Title: Simulate Experimental Crosses
Description: Simulate and plot general experimental crosses. The focus is on simulating genotypes with an aim towards flexibility rather than speed. Meiosis is simulated following the Stahl model, in which chiasma locations are the superposition of two processes: a proportion p coming from a process exhibiting no interference, and the remainder coming from a process following the chi-square model.
Author: Karl W Broman [aut, cre]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between simcross versions 0.8 dated 2026-05-01 and 0.10 dated 2026-06-08
DESCRIPTION | 10 +++++----- MD5 | 19 +++++++++++-------- NEWS.md | 10 ++++++++++ R/plot_cross.R | 27 ++++++++++++++++++++++----- R/simcross-package.R |only README.md | 18 +++++++++++++++++- inst/doc/simcross.Rmd | 8 ++++++++ inst/doc/simcross.html | 9 +++++++++ man/CCcolors.Rd | 12 ++++++++++-- man/figures |only man/simcross-package.Rd |only vignettes/simcross.Rmd | 8 ++++++++ 12 files changed, 100 insertions(+), 21 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2019) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] ,
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.40 dated 2026-05-04 and 0.42 dated 2026-06-08
DESCRIPTION | 8 - MD5 | 133 +++++++++++++++++------------ NAMESPACE | 13 ++ NEWS.md | 45 ++++++++++ R/RcppExports.R | 56 ++++++------ R/calc_hotspots.R |only R/cbind_phasedgeno.R |only R/cbind_viterbi.R | 47 ---------- R/find_peaks.R | 4 R/fit1.R | 56 ++++++++---- R/fit1_pg.R | 39 ++++++-- R/guess_phase.R | 3 R/plot_ci.R | 127 ++++++++++++++-------------- R/plot_cistrans.R |only R/plot_colorscale.R |only R/plot_geno.R |only R/plot_genoprob.R | 2 R/plot_lodpeaks.R | 2 R/plot_onegeno.R | 2 R/plot_scan1.R | 2 R/plot_scan1_heatmap.R |only R/qtl2-package.R | 5 + R/rbind_phasedgeno.R |only R/rbind_viterbi.R | 2 R/read_cross2.R | 3 R/read_pheno.R | 23 ++++- R/scan1coef.R | 2 R/subset_phasedgeno.R |only R/subset_viterbi.R | 2 README.md | 22 ++++ man/calc_hotspots.Rd |only man/cbind.phasedgeno.Rd |only man/figures |only man/fit1.Rd | 6 + man/guess_phase.Rd | 2 man/plot_ci.Rd | 11 ++ man/plot_cistrans.Rd |only man/plot_colorscale.Rd |only man/plot_geno.Rd |only man/plot_genoprob.Rd | 2 man/plot_lodpeaks.Rd | 2 man/plot_onegeno.Rd | 3 man/plot_scan1.Rd | 2 man/plot_scan1_heatmap.Rd |only man/qtl2-package.Rd | 10 ++ man/rbind.phasedgeno.Rd |only man/rbind.viterbi.Rd | 2 man/scan1coef.Rd | 4 man/subset.phasedgeno.Rd |only man/subset.viterbi.Rd | 3 src/RcppExports.cpp | 131 +++++++++++++++++------------ src/binreg.cpp | 3 src/binreg.h | 1 src/binreg_eigen.cpp | 23 ++++- src/binreg_eigen.h | 1 src/binreg_weighted.cpp | 3 src/binreg_weighted.h | 1 src/binreg_weighted_eigen.cpp | 23 ++++- src/binreg_weighted_eigen.h | 1 src/fit1_binary.cpp | 10 +- src/fit1_binary.h | 2 src/fit1_hk.cpp | 8 + src/fit1_hk.h | 2 src/fit1_pg.cpp | 8 + src/fit1_pg.h | 2 src/linreg.cpp | 4 src/linreg.h | 3 src/linreg_eigen.cpp | 45 ++++++++-- src/linreg_eigen.h | 3 src/running_count.cpp |only src/running_count.h |only tests/testthat/test-binreg.R | 48 ++++++++++ tests/testthat/test-calc_hotspots.R |only tests/testthat/test-fit1.R | 144 +++++++++++++++++++++++++++++++- tests/testthat/test-fit1_binary.R | 61 +++++++++++++ tests/testthat/test-guess_phase.R | 1 tests/testthat/test-linreg.R | 34 +++++++ tests/testthat/test-subset_phasedgeno.R |only 78 files changed, 886 insertions(+), 321 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman [aut, cre] ,
Aimee Teo Broman [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between broman versions 0.92 dated 2025-12-08 and 0.94 dated 2026-06-08
DESCRIPTION | 10 +++--- MD5 | 35 +++++++++++---------- NEWS.md | 11 ++++++ R/brocolors.R | 67 ++++++++++++++++++++++++++++++++++++++---- R/broman-package.R |only data/numbers-cap.RData |binary data/numbers.RData |binary man/broman-package.Rd |only man/crayons.Rd | 14 ++++++++ man/figures |only man/myround.Rd | 2 - man/objectsizes.Rd | 2 - man/paste..Rd | 2 - man/paste00.Rd | 2 - man/plot_crayons.Rd | 8 ++++- man/qqline2.Rd | 6 +-- man/revrainbow.Rd | 6 +-- man/rmvn.Rd | 2 - man/twocolorpal.Rd | 2 - tests/testthat/test-crayons.R | 24 +++++++++++++++ 20 files changed, 152 insertions(+), 41 deletions(-)
Title: A Bias Bound Approach to Non-Parametric Inference
Description: A novel bias-bound approach for non-parametric inference is introduced,
focusing on both density and conditional expectation estimation.
It constructs valid confidence intervals that account for the presence of
a non-negligible bias and thus make it possible to perform inference with
optimal mean squared error minimizing bandwidths.
This package is based on Schennach (2020) <doi:10.1093/restud/rdz065>.
Author: Xinyu DAI [aut, cre],
Susanne M Schennach [aut]
Maintainer: Xinyu DAI <xinyu_dai@brown.edu>
Diff between rbbnp versions 0.3.0 dated 2025-04-30 and 1.1.0 dated 2026-06-08
DESCRIPTION | 17 MD5 | 171 ++-- NAMESPACE | 66 + NEWS.md | 108 +- R/bandwidths.R | 556 +++++++++---- R/config.R | 246 +++--- R/gen_sample.R | 176 ++-- R/globals.R | 56 - R/kernels.R | 296 +++---- R/main.R | 789 ++++++++++--------- R/methods-extractors.R |only R/methods-plot.R |only R/methods-print.R |only R/methods-summary.R |only R/rbbnp-pkg.R | 74 + R/s3-constructors.R |only R/utils.R | 1194 +++++++++++++++++++----------- README.md | 262 ++---- build |only inst/CITATION | 19 inst/doc |only man/DATA_PATH.Rd | 23 man/EXT_DATA_PATH.Rd | 25 man/W_kernel.Rd | 43 - man/W_kernel_ft.Rd | 45 - man/biasBound_condExpectation.Rd | 207 ++--- man/biasBound_density.Rd | 191 ++-- man/coef.bbnp_density.Rd |only man/coef.bbnp_regression.Rd |only man/confint.bbnp_density.Rd |only man/confint.bbnp_regression.Rd |only man/create_biasBound_config.Rd | 124 +-- man/create_kernel_functions.Rd | 50 - man/cv_bandwidth.Rd | 86 +- man/dot-has_lp_solver.Rd |only man/dot-noise_floor_avg_dphi.Rd |only man/dot-prepare_lp_problem.Rd |only man/dot-snr_window.Rd |only man/dot-solve_lp_envelope.Rd |only man/epanechnikov_kernel.Rd | 35 man/epanechnikov_kernel_ft.Rd | 35 man/figures |only man/fitted.bbnp_regression.Rd |only man/fun_approx.Rd | 83 +- man/gen_sample_data.Rd | 63 - man/get_avg_f1x.Rd | 47 - man/get_avg_fyx.Rd | 51 - man/get_avg_phi.Rd | 45 - man/get_avg_phi_log.Rd | 45 - man/get_conditional_var.Rd | 62 - man/get_conditional_var_loop.Rd |only man/get_est_Ar.Rd | 79 + man/get_est_Ar_grid.Rd |only man/get_est_Ar_lp.Rd |only man/get_est_B.Rd | 35 man/get_est_b1x.Rd | 51 - man/get_est_byx.Rd | 43 - man/get_est_vy.Rd | 29 man/get_sigma.Rd | 47 - man/get_sigma_yx.Rd | 53 - man/get_xi_interval.Rd | 71 + man/kernel_reg.Rd | 51 - man/new_bbnp_density.Rd |only man/new_bbnp_regression.Rd |only man/normal_kernel.Rd | 35 man/normal_kernel_ft.Rd | 35 man/plot.bbnp_density.Rd |only man/plot.bbnp_regression.Rd |only man/plot_density_internal.Rd |only man/plot_ft.Rd | 71 - man/plot_ft_internal.Rd |only man/plot_regression_internal.Rd |only man/print.bbnp_density.Rd |only man/print.bbnp_regression.Rd |only man/print.summary.bbnp_density.Rd |only man/print.summary.bbnp_regression.Rd |only man/rbbnp-package.Rd |only man/rpoly01.Rd | 43 - man/sample_data.Rd | 40 - man/select_bandwidth.Rd | 88 +- man/silverman_bandwidth.Rd | 50 - man/sinc.Rd | 35 man/sinc_ft.Rd | 35 man/summary.bbnp_density.Rd |only man/summary.bbnp_regression.Rd |only man/true_density_2fold.Rd | 35 tests/testthat/test-bandwidths.R | 282 +++++-- tests/testthat/test-deprecated.R |only tests/testthat/test-equation-audit.R |only tests/testthat/test-integration-s3.R |only tests/testthat/test-kernel-factory.R | 22 tests/testthat/test-kernels.R | 54 - tests/testthat/test-main.R | 209 ++--- tests/testthat/test-methods-extractors.R |only tests/testthat/test-methods-plot.R |only tests/testthat/test-methods-print.R |only tests/testthat/test-methods-summary.R |only tests/testthat/test-s3-constructors.R |only tests/testthat/test-utils.R | 534 ++++++++++--- tests/testthat/test-validation-envelope.R |only tests/testthat/test-validation-golden.R |only tests/testthat/test-window-snr.R |only vignettes |only 103 files changed, 4345 insertions(+), 2972 deletions(-)
Title: Advanced Continuous Glucose Monitoring Analysis with
High-Performance C++ Backend
Description: Tools for advanced analysis of continuous glucose monitoring (CGM)
time-series, implementing GRID (Glucose Rate Increase Detector) and GRID-based
algorithms for postprandial peak detection, and detection of hypoglycemic and
hyperglycemic episodes (Levels 1/2/Extended) aligned with international consensus
CGM metrics. Core algorithms are implemented in optimized C++ using 'Rcpp' to
provide accurate and fast analysis on large datasets.
Author: Sang Ho Park [aut, cre],
Rosa Oh [aut, ctb],
Sang-Man Jin [aut, ctb]
Maintainer: Sang Ho Park <shstat1729@gmail.com>
Diff between cgmguru versions 1.0.0 dated 2026-05-14 and 1.1.0 dated 2026-06-08
DESCRIPTION | 6 MD5 | 91 +++---- NEWS.md | 43 +++ R/RcppExports.R | 6 R/cgmguru-functions-docs.R | 191 +++++++++----- R/function_overrides.R | 13 - R/sensor_wear.R | 11 build/vignette.rds |binary inst/doc/cgmguru.R |only inst/doc/cgmguru.Rmd |only inst/doc/cgmguru.pdf |only inst/doc/detect_all_events.html | 172 ++++++------- inst/doc/detect_hyperglycemic_events.html | 180 ++++++------- inst/doc/detect_hypoglycemic_events.html | 166 ++++++------ inst/doc/examples.html | 273 ++++++++++----------- inst/doc/grid.html | 4 inst/doc/intro.R | 10 inst/doc/intro.Rmd | 10 inst/doc/intro.html | 132 +++++----- inst/doc/maxima_grid.html | 63 ++-- inst/examples/detect_all_events.R | 10 inst/examples/detect_hyperglycemic_events.R | 2 inst/examples/detect_hypoglycemic_events.R | 6 man/detect_all_events.Rd | 119 ++++++--- man/detect_hyperglycemic_events.Rd | 16 - man/detect_hypoglycemic_events.Rd | 16 - man/sensor_wear.Rd | 42 +-- src/RcppExports.cpp | 14 - src/detect_all_events.cpp | 261 +++++++++++++------- src/detect_between_maxima.cpp | 19 + src/detect_hyperglycemic_events.cpp | 15 - src/detect_hypoglycemic_events.cpp | 27 +- src/event_preprocessing.h | 106 +++++++- src/interpolate_cgm.cpp | 3 src/maxima_grid.cpp | 26 +- src/sensor_wear.cpp | 147 +++++++++-- tests/testthat/test-event-interpolation-segments.R | 65 ++++- tests/testthat/test-events.R | 107 +++++--- tests/testthat/test-function_overrides.R | 24 + tests/testthat/test-grid_maxima_excursion.R | 18 + tests/testthat/test-iglu-episode-parity.R | 80 ++++++ tests/testthat/test-interpolate-cgm.R | 7 tests/testthat/test-overrides-errors.R | 2 tests/testthat/test-pre-recovery-events.R | 81 +++--- tests/testthat/test-sensor-wear.R | 40 ++- tests/testthat/test-transform-between.R | 25 + vignettes/cgmguru.Rmd |only vignettes/cgmguru.html |only vignettes/intro.Rmd | 10 49 files changed, 1718 insertions(+), 941 deletions(-)
Title: Bayesian Screening and Variable Selection
Description: Performs Bayesian variable screening and selection for ultra-high dimensional linear regression models.Also contains an user friendly web application to perform multi trait GWAS.
Author: Dongjin Li [aut, cre],
Debarshi Chakraborty [aut],
Somak Dutta [aut],
Vivekananda Roy [ctb]
Maintainer: Dongjin Li <liyangxiaobei@gmail.com>
Diff between bravo versions 4.0.0 dated 2026-05-27 and 4.1.0 dated 2026-06-08
DESCRIPTION | 8 +-- MD5 | 41 ++++++++++---------- R/calc_functions.R | 87 ++++++++----------------------------------- R/dense2sparse.R |only R/svenetics.R | 4 - man/FDR_WS.Rd | 1 man/FDR_corrected.Rd | 1 man/FPR_WS.Rd | 1 man/FPR_corrected.Rd | 1 man/TPR_WS.Rd | 1 man/TPR_corrected.Rd | 1 man/basic.sven.model.Rd | 1 man/bwas.Rd | 1 man/clean.Rd | 1 man/create_param_mat.Rd | 1 man/dense2sparse.Rd | 22 ++++++++-- man/jcidx.Rd | 1 man/pipeline_single_trait.Rd | 1 man/run_all_params.Rd | 1 man/tune.sven.Rd | 1 man/tune.sven.all.Rd | 1 man/unite.sven.Rd | 1 22 files changed, 77 insertions(+), 101 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
(Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>)
for supervised learning and Bayesian Causal Forests (BCF)
(Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>)
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Includes the grow-from-root algorithm for accelerated forest sampling
(He and Hahn (2021) <doi:10.1080/01621459.2021.1942012>),
a log-linear leaf model for forest-based heteroskedasticity (Murray (2020) <doi:10.1080/01621459.2020.1813587>),
and the cloglog BART model of Alam and Linero (2025) <doi:10.48550/arXiv.2502.00606> for ordinal outcomes.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
Entejar Alam [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.4.2 dated 2026-04-28 and 0.4.4 dated 2026-06-08
DESCRIPTION | 6 MD5 | 34 ++-- NEWS.md | 17 ++ R/bart.R | 88 ++++------ R/bcf.R | 207 ++++++++++++++++++++---- R/kernel.R | 2 R/model.R | 4 R/posterior_transformation.R | 11 + R/utils.R | 11 - configure | 18 +- configure.ac | 2 man/ForestKernelComputation.Rd | 2 man/computeBCFPosteriorInterval.Rd | 11 + man/predict.bcfmodel.Rd | 13 + tests/testthat/test-bcf.R | 101 +++++++++++ tests/testthat/test-data-preprocessing.R | 48 +++++ tests/testthat/test-predict.R | 59 +++++++ tests/testthat/test-serialization.R | 261 +++++++++++++++++++++++++++++++ 18 files changed, 766 insertions(+), 129 deletions(-)
Title: Likelihood-Based Confidence Interval in Structural Equation
Models
Description: Forms likelihood-based confidence intervals
(LBCIs) for parameters in structural equation modeling,
introduced in Cheung and Pesigan (2023)
<doi:10.1080/10705511.2023.2183860>. Currently
implements the algorithm illustrated by Pek and Wu
(2018) <doi:10.1037/met0000163>, and supports the robust
LBCI proposed by Falk (2018)
<doi:10.1080/10705511.2017.1367254>.
Author: Shu Fai Cheung [aut, cre] ,
Ivan Jacob Agaloos Pesigan [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semlbci versions 0.11.5 dated 2025-12-06 and 0.11.6 dated 2026-06-08
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 16 +++++++++++++++- R/check_sem_out.R | 2 +- R/ci_bound_ur_i_helpers.R | 4 ++-- README.md | 2 +- build/partial.rdb |binary build/vignette.rds |binary man/check_sem_out.Rd | 2 +- man/ci_bound_ur.Rd | 2 +- man/ci_bound_ur_i.Rd | 2 +- man/ci_bound_wn_i.Rd | 2 +- man/gen_userp.Rd | 6 +++--- man/loglikelihood.Rd | 2 +- man/plot.loglike_compare.Rd | 4 ++-- man/semlbci-package.Rd | 5 +++++ tests/testthat/test-check_sem_out.R | 3 ++- 17 files changed, 56 insertions(+), 36 deletions(-)
Title: Functions to Help in your Coding Etiquette
Description: Adds some functions to help in your coding etiquette.
'tinycodet' primarily focuses on 4 aspects.
1) Safer decimal (in)equality testing,
standard-evaluated alternatives to with() and aes(),
and other functions for safer coding.
2) A new package import system,
that attempts to combine the benefits of using a package without attaching it,
with the benefits of attaching a package.
3) Extending the string manipulation capabilities of the 'stringi' R package.
4) Reducing repetitive code.
Besides linking to 'Rcpp', 'tinycodet' has only one other dependency, namely 'stringi'.
Author: Tony Wilkes [aut, cre, cph]
Maintainer: Tony Wilkes <tony_a_wilkes@outlook.com>
Diff between tinycodet versions 0.6.2 dated 2026-03-05 and 0.7.0 dated 2026-06-08
tinycodet-0.6.2/tinycodet/R/logic_ops.R |only tinycodet-0.6.2/tinycodet/inst/tinytest/test-logic_ops.R |only tinycodet-0.6.2/tinycodet/man/logic_ops.Rd |only tinycodet-0.7.0/tinycodet/DESCRIPTION | 6 +++--- tinycodet-0.7.0/tinycodet/MD5 | 13 +++++-------- tinycodet-0.7.0/tinycodet/NAMESPACE | 6 ------ tinycodet-0.7.0/tinycodet/NEWS.md | 3 +++ tinycodet-0.7.0/tinycodet/R/aaa5_tinycodet_misc.R | 1 - tinycodet-0.7.0/tinycodet/man/aaa5_tinycodet_misc.Rd | 1 - 9 files changed, 11 insertions(+), 19 deletions(-)
Title: Interactive Tool for Statistics and Probability
Description: A Shiny application designed to support the learning of basic
concepts in statistics and probability. The tool provides an interactive
interface that allows students to explore and visualize different
statistical concepts intuitively, including descriptive statistics for
continuous and qualitative variables, and probability distributions.
Author: Javier De La Hoz Maestre [cre, aut] ,
Humberto Llinas Solano [aut] ,
Alexander Rangel Vizcaino [aut]
Maintainer: Javier De La Hoz Maestre <jdelahoz@unimagdalena.edu.co>
Diff between StatisticTeach1 versions 0.1.0 dated 2026-05-30 and 0.1.2 dated 2026-06-08
StatisticTeach1-0.1.0/StatisticTeach1/R/header.R |only StatisticTeach1-0.1.0/StatisticTeach1/R/sidebar.R |only StatisticTeach1-0.1.0/StatisticTeach1/build |only StatisticTeach1-0.1.0/StatisticTeach1/inst/StatisticTeach1App |only StatisticTeach1-0.1.0/StatisticTeach1/inst/doc |only StatisticTeach1-0.1.0/StatisticTeach1/vignettes |only StatisticTeach1-0.1.2/StatisticTeach1/DESCRIPTION | 41 +-- StatisticTeach1-0.1.2/StatisticTeach1/MD5 | 105 +++---- StatisticTeach1-0.1.2/StatisticTeach1/NAMESPACE | 73 +++-- StatisticTeach1-0.1.2/StatisticTeach1/NEWS.md |only StatisticTeach1-0.1.2/StatisticTeach1/R/ST_freq_factor.R | 88 ++---- StatisticTeach1-0.1.2/StatisticTeach1/R/ST_freq_numeric.R | 133 ++++------ StatisticTeach1-0.1.2/StatisticTeach1/R/runStatisticTeach1.R | 110 ++++---- StatisticTeach1-0.1.2/StatisticTeach1/R/zzz.R | 5 StatisticTeach1-0.1.2/StatisticTeach1/README.md | 24 + StatisticTeach1-0.1.2/StatisticTeach1/inst/SatisticTeach1App |only StatisticTeach1-0.1.2/StatisticTeach1/man/ST_freq_factor.Rd | 20 - StatisticTeach1-0.1.2/StatisticTeach1/man/ST_freq_numeric.Rd | 22 - StatisticTeach1-0.1.2/StatisticTeach1/man/runStatisticTeach1.Rd | 43 +-- StatisticTeach1-0.1.2/StatisticTeach1/tests |only 20 files changed, 330 insertions(+), 334 deletions(-)
More information about StatisticTeach1 at CRAN
Permanent link
Title: Accessing and Validating Marine Environmental Data from 'SHARK'
and Related Databases
Description: Provides functions to retrieve, process, analyze, and
quality-control marine physical, chemical, and biological data. The
main focus is on Swedish monitoring data available through the 'SHARK'
database <https://shark.smhi.se/en/>, with additional API support for 'Nordic
Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa'
<https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>,
'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service
<https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) -
UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins
<https://toxins.hais.ioc-unesco.org/>.
