStats/R/EngineGraphQLGitLab.R | 143 -- GitStats-2.5.0/GitStats/R/EngineRestGitHub.R | 33 GitStats-2.5.0/GitStats/R/EngineRestGitLab.R | 70 + GitStats-2.5.0/GitStats/R/GQLQueryGitHub.R | 18 GitStats-2.5.0/GitStats/R/GQLQueryGitLab.R | 75 - GitStats-2.5.0/GitStats/R/GitHost.R | 117 +- GitStats-2.5.0/GitStats/R/GitHostGitHub.R | 44 GitStats-2.5.0/GitStats/R/GitHostGitLab.R | 206 +++- GitStats-2.5.0/GitStats/R/GitStats-package.R | 1 GitStats-2.5.0/GitStats/R/GitStats.R | 486 ++++++++-- GitStats-2.5.0/GitStats/R/Storage.R |only GitStats-2.5.0/GitStats/R/get_repos.R | 16 GitStats-2.5.0/GitStats/R/global.R | 1 GitStats-2.5.0/GitStats/R/utils.R | 59 + GitStats-2.5.0/GitStats/README.md | 37 GitStats-2.5.0/GitStats/build/vignette.rds |binary GitStats-2.5.0/GitStats/inst/doc/set_hosts.R | 24 GitStats-2.5.0/GitStats/inst/doc/set_hosts.Rmd | 4 GitStats-2.5.0/GitStats/inst/doc/store_data.R |only GitStats-2.5.0/GitStats/inst/doc/store_data.Rmd |only GitStats-2.5.0/GitStats/inst/doc/store_data.html |only GitStats-2.5.0/GitStats/man/create_gitstats.Rd | 2 GitStats-2.5.0/GitStats/man/get_repos.Rd | 14 GitStats-2.5.0/GitStats/man/get_storage.Rd | 2 GitStats-2.5.0/GitStats/man/get_storage_metadata.Rd |only GitStats-2.5.0/GitStats/man/is_verbose.Rd | 2 GitStats-2.5.0/GitStats/man/remove_from_storage.Rd |only GitStats-2.5.0/GitStats/man/remove_postgres_storage.Rd |only GitStats-2.5.0/GitStats/man/remove_sqlite_storage.Rd |only GitStats-2.5.0/GitStats/man/set_local_storage.Rd |only GitStats-2.5.0/GitStats/man/set_parallel.Rd |only GitStats-2.5.0/GitStats/man/set_postgres_storage.Rd |only GitStats-2.5.0/GitStats/man/set_sqlite_storage.Rd |only GitStats-2.5.0/GitStats/man/show_hosts.Rd | 2 GitStats-2.5.0/GitStats/man/show_orgs.Rd | 2 GitStats-2.5.0/GitStats/man/verbose_off.Rd | 2 GitStats-2.5.0/GitStats/man/verbose_on.Rd | 2 GitStats-2.5.0/GitStats/tests/testthat/_snaps/01-get_repos-GitHub.md | 4 GitStats-2.5.0/GitStats/tests/testthat/_snaps/01-get_repos-GitLab.md | 33 GitStats-2.5.0/GitStats/tests/testthat/_snaps/02-get_commits-GitLab.md | 2 GitStats-2.5.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitHub.md | 15 GitStats-2.5.0/GitStats/tests/testthat/_snaps/03-get_files_structure-GitLab.md | 13 GitStats-2.5.0/GitStats/tests/testthat/_snaps/z-GitStats.md | 8 GitStats-2.5.0/GitStats/tests/testthat/helper-fixtures-repos.R | 71 + GitStats-2.5.0/GitStats/tests/testthat/helper.R | 13 GitStats-2.5.0/GitStats/tests/testthat/setup.R | 2 GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitHub.R | 6 GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitLab.R | 394 +++++++- GitStats-2.5.0/GitStats/tests/testthat/test-01-get_repos-GitStats.R | 5 GitStats-2.5.0/GitStats/tests/testthat/test-03-get_files_structure-GitHub.R | 190 --- GitStats-2.5.0/GitStats/tests/testthat/test-03-get_files_structure-GitLab.R | 201 ---- GitStats-2.5.0/GitStats/tests/testthat/test-GitHost-helpers.R | 37 GitStats-2.5.0/GitStats/tests/testthat/test-get_files_tree-REST.R |only GitStats-2.5.0/GitStats/tests/testthat/test-get_storage.R | 6 GitStats-2.5.0/GitStats/tests/testthat/test-get_urls_repos-GitStats.R | 21 GitStats-2.5.0/GitStats/tests/testthat/test-incremental-cache.R |only GitStats-2.5.0/GitStats/tests/testthat/test-parallel.R |only GitStats-2.5.0/GitStats/tests/testthat/test-set_storage.R |only GitStats-2.5.0/GitStats/tests/testthat/test-utils.R | 114 ++ GitStats-2.5.0/GitStats/tests/testthat/test-z-GitStats.R | 44 GitStats-2.5.0/GitStats/vignettes/set_hosts.Rmd | 4 GitStats-2.5.0/GitStats/vignettes/store_data.Rmd |only 73 files changed, 1887 insertions(+), 952 deletions(-)
Title: Access Finnish Geospatial Data
Description: Designed to simplify geospatial data access from the Statistics Finland Web Feature Service API <https://geo.stat.fi/geoserver/index.html>, the geofi package offers researchers and analysts a set of tools to obtain and harmonize administrative spatial data for a wide range of applications, from urban planning to environmental research. The package contains annually updated time series of municipality key datasets that can be used for data aggregation and language translations.
Author: Markus Kainu [aut, cre] ,
Joona Lehtomaki [aut] ,
Juuso Parkkinen [ctb] ,
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Sampo Vesanen [ctb],
Leo Lahti [aut]
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.2.0 dated 2026-03-02 and 1.2.1 dated 2026-04-02
DESCRIPTION | 10 MD5 | 48 +-- NEWS.md | 4 R/check_api_access.R | 2 R/firstlib.R | 7 R/get_municipalities.R | 4 R/get_municipality_pop.R | 4 R/get_population_grid.R | 4 R/get_statistical_grid.R | 4 R/get_zipcodes.R | 4 R/ogc_api_nls.R | 1 R/wfs_api.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/geofi_datasets.html | 4 inst/doc/geofi_joining_attribute_data.html | 4 inst/doc/geofi_making_maps.html | 365 ++++++++++++----------------- inst/doc/geofi_nls_ogc.html | 4 inst/doc/geofi_spatial_analysis.Rmd | 2 inst/doc/geofi_spatial_analysis.html | 6 inst/doc/geofi_statfi_ogc.html | 4 inst/extdata/wfs_providers.yaml | 4 man/check_api_access.Rd | 2 man/wfs_api.Rd | 4 vignettes/geofi_spatial_analysis.Rmd | 2 25 files changed, 222 insertions(+), 279 deletions(-)
Title: F1 Pit Stop Datasets
Description: Formula 1 pit stop data. The package provides information on teams and drivers across seasons (2019 or higher). It also includes a function to visualize pit stop performance.
Author: Jose Jordan-Soria [aut, cre]
Maintainer: Jose Jordan-Soria <jjose.jjordan@gmail.com>
Diff between f1pits versions 0.2.0 dated 2026-03-08 and 1.2.0 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 1 + NEWS.md | 14 ++++++++++++-- R/pitchamp.R |only R/pitplot.R | 3 +++ R/pits.R | 2 +- inst/CITATION | 2 +- inst/doc/f1pits-intro.R | 6 ++++++ inst/doc/f1pits-intro.Rmd | 13 +++++++++++-- inst/doc/f1pits-intro.html | 22 +++++++++++++++++----- man/pitchamp.Rd |only man/pits.Rd | 2 +- tests/testthat/test-pitchamp.R |only tests/testthat/testdata/2015.csv |only vignettes/f1pits-intro.Rmd | 13 +++++++++++-- 16 files changed, 83 insertions(+), 29 deletions(-)
Title: Functions for Declared Missing Values
Description: A zero dependency package containing functions to declare labels
and missing values, coupled with associated functions to create (weighted)
tables of frequencies and various other summary measures.
Some of the base functions have been rewritten to make use of the specific
information about the missing values, most importantly to distinguish
between empty NA and declared NA values.
Some functions have similar functionality with the corresponding ones from
packages "haven" and "labelled". The aim is to ensure as much compatibility
as possible with these packages, while offering an alternative in the
objects of class "declared".
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between declared versions 0.25 dated 2024-09-08 and 0.26 dated 2026-04-02
declared-0.25/declared/R/w_IQR.R |only declared-0.25/declared/R/w_fivenum.R |only declared-0.25/declared/R/w_mean.R |only declared-0.25/declared/R/w_median.R |only declared-0.25/declared/R/w_mode.R |only declared-0.25/declared/R/w_quantile.R |only declared-0.25/declared/R/w_sd.R |only declared-0.25/declared/R/w_standardize.R |only declared-0.25/declared/R/w_summary.R |only declared-0.25/declared/R/w_table.R |only declared-0.25/declared/R/w_var.R |only declared-0.26/declared/DESCRIPTION | 16 -- declared-0.26/declared/MD5 | 54 ++++----- declared-0.26/declared/NAMESPACE | 18 ++- declared-0.26/declared/R/class_methods.R | 22 +++ declared-0.26/declared/R/declared.R | 87 ++++++++++++++- declared-0.26/declared/R/declared_package.R | 4 declared-0.26/declared/R/drop_undeclare.R | 2 declared-0.26/declared/R/internals.R | 38 +++--- declared-0.26/declared/R/measurement.R | 6 - declared-0.26/declared/R/onLoad.R | 137 ++++++++++++++++++++++++ declared-0.26/declared/R/print.R | 92 ++++++++++------ declared-0.26/declared/R/wIQR.R |only declared-0.26/declared/R/wfivenum.R |only declared-0.26/declared/R/wmean.R |only declared-0.26/declared/R/wmedian.R |only declared-0.26/declared/R/wmode.R |only declared-0.26/declared/R/wquantile.R |only declared-0.26/declared/R/wsd.R |only declared-0.26/declared/R/wstandardize.R |only declared-0.26/declared/R/wsummary.R |only declared-0.26/declared/R/wtable.R |only declared-0.26/declared/R/wvar.R |only declared-0.26/declared/man/declared.Rd | 8 + declared-0.26/declared/man/declared_internal.Rd | 51 ++++++++ declared-0.26/declared/man/declared_package.Rd | 4 declared-0.26/declared/man/measurement.Rd | 4 declared-0.26/declared/man/weighted.Rd | 88 +++++++-------- declared-0.26/declared/src/declared.c | 19 +++ 39 files changed, 496 insertions(+), 154 deletions(-)
Title: Acknowledge all Contributors to a Project
Description: Acknowledge all contributors to a project via a single
function call. The function appends to a 'README' or other specified
file(s) a table with names of all individuals who contributed via code
or repository issues. The package also includes several additional
functions to extract and quantify contributions to any repository.
Author: Mark Padgham [aut, cre],
Chris Hartgerink [aut],
Maelle Salmon [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between allcontributors versions 0.2.2 dated 2024-10-23 and 0.2.3 dated 2026-04-02
allcontributors-0.2.2/allcontributors/tests/testthat/getcontribs/gh-api/geodist/contributors-7ad99d-38c41e.json |only allcontributors-0.2.2/allcontributors/tests/testthat/getcontribs/gh-api/rate_limit-38c41e.json |only allcontributors-0.2.3/allcontributors/DESCRIPTION | 9 allcontributors-0.2.3/allcontributors/MD5 | 30 +- allcontributors-0.2.3/allcontributors/NEWS.md | 16 + allcontributors-0.2.3/allcontributors/R/add-contributors.R | 4 allcontributors-0.2.3/allcontributors/R/github.R | 20 + allcontributors-0.2.3/allcontributors/README.md | 148 +++++++++- allcontributors-0.2.3/allcontributors/build/vignette.rds |binary allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.R | 2 allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.Rmd | 2 allcontributors-0.2.3/allcontributors/inst/doc/allcontributors.html | 50 +-- allcontributors-0.2.3/allcontributors/man/get_contributors.Rd | 4 allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/geodist/contributors-7ad99d.json |only allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/graphql-8cf72c-POST.json | 130 ++++++++ allcontributors-0.2.3/allcontributors/tests/testthat/getcontribs/gh-api/rate_limit.json |only allcontributors-0.2.3/allcontributors/tests/testthat/test-get-contribs.R | 6 allcontributors-0.2.3/allcontributors/vignettes/allcontributors.Rmd | 2 18 files changed, 347 insertions(+), 76 deletions(-)
More information about allcontributors at CRAN
Permanent link
Title: Collection of Utility Functions for Data Analysis and Computing
Description: Provides utility functions for data analysis and computing. Includes functions for logging, parallel processing, and other computational tasks to streamline workflows.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisutils versions 0.4.3 dated 2026-03-06 and 0.4.4 dated 2026-04-02
DESCRIPTION | 12 MD5 | 53 ++- NAMESPACE | 10 NEWS.md | 16 + R/RcppExports.R | 18 - R/computation.R | 37 +- R/lisi.R |only R/log_message.R | 647 +++++++++++++++++++++++++++++++++++-------- R/parallelize_fun.R | 253 +++++++++++----- R/reexports.R | 2 R/sparse_cor.R | 5 R/thisutils-package.R | 2 R/utils.R | 57 ++- README.md | 2 man/compute_lisi.Rd |only man/compute_simpson_index.Rd |only man/is_apple_silicon.Rd |only man/is_linux.Rd |only man/is_osx.Rd |only man/is_windows.Rd |only man/log_message.Rd | 22 + man/parallelize_fun.Rd | 4 man/unnest_fun.Rd | 2 src/RcppExports.cpp | 55 +++ src/lisi.cpp |only src/matrix_to_table.cpp | 12 src/table_to_matrix.cpp | 55 ++- tests |only 28 files changed, 986 insertions(+), 278 deletions(-)
Title: Read and Write 'las' and 'laz' Binary File Formats Used for
Remote Sensing Data
Description: Read and write 'las' and 'laz' binary file formats. The LAS file format is a public file format for the interchange of 3-dimensional point cloud data between data users. The LAS specifications are approved by the American Society for Photogrammetry and Remote Sensing <https://community.asprs.org/leadership-restricted/leadership-content/public-documents/standards>. The LAZ file format is an open and lossless compression scheme for binary LAS format versions 1.0 to 1.4 <https://laszip.org/>.
Author: Jean-Romain Roussel [aut, cre, cph],
Florian De Boissieu [aut, ctb] ,
Martin Isenburg [cph] ,
David Auty [ctb] ,
Pierrick Marie [ctb] ,
Tiago de Conto [ctb]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between rlas versions 1.8.4 dated 2026-01-29 and 1.8.5 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/altrep_compact_replication.cpp | 5 +++-- src/rlasstreamer.cpp | 4 ++-- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [ctb] , [...truncated...]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3 versions 1.5.0 dated 2026-02-27 and 1.6.0 dated 2026-04-02
mlr3-1.5.0/mlr3/man/figures/block.png |only mlr3-1.5.0/mlr3/man/figures/block.svg |only mlr3-1.5.0/mlr3/man/figures/mlr3verse.svg |only mlr3-1.6.0/mlr3/DESCRIPTION | 8 mlr3-1.6.0/mlr3/MD5 | 457 ++++------ mlr3-1.6.0/mlr3/NEWS.md | 8 mlr3-1.6.0/mlr3/R/BenchmarkResult.R | 184 ++-- mlr3-1.6.0/mlr3/R/CallbackResample.R | 48 - mlr3-1.6.0/mlr3/R/ContextResample.R | 5 mlr3-1.6.0/mlr3/R/DataBackend.R | 4 mlr3-1.6.0/mlr3/R/DataBackendCbind.R | 7 mlr3-1.6.0/mlr3/R/DataBackendDataTable.R | 11 mlr3-1.6.0/mlr3/R/DataBackendRbind.R | 7 mlr3-1.6.0/mlr3/R/DataBackendRename.R | 6 mlr3-1.6.0/mlr3/R/HotstartStack.R | 38 mlr3-1.6.0/mlr3/R/Learner.R | 327 +++++-- mlr3-1.6.0/mlr3/R/LearnerClassif.R | 40 mlr3-1.6.0/mlr3/R/LearnerClassifDebug.R | 90 + mlr3-1.6.0/mlr3/R/LearnerClassifFeatureless.R | 27 mlr3-1.6.0/mlr3/R/LearnerClassifRpart.R | 29 mlr3-1.6.0/mlr3/R/LearnerRegr.R | 57 - mlr3-1.6.0/mlr3/R/LearnerRegrDebug.R | 14 mlr3-1.6.0/mlr3/R/LearnerRegrFeatureless.R | 19 mlr3-1.6.0/mlr3/R/LearnerRegrRpart.R | 17 mlr3-1.6.0/mlr3/R/Measure.R | 155 ++- mlr3-1.6.0/mlr3/R/MeasureAIC.R | 18 mlr3-1.6.0/mlr3/R/MeasureBIC.R | 18 mlr3-1.6.0/mlr3/R/MeasureClassif.R | 39 mlr3-1.6.0/mlr3/R/MeasureClassifCosts.R | 12 mlr3-1.6.0/mlr3/R/MeasureDebug.R | 3 mlr3-1.6.0/mlr3/R/MeasureElapsedTime.R | 10 mlr3-1.6.0/mlr3/R/MeasureInternalValidScore.R | 3 mlr3-1.6.0/mlr3/R/MeasureOOBError.R | 3 mlr3-1.6.0/mlr3/R/MeasureRegr.R | 39 mlr3-1.6.0/mlr3/R/MeasureRegrPinball.R | 3 mlr3-1.6.0/mlr3/R/MeasureRegrRQR.R | 7 mlr3-1.6.0/mlr3/R/MeasureRegrRSQ.R | 13 mlr3-1.6.0/mlr3/R/MeasureSelectedFeatures.R | 3 mlr3-1.6.0/mlr3/R/MeasureSimilarity.R | 38 mlr3-1.6.0/mlr3/R/MeasureSimple.R | 60 - mlr3-1.6.0/mlr3/R/Prediction.R | 29 mlr3-1.6.0/mlr3/R/PredictionClassif.R | 29 mlr3-1.6.0/mlr3/R/PredictionData.R | 13 mlr3-1.6.0/mlr3/R/PredictionDataClassif.R | 26 mlr3-1.6.0/mlr3/R/PredictionDataRegr.R | 26 mlr3-1.6.0/mlr3/R/PredictionRegr.R | 33 mlr3-1.6.0/mlr3/R/ResampleResult.R | 65 + mlr3-1.6.0/mlr3/R/Resampling.R | 36 mlr3-1.6.0/mlr3/R/ResamplingBootstrap.R | 15 mlr3-1.6.0/mlr3/R/ResamplingCV.R | 8 mlr3-1.6.0/mlr3/R/ResamplingCustom.R | 12 mlr3-1.6.0/mlr3/R/ResamplingCustomCV.R | 12 mlr3-1.6.0/mlr3/R/ResamplingHoldout.R | 9 mlr3-1.6.0/mlr3/R/ResamplingInsample.R | 9 mlr3-1.6.0/mlr3/R/ResamplingLOO.R | 4 mlr3-1.6.0/mlr3/R/ResamplingRepeatedCV.R | 15 mlr3-1.6.0/mlr3/R/ResamplingSubsampling.R | 28 mlr3-1.6.0/mlr3/R/ResultData.R | 165 ++- mlr3-1.6.0/mlr3/R/Task.R | 298 ++++-- mlr3-1.6.0/mlr3/R/TaskClassif.R | 12 mlr3-1.6.0/mlr3/R/TaskClassif_breast_cancer.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_german_credit.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_penguins.R | 9 mlr3-1.6.0/mlr3/R/TaskClassif_pima.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_sonar.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_spam.R | 3 mlr3-1.6.0/mlr3/R/TaskClassif_wine.R | 6 mlr3-1.6.0/mlr3/R/TaskGenerator.R | 22 mlr3-1.6.0/mlr3/R/TaskGenerator2DNormals.R | 15 mlr3-1.6.0/mlr3/R/TaskGeneratorCassini.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorCircle.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorFriedman1.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorMoons.R | 12 mlr3-1.6.0/mlr3/R/TaskGeneratorSimplex.R | 19 mlr3-1.6.0/mlr3/R/TaskGeneratorSmiley.R | 13 mlr3-1.6.0/mlr3/R/TaskGeneratorSpirals.R | 15 mlr3-1.6.0/mlr3/R/TaskGeneratorXor.R | 13 mlr3-1.6.0/mlr3/R/TaskRegr.R | 12 mlr3-1.6.0/mlr3/R/TaskSupervised.R | 5 mlr3-1.6.0/mlr3/R/TaskUnsupervised.R | 6 mlr3-1.6.0/mlr3/R/as_benchmark_result.R | 6 mlr3-1.6.0/mlr3/R/as_data_backend.R | 9 mlr3-1.6.0/mlr3/R/as_learner.R | 15 mlr3-1.6.0/mlr3/R/as_measure.R | 21 mlr3-1.6.0/mlr3/R/as_prediction.R | 16 mlr3-1.6.0/mlr3/R/as_prediction_classif.R | 11 mlr3-1.6.0/mlr3/R/as_prediction_data.R | 13 mlr3-1.6.0/mlr3/R/as_prediction_regr.R | 6 mlr3-1.6.0/mlr3/R/as_resample_result.R | 19 mlr3-1.6.0/mlr3/R/as_resampling.R | 15 mlr3-1.6.0/mlr3/R/as_result_data.R | 38 mlr3-1.6.0/mlr3/R/as_task.R | 15 mlr3-1.6.0/mlr3/R/as_task_classif.R | 42 mlr3-1.6.0/mlr3/R/as_task_regr.R | 21 mlr3-1.6.0/mlr3/R/as_task_unsupervised.R | 15 mlr3-1.6.0/mlr3/R/assertions.R | 211 +++- mlr3-1.6.0/mlr3/R/auto_convert.R | 7 mlr3-1.6.0/mlr3/R/benchmark.R | 52 - 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Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- common effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- three-level meta-analysis model;
- generalised linear mixed model;
- logistic regression with penalised likelihood for rare events;
- Hartung-Knapp method for random effects model;
- Kenward-Roger method for random effects model;
- prediction interval and density of the prediction distribution;
- expected proportion of comparable studies with clinically important benefit or harm;
- statistical tests for funnel plot asymmetry;
- trim-and-fill method to evaluate bias in meta-analysis;
- meta-regression;
- cumulative meta-analysis and leave-one-out meta-analysis;
- import data from 'RevMan 5';
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between meta versions 8.2-1 dated 2025-09-01 and 8.3-0 dated 2026-04-02
DESCRIPTION | 20 MD5 | 321 +++--- NAMESPACE | 12 NEWS.md | 102 + R/JAMAlabels.R | 17 R/amlodipine.R | 11 R/as.data.frame.meta.R | 57 - R/barplot.rob.R | 29 R/baujat.R | 77 - R/blup.meta.R | 15 R/bracket.longarm.R | 6 R/bracket.pairwise.R | 6 R/bubble.R | 8 R/caffeine.R | 8 R/catmeth-internal.R | 40 R/catmeth.R | 298 ++--- R/ci.R | 15 R/cidprop.R | 141 +- R/compsplit.R | 2 R/drapery.R | 275 ++--- R/estimates.R | 263 ++-- R/forest-internal.R | 437 ++++---- R/forest.R | 472 +++++--- R/forest.metabind.R | 190 +-- R/forest.metacum.R | 14 R/forest.metainf.R | 23 R/funnel.R | 247 ++-- R/gm.R | 38 R/gs.R | 1 R/hetcalc.R | 219 ++-- R/labbe.R | 186 +-- R/labels.meta.R | 19 R/longarm-internal.R | 10 R/longarm.R | 151 +- R/mean-sd-internal.R | 130 +- R/meta-aux.R | 286 ++--- R/meta-chk.R | 166 +-- R/meta-ci.R | 78 - R/meta-format.R | 50 R/meta-het.R | 80 - R/meta-internal.R | 355 +++--- R/meta-is.R | 14 R/meta-math.R | 200 +-- R/meta-object.R | 81 - R/meta-package.R | 21 R/meta-set.R | 64 - R/meta-transf.R | 123 +- R/meta-xlab.R | 70 - R/metaadd.R | 51 R/metabias.R | 276 ++--- R/metabias.rm5.R | 42 R/metabin.R | 547 +++++----- R/metabind-internal.R | 234 ++-- R/metabind.R | 377 +++---- R/metacont.R | 645 ++++++------ R/metacor.R | 355 +++--- R/metacr.R | 375 +++---- R/metacum.R | 226 ++-- R/metagen.R | 805 +++++++-------- R/metainc.R | 407 +++---- R/metainf.R | 234 ++-- R/metamean.R | 533 ++++------ R/metamerge-internal.R | 248 ++-- R/metamerge.R | 459 ++++---- R/metaprop.R | 531 ++++----- R/metarate.R | 469 ++++---- R/metareg.R | 133 +- R/nnt.R | 233 ++-- R/or2smd.R | 99 - R/pairwise-internal.R |only R/pairwise.R | 2395 +++++++++++++++++++++++---------------------- R/plot.cidprop.R | 19 R/print.meta.R | 514 ++++----- R/print.metacum.R | 12 R/print.metainf.R | 10 R/print.rm5.R | 25 R/print.summary.meta.R | 259 ++-- R/radial.R | 104 - R/rd.R |only R/read.cdir.R | 210 +-- R/read.mtv.R | 55 - R/read.rm5-internal.R | 484 ++++----- R/read.rm5.R | 19 R/rob-internal.R | 48 R/rob.R | 244 ++-- R/se-internal.R | 58 - R/settings.meta-internal.R | 56 - R/settings.meta.R | 459 ++++---- R/smd2or.R | 107 -- R/smlab.R | 4 R/smoking.R | 9 R/subgroup-internal.R | 16 R/subgroup.R | 456 ++++---- R/subset.longarm.R | 21 R/subset.pairwise.R | 18 R/summary.meta.R | 114 +- R/summary.rm5.R | 48 R/traffic_light.R | 31 R/trimfill.R | 326 +++--- R/trimfill.rm5.R | 68 - R/update.meta.R | 648 ++++++------ R/weights.meta.R | 29 R/woodyplants.R | 13 build/vignette.rds |binary inst/CITATION | 4 inst/doc/meta-tutorial.pdf |binary inst/doc/meta-workflow.pdf |binary man/amlodipine.Rd | 10 man/as.data.frame.meta.Rd | 12 man/barplot.rob.Rd | 8 man/baujat.meta.Rd | 20 man/blup.meta.Rd | 15 man/bubble.metareg.Rd | 6 man/caffeine.Rd | 8 man/cidprop.Rd | 12 man/drapery.Rd | 10 man/estimates.Rd | 25 man/forest.meta.Rd | 183 ++- man/forest.metabind.Rd | 12 man/forest.metacum.Rd | 14 man/forest.metainf.Rd | 14 man/funnel.meta.Rd | 12 man/labbe.Rd | 16 man/meta-object.Rd | 81 - man/meta-package.Rd | 13 man/metaadd.Rd | 10 man/metabias.Rd | 30 man/metabin.Rd | 66 - man/metabind.Rd | 32 man/metacont.Rd | 26 man/metacor.Rd | 18 man/metacr.Rd | 4 man/metacum.Rd | 24 man/metagen.Rd | 16 man/metainc.Rd | 20 man/metainf.Rd | 32 man/metamean.Rd | 20 man/metamerge.Rd | 66 - man/metaprop.Rd | 92 - man/metarate.Rd | 34 man/metareg.Rd | 48 man/nnt.Rd | 6 man/or2smd.Rd | 8 man/pairwise.Rd | 104 + man/plot.cidprop.Rd | 10 man/print.metacum.Rd | 10 man/print.metainf.Rd | 10 man/print.summary.meta.Rd | 10 man/radial.Rd | 4 man/rd.Rd |only man/rob.Rd | 8 man/smd2or.Rd | 10 man/smoking.Rd | 8 man/sub-.longarm.Rd | 4 man/sub-.pairwise.Rd | 4 man/subset.longarm.Rd | 2 man/subset.pairwise.Rd | 4 man/summary.meta.Rd | 10 man/traffic_light.Rd | 8 man/trimfill.Rd | 16 man/update.meta.Rd | 14 man/woodyplants.Rd | 12 vignettes/references.bib | 2 163 files changed, 10728 insertions(+), 10155 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] ,
Florian De Boissieu [ctb] ,
Andrew Sanchez Meador [ctb] for
segment_snags),
Bourdon Jean-Francois [ctb] for
track_sensor),
Gatziolis Demetrios [ctb] for
track_sensor),
Leon Steinmeier [c [...truncated...]
