Title: Threshold-Sweep QCA
Description: Provides threshold sweep methods for Qualitative Comparative
Analysis (QCA). Implements Condition Threshold Sweep-Single (CTS-S),
Condition Threshold Sweep-Multiple (CTS-M), Outcome Threshold Sweep (OTS),
and Dual Threshold Sweep (DTS) for systematic exploration of threshold
calibration effects on crisp-set QCA results. These methods extend
traditional robustness approaches by treating threshold variation as an
exploratory tool for discovering causal structures. Also provides Fiss
(2011) <doi:10.5465/amj.2011.60263120> core/peripheral condition
classification via compute_fiss_core() and generate_fiss_chart(), enabling
four-symbol configuration charts that distinguish core conditions (present
in both parsimonious and intermediate solutions) from peripheral conditions
(intermediate only). Built on top of the 'QCA' package by Dusa (2019)
<doi:10.1007/978-3-319-75668-4>, with function arguments following 'QCA'
conventions. Based on set-theoretic methods by Ragin (2008)
<doi: [...truncated...]
Author: Yuki Toyoda [aut, cre],
Japan Society for the Promotion of Science [fnd]
Maintainer: Yuki Toyoda <yuki.toyoda.ds@hosei.ac.jp>
Diff between ThSQCA versions 2.0.2 dated 2026-07-15 and 2.0.4 dated 2026-07-22
DESCRIPTION | 9 - MD5 | 26 ++-- NEWS.md | 77 ++++++++++++ R/tsqca_config_chart.R | 79 ++++++------- R/tsqca_core.R | 126 +++++++++++---------- R/tsqca_helpers.R | 89 +++++++------- R/tsqca_report.R | 23 +++ README.md | 6 - inst/doc/ThSQCA_Reproducible_EN.html | 2 inst/doc/ThSQCA_Tutorial_EN.html | 2 tests/testthat/helper-fixtures.R |only tests/testthat/test-edge-inputs.R |only tests/testthat/test-endtoend-cyclic.R |only tests/testthat/test-extractor-consistency-stress.R |only tests/testthat/test-generate-report-e2e.R |only tests/testthat/test-intermediate-covS.R |only tests/testthat/test-multisolution-covS.R |only tests/testthat/test-report-chart-extractors.R |only 18 files changed, 282 insertions(+), 157 deletions(-)
Title: Nonparametric Item Response Theory
Description: Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Author: Angelo Mazza [aut],
Antonio Punzo [aut],
Brian McGuire [aut, cre]
Maintainer: Brian McGuire <mcguirebc@gmail.com>
Diff between KernSmoothIRT versions 6.4 dated 2020-02-17 and 6.6 dated 2026-07-22
KernSmoothIRT-6.4/KernSmoothIRT/src/Makevars |only KernSmoothIRT-6.4/KernSmoothIRT/src/Makevars.win |only KernSmoothIRT-6.6/KernSmoothIRT/DESCRIPTION | 20 +++++++---- KernSmoothIRT-6.6/KernSmoothIRT/MD5 | 17 ++++----- KernSmoothIRT-6.6/KernSmoothIRT/NAMESPACE | 2 - KernSmoothIRT-6.6/KernSmoothIRT/inst/CITATION | 16 ++++---- KernSmoothIRT-6.6/KernSmoothIRT/man/KernSmoothIRT-package.Rd | 4 +- KernSmoothIRT-6.6/KernSmoothIRT/man/ksIRT.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/man/plot.ksIRT.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/man/subjOCCDIF.Rd | 2 - KernSmoothIRT-6.6/KernSmoothIRT/src/init.c |only 11 files changed, 36 insertions(+), 29 deletions(-)
Title: Process Command Line Arguments
Description: Process command line arguments, allowing scripts to
behave like functions, with well-defined inputs and outputs.
Helps make data analysis workflows more modular,
and therefore more transparent, flexible, and reliable.
Author: John Bryant [aut, cre],
Bayesian Demography Limited [cph]
Maintainer: John Bryant <john@bayesiandemography.com>
Diff between command versions 0.1.3 dated 2025-11-22 and 0.2.0 dated 2026-07-22
DESCRIPTION | 21 ++---- MD5 | 53 ++++++++------- NAMESPACE | 1 NEWS.md | 35 ++++++++++ R/check-functions.R | 14 ++-- R/cmd_assign.R | 3 R/command-package.R | 13 ++- R/extract_make.R | 5 - R/extract_shell.R | 5 - R/helper-functions.R | 107 ++++++++++++++++++++++++++++--- R/makefile.R | 9 +- R/shell_script.R | 9 +- R/use_renv.R |only man/cmd_assign.Rd | 3 man/command-package.Rd | 17 +++-- man/extract_make.Rd | 3 man/extract_shell.Rd | 3 man/makefile.Rd | 5 - man/shell_script.Rd | 5 - man/use_renv.Rd |only tests/testthat/helper.R | 26 +++++++ tests/testthat/test-check-functions.R | 12 +-- tests/testthat/test-cmd_assign.R | 61 ++++++++++++++++++ tests/testthat/test-extract_make.R | 11 +-- tests/testthat/test-extract_shell.R | 12 +-- tests/testthat/test-helper-functions.R | 111 +++++++++++++++++++++++++++++++++ tests/testthat/test-makefile.R | 17 ++--- tests/testthat/test-shell_script.R | 13 --- tests/testthat/test-use_renv.R |only 29 files changed, 447 insertions(+), 127 deletions(-)
Title: Lossless CDISC-Native Input and Output for Clinical Datasets
Description: Reads and writes clinical-trial datasets losslessly across
'SAS' XPORT (XPT), Clinical Data Interchange Standards Consortium
(CDISC) Dataset-JSON, and 'Apache Parquet', applying a specification to
produce submission-ready Study Data Tabulation Model (SDTM) and
Analysis Data Model (ADaM) datasets. A single canonical metadata model
carries labels, CDISC data types, lengths, 'SAS' display formats,
controlled-terminology references, and sort keys identically across
every format, so conversion between any two formats is lossless by
construction. Pure 'R' and lightweight, with no external 'SAS' or
'Java' runtime. Implements the published format specifications for
CDISC Dataset-JSON
(<https://cdisc-org.github.io/DataExchange-DatasetJson/doc/dataset-json1-1.html>)
and 'SAS' XPORT
(<https://www.loc.gov/preservation/digital/formats/fdd/fdd000466.shtml>).
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between artoo versions 0.1.2 dated 2026-07-01 and 0.1.3 dated 2026-07-22
DESCRIPTION | 6 MD5 | 46 +++--- NEWS.md | 34 ++++ R/check_spec.R | 25 +++ R/checks.R | 7 R/codec_json.R | 7 R/codec_ndjson.R | 6 R/codec_parquet.R | 6 R/codec_xpt.R | 45 +++++ R/encoding.R | 279 +++++++++++++++++++++++++++++++++---- inst/WORDLIST | 111 ++++++++------ inst/spec_rules.json | 11 + man/artoo_checks.Rd | 6 man/write_json.Rd | 7 man/write_ndjson.Rd | 6 man/write_parquet.Rd | 6 man/write_xpt.Rd | 28 ++- tests/testthat/_snaps/checks.md | 2 tests/testthat/_snaps/codec_xpt.md | 10 + tests/testthat/_snaps/encoding.md | 20 ++ tests/testthat/test-check_spec.R | 43 +++++ tests/testthat/test-codec_xpt.R | 42 +++++ tests/testthat/test-encoding.R | 200 ++++++++++++++++++++++++++ tests/testthat/test-members.R | 4 24 files changed, 831 insertions(+), 126 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-30 1.0.0
Title: Reference Based Multiple Imputation
Description: Implements standard and reference based multiple imputation methods for continuous
longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular,
this package supports deterministic conditional mean imputation and jackknifing as described
in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described
in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum
likelihood imputation as described in von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>.
Author: Lukas A. Widmer [aut, cre] ,
Craig Gower-Page [aut],
Isaac Gravestock [aut] ,
Alessandro Noci [aut],
Marcel Wolbers [aut] ,
Daniel Sabanes Bove [aut] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Lukas A. Widmer <lukas_andreas.widmer@novartis.com>
Diff between rbmi versions 1.6.0 dated 2026-01-23 and 1.6.1 dated 2026-07-22
rbmi-1.6.0/rbmi/R/rbmi.R |only rbmi-1.6.0/rbmi/man/extract_data_nmar_as_na.Rd |only rbmi-1.6.0/rbmi/vignettes/retrieved_dropout.asis |only rbmi-1.6.0/rbmi/vignettes/retrieved_dropout.html |only rbmi-1.6.1/rbmi/DESCRIPTION | 34 - rbmi-1.6.1/rbmi/MD5 | 235 +++++----- rbmi-1.6.1/rbmi/NAMESPACE | 1 rbmi-1.6.1/rbmi/NEWS.md | 46 +- rbmi-1.6.1/rbmi/R/analyse.R | 14 rbmi-1.6.1/rbmi/R/ancova.R | 38 + rbmi-1.6.1/rbmi/R/as_ascii_table.R | 8 rbmi-1.6.1/rbmi/R/bootstrap.R | 2 rbmi-1.6.1/rbmi/R/controls.R | 18 rbmi-1.6.1/rbmi/R/dataclasses.R | 9 rbmi-1.6.1/rbmi/R/delta.R | 14 rbmi-1.6.1/rbmi/R/draws.R | 70 ++- rbmi-1.6.1/rbmi/R/expand.R | 10 rbmi-1.6.1/rbmi/R/impute.R | 14 rbmi-1.6.1/rbmi/R/longData.R | 46 +- rbmi-1.6.1/rbmi/R/mcmc.R | 16 rbmi-1.6.1/rbmi/R/methods.R | 26 + rbmi-1.6.1/rbmi/R/mmrm.R | 10 rbmi-1.6.1/rbmi/R/parallel.R | 9 rbmi-1.6.1/rbmi/R/pool.R | 99 ++++ rbmi-1.6.1/rbmi/R/rbmi-package.R |only rbmi-1.6.1/rbmi/R/scaling.R | 2 rbmi-1.6.1/rbmi/R/simulate.R | 14 rbmi-1.6.1/rbmi/R/simulate_data.R | 90 +++- rbmi-1.6.1/rbmi/R/stack.R | 6 rbmi-1.6.1/rbmi/R/strategies.R | 34 + rbmi-1.6.1/rbmi/R/utilities.R | 43 + rbmi-1.6.1/rbmi/R/validate.R | 6 rbmi-1.6.1/rbmi/R/validate_datalong.R | 14 rbmi-1.6.1/rbmi/README.md | 4 rbmi-1.6.1/rbmi/build/partial.rdb |binary rbmi-1.6.1/rbmi/build/vignette.rds |binary rbmi-1.6.1/rbmi/inst/WORDLIST |only rbmi-1.6.1/rbmi/inst/doc/CondMean_Inference.html | 6 rbmi-1.6.1/rbmi/inst/doc/advanced.html | 8 rbmi-1.6.1/rbmi/inst/doc/quickstart.html | 58 +- rbmi-1.6.1/rbmi/inst/doc/retrieved_dropout.html |only rbmi-1.6.1/rbmi/inst/doc/retrieved_dropout.html.asis |only rbmi-1.6.1/rbmi/inst/doc/stat_specs.html | 14 rbmi-1.6.1/rbmi/man/STAN_BLOCKS.Rd | 5 rbmi-1.6.1/rbmi/man/Stack.Rd | 106 ++-- rbmi-1.6.1/rbmi/man/add_class.Rd | 4 rbmi-1.6.1/rbmi/man/analyse.Rd | 9 rbmi-1.6.1/rbmi/man/ancova.Rd | 39 + rbmi-1.6.1/rbmi/man/as_ascii_table.Rd | 2 rbmi-1.6.1/rbmi/man/as_class.Rd | 4 rbmi-1.6.1/rbmi/man/as_dataframe.Rd | 2 rbmi-1.6.1/rbmi/man/as_mmrm_df.Rd | 2 rbmi-1.6.1/rbmi/man/as_mmrm_formula.Rd | 4 rbmi-1.6.1/rbmi/man/as_model_df.Rd | 2 rbmi-1.6.1/rbmi/man/as_stan_array.Rd | 4 rbmi-1.6.1/rbmi/man/as_stan_fragments.Rd | 2 rbmi-1.6.1/rbmi/man/as_strata.Rd | 2 rbmi-1.6.1/rbmi/man/control.Rd | 23 - rbmi-1.6.1/rbmi/man/convert_to_imputation_list_df.Rd | 6 rbmi-1.6.1/rbmi/man/delta_template.Rd | 13 rbmi-1.6.1/rbmi/man/draws.Rd | 57 ++ rbmi-1.6.1/rbmi/man/ensure_rstan.Rd | 2 rbmi-1.6.1/rbmi/man/eval_mmrm.Rd | 4 rbmi-1.6.1/rbmi/man/expand.Rd | 8 rbmi-1.6.1/rbmi/man/extract_data_mnar_as_na.Rd |only rbmi-1.6.1/rbmi/man/extract_imputed_df.Rd | 2 rbmi-1.6.1/rbmi/man/figures/lifecycle-deprecated.svg |only rbmi-1.6.1/rbmi/man/figures/lifecycle-experimental.svg |only rbmi-1.6.1/rbmi/man/figures/lifecycle-stable.svg |only rbmi-1.6.1/rbmi/man/figures/lifecycle-superseded.svg |only rbmi-1.6.1/rbmi/man/fit_mcmc.Rd | 4 rbmi-1.6.1/rbmi/man/getStrategies.Rd | 6 rbmi-1.6.1/rbmi/man/get_draws_mle.Rd | 2 rbmi-1.6.1/rbmi/man/get_example_data.Rd | 13 rbmi-1.6.1/rbmi/man/has_class.Rd | 1 rbmi-1.6.1/rbmi/man/imputation_list_df.Rd | 2 rbmi-1.6.1/rbmi/man/imputation_list_single.Rd | 6 rbmi-1.6.1/rbmi/man/impute.Rd | 8 rbmi-1.6.1/rbmi/man/impute_data_individual.Rd | 2 rbmi-1.6.1/rbmi/man/invert.Rd | 2 rbmi-1.6.1/rbmi/man/locf.Rd | 5 rbmi-1.6.1/rbmi/man/longDataConstructor.Rd | 372 +++++++++-------- rbmi-1.6.1/rbmi/man/make_rbmi_cluster.Rd | 6 rbmi-1.6.1/rbmi/man/mcse_internal.Rd | 13 rbmi-1.6.1/rbmi/man/method.Rd | 29 + rbmi-1.6.1/rbmi/man/par_lapply.Rd | 6 rbmi-1.6.1/rbmi/man/pool.Rd | 83 +++ rbmi-1.6.1/rbmi/man/pool_internal.Rd | 7 rbmi-1.6.1/rbmi/man/prepare_prior_params.Rd | 4 rbmi-1.6.1/rbmi/man/progressLogger.Rd | 132 +++--- rbmi-1.6.1/rbmi/man/rbmi-package.Rd | 11 rbmi-1.6.1/rbmi/man/recursive_reduce.Rd | 2 rbmi-1.6.1/rbmi/man/sample_mvnorm.Rd | 4 rbmi-1.6.1/rbmi/man/scalerConstructor.Rd | 183 ++++---- rbmi-1.6.1/rbmi/man/set_simul_pars.Rd | 30 + rbmi-1.6.1/rbmi/man/set_vars.Rd | 8 rbmi-1.6.1/rbmi/man/simulate_data.Rd | 48 ++ rbmi-1.6.1/rbmi/man/simulate_ice.Rd | 2 rbmi-1.6.1/rbmi/man/simulate_test_data.Rd | 14 rbmi-1.6.1/rbmi/man/strategies.Rd | 29 + rbmi-1.6.1/rbmi/man/string_pad.Rd | 2 rbmi-1.6.1/rbmi/man/validate.Rd | 6 rbmi-1.6.1/rbmi/man/validate.ivars.Rd | 2 rbmi-1.6.1/rbmi/man/validate_analyse_pars.Rd | 5 rbmi-1.6.1/rbmi/man/validate_datalong.Rd | 16 rbmi-1.6.1/rbmi/tests/scripts/core.sh | 4 rbmi-1.6.1/rbmi/tests/scripts/cran.sh | 42 + rbmi-1.6.1/rbmi/tests/scripts/documentation.sh | 7 rbmi-1.6.1/rbmi/tests/scripts/extended.sh | 4 rbmi-1.6.1/rbmi/tests/scripts/vignettes.sh | 2 rbmi-1.6.1/rbmi/tests/testthat/_snaps/impute.md | 2 rbmi-1.6.1/rbmi/tests/testthat/helper-misc.R | 12 rbmi-1.6.1/rbmi/tests/testthat/test-draws.R | 12 rbmi-1.6.1/rbmi/tests/testthat/test-impute.R | 42 - rbmi-1.6.1/rbmi/tests/testthat/test-longData.R | 215 +++++---- rbmi-1.6.1/rbmi/tests/testthat/test-simulate.R | 48 ++ rbmi-1.6.1/rbmi/tests/testthat/test-spelling.R |only rbmi-1.6.1/rbmi/vignettes/CondMean_Inference.Rmd | 8 rbmi-1.6.1/rbmi/vignettes/FAQ.Rmd | 4 rbmi-1.6.1/rbmi/vignettes/FAQ.html | 4 rbmi-1.6.1/rbmi/vignettes/advanced.Rmd | 4 rbmi-1.6.1/rbmi/vignettes/build.R | 2 rbmi-1.6.1/rbmi/vignettes/quickstart.Rmd | 10 rbmi-1.6.1/rbmi/vignettes/retrieved_dropout.Rmd | 4 rbmi-1.6.1/rbmi/vignettes/retrieved_dropout.html.asis |only rbmi-1.6.1/rbmi/vignettes/stat_specs.Rmd | 14 126 files changed, 1949 insertions(+), 876 deletions(-)
Title: Moments and Distributions of Ratios of Quadratic Forms Using
Recursion
Description: Evaluates moments of ratios (and products) of quadratic forms
in normal variables, specifically using recursive algorithms developed by
Bao and Kan (2013) <doi:10.1016/j.jmva.2013.03.002> and Hillier et al.
(2014) <doi:10.1017/S0266466613000364>. Also provides distribution,
quantile, and probability density functions of simple ratios of quadratic
forms in normal variables with several algorithms. Originally developed as
a supplement to Watanabe (2023) <doi:10.1007/s00285-023-01930-8> for
evaluating average evolvability measures in evolutionary quantitative
genetics, but can be used for a broader class of statistics. Generating
functions for these moments are also closely related to the top-order zonal
and invariant polynomials of matrix arguments.
Author: Junya Watanabe [aut, cre, cph] ,
Patrick Alken [cph] ,
Brian Gough [cph] ,
Pavel Holoborodko [cph] ,
Gerard Jungman [cph] ,
Reid Priedhorsky [cph] ,
Free Software Foundation, Inc. [cph]
Maintainer: Junya Watanabe <Junya.Watanabe@vetmeduni.ac.at>
Diff between qfratio versions 1.1.1 dated 2024-02-08 and 1.1.2 dated 2026-07-22
DESCRIPTION | 19 MD5 | 240 ++++----- NAMESPACE | 1 NEWS.md | 8 R/dist_funs.R | 836 +++++++++++++++++++------------ R/dk_funs.R | 248 ++++----- R/hgs_funs.R | 16 R/qfratio-package.R | 8 R/ratio_fun.R | 421 ++++++--------- R/rqf_funs.R | 116 ++-- R/utils.R | 82 ++- README.md | 22 build/partial.rdb |binary build/vignette.rds |binary configure | 692 ++++++++++++++------------ configure.ac | 27 - inst/doc/qfratio.R | 12 inst/doc/qfratio.Rmd | 58 +- inst/doc/qfratio.html | 423 ++++++++------- inst/doc/qfratio_distr.R | 161 +++--- inst/doc/qfratio_distr.Rmd | 125 +++- inst/doc/qfratio_distr.html | 894 +++++++++++++++++---------------- man/dot-run_check_conv.Rd |only man/pqfr.Rd | 325 ++---------- man/pqfr_int.Rd |only man/qfmrm.Rd | 20 man/qfpm.Rd | 7 man/qfratio-package.Rd | 26 man/qfrm.Rd | 31 - man/rqfr.Rd | 131 +++- src/config.h.in | 11 src/gsl/build.h |only src/gsl/err/error.c | 2 src/gsl/err/gsl_errno.h | 2 src/gsl/err/strerror.c | 2 src/gsl/gsl_inline.h | 2 src/gsl/gsl_machine.h | 2 src/gsl/gsl_math.h | 2 src/gsl/gsl_minmax.h | 2 src/gsl/gsl_mode.h | 2 src/gsl/gsl_nan.h | 2 src/gsl/gsl_pow_int.h | 2 src/gsl/gsl_precision.h | 2 src/gsl/gsl_types.h | 2 src/gsl/integration/err.c | 2 src/gsl/integration/gsl_integration.h | 21 src/gsl/integration/initialise.c | 2 src/gsl/integration/positivity.c | 2 src/gsl/integration/qags.c | 2 src/gsl/integration/qelg.c | 2 src/gsl/integration/qk.c | 2 src/gsl/integration/qk15.c | 2 src/gsl/integration/qpsrt.c | 2 src/gsl/integration/qpsrt2.c | 2 src/gsl/integration/reset.c | 2 src/gsl/integration/set_initial.c | 2 src/gsl/integration/util.c | 2 src/gsl/integration/workspace.c | 2 src/gsl/poly/eval.c |only src/gsl/poly/gsl_poly.h | 2 src/gsl/roots/brent.c | 2 src/gsl/roots/convergence.c | 2 src/gsl/roots/fsolver.c | 2 src/gsl/roots/gsl_roots.h | 2 src/gsl/roots/roots.h | 2 src/gsl/specfunc/bessel.c | 2 src/gsl/specfunc/bessel.h | 2 src/gsl/specfunc/bessel_I0.c | 2 src/gsl/specfunc/bessel_I1.c | 2 src/gsl/specfunc/bessel_In.c | 2 src/gsl/specfunc/bessel_Inu.c | 2 src/gsl/specfunc/bessel_J1.c | 2 src/gsl/specfunc/bessel_K0.c | 2 src/gsl/specfunc/bessel_Knu.c | 2 src/gsl/specfunc/bessel_amp_phase.c | 2 src/gsl/specfunc/bessel_amp_phase.h | 2 src/gsl/specfunc/bessel_temme.c | 2 src/gsl/specfunc/bessel_temme.h | 2 src/gsl/specfunc/beta.c | 2 src/gsl/specfunc/cheb_eval.c | 2 src/gsl/specfunc/chebyshev.h | 2 src/gsl/specfunc/check.h | 2 src/gsl/specfunc/elementary.c | 2 src/gsl/specfunc/error.h | 2 src/gsl/specfunc/eval.h | 2 src/gsl/specfunc/exp.c | 5 src/gsl/specfunc/gamma.c | 4 src/gsl/specfunc/gsl_sf_bessel.h | 2 src/gsl/specfunc/gsl_sf_elementary.h | 2 src/gsl/specfunc/gsl_sf_exp.h | 2 src/gsl/specfunc/gsl_sf_gamma.h | 2 src/gsl/specfunc/gsl_sf_hyperg.h | 2 src/gsl/specfunc/gsl_sf_laguerre.h | 2 src/gsl/specfunc/gsl_sf_log.h | 2 src/gsl/specfunc/gsl_sf_pow_int.h | 2 src/gsl/specfunc/gsl_sf_psi.h | 2 src/gsl/specfunc/gsl_sf_result.h | 2 src/gsl/specfunc/gsl_sf_trig.h | 2 src/gsl/specfunc/gsl_sf_zeta.h | 2 src/gsl/specfunc/hyperg.c | 2 src/gsl/specfunc/hyperg.h | 2 src/gsl/specfunc/hyperg_1F1.c | 18 src/gsl/specfunc/hyperg_2F1.c | 2 src/gsl/specfunc/hyperg_U.c | 25 src/gsl/specfunc/laguerre.c | 2 src/gsl/specfunc/log.c | 2 src/gsl/specfunc/poch.c | 7 src/gsl/specfunc/pow_int.c | 2 src/gsl/specfunc/psi.c | 2 src/gsl/specfunc/result.c | 2 src/gsl/specfunc/trig.c | 2 src/gsl/specfunc/zeta.c | 2 src/gsl/sys/coerce.c | 2 src/gsl/sys/fdiv.c | 2 src/gsl/sys/gsl_sys.h | 2 src/gsl/sys/infnan.c | 2 src/hgs_funs.cpp | 26 src/scripts/SOURCES_GSL.mkf | 1 tests/testthat/test_distr.R | 20 tools/config.guess | 33 - tools/config.sub | 901 +++++++++++++++++++++++++--------- vignettes/qfratio.Rmd | 58 +- vignettes/qfratio_distr.Rmd | 125 +++- 123 files changed, 3683 insertions(+), 2675 deletions(-)
Title: Testing DBI Backends
Description: A helper that tests DBI back ends for conformity to the
interface.