Author: Markus Lindh [aut] ,
Anders Torstensson [aut, cre] ,
Mikael Hedblom [ctb] ,
Bengt Karlson [ctb] ,
Peter Thor [ctb] ,
Marie Johansen [ctb] ,
SHARK [cph],
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between SHARK4R versions 1.1.1 dated 2026-03-12 and 1.2.0 dated 2026-06-08
DESCRIPTION | 25 MD5 | 140 +- NAMESPACE | 18 NEWS.md | 19 R/SHARK4R-package.R | 14 R/algaebase_api_functions.R | 16 R/check_codes.R | 17 R/check_depth.R | 4 R/check_fields.R | 138 +- R/check_logical.R | 85 - R/check_onland.R | 17 R/check_outliers.R | 22 R/check_stations.R | 41 R/defunct.R | 59 R/dyntaxa_api_functions.R | 211 +-- R/hab_api_functions.R | 88 + R/iRfcb_functions.R | 202 +-- R/nua_api_functions.R | 48 R/pie_map.R |only R/plankton_toolbox.R | 30 R/plot_map_leaflet.R | 7 R/read_delivery_template.R | 12 R/run_qc_app.R | 19 R/scatterplot.R | 20 R/shark_api_functions.R | 109 - R/shark_read.R | 26 R/util.R | 167 +- R/worms_api_functions.R | 80 - R/xylookup.R | 10 R/zooplankton.R |only R/zzz.R | 123 - build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST | 84 + inst/doc/quality_control.html | 33 inst/doc/retrieve_hab_data.R | 23 inst/doc/retrieve_hab_data.Rmd | 25 inst/doc/retrieve_hab_data.html | 66 - inst/doc/retrieve_nordic_microalgae_data.html | 90 - inst/doc/retrieve_shark_data.html | 8 inst/doc/retrieve_worms_data.html | 72 - inst/extdata/Mesozooplankton_Kattegat_Skagerrak_taxa_and_biomass_calculations.xlsx |only inst/extdata/threshold_values.csv |only inst/shiny/shark-qc/rsconnect |only inst/shiny/shark-qc/server.R | 179 +- inst/shiny/shark-qc/ui.R | 623 +++++----- man/SHARK4R-package.Rd | 3 man/build_pie_polygons.Rd |only man/cache_coastline_shape.Rd |only man/calc_zooplankton_biomass.Rd |only man/calc_zooplankton_dry_weight.Rd |only man/check_datatype.Rd | 2 man/check_depth.Rd | 4 man/check_fields.Rd | 8 man/clamp_pie_centers.Rd |only man/create_pie_map.Rd |only man/defunct.Rd | 66 + man/find_required_fields.Rd | 2 man/get_toxin_list.Rd | 29 man/load_shark4r_fields.Rd | 6 man/place_pie_labels.Rd |only man/positions_are_near_land.Rd | 22 man/repel_pie_centers.Rd |only man/which_basin.Rd | 6 tests/testthat/test-check_logical.R | 22 tests/testthat/test-check_outliers.R | 22 tests/testthat/test-check_stations.R | 26 tests/testthat/test-dyntaxa_api_functions.R | 11 tests/testthat/test-iRfcb_functions.R | 2 tests/testthat/test-pie_map.R |only tests/testthat/test-plankton_toolbox.R | 4 tests/testthat/test-run_qc_app.R | 12 tests/testthat/test-shark_api_functions.R | 2 tests/testthat/test-shark_read.R | 8 tests/testthat/test-worms_api_functions.R | 2 tests/testthat/test-zooplankton_biomass.R |only tests/testthat/test-zooplankton_dry_weight.R |only vignettes/retrieve_hab_data.Rmd | 25 79 files changed, 1801 insertions(+), 1457 deletions(-)
Title: Automatic Generation of Initial Estimates for Population
Pharmacokinetic Modeling
Description: Provides automated methods for generating initial parameter estimates
in population pharmacokinetic modeling. The pipeline integrates adaptive single-point
methods, naive pooled graphic approaches, noncompartmental analysis methods, and parameter
sweeping across pharmacokinetic models. It estimates residual unexplained variability
using either data-driven or fixed-fraction approaches and assigns pragmatic initial values
for inter-individual variability. These strategies are designed to improve model
robustness and convergence in 'nlmixr2' workflows. For more details see
Huang Z, Fidler M, Lan M, Cheng IL, Kloprogge F, Standing JF (2025)
<doi:10.1007/s10928-025-10000-z>.
Author: Zhonghui Huang [aut, cre],
Joseph Standing [ctb],
Matthew Fidler [ctb],
Frank Kloprogge [ctb]
Maintainer: Zhonghui Huang <huangzhonghui22@gmail.com>
Diff between nlmixr2autoinit versions 1.0.0 dated 2025-11-13 and 1.0.1 dated 2026-06-08
nlmixr2autoinit-1.0.0/nlmixr2autoinit/R/run_modelfit.R |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_1cmpt_iv.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_1cmpt_mm_iv.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_1cmpt_mm_oral.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_1cmpt_oral.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_2cmpt_iv.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_2cmpt_oral.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_3cmpt_iv.Rd |only nlmixr2autoinit-1.0.0/nlmixr2autoinit/man/run_npd_3cmpt_oral.Rd |only nlmixr2autoinit-1.0.1/nlmixr2autoinit/DESCRIPTION | 11 nlmixr2autoinit-1.0.1/nlmixr2autoinit/MD5 | 165 nlmixr2autoinit-1.0.1/nlmixr2autoinit/NAMESPACE | 140 nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/approx.vc.R | 424 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/bin.time.R | 246 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/calculate_tad.R | 300 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/evaluation.R | 905 ++-- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/extra_ka.R | 1130 ++--- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/find_best_lambdaz.R | 458 +- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/force_find_lambdaz.R | 248 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/getOmegas.R | 210 nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/getPPKinits.R | 2167 +++++---- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/get_hf.R | 314 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/get_pooled_data.R | 470 +- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/getnca.R | 818 +-- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/getsigma.R | 406 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/global.R | 238 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/initsControl.R | 182 nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/is_ss.R | 614 +- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/nmpkconvert.R | 116 nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/npd_modelcodes.R | 2178 +++++----- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/processData.R | 1180 ++--- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/run_graphcal.R | 676 +-- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/run_pooled_nca.R | 476 +- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/run_single_point_base.R | 1148 ++--- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/run_single_point_extra.R | 692 +-- nlmixr2autoinit-1.0.1/nlmixr2autoinit/R/sim_sens_params.R | 1873 ++++---- nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_1cmpt_iv.Rd | 144 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_1cmpt_mm_iv.Rd | 154 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_1cmpt_mm_oral.Rd | 162 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_1cmpt_oral.Rd | 154 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_2cmpt_iv.Rd | 166 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_2cmpt_oral.Rd | 162 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_3cmpt_iv.Rd | 184 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/Fit_3cmpt_oral.Rd | 166 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/approx.vc.Rd | 154 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/bin.time.Rd | 122 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/calculate_cl.Rd | 162 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/calculate_tad.Rd | 90 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/calculate_vd.Rd | 154 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/eval_perf_1cmpt.Rd | 121 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/fallback_control.Rd | 72 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/find_best_lambdaz.Rd | 180 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/force_find_lambdaz.Rd | 114 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/getOmegas.Rd | 58 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/getPPKinits.Rd | 140 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/get_hf.Rd | 132 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/get_pooled_data.Rd | 124 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/getnca.Rd | 182 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/getsigma.Rd | 100 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/getsigmas.Rd | 114 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/graphcal_iv.Rd | 82 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/graphcal_oral.Rd | 92 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/hybrid_eval_perf_1cmpt.Rd | 196 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/initsControl.Rd | 124 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/is_ss.Rd | 102 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/ka_calculation_md.Rd | 104 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/ka_calculation_sd.Rd | 102 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/ka_wanger_nelson.Rd | 156 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/mark_dose_number.Rd | 56 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/metrics..Rd | 120 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/nca_control.Rd | 98 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/nmpkconvert.Rd | 78 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/pooled_control.Rd | 78 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/print.getPPKinits.Rd | 70 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/processData.Rd | 238 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_graphcal.Rd | 140 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_ka_solution.Rd | 124 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_pooled_nca.Rd | 128 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_single_point.Rd | 144 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_single_point_base.Rd | 136 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/run_single_point_extra.Rd | 214 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/sim_sens_1cmpt_mm.Rd | 176 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/sim_sens_2cmpt.Rd | 190 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/sim_sens_3cmpt.Rd | 230 - nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/ss_control.Rd | 134 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/trapezoidal_linear.Rd | 58 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/trapezoidal_linear_up_log_down.Rd | 68 nlmixr2autoinit-1.0.1/nlmixr2autoinit/man/trimmed_geom_mean.Rd | 60 88 files changed, 12341 insertions(+), 12253 deletions(-)
More information about nlmixr2autoinit at CRAN
Permanent link
Title: Simulation-Based Inference for Regression Models
Description: Performs simulation-based inference as an alternative to the delta method for obtaining valid confidence intervals and p-values for regression post-estimation quantities, such as average marginal effects and predictions at representative values. This framework for simulation-based inference is especially useful when the resulting quantity is not normally distributed and the delta method approximation fails. The methodology is described in Greifer, et al. (2025) <doi:10.32614/RJ-2024-015>. 'clarify' is meant to replace some of the functionality of the archived package 'Zelig'; see the vignette "Translating Zelig to clarify" for replicating this functionality.
Author: Noah Greifer [aut, cre] ,
Steven Worthington [aut] ,
Stefano Iacus [aut] ,
Gary King [aut]
Maintainer: Noah Greifer <ngreifer@iq.harvard.edu>
Diff between clarify versions 0.2.2 dated 2025-09-19 and 0.2.3 dated 2026-06-08
DESCRIPTION | 14 - MD5 | 82 +++--- NEWS.md | 28 +- R/checks.R | 143 ++++------- R/clarify_est_methods.R | 20 - R/clarify_predict.R | 2 R/get_model_components.R | 4 R/misim.R | 45 +-- R/plot.clarify_adrf.R | 6 R/plot.clarify_est.R | 6 R/plot.clarify_setx.R | 34 +- R/sim.R | 59 ++-- R/sim_adrf.R | 129 +++++----- R/sim_ame.R | 168 ++++++------- R/sim_apply.R | 95 ++++--- R/sim_setx.R | 96 +++---- R/summary.clarify_est.R | 42 +-- R/transform.clarify_est.R | 33 +- R/utils.R | 209 +++-------------- README.md | 53 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Zelig.Rmd | 90 +++---- inst/doc/Zelig.html | 180 +++++++------- inst/doc/clarify.Rmd | 84 +++--- inst/doc/clarify.html | 376 +++++++++++++++---------------- man/clarify-package.Rd | 3 man/figures/README-example-1.png |binary man/figures/README-example2-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/misim.Rd | 4 man/plot.clarify_adrf.Rd | 6 man/plot.clarify_setx.Rd | 6 man/sim.Rd | 2 man/sim_adrf.Rd | 38 +-- man/sim_ame.Rd | 62 ++--- man/sim_apply.Rd | 32 +- man/sim_setx.Rd | 37 +-- man/summary.clarify_est.Rd | 10 man/transform.clarify_est.Rd | 14 - vignettes/Zelig.Rmd | 90 +++---- vignettes/clarify.Rmd | 84 +++--- 42 files changed, 1096 insertions(+), 1290 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions.
Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc.
Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM)
for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates).
A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc.
Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of larg [...truncated...]
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@gmail.com>
Diff between wrMisc versions 2.0.2 dated 2026-04-29 and 2.1.0 dated 2026-06-08
DESCRIPTION | 8 MD5 | 83 ++++---- NAMESPACE | 4 R/addBeforFileExtension.R | 45 ++++ R/adjBy2ptReg.R | 144 +++++++++----- R/blockNormalize.R |only R/checkGroupOrderSEM.R | 62 +++--- R/exclExtrValues.R | 26 +- R/extrSpcText.R | 11 - R/findHeadAndTail.R | 8 R/findUsableGroupRange.R | 41 ++-- R/getPWseparator.R | 2 R/getPairwiseSetup.R | 13 - R/moderTest2grp.R | 12 - R/moderTestXgrp.R | 16 - R/normalizeThis.R | 9 R/readTabulatedBatch.R | 2 R/readXlsxBatch.R | 2 R/rowGrpNA.R | 115 +++++++++-- R/scaleXY.R | 70 +++++-- R/searchLinesAtGivenSlope.R | 7 R/stableMode.R | 2 R/vectorDistAngle.R |only R/volcanoFilter.R |only build/vignette.rds |binary inst/doc/wrMiscVignette1.R | 77 ++++++- inst/doc/wrMiscVignette1.Rmd | 191 +++++++++++++++---- inst/doc/wrMiscVignette1.html | 408 +++++++++++++++++++++++++++++------------ man/addBeforFileExtension.Rd | 11 - man/addBeforeFileExtension.Rd |only man/adjBy2ptReg.Rd | 41 ++-- man/blockNormalize.Rd |only man/checkGrpOrderSEM.Rd | 31 +-- man/dot-retain1stPart.Rd | 2 man/dot-scale01.Rd | 2 man/dot-scaleXY.Rd | 2 man/exclExtrValues.Rd | 9 man/extrSpcText.Rd | 2 man/findUsableGroupRange.Rd | 28 ++ man/normalizeThis.Rd | 4 man/rowGrpNA.Rd | 72 +++++-- man/scaleXY.Rd | 57 ++++- man/searchLinesAtGivenSlope.Rd | 2 man/vectorDistAngle.Rd |only man/volcanoFilter.Rd |only vignettes/wrMiscVignette1.Rmd | 191 +++++++++++++++---- 46 files changed, 1304 insertions(+), 508 deletions(-)
Title: 'Shiny' Bindings for Designsystemet Components
Description: Provides 'R' wrappers for the Designsystemet component library
<https://designsystemet.no>, enabling use of Norwegian government design system
components in 'Shiny' applications. Includes web components and CSS-based
HTML components with full 'Shiny' input binding support.
Author: Novica Nakov [aut, cre, cph]
Maintainer: Novica Nakov <nnovica@gmail.com>
Diff between shinyds versions 0.2.2 dated 2026-06-04 and 0.3.0 dated 2026-06-08
DESCRIPTION | 10 MD5 | 66 ++-- NAMESPACE | 5 NEWS.md | 6 R/ds-button.R | 36 +- R/ds-dependencies.R | 64 +++ R/ds-details.R | 71 +++- R/ds-misc.R | 68 +++- R/ds-tooltip.R | 19 - README.md | 4 inst/doc/getting-started.R | 62 +++ inst/doc/getting-started.html | 561 +++++++++++++++++++---------------- inst/doc/getting-started.qmd | 90 +++++ inst/doc/reactivity-patterns.R | 45 +- inst/doc/reactivity-patterns.html | 213 ++++++------- inst/doc/reactivity-patterns.qmd | 59 +-- inst/examples/faithful/app.R | 3 inst/examples/showcase/app.R | 95 ++++- inst/www/js/ds-bindings-generated.js | 78 ---- inst/www/js/ds-bindings.js | 12 man/ds_badge.Rd | 13 man/ds_button.Rd | 30 + man/ds_chip_group.Rd |only man/ds_dialog.Rd | 6 man/ds_dropdown.Rd | 6 man/ds_search.Rd | 4 man/ds_theme.Rd |only man/ds_tooltip.Rd | 13 man/hide_ds_dialog.Rd |only man/show_ds_dialog.Rd |only tests/testthat/test-components.R | 32 + tests/testthat/test-dependencies.R | 2 tests/testthat/test-dialog.R |only tests/testthat/test-showcase.R | 27 + tests/testthat/test-theme.R |only vignettes/getting-started.qmd | 90 +++++ vignettes/reactivity-patterns.qmd | 59 +-- 37 files changed, 1185 insertions(+), 664 deletions(-)
Title: Deploy Docs, Apps, and APIs to 'Posit Connect', 'shinyapps.io',
and 'RPubs'
Description: Programmatic deployment interface for 'RPubs',
'shinyapps.io', and 'Posit Connect'. Supported content types include R
Markdown documents, Shiny applications, Plumber APIs, plots, and
static web content.
Author: Aron Atkins [aut, cre],
Toph Allen [aut],
Hadley Wickham [aut],
Jonathan McPherson [aut],
JJ Allaire [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Aron Atkins <aron@posit.co>
Diff between rsconnect versions 1.8.0 dated 2026-04-10 and 1.10.0 dated 2026-06-08
DESCRIPTION | 16 +- MD5 | 98 ++++++------- NAMESPACE | 1 NEWS.md | 42 +++++ R/accounts.R | 169 +++++++++++++++++++---- R/appDependencies.R | 16 +- R/appMetadata.R | 56 +++++++ R/bundle.R | 36 ++++ R/bundleFiles.R | 3 R/bundlePackage.R | 17 +- R/bundlePackageRenv.R | 35 +++- R/client-cloudAuth.R | 19 ++ R/client-connectCloud.R | 33 +++- R/config.R | 12 + R/deployApp.R | 107 +++++++++++++- R/deployments.R | 31 +++- R/http-httr2.R | 2 R/http-libcurl.R | 2 R/http.R | 4 R/servers.R | 17 ++ R/writeManifest.R | 9 + README.md | 2 man/accounts.Rd | 9 - man/appDependencies.Rd | 17 +- man/applications.Rd | 12 - man/connectApiUser.Rd | 9 - man/connectCloudClientCredentials.Rd |only man/connectCloudUser.Rd | 9 - man/deployAPI.Rd | 12 - man/deployApp.Rd | 46 ++++-- man/deployDoc.Rd | 12 - man/deploySite.Rd | 12 - man/deployTFModel.Rd | 12 - man/rsconnect-package.Rd | 3 man/setAccountInfo.Rd | 9 - man/writeManifest.Rd | 32 +++- tests/integration/test-deploy.R | 8 - tests/testthat/_snaps/bundlePackageRenv.md | 12 + tests/testthat/_snaps/deployments.md | 35 ++++ tests/testthat/_snaps/servers.md | 1 tests/testthat/helper.R | 1 tests/testthat/test-accounts.R | 157 +++++++++++++++++++++ tests/testthat/test-appDependencies.R | 5 tests/testthat/test-appMetadata.R | 211 ++++++++++++++++++++++++++++- tests/testthat/test-bundleNodejs.R |only tests/testthat/test-bundlePackageRenv.R | 60 +++++++- tests/testthat/test-client-connectCloud.R | 75 ++++++++++ tests/testthat/test-deployApp.R | 107 ++++++++++++++ tests/testthat/test-deployments.R | 43 +++++ tests/testthat/test-servers.R | 49 ++++++ tests/testthat/test-writeManifest.R | 125 +++++++++++++++++ 51 files changed, 1582 insertions(+), 228 deletions(-)
Title: Bayesian Mixture Log-Normal Survival Model
Description: Bayesian Survival models via the mixture of Log-Normal distribution extends the well-known survival models and accommodates different behaviour over time and considers higher censored survival times. The proposal combines mixture distributions Fruhwirth-Schnatter(2006) <doi:10.1007/s11336-009-9121-4>, and data augmentation techniques Tanner and Wong (1987) <doi:10.1080/01621459.1987.10478458>.
Author: Viviana das Gracas Ribeiro Lobo [cre],
Thais Cristina Oliveira da Fonseca [aut],
Mariane Branco Alves [aut],
Vitor Capdeville [aut],
Victor Hugo Soares Ney [aut]
Maintainer: Viviana das Gracas Ribeiro Lobo <viviana@dme.ufrj.br>
This is a re-admission after prior archival of version 3.1.6 dated 2024-09-03
Diff between lnmixsurv versions 3.1.6 dated 2024-09-03 and 3.1.7 dated 2026-06-08
DESCRIPTION | 28 - MD5 | 98 ++-- NAMESPACE | 1 R/fit_metrics.R |only R/join_empirical_hazard.R | 2 R/simulate_data.R | 2 R/survival_ln_mixture-fit.R | 5 R/survival_ln_mixture-predict.R | 6 R/survival_ln_mixture-print-summary.R | 4 R/survival_ln_mixture_em-fit.R | 63 +- R/survival_ln_mixture_em-methods.R | 8 R/survival_ln_mixture_em-print-summary.R | 2 R/tidiers.R | 32 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/compare.R | 25 - inst/doc/compare.Rmd | 25 - inst/doc/compare.html | 54 +- inst/doc/expectation_maximization.R | 22 inst/doc/expectation_maximization.Rmd | 18 inst/doc/expectation_maximization.html | 94 --- inst/doc/intercept_only.R | 30 - inst/doc/intercept_only.Rmd | 28 - inst/doc/intercept_only.html | 37 - inst/doc/lnmixsurv.R | 55 +- inst/doc/lnmixsurv.Rmd | 15 inst/doc/lnmixsurv.html | 56 +- inst/doc/parallel_computation.R | 20 inst/doc/parallel_computation.Rmd | 20 inst/doc/parallel_computation.html | 29 - man/fit_metrics.Rd |only man/lnmixsurv-package.Rd | 4 man/reexports.Rd | 4 man/tidy.survival_ln_mixture.Rd | 2 tests/testthat/_snaps/plot_fit_on_data.md | 240 +++++----- tests/testthat/_snaps/survival_ln_mixture-print-summary.md | 16 tests/testthat/_snaps/survival_ln_mixture_em-print-summary.md | 64 +- tests/testthat/fixtures/test-fixture.R | 20 tests/testthat/test-join_empirical_hazard.R | 2 tests/testthat/test-plot_fit_on_data.R | 64 +- tests/testthat/test-simulate_data.R | 5 tests/testthat/test-survival_ln_mixture-fit.R | 9 tests/testthat/test-survival_ln_mixture-predict.R | 94 ++- tests/testthat/test-survival_ln_mixture_em-fit.R | 20 tests/testthat/test-survival_ln_mixture_em-predict.R | 102 ++-- tests/testthat/test-tidiers.R | 2 vignettes/compare.Rmd | 25 - vignettes/expectation_maximization.Rmd | 18 vignettes/intercept_only.Rmd | 28 - vignettes/lnmixsurv.Rmd | 15 vignettes/parallel_computation.Rmd | 20 51 files changed, 790 insertions(+), 743 deletions(-)
Title: Core Survey Analysis Infrastructure
Description: A modern, 'S7'-based foundation for survey analysis
spanning both probability and non-probability samples. Probability
sample designs include Taylor series linearization, replicate
weights (BRR, Fay, jackknife, bootstrap), and two-phase
estimation, following 'Lumley' (2004) <doi:10.18637/jss.v009.i08>.
Non-probability sample designs support bootstrap and jackknife
variance estimation for opt-in panels and convenience samples.
Provides a unified estimator interface for means, frequencies,
totals, quantiles, ratios, correlations, regression, and t-tests,
with weighted 'polychoric' and 'polyserial' correlation following
'Mannan' (2025) <doi:10.2139/ssrn.6580480>. A metadata system
preserves 'haven'-style variable labels, value labels, and
question-preface attributes through all operations. Uses a
'tidyselect' interface throughout.
