Title: Computes R Squared for Mixed (Multilevel) Models
Description: The model R squared and semi-partial R squared for the linear and
generalized linear mixed model (LMM and GLMM) are computed with confidence
limits. The R squared measure from Edwards et.al (2008) <DOI:10.1002/sim.3429>
is extended to the GLMM using penalized quasi-likelihood (PQL) estimation
(see Jaeger et al. 2016 <DOI:10.1080/02664763.2016.1193725>). Three methods
of computation are provided and described as follows. First, The
Kenward-Roger approach. Due to some inconsistency between the 'pbkrtest'
package and the 'glmmPQL' function, the Kenward-Roger approach in the
'r2glmm' package is limited to the LMM. Second, The method introduced
by Nakagawa and Schielzeth (2013) <DOI:10.1111/j.2041-210x.2012.00261.x>
and later extended by Johnson (2014) <DOI:10.1111/2041-210X.12225>.
The 'r2glmm' package only computes marginal R squared for the LMM and does
not generalize the statistic to the GLMM; however, confidence limits and
semi-partial R squared for fixed effect [...truncated...]
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <byron.jaeger@gmail.com>
Diff between r2glmm versions 0.1.2 dated 2017-08-05 and 0.1.3 dated 2025-04-28
DESCRIPTION | 17 +-- MD5 | 29 ++--- NEWS.md |only R/cmpR2_Function.R | 17 +-- R/glm_PQL_Function.R | 3 R/r2_sgv_est_Function.R | 6 - R/r2beta_Function.R | 10 - R/r2beta_glmmPQL_Function.R | 15 +- R/r2beta_lme_Function.R | 13 +- R/r2beta_lmerMod_Function.R | 33 +++++- README.md | 226 +++++++++++++++++++++++++++++--------------- man/plot.R2.Rd | 12 +- man/pqlmer.Rd | 2 man/r2beta.Rd | 10 - man/r2dt.Rd | 12 +- tests/testthat/test_R2.R | 30 +++++ 16 files changed, 292 insertions(+), 143 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization, Stochastic dominance and Advanced Monte Carlo sampling. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre],
Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 11.2 dated 2025-03-25 and 11.3 dated 2025-04-28
DESCRIPTION | 8 - MD5 | 18 +- R/Nowcast.R | 3 R/Partial_Moments.R | 202 ++++++++++++++++++++---------- README.md | 4 inst/doc/NNSvignette_Partial_Moments.html | 2 man/NNS.nowcast.Rd | 1 src/fast_lm.cpp | 79 +++++++++-- tests/testthat/Rplots.pdf |binary tests/testthat/test_Partial_Moments.R | 2 10 files changed, 222 insertions(+), 97 deletions(-)
Title: High Density Genetic Linkage Mapping using Multidimensional
Scaling
Description: Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.
Author: Katharine F. Preedy [aut],
Christine A. Hackett [aut],
Bram Boskamp [cre]
Maintainer: Bram Boskamp <bram.boskamp@bioss.ac.uk>
Diff between MDSMap versions 1.1 dated 2018-08-09 and 1.3 dated 2025-04-28
DESCRIPTION | 31 MD5 | 62 NAMESPACE | 54 R/MDSmap-package.R | 4 R/mds.R | 139 build/vignette.rds |binary inst/doc/MDSMap.pdf |binary inst/extdata/lgV.txt |56408 ++++++++++++++++++++--------------------- man/MDSMap-package.Rd | 70 man/calc.maps.pc.Rd | 206 man/calc.maps.sphere.Rd | 220 man/calc.nnfit.Rd | 78 man/calc.nnfit.from.file.Rd | 163 man/calc.nnfit.loci.Rd | 72 man/calc.nswaps.Rd | 64 man/calc.pair.rf.lod.Rd | 114 man/convert.polar.Rd | 80 man/dmap.Rd | 56 man/dmap.check.Rd | 62 man/estimate.map.Rd | 264 man/get.dist.loci.Rd | 54 man/get.nearest.informative.Rd | 48 man/invert.map.Rd | 50 man/lgI.txt.Rd | 84 man/lgV.txt.Rd | 84 man/map.to.interval.Rd | 86 man/meandist.from.truth.Rd | 92 man/plot.pcmap.Rd | 105 man/plot.pcmap3d.Rd | 125 man/plot.spheremap.Rd | 116 man/recalc.nnfit.from.map.Rd | 72 man/sim.bc.rflod.file.Rd | 82 32 files changed, 29602 insertions(+), 29543 deletions(-)
Title: Annual Regional Database of the European Commission (ARDECO)
Description: A set of functions to access the 'ARDECO' (Annual Regional Database
of the European Commission) data directly from the official ARDECO public
repository through the exploitation of the 'ARDECO' APIs.
The APIs are completely transparent to the user and the provided functions
provide a direct access to the 'ARDECO' data.
The 'ARDECO' database is a collection of variables related to demography,
employment, labour market, domestic product, capital formation.
Each variable can be exposed in one or more units of measure as well as
refers to total values plus additional dimensions like economic sectors, gender,
age classes. Data can be also aggregated at country level according
to the tercet classes as defined by EUROSTAT.
The description of the 'ARDECO' database can be found at the following URL
<https://urban.jrc.ec.europa.eu/ardeco>.