Author: Kirill Mueller [aut, cre] ,
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between DBItest versions 1.8.2 dated 2024-12-07 and 1.8.3 dated 2026-07-22
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Title: 'SAS Studio'-Style Interactive Dataset Viewer
Description: An interactive dataset viewer that renders a fast, scrollable
grid with a column-selection panel, per-column property metadata, and
a names-versus-labels header toggle, modelled on the 'SAS Studio' table
viewer. Runs from one codebase in interactive 'Shiny' apps and in static
HTML documents, with a free-text row filter, header sort, and CSV
export, and handles large datasets without row sampling by querying
them in the browser with 'DuckDB-WASM'.
Author: Vignesh Thanikachalam [aut, cre, cph]
Maintainer: Vignesh Thanikachalam <about.vignesh@gmail.com>
Diff between datasetviewer versions 0.1.1 dated 2026-07-09 and 0.2.0 dated 2026-07-22
DESCRIPTION | 6 - MD5 | 12 +- NEWS.md | 10 ++ README.md | 2 inst/doc/datasetviewer.html | 174 ++++++++++++++++++------------------- inst/htmlwidgets/datasetviewer.css | 2 inst/htmlwidgets/datasetviewer.js | 164 +++++++++++++++++----------------- 7 files changed, 191 insertions(+), 179 deletions(-)
Title: Beta Product Confidence Procedure for Right Censored Data
Description: Calculates nonparametric pointwise confidence intervals for the survival distribution for right censored data, and for medians [Fay and Brittain <DOI:10.1002/sim.6905>]. Has two-sample tests for dissimilarity (e.g., difference, ratio or odds ratio) in survival at a fixed time, and differences in medians [Fay, Proschan, and Brittain <DOI:10.1111/biom.12231>]. Basically, the package gives exact inference methods for one- and two-sample exact inferences for Kaplan-Meier curves (e.g., generalizing Fisher's exact test to allow for right censoring), which are especially important for latter parts of the survival curve, small sample sizes or heavily censored data. Includes mid-p options.
Author: Michael P. Fay [aut, cre],
Allyson Mateja [ctb],
Megan Grieco [ctb]
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between bpcp versions 1.5.4 dated 2026-07-21 and 1.5.5 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 12 +-- NAMESPACE | 2 NEWS | 3 R/delta2samp.R | 170 +++++++++++++++++++++++++++++++--------------- inst/doc/discreteBPCP.pdf |binary man/bpcp-internal.Rd | 16 ++-- 7 files changed, 139 insertions(+), 72 deletions(-)
Title: Biomonitoring and Bioassessment Calculations
Description: An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa,
subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) <https://archive.epa.gov/water/archive/web/html/index-14.html>.
Author: Erik W. Leppo [aut, cre] ,
Jen Stamp [ctb],
John van Sickles [ctb],
Ben Block [ctb]
Maintainer: Erik W. Leppo <Erik.Leppo@tetratech.com>
Diff between BioMonTools versions 1.2.4 dated 2025-10-09 and 1.3.1 dated 2026-07-22
DESCRIPTION | 13 MD5 | 116 +-- NAMESPACE | 6 NEWS | 243 ++++++ NEWS.md | 243 ++++++ R/BioMonTools.R |only R/MapTaxaObs.R | 6 R/assign_indexclass.R | 8 R/data.R | 80 ++ R/markExcluded.R | 9 R/metric_stats.R | 61 - R/metric_stats2.R | 20 R/metric_values.R | 1178 ++++++++++++++++++++++++++----- R/qc_taxa.R | 272 ------- R/qc_taxa_match_official.R |only R/qc_taxa_names_proof.R |only R/qc_taxa_phylo.R |only R/qc_taxa_values_character.R |only R/qc_taxa_values_logical.R |only R/qc_taxa_values_numeric.R |only R/rarify.R | 5 R/taxa_translate.R | 2 README.md | 30 build/vignette.rds |binary data/data_algae_names_official.rda |only data/data_algae_names_user.rda |only data/data_benthos_MBSS.rda |binary data/data_benthos_PacNW.rda |binary data/data_diatom_mmi_dev.rda |binary data/data_mmi_dev_small.rda |binary data/data_taxa_names_issues.rda |only inst/doc/vignette_BioMonTools.R | 9 inst/doc/vignette_BioMonTools.Rmd | 11 inst/doc/vignette_BioMonTools.html | 157 ++-- inst/doc/vignette_MapTaxaObs.html | 4 inst/doc/vignette_NewIndex.Rmd | 2 inst/doc/vignette_NewIndex.html | 4 inst/extdata/MetricNames.xlsx |binary inst/extdata/MetricScoring.xlsx |binary man/BioMonTools-package.Rd |only man/MapTaxaObs.Rd | 3 man/data_algae_names_official.Rd |only man/data_algae_names_user.Rd |only man/data_benthos_MBSS.Rd | 2 man/data_benthos_PacNW.Rd | 2 man/data_coral_bcg_metric_qc.Rd | 3 man/data_diatom_mmi_dev.Rd | 13 man/data_mmi_dev_small.Rd | 4 man/data_taxa_names_issues.Rd |only man/markExcluded.Rd | 3 man/metric.stats2.Rd | 8 man/metric.values.Rd | 4 man/metric.values.algae.Rd | 3 man/qc_taxa.Rd | 76 -- man/qc_taxa_match_official.Rd |only man/qc_taxa_names_proof.Rd |only man/qc_taxa_phylo.Rd |only man/qc_taxa_values_character.Rd |only man/qc_taxa_values_logical.Rd |only man/qc_taxa_values_numeric.Rd |only man/rarify.Rd | 2 man/taxa_translate.Rd | 2 tests/testthat/test_markExcluded.R | 5 tests/testthat/test_metric_calc.R | 1107 ++++++++++++++++++++++++++++- tests/testthat/test_metric_names.R | 13 tests/testthat/test_metric_stats.R | 36 tests/testthat/test_metric_values.R |only tests/testthat/test_qc_taxa_values_foo.R |only vignettes/vignette_BioMonTools.Rmd | 11 vignettes/vignette_NewIndex.Rmd | 2 70 files changed, 2984 insertions(+), 794 deletions(-)
Title: Interactive Fixed Effects Estimator for Panel Data
Description: Implements the interactive fixed effects ('IFE') panel estimator of
Bai (2009) <doi:10.3982/ECTA6135> for balanced and unbalanced panels, with
optional additive unit and/or time fixed effects. Provides analytical
standard errors ('homoskedastic', 'HC1' heteroskedasticity-robust,
cluster-robust by unit, and heteroskedasticity- and autocorrelation-
consistent), together with asymptotic incidental-parameter bias correction
for large panels, including a dynamic extension for predetermined
(lagged-dependent) regressors following Moon and Weidner (2017)
<doi:10.1017/S0266466615000328>. The number of factors is chosen by
information criteria (Bai and Ng 2002 <doi:10.1111/1468-0262.00273>) or by
singular value thresholding. Unbalanced panels are handled by an
expectation-maximisation algorithm with nuclear-norm-regularised
initialisation, with estimation, analytical inference, and bias correction
following Su, Wang and Wang (2025) <doi:10.2139/ssrn.5177283> and building [...truncated...]
Author: Binzhi Chen [aut, cre]
Maintainer: Binzhi Chen <Binzhi.Chen9@gmail.com>
Diff between xtife versions 0.1.3 dated 2026-04-21 and 0.1.4 dated 2026-07-22
DESCRIPTION | 33 MD5 | 32 NAMESPACE | 3 R/ife.R | 256 +++-- R/ife_unbalanced.R |only README.md | 213 +++- build/vignette.rds |binary inst/CITATION |only inst/doc/xtife-introduction.R | 218 +++- inst/doc/xtife-introduction.Rmd | 821 +++++++++++++++--- inst/doc/xtife-introduction.html | 1135 ++++++++++++++++++++----- man/dot-bias_correct.Rd | 5 man/dot-bias_correct_mw.Rd | 8 man/ife.Rd | 10 man/ife_select_r_unb.Rd |only man/ife_unbalanced.Rd |only tests/testthat/test-ife-unbalanced-inference.R |only tests/testthat/test-ife-unbalanced.R |only tests/testthat/test-ife.R | 57 + vignettes/xtife-introduction.Rmd | 821 +++++++++++++++--- 20 files changed, 2874 insertions(+), 738 deletions(-)
Title: Classification Models with Copula Functions
Description: Provides several classifiers based on probabilistic models. These classifiers allow to model the dependence structure of continuous features through bivariate copula functions and graphical models, see Salinas-Gutiérrez et al. (2014) <doi:10.1007/s00180-013-0457-y>.
Author: Rogelio Salinas Gutierrez [aut, cre, cph] ,
Angelica Hernandez Quintero [aut, cph] ,
Pedro Abraham Montoya Calzada [aut, cph] ,
Carlos Alberto Lopez Hernandez [aut, cph] ,
Juan Manuel Marquez Romero [aut, cph]
Maintainer: Rogelio Salinas Gutierrez <rogelio.salinas@edu.uaa.mx>
This is a re-admission after prior archival of version 1.1.0 dated 2025-09-19
Diff between MLCOPULA versions 1.1.0 dated 2025-09-19 and 1.1.1 dated 2026-07-22
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 2 - R/classification_report.R | 62 +++++++++++++++++++++++++++++++++++++--------- R/norm_test.R | 10 ++++++- build/partial.rdb |binary 6 files changed, 71 insertions(+), 23 deletions(-)
Title: Fuzzy Rule-Based Systems for Classification and Regression Tasks
Description: An implementation of various learning algorithms based on fuzzy rule-based systems (FRBSs) for dealing with classification and regression tasks. Moreover, it allows to construct an FRBS model defined by human experts.
FRBSs are based on the concept of fuzzy sets, proposed by Zadeh in 1965, which aims at
representing the reasoning of human experts in a set of IF-THEN rules, to
handle real-life problems in, e.g., control, prediction and inference, data
mining, bioinformatics data processing, and robotics. FRBSs are also known
as fuzzy inference systems and fuzzy models. During the modeling of an
FRBS, there are two important steps that need to be conducted: structure
identification and parameter estimation. Nowadays, there exists a wide
variety of algorithms to generate fuzzy IF-THEN rules automatically from
numerical data, covering both steps. Approaches that have been used in the
past are, e.g., heuristic procedures, neuro-fuzzy techniques, clustering
methods, genetic algorithms, squar [...truncated...]
Author: Lala Septem Riza [aut],
Christoph Bergmeir [aut, cre],
Francisco Herrera [aut],
Jose Manuel Benitez [aut]
Maintainer: Christoph Bergmeir <c.bergmeir@decsai.ugr.es>
Diff between frbs versions 3.2-0 dated 2019-12-15 and 3.3-0 dated 2026-07-22
DESCRIPTION | 29 ++++++++++++++++++++++------- MD5 | 33 +++++++++++++++++---------------- NAMESPACE | 1 + NEWS.md |only R/FRBS.MainFunction.R | 3 ++- build/vignette.rds |binary inst/CITATION | 16 ++++++++-------- inst/doc/lala2015frbs.ltx | 6 +++--- inst/doc/lala2015frbs.pdf |binary inst/doc/lala2015pmml.R | 1 - inst/doc/lala2015pmml.Rtex | 10 +++++----- inst/doc/lala2015pmml.pdf |binary man/frbs-package.Rd | 4 ++-- man/summary.frbs.Rd | 4 ++-- vignettes/lala2015frbs.bib | 43 +++++++++++++++++++++++++++++++------------ vignettes/lala2015frbs.ltx | 6 +++--- vignettes/lala2015pmml.Rtex | 10 +++++----- vignettes/lala2015pmml.bib | 4 ++-- 18 files changed, 103 insertions(+), 67 deletions(-)
Title: Your Go-to Motif Accountant
Description: Provides the 'C++' header-only library 'barry' for use in R packages.
'barry' is a 'C++' template library for counting sufficient statistics on binary
arrays and building discrete exponential-family models. It provides tools for
sparse arrays, user-defined count statistics, support set constraints,
power set generation, and includes modules for Discrete Exponential Family Models
(DEFMs) and network statistics. By placing these headers in this package, we
offer an efficient distribution system for CRAN as replication of this code in
the sources of other packages is avoided. This package follows the same
approach as the 'BH' package which provides 'Boost' headers for R packages.
Author: George Vega Yon [aut, cre] ,
U.S. Army Medical Research Acquisition Activity [fnd] ,
National Cancer Institute [fnd]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between barry versions 0.2.1 dated 2025-12-01 and 0.2.2 dated 2026-07-22
DESCRIPTION | 17 ++- MD5 | 18 +-- NEWS.md | 14 +++ README.md | 102 +++++++++++++--------- inst/include/barry/barry.hpp | 2 inst/include/barry/freqtable.hpp | 122 ++++++++++++++++++++++----- inst/include/barry/model-meat.hpp | 74 +++++----------- inst/include/barry/models/defm/defm-meat.hpp | 9 + inst/include/barry/typedefs.hpp | 35 ++++++- man/barry-package.Rd | 6 + 10 files changed, 266 insertions(+), 133 deletions(-)
Title: Declarative API for Staged Survey Weights
Description: Builds survey weights from design base weights by chaining
hierarchical adjustments (unknown eligibility, nonresponse and calibration)
through a declarative, pipeable, 'tidymodels'-style API. Calibration follows
Deville and Sarndal (1992) <doi:10.2307/2290268>. Variances are obtained with
a bootstrap that resamples primary sampling units and re-applies the whole
recipe on each replicate, following the rescaling bootstrap of Rao and Wu
(1988) <doi:10.1080/01621459.1988.10478591>, so the replicate weights carry
the variability of every adjustment. The weights also bridge to the 'survey'
and 'srvyr' packages for design-based inference.
Author: Juan Pablo Ferreira [aut, cre]
Maintainer: Juan Pablo Ferreira <juanpablo.ferreira@fcea.edu.uy>
Diff between weightflow versions 0.1.0 dated 2026-06-30 and 0.2.0 dated 2026-07-22
DESCRIPTION | 11 MD5 | 135 +++- NAMESPACE | 5 NEWS.md | 168 ++++- R/adjustments.R | 777 ++++++++++++++++++++++-- R/data.R | 3 R/plots.R | 3 R/prep.R | 102 +++ R/print.R | 6 R/r-indicators.R |only R/report.R | 202 +++++- R/spec.R | 438 +++++++++++-- R/variance.R | 218 ++++++ README.md | 289 ++++++++ build/vignette.rds |binary data/sample_one.rda |binary inst/WORDLIST | 87 ++ inst/doc/advanced-methods.R |only inst/doc/advanced-methods.Rmd |only inst/doc/advanced-methods.html |only inst/doc/calibration-totals.R |only inst/doc/calibration-totals.Rmd |only inst/doc/calibration-totals.html |only inst/doc/calibration.R |only inst/doc/calibration.Rmd |only inst/doc/calibration.html |only inst/doc/model-calibration.R |only inst/doc/model-calibration.Rmd |only inst/doc/model-calibration.html |only inst/doc/nonresponse-propensities.R |only inst/doc/nonresponse-propensities.Rmd |only inst/doc/nonresponse-propensities.html |only inst/doc/preparing-the-sample.R |only inst/doc/preparing-the-sample.Rmd |only inst/doc/preparing-the-sample.html |only inst/doc/quickstart.R |only inst/doc/quickstart.Rmd |only inst/doc/quickstart.html |only inst/doc/validation-against-survey.R |only inst/doc/validation-against-survey.Rmd |only inst/doc/validation-against-survey.html |only inst/doc/variance-estimation.R | 12 inst/doc/variance-estimation.Rmd | 72 +- inst/doc/variance-estimation.html | 188 +++-- inst/doc/weightflow.R |only inst/doc/weightflow.Rmd |only inst/doc/weightflow.html |only man/as_svydesign.Rd | 16 man/collect_replicate_weights.Rd | 2 man/figures |only man/jackknife_estimate.Rd |only man/jackknife_weights.Rd |only man/plot.prepped_weighting_spec.Rd | 3 man/prep.Rd | 15 man/report_weighting.Rd | 9 man/sample_one.Rd | 3 man/step_assert.Rd | 4 man/step_calibrate.Rd | 158 ++++ man/step_drop_ineligible.Rd | 3 man/step_model_calibration.Rd | 76 ++ man/step_nonresponse.Rd | 56 + man/step_rescale.Rd | 3 man/step_round.Rd | 3 man/step_select_within.Rd | 21 man/step_trim.Rd | 3 man/step_trim_weights.Rd | 32 man/step_unknown_eligibility.Rd | 3 man/y_model.Rd | 7 tests/testthat/_snaps |only tests/testthat/test-advanced-methods.R |only tests/testthat/test-alerts.R |only tests/testthat/test-calibrate-by-domain.R |only tests/testthat/test-calibrate-totals.R |only tests/testthat/test-calibrate-vs-survey.R |only tests/testthat/test-coverage-branches.R |only tests/testthat/test-engines.R |only tests/testthat/test-guardrails.R |only tests/testthat/test-invariants.R |only tests/testthat/test-jackknife.R |only tests/testthat/test-model-calibration-cluster.R |only tests/testthat/test-model-calibration-xtotals.R |only tests/testthat/test-r-indicator.R |only tests/testthat/test-report-convergence.R |only tests/testthat/test-report-plots.R |only tests/testthat/test-scale.R |only tests/testthat/test-select-within-nselected.R |only tests/testthat/test-snapshot.R |only tests/testthat/test-survey-validation.R |only vignettes/advanced-methods.Rmd |only vignettes/calibration-totals.Rmd |only vignettes/calibration.Rmd |only vignettes/model-calibration.Rmd |only vignettes/nonresponse-propensities.Rmd |only vignettes/preparing-the-sample.Rmd |only vignettes/quickstart.Rmd |only vignettes/validation-against-survey.Rmd |only vignettes/variance-estimation.Rmd | 72 +- vignettes/weightflow.Rmd |only 98 files changed, 2782 insertions(+), 423 deletions(-)
Title: Seamless AWS Cloud Bursting for Parallel R Workloads
Description: A 'future' backend that enables seamless execution of parallel R
workloads on 'Amazon Web Services' ('AWS', <https://aws.amazon.com>),
including 'EC2' and 'Fargate'. 'staRburst' handles environment
synchronization, data transfer, quota management, and worker orchestration
automatically, allowing users to scale from local execution to 100+ cloud
workers with a single line of code change.
Author: Scott Friedman [aut, cre]
Maintainer: Scott Friedman <help@starburst.ing>
Diff between starburst versions 0.3.8 dated 2026-03-19 and 0.3.9 dated 2026-07-22
DESCRIPTION | 12 MD5 | 269 ++-- NEWS.md | 141 ++ R/aws-clients.R |only R/cost.R |only R/ec2-pool.R | 35 R/errors.R | 2 R/future-starburst.R | 4 R/images.R |only R/network.R |only R/plan-starburst.R | 34 R/s3-io.R |only R/session-api.R | 95 + R/setup.R | 122 +- R/starburst-estimate.R | 22 R/starburst-map.R | 75 - R/task-definition.R |only R/task-registry.R |only R/utils.R | 1650 ----------------------------- README.md | 171 +-- build/vignette.rds |binary inst/doc/detached-sessions.R | 45 inst/doc/detached-sessions.Rmd | 56 inst/doc/detached-sessions.html | 70 - inst/doc/example-api-calls.R | 26 inst/doc/example-api-calls.Rmd | 82 - inst/doc/example-api-calls.html | 140 -- inst/doc/example-bootstrap.R | 6 inst/doc/example-bootstrap.Rmd | 55 inst/doc/example-bootstrap.html | 56 inst/doc/example-feature-engineering.R | 4 inst/doc/example-feature-engineering.Rmd | 50 inst/doc/example-feature-engineering.html | 53 inst/doc/example-geospatial.R | 4 inst/doc/example-geospatial.Rmd | 60 - inst/doc/example-geospatial.html | 98 + inst/doc/example-grid-search.R | 16 inst/doc/example-grid-search.Rmd | 63 - inst/doc/example-grid-search.html | 109 - inst/doc/example-monte-carlo.R | 8 inst/doc/example-monte-carlo.Rmd | 75 - inst/doc/example-monte-carlo.html | 121 -- inst/doc/example-reports.R | 2 inst/doc/example-reports.Rmd | 49 inst/doc/example-reports.html | 86 - inst/doc/example-risk-modeling.R | 17 inst/doc/example-risk-modeling.Rmd | 57 - inst/doc/example-risk-modeling.html | 103 - inst/doc/getting-started.R | 242 +--- inst/doc/getting-started.Rmd | 396 +++--- inst/doc/getting-started.html | 697 ++++++------ inst/doc/performance.R |only inst/doc/performance.Rmd |only inst/doc/performance.html |only inst/doc/troubleshooting.Rmd | 7 inst/doc/troubleshooting.html | 9 inst/doc/workload-shapes.R |only inst/doc/workload-shapes.Rmd |only inst/doc/workload-shapes.html |only inst/templates/Dockerfile.base | 6 man/StarburstFuture.Rd | 2 man/aws-clients.Rd |only man/build_base_image.Rd | 2 man/build_environment_image.Rd | 2 man/build_initial_environment.Rd | 2 man/calculate_task_cost.Rd | 2 man/calculate_total_cost.Rd | 2 man/check_aws_credentials.Rd | 2 man/check_ecr_image_age.Rd | 2 man/check_ecr_image_exists.Rd | 2 man/cleanup_s3_files.Rd | 2 man/compute_env_hash.Rd | 2 man/cost.Rd |only man/create_ecr_lifecycle_policy.Rd | 2 man/create_task.Rd | 2 man/dot-static_ec2_prices.Rd |only man/ensure_base_image.Rd | 2 man/ensure_buildx_builder.Rd |only man/ensure_environment.Rd | 2 man/ensure_log_group.Rd | 2 man/estimate_cost.Rd | 16 man/extract_region_from_key.Rd | 2 man/figures/logo.png |binary man/get_aws_account_id.Rd | 2 man/get_base_image_source.Rd | 2 man/get_base_image_uri.Rd | 2 man/get_ec2_client.Rd | 8 man/get_ec2_instance_price.Rd | 13 man/get_ec2_ondemand_price.Rd |only man/get_ec2_spot_price.Rd |only man/get_ecr_client.Rd | 2 man/get_ecs_client.Rd | 2 man/get_execution_role_arn.Rd | 2 man/get_instance_vcpus.Rd | 2 man/get_or_create_security_group.Rd | 2 man/get_or_create_subnets.Rd | 2 man/get_or_create_task_definition.Rd | 2 man/get_s3_client.Rd | 2 man/get_service_quotas_client.Rd | 2 man/get_starburst_bucket.Rd | 2 man/get_starburst_security_groups.Rd | 2 man/get_starburst_subnets.Rd | 2 man/get_task_arn.Rd | 2 man/get_task_registry.Rd | 2 man/get_task_role_arn.Rd | 2 man/get_vpc_config.Rd | 2 man/images.Rd |only man/list_active_clusters.Rd | 2 man/list_task_arns.Rd | 2 man/network.Rd |only man/poll_for_result.Rd | 2 man/public_base_image_exists.Rd |only man/result_exists.Rd | 2 man/run.StarburstFuture.Rd | 2 man/s3-io.Rd |only man/serialize_and_upload.Rd | 2 man/should_cleanup_s3.Rd |only man/starburst-package.Rd | 5 man/starburst_cluster.Rd | 23 man/starburst_config.Rd | 42 man/starburst_map.Rd | 24 man/starburst_session.Rd | 61 - man/starburst_setup.Rd | 22 man/stop_running_tasks.Rd | 2 man/store_task_arn.Rd | 2 man/task-definition.Rd |only man/task-registry.Rd |only man/utils.Rd | 6 tests/testthat/helper-aws.R | 14 tests/testthat/test-cost.R | 90 + tests/testthat/test-detached-sessions.R | 69 + tests/testthat/test-docker.R | 140 ++ tests/testthat/test-ec2-pool.R |only tests/testthat/test-integration-examples.R | 9 tests/testthat/test-plan.R | 35 tests/testthat/test-security.R | 52 tests/testthat/test-setup.R |only tools |only vignettes/detached-sessions.Rmd | 56 vignettes/example-api-calls.Rmd | 82 - vignettes/example-bootstrap.Rmd | 55 vignettes/example-feature-engineering.Rmd | 50 vignettes/example-geospatial.Rmd | 60 - vignettes/example-grid-search.Rmd | 63 - vignettes/example-monte-carlo.Rmd | 75 - vignettes/example-reports.Rmd | 49 vignettes/example-risk-modeling.Rmd | 57 - vignettes/getting-started.Rmd | 396 +++--- vignettes/performance.Rmd |only vignettes/troubleshooting.Rmd | 7 vignettes/workload-shapes.Rmd |only 151 files changed, 3212 insertions(+), 3955 deletions(-)
Title: Quadratic Inference Function
Description: Developed to perform the estimation and inference for regression
coefficient parameters in longitudinal marginal models using the method of
quadratic inference functions. Like generalized estimating equations, this
method is also a quasi-likelihood inference method. It has been showed that
the method gives consistent estimators of the regression coefficients even if
the correlation structure is misspecified, and it is more efficient than GEE
when the correlation structure is misspecified. Based on Qu, A., Lindsay,
B.G. and Li, B. (2000) <doi:10.1093/biomet/87.4.823>.