Author: Jacob Dennen [aut, cre, cph] ,
Thomas Lumley [ctb, cph]
Maintainer: Jacob Dennen <jdenn0514@gmail.com>
Diff between surveycore versions 0.8.3 dated 2026-05-05 and 1.0.0 dated 2026-06-08
DESCRIPTION | 35 MD5 | 320 ++-- NAMESPACE | 7 NEWS.md | 116 + R/analysis-corr-helpers.R | 20 R/analysis-corr-latent.R | 58 R/analysis-corr.R | 60 R/analysis-covariance-helpers.R | 44 R/analysis-covariance.R | 15 R/analysis-diffs-helpers.R | 154 + R/analysis-diffs.R | 158 + R/analysis-effective-n.R |only R/analysis-freqs-helpers.R | 48 R/analysis-freqs.R | 15 R/analysis-helpers.R | 67 R/analysis-means-helpers.R | 80 - R/analysis-means.R | 37 R/analysis-meta.R | 46 R/analysis-quantiles-helpers.R | 3 R/analysis-quantiles.R | 33 R/analysis-ratios.R | 12 R/analysis-t-test.R | 148 + R/analysis-totals-helpers.R | 74 R/analysis-totals.R | 21 R/analysis-variance-helpers.R | 34 R/analysis-variance.R | 31 R/calibration.R |only R/core-classes.R | 193 +- R/core-constructors.R | 599 ++++++- R/core-metadata.R | 647 +++++++- R/core-validators.R | 28 R/data.R | 104 + R/glm-anova-dispatch.R | 35 R/glm-anova.R | 62 R/glm-clean.R | 21 R/glm-methods.R | 15 R/glm.R | 72 R/metadata-infer.R | 11 R/methods-compat.R | 2 R/methods-conversion.R | 55 R/methods-print.R | 60 R/srr-stats-standards.R | 8 R/survey-collection.R | 78 R/update-design.R | 59 R/utils.R | 45 R/variance-replicate.R | 31 R/variance-taylor.R | 72 R/variance-twophase.R | 9 R/zzz.R | 5 README.md | 2 data/ca_api_2000.rda |only inst/doc/creating-survey-objects.R | 25 inst/doc/creating-survey-objects.Rmd | 359 ++-- inst/doc/creating-survey-objects.html | 561 +++---- inst/doc/getting-started.R | 168 +- inst/doc/getting-started.Rmd | 434 +++-- inst/doc/getting-started.html | 1203 +++++++++++---- inst/doc/surveycore-vs-survey.html | 375 +++- man/SURVEYCORE_DOMAIN_COL.Rd | 2 man/acs_pums_wy.Rd | 3 man/add_survey.Rd | 19 man/anova.survey_glm_fit.Rd |only man/as_caldata.Rd |only man/as_survey.Rd | 56 man/as_survey_collection.Rd | 21 man/as_survey_nonprob.Rd | 206 ++ man/as_survey_replicate.Rd | 50 man/as_survey_twophase.Rd | 28 man/as_svydesign.Rd | 10 man/as_tbl_svy.Rd | 19 man/ca_api_2000.Rd |only man/classify_question_type.Rd | 21 man/clean.Rd | 11 man/dot-get_design_vars_flat.Rd | 1 man/extract_higher_is.Rd |only man/extract_metadata.Rd | 14 man/extract_missing_codes.Rd | 17 man/extract_question_preface.Rd | 14 man/extract_reverse_coded.Rd |only man/extract_sata.Rd | 14 man/extract_universe.Rd | 14 man/extract_val_labels.Rd | 17 man/extract_var_label.Rd | 14 man/extract_var_note.Rd | 14 man/from_svydesign.Rd | 12 man/from_tbl_svy.Rd | 16 man/get_anova.Rd | 23 man/get_corr.Rd | 56 man/get_covariance.Rd | 2 man/get_diffs.Rd | 34 man/get_effective_n.Rd |only man/get_freqs.Rd | 16 man/get_means.Rd | 23 man/get_pairwise.Rd | 22 man/get_quantiles.Rd | 36 man/get_ratios.Rd | 7 man/get_t_test.Rd | 22 man/get_totals.Rd | 22 man/get_variance.Rd | 17 man/infer_question_prefaces.Rd | 15 man/meta.Rd | 29 man/ns_wave1.Rd | 2 man/print.survey_anova.Rd |only man/print.survey_diffs.Rd | 1 man/print.survey_effective_n.Rd |only man/print.survey_pairwise.Rd |only man/print.survey_result.Rd | 17 man/print.survey_t_test.Rd |only man/remove_survey.Rd | 22 man/set_collection_id.Rd | 10 man/set_collection_if_missing_var.Rd | 10 man/set_higher_is.Rd |only man/set_missing_codes.Rd | 16 man/set_question_preface.Rd | 14 man/set_reverse_coded.Rd |only man/set_sata.Rd | 14 man/set_universe.Rd | 16 man/set_val_labels.Rd | 14 man/set_var_label.Rd | 21 man/set_var_note.Rd | 14 man/survey_collection.Rd | 10 man/survey_data.Rd | 24 man/survey_glm.Rd | 17 man/survey_glm_fit.Rd | 26 man/survey_metadata.Rd | 17 man/survey_nonprob.Rd | 63 man/survey_replicate.Rd | 47 man/survey_taylor.Rd | 37 man/survey_twophase.Rd | 13 man/survey_weighting_history.Rd | 16 man/update_design.Rd | 25 tests/testthat/_snaps/analysis-corr-latent-variance.md | 2 tests/testthat/_snaps/analysis-corr-latent.md | 6 tests/testthat/_snaps/analysis-corr.md | 20 tests/testthat/_snaps/analysis-diffs.md | 48 tests/testthat/_snaps/analysis-helpers.md | 22 tests/testthat/_snaps/analysis-t-test.md | 2 tests/testthat/_snaps/calibration.md |only tests/testthat/_snaps/constructors.md | 258 +++ tests/testthat/_snaps/effective-n.md |only tests/testthat/_snaps/glm-methods.md | 19 tests/testthat/_snaps/glm.md | 21 tests/testthat/_snaps/metadata-system.md | 141 + tests/testthat/_snaps/methods-print.md | 285 +++ tests/testthat/_snaps/nonprob-bootstrap-variance.md |only tests/testthat/_snaps/survey-collection.md | 9 tests/testthat/_snaps/update-design.md |only tests/testthat/_snaps/validators.md |only tests/testthat/_snaps/variance-taylor.md |only tests/testthat/helper-test-data.R | 8 tests/testthat/test-analysis-corr-latent.R | 518 +++--- tests/testthat/test-analysis-corr.R | 242 +++ tests/testthat/test-analysis-diffs.R | 471 +++++ tests/testthat/test-analysis-helpers.R | 104 + tests/testthat/test-analysis-t-test.R | 292 +++ tests/testthat/test-calibration.R |only tests/testthat/test-constructors.R | 912 +++++++++++ tests/testthat/test-effective-n.R |only tests/testthat/test-glm-methods.R | 163 +- tests/testthat/test-glm-numerical.R | 7 tests/testthat/test-glm.R | 197 ++ tests/testthat/test-metadata-system.R | 1353 ++++++++++++++--- tests/testthat/test-methods-print.R | 281 +++ tests/testthat/test-nonprob-bootstrap-variance.R |only tests/testthat/test-s7-classes.R | 552 ++++-- tests/testthat/test-survey-collection.R | 63 tests/testthat/test-update-design.R | 21 tests/testthat/test-utils.R | 11 tests/testthat/test-validators.R | 72 tests/testthat/test-variance-taylor.R | 728 ++++++--- vignettes/creating-survey-objects.Rmd | 359 ++-- vignettes/getting-started.Rmd | 434 +++-- vignettes/references.bib | 18 173 files changed, 12263 insertions(+), 3733 deletions(-)
Title: Multiple Imputation in Cluster Analysis
Description: Implementation of a framework for cluster analysis with selection
of the final number of clusters and an optional variable selection
procedure. The package is designed to integrate the results of multiple
imputed datasets while accounting for the uncertainty that the imputations
introduce in the final results. In addition, the package can also be used
for a cluster analysis of the complete cases of a single dataset. The
package also includes specific methods to summarize and plot the results.
The methods are described in Basagana et al. (2013) <doi:10.1093/aje/kws289>.
Author: Jose Barrera-Gomez [aut, cre] ,
Xavier Basagana [aut]
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between miclust versions 1.2.8 dated 2022-02-07 and 1.3.0 dated 2026-06-08
miclust-1.2.8/miclust/R/plot.miclust.R |only miclust-1.2.8/miclust/R/print.miclust.R |only miclust-1.2.8/miclust/R/print.summary.miclust.R |only miclust-1.2.8/miclust/man/assignprobandkappas.Rd |only miclust-1.2.8/miclust/man/centerdata.Rd |only miclust-1.2.8/miclust/man/centroid.Rd |only miclust-1.2.8/miclust/man/doclusterkmeans.Rd |only miclust-1.2.8/miclust/man/doclusterkmeansbackward.Rd |only miclust-1.2.8/miclust/man/doclusterkmeansforward.Rd |only miclust-1.2.8/miclust/man/doclusterkmeansforwardhc.Rd |only miclust-1.2.8/miclust/man/doclusterkmeansforwardrand.Rd |only miclust-1.2.8/miclust/man/doclusterkmeansnone.Rd |only miclust-1.2.8/miclust/man/euclidean.Rd |only miclust-1.2.8/miclust/man/getcritcfkcca.Rd |only miclust-1.2.8/miclust/man/getinitialcentroids.Rd |only miclust-1.2.8/miclust/man/manhattan.Rd |only miclust-1.2.8/miclust/man/plot.miclust.Rd |only miclust-1.2.8/miclust/man/print.miclust.Rd |only miclust-1.2.8/miclust/man/print.summary.miclust.Rd |only miclust-1.2.8/miclust/man/relabelclusters.Rd |only miclust-1.2.8/miclust/man/standardizedata.Rd |only miclust-1.3.0/miclust/DESCRIPTION | 29 miclust-1.3.0/miclust/MD5 | 89 +- miclust-1.3.0/miclust/NEWS.md | 42 + miclust-1.3.0/miclust/R/assignprobandkappas.R | 14 miclust-1.3.0/miclust/R/centerdata.R | 4 miclust-1.3.0/miclust/R/centroid.R | 6 miclust-1.3.0/miclust/R/doclusterkmeans.R | 2 miclust-1.3.0/miclust/R/doclusterkmeansbackward.R | 10 miclust-1.3.0/miclust/R/doclusterkmeansforward.R | 2 miclust-1.3.0/miclust/R/doclusterkmeansforwardhc.R | 6 miclust-1.3.0/miclust/R/doclusterkmeansforwardrand.R | 6 miclust-1.3.0/miclust/R/doclusterkmeansnone.R | 6 miclust-1.3.0/miclust/R/euclidean.R | 2 miclust-1.3.0/miclust/R/get_miclust_verbose.R |only miclust-1.3.0/miclust/R/getcritcfkcca.R | 2 miclust-1.3.0/miclust/R/getdata.R | 50 - miclust-1.3.0/miclust/R/getinitialcentroids.R | 2 miclust-1.3.0/miclust/R/getvariablesfrequency.R | 23 miclust-1.3.0/miclust/R/kappaunweighted.R |only miclust-1.3.0/miclust/R/manhattan.R | 6 miclust-1.3.0/miclust/R/miclust-package.R | 27 miclust-1.3.0/miclust/R/miclust.R | 454 +++++++++++++-- miclust-1.3.0/miclust/R/minhanes.R | 14 miclust-1.3.0/miclust/R/relabelclusters.R | 16 miclust-1.3.0/miclust/R/standardizedata.R | 4 miclust-1.3.0/miclust/R/summary.miclust.R | 329 ++++++++-- miclust-1.3.0/miclust/README.md | 105 --- miclust-1.3.0/miclust/data/minhanes.RData |binary miclust-1.3.0/miclust/man/figures/README-ex1plot-1.png |binary miclust-1.3.0/miclust/man/figures/README-ex1selvar-1.png |binary miclust-1.3.0/miclust/man/getdata.Rd | 48 - miclust-1.3.0/miclust/man/getvariablesfrequency.Rd | 17 miclust-1.3.0/miclust/man/miclust-package.Rd | 33 - miclust-1.3.0/miclust/man/miclust.Rd | 116 ++- miclust-1.3.0/miclust/man/minhanes.Rd | 14 miclust-1.3.0/miclust/man/summary.miclust.Rd | 64 +- 57 files changed, 1063 insertions(+), 479 deletions(-)
Title: Proper Scoring Rules for Missing Value Imputation
Description: Provides tools for evaluating and ranking missing value
imputation methods using proper scoring rules.
Implements the Energy-I-Score and the DR-I-Score for the assessment
of deterministic, stochastic and multiple imputation methods
for numerical and mixed datasets, following Näf et al. (2022)
<doi:10.48550/arXiv.2106.03742> and Näf et al. (2025)
<doi:10.48550/arXiv.2507.11297>.
Author: Krystyna Grzesiak [aut, cre] ,
Loris Michel [aut, ctb],
Meta-Lina Spohn [aut, ctb],
Jeffrey Naef [aut, ctb]
Maintainer: Krystyna Grzesiak <krygrz11@gmail.com>
This is a re-admission after prior archival of version 1.1.0 dated 2022-01-04
Diff between Iscores versions 1.1.0 dated 2022-01-04 and 1.2.0 dated 2026-06-08
Iscores-1.1.0/Iscores/R/Iscores.R |only Iscores-1.1.0/Iscores/R/helpers.R |only Iscores-1.1.0/Iscores/man/Iscores.Rd |only Iscores-1.1.0/Iscores/man/doevaluation.Rd |only Iscores-1.1.0/Iscores/man/sample.vars.proj.Rd |only Iscores-1.2.0/Iscores/DESCRIPTION | 50 +++ Iscores-1.2.0/Iscores/MD5 | 65 +++- Iscores-1.2.0/Iscores/NAMESPACE | 29 +- Iscores-1.2.0/Iscores/R/DR-I-Score.R |only Iscores-1.2.0/Iscores/R/I-Score.R |only Iscores-1.2.0/Iscores/R/energy-I-Score.R |only Iscores-1.2.0/Iscores/R/energy-I-Score_cat.R |only Iscores-1.2.0/Iscores/R/energy_dist.R |only Iscores-1.2.0/Iscores/R/random_na_data.R |only Iscores-1.2.0/Iscores/README.md | 240 ++++++++++++++---- Iscores-1.2.0/Iscores/build |only Iscores-1.2.0/Iscores/inst |only Iscores-1.2.0/Iscores/man/DR_IScore.Rd |only Iscores-1.2.0/Iscores/man/class.balancing.Rd | 11 Iscores-1.2.0/Iscores/man/combine2Forests.Rd | 13 Iscores-1.2.0/Iscores/man/combineForests.Rd | 11 Iscores-1.2.0/Iscores/man/compare_Iscores.Rd |only Iscores-1.2.0/Iscores/man/compute_drScore.Rd | 13 Iscores-1.2.0/Iscores/man/densityRatioScore.Rd | 51 ++- Iscores-1.2.0/Iscores/man/do_one_hot.Rd |only Iscores-1.2.0/Iscores/man/edistance.Rd |only Iscores-1.2.0/Iscores/man/energy_IScore.Rd |only Iscores-1.2.0/Iscores/man/energy_Iscore_cat.Rd |only Iscores-1.2.0/Iscores/man/energy_Iscore_num.Rd |only Iscores-1.2.0/Iscores/man/exp_imputation.Rd |only Iscores-1.2.0/Iscores/man/factor_to_numeric.Rd |only Iscores-1.2.0/Iscores/man/factor_to_onehot.Rd |only Iscores-1.2.0/Iscores/man/get_pattern_data.Rd |only Iscores-1.2.0/Iscores/man/median_mode_imputation.Rd |only Iscores-1.2.0/Iscores/man/merge_singleton_patterns.Rd |only Iscores-1.2.0/Iscores/man/norm_imputation.Rd |only Iscores-1.2.0/Iscores/man/random_mcar_data.Rd |only Iscores-1.2.0/Iscores/man/random_mcar_mixed_data.Rd |only Iscores-1.2.0/Iscores/man/sample_vars_proj.Rd |only Iscores-1.2.0/Iscores/man/truncProb.Rd | 3 Iscores-1.2.0/Iscores/tests |only Iscores-1.2.0/Iscores/vignettes |only 42 files changed, 366 insertions(+), 120 deletions(-)
Title: Parametric Time-to-Event Analysis with Variable Incubation
Phases
Description: Fit parametric models for time-to-event data that show an initial
'incubation period', i.e. a variable delay phase where no events occur.
The delayed Weibull distribution serves as the foundational data model.
For parameter estimation, different flavours of maximum likelihood
estimation ('MLE') and the method of maximum product of spacings estimation
('MPSE') are implemented. Bootstrap confidence intervals for parameters and
significance tests in a two group setting are provided.
Author: Matthias Kuhn [aut, cre, cph]
Maintainer: Matthias Kuhn <matthias.kuhn@tu-dresden.de>
Diff between incubate versions 1.4.0 dated 2026-03-22 and 1.4.1 dated 2026-06-08
incubate-1.4.0/incubate/R/integration.R |only incubate-1.4.1/incubate/DESCRIPTION | 23 incubate-1.4.1/incubate/MD5 | 65 - incubate-1.4.1/incubate/NEWS.md | 15 incubate-1.4.1/incubate/R/S3_integration.R |only incubate-1.4.1/incubate/R/cpp11.R | 8 incubate-1.4.1/incubate/R/data.R | 14 incubate-1.4.1/incubate/R/delay.R | 150 +++ incubate-1.4.1/incubate/R/delay_estimation.R | 381 ++++++---- incubate-1.4.1/incubate/R/delay_test.R | 31 incubate-1.4.1/incubate/data/measles_sailer.rda |binary incubate-1.4.1/incubate/inst/doc/delayed-dist.Rmd | 124 ++- incubate-1.4.1/incubate/inst/doc/delayed-dist.html | 181 +++- incubate-1.4.1/incubate/inst/scripts/simul_MLEweights.R | 67 + incubate-1.4.1/incubate/man/DelayedExponential.Rd | 4 incubate-1.4.1/incubate/man/DelayedWeibull.Rd | 2 incubate-1.4.1/incubate/man/bsDataStep.Rd | 20 incubate-1.4.1/incubate/man/coef.incubate_fit.Rd | 2 incubate-1.4.1/incubate/man/confint.incubate_fit.Rd | 9 incubate-1.4.1/incubate/man/delay_fit.Rd | 6 incubate-1.4.1/incubate/man/getVariance.Rd |only incubate-1.4.1/incubate/man/incubate.Rd | 7 incubate-1.4.1/incubate/man/lines.incubate_fit.Rd | 2 incubate-1.4.1/incubate/man/logLik.incubate_fit.Rd | 2 incubate-1.4.1/incubate/man/long2017.Rd | 4 incubate-1.4.1/incubate/man/measles_sailer.Rd | 10 incubate-1.4.1/incubate/man/plot.incubate_fit.Rd | 18 incubate-1.4.1/incubate/man/power_diff.Rd | 31 incubate-1.4.1/incubate/man/transform.incubate_fit.Rd | 2 incubate-1.4.1/incubate/src/cpp11.cpp | 20 incubate-1.4.1/incubate/src/utils.cpp | 89 ++ incubate-1.4.1/incubate/tests/testthat/test-delay.R | 100 +- incubate-1.4.1/incubate/tests/testthat/test-delay_estimation.R | 124 +++ incubate-1.4.1/incubate/tests/testthat/test-utils.R | 100 ++ incubate-1.4.1/incubate/vignettes/delayed-dist.Rmd | 124 ++- 35 files changed, 1258 insertions(+), 477 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane [aut, cre] ,
John W. Emerson [aut],
Peter Haverty [aut],
Charles Determan [aut]
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.6.4 dated 2024-01-09 and 4.6.6 dated 2026-06-08
DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- NEWS | 10 ++++++++++ R/hello-bigmemory.R | 7 +++---- configure | 2 +- tests/testthat/test_readonly.R | 20 +++++++++++++------- 6 files changed, 38 insertions(+), 22 deletions(-)
Title: Data Thinning of Species Occurrences in Environmental Space
Description: A suite of tools to mitigate sampling bias in species occurrence
records by thinning data in the environmental space (E-space). This process
can improve the accuracy and precision of species distribution models (SDM,
also known as ecological niche models, ENM). The package offers a
data-driven protocol to determine thinning parameters using kernel-density
bandwidth selection. Two thinning methods are provided (stochastic and
deterministic) to reduce over-sampled environmental conditions and down-weight
outlier observations. The name 'bean' reflects the core principle of the
method: each 'pod' (a grid cell in E-space) is allowed to contain only a
limited number of 'beans' (occurrence points). See Silverman (1986,
ISBN:978-0-412-24620-3) and Rousseeuw and Leroy (2003,
ISBN:978-0-471-48855-2) for the underlying statistical methods.
Author: Paanwaris Paansri [cre, aut] ,
Luis E. Escobar [aut, ctb]
Maintainer: Paanwaris Paansri <paanwaris@vt.edu>
Diff between bean versions 0.2.0 dated 2026-05-30 and 0.2.1 dated 2026-06-08
bean-0.2.0/bean/R/methods.R |only bean-0.2.0/bean/man/predict.bean_ellipsoid.Rd |only bean-0.2.1/bean/DESCRIPTION | 6 bean-0.2.1/bean/MD5 | 26 +- bean-0.2.1/bean/NAMESPACE | 1 bean-0.2.1/bean/NEWS.md | 32 +++ bean-0.2.1/bean/R/fit_ellipsoid.R | 76 +++++++ bean-0.2.1/bean/README.md | 51 +++-- bean-0.2.1/bean/data/origin_ellipse.rda |binary bean-0.2.1/bean/inst/doc/niche-modeling.R | 131 ++++-------- bean-0.2.1/bean/inst/doc/niche-modeling.Rmd | 174 ++++++----------- bean-0.2.1/bean/inst/doc/niche-modeling.html | 202 ++++++++------------ bean-0.2.1/bean/man/fit_ellipsoid.Rd | 36 +++ bean-0.2.1/bean/tests/testthat/test-fit_ellipsoid.R | 48 +++- bean-0.2.1/bean/vignettes/niche-modeling.Rmd | 174 ++++++----------- 15 files changed, 483 insertions(+), 474 deletions(-)
Title: Testing Differences Between Families of Trees
Description: Perform test to detect differences in structure between families of
trees. The method is based on cophenetic distances and aggregated
Student's tests.
Author: Nathalie Vialaneix [aut, cre] ,
Gwendaelle Cardenas [aut],
Marie Chavent [aut] ,
Sylvain Foissac [aut] ,
Elise Maigne [aut],
Pierre Neuvial [aut] ,
Nathanael Randriamihamison [aut]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between treediff versions 0.2.2 dated 2026-01-30 and 0.2.3 dated 2026-06-08
treediff-0.2.2/treediff/man/HiCDOCDataSet.Rd |only treediff-0.2.3/treediff/DESCRIPTION | 14 +- treediff-0.2.3/treediff/MD5 | 12 +- treediff-0.2.3/treediff/NAMESPACE | 14 +- treediff-0.2.3/treediff/NEWS.md | 6 + treediff-0.2.3/treediff/R/HiC2Tree.R | 94 ++++++++++------- treediff-0.2.3/treediff/man/HiCDataSet.Rd |only treediff-0.2.3/treediff/tests/testthat/test-HiC2Tree.R | 12 +- 8 files changed, 89 insertions(+), 63 deletions(-)
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 0.4.1 dated 2026-04-07 and 0.5.0 dated 2026-06-08
DESCRIPTION | 9 +- MD5 | 11 +-- NEWS.md | 14 ++++ R/packages.R | 129 ++++++++++++++++++++++++++++++++--------- R/version.R | 4 - man/shinylive-package.Rd | 1 tests/testthat/test-packages.R |only 7 files changed, 131 insertions(+), 37 deletions(-)
More information about NeutroRCDsAnalysis at CRAN
Permanent link
More information about FastSegmentation at CRAN
Permanent link
Title: Bootstrap Hyperparameter Selection for PLS Models and Extensions
Description: Several implementations of non-parametric stable bootstrap-based techniques to determine the numbers of components for Partial Least Squares linear or generalized linear regression models as well as and sparse Partial Least Squares linear or generalized linear regression models. The package collects techniques that were published in a book chapter (Magnanensi et al. 2016, 'The Multiple Facets of Partial Least Squares and Related Methods', <doi:10.1007/978-3-319-40643-5_18>) and two articles (Magnanensi et al. 2017, 'Statistics and Computing', <doi:10.1007/s11222-016-9651-4>) and (Magnanensi et al. 2021, 'Frontiers in Applied Mathematics and Statistics', <doi:10.3389/fams.2021.693126>).
Author: Frederic Bertrand [cre, aut] ,
Jeremy Magnanensi [aut],
Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between bootPLS versions 1.1.0 dated 2025-09-13 and 1.2.0 dated 2026-06-08
DESCRIPTION | 14 +++++----- MD5 | 21 ++++++++------- NEWS.md | 6 +++- R/YTplsR.R | 8 ++--- R/internal-bootPLS.R | 46 +++++++++++++++++++++++++++++++++- R/sgpls_bootYT.R | 12 ++++---- R/spls.R | 12 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/doc/UseNbcomp.html | 9 +++--- man/bootPLS-package.Rd | 4 +- tests/testthat/test-confints-compat.R |only 12 files changed, 91 insertions(+), 41 deletions(-)
More information about aisdk.providers at CRAN
Permanent link
Title: Estimate Step Counts from 'Accelerometry' Data
Description: Interfaces the 'stepcount' Python
module <https://github.com/OxWearables/stepcount> to estimate
step counts and other activities from 'accelerometry' data.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between stepcount versions 0.3.2 dated 2024-10-02 and 0.5.0 dated 2026-06-08
stepcount-0.3.2/stepcount/R/conda_create_env.R |only stepcount-0.3.2/stepcount/R/use_stepcount_condaenv.R |only stepcount-0.3.2/stepcount/man/conda_create_walking_env.Rd |only stepcount-0.3.2/stepcount/man/pipe.Rd |only stepcount-0.3.2/stepcount/man/use_stepcount_condaenv.Rd |only stepcount-0.5.0/stepcount/DESCRIPTION | 17 stepcount-0.5.0/stepcount/MD5 | 36 - stepcount-0.5.0/stepcount/NAMESPACE | 7 stepcount-0.5.0/stepcount/NEWS.md | 10 stepcount-0.5.0/stepcount/R/aaa_base.R | 20 stepcount-0.5.0/stepcount/R/install_stepcount.R | 30 - stepcount-0.5.0/stepcount/R/sc_read.R | 9 stepcount-0.5.0/stepcount/R/stepcount.R | 61 +- stepcount-0.5.0/stepcount/R/utils-pipe.R | 12 stepcount-0.5.0/stepcount/R/zzz.R |only stepcount-0.5.0/stepcount/README.md | 67 -- stepcount-0.5.0/stepcount/man/sc_read.Rd | 9 stepcount-0.5.0/stepcount/man/stepcount.Rd | 11 stepcount-0.5.0/stepcount/man/stepcount_setup.Rd | 25 stepcount-0.5.0/stepcount/tests/testthat.R | 7 stepcount-0.5.0/stepcount/tests/testthat/helper-fakes.R |only stepcount-0.5.0/stepcount/tests/testthat/test-full_run.R |only stepcount-0.5.0/stepcount/tests/testthat/test-stepcount.R | 359 +++++++++++--- 23 files changed, 445 insertions(+), 235 deletions(-)
Title: Help with Preparing a New Version of an R Package
Description: Helps to prepare a release. Before releasing an R package it is important to update the DESCRIPTION file and the changelog. This package prepares these files and also updates the versions according to the branches. It relies heavily on the 'desc' packages.