Author: Carmelo Attardo [cre],
Giuseppe Bucciarelli [aut],
European Commission, JRC [cph]
Maintainer: Carmelo Attardo <carmelo.attardo@ec.europa.eu>
Diff between ARDECO versions 2.2.1 dated 2025-04-18 and 2.2.2 dated 2025-04-28
ARDECO-2.2.1/ARDECO/inst/doc/introArdeco.R |only ARDECO-2.2.2/ARDECO/DESCRIPTION | 6 ARDECO-2.2.2/ARDECO/MD5 | 14 ARDECO-2.2.2/ARDECO/NEWS | 2 ARDECO-2.2.2/ARDECO/build/vignette.rds |binary ARDECO-2.2.2/ARDECO/inst/doc/introArdeco.Rmd | 422 +++++++++++++++++++-- ARDECO-2.2.2/ARDECO/inst/doc/introArdeco.html | 302 +++++++-------- ARDECO-2.2.2/ARDECO/vignettes/introArdeco.Rmd | 422 +++++++++++++++++++-- ARDECO-2.2.2/ARDECO/vignettes/introArdeco.Rmd.orig |only 9 files changed, 937 insertions(+), 231 deletions(-)
Title: Easily Install and Load 'tesselle' Packages
Description: Easy install and load key packages from the 'tesselle' suite
in a single step. The 'tesselle' suite is a collection of packages for
research and teaching in archaeology. These packages focus on
quantitative analysis methods developed for archaeology. The
'tesselle' packages are designed to work seamlessly together and to
complement general-purpose and other specialized statistical packages.
These packages can be used to explore and analyze common data types in
archaeology: count data, compositional data and chronological data.
Learn more about 'tesselle' at <https://www.tesselle.org>.
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [art] ,
Universite Bordeaux Montaigne [fnd] ,
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tesselle versions 1.5.0 dated 2024-12-10 and 1.6.0 dated 2025-04-28
DESCRIPTION | 34 ++++++++++++++++++++-------------- MD5 | 19 +++++++++++-------- NEWS.md | 9 +++++++++ R/attach.R | 2 +- R/tesselle-internal.R | 5 +++++ R/tesselle-package.R | 2 +- README.md | 27 +++++++++++++-------------- inst/CITATION | 8 ++++---- inst/po |only man/tesselle-package.Rd | 6 +++--- po |only 11 files changed, 67 insertions(+), 45 deletions(-)
Title: Formatted Survey Estimates
Description: Short and understandable commands that generate tabulated,
formatted, and rounded survey estimates. Mostly a wrapper for the
'survey' package (Lumley (2004) <doi:10.18637/jss.v009.i08>
<https://CRAN.R-project.org/package=survey>) that identifies
low-precision estimates using the National Center for Health
Statistics (NCHS) presentation standards (Parker et al. (2017)
<https://www.cdc.gov/nchs/data/series/sr_02/sr02_175.pdf>,
Parker et al. (2023) <doi:10.15620/cdc:124368>).
Author: Alex Strashny [aut, cre]
Maintainer: Alex Strashny <alex.strashny@gmail.com>
Diff between surveytable versions 0.9.6 dated 2025-03-13 and 0.9.7 dated 2025-04-28
DESCRIPTION | 6 MD5 | 50 - NEWS.md | 4 R/set_survey.R | 214 +++--- R/survey_subset.R | 76 +- R/tab.R | 6 R/total.R | 4 R/var_all.R | 64 +- R/var_any.R | 68 +- R/var_case.R | 100 +-- R/var_collapse.R | 62 - R/var_copy.R | 62 - R/var_list.R | 112 +-- R/var_not.R | 52 - R/z_utils.R | 98 +-- README.md | 4 inst/WORDLIST | 1 inst/doc/Advanced-topics.html | 8 inst/doc/Example-National-Ambulatory-Medical-Care-Survey-NAMCS-tables.html | 294 ++++----- inst/doc/Example-Residential-Care-Community-Services-User-NSLTCP-RCC-SU-report.html | 72 +- inst/doc/Printing-HTML.html | 295 ++++----- inst/doc/Printing-PDF.pdf |binary inst/doc/surveytable.Rmd | 2 inst/doc/surveytable.html | 317 +++++----- man/set_survey.Rd | 4 vignettes/surveytable.Rmd | 2 26 files changed, 995 insertions(+), 982 deletions(-)
Title: Working with netCDF for Essential Biodiversity Variables
Description: The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>)
comes with a data structure based on the Network Common Data Form (netCDF).