Author: Zhichang Jiang [aut],
Peter Song [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between qif versions 1.5 dated 2019-07-20 and 1.5.1 dated 2026-07-22
DESCRIPTION | 14 MD5 | 22 NAMESPACE | 28 R/data.R | 68 +- R/qif.r | 1564 +++++++++++++++++++++++------------------------ README.md | 218 +++--- man/epil.Rd | 70 +- man/exacerb.Rd | 42 - man/print.qif.Rd | 67 -- man/print.summary.qif.Rd | 71 +- man/qif.Rd | 282 ++++---- man/summary.qif.Rd | 56 - 12 files changed, 1256 insertions(+), 1246 deletions(-)
Title: Viewing Observational Health Data Sciences and Informatics
Results via 'shiny' Modules
Description: Users can build a single 'shiny' app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in 'HADES' (see <https://ohdsi.github.io/Hades/>). Learn more about 'OhdsiShinyAppBuilder' at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.
Author: Jenna Reps [aut, cre],
Nathan Hall [aut],
Josh Ide [aut],
Jamie Gibert [aut]
Maintainer: Jenna Reps <jreps@its.jnj.com>
Diff between OhdsiShinyAppBuilder versions 1.0.0 dated 2024-12-10 and 1.1.0 dated 2026-07-22
DESCRIPTION | 18 +- MD5 | 70 ++++----- R/AddConfig.R | 6 R/CreateConfig.R | 29 ++- R/ViewShiny.R | 21 +- R/createResultDatabaseSettings.R | 3 R/saveLoadConfig.R | 6 R/ui.R | 111 ++++++++++++--- build/vignette.rds |binary inst/doc/shinyAppModules.R | 2 inst/doc/shinyAppModules.Rmd | 2 inst/doc/shinyAppModules.html | 207 ++++++++++++---------------- man/OhdsiShinyAppBuilder.Rd | 1 man/addModuleConfig.Rd | 7 man/createDefaultAboutConfig.Rd | 17 ++ man/createDefaultCharacterizationConfig.Rd | 17 ++ man/createDefaultCohortDiagnosticsConfig.Rd | 17 ++ man/createDefaultCohortGeneratorConfig.Rd | 17 ++ man/createDefaultCohortMethodConfig.Rd | 17 ++ man/createDefaultDatasourcesConfig.Rd | 17 ++ man/createDefaultEstimationConfig.Rd | 17 ++ man/createDefaultEvidenceSynthesisConfig.Rd | 17 ++ man/createDefaultHomeConfig.Rd | 17 ++ man/createDefaultPhevaluatorConfig.Rd | 17 ++ man/createDefaultPredictionConfig.Rd | 17 ++ man/createDefaultReportConfig.Rd | 17 ++ man/createDefaultResultDatabaseSettings.Rd | 1 man/createDefaultSccsConfig.Rd | 17 ++ man/createModuleConfig.Rd | 17 ++ man/createShinyApp.Rd | 8 + man/initializeModuleConfig.Rd | 7 man/loadConfig.Rd | 7 man/saveConfig.Rd | 7 man/viewShiny.Rd | 10 + tests/testthat/test-addConfig.R | 8 - vignettes/shinyAppModules.Rmd | 2 36 files changed, 557 insertions(+), 214 deletions(-)
More information about OhdsiShinyAppBuilder at CRAN
Permanent link
Title: 'Rcpp' Integration for the 'mlpack' Library
Description: A fast, flexible machine learning library, written in C++, that
aims to provide fast, extensible implementations of cutting-edge
machine learning algorithms. See also Curtin et al. (2023)
<doi:10.21105/joss.05026>.
Author: Yashwant Singh Parihar [aut, ctb, cph],
Ryan Curtin [aut, ctb, cph, cre],
Dirk Eddelbuettel [aut, ctb, cph],
James Balamuta [aut, ctb, cph],
Bill March [ctb, cph],
Dongryeol Lee [ctb, cph],
Nishant Mehta [ctb, cph],
Parikshit Ram [ctb, cph],
James Cl [...truncated...]
Maintainer: Ryan Curtin <ryan@ratml.org>
Diff between mlpack versions 4.8.0 dated 2026-07-16 and 4.8.0-1 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 32 +++++----- inst/include/mlpack.h | 16 +++++ inst/include/mlpack/config.hpp | 19 +++++ inst/include/mlpack/core/audio/audio.hpp | 4 + inst/include/mlpack/core/data/image_letterbox.hpp | 19 +++++ inst/include/mlpack/core/data/image_resize_crop.hpp | 26 ++++++++ inst/include/mlpack/core/data/imputation_methods/mean_imputation.hpp | 4 - inst/include/mlpack/core/data/imputation_methods/median_imputation.hpp | 4 - inst/include/mlpack/core/data/load_audio.hpp | 19 +++++ inst/include/mlpack/core/data/load_image.hpp | 17 +++++ inst/include/mlpack/core/data/save_audio.hpp | 17 +++++ inst/include/mlpack/core/data/save_image.hpp | 12 +++ inst/include/mlpack/core/stb/stb.hpp | 4 + inst/include/mlpack/methods/ann/models/yolov3/yolov3_impl.hpp | 1 inst/include/mlpack/methods/ann/models/yolov3/yolov3_tiny_impl.hpp | 2 src/rcpp_mlpack.h | 24 +++++-- 17 files changed, 196 insertions(+), 32 deletions(-)
Title: API Wrapper for 'Ipeadata'
Description: Provides direct access to the macroeconomic, financial,
and regional database maintained by the Institute for
Applied Economic Research (Ipea) via the Ipeadata API.
For more information, see <https://www.ipeadata.gov.br/>.
Author: Luiz Eduardo Gomes [aut, cre] ,
Daniel Herszenhut [ctb] ,
Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Luiz Eduardo Gomes <luiz.gomes@ipea.gov.br>
Diff between ipeadatar versions 0.2.0 dated 2026-05-28 and 0.2.1 dated 2026-07-22
ipeadatar-0.2.0/ipeadatar/man/figures/README-pressure-1.png |only ipeadatar-0.2.1/ipeadatar/DESCRIPTION | 6 ipeadatar-0.2.1/ipeadatar/MD5 | 33 +-- ipeadatar-0.2.1/ipeadatar/NEWS.md | 26 ++ ipeadatar-0.2.1/ipeadatar/R/available_series.R | 60 +++++- ipeadatar-0.2.1/ipeadatar/R/available_subjects.R | 47 +++- ipeadatar-0.2.1/ipeadatar/R/available_territories.R | 49 ++++ ipeadatar-0.2.1/ipeadatar/R/ipeadata.R | 118 +++++++++--- ipeadatar-0.2.1/ipeadatar/R/metadata.R | 107 ++++++++-- ipeadatar-0.2.1/ipeadatar/R/search_series.R | 12 - ipeadatar-0.2.1/ipeadatar/inst/WORDLIST | 4 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.R | 2 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.Rmd | 4 ipeadatar-0.2.1/ipeadatar/inst/doc/ipeadatar.html | 6 ipeadatar-0.2.1/ipeadatar/man/ipeadata.Rd | 8 ipeadatar-0.2.1/ipeadatar/man/metadata.Rd | 5 ipeadatar-0.2.1/ipeadatar/man/search_series.Rd | 5 ipeadatar-0.2.1/ipeadatar/vignettes/ipeadatar.Rmd | 4 18 files changed, 381 insertions(+), 115 deletions(-)
Title: Tools for Scoring and Evaluating Hubverse Model Outputs
Description: Provides tools for scoring and evaluating 'hubverse' model outputs
against observed data, wrapping scoring workflows from the
'scoringutils' package and bridging hubverse model output formats
to 'scoringutils' forecast classes.
Author: Anna Krystalli [aut, cre] ,
Nicholas Reich [aut] ,
Evan Ray [aut],
Nikos Bosse [aut] ,
Kimberlyn Roosa [aut],
Zhian Kamvar [ctb] ,
Li Shandross [ctb] ,
Becky Sweger [ctb],
Lucie Contamin [ctb],
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Anna Krystalli <annakrystalli@googlemail.com>
Diff between hubEvals versions 0.3.1 dated 2026-07-17 and 0.4.0 dated 2026-07-22
hubEvals-0.3.1/hubEvals/tests/testthat/helper-suppress_wilcox_ties.R |only hubEvals-0.4.0/hubEvals/DESCRIPTION | 6 hubEvals-0.4.0/hubEvals/MD5 | 13 hubEvals-0.4.0/hubEvals/NEWS.md | 6 hubEvals-0.4.0/hubEvals/R/score_model_out.R | 53 ++ hubEvals-0.4.0/hubEvals/man/score_model_out.Rd | 5 hubEvals-0.4.0/hubEvals/tests/testthat/test-score_model_out.R | 219 ++++++++++ hubEvals-0.4.0/hubEvals/tests/testthat/test-score_model_out_rel_metrics.R | 133 ++---- 8 files changed, 347 insertions(+), 88 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2023, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Tim Gyger [aut],
Pascal Kuendig [aut],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the incl [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 1.7.0.1 dated 2026-07-13 and 1.7.1 dated 2026-07-22
DESCRIPTION | 8 MD5 | 52 R/GPModel.R | 237 R/gpb.Booster.R | 22 R/gpb.Dataset.R | 28 R/gpb.train.R | 16 configure.ac | 2 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 10 man/GPModel.Rd | 83 man/GPModel_shared_params.Rd | 102 man/fitGPModel.Rd | 83 src/Vecchia_utils.cpp | 148 src/include/GPBoost/CG_utils.h | 4 src/include/GPBoost/Vecchia_utils.h | 6 src/include/GPBoost/cov_fcts.h | 421 + src/include/GPBoost/egpd_utils.h |only src/include/GPBoost/likelihoods.h | 3267 +++++++++- src/include/GPBoost/re_comp.h | 143 src/include/GPBoost/re_model.h | 2 src/include/GPBoost/re_model_template.h | 98 src/include/GPBoost/tweedie_utils.h |only src/objective/regression_objective.hpp | 2 src/re_model.cpp | 11 tests/testthat/Rplots.pdf |binary tests/testthat/test_GPModel_ar1_multifidelity.R |only tests/testthat/test_GPModel_egpd.R |only tests/testthat/test_GPModel_non_Gaussian_data.R | 204 tests/testthat/test_GPModel_tweedie.R |only tests/testthat/test_GPModel_zero_inflated_hurdle.R |only tests/testthat/test_z_GPBoost_algorithm_non_Gaussian_data.R | 12 30 files changed, 4368 insertions(+), 593 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf cla [...truncated...]
Author: Daniel Adler [aut],
Christian Glaeser [ctb],
Oleg Nenadic [ctb],
Jens Oehlschlaegel [aut, cre],
Martijn Schuemie [ctb],
Walter Zucchini [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 4.5.2 dated 2025-01-12 and 4.5.3 dated 2026-07-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/array.R | 2 +- R/ffbit.R | 8 ++++++-- R/hi.R | 4 ++-- R/zzz.R | 6 +++++- tests/testthat/test-zero_lengths.R | 10 +++++----- 7 files changed, 29 insertions(+), 21 deletions(-)
Title: Sparse Functional Data Analysis Methods
Description: Provides algorithms to fit linear regression models under several popular penalization techniques and functional linear regression models based on Majorizing-Minimizing (MM) and Alternating Direction Method of Multipliers (ADMM) techniques.
See Boyd et al (2010) <doi:10.1561/2200000016> for complete introduction to the method.
Author: Mauro Bernardi [aut, cre],
Marco Stefanucci [aut],
Antonio Canale [ctb]
Maintainer: Mauro Bernardi <mauro.bernardi@unipd.it>
Diff between fdaSP versions 1.1.2 dated 2026-04-27 and 1.1.3 dated 2026-07-22
DESCRIPTION | 10 - MD5 | 13 + NEWS.md |only R/dof_utils.R | 147 ++++++++++----------- R/f2sreg.R | 366 +++++++++++++++++++++++++++++++++--------------------- build/partial.rdb |binary man/f2sSP.Rd | 104 ++++++++++----- man/f2sSP_cv.Rd | 82 +++++++----- 8 files changed, 433 insertions(+), 289 deletions(-)
Title: General Bivariate Copula Theory and Many Utility Functions
Description: Extensive functions for bivariate copula (bicopula) computations and related operations
for bicopula theory. The lower, upper, product, and select other bicopula are implemented along
with operations including the diagonal, survival copula, dual of a copula, co-copula, and
numerical bicopula density. Level sets, horizontal and vertical sections are supported. Numerical
derivatives and inverses of a bicopula are provided through which simulation is implemented.
Bicopula composition, convex combination, asymmetry extension, and products also are provided.
Support extends to the Kendall Function as well as the Lmoments thereof. Kendall Tau,
Spearman Rho and Footrule, Gini Gamma, Blomqvist Beta, Hoeffding Phi, Schweizer-
Wolff Sigma, tail dependency, tail order, skewness, and bivariate Lmoments are implemented, and
positive/negative quadrant dependency, left (right) increasing (decreasing) are available.
Other features include Kullback-Leibler Divergence, Vuong Procedure, spectral measure, [...truncated...]
Author: William Asquith [aut, cre]
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between copBasic versions 2.2.14 dated 2026-05-22 and 2.2.15 dated 2026-07-22
DESCRIPTION | 8 +- MD5 | 35 ++++++---- NAMESPACE | 3 NEWS | 16 ++++ R/EuvCOP.R | 2 R/EvuCOP.R | 2 R/LMRuvCOP.R |only R/LMRvuCOP.R |only R/TRIcop.R |only R/wolfCOPtest.R | 131 ++++++++++++++++++++++++++++++------- inst/LMRvuDEMO.R |only man/EMPIRgrid_fast.Rd | 6 - man/EuvCOP.Rd | 4 - man/EvuCOP.Rd | 4 - man/LMRuvCOP.Rd |only man/LMRvuCOP.Rd |only man/TRIcop.Rd |only man/copBasic-package.Rd | 16 +++- man/prod2COP.Rd | 2 man/wolfCOP.Rd | 13 ++- man/wolfCOPtest.Rd | 142 +++++++++++++++++++++++++++++++++++++---- man/wolfCOPtest_data_smlsam.Rd | 2 22 files changed, 310 insertions(+), 76 deletions(-)
Title: Zero-Modified Complex 'Tri-Parametric' Pearson Distribution for
Overdispersed Count Data
Description: Implements zero-modified versions of the Complex 'Tri-Parametric'
Pearson distribution for overdispersed count data. The package addresses
limitations of existing implementations when the parameter b approaches
zero. It provides distribution functions, maximum likelihood estimation,
and diagnostic tools for modeling count data with excess zeros. The
methodology is based on 'Rodriguez-Avi' and coauthors (2003)
<doi:10.1007/s00362-002-0134-7>.
Author: Rasheedat Oladoja [aut, cre]
Maintainer: Rasheedat Oladoja <roladoja@ttu.edu>
Diff between zmctp versions 0.1.1 dated 2026-07-09 and 0.1.2 dated 2026-07-22
DESCRIPTION | 6 +- MD5 | 21 +++++---- NEWS.md |only R/ctp_fit.R | 8 +++ R/moments.R | 78 ++++++++++++++++++++++++++--------- R/zictp_fit.R | 7 ++- inst/WORDLIST | 48 ++++++++++----------- inst/doc/introduction.html | 6 +- man/mean_ctp.Rd | 16 +------ man/mean_zictp.Rd | 9 +--- man/mode_ctp.Rd |only man/mode_zictp.Rd |only tests/testthat/test-moments.R | 92 ++++++++++++++++++++++++++++++++++++++++++ 13 files changed, 213 insertions(+), 78 deletions(-)
Title: Extract Drug Dosages from Free-Text Prescriptions
Description: Utilities for converting unstructured electronic prescribing instructions into structured medication data. Extracts drug dose, units, daily dosing frequency and intervals from English-language prescriptions. Based on Karystianis et al. (2015) <doi:10.1186/s12911-016-0255-x>.
Author: David Selby [aut, cre] ,
Belay Birlie Yimer [ctb],
Ben Marwick [ctb]
Maintainer: David Selby <david_antony.selby@dfki.de>
This is a re-admission after prior archival of version 0.1.2 dated 2021-07-19
Diff between doseminer versions 0.1.2 dated 2021-07-19 and 0.2.1 dated 2026-07-22
DESCRIPTION | 16 LICENSE | 4 MD5 | 66 +- NEWS.md | 30 - R/data.R | 184 +++--- R/doseminer-package.R | 16 R/extract.R | 386 ++++++------ R/numbers.R | 662 +++++++++++----------- R/units.R | 160 ++--- README.md | 296 +++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/case_study.R | 78 +- inst/doc/case_study.Rmd | 198 +++--- inst/doc/case_study.html | 830 ++++++++++++++------------- inst/doc/introduction.R | 76 +- inst/doc/introduction.Rmd | 238 +++---- inst/doc/introduction.html | 1170 +++++++++++++++++++-------------------- man/doseminer-package.Rd | 61 +- man/drug_units.Rd | 39 - man/example_cprd.Rd | 5 man/example_prescriptions.Rd | 5 man/extract_from_prescription.Rd | 74 +- man/hourly_to_daily.Rd | 34 - man/latin_medical_terms.Rd | 5 man/multiply_dose.Rd | 42 - man/numb_replacements.Rd | 9 man/regex_numbers.Rd | 7 man/weekly_to_daily.Rd | 34 - tests/testthat.R | 8 tests/testthat/test-examples.R |only tests/testthat/test-numbers.R | 78 +- tests/testthat/test-utils.R | 94 +-- vignettes/case_study.Rmd | 198 +++--- vignettes/introduction.Rmd | 238 +++---- 35 files changed, 2701 insertions(+), 2640 deletions(-)
Title: Systematic Comparison of Trip Distribution Laws and Models
Description: The main purpose of this package is to propose a rigorous framework to fairly compare trip distribution laws and models as described in Lenormand et al. (2016) <doi:10.1016/j.jtrangeo.2015.12.008>.
Author: Maxime Lenormand [aut, cre]
Maintainer: Maxime Lenormand <maxime.lenormand@inrae.fr>
Diff between TDLM versions 1.1.3 dated 2025-10-03 and 1.1.4 dated 2026-07-22
TDLM-1.1.3/TDLM/man/figures/GravVsOpp.png |only TDLM-1.1.3/TDLM/man/figures/Inputs.png |only TDLM-1.1.3/TDLM/man/figures/Models.png |only TDLM-1.1.3/TDLM/man/figures/OD.png |only TDLM-1.1.3/TDLM/man/figures/Proba.png |only TDLM-1.1.4/TDLM/DESCRIPTION | 8 TDLM-1.1.4/TDLM/MD5 | 51 ++-- TDLM-1.1.4/TDLM/NEWS.md | 32 ++ TDLM-1.1.4/TDLM/R/run_law.R | 5 TDLM-1.1.4/TDLM/R/run_law_model.R | 21 + TDLM-1.1.4/TDLM/R/run_model.R | 33 +- TDLM-1.1.4/TDLM/README.md | 4 TDLM-1.1.4/TDLM/build/vignette.rds |binary TDLM-1.1.4/TDLM/inst/doc/TDLM.Rmd | 40 ++- TDLM-1.1.4/TDLM/inst/doc/TDLM.html | 258 ++++++++++----------- TDLM-1.1.4/TDLM/inst/java/Sij.jar |binary TDLM-1.1.4/TDLM/inst/java/TDLM.class |binary TDLM-1.1.4/TDLM/inst/java/TDLM.jar |binary TDLM-1.1.4/TDLM/inst/java/TDM.class |binary TDLM-1.1.4/TDLM/inst/java/TDM.jar |binary TDLM-1.1.4/TDLM/java/TDLM.java | 24 + TDLM-1.1.4/TDLM/java/TDM.java | 21 - TDLM-1.1.4/TDLM/man/extract_spatial_information.Rd | 2 TDLM-1.1.4/TDLM/man/figures/Fig1.png |only TDLM-1.1.4/TDLM/man/figures/Fig2.png |only TDLM-1.1.4/TDLM/man/figures/Fig3.png |only TDLM-1.1.4/TDLM/man/figures/Fig4.png |only TDLM-1.1.4/TDLM/man/figures/Fig5.png |only TDLM-1.1.4/TDLM/man/figures/Fig6.png |only TDLM-1.1.4/TDLM/man/run_law_model.Rd | 12 TDLM-1.1.4/TDLM/man/run_model.Rd | 28 +- TDLM-1.1.4/TDLM/vignettes/TDLM.Rmd | 40 ++- 32 files changed, 339 insertions(+), 240 deletions(-)
Title: Adaptive Machine Learning-Powered, Context-Matching Tool for
Single-Cell and Spatial Transcriptomics Annotation
Description: Annotates single-cell and spatial-transcriptomic (ST) data using context-matching marker datasets. It creates a unified marker list (`Markers_list`) from multiple sources: built-in curated databases ('Cellmarker2', 'PanglaoDB', 'ScType', 'scIBD', 'TCellSI', 'PCTIT', 'PCTAM'), Seurat objects with cell labels, or user-provided Excel tables. SlimR first uses adaptive machine learning for parameter optimization, and then offers two automated annotation approaches: 'cluster-based' and 'per-cell'. Cluster-based annotation assigns one label per cluster, expression-based probability calculation, and AUC validation. Per-cell annotation assigns labels to individual cells using three scoring methods with adaptive thresholds and ratio-based confidence filtering, plus optional UMAP spatial smoothing, making it ideal for heterogeneous clusters and rare cell types. The package also supports semi-automated workflows with heatmaps, feature plots, and combined visualizations for manual annotation. For m [...truncated...]