Author: Tanguy Barthelemy [aut, cre, art]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between releaser versions 1.1.0 dated 2026-03-10 and 1.1.1 dated 2026-06-08
DESCRIPTION | 8 +-- MD5 | 16 +++--- NEWS.md | 10 +++ R/cran-check.R | 56 +++++++++++++-------- R/get_information.R | 15 +++-- man/check_docs.Rd | 3 - man/get_github_branches.Rd | 3 - man/get_latest_version.Rd | 3 - tests/testthat/test-get_different_future_version.R | 4 + 9 files changed, 76 insertions(+), 42 deletions(-)
Title: Conditional Forecasting and Scenario Analysis Using VAR Models
Description: Provides tools for interpretable conditional forecasting and scenario analysis in reduced-form vector autoregressive (VAR) models.
Implements a Kalman smoothing framework to generate forecasts under
path restrictions on selected variables. The package enables decomposition
of conditional forecasts into variable-specific contributions, and extraction
of observation weights. It also computes measures of overall and marginal variable importance to enhance
the economic interpretation of forecast revisions. The framework is
structurally agnostic and suited for policy analysis, stress testing,
and macro-financial applications. The methodology is described in more detail in
Caspi and Ginker (2026) <doi:10.13140/RG.2.2.25225.51040>.
Author: Tim Ginker [aut, cre]
Maintainer: Tim Ginker <tim.ginker@gmail.com>
Diff between cforecast versions 0.1.0 dated 2026-03-09 and 0.1.1 dated 2026-06-08
DESCRIPTION | 18 - MD5 | 38 +- NAMESPACE | 3 NEWS.md | 8 R/cforecast.R | 95 +++++ R/cforecast_composition.R | 10 R/fct_weights.R | 12 R/state_space_representation.R | 6 R/variable_importance_stat.R | 17 - README.md | 511 +++++++++++++++---------------- man/cforecast.Rd | 60 ++- man/cforecast_composition.Rd | 3 man/fct_weights.Rd | 9 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/state_space_representation.Rd | 6 man/variable_importance_stat.Rd | 15 20 files changed, 488 insertions(+), 323 deletions(-)
More information about OlinkAnalyzeVignettes at CRAN
Permanent link
Title: Building Augmented Data to Run Multi-State Models with 'msm'
Package
Description: A fast and general method for restructuring classical longitudinal
observational data into augmented transition data suitable for multi-state
modeling with the 'msm' package. Works with any longitudinal data where
subjects accumulate repeated observations with start and end times and an
optional terminal outcome. Methods are described in Grossetti, Ieva and
Paganoni (2018) <doi:10.1007/s10729-017-9400-z>.
Author: Francesco Grossetti [aut, cre]
Maintainer: Francesco Grossetti <francesco.grossetti@unibocconi.it>
This is a re-admission after prior archival of version 2.0.1 dated 2021-04-12
Diff between msmtools versions 2.0.1 dated 2021-04-12 and 2.2.1 dated 2026-06-08
msmtools-2.0.1/msmtools/man/msmtools.Rd |only msmtools-2.0.1/msmtools/tests/testthat/test_dataset_return.R |only msmtools-2.2.1/msmtools/DESCRIPTION | 33 msmtools-2.2.1/msmtools/MD5 | 56 msmtools-2.2.1/msmtools/NAMESPACE | 30 msmtools-2.2.1/msmtools/NEWS.md | 408 ++++ msmtools-2.2.1/msmtools/R/augment-helpers.R |only msmtools-2.2.1/msmtools/R/augment.R | 903 ++-------- msmtools-2.2.1/msmtools/R/hosp.R | 49 msmtools-2.2.1/msmtools/R/msmtools.R | 23 msmtools-2.2.1/msmtools/R/onAttach.R | 12 msmtools-2.2.1/msmtools/R/plot-helpers.R |only msmtools-2.2.1/msmtools/R/polish.R | 379 ++-- msmtools-2.2.1/msmtools/R/preprocess-helpers.R |only msmtools-2.2.1/msmtools/R/prevplot.R | 327 ++- msmtools-2.2.1/msmtools/R/survplot.R | 449 ++--- msmtools-2.2.1/msmtools/R/verbosity.R |only msmtools-2.2.1/msmtools/README.md | 148 + msmtools-2.2.1/msmtools/build/partial.rdb |only msmtools-2.2.1/msmtools/build/vignette.rds |binary msmtools-2.2.1/msmtools/inst/doc/msmtools.Rmd | 550 +----- msmtools-2.2.1/msmtools/inst/doc/msmtools.html | 930 +++++------ msmtools-2.2.1/msmtools/man/augment.Rd | 275 +-- msmtools-2.2.1/msmtools/man/hosp.Rd | 48 msmtools-2.2.1/msmtools/man/msmtools-package.Rd |only msmtools-2.2.1/msmtools/man/polish.Rd | 112 - msmtools-2.2.1/msmtools/man/prevplot.Rd | 138 + msmtools-2.2.1/msmtools/man/survplot.Rd | 178 +- msmtools-2.2.1/msmtools/tests/testthat/fixtures |only msmtools-2.2.1/msmtools/tests/testthat/helper-msmtools.R |only msmtools-2.2.1/msmtools/tests/testthat/test-augment.R |only msmtools-2.2.1/msmtools/tests/testthat/test-invariants.R |only msmtools-2.2.1/msmtools/tests/testthat/test-plots.R |only msmtools-2.2.1/msmtools/tests/testthat/test-polish.R |only msmtools-2.2.1/msmtools/vignettes/msmtools.Rmd | 550 +----- msmtools-2.2.1/msmtools/vignettes/references.bib | 10 36 files changed, 2609 insertions(+), 2999 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.5.4 dated 2025-11-16 and 3.0.0 dated 2026-06-08
mizer-2.5.4/mizer/inst/doc/mizer_vignette.pdf |only mizer-2.5.4/mizer/man/animateSpectra.Rd |only mizer-2.5.4/mizer/man/finalNOther.Rd |only mizer-2.5.4/mizer/man/getComponent.Rd |only mizer-2.5.4/mizer/man/get_required_reproduction.Rd |only mizer-2.5.4/mizer/man/plot-MizerParams-missing-method.Rd |only mizer-2.5.4/mizer/man/summary-MizerParams-method.Rd |only mizer-2.5.4/mizer/man/summary-MizerSim-method.Rd |only mizer-2.5.4/mizer/tests/testthat/_snaps/age_mat.md |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-feeding-level-critical.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-feeding-level.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-single-growth-curve.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-yield-by-gear.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plot-yield.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plotfishing-mortality.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plotfmort-truncated.svg |only mizer-2.5.4/mizer/tests/testthat/_snaps/plots/plotpredation-mortality.svg |only mizer-2.5.4/mizer/vignettes/mizer_vignette.html |only mizer-2.5.4/mizer/vignettes/vignette_images |only mizer-3.0.0/mizer/DESCRIPTION | 44 mizer-3.0.0/mizer/MD5 | 756 + mizer-3.0.0/mizer/NAMESPACE | 286 mizer-3.0.0/mizer/NEWS.md | 412 mizer-3.0.0/mizer/R/ArraySpeciesBySize-class.R |only mizer-3.0.0/mizer/R/ArrayTimeBySpecies-class.R |only mizer-3.0.0/mizer/R/ArrayTimeBySpeciesBySize-class.R |only mizer-3.0.0/mizer/R/MizerParams-class.R | 287 mizer-3.0.0/mizer/R/MizerSim-class.R | 317 mizer-3.0.0/mizer/R/RcppExports.R | 4 mizer-3.0.0/mizer/R/age_mat.R | 74 mizer-3.0.0/mizer/R/animateSpectra.R | 317 mizer-3.0.0/mizer/R/background.R |only mizer-3.0.0/mizer/R/calibrate.R | 44 mizer-3.0.0/mizer/R/compareParams.R | 80 mizer-3.0.0/mizer/R/customFunction.R | 2 mizer-3.0.0/mizer/R/data.R | 6 mizer-3.0.0/mizer/R/defaults_edition.R | 17 mizer-3.0.0/mizer/R/deprecated.R | 60 mizer-3.0.0/mizer/R/diffusion.R |only mizer-3.0.0/mizer/R/extension.R | 253 mizer-3.0.0/mizer/R/generic_methods.R |only mizer-3.0.0/mizer/R/getRequiredRDD.R |only mizer-3.0.0/mizer/R/get_initial_n.R | 60 mizer-3.0.0/mizer/R/helpers.R | 77 mizer-3.0.0/mizer/R/indicator_functions.R |only mizer-3.0.0/mizer/R/manipulate_species.R | 434 - mizer-3.0.0/mizer/R/match.R | 102 mizer-3.0.0/mizer/R/matchGrowth.R | 40 mizer-3.0.0/mizer/R/mizer-package.R | 2 mizer-3.0.0/mizer/R/newMultispeciesParams.R | 151 mizer-3.0.0/mizer/R/newSingleSpeciesParams.R | 35 mizer-3.0.0/mizer/R/numerical_methods.R |only mizer-3.0.0/mizer/R/plotBiomassObservedVsModel.R | 50 mizer-3.0.0/mizer/R/plotYieldObservedVsModel.R | 59 mizer-3.0.0/mizer/R/plots.R | 2645 +++++- mizer-3.0.0/mizer/R/pred_kernel_funcs.R | 8 mizer-3.0.0/mizer/R/project.R | 570 - mizer-3.0.0/mizer/R/project_methods.R | 340 mizer-3.0.0/mizer/R/project_n.R |only mizer-3.0.0/mizer/R/rate_functions.R | 1652 ++- mizer-3.0.0/mizer/R/registerExtensions.R |only mizer-3.0.0/mizer/R/reproduction.R | 119 mizer-3.0.0/mizer/R/resource_dynamics.R | 3 mizer-3.0.0/mizer/R/resource_logistic.R | 27 mizer-3.0.0/mizer/R/resource_semichemostat.R | 25 mizer-3.0.0/mizer/R/saveParams.R | 185 mizer-3.0.0/mizer/R/scaleRates.R |only mizer-3.0.0/mizer/R/selectivity_funcs.R | 47 mizer-3.0.0/mizer/R/setBevertonHolt.R | 73 mizer-3.0.0/mizer/R/setColours.R | 30 mizer-3.0.0/mizer/R/setExtDiffusion.R |only mizer-3.0.0/mizer/R/setExtEncounter.R | 116 mizer-3.0.0/mizer/R/setExtMort.R | 53 mizer-3.0.0/mizer/R/setFishing.R | 264 mizer-3.0.0/mizer/R/setInitialValues.R | 146 mizer-3.0.0/mizer/R/setInteraction.R | 36 mizer-3.0.0/mizer/R/setMaxIntakeRate.R | 74 mizer-3.0.0/mizer/R/setMetabolicRate.R | 74 mizer-3.0.0/mizer/R/setMetadata.R | 20 mizer-3.0.0/mizer/R/setPredKernel.R | 76 mizer-3.0.0/mizer/R/setReproduction.R | 102 mizer-3.0.0/mizer/R/setResource.R | 132 mizer-3.0.0/mizer/R/setSearchVolume.R | 80 mizer-3.0.0/mizer/R/species_params.R | 168 mizer-3.0.0/mizer/R/steady.R | 104 mizer-3.0.0/mizer/R/steadySingleSpecies.R | 99 mizer-3.0.0/mizer/R/summary_methods.R | 919 +- mizer-3.0.0/mizer/R/transport.R |only mizer-3.0.0/mizer/R/upgrade.R | 183 mizer-3.0.0/mizer/R/validSpeciesParams.R | 24 mizer-3.0.0/mizer/R/wrapper_functions.R | 114 mizer-3.0.0/mizer/README.md | 32 mizer-3.0.0/mizer/build/vignette.rds |binary mizer-3.0.0/mizer/data/NS_params.rda |binary mizer-3.0.0/mizer/data/NS_sim.rda |binary mizer-3.0.0/mizer/data/NS_species_params.rda |binary mizer-3.0.0/mizer/data/NS_species_params_gears.rda |binary mizer-3.0.0/mizer/inst/WORDLIST | 88 mizer-3.0.0/mizer/inst/doc/mizer_vignette.Rmd | 4 mizer-3.0.0/mizer/inst/doc/mizer_vignette.html |only mizer-3.0.0/mizer/man/ArraySpeciesBySize.Rd |only mizer-3.0.0/mizer/man/ArrayTimeBySpecies.Rd |only mizer-3.0.0/mizer/man/ArrayTimeBySpeciesBySize.Rd |only mizer-3.0.0/mizer/man/BevertonHoltRDD.Rd | 12 mizer-3.0.0/mizer/man/MizerParams-class.Rd | 26 mizer-3.0.0/mizer/man/MizerParams.Rd | 17 mizer-3.0.0/mizer/man/MizerSim-class.Rd | 16 mizer-3.0.0/mizer/man/N.Rd | 4 mizer-3.0.0/mizer/man/NOther.Rd | 22 mizer-3.0.0/mizer/man/NS_interaction.Rd | 4 mizer-3.0.0/mizer/man/NS_params.Rd | 2 mizer-3.0.0/mizer/man/NS_sim.Rd | 2 mizer-3.0.0/mizer/man/NS_species_params.Rd | 2 mizer-3.0.0/mizer/man/RickerRDD.Rd | 12 mizer-3.0.0/mizer/man/SheperdRDD.Rd | 12 mizer-3.0.0/mizer/man/addPlot.Rd |only mizer-3.0.0/mizer/man/addSpecies.Rd | 26 mizer-3.0.0/mizer/man/age_mat.Rd | 10 mizer-3.0.0/mizer/man/age_mat_vB.Rd | 7 mizer-3.0.0/mizer/man/animate.Rd |only mizer-3.0.0/mizer/man/as.data.frame.Rd |only mizer-3.0.0/mizer/man/assertExtensionChain.Rd |only mizer-3.0.0/mizer/man/baseMizerClass.Rd |only mizer-3.0.0/mizer/man/box_pred_kernel.Rd | 14 mizer-3.0.0/mizer/man/calc_selectivity.Rd | 6 mizer-3.0.0/mizer/man/calibrateBiomass.Rd | 9 mizer-3.0.0/mizer/man/calibrateNumber.Rd | 9 mizer-3.0.0/mizer/man/calibrateYield.Rd | 7 mizer-3.0.0/mizer/man/cdf_y_label.Rd |only mizer-3.0.0/mizer/man/clearExtensionChain.Rd |only mizer-3.0.0/mizer/man/coerceToExtensionClass.Rd |only mizer-3.0.0/mizer/man/compareExtensionChains.Rd |only mizer-3.0.0/mizer/man/compareParams.Rd | 10 mizer-3.0.0/mizer/man/completeSpeciesParams.Rd | 10 mizer-3.0.0/mizer/man/constantEggRDI.Rd | 17 mizer-3.0.0/mizer/man/constantRDD.Rd | 12 mizer-3.0.0/mizer/man/convert_plot_size_axis.Rd |only mizer-3.0.0/mizer/man/customFunction.Rd | 4 mizer-3.0.0/mizer/man/defaults_edition.Rd | 17 mizer-3.0.0/mizer/man/defineExtensionClasses.Rd |only mizer-3.0.0/mizer/man/defineOrCheckClass.Rd |only mizer-3.0.0/mizer/man/dispatchExtensions.Rd |only mizer-3.0.0/mizer/man/distanceMaxRelRDI.Rd | 7 mizer-3.0.0/mizer/man/distanceSSLogN.Rd | 7 mizer-3.0.0/mizer/man/dot-checkRateFunctionOutput.Rd |only mizer-3.0.0/mizer/man/double_sigmoid_length.Rd | 24 mizer-3.0.0/mizer/man/ensureExtensionNamespaces.Rd |only mizer-3.0.0/mizer/man/expandSizeGrid.Rd |only mizer-3.0.0/mizer/man/figures/unnamed-chunk-4-1.png |binary mizer-3.0.0/mizer/man/filter_plot_length_limits.Rd |only mizer-3.0.0/mizer/man/finalN.Rd | 4 mizer-3.0.0/mizer/man/finalParams.Rd |only mizer-3.0.0/mizer/man/flux_from_rates.Rd |only mizer-3.0.0/mizer/man/flux_units.Rd |only mizer-3.0.0/mizer/man/formatExtensionChain.Rd |only mizer-3.0.0/mizer/man/gear_params.Rd | 27 mizer-3.0.0/mizer/man/getBiomass.Rd | 50 mizer-3.0.0/mizer/man/getCommunitySlope.Rd | 33 mizer-3.0.0/mizer/man/getCriticalFeedingLevel.Rd | 2 mizer-3.0.0/mizer/man/getDiet.Rd | 28 mizer-3.0.0/mizer/man/getDiffusion.Rd |only mizer-3.0.0/mizer/man/getEGrowth.Rd | 86 mizer-3.0.0/mizer/man/getERepro.Rd | 86 mizer-3.0.0/mizer/man/getEReproAndGrowth.Rd | 103 mizer-3.0.0/mizer/man/getESpawning.Rd | 86 mizer-3.0.0/mizer/man/getEncounter.Rd | 98 mizer-3.0.0/mizer/man/getFMort.Rd | 80 mizer-3.0.0/mizer/man/getFMortGear.Rd | 60 mizer-3.0.0/mizer/man/getFeedingLevel.Rd | 83 mizer-3.0.0/mizer/man/getFlux.Rd |only mizer-3.0.0/mizer/man/getGrowthCurves.Rd | 16 mizer-3.0.0/mizer/man/getM2.Rd | 81 mizer-3.0.0/mizer/man/getM2Background.Rd | 30 mizer-3.0.0/mizer/man/getMeanMaxWeight.Rd | 40 mizer-3.0.0/mizer/man/getMeanWeight.Rd | 24 mizer-3.0.0/mizer/man/getMort.Rd | 89 mizer-3.0.0/mizer/man/getN.Rd | 25 mizer-3.0.0/mizer/man/getParams.Rd | 48 mizer-3.0.0/mizer/man/getPhiPrey.Rd | 12 mizer-3.0.0/mizer/man/getPredMort.Rd | 81 mizer-3.0.0/mizer/man/getPredRate.Rd | 87 mizer-3.0.0/mizer/man/getProportionOfLargeFish.Rd | 48 mizer-3.0.0/mizer/man/getRDD.Rd | 79 mizer-3.0.0/mizer/man/getRDI.Rd | 75 mizer-3.0.0/mizer/man/getRates.Rd | 60 mizer-3.0.0/mizer/man/getRegisteredExtensions.Rd |only mizer-3.0.0/mizer/man/getReproductionLevel.Rd | 1 mizer-3.0.0/mizer/man/getRequiredRDD.Rd |only mizer-3.0.0/mizer/man/getResourceMort.Rd | 30 mizer-3.0.0/mizer/man/getSSB.Rd | 33 mizer-3.0.0/mizer/man/getSimParams.Rd |only mizer-3.0.0/mizer/man/getTimes.Rd | 2 mizer-3.0.0/mizer/man/getTrophicLevel.Rd |only mizer-3.0.0/mizer/man/getTrophicLevelBySpecies.Rd |only mizer-3.0.0/mizer/man/getYield.Rd | 30 mizer-3.0.0/mizer/man/getYieldGear.Rd | 20 mizer-3.0.0/mizer/man/getZ.Rd | 89 mizer-3.0.0/mizer/man/get_ArraySpeciesBySize_w.Rd |only mizer-3.0.0/mizer/man/get_f0_default.Rd | 8 mizer-3.0.0/mizer/man/get_gamma_default.Rd | 8 mizer-3.0.0/mizer/man/get_h_default.Rd | 8 mizer-3.0.0/mizer/man/get_initial_n.Rd | 7 mizer-3.0.0/mizer/man/get_ks_default.Rd | 8 mizer-3.0.0/mizer/man/get_sim_rate_slice.Rd |only mizer-3.0.0/mizer/man/get_sim_rate_time_elements.Rd |only mizer-3.0.0/mizer/man/get_size_range_array.Rd | 4 mizer-3.0.0/mizer/man/get_species_size_rate_from_sim.Rd |only mizer-3.0.0/mizer/man/get_species_time_rate_from_sim.Rd |only mizer-3.0.0/mizer/man/get_steady_state_n.Rd |only mizer-3.0.0/mizer/man/get_time_elements.Rd | 23 mizer-3.0.0/mizer/man/indicator_functions.Rd | 18 mizer-3.0.0/mizer/man/initialN-set.Rd | 10 mizer-3.0.0/mizer/man/initialNOther-set.Rd | 11 mizer-3.0.0/mizer/man/initialNResource-set.Rd | 4 mizer-3.0.0/mizer/man/initialParams.Rd |only mizer-3.0.0/mizer/man/initial_effort.Rd | 11 mizer-3.0.0/mizer/man/is.ArraySpeciesBySize.Rd |only mizer-3.0.0/mizer/man/is.ArrayTimeBySpecies.Rd |only mizer-3.0.0/mizer/man/is.ArrayTimeBySpeciesBySize.Rd |only mizer-3.0.0/mizer/man/isSuffixChain.Rd |only mizer-3.0.0/mizer/man/isVersionRequirement.Rd |only mizer-3.0.0/mizer/man/knife_edge.Rd | 17 mizer-3.0.0/mizer/man/log_breaks.Rd | 2 mizer-3.0.0/mizer/man/lognormal_pred_kernel.Rd | 8 mizer-3.0.0/mizer/man/make_linesize.Rd |only mizer-3.0.0/mizer/man/make_mizer_plot.Rd |only mizer-3.0.0/mizer/man/markBackground.Rd |only mizer-3.0.0/mizer/man/matchBiomasses.Rd | 9 mizer-3.0.0/mizer/man/matchGrowth.Rd | 13 mizer-3.0.0/mizer/man/matchNumbers.Rd | 13 mizer-3.0.0/mizer/man/matchYields.Rd | 9 mizer-3.0.0/mizer/man/mizer-package.Rd | 1 mizer-3.0.0/mizer/man/mizerDiffusion.Rd |only mizer-3.0.0/mizer/man/mizerEGrowth.Rd | 40 mizer-3.0.0/mizer/man/mizerERepro.Rd | 41 mizer-3.0.0/mizer/man/mizerEReproAndGrowth.Rd | 66 mizer-3.0.0/mizer/man/mizerEncounter.Rd | 53 mizer-3.0.0/mizer/man/mizerFMort.Rd | 34 mizer-3.0.0/mizer/man/mizerFMortGear.Rd | 30 mizer-3.0.0/mizer/man/mizerFeedingLevel.Rd | 34 mizer-3.0.0/mizer/man/mizerMort.Rd | 34 mizer-3.0.0/mizer/man/mizerPredMort.Rd | 39 mizer-3.0.0/mizer/man/mizerPredRate.Rd | 34 mizer-3.0.0/mizer/man/mizerRDI.Rd | 71 mizer-3.0.0/mizer/man/mizerRates.Rd | 34 mizer-3.0.0/mizer/man/mizerResourceMort.Rd | 34 mizer-3.0.0/mizer/man/mizer_rates_subset.Rd |only mizer-3.0.0/mizer/man/mizer_tooltip_vars.Rd |only mizer-3.0.0/mizer/man/needed_rates.Rd |only mizer-3.0.0/mizer/man/newCommunityParams.Rd | 27 mizer-3.0.0/mizer/man/newMultispeciesParams.Rd | 118 mizer-3.0.0/mizer/man/newSingleSpeciesParams.Rd | 27 mizer-3.0.0/mizer/man/newTraitParams.Rd | 32 mizer-3.0.0/mizer/man/noRDD.Rd | 12 mizer-3.0.0/mizer/man/objectExtensions.Rd |only mizer-3.0.0/mizer/man/parseTimePlotLog.Rd |only mizer-3.0.0/mizer/man/plot.Rd |only mizer-3.0.0/mizer/man/plot2.Rd |only mizer-3.0.0/mizer/man/plotBiomass.Rd | 121 mizer-3.0.0/mizer/man/plotBiomassObservedVsModel.Rd | 24 mizer-3.0.0/mizer/man/plotCDF.Rd |only mizer-3.0.0/mizer/man/plotCDF2.Rd |only mizer-3.0.0/mizer/man/plotComparisonDataFrame.Rd |only mizer-3.0.0/mizer/man/plotDataFrame.Rd | 4 mizer-3.0.0/mizer/man/plotDiet.Rd | 82 mizer-3.0.0/mizer/man/plotFMort.Rd | 86 mizer-3.0.0/mizer/man/plotFeedingLevel.Rd | 103 mizer-3.0.0/mizer/man/plotGrowthCurves.Rd | 71 mizer-3.0.0/mizer/man/plotHover.Rd |only mizer-3.0.0/mizer/man/plotM2.Rd | 82 mizer-3.0.0/mizer/man/plotMizerParams.Rd |only mizer-3.0.0/mizer/man/plotMizerSim.Rd | 49 mizer-3.0.0/mizer/man/plotPredMort.Rd | 86 mizer-3.0.0/mizer/man/plotRelative.Rd |only mizer-3.0.0/mizer/man/plotRelativeDataFrame.Rd |only mizer-3.0.0/mizer/man/plotSpectra.Rd | 137 mizer-3.0.0/mizer/man/plotSpectra2.Rd |only mizer-3.0.0/mizer/man/plotSpectraRelative.Rd |only mizer-3.0.0/mizer/man/plotYield.Rd | 89 mizer-3.0.0/mizer/man/plotYieldGear.Rd | 64 mizer-3.0.0/mizer/man/plotYieldObservedVsModel.Rd | 15 mizer-3.0.0/mizer/man/plot_cdf.Rd |only mizer-3.0.0/mizer/man/plot_diet.Rd |only mizer-3.0.0/mizer/man/plot_feeding_level.Rd |only mizer-3.0.0/mizer/man/plot_growth_curves.Rd |only mizer-3.0.0/mizer/man/plot_size_axis.Rd |only mizer-3.0.0/mizer/man/plot_size_tooltip.Rd |only mizer-3.0.0/mizer/man/plot_size_x_var.Rd |only mizer-3.0.0/mizer/man/plot_size_xlab.Rd |only mizer-3.0.0/mizer/man/plot_size_xlim.Rd |only mizer-3.0.0/mizer/man/plot_spectra.Rd |only mizer-3.0.0/mizer/man/plotting_functions.Rd | 106 mizer-3.0.0/mizer/man/power_law_pred_kernel.Rd | 10 mizer-3.0.0/mizer/man/prepare_spectra_cdf_data.Rd |only mizer-3.0.0/mizer/man/print.Rd |only mizer-3.0.0/mizer/man/project.Rd | 101 mizer-3.0.0/mizer/man/projectRDD.Rd |only mizer-3.0.0/mizer/man/projectToSteady.Rd | 17 mizer-3.0.0/mizer/man/project_n.Rd |only mizer-3.0.0/mizer/man/project_n_2.Rd |only mizer-3.0.0/mizer/man/project_simple.Rd | 29 mizer-3.0.0/mizer/man/reexports.Rd | 2 mizer-3.0.0/mizer/man/registerExtension.Rd |only mizer-3.0.0/mizer/man/registerExtensions.Rd |only mizer-3.0.0/mizer/man/relative_difference.Rd |only mizer-3.0.0/mizer/man/removeBackgroundSpecies.Rd |only mizer-3.0.0/mizer/man/removeSpecies.Rd | 14 mizer-3.0.0/mizer/man/renameGear.Rd | 9 mizer-3.0.0/mizer/man/renameSpecies.Rd | 9 mizer-3.0.0/mizer/man/resource_constant.Rd | 6 mizer-3.0.0/mizer/man/resource_logistic.Rd | 16 mizer-3.0.0/mizer/man/resource_semichemostat.Rd | 14 mizer-3.0.0/mizer/man/saveParams.Rd | 45 mizer-3.0.0/mizer/man/scaleModel.Rd | 4 mizer-3.0.0/mizer/man/scaleRates.Rd |only mizer-3.0.0/mizer/man/setBevertonHolt.Rd | 20 mizer-3.0.0/mizer/man/setComponent.Rd | 41 mizer-3.0.0/mizer/man/setExtDiffusion.Rd |only mizer-3.0.0/mizer/man/setExtEncounter.Rd | 55 mizer-3.0.0/mizer/man/setExtMort.Rd | 47 mizer-3.0.0/mizer/man/setFishing.Rd | 35 mizer-3.0.0/mizer/man/setInitialValues.Rd | 48 mizer-3.0.0/mizer/man/setInteraction.Rd | 35 mizer-3.0.0/mizer/man/setMaxIntakeRate.Rd | 53 mizer-3.0.0/mizer/man/setMetabolicRate.Rd | 54 mizer-3.0.0/mizer/man/setMetadata.Rd | 18 mizer-3.0.0/mizer/man/setParams.Rd | 133 mizer-3.0.0/mizer/man/setPredKernel.Rd | 34 mizer-3.0.0/mizer/man/setRateFunction.Rd | 24 mizer-3.0.0/mizer/man/setReproduction.Rd | 74 mizer-3.0.0/mizer/man/setResource.Rd | 34 mizer-3.0.0/mizer/man/setRmax.Rd | 13 mizer-3.0.0/mizer/man/setSearchVolume.Rd | 50 mizer-3.0.0/mizer/man/set_multispecies_model.Rd | 21 mizer-3.0.0/mizer/man/set_species_param_default.Rd | 2 mizer-3.0.0/mizer/man/set_trait_model.Rd | 8 mizer-3.0.0/mizer/man/sigmoid_length.Rd | 20 mizer-3.0.0/mizer/man/sigmoid_weight.Rd | 20 mizer-3.0.0/mizer/man/simExtensionClass.Rd |only mizer-3.0.0/mizer/man/sim_size_rate.Rd |only mizer-3.0.0/mizer/man/sim_species_rate.Rd |only mizer-3.0.0/mizer/man/species_params.Rd | 64 mizer-3.0.0/mizer/man/spectra_bin_width.Rd |only mizer-3.0.0/mizer/man/spectra_y_label.Rd |only mizer-3.0.0/mizer/man/steady.Rd | 14 mizer-3.0.0/mizer/man/steadySingleSpecies.Rd | 23 mizer-3.0.0/mizer/man/str.MizerParams.Rd |only mizer-3.0.0/mizer/man/str.MizerSim.Rd |only mizer-3.0.0/mizer/man/str.Rd |only mizer-3.0.0/mizer/man/summary.MizerParams.Rd |only mizer-3.0.0/mizer/man/summary.MizerSim.Rd |only mizer-3.0.0/mizer/man/summary.Rd |only mizer-3.0.0/mizer/man/summary_functions.Rd | 2 mizer-3.0.0/mizer/man/truncated_lognormal_pred_kernel.Rd | 8 