Maintainer: Jean-Romain Roussel <info@r-lidar.com>
Diff between lidR versions 4.2.3 dated 2026-01-08 and 4.3.0 dated 2026-04-02
DESCRIPTION | 8 - MD5 | 78 ++++++++++++------- NAMESPACE | 4 NEWS.md | 8 + R/RcppExports.R | 8 + R/algorithm-dsm.R | 97 ++++++++++++++++++++++++ R/algorithm-gnd.R | 84 ++++++++++++++++++++ R/catalog_boundaries.R | 22 +++++ R/classify.R | 4 inst/doc/lidR-LAS-class.html | 5 - inst/doc/lidR-LAScatalog-class.html | 5 - inst/doc/lidR-LAScatalog-engine.html | 5 - inst/doc/lidR-catalog-apply-examples.html | 5 - inst/doc/lidR-computation-speed-LAScatalog.html | 5 - inst/include/lidR/Grid3D.h | 2 man/catalog_split_clusters.Rd |only man/classify.Rd | 4 man/dsm_pitfree.Rd | 1 man/dsm_point2raster.Rd | 1 man/dsm_spikefree.Rd |only man/dsm_tin.Rd | 3 man/gnd_csf.Rd | 3 man/gnd_mcc.Rd | 3 man/gnd_pmf.Rd | 3 man/ptd.Rd |only src/C_ptd.cpp |only src/C_spikefree.cpp |only src/LAS.cpp | 8 - src/Makevars | 22 +++++ src/RcppExports.cpp | 34 ++++++++ src/hporro |only src/knn.cpp | 2 src/nanoflann |only src/ptd |only src/spikefree |only tests/testthat/Rplots.pdf |binary tests/testthat/test-classify_ground.R | 15 +++ tests/testthat/test-rasterize_canopy.R | 18 ++++ 38 files changed, 401 insertions(+), 56 deletions(-)
Title: Using CF-Compliant Calendars with Climate Projection Data
Description: Support for all calendars as specified in the Climate and Forecast
(CF) Metadata Conventions for climate and forecasting data. The CF Metadata
Conventions is widely used for distributing files with climate observations
or projections, including the Coupled Model Intercomparison Project (CMIP)
data used by climate change scientists and the Intergovernmental Panel on
Climate Change (IPCC). This package specifically allows the user to work
with any of the CF-compliant calendars (many of which are not compliant with
POSIXt). The CF time coordinate is formally defined in the CF Metadata
Conventions document available at <https://cf-convention.github.io/Data/cf-conventions/cf-conventions-1.13/cf-conventions.html#time-coordinate>.
Author: Patrick Van Laake [aut, cre, cph]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between CFtime versions 1.7.2 dated 2025-11-12 and 1.7.3 dated 2026-04-02
DESCRIPTION | 8 - LICENSE | 2 MD5 | 68 +++++----- NAMESPACE | 1 NEWS.md | 141 ++++++---------------- R/CFCalendar.R | 17 ++ R/CFCalendar360.R | 10 + R/CFCalendar365.R | 11 + R/CFCalendar366.R | 11 + R/CFCalendarNone.R | 13 ++ R/CFCalendarProleptic.R | 2 R/CFClimatology.R | 10 - R/CFtime-package.R | 7 - R/CFtime.R | 224 +++++++++++++++++++++--------------- R/api.R | 125 ++++++++++++-------- R/helpers.R | 8 - README.md | 36 +++-- TODO | 1 man/CFCalendar.Rd | 28 ++++ man/CFCalendar360.Rd | 24 +++ man/CFCalendar365.Rd | 24 +++ man/CFCalendar366.Rd | 24 +++ man/CFCalendarJulian.Rd | 1 man/CFCalendarNone.Rd | 23 +++ man/CFCalendarProleptic.Rd | 1 man/CFCalendarStandard.Rd | 1 man/CFCalendarTAI.Rd | 1 man/CFCalendarUTC.Rd | 1 man/CFClimatology.Rd | 3 man/CFTime.Rd | 52 +++++--- man/CFtime-package.Rd | 7 - man/plus-.CFTime.Rd | 56 +++++---- tests/testthat/test-CFtime.R | 18 +- tests/testthat/test-functions.R | 34 +++-- tests/testthat/test-parse_deparse.R | 22 +-- 35 files changed, 629 insertions(+), 386 deletions(-)
Title: Utility Functions for Plotting
Description: Provides utility functions for plotting. Includes functions for color manipulation, plot customization, panel size control, data optimization for plots, and layout adjustments.
Author: Meng Xu [aut, cre]
Maintainer: Meng Xu <mengxu98@qq.com>
Diff between thisplot versions 0.3.6 dated 2026-03-07 and 0.3.7 dated 2026-04-02
DESCRIPTION | 19 - MD5 | 26 +- NAMESPACE | 2 NEWS.md | 14 + R/GraphPlot.R |only R/StatPlot.R | 74 +++++- R/compute_velocity_on_grid.R |only R/heatmap.R | 5 R/palettes.R | 2 R/sankey.R | 371 +++++++++++++++++++++------------- README.md | 2 man/GraphPlot.Rd |only man/annotation_block_fill_graphics.Rd | 2 man/build_heatmap_annotation.Rd | 2 man/compute_velocity_on_grid.Rd |only man/palette_colors.Rd | 2 16 files changed, 342 insertions(+), 179 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.5-1 dated 2026-02-01 and 3.6-0 dated 2026-04-02
DESCRIPTION | 16 +- MD5 | 36 ++--- NEWS | 10 + build/vignette.rds |binary inst/doc/NAobjects.pdf |binary inst/doc/bugfixes.Rnw | 10 + inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 323 +++++++++++++++++++++++++++++++++++++++++++-- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 1 man/macros/defns.Rd | 3 vignettes/bugfixes.Rnw | 10 + vignettes/updates.Rnw | 323 +++++++++++++++++++++++++++++++++++++++++++-- 19 files changed, 677 insertions(+), 56 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically regular time series and air quality
measurement, meteorological data and dispersion model output can be
analysed. The package is described in Carslaw and Ropkins (2012,
<doi:10.1016/j.envsoft.2011.09.008>) and subsequent papers.
Author: David Carslaw [aut, cre] ,
Jack Davison [aut] ,
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 2.19.0 dated 2025-08-28 and 3.0.0 dated 2026-04-02
openair-2.19.0/openair/R/calcFno2.R |only openair-2.19.0/openair/R/date.breaks.R |only openair-2.19.0/openair/R/drawOpenKey.R |only openair-2.19.0/openair/R/linearRelation.R |only openair-2.19.0/openair/R/samp.boot.block.R |only openair-2.19.0/openair/R/summaryPlot.R |only openair-2.19.0/openair/R/zzz.R |only openair-2.19.0/openair/man/calcFno2.Rd |only openair-2.19.0/openair/man/drawOpenKey.Rd |only openair-2.19.0/openair/man/linearRelation.Rd |only openair-2.19.0/openair/man/summaryPlot.Rd |only openair-2.19.0/openair/src/Makevars |only openair-2.19.0/openair/src/Makevars.win |only openair-2.19.0/openair/src/init.c |only openair-2.19.0/openair/tests/testthat/test-bootMean.R |only openair-2.19.0/openair/tests/testthat/test-utilities.R |only openair-3.0.0/openair/DESCRIPTION | 23 openair-3.0.0/openair/MD5 | 300 openair-3.0.0/openair/NAMESPACE | 215 openair-3.0.0/openair/NEWS.md | 2558 +++--- openair-3.0.0/openair/R/GaussianSmooth.R |only openair-3.0.0/openair/R/RColorBrewer.R | 3586 ++++----- openair-3.0.0/openair/R/RcppExports.R |only openair-3.0.0/openair/R/TaylorDiagram.R | 1484 +-- openair-3.0.0/openair/R/TheilSen.R | 1498 +--- openair-3.0.0/openair/R/WhittakerSmooth.R |only openair-3.0.0/openair/R/aqStats.R | 746 -- openair-3.0.0/openair/R/bootMeans.R | 570 - openair-3.0.0/openair/R/calcPercentile.R | 262 openair-3.0.0/openair/R/calendarPlot.R | 1497 ++-- openair-3.0.0/openair/R/checkPrep.R | 345 openair-3.0.0/openair/R/conditionalEval.R | 1080 +- openair-3.0.0/openair/R/conditionalQuantile.R | 870 +- openair-3.0.0/openair/R/corPlot.R | 1172 +-- openair-3.0.0/openair/R/cutData.R | 1653 ++-- openair-3.0.0/openair/R/datePad.R |only openair-3.0.0/openair/R/facet_wd.R |only openair-3.0.0/openair/R/ggplot2-utils.R |only openair-3.0.0/openair/R/importADMS.R | 2461 +++--- openair-3.0.0/openair/R/importEurope.R | 435 - openair-3.0.0/openair/R/importImperial.R | 876 +- openair-3.0.0/openair/R/importMeta.R | 747 +- openair-3.0.0/openair/R/importTraj.R | 360 openair-3.0.0/openair/R/importUKAQ-utils.R | 1144 +-- openair-3.0.0/openair/R/importUKAQ.R | 1439 +-- openair-3.0.0/openair/R/layer_stroked_path.R |only openair-3.0.0/openair/R/layer_windflow.R |only openair-3.0.0/openair/R/modStats.R | 808 +- openair-3.0.0/openair/R/mydata.R | 62 openair-3.0.0/openair/R/openColours.R | 1190 +-- openair-3.0.0/openair/R/openair-package.R | 267 openair-3.0.0/openair/R/openair.generics.R | 74 openair-3.0.0/openair/R/percentileRose.R | 1277 +-- openair-3.0.0/openair/R/polarAnnulus.R | 1521 +--- openair-3.0.0/openair/R/polarCluster.R | 999 +- openair-3.0.0/openair/R/polarDiff.R | 401 - openair-3.0.0/openair/R/polarFreq.R | 948 +- openair-3.0.0/openair/R/polarPlot.R | 3559 ++++----- openair-3.0.0/openair/R/quickText.R | 438 - openair-3.0.0/openair/R/rollingMean.R | 276 openair-3.0.0/openair/R/rollingQuantile.R |only openair-3.0.0/openair/R/runRegression.R | 329 openair-3.0.0/openair/R/scatterPlot.R | 3715 ++++------ openair-3.0.0/openair/R/selectByDate.R | 359 openair-3.0.0/openair/R/selectRunning.R | 309 openair-3.0.0/openair/R/senTheil.R | 22 openair-3.0.0/openair/R/shared-docs.R |only openair-3.0.0/openair/R/smoothTrend.R | 1278 +-- openair-3.0.0/openair/R/splitByDate.R | 252 openair-3.0.0/openair/R/timeAverage.R | 1353 +-- openair-3.0.0/openair/R/timePlot.R | 1636 ++-- openair-3.0.0/openair/R/timeProp.R | 698 - openair-3.0.0/openair/R/timeVariation.R | 1924 +---- openair-3.0.0/openair/R/trajCluster.R | 587 - openair-3.0.0/openair/R/trajLevel.R | 1662 ++-- openair-3.0.0/openair/R/trajPlot.R | 771 -- openair-3.0.0/openair/R/trendLevel.R | 1313 +-- openair-3.0.0/openair/R/utilities.R | 1158 --- openair-3.0.0/openair/R/variationPlot.R |only openair-3.0.0/openair/R/windRose.R | 2225 +++-- openair-3.0.0/openair/R/windflowOpts.R |only openair-3.0.0/openair/README.md | 196 openair-3.0.0/openair/build/partial.rdb |binary openair-3.0.0/openair/inst/CITATION | 42 openair-3.0.0/openair/inst/WORDLIST | 1007 +- openair-3.0.0/openair/man/GaussianSmooth.Rd |only openair-3.0.0/openair/man/TaylorDiagram.Rd | 585 - openair-3.0.0/openair/man/TheilSen.Rd | 577 - openair-3.0.0/openair/man/WhittakerSmooth.Rd |only openair-3.0.0/openair/man/aqStats.Rd | 228 openair-3.0.0/openair/man/bootMeans.Rd | 179 openair-3.0.0/openair/man/calcPercentile.Rd | 242 openair-3.0.0/openair/man/calc_sqtba_cpp.Rd |only openair-3.0.0/openair/man/calendarPlot.Rd | 518 - openair-3.0.0/openair/man/conditionalEval.Rd | 359 openair-3.0.0/openair/man/conditionalQuantile.Rd | 374 - openair-3.0.0/openair/man/corPlot.Rd | 353 openair-3.0.0/openair/man/cutData.Rd | 318 openair-3.0.0/openair/man/datePad.Rd |only openair-3.0.0/openair/man/distAngle.Rd |only openair-3.0.0/openair/man/distEuclid.Rd |only openair-3.0.0/openair/man/figures/feature-banner.png |binary openair-3.0.0/openair/man/importADMS.Rd | 386 - openair-3.0.0/openair/man/importEurope.Rd | 124 openair-3.0.0/openair/man/importImperial.Rd | 392 - openair-3.0.0/openair/man/importMeta.Rd | 236 openair-3.0.0/openair/man/importTraj.Rd | 312 openair-3.0.0/openair/man/importUKAQ-wrapper.Rd | 506 - openair-3.0.0/openair/man/importUKAQ.Rd | 472 - openair-3.0.0/openair/man/modStats.Rd | 378 - openair-3.0.0/openair/man/mydata.Rd | 98 openair-3.0.0/openair/man/openColours.Rd | 252 openair-3.0.0/openair/man/openair-package.Rd | 249 openair-3.0.0/openair/man/percentileRose.Rd | 432 - openair-3.0.0/openair/man/polarAnnulus.Rd | 570 - openair-3.0.0/openair/man/polarCluster.Rd | 805 +- openair-3.0.0/openair/man/polarDiff.Rd | 615 - openair-3.0.0/openair/man/polarFreq.Rd | 503 - openair-3.0.0/openair/man/polarPlot.Rd | 948 +- openair-3.0.0/openair/man/pollutionRose.Rd | 464 - openair-3.0.0/openair/man/quickText.Rd | 104 openair-3.0.0/openair/man/rollingMean.Rd | 134 openair-3.0.0/openair/man/rollingQuantile.Rd |only openair-3.0.0/openair/man/rolling_gaussian_cpp.Rd |only openair-3.0.0/openair/man/runRegression.Rd | 145 openair-3.0.0/openair/man/scatterPlot.Rd | 736 - openair-3.0.0/openair/man/selectByDate.Rd | 145 openair-3.0.0/openair/man/selectRunning.Rd | 164 openair-3.0.0/openair/man/shared_openair_params.Rd |only openair-3.0.0/openair/man/smoothTrend.Rd | 498 - openair-3.0.0/openair/man/splitByDate.Rd | 142 openair-3.0.0/openair/man/timeAverage.Rd | 420 - openair-3.0.0/openair/man/timePlot.Rd | 679 - openair-3.0.0/openair/man/timeProp.Rd | 338 openair-3.0.0/openair/man/timeVariation.Rd | 647 - openair-3.0.0/openair/man/trajCluster.Rd | 308 openair-3.0.0/openair/man/trajLevel.Rd | 619 - openair-3.0.0/openair/man/trajPlot.Rd | 428 - openair-3.0.0/openair/man/trendLevel.Rd | 429 - openair-3.0.0/openair/man/variationPlot.Rd |only openair-3.0.0/openair/man/windRose.Rd | 548 - openair-3.0.0/openair/man/windflowOpts.Rd |only openair-3.0.0/openair/src/Gaus_smooth.cpp |only openair-3.0.0/openair/src/RcppExports.cpp |only openair-3.0.0/openair/src/cluster.cpp | 180 openair-3.0.0/openair/src/rolling.cpp | 258 openair-3.0.0/openair/src/sqtba.cpp |only openair-3.0.0/openair/src/time_average.cpp |only openair-3.0.0/openair/src/whittaker_baseline.cpp |only openair-3.0.0/openair/src/whittaker_gcv.cpp |only openair-3.0.0/openair/tests/testthat.R | 26 openair-3.0.0/openair/tests/testthat/test-GaussianSmooth.R |only openair-3.0.0/openair/tests/testthat/test-TaylorDiagram.R |only openair-3.0.0/openair/tests/testthat/test-TheilSen.R |only openair-3.0.0/openair/tests/testthat/test-WhittakerSmooth.R |only openair-3.0.0/openair/tests/testthat/test-aqStats.R | 203 openair-3.0.0/openair/tests/testthat/test-bootMeans.R |only openair-3.0.0/openair/tests/testthat/test-calcPercentile.R | 189 openair-3.0.0/openair/tests/testthat/test-calendarPlot.R |only openair-3.0.0/openair/tests/testthat/test-conditionalEval.R |only openair-3.0.0/openair/tests/testthat/test-conditionalQuantile.R |only openair-3.0.0/openair/tests/testthat/test-corPlot.R |only openair-3.0.0/openair/tests/testthat/test-cutData.R | 310 openair-3.0.0/openair/tests/testthat/test-datePad.R |only openair-3.0.0/openair/tests/testthat/test-modStats.R |only openair-3.0.0/openair/tests/testthat/test-openColours.R | 240 openair-3.0.0/openair/tests/testthat/test-percentileRose.R |only openair-3.0.0/openair/tests/testthat/test-polarAnnulus.R |only openair-3.0.0/openair/tests/testthat/test-polarCluster.R |only openair-3.0.0/openair/tests/testthat/test-polarDiff.R |only openair-3.0.0/openair/tests/testthat/test-polarFreq.R |only openair-3.0.0/openair/tests/testthat/test-polarPlot.R |only openair-3.0.0/openair/tests/testthat/test-rollingMean.R | 232 openair-3.0.0/openair/tests/testthat/test-rollingQuantile.R |only openair-3.0.0/openair/tests/testthat/test-scatterPlot.R |only openair-3.0.0/openair/tests/testthat/test-selectByDate.R |only openair-3.0.0/openair/tests/testthat/test-selectRunning.R | 239 openair-3.0.0/openair/tests/testthat/test-smoothTrend.R |only openair-3.0.0/openair/tests/testthat/test-splitByDate.R | 152 openair-3.0.0/openair/tests/testthat/test-timeAverage.R | 389 - openair-3.0.0/openair/tests/testthat/test-timePlot.R |only openair-3.0.0/openair/tests/testthat/test-timeProp.R |only openair-3.0.0/openair/tests/testthat/test-trajCluster.R |only openair-3.0.0/openair/tests/testthat/test-trajLevel.R |only openair-3.0.0/openair/tests/testthat/test-trajPlot.R |only openair-3.0.0/openair/tests/testthat/test-trendLevel.R |only openair-3.0.0/openair/tests/testthat/test-variationPlot.R |only openair-3.0.0/openair/tests/testthat/test-windRose.R |only 188 files changed, 38150 insertions(+), 40204 deletions(-)
Title: Download and Analyze Spatial Development Data from 'INKAR'
Description: A professional R interface to download and analyze spatial
development indicators from the 'BBSR' 'INKAR' (Indikatoren und Karten zur Raum-
und Stadtentwicklung) database. Features a bilingual interactive wizard,
fuzzy search, multi-indicator downloads with automatic tidy merging (long/wide),
robust disk caching, and premium 'ggplot2' themes for regional mapping.
Author: Omer Furkan Coban [aut, cre]
Maintainer: Omer Furkan Coban <oemer.furkan.coban@uni-oldenburg.de>
This is a re-admission after prior archival of version 0.6.1 dated 2026-03-17
Diff between inkaR versions 0.6.1 dated 2026-03-17 and 0.6.2 dated 2026-04-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 12 ++++++++++++ R/api.R | 16 ++++++++++++++-- 4 files changed, 32 insertions(+), 8 deletions(-)
Title: Estimating and Testing the Number of Interesting Components in
Linear Dimension Reduction
Description: For different linear dimension reduction methods like principal components analysis (PCA), independent components analysis (ICA) and supervised linear dimension reduction tests and estimates for the number of interesting components (ICs) are provided.
Author: Klaus Nordhausen [aut, cre] ,
Hannu Oja [aut] ,
Katariina Perkonoja [aut] ,
David E. Tyler [aut],
Joni Virta [aut]
Maintainer: Klaus Nordhausen <klausnordhausenR@gmail.com>
Diff between ICtest versions 0.3-6 dated 2025-05-27 and 0.3-7 dated 2026-04-02
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- R/components.R | 3 ++- inst/ChangeLog | 5 +++++ inst/doc/ICA.html | 8 ++++---- inst/doc/PCA.html | 10 +++++----- inst/doc/SIR.html | 10 +++++----- man/components.ictest.Rd | 11 +++++++---- src/Makevars | 2 +- src/Makevars.win | 3 +-- 11 files changed, 45 insertions(+), 37 deletions(-)
Title: Making "Deduplicated" Functions
Description: Contains one main function deduped() which speeds up slow,
vectorized functions by only performing computations on the unique values
of the input and expanding the results at the end.
Author: Or Gadish [aut, cre, cph]
Maintainer: Or Gadish <orgadish@gmail.com>
Diff between deduped versions 0.3.0 dated 2025-11-29 and 0.4.0 dated 2026-04-02
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 13 ++++++++ R/deduped.R | 42 ++++++++++++++++++++++------ README.md | 54 ++++++++++++++++++++++++++++++------- inst/WORDLIST | 1 man/deduped.Rd | 5 ++- tests/testthat/test-deduped.R | 39 ++++++++++++++++++++++++++ tests/testthat/test-with_deduped.R | 25 ++++++++++++++--- 9 files changed, 167 insertions(+), 38 deletions(-)
Title: A Swiss-Army Knife for Data I/O
Description: Streamlined data import and export by making assumptions that
the user is probably willing to make: 'import()' and 'export()' determine
the data format from the file extension, reasonable defaults are used for
data import and export, web-based import is natively supported (including
from SSL/HTTPS), compressed files can be read directly, and fast import
packages are used where appropriate. An additional convenience function,
'convert()', provides a simple method for converting between file types.
Author: Jason Becker [aut],
Chung-hong Chan [aut, cre] ,
David Schoch [aut] ,
Geoffrey CH Chan [ctb],
Thomas J. Leeper [aut] ,
Christopher Gandrud [ctb],
Andrew MacDonald [ctb],
Ista Zahn [ctb],
Stanislaus Stadlmann [ctb],
Ruaridh Williamson [ctb],
Patrick K [...truncated...]