Author: Zhaoqing Wang [aut, cre]
Maintainer: Zhaoqing Wang <zhaoqingwang@mail.sdu.edu.cn>
Diff between SlimR versions 1.1.6 dated 2026-06-30 and 1.1.7 dated 2026-07-22
SlimR-1.1.6/SlimR/R/plot_pheatmap.R |only SlimR-1.1.7/SlimR/DESCRIPTION | 12 - SlimR-1.1.7/SlimR/MD5 | 33 +- SlimR-1.1.7/SlimR/NAMESPACE | 16 + SlimR-1.1.7/SlimR/NEWS.md | 13 + SlimR-1.1.7/SlimR/R/Compute_Gene_AUC_ROC.R | 2 SlimR-1.1.7/SlimR/R/Plot_Hierarchy_Proportion.R |only SlimR-1.1.7/SlimR/R/Plot_Voronoi_Diagram.R |only SlimR-1.1.7/SlimR/R/Plot_pheatmap.R |only SlimR-1.1.7/SlimR/R/paletteDiscrete.R |only SlimR-1.1.7/SlimR/README.md | 173 ++++++++++++++- SlimR-1.1.7/SlimR/man/ArchRPalettes.Rd |only SlimR-1.1.7/SlimR/man/Celltype_Compare.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Cellmarker2.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Excel.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_PanglaoDB.Rd | 5 SlimR-1.1.7/SlimR/man/Celltype_annotation_Seurat.Rd | 5 SlimR-1.1.7/SlimR/man/Compute_Gene_AUC_ROC.Rd | 7 SlimR-1.1.7/SlimR/man/Plot_Hierarchy_Proportion.Rd |only SlimR-1.1.7/SlimR/man/Plot_Voronoi_diagram.Rd |only SlimR-1.1.7/SlimR/man/paletteDiscrete.Rd |only SlimR-1.1.7/SlimR/man/plot.pheatmap.Rd | 2 22 files changed, 254 insertions(+), 29 deletions(-)
Title: R Client for the BIODATACR Biodiversity Data Platform of Costa
Rica
Description: Provides functions to query occurrence records, species
information, and datasets from BIODATACR
<https://biodiversidad.go.cr>, the national biodiversity information
platform of Costa Rica managed by the Technical Office of CONAGEBIO.
Built on the Atlas of Living Australia (ALA) API infrastructure.
Author: Manuel Spinola [aut, cre]
Maintainer: Manuel Spinola <mspinola10@gmail.com>
Diff between rbiodatacr versions 0.1.1 dated 2026-05-05 and 0.1.2 dated 2026-07-22
DESCRIPTION | 10 ++--- MD5 | 12 +++--- NEWS.md | 14 +++++++ R/bdcr_occurrences.R | 75 ++++++++++++++++++++++++++++++++++++------ R/bdcr_occurrences_batch.R | 34 ++++++++++++++----- man/bdcr_occurrences.Rd | 18 ++++++++-- man/bdcr_occurrences_batch.Rd | 14 ++++++- 7 files changed, 142 insertions(+), 35 deletions(-)
Title: Another Approach to Package Installation
Description: The goal of 'pak' is to make package installation faster and
more reliable. In particular, it performs all HTTP operations in
parallel, so metadata resolution and package downloads are fast.
Metadata and package files are cached on the local disk as well. 'pak'
has a dependency solver, so it finds version conflicts before
performing the installation. This version of 'pak' supports CRAN,
'Bioconductor' and 'GitHub' packages as well.
Author: Gabor Csardi [aut, cre],
Jim Hester [aut],
Posit Software, PBC [cph, fnd] ,
Winston Chang [ctb] ,
Ascent Digital Services [cph, fnd] ,
Hadley Wickham [ctb, cph] ,
Jeroen Ooms [ctb] ,
Maelle Salmon [ctb] ,
Duncan Temple Lang [ctb] ,
Lloyd Hilaiel [cph [...truncated...]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between pak versions 0.11.0 dated 2026-07-15 and 0.11.1 dated 2026-07-22
DESCRIPTION | 6 MD5 | 97 +++++----- NEWS.md | 8 man/chunks/install.Rmd | 16 - man/install.Rd | 16 - src/library/pkgdepends/DESCRIPTION | 2 src/library/pkgdepends/R/dep-utils.R | 16 + src/library/pkgdepends/R/gh-app.R | 72 +++++-- src/library/pkgdepends/R/install-plan.R | 101 +++++++++-- src/library/pkgdepends/R/pkg-plan.R | 1 src/library/pkgdepends/R/solve.R | 1 src/library/pkgdepends/R/sysreqs2.R | 4 src/library/pkgdepends/R/tojson.R | 3 src/library/pkgdepends/R/type-github.R | 37 +++- src/library/pkgdepends/R/zzz-pkgdepends-config.R | 8 src/library/pkgdepends/inst/WORDLIST | 1 src/library/pkgdepends/inst/docs/pak-config-docs.rds |binary src/library/pkgdepends/inst/sysreqs/HEAD | 2 src/library/pkgdepends/inst/sysreqs/rules/Abseil.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/blosc.json | 19 +- src/library/pkgdepends/inst/sysreqs/rules/chrome.json | 27 -- src/library/pkgdepends/inst/sysreqs/rules/cln.json | 18 + src/library/pkgdepends/inst/sysreqs/rules/dotnet10.json |only src/library/pkgdepends/inst/sysreqs/rules/dotnet8.json |only src/library/pkgdepends/inst/sysreqs/rules/dotnet9.json |only src/library/pkgdepends/inst/sysreqs/rules/exiftool.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/faiss.json |only src/library/pkgdepends/inst/sysreqs/rules/fluidsynth.json | 15 + src/library/pkgdepends/inst/sysreqs/rules/ginac.json | 5 src/library/pkgdepends/inst/sysreqs/rules/grpcpp.json | 10 - src/library/pkgdepends/inst/sysreqs/rules/gtkmm2.json |only src/library/pkgdepends/inst/sysreqs/rules/haveged.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/hdf5.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/hiredis.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/imagemagick.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/libavif.json |only src/library/pkgdepends/inst/sysreqs/rules/libbsd.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/libgit2.json | 17 - src/library/pkgdepends/inst/sysreqs/rules/libmecab.json | 42 ---- src/library/pkgdepends/inst/sysreqs/rules/libsodium.json | 30 --- src/library/pkgdepends/inst/sysreqs/rules/libssh.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/libssh2.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/ncurses.json |only src/library/pkgdepends/inst/sysreqs/rules/netcdf4.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/openbabel.json | 15 - src/library/pkgdepends/inst/sysreqs/rules/opencv.json | 20 -- src/library/pkgdepends/inst/sysreqs/rules/openmpt.json | 15 + src/library/pkgdepends/inst/sysreqs/rules/protobuf-grpc.json | 20 -- src/library/pkgdepends/inst/sysreqs/rules/redland.json | 3 src/library/pkgdepends/inst/sysreqs/rules/sdl2.json | 20 ++ src/library/pkgdepends/inst/sysreqs/rules/udunits2.json | 46 ++--- src/library/pkgdepends/inst/sysreqs/rules/v8.json | 2 src/library/pkgdepends/inst/sysreqs/rules/zeromq.json | 30 --- 53 files changed, 433 insertions(+), 526 deletions(-)
Title: Multi-Resolution Scanning for Cross-Sample and Cross-Group
Differences
Description: Implements the multi-resolution scanning (MRS) method for
cross-sample distribution comparisons, as described in Soriano and Ma (2017)
<doi:10.1111/rssb.12180>, and the analysis of distributional variation
(ANDOVA) method for cross-group comparisons introduced in Ma and Soriano
(2018) <doi:10.1080/10618600.2017.1402774>. Both methods use nonparametric
models on multi-resolution partition trees to detect and characterize
differences among distributions, with tools for visualizing the results.
Author: Jacopo Soriano [aut],
Li Ma [aut, cre]
Maintainer: Li Ma <mastatlab@gmail.com>
This is a re-admission after prior archival of version 1.2.6 dated 2023-12-11
Diff between MRS versions 1.2.6 dated 2023-12-11 and 1.3.2 dated 2026-07-22
DESCRIPTION | 43 ++- MD5 | 63 ++-- NAMESPACE | 8 NEWS.md |only R/RcppExports.R | 8 R/andova.R | 225 ++++++++--------- R/bFDR.R |only R/mrs.R | 158 ++++------- R/plot1D.R | 167 +++++++----- R/plot1DSigWindows.R |only R/plot2D.R | 217 +++++++++------- R/plotTree.R | 280 +++++++++++++++------ R/print.summary.mrs.R | 38 +- R/summary.mrs.R | 84 +++--- R/utils.R |only README.md |only build/partial.rdb |binary demo |only man/andova.Rd | 49 ++- man/mrs.Rd | 34 +- man/plot1D.Rd | 31 +- man/plot1DSigWindows.Rd |only man/plot2D.Rd | 33 +- man/plotTree.Rd | 31 +- man/print.summary.mrs.Rd | 18 - man/summary.mrs.Rd | 10 src/RcppExports.cpp | 27 +- src/helpers.cpp | 41 +-- src/helpers.h | 2 src/main.cpp | 113 ++++++++ src/recursion.cpp | 619 +++++++++++++++++++++++++++++++++++++++++++---- src/recursion.h | 57 +++- tests |only 33 files changed, 1649 insertions(+), 707 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] ,
Christoph Burow [aut, trl, dtc] ,
Michael Dietze [aut] ,
Margret C. Fuchs [aut] ,
Christoph Schmidt [aut] ,
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] ,
Norbert Mercier [aut] ,
Rachel K. Smedley [ct [...truncated...]
Maintainer: Sebastian Kreutzer <maintainer_luminescence@r-luminescence.org>
Diff between Luminescence versions 1.2.1 dated 2026-03-25 and 1.3.0 dated 2026-07-22
Luminescence-1.2.1/Luminescence/man/as.Rd |only Luminescence-1.3.0/Luminescence/DESCRIPTION | 28 Luminescence-1.3.0/Luminescence/MD5 | 568 ++--- Luminescence-1.3.0/Luminescence/NAMESPACE | 1 Luminescence-1.3.0/Luminescence/NEWS.md | 410 +++ Luminescence-1.3.0/Luminescence/R/Luminescence-generics.R | 26 Luminescence-1.3.0/Luminescence/R/Luminescence-package.R | 8 Luminescence-1.3.0/Luminescence/R/RLum.Analysis-class.R | 56 Luminescence-1.3.0/Luminescence/R/RLum.Data.Curve-class.R | 30 Luminescence-1.3.0/Luminescence/R/RLum.Data.Image-class.R | 13 Luminescence-1.3.0/Luminescence/R/RLum.Data.Spectrum-class.R | 14 Luminescence-1.3.0/Luminescence/R/RLum.Results-class.R | 30 Luminescence-1.3.0/Luminescence/R/RcppExports.R | 16 Luminescence-1.3.0/Luminescence/R/analyse_Al2O3C_CrossTalk.R | 2 Luminescence-1.3.0/Luminescence/R/analyse_Al2O3C_ITC.R | 2 Luminescence-1.3.0/Luminescence/R/analyse_FadingMeasurement.R | 130 - Luminescence-1.3.0/Luminescence/R/analyse_IRSAR.RF.R | 332 +-- Luminescence-1.3.0/Luminescence/R/analyse_SAR.CWOSL.R | 1060 ++++------ Luminescence-1.3.0/Luminescence/R/analyse_SAR.NCF.R |only Luminescence-1.3.0/Luminescence/R/analyse_SAR.TL.R | 41 Luminescence-1.3.0/Luminescence/R/analyse_baSAR.R | 741 ++---- Luminescence-1.3.0/Luminescence/R/analyse_pIRIRSequence.R | 75 Luminescence-1.3.0/Luminescence/R/analyse_portableOSL.R | 22 Luminescence-1.3.0/Luminescence/R/apply_EfficiencyCorrection.R | 59 Luminescence-1.3.0/Luminescence/R/calc_AliquotSize.R | 29 Luminescence-1.3.0/Luminescence/R/calc_FastRatio.R | 15 Luminescence-1.3.0/Luminescence/R/calc_Huntley2006.R | 128 - Luminescence-1.3.0/Luminescence/R/calc_IEU.R | 8 Luminescence-1.3.0/Luminescence/R/calc_Lamothe2003.R | 2 Luminescence-1.3.0/Luminescence/R/calc_MinDose.R | 161 - Luminescence-1.3.0/Luminescence/R/calc_OSLLxTxRatio.R | 247 +- Luminescence-1.3.0/Luminescence/R/calc_SourceDoseRate.R | 54 Luminescence-1.3.0/Luminescence/R/calc_Statistics.R | 191 - Luminescence-1.3.0/Luminescence/R/convert_CW2pHMi.R | 15 Luminescence-1.3.0/Luminescence/R/convert_CW2pLMi.R | 40 Luminescence-1.3.0/Luminescence/R/convert_CW2pPMi.R | 14 Luminescence-1.3.0/Luminescence/R/convert_Second2Gray.R | 20 Luminescence-1.3.0/Luminescence/R/extract_IrradiationTimes.R | 5 Luminescence-1.3.0/Luminescence/R/fit_DoseResponseCurve.R | 825 ++++--- Luminescence-1.3.0/Luminescence/R/fit_EmissionSpectra.R | 62 Luminescence-1.3.0/Luminescence/R/fit_LMCurve.R | 4 Luminescence-1.3.0/Luminescence/R/fit_OSLLifeTimes.R | 2 Luminescence-1.3.0/Luminescence/R/get_Layout.R | 2 Luminescence-1.3.0/Luminescence/R/internal_as.latex.table.R | 4 Luminescence-1.3.0/Luminescence/R/internals_RLum.R | 129 - Luminescence-1.3.0/Luminescence/R/merge_RLum.Results.R | 13 Luminescence-1.3.0/Luminescence/R/methods_RLum.R | 4 Luminescence-1.3.0/Luminescence/R/plot_AbanicoPlot.R | 519 +--- Luminescence-1.3.0/Luminescence/R/plot_DRTResults.R | 50 Luminescence-1.3.0/Luminescence/R/plot_DetPlot.R | 98 Luminescence-1.3.0/Luminescence/R/plot_DoseResponseCurve.R | 59 Luminescence-1.3.0/Luminescence/R/plot_GrowthCurve.R | 42 Luminescence-1.3.0/Luminescence/R/plot_Histogram.R | 94 Luminescence-1.3.0/Luminescence/R/plot_KDE.R | 287 -- Luminescence-1.3.0/Luminescence/R/plot_NRt.R | 8 Luminescence-1.3.0/Luminescence/R/plot_RLum.Analysis.R | 6 Luminescence-1.3.0/Luminescence/R/plot_RLum.Data.Spectrum.R | 122 - Luminescence-1.3.0/Luminescence/R/plot_RLum.Results.R | 157 - Luminescence-1.3.0/Luminescence/R/plot_RadialPlot.R | 189 - Luminescence-1.3.0/Luminescence/R/plot_ViolinPlot.R | 24 Luminescence-1.3.0/Luminescence/R/read_BIN2R.R | 9 Luminescence-1.3.0/Luminescence/R/read_Daybreak2R.R | 57 Luminescence-1.3.0/Luminescence/R/read_XSYG2R.R | 6 Luminescence-1.3.0/Luminescence/R/scale_GammaDose.R | 31 Luminescence-1.3.0/Luminescence/R/tune_Data.R | 28 Luminescence-1.3.0/Luminescence/R/use_DRAC.R | 2 Luminescence-1.3.0/Luminescence/R/verify_SingleGrainData.R | 263 -- Luminescence-1.3.0/Luminescence/README.md | 9 Luminescence-1.3.0/Luminescence/build/partial.rdb |binary Luminescence-1.3.0/Luminescence/build/vignette.rds |binary Luminescence-1.3.0/Luminescence/inst/WORDLIST | 25 Luminescence-1.3.0/Luminescence/inst/doc/crosstalk.html | 62 Luminescence-1.3.0/Luminescence/inst/extdata/NCF.binx |only Luminescence-1.3.0/Luminescence/man/ExampleData.Al2O3C.Rd | 2 Luminescence-1.3.0/Luminescence/man/ExampleData.BINfileData.Rd | 2 Luminescence-1.3.0/Luminescence/man/ExampleData.Fading.Rd | 2 Luminescence-1.3.0/Luminescence/man/ExampleData.RF70Curves.Rd | 6 Luminescence-1.3.0/Luminescence/man/ExampleData.RLum.Analysis.Rd | 4 Luminescence-1.3.0/Luminescence/man/ExampleData.RLum.Data.Image.Rd | 6 Luminescence-1.3.0/Luminescence/man/ExampleData.TR_OSL.Rd | 4 Luminescence-1.3.0/Luminescence/man/ExampleData.XSYG.Rd | 8 Luminescence-1.3.0/Luminescence/man/ExampleData.portableOSL.Rd | 4 Luminescence-1.3.0/Luminescence/man/Luminescence-package.Rd | 3 Luminescence-1.3.0/Luminescence/man/RLum-class.Rd | 18 Luminescence-1.3.0/Luminescence/man/RLum.Analysis-class.Rd | 6 Luminescence-1.3.0/Luminescence/man/RLum.Data-class.Rd | 4 Luminescence-1.3.0/Luminescence/man/RLum.Data.Curve-class.Rd | 4 Luminescence-1.3.0/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-1.3.0/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-1.3.0/Luminescence/man/RLum.Results-class.Rd | 4 Luminescence-1.3.0/Luminescence/man/Risoe.BINfileData-class.Rd | 4 Luminescence-1.3.0/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 24 Luminescence-1.3.0/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 6 Luminescence-1.3.0/Luminescence/man/analyse_Al2O3C_ITC.Rd | 6 Luminescence-1.3.0/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 8 Luminescence-1.3.0/Luminescence/man/analyse_FadingMeasurement.Rd | 8 Luminescence-1.3.0/Luminescence/man/analyse_IRSAR.RF.Rd | 39 Luminescence-1.3.0/Luminescence/man/analyse_SAR.CWOSL.Rd | 108 - Luminescence-1.3.0/Luminescence/man/analyse_SAR.NCF.Rd |only Luminescence-1.3.0/Luminescence/man/analyse_SAR.TL.Rd | 14 Luminescence-1.3.0/Luminescence/man/analyse_baSAR.Rd | 26 Luminescence-1.3.0/Luminescence/man/analyse_pIRIRSequence.Rd | 28 Luminescence-1.3.0/Luminescence/man/analyse_portableOSL.Rd | 12 Luminescence-1.3.0/Luminescence/man/apply_CosmicRayRemoval.Rd | 16 Luminescence-1.3.0/Luminescence/man/apply_Crosstalk.Rd | 4 Luminescence-1.3.0/Luminescence/man/apply_EfficiencyCorrection.Rd | 22 Luminescence-1.3.0/Luminescence/man/bin_RLum.Data.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_AliquotSize.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_AverageDose.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_CentralDose.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_CobbleDoseRate.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_CommonDose.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_CosmicDoseRate.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_EED_Model.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_FadingCorr.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_FastRatio.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_FiniteMixture.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_FuchsLang2001.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_HomogeneityTest.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_Huntley2006.Rd | 14 Luminescence-1.3.0/Luminescence/man/calc_IEU.Rd | 8 Luminescence-1.3.0/Luminescence/man/calc_Lamothe2003.Rd | 10 Luminescence-1.3.0/Luminescence/man/calc_MaxDose.Rd | 18 Luminescence-1.3.0/Luminescence/man/calc_MinDose.Rd | 34 Luminescence-1.3.0/Luminescence/man/calc_MoransI.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_OSLLxTxRatio.Rd | 148 - Luminescence-1.3.0/Luminescence/man/calc_SourceDoseRate.Rd | 40 Luminescence-1.3.0/Luminescence/man/calc_Statistics.Rd | 12 Luminescence-1.3.0/Luminescence/man/calc_TLLxTxRatio.Rd | 14 Luminescence-1.3.0/Luminescence/man/calc_ThermalLifetime.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_WodaFuchs2008.Rd | 4 Luminescence-1.3.0/Luminescence/man/calc_gSGC.Rd | 6 Luminescence-1.3.0/Luminescence/man/calc_gSGC_feldspar.Rd | 6 Luminescence-1.3.0/Luminescence/man/combine_De_Dr.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_Activity2Concentration.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_BIN2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_CW2pHMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_CW2pLM.Rd | 10 Luminescence-1.3.0/Luminescence/man/convert_CW2pLMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_CW2pPMi.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_Concentration2DoseRate.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_Daybreak2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_PSL2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/convert_PSL2Risoe.BINfileData.Rd | 20 Luminescence-1.3.0/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 18 Luminescence-1.3.0/Luminescence/man/convert_SG2MG.Rd | 10 Luminescence-1.3.0/Luminescence/man/convert_Second2Gray.Rd | 15 Luminescence-1.3.0/Luminescence/man/convert_Wavelength2Energy.Rd | 8 Luminescence-1.3.0/Luminescence/man/convert_XSYG2CSV.Rd | 4 Luminescence-1.3.0/Luminescence/man/correct_PMTLinearity.Rd | 4 Luminescence-1.3.0/Luminescence/man/dot-as.latex.table.Rd | 2 Luminescence-1.3.0/Luminescence/man/extract_IrradiationTimes.Rd | 30 Luminescence-1.3.0/Luminescence/man/extract_ROI.Rd | 10 Luminescence-1.3.0/Luminescence/man/fit_CWCurve.Rd | 10 Luminescence-1.3.0/Luminescence/man/fit_DoseResponseCurve.Rd | 158 - Luminescence-1.3.0/Luminescence/man/fit_EmissionSpectra.Rd | 8 Luminescence-1.3.0/Luminescence/man/fit_LMCurve.Rd | 6 Luminescence-1.3.0/Luminescence/man/fit_OSLLifeTimes.Rd | 8 Luminescence-1.3.0/Luminescence/man/fit_SurfaceExposure.Rd | 2 Luminescence-1.3.0/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-1.3.0/Luminescence/man/get_Layout.Rd | 2 Luminescence-1.3.0/Luminescence/man/get_RLum.Rd | 46 Luminescence-1.3.0/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-1.3.0/Luminescence/man/import_Data.Rd | 6 Luminescence-1.3.0/Luminescence/man/length_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/melt_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/merge_RLum.Analysis.Rd | 32 Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Curve.Rd | 10 Luminescence-1.3.0/Luminescence/man/merge_RLum.Data.Spectrum.Rd | 12 Luminescence-1.3.0/Luminescence/man/merge_RLum.Rd | 24 Luminescence-1.3.0/Luminescence/man/merge_RLum.Results.Rd | 13 Luminescence-1.3.0/Luminescence/man/merge_Risoe.BINfileData.Rd | 14 Luminescence-1.3.0/Luminescence/man/metadata.Rd | 32 Luminescence-1.3.0/Luminescence/man/methods_RLum.Rd | 14 Luminescence-1.3.0/Luminescence/man/names_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/normalise_RLum.Rd | 20 Luminescence-1.3.0/Luminescence/man/plot_AbanicoPlot.Rd | 28 Luminescence-1.3.0/Luminescence/man/plot_DRCSummary.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_DRTResults.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_DetPlot.Rd | 59 Luminescence-1.3.0/Luminescence/man/plot_DoseResponseCurve.Rd | 14 Luminescence-1.3.0/Luminescence/man/plot_FilterCombinations.Rd | 6 Luminescence-1.3.0/Luminescence/man/plot_GrowthCurve.Rd | 41 Luminescence-1.3.0/Luminescence/man/plot_Histogram.Rd | 22 Luminescence-1.3.0/Luminescence/man/plot_KDE.Rd | 6 Luminescence-1.3.0/Luminescence/man/plot_MoranScatterplot.Rd | 4 Luminescence-1.3.0/Luminescence/man/plot_NRt.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_OSLAgeSummary.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RLum.Analysis.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Curve.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Image.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 22 Luminescence-1.3.0/Luminescence/man/plot_RLum.Rd | 18 Luminescence-1.3.0/Luminescence/man/plot_RLum.Results.Rd | 18 Luminescence-1.3.0/Luminescence/man/plot_ROI.Rd | 8 Luminescence-1.3.0/Luminescence/man/plot_RadialPlot.Rd | 27 Luminescence-1.3.0/Luminescence/man/plot_Risoe.BINfileData.Rd | 10 Luminescence-1.3.0/Luminescence/man/plot_SingleGrainDisc.Rd | 4 Luminescence-1.3.0/Luminescence/man/plot_ViolinPlot.Rd | 4 Luminescence-1.3.0/Luminescence/man/read_BIN2R.Rd | 14 Luminescence-1.3.0/Luminescence/man/read_BINXLOG2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_Daybreak2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_HeliosOSL2R.Rd | 8 Luminescence-1.3.0/Luminescence/man/read_PSL2R.Rd | 12 Luminescence-1.3.0/Luminescence/man/read_RF2R.Rd | 10 Luminescence-1.3.0/Luminescence/man/read_SPE2R.Rd | 18 Luminescence-1.3.0/Luminescence/man/read_TIFF2R.Rd | 6 Luminescence-1.3.0/Luminescence/man/read_XSYG2R.Rd | 10 Luminescence-1.3.0/Luminescence/man/remove_RLum.Rd | 18 Luminescence-1.3.0/Luminescence/man/remove_SignalBackground.Rd | 16 Luminescence-1.3.0/Luminescence/man/replicate_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/report_RLum.Rd | 2 Luminescence-1.3.0/Luminescence/man/sTeve.Rd | 2 Luminescence-1.3.0/Luminescence/man/scale_GammaDose.Rd | 2 Luminescence-1.3.0/Luminescence/man/set_RLum.Rd | 28 Luminescence-1.3.0/Luminescence/man/set_Risoe.BINfileData.Rd | 10 Luminescence-1.3.0/Luminescence/man/show.Rd | 2 Luminescence-1.3.0/Luminescence/man/smooth_RLum.Rd | 12 Luminescence-1.3.0/Luminescence/man/sort_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/structure_RLum.Rd | 16 Luminescence-1.3.0/Luminescence/man/subset_SingleGrainData.Rd | 8 Luminescence-1.3.0/Luminescence/man/template_DRAC.Rd | 2 Luminescence-1.3.0/Luminescence/man/trim_RLum.Data.Rd | 12 Luminescence-1.3.0/Luminescence/man/tune_Data.Rd | 12 Luminescence-1.3.0/Luminescence/man/use_DRAC.Rd | 4 Luminescence-1.3.0/Luminescence/man/verify_SingleGrainData.Rd | 22 Luminescence-1.3.0/Luminescence/man/view.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_R2BIN.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_R2TIFF.Rd | 10 Luminescence-1.3.0/Luminescence/man/write_RLum2CSV.Rd | 12 Luminescence-1.3.0/Luminescence/src/Makevars | 2 Luminescence-1.3.0/Luminescence/src/Makevars.win | 2 Luminescence-1.3.0/Luminescence/src/RcppExports.cpp | 59 Luminescence-1.3.0/Luminescence/src/src_EED_Calc_Overall_StatUncertainty.cpp | 13 Luminescence-1.3.0/Luminescence/src/src_fit_functions.cpp | 37 Luminescence-1.3.0/Luminescence/tests/testthat/_data/LxTx_Bluszcz.rds |only Luminescence-1.3.0/Luminescence/tests/testthat/setup.R | 9 Luminescence-1.3.0/Luminescence/tests/testthat/test_RLum.Analysis-class.R | 16 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_CrossTalk.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_ITC.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_Al2O3C_Measurement.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_FadingMeasurement.R | 10 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_IRSAR.RF.R | 14 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.CWOSL.R | 174 + Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.NCF.R |only Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_SAR.TL.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_baSAR.R | 40 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_pIRIRSequence.R | 37 Luminescence-1.3.0/Luminescence/tests/testthat/test_analyse_portableOSL.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_apply_EfficiencyCorrection.R | 19 Luminescence-1.3.0/Luminescence/tests/testthat/test_as_latex_table.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_Huntley2006.R | 89 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_IEU.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_MinDose.R | 31 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_OSLLxTxRatio.R | 100 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_SourceDoseRate.R | 69 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_Statistics.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_calc_TLLxTxRatio.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_convert_CW2pX.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_convert_Second2Gray.R | 5 Luminescence-1.3.0/Luminescence/tests/testthat/test_extract_IrradiationTimes.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_DoseResponseCurve.R | 305 ++ Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_EmissionSpectra.R | 29 Luminescence-1.3.0/Luminescence/tests/testthat/test_fit_OSLLifeTimes.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_get_RLum.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_internals.R | 22 Luminescence-1.3.0/Luminescence/tests/testthat/test_merge_RLum.Results.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_methods_S3.R | 3 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_AbanicoPlot.R | 24 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DRCSummary.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DRTResults.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DetPlot.R | 20 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_DoseResponseCurve.R | 41 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_GrowthCurve.R | 26 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_Histogram.R | 4 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_KDE.R | 11 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_NRt.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Analysis.R | 2 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 59 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RLum.Results.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_RadialPlot.R | 36 Luminescence-1.3.0/Luminescence/tests/testthat/test_plot_ViolinPlot.R | 7 Luminescence-1.3.0/Luminescence/tests/testthat/test_read_Daybreak2R.R | 8 Luminescence-1.3.0/Luminescence/tests/testthat/test_read_XSYG2R.R | 6 Luminescence-1.3.0/Luminescence/tests/testthat/test_set_RLum.R | 25 Luminescence-1.3.0/Luminescence/tests/testthat/test_verify_SingleGrainData.R | 40 Luminescence-1.3.0/Luminescence/tests/testthat/test_zzz.R | 21 288 files changed, 5955 insertions(+), 5506 deletions(-)
Title: Geolocalização De Endereços Brasileiros (Geocoding Brazilian
Addresses)
Description: Método simples e eficiente de geolocalizar dados no Brasil. O
pacote é baseado em conjuntos de dados espaciais abertos de endereços
brasileiros, utilizando como fonte principal o Cadastro Nacional de Endereços
para Fins Estatísticos (CNEFE). O CNEFE é publicado pelo Instituto Brasileiro
de Geografia e Estatística (IBGE), órgão oficial de estatísticas e geografia
do Brasil. (A simple and efficient method for geolocating data in Brazil. The
package is based on open spatial datasets of Brazilian addresses, primarily
using the Cadastro Nacional de Endereços para Fins Estatísticos (CNEFE),
published by the Instituto Brasileiro de Geografia e Estatística (IBGE),
Brazil's official statistics and geography agency.)