mizer-3.0.0/mizer/man/use_predation_diffusion.Rd |only mizer-3.0.0/mizer/man/usesExtensionDispatch.Rd |only mizer-3.0.0/mizer/man/validEffortVector.Rd |only mizer-3.0.0/mizer/man/validParams.Rd | 5 mizer-3.0.0/mizer/man/validSim.Rd | 7 mizer-3.0.0/mizer/man/validSpeciesParams.Rd | 10 mizer-3.0.0/mizer/man/valid_gears_arg.Rd | 4 mizer-3.0.0/mizer/man/validateExtensionsVector.Rd |only mizer-3.0.0/mizer/src/RcppExports.cpp | 17 mizer-3.0.0/mizer/src/inner_project_loop.cpp | 1 mizer-3.0.0/mizer/src/project_n_loop.cpp |only mizer-3.0.0/mizer/tests/testthat/Rplots.pdf |binary mizer-3.0.0/mizer/tests/testthat/_snaps/indicator_functions.md |only mizer-3.0.0/mizer/tests/testthat/_snaps/newSingleSpeciesParams.md |only mizer-3.0.0/mizer/tests/testthat/_snaps/plotBiomassObservedVsModel/plotbiomassobservedvsmodel.svg | 140 mizer-3.0.0/mizer/tests/testthat/_snaps/plotYieldObservedVsModel/plotyieldobservedvsmodel.svg | 116 mizer-3.0.0/mizer/tests/testthat/_snaps/plots/plot-biomass.svg | 38 mizer-3.0.0/mizer/tests/testthat/_snaps/plots/plot-diet.svg | 81 mizer-3.0.0/mizer/tests/testthat/_snaps/plots/plot-spectra.svg | 58 mizer-3.0.0/mizer/tests/testthat/_snaps/project.md | 122 mizer-3.0.0/mizer/tests/testthat/_snaps/project_methods.md | 236 mizer-3.0.0/mizer/tests/testthat/_snaps/project_n.md |only mizer-3.0.0/mizer/tests/testthat/_snaps/steady.md | 8 mizer-3.0.0/mizer/tests/testthat/_snaps/summary_methods.md | 4262 ---------- mizer-3.0.0/mizer/tests/testthat/helper.R | 75 mizer-3.0.0/mizer/tests/testthat/test-ArraySpeciesBySize.R |only mizer-3.0.0/mizer/tests/testthat/test-ArrayTimeBySpecies.R |only mizer-3.0.0/mizer/tests/testthat/test-ArrayTimeBySpeciesBySize.R |only mizer-3.0.0/mizer/tests/testthat/test-MizerParams-class.R | 38 mizer-3.0.0/mizer/tests/testthat/test-MizerSim-class.R | 78 mizer-3.0.0/mizer/tests/testthat/test-age_mat.R | 38 mizer-3.0.0/mizer/tests/testthat/test-analytic_results.R | 62 mizer-3.0.0/mizer/tests/testthat/test-analytic_transport.R |only mizer-3.0.0/mizer/tests/testthat/test-animateSpectra.R | 311 mizer-3.0.0/mizer/tests/testthat/test-backwards_compatibility.R | 85 mizer-3.0.0/mizer/tests/testthat/test-calc-selectivity.R | 43 mizer-3.0.0/mizer/tests/testthat/test-calibrate.R | 106 mizer-3.0.0/mizer/tests/testthat/test-compareParams.R | 16 mizer-3.0.0/mizer/tests/testthat/test-customFunction.R | 6 mizer-3.0.0/mizer/tests/testthat/test-defaults_edition.R |only mizer-3.0.0/mizer/tests/testthat/test-diffusion.R |only mizer-3.0.0/mizer/tests/testthat/test-extension-dispatch.R |only mizer-3.0.0/mizer/tests/testthat/test-extension.R | 157 mizer-3.0.0/mizer/tests/testthat/test-getFlux.R |only mizer-3.0.0/mizer/tests/testthat/test-getRequiredRDD.R |only mizer-3.0.0/mizer/tests/testthat/test-get_initial_n.R | 25 mizer-3.0.0/mizer/tests/testthat/test-get_steady_state_n.R |only mizer-3.0.0/mizer/tests/testthat/test-helpers-plot.R | 34 mizer-3.0.0/mizer/tests/testthat/test-helpers.R | 38 mizer-3.0.0/mizer/tests/testthat/test-idxFinalT.R | 32 mizer-3.0.0/mizer/tests/testthat/test-indicator_functions.R |only mizer-3.0.0/mizer/tests/testthat/test-io.R | 56 mizer-3.0.0/mizer/tests/testthat/test-manipulate_species.R | 336 mizer-3.0.0/mizer/tests/testthat/test-match.R | 95 mizer-3.0.0/mizer/tests/testthat/test-matchGrowth.R | 69 mizer-3.0.0/mizer/tests/testthat/test-newMultispeciesParams.R | 70 mizer-3.0.0/mizer/tests/testthat/test-newSingleSpeciesParams.R | 11 mizer-3.0.0/mizer/tests/testthat/test-plotBiomass-cutoff.R |only mizer-3.0.0/mizer/tests/testthat/test-plotBiomassObservedVsModel.R | 52 mizer-3.0.0/mizer/tests/testthat/test-plotYieldObservedVsModel.R | 82 mizer-3.0.0/mizer/tests/testthat/test-plots.R | 574 + mizer-3.0.0/mizer/tests/testthat/test-pred_kernel_funcs.R | 28 mizer-3.0.0/mizer/tests/testthat/test-project-time-resampling.R |only mizer-3.0.0/mizer/tests/testthat/test-project.R | 292 mizer-3.0.0/mizer/tests/testthat/test-project_methods.R | 482 - mizer-3.0.0/mizer/tests/testthat/test-project_n.R |only mizer-3.0.0/mizer/tests/testthat/test-project_simple.R | 79 mizer-3.0.0/mizer/tests/testthat/test-rate_functions.R | 8 mizer-3.0.0/mizer/tests/testthat/test-reexports.R |only mizer-3.0.0/mizer/tests/testthat/test-registerExtensions.R |only mizer-3.0.0/mizer/tests/testthat/test-reproduction.R | 89 mizer-3.0.0/mizer/tests/testthat/test-resource_dynamics.R | 31 mizer-3.0.0/mizer/tests/testthat/test-resource_logistic.R | 56 mizer-3.0.0/mizer/tests/testthat/test-resource_semichemostat.R | 57 mizer-3.0.0/mizer/tests/testthat/test-scaleRates.R |only mizer-3.0.0/mizer/tests/testthat/test-selectivity_funcs.R | 73 mizer-3.0.0/mizer/tests/testthat/test-setBevertonHolt.R | 170 mizer-3.0.0/mizer/tests/testthat/test-setColours.R | 8 mizer-3.0.0/mizer/tests/testthat/test-setExtDiffusion.R |only mizer-3.0.0/mizer/tests/testthat/test-setExtEncounter.R | 55 mizer-3.0.0/mizer/tests/testthat/test-setExtMort.R | 62 mizer-3.0.0/mizer/tests/testthat/test-setFishing.R | 59 mizer-3.0.0/mizer/tests/testthat/test-setInitialValues.R | 101 mizer-3.0.0/mizer/tests/testthat/test-setInteraction.R | 40 mizer-3.0.0/mizer/tests/testthat/test-setMaxIntakeRate.R | 28 mizer-3.0.0/mizer/tests/testthat/test-setMetabolicRate.R | 37 mizer-3.0.0/mizer/tests/testthat/test-setMetadata.R | 22 mizer-3.0.0/mizer/tests/testthat/test-setPredKernel.R | 47 mizer-3.0.0/mizer/tests/testthat/test-setReproduction.R | 44 mizer-3.0.0/mizer/tests/testthat/test-setResource.R | 52 mizer-3.0.0/mizer/tests/testthat/test-setSearchVolume.R | 36 mizer-3.0.0/mizer/tests/testthat/test-single_species.R | 4 mizer-3.0.0/mizer/tests/testthat/test-species_params.R | 101 mizer-3.0.0/mizer/tests/testthat/test-steady.R | 312 mizer-3.0.0/mizer/tests/testthat/test-steadySingleSpecies.R | 102 mizer-3.0.0/mizer/tests/testthat/test-summary_methods.R | 321 mizer-3.0.0/mizer/tests/testthat/test-transport.R |only mizer-3.0.0/mizer/tests/testthat/test-upgrade.R | 105 mizer-3.0.0/mizer/tests/testthat/test-validSpeciesParams.R | 91 mizer-3.0.0/mizer/tests/testthat/test-wrapper_functions.R | 66 mizer-3.0.0/mizer/vignettes/_quarto.yml |only mizer-3.0.0/mizer/vignettes/diffusion_references.bib |only mizer-3.0.0/mizer/vignettes/mizer_vignette.Rmd | 4 mizer-3.0.0/mizer/vignettes/reflib.bib | 6 458 files changed, 17740 insertions(+), 10973 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' 'R' packages. It helps to build reproducible and robust bioinformatics pipelines in 'R'. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
This is a re-admission after prior archival of version 0.14.4 dated 2025-09-30
Diff between MiscMetabar versions 0.14.4 dated 2025-09-30 and 0.16.8 dated 2026-06-08
MiscMetabar-0.14.4/MiscMetabar/tests/testthat/log.txt |only MiscMetabar-0.16.8/MiscMetabar/DESCRIPTION | 34 MiscMetabar-0.16.8/MiscMetabar/MD5 | 373 MiscMetabar-0.16.8/MiscMetabar/NAMESPACE | 39 MiscMetabar-0.16.8/MiscMetabar/NEWS.md | 312 MiscMetabar-0.16.8/MiscMetabar/R/Deseq2_edgeR.R | 147 MiscMetabar-0.16.8/MiscMetabar/R/MiscMetabar-package.R | 184 MiscMetabar-0.16.8/MiscMetabar/R/alpha_div_test.R | 323 MiscMetabar-0.16.8/MiscMetabar/R/beta_div_test.R | 854 + MiscMetabar-0.16.8/MiscMetabar/R/blast.R | 430 MiscMetabar-0.16.8/MiscMetabar/R/controls.R | 100 MiscMetabar-0.16.8/MiscMetabar/R/dada_phyloseq.R | 2565 ++++- MiscMetabar-0.16.8/MiscMetabar/R/data.R | 62 MiscMetabar-0.16.8/MiscMetabar/R/funguild.R | 93 MiscMetabar-0.16.8/MiscMetabar/R/hill_divent.R |only MiscMetabar-0.16.8/MiscMetabar/R/hill_helpers.R |only MiscMetabar-0.16.8/MiscMetabar/R/krona.R | 28 MiscMetabar-0.16.8/MiscMetabar/R/lulu.R | 165 MiscMetabar-0.16.8/MiscMetabar/R/miscellanous.R | 172 MiscMetabar-0.16.8/MiscMetabar/R/mmseqs2.R |only MiscMetabar-0.16.8/MiscMetabar/R/normalize_pq.R |only MiscMetabar-0.16.8/MiscMetabar/R/plot_functions.R | 4320 +++++++--- MiscMetabar-0.16.8/MiscMetabar/R/speedyseq_functions.R | 278 MiscMetabar-0.16.8/MiscMetabar/R/table_functions.R | 291 MiscMetabar-0.16.8/MiscMetabar/R/targets_misc.R | 147 MiscMetabar-0.16.8/MiscMetabar/R/taxonomy.R | 367 MiscMetabar-0.16.8/MiscMetabar/R/vsearch.R | 804 + MiscMetabar-0.16.8/MiscMetabar/README.md | 38 MiscMetabar-0.16.8/MiscMetabar/inst/WORDLIST | 117 MiscMetabar-0.16.8/MiscMetabar/inst/benchmark |only MiscMetabar-0.16.8/MiscMetabar/inst/doc/MiscMetabar.R | 2 MiscMetabar-0.16.8/MiscMetabar/inst/doc/MiscMetabar.Rmd | 2 MiscMetabar-0.16.8/MiscMetabar/inst/doc/MiscMetabar.html | 117 MiscMetabar-0.16.8/MiscMetabar/man/LCBD_pq.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/SRS_curve_pq.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/accu_plot.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/accu_plot_balanced_modality.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/accu_samp_threshold.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/add_blast_info.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/add_dna_to_phyloseq.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/add_new_taxonomy_pq.Rd | 7 MiscMetabar-0.16.8/MiscMetabar/man/adonis_pq.Rd | 46 MiscMetabar-0.16.8/MiscMetabar/man/adonis_rarperm_pq.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/aldex_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/all_object_size.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/ancombc_pq.Rd | 13 MiscMetabar-0.16.8/MiscMetabar/man/are_modality_even_depth.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/assign_blastn.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/assign_mmseqs2.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/assign_sintax.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/assign_vsearch_lca.Rd | 17 MiscMetabar-0.16.8/MiscMetabar/man/biplot_pq.Rd | 53 MiscMetabar-0.16.8/MiscMetabar/man/blast_pq.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/blast_to_derep.Rd | 16 MiscMetabar-0.16.8/MiscMetabar/man/build_phytree_pq.Rd | 14 MiscMetabar-0.16.8/MiscMetabar/man/chimera_detection_vs.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/chimera_removal_vs.Rd | 27 MiscMetabar-0.16.8/MiscMetabar/man/circle_pq.Rd | 12 MiscMetabar-0.16.8/MiscMetabar/man/clean_pq.Rd | 54 MiscMetabar-0.16.8/MiscMetabar/man/compare_pairs_pq.Rd | 16 MiscMetabar-0.16.8/MiscMetabar/man/css_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/cutadapt_remove_primers.Rd | 25 MiscMetabar-0.16.8/MiscMetabar/man/dist_bycol.Rd | 7 MiscMetabar-0.16.8/MiscMetabar/man/distri_1_taxa.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/divent_hill_matrix_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/fac2col.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/figures/README-example-1.png |binary MiscMetabar-0.16.8/MiscMetabar/man/figures/README-unnamed-chunk-6-1.png |binary MiscMetabar-0.16.8/MiscMetabar/man/figures/README-unnamed-chunk-8-1.png |binary MiscMetabar-0.16.8/MiscMetabar/man/filter_asv_blast.Rd | 13 MiscMetabar-0.16.8/MiscMetabar/man/filter_trim.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/find_mmseqs2.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/find_vsearch.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/format2dada2.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/format2dada2_species.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/format2sintax.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/funguild_assign.Rd | 9 MiscMetabar-0.16.8/MiscMetabar/man/funky_color.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/get_file_extension.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/get_funguild_db.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/ggaluv_pq.Rd | 30 MiscMetabar-0.16.8/MiscMetabar/man/ggbetween_pq.Rd | 48 MiscMetabar-0.16.8/MiscMetabar/man/ggscatt_pq.Rd | 32 MiscMetabar-0.16.8/MiscMetabar/man/ggvenn_pq.Rd | 32 MiscMetabar-0.16.8/MiscMetabar/man/glmutli_pq.Rd | 34 MiscMetabar-0.16.8/MiscMetabar/man/gmpr_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/hill_acc_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/hill_bar_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/hill_curves_pq.Rd | 20 MiscMetabar-0.16.8/MiscMetabar/man/hill_pq.Rd | 52 MiscMetabar-0.16.8/MiscMetabar/man/hill_test_rarperm_pq.Rd | 35 MiscMetabar-0.16.8/MiscMetabar/man/hill_tuckey_pq.Rd | 43 MiscMetabar-0.16.8/MiscMetabar/man/iNEXT_pq.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/install_mmseqs2.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/install_vsearch.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/is_mmseqs2_installed.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/is_vsearch_installed.Rd | 7 MiscMetabar-0.16.8/MiscMetabar/man/lefser_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/lulu.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/lulu_pq.Rd | 8 MiscMetabar-0.16.8/MiscMetabar/man/mcknight_residuals_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/merge_samples2.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/merge_taxa_vec.Rd | 39 MiscMetabar-0.16.8/MiscMetabar/man/mmseqs2_clustering.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/multi_biplot_pq.Rd | 5 MiscMetabar-0.16.8/MiscMetabar/man/multipatt_pq.Rd | 13 MiscMetabar-0.16.8/MiscMetabar/man/mumu_pq.Rd | 18 MiscMetabar-0.16.8/MiscMetabar/man/no_legend.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/normalize_prop_pq.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/perc.Rd | 5 MiscMetabar-0.16.8/MiscMetabar/man/phyloseq_to_edgeR.Rd | 12 MiscMetabar-0.16.8/MiscMetabar/man/physeq_or_string_to_dna.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/plot_LCBD_pq.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/plot_SCBD_pq.Rd | 10 MiscMetabar-0.16.8/MiscMetabar/man/plot_ancombc_pq.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/plot_mt.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/plot_ordination_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/plot_refseq_extremity_pq.Rd | 34 MiscMetabar-0.16.8/MiscMetabar/man/plot_refseq_pq.Rd | 14 MiscMetabar-0.16.8/MiscMetabar/man/plot_seq_ratio_pq.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/plot_tsne_pq.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/plot_var_part_pq.Rd | 28 MiscMetabar-0.16.8/MiscMetabar/man/postcluster_pq.Rd | 42 MiscMetabar-0.16.8/MiscMetabar/man/profile_hill_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/psmelt_samples_pq.Rd | 59 MiscMetabar-0.16.8/MiscMetabar/man/rarefy_even_depth_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/rarefy_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/reorder_distinct_colors.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/reorder_taxa_pq.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/resolve_vector_ranks.Rd | 7 MiscMetabar-0.16.8/MiscMetabar/man/ridges_sam_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/rotl_pq.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/sam_data_matching_names.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/sample_data_with_new_names.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/select_taxa-methods.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/signif_ancombc.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/simplify_taxo.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/srs_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/subset_samples_pq.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/subset_taxa_pq.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/summary_plot_pq.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/swarm_clustering.Rd | 30 MiscMetabar-0.16.8/MiscMetabar/man/tax_bar_pq.Rd | 111 MiscMetabar-0.16.8/MiscMetabar/man/taxa_as_columns.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/taxa_as_rows.Rd | 3 MiscMetabar-0.16.8/MiscMetabar/man/taxa_only_in_one_level.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/tmm_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/track_wkflow.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/track_wkflow_samples.Rd | 15 MiscMetabar-0.16.8/MiscMetabar/man/transform_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/transp.Rd | 4 MiscMetabar-0.16.8/MiscMetabar/man/treemap_pq.Rd | 49 MiscMetabar-0.16.8/MiscMetabar/man/tsne_pq.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/umap_pq.Rd | 68 MiscMetabar-0.16.8/MiscMetabar/man/unique_or_na.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/unwanted_tax_patterns.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/upset_pq.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/upset_test_pq.Rd | 7 MiscMetabar-0.16.8/MiscMetabar/man/var_par_pq.Rd | 2 MiscMetabar-0.16.8/MiscMetabar/man/var_par_rarperm_pq.Rd | 17 MiscMetabar-0.16.8/MiscMetabar/man/verify_pq.Rd | 19 MiscMetabar-0.16.8/MiscMetabar/man/verify_tax_table.Rd |only MiscMetabar-0.16.8/MiscMetabar/man/vs_search_global.Rd | 6 MiscMetabar-0.16.8/MiscMetabar/man/vsearch_clustering.Rd | 11 MiscMetabar-0.16.8/MiscMetabar/man/vst_pq.Rd |only MiscMetabar-0.16.8/MiscMetabar/tests/spelling.R | 3 MiscMetabar-0.16.8/MiscMetabar/tests/testthat.R | 2 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/Rplots.pdf |binary MiscMetabar-0.16.8/MiscMetabar/tests/testthat/inst/extdata/General_EUK_ITS_v2.0_MINI.fasta |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/inst/extdata/mini_UNITE_fungi.fasta.gz |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/inst/extdata/sh_general_release_dynamic_19.02.2025_MINI.fasta |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_adonis.R | 26 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_alpha_div.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_ancombc.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_assignment.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_beta_div.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_blast.R | 322 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_clean_pq.R | 130 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_controls.R | 79 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_cutadapt.R | 39 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_dada_phyloseq.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_data_manipulation.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_deprecated.R | 110 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_deseq2_edgeR.R | 170 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_fact_one_sample.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_alpha_div.R | 139 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_beta_div.R | 175 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_biplot.R | 80 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_misc.R | 31 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_summary_plot.R | 12 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_figures_taxo.R | 370 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_filtering.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_format_conversion.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_funguild.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_krona.R | 21 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_misc.R | 155 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_mmseqs2.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_normalize_pq.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_phyloseq_class.R | 225 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_plot_funcs.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_plot_utilities.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_rw.R | 54 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_subset.R | 43 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_swarm.R | 18 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_table_functions.R | 100 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_targets.R | 399 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_taxonomy.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_taxonomy_utils.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_tuckey.R | 24 MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_utils.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_visualization.R |only MiscMetabar-0.16.8/MiscMetabar/tests/testthat/test_vsearch.R | 141 MiscMetabar-0.16.8/MiscMetabar/vignettes/MiscMetabar.Rmd | 2 MiscMetabar-0.16.8/MiscMetabar/vignettes/bibliography.bib | 124 214 files changed, 12698 insertions(+), 4226 deletions(-)
Title: A Modular Two-Step Convex Optimization Estimator for Ill-Posed
Problems
Description: Convex Least Squares Programming (CLSP) is a two-step estimator
for solving underdetermined, ill-posed, or structurally constrained
least-squares problems. It combines pseudoinverse-based estimation with
convex-programming correction methods inspired by Lasso, Ridge, and
Elastic Net to ensure numerical stability, constraint enforcement, and
interpretability. The package also provides numerical stability analysis
and CLSP-specific diagnostics, including partial R^2, normalized RMSE
(NRMSE), Monte Carlo t-tests for mean NRMSE, and condition-number-based
confidence bands.