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between rio versions 1.2.4 dated 2025-09-26 and 1.3.0 dated 2026-04-02
rio-1.2.4/rio/po |only rio-1.2.4/rio/tests/testthat/test_format_qs.R |only rio-1.3.0/rio/DESCRIPTION | 10 - rio-1.3.0/rio/MD5 | 38 +++--- rio-1.3.0/rio/NAMESPACE | 2 rio-1.3.0/rio/NEWS.md | 12 ++ rio-1.3.0/rio/R/export.R | 5 rio-1.3.0/rio/R/export_methods.R | 8 - rio-1.3.0/rio/R/import.R | 5 rio-1.3.0/rio/R/import_methods.R | 6 - rio-1.3.0/rio/R/sysdata.rda |binary rio-1.3.0/rio/README.md | 142 ++++++++++++------------ rio-1.3.0/rio/build/vignette.rds |binary rio-1.3.0/rio/inst/doc/labelled.html | 4 rio-1.3.0/rio/inst/doc/philosophy.Rmd | 2 rio-1.3.0/rio/inst/doc/philosophy.html | 2 rio-1.3.0/rio/inst/doc/rio.html | 32 ++--- rio-1.3.0/rio/man/export.Rd | 5 rio-1.3.0/rio/man/import.Rd | 5 rio-1.3.0/rio/tests/testthat/test_import_list.R | 3 rio-1.3.0/rio/vignettes/philosophy.Rmd | 2 21 files changed, 130 insertions(+), 153 deletions(-)
Title: Headers and Static Libraries for 'HDF5'
Description: Provides a self-contained, static build of the 'HDF5'
(Hierarchical Data Format 5) 'C' library (release 2.1.1) for R
package developers. Designed for use in the 'LinkingTo' field,
it enables zero-dependency integration by building the library
entirely from source during installation. Additionally, it compiles
and internally links a comprehensive suite of advanced compression
filters and their 'HDF5' plugins (Zstd, LZ4, Blosc/Blosc2, Snappy,
ZFP, Bzip2, LZF, Bitshuffle, szip, and gzip). These plugins are
integrated out-of-the-box, allowing downstream packages to utilize
high-performance compression directly through the standard 'HDF5'
API while keeping the underlying third-party headers fully
encapsulated. 'HDF5' is developed by The HDF Group
<https://www.hdfgroup.org/>.
Author: Daniel P. Smith [aut, cre] ,
Alkek Center for Metagenomics and Microbiome Research [cph, fnd],
The HDF Group [ctb, cph] ,
The Board of Trustees of the University of Illinois [cph] ,
Jean-loup Gailly [ctb, cph] ,
Mark Adler [ctb, cph] ,
Kiyoshi Masui [...truncated...]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Diff between hdf5lib versions 2.0.0.6 dated 2026-02-19 and 2.1.1.0 dated 2026-04-02
hdf5lib-2.0.0.6/hdf5lib/src/H5pubconf.h |only hdf5lib-2.0.0.6/hdf5lib/src/find_byte_widths.c |only hdf5lib-2.0.0.6/hdf5lib/src/hdf5-2.0.0.tar.gz |only hdf5lib-2.0.0.6/hdf5lib/src/zlib-1.3.1.tar.gz |only hdf5lib-2.0.0.6/hdf5lib/tests/src |only hdf5lib-2.0.0.6/hdf5lib/tests/testthat |only hdf5lib-2.0.0.6/hdf5lib/tests/testthat.r |only hdf5lib-2.1.1.0/hdf5lib/DESCRIPTION | 79 +++- hdf5lib-2.1.1.0/hdf5lib/LICENSE | 2 hdf5lib-2.1.1.0/hdf5lib/MD5 | 105 +++++- hdf5lib-2.1.1.0/hdf5lib/NEWS.md | 8 hdf5lib-2.1.1.0/hdf5lib/R/flags.r | 52 +- hdf5lib-2.1.1.0/hdf5lib/README.md | 86 ++-- hdf5lib-2.1.1.0/hdf5lib/configure | 434 ++++++++++++++++++++----- hdf5lib-2.1.1.0/hdf5lib/inst/COPYRIGHTS | 310 +++++++++++++++++ hdf5lib-2.1.1.0/hdf5lib/man/figures/logo.png |binary hdf5lib-2.1.1.0/hdf5lib/src/config |only hdf5lib-2.1.1.0/hdf5lib/src/dummy.c |only hdf5lib-2.1.1.0/hdf5lib/src/filters |only hdf5lib-2.1.1.0/hdf5lib/src/hdf5-2.1.0.tar.gz |only hdf5lib-2.1.1.0/hdf5lib/src/hdf5-2.1.1.tar.gz |only hdf5lib-2.1.1.0/hdf5lib/src/install.libs.R |only hdf5lib-2.1.1.0/hdf5lib/src/lib |only hdf5lib-2.1.1.0/hdf5lib/src/patches |only hdf5lib-2.1.1.0/hdf5lib/src/plugins |only hdf5lib-2.1.1.0/hdf5lib/tests/Makevars |only hdf5lib-2.1.1.0/hdf5lib/tests/interop |only hdf5lib-2.1.1.0/hdf5lib/tests/smoke_test.c |only hdf5lib-2.1.1.0/hdf5lib/tests/test-flags.r |only hdf5lib-2.1.1.0/hdf5lib/tests/test-hdf5.r |only 30 files changed, 885 insertions(+), 191 deletions(-)
Title: A Collection of Functions for Graphing Correlation Matrices
Description: Routines for the graphical representation of correlation matrices by means of correlograms, MDS maps and biplots obtained by PCA, PFA or WALS (weighted alternating least squares); See Graffelman & De Leeuw (2023) <doi: 10.1080/00031305.2023.2186952>.
Author: Jan Graffelman [aut, cre],
Jan De Leeuw [aut]
Maintainer: Jan Graffelman <jan.graffelman@upc.edu>
Diff between Correlplot versions 1.1.2 dated 2025-07-25 and 1.1.3 dated 2026-04-02
DESCRIPTION | 8 MD5 | 48 ++- NAMESPACE | 4 R/FitAllModelsRxy.R |only R/FitRxy.R |only R/LastFunctions.R |only R/genloss.R |only R/ggbplot.R | 132 ++++++---- R/ggtally.R | 139 ++++++++-- R/rmse.rxy.R |only data/achievement.rda |only inst/doc/CorrelplotManual.R | 288 ++++++++++++++++++++-- inst/doc/CorrelplotManual.Rmd | 357 +++++++++++++++++++++++++-- inst/doc/CorrelplotManual.html | 526 +++++++++++++++++++++++++++++++++-------- man/FitAllModelsRxy.Rd |only man/FitRDeltaQSym.Rd | 3 man/FitRwithPCAandWALS.Rd | 4 man/FitRxy.Rd |only man/Keller.Rd | 2 man/achievement.Rd |only man/ggbplot.Rd | 42 +-- man/ggtally.Rd | 37 ++ man/ipSymLS.Rd | 2 man/rmse.Rd | 3 man/rmse.rxy.Rd |only man/rmsePCAandWALS.Rd | 2 man/tally.Rd | 4 man/wAddPCA.Rd | 2 vignettes/Correlplot.bib | 13 - vignettes/CorrelplotManual.Rmd | 357 +++++++++++++++++++++++++-- 30 files changed, 1651 insertions(+), 322 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-30 1.0.6
2023-08-17 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-20 1.0.32
2023-11-10 1.0.31
2022-10-13 1.0.3
2020-10-28 1.0.2
2020-05-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-11-17 1.0.0
2025-09-01 0.3.2
2024-02-28 0.3.0
2023-12-13 0.2.39
2023-01-28 0.2.30
2022-06-30 0.2.27
Title: Design-Based Causal Inference Method for Incomplete Block
Designs
Description: This R package implements methods for estimation and inference under Incomplete Block Designs and Balanced Incomplete Block Designs within a design-based finite-population framework. Based on 'Koo and Pashley' (2026) <doi:10.1093/biomet/asag013>, it includes block-level estimators and extends to unit-level effects using 'Horvitz-Thompson' and 'Hájek' estimators. The package also provides asymptotic confidence intervals to support valid statistical inference.
Author: Taehyeon Koo [aut, cre],
Nicole Pashley [ctb]
Maintainer: Taehyeon Koo <tk3077@cumc.columbia.edu>
Diff between IBDInfer versions 0.0.1 dated 2025-04-16 and 0.1.0 dated 2026-04-01
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- R/IBDInfer.R | 44 ++++++++++++++++++++++++++++++++++---------- 3 files changed, 42 insertions(+), 18 deletions(-)
Title: R Wrappers for EXPOKIT; Other Matrix Functions
Description: Wraps some of the matrix exponentiation
utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>),
a FORTRAN library that is widely recommended for matrix
exponentiation (Sidje RB, 1998. "Expokit: A Software Package
for Computing Matrix Exponentials." ACM Trans. Math. Softw.
24(1): 130-156). EXPOKIT includes functions for
exponentiating both small, dense matrices, and large, sparse
matrices (in sparse matrices, most of the cells have value 0).
Rapid matrix exponentiation is useful in phylogenetics when we
have a large number of states (as we do when we are inferring
the history of transitions between the possible geographic
ranges of a species), but is probably useful in other ways as
well. NOTE: In case FORTRAN checks temporarily get rexpokit
archived on CRAN, see archived binaries at GitHub in:
nmatzke/Matzke_R_binaries (binaries install without compilation
of source code).
Author: Nicholas J. Matzke [aut, cre, cph],
Roger B. Sidje [aut, cph],
Drew Schmidt [aut]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>
This is a re-admission after prior archival of version 0.26.6.14 dated 2023-11-22
Diff between rexpokit versions 0.26.6.14 dated 2023-11-22 and 0.26.6.15 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NAMESPACE | 3 ++- NEWS | 22 ++++++++++++++++++++++ R/expm.r | 2 +- R/rexpokit-package.R | 4 ++-- build/partial.rdb |binary demo/expm.r | 2 +- demo/expm_check.r | 2 +- man/00_rexpokit-package.Rd | 7 ++----- man/01_expm.Rd | 14 ++++++-------- tests/expm.R | 8 ++++---- 12 files changed, 57 insertions(+), 39 deletions(-)
Title: Meta Fuzzy Functions
Description: Implements Meta Fuzzy Functions (MFFs) for regression Tak and Ucan (2026) <doi:10.1016/j.asoc.2026.114592> by aggregating predictions from multiple base learners using membership weights learned in the prediction space of validation set. The package supports fuzzy and crisp meta-ensemble structures via Fuzzy C-Means (FCM) Tak (2018) <doi:10.1016/j.asoc.2018.08.009>, Possibilistic FCM (PFCM) Tak (2021) <doi:10.1016/j.ins.2021.01.024>, Gustafson–Kessel (GK) clustering, and k-means, and provides a workflow to (i) generate validation/test prediction matrices from common regression learners (linear and penalized regression via 'glmnet', random forests, gradient boosting with 'xgboost' and 'lightgbm'), (ii) fit cluster-wise meta fuzzy functions and compute membership-based weights, (iii) tune clustering-related hyperparameters (number of clusters/functions, fuzziness exponent, possibilistic regularization) via grid search on validation loss, and (iv) predict on new/test pre [...truncated...]
Author: Nihat Tak [aut, cre],
Sadik Coban [aut]
Maintainer: Nihat Tak <nihattak@gmail.com>
Diff between MFF versions 0.1.0 dated 2026-02-13 and 0.2.0 dated 2026-04-01
MFF-0.1.0/MFF/man/dot-weight_kmeans.Rd |only MFF-0.2.0/MFF/DESCRIPTION | 11 +- MFF-0.2.0/MFF/MD5 | 25 ++--- MFF-0.2.0/MFF/NAMESPACE | 9 + MFF-0.2.0/MFF/R/MFF-package.R | 27 +++-- MFF-0.2.0/MFF/R/boot.train.R |only MFF-0.2.0/MFF/R/evaluate.R | 2 MFF-0.2.0/MFF/R/mff.R | 80 ++++++++++++++--- MFF-0.2.0/MFF/R/tune.mff.R | 153 +++++++++++++++++---------------- MFF-0.2.0/MFF/R/utils-clustering.R | 1 MFF-0.2.0/MFF/man/MFF-package.Rd | 24 +++-- MFF-0.2.0/MFF/man/boot.train.Rd |only MFF-0.2.0/MFF/man/evaluate.Rd | 2 MFF-0.2.0/MFF/man/mff.Rd | 30 ++++-- MFF-0.2.0/MFF/man/tune.mff.Rd | 20 +++- 15 files changed, 252 insertions(+), 132 deletions(-)
More information about likelihood.contr at CRAN
Permanent link
Title: Ensemble Models for Lactation Curves
Description: Lactation curves describe temporal changes in milk yield and are key to breeding and managing dairy animals more efficiently. The use of ensemble modeling, which consists of combining predictions from multiple models, has the potential to yields more accurate and robust estimates of lactation patterns than relying solely on single model estimates. The package EMOTIONS fits 47 models for lactation curves and creates ensemble models using model averaging based on Akaike information criterion (AIC), Bayesian information criterion (BIC), root mean square percentage error (RMSPE) and mean squared error (MAE), variance of the predictions, cosine similarity for each model's predictions, and Bayesian Model Average (BMA). The daily production values predicted through the ensemble models can be used to estimate resilience indicators in the package. The package allows the graphical visualization of the model ranks and the predicted lactation curves. Additionally, the packages allows the user to d [...truncated...]
Author: Pablo Fonseca [aut, cre],
Marcos Prates [aut],
Aroa Suarez-Vega [aut],
Ruth Arribas Gonzalo [aut],
Beatriz Gutierrez-Gil [aut],
Juan Jose Arranz [aut]
Maintainer: Pablo Fonseca <p.fonseca@csic.es>
Diff between EMOTIONS versions 1.2 dated 2026-03-27 and 1.3 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS | 6 ++---- R/PlotMilkLoss.R | 46 +++++++++++++++++++++++++++++++++++++--------- R/global_variables.R | 2 +- inst/doc/EMOTIONS.html | 6 +++--- 7 files changed, 53 insertions(+), 26 deletions(-)
Title: Clustering on Network of Samples
Description: Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.
Author: Viktor Petukhov [aut],
Nikolas Barkas [aut],
Peter Kharchenko [aut],
Weiliang Qiu [ctb],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
This is a re-admission after prior archival of version 1.5.2 dated 2024-02-26
Diff between conos versions 1.5.2 dated 2024-02-26 and 1.5.3 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 2 +- src/Makevars | 2 +- src/Makevars.win | 2 +- tests/testthat/test_functions.R | 28 ++++++++++++++++++++++++++-- 6 files changed, 37 insertions(+), 13 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
Diff between RTMBdist versions 1.0.2 dated 2026-03-16 and 1.0.3 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 6 ++++++ R/aaa_utils.R | 9 +++++---- R/skewt.R | 12 ++++++------ R/skewt2.R | 4 ++-- R/zibeta.R | 2 +- R/zibinom.R | 2 +- R/zigamma.R | 3 +-- R/ziinvgauss.R | 2 +- R/zilnorm.R | 2 +- R/zipois.R | 2 +- R/ziweibull.R |only R/zoibeta.R | 8 ++++++-- build/vignette.rds |binary inst/doc/Examples.html | 10 +++++----- inst/doc/distlist.Rmd | 10 ++++++---- inst/doc/distlist.html | 15 +++++++++------ man/ziweibull.Rd |only vignettes/distlist.Rmd | 10 ++++++---- 20 files changed, 81 insertions(+), 62 deletions(-)
Title: Tools for Working with Posterior Distributions
Description: Provides useful tools for both users and developers of packages
for fitting Bayesian models or working with output from Bayesian models.
The primary goals of the package are to:
(a) Efficiently convert between many different useful formats of
draws (samples) from posterior or prior distributions.
(b) Provide consistent methods for operations commonly performed on draws,
for example, subsetting, binding, or mutating draws.
(c) Provide various summaries of draws in convenient formats.
(d) Provide lightweight implementations of state of the art posterior
inference diagnostics. References: Vehtari et al. (2021)
<doi:10.1214/20-BA1221>.
Author: Paul-Christian Buerkner [aut, cre],
Jonah Gabry [aut],
Matthew Kay [aut],
Aki Vehtari [aut],
Mans Magnusson [ctb],
Rok Česnovar [ctb],
Ben Lambert [ctb],
Ozan Adiguezel [ctb],
Jacob Socolar [ctb],
Noa Kallioinen [ctb],
Teemu Saeilynoja [ctb]
Maintainer: Paul-Christian Buerkner <paul.buerkner@gmail.com>
Diff between posterior versions 1.6.1 dated 2025-02-27 and 1.7.0 dated 2026-04-01
posterior-1.6.1/posterior/man/figures/stanlogo.png |only posterior-1.7.0/posterior/DESCRIPTION | 21 - posterior-1.7.0/posterior/MD5 | 96 +++--- posterior-1.7.0/posterior/NAMESPACE | 19 + posterior-1.7.0/posterior/NEWS.md | 17 + posterior-1.7.0/posterior/R/extract_list_of_variable_arrays.R |only posterior-1.7.0/posterior/R/extract_variable_array.R | 39 ++ posterior-1.7.0/posterior/R/gpd.R | 141 +++++++-- posterior-1.7.0/posterior/R/misc.R | 28 + posterior-1.7.0/posterior/R/pareto_smooth.R | 152 +++++----- posterior-1.7.0/posterior/R/pit.R |only posterior-1.7.0/posterior/R/posterior-package.R | 2 posterior-1.7.0/posterior/R/rvar-.R | 1 posterior-1.7.0/posterior/R/rvar-print.R | 2 posterior-1.7.0/posterior/R/rvar-slice.R | 2 posterior-1.7.0/posterior/R/subset_draws.R | 12 posterior-1.7.0/posterior/R/uniformity_test.R |only posterior-1.7.0/posterior/R/weight_draws.R | 3 posterior-1.7.0/posterior/README.md | 98 +++--- posterior-1.7.0/posterior/build/partial.rdb |binary posterior-1.7.0/posterior/build/vignette.rds |binary posterior-1.7.0/posterior/inst/doc/pareto_diagnostics.html | 43 +- posterior-1.7.0/posterior/inst/doc/posterior.R | 12 posterior-1.7.0/posterior/inst/doc/posterior.html | 3 posterior-1.7.0/posterior/inst/doc/rvar.R | 2 posterior-1.7.0/posterior/inst/doc/rvar.html | 16 - posterior-1.7.0/posterior/man/extract_list_of_variable_arrays.Rd |only posterior-1.7.0/posterior/man/extract_variable.Rd | 8 posterior-1.7.0/posterior/man/extract_variable_array.Rd | 19 - posterior-1.7.0/posterior/man/extract_variable_matrix.Rd | 8 posterior-1.7.0/posterior/man/figures/logo.svg | 97 ------ posterior-1.7.0/posterior/man/gpdfit.Rd |only posterior-1.7.0/posterior/man/is_constant.Rd |only posterior-1.7.0/posterior/man/pareto_pit.Rd |only posterior-1.7.0/posterior/man/pgeneralized_pareto.Rd |only posterior-1.7.0/posterior/man/pit.Rd |only posterior-1.7.0/posterior/man/posterior-package.Rd | 5 posterior-1.7.0/posterior/man/print.rvar.Rd | 2 posterior-1.7.0/posterior/man/ps_convergence_rate.Rd | 1 posterior-1.7.0/posterior/man/ps_khat_threshold.Rd | 1 posterior-1.7.0/posterior/man/ps_min_ss.Rd | 1 posterior-1.7.0/posterior/man/ps_tail.Rd |only posterior-1.7.0/posterior/man/ps_tail_length.Rd | 1 posterior-1.7.0/posterior/man/qgeneralized_pareto.Rd |only posterior-1.7.0/posterior/man/rvar-slice.Rd | 2 posterior-1.7.0/posterior/man/subset_draws.Rd | 4 posterior-1.7.0/posterior/man/uniformity_test.Rd |only posterior-1.7.0/posterior/tests/testthat/test-draws-index.R | 5 posterior-1.7.0/posterior/tests/testthat/test-extract_list_of_variable_arrays.R |only posterior-1.7.0/posterior/tests/testthat/test-extract_variable_array.R | 130 +++++++- posterior-1.7.0/posterior/tests/testthat/test-gpd-distributions.R |only posterior-1.7.0/posterior/tests/testthat/test-gpdfit.R |only posterior-1.7.0/posterior/tests/testthat/test-log_sum_exp.R |only posterior-1.7.0/posterior/tests/testthat/test-pareto_pit.R |only posterior-1.7.0/posterior/tests/testthat/test-pareto_smooth.R | 61 +++- posterior-1.7.0/posterior/tests/testthat/test-pit.R |only posterior-1.7.0/posterior/tests/testthat/test-rvar-.R | 5 posterior-1.7.0/posterior/tests/testthat/test-subset_draws.R | 97 ++++++ posterior-1.7.0/posterior/tests/testthat/test-uniformity_test.R |only 59 files changed, 787 insertions(+), 369 deletions(-)
Title: Lagged Cross-Correlation Analysis of Environmental Time Series
Description: Tools for analysing lagged relationships between environmental variables and ecological or epidemiological time series. The package implements a workflow to aggregate meteorological data over multiple lagged intervals, fit regression models, including mixed-effect models using 'glmmTMB', for each lag window, and visualise varied models outcomes (effect strength and direction, model prediction error...) using cross-correlation maps ('CCM').
Author: Nicolas Moiroux [aut, cre] ,
Colombine Bartholomee [aut] ,
Paul Taconet [aut]
Maintainer: Nicolas Moiroux <nicolas.moiroux@ird.fr>
Diff between ecoXCorr versions 0.1.9 dated 2026-03-24 and 0.2.1 dated 2026-04-01
DESCRIPTION | 6 MD5 | 18 - NEWS.md |only R/funs.R | 284 +++++++++++++---------- README.md | 217 +++++++++++++---- build/partial.rdb |binary inst/CITATION | 2 man/aggregate_lagged_intervals.Rd | 25 +- man/ecoXCorr.Rd | 4 man/plotCCM.Rd | 8 tests/testthat/test-aggregate_lagged_intervals.R |only 11 files changed, 381 insertions(+), 183 deletions(-)
Title: Parse 'User-Agent' Strings
Description: Despite there being a section in RFC 7231
<https://datatracker.ietf.org/doc/html/rfc7231#section-5.5.3> defining a suggested
structure for 'User-Agent' headers this data is notoriously difficult
to parse consistently. Tools are provided that will take in user agent
strings and return structured R objects. This is a 'V8'-backed package
based on the 'ua-parser' project <https://github.com/ua-parser>.
Author: Bob Rudis [aut, cph],
Greg Hunt [aut, cre, cph],
Lindsey Simon [aut] ,
Tobie Langel [aut] ,
Colman Humphrey [ctb]
Maintainer: Greg Hunt <greg@firmansyah.com>
Diff between uaparserjs versions 0.3.6 dated 2026-03-23 and 0.3.7 dated 2026-04-01
uaparserjs-0.3.6/uaparserjs/inst/js/bld |only uaparserjs-0.3.6/uaparserjs/inst/js/index.js |only uaparserjs-0.3.6/uaparserjs/inst/js/newbuild |only uaparserjs-0.3.7/uaparserjs/DESCRIPTION | 18 +++--- uaparserjs-0.3.7/uaparserjs/LICENSE | 4 - uaparserjs-0.3.7/uaparserjs/MD5 | 31 ++++++------ uaparserjs-0.3.7/uaparserjs/NEWS.md | 9 +++ uaparserjs-0.3.7/uaparserjs/R/uaparser.R | 21 +++++++- uaparserjs-0.3.7/uaparserjs/R/uaparserjs-package.R | 22 +++++++- uaparserjs-0.3.7/uaparserjs/R/utils-mappers.R | 17 +++++- uaparserjs-0.3.7/uaparserjs/R/zzz.r | 14 +++++ uaparserjs-0.3.7/uaparserjs/inst/js/bundle.js | 9 --- uaparserjs-0.3.7/uaparserjs/inst/tinytest/test_exhaustive.R |only uaparserjs-0.3.7/uaparserjs/inst/tinytest/test_uaparserjs.R | 15 +++++ uaparserjs-0.3.7/uaparserjs/inst/tinytest/tests |only uaparserjs-0.3.7/uaparserjs/man/ua_parse.Rd | 4 - uaparserjs-0.3.7/uaparserjs/man/uaparserjs.Rd | 14 +++++ uaparserjs-0.3.7/uaparserjs/tests/tinytest.R | 14 +++++ 18 files changed, 147 insertions(+), 45 deletions(-)
Title: Execute and Control System Processes
Description: Tools to run system processes in the background. It can
check if a background process is running; wait on a background process
to finish; get the exit status of finished processes; kill background
processes. It can read the standard output and error of the processes,
using non-blocking connections. 'processx' can poll a process for
standard output or error, with a timeout. It can also poll several
processes at once.