Author: Rafael H. M. Pereira [aut, cre] ,
Daniel Herszenhut [aut] ,
Gabriel Garcia de Almeida [aut] ,
Arthur Bazolli [ctb],
Pedro Milreu Cunha [ctb],
ITpS - Instituto Todos pela Saude [fnd],
Ipea - Instituto de Pesquisa Economica Aplicada [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geocodebr versions 0.6.3 dated 2026-05-24 and 0.6.4 dated 2026-07-22
DESCRIPTION | 6 - MD5 | 26 +++---- NEWS.md | 11 ++- R/geocode.R | 2 build/vignette.rds |binary inst/doc/geocode.R | 52 +++++++------- inst/doc/geocode.html | 41 ----------- inst/doc/geocode_reverso.R | 38 +++++----- inst/doc/geocode_reverso.html | 50 ++++--------- inst/doc/geocodebr.R | 116 ++++++++++++++++---------------- inst/doc/geocodebr.html | 24 +----- tests/testthat/_snaps/cache.md | 60 ++++++++-------- tests/testthat/_snaps/definir_campos.md | 16 ++-- tests/testthat/_snaps/message.md | 14 +-- 14 files changed, 201 insertions(+), 255 deletions(-)
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.6 dated 2026-02-05 and 1.4.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 160 +++--- NAMESPACE | 7 NEWS.md | 11 R/check_bare_col.R |only R/flux_calc.R | 101 ++- R/flux_calc_frac.R |only R/flux_calc_vol.R |only R/flux_conc.R |only R/flux_diff.R | 10 R/flux_drygas.R | 22 R/flux_fitting.R | 31 - R/flux_fitting_exptz.R | 3 R/flux_fitting_hm.R | 3 R/flux_fitting_lm.R | 3 R/flux_fitting_quadratic.R | 3 R/flux_fitting_zhao18.R | 3 R/flux_flag_count.R | 30 - R/flux_fortify.R | 13 R/flux_gep.R | 3 R/flux_gpp.R | 14 R/flux_lrc.R | 17 R/flux_match.R | 65 -- R/flux_plot.R | 27 - R/flux_quality.R | 82 ++- R/flux_units.R | 12 R/stupeflux.R | 18 README.md | 49 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/data-prep.Rmd | 1 inst/doc/data-prep.html | 5 inst/doc/fluxible.R | 4 inst/doc/fluxible.Rmd | 6 inst/doc/fluxible.html | 82 +-- inst/doc/li7500.html | 16 inst/doc/two-gases.html | 2 inst/doc/vol_conc.R |only inst/doc/vol_conc.Rmd |only inst/doc/vol_conc.html |only man/check_bare_col.Rd |only man/figures/README-short-example-1.png |binary man/flux_calc.Rd | 37 + man/flux_calc_frac.Rd |only man/flux_calc_vol.Rd |only man/flux_conc.Rd |only man/flux_diff.Rd | 4 man/flux_drygas.Rd | 11 man/flux_fitting.Rd | 17 man/flux_flag_count.Rd | 14 man/flux_fortify.Rd | 3 man/flux_gpp.Rd | 7 man/flux_lrc.Rd | 10 man/flux_match.Rd | 28 - man/flux_plot.Rd | 15 man/flux_quality.Rd | 78 +-- man/flux_units.Rd | 3 man/fluxible-package.Rd | 1 man/stupeflux.Rd | 12 tests/testthat/_snaps/flux_calc.md | 31 - tests/testthat/_snaps/flux_conc.md |only tests/testthat/_snaps/flux_fitting.md | 52 +- tests/testthat/_snaps/flux_flag_count.md | 46 - tests/testthat/_snaps/flux_plot.md | 256 ---------- tests/testthat/_snaps/flux_plot/facet-ordering.svg |only tests/testthat/_snaps/flux_plot/flux-diff-and-lm.svg | 26 - tests/testthat/_snaps/flux_plot/ggssave-and-print.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-as-an-object.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-for-exp-hm-fit.svg | 72 +- tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit-with-mid-missing-data.svg | 32 - tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit.svg | 32 - tests/testthat/_snaps/flux_plot/plot-for-kappamax-fit.svg | 94 +-- tests/testthat/_snaps/flux_plot/plot-for-linear-fit.svg | 58 +- tests/testthat/_snaps/flux_plot/plot-for-quadratic-fit-with-mid-missing-data.svg | 44 - tests/testthat/_snaps/flux_plot/plot-with-custom-facet-id.svg | 58 +- tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-hm.svg | 10 tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-exp-tz.svg | 12 tests/testthat/_snaps/flux_plot/slope-crosses-fit-at-tz-with-quadratic.svg | 10 tests/testthat/test-flux_calc.R | 38 + tests/testthat/test-flux_conc.R |only tests/testthat/test-flux_fitting.R | 16 tests/testthat/test-flux_match.R | 64 -- tests/testthat/test-flux_plot.R | 81 +-- tests/testthat/test-flux_quality.R | 8 tests/testthat/test-flux_units.R | 9 vignettes/data-prep.Rmd | 1 vignettes/ex_data/sample_vol_conc.csv |only vignettes/fluxible.Rmd | 6 vignettes/vol_conc.Rmd |only 89 files changed, 1092 insertions(+), 1133 deletions(-)
Title: Estimation of Life Expectancies Using Multi-State Models
Description: Functions to compute state-specific and marginal life expectancies. The computation is based on a fitted continuous-time multi-state model that includes an absorbing death state; see Van den Hout (2017, ISBN:9781466568402). The fitted multi-state model model should be estimated using the 'msm' package using age as the time-scale.
Author: Ardo van den Hout [aut, cre],
Mei Sum Chan [aut]
Maintainer: Ardo van den Hout <ardo.vandenhout@ucl.ac.uk>
Diff between elect versions 1.2 dated 2019-04-03 and 1.2.1 dated 2026-07-22
DESCRIPTION | 18 +++++++++++++----- MD5 | 8 ++++---- NEWS | 5 +++++ man/electData.Rd | 4 ++-- man/summary.elect.Rd | 2 +- 5 files changed, 25 insertions(+), 12 deletions(-)
Title: Goodness-of-Fit and Calibration Tests for Logistic Regression
Description: Provides a unified battery of goodness-of-fit and calibration tests
for binary logistic regression, runnable in a single call via
'run.all.gof()'. The package introduces the author's own tests aimed at
sparse data --- the omnibus Ebrahim-Farrington (EF) test, the Directed EF
('EDGE') test that targets smooth calibration-shape departures, and a
Cauchy-combination ensemble --- and aggregates a wide range of classical and
modern tests for comparison, including Hosmer-Lemeshow, McCullagh,
Osius-Rojek, le Cessie-van Houwelingen, Stute-Zhu, the binary-adaptive
'BAGofT' test, and the 'GiViTI' calibration test (each obtained from its own
package, where installed, and attributed to its authors). The tools are
particularly suited to sparse data, where the Hosmer-Lemeshow test loses
power. For more details see Hosmer (1980) <doi:10.1080/03610928008827941> and
Farrington (1996) <doi:10.1111/j.2517-6161.1996.tb02086.x>.
Author: Ebrahim Khaled Ebrahim [aut, cre]
Maintainer: Ebrahim Khaled Ebrahim <ebrahimkhaled@alexu.edu.eg>
Diff between ebrahim.gof versions 2.1.0 dated 2026-06-17 and 2.4.0 dated 2026-07-22
DESCRIPTION | 40 +- MD5 | 42 ++- NAMESPACE | 3 NEWS.md | 106 +++++++ R/data.R |only R/def_ensemble_gof.R | 29 ++ R/def_gof.R | 5 R/ebrahim.gof-package.R |only R/edge_gof.R |only R/install_suggests.R |only R/run_all_gof.R | 442 ++++++++++++++++++++++++++++----- R/zzz.R |only README.md | 149 ++++++++++- build/partial.rdb |only build/vignette.rds |binary data |only inst/CITATION |only inst/doc/ebrahim-farrington-intro.html | 99 +++---- inst/doc/ebrahim-gof-toolbox.R |only inst/doc/ebrahim-gof-toolbox.Rmd |only inst/doc/ebrahim-gof-toolbox.html |only man/def.gof.Rd | 5 man/ebrahim.gof-package.Rd |only man/edge.gof.Rd |only man/edges.gof.Rd |only man/gof_demo.Rd |only man/gof_demo_grouped.Rd |only man/gof_install_suggests.Rd |only man/run.all.gof.Rd | 134 +++++++++- tests/testthat/test-parallel.R |only vignettes/ebrahim-gof-toolbox.Rmd |only 31 files changed, 891 insertions(+), 163 deletions(-)
Title: Conway-Maxwell Poisson (COM-Poisson) Regression
Description: Fit Conway-Maxwell Poisson (COM-Poisson or CMP) regression models
to count data (Sellers & Shmueli, 2010) <doi:10.1214/09-AOAS306>. The
package provides functions for model estimation, dispersion testing, and
diagnostics. Zero-inflated CMP regression (Sellers & Raim, 2016)
<doi:10.1016/j.csda.2016.01.007> is also supported.
Author: Kimberly Sellers [aut],
Thomas Lotze [aut],
Andrew Raim [cre, aut]
Maintainer: Andrew Raim <andrew.raim@gmail.com>
Diff between COMPoissonReg versions 0.8.1 dated 2023-11-29 and 0.8.2 dated 2026-07-22
COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.R |only COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.Rmd |only COMPoissonReg-0.8.1/COMPoissonReg/inst/doc/vignette.pdf |only COMPoissonReg-0.8.1/COMPoissonReg/man/COMPoissonReg-options.Rd |only COMPoissonReg-0.8.1/COMPoissonReg/vignettes/vignette.Rmd |only COMPoissonReg-0.8.1/COMPoissonReg/vignettes/vignette_files |only COMPoissonReg-0.8.2/COMPoissonReg/DESCRIPTION | 33 +++- COMPoissonReg-0.8.2/COMPoissonReg/MD5 | 72 +++------- COMPoissonReg-0.8.2/COMPoissonReg/NEWS.md |only COMPoissonReg-0.8.2/COMPoissonReg/R/S3methods.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/R/cmp-reg.R | 38 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/cmp.R | 6 COMPoissonReg-0.8.2/COMPoissonReg/R/glm.R | 39 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/helpers.R | 65 +++++---- COMPoissonReg-0.8.2/COMPoissonReg/R/package.R | 31 ---- COMPoissonReg-0.8.2/COMPoissonReg/R/util.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/R/zicmp-reg.R | 41 ++--- COMPoissonReg-0.8.2/COMPoissonReg/R/zicmp.R | 4 COMPoissonReg-0.8.2/COMPoissonReg/R/zip.R | 2 COMPoissonReg-0.8.2/COMPoissonReg/build/vignette.rds |binary COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.R |only COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.pdf |only COMPoissonReg-0.8.2/COMPoissonReg/inst/doc/COMPoissonReg.qmd |only COMPoissonReg-0.8.2/COMPoissonReg/man/CMP-Distribution.Rd | 4 COMPoissonReg-0.8.2/COMPoissonReg/man/COMPoissonReg-package.Rd | 14 + COMPoissonReg-0.8.2/COMPoissonReg/man/ZICMP-Distribution.Rd | 4 COMPoissonReg-0.8.2/COMPoissonReg/man/get.control.Rd | 14 + COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-CMP-support.Rd | 24 +-- COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-ZICMP-support.Rd | 17 +- COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp-raw.Rd | 6 COMPoissonReg-0.8.2/COMPoissonReg/man/glm.cmp.Rd | 2 COMPoissonReg-0.8.2/COMPoissonReg/src/cmp.cpp | 4 COMPoissonReg-0.8.2/COMPoissonReg/vignettes/COMPoissonReg.qmd |only COMPoissonReg-0.8.2/COMPoissonReg/vignettes/common.sty | 58 ++++++-- 34 files changed, 259 insertions(+), 223 deletions(-)
Title: Extensible Framework for Data Pattern Exploration
Description: A framework for systematic exploration of
association rules (Agrawal et al., 1994, <https://www.vldb.org/conf/1994/P487.PDF>),
contrast patterns (Chen, 2022, <doi:10.48550/arXiv.2209.13556>),
emerging patterns (Dong et al., 1999, <doi:10.1145/312129.312191>),
subgroup discovery (Atzmueller, 2015, <doi:10.1002/widm.1144>),
and conditional correlations (Hájek, 1978, <doi:10.1007/978-3-642-66943-9>).
User-defined functions may also be supplied to guide custom pattern searches.
Supports both crisp (Boolean) and fuzzy data. Generates candidate conditions
expressed as elementary conjunctions, evaluates them on a dataset, and
inspects the induced sub-data for statistical, logical, or structural
properties such as associations, correlations, or contrasts. Includes methods
for visualization of logical structures and supports interactive exploration
through integrated Shiny applications.
Author: Michal Burda [aut, cre]
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between nuggets versions 2.2.1 dated 2026-06-10 and 2.2.2 dated 2026-07-22
nuggets-2.2.1/nuggets/src/dig/TautologyTree.h |only nuggets-2.2.1/nuggets/src/test-dig-TautologyTree.cpp |only nuggets-2.2.2/nuggets/DESCRIPTION | 12 nuggets-2.2.2/nuggets/MD5 | 101 nuggets-2.2.2/nuggets/NAMESPACE | 1 nuggets-2.2.2/nuggets/NEWS.md | 144 - nuggets-2.2.2/nuggets/R/cluster_associations.R | 4 nuggets-2.2.2/nuggets/R/dig.R | 22 nuggets-2.2.2/nuggets/R/dig_associations.R | 19 nuggets-2.2.2/nuggets/R/dig_baseline_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_complement_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_correlations.R | 12 nuggets-2.2.2/nuggets/R/dig_grid.R | 12 nuggets-2.2.2/nuggets/R/dig_paired_baseline_contrasts.R | 12 nuggets-2.2.2/nuggets/R/dig_tautologies.R | 45 nuggets-2.2.2/nuggets/R/helper-format_percent.R |only nuggets-2.2.2/nuggets/R/nuggets-package.R | 1 nuggets-2.2.2/nuggets/R/parse_condition.R | 5 nuggets-2.2.2/nuggets/R/partition.R | 11 nuggets-2.2.2/nuggets/R/ui-associationsClusterModule.R | 138 + nuggets-2.2.2/nuggets/R/ui-exploreApp.R | 20 nuggets-2.2.2/nuggets/R/ui-numericFilterModule.R | 2 nuggets-2.2.2/nuggets/R/ui-variableFilterModule.R | 2 nuggets-2.2.2/nuggets/build/partial.rdb |binary nuggets-2.2.2/nuggets/build/vignette.rds |binary nuggets-2.2.2/nuggets/inst/doc/association-rules.R |only nuggets-2.2.2/nuggets/inst/doc/association-rules.Rmd |only nuggets-2.2.2/nuggets/inst/doc/association-rules.html |only nuggets-2.2.2/nuggets/inst/doc/data-preparation.R | 51 nuggets-2.2.2/nuggets/inst/doc/data-preparation.Rmd | 218 + nuggets-2.2.2/nuggets/inst/doc/data-preparation.html | 1471 +++++++----- nuggets-2.2.2/nuggets/inst/doc/nuggets.Rmd | 4 nuggets-2.2.2/nuggets/inst/doc/nuggets.html | 7 nuggets-2.2.2/nuggets/man/dig.Rd | 22 nuggets-2.2.2/nuggets/man/dig_associations.Rd | 19 nuggets-2.2.2/nuggets/man/dig_baseline_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_complement_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_correlations.Rd | 12 nuggets-2.2.2/nuggets/man/dig_grid.Rd | 12 nuggets-2.2.2/nuggets/man/dig_paired_baseline_contrasts.Rd | 12 nuggets-2.2.2/nuggets/man/dig_tautologies.Rd | 24 nuggets-2.2.2/nuggets/man/nuggets-package.Rd | 4 nuggets-2.2.2/nuggets/src/Makevars | 3 nuggets-2.2.2/nuggets/src/dig.cpp | 123 - nuggets-2.2.2/nuggets/src/dig/BaseChain.h | 33 nuggets-2.2.2/nuggets/src/dig/Clause.h | 9 nuggets-2.2.2/nuggets/src/dig/DeductionEngine.h |only nuggets-2.2.2/nuggets/src/dig/Digger.h | 70 nuggets-2.2.2/nuggets/src/dig/SparseBitChain.h |only nuggets-2.2.2/nuggets/src/test-dig-DeductionEngine.cpp |only nuggets-2.2.2/nuggets/src/test-dig-SparseBitChain.cpp |only nuggets-2.2.2/nuggets/tests/testthat/test-dig.R | 91 nuggets-2.2.2/nuggets/tests/testthat/test-parse_condition.R | 2 nuggets-2.2.2/nuggets/tests/testthat/test-partition.R | 320 +- nuggets-2.2.2/nuggets/vignettes/association-rules.Rmd |only nuggets-2.2.2/nuggets/vignettes/data-preparation.Rmd | 218 + nuggets-2.2.2/nuggets/vignettes/nuggets.Rmd | 4 57 files changed, 2207 insertions(+), 1133 deletions(-)
Title: Langa-Weir Classification of Cognitive Function for 2022 HRS
Data
Description: Generates the Langa-Weir classification of cognitive function for
the 2022 Health and Retirement Study (HRS) cognition data. It is
particularly useful for researchers studying cognitive aging who wish to
work with the most recent release of HRS data. The package provides
user-friendly functions for data preprocessing, scoring, and classification
allowing users to easily apply the Langa-Weir classification system.
For details regarding the;
HRS <https://hrsdata.isr.umich.edu/> and
Langa-Weir classifications <https://hrsdata.isr.umich.edu/data-products/langa-weir-classification-cognitive-function-1995-2022>.
Author: Cormac Monaghan [cph, aut, cre] ,
Rafael de Andrade Moral [aut] ,
Joanna McHugh Power [aut]
Maintainer: Cormac Monaghan <cormacmonaghan@protonmail.com>
Diff between lwc2022 versions 1.0.0 dated 2024-11-20 and 1.0.1 dated 2026-07-22
DESCRIPTION | 32 ++--- LICENSE | 4 MD5 | 52 ++++---- NAMESPACE | 28 ++-- R/classify.R | 146 ++++++++++++---------- R/data.R | 169 +++++++++++++------------- R/extract.R | 95 +++++++------- R/globals.R | 42 +++--- R/score.R | 175 +++++++++++++++------------ R/score_recall.R | 56 ++++---- R/score_subtraction.R | 68 +++++----- build/vignette.rds |binary inst/doc/example_data.R | 18 +- inst/doc/example_data.Rmd | 287 ++++++++++++++++++++++----------------------- inst/doc/example_data.html | 27 ++-- inst/doc/lwc2022.R | 7 - inst/doc/lwc2022.Rmd | 186 ++++++++++++++--------------- inst/doc/lwc2022.html | 90 +++++++------- man/classify.Rd | 80 ++++++------ man/cog_data.Rd | 136 ++++++++++----------- man/cog_data_score.Rd | 70 +++++----- man/extract.Rd | 80 ++++++------ man/score.Rd | 78 ++++++------ man/score_recall.Rd | 68 +++++----- man/score_subtraction.Rd | 80 ++++++------ vignettes/example_data.Rmd | 287 ++++++++++++++++++++++----------------------- vignettes/lwc2022.Rmd | 186 ++++++++++++++--------------- 27 files changed, 1299 insertions(+), 1248 deletions(-)
Title: Fast Library for Number Theory
Description: An R interface to 'FLINT' <https://flintlib.org/>, a C library for
number theory. 'FLINT' extends GNU 'MPFR' <https://www.mpfr.org/>
and GNU 'MP' <https://gmplib.org/> with support for operations on
standard rings (the integers, the integers modulo n, finite
fields, the rational, p-adic, real, and complex numbers) as well
as matrices and polynomials over rings. 'FLINT' implements
midpoint-radius interval arithmetic, also known as ball
arithmetic, in the real and complex numbers, enabling computation
in arbitrary precision with rigorous propagation of rounding and
other errors; see Johansson (2017) <doi:10.1109/TC.2017.2690633>.