Author: Ilya Bolotov [aut, cre]
Maintainer: Ilya Bolotov <ilya.bolotov@vse.cz>
Diff between rclsp versions 1.1.0 dated 2026-06-07 and 2.0.0 dated 2026-06-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 10 ++++++++++ R/clsp.R | 4 ++-- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Optimal PK/PD Index Finder
Description: Fits Emax models to pharmacokinetic/pharmacodynamic (PK/PD) data, estimate key parameters, and visualise model fits for multiple PK/PD indices. Methods are described in Macdougall J (2006) <doi:10.1007/0-387-33706-7_9>, Spiess AN, Neumeyer N (2010) <doi:10.1186/1471-2210-10-6>, and Burnham KP, Anderson DR (2004) <doi:10.1177/0049124104268644>.
Author: Najla Alabdulkarim [aut, cre],
Joseph F Standing [aut]
Maintainer: Najla Alabdulkarim <naaalabdulkarim@hotmail.com>
Diff between PKPDindex versions 0.2.0 dated 2025-10-09 and 0.2.1 dated 2026-06-08
DESCRIPTION | 8 ++--- MD5 | 8 ++--- NEWS.md | 8 +++++ R/PKPDindex.R | 84 +++++++++++++++++++++++++++---------------------------- man/PKPDindex.Rd | 8 ++--- 5 files changed, 62 insertions(+), 54 deletions(-)
Title: Supporting Functions Maintained by Zhen Lu
Description: Miscellaneous functions commonly used by LuLab. This package aims to help more researchers on epidemiology to perform data management and visualization more efficiently.
Author: Zhen Lu [aut, cre]
Maintainer: Zhen Lu <Zhen.Lu.VA@gmail.com>
Diff between lulab.utils versions 1.0.0 dated 2025-10-09 and 1.0.2 dated 2026-06-08
DESCRIPTION | 19 - MD5 | 39 +- NAMESPACE | 1 NEWS.md | 59 ++- R/SCI_TFL.R | 441 ++++++++++++++------------- R/regression_utilities.R | 16 R/utilities.R | 39 +- README.md | 24 + build/vignette.rds |binary inst/doc/lulab_utils.R | 23 + inst/doc/lulab_utils.Rmd | 37 ++ inst/doc/lulab_utils.html | 46 ++ man/Table1.Rd |only man/lulab.utils-package.Rd | 7 man/round2.Rd | 44 +- tests/testthat/test-Table1.R | 69 ++-- tests/testthat/test-check_cha.R | 14 tests/testthat/test-extract_logistic_model.R |only tests/testthat/test-round2.R |only tests/testthat/test-test_mirror.R | 2 tests/testthat/test-use_wget.R | 20 - vignettes/lulab_utils.Rmd | 37 ++ 22 files changed, 596 insertions(+), 341 deletions(-)
Title: Markov Model for Online Multi-Channel Attribution
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. This is called online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identify structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.io>
Diff between ChannelAttribution versions 2.2.4 dated 2025-11-19 and 2.2.5 dated 2026-06-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/ChannelAttribution.R | 4 ++-- man/ChannelAttribution-package.Rd | 4 ++-- src/Makevars | 2 +- src/Makevars.win | 2 +- 6 files changed, 15 insertions(+), 15 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Description: A comprehensive suite of tools for managing, processing, and
analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports
quality control, geospatial analysis, and preparation of IFCB data for
publication in databases like <https://www.gbif.org>,
<https://www.obis.org>, <https://emodnet.ec.europa.eu/en>,
<https://shark.smhi.se/en/>, and <https://www.ecotaxa.org>. The package
integrates with the MATLAB 'ifcb-analysis' tool, which is described in
Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides
features for working with raw, manually classified, and machine
learning–classified image datasets. Key functionalities include image
extraction, particle size distribution analysis, taxonomic data
handling, and biomass concentration calculations, essential for
plankton research.
Author: Anders Torstensson [aut, cre] ,
Kendra Hayashi [ctb] ,
Jamie Enslein [ctb],
Raphael Kudela [ctb] ,
Alle Lie [ctb] ,
Jayme Smith [ctb] ,
DTO-BioFlow [fnd] ,
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between iRfcb versions 0.8.1 dated 2026-03-01 and 0.9.0 dated 2026-06-08
DESCRIPTION | 14 LICENSE | 4 LICENSE.note | 64 MD5 | 461 ++-- NAMESPACE | 429 +-- NEWS.md | 19 R/defunct.R | 56 R/iRfcb-package.R | 60 R/ifcb_adjust_classes.R | 116 - R/ifcb_annotate_batch.R | 350 +-- R/ifcb_annotate_samples.R | 439 +-- R/ifcb_classify_images.R | 975 ++++---- R/ifcb_classify_models.R | 157 - R/ifcb_classify_sample.R | 211 - R/ifcb_convert_filenames.R | 143 - R/ifcb_correct_annotation.R | 228 - R/ifcb_count_mat_annotations.R | 267 +- R/ifcb_create_class2use.R | 96 R/ifcb_create_empty_manual_file.R | 136 - R/ifcb_create_manifest.R | 134 - R/ifcb_create_manual_file.R | 122 - R/ifcb_download_dashboard_data.R | 778 +++--- R/ifcb_download_dashboard_metadata.R | 143 - R/ifcb_download_test_data.R | 266 +- R/ifcb_download_whoi_plankton.R | 348 +-- R/ifcb_extract_annotated_images.R | 356 +-- R/ifcb_extract_biovolumes.R | 777 +++--- R/ifcb_extract_classified_images.R | 314 +- R/ifcb_extract_features.R |only R/ifcb_extract_pngs.R | 400 +-- R/ifcb_get_ecotaxa_example.R | 83 R/ifcb_get_ferrybox_data.R | 425 +-- R/ifcb_get_mat_names.R | 90 R/ifcb_get_mat_variable.R | 121 - R/ifcb_get_runtime.R | 156 - R/ifcb_get_shark_colnames.R | 80 R/ifcb_get_shark_example.R | 48 R/ifcb_get_trophic_type.R | 166 - R/ifcb_helper_functions.R | 1942 ++++++++--------- R/ifcb_is_diatom.R | 156 - R/ifcb_is_in_basin.R | 183 - R/ifcb_is_near_land.R | 552 ++-- R/ifcb_list_dashboard_bins.R | 134 - R/ifcb_match_taxa_names.R | 230 +- R/ifcb_merge_manual.R | 407 +-- R/ifcb_prepare_whoi_plankton.R | 688 +++--- R/ifcb_psd.R | 511 ++-- R/ifcb_psd_plot.R | 329 +- R/ifcb_py_install.R | 262 +- R/ifcb_read_features.R | 179 - R/ifcb_read_hdr_data.R | 232 +- R/ifcb_read_mat.R | 122 - R/ifcb_read_summary.R | 352 +-- R/ifcb_replace_mat_values.R | 148 - R/ifcb_run_image_gallery.R | 91 R/ifcb_save_classification.R | 477 ++-- R/ifcb_summarize_biovolumes.R | 427 +-- R/ifcb_summarize_class_counts.R | 273 +- R/ifcb_summarize_png_counts.R | 368 +-- R/ifcb_summarize_png_metadata.R | 176 - R/ifcb_volume_analyzed.R | 131 - R/ifcb_volume_analyzed_from_adc.R | 178 - R/ifcb_which_basin.R | 195 - R/ifcb_zip_images_by_class.R | 240 +- R/ifcb_zip_matlab.R | 653 ++--- R/ifcb_zip_pngs.R | 396 +-- R/zzz.R | 135 - README.md | 222 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 22 inst/WORDLIST | 416 +-- inst/doc/introduction.R | 418 +-- inst/doc/introduction.Rmd | 682 +++-- inst/doc/introduction.html | 1680 +++++++------- inst/exdata/MATLAB-template.md | 232 +- inst/exdata/README-template.md | 36 inst/exdata/ecotaxa_table_minimum.tsv | 10 inst/exdata/ecotaxa_table_with_classification.tsv | 22 inst/exdata/ecotaxa_table_without_classification.tsv | 18 inst/exdata/example.txt | 6 inst/exdata/example_ferrybox.txt | 6 inst/python/create_manual_mat.py | 78 inst/python/edit_manual_file.py | 32 inst/python/extract_slim_features.py |only inst/python/psd.py | 920 ++++---- inst/python/read_mat_file.py | 150 - inst/python/replace_value_in_classlist.py | 56 inst/python/requirements.txt | 6 inst/python/save_class2use_to_mat.py | 20 inst/python/save_class_mat.py | 100 inst/python/start_mc_adjust_classes_user_training.py | 62 inst/shiny/ifcb_image_gallery/server.R | 290 +- inst/shiny/ifcb_image_gallery/ui.R | 66 man/create_package_manifest.Rd | 50 man/defunct.Rd | 32 man/figures/lifecycle-archived.svg | 42 man/figures/lifecycle-defunct.svg | 42 man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-maturing.svg | 42 man/figures/lifecycle-questioning.svg | 42 man/figures/lifecycle-soft-deprecated.svg | 42 man/figures/lifecycle-stable.svg | 58 man/figures/lifecycle-superseded.svg | 42 man/iRfcb-package.Rd | 77 man/ifcb_adjust_classes.Rd | 94 man/ifcb_annotate_batch.Rd | 176 - man/ifcb_annotate_samples.Rd | 204 - man/ifcb_classify_images.Rd | 161 - man/ifcb_classify_models.Rd | 80 man/ifcb_classify_sample.Rd | 183 - man/ifcb_convert_filenames.Rd | 84 man/ifcb_correct_annotation.Rd | 146 - man/ifcb_count_mat_annotations.Rd | 122 - man/ifcb_create_class2use.Rd | 86 man/ifcb_create_empty_manual_file.Rd | 136 - man/ifcb_create_manifest.Rd | 84 man/ifcb_create_manual_file.Rd | 126 - man/ifcb_download_dashboard_data.Rd | 198 - man/ifcb_download_dashboard_metadata.Rd | 78 man/ifcb_download_test_data.Rd | 112 man/ifcb_download_whoi_plankton.Rd | 94 man/ifcb_extract_annotated_images.Rd | 208 - man/ifcb_extract_biovolumes.Rd | 298 +- man/ifcb_extract_classified_images.Rd | 198 - man/ifcb_extract_features.Rd |only man/ifcb_extract_pngs.Rd | 154 - man/ifcb_get_ecotaxa_example.Rd | 76 man/ifcb_get_ferrybox_data.Rd | 122 - man/ifcb_get_mat_names.Rd | 86 man/ifcb_get_mat_variable.Rd | 114 man/ifcb_get_runtime.Rd | 68 man/ifcb_get_shark_colnames.Rd | 62 man/ifcb_get_shark_example.Rd | 48 man/ifcb_get_trophic_type.Rd | 74 man/ifcb_is_diatom.Rd | 124 - man/ifcb_is_in_basin.Rd | 86 man/ifcb_is_near_land.Rd | 176 - man/ifcb_list_dashboard_bins.Rd | 76 man/ifcb_match_taxa_names.Rd | 130 - man/ifcb_merge_manual.Rd | 162 - man/ifcb_prepare_whoi_plankton.Rd | 258 +- man/ifcb_psd.Rd | 306 +- man/ifcb_psd_plot.Rd | 144 - man/ifcb_py_install.Rd | 137 - man/ifcb_read_features.Rd | 106 man/ifcb_read_hdr_data.Rd | 84 man/ifcb_read_mat.Rd | 78 man/ifcb_read_summary.Rd | 108 man/ifcb_replace_mat_values.Rd | 106 man/ifcb_run_image_gallery.Rd | 68 man/ifcb_save_classification.Rd | 197 - man/ifcb_summarize_biovolumes.Rd | 290 +- man/ifcb_summarize_class_counts.Rd | 110 man/ifcb_summarize_png_counts.Rd | 128 - man/ifcb_summarize_png_metadata.Rd | 78 man/ifcb_volume_analyzed.Rd | 78 man/ifcb_volume_analyzed_from_adc.Rd | 80 man/ifcb_which_basin.Rd | 86 man/ifcb_zip_images_by_class.Rd | 104 man/ifcb_zip_matlab.Rd | 190 - man/ifcb_zip_pngs.Rd | 136 - man/process_ifcb_string.Rd | 70 man/read_hdr_file.Rd | 34 man/retrieve_worms_records.Rd | 74 man/split_large_zip.Rd | 56 man/summarize_TBclass.Rd | 52 man/vol2C_lgdiatom.Rd | 54 man/vol2C_nondiatom.Rd | 54 tests/spelling.R | 6 tests/testthat.R | 24 tests/testthat/helper.R | 307 +- tests/testthat/setup-venv.R | 50 tests/testthat/test-defunct.R | 14 tests/testthat/test-get_latest_github_release.R |only tests/testthat/test-ifcb_adjust_classes.R | 122 - tests/testthat/test-ifcb_annotate_batch.R | 266 +- tests/testthat/test-ifcb_annotate_samples.R | 360 +-- tests/testthat/test-ifcb_classify_images.R | 380 +-- tests/testthat/test-ifcb_classify_models.R | 24 tests/testthat/test-ifcb_classify_sample.R | 266 +- tests/testthat/test-ifcb_convert_filenames.R | 196 - tests/testthat/test-ifcb_correct_annotation.R | 466 ++-- tests/testthat/test-ifcb_count_mat_annotations.R | 142 - tests/testthat/test-ifcb_create_class2use.R | 46 tests/testthat/test-ifcb_create_empty_manual_file.R | 72 tests/testthat/test-ifcb_create_manifest.R | 220 - tests/testthat/test-ifcb_create_manual_file.R | 96 tests/testthat/test-ifcb_download_dashboard_data.R | 324 +- tests/testthat/test-ifcb_download_dashboard_metadata.R | 28 tests/testthat/test-ifcb_download_test_data.R | 90 tests/testthat/test-ifcb_download_whoi_plankton.R | 42 tests/testthat/test-ifcb_extract_annotated_images.R | 306 +- tests/testthat/test-ifcb_extract_biovolumes.R | 446 +-- tests/testthat/test-ifcb_extract_classified_images.R | 482 ++-- tests/testthat/test-ifcb_extract_features.R |only tests/testthat/test-ifcb_extract_pngs.R | 194 - tests/testthat/test-ifcb_get_ecotaxa_example.R | 76 tests/testthat/test-ifcb_get_ferrybox_data.R | 340 +- tests/testthat/test-ifcb_get_mat_names.R | 92 tests/testthat/test-ifcb_get_mat_variable.R | 124 - tests/testthat/test-ifcb_get_runtime.R | 150 - tests/testthat/test-ifcb_get_shark_colnames.R | 74 tests/testthat/test-ifcb_get_shark_example.R | 58 tests/testthat/test-ifcb_get_trophic_type.R | 80 tests/testthat/test-ifcb_is_diatom.R | 150 - tests/testthat/test-ifcb_is_in_basin.R | 118 - tests/testthat/test-ifcb_is_near_land.R | 162 - tests/testthat/test-ifcb_list_dashboard_bins.R | 36 tests/testthat/test-ifcb_match_taxa_names.R | 64 tests/testthat/test-ifcb_merge_manual.R | 266 +- tests/testthat/test-ifcb_prepare_whoi_plankton.R | 304 +- tests/testthat/test-ifcb_psd.R | 252 +- tests/testthat/test-ifcb_psd_plot.R | 196 - tests/testthat/test-ifcb_py_install.R | 116 - tests/testthat/test-ifcb_read_features.R | 132 - tests/testthat/test-ifcb_read_hdr_data.R | 156 - tests/testthat/test-ifcb_read_summary.R | 220 - tests/testthat/test-ifcb_replace_mat_values.R | 280 +- tests/testthat/test-ifcb_run_image_gallery.R | 34 tests/testthat/test-ifcb_save_classification.R | 952 ++++---- tests/testthat/test-ifcb_summarize_biovolumes.R | 230 +- tests/testthat/test-ifcb_summarize_class_counts.R | 88 tests/testthat/test-ifcb_summarize_png_counts.R | 234 +- tests/testthat/test-ifcb_summarize_png_metadata.R | 132 - tests/testthat/test-ifcb_volume_analyzed.R | 94 tests/testthat/test-ifcb_volume_analyzed_from_adc.R | 80 tests/testthat/test-ifcb_which_basin.R | 130 - tests/testthat/test-ifcb_zip_images_by_class.R | 224 - tests/testthat/test-ifcb_zip_matlab.R | 346 +-- tests/testthat/test-ifcb_zip_pngs.R | 168 - tests/testthat/test-read_class_file.R | 358 +-- vignettes/introduction.Rmd | 682 +++-- 234 files changed, 22817 insertions(+), 22344 deletions(-)
Title: Scalable Statistical Computing with HDF5-Backed Matrices
Description: A framework for 'scalable' statistical computing on large on-disk
matrices stored in 'HDF5' files. It provides efficient block-wise
implementations of core linear-algebra operations (matrix multiplication,
SVD, PCA, QR decomposition, and canonical correlation analysis) written
in C++ and R. These building blocks are designed not only for direct use,
but also as foundational components for developing new statistical methods
that must operate on datasets too large to fit in memory. The package
supports data provided either as 'HDF5' files or standard R objects, and is
intended for high-dimensional applications such as 'omics' and
precision-medicine research.
Author: Dolors Pelegri-Siso [aut, cre] ,
Juan R. Gonzalez [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri@isglobal.org>
Diff between BigDataStatMeth versions 2.0.1 dated 2026-05-17 and 2.0.2 dated 2026-06-08
BigDataStatMeth-2.0.1/BigDataStatMeth/inst/include/hdf5Algebra/matrixDiagonal_OLD.hpp |only BigDataStatMeth-2.0.1/BigDataStatMeth/inst/include/hdf5Utilities/hdf5Files.hpp.bck |only BigDataStatMeth-2.0.2/BigDataStatMeth/DESCRIPTION | 10 BigDataStatMeth-2.0.2/BigDataStatMeth/MD5 | 80 - BigDataStatMeth-2.0.2/BigDataStatMeth/NEWS.md | 43 BigDataStatMeth-2.0.2/BigDataStatMeth/R/HDF5Matrix_op_normalize.R | 22 BigDataStatMeth-2.0.2/BigDataStatMeth/R/RcppExports.R | 4 BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_bind.R | 136 ++ BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_decompositions.R | 1 BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_normalize.R | 44 BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_operations.R | 81 + BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_split.R | 14 BigDataStatMeth-2.0.2/BigDataStatMeth/R/S3_standalone.R | 50 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/doc/BigDataStatMeth.R | 33 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/doc/BigDataStatMeth.Rmd | 84 + BigDataStatMeth-2.0.2/BigDataStatMeth/inst/doc/BigDataStatMeth.html | 124 +- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/Utilities/system-utils.hpp | 131 +- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/crossprod.hpp | 120 ++ BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixAggregations.hpp | 311 ++++- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixCorrelation.hpp | 32 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixInvCholesky.hpp | 132 -- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixNormalization.hpp | 124 +- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixPCA.hpp | 45 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixQR.hpp | 19 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixSvd.hpp | 6 BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/matrixSvdBlock.hpp | 222 ++-- BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/multiplication.hpp | 524 ++++------ BigDataStatMeth-2.0.2/BigDataStatMeth/inst/include/hdf5Algebra/tcrossprod.hpp | 151 ++ BigDataStatMeth-2.0.2/BigDataStatMeth/man/apply_function.Rd | 27 BigDataStatMeth-2.0.2/BigDataStatMeth/man/cbind.HDF5Matrix.Rd | 5 BigDataStatMeth-2.0.2/BigDataStatMeth/man/hdf5_apply.Rd | 33 BigDataStatMeth-2.0.2/BigDataStatMeth/man/hdf5_reduce.Rd | 14 BigDataStatMeth-2.0.2/BigDataStatMeth/man/rbind.HDF5Matrix.Rd | 5 BigDataStatMeth-2.0.2/BigDataStatMeth/man/reduce.Rd | 24 BigDataStatMeth-2.0.2/BigDataStatMeth/man/scale.Rd | 30 BigDataStatMeth-2.0.2/BigDataStatMeth/man/split.HDF5Matrix.Rd | 31 BigDataStatMeth-2.0.2/BigDataStatMeth/man/split_dataset.Rd | 13 BigDataStatMeth-2.0.2/BigDataStatMeth/src/RcppExports.cpp | 10 BigDataStatMeth-2.0.2/BigDataStatMeth/src/hdf5_r6_normalize.cpp | 37 BigDataStatMeth-2.0.2/BigDataStatMeth/src/hdf5_r6_subset.cpp | 6 BigDataStatMeth-2.0.2/BigDataStatMeth/src/hdf5_writeDimnames.cpp | 6 BigDataStatMeth-2.0.2/BigDataStatMeth/vignettes/BigDataStatMeth.Rmd | 84 + 42 files changed, 1977 insertions(+), 891 deletions(-)
More information about BigDataStatMeth at CRAN
Permanent link
Title: Automated Functional Annotation of Genetic Variants and Linked
Proxies
Description: To automated functional annotation of genetic variants and linked proxies. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.