Author: Gabor Csardi [aut, cre, cph] ,
Winston Chang [aut],
Posit Software, PBC [cph, fnd] ,
Ascent Digital Services [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between processx versions 3.8.6 dated 2025-02-21 and 3.8.7 dated 2026-04-01
DESCRIPTION | 17 - LICENSE | 2 MD5 | 141 +++++---- NEWS.md | 4 R/aaa-import-standalone-rstudio-detect.R | 78 ++--- R/aaassertthat.R | 39 +- R/assertions.R | 21 - R/base64.R | 1 R/cleancall.R | 1 R/client-lib.R | 20 - R/connections.R | 112 +++++-- R/initialize.R | 97 ++++-- R/io.R | 37 +- R/named_pipe.R | 12 R/on-load.R | 11 R/poll.R | 4 R/print.R | 6 R/process-helpers.R | 1 R/process.R | 343 ++++++++++++------------ R/run.R | 273 ++++++++++++++----- R/standalone-errors.R | 414 +++++++++++++++++++---------- R/supervisor.R | 49 +-- R/utils.R | 87 +++--- README.md | 21 - man/process.Rd | 31 +- src/cleancall.c | 6 src/init.c | 2 src/install.libs.R | 10 tests/testthat.R | 8 tests/testthat/_snaps/Darwin |only tests/testthat/_snaps/Linux |only tests/testthat/_snaps/Windows |only tests/testthat/_snaps/assertions.md |only tests/testthat/_snaps/fifo.md |only tests/testthat/_snaps/io.md |only tests/testthat/_snaps/process.md |only tests/testthat/_snaps/pty.md |only tests/testthat/_snaps/standalone-errors.md | 36 +- tests/testthat/_snaps/unix-sockets.md |only tests/testthat/_snaps/utils.md |only tests/testthat/helper.R | 92 +++++- tests/testthat/test-assertions.R | 62 ++-- tests/testthat/test-chr-io.R | 4 tests/testthat/test-cleanup.R | 3 tests/testthat/test-client-lib.R | 31 +- tests/testthat/test-connections.R | 27 - tests/testthat/test-env.R | 7 tests/testthat/test-err-output.R | 66 +++- tests/testthat/test-errors.R | 31 +- tests/testthat/test-extra-connections.R | 34 +- tests/testthat/test-fifo.R | 24 + tests/testthat/test-io.R | 47 +-- tests/testthat/test-kill-tree.R | 91 ++++-- tests/testthat/test-poll-connections.R | 12 tests/testthat/test-poll-curl.R | 65 +++- tests/testthat/test-poll-stress.R | 11 tests/testthat/test-poll.R | 92 ++++-- tests/testthat/test-poll2.R | 29 +- tests/testthat/test-poll3.R | 56 ++- tests/testthat/test-print.R | 2 tests/testthat/test-process.R | 40 ++ tests/testthat/test-ps-methods.R | 9 tests/testthat/test-pty.R | 34 +- tests/testthat/test-run.R | 53 ++- tests/testthat/test-set-std.R | 16 - tests/testthat/test-sigchld.R | 33 +- tests/testthat/test-standalone-errors.R | 199 ++++--------- tests/testthat/test-stdin.R | 6 tests/testthat/test-stress.R | 12 tests/testthat/test-unix-sockets.R | 62 +++- tests/testthat/test-utf8.R | 5 tests/testthat/test-utils.R | 31 +- tests/testthat/test-wait.R | 18 - tools |only 74 files changed, 1953 insertions(+), 1235 deletions(-)
Title: Download Data from the FAOSTAT Database
Description: Download Data from the FAOSTAT Database of the Food and Agricultural Organization (FAO) of the United Nations.
A list of functions to download statistics from FAOSTAT (database of the FAO <https://www.fao.org/faostat/>)
and WDI (database of the World Bank <https://data.worldbank.org/>), and to perform some harmonization operations.
Author: Michael C. J. [aut],
Markus Gesmann [aut],
Filippo Gheri [aut],
Paul Rougieux [aut, cre],
Sebastian Campbell [aut]
Maintainer: Paul Rougieux <paul.rougieux@gmail.com>
Diff between FAOSTAT versions 2.4.0 dated 2024-05-22 and 2.4.2 dated 2026-04-01
DESCRIPTION | 34 +++++- MD5 | 31 +++-- NAMESPACE | 3 R/faostat_bulk_download.R | 110 ++++++++++++++------- R/read_fao.R | 2 R/rest.R | 88 ++++++++++++++++ R/utils.R | 4 build/vignette.rds |binary data/FAOregionProfile.RData |binary inst/doc/FAOSTAT.R | 224 ++++++++++++++++++++++--------------------- inst/doc/FAOSTAT.Rnw | 58 ++++++++--- inst/doc/FAOSTAT.pdf |binary man/FAOSTAT-package.Rd | 12 ++ man/change_case.Rd | 4 man/download_faostat_bulk.Rd | 46 ++++++-- man/faostat_login.Rd |only vignettes/FAOSTAT.Rnw | 58 ++++++++--- 17 files changed, 463 insertions(+), 211 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
Author: Tim Stuart [aut, cre] ,
Avi Srivastava [aut] ,
Paul Hoffman [ctb] ,
Rahul Satija [ctb]
Maintainer: Tim Stuart <stuartt@a-star.edu.sg>
Diff between Signac versions 1.16.0 dated 2025-10-10 and 1.17.0 dated 2026-04-01
Signac-1.16.0/Signac/man/AddChromatinModule.Rd |only Signac-1.16.0/Signac/man/RunChromVAR.Rd |only Signac-1.17.0/Signac/DESCRIPTION | 29 Signac-1.17.0/Signac/MD5 | 262 ++-- Signac-1.17.0/Signac/NAMESPACE | 36 Signac-1.17.0/Signac/NEWS.md | 35 Signac-1.17.0/Signac/R/Signac-package.R |only Signac-1.17.0/Signac/R/data.R | 61 Signac-1.17.0/Signac/R/dimension_reduction.R | 93 - Signac-1.17.0/Signac/R/footprinting.R | 12 Signac-1.17.0/Signac/R/fragments.R | 40 Signac-1.17.0/Signac/R/generics.R | 161 +- Signac-1.17.0/Signac/R/genomeinfodb-methods.R | 12 Signac-1.17.0/Signac/R/granges-methods.R | 14 Signac-1.17.0/Signac/R/heatmaps.R | 4 Signac-1.17.0/Signac/R/iranges-methods.R | 78 - Signac-1.17.0/Signac/R/links.R | 22 Signac-1.17.0/Signac/R/mito.R | 14 Signac-1.17.0/Signac/R/motifs.R | 144 -- Signac-1.17.0/Signac/R/objects.R | 74 - Signac-1.17.0/Signac/R/ontology.R |only Signac-1.17.0/Signac/R/peaks.R | 22 Signac-1.17.0/Signac/R/preprocessing.R | 770 +++++++++++- Signac-1.17.0/Signac/R/quantification.R | 24 Signac-1.17.0/Signac/R/region-enrichment.R | 7 Signac-1.17.0/Signac/R/utilities.R | 129 -- Signac-1.17.0/Signac/R/visualization.R | 103 - Signac-1.17.0/Signac/README.md | 12 Signac-1.17.0/Signac/data/blacklist_ce10.rda |binary Signac-1.17.0/Signac/data/blacklist_ce11.rda |binary Signac-1.17.0/Signac/data/blacklist_dm3.rda |binary Signac-1.17.0/Signac/data/blacklist_dm6.rda |binary Signac-1.17.0/Signac/data/blacklist_hg19.rda |binary Signac-1.17.0/Signac/data/blacklist_hg38.rda |binary Signac-1.17.0/Signac/data/blacklist_hg38_unified.rda |binary Signac-1.17.0/Signac/data/blacklist_mm10.rda |binary Signac-1.17.0/Signac/man/ATACqc.Rd |only Signac-1.17.0/Signac/man/AddMotifs.Rd | 6 Signac-1.17.0/Signac/man/AggregateTiles.Rd | 4 Signac-1.17.0/Signac/man/AlleleFreq.Rd | 2 Signac-1.17.0/Signac/man/Annotation.Rd | 4 Signac-1.17.0/Signac/man/AnnotationPlot.Rd | 4 Signac-1.17.0/Signac/man/BigwigTrack.Rd | 2 Signac-1.17.0/Signac/man/BinarizeCounts.Rd | 4 Signac-1.17.0/Signac/man/CallPeaks.Rd | 8 Signac-1.17.0/Signac/man/Cells.Rd | 8 Signac-1.17.0/Signac/man/ChromatinAssay-class.Rd | 24 Signac-1.17.0/Signac/man/ClosestFeature.Rd | 4 Signac-1.17.0/Signac/man/ClusterClonotypes.Rd | 2 Signac-1.17.0/Signac/man/ConnectionsToLinks.Rd | 2 Signac-1.17.0/Signac/man/CountFragments.Rd | 10 Signac-1.17.0/Signac/man/CountsInRegion.Rd | 4 Signac-1.17.0/Signac/man/CoverageBrowser.Rd | 6 Signac-1.17.0/Signac/man/CoveragePlot.Rd | 8 Signac-1.17.0/Signac/man/CreateChromatinAssay.Rd | 26 Signac-1.17.0/Signac/man/CreateMotifMatrix.Rd | 8 Signac-1.17.0/Signac/man/CreateMotifObject.Rd | 6 Signac-1.17.0/Signac/man/DepthCor.Rd | 6 Signac-1.17.0/Signac/man/DownsampleFeatures.Rd | 4 Signac-1.17.0/Signac/man/EnrichedTerms.Rd |only Signac-1.17.0/Signac/man/Extend.Rd | 2 Signac-1.17.0/Signac/man/FRiP.Rd | 6 Signac-1.17.0/Signac/man/FeatureMatrix.Rd | 6 Signac-1.17.0/Signac/man/FindClonotypes.Rd | 8 Signac-1.17.0/Signac/man/FindMotifs.Rd | 6 Signac-1.17.0/Signac/man/FindTopFeatures.Rd | 10 Signac-1.17.0/Signac/man/FitMeanVar.Rd |only Signac-1.17.0/Signac/man/Footprint.Rd | 2 Signac-1.17.0/Signac/man/FractionCountsInRegion.Rd | 4 Signac-1.17.0/Signac/man/Fragment-class.Rd | 2 Signac-1.17.0/Signac/man/FragmentHistogram.Rd | 2 Signac-1.17.0/Signac/man/Fragments.Rd | 4 Signac-1.17.0/Signac/man/GRangesToString.Rd | 3 Signac-1.17.0/Signac/man/GenomeBinMatrix.Rd | 6 Signac-1.17.0/Signac/man/GetFootprintData.Rd | 14 Signac-1.17.0/Signac/man/GetFragmentData.Rd | 4 Signac-1.17.0/Signac/man/GetGRangesFromEnsDb.Rd | 2 Signac-1.17.0/Signac/man/GetIntersectingFeatures.Rd | 4 Signac-1.17.0/Signac/man/GetMotifData.Rd | 2 Signac-1.17.0/Signac/man/InsertionBias.Rd | 2 Signac-1.17.0/Signac/man/IntersectMatrix.Rd | 4 Signac-1.17.0/Signac/man/LinkPeaks.Rd | 16 Signac-1.17.0/Signac/man/LinkPlot.Rd | 4 Signac-1.17.0/Signac/man/Links.Rd | 2 Signac-1.17.0/Signac/man/MatchRegionStats.Rd | 4 Signac-1.17.0/Signac/man/Motif-class.Rd | 2 Signac-1.17.0/Signac/man/MotifCounts.Rd | 6 Signac-1.17.0/Signac/man/MotifPlot.Rd | 4 Signac-1.17.0/Signac/man/Motifs.Rd | 2 Signac-1.17.0/Signac/man/NucleosomeSignal.Rd | 4 Signac-1.17.0/Signac/man/PeakPlot.Rd | 6 Signac-1.17.0/Signac/man/PearsonResidualVar.Rd |only Signac-1.17.0/Signac/man/RegionHeatmap.Rd | 10 Signac-1.17.0/Signac/man/RegionMatrix.Rd | 4 Signac-1.17.0/Signac/man/RegionPlot.Rd | 8 Signac-1.17.0/Signac/man/RegionStats.Rd | 4 Signac-1.17.0/Signac/man/RunSVD.Rd | 43 Signac-1.17.0/Signac/man/RunTFIDF.Rd | 26 Signac-1.17.0/Signac/man/SetMotifData.Rd | 2 Signac-1.17.0/Signac/man/Signac-package.Rd | 16 Signac-1.17.0/Signac/man/SortIdents.Rd | 6 Signac-1.17.0/Signac/man/StringToGRanges.Rd | 5 Signac-1.17.0/Signac/man/TSSEnrichment.Rd | 4 Signac-1.17.0/Signac/man/TSSPlot.Rd | 9 Signac-1.17.0/Signac/man/TilePlot.Rd | 2 Signac-1.17.0/Signac/man/UnifyPeaks.Rd | 8 Signac-1.17.0/Signac/man/UpdatePath.Rd | 4 Signac-1.17.0/Signac/man/ValidateCells.Rd | 4 Signac-1.17.0/Signac/man/ValidateFragments.Rd | 4 Signac-1.17.0/Signac/man/ValidateHash.Rd | 2 Signac-1.17.0/Signac/man/VariantPlot.Rd | 2 Signac-1.17.0/Signac/man/as.ChromatinAssay.Rd | 16 Signac-1.17.0/Signac/man/atac_small.Rd | 8 Signac-1.17.0/Signac/man/blacklist_ce10.Rd | 3 Signac-1.17.0/Signac/man/blacklist_ce11.Rd | 3 Signac-1.17.0/Signac/man/blacklist_dm3.Rd | 3 Signac-1.17.0/Signac/man/blacklist_dm6.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg19.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg38.Rd | 3 Signac-1.17.0/Signac/man/blacklist_hg38_unified.Rd | 4 Signac-1.17.0/Signac/man/blacklist_mm10.Rd | 3 Signac-1.17.0/Signac/man/corSparse.Rd | 2 Signac-1.17.0/Signac/man/coverage-ChromatinAssay-method.Rd | 22 Signac-1.17.0/Signac/man/figures/lifecycle-deprecated.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-experimental.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-stable.svg |only Signac-1.17.0/Signac/man/figures/lifecycle-superseded.svg |only Signac-1.17.0/Signac/man/findOverlaps-methods.Rd | 22 Signac-1.17.0/Signac/man/granges-methods.Rd | 16 Signac-1.17.0/Signac/man/head.Fragment.Rd | 2 Signac-1.17.0/Signac/man/inter-range-methods.Rd | 22 Signac-1.17.0/Signac/man/nearest-methods.Rd | 24 Signac-1.17.0/Signac/man/seqinfo-methods.Rd | 12 Signac-1.17.0/Signac/man/subset.Fragment.Rd | 6 Signac-1.17.0/Signac/man/subset.Motif.Rd | 6 Signac-1.17.0/Signac/man/theme_browser.Rd | 2 Signac-1.17.0/Signac/tests/testthat/test-dimreduc.R | 4 Signac-1.17.0/Signac/tests/testthat/test-preprocessing.R | 2 138 files changed, 1777 insertions(+), 1030 deletions(-)
Title: Convert Gene IDs Between Each Other and Fetch Annotations from
Biomart
Description: Gene Symbols or Ensembl Gene IDs are converted using the Bimap interface in 'AnnotationDbi' in convertId2() but
that function is only provided as fallback mechanism for the most common use cases in data analysis. The main function
in the package is convert.bm() which queries BioMart using the full capacity of the API provided through the
'biomaRt' package. Presets and defaults are provided for convenience but all "marts", "filters" and "attributes"
can be set by the user. Function convert.alias() converts Gene Symbols to Aliases and vice versa and function likely_symbol()
attempts to determine the most likely current Gene Symbol.
Author: Vidal Fey [aut, cre],
Henrik Edgren [aut]
Maintainer: Vidal Fey <vidal.fey@gmail.com>
Diff between convertid versions 0.2.1 dated 2026-02-05 and 0.3.0 dated 2026-04-01
convertid-0.2.1/convertid/R/get_symbol_aliases.R |only convertid-0.3.0/convertid/DESCRIPTION | 13 +++--- convertid-0.3.0/convertid/MD5 | 19 ++++++--- convertid-0.3.0/convertid/NAMESPACE | 1 convertid-0.3.0/convertid/R/convertId2.R | 6 ++- convertid-0.3.0/convertid/R/likely_symbol.R |only convertid-0.3.0/convertid/R/unify_gene_ids.R |only convertid-0.3.0/convertid/man/convert.bm.Rd | 3 + convertid-0.3.0/convertid/man/likely_symbol.Rd | 46 ++++++++++++++++++++--- convertid-0.3.0/convertid/man/unify_gene_ids.Rd |only convertid-0.3.0/convertid/tests |only 11 files changed, 68 insertions(+), 20 deletions(-)
Title: Classify Names by Gender, U.S. Ethnicity, and Leaf Nationality
Description: Functions to use the 'NamePrism' API <https://www.name-prism.com/api> or 'NamSor' API v2 <https://namsor.app/> for classifying names based on gender, 6 U.S. ethnicities, or 39 leaf nationalities. Updated to work with current API endpoints.
Author: Charles Crabtree [aut, cre],
Volha Chykina [aut],
Micah Gell-Redman [aut],
Christian Chacua [aut]
Maintainer: Charles Crabtree <charles.crabtree@monash.edu>
This is a re-admission after prior archival of version 1.0.0 dated 2017-11-04
Diff between nomine versions 1.0.0 dated 2017-11-04 and 1.0.2 dated 2026-04-01
DESCRIPTION | 27 ++++---- LICENSE | 4 - MD5 | 18 ++--- R/ethnicites.R | 56 +++++++++++++----- R/gender.r | 26 ++++---- R/nationalities.r | 95 +++++++++++++++++-------------- README.md | 143 ++++++++++++++++++++++++++++++++++++++++++----- man/get_ethnicities.Rd | 30 +++++++-- man/get_gender.Rd | 20 +++--- man/get_nationalities.Rd | 28 +++++++-- 10 files changed, 315 insertions(+), 132 deletions(-)
Title: A Multi-Modal Simulator for Spearheading Single-Cell Omics
Analyses
Description: A novel, multi-modal simulation engine for
studying dynamic cellular processes at single-cell resolution. 'dyngen'
is more flexible than current single-cell simulation engines. It
allows better method development and benchmarking, thereby stimulating
development and testing of novel computational methods. Cannoodt et
al. (2021) <doi:10.1038/s41467-021-24152-2>.
Author: Robrecht Cannoodt [aut, cre, cph] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dyngen versions 1.1.0 dated 2026-03-17 and 1.1.1 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/8_convert.R | 12 ++++++++---- build/vignette.rds |binary man/convert.Rd | 12 ++++++++---- 6 files changed, 28 insertions(+), 16 deletions(-)
Title: Single-Case Data Analyses for Single and Multiple Baseline
Designs
Description: A collection of procedures for analysing, visualising,
and managing single-case data. Multi-phase and multi-baseline designs are
supported. Analysing methods include regression models
(multilevel, multivariate, bayesian), between case standardised mean difference,
overlap indices ('PND', 'PEM', 'PAND', 'NAP', 'PET', 'tau-u', 'IRD', 'baseline corrected tau',
'CDC'), and randomization tests. Data preparation functions support outlier
detection, handling missing values, scaling, and custom transformations.
An export function helps to generate html, word, and latex tables in a
publication friendly style. A shiny app allows to use scan in a graphical
user interface.
More details can be found in the online book 'Analyzing single-case data with
R and scan', Juergen Wilbert (2026)
<https://jazznbass.github.io/scan-Book/>.
Author: Juergen Wilbert [cre, aut] ,
Timo Lueke [aut]
Maintainer: Juergen Wilbert <juergen.wilbert@uni-muenster.de>
Diff between scan versions 0.67.0 dated 2025-09-11 and 0.68.0 dated 2026-04-01
scan-0.67.0/scan/man/example_data.Rd |only scan-0.68.0/scan/DESCRIPTION | 17 scan-0.68.0/scan/MD5 | 332 ++++++++-------- scan-0.68.0/scan/NAMESPACE | 2 scan-0.68.0/scan/NEWS.md | 25 + scan-0.68.0/scan/R/add_l2.R | 43 +- scan-0.68.0/scan/R/anova.R | 17 scan-0.68.0/scan/R/as.data.frame.scdf.R | 7 scan-0.68.0/scan/R/autocorr.R | 9 scan-0.68.0/scan/R/batch_apply.R | 10 scan-0.68.0/scan/R/between_smd.R | 10 scan-0.68.0/scan/R/bplm.R | 44 +- scan-0.68.0/scan/R/cdc.R | 5 scan-0.68.0/scan/R/coefficents.sc_plm.R | 4 scan-0.68.0/scan/R/convert.R | 14 scan-0.68.0/scan/R/corrected_tau.R | 73 ++- scan-0.68.0/scan/R/describe.R | 8 scan-0.68.0/scan/R/design.R | 10 scan-0.68.0/scan/R/estimate_design.R | 33 + scan-0.68.0/scan/R/export.R | 8 scan-0.68.0/scan/R/export.sc_desc.R | 5 scan-0.68.0/scan/R/fetch.R | 35 + scan-0.68.0/scan/R/fill_missing.R | 156 +++++-- scan-0.68.0/scan/R/hplm.R | 61 ++- scan-0.68.0/scan/R/importer-gadget.R | 37 + scan-0.68.0/scan/R/inherit_roxygen_descriptions.R | 10 scan-0.68.0/scan/R/ird.R | 5 scan-0.68.0/scan/R/mplm.R | 10 scan-0.68.0/scan/R/nap.R | 9 scan-0.68.0/scan/R/outlier.R | 3 scan-0.68.0/scan/R/overlap.R | 6 scan-0.68.0/scan/R/pand.R | 5 scan-0.68.0/scan/R/pem.R | 12 scan-0.68.0/scan/R/pet.R | 10 scan-0.68.0/scan/R/plm.R | 22 - scan-0.68.0/scan/R/plm_contrasts.R | 7 scan-0.68.0/scan/R/pnd.R | 8 scan-0.68.0/scan/R/power_test.R | 8 scan-0.68.0/scan/R/print-export-plm.R | 1 scan-0.68.0/scan/R/private_check.R | 21 - scan-0.68.0/scan/R/private_kendall.R | 2 scan-0.68.0/scan/R/private_options.R | 2 scan-0.68.0/scan/R/rand_test.R | 20 - scan-0.68.0/scan/R/random_scdf.R | 12 scan-0.68.0/scan/R/rci.R | 12 scan-0.68.0/scan/R/read_scdf.R | 5 scan-0.68.0/scan/R/rescale.R | 7 scan-0.68.0/scan/R/sample_names.R | 14 scan-0.68.0/scan/R/scan-Data.R | 156 +++++-- scan-0.68.0/scan/R/scan-package.R | 3 scan-0.68.0/scan/R/scdf-functions.R | 39 + scan-0.68.0/scan/R/scdf.R | 36 + scan-0.68.0/scan/R/select_cases.R | 10 scan-0.68.0/scan/R/select_phases.R | 25 + scan-0.68.0/scan/R/set_vars.R | 8 scan-0.68.0/scan/R/shinyscan.R | 4 scan-0.68.0/scan/R/smd.R | 6 scan-0.68.0/scan/R/subset.scdf.R | 7 scan-0.68.0/scan/R/summary.scdf.R | 13 scan-0.68.0/scan/R/tau_u.R | 12 scan-0.68.0/scan/R/transform.scdf.R | 4 scan-0.68.0/scan/R/trend.R | 21 - 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-03-12 2.2.9
2024-01-08 2.2.8
2023-03-30 2.1.2
Title: Utilities to Support Lidar Applications at the Landscape,
Forest, and Tree Scale
Description: Implements algorithms for terrestrial, mobile, and airborne lidar processing, tree detection,
segmentation, and attribute estimation (Donager et al., 2021)
<doi:10.3390/rs13122297>, and a hierarchical patch delineation algorithm
'PatchMorph' (Girvetz & Greco, 2007) <doi:10.1007/s10980-007-9104-8>. Tree
detection uses rasterized point cloud metrics (relative neighborhood density and
verticality) combined with RANSAC cylinder fitting to locate tree boles and estimate
diameter at breast height. Tree segmentation applies graph-theory approaches inspired
by Tao et al. (2015) <doi:10.1016/j.isprsjprs.2015.08.007> with cylinder fitting
methods from de Conto et al. (2017) <doi:10.1016/j.compag.2017.07.019>. PatchMorph
delineates habitat patches across spatial scales using organism-specific thresholds.
Built on 'lidR' (Roussel et al., 2020) <doi:10.1016/j.rse.2020.112061>.
Author: Andrew Sanchez Meador [aut, cre, ctb] ,
Jonathon Donager [aut, ctb] ,
Blackburn Ryan [aut, ctb] ,
Cannon Jeffery [ctb] ,
Tiago de Conto [ctb, cph] ,
Keith O'Hara [ctb, cph]
Maintainer: Andrew Sanchez Meador <Andrew.SanchezMeador@nau.edu>
Diff between spanner versions 1.0.3 dated 2026-03-26 and 1.0.4 dated 2026-04-01
DESCRIPTION | 8 MD5 | 38 +- NEWS.md | 163 ++++----- R/Patch_Morph.R | 404 +++++++++++------------ R/PostProcess_TreeLocations.R | 492 ++++++++++++++-------------- R/Segment_Graph.R | 630 ++++++++++++++++++------------------ R/spanner-package.R | 38 +- R/utils.R | 62 ++- build/stage23.rdb |binary man/colorize_las.Rd | 180 +++++----- man/compute_pcv.Rd | 72 ++-- man/compute_ssao.Rd | 90 ++--- man/create_rotation_gif.Rd | 33 - man/download_naip_for_las.Rd | 126 +++---- man/eigen_metrics.Rd | 126 +++---- man/merge_las_colors.Rd | 124 +++---- man/segment_graph.Rd | 304 ++++++++--------- src/Progress.cpp | 5 tests/testthat/test-eigen-metrics.R | 120 +++--- tests/testthat/test-segmentation.R | 224 ++++++------ 20 files changed, 1627 insertions(+), 1612 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut],
Marly Gotti [aut],
Eli Miller [cre, aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Meth [...truncated...]