Finally, 'FLINT' provides ball arithmetic implementations of many
special mathematical functions, with high coverage of reference
works such as the NIST Digital Library of Mathematical Functions
<https://dlmf.nist.gov/>. The R interface defines S4 classes,
generic functions, and methods for representation and basic
operations as [...truncated...]
Author: Mikael Jagan [aut, cre] ,
Martin Maechler [ctb]
Maintainer: Mikael Jagan <jaganmn2@gmail.com>
Diff between flint versions 0.1.4 dated 2025-12-19 and 0.1.5 dated 2026-07-22
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/acb_special.R | 16 ++++++++-------- R/flint.R | 38 ++++++++++++++++++++++++++++++++++---- build/partial.rdb |binary configure | 34 +++++++++++++++++----------------- configure.ac | 6 +++--- inst/NEWS.Rd | 33 ++++++++++++++++++++++++++++----- man/flint-class.Rd | 13 +++++++++++-- src/flint.h | 3 +++ src/utils.c | 33 ++++++++++++++++++++++++++------- tests/reg-tests.R | 6 ++++++ 13 files changed, 155 insertions(+), 65 deletions(-)
Title: Co-Occurrence Network Construction and Manipulation
Description: Constructs co-occurrence networks from several types of input
data, such as delimited fields, long/bipartite tables, binary
matrices, or wide sequences. Returns tidy edge data frames and
supports optional scaling, splitting into several networks,
thresholding, and subsetting. Provides eight similarity measures,
including Jaccard, cosine, and association strength. Supports export
to several network and file formats. Network construction and
analysis methods follow Saqr, Lopez-Pernas, Conde, and
Hernandez-Garcia (2024, <doi:10.1007/978-3-031-54464-4_15>).
Author: Mohammed Saqr [aut, cre, cph],
Sonsoles Lopez-Pernas [aut, cph],
Kamila Misiejuk [aut, cph]
Maintainer: Mohammed Saqr <saqr@saqr.me>
Diff between cooccure versions 0.1.1 dated 2026-04-24 and 0.4.0 dated 2026-07-22
DESCRIPTION | 6 MD5 | 41 - NAMESPACE | 2 NEWS.md | 137 +++ R/converters.R | 29 R/cooccurrence.R | 824 +++++++++++++++++++++-- R/data.R | 19 R/methods.R | 409 ++++++++++- data/demo.rda |binary inst/WORDLIST | 11 inst/doc/imdb-tutorial.R | 6 inst/doc/imdb-tutorial.Rmd | 11 inst/doc/imdb-tutorial.html | 967 +++++++++++++++------------ man/as.data.frame.summary.cooccurrence.Rd |only man/cooccurrence.Rd | 150 ++++ man/demo.Rd | 19 man/plot.cooccurrence.Rd | 11 man/print.cooccurrence.Rd | 2 man/print.summary.cooccurrence.Rd |only man/summary.cooccurrence.Rd | 18 tests/testthat/test-cooccurrence.R | 974 +++++++++++++++++++++++++++- tests/testthat/test-nestimate-equivalence.R |only vignettes/imdb-tutorial.Rmd | 11 23 files changed, 3034 insertions(+), 613 deletions(-)
Title: Comparison of Variance - Covariance Patterns
Description: Comparison of variance - covariance patterns using relative principal component analysis (relative eigenanalysis), as described in Le Maitre and Mitteroecker (2019) <doi:10.1111/2041-210X.13253>. Also provides functions to compute group covariance matrices, distance matrices, and perform proportionality tests. A worked sample on the body shape of cichlid fishes is included, based on the dataset from Kerschbaumer et al. (2013) <doi:10.5061/dryad.fc02f>.
Author: Anne Le Maitre [aut, cre] ,
Philipp Mitteroecker [aut]
Maintainer: Anne Le Maitre <anne.le.maitre@univie.ac.at>
Diff between vcvComp versions 1.0.2 dated 2020-12-17 and 1.0.3 dated 2026-07-22
vcvComp-1.0.2/vcvComp/NEWS |only vcvComp-1.0.3/vcvComp/DESCRIPTION | 22 vcvComp-1.0.3/vcvComp/MD5 | 23 vcvComp-1.0.3/vcvComp/NEWS.md |only vcvComp-1.0.3/vcvComp/R/Tropheus-IK-coord-dataset.R | 20 vcvComp-1.0.3/vcvComp/R/Tropheus-dataset.R | 22 vcvComp-1.0.3/vcvComp/R/relative.eigen.R | 2 vcvComp-1.0.3/vcvComp/build/partial.rdb |only vcvComp-1.0.3/vcvComp/build/vignette.rds |binary vcvComp-1.0.3/vcvComp/inst/CITATION | 4 vcvComp-1.0.3/vcvComp/inst/doc/vcvComp-worked-example.html | 1128 +++++++++---- vcvComp-1.0.3/vcvComp/man/Tropheus.IK.coord.Rd | 20 vcvComp-1.0.3/vcvComp/man/Tropheus.Rd | 22 vcvComp-1.0.3/vcvComp/man/relative.eigen.Rd | 2 14 files changed, 859 insertions(+), 406 deletions(-)
Title: Distributions Compatible with Automatic Differentiation by
'RTMB'
Description: Extends the functionality of the 'RTMB' <https://kaskr.r-universe.dev/RTMB> package by providing a collection of non-standard probability distributions compatible with automatic differentiation (AD). While 'RTMB' enables flexible and efficient modelling, including random effects, its built-in support is limited to standard distributions. The package adds additional AD-compatible distributions, broadening the range of models that can be implemented and estimated using 'RTMB'. Automatic differentiation and Laplace approximation are described in Kristensen et al. (2016) <doi:10.18637/jss.v070.i05>.
Author: Jan-Ole Fischer [aut, cre]
Maintainer: Jan-Ole Fischer <jan-ole.fischer@mailbox.org>
This is a re-admission after prior archival of version 1.0.4 dated 2026-04-09
Diff between RTMBdist versions 1.0.4 dated 2026-04-09 and 1.0.5 dated 2026-07-22
RTMBdist-1.0.4/RTMBdist/tests/testthat/test-myfunction.R |only RTMBdist-1.0.5/RTMBdist/DESCRIPTION | 8 RTMBdist-1.0.5/RTMBdist/MD5 | 306 ++++++---- RTMBdist-1.0.5/RTMBdist/NAMESPACE | 14 RTMBdist-1.0.5/RTMBdist/R/aaa_utils.R | 22 RTMBdist-1.0.5/RTMBdist/R/bccg.R | 16 RTMBdist-1.0.5/RTMBdist/R/bcpe.R | 34 - RTMBdist-1.0.5/RTMBdist/R/bct.R | 14 RTMBdist-1.0.5/RTMBdist/R/beta2.R | 8 RTMBdist-1.0.5/RTMBdist/R/betabinom.R | 2 RTMBdist-1.0.5/RTMBdist/R/betaprime.R | 2 RTMBdist-1.0.5/RTMBdist/R/dirichlet.R | 5 RTMBdist-1.0.5/RTMBdist/R/dirmult.R | 3 RTMBdist-1.0.5/RTMBdist/R/exgauss.R | 12 RTMBdist-1.0.5/RTMBdist/R/foldnorm.R | 2 RTMBdist-1.0.5/RTMBdist/R/gamma2.R | 3 RTMBdist-1.0.5/RTMBdist/R/gengamma.R | 4 RTMBdist-1.0.5/RTMBdist/R/genpois.R | 2 RTMBdist-1.0.5/RTMBdist/R/gmrf.R | 14 RTMBdist-1.0.5/RTMBdist/R/gompertz.R |only RTMBdist-1.0.5/RTMBdist/R/gumbel.R | 2 RTMBdist-1.0.5/RTMBdist/R/invchisq.R | 6 RTMBdist-1.0.5/RTMBdist/R/invgamma.R | 5 RTMBdist-1.0.5/RTMBdist/R/invgauss.R | 1 RTMBdist-1.0.5/RTMBdist/R/kumar.R | 15 RTMBdist-1.0.5/RTMBdist/R/laplace.R | 2 RTMBdist-1.0.5/RTMBdist/R/llogis.R |only RTMBdist-1.0.5/RTMBdist/R/mcreport.R | 14 RTMBdist-1.0.5/RTMBdist/R/mvt.R | 3 RTMBdist-1.0.5/RTMBdist/R/nbinom2.R | 36 - RTMBdist-1.0.5/RTMBdist/R/oibeta.R | 8 RTMBdist-1.0.5/RTMBdist/R/oibeta2.R | 5 RTMBdist-1.0.5/RTMBdist/R/pareto.R | 6 RTMBdist-1.0.5/RTMBdist/R/pgweibull.R | 6 RTMBdist-1.0.5/RTMBdist/R/powerexp.R | 14 RTMBdist-1.0.5/RTMBdist/R/skewnorm.R | 20 RTMBdist-1.0.5/RTMBdist/R/skewnorm2.R | 16 RTMBdist-1.0.5/RTMBdist/R/skewt.R | 18 RTMBdist-1.0.5/RTMBdist/R/skewt2.R | 4 RTMBdist-1.0.5/RTMBdist/R/t2.R | 18 RTMBdist-1.0.5/RTMBdist/R/truncnorm.R | 6 RTMBdist-1.0.5/RTMBdist/R/trunct.R | 3 RTMBdist-1.0.5/RTMBdist/R/trunct2.R | 2 RTMBdist-1.0.5/RTMBdist/R/vm.R | 13 RTMBdist-1.0.5/RTMBdist/R/vmf.R | 7 RTMBdist-1.0.5/RTMBdist/R/vmf2.R | 6 RTMBdist-1.0.5/RTMBdist/R/wishart.R | 4 RTMBdist-1.0.5/RTMBdist/R/wrpcauchy.R | 2 RTMBdist-1.0.5/RTMBdist/R/zibeta.R | 5 RTMBdist-1.0.5/RTMBdist/R/zibeta2.R | 3 RTMBdist-1.0.5/RTMBdist/R/zibinom.R | 3 RTMBdist-1.0.5/RTMBdist/R/zigamma.R | 3 RTMBdist-1.0.5/RTMBdist/R/zigamma2.R | 13 RTMBdist-1.0.5/RTMBdist/R/ziinvgauss.R | 6 RTMBdist-1.0.5/RTMBdist/R/zilnorm.R | 3 RTMBdist-1.0.5/RTMBdist/R/zinbinom.R | 5 RTMBdist-1.0.5/RTMBdist/R/zinbinom2.R | 3 RTMBdist-1.0.5/RTMBdist/R/zipois.R | 3 RTMBdist-1.0.5/RTMBdist/R/ziweibull.R | 3 RTMBdist-1.0.5/RTMBdist/R/zoibeta.R | 8 RTMBdist-1.0.5/RTMBdist/R/zoibeta2.R | 4 RTMBdist-1.0.5/RTMBdist/README.md | 5 RTMBdist-1.0.5/RTMBdist/build/vignette.rds |binary RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.R | 63 +- RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.Rmd | 71 +- RTMBdist-1.0.5/RTMBdist/inst/doc/Examples.html | 134 ++-- RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.R |only RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.Rmd |only RTMBdist-1.0.5/RTMBdist/inst/doc/adding-a-distribution.html |only RTMBdist-1.0.5/RTMBdist/inst/doc/distlist.Rmd | 4 RTMBdist-1.0.5/RTMBdist/inst/doc/distlist.html | 6 RTMBdist-1.0.5/RTMBdist/man/bccg.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/bcpe.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/bct.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/beta2.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/betabinom.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/betaprime.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/dirichlet.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/dirmult.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/exgauss.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/figures/README-sim_residuals-1.png |binary RTMBdist-1.0.5/RTMBdist/man/foldnorm.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/gamma2.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/gengamma.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/genpois.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/gompertz.Rd |only RTMBdist-1.0.5/RTMBdist/man/gumbel.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/invchisq.Rd | 4 RTMBdist-1.0.5/RTMBdist/man/invgamma.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/invgauss.Rd | 2 RTMBdist-1.0.5/RTMBdist/man/kumar.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/laplace.Rd | 2 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RTMBdist-1.0.5/RTMBdist/man/zibinom.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zigamma.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zigamma2.Rd | 11 RTMBdist-1.0.5/RTMBdist/man/ziinvgauss.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zilnorm.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zinbinom.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zinbinom2.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zipois.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/ziweibull.Rd | 3 RTMBdist-1.0.5/RTMBdist/man/zoibeta.Rd | 5 RTMBdist-1.0.5/RTMBdist/man/zoibeta2.Rd | 4 RTMBdist-1.0.5/RTMBdist/tests/testthat/helper-distcheck.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bccg.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bcpe.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-bct.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-beta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-betabinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-betaprime.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-dirichlet.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-dirmult.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-exgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-foldnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gamma2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gengamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-genpois.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gmrf.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gompertz.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-gumbel.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invchisq.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invgamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-invgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-kumar.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-laplace.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-llogis.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-mvt.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-nbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-oibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-oibeta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-pgweibull.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-powerexp.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skellam.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewnorm2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewt.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-skewt2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-t2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-truncnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-trunct.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-trunct2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vmf.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-vmf2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-wishart.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-wrpcauchy.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zibinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zigamma.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zigamma2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ziinvgauss.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zilnorm.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zinbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zinbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zipois.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ziweibull.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zoibeta.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-zoibeta2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztnbinom.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztnbinom2.R |only RTMBdist-1.0.5/RTMBdist/tests/testthat/test-ztpois.R |only RTMBdist-1.0.5/RTMBdist/vignettes/Examples.Rmd | 71 +- RTMBdist-1.0.5/RTMBdist/vignettes/adding-a-distribution.Rmd |only RTMBdist-1.0.5/RTMBdist/vignettes/distlist.Rmd | 4 188 files changed, 940 insertions(+), 426 deletions(-)
Title: Nonparametric Hazard Rate Estimation
Description: Provides functions and examples for histogram, kernel (classical, variable bandwidth and transformations based, see e.g. Bagkavos (2008), <doi:10.1080/10485250802440184>, discrete and semiparametric hazard rate estimators.
Author: Dimitrios Bagkavos [aut, cre]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between NPHazardRate versions 0.1 dated 2018-11-02 and 0.3 dated 2026-07-22
DESCRIPTION | 12 ++-- MD5 | 18 +++--- man/DefVarBandRule.Rd | 10 --- man/DiscHazRateAuxFunctions.Rd | 19 +----- man/NP.M.Estimate.Rd | 2 man/SimpsonInt.Rd | 2 man/TransHazRateEst.Rd | 17 +---- man/TutzPritscher.Rd | 121 ++++++++++++++++++----------------------- man/VarBandHazEst.Rd | 9 +-- man/WeibHazFunctionals.Rd | 2 10 files changed, 87 insertions(+), 125 deletions(-)
Title: Numerical Tools for 'Rcpp' and Lambda Functions
Description: Provides a 'C++' API for routinely used numerical tools such as integration,
root-finding, and optimization, where function arguments are given as
lambdas. This facilitates 'Rcpp' programming, enabling the development of
'R'-like code in 'C++' where functions can be defined on the fly and use
variables in the surrounding environment.
Author: Andrew M. Raim [aut, cre]
Maintainer: Andrew M. Raim <andrew.raim@gmail.com>
Diff between fntl versions 0.1.2 dated 2024-11-12 and 0.1.3 dated 2026-07-22
DESCRIPTION | 14 MD5 | 111 NAMESPACE | 2 NEWS.md | 6 R/RcppExports.R | 37 build/vignette.rds |binary inst/doc/examples |only inst/doc/fntl.R | 74 inst/doc/fntl.pdf |binary inst/doc/fntl.qmd | 714 +++--- inst/include/args.h | 6 inst/include/findroot-bisect.h | 6 inst/include/findroot-brent.h | 6 inst/include/goldensection.h | 2 inst/include/gradient.h | 4 inst/include/integrate.h | 2 inst/include/jacobian.h | 4 inst/include/log-sum-exp.h | 4 inst/include/optimize-brent.h | 2 inst/include/outer.h | 61 inst/include/result.h | 43 inst/include/trunc.h | 69 inst/include/typedefs-rcpp.h | 1 inst/include/util.h | 30 inst/tinytest/test-outer.R |only man/fntl-package.Rd | 5 man/outer.Rd | 32 src/RcppExports.cpp | 29 src/rcpp-interface.cpp | 39 src/rcpp-interface.h | 38 vignettes/.install_extras |only vignettes/common.sty | 2 vignettes/examples/arma.cpp |only vignettes/examples/first.cpp | 2 vignettes/examples/logger.cpp |only vignettes/examples/outer-sp.cpp |only vignettes/examples/outer.cpp | 11 vignettes/fntl.html | 4444 +++++++++++++++++++++++++++++++++++----- vignettes/fntl.html.md |only vignettes/fntl.qmd | 714 +++--- vignettes/references.bib | 66 41 files changed, 5323 insertions(+), 1257 deletions(-)
Title: VCG Sampling using Energy-Based Covariate Balancing
Description: Provides a principled framework for sampling Virtual Control Group (VCG) using energy distance-based covariate balancing. The package offers visualization tools to assess covariate balance and includes a permutation test to evaluate the statistical significance of observed deviations.
Author: Andreas Schulz [aut, cre] ,
Sanofi [cph, fnd]
Maintainer: Andreas Schulz <andreas.schulz2@sanofi.com>
Diff between eVCGsampler versions 1.1.0 dated 2026-07-06 and 1.1.2 dated 2026-07-22
DESCRIPTION | 6 +-- MD5 | 19 +++++----- NEWS.md |only R/VCG_sampler.R | 59 +++++++++++++++++++++++++++++--- R/combine_variables.R | 4 +- R/energy_distance.R | 2 - R/find_outliers.R | 4 +- R/robust_scale.R | 19 ++++++---- inst/doc/eVCGsampler_user_guide.html | 56 +++++++++++++++--------------- man/robust_scale.Rd | 5 +- tests/testthat/test-combine_variables.R | 2 - 11 files changed, 117 insertions(+), 59 deletions(-)
Title: Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indexes, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [aut] ,
Ned Horning [aut],
Jakob Schwalb-Willmann [aut] ,
Robert J. Hijmans [ctb] ,
Konstantin Mueller [aut, cre]
Maintainer: Konstantin Mueller <konstantinfinn.mueller@gmx.de>
Diff between RStoolbox versions 1.0.2.2 dated 2025-10-02 and 1.0.2.3 dated 2026-07-22
DESCRIPTION | 12 +++++------ MD5 | 21 ++++++++++--------- NEWS.md | 6 +++++ R/mesma.R | 39 ++++++++++++++++++++++++------------- README.md | 19 ++++++++---------- man/mesma.Rd | 5 ++-- man/rescaleImage.Rd | 2 - man/spectralIndices.Rd | 26 ------------------------ tests/testthat/Rplots.pdf |only tests/testthat/test-mesma.R | 14 ++++++------- tests/testthat/test-oneHotEncode.R | 6 +++-- tests/testthat/test-superClass.R | 4 +++ 12 files changed, 77 insertions(+), 77 deletions(-)
Title: 'GGML' Tensor Operations for Machine Learning
Description: Provides 'R' bindings to the 'GGML' tensor library for machine
learning, optimized for 'Vulkan' GPU acceleration with a transparent CPU
fallback. The package features a 'Keras'-like sequential API and a
'PyTorch'-style 'autograd' engine for building, training, and deploying
neural networks. Key capabilities include high-performance 5D tensor
operations, 'f16' precision, and efficient quantization. It supports
native 'ONNX' model import (50+ operators) and 'GGUF' weight loading
from the 'llama.cpp' and 'Hugging Face' ecosystems. Designed for
zero-overhead inference via dedicated weight buffering, it integrates
seamlessly as a 'parsnip' engine for 'tidymodels' and provides
first-class learners for the 'mlr3' framework.
See <https://github.com/ggml-org/ggml> for more information about the
underlying library.
Author: Yuri Baramykov [aut, cre] ,
Georgi Gerganov [ctb, cph] ,
Jeffrey Quesnelle [ctb, cph] ,
Bowen Peng [ctb, cph] ,
Mozilla Foundation [ctb, cph]
Maintainer: Yuri Baramykov <lbsbmsu@mail.ru>
Diff between ggmlR versions 0.8.1 dated 2026-07-13 and 0.8.2 dated 2026-07-22
DESCRIPTION | 6 +-- MD5 | 19 ++++++------ NEWS.md | 4 ++ R/gpu_linalg.R | 16 ++++++++++ R/sc_contracts.R | 10 ++++++ R/sc_umap.R | 6 +++ README.md | 10 ++++++ inst/examples/profile_tests.R |only tests/testthat.R | 3 + tests/testthat/test-mlr3-autograd.R | 55 ++++++++++++++++++++++++++++++++---- tests/testthat/test-sc-umap.R | 19 +++++------- 11 files changed, 119 insertions(+), 29 deletions(-)
Title: Hasse Diagram of the Layout Structure and Restricted Layout
Structure
Description: Returns a Hasse diagram of the layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918173> or the restricted layout structure (Bate and Chatfield (2016)) <doi:10.1080/00224065.2016.11918174> of an experimental design.
Author: Damianos Michaelides [aut, cre],
Simon Bate [aut],
Marion Chatfield [aut]
Maintainer: Damianos Michaelides <dm3g15@soton.ac.uk>
Diff between hassediagrams versions 2.0 dated 2026-01-17 and 2.1 dated 2026-07-22
DESCRIPTION | 8 +++---- MD5 | 6 ++--- R/internal.R | 13 +++++++++-- inst/doc/Introduction_to_hassediagrams.html | 32 ++++++++++++---------------- 4 files changed, 32 insertions(+), 27 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow the user to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 1.2.4 dated 2026-06-19 and 1.2.5 dated 2026-07-22
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/RcppExports.R | 8 ++++++++ R/graphlayouts.R | 1 + R/layout_tree.R |only R/layouts.R | 25 +++++++++++++++++++++++++ man/graphlayouts-package.Rd | 6 ++++++ man/layout_tree_unrooted.Rd |only src/RcppExports.cpp | 32 ++++++++++++++++++++++++++++++++ src/unrooted_tree.cpp |only tests/testthat/test-layout_tree.R |only 13 files changed, 93 insertions(+), 11 deletions(-)
Title: Discrete-Time Multistate Models
Description: Discrete-time multistate models with a user-friendly workflow. The package provides tools for processing data, several ways of estimating parametric and nonparametric multistate models, and an extensive set of Markov chain methods which use transition probabilities derived from the multistate model. Some of the implemented methods are described in Schneider et al. (2024) <doi:10.1080/00324728.2023.2176535>, Dudel (2021) <doi:10.1177/0049124118782541>, Dudel & Myrskylä (2020) <doi:10.1186/s12963-020-00217-0>, van den Hout (2017) <doi:10.1201/9781315374321>.
Author: Christian Dudel [aut, cre]
Maintainer: Christian Dudel <dudel@demogr.mpg.de>
Diff between dtms versions 0.4.2 dated 2026-02-25 and 0.5.0 dated 2026-07-22
DESCRIPTION | 8 LICENSE | 4 MD5 | 37 ++-- NAMESPACE | 1 NEWS.md | 13 + R/dtms.R | 3 R/dtms_censoring.R | 6 R/dtms_expectancy.R | 2 R/dtms_impute.R |only R/dtms_matrix.R | 2 R/dtms_transitions.R | 26 ++- README.md | 249 ++++++++++++++++++----------- man/dtms.Rd | 93 +++++----- man/dtms_aggregate.Rd | 106 ++++++------ man/dtms_duration.Rd | 134 +++++++-------- man/dtms_expectancy.Rd | 2 man/dtms_impute.Rd |only man/dtms_matrix.Rd | 2 man/dtms_occurrence.Rd | 140 ++++++++-------- man/dtms_survivor.Rd | 140 ++++++++-------- man/figures/README-regressionpredict-1.png |only 21 files changed, 537 insertions(+), 431 deletions(-)
Title: Alternative and Fast ROC Analysis
Description: Alternative and fast algorithms for the analysis of receiver operating
characteristics curves (ROC curves) as described in Thomas et al. (2017)
<doi:10.1186/s41512-017-0017-y> and Thomas et al. (2023) <doi:10.1016/j.ajogmf.2023.101110>.