Author: Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Diff between SNPannotator versions 1.4.6 dated 2026-01-08 and 1.4.7 dated 2026-06-08
SNPannotator-1.4.6/SNPannotator/man/mergeResultFiles.Rd |only SNPannotator-1.4.7/SNPannotator/DESCRIPTION | 8 SNPannotator-1.4.7/SNPannotator/MD5 | 35 +-- SNPannotator-1.4.7/SNPannotator/NAMESPACE | 2 SNPannotator-1.4.7/SNPannotator/R/aaa.R | 2 SNPannotator-1.4.7/SNPannotator/R/configFile_funcs.R | 90 ++++++-- SNPannotator-1.4.7/SNPannotator/R/demo.R | 4 SNPannotator-1.4.7/SNPannotator/R/ensembl_funcs.R | 61 +++-- SNPannotator-1.4.7/SNPannotator/R/inSilicoSeqPipeline.R | 2 SNPannotator-1.4.7/SNPannotator/R/merge_funcs.R |only SNPannotator-1.4.7/SNPannotator/R/misc_files.R | 109 +++++----- SNPannotator-1.4.7/SNPannotator/R/parse_funcs.R | 8 SNPannotator-1.4.7/SNPannotator/R/runPipelineOnlist.R | 32 +- SNPannotator-1.4.7/SNPannotator/R/stringDB_funcs.R | 33 ++- SNPannotator-1.4.7/SNPannotator/inst/extdata/demo_config.ini | 6 SNPannotator-1.4.7/SNPannotator/inst/extdata/inSilicoSeqConfig.ini | 39 ++- SNPannotator-1.4.7/SNPannotator/inst/rmd/variantReport.Rmd | 5 SNPannotator-1.4.7/SNPannotator/man/EnsemblDatabases.Rd | 4 SNPannotator-1.4.7/SNPannotator/man/EnsemblReleases.Rd | 4 SNPannotator-1.4.7/SNPannotator/man/merge_annotations.Rd |only 20 files changed, 279 insertions(+), 165 deletions(-)
Title: Personalised Synthetic Controls
Description: Allows the comparison of data cohorts (DC) against a Counter
Factual Model (CFM) and measures the difference in terms of an efficacy
parameter. Allows the application of Personalised Synthetic Controls.
Author: Richard Jackson [cre, aut, cph]
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Diff between psc versions 2.0.1 dated 2026-01-12 and 2.1.0 dated 2026-06-08
DESCRIPTION | 6 +++--- MD5 | 26 ++++++++++++++------------ NAMESPACE | 1 + NEWS.md | 2 ++ R/lik.flexsurvreg.R | 1 + R/pscComb.R |only R/pscEst.R | 4 ++-- R/pscEst_run.R | 14 +++++++------- R/pscEst_start.R | 17 ++++++++++------- R/pscfit.R | 4 ++-- README.md | 15 ++++++++------- inst/doc/psc.html | 26 +++++++++++++------------- man/figures/README-pressure-1.png |binary man/pscComb.Rd |only man/pscfit.Rd | 2 +- 15 files changed, 64 insertions(+), 54 deletions(-)
Title: Translate Text
Description: Provide easy methods to translate pieces of text.
Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <iwantomer@hotmail.com>
Diff between polyglotr versions 1.7.1 dated 2026-01-11 and 1.7.4 dated 2026-06-08
polyglotr-1.7.1/polyglotr/R/linguee_external_sources.R |only polyglotr-1.7.1/polyglotr/R/linguee_translation_examples.R |only polyglotr-1.7.1/polyglotr/R/linguee_word_translation.R |only polyglotr-1.7.1/polyglotr/inst/doc/Linguee.R |only polyglotr-1.7.1/polyglotr/inst/doc/Linguee.Rmd |only polyglotr-1.7.1/polyglotr/inst/doc/Linguee.html |only polyglotr-1.7.1/polyglotr/man/linguee_external_sources.Rd |only polyglotr-1.7.1/polyglotr/man/linguee_translation_examples.Rd |only polyglotr-1.7.1/polyglotr/man/linguee_word_translation.Rd |only polyglotr-1.7.1/polyglotr/vignettes/Linguee.Rmd |only polyglotr-1.7.4/polyglotr/DESCRIPTION | 6 polyglotr-1.7.4/polyglotr/MD5 | 86 +-- polyglotr-1.7.4/polyglotr/NAMESPACE | 3 polyglotr-1.7.4/polyglotr/NEWS.md | 15 polyglotr-1.7.4/polyglotr/R/apertium_get_language_pairs.R | 6 polyglotr-1.7.4/polyglotr/R/create_translation_table.R | 2 polyglotr-1.7.4/polyglotr/R/create_transliteration_table.R | 2 polyglotr-1.7.4/polyglotr/R/google_get_supported_languages.R | 6 polyglotr-1.7.4/polyglotr/R/google_translate.R | 91 ++- polyglotr-1.7.4/polyglotr/R/google_translate_long_text.R | 25 - polyglotr-1.7.4/polyglotr/R/google_transliterate.R | 43 - polyglotr-1.7.4/polyglotr/R/language_detect.R | 6 polyglotr-1.7.4/polyglotr/R/microsoft_supported_languages.R | 6 polyglotr-1.7.4/polyglotr/R/mymemory_translate.R | 6 polyglotr-1.7.4/polyglotr/R/pons_dictionaries.R | 6 polyglotr-1.7.4/polyglotr/R/pons_translate.R | 42 - polyglotr-1.7.4/polyglotr/R/qcri_get_domains.R | 9 polyglotr-1.7.4/polyglotr/R/qcri_get_language_pairs.R | 12 polyglotr-1.7.4/polyglotr/R/qcri_translate_text.R | 12 polyglotr-1.7.4/polyglotr/R/translate_apertium.R | 9 polyglotr-1.7.4/polyglotr/R/translate_to_morse.R | 21 polyglotr-1.7.4/polyglotr/R/translate_to_morse_audio.R | 27 - polyglotr-1.7.4/polyglotr/R/utils-http.R |only polyglotr-1.7.4/polyglotr/R/wikimedia_detect_language.R | 6 polyglotr-1.7.4/polyglotr/R/wikipedia_get_language_names.R | 9 polyglotr-1.7.4/polyglotr/R/wmcloud_translate.R | 6 polyglotr-1.7.4/polyglotr/README.md | 230 +--------- polyglotr-1.7.4/polyglotr/build/vignette.rds |binary polyglotr-1.7.4/polyglotr/inst/doc/Movie_Reviews.html | 5 polyglotr-1.7.4/polyglotr/inst/doc/apertium-intro.html | 5 polyglotr-1.7.4/polyglotr/inst/doc/language-detection-conditional-translation.html | 5 polyglotr-1.7.4/polyglotr/inst/doc/polyglotr.html | 5 polyglotr-1.7.4/polyglotr/inst/doc/translation-table-workflow.html | 5 polyglotr-1.7.4/polyglotr/inst/examples/launch_shiny_app.R | 2 polyglotr-1.7.4/polyglotr/inst/shiny-app/README.md | 3 polyglotr-1.7.4/polyglotr/inst/shiny-app/server.R | 14 polyglotr-1.7.4/polyglotr/inst/shiny-app/ui.R | 2 polyglotr-1.7.4/polyglotr/man/google_translate.Rd | 1 polyglotr-1.7.4/polyglotr/man/wikipedia_get_language_names.Rd | 3 polyglotr-1.7.4/polyglotr/tests/testthat/test-google_translate.R |only 50 files changed, 271 insertions(+), 471 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Package including functions and interactive shiny application
for the psychometric analysis of educational tests, psychological
assessments, health-related and other types of multi-item
measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre] ,
Adela Hladka [aut] ,
Jan Netik [aut] ,
Ondrej Leder [ctb],
Jakub Houdek [ctb],
Lubomir Stepanek [ctb],
Tomas Jurica [ctb],
Jana Vorlickova [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.5.5 dated 2025-07-10 and 1.6.0 dated 2026-06-08
DESCRIPTION | 18 MD5 | 256 - NAMESPACE | 1 NEWS.md | 16 R/DDplot.R | 85 R/DistractorAnalysis.R | 83 R/ICCrestricted.R | 36 R/ItemAnalysis.R | 33 R/Logistik_edited.R | 63 R/ShinyItemAnalysis-package.R | 4 R/blis.R | 224 + R/cronbach_alpha.R | 2 R/delta_method.R | 4 R/difLogistic_edited.R | 148 - R/difLord_edited.R | 163 - R/difMH_edited.R | 177 - R/difRaju_edited.R | 157 - R/difSIBTEST_edited.R | 72 R/fa_parallel.R | 139 R/gDiscrim.R | 25 R/ggWrightMap.R | 87 R/onAttach.R | 3 R/plotAdjacent.R | 46 R/plotCumulative.R | 113 R/plotDIFLogistic.R | 50 R/plotDIFirt.R | 71 R/plotDistractorAnalysis.R | 97 R/plotMultinomial.R | 47 R/plot_corr.R | 75 R/recode_nr.R | 11 R/startShinyItemAnalysis.R | 16 README.md | 57 build/partial.rdb |binary inst/CITATION | 25 inst/ShinyItemAnalysis/global.R | 10 inst/ShinyItemAnalysis/reporthtml.Rmd | 20 inst/ShinyItemAnalysis/reportpdf.Rmd | 50 inst/ShinyItemAnalysis/sc/data |only inst/ShinyItemAnalysis/sc/dif/adj.R | 10 inst/ShinyItemAnalysis/sc/dif/adj_it.R | 10 inst/ShinyItemAnalysis/sc/dif/cum.R | 10 inst/ShinyItemAnalysis/sc/dif/cum_it.R | 10 inst/ShinyItemAnalysis/sc/dif/delta_plt.R | 14 inst/ShinyItemAnalysis/sc/dif/log.R | 18 inst/ShinyItemAnalysis/sc/dif/log_it.R | 9 inst/ShinyItemAnalysis/sc/dif/lord.R | 25 inst/ShinyItemAnalysis/sc/dif/lord_it.R | 25 inst/ShinyItemAnalysis/sc/dif/mh.R | 8 inst/ShinyItemAnalysis/sc/dif/mh_it.R | 13 inst/ShinyItemAnalysis/sc/dif/mult.R | 11 inst/ShinyItemAnalysis/sc/dif/mult_it.R | 11 inst/ShinyItemAnalysis/sc/dif/nlr.R | 20 inst/ShinyItemAnalysis/sc/dif/nlr_it.R | 10 inst/ShinyItemAnalysis/sc/dif/raju.R | 25 inst/ShinyItemAnalysis/sc/dif/raju_it.R | 25 inst/ShinyItemAnalysis/sc/dif/sibtest.R | 16 inst/ShinyItemAnalysis/sc/dif/tot_scores.R | 26 inst/ShinyItemAnalysis/sc/irt/1pl.R | 22 inst/ShinyItemAnalysis/sc/irt/1pl_item.R | 9 inst/ShinyItemAnalysis/sc/irt/2pl.R | 7 inst/ShinyItemAnalysis/sc/irt/3pl.R | 7 inst/ShinyItemAnalysis/sc/irt/bock.R | 19 inst/ShinyItemAnalysis/sc/irt/comp.R | 6 inst/ShinyItemAnalysis/sc/irt/gpcm.R |only inst/ShinyItemAnalysis/sc/irt/gpcm_comparison.R |only inst/ShinyItemAnalysis/sc/irt/grm.R |only inst/ShinyItemAnalysis/sc/irt/rasch.R | 7 inst/ShinyItemAnalysis/sc/irt/train_dich.R | 24 inst/ShinyItemAnalysis/sc/irt/train_poly_gpcm.R | 3 inst/ShinyItemAnalysis/sc/irt/train_poly_grm.R | 51 inst/ShinyItemAnalysis/sc/irt/train_poly_nrm.R | 2 inst/ShinyItemAnalysis/sc/regr/adj.R | 6 inst/ShinyItemAnalysis/sc/regr/compar.R | 12 inst/ShinyItemAnalysis/sc/regr/cum.R | 18 inst/ShinyItemAnalysis/sc/regr/log.R | 9 inst/ShinyItemAnalysis/sc/regr/log_irt_z.R | 9 inst/ShinyItemAnalysis/sc/regr/log_z.R | 9 inst/ShinyItemAnalysis/sc/regr/nlr_3.R | 15 inst/ShinyItemAnalysis/sc/regr/nlr_4.R | 15 inst/ShinyItemAnalysis/sc/reliability/restr_range.R | 33 inst/ShinyItemAnalysis/sc/scores/total.R | 11 inst/ShinyItemAnalysis/sc/tia/crit_val_it.R | 8 inst/ShinyItemAnalysis/sc/tia/distr.R | 16 inst/ShinyItemAnalysis/sc/validity/crit_val.R | 5 inst/ShinyItemAnalysis/server.R | 9 inst/ShinyItemAnalysis/server/DIF.R | 2869 +++++++++++++------- inst/ShinyItemAnalysis/server/Data.R | 438 +-- inst/ShinyItemAnalysis/server/IRT.R | 359 +- inst/ShinyItemAnalysis/server/IRT/gpcm.R |only inst/ShinyItemAnalysis/server/IRT/grm.R |only inst/ShinyItemAnalysis/server/IRT/polytomous.R | 153 - inst/ShinyItemAnalysis/server/IRT/training.R | 787 ++++- inst/ShinyItemAnalysis/server/Modules.R | 59 inst/ShinyItemAnalysis/server/Regression.R | 525 ++- inst/ShinyItemAnalysis/server/Reliability.R | 59 inst/ShinyItemAnalysis/server/Reports.R | 502 ++- inst/ShinyItemAnalysis/server/Scores.R | 40 inst/ShinyItemAnalysis/server/TraditionalAnalysis.R | 287 +- inst/ShinyItemAnalysis/server/Validity.R | 348 +- inst/ShinyItemAnalysis/ui.R | 24 inst/ShinyItemAnalysis/ui/uiAbout.R | 333 +- inst/ShinyItemAnalysis/ui/uiDIF.R | 749 +++-- inst/ShinyItemAnalysis/ui/uiDIF/adjacent.R | 130 inst/ShinyItemAnalysis/ui/uiDIF/cumulative.R | 169 - inst/ShinyItemAnalysis/ui/uiDIF/logistic.R | 175 - inst/ShinyItemAnalysis/ui/uiDIF/multinomial.R | 162 - inst/ShinyItemAnalysis/ui/uiDIF/uiTDIF.R | 256 + inst/ShinyItemAnalysis/ui/uiData.R | 139 inst/ShinyItemAnalysis/ui/uiIRT.R | 127 inst/ShinyItemAnalysis/ui/uiIRT/uiDIRT.R | 360 +- inst/ShinyItemAnalysis/ui/uiIRT/uiPolyIRT.R | 79 inst/ShinyItemAnalysis/ui/uiIRT/uiPolyTraining.R | 447 ++- inst/ShinyItemAnalysis/ui/uiIRT/ui_gpcm.R |only inst/ShinyItemAnalysis/ui/uiIRT/ui_grm.R |only inst/ShinyItemAnalysis/ui/uiModules.R | 27 inst/ShinyItemAnalysis/ui/uiReferences.R | 47 inst/ShinyItemAnalysis/ui/uiRegression.R | 413 ++ inst/ShinyItemAnalysis/ui/uiReliability.R | 100 inst/ShinyItemAnalysis/ui/uiReports.R | 111 inst/ShinyItemAnalysis/ui/uiScores.R | 60 inst/ShinyItemAnalysis/ui/uiSetting.R | 100 inst/ShinyItemAnalysis/ui/uiTraditionalAnalysis.R | 207 - inst/ShinyItemAnalysis/ui/uiValidity.R | 108 man/BlisClass-class.Rd | 14 man/blis2blirt.Rd | 2 man/coef-BlisClass-method.Rd | 16 man/fa_parallel.Rd | 8 man/fit_blis.Rd | 23 man/get_orig_levels.Rd | 12 man/nominal_to_int.Rd | 12 man/obtain_nrm_def.Rd | 10 man/plot_corr.Rd | 7 man/print.blis_coefs.Rd | 10 133 files changed, 9782 insertions(+), 4193 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: Mediation, Moderation and Moderated-Mediation After Model
Fitting
Description: Computes indirect effects, conditional effects, and conditional
indirect effects in a structural equation model or path model after model
fitting, with no need to define any user parameters or label any paths in
the model syntax, using the approach presented in Cheung and Cheung
(2024) <doi:10.3758/s13428-023-02224-z>. Can also form bootstrap
confidence intervals by doing bootstrapping only once and reusing the
bootstrap estimates in all subsequent computations. Supports bootstrap
confidence intervals for standardized (partially or completely) indirect
effects, conditional effects, and conditional indirect effects as described
in Cheung (2009) <doi:10.3758/BRM.41.2.425> and Cheung, Cheung, Lau, Hui,
and Vong (2022) <doi:10.1037/hea0001188>. Model fitting can be done by
structural equation modeling using lavaan() or regression using lm().
Author: Shu Fai Cheung [aut, cre] ,
Sing-Hang Cheung [aut] ,
Rong Wei Sun [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between manymome versions 0.3.5 dated 2026-06-01 and 0.3.6 dated 2026-06-08
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 2 +- README.md | 2 +- inst/doc/mod_levels.html | 6 +++--- tests/testthat/test_mg_boot.R | 3 ++- tests/testthat/test_sam.R | 8 ++++++++ tests/testthat/test_sam_indirect_effect_std.R | 6 ++++-- tests/testthat/test_sam_mediation_mg.R | 3 ++- tests/testthat/test_sam_q_mediation.R | 10 ++++++++-- tests/testthat/test_sam_update_internal.R | 7 +++++-- 11 files changed, 47 insertions(+), 26 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Balasubramanian Narasimhan [aut],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.12.0-3 dated 2026-02-08 and 1.14.0-2 dated 2026-06-08
highs-1.12.0-3/highs/inst/HiGHS/HiGHS.sln |only highs-1.12.0-3/highs/inst/HiGHS/highs/io/FilereaderEms.cpp |only highs-1.12.0-3/highs/inst/HiGHS/highs/io/FilereaderEms.h |only highs-1.12.0-3/highs/inst/HiGHS/highs/ipm/hipo/ipm/CurtisReidScaling.cpp |only highs-1.12.0-3/highs/inst/HiGHS/highs/ipm/hipo/ipm/CurtisReidScaling.h |only highs-1.14.0-2/highs/DESCRIPTION | 15 highs-1.14.0-2/highs/MD5 | 442 +-- highs-1.14.0-2/highs/NAMESPACE | 14 highs-1.14.0-2/highs/NEWS.md | 6 highs-1.14.0-2/highs/R/RcppExports.R | 44 highs-1.14.0-2/highs/R/constants.R | 61 highs-1.14.0-2/highs/R/highs.R | 32 highs-1.14.0-2/highs/R/options.R | 204 - highs-1.14.0-2/highs/R/solver-api.R | 291 ++ highs-1.14.0-2/highs/README.md | 72 highs-1.14.0-2/highs/build |only highs-1.14.0-2/highs/cleanup | 4 highs-1.14.0-2/highs/configure | 14 highs-1.14.0-2/highs/configure.win | 13 highs-1.14.0-2/highs/inst/HiGHS/CMakeLists.txt | 44 highs-1.14.0-2/highs/inst/HiGHS/CONTRIBUTING.md | 4 highs-1.14.0-2/highs/inst/HiGHS/FEATURES.md | 64 highs-1.14.0-2/highs/inst/HiGHS/LICENSE.txt | 2 highs-1.14.0-2/highs/inst/HiGHS/MODULE.bazel | 18 highs-1.14.0-2/highs/inst/HiGHS/README.md | 4 highs-1.14.0-2/highs/inst/HiGHS/THIRD_PARTY_NOTICES.md | 6 highs-1.14.0-2/highs/inst/HiGHS/Version.txt | 2 highs-1.14.0-2/highs/inst/HiGHS/cmake/FindHipoDeps.cmake | 14 highs-1.14.0-2/highs/inst/HiGHS/cmake/cpp-highs.cmake | 2 highs-1.14.0-2/highs/inst/HiGHS/cmake/sources-python.cmake | 18 highs-1.14.0-2/highs/inst/HiGHS/cmake/sources.cmake | 23 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/SuiteSparse_config.c | 6 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/SuiteSparse_config.h | 12 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd.h | 16 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_1.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_2.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_control.c | 19 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_defaults.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_info.c | 29 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_order.c | 44 highs-1.14.0-2/highs/inst/HiGHS/extern/amd/amd_valid.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/GKlib/error.c | 9 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/GKlib/gk_macros.h | 6 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/GKlib/mcore.c | 19 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/auxapi.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/balance.c | 30 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/coarsen.c | 18 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/compress.c | 6 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/fm.c | 32 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/initpart.c | 23 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/ometis.c | 8 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/options.c | 80 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/proto.h | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/sfm.c | 18 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/libmetis/srefine.c | 2 highs-1.14.0-2/highs/inst/HiGHS/extern/metis/metis.h | 4 highs-1.14.0-2/highs/inst/HiGHS/extern/rcm/rcm.cpp | 31 highs-1.14.0-2/highs/inst/HiGHS/extern/rcm/rcm.h | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/CMakeLists.txt | 92 highs-1.14.0-2/highs/inst/HiGHS/highs/HConfig.h.bazel.in | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/Highs.h | 11 highs-1.14.0-2/highs/inst/HiGHS/highs/highspy/highs.py | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/io/Filereader.cpp | 32 highs-1.14.0-2/highs/inst/HiGHS/highs/io/Filereader.h | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/io/FilereaderLp.cpp | 10 highs-1.14.0-2/highs/inst/HiGHS/highs/io/HMPSIO.cpp | 18 highs-1.14.0-2/highs/inst/HiGHS/highs/io/HMPSIO.h | 12 highs-1.14.0-2/highs/inst/HiGHS/highs/io/HMpsFF.cpp | 167 - highs-1.14.0-2/highs/inst/HiGHS/highs/io/HMpsFF.h | 6 highs-1.14.0-2/highs/inst/HiGHS/highs/io/HighsIO.cpp | 159 - highs-1.14.0-2/highs/inst/HiGHS/highs/io/HighsIO.h | 15 highs-1.14.0-2/highs/inst/HiGHS/highs/io/LoadOptions.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/io/LoadOptions.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/io/filereaderlp/reader.cpp | 68 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/IpxWrapper.cpp | 134 - highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/IpxWrapper.h | 14 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/Auxiliary.cpp | 84 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/Auxiliary.h | 15 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/OrderingPrint.h |only highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/auxiliary/VectorOperations.cpp | 32 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Analyse.cpp | 276 +- highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Analyse.h | 9 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/CliqueStack.cpp | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/DataCollector.cpp | 59 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FactorHiGHS.cpp | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FactorHiGHS.h | 12 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FactorHiGHSSettings.h | 3 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Factorise.cpp | 28 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/FormatHandler.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridHybridFormatHandler.cpp | 30 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/HybridHybridFormatHandler.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/KrylovMethodsIpm.cpp | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Symbolic.cpp | 3 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Symbolic.h | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/factorhighs/Timing.h | 1 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Control.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/FactorHiGHSSolver.cpp | 469 ++- highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/FactorHiGHSSolver.h | 22 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Info.h | 9 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Iterate.cpp | 313 +- highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Iterate.h | 62 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/LinearSolver.h | 7 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Model.cpp | 529 +--- highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Model.h | 68 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Options.h | 38 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Parameters.h | 8 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/PreProcess.cpp |only highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/PreProcess.h |only highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Refine.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Solver.cpp | 361 +- highs-1.14.0-2/highs/inst/HiGHS/highs/ipm/hipo/ipm/Solver.h | 46 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HConst.h | 53 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/Highs.cpp | 401 +-- highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsDebug.cpp | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsDebug.h | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsDeprecated.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsIis.cpp | 367 ++ highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsIis.h | 63 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsInfo.cpp | 75 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsInfo.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsInterface.cpp | 821 ++---- highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsLpUtils.cpp | 18 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsLpUtils.h | 18 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsModelUtils.cpp | 182 - highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsModelUtils.h | 30 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsOptions.cpp | 196 + highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsOptions.h | 171 - highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolution.cpp | 335 ++ highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolution.h | 11 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolutionDebug.cpp | 14 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolutionDebug.h | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolve.cpp | 33 highs-1.14.0-2/highs/inst/HiGHS/highs/lp_data/HighsSolve.h | 1 highs-1.14.0-2/highs/inst/HiGHS/highs/meson.build | 7 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsCliqueTable.cpp | 297 -- highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsCliqueTable.h | 8 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsDomain.cpp | 100 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsDomain.h | 3 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsImplications.cpp | 60 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsImplications.h | 8 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsLpRelaxation.cpp | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/mip/HighsMipSolver.cpp | 7 highs-1.14.0-2/highs/inst/HiGHS/highs/model/HighsHessian.cpp | 47 highs-1.14.0-2/highs/inst/HiGHS/highs/model/HighsHessian.h | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/model/HighsHessianUtils.cpp | 363 +- highs-1.14.0-2/highs/inst/HiGHS/highs/parallel/HighsBinarySemaphore.h | 4 highs-1.14.0-2/highs/inst/HiGHS/highs/parallel/HighsTask.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/CupdlpWrapper.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/CupdlpWrapper.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/HiPdlpTimer.h |only highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/HiPdlpWrapper.cpp |only highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/HiPdlpWrapper.h |only highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cuda/CMakeLists.txt | 24 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cuda/test_cublas.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cuda/test_cuda_linalg.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_cs.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_cs.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_defs.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_linalg.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_linalg.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_proj.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_proj.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_restart.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_restart.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_scaling.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_scaling.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_solver.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_solver.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_step.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_step.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_utils.c | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/cupdlp_utils.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/cupdlp/glbopts.h | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/pdlp/hipdlp |only highs-1.14.0-2/highs/inst/HiGHS/highs/presolve/HPresolve.cpp | 1239 ++++++---- highs-1.14.0-2/highs/inst/HiGHS/highs/presolve/HPresolve.h | 29 highs-1.14.0-2/highs/inst/HiGHS/highs/presolve/HPresolveAnalysis.cpp | 78 highs-1.14.0-2/highs/inst/HiGHS/highs/presolve/HPresolveAnalysis.h | 3 highs-1.14.0-2/highs/inst/HiGHS/highs/qpsolver/basis.cpp | 10 highs-1.14.0-2/highs/inst/HiGHS/highs/qpsolver/quass.cpp | 5 highs-1.14.0-2/highs/inst/HiGHS/highs/simplex/HApp.h | 33 highs-1.14.0-2/highs/inst/HiGHS/highs/simplex/HEkkPrimal.cpp | 2 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsMatrixPic.cpp | 6 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsMatrixPic.h | 6 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsMatrixUtils.cpp | 137 - highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsMatrixUtils.h | 15 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsSparseMatrix.cpp | 8 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsUtils.cpp | 29 highs-1.14.0-2/highs/inst/HiGHS/highs/util/HighsUtils.h | 29 highs-1.14.0-2/highs/inst/HiGHS/meson.build | 2 highs-1.14.0-2/highs/inst/HiGHS/nuget/README.md | 2 highs-1.14.0-2/highs/inst/HiGHS/pyproject.toml | 10 highs-1.14.0-2/highs/inst/HiGHS/tests/test_highspy.py | 8 highs-1.14.0-2/highs/inst/build_cran_like.sh |only highs-1.14.0-2/highs/inst/build_highs.sh | 17 highs-1.14.0-2/highs/inst/doc |only highs-1.14.0-2/highs/inst/tinytest/test_dual-ray.R |only highs-1.14.0-2/highs/inst/tinytest/test_lp-solver.R | 3 highs-1.14.0-2/highs/inst/tinytest/test_misc-features.R |only highs-1.14.0-2/highs/inst/tinytest/test_ranging.R |only highs-1.14.0-2/highs/inst/tinytest/test_solver-api.R | 30 highs-1.14.0-2/highs/inst/tinytest/test_solver-modification.R |only highs-1.14.0-2/highs/inst/tinytest/test_stdout-stderr.R |only highs-1.14.0-2/highs/inst/tinytest/test_warm-start.R |only highs-1.14.0-2/highs/man/hi_solver_change_constraint_bounds.Rd | 7 highs-1.14.0-2/highs/man/hi_solver_clear_basis.Rd |only highs-1.14.0-2/highs/man/hi_solver_get_basis.Rd |only highs-1.14.0-2/highs/man/hi_solver_get_dual_ray.Rd |only highs-1.14.0-2/highs/man/hi_solver_get_primal_ray.Rd |only highs-1.14.0-2/highs/man/hi_solver_get_ranging.Rd |only highs-1.14.0-2/highs/man/hi_solver_get_run_time.Rd |only highs-1.14.0-2/highs/man/hi_solver_postsolve.Rd |only highs-1.14.0-2/highs/man/hi_solver_presolve.Rd |only highs-1.14.0-2/highs/man/hi_solver_read_model.Rd |only highs-1.14.0-2/highs/man/hi_solver_run.Rd | 12 highs-1.14.0-2/highs/man/hi_solver_set_basis.Rd |only highs-1.14.0-2/highs/man/hi_solver_set_option.Rd | 2 highs-1.14.0-2/highs/man/hi_solver_set_options.Rd | 4 highs-1.14.0-2/highs/man/hi_solver_set_solution.Rd |only highs-1.14.0-2/highs/man/hi_solver_set_sparse_solution.Rd |only highs-1.14.0-2/highs/man/hi_solver_set_start.Rd |only highs-1.14.0-2/highs/man/hi_solver_version.Rd |only highs-1.14.0-2/highs/man/highs_solve.Rd | 5 highs-1.14.0-2/highs/src/Makevars.in | 2 highs-1.14.0-2/highs/src/RcppExports.cpp | 139 + highs-1.14.0-2/highs/src/highs_interface.cpp | 212 + highs-1.14.0-2/highs/vignettes |only 228 files changed, 6666 insertions(+), 4315 deletions(-)
Title: Reparameterized Regression Models
Description: Provides estimation and data generation tools for several new regression models,
including the gamma, beta, inverse gamma and beta prime distributions. These models can be
parameterized based on the mean, median, mode, geometric mean and harmonic mean, as
specified by the user.