Maintainer: Eli Miller <eli.miller@atorusresearch.com>
Diff between riskmetric versions 0.2.6 dated 2026-01-13 and 0.2.7 dated 2026-04-01
DESCRIPTION | 10 - MD5 | 56 +++---- NAMESPACE | 4 NEWS.md | 10 + R/assess_last_30_bugs_status.R | 10 - R/metric_score.R | 7 R/pkg_ref_cache.R | 2 R/pkg_ref_cache_archive_release_date.R | 1 R/pkg_ref_cache_bug_reports.R | 5 R/pkg_ref_cache_description.R | 4 R/pkg_ref_cache_examples.R | 2 R/pkg_ref_cache_help_aliases.R | 4 R/pkg_ref_cache_license.R | 3 R/pkg_ref_cache_maintainer.R | 5 R/pkg_ref_cache_news.R | 6 R/pkg_ref_cache_r_cmd_check.R | 1 R/pkg_ref_cache_release_date.R | 6 R/pkg_ref_cache_repo_base_url.R | 3 R/pkg_ref_cache_tarball_url.R | 3 R/pkg_ref_cache_vignettes.R | 8 - R/pkg_ref_cache_web_url.R | 4 R/pkg_ref_cache_website_urls.R | 6 R/pkg_ref_class.R | 238 ++++++++++++++++++++------------- inst/doc/extending-riskmetric.R | 6 inst/doc/extending-riskmetric.html | 14 - inst/doc/riskmetric.R | 16 +- inst/doc/riskmetric.html | 30 ++-- man/pkg_ref.Rd | 28 +-- tests/testthat/setup_test_packages.R | 63 +++++--- 29 files changed, 322 insertions(+), 233 deletions(-)
Title: A Fast and Flexible Pipeline for Text Classification
Description: A high-level pipeline that simplifies text classification into three streamlined steps:
preprocessing, model training, and standardized prediction.
It unifies the interface for multiple algorithms (including 'glmnet', 'ranger',
'xgboost', and 'naivebayes') and memory-efficient sparse matrix vectorization
methods (Bag-of-Words, Term Frequency, TF-IDF, and Binary). Users can go from
raw text to a fully evaluated sentiment model, complete with ROC-optimized
thresholds, in just a few function calls. The resulting model artifact
automatically aligns the vocabulary of new datasets during the prediction phase,
safely appending predicted classes and probability matrices directly to the
user's original dataframe to preserve metadata.
Author: Alabhya Dahal [aut, cre]
Maintainer: Alabhya Dahal <alabhya.dahal@gmail.com>
Diff between quickSentiment versions 0.3.2 dated 2026-03-20 and 0.3.3 dated 2026-04-01
DESCRIPTION | 6 ++--- MD5 | 15 ++++++------- NAMESPACE | 1 NEWS.md | 12 +++------- R/evaluate_performance.R | 45 ++++++++++++++++++++++++++++++++++++--- R/print.quickSentiment_eval.R | 30 ++++++++++++++++++++++++++ README.md | 1 man/evaluate_performance.Rd | 4 ++- man/print.quickSentiment_eval.Rd |only 9 files changed, 92 insertions(+), 22 deletions(-)
More information about quickSentiment at CRAN
Permanent link
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package and then
attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Winston Chang [aut],
Jim Hester [aut],
Lionel Henry [aut, cre],
Posit Software, PBC [cph, fnd],
R Core team [ctb]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between pkgload versions 1.5.0 dated 2026-02-03 and 1.5.1 dated 2026-04-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/namespace-env.R | 5 ++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989) <DOI:10.2307/1912557>.
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is partially based on
work supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle [aut, cre],
Dongjun You [aut],
Lennart Schneider [ctb],
Mauricio Garnier-Villarreal [ctb],
Seongho Bae [ctb],
Phil Chalmers [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.5-8 dated 2024-08-28 and 0.5-9 dated 2026-04-01
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NEWS | 4 ++++ R/icci.R | 4 ++-- R/vuongtest.R | 9 ++++++--- README.md | 28 ++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/nonnest2.R | 10 +++++----- inst/doc/nonnest2.pdf |binary tests/testthat/test_discreteclass.R |only 10 files changed, 59 insertions(+), 23 deletions(-)
Title: MCMC, Particle Filtering, and Programmable Hierarchical Modeling
Description: A system for writing hierarchical statistical models largely
compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models
and do basic R-style math, and compiling both models and nimbleFunctions via
custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace
Approximation, deterministic nested approximations, Monte Carlo Expectation
Maximization, and some other tools.
The nimbleFunction system makes it easy to do things like implement new MCMC
samplers from R, customize the assignment of samplers to different parts of
a model from R, and compile the new samplers automatically via C++ alongside
the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language
by making it extensible: New distributions and functions can be added,
including as calls to external compiled code. Although most people think
of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models,
one can use 'NIMBLE' for writing arbitrary other kinds of model-generic
al [...truncated...]
Author: Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] ,
Abel Rodriguez [aut] ,
Duncan Temple Lang [aut] ,
Wei Zhang [aut] ,
[...truncated...]
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 1.4.1 dated 2026-02-13 and 1.4.2 dated 2026-04-01
DESCRIPTION | 8 INSTALL | 6 MD5 | 30 +-- R/MCMC_configuration.R | 10 - R/cppDefs_nimbleFunction.R | 2 R/cppDefs_nimbleList.R | 50 +---- inst/CppCode/RcppNimbleUtils.cpp | 162 ++++++++--------- inst/CppCode/RcppUtils.cpp | 77 ++++---- inst/CppCode/accessorClasses.cpp | 56 ++---- inst/CppCode/eigenUsingClasses.cpp | 54 ++--- inst/CppCode/nimOptim.cpp | 16 - inst/CppCode/predefinedNimbleLists.cpp | 306 ++++++++++++++------------------- inst/NEWS.md | 12 + inst/include/nimble/RcppNimbleUtils.h | 57 ++---- inst/include/nimble/Utils.h | 52 +++++ inst/include/nimble/accessorClasses.h | 215 ++++------------------- 16 files changed, 489 insertions(+), 624 deletions(-)
Title: Multimodal Access and Interactive Data Representation
Description: Provides accessible, interactive visualizations through the 'MAIDR'
(Multimodal Access and Interactive Data Representation) system. Converts
'ggplot2' and Base R plots into accessible HTML/SVG formats with keyboard
navigation, screen reader support, and 'sonification' capabilities. Supports
bar charts (simple, grouped, stacked), histograms, line plots, scatter plots,
box plots, violin plots, heat maps, density/smooth curves, faceted plots,
multi-panel layouts (including patchwork), and multi-layered plot combinations. Enables
data exploration for users with visual impairments through multiple sensory
modalities. For more details see the 'MAIDR' project
<https://maidr.ai/>.
Author: JooYoung Seo [aut, cph],
Niranjan Kalaiselvan [aut, cre]
Maintainer: Niranjan Kalaiselvan <nk46@illinois.edu>
Diff between maidr versions 0.2.0 dated 2026-03-07 and 0.3.0 dated 2026-04-01
maidr-0.2.0/maidr/inst/doc/plot-types.R |only maidr-0.2.0/maidr/inst/doc/plot-types.Rmd |only maidr-0.2.0/maidr/inst/doc/plot-types.html |only maidr-0.2.0/maidr/inst/htmlwidgets/lib/maidr-3.55.2 |only maidr-0.2.0/maidr/vignettes/plot-types.Rmd |only maidr-0.3.0/maidr/DESCRIPTION | 9 maidr-0.3.0/maidr/MD5 | 49 ++-- maidr-0.3.0/maidr/R/base_r_point_layer_processor.R | 94 +++++++ maidr-0.3.0/maidr/R/base_r_processor_factory.R | 2 maidr-0.3.0/maidr/R/examples.R | 12 + maidr-0.3.0/maidr/R/ggplot2_line_layer_processor.R | 4 maidr-0.3.0/maidr/R/ggplot2_point_layer_processor.R | 120 +++++++++- maidr-0.3.0/maidr/R/html_dependencies.R | 2 maidr-0.3.0/maidr/R/maidr-package.R |only maidr-0.3.0/maidr/R/svg_utils.R | 4 maidr-0.3.0/maidr/build/vignette.rds |binary maidr-0.3.0/maidr/inst/doc/getting-started.Rmd | 4 maidr-0.3.0/maidr/inst/doc/getting-started.html | 10 maidr-0.3.0/maidr/inst/doc/shiny-integration.Rmd | 2 maidr-0.3.0/maidr/inst/doc/shiny-integration.html | 8 maidr-0.3.0/maidr/inst/htmlwidgets/lib/maidr-3.59.0 |only maidr-0.3.0/maidr/man/BaseRPointLayerProcessor.Rd | 10 maidr-0.3.0/maidr/man/Ggplot2PointLayerProcessor.Rd | 49 +++- maidr-0.3.0/maidr/man/maidr-package.Rd |only maidr-0.3.0/maidr/tests/testthat/Rplots.pdf |binary maidr-0.3.0/maidr/tests/testthat/test-base-r-point-layer-processor.R | 114 ++++++++- maidr-0.3.0/maidr/tests/testthat/test-ggplot2-point-layer-processor.R |only maidr-0.3.0/maidr/vignettes/getting-started.Rmd | 4 maidr-0.3.0/maidr/vignettes/shiny-integration.Rmd | 2 29 files changed, 426 insertions(+), 73 deletions(-)
Title: Calculation of Sample Size and Power for ICC
Description: Provides functions to calculate the requisite sample size for studies where ICC is
the primary outcome. Can also be used for calculation of power. In both cases it
allows the user to test the impact of changing input variables by calculating the outcome
for several different values of input variables. Based off the work of Zou.
Zou, G. Y. (2012). Sample size formulas for estimating intraclass correlation coefficients with
precision and assurance. Statistics in medicine, 31(29), 3972-3981.
Author: Alasdair Rathbone [aut, cre],
Saurabh Shaw [aut],
Dinesh Kumbhare [aut]
Maintainer: Alasdair Rathbone <alasdair.rathbone@gmail.com>
Diff between ICC.Sample.Size versions 1.0 dated 2015-09-03 and 1.1 dated 2026-04-01
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 11 ++++++----- NEWS.md |only R/calculateAchievablep0.R | 11 +++++------ man/calculateAchieveablep0.Rd | 2 +- man/calculateIccPower.Rd | 2 +- man/calculateIccSampleSize.Rd | 2 +- 7 files changed, 33 insertions(+), 21 deletions(-)
More information about ICC.Sample.Size at CRAN
Permanent link
Title: Robust Inference in Difference-in-Differences and Event Study
Designs
Description: Provides functions to conduct robust inference in difference-in-differences and event study designs by implementing the methods developed in Rambachan & Roth (2023) <doi:10.1093/restud/rdad018>, "A More Credible Approach to Parallel Trends" [Previously titled "An Honest Approach..."]. Inference is conducted under a weaker version of the parallel trends assumption. Uniformly valid confidence sets are constructed based upon conditional confidence sets, fixed-length confidence sets and hybridized confidence sets.
Author: Ashesh Rambachan [aut, cph, cre],
Jonathan Roth [aut, cph]
Maintainer: Ashesh Rambachan <ashesh.a.rambachan@gmail.com>
Diff between HonestDiD versions 0.2.6 dated 2024-07-14 and 0.2.7 dated 2026-04-01
DESCRIPTION | 8 +++---- MD5 | 11 +++++----- NEWS.md |only R/arp-nuisance.R | 4 +-- R/flci.R | 53 ++++++++++++++++++++++++++++++++++++------------- R/sensitivityresults.R | 4 +++ R/utilities.R | 30 ++++++++++++++++++++++----- 7 files changed, 80 insertions(+), 30 deletions(-)
Title: Parallelize Common Functions via One Magic Function
Description: The futurize() function transpiles calls to sequential map-reduce functions such as base::lapply(), purrr::map(), 'foreach::foreach() %do% { ... }' into concurrent alternatives, providing you with a simple, straightforward path to scalable parallel computing via the 'future' ecosystem <doi:10.32614/RJ-2021-048>. By combining this function with R's native pipe operator, you have a convenient way for speeding up iterative computations with minimal refactoring, e.g. 'lapply(xs, fcn) |> futurize()', 'purrr::map(xs, fcn) |> futurize()', and 'foreach::foreach(x = xs) %do% { fcn(x) } |> futurize()'. Other map-reduce packages that can be "futurized" are 'BiocParallel', 'plyr', 'crossmap', 'pbapply' packages. There is also support for a growing set of domain-specific packages on CRAN (e.g. 'boot', 'caret', 'fgsea', 'fwb', 'gamlss', 'glmmTMB', 'glmnet', 'kernelshap', 'lme4', 'metafor', 'mgcv', 'partykit', 'riskRegression', 'seriation', 'shapr', 'SimDesign', 'strucchange', 'tm', 'T [...truncated...]
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between futurize versions 0.2.0 dated 2026-03-18 and 0.3.0 dated 2026-04-01
futurize-0.2.0/futurize/inst/testme/test-furrr-future_invoke-map.R |only futurize-0.2.0/futurize/tests/test-furrr-future_invoke-map.R |only futurize-0.3.0/futurize/DESCRIPTION | 9 futurize-0.3.0/futurize/MD5 | 218 ++++------ futurize-0.3.0/futurize/NAMESPACE | 1 futurize-0.3.0/futurize/NEWS.md | 20 futurize-0.3.0/futurize/R/000.bquote.R | 2 futurize-0.3.0/futurize/R/addons-BiocParallel.R | 11 futurize-0.3.0/futurize/R/addons-DESeq2.R | 6 futurize-0.3.0/futurize/R/addons-GSVA.R | 5 futurize-0.3.0/futurize/R/addons-GenomicAlignments.R | 5 futurize-0.3.0/futurize/R/addons-Rsamtools.R | 5 futurize-0.3.0/futurize/R/addons-SimDesign.R | 12 futurize-0.3.0/futurize/R/addons-SingleCellExperiment.R | 5 futurize-0.3.0/futurize/R/addons-TSP.R | 6 futurize-0.3.0/futurize/R/addons-boot.R | 12 futurize-0.3.0/futurize/R/addons-caret.R | 15 futurize-0.3.0/futurize/R/addons-fgsea.R | 5 futurize-0.3.0/futurize/R/addons-foreach.R | 8 futurize-0.3.0/futurize/R/addons-fwb.R | 24 - futurize-0.3.0/futurize/R/addons-gamlss.R | 21 futurize-0.3.0/futurize/R/addons-glmmTMB.R | 14 futurize-0.3.0/futurize/R/addons-glmnet.R | 5 futurize-0.3.0/futurize/R/addons-kernelshap.R | 6 futurize-0.3.0/futurize/R/addons-lme4.R | 5 futurize-0.3.0/futurize/R/addons-metafor.R | 15 futurize-0.3.0/futurize/R/addons-mgcv.R | 11 futurize-0.3.0/futurize/R/addons-partykit.R | 3 futurize-0.3.0/futurize/R/addons-pbapply.R | 11 futurize-0.3.0/futurize/R/addons-plyr.R | 8 futurize-0.3.0/futurize/R/addons-riskRegression.R | 10 futurize-0.3.0/futurize/R/addons-scater.R | 5 futurize-0.3.0/futurize/R/addons-scuttle.R | 5 futurize-0.3.0/futurize/R/addons-seriation.R | 6 futurize-0.3.0/futurize/R/addons-shapr.R | 10 futurize-0.3.0/futurize/R/addons-strucchange.R | 5 futurize-0.3.0/futurize/R/addons-sva.R | 5 futurize-0.3.0/futurize/R/addons-tm.R | 11 futurize-0.3.0/futurize/R/addons-vegan.R | 2 futurize-0.3.0/futurize/R/make_addon_transpilers.R | 11 futurize-0.3.0/futurize/R/make_options_for_furrr.R | 16 futurize-0.3.0/futurize/R/make_options_for_future.apply.R | 5 futurize-0.3.0/futurize/R/transpile.R | 17 futurize-0.3.0/futurize/R/transpiler-unwrap.R | 3 futurize-0.3.0/futurize/README.md | 2 futurize-0.3.0/futurize/inst/doc/futurize-21-purrr.html | 9 futurize-0.3.0/futurize/inst/doc/futurize-21-purrr.md | 9 futurize-0.3.0/futurize/inst/doc/futurize-22-crossmap.html | 2 futurize-0.3.0/futurize/inst/doc/futurize-22-crossmap.md | 2 futurize-0.3.0/futurize/inst/testme/run.R | 15 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,errors.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_colon.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,nested_dofuture.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture,rng.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture-options,nested.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-foreach_dofuture.R | 1 futurize-0.3.0/futurize/inst/testme/test-doFuture-times.R | 1 futurize-0.3.0/futurize/inst/testme/test-furrr-future_imap.R | 6 futurize-0.3.0/futurize/inst/testme/test-furrr-future_map.R | 11 futurize-0.3.0/futurize/inst/testme/test-furrr-future_map2.R | 12 futurize-0.3.0/futurize/inst/testme/test-furrr-future_modify.R | 1 futurize-0.3.0/futurize/inst/testme/test-furrr-future_pmap.R | 12 futurize-0.3.0/futurize/inst/testme/test-furrr-future_walk.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_Filter.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_apply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_by.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_eapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_kernapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply,RNG.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_lapply.R | 2 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_mapply,globals.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_mapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_replicate.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_sapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_tapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-future_vapply.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-globals,tricky2.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-globals,tricky_recursive.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-options,nested.R | 1 futurize-0.3.0/futurize/inst/testme/test-future.apply-stdout.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-BiocParallel.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-DESeq2.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-Rsamtools.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-SimDesign.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-TSP.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-base-stats.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-boot.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-caret.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-crossmap.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-fgsea.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-foreach.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-fwb.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-gamlss.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-kernelshap.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-lme4.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-metafor.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-mgcv.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-partykit.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-purrr.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-seriation.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-shapr.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-strucchange.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-tm.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-vegan.R | 1 futurize-0.3.0/futurize/inst/testme/test-futurize-wrapped.R | 28 + futurize-0.3.0/futurize/inst/testme/test-internals-futurize.R | 1 futurize-0.3.0/futurize/man/transpile.Rd | 4 futurize-0.3.0/futurize/vignettes/futurize-21-purrr.md | 9 futurize-0.3.0/futurize/vignettes/futurize-22-crossmap.md | 2 111 files changed, 471 insertions(+), 285 deletions(-)
Title: Breaks for Additive Season and Trend
Description: Decomposition of time series into
trend, seasonal, and remainder components with methods for detecting and
characterizing abrupt changes within the trend and seasonal components. 'BFAST'
can be used to analyze different types of satellite image time series and can
be applied to other disciplines dealing with seasonal or non-seasonal time
series, such as hydrology, climatology, and econometrics. The algorithm can be
extended to label detected changes with information on the parameters of the
fitted piecewise linear models. 'BFAST' monitoring functionality is described
in Verbesselt et al. (2010) <doi:10.1016/j.rse.2009.08.014>. 'BFAST monitor'
provides functionality to detect disturbance in near real-time based on 'BFAST'-
type models, and is described in Verbesselt et al. (2012) <doi:10.1016/j.rse.2012.02.022>.
'BFAST Lite' approach is a flexible approach that handles missing data
without interpolation, and will be described in an upcoming paper.
Furthermore, different mode [...truncated...]
Author: Jan Verbesselt [aut],
Dainius Masiliūnas [aut, cre] ,
Achim Zeileis [aut],
Rob Hyndman [ctb],
Marius Appel [aut],
Martin Jung [ctb],
Andrei Mîrț [ctb] ,
Paulo Negri Bernardino [ctb],
Dongdong Kong [ctb]
Maintainer: Dainius Masiliūnas <pastas4@gmail.com>
Diff between bfast versions 1.7.1 dated 2025-08-18 and 1.7.2 dated 2026-04-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 5 +++++ build/partial.rdb |binary man/bfastlite.Rd | 3 ++- man/bfastpp.Rd | 6 +++--- tests/Examples/bfast-Ex.Rout.save | 12 +++++++++--- 7 files changed, 29 insertions(+), 17 deletions(-)
Title: Spatial Component Analysis for Spatial Sequencing Data
Description: Spatial components offer tools for dimension reduction and
spatially variable gene detection for high dimensional spatial transcriptomics
data. Construction of a projection onto low-dimensional feature space of
spatially dependent metagenes offers pre-processing to clustering, testing for
spatial variability and denoising of spatial expression patterns. For more
details, see Koehler et al. (2026) <doi:10.1093/bioinformatics/btag052>.
Author: David Koehler [aut, cre]
Maintainer: David Koehler <koehler@imbie.uni-bonn.de>
Diff between SPACO versions 1.0.0 dated 2026-03-31 and 1.0.1 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Rcpp_Functions.cpp | 3 +++ tests/testthat/test-SCA.R | 13 +++++++++---- 4 files changed, 18 insertions(+), 10 deletions(-)
Title: Simulate and Analyse Social Interaction Data
Description: Provides tools to simulate and analyse datasets of social interactions
between individuals using hierarchical Bayesian models implemented in Stan.
Model fitting is performed via the 'rstan' package. Users can generate
realistic interaction data where individual phenotypes influence and respond
to those of their partners, with control over sampling design parameters such
as the number of individuals, partners, and repeated dyads. The simulation
framework allows flexible control over variation and correlation in mean trait
values, social responsiveness, and social impact, making it suitable for
research on interacting phenotypes and on direct and indirect genetic effects
('DGEs' and 'IGEs'). The package also includes functions to fit and compare
alternative models of social effects, including impact–responsiveness,
variance–partitioning, and trait-based models, and to summarise model
performance in terms of bias and dispersion. For a more detailed description
of the available models and [...truncated...]
Author: Rori Efrain Wijnhorst [aut, cre]
Maintainer: Rori Efrain Wijnhorst <roriwijnhorst@proton.me>
Diff between socialSim versions 0.1.8 dated 2026-01-30 and 0.1.9 dated 2026-03-31
DESCRIPTION | 12 - MD5 | 28 +-- NEWS.md | 8 R/run_model.R | 302 +++++++++++++++++------------------ R/simulate_data.R | 362 +++++++++++++++++++++--------------------- R/summarise_results.R | 164 +++++++++---------- README.md | 8 inst/doc/getting-started.Rmd | 198 +++++++++++----------- inst/stan/I&R.stan | 250 ++++++++++++++--------------- inst/stan/Trait.stan | 250 ++++++++++++++--------------- inst/stan/Trait_EIV.stan | 218 ++++++++++++------------- inst/stan/Trait_RS.stan | 260 +++++++++++++++--------------- inst/stan/Trait_only.stan | 180 ++++++++++---------- inst/stan/VP.stan | 160 +++++++++--------- vignettes/getting-started.Rmd | 198 +++++++++++----------- 15 files changed, 1299 insertions(+), 1299 deletions(-)
Title: Sequential Trial Emulation
Description: Implementation of sequential trial emulation for the analysis of observational databases.
The 'SEQTaRget' software accommodates time-varying treatments and confounders, as well as binary
and failure time outcomes. 'SEQTaRget' allows to compare both static and dynamic strategies,
can be used to estimate observational analogs of intention-to-treat
and per-protocol effects, and can adjust for potential selection bias
induced by losses-to-follow-up. (Paper to come).
Author: Ryan O'Dea [aut, cre] ,
Alejandro Szmulewicz [aut] ,
Tom Palmer [aut] ,
Paul Madley-Dowd [aut] ,
Miguel Hernan [aut] ,
The President and Fellows of Harvard College [cph]
Maintainer: Ryan O'Dea <ryan.odea@psi.ch>
Diff between SEQTaRget versions 1.3.6 dated 2026-02-16 and 1.4.1 dated 2026-03-31
DESCRIPTION | 17 +- MD5 | 115 +++++++++--------- NAMESPACE | 1 NEWS.md | 55 ++++++++ R/SEQexpand.R | 50 ++++---- R/SEQopts.R | 34 ++++- R/SEQuential.R | 74 +++++++++-- R/class_definitions.R | 9 - R/class_methods.R | 66 ++++++---- R/class_setters.R | 6 R/data.R | 12 - R/internal_analysis.R | 58 +++++---- R/internal_fatglmHelpers.R | 46 +++---- R/internal_hazard.R | 28 ++-- R/internal_misc.R | 67 +++++++--- R/internal_models.R | 2 R/internal_multinomial.R | 84 ++++++++----- R/internal_plot.R | 5 R/internal_survival.R | 145 ++++++++++++++--------- R/internal_weights.R | 103 ++++++++-------- README.md | 34 +++-- build/vignette.rds |binary data/SEQdata.LTFU.rda |binary data/SEQdata.multitreatment.rda |binary data/SEQdata.rda |binary inst/doc/ITT.R | 2 inst/doc/ITT.Rmd | 2 inst/doc/SEQuential.R | 4 inst/doc/SEQuential.Rmd | 15 +- inst/doc/SEQuential.html | 248 +++++++++++++++++++++++++++++++--------- inst/doc/censoring.R | 10 - inst/doc/censoring.Rmd | 10 - inst/doc/censoring.html | 172 ++++++++++----------------- inst/doc/doseresponse.R | 2 inst/doc/doseresponse.Rmd | 12 + inst/doc/doseresponse.html | 8 - man/SEQdata.LTFU.Rd | 5 man/SEQdata.Rd | 6 man/SEQdata.multitreatment.Rd | 2 man/SEQopts.Rd | 12 - man/SEQuential.Rd | 2 man/check_separation.Rd |only man/compevent.Rd | 2 man/create.risk.Rd | 2 man/denominator.Rd | 2 man/dot-coef_table.Rd |only man/hazard_ratio.Rd | 2 man/km_curve.Rd | 2 man/km_data.Rd | 2 man/prepare.output.Rd | 1 tests/testthat/test_coverage.R |only tests/testthat/test_errors.R | 13 ++ tests/testthat/test_methods.R | 4 tests/testthat/test_misc.R | 12 + tests/testthat/test_survival.R | 19 ++- tests/testthat/test_warnings.R | 23 +++ vignettes/ITT.Rmd | 2 vignettes/SEQuential.Rmd | 15 +- vignettes/censoring.Rmd | 10 - vignettes/doseresponse.Rmd | 12 + 60 files changed, 1031 insertions(+), 615 deletions(-)
Title: Analyzing Revisions in Real-Time Time Series Vintages
Description: Analyzes revisions in real-time time series vintages. The
package converts between wide revision triangles and tidy long
vintages, extracts selected releases, computes revision series,
visualizes vintage paths, and summarizes revision properties such as
bias, dispersion, autocorrelation, and news-noise diagnostics. It
also identifies efficient releases and estimates state-space models
for revision nowcasting. Methods are based on Howrey (1978)
<doi:10.2307/1924972>, Jacobs and Van Norden (2011)
<doi:10.1016/j.jeconom.2010.04.010>, and Kishor and Koenig (2012)
<doi:10.1198/jbes.2010.08169>.