Author: Gregoire Thomas [aut, cre] ,
Robin Tuytten [ctb] ,
Jef Moerman [ctb],
Xavier Robin [cph] ,
Stefan Siegert [cph]
Maintainer: Gregoire Thomas <gregoire.thomas@SQU4RE.com>
Diff between alternativeROC versions 1.0.4 dated 2025-11-24 and 1.0.5 dated 2026-07-22
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 5 +++++ R/alternativeROC-common-args.R | 4 +++- R/rocperf.R | 20 +++++++++++--------- build/partial.rdb |binary man/alternativeROC-common-args.Rd | 4 ++++ man/alternativeROC-package.Rd | 5 +++++ man/rocperf.Rd | 3 +++ tests/testthat/test_rocperf.R | 10 ++++++++++ 10 files changed, 55 insertions(+), 24 deletions(-)
More information about alternativeROC at CRAN
Permanent link
Title: Uniform Data Model and 'Zarr' Interchange for Single-Cell Omics
Description: A lightweight interchange layer for single-cell and spatial omics
data, built on the L-star model of labelled axes and typed fields over them,
serialized to the 'Zarr' format. Provides bidirectional converters
("profiles") for 'Seurat', 'SingleCellExperiment', 'Conos', and 'pagoda2'
objects, including collections of heterogeneous samples, via a shared C++
core ('libstar') so the same store is readable from R, 'Python', and C++.
Author: Peter Kharchenko [aut, cre]
Maintainer: Peter Kharchenko <pk.restricted@gmail.com>
Diff between lstar versions 0.1.0 dated 2026-06-22 and 0.2.1 dated 2026-07-22
lstar-0.1.0/lstar/man/write_pagoda2.Rd |only lstar-0.2.1/lstar/DESCRIPTION | 14 lstar-0.2.1/lstar/MD5 | 63 - lstar-0.2.1/lstar/NAMESPACE | 6 lstar-0.2.1/lstar/NEWS.md | 131 ++ lstar-0.2.1/lstar/R/backed.R | 8 lstar-0.2.1/lstar/R/cpp11.R | 16 lstar-0.2.1/lstar/R/lstar.R | 28 lstar-0.2.1/lstar/R/profile_pagoda2.R | 134 +- lstar-0.2.1/lstar/R/profile_sce.R | 1 lstar-0.2.1/lstar/R/profile_seurat.R | 91 + lstar-0.2.1/lstar/R/view.R |only lstar-0.2.1/lstar/R/viewer.R |only lstar-0.2.1/lstar/inst/include/libzarr |only lstar-0.2.1/lstar/inst/include/lstar/lstar.hpp | 845 +++++++++++++----- lstar-0.2.1/lstar/man/dot-lstar_drop_cache.Rd |only lstar-0.2.1/lstar/man/extend_for_viewer.Rd |only lstar-0.2.1/lstar/man/lstar_read.Rd | 2 lstar-0.2.1/lstar/man/lstar_write.Rd | 16 lstar-0.2.1/lstar/man/lstar_write_viewer.Rd |only lstar-0.2.1/lstar/man/read_pagoda2.Rd |only lstar-0.2.1/lstar/man/view.Rd |only lstar-0.2.1/lstar/man/viewer_extend.Rd |only lstar-0.2.1/lstar/man/write_seurat.Rd | 11 lstar-0.2.1/lstar/src/Makevars | 24 lstar-0.2.1/lstar/src/cpp11.cpp | 32 lstar-0.2.1/lstar/src/lstar_cpp.cpp | 88 + lstar-0.2.1/lstar/tests/testthat/test-pagoda2.R | 20 lstar-0.2.1/lstar/tests/testthat/test-roundtrip.R | 12 lstar-0.2.1/lstar/tests/testthat/test-view.R |only lstar-0.2.1/lstar/tests/testthat/test-viewer-export.R |only 31 files changed, 1177 insertions(+), 365 deletions(-)
Title: Make Symmetric and Asymmetric ARDL Estimations
Description: Implements estimation procedures for Autoregressive Distributed Lag (ARDL)
and Nonlinear ARDL (NARDL) models, which allow researchers to investigate both
short- and long-run relationships in time series data under mixed orders of integration.
The package supports simultaneous modeling of symmetric and asymmetric regressors,
flexible treatment of short-run and long-run asymmetries, and automated equation handling.
It includes several cointegration testing approaches such as the Pesaran-Shin-Smith F
and t bounds tests, and narayan test.
Methodological foundations are provided in Pesaran, Shin, and Smith (2001)
<doi:10.1016/S0304-4076(01)00049-5> and Shin, Yu, and Greenwood-Nimmo (2014, ISBN:9780123855079).
Author: Huseyin karamelikli [aut, cre] ,
Huseyin Utku Demir [aut]
Maintainer: Huseyin karamelikli <hakperest@gmail.com>
Diff between kardl versions 2.0.4 dated 2026-07-17 and 2.0.5 dated 2026-07-22
DESCRIPTION | 6 MD5 | 32 ++-- R/multipliers.R | 8 - R/print.R | 229 ++++++++++++++------------------ R/tests.R | 11 - inst/doc/intro.R | 6 inst/doc/intro.Rmd | 6 inst/doc/intro.html | 253 +++++++++++++++++------------------- man/bootstrap.Rd | 20 ++ man/ecm.Rd | 16 -- man/kardl.Rd | 16 -- man/mplier.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-print-summary.R | 6 tests/testthat/test-print.R | 2 tests/testthat/test-tests.R | 7 vignettes/intro.Rmd | 6 17 files changed, 298 insertions(+), 331 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Maelle Salmon [aut] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.3.1 dated 2026-01-11 and 2.4.0 dated 2026-07-22
gert-2.3.1/gert/NEWS |only gert-2.4.0/gert/DESCRIPTION | 13 + gert-2.4.0/gert/MD5 | 142 +++++++++++---------- gert-2.4.0/gert/NAMESPACE | 15 ++ gert-2.4.0/gert/NEWS.md |only gert-2.4.0/gert/R/archive.R | 3 gert-2.4.0/gert/R/branch.R | 71 ++++++++++ gert-2.4.0/gert/R/commit.R | 172 ++++++++++++++++++++++---- gert-2.4.0/gert/R/config.R | 131 ++++++++++++++----- gert-2.4.0/gert/R/diff.R | 10 + gert-2.4.0/gert/R/errors.R | 4 gert-2.4.0/gert/R/fetch.R | 68 ++++++++-- gert-2.4.0/gert/R/gert-package.R | 39 +++++ gert-2.4.0/gert/R/ignore.R | 2 gert-2.4.0/gert/R/init.R | 10 - gert-2.4.0/gert/R/merge.R | 36 +++-- gert-2.4.0/gert/R/open.R | 4 gert-2.4.0/gert/R/pr.R | 12 + gert-2.4.0/gert/R/rebase.R | 46 ++++-- gert-2.4.0/gert/R/remotes.R | 47 +++++-- gert-2.4.0/gert/R/repository.R | 24 ++- gert-2.4.0/gert/R/restore.R |only gert-2.4.0/gert/R/roxygen2.R |only gert-2.4.0/gert/R/signature.R | 5 gert-2.4.0/gert/R/stash.R | 1 gert-2.4.0/gert/R/submodules.R | 9 - gert-2.4.0/gert/R/tag.R | 3 gert-2.4.0/gert/R/utils-sha.R |only gert-2.4.0/gert/R/worktree.R | 1 gert-2.4.0/gert/build/vignette.rds |binary gert-2.4.0/gert/cleanup | 1 gert-2.4.0/gert/configure | 4 gert-2.4.0/gert/inst/doc/gert.html | 13 + gert-2.4.0/gert/man/gert-package.Rd | 5 gert-2.4.0/gert/man/git_archive.Rd | 25 ++- gert-2.4.0/gert/man/git_branch.Rd | 88 +++++++++++-- gert-2.4.0/gert/man/git_commit.Rd | 80 ++++-------- gert-2.4.0/gert/man/git_config.Rd | 92 ++++++++++--- gert-2.4.0/gert/man/git_diff.Rd | 35 +++-- gert-2.4.0/gert/man/git_fetch.Rd | 40 ++++-- gert-2.4.0/gert/man/git_history.Rd |only gert-2.4.0/gert/man/git_ignore.Rd | 29 ++-- gert-2.4.0/gert/man/git_merge.Rd | 61 +++++---- gert-2.4.0/gert/man/git_open.Rd | 4 gert-2.4.0/gert/man/git_rebase.Rd | 51 ++++--- gert-2.4.0/gert/man/git_remote.Rd | 32 +++- gert-2.4.0/gert/man/git_repo.Rd | 59 ++++++-- gert-2.4.0/gert/man/git_reset.Rd | 25 ++- gert-2.4.0/gert/man/git_restore.Rd |only gert-2.4.0/gert/man/git_revert.Rd |only gert-2.4.0/gert/man/git_signature.Rd | 25 ++- gert-2.4.0/gert/man/git_stash.Rd | 27 ++-- gert-2.4.0/gert/man/git_submodule.Rd | 9 - gert-2.4.0/gert/man/git_tag.Rd | 29 ++-- gert-2.4.0/gert/man/git_worktree.Rd | 27 ++-- gert-2.4.0/gert/man/github.Rd | 6 gert-2.4.0/gert/man/user_is_configured.Rd | 2 gert-2.4.0/gert/src/branch.c | 14 -- gert-2.4.0/gert/src/clone.c | 28 ++-- gert-2.4.0/gert/src/commit.c | 85 ++++++++---- gert-2.4.0/gert/src/config.c | 64 ++++++--- gert-2.4.0/gert/src/files.c | 32 +++- gert-2.4.0/gert/src/init.c | 20 +-- gert-2.4.0/gert/src/utils.c | 11 + gert-2.4.0/gert/src/utils.h | 3 gert-2.4.0/gert/tests/spelling.R | 10 + gert-2.4.0/gert/tests/testthat/test-auth.R | 68 ++++++++-- gert-2.4.0/gert/tests/testthat/test-branch.R |only gert-2.4.0/gert/tests/testthat/test-clone.R | 53 +++++++- gert-2.4.0/gert/tests/testthat/test-commit.R | 113 ++++++++++++++++- gert-2.4.0/gert/tests/testthat/test-config.R | 53 +++++++- gert-2.4.0/gert/tests/testthat/test-ignore.R | 21 +-- gert-2.4.0/gert/tests/testthat/test-merge.R | 5 gert-2.4.0/gert/tests/testthat/test-rebase.R | 88 ++++++++++--- gert-2.4.0/gert/tests/testthat/test-remotes.R | 99 +++++++++++++- gert-2.4.0/gert/tests/testthat/test-restore.R |only gert-2.4.0/gert/tools/winlibs.R | 10 - 77 files changed, 1769 insertions(+), 645 deletions(-)
Title: Prediction and Interpretation in Decision Trees for
Classification and Regression
Description: Optimization of conditional inference trees from the package 'party'
for classification and regression.
For optimization, the model space is searched for the best tree on the full sample by
means of repeated subsampling. Restrictions are allowed so that only trees are accepted
which do not include pre-specified uninterpretable split results (cf. Weihs & Buschfeld, 2021a).
The function PrInDT() represents the basic resampling loop for 2-class classification (cf. Weihs
& Buschfeld, 2021a). The function RePrInDT() (repeated PrInDT()) allows for repeated
applications of PrInDT() for different percentages of the observations of the large and the
small classes (cf. Weihs & Buschfeld, 2021c). The function NesPrInDT() (nested PrInDT())
allows for an extra layer of subsampling for a specific factor variable (cf. Weihs & Buschfeld,
2021b). The functions PrInDTMulev() and PrInDTMulab() deal with multilevel and multilabel
classification. In addition to these PrInDT() variants for c [...truncated...]
Author: Claus Weihs [aut, cre],
Sarah Buschfeld [aut],
Niklas Nitsch [ctb]
Maintainer: Claus Weihs <claus.weihs@tu-dortmund.de>
Diff between PrInDT versions 2.0.2 dated 2025-09-11 and 2.0.3 dated 2026-07-22
DESCRIPTION | 14 +++++++------- MD5 | 6 +++--- R/SimMixPrInDT.R | 2 +- man/SimMixPrInDT.Rd | 2 +- 4 files changed, 12 insertions(+), 12 deletions(-)
Title: NWS Hydrology Models: SAC-SMA, SNOW17, UH, CONSUSE, CHANLOSS
Description: Interface to the National Weather Service operational
hydrology models, Sacramento Soil Moisture Accounting (SAC-SMA),
Snow Accumulation and Ablation (SNOW17). Also provides an
interface to the unit hydrograph routing model (UH), consumptive use (CONSUSE)
and channel loss/gain modules (CHANLOSS). The Fortran code used in this package
is considered "legacy" and is not supported officially by NWS,
but it should not have any significant differences from current
operational models.
Author: Cameron Bracken [aut, cre] ,
Geoffrey Walters [aut] ,
Eric Anderson [ctb] ),
George F. Smith [ctb] ),
Janice M. Lewis [ctb] ),
John E. Pask [ctb] ; see
inst/COPYRIGHTS),
Ondrej Certik [ctb] ,
John Burkardt [ctb] ,
National Oceanic and Atmospheric Adm [...truncated...]
Maintainer: Cameron Bracken <cameron.bracken@pnnl.gov>
Diff between nwsrfsr versions 1.0.2 dated 2026-07-17 and 1.0.3 dated 2026-07-22
nwsrfsr-1.0.2/nwsrfsr/src/Makevars |only nwsrfsr-1.0.3/nwsrfsr/DESCRIPTION | 12 ++--- nwsrfsr-1.0.3/nwsrfsr/MD5 | 28 +++++++------ nwsrfsr-1.0.3/nwsrfsr/NEWS.md | 35 ++++++++++++++++ nwsrfsr-1.0.3/nwsrfsr/R/sac-snow-uh.R | 70 ++++++++++++++++++++++++++++----- nwsrfsr-1.0.3/nwsrfsr/cleanup |only nwsrfsr-1.0.3/nwsrfsr/configure |only nwsrfsr-1.0.3/nwsrfsr/man/nwsrfsr.Rd | 2 nwsrfsr-1.0.3/nwsrfsr/man/rsnwelev.Rd | 32 ++++++++++++--- nwsrfsr-1.0.3/nwsrfsr/src/Makevars.in |only nwsrfsr-1.0.3/nwsrfsr/src/Makevars.win | 24 +++++++---- nwsrfsr-1.0.3/nwsrfsr/src/aesc19.f | 6 ++ nwsrfsr-1.0.3/nwsrfsr/src/fka7.f | 5 ++ nwsrfsr-1.0.3/nwsrfsr/src/flag7.f | 11 ++++- nwsrfsr-1.0.3/nwsrfsr/src/pin7.f | 5 ++ nwsrfsr-1.0.3/nwsrfsr/src/umemst.f | 7 ++- nwsrfsr-1.0.3/nwsrfsr/src/zero19.f | 9 +++- 17 files changed, 199 insertions(+), 47 deletions(-)
More information about NeutroCrdRcbdAnalysis at CRAN
Permanent link
Title: Toolkit for HLA Immunogenomics
Description: A toolkit for the analysis and management of data for genes in the so-called "Human Leukocyte Antigen" (HLA) region. Functions extract reference data from the Anthony Nolan HLA Informatics Group/ImmunoGeneTics HLA 'GitHub' repository (ANHIG/IMGTHLA) <https://github.com/ANHIG/IMGTHLA>, validate Genotype List (GL) Strings, convert between UNIFORMAT and GL String Code (GLSC) formats, translate HLA alleles and GLSCs across ImmunoPolymorphism Database (IPD) IMGT/HLA Database release versions, identify differences between pairs of alleles at a locus, generate customized, multi-position sequence alignments, trim and convert allele-names across nomenclature epochs, and extend existing data-analysis methods. Tran et al., (2025) <doi:10.1111/iji.70013>.
Author: Livia Tran [aut],
Ryan Nickens [aut],
Leamon Crooms IV [aut],
Derek Pappas [aut],
Vinh Luu [ctb],
Josh Bredeweg [ctb],
Steven Mack [aut, cre]
Maintainer: Steven Mack <Steven.Mack@ucsf.edu>
Diff between HLAtools versions 1.6.3 dated 2025-07-21 and 1.11.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 64 + NAMESPACE | 2 NEWS.md | 47 + R/SearchandBuildAlignments.R | 2 R/UpdateAll.R | 28 R/VersionValidation.R | 18 R/atlasMaker.R | 1321 +++++++++++++++++++-------------------- R/buildAlignments.R | 177 ++--- R/buildGazetteer.R | 20 R/compareSequences.R | 91 +- R/data.R | 32 R/extractGenomicReferenceGenes.R |only R/globals.R | 3 R/locusValidator.R | 18 README.md | 37 - build/vignette.rds |binary data/HLAatlas.rda |binary data/HLAgazetteer.rda |binary data/IMGTGenomicReferences.rda |only data/IMGTHLAGeneTypes.rda |binary data/fragmentFeatureNames.rda |binary inst/doc/HLAtools.Rmd | 31 inst/doc/HLAtools.html | 56 + man/HLAatlas.Rd | 2 man/HLAgazetteer.Rd | 11 man/IMGTGenomicReferences.Rd |only man/buildAlignments.Rd | 6 man/buildGazetteer.Rd | 13 man/buildGenomicReferences.Rd |only man/compareSequences.Rd | 17 man/getLatestVersion.Rd | 2 man/multiLocusValidation.Rd | 4 man/updateAll.Rd | 4 vignettes/HLAtools.Rmd | 31 35 files changed, 1163 insertions(+), 884 deletions(-)
Title: Modelling Structured Dynamical Systems in 'greta'
Description: A 'greta' extension for analysing transition matrices and
ordinary differential equations representing dynamical systems. Provides
functions for analysing transition matrices by iteration, and solving
ordinary differential equations. This is an extension to the 'greta'
software, Golding (2019) <doi:10.21105/joss.01601>.
Author: Nick Golding [aut, cph] ,
Nicholas Tierney [aut, cre]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
This is a re-admission after prior archival of version 0.2.2 dated 2024-11-13
Diff between greta.dynamics versions 0.2.2 dated 2024-11-13 and 0.2.3 dated 2026-07-22
DESCRIPTION | 17 +++-- MD5 | 28 ++++---- NEWS.md | 21 ++++++ R/greta.dynamics-package.R | 2 R/iterate_dynamic_function.R | 22 ++++++ R/iterate_dynamic_matrix.R | 30 +++++++++ R/iterate_matrix.R | 4 - README.md | 2 build/vignette.rds |binary inst/doc/iterate-matrix-example.html | 112 +++++++++++++++++------------------ inst/doc/ode-solve-example.html | 20 +++--- man/greta.dynamics.Rd | 3 man/iterate_dynamic_function.Rd | 23 ++++++- man/iterate_dynamic_matrix.Rd | 31 +++++++++ man/iterate_matrix.Rd | 4 - 15 files changed, 223 insertions(+), 96 deletions(-)
More information about greta.dynamics at CRAN
Permanent link
Title: GeoServer REST API R Interface
Description: Provides an R interface to the GeoServer REST API, allowing to upload
and publish data in a GeoServer web-application and expose data to OGC Web-Services.
The package currently supports all CRUD (Create,Read,Update,Delete) operations
on GeoServer workspaces, namespaces, datastores (stores of vector data), featuretypes,
layers, styles, as well as vector data upload operations. For more information about
the GeoServer REST API, see <https://docs.geoserver.org/main/en/user/rest/>.
Author: Emmanuel Blondel [aut, cre]
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geosapi versions 0.8 dated 2026-01-12 and 0.8-1 dated 2026-07-22
DESCRIPTION | 10 +- MD5 | 36 ++++----- NEWS.md | 14 ++- R/GSAccessControlListManager.R | 116 ++++++++++++++++++++++++----- R/GSCoverageStoreManager.R | 2 R/GSLayerRule.R | 2 R/GSRestRule.R | 10 -- R/GSRule.R | 6 - R/GSServiceRule.R | 2 R/geosapi.R | 2 README.md | 2 inst/doc/geosapi.Rmd | 16 ++-- inst/doc/geosapi.html | 16 ++-- man/GSAccessControlListManager.Rd | 152 +++++++++++++++++++++++++++++++++++--- man/GSCoverageStoreManager.Rd | 2 man/GSRestRule.Rd | 10 -- man/GSRule.Rd | 4 - man/geosapi.Rd | 2 vignettes/geosapi.Rmd | 16 ++-- 19 files changed, 308 insertions(+), 112 deletions(-)
Title: The Environmental Costs of Flow Regulation
Description: An application to calculate the daily environmental costs of river
flow regulation by dams based on García de Jalón et al. (2017)
<doi:10.1007/s11269-017-1663-0>.
Author: Silvestre Garcia de Jalon [aut],
Javier Martinez-Lopez [aut, cre],
Marta Gonzalez del Tanago [aut],
Carlos Alonso [aut],
Diego Garcia de Jalon [aut]
Maintainer: Javier Martinez-Lopez <javi.martinez.lopez@gmail.com>
Diff between FlowRegEnvCost versions 0.1.1 dated 2017-10-18 and 0.1.2 dated 2026-07-22
DESCRIPTION | 35 +++++++++++++++++++++++++++++------ MD5 | 10 ++++++---- NEWS.md |only R/data.R | 6 +++--- build |only inst/CITATION | 41 +++++++++++++++++++++-------------------- man/flowdata.Rd | 6 +++--- 7 files changed, 62 insertions(+), 36 deletions(-)
More information about FlowRegEnvCost at CRAN
Permanent link
Title: Data Sets to Accompany Designing Experiments and Analyzing Data:
A Model Comparison Perspective (Maxwell, Delaney, and Kelley,
2027, 4th Edition)
Description: Data sets that accompany the book "Designing experiments and
analyzing data: A model comparison perspective" (4th ed.) by
Maxwell, Delaney, and Kelley (2027; ISBN 978-1-041-25384-6; Routledge).
Contains all of the data sets in the book's chapters and end-of-chapter
exercises. Beginning with version 2.0, the package is tailored to the 4th
edition of the book; for the data as distributed with the 3rd edition
(2018), install the archived version 1.0.2 from CRAN. We recommend the
'DMAR' package as the companion for carrying out the book's analyses; these
analyses are illustrated in the book itself using the 'MBESS' package, which
may be used as well. The book's companion website is available at
<https://designingexperiments.com/> and its publisher page at
<https://www.routledge.com/Designing-Experiments-and-Analyzing-Data-A-Model-Comparison-Perspective/Maxwell-Delaney-Kelley/p/book/9781041253846>.