For details, see Bourguignon and Gallardo (2025a) <doi:10.1016/j.chemolab.2025.105382> and
Bourguignon and Gallardo (2025b) <doi:10.1111/stan.70007>.
Additional tools are provided for higher-order likelihood inference through
Skovgaard-adjusted likelihood ratio statistics and for predictive shrinkage
estimation in reparameterized beta regression models.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut],
Marcia Brandao [aut],
Tiago Magalhaes [ctb],
Rafael Izbicki [ctb]
Maintainer: Diego Gallardo <dgallardo@ubiobio.cl>
Diff between rregm versions 1.1 dated 2026-04-10 and 1.2 dated 2026-06-08
DESCRIPTION | 19 +++++++++++++------ INDEX | 14 ++++++++------ MD5 | 14 +++++++++----- NAMESPACE | 8 +++++--- NEWS.md | 6 ++++++ R/RBE.predictive.R |only R/RBE.skovgaard.R |only R/print.LRskov.R |only man/RBE.skov.Rd |only man/tools.rregm.Rd | 4 +++- 10 files changed, 44 insertions(+), 21 deletions(-)
Title: Miscellaneous Utilities for 'rerddap'
Description: The 'rerddapUtils' package is an 'R' package that is a set of four main
functions designed to work with and extend the 'rerddap' package. These functions includes one for restricting by season,
one for splitting large requests, and two for working with projected datasets. There are also two utility functions
that provide estimates of the size of a proposed 'rerddap::griddap()' request.
Author: Roy Mendelssohn [aut, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
This is a re-admission after prior archival of version 1.0.1 dated 2026-05-21
Diff between rerddapUtils versions 1.0.1 dated 2026-05-21 and 1.0.2 dated 2026-06-08
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- NEWS.md | 6 ++++- R/conversion.R | 62 ++++++++++++++++++++++++++-------------------------- R/griddap_season.R | 3 +- R/griddap_split.R | 6 +++-- R/iceInfo.R | 3 +- R/proj_extract.R | 3 +- R/utils.R | 6 +++-- R/wind_info.R | 3 +- man/iceInfo.Rd | 3 +- man/proj_extract.Rd | 3 +- man/wind_info.Rd | 3 +- man/xy_to_latlon.Rd | 3 +- 14 files changed, 78 insertions(+), 60 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions and flexible iterators implemented in
C++ for solving problems in combinatorics and computational mathematics.
Handles various combinatorial objects including combinations, permutations,
integer partitions and compositions, Cartesian products, unordered
Cartesian products, and partition of groups. Utilizes the RMatrix class
from 'RcppParallel' for thread safety. The combination and permutation
functions contain constraint parameters that allow for generation of all
results of a vector meeting specific criteria (e.g. finding all
combinations such that the sum is between two bounds). Capable of
ranking/unranking combinatorial objects efficiently (e.g. retrieve only the
nth lexicographical result) which sets up nicely for parallelization as
well as random sampling. Gmp support permits exploration where the total
number of results is large (e.g. comboSample(10000, 500, n = 4)).
Additionally, there are several high performance number theoretic
functions that are [...truncated...]
Author: Joseph Wood [aut, cre]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.10.0 dated 2026-03-08 and 2.10.1 dated 2026-06-08
DESCRIPTION | 6 - MD5 | 88 +++++++-------- NEWS.md | 17 ++ R/Utility.R | 8 + R/zzz.R | 64 ++--------- README.md | 2 inst/CITATION | 4 inst/NEWS.Rd | 184 +++++++++++++++++--------------- inst/doc/CombPermConstraints.Rmd | 28 ++-- inst/doc/CombPermConstraints.html | 30 ++--- inst/doc/CombinatorialSampling.Rmd | 24 ++-- inst/doc/CombinatorialSampling.html | 26 ++-- inst/doc/CombinatoricsIterators.Rmd | 146 ++++++++++++------------- inst/doc/CombinatoricsIterators.html | 158 +++++++++++++-------------- inst/doc/ComputationalMathematics.Rmd | 36 +++--- inst/doc/ComputationalMathematics.html | 38 +++--- inst/doc/GeneralCombinatorics.Rmd | 28 ++-- inst/doc/GeneralCombinatorics.html | 28 ++-- inst/doc/HighPerformanceBenchmarks.Rmd | 116 ++++++++++---------- inst/doc/HighPerformanceBenchmarks.html | 118 ++++++++++---------- inst/doc/IntegerCompositions.Rmd | 18 +-- inst/doc/IntegerCompositions.html | 20 +-- inst/doc/IntegerPartitions.Rmd | 14 +- inst/doc/IntegerPartitions.html | 16 +- inst/doc/OtherCombinatorics.Rmd | 26 ++-- inst/doc/OtherCombinatorics.html | 28 ++-- inst/doc/SubsetSum.Rmd | 32 ++--- inst/doc/SubsetSum.html | 34 ++--- man/combinatoricsGeneral.Rd | 2 man/comboGroups.Rd | 2 man/stdThreadMax.Rd | 2 src/NextComposition.cpp | 4 src/PartitionsCount.cpp | 13 ++ src/version.cpp | 2 tests/testthat/testPermuteGeneral.R | 8 + vignettes/CombPermConstraints.Rmd | 28 ++-- vignettes/CombinatorialSampling.Rmd | 24 ++-- vignettes/CombinatoricsIterators.Rmd | 146 ++++++++++++------------- vignettes/ComputationalMathematics.Rmd | 36 +++--- vignettes/GeneralCombinatorics.Rmd | 28 ++-- vignettes/HighPerformanceBenchmarks.Rmd | 116 ++++++++++---------- vignettes/IntegerCompositions.Rmd | 18 +-- vignettes/IntegerPartitions.Rmd | 14 +- vignettes/OtherCombinatorics.Rmd | 26 ++-- vignettes/SubsetSum.Rmd | 32 ++--- 45 files changed, 933 insertions(+), 905 deletions(-)
Title: Interactive Topic Modeling and Bibliometric Analysis via Shiny
Description: Provides a 'Shiny' graphical interface for the complete workflow of
Latent Dirichlet Allocation (LDA) topic modelling on bibliometric data from
Scopus and Web of Science. Steps include data import and deduplication, text
preprocessing (stopword removal, stemming, n-grams, sparse-term filtering),
statistical inference to select the optimal number of topics via coherence,
final model training, and topic trend analysis over time using linear
regression. All results can be exported as Excel files, RDS objects, and
publication-quality plots.
Author: Javier De La Hoz-M [aut, cre]
Maintainer: Javier De La Hoz-M <jdelahoz@unimagdalena.edu.co>
This is a re-admission after prior archival of version 0.9.3 dated 2021-03-29
Diff between LDAShiny versions 0.9.3 dated 2021-03-29 and 1.0.0 dated 2026-06-08
LDAShiny-0.9.3/LDAShiny/R/crude.R |only LDAShiny-0.9.3/LDAShiny/R/removeSparseTerms.R |only LDAShiny-0.9.3/LDAShiny/R/runLDAShiny.R |only LDAShiny-0.9.3/LDAShiny/data |only LDAShiny-0.9.3/LDAShiny/inst/doc/A_brief_introduction_to_LDAShiny.R |only LDAShiny-0.9.3/LDAShiny/inst/doc/A_brief_introduction_to_LDAShiny.Rmd |only LDAShiny-0.9.3/LDAShiny/inst/doc/A_brief_introduction_to_LDAShiny.html |only LDAShiny-0.9.3/LDAShiny/inst/doc/Una_breve_introducci-n_a_LDAShiny.R |only LDAShiny-0.9.3/LDAShiny/inst/doc/Una_breve_introducci-n_a_LDAShiny.Rmd |only LDAShiny-0.9.3/LDAShiny/inst/doc/Una_breve_introducci-n_a_LDAShiny.html |only LDAShiny-0.9.3/LDAShiny/inst/extdata |only LDAShiny-0.9.3/LDAShiny/inst/img |only LDAShiny-0.9.3/LDAShiny/inst/shinyLDA |only LDAShiny-0.9.3/LDAShiny/man/crude.Rd |only LDAShiny-0.9.3/LDAShiny/man/removeSparseTerms.Rd |only LDAShiny-0.9.3/LDAShiny/man/runLDAShiny.Rd |only LDAShiny-0.9.3/LDAShiny/vignettes/A_brief_introduction_to_LDAShiny.Rmd |only LDAShiny-0.9.3/LDAShiny/vignettes/Una_breve_introducci-n_a_LDAShiny.Rmd |only LDAShiny-1.0.0/LDAShiny/DESCRIPTION | 78 +---- LDAShiny-1.0.0/LDAShiny/MD5 | 82 +++-- LDAShiny-1.0.0/LDAShiny/NAMESPACE | 156 +++++++++- LDAShiny-1.0.0/LDAShiny/R/app_config.R |only LDAShiny-1.0.0/LDAShiny/R/app_server.R |only LDAShiny-1.0.0/LDAShiny/R/app_ui.R |only LDAShiny-1.0.0/LDAShiny/R/globals.R |only LDAShiny-1.0.0/LDAShiny/R/golem_utils_server.R |only LDAShiny-1.0.0/LDAShiny/R/golem_utils_ui.R |only LDAShiny-1.0.0/LDAShiny/R/mod_about.R |only LDAShiny-1.0.0/LDAShiny/R/mod_import_bibliometrics.R |only LDAShiny-1.0.0/LDAShiny/R/mod_inference.R |only LDAShiny-1.0.0/LDAShiny/R/mod_lda_train.R |only LDAShiny-1.0.0/LDAShiny/R/mod_preprocess.R |only LDAShiny-1.0.0/LDAShiny/R/mod_trend.R |only LDAShiny-1.0.0/LDAShiny/R/run_LDAShiny.R |only LDAShiny-1.0.0/LDAShiny/R/zzz.R |only LDAShiny-1.0.0/LDAShiny/build/vignette.rds |binary LDAShiny-1.0.0/LDAShiny/inst/WORDLIST |only LDAShiny-1.0.0/LDAShiny/inst/app |only LDAShiny-1.0.0/LDAShiny/inst/doc/LDAShiny-introduction.R |only LDAShiny-1.0.0/LDAShiny/inst/doc/LDAShiny-introduction.Rmd |only LDAShiny-1.0.0/LDAShiny/inst/doc/LDAShiny-introduction.html |only LDAShiny-1.0.0/LDAShiny/inst/golem-config.yml |only LDAShiny-1.0.0/LDAShiny/man/lda_themes.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_about_server.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_about_ui.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_import_bibliometrics_server.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_import_bibliometrics_ui.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_inference_server.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_inference_ui.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_lda_train.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_preprocess_server.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_preprocess_ui.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_trend_server.Rd |only LDAShiny-1.0.0/LDAShiny/man/mod_trend_ui.Rd |only LDAShiny-1.0.0/LDAShiny/man/parse_wos.Rd |only LDAShiny-1.0.0/LDAShiny/man/run_LDAShiny.Rd |only LDAShiny-1.0.0/LDAShiny/man/standardize_scopus.Rd |only LDAShiny-1.0.0/LDAShiny/tests |only LDAShiny-1.0.0/LDAShiny/vignettes/LDAShiny-introduction.Rmd |only 59 files changed, 229 insertions(+), 87 deletions(-)
Title: Automated Eye Tracking Data Quality Determination for
Screen-Based Eye Trackers
Description: Compute common data quality metrics for accuracy, precision and data loss
for screen-based eye trackers. The package supports gaze input in screen pixels or
degrees and reports angular measures in degrees where appropriate. If you use this
package, please cite Niehorster, D.C., Nyström, M., Hessels, R.S., Benjamins, J.S.,
Andersson, R., and Hooge, I.T.C. (2026). The fundamentals of eye tracking, Part 7:
Determining data quality. Behavior Research Methods. <doi:10.3758/s13428-026-03039-4>.
Author: Diederick Niehorster [aut, cre, cph]
Maintainer: Diederick Niehorster <diederick_c.niehorster@humlab.lu.se>
Diff between ETDQualitizer versions 1.0.0 dated 2026-05-21 and 1.1.0 dated 2026-06-08
DESCRIPTION | 8 +- MD5 | 6 - R/ETDQualitizer.R | 100 ++++++++++++++++++++++++++--- tests/testthat/test-data_quality_metrics.R | 37 ++++++++++ 4 files changed, 137 insertions(+), 14 deletions(-)
Title: Multi-Context Colocalization Analysis for QTL and GWAS Studies
Description: A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects,
based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero
effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS)
and quantitative trait loci (QTL) studies.
The ColocBoost model is described in Cao et. al. (2025) <doi:10.1101/2025.04.17.25326042>.
Author: Xuewei Cao [cre, aut, cph],
Haochen Sun [aut, cph],
Ru Feng [aut, cph],
Daniel Nachun [aut, cph],
Kushal Dey [aut, cph],
Gao Wang [aut, cph]
Maintainer: Xuewei Cao <xc2270@cumc.columbia.edu>
Diff between colocboost versions 1.0.8 dated 2026-06-07 and 1.0.9 dated 2026-06-08
DESCRIPTION | 8 MD5 | 12 inst/doc/Individual_Level_Colocalization.html | 12 inst/doc/announcements.Rmd | 2 inst/doc/announcements.html | 2 tests/testthat/test_inference.R | 467 ++++++++------------------ vignettes/announcements.Rmd | 2 7 files changed, 176 insertions(+), 329 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting and Doubly Robust Estimation
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects based on different identification strategies (unconfoundedness, instruments, difference-in-differences, regression discontinuity designs).
Author: Hugo Bodory [aut, cre] ,
Martin Huber [aut] ,
Jannis Kueck [aut]
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
This is a re-admission after prior archival of version 1.1.4 dated 2025-12-01
Diff between causalweight versions 1.1.4 dated 2025-12-01 and 1.1.5 dated 2026-06-08
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 -- R/attrlateweight.R | 1 - R/dyntreatDML.R | 2 +- R/functions.R | 8 ++------ R/medDML.R | 9 ++++----- R/medweightcont.R | 2 +- R/paneltestDML.R | 2 +- man/dyntreatDML.Rd | 2 +- man/medDML.Rd | 3 --- man/medweightcont.Rd | 2 +- man/paneltestDML.Rd | 2 +- 13 files changed, 29 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-05-25 1.1.0
2026-05-04 1.0.2
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.92 dated 2026-03-22 and 0.7.0 dated 2026-06-08
inti-0.6.92/inti/R/jc_tombola.R |only inti-0.6.92/inti/inst/extdata/_extensions/scihub/article.zp |only inti-0.6.92/inti/inst/extdata/_extensions/scihub/files/template.docx |only inti-0.6.92/inti/inst/extdata/_extensions/scihub/manuscript/Figure-1.jpg |only inti-0.6.92/inti/man/jc_tombola.Rd |only inti-0.7.0/inti/DESCRIPTION | 13 inti-0.7.0/inti/MD5 | 79 ++-- inti-0.7.0/inti/NAMESPACE | 2 inti-0.7.0/inti/NEWS.md | 9 inti-0.7.0/inti/R/design_noreps.R | 12 inti-0.7.0/inti/R/design_repblock.R | 16 inti-0.7.0/inti/R/gdoc2qmd.R | 11 inti-0.7.0/inti/R/rticle.R |only inti-0.7.0/inti/R/tarpuy_design.R | 20 - inti-0.7.0/inti/R/tarpuy_plex.R | 87 ++-- inti-0.7.0/inti/build/partial.rdb |binary inti-0.7.0/inti/build/vignette.rds |binary inti-0.7.0/inti/inst/doc/apps.html | 8 inti-0.7.0/inti/inst/doc/apps.qmd | 6 inti-0.7.0/inti/inst/doc/policy.html | 4 inti-0.7.0/inti/inst/doc/policy.qmd | 4 inti-0.7.0/inti/inst/doc/rticles.html | 2 inti-0.7.0/inti/inst/doc/rticles.qmd | 2 inti-0.7.0/inti/inst/doc/tarpuy.html | 2 inti-0.7.0/inti/inst/doc/tarpuy.qmd | 2 inti-0.7.0/inti/inst/doc/yupana.Rmd | 2 inti-0.7.0/inti/inst/doc/yupana.html | 2 inti-0.7.0/inti/inst/extdata/_extensions/scihub/ReadMe.qmd | 9 inti-0.7.0/inti/inst/extdata/_extensions/scihub/article.qmd | 35 - inti-0.7.0/inti/inst/extdata/_extensions/scihub/draft.md |only inti-0.7.0/inti/inst/extdata/_extensions/scihub/files/style.css |only inti-0.7.0/inti/inst/extdata/_extensions/scihub/files/style.docx |only inti-0.7.0/inti/inst/extdata/_extensions/scihub/manuscript/Figure_1.jpg |only inti-0.7.0/inti/inst/tarpuy/server.R | 195 +++++++--- inti-0.7.0/inti/inst/tarpuy/ui.R | 103 +---- inti-0.7.0/inti/man/design_noreps.Rd | 8 inti-0.7.0/inti/man/design_repblock.Rd | 10 inti-0.7.0/inti/man/reexports.Rd | 2 inti-0.7.0/inti/man/rticle.Rd |only inti-0.7.0/inti/man/tarpuy_design.Rd | 8 inti-0.7.0/inti/man/tarpuy_plex.Rd | 26 - inti-0.7.0/inti/vignettes/apps.qmd | 6 inti-0.7.0/inti/vignettes/policy.qmd | 4 inti-0.7.0/inti/vignettes/rticles.qmd | 2 inti-0.7.0/inti/vignettes/tarpuy.qmd | 2 inti-0.7.0/inti/vignettes/yupana.Rmd | 2 46 files changed, 378 insertions(+), 317 deletions(-)
Title: Automated Data Quality Checks for Recurring Dataset Deliveries
Description: Automates quality verification of recurring external dataset deliveries.
For each new file arrival, it runs single-snapshot quality checks, compares
the file to the previous delivery, writes a self-contained 'HTML' report, and
records summary statistics in a local 'SQLite' database for long-term trend
tracking. Supports 'CSV' and fixed-width formats. Custom organisation-specific
checks can be supplied as plain R files.
Author: Mick Mioduszewski [aut, cre]
Maintainer: Mick Mioduszewski <mick@mioduszewski.net>
Diff between dqcheckr versions 0.2.0 dated 2026-06-01 and 0.2.1 dated 2026-06-08
DESCRIPTION | 8 +- MD5 | 56 +++++++++---------- NEWS.md | 23 +++++++ R/checks_custom.R | 17 +++-- R/checks_generic.R | 6 +- R/compare.R | 4 - R/dqcheckr-package.R | 9 ++- R/drift.R | 56 ++++++------------- R/ingest.R | 26 ++++++-- R/report.R | 10 ++- R/snapshot.R | 30 +++++----- R/utils.R | 9 ++- README.md |only build/vignette.rds |binary inst/doc/specification.Rmd | 10 +-- inst/doc/specification.html | 8 +- man/check_min_row_count.Rd | 6 +- man/run_custom_checks.Rd | 2 tests/testthat/helper.R |only tests/testthat/test-checks.R | 103 +++++++++++------------------------ tests/testthat/test-col-threshold.R | 2 tests/testthat/test-compare.R | 24 +------- tests/testthat/test-drift.R | 15 ----- tests/testthat/test-ingest.R | 5 - tests/testthat/test-integration.R | 2 tests/testthat/test-report-tempdir.R | 2 tests/testthat/test-snapshot.R | 46 +++------------ tests/testthat/test-type-override.R | 2 tests/testthat/test-utils.R | 2 vignettes/specification.Rmd | 10 +-- 30 files changed, 212 insertions(+), 281 deletions(-)