Author: Marc Burri [aut, cre, cph] ,
Philipp Wegmueller [aut, cph]
Maintainer: Marc Burri <marc.burri91@gmail.com>
Diff between reviser versions 0.1.0 dated 2026-03-29 and 0.1.1 dated 2026-03-31
reviser-0.1.0/reviser/man/figures/README-unnamed-chunk-3-1.png |only reviser-0.1.0/reviser/tests/testthat/tests-kk.R |only reviser-0.1.1/reviser/DESCRIPTION | 11 - reviser-0.1.1/reviser/MD5 | 22 +- reviser-0.1.1/reviser/NEWS.md | 13 + reviser-0.1.1/reviser/R/jvn.R | 55 +++---- reviser-0.1.1/reviser/R/kk.R | 19 +- reviser-0.1.1/reviser/R/reviser-package.R | 4 reviser-0.1.1/reviser/README.md | 75 ++++++---- reviser-0.1.1/reviser/inst/CITATION | 5 reviser-0.1.1/reviser/inst/examples/sticker.R | 2 reviser-0.1.1/reviser/man/figures/README-readme-example-1.png |only reviser-0.1.1/reviser/man/reviser-package.Rd | 11 + reviser-0.1.1/reviser/tests/testthat/test-kk.R |only 14 files changed, 132 insertions(+), 85 deletions(-)
Title: Spatial Estimation and Prediction for Censored/Missing Responses
Description: It provides functions for estimating parameters in linear spatial models with censored or missing responses using the Expectation-Maximization (EM), Stochastic Approximation EM (SAEM), and Monte Carlo EM (MCEM) algorithms. These methods are widely used to obtain maximum likelihood (ML) estimates in the presence of incomplete data. The EM algorithm computes ML estimates when a closed-form expression for the conditional expectation of the complete-data log-likelihood is available. The MCEM algorithm replaces this expectation with a Monte Carlo approximation based on independent simulations of the missing data. In contrast, the SAEM algorithm decomposes the E-step into simulation and stochastic approximation steps, improving computational efficiency in complex settings. In addition, the package provides standard error estimation based on the Louis method. It also includes functionality for spatial prediction at new locations.
References used for this package: Galarza, C. E., Matos, L. A., [...truncated...]
Author: Katherine A. L. Valeriano [aut, cre] ,
Christian Galarza Morales [ctb] ,
Larissa Avila Matos [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>
This is a re-admission after prior archival of version 0.3.0 dated 2022-06-27
Diff between RcppCensSpatial versions 0.3.0 dated 2022-06-27 and 1.0.0 dated 2026-03-31
DESCRIPTION | 40 ++++---------- MD5 | 44 +++++++-------- NEWS.md | 16 +++-- R/Algorithm_utils.R | 19 +++++- R/AuxiliaryFunctions_USER.R | 20 +++---- R/EstEMspatial_USER.R | 26 ++++----- R/EstMCEMspatial_USER.R | 29 +++++----- R/EstSAEMspatial_USER.R | 40 +++++++------- R/RcppExports.R | 8 +- R/rCensspatial_USER.R | 6 +- README.md | 125 ++++++++++++++++++++++---------------------- build/partial.rdb |binary man/CovMat.Rd | 4 - man/EM.sclm.Rd | 26 ++++----- man/MCEM.sclm.Rd | 29 +++++----- man/SAEM.sclm.Rd | 40 +++++++------- man/dist2Dmatrix.Rd | 4 - man/predict.sclm.Rd | 8 +- man/rCensSp.Rd | 6 +- src/AuxiliaryFunctions.cpp | 14 +--- src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 18 +++--- 23 files changed, 262 insertions(+), 262 deletions(-)
More information about RcppCensSpatial at CRAN
Permanent link
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharche [...truncated...]
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Rasmus Rydbirk [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
This is a re-admission after prior archival of version 1.0.14 dated 2026-03-08
Diff between pagoda2 versions 1.0.14 dated 2026-03-08 and 1.0.15 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- README.md | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Measles Epidemiological Models
Description: A specialized collection of measles epidemiological models built on the 'epiworldR' framework. This package is a spinoff from 'epiworldR' focusing specifically on measles transmission dynamics. It includes models for school settings with quarantine and isolation policies, mixing models with population groups, and risk-based quarantine strategies. The models use Agent-Based Models (ABM) with a fast 'C++' backend from the 'epiworld' library. Ideal for studying measles outbreaks, vaccination strategies, and intervention policies.
Author: George Vega Yon [aut, cre] ,
Damon Toth [ctb] ,
Jake Wagoner [ctb] ,
Olivia Banks [ctb] ,
Centers for Disease Control and Prevention [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
This is a re-admission after prior archival of version 0.1.1 dated 2026-02-21
Diff between measles versions 0.1.1 dated 2026-02-21 and 0.2.0 dated 2026-03-31
DESCRIPTION | 8 MD5 | 35 +-- NEWS.md | 13 + R/ModelMeaslesMixing.R | 22 ++ R/ModelMeaslesMixingRiskQuarantine.R | 3 R/ModelMeaslesSchool.R | 3 README.md | 256 ++++++++++++++++++++++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/short-creek.R | 17 + inst/doc/short-creek.html | 147 +++++++------- inst/doc/short-creek.qmd | 25 +- inst/tinytest/test-measles-quarantine-errors.R | 1 inst/tinytest/test-measles-quarantine-math.R | 16 - man/ModelMeaslesMixing.Rd | 22 ++ man/ModelMeaslesMixingRiskQuarantine.Rd | 3 man/ModelMeaslesSchool.Rd | 3 man/figures/README-outbreak-size-plot-1.png |only vignettes/short-creek.qmd | 25 +- 19 files changed, 483 insertions(+), 116 deletions(-)
Title: Model-Based Geostatistics
Description: Modern model-based geostatistics for point-referenced data. This package provides a
simple interface to run spatial machine learning models and geostatistical models
that estimate a continuous (raster) surface from point-referenced outcomes and,
optionally, a set of raster covariates. The package also includes functions to
summarize raster outcomes by (polygon) region while preserving uncertainty.
Author: Nathaniel Henry [aut, cre] ,
Benjamin Mayala [aut],
Roy Burstein [ctb] ,
Nafis Sadat [ctb],
Michael Richards [ctb],
Michael Collison [ctb],
Michael Cork [ctb]
Maintainer: Nathaniel Henry <nat@henryspatialanalysis.com>
Diff between mbg versions 1.1.2 dated 2026-03-10 and 1.2.0 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/aggregate_grid_to_polygons.R | 4 ++++ 3 files changed, 9 insertions(+), 5 deletions(-)
Title: Image Statistics Based on Processing Fluency
Description: Get image statistics based on processing fluency theory. The
functions provide scores for several basic aesthetic principles that
facilitate fluent cognitive processing of images: contrast,
complexity / simplicity, self-similarity, symmetry, and typicality.
See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr
(2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Author: Stefan Mayer [aut, cre]
Maintainer: Stefan Mayer <stefan@mayer-de.com>
This is a re-admission after prior archival of version 0.2.5 dated 2024-02-22
Diff between imagefluency versions 0.2.5 dated 2024-02-22 and 1.0.0 dated 2026-03-31
DESCRIPTION | 17 MD5 | 75 +- NEWS.md | 12 R/complexity.R | 147 +--- R/contrast.R | 8 R/imagefluency-package.R | 2 R/self-similarity.R | 74 +- R/simplicity.R | 2 R/symmetry.R | 15 R/typicality.R | 15 R/utils.R | 48 + README.md | 42 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/getting-started.R | 152 ++-- inst/doc/getting-started.Rmd | 26 inst/doc/getting-started.html | 831 +++++++++++++++++------ inst/imagefluencyApp/app.R | 1228 ++++++++++++++++++++++++++++------ man/dot-compl.Rd | 2 man/dot-compress_and_get_size.Rd |only man/dot-typ.Rd | 2 man/figures/dashboard.png |only man/imagefluency-package.Rd | 2 man/img_complexity.Rd | 2 man/img_simplicity.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test_complexity.R | 34 tests/testthat/test_contrast.R | 6 tests/testthat/test_imagefluencyApp.R | 2 tests/testthat/test_self_similarity.R | 13 tests/testthat/test_symmetry.R | 3 tests/testthat/test_typicality.R | 6 tests/testthat/test_utils.R | 8 vignettes/example_images |only vignettes/getting-started.Rmd | 26 35 files changed, 2051 insertions(+), 753 deletions(-)
Title: Online Changepoint Detection in Univariate and Multivariate Data
Streams
Description: Provides high-performance online changepoint detection in univariate and multivariate data
streams. Implements efficient 'C++' backends for the 'focus', 'md-focus' and 'np-focus'
algorithms, with an 'R' interface for real-time monitoring and offline analysis.
The package bundles code from 'Qhull' <http://www.qhull.org/>, by C. B. Barber and
The Geometry Center. See 'inst/COPYRIGHTS' for details.
Author: Gaetano Romano [aut, cre, trl],
Kes Ward [aut],
Yuntang Fan [aut],
Guillem Rigaill [aut],
Vincent Runge [aut],
Paul Fearnhead [aut],
Idris A. Eckley [aut],
C. B. Barber [ctb, cph] ,
The Geometry Center [cph]
Maintainer: Gaetano Romano <g.romano@lancaster.ac.uk>
Diff between focus versions 0.1.2 dated 2026-03-30 and 0.1.3 dated 2026-03-31
DESCRIPTION | 6 MD5 | 28 +- R/RcppExports.R | 59 ++--- README.md | 18 - man/detector_candidates.Rd | 4 man/detector_info_n.Rd | 4 man/detector_info_sn.Rd | 4 man/detector_pieces_len.Rd | 4 man/detector_update.Rd | 4 man/focus_offline.Rd | 9 man/generate_projection_indexes.Rd | 12 - man/get_statistics.Rd | 4 src/MultivariateInfo.h | 378 +++++++++++-------------------------- src/RcppExports.cpp | 56 ++--- src/focus_rcpp_module.cpp | 61 ++--- 15 files changed, 242 insertions(+), 409 deletions(-)
Title: Representing and Inferring Single-Cell Trajectories
Description: Provides functionality to infer trajectories from single-cell data,
represent them into a common format, and adapt them. Other biological information
can also be added, such as cellular grouping, RNA velocity and annotation.
Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
Author: Robrecht Cannoodt [aut, cre] ,
Wouter Saelens [aut]
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
This is a re-admission after prior archival of version 1.2.5 dated 2025-11-26
Diff between dynwrap versions 1.2.5 dated 2025-11-26 and 1.3.0 dated 2026-03-31
dynwrap-1.2.5/dynwrap/man/dynwrap.Rd |only dynwrap-1.3.0/dynwrap/DESCRIPTION | 14 dynwrap-1.3.0/dynwrap/MD5 | 180 +++++----- dynwrap-1.3.0/dynwrap/NAMESPACE | 4 dynwrap-1.3.0/dynwrap/NEWS.md | 18 + dynwrap-1.3.0/dynwrap/R/adapt_orient_topology.R | 22 - dynwrap-1.3.0/dynwrap/R/add_regulatory_network.R | 2 dynwrap-1.3.0/dynwrap/R/calculate_average.R | 6 dynwrap-1.3.0/dynwrap/R/calculate_geodesic_distances.R | 69 +-- dynwrap-1.3.0/dynwrap/R/calculate_trajectory_dimred.R | 72 +--- dynwrap-1.3.0/dynwrap/R/classify_milestone_network.R | 8 dynwrap-1.3.0/dynwrap/R/convert_milestone_percentages_to_progressions.R | 28 - dynwrap-1.3.0/dynwrap/R/convert_progressions_to_milestone_percentages.R | 20 - dynwrap-1.3.0/dynwrap/R/method_create_ti_method_container.R | 6 dynwrap-1.3.0/dynwrap/R/method_create_ti_method_r.R | 6 dynwrap-1.3.0/dynwrap/R/method_execute.R | 6 dynwrap-1.3.0/dynwrap/R/method_extract_args.R | 16 dynwrap-1.3.0/dynwrap/R/method_get_ti_methods.R | 12 dynwrap-1.3.0/dynwrap/R/method_process_definition.R | 2 dynwrap-1.3.0/dynwrap/R/package.R | 7 dynwrap-1.3.0/dynwrap/R/project_waypoints.R | 4 dynwrap-1.3.0/dynwrap/R/simplify_igraph_network.R | 72 ++-- dynwrap-1.3.0/dynwrap/R/simplify_trajectory.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_branch_trajectory.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_cell_graph.R | 53 +- dynwrap-1.3.0/dynwrap/R/wrap_add_cell_waypoints.R | 52 +- dynwrap-1.3.0/dynwrap/R/wrap_add_cluster_graph.R | 34 - dynwrap-1.3.0/dynwrap/R/wrap_add_cyclic_trajectory.R | 10 dynwrap-1.3.0/dynwrap/R/wrap_add_dimred.R | 36 +- dynwrap-1.3.0/dynwrap/R/wrap_add_dimred_projection.R | 26 - dynwrap-1.3.0/dynwrap/R/wrap_add_end_state_probabilities.R | 14 dynwrap-1.3.0/dynwrap/R/wrap_add_expression.R | 4 dynwrap-1.3.0/dynwrap/R/wrap_add_feature_importance.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_grouping.R | 42 +- dynwrap-1.3.0/dynwrap/R/wrap_add_prior_information.R | 26 - dynwrap-1.3.0/dynwrap/R/wrap_add_pseudotime.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_root.R | 27 - dynwrap-1.3.0/dynwrap/R/wrap_add_timings.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_add_trajectory.R | 42 +- dynwrap-1.3.0/dynwrap/R/wrap_add_waypoints.R | 60 +-- dynwrap-1.3.0/dynwrap/R/wrap_data.R | 2 dynwrap-1.3.0/dynwrap/R/wrap_gather_cells_at_milestones.R | 10 dynwrap-1.3.0/dynwrap/R/wrap_label_milestones.R | 28 - dynwrap-1.3.0/dynwrap/build/vignette.rds |binary dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_container.Rmd | 4 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_container.html | 28 - dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_definition.Rmd | 6 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_definition.html | 13 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_r.Rmd | 2 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_r.html | 6 dynwrap-1.3.0/dynwrap/inst/doc/create_ti_method_wrappers.html | 44 +- dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_comp1.R | 10 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_identity.R | 8 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_random.R | 10 dynwrap-1.3.0/dynwrap/inst/tests/testthat/helper-ti_shuffle.R | 12 dynwrap-1.3.0/dynwrap/man/add_trajectory.Rd | 6 dynwrap-1.3.0/dynwrap/man/create_ti_method_r.Rd | 2 dynwrap-1.3.0/dynwrap/man/dynwrap-package.Rd |only dynwrap-1.3.0/dynwrap/man/simplify_igraph_network.Rd | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-adapt_orient_topology.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_average.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_geodesic_distances.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-calculate_trajectory_dimred.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-classify_milestone_network.R | 24 - dynwrap-1.3.0/dynwrap/tests/testthat/test-method_create_ti_method_r.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-method_infer_trajectory.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-method_parse_parameter_definition.R | 22 - dynwrap-1.3.0/dynwrap/tests/testthat/test-milestone_convertors.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-simplify_igraph_network.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-simplify_trajectory.R | 44 +- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_branch_trajectory.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cell_graph.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cell_waypoints.R | 18 - dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_cyclic_trajectory.R | 12 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_dimred.R | 50 +- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_dimred_projection.R | 6 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_end_state_probabilities.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_expression.R | 16 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_grouping.R | 12 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_linear_trajectory.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_prior_information.R | 84 ++-- dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_pseudotime.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_root_and_add_pseudotime.R | 4 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_timings.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_trajectory.R | 2 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_add_waypoints.R | 10 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_cell_group.R | 14 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_cluster_graph.R | 8 dynwrap-1.3.0/dynwrap/tests/testthat/test-wrap_label_milestones.R | 8 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_container.Rmd | 4 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_definition.Rmd | 6 dynwrap-1.3.0/dynwrap/vignettes/create_ti_method_r.Rmd | 2 92 files changed, 858 insertions(+), 857 deletions(-)
Title: Community Assembly by Traits: Individuals and Beyond
Description: Detect and quantify community assembly processes using trait values of individuals or populations, the T-statistics and other metrics, and dedicated null models. Provides tools to analyse 'intraspecific' trait variability and its consequences for community assembly. Implements a framework using individual-level trait data to decompose variance at the population, species, and community levels. Methods are described in 'Taudiere' and 'Violle' (2016) <doi:10.1111/ecog.01433>.
Author: Adrien Taudiere [aut, cre, cph] ,
Cyrille Violle [aut] ,
Francois Munoz [ctb]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between cati versions 0.99.4 dated 2022-02-25 and 0.99.6 dated 2026-03-31
DESCRIPTION | 37 MD5 | 62 NAMESPACE | 112 NEWS.md |only R/allfunctions_cati.R |10942 +++++++++++++++++++++++++++++----------------- R/cati-package.R |only README.md |only build |only inst/CITATION | 26 inst/WORDLIST |only man/ComIndex.Rd | 2 man/ComIndexMulti.Rd | 61 man/Fred.Rd | 20 man/IndexByGroups.Rd | 4 man/MinMaxMST.Rd | 4 man/RaoRel.Rd | 71 man/SumBL.Rd | 4 man/Tstats.Rd | 26 man/as.listofindex.Rd | 2 man/cati-package.Rd |only man/decompCTRE.Rd | 8 man/partvar.Rd | 2 man/plotCorTstats.Rd | 2 man/plotDistri.Rd | 2 man/plotRandtest.Rd | 22 man/plotSESvar.Rd | 2 man/plotSpPop.Rd | 2 man/plotSpVar.Rd | 2 man/samplingSubsetData.Rd | 8 man/ses.Rd | 2 man/ses.listofindex.Rd | 10 man/traitflex.anova.Rd | 11 tests |only 33 files changed, 7341 insertions(+), 4105 deletions(-)
Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus
genotype-by-environment) and GGB (genotype plus
genotype-by-block-of-environments) models. See Laffont et al. (2013)
<doi:10.2135/cropsci2013.03.0178>.
Author: Kevin Wright [aut, cre, cph] ,
Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between gge versions 1.9 dated 2024-10-28 and 1.10 dated 2026-03-31
gge-1.10/gge/DESCRIPTION | 11 ++++---- gge-1.10/gge/MD5 | 22 ++++++++-------- gge-1.10/gge/NAMESPACE | 1 gge-1.10/gge/NEWS.md | 11 +++++--- gge-1.10/gge/R/gge.r |only gge-1.10/gge/build/partial.rdb |binary gge-1.10/gge/build/vignette.rds |binary gge-1.10/gge/inst/doc/gge_examples.R | 44 ++++++++++++++++---------------- gge-1.10/gge/inst/doc/gge_examples.html | 19 +++++++------ gge-1.10/gge/man/RedGrayBlue.Rd | 2 - gge-1.10/gge/man/gge.Rd | 17 ++++++++---- gge-1.10/gge/tests/testthat/test_gge.R | 37 ++++++++++++++++++++++---- gge-1.9/gge/R/gge.R |only 13 files changed, 100 insertions(+), 64 deletions(-)
Title: Automated Analysis of Phenotypic Data
Description: Provides functions to analyze and visualize meristic and mensural
phenotypic data in a comparative framework. The package implements an
automated pipeline that summarizes traits, identifies diagnostic variables
among groups, performs multivariate and univariate statistical analyses, and
produces publication-ready graphics. Earlier implementation are
described in Torres (2025) <doi:10.64898/2025.12.18.695244> (v1.0.0)
and Torres (2026) <doi:10.1002/ece3.73111> (v2.0.0).
Author: Javier Torres [aut, cre]
Maintainer: Javier Torres <metalofis@gmail.com>
Diff between Orangutan versions 2.0.0 dated 2026-02-04 and 2.1.0 dated 2026-03-31
DESCRIPTION | 17 MD5 | 16 NAMESPACE | 11 R/Orangutan.R | 1269 ++++++++++++++++++++++++++++++-------------- R/globals.R | 4 R/html_report.R |only R/imports.R | 17 README.md |only man/categorical_analyses.Rd |only man/generate_html_report.Rd |only man/run_orangutan.Rd | 6 11 files changed, 924 insertions(+), 416 deletions(-)
Title: Accessing Data Stored in 'LaBB-CAT' Instances
Description: 'LaBB-CAT' is a web-based language corpus management
system developed by the New Zealand Institute of Language, Brain
and Behaviour (NZILBB) - see <https://labbcat.canterbury.ac.nz>.
This package defines functions for accessing corpus data in a 'LaBB-CAT'
instance. You must have at least version 20230818.1400 of 'LaBB-CAT'
to use this package.
For more information about 'LaBB-CAT', see
Robert Fromont and Jennifer Hay (2008) <doi:10.3366/E1749503208000142>
or
Robert Fromont (2017) <doi:10.1016/j.csl.2017.01.004>.
Author: Robert Fromont [aut, cre]
Maintainer: Robert Fromont <robert.fromont@canterbury.ac.nz>
Diff between nzilbb.labbcat versions 1.5-0 dated 2025-08-19 and 1.5-1 dated 2026-03-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/nzilbb.labbcat.R | 20 +++++++++++++------- build/partial.rdb |binary tests/testthat/test-getMatches.R | 3 ++- 6 files changed, 30 insertions(+), 17 deletions(-)
More information about nzilbb.labbcat at CRAN
Permanent link
Title: Run 'shiny' Applications in the Browser
Description: Exporting 'shiny' applications with 'shinylive' allows you to
run them entirely in a web browser, without the need for a separate R
server. The traditional way of deploying 'shiny' applications involves
in a separate server and client: the server runs R and 'shiny', and
clients connect via the web browser. When an application is deployed
with 'shinylive', R and 'shiny' run in the web browser (via 'webR'):
the browser is effectively both the client and server for the
application. This allows for your 'shiny' application exported by
'shinylive' to be hosted by a static web server.
Author: Barret Schloerke [aut, cre] ,
Winston Chang [aut] ,
George Stagg [aut],
Garrick Aden-Buie [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinylive versions 0.3.0 dated 2024-11-12 and 0.4.0 dated 2026-03-31
DESCRIPTION | 26 +++--- MD5 | 53 +++++++------ NAMESPACE | 1 NEWS.md | 24 ++++++ R/app_json.R | 46 +++++++---- R/assets.R | 45 ++++++----- R/cli.R | 39 +++++++-- R/deps.R | 47 +++++++---- R/export.R | 58 +++++++------- R/packages.R | 136 +++++++++++++++++++++++++--------- R/quarto_ext.R | 39 ++++++--- R/shinylive-package.R | 1 R/utils.R | 42 ++++++++-- R/version.R | 4 - README.md | 2 inst/WORDLIST | 6 - man/export.Rd | 6 - man/figures |only man/shinylive-package.Rd | 2 tests/testthat/apps/app-r/app.R | 2 tests/testthat/apps/server-r/global.R | 2 tests/testthat/apps/server-r/server.R | 2 tests/testthat/apps/server-r/ui.R | 2 tests/testthat/setup-skip.R | 5 + tests/testthat/test-assertions.R |only tests/testthat/test-export.R | 53 ++++++++++--- tests/testthat/test-quarto_ext.R | 50 +++++++++++- 27 files changed, 485 insertions(+), 208 deletions(-)
Title: Analysis and Visualization of Complex Networks
Description: Provides tools for the analysis, visualization, and manipulation
of dynamical, social (Saqr et al. (2024) <doi:10.1007/978-3-031-54464-4_10>) and
complex networks (Saqr et al. (2025) <doi:10.1145/3706468.3706513>). The package
supports multiple network formats and offers flexible tools for heterogeneous,
multi-layer, and hierarchical network analysis with simple syntax and
extensive toolset.
Author: Mohammed Saqr [aut, cph],
Sonsoles Lopez-Pernas [aut, cre, cph],
Santtu Tikka [aut]
Maintainer: Sonsoles Lopez-Pernas <sonsoles.lopez@uef.fi>
Diff between cograph versions 1.5.2 dated 2026-03-02 and 2.0.0 dated 2026-03-31
cograph-1.5.2/cograph/inst/doc/basic_example.R |only cograph-1.5.2/cograph/inst/doc/basic_example.Rmd |only cograph-1.5.2/cograph/inst/doc/basic_example.html |only cograph-1.5.2/cograph/inst/doc/co_pvalue.R |only cograph-1.5.2/cograph/inst/doc/co_pvalue.Rmd |only cograph-1.5.2/cograph/inst/doc/co_pvalue.html |only cograph-1.5.2/cograph/inst/doc/multi_network.R |only cograph-1.5.2/cograph/inst/doc/multi_network.Rmd |only cograph-1.5.2/cograph/inst/doc/multi_network.html |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.R |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.Rmd |only cograph-1.5.2/cograph/inst/doc/pie_donut_guide.html |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.R |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.Rmd |only cograph-1.5.2/cograph/inst/doc/qgraph-to-splot.html |only cograph-1.5.2/cograph/man/as_cograph_network.Rd |only cograph-1.5.2/cograph/man/figures/README-unnamed-chunk-10-1.jpeg |only 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cograph-2.0.0/cograph/tests/testthat/test-sn-edges.R | 132 - cograph-2.0.0/cograph/tests/testthat/test-sn-nodes.R | 169 -- cograph-2.0.0/cograph/tests/testthat/test-sn-save.R | 9 cograph-2.0.0/cograph/tests/testthat/test-soplot.R | 199 -- cograph-2.0.0/cograph/tests/testthat/test-splot.R | 557 +------ cograph-2.0.0/cograph/tests/testthat/test-themes-extended.R | 12 cograph-2.0.0/cograph/tests/testthat/test-tna-integration.R |only cograph-2.0.0/cograph/tests/testthat/test-tna-temporal.R |only cograph-2.0.0/cograph/tests/testthat/test-validate-nestimate-bootstrap-permutation.R |only cograph-2.0.0/cograph/vignettes/articles |only cograph-2.0.0/cograph/vignettes/input-formats.Rmd |only cograph-2.0.0/cograph/vignettes/introduction.Rmd |only 590 files changed, 6724 insertions(+), 4121 deletions(-)
Title: Rapid Manipulation of the Variant Call Format (VCF)
Description: The 'vcfpp.h' (<https://github.com/Zilong-Li/vcfpp>) provides an easy-to-use 'C++' 'API' of 'htslib', offering full functionality for manipulating Variant Call Format (VCF) files. The 'vcfppR' package serves as the R bindings of the 'vcfpp.h' library, enabling rapid processing of both compressed and uncompressed VCF files. Explore a range of powerful features for efficient VCF data manipulation.