The 'ebvcube' 'R' package provides functionality to easily create, access and
visualise this data. The EBV netCDFs can be downloaded from the EBV Data
Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
Author: Luise Quoss [aut, cre] ,
Nestor Fernandez [aut] ,
Christian Langer [aut] ,
Jose Valdez [aut] ,
Henrique Miguel Pereira [aut]
Maintainer: Luise Quoss <luise.quoss@idiv.de>
Diff between ebvcube versions 0.4.0 dated 2025-03-05 and 0.5.0 dated 2025-04-28
ebvcube-0.4.0/ebvcube/inst/docs/ebvcube_0.4.0.pdf |only ebvcube-0.5.0/ebvcube/DESCRIPTION | 8 ebvcube-0.5.0/ebvcube/MD5 | 32 ebvcube-0.5.0/ebvcube/NEWS.md | 357 - ebvcube-0.5.0/ebvcube/R/ebv_create_taxonomy.R | 2370 +++++----- ebvcube-0.5.0/ebvcube/R/ebv_properties.R | 987 ++-- ebvcube-0.5.0/ebvcube/R/zzz.R | 10 ebvcube-0.5.0/ebvcube/README.md | 40 ebvcube-0.5.0/ebvcube/inst/docs/ebvcube_0.5.0.pdf |only ebvcube-0.5.0/ebvcube/inst/extdata/testdata/id5_taxid.csv | 2 ebvcube-0.5.0/ebvcube/man/EBV-netCDF-properties-class.Rd | 4 ebvcube-0.5.0/ebvcube/man/ebv_create_taxonomy.Rd | 34 ebvcube-0.5.0/ebvcube/tests/testthat/test-ebv-read.R | 156 ebvcube-0.5.0/ebvcube/tests/testthat/test-ebv_create_taxonomy.R | 309 - ebvcube-0.5.0/ebvcube/tests/testthat/test-ebv_manipulate.R | 334 - ebvcube-0.5.0/ebvcube/tests/testthat/test-plots.R | 212 ebvcube-0.5.0/ebvcube/tests/testthat/test-resample.R | 70 ebvcube-0.5.0/ebvcube/tests/testthat/test-write.R | 129 18 files changed, 2557 insertions(+), 2497 deletions(-)
Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut],
Timo Bechger [aut],
Jesse Koops [aut, cre],
Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>
Diff between dexter versions 1.6.0 dated 2025-04-07 and 1.6.1 dated 2025-04-28
dexter-1.6.0/dexter/tests/testthat/sufstats_dich.RData |only dexter-1.6.0/dexter/tests/testthat/sufstats_poly.RData |only dexter-1.6.0/dexter/tests/testthat/verbAggression.db |only dexter-1.6.0/dexter/tests/testthat/verbal_oplm |only dexter-1.6.1/dexter/DESCRIPTION | 6 dexter-1.6.1/dexter/MD5 | 88 ++--- dexter-1.6.1/dexter/NAMESPACE | 13 dexter-1.6.1/dexter/NEWS.md | 14 dexter-1.6.1/dexter/R/ability.R | 15 dexter-1.6.1/dexter/R/database.R | 27 - dexter-1.6.1/dexter/R/dexter.R | 26 - dexter-1.6.1/dexter/R/equating.R | 2 dexter-1.6.1/dexter/R/fit_enorm.R | 56 --- dexter-1.6.1/dexter/R/misc.R | 34 + dexter-1.6.1/dexter/R/misc_anon.R | 1 dexter-1.6.1/dexter/R/oplike.R | 5 dexter-1.6.1/dexter/R/param.R | 75 +++- dexter-1.6.1/dexter/R/plots.R | 174 +++++----- dexter-1.6.1/dexter/R/resp_data.R | 9 dexter-1.6.1/dexter/R/standards.R | 2 dexter-1.6.1/dexter/R/suf_stats.R | 38 ++ dexter-1.6.1/dexter/inst/doc/DIF_vignette.html | 4 dexter-1.6.1/dexter/inst/doc/Equating.html | 10 dexter-1.6.1/dexter/inst/doc/Plausible_Values.html | 16 dexter-1.6.1/dexter/inst/doc/Test_Individual_differences.html | 14 dexter-1.6.1/dexter/inst/doc/dexter.html | 54 +-- dexter-1.6.1/dexter/inst/doc/profile-plots.html | 4 dexter-1.6.1/dexter/man/plot.enorm.Rd | 8 dexter-1.6.1/dexter/src/ability.cpp | 39 +- dexter-1.6.1/dexter/tests/testthat/setup.R |only dexter-1.6.1/dexter/tests/testthat/test_ability.R | 64 +++ dexter-1.6.1/dexter/tests/testthat/test_data_selection.R | 2 dexter-1.6.1/dexter/tests/testthat/test_database.R | 19 - dexter-1.6.1/dexter/tests/testthat/test_elsym.R | 8 dexter-1.6.1/dexter/tests/testthat/test_enorm.R | 19 - dexter-1.6.1/dexter/tests/testthat/test_interaction.R | 2 dexter-1.6.1/dexter/tests/testthat/test_latent_cor.R | 2 dexter-1.6.1/dexter/tests/testthat/test_p2p.R | 2 dexter-1.6.1/dexter/tests/testthat/test_plausible_scores.R | 2 dexter-1.6.1/dexter/tests/testthat/test_plausible_values.R | 26 - dexter-1.6.1/dexter/tests/testthat/test_profiles.R | 2 dexter-1.6.1/dexter/tests/testthat/test_theta.R | 2 dexter-1.6.1/dexter/tests/testthat/testdata |only 43 files changed, 517 insertions(+), 367 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut, ctb],
Diego Salles [aut, ths],
Janio Lima [aut, ths],
Lucas Tavares [aut, ths],
Diego Carvalho [aut, ths],
Eduardo Bezerra [aut, ths],
Rafaelli Coutinho [aut, ths],
Federal Center for Technolog [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.1.737 dated 2025-04-21 and 1.1.747 dated 2025-04-28