Author: Scott E. Maxwell [aut],
Harold D. Delaney [aut],
Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between AMCP versions 1.0.2 dated 2024-06-07 and 2.0.0 dated 2026-07-22
AMCP-1.0.2/AMCP/data/C12T21.rda |only AMCP-1.0.2/AMCP/data/C13T12.rda |only AMCP-1.0.2/AMCP/data/C13T14.rda |only AMCP-1.0.2/AMCP/data/C4T7.rda |only AMCP-1.0.2/AMCP/data/C7T15.rda |only AMCP-1.0.2/AMCP/data/C7T23.rda |only AMCP-1.0.2/AMCP/data/C9T11.rda |only AMCP-1.0.2/AMCP/data/chapter_12_table_21.rda |only AMCP-1.0.2/AMCP/data/chapter_13_table_12.rda |only AMCP-1.0.2/AMCP/data/chapter_13_table_14.rda |only AMCP-1.0.2/AMCP/data/chapter_4_table_7.rda |only AMCP-1.0.2/AMCP/data/chapter_7_table_15.rda |only AMCP-1.0.2/AMCP/data/chapter_7_table_23.rda |only AMCP-1.0.2/AMCP/data/chapter_9_table_11.rda |only AMCP-1.0.2/AMCP/man/chapter_12_table_21.Rd |only AMCP-1.0.2/AMCP/man/chapter_13_table_12.Rd |only AMCP-1.0.2/AMCP/man/chapter_13_table_14.Rd |only AMCP-1.0.2/AMCP/man/chapter_4_table_7.Rd |only AMCP-1.0.2/AMCP/man/chapter_7_table_15.Rd |only AMCP-1.0.2/AMCP/man/chapter_7_table_23.Rd |only AMCP-1.0.2/AMCP/man/chapter_9_table_11.Rd |only AMCP-2.0.0/AMCP/DESCRIPTION | 49 AMCP-2.0.0/AMCP/MD5 | 405 + AMCP-2.0.0/AMCP/NEWS.md |only AMCP-2.0.0/AMCP/R/AMCP.R | 44 AMCP-2.0.0/AMCP/R/documentation.R | 2822 ++++++++----- AMCP-2.0.0/AMCP/README.md | 41 AMCP-2.0.0/AMCP/build |only AMCP-2.0.0/AMCP/data/C12E22.rda |only AMCP-2.0.0/AMCP/data/C12E23.rda |only AMCP-2.0.0/AMCP/data/C12E24.rda |only AMCP-2.0.0/AMCP/data/C12E25.rda |only AMCP-2.0.0/AMCP/data/C12E26.rda |only AMCP-2.0.0/AMCP/data/C12E27.rda |only AMCP-2.0.0/AMCP/data/C12T29.rda |only AMCP-2.0.0/AMCP/data/C13T10.rda |only AMCP-2.0.0/AMCP/data/C13T5.rda |only AMCP-2.0.0/AMCP/data/C14E10.rda |binary AMCP-2.0.0/AMCP/data/C14T10.rda |binary AMCP-2.0.0/AMCP/data/C14T13.rda |only AMCP-2.0.0/AMCP/data/C14T7.rda |only AMCP-2.0.0/AMCP/data/C14T8.rda |binary AMCP-2.0.0/AMCP/data/C14T9.rda |only AMCP-2.0.0/AMCP/data/C15E19.rda |binary AMCP-2.0.0/AMCP/data/C16E5.rda |binary AMCP-2.0.0/AMCP/data/C16T1.rda |binary AMCP-2.0.0/AMCP/data/C1E22.rda |binary AMCP-2.0.0/AMCP/data/C4E18.rda |only AMCP-2.0.0/AMCP/data/C4E21.rda 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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-20 2019-12.4
2016-08-08 2016-8.8
2014-12-05 2013-10.28
2013-11-08 2013-10.27
Title: Fit 'TabNet' Models for Classification and Regression
Description: Implements the 'TabNet' model by Sercan O. Arik et al. (2019)
<doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical
Multi-label Classification Networks' by Giunchiglia et al.
<doi:10.48550/arXiv.2010.10151> and provides a consistent interface
for fitting and creating predictions. It's also fully compatible with
the 'tidymodels' ecosystem.
Author: Daniel Falbel [aut],
RStudio [cph],
Christophe Regouby [cre, ctb],
Egill Fridgeirsson [ctb],
Philipp Haarmeyer [ctb],
Sven Verweij [ctb]
Maintainer: Christophe Regouby <christophe.regouby@free.fr>
Diff between tabnet versions 0.9.0 dated 2026-06-12 and 0.9.1 dated 2026-07-22
tabnet-0.9.0/tabnet/build/partial.rdb |only tabnet-0.9.0/tabnet/man/tabnet-package.Rd |only tabnet-0.9.1/tabnet/DESCRIPTION | 18 ++- tabnet-0.9.1/tabnet/MD5 | 46 ++++------ tabnet-0.9.1/tabnet/NEWS.md | 4 tabnet-0.9.1/tabnet/R/hardhat.R | 1 tabnet-0.9.1/tabnet/README.md | 8 - tabnet-0.9.1/tabnet/build/vignette.rds |binary tabnet-0.9.1/tabnet/inst/WORDLIST | 3 tabnet-0.9.1/tabnet/inst/doc/Hierarchical_classification.R | 1 tabnet-0.9.1/tabnet/inst/doc/Hierarchical_classification.Rmd | 1 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.R | 3 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.Rmd | 3 tabnet-0.9.1/tabnet/inst/doc/Missing_data_predictors.html | 6 - tabnet-0.9.1/tabnet/inst/doc/interpretation.R | 1 tabnet-0.9.1/tabnet/inst/doc/interpretation.Rmd | 1 tabnet-0.9.1/tabnet/man/figures/README-model-explain-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-model-fit-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-step-explain-1.png |binary tabnet-0.9.1/tabnet/man/figures/README-step-pretrain-1.png |binary tabnet-0.9.1/tabnet/tests/testthat/Rplots.pdf |binary tabnet-0.9.1/tabnet/tests/testthat/test-parsnip.R | 5 - tabnet-0.9.1/tabnet/vignettes/Hierarchical_classification.Rmd | 1 tabnet-0.9.1/tabnet/vignettes/Missing_data_predictors.Rmd | 3 tabnet-0.9.1/tabnet/vignettes/interpretation.Rmd | 1 25 files changed, 62 insertions(+), 44 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] ,
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] ,
Pedro Despouy [aut],
Salim Brueggemann [ctb] ,
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.12.0 dated 2026-01-24 and 4.12.1 dated 2026-07-22
DESCRIPTION | 10 +- MD5 | 40 ++++----- NAMESPACE | 5 - NEWS.md | 16 +++ R/ggplotly.R | 23 ++++- R/imports.R | 1 R/kaleido.R | 52 ++++++++++-- R/layout.R | 4 R/plotly.R | 3 R/plotly_build.R | 3 R/utils.R | 2 README.md | 2 man/config.Rd | 4 man/figures/README-volcano-surface.png |only man/plot_ly.Rd | 3 tests/testthat/_snaps/ggplot-size/size-global-scaling.svg | 2 tests/testthat/_snaps/ggplot-theme/theme-marker-default.svg | 2 tests/testthat/test-ggplot-facets.R | 6 - tests/testthat/test-ggplot-legend.R | 12 +- tests/testthat/test-group2NA.R | 2 tests/testthat/test-kaleido.R |only tests/testthat/test-plotly.R | 6 + 22 files changed, 139 insertions(+), 59 deletions(-)
Title: Test of No Main and/or Interaction Effects in Functional Data
Description: Distribution free heteroscedastic tests for functional data.
The following tests are included in this package: test of no main treatment or contrast
effect and no simple treatment effect given in
Wang, Higgins, and Blasi (2010) <doi:10.1016/j.spl.2009.11.016>,
no main time effect, and no interaction effect based on
original observations given in Wang and Akritas (2010a)
<doi:10.1080/10485250903171621>
and tests based on ranks given in Wang and Akritas (2010b)
<doi:10.1016/j.jmva.2010.03.012>.
Author: Haiyan Wang [aut, cre],
Michael Akritas [aut],
James Higgins [aut],
Dale Blasi [aut]
Maintainer: Haiyan Wang <hwang@ksu.edu>
Diff between HeterFunctionalData versions 0.1.0 dated 2020-08-20 and 1.0 dated 2026-07-22
HeterFunctionalData-0.1.0/HeterFunctionalData/man/fun.sigijj12.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/DESCRIPTION | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/MD5 | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/NAMESPACE | 22 +- HeterFunctionalData-1.0/HeterFunctionalData/R/functions.R | 102 +++++++--- HeterFunctionalData-1.0/HeterFunctionalData/man/eu.Rd | 6 HeterFunctionalData-1.0/HeterFunctionalData/man/fun.sigijj12R.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigijj12C.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4.Rd | 21 +- HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4R.Rd |only HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4bootstrap.Rd | 4 HeterFunctionalData-1.0/HeterFunctionalData/man/sigma4jackknife.Rd | 4 HeterFunctionalData-1.0/HeterFunctionalData/man/taufun.Rd | 2 HeterFunctionalData-1.0/HeterFunctionalData/src |only 14 files changed, 141 insertions(+), 64 deletions(-)
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Title: Generalized Elastic Nets
Description: Implements several extensions of the elastic net regularization
scheme. These extensions include individual feature penalties for the L1 term,
feature-feature penalties for the L2 term, as well as translation coefficients
for the latter.
Author: Artem Sokolov [aut, cre]
Maintainer: Artem Sokolov <artem.sokolov@gmail.com>
Diff between gelnet versions 1.2.1 dated 2016-04-05 and 1.2.2 dated 2026-07-22
CHANGES | 8 DESCRIPTION | 15 MD5 | 37 +- NAMESPACE | 3 R/gelnet.R | 5 build/vignette.rds |binary inst/doc/basics.R | 20 - inst/doc/basics.Rmd | 2 inst/doc/basics.html | 822 ++++++++++++++++++++++++++------------------- man/L1.ceiling.Rd | 13 man/adj2lapl.Rd | 1 man/adj2nlapl.Rd | 1 man/gelnet.Rd | 24 + man/gelnet.cv.Rd | 23 - man/gelnet.ker.Rd | 17 man/gelnet.lin.obj.Rd | 15 man/gelnet.logreg.obj.Rd | 17 man/gelnet.oneclass.obj.Rd | 12 src/init.c |only vignettes/basics.Rmd | 2 20 files changed, 625 insertions(+), 412 deletions(-)
Title: Relationship Matrices for Diploid and Autopolyploid Species
Description: Fast computation of A (pedigree), G (genomic-base), and H (A corrected
by G) relationship matrices for diploid and autopolyploid species. Several methods
are implemented considering additive and non-additive models.
Author: Rodrigo Amadeu [aut, cre],
Luis Ferrao [aut, ctb],
Thiago Oliveira [aut, ctb],
Catherine Cellon [ctb],
Leticia Lara [ctb],
Marcio Resende [ctb],
Ivone Oliveira [ctb],
Patricio Munoz [ctb],
Augusto Garcia [ctb]
Maintainer: Rodrigo Amadeu <rramadeu@gmail.com>
Diff between AGHmatrix versions 2.1.4 dated 2023-10-03 and 3.0.1 dated 2026-07-22
DESCRIPTION | 51 - MD5 | 120 +- NAMESPACE | 34 R/Amatrix.R | 524 ++++------ R/AmatrixPolyCross.R | 379 +++---- R/Gmatrix.R | 786 +++++++-------- R/Hmatrix.R | 451 +++++--- R/Mcheck.R | 326 +++--- R/RcppExports.R |only R/datatreat.R | 392 ++----- R/expandAmatrix.R | 162 +-- R/filterpedigree.R | 114 +- R/formatmatrix.R | 180 +-- R/missingdata.R | 182 +-- R/ped.mrode-data.R | 38 R/ped.sol-data.R | 38 R/snp.pine-data.R | 38 R/snp.sol-data.R | 38 README.md | 712 +++++++------- build/vignette.rds |binary data/datalist | 8 inst/CITATION | 32 inst/doc/Tutorial_AGHmatrix.R | 472 ++++----- inst/doc/Tutorial_AGHmatrix.Rmd | 820 ++++++++-------- inst/doc/Tutorial_AGHmatrix.html | 1974 +++++++++++++++++++-------------------- inst/misc/ISSUE | 4 inst/misc/Tutorial_AGHmatrix.R | 380 +++---- inst/misc/Tutorial_AGHmatrix.Rmd | 640 ++++++------ inst/misc/converttofrequency.R | 224 ++-- inst/misc/explorematrix.R | 122 +- inst/misc/misc.R | 180 +-- man/Amatrix.Rd | 201 ++- man/AmatrixPolyCross.Rd | 110 +- man/Gmatrix.Rd | 283 +++-- man/H_martini_blocks.Rd |only man/Hmatrix.Rd | 182 +-- man/Mcheck.Rd | 6 man/asciitonumber.Rd |only man/datatreat.Rd | 65 - man/expandAmatrix.Rd | 76 - man/filterpedigree.Rd | 54 - man/formatmatrix.Rd | 110 +- man/missingdata.Rd | 54 - man/munoz_var_mean_by_Aclass.Rd |only man/ped.mrode.Rd | 46 man/ped.sol.Rd | 48 man/snp.pine.Rd | 48 man/snp.sol.Rd | 48 src |only tests |only vignettes/Tutorial_AGHmatrix.Rmd | 820 ++++++++-------- 51 files changed, 5820 insertions(+), 5752 deletions(-)
Title: Anomaly Detection in Temporal Networks
Description: Anomaly detection in dynamic, temporal networks. The package
'oddnet' uses a feature-based method to identify anomalies. First, it computes
many features for each network. Then it models the features using time series
methods. Using time series residuals it detects anomalies. This way, the
temporal dependencies are accounted for when identifying anomalies
(Kandanaarachchi, Sanderson, Hyndman 2024) <doi:10.1109/ISCMI63661.2024.10851659>.
Author: Sevvandi Kandanaarachchi [aut, cre] ,
Rob Hyndman [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between oddnet versions 0.1.1 dated 2024-02-11 and 0.1.2 dated 2026-07-22
DESCRIPTION | 22 ++++++++-------- MD5 | 21 ++++++++------- R/anomaly_detection.R | 17 +++++++++--- R/features.R | 7 +++-- R/laplacian_eigenvalue_method.R | 6 ++-- build/partial.rdb |only build/vignette.rds |binary inst/doc/oddnet.html | 53 ++++++++++++++++++++++++++-------------- man/anomalous_networks.Rd | 11 +++++--- man/compute_features.Rd | 2 - man/lad.Rd | 6 ++-- man/oddnet-package.Rd | 4 ++- 12 files changed, 92 insertions(+), 57 deletions(-)
Title: Multistate Model Bias-Corrected Robust Variance
Description: Computes robust and bias-corrected sandwich variance estimators for multi-state Cox models with clustered time-to-event data. Also provides Wald tests for heterogeneity, generalized least-squares linear trends, and order-restricted trends among transition-specific coefficients. The methodology extends the marginal Cox model bias-correction framework of Wang et al. (2023) <doi:10.1002/bimj.202200113> to the multi-state setting.
Author: Can Meng [aut, cre],
Denise Esserman [aut],
Fan Li [aut],
Erich Greene [aut]
Maintainer: Can Meng <can.meng@yale.edu>
Diff between mmbcv versions 0.3.0 dated 2026-03-31 and 1.0.0 dated 2026-07-22
DESCRIPTION | 10 MD5 | 23 NAMESPACE | 3 NEWS.md |only R/dissipation-tests-helper.R |only R/heterogeneity-test.R |only R/linear-trend-test.R |only R/order-restricted-test.R |only inst/doc/mmbcv-intro.R | 120 ++ inst/doc/mmbcv-intro.Rmd | 1394 ++++++++++++++++++++++---------- inst/doc/mmbcv-intro.html | 1321 +++++++++++++++++++++++------- man/heterogeneity_test.Rd |only man/linear_trend_test.Rd |only man/order_restricted_test.Rd |only tests/testthat/test-dissipation-tests.R |only vignettes/mmbcv-intro.Rmd | 1394 ++++++++++++++++++++++---------- vignettes/references.bib | 129 ++ 17 files changed, 3253 insertions(+), 1141 deletions(-)
Title: Calculate Generalized Eigenvalues, the Generalized Schur
Decomposition and the Generalized Singular Value Decomposition
of a Matrix Pair with Lapack
Description: Functions to compute generalized eigenvalues and eigenvectors,
the generalized Schur decomposition and
the generalized Singular Value Decomposition of a matrix pair,
using Lapack routines.
Author: Berend Hasselman [aut],
Jonathan M. Lees [cre],
Lapack authors [aut, cph]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between geigen versions 2.3 dated 2019-05-30 and 2.4 dated 2026-07-22
DESCRIPTION | 24 +++++++++++++++--------- MD5 | 14 +++++++------- build/partial.rdb |binary man/geigen.Rd | 6 +++--- man/gevalues.Rd | 2 +- man/gqz.Rd | 8 ++++---- man/gsvd.Rd | 14 +++++++------- src/zggsvdall.f | 12 ++++++------ 8 files changed, 43 insertions(+), 37 deletions(-)
Title: Recursive Two-Stage Models to Address Endogeneity
Description: Various recursive two-stage models to address the endogeneity issue of treatment variables in observational study or mediators in experiments. The details of the models are discussed in Peng (2023) <doi:10.1287/isre.2022.1113>.
Author: Jing Peng [aut, cre]
Maintainer: Jing Peng <jing.peng@uconn.edu>
Diff between endogeneity versions 2.1.5 dated 2025-10-12 and 2.1.6 dated 2026-07-22
DESCRIPTION | 8 ++++---- MD5 | 34 +++++++++++++++++----------------- R/pln.R | 10 +++++++++- R/probit_linearRE.R | 7 ++++--- build/vignette.rds |binary inst/doc/vignette.html | 6 +++--- man/bilinear.Rd | 22 +++++++++++----------- man/biprobit.Rd | 22 +++++++++++----------- man/biprobit_latent.Rd | 22 +++++++++++----------- man/biprobit_partial.Rd | 22 +++++++++++----------- man/linear_probit.Rd | 22 +++++++++++----------- man/pln.Rd | 5 +++++ man/pln_linear.Rd | 22 +++++++++++----------- man/pln_probit.Rd | 22 +++++++++++----------- man/probit_linear.Rd | 22 +++++++++++----------- man/probit_linearRE.Rd | 27 +++++++++++++++------------ man/probit_linear_latent.Rd | 22 +++++++++++----------- man/probit_linear_partial.Rd | 22 +++++++++++----------- 18 files changed, 167 insertions(+), 150 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability distributions
using S3. Generics pdf(), cdf(), quantile(), and random() provide
replacements for base R's d/p/q/r style functions. Functions and
arguments have been named carefully to minimize confusion for students
in intro stats courses. The documentation for each distribution
contains detailed mathematical notes.
Author: Alex Hayes [aut] ,
Ralph Moller-Trane [aut] ,
Daniel Jordan [aut],
Paul Northrop [aut] ,
Moritz N. Lang [aut] ,
Achim Zeileis [aut, cre] ,
Emil Hvitfeldt [ctb] ,
Bruna Wundervald [ctb] ,
Alessandro Gasparini [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between distributions3 versions 0.2.3 dated 2025-09-12 and 0.2.4 dated 2026-07-22
DESCRIPTION | 55 +++--- LICENSE | 2 MD5 | 234 ++++++++++++++-------------- NEWS.md | 10 + R/Bernoulli.R | 2 R/Binomial.R | 2 R/Cauchy.R | 2 R/ChiSquare.R | 2 R/Exponential.R | 4 R/FisherF.R | 2 R/Frechet.R | 2 R/Gamma.R | 2 R/GeneralisedExtremeValue.R | 4 R/GeneralisedPareto.R | 2 R/Geometric.R | 4 R/Gumbel.R | 2 R/HurdleNegativeBinomial.R | 2 R/HurdlePoisson.R | 2 R/HyperGeometric.R | 6 R/LogNormal.R | 2 R/Logistic.R | 2 R/Multinomial.R | 2 R/NegativeBinomial.R | 4 R/Normal.R | 2 R/Poisson.R | 2 R/PoissonBinomial.R | 2 R/ReversedWeibull.R | 2 R/StudentsT.R | 2 R/Tukey.R | 2 R/Weibull.R | 16 - R/ZINegativeBinomial.R | 2 R/ZIPoisson.R | 2 R/ZTNegativeBinomial.R | 2 R/ZTPoisson.R | 2 README.md | 13 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-hypothesis-testing.html | 2 inst/doc/one-sample-sign-tests.html | 2 inst/doc/one-sample-t-test.html | 2 inst/doc/one-sample-z-test-for-proportion.R | 12 - inst/doc/one-sample-z-test.html | 2 inst/doc/paired-tests.html | 22 +- inst/doc/poisson.html | 27 +-- inst/doc/two-sample-z-test.html | 6 man/Bernoulli.Rd | 32 +-- man/Beta.Rd | 38 ++-- man/Binomial.Rd | 32 +-- man/Categorical.Rd | 30 +-- man/Cauchy.Rd | 40 ++-- man/ChiSquare.Rd | 40 ++-- man/Erlang.Rd | 38 ++-- man/Exponential.Rd | 40 ++-- man/FisherF.Rd | 40 ++-- man/Frechet.Rd | 40 ++-- man/GEV.Rd | 40 ++-- man/GP.Rd | 40 ++-- man/Gamma.Rd | 40 ++-- man/Geometric.Rd | 32 +-- man/Gumbel.Rd | 40 ++-- man/HurdleNegativeBinomial.Rd | 32 +-- man/HurdlePoisson.Rd | 32 +-- man/HyperGeometric.Rd | 32 +-- man/LogNormal.Rd | 40 ++-- man/Logistic.Rd | 40 ++-- man/Multinomial.Rd | 32 +-- man/NegativeBinomial.Rd | 32 +-- man/Normal.Rd | 40 ++-- man/Poisson.Rd | 32 +-- man/PoissonBinomial.Rd | 32 +-- man/RevWeibull.Rd | 40 ++-- man/StudentsT.Rd | 40 ++-- man/Tukey.Rd | 40 ++-- man/Uniform.Rd | 38 ++-- man/Weibull.Rd | 42 ++--- man/ZINegativeBinomial.Rd | 32 +-- man/ZIPoisson.Rd | 32 +-- man/ZTNegativeBinomial.Rd | 32 +-- man/ZTPoisson.Rd | 32 +-- man/cdf.Geometric.Rd | 8 man/cdf.HyperGeometric.Rd | 8 man/cdf.LogNormal.Rd | 10 - man/cdf.Logistic.Rd | 8 man/cdf.NegativeBinomial.Rd | 8 man/cdf.Normal.Rd | 8 man/cdf.StudentsT.Rd | 8 man/cdf.Tukey.Rd | 4 man/cdf.Weibull.Rd | 8 man/distributions3-package.Rd | 11 - man/fit_mle.LogNormal.Rd | 10 - man/fit_mle.Normal.Rd | 8 man/geom_auc.Rd | 2 man/pdf.Geometric.Rd | 8 man/pdf.HyperGeometric.Rd | 8 man/pdf.LogNormal.Rd | 10 - man/pdf.Logistic.Rd | 8 man/pdf.Multinomial.Rd | 4 man/pdf.NegativeBinomial.Rd | 8 man/pdf.Normal.Rd | 8 man/pdf.StudentsT.Rd | 8 man/pdf.Weibull.Rd | 8 man/quantile.Geometric.Rd | 8 man/quantile.HyperGeometric.Rd | 8 man/quantile.LogNormal.Rd | 10 - man/quantile.Logistic.Rd | 8 man/quantile.NegativeBinomial.Rd | 8 man/quantile.Normal.Rd | 8 man/quantile.StudentsT.Rd | 8 man/quantile.Tukey.Rd | 4 man/quantile.Weibull.Rd | 8 man/random.Geometric.Rd | 8 man/random.HyperGeometric.Rd | 8 man/random.LogNormal.Rd | 10 - man/random.Logistic.Rd | 8 man/random.Multinomial.Rd | 4 man/random.NegativeBinomial.Rd | 8 man/random.StudentsT.Rd | 8 man/random.Weibull.Rd | 8 118 files changed, 1009 insertions(+), 1003 deletions(-)
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Title: Color Schemes for Dichromats
Description: Collapse red-green or green-blue distinctions to simulate the effects of different types of color-blindness
based on the work of Françoise Viénot and co-authors, especially <doi:10.1038/376127a0> and <doi:10.1364/josaa.14.002647>.
More recent functions for simulating color vision deficiency are provided in the 'colorspace' package.
Author: Thomas Lumley [aut] ,
Achim Zeileis [aut, cre] ,
Kenneth Knoblauch [ctb] ,
Scott Waichler [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between dichromat versions 2.0-0.1 dated 2022-05-02 and 2.0-1 dated 2026-07-22
DESCRIPTION | 44 ++++++++++++++++++++++++-------------------- MD5 | 18 +++++++++++------- NAMESPACE | 4 ++-- NEWS.md |only R/sysdata.rda |binary R/zzz.R |only README.md |only build |only data/dalton.rda |binary man/colorschemes.Rd | 5 +---- man/dalton.Rd | 20 +++++++++++--------- man/dichromat.Rd | 15 +++++++++------ 12 files changed, 58 insertions(+), 48 deletions(-)