Author: Zilong Li [aut, cre] ,
Bonfield, James K and Marshall, John and Danecek, Petr and Li, Heng and
Ohan, Valeriu and Whitwham, Andrew and Keane, Thomas and Davies,
Robert M [cph]
Maintainer: Zilong Li <zilong.dk@gmail.com>
Diff between vcfppR versions 0.8.2 dated 2025-11-06 and 0.8.3 dated 2026-03-31
vcfppR-0.8.2/vcfppR/src/vcf-popgen.cpp |only vcfppR-0.8.3/vcfppR/DESCRIPTION | 6 vcfppR-0.8.3/vcfppR/MD5 | 33 +- vcfppR-0.8.3/vcfppR/NAMESPACE | 2 vcfppR-0.8.3/vcfppR/NEWS.md | 4 vcfppR-0.8.3/vcfppR/R/RcppExports.R | 16 vcfppR-0.8.3/vcfppR/R/common.R | 60 ++- vcfppR-0.8.3/vcfppR/R/vcf-compare.R | 6 vcfppR-0.8.3/vcfppR/R/vcf-info.R | 4 vcfppR-0.8.3/vcfppR/R/vcf-plot.R | 273 +++++++++++++++++ vcfppR-0.8.3/vcfppR/inst/include/vcfpp.h | 32 + vcfppR-0.8.3/vcfppR/man/plot_variants_per_haplotype.Rd |only vcfppR-0.8.3/vcfppR/man/vcfpp_calc_info_persite.Rd |only vcfppR-0.8.3/vcfppR/man/vcfreader.Rd | 2 vcfppR-0.8.3/vcfppR/src/RcppExports.cpp | 44 +- vcfppR-0.8.3/vcfppR/src/htslib-1.21/config.status | 12 vcfppR-0.8.3/vcfppR/src/vcf-reader.cpp | 3 vcfppR-0.8.3/vcfppR/src/vcf-utils.cpp |only vcfppR-0.8.3/vcfppR/tests/testthat/test-clearinfo.R |only vcfppR-0.8.3/vcfppR/tests/testthat/test-vcf-plot.R | 69 +++- 20 files changed, 496 insertions(+), 70 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/data-documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre]
Maintainer: Benjamin Skinner <ben@btskinner.io>
Diff between rscorecard versions 0.32.0 dated 2025-05-12 and 0.33.0 dated 2026-03-31
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/sysdata.rda |binary 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Compact Inline Widgets for 'shiny' Apps
Description: Provides a basic set of compact widgets for 'shiny' apps which
occupy less space and can appear inline with surrounding text.
Author: Nick Davies [aut, cre]
Maintainer: Nick Davies <nicholas.davies@lshtm.ac.uk>
Diff between inshiny versions 0.1.3 dated 2026-03-20 and 0.1.4 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 6 ++++++ R/date.R | 5 +++-- R/inline.R | 18 ++++++++++++++++++ R/number.R | 5 +++-- R/select.R | 6 ++++-- R/slider.R | 4 ++-- R/text.R | 10 ++++++++-- inst/www/inshiny/inshiny.css | 18 +++++++++++++++++- man/inline.Rd | 18 ++++++++++++++++++ man/inline_date.Rd | 6 ++++++ man/inline_number.Rd | 16 +++++++++++----- man/inline_select.Rd | 14 +++++++++++++- man/inline_slider.Rd | 8 +++++++- man/inline_text.Rd | 13 ++++++++++++- tests/testthat/_snaps/date.md | 2 +- tests/testthat/_snaps/number.md | 2 +- tests/testthat/_snaps/select.md | 2 +- tests/testthat/_snaps/slider.md | 2 +- tests/testthat/_snaps/text.md | 2 +- 21 files changed, 156 insertions(+), 47 deletions(-)
Title: Nonlinear Longitudinal Process in Structural Equation Modeling
Description: Provides computational tools for nonlinear longitudinal models, in particular the intrinsically nonlinear models, in four scenarios: (1) univariate longitudinal processes with growth factors, with or without covariates including time-invariant covariates (TICs) and time-varying covariates (TVCs); (2) multivariate longitudinal processes that facilitate the assessment of correlation or causation between multiple longitudinal variables; (3) multiple-group models for scenarios (1) and (2) to evaluate differences among manifested groups, and (4) longitudinal mixture models for scenarios (1) and (2), with an assumption that trajectories are from multiple latent classes. The methods implemented are introduced in Liu (2025) <doi:10.3758/s13428-025-02596-4>.
Author: Jin Liu [aut, cre]
Maintainer: Jin Liu <Veronica.Liu0206@gmail.com>
Diff between nlpsem versions 0.3 dated 2023-09-12 and 0.4 dated 2026-03-31
nlpsem-0.3/nlpsem/man/getFitFig.Rd |only nlpsem-0.3/nlpsem/man/getLCSM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getLCSM.output.Rd |only nlpsem-0.3/nlpsem/man/getLGCM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getLGCM.output.Rd |only nlpsem-0.3/nlpsem/man/getMED.initial.Rd |only nlpsem-0.3/nlpsem/man/getMED.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMED.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMED.output.Rd |only nlpsem-0.3/nlpsem/man/getMGM.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMGM.output.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.initial.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMGroup.output.Rd |only nlpsem-0.3/nlpsem/man/getMIX.initial.Rd |only nlpsem-0.3/nlpsem/man/getMIX.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getMIX.output.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MED.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MULTI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMIX_MULTI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMIX_TVC.info.Rd |only nlpsem-0.3/nlpsem/man/getMIX_UNI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMIX_UNI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.initial.Rd |only nlpsem-0.3/nlpsem/man/getMULTI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getTVC.info.Rd |only nlpsem-0.3/nlpsem/man/getTVC.initial.Rd |only nlpsem-0.3/nlpsem/man/getTVC.mxModel.Rd |only nlpsem-0.3/nlpsem/man/getTVC.output.Rd |only nlpsem-0.3/nlpsem/man/getUNI.GF.Rd |only nlpsem-0.3/nlpsem/man/getUNI.addpara.Rd |only nlpsem-0.3/nlpsem/man/getUNI.initial.Rd |only nlpsem-0.3/nlpsem/man/getUNI.loadings.Rd |only nlpsem-0.3/nlpsem/man/getsub.LCSM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.LCSM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.LGCM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.LGCM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.MED_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.MED_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.MGM_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.MGM_m.Rd |only nlpsem-0.3/nlpsem/man/getsub.TVC_l.Rd |only nlpsem-0.3/nlpsem/man/getsub.TVC_m.Rd |only nlpsem-0.4/nlpsem/DESCRIPTION | 21 nlpsem-0.4/nlpsem/MD5 | 309 +-- nlpsem-0.4/nlpsem/NAMESPACE | 9 nlpsem-0.4/nlpsem/NEWS.md |only nlpsem-0.4/nlpsem/R/FitFig_helper.R | 164 + nlpsem-0.4/nlpsem/R/LCSM.mxModel_helper.R | 189 - nlpsem-0.4/nlpsem/R/LCSM.output_helper.R | 38 nlpsem-0.4/nlpsem/R/LGCM.mxModel_helper.R | 253 +- nlpsem-0.4/nlpsem/R/LGCM.output_helper.R | 11 nlpsem-0.4/nlpsem/R/MED.Initial_helper.R | 117 - nlpsem-0.4/nlpsem/R/MED.loading_helper.R | 7 nlpsem-0.4/nlpsem/R/MED.mxModel_helper.R | 189 - nlpsem-0.4/nlpsem/R/MED.output_helper.R | 17 nlpsem-0.4/nlpsem/R/MGM.mxModel_helper.R | 226 +- nlpsem-0.4/nlpsem/R/MGM.output_helper.R | 45 nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.LCSM_helper.R | 213 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.LGCM_helper.R | 279 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.MED_helper.R | 147 - nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.MGM_helper.R | 226 +- nlpsem-0.4/nlpsem/R/MGroup.SUBMODEL.TVC_helper.R | 1175 +++++------ nlpsem-0.4/nlpsem/R/MGroup.initial_helper.R | 26 nlpsem-0.4/nlpsem/R/MGroup.mxModel_helper.R | 1 nlpsem-0.4/nlpsem/R/MGroup.output_helper.R | 529 ++--- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.LCSM_helper.R | 237 +- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.LGCM_helper.R | 311 +-- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.MED_helper.R | 155 - nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.MGM_helper.R | 254 +- nlpsem-0.4/nlpsem/R/MIX.SUBMODEL.TVC_helper.R | 1287 ++++++------- nlpsem-0.4/nlpsem/R/MIX.initial_helper.R | 63 nlpsem-0.4/nlpsem/R/MIX.mxModel_helper.R | 5 nlpsem-0.4/nlpsem/R/MIX.output_helper.R | 532 ++--- nlpsem-0.4/nlpsem/R/MIX_MED.loading_helper.R | 7 nlpsem-0.4/nlpsem/R/MIX_MULTI.addpara_helper.R | 11 nlpsem-0.4/nlpsem/R/MIX_MULTI.loading_helper.R | 11 nlpsem-0.4/nlpsem/R/MIX_TVC.info_helper.R | 41 nlpsem-0.4/nlpsem/R/MIX_UNI.addpara_helper.R | 9 nlpsem-0.4/nlpsem/R/MIX_UNI.loading_helper.R | 10 nlpsem-0.4/nlpsem/R/MULTI.addpara_helper.R | 11 nlpsem-0.4/nlpsem/R/MULTI.initial_helper.R | 168 + nlpsem-0.4/nlpsem/R/MULTI.loading_helper.R | 13 nlpsem-0.4/nlpsem/R/StandardMethods.R | 118 - nlpsem-0.4/nlpsem/R/TVC.info_helper.R | 41 nlpsem-0.4/nlpsem/R/TVC.initial_helper.R | 284 ++ nlpsem-0.4/nlpsem/R/TVC.mxModel_helper.R | 1109 +++++------ nlpsem-0.4/nlpsem/R/TVC.output_helper.R | 18 nlpsem-0.4/nlpsem/R/UNI.GF_helper.R | 254 ++ nlpsem-0.4/nlpsem/R/UNI.addpara_helper.R | 9 nlpsem-0.4/nlpsem/R/UNI.initial_helper.R | 159 + nlpsem-0.4/nlpsem/R/UNI.loading_helper.R | 10 nlpsem-0.4/nlpsem/R/getEstimateStats.R | 110 - nlpsem-0.4/nlpsem/R/getFigure.R | 160 - nlpsem-0.4/nlpsem/R/getIndFS.R | 7 nlpsem-0.4/nlpsem/R/getLCSM.R | 37 nlpsem-0.4/nlpsem/R/getLGCM.R | 49 nlpsem-0.4/nlpsem/R/getLRT.R | 8 nlpsem-0.4/nlpsem/R/getLatentKappa.R | 20 nlpsem-0.4/nlpsem/R/getMGM.R | 64 nlpsem-0.4/nlpsem/R/getMGroup.R | 117 - nlpsem-0.4/nlpsem/R/getMIX.R | 118 - nlpsem-0.4/nlpsem/R/getMediation.R | 64 nlpsem-0.4/nlpsem/R/getPosterior.R | 38 nlpsem-0.4/nlpsem/R/getSummary.R | 22 nlpsem-0.4/nlpsem/R/getTVCmodel.R | 75 nlpsem-0.4/nlpsem/R/global_vars.R | 21 nlpsem-0.4/nlpsem/R/initial_helpers_common.R |only nlpsem-0.4/nlpsem/R/multi_cov_helpers.R |only nlpsem-0.4/nlpsem/R/output_helpers_common.R |only nlpsem-0.4/nlpsem/R/paramNames_helper.R |only nlpsem-0.4/nlpsem/R/validation_helpers.R |only nlpsem-0.4/nlpsem/build/partial.rdb |binary nlpsem-0.4/nlpsem/build/vignette.rds |binary nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.R | 118 - nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.Rmd | 30 nlpsem-0.4/nlpsem/inst/doc/getLCSM_examples.html | 61 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.R | 90 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.Rmd | 18 nlpsem-0.4/nlpsem/inst/doc/getLGCM_examples.html | 89 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.R | 85 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.Rmd | 28 nlpsem-0.4/nlpsem/inst/doc/getMGM_examples.html | 46 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.R | 83 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.Rmd | 39 nlpsem-0.4/nlpsem/inst/doc/getMGroup_examples.html | 50 nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.R | 114 - nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.Rmd | 37 nlpsem-0.4/nlpsem/inst/doc/getMIX_examples.html | 209 +- nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.R | 102 - nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.Rmd | 44 nlpsem-0.4/nlpsem/inst/doc/getMediation_examples.html | 257 +- nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.R | 152 - nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.Rmd | 52 nlpsem-0.4/nlpsem/inst/doc/getTVCmodel_examples.html | 183 - nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.R |only nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.Rmd |only nlpsem-0.4/nlpsem/inst/doc/nlpsem_overview.html |only nlpsem-0.4/nlpsem/inst/extdata/getLCSM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getLGCM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMGM_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMGroup_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMIX_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getMediation_examples.RData |binary nlpsem-0.4/nlpsem/inst/extdata/getTVCmodel_examples.RData |binary nlpsem-0.4/nlpsem/man/KappaOutput-class.Rd | 2 nlpsem-0.4/nlpsem/man/ModelSummary-myMxOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/ModelSummary.Rd | 26 nlpsem-0.4/nlpsem/man/getEstimateStats.Rd | 28 nlpsem-0.4/nlpsem/man/getFigure.Rd | 31 nlpsem-0.4/nlpsem/man/getIndFS.Rd | 8 nlpsem-0.4/nlpsem/man/getLCSM.Rd | 16 nlpsem-0.4/nlpsem/man/getLGCM.Rd | 27 nlpsem-0.4/nlpsem/man/getLRT.Rd | 7 nlpsem-0.4/nlpsem/man/getLatentKappa.Rd | 12 nlpsem-0.4/nlpsem/man/getMGM.Rd | 41 nlpsem-0.4/nlpsem/man/getMGroup.Rd | 53 nlpsem-0.4/nlpsem/man/getMIX.Rd | 59 nlpsem-0.4/nlpsem/man/getMediation.Rd | 47 nlpsem-0.4/nlpsem/man/getPosterior.Rd | 9 nlpsem-0.4/nlpsem/man/getSummary.Rd | 11 nlpsem-0.4/nlpsem/man/getTVCmodel.Rd | 52 nlpsem-0.4/nlpsem/man/myMxOutput-class.Rd | 2 nlpsem-0.4/nlpsem/man/printTable-FSOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-KappaOutput-method.Rd | 8 nlpsem-0.4/nlpsem/man/printTable-StatsOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-myMxOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable-postOutput-method.Rd | 4 nlpsem-0.4/nlpsem/man/printTable.Rd | 28 nlpsem-0.4/nlpsem/man/show-figOutput-method.Rd | 3 nlpsem-0.4/nlpsem/tests |only nlpsem-0.4/nlpsem/vignettes/getLCSM_examples.Rmd | 30 nlpsem-0.4/nlpsem/vignettes/getLGCM_examples.Rmd | 18 nlpsem-0.4/nlpsem/vignettes/getMGM_examples.Rmd | 28 nlpsem-0.4/nlpsem/vignettes/getMGroup_examples.Rmd | 39 nlpsem-0.4/nlpsem/vignettes/getMIX_examples.Rmd | 37 nlpsem-0.4/nlpsem/vignettes/getMediation_examples.Rmd | 44 nlpsem-0.4/nlpsem/vignettes/getTVCmodel_examples.Rmd | 52 nlpsem-0.4/nlpsem/vignettes/nlpsem_overview.Rmd |only 180 files changed, 6751 insertions(+), 6102 deletions(-)
Title: Income Tax Calculations (UK)
Description: Income tax calculations for England, Northern Ireland and Wales. Estimate annual income tax within the different taxation bands at specified levels of both taxable income and the Personal Allowance, emulating the results obtained at <https://www.gov.uk/estimate-income-tax>. Calculate the standard Personal Allowance at various levels of taxable income. Estimate the personal allowance required to recoup a specified amount of income tax.
Author: Mark Eisler [aut, cre, cph]
Maintainer: Mark Eisler <mark@markeisler.com>
Diff between Fiscal versions 1.0.1 dated 2026-03-24 and 1.0.2 dated 2026-03-31
DESCRIPTION | 8 ++--- MD5 | 20 +++++++------- NEWS.md | 6 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/incometax.R | 12 ++++++-- inst/doc/incometax.Rnw | 67 +++++++++++++++++++++++++++--------------------- inst/doc/incometax.pdf |binary man/allowance.Rd | 14 +++++----- man/tax_opts.Rd | 31 ++++++++++------------ vignettes/incometax.Rnw | 67 +++++++++++++++++++++++++++--------------------- 11 files changed, 127 insertions(+), 98 deletions(-)
Title: Surrogate Functional False Discovery Rates for Genome-Wide
Association Studies
Description: Pleiotropy-informed significance analysis of genome-wide association studies with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and $q$-value, and uses these estimates to derive a functional $p$-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization).
Author: Andrew Bass [aut, cre],
Chris Wallace [aut]
Maintainer: Andrew Bass <ab3105@cam.ac.uk>
Diff between sffdr versions 1.1.0 dated 2026-02-11 and 1.1.2 dated 2026-03-31
DESCRIPTION | 11 - MD5 | 62 +++--- NAMESPACE | 14 + NEWS.md | 10 + R/RcppExports.R |only R/fpi0est.R | 300 ++++++++++++++++++++++++++------ R/fpvalues.R | 42 ---- R/kernelEstimator.R | 204 ++++++++++++++------- R/null_overlap.R |only R/pi0_model.R | 290 +++++++++++++++++++++++------- R/plot.R | 3 R/sffdr.R | 130 ++++++++++++- README.md | 48 ++++- inst/doc/sffdr.R | 17 + inst/doc/sffdr.Rmd | 39 +++- inst/doc/sffdr.html | 219 ++++++++++++++--------- man/decorrelate_informative.Rd |only man/discover_empirical_nulls.Rd |only man/estimate_rho_overlap.Rd |only man/fit_bivariate_density.Rd | 6 man/fit_strategy_final.Rd | 3 man/fit_univariate_density.Rd | 2 man/fpi0est.Rd | 9 man/kernelEstimator.Rd | 27 +- man/monoSmooth_conditional.Rd |only man/monoSmooth_pava.Rd |only man/overlap_null_density.Rd |only man/pi0_model.Rd | 21 +- man/plot.sffdr.Rd | 3 man/run_empirical_overlap_correction.Rd |only man/sffdr.Rd | 20 ++ src |only tests/testthat/test-fpi0est.R | 127 +++++++++++++ tests/testthat/test-kernelEstimator.R | 25 -- tests/testthat/test-null_overlap.R |only tests/testthat/test-sffdr.R | 151 ++++++++++++++++ vignettes/sffdr.Rmd | 39 +++- 37 files changed, 1408 insertions(+), 414 deletions(-)
Title: Reliability Growth Analysis
Description: Modeling and plotting functions for Reliability Growth Analysis (RGA). Models include the Duane (1962) <doi:10.1109/TA.1964.4319640>, Non-Homogeneous Poisson Process (NHPP) by Crow (1975) (No. AMSAATR138), Piecewise Weibull NHPP by Guo et al. (2010) <doi:10.1109/RAMS.2010.5448029>, and Piecewise Weibull NHPP with Change Point Detection based on the 'segmented' package by Muggeo (2024) <https://cran.r-project.org/package=segmented>.
Author: Paul Govan [aut, cre, cph]
Maintainer: Paul Govan <paul.govan2@gmail.com>
Diff between ReliaGrowR versions 0.3.2 dated 2025-12-09 and 0.4 dated 2026-03-31
DESCRIPTION | 10 MD5 | 60 ++-- NAMESPACE | 9 NEWS.md | 21 + R/ReliaGrowR-package.R | 68 ++++ R/grwr_api.R | 4 R/rdt.R | 25 + R/rga.R | 470 +++++++++++++++++++++++++++++++-- R/sim_failures.R |only build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 3 inst/doc/RGF.R |only inst/doc/RGF.Rmd |only inst/doc/RGF.html |only inst/plumber/plumb-duane.R | 152 ---------- inst/plumber/plumb-gof.R | 80 ----- inst/plumber/plumb-rga.R | 218 --------------- inst/plumber/plumber.R | 354 +++++++++++++++++++----- man/ReliaGrowR-package.Rd | 70 ++++ man/grwr_api.Rd | 5 man/plot.rga.Rd | 3 man/plot.rga_predict.Rd |only man/predict_rga.Rd |only man/print.rga.Rd | 3 man/print.rga_predict.Rd |only man/rdt.Rd | 15 - man/rga.Rd | 38 ++ man/sim_failures.Rd |only man/weibull_to_rga.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-srr-duane.R | 3 tests/testthat/test-srr-rga.R | 376 +++++++++++++++++++++++++- tests/testthat/test-srr-sim_failures.R |only tests/testthat/test-srr_rdt.R | 94 ++++++ vignettes/RGF.Rmd |only 36 files changed, 1497 insertions(+), 594 deletions(-)
Title: List, Query, Manipulate System Processes
Description: List, query and manipulate all system processes, on
'Windows', 'Linux' and 'macOS'.
Author: Jay Loden [aut],
Dave Daeschler [aut],
Giampaolo Rodola' [aut],
Gabor Csardi [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between ps versions 1.9.1 dated 2025-04-12 and 1.9.2 dated 2026-03-31
DESCRIPTION | 12 LICENSE | 2 MD5 | 99 +-- NAMESPACE | 1 NEWS.md | 4 R/cleancall.R | 1 R/compat-vctrs.R | 1003 ++++++++++++++++----------------- R/disk.R | 16 R/errno.R | 1 R/error.R | 4 R/glob.R | 21 R/iso-date.R | 49 - R/kill-tree.R | 9 R/linux.R | 127 ++-- R/low-level.R | 180 +++-- R/macos.R | 36 - R/memoize.R | 7 R/memory.R | 76 +- R/os.R | 17 R/package.R | 7 R/posix.R | 6 R/ps.R | 193 ++++-- R/rematch2.R | 14 R/string.R |only R/system.R | 63 +- R/testthat-reporter.R | 149 +++- R/utils.R | 126 ++-- README.md | 297 +++++---- inst/tools/error-codes.R | 23 inst/tools/winver.R | 21 man/ps_handle.Rd | 4 man/ps_string.Rd |only src/cleancall.c | 6 src/install.libs.R | 9 tests/testthat.R | 7 tests/testthat/helpers.R | 57 + tests/testthat/test-cleanup-reporter.R | 253 +++++--- tests/testthat/test-common.R | 30 tests/testthat/test-connections.R | 152 +++-- tests/testthat/test-finished.R | 21 tests/testthat/test-kill-tree.R | 88 ++ tests/testthat/test-linux.R | 12 tests/testthat/test-macos.R | 5 tests/testthat/test-pid-reuse.R | 17 tests/testthat/test-posix-zombie.R | 5 tests/testthat/test-posix.R | 29 tests/testthat/test-ps.R | 5 tests/testthat/test-system.R | 12 tests/testthat/test-utils.R | 3 tests/testthat/test-windows.R | 5 tests/testthat/test-winver.R | 26 tests/testthat/test-z-string.R |only 52 files changed, 1954 insertions(+), 1356 deletions(-)
Title: Apply Mapping Functions in Parallel using Futures
Description: Implementations of the family of map() functions from 'purrr'
that can be resolved using any 'future'-supported backend, e.g.
parallel on the local machine or distributed on a compute cluster.