DESCRIPTION | 19 +++-- MD5 | 142 ++++++++++++++++++++++---------------------- NAMESPACE | 4 - R/autoenc_adv_e.R | 9 +- R/autoenc_adv_ed.R | 9 +- R/autoenc_conv_e.R | 9 +- R/autoenc_conv_ed.R | 5 - R/autoenc_denoise_e.R | 9 +- R/autoenc_denoise_ed.R | 9 +- R/autoenc_e.R | 9 +- R/autoenc_ed.R | 9 +- R/autoenc_lstm_e.R | 9 +- R/autoenc_lstm_ed.R | 9 +- R/autoenc_stacked_e.R | 9 +- R/autoenc_stacked_ed.R | 9 +- R/autoenc_variational_e.R | 9 +- R/autoenc_variational_ed.R | 9 +- R/cla_classification.R | 2 R/cla_dtree.R | 4 - R/cla_knn.R | 4 - R/cla_majority.R | 4 - R/cla_mlp.R | 4 - R/cla_nb.R | 4 - R/cla_rf.R | 4 - R/cla_svm.R | 4 - R/cla_tune.R | 3 R/clu_clusterer.R | 8 +- R/clu_dbscan.R | 4 - R/clu_kmeans.R | 2 R/clu_pam.R | 2 R/clu_tune.R | 1 R/dal_base.R | 7 +- R/dal_learner.R | 7 -- R/dal_predictor.R | 4 - R/dal_tune.R | 2 R/reg_dtree.R | 4 - R/reg_knn.R | 3 R/reg_mlp.R | 4 - R/reg_regression.R | 2 R/reg_rf.R | 4 - R/reg_svm.R | 4 - R/reg_tune.R | 3 R/trans_categ_mapping.R | 2 R/trans_dt_pca.R | 5 - R/trans_fit_curvature_max.R | 2 R/trans_fit_curvature_min.R | 2 R/trans_norm_minmax.R | 7 -- R/trans_norm_zscore.R | 6 - R/trans_outliers.R | 4 - R/trans_sample.R | 4 - R/trans_sample_random.R | 4 - R/trans_sample_strat.R | 4 - R/trans_smoothing.R | 6 - R/trans_smoothing_cluster.R | 2 R/trans_smoothing_freq.R | 2 R/trans_smoothing_inter.R | 2 R/trans_transform.R | 6 - R/ts_arima.R | 12 ++- R/ts_conv1d.R | 16 ---- R/ts_elm.R | 4 - R/ts_knn.R | 4 - R/ts_lstm.R | 18 ----- R/ts_mlp.R | 2 R/ts_norm_an.R | 6 - R/ts_norm_diff.R | 6 - R/ts_norm_gminmax.R | 6 - R/ts_norm_swminmax.R | 6 - R/ts_reg.R | 5 - R/ts_regsw.R | 6 - R/ts_rf.R | 4 - R/ts_svm.R | 4 - R/ts_tune.R | 2 72 files changed, 256 insertions(+), 284 deletions(-)
Title: Prediction Explanation with Dependence-Aware Shapley Values
Description: Complex machine learning models are often hard to interpret. However, in
many situations it is crucial to understand and explain why a model made a specific
prediction. Shapley values is the only method for such prediction explanation framework
with a solid theoretical foundation. Previously known methods for estimating the Shapley
values do, however, assume feature independence. This package implements methods which accounts for any feature
dependence, and thereby produces more accurate estimates of the true Shapley values.
An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.
Author: Martin Jullum [cre, aut] ,
Lars Henry Berge Olsen [aut] ,
Annabelle Redelmeier [aut],
Jon Lachmann [aut] ,
Nikolai Sellereite [aut] ,
Anders Loeland [ctb],
Jens Christian Wahl [ctb],
Camilla Lingjaerde [ctb],
Norsk Regnesentral [cph, fnd]
Maintainer: Martin Jullum <Martin.Jullum@nr.no>
Diff between shapr versions 1.0.3 dated 2025-04-01 and 1.0.4 dated 2025-04-28
DESCRIPTION | 10 MD5 | 261 NEWS.md | 35 R/approach_categorical.R | 500 R/approach_copula.R | 346 R/approach_ctree.R | 602 R/approach_empirical.R | 1218 - R/approach_gaussian.R | 346 R/approach_regression_separate.R | 1010 - R/approach_regression_surrogate.R | 6 R/approach_timeseries.R | 2 R/approach_vaeac.R | 310 R/approach_vaeac_torch_modules.R | 4093 +++--- R/asymmetric_and_casual_Shapley.R | 1042 - R/check_convergence.R | 16 R/cli.R | 277 R/compute_estimates.R | 77 R/compute_vS.R | 608 R/explain.R | 52 R/explain_forecast.R | 910 - R/finalize_explanation.R | 459 R/get_feature_specs.R | 144 R/get_predict_model.R | 173 R/model.R | 351 R/model_ar.R | 64 R/model_arima.R | 180 R/model_glm.R | 70 R/model_lm.R | 64 R/model_mgcv_gam.R | 82 R/model_ranger.R | 175 R/model_workflow.R | 62 R/model_xgboost.R | 102 R/plot.R | 287 R/prepare_next_iteration.R | 182 R/print_iter.R | 14 R/setup.R | 3558 ++--- R/shapley_setup.R | 473 R/zzz.R | 339 README.md | 588 inst/CITATION | 52 inst/doc/asymmetric_causal.Rmd | 4232 +++--- inst/doc/asymmetric_causal.html | 1706 +- inst/doc/general_usage.Rmd | 5005 ++++---- inst/doc/general_usage.html | 1658 +- inst/doc/regression.Rmd | 6238 +++++----- inst/doc/regression.html | 3704 +++-- inst/doc/vaeac.Rmd | 2480 ++- inst/doc/vaeac.html | 1004 - man/check_verbose.Rd | 9 man/cli_iter.Rd | 9 man/cli_startup.Rd | 9 man/cli_topline.Rd |only man/compute_vS.Rd | 6 man/create_coalition_table.Rd | 45 man/create_ctree.Rd | 2 man/exact_coalition_table.Rd | 1 man/explain.Rd | 46 man/explain_forecast.Rd | 11 man/get_extra_comp_args_default.Rd | 15 man/plot.shapr.Rd | 178 man/plot_SV_several_approaches.Rd | 2 man/regression.check_namespaces.Rd | 2 man/regression.train_model.Rd | 9 man/sample_coalition_table.Rd | 63 man/setup.Rd | 9 man/vaeac_check_cuda.Rd | 18 man/vaeac_check_epoch_values.Rd | 19 man/vaeac_check_parameters.Rd | 9 man/vaeac_check_save_parameters.Rd | 19 man/vaeac_get_mask_generator_name.Rd | 9 man/vaeac_impute_missing_entries.Rd | 9 man/vaeac_train_model.Rd | 9 man/vaeac_train_model_auxiliary.Rd | 9 man/vaeac_train_model_continue.Rd | 9 tests/testthat/helper-ar-arima.R | 2 tests/testthat/test-asymmetric-causal-output.R | 1096 - tests/testthat/test-asymmetric-causal-setup.R | 784 - tests/testthat/test-forecast-setup.R | 1478 +- tests/testthat/test-iterative-output.R | 403 tests/testthat/test-iterative-setup.R | 863 - tests/testthat/test-plot.R | 631 - tests/testthat/test-regression-output.R | 640 - tests/testthat/test-regression-setup.R | 23 tests/testthat/test-regular-output.R | 1167 - tests/testthat/test-regular-setup.R | 68 tests/testthat/test-semi-deterministic-output.R |only tests/testthat/test-semi-deterministic-setup.R |only vignettes/asymmetric_causal.Rmd | 4232 +++--- vignettes/figure_asymmetric_causal/compare_plots-1.png |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_SV-1.png |binary vignettes/figure_asymmetric_causal/explanation_asym_cau_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/explanation_asym_con_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/explanation_sym_cau_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/explanation_sym_con_SV-1.png |binary vignettes/figure_asymmetric_causal/explanation_sym_con_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/explanation_sym_mar_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_SV-1.png |binary vignettes/figure_asymmetric_causal/n_coalitions_plot_beeswarm-1.png |binary vignettes/figure_asymmetric_causal/scatter_plots-1.png |binary vignettes/figure_asymmetric_causal/sym_and_asym_Shapley_values-1.png |binary vignettes/figure_asymmetric_causal/two_dates_1-1.png |binary vignettes/figure_asymmetric_causal/two_dates_2-1.png |binary vignettes/figure_asymmetric_causal/two_dates_3-1.png |binary vignettes/figure_general_usage/combined-1-1.png |binary vignettes/figure_general_usage/custom-1.png |binary vignettes/figure_general_usage/custom-2.png |binary vignettes/figure_general_usage/factor-1.png |binary vignettes/figure_general_usage/group-1.png |binary vignettes/figure_general_usage/plot-beeswarm-1.png |binary vignettes/figure_general_usage/plot-scatter-1.png |binary vignettes/figure_general_usage/plot-waterfall-1.png |binary vignettes/figure_general_usage/setup-2-1.png |binary vignettes/figure_regression/MSEv-sum-1.png |binary vignettes/figure_regression/MSEv-sum-2-1.png |binary vignettes/figure_regression/SV-sum-1.png |binary vignettes/figure_regression/SV-sum-2-1.png |binary vignettes/figure_regression/SV-sum-2.png |binary vignettes/figure_regression/SV-sum-3.png |binary vignettes/figure_regression/dt-cv-plot-1.png |binary vignettes/figure_regression/mixed-plot-1.png |binary vignettes/figure_regression/mixed-plot-2-1.png |binary vignettes/figure_regression/mixed-plot-3-1.png |binary vignettes/figure_regression/mixed-plot-4-1.png |binary vignettes/figure_regression/ppr-plot-1.png |binary vignettes/figure_regression/surrogate-plot-1.png |binary vignettes/figure_vaeac/check-n_coalitions-1.png |binary vignettes/figure_vaeac/continue-training-2.png |binary vignettes/figure_vaeac/continue-training-5.png |binary vignettes/figure_vaeac/first-vaeac-plots-1.png |binary vignettes/figure_vaeac/vaeac-grouping-of-features-1.png |binary vignettes/general_usage.Rmd | 5005 ++++---- vignettes/regression.Rmd | 6238 +++++----- vignettes/vaeac.Rmd | 2480 ++- 133 files changed, 37098 insertions(+), 33705 deletions(-)
Title: Efficient Monitoring of Global Biodiversity Portfolios
Description: Biodiversity areas, especially primary forest, serve a
multitude of functions for local economy, regional functionality of
the ecosystems as well as the global health of our planet. Recently,
adverse changes in human land use practices and climatic responses to
increased greenhouse gas emissions, put these biodiversity areas under
a variety of different threats. The present package helps to analyse a
number of biodiversity indicators based on freely available
geographical datasets. It supports computational efficient routines
that allow the analysis of potentially global biodiversity portfolios.