Author: Davis Vaughan [aut, cre] ,
Henrik Bengtsson [aut] ,
Matt Dancho [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between furrr versions 0.3.1 dated 2022-08-15 and 0.4.0 dated 2026-03-31
furrr-0.3.1/furrr/R/future-invoke-map.R |only furrr-0.3.1/furrr/man/future_invoke_map.Rd |only furrr-0.3.1/furrr/man/future_options.Rd |only furrr-0.3.1/furrr/tests/testthat/_snaps/deprecation.md |only furrr-0.3.1/furrr/tests/testthat/test-deprecation.R |only furrr-0.3.1/furrr/tests/testthat/test-future-invoke-map.R |only furrr-0.4.0/furrr/DESCRIPTION | 37 - furrr-0.4.0/furrr/MD5 | 80 +-- furrr-0.4.0/furrr/NAMESPACE | 17 furrr-0.4.0/furrr/NEWS.md | 79 ++- furrr-0.4.0/furrr/R/chunks.R | 24 furrr-0.4.0/furrr/R/furrr-options.R | 159 +++--- furrr-0.4.0/furrr/R/future-imap.R | 129 +++-- furrr-0.4.0/furrr/R/future-map.R | 261 ++++++---- furrr-0.4.0/furrr/R/future-map2.R | 190 ++++--- furrr-0.4.0/furrr/R/future-modify.R | 341 +++++++------- furrr-0.4.0/furrr/R/future-pmap.R | 148 +++--- furrr-0.4.0/furrr/R/future-walk.R | 67 +- furrr-0.4.0/furrr/R/globals.R | 28 - furrr-0.4.0/furrr/R/progress.R | 7 furrr-0.4.0/furrr/R/recycle.R | 10 furrr-0.4.0/furrr/R/seed.R | 28 - furrr-0.4.0/furrr/R/template.R | 193 +++++-- furrr-0.4.0/furrr/R/utils-purrr.R | 34 + furrr-0.4.0/furrr/R/utils.R | 1 furrr-0.4.0/furrr/README.md | 42 - furrr-0.4.0/furrr/man/furrr-package.Rd | 9 furrr-0.4.0/furrr/man/furrr_options.Rd | 40 + furrr-0.4.0/furrr/man/future_imap.Rd | 50 +- furrr-0.4.0/furrr/man/future_map.Rd | 64 +- furrr-0.4.0/furrr/man/future_map2.Rd | 71 +- furrr-0.4.0/furrr/man/future_map_if.Rd | 56 +- furrr-0.4.0/furrr/man/future_modify.Rd | 54 +- furrr-0.4.0/furrr/tests/testthat/_snaps/future-map.md |only furrr-0.4.0/furrr/tests/testthat/_snaps/future-map2.md |only furrr-0.4.0/furrr/tests/testthat/_snaps/future-pmap.md |only furrr-0.4.0/furrr/tests/testthat/helper-furrr-test-that.R | 12 furrr-0.4.0/furrr/tests/testthat/helper-state.R |only furrr-0.4.0/furrr/tests/testthat/test-chunks.R | 19 furrr-0.4.0/furrr/tests/testthat/test-furrr-options.R | 78 ++- furrr-0.4.0/furrr/tests/testthat/test-future-imap.R | 48 + furrr-0.4.0/furrr/tests/testthat/test-future-map.R | 99 +++- furrr-0.4.0/furrr/tests/testthat/test-future-map2.R | 121 +++- furrr-0.4.0/furrr/tests/testthat/test-future-modify.R | 61 ++ furrr-0.4.0/furrr/tests/testthat/test-future-pmap.R | 139 ++++- furrr-0.4.0/furrr/tests/testthat/test-future-walk.R | 24 46 files changed, 1799 insertions(+), 1021 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrology and Water Quality
Data
Description: Collection of functions to help retrieve U.S. Geological Survey
and U.S. Environmental Protection Agency water quality and
hydrology data from web services.
Author: Laura DeCicco [aut, cre] ,
Robert Hirsch [aut] ,
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Platt [ctb],
David Watkins [aut] ,
David Blodgett [aut] ,
Mike Johnson [aut] ,
Aliesha Krall [ctb] ,
Lee Stanish [ctb] ,
Joseph Zemme [...truncated...]
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.23 dated 2026-03-10 and 2.7.24 dated 2026-03-31
DESCRIPTION | 9 MD5 | 162 +++--- NEWS | 7 R/AAA.R | 135 +++-- R/addWaterYear.R | 41 + R/checkWQPdates.R | 12 R/citations.R | 68 +- R/constructNWISURL.R | 552 ++++++++++---------- R/construct_api_requests.R | 572 +++++++++++---------- R/dataRetrieval-package.R | 29 - R/deal_with_empty.R | 72 +- R/findNLDI.R | 94 ++- R/getWebServiceData.R | 90 +-- R/get_ogc_data.R | 228 ++++---- R/get_ogc_documentation.R | 129 ++-- R/importNGWMN_wml2.R | 162 ++++-- R/importRDB1.R | 150 +++-- R/importWQP.R | 225 ++++---- R/importWaterML1.R | 193 +++++-- R/pcode_to_name.R | 44 - R/readNGWMNdata.R | 88 ++- R/readNWISdata.R | 365 ++++++++----- R/readNWISdv.R | 33 - R/readNWISpCode.R | 50 + R/readNWISsite.R | 36 - R/readNWISunit.R | 121 ++-- R/readWQPdata.R | 282 +++++----- R/readWQPdots.R | 65 +- R/readWQPqw.R | 48 - R/read_waterdata.R | 96 +-- R/read_waterdata_channel.R | 98 +-- R/read_waterdata_combined_meta.R | 180 +++--- R/read_waterdata_continuous.R | 114 ++-- R/read_waterdata_daily.R | 84 +-- R/read_waterdata_field_measurements.R | 94 +-- R/read_waterdata_field_meta.R | 74 +- R/read_waterdata_latest_continuous.R | 76 +- R/read_waterdata_latest_daily.R | 76 +- R/read_waterdata_metadata.R | 40 - R/read_waterdata_monitoring_location.R | 125 ++-- R/read_waterdata_parameter_codes.R | 62 +- R/read_waterdata_samples.R | 795 +++++++++++++++--------------- R/read_waterdata_stats.R | 233 ++++---- R/read_waterdata_ts_meta.R | 100 +-- R/rejigger_cols.R | 58 +- R/renameColumns.R | 24 R/setAccess.R | 22 R/walk_pages.R | 147 +++-- R/whatNWISdata.R | 89 ++- R/whatNWISsites.R | 65 +- R/whatWQPdata.R | 216 ++++---- R/whatWQPsites.R | 79 +- build/vignette.rds |binary inst/CITATION | 4 inst/doc/dataRetrieval.html | 6 man/create_NWIS_bib.Rd | 4 man/importNGWMN.Rd | 2 man/importWaterML1.Rd | 6 man/parse_WQP.Rd | 2 man/readWQPdata.Rd | 22 man/readWQPqw.Rd | 8 man/read_waterdata.Rd | 2 man/read_waterdata_channel.Rd | 5 man/read_waterdata_combined_meta.Rd | 10 man/read_waterdata_continuous.Rd | 19 man/read_waterdata_daily.Rd | 14 man/read_waterdata_field_measurements.Rd | 8 man/read_waterdata_field_meta.Rd | 4 man/read_waterdata_latest_continuous.Rd | 6 man/read_waterdata_latest_daily.Rd | 4 man/read_waterdata_monitoring_location.Rd | 15 man/read_waterdata_parameter_codes.Rd | 4 man/read_waterdata_samples.Rd | 6 man/read_waterdata_stats.Rd | 10 man/read_waterdata_ts_meta.Rd | 4 man/wqp_check_status.Rd | 2 tests/testthat/test_waterdata_stats.R | 140 ++--- tests/testthat/tests_general.R | 512 +++++++++++-------- tests/testthat/tests_imports.R | 152 +++-- tests/testthat/tests_nldi.R | 196 +++++-- tests/testthat/tests_samples.R | 203 ++++--- tests/testthat/tests_userFriendly_fxns.R | 446 ++++++++++------ 82 files changed, 4975 insertions(+), 3850 deletions(-)
Title: 'DuckDB' High Throughput Sequencing File Formats Reader
Extension
Description: Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput
Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API
<https://duckdb.org/docs/stable/clients/c/api> and its 'htslib' dependency are
compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>.
Author: Sounkou Mahamane Toure [aut, cre],
James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan,
Andrew Whitwham,Thomas Keane , Robert M Davies [ctb] ,
Giulio Genovese [cph] ,
DuckDB C Extension API Authors [ctb]
Maintainer: Sounkou Mahamane Toure <sounkoutoure@gmail.com>
Diff between Rduckhts versions 0.1.3-0.0.2 dated 2026-02-24 and 1.1.4-0.0.1 dated 2026-03-31
DESCRIPTION | 11 MD5 | 117 +- NAMESPACE | 12 NEWS.md | 60 + R/bootstrap.R | 37 R/duckhts.R | 804 +++++++++++++++- configure | 2 configure.win | 2 inst/duckhts_extension/bam_reader.c | 168 ++- inst/duckhts_extension/bcf_reader.c | 150 ++ inst/duckhts_extension/bcftools_filter.c |only inst/duckhts_extension/bcftools_shim.c |only inst/duckhts_extension/bgzip.c |only inst/duckhts_extension/duckhts.c | 226 ++++ inst/duckhts_extension/hts_index_builder.c |only inst/duckhts_extension/hts_meta_reader.c | 288 +++-- inst/duckhts_extension/include/bcftools_filter_config.h |only inst/duckhts_extension/include/bcftools_shim.h |only inst/duckhts_extension/include/filter.h |only inst/duckhts_extension/include/quality_encoding.h |only inst/duckhts_extension/include/seq_encoding.h |only inst/duckhts_extension/include/vep_parser.h | 10 inst/duckhts_extension/interval_udf.c |only inst/duckhts_extension/kmer_udf.c |only inst/duckhts_extension/liftover_udf.c |only inst/duckhts_extension/munge_udf.c |only inst/duckhts_extension/quality_encoding.c |only inst/duckhts_extension/quality_encoding_reader.c |only inst/duckhts_extension/score_udf.c |only inst/duckhts_extension/seq_reader.c | 235 ++++ inst/duckhts_extension/tabix_reader.c | 17 inst/duckhts_extension/vep_parser.c | 247 ++++ inst/extdata/colheaders.tsv |only inst/extdata/legacy_phred64.fq |only inst/extdata/score_as.vcf |only inst/extdata/score_chrprefix.vcf |only inst/extdata/score_columns.tsv |only inst/extdata/score_dosage.vcf |only inst/extdata/score_gwas_summary.vcf |only inst/extdata/score_input.vcf |only inst/extdata/score_missing_ds.vcf |only inst/extdata/score_missing_gt.vcf |only inst/extdata/score_regions.txt |only inst/extdata/score_summary.tsv |only inst/extdata/score_summary_bolt.tsv |only inst/extdata/score_summary_custom.tsv |only inst/extdata/score_summary_log10p.tsv |only inst/extdata/score_summary_metal.tsv |only inst/extdata/score_summary_mismatch.tsv |only inst/extdata/score_summary_na.tsv |only inst/extdata/score_summary_no_snp.tsv |only inst/extdata/score_summary_or.tsv |only inst/extdata/score_summary_pgs.tsv |only inst/extdata/score_summary_plink2.tsv |only inst/extdata/score_summary_regenie.tsv |only inst/extdata/score_summary_rsid.tsv |only inst/extdata/score_summary_saige.tsv |only inst/extdata/score_summary_smallp.tsv |only inst/extdata/score_summary_ssf.tsv |only inst/extdata/score_targets.txt |only inst/extdata/targets.bed |only inst/function_catalog |only inst/tinytest/test_basic.R | 154 ++- inst/tinytest/test_cigar_utils.R |only inst/tinytest/test_indexes_bgzip.R |only inst/tinytest/test_integration.R | 39 inst/tinytest/test_intervals.R |only inst/tinytest/test_liftover.R |only inst/tinytest/test_liftover_stress.R |only inst/tinytest/test_munge.R |only inst/tinytest/test_quality_encoding.R |only inst/tinytest/test_score.R |only inst/tinytest/test_seq_ops.R |only man/Rduckhts.Rd | 1 man/rduckhts_bam.Rd | 18 man/rduckhts_bam_index.Rd |only man/rduckhts_bcf.Rd | 4 man/rduckhts_bcf_index.Rd |only man/rduckhts_bed.Rd |only man/rduckhts_bgunzip.Rd |only man/rduckhts_bgzip.Rd |only man/rduckhts_detect_quality_encoding.Rd |only man/rduckhts_fasta.Rd | 5 man/rduckhts_fasta_nuc.Rd |only man/rduckhts_fastq.Rd | 15 man/rduckhts_functions.Rd |only man/rduckhts_gff.Rd | 15 man/rduckhts_gtf.Rd | 15 man/rduckhts_liftover.Rd |only man/rduckhts_munge.Rd |only man/rduckhts_score.Rd |only man/rduckhts_tabix_index.Rd |only 92 files changed, 2362 insertions(+), 290 deletions(-)
Title: Approximate Optimal Experimental Designs Using Generalised
Linear Mixed Models
Description: Optimal design analysis algorithms for any study design that can be represented or
modelled as a generalised linear mixed model including cluster randomised trials,
cohort studies, spatial and temporal epidemiological studies, and split-plot designs.
See <https://github.com/samuel-watson/glmmrBase/blob/master/README.md> for a
detailed manual on model specification. A detailed discussion of the methods in this
package can be found in Watson, Hemming, and Girling (2023) <doi:10.1177/09622802231202379>.
Author: Sam Watson [aut, cre],
Yi Pan [aut]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrOptim versions 0.3.6 dated 2024-12-17 and 0.3.7 dated 2026-03-31
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/R6designspace.R | 4 ++-- build/partial.rdb |binary inst/include/optim/optimclass.h | 1 + src/gd_search.cpp | 1 + 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Tools for Various R Functions Helpers
Description: Contains miscellaneous functions useful for managing 'NetCDF' files (see <https://en.wikipedia.org/wiki/NetCDF>), get moon phase and time for sun rise and fall, tide level, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot [aut, cre]
Maintainer: Marc Girondot <marc.girondot@gmail.com>
Diff between HelpersMG versions 2026.2.28 dated 2026-02-28 and 2026.3.31 dated 2026-03-31
HelpersMG-2026.2.28/HelpersMG/R/Probability_Best_Model_WAIC.R |only HelpersMG-2026.2.28/HelpersMG/man/Probability_Best_Model_WAIC.Rd |only HelpersMG-2026.3.31/HelpersMG/DESCRIPTION | 10 - HelpersMG-2026.3.31/HelpersMG/MD5 | 54 +++++----- HelpersMG-2026.3.31/HelpersMG/NAMESPACE | 6 - HelpersMG-2026.3.31/HelpersMG/NEWS | 15 ++ HelpersMG-2026.3.31/HelpersMG/R/AddPriors.R |only HelpersMG-2026.3.31/HelpersMG/R/ELPDweight.R |only HelpersMG-2026.3.31/HelpersMG/R/HelpersMG-package.R | 4 HelpersMG-2026.3.31/HelpersMG/R/MHalgoGen.R | 49 +++++++-- HelpersMG-2026.3.31/HelpersMG/R/plot.mcmcComposite.R | 21 +++ HelpersMG-2026.3.31/HelpersMG/R/setPriors1.R |only HelpersMG-2026.3.31/HelpersMG/inst/shiny/cutter/ui.R | 2 HelpersMG-2026.3.31/HelpersMG/man/ELPDweight.Rd |only HelpersMG-2026.3.31/HelpersMG/man/ExtractAIC.glm.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/FormatCompareAIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/HelpersMG-package.Rd | 4 HelpersMG-2026.3.31/HelpersMG/man/MHalgoGen.Rd | 21 +++ HelpersMG-2026.3.31/HelpersMG/man/as.mcmc.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/as.parameters.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/as.quantiles.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_AIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_AICc.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/compare_BIC.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/figures/TB.png |binary HelpersMG-2026.3.31/HelpersMG/man/merge.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plot.PriorsmcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plot.mcmcComposite.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/plus-.PriorsmcmcComposite.Rd |only HelpersMG-2026.3.31/HelpersMG/man/setPriors.Rd | 2 HelpersMG-2026.3.31/HelpersMG/man/setPriors1.Rd |only HelpersMG-2026.3.31/HelpersMG/man/summary.mcmcComposite.Rd | 4 32 files changed, 156 insertions(+), 58 deletions(-)
Title: Generalised Linear Mixed Models in R
Description: Specification, analysis, simulation, and fitting of generalised linear mixed models.
Includes Markov Chain Monte Carlo Maximum likelihood model fitting for a range of models,
non-linear fixed effect specifications, a wide range of flexible covariance functions that can be combined arbitrarily,
robust and bias-corrected standard error estimation, power calculation, data simulation, and more.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <S.I.Watson@bham.ac.uk>
Diff between glmmrBase versions 1.2.1 dated 2026-01-27 and 1.3.0 dated 2026-03-31
glmmrBase-1.2.1/glmmrBase/inst/include/glmmr/modelmcmc.hpp |only glmmrBase-1.3.0/glmmrBase/DESCRIPTION | 8 glmmrBase-1.3.0/glmmrBase/MD5 | 35 glmmrBase-1.3.0/glmmrBase/R/Betadist.R | 4 glmmrBase-1.3.0/glmmrBase/R/R6Model.R | 229 ++-- glmmrBase-1.3.0/glmmrBase/R/R6covariance.R | 33 glmmrBase-1.3.0/glmmrBase/R/RcppExports.R | 12 glmmrBase-1.3.0/glmmrBase/build/partial.rdb |binary glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/covariance.hpp | 42 glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/hsgpcovariance.hpp | 498 +++++++-- glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/modelmatrix.hpp | 147 ++ glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/modeloptim.hpp | 515 +++++++++- glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/nngpcovariance.hpp | 100 - glmmrBase-1.3.0/glmmrBase/inst/include/glmmr/randomeffects.hpp | 71 + glmmrBase-1.3.0/glmmrBase/man/Model.Rd | 48 glmmrBase-1.3.0/glmmrBase/man/exponential.Rd | 34 glmmrBase-1.3.0/glmmrBase/src/RcppExports.cpp | 35 glmmrBase-1.3.0/glmmrBase/src/model_module.cpp | 40 glmmrBase-1.3.0/glmmrBase/src/stanExports_mcml.cc | 34 19 files changed, 1317 insertions(+), 568 deletions(-)
Title: An Abstracted System for Easily Working with Databases with
Large Datasets
Description: Provides object-oriented database management tools for working with large datasets across multiple database systems. Features include robust connection management for 'PostgreSQL' databases, advanced table operations with bulk data loading and upsert functionality, comprehensive data validation through customizable field type and content validators, efficient index management, and cross-database compatibility. Designed for high-performance data operations in surveillance systems and large-scale data processing workflows.
Author: Richard Aubrey White [aut, cre] ,
August Soerli Mathisen [aut]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Diff between csdb versions 2025.7.30 dated 2025-08-18 and 2026.2.2 dated 2026-03-31
DESCRIPTION | 22 +++++++--------- MD5 | 18 +++++++------ NAMESPACE | 2 + NEWS.md | 10 +++++++ R/3_onAttach.R | 8 ++--- R/r6_DBConnection_v9.R | 63 +++++++++++++++++++++++++++++++++++++++++++++- README.md | 36 ++++---------------------- build/vignette.rds |binary inst/doc/csdb.html | 5 ++- man/csdb_get_auth_hook.Rd |only man/csdb_set_auth_hook.Rd |only 11 files changed, 107 insertions(+), 57 deletions(-)
Title: Pan-European Phenological Data Analysis
Description: Provides a framework for quality-aware analysis of ground-based
phenological data from the PEP725 Pan-European Phenology Database
(Templ et al. (2018) <doi:10.1007/s00484-018-1512-8>;
Templ et al. (2026) <doi:10.1111/nph.70869>) and similar observation
networks. Implements station-level data quality grading, outlier
detection, phenological normals (climate baselines), anomaly detection,
elevation and latitude gradient estimation with robust regression,
spatial synchrony quantification, partial least squares (PLS) regression
for identifying temperature-sensitive periods, and sequential
Mann-Kendall trend analysis. Supports data import from PEP725 files,
conversion of user-supplied data, and downloadable synthetic datasets
for teaching without barriers of registration.
All analysis outputs provide 'print', 'summary', and
'plot' methods. Interactive spatial visualization is available via
'leaflet'.
Author: Matthias Templ [aut, cre] ,
Barbara Templ [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between pep725 versions 1.0.0 dated 2026-03-09 and 1.0.2 dated 2026-03-31
DESCRIPTION | 6 MD5 | 22 NEWS.md | 11 R/pep_class.R | 13 R/pep_download.R | 29 R/pep_simulate.R | 5 inst/doc/data-quality.html | 787 ++++++++-------- inst/doc/getting-started.html | 1696 +++++++++++++++++------------------- inst/doc/phenological-analysis.html | 1605 +++++++++++++++++----------------- inst/doc/spatial-patterns.html | 1197 ++++++++++++------------- man/pep_coverage.Rd | 13 man/pep_simulate.Rd | 5 12 files changed, 2705 insertions(+), 2684 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.3.3 dated 2026-03-15 and 0.3.4 dated 2026-03-31
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 6 ++++++ R/OrgHeatmap.R | 13 ++++++------- README.md | 2 +- inst/doc/introduction.Rmd | 2 +- inst/doc/introduction.html | 2 +- man/OrgHeatmap.Rd | 3 +++ vignettes/introduction.Rmd | 2 +- 9 files changed, 30 insertions(+), 22 deletions(-)
Title: Reinforcement Learning Tools for Multi-Armed Bandit
Description: A flexible general-purpose toolbox for implementing Rescorla-Wagner models
in multi-armed bandit tasks.
As the successor and functional extension of the 'binaryRL' package,
'multiRL' modularizes the Markov Decision Process (MDP) into six core
components. This framework enables users to construct custom models via
intuitive if-else syntax and define latent learning rules for agents.
For parameter estimation, it provides both likelihood-based
inference (MLE and MAP) and simulation-based inference (ABC and
RNN), with full support for parallel processing across subjects.
The workflow is highly standardized, featuring four main functions
that strictly follow the four-step protocol (and ten rules)
proposed by Wilson & Collins (2019) <doi:10.7554/eLife.49547>.
Beyond the three built-in models (TD, RSTD, and Utility), users
can easily derive new variants by declaring which variables are
treated as free parameters.
Author: YuKi [aut, cre] ,
Xinyu [aut]
Maintainer: YuKi <hmz1969a@gmail.com>
Diff between multiRL versions 0.2.3 dated 2026-01-26 and 0.3.7 dated 2026-03-31
DESCRIPTION | 10 MD5 | 187 +++++++------ NAMESPACE | 3 R/base_plot.R | 7 R/base_setClass.R | 5 R/base_summary.R | 3 R/document_algorithm.R | 22 - R/document_behrule.R | 6 R/document_colnames.R | 4 R/document_control.R | 563 +++++++++++++++++++++++++++--------------- R/document_data.R | 2 R/document_estimate.R | 209 ++++++++------- R/document_funcs.R | 285 ++++++++++----------- R/document_layer.R |only R/document_params.R | 538 ++++++++++++++++++++++------------------ R/document_reduction.R |only R/engine_ABC.R | 16 - R/engine_RNN.R | 347 +++++++++++++++++++------ R/engine_RNN3.R |only R/estimate_0_ENV.R | 6 R/estimate_1_LBI.R | 225 ++++++++++------ R/estimate_1_MAP.R | 308 ++++++++++++---------- R/estimate_1_MLE.R | 199 +++++++------- R/estimate_2_ABC.R | 338 ++++++++++++++----------- R/estimate_2_RNN.R | 140 +++++++--- R/estimate_2_SBI.R | 17 - R/estimation_methods.R | 115 ++++---- R/func_alpha.R | 20 + R/func_beta.R | 27 +- R/func_delta.R | 94 ++++++- R/func_epsilon.R | 56 +--- R/func_gamma.R | 20 + R/func_zeta.R | 20 + R/model_RSTD.R | 2 R/model_TD.R | 2 R/model_Utility.R | 2 R/multiRL-package.R | 12 R/plot_fitting.R | 62 +--- R/plot_recovery.R | 150 ++++++++++- R/process_1_input.R | 6 R/process_3_record.R | 4 R/process_4_output.R | 91 ++++-- R/process_5_metric.R | 30 +- R/step_1_run_m.R | 6 R/step_2_rcv_d.R | 246 +++++++++--------- R/step_3_fit_p.R | 202 ++++++++------- R/step_4_rpl_e.R | 2 R/tool_check_dependency.R | 18 - R/tool_df2matrix.R | 64 ++-- R/tool_extract_abc.R | 6 R/tool_fix_params.r |only R/tool_for_abc.R | 28 +- R/tool_name_abcouts.R |only R/tool_name_rnnouts.R |only R/tool_reduce_sumstats.R |only R/tool_remove_slot.R | 4 R/tool_replay.R | 43 +-- R/tool_restructure_settings.R | 4 R/tool_return_result.R | 2 R/zzz.R | 13 build/partial.rdb |binary man/RSTD.Rd | 2 man/TD.Rd | 2 man/Utility.Rd | 2 man/algorithm.Rd | 22 - man/behrule.Rd | 6 man/colnames.Rd | 4 man/control.Rd | 541 ++++++++++++++++++++++++++-------------- man/data.Rd | 2 man/engine_ABC.Rd | 2 man/engine_RNN.Rd | 41 ++- man/estimate.Rd | 167 ++++++------ man/estimate_0_ENV.Rd | 2 man/estimate_1_LBI.Rd | 23 - man/estimate_1_MAP.Rd | 24 - man/estimate_1_MLE.Rd | 16 - man/estimate_2_ABC.Rd | 10 man/estimate_2_RNN.Rd | 8 man/estimate_2_SBI.Rd | 6 man/estimation_methods.Rd | 20 - man/fit_p.Rd | 21 - man/func_alpha.Rd | 20 + man/func_beta.Rd | 26 + man/func_delta.Rd | 55 +++- man/func_epsilon.Rd | 39 +- man/func_gamma.Rd | 19 + man/func_zeta.Rd | 20 + man/funcs.Rd | 229 ++++++++--------- man/layer.Rd |only man/multiRL-package.Rd | 12 man/params.Rd | 506 +++++++++++++++++++++---------------- man/plot.multiRL.replay.Rd | 5 man/rcv_d.Rd | 35 +- man/reduction.Rd |only man/rpl_e.Rd | 2 man/run_m.Rd | 6 src/process_4_output.cpp | 100 +++++-- src/tool_record_shown.cpp | 9 src/tool_sample_choice.cpp | 40 +- 99 files changed, 4122 insertions(+), 2713 deletions(-)