The primary use case of the package is to support evidence based
reporting of an organization's effort to protect biodiversity areas
under threat and to identify regions were intervention is most duly
needed.
Author: Darius A. Goergen [aut] ,
Om Prakash Bhandari [aut],
Andreas Petutschnig [ctb] ,
Sven Bergtold [ctb, cre],
Zivan Karaman [ctb] ,
MAPME-Initiative [cph, fnd]
Maintainer: Sven Bergtold <sven.bergtold@gmail.com>
Diff between mapme.biodiversity versions 0.9.3 dated 2024-10-21 and 0.9.4 dated 2025-04-28
mapme.biodiversity-0.9.3/mapme.biodiversity/tests/testthat/_snaps/calc_precipitation_chirps.md |only mapme.biodiversity-0.9.4/mapme.biodiversity/DESCRIPTION | 33 mapme.biodiversity-0.9.4/mapme.biodiversity/MD5 | 153 - mapme.biodiversity-0.9.4/mapme.biodiversity/NEWS.md | 722 ++--- mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_ecoregion.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_exposed_population_acled.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_exposed_population_ucdp.R | 10 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_fatalities_ucdp.R | 8 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_gsw_occurrence.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_gsw_recurrence.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_ipbes_biomes.R | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_precipitation_wc.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_traveltime.R | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_traveltime_2000.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_treecover_area_and_emissions.R | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_treecoverloss_emissions.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/calc_tri.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/chunking.R | 58 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_acled.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_biodiversity_intactness_index.R | 9 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_chelsa.R | 10 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_esalandcover.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_fritz_et_al.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_gfw_lossyear.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_gmw.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_gsw.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_gsw_time_series.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_hfp.R | 15 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_iucn.R | 3 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_key_biodiversity_areas.R | 31 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_mcd64A1.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_nelson_et_al.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_soilgrids.R | 10 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_ucdp_ged.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/get_worldclim.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/portfolio.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/register.R | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/R/spatial-utils.R | 73 mapme.biodiversity-0.9.4/mapme.biodiversity/R/utils.R | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/README.md | 169 - mapme.biodiversity-0.9.4/mapme.biodiversity/build/partial.rdb |binary mapme.biodiversity-0.9.4/mapme.biodiversity/build/vignette.rds |binary mapme.biodiversity-0.9.4/mapme.biodiversity/inst/WORDLIST | 329 +- mapme.biodiversity-0.9.4/mapme.biodiversity/inst/doc/quickstart.R | 226 - mapme.biodiversity-0.9.4/mapme.biodiversity/inst/doc/quickstart.Rmd | 234 - mapme.biodiversity-0.9.4/mapme.biodiversity/inst/doc/quickstart.html | 1324 +++++----- mapme.biodiversity-0.9.4/mapme.biodiversity/inst/doc/terminology.R | 28 mapme.biodiversity-0.9.4/mapme.biodiversity/inst/doc/terminology.html | 660 ++-- mapme.biodiversity-0.9.4/mapme.biodiversity/man/acled.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/biodiversity_intactness_index_resource.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/calc_exposed_population_acled.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/check_available_years.Rd | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/man/chelsa.Rd | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/man/esalandcover.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/exposed_population_ucdp.Rd | 10 mapme.biodiversity-0.9.4/mapme.biodiversity/man/fatalities_ucpd.Rd | 8 mapme.biodiversity-0.9.4/mapme.biodiversity/man/fritz_et_al.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/gmw.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/humanfootprint_resource.Rd | 8 mapme.biodiversity-0.9.4/mapme.biodiversity/man/iucn.Rd | 1 mapme.biodiversity-0.9.4/mapme.biodiversity/man/make_footprints.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/mapme.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/mcd64a1.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/nelson_et_al.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/precipitation_wc.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/soilgrids.Rd | 10 mapme.biodiversity-0.9.4/mapme.biodiversity/man/traveltime.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/treecover_area_and_emissions.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/treecoverloss_emissions.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/man/ucdp_ged.Rd | 2 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-calc_indicator.R | 135 - mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-calc_precipitation_chirps.R | 78 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-chunking.R | 13 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-get_biodiversity_intactness_index.R | 6 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-get_chelsa.R |only mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-get_chirps.R | 22 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-get_resources.R | 4 mapme.biodiversity-0.9.4/mapme.biodiversity/tests/testthat/test-spatial-utils.R |only mapme.biodiversity-0.9.4/mapme.biodiversity/vignettes/quickstart.Rmd | 234 - 79 files changed, 2367 insertions(+), 2363 deletions(-)
More information about mapme.biodiversity at CRAN
Permanent link
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.4.3 dated 2025-03-10 and 1.5.0 dated 2025-04-28
DESCRIPTION | 11 +++--- MD5 | 57 ++++++++++++++++---------------- NAMESPACE | 14 +++++++ NEWS.md | 14 +++++++ R/accessors.R | 27 +++++---------- R/epiweek-class.R | 24 ++++++++----- R/int_period-class.R | 6 +++ R/isoweek-class.R | 24 ++++++++----- R/month-class.R | 17 +++++---- R/month-utils.R | 9 +---- R/period-class.R | 8 +++- R/utils.R | 11 ------ R/year-class.R | 8 +++- R/yearmonth-class.R | 19 ++++++---- R/yearquarter-class.R | 8 +++- R/yearweek-class.R | 67 ++++++++++++++++++++++---------------- inst/doc/grates.Rmd | 1 inst/doc/grates.html | 22 ++++++------ man/grouped_date_accessors.Rd | 3 - tests/testthat/test-epiweek.R | 1 tests/testthat/test-int_period.R | 1 tests/testthat/test-isoweek.R | 1 tests/testthat/test-month.R | 1 tests/testthat/test-period.R | 2 + tests/testthat/test-refactoring.R |only tests/testthat/test-year.R | 2 + tests/testthat/test-yearmonth.R | 1 tests/testthat/test-yearquarter.R | 1 tests/testthat/test-yearweek.R | 1 vignettes/grates.Rmd | 1 30 files changed, 216 insertions(+), 146 deletions(-)
More information about forensicpopdata at CRAN
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Title: The Ultimate Tool for Reading Data in Bulk
Description: Designed to simplify and streamline the process of reading
and processing large volumes of data in R, this package offers a
collection of functions tailored for bulk data operations. It enables
users to efficiently read multiple sheets from Microsoft Excel and
Google Sheets workbooks, as well as various CSV files from a
directory. The data is returned as organized data frames, facilitating
further analysis and manipulation. Ideal for handling extensive data
sets or batch processing tasks, bulkreadr empowers users to manage
data in bulk effortlessly, saving time and effort in data preparation
workflows. Additionally, the package seamlessly works with labelled
data from SPSS and Stata.
Author: Ezekiel Ogundepo [aut, cre] ,
Ernest Fokoue [ctb] ,
Golibe Ezeechesi [ctb],
Fatimo Adebanjo [ctb],
Isaac Ajao [ctb]
Maintainer: Ezekiel Ogundepo <gbganalyst@gmail.com>
Diff between bulkreadr versions 1.1.1 dated 2024-05-26 and 1.2.0 dated 2025-04-28
bulkreadr-1.1.1/bulkreadr/inst/doc/bulkreadr.R |only bulkreadr-1.1.1/bulkreadr/inst/doc/bulkreadr.Rmd |only bulkreadr-1.1.1/bulkreadr/inst/doc/bulkreadr.html |only bulkreadr-1.1.1/bulkreadr/vignettes/bulkreadr.Rmd |only bulkreadr-1.2.0/bulkreadr/DESCRIPTION | 10 bulkreadr-1.2.0/bulkreadr/MD5 | 61 - bulkreadr-1.2.0/bulkreadr/NAMESPACE | 4 bulkreadr-1.2.0/bulkreadr/NEWS.md | 148 ++-- bulkreadr-1.2.0/bulkreadr/R/bulkreadr-package.R | 58 - bulkreadr-1.2.0/bulkreadr/R/fill_missing_values.R | 262 +++---- bulkreadr-1.2.0/bulkreadr/R/onload.R | 6 bulkreadr-1.2.0/bulkreadr/R/read_excel_workbook.R | 14 bulkreadr-1.2.0/bulkreadr/R/read_gsheets.R | 12 bulkreadr-1.2.0/bulkreadr/R/utils.R | 126 +-- bulkreadr-1.2.0/bulkreadr/R/write_excel_sheets_to_csv.R |only bulkreadr-1.2.0/bulkreadr/build/vignette.rds |binary bulkreadr-1.2.0/bulkreadr/inst/doc/intro-to-bulkreadr.R |only bulkreadr-1.2.0/bulkreadr/inst/doc/intro-to-bulkreadr.Rmd |only bulkreadr-1.2.0/bulkreadr/inst/doc/intro-to-bulkreadr.html |only bulkreadr-1.2.0/bulkreadr/inst/doc/labelled-data.Rmd | 256 +++---- bulkreadr-1.2.0/bulkreadr/inst/doc/labelled-data.html | 2 bulkreadr-1.2.0/bulkreadr/inst/doc/other-functions.R | 19 bulkreadr-1.2.0/bulkreadr/inst/doc/other-functions.Rmd | 352 +++++----- bulkreadr-1.2.0/bulkreadr/inst/doc/other-functions.html | 94 +- bulkreadr-1.2.0/bulkreadr/man/fill_missing_values.Rd | 19 bulkreadr-1.2.0/bulkreadr/man/pipe.Rd | 40 - bulkreadr-1.2.0/bulkreadr/man/read_csv_files_from_dir.Rd | 140 +-- bulkreadr-1.2.0/bulkreadr/man/read_excel_workbook.Rd | 2 bulkreadr-1.2.0/bulkreadr/man/read_gsheets.Rd | 3 bulkreadr-1.2.0/bulkreadr/man/write_excel_sheets_to_csv.Rd |only bulkreadr-1.2.0/bulkreadr/tests/testthat/extdata/airquality_mean.csv | 308 ++++---- bulkreadr-1.2.0/bulkreadr/tests/testthat/test-fill_missing_values.R | 24 bulkreadr-1.2.0/bulkreadr/tests/testthat/test-utils.R | 56 - bulkreadr-1.2.0/bulkreadr/tests/testthat/test-write_excel_sheets_to_csv.R |only bulkreadr-1.2.0/bulkreadr/vignettes/intro-to-bulkreadr.Rmd |only bulkreadr-1.2.0/bulkreadr/vignettes/labelled-data.Rmd | 256 +++---- bulkreadr-1.2.0/bulkreadr/vignettes/other-functions.Rmd | 352 +++++----- 37 files changed, 1299 insertions(+), 1325 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <officialeasystats@gmail.com>
Diff between bayestestR versions 0.15.2 dated 2025-02-07 and 0.15.3 dated 2025-04-28
DESCRIPTION | 16 +- MD5 | 156 ++++++++++---------- NEWS.md | 19 ++ R/bayesfactor.R | 3 R/bayesfactor_inclusion.R | 5 R/bayesfactor_models.R | 5 R/bayesfactor_parameters.R | 10 - R/bayesfactor_restricted.R | 7 R/bci.R | 35 +--- R/check_prior.R | 9 - R/ci.R | 61 ++++--- R/describe_posterior.R | 152 +++++++++---------- R/describe_prior.R | 11 - R/diagnostic_posterior.R | 71 ++++++--- R/effective_sample.R | 148 ++++++++++--------- R/equivalence_test.R | 60 ++++--- R/estimate_density.R | 64 ++------ R/eti.R | 60 +++++-- R/hdi.R | 128 ++++++++++------ R/map_estimate.R | 118 +++++++++++---- R/mcse.R | 16 -- R/mediation.R | 5 R/p_direction.R | 86 +++++++---- R/p_map.R | 68 +++++--- R/p_rope.R | 31 +--- R/p_significance.R | 43 +++-- R/point_estimate.R | 69 ++++++-- R/print.equivalence_test.R | 2 R/rope.R | 239 +++++++++++++++++++++---------- R/si.R | 13 - R/simulate_priors.R | 19 -- R/spi.R | 33 ++-- R/unupdate.R | 6 R/utils.R | 12 + R/utils_print_data_frame.R | 38 ++-- R/weighted_posteriors.R | 10 - README.md | 31 +--- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 2 man/bayesfactor.Rd | 7 man/bayesfactor_inclusion.Rd | 5 man/bayesfactor_models.Rd | 5 man/bayesfactor_parameters.Rd | 84 ++++++---- man/bayesfactor_restricted.Rd | 34 +++- man/bayestestR-package.Rd | 2 man/bci.Rd | 118 ++++++++------- man/check_prior.Rd | 41 +++++ man/ci.Rd | 103 +++++++------ man/describe_posterior.Rd | 171 ++++++++++++---------- man/describe_prior.Rd | 16 -- man/diagnostic_draws.Rd | 4 man/diagnostic_posterior.Rd | 54 +++++-- man/effective_sample.Rd | 115 +++++++++++--- man/equivalence_test.Rd | 84 +++++++--- man/estimate_density.Rd | 73 +++++++++ man/eti.Rd | 93 ++++++++---- man/figures/unnamed-chunk-8-1.png |binary man/hdi.Rd | 113 +++++++++----- man/map_estimate.Rd | 77 +++++++-- man/mcse.Rd | 62 ++++++-- man/mediation.Rd | 14 - man/p_direction.Rd | 113 ++++++-------- man/p_map.Rd | 72 ++++++--- man/p_rope.Rd | 71 ++++++--- man/p_significance.Rd | 71 ++++++--- man/point_estimate.Rd | 74 ++++++--- man/rope.Rd | 92 +++++++---- man/si.Rd | 60 ++----- man/simulate_prior.Rd | 40 +++++ man/spi.Rd | 42 ++--- man/unupdate.Rd | 6 man/weighted_posteriors.Rd | 52 ++---- tests/testthat/test-blavaan.R | 28 ++- tests/testthat/test-describe_posterior.R | 27 +++ tests/testthat/test-effective_sample.R | 33 +++- tests/testthat/test-map_estimate.R | 17 ++ tests/testthat/test-marginaleffects.R | 22 ++ tests/testthat/test-point_estimate.R | 17 ++ 79 files changed, 2471 insertions(+), 1502 deletions(-)
Title: Access the Weekly 'TidyTuesday' Project Dataset
Description: 'TidyTuesday' is a project by the 'Data Science Learning
Community' in which they post a weekly dataset in a public data
repository (<https://github.com/rfordatascience/tidytuesday>) for
people to analyze and visualize. This package provides the tools to
easily download this data and the description of the source.
Author: Jon Harmon [aut, cre] ,
Ellis Hughes [aut],
Thomas Mock [ctb],
Data Science Learning Community [dtc]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between tidytuesdayR versions 1.1.2 dated 2024-09-09 and 1.2.0 dated 2025-04-28
DESCRIPTION | 18 +- MD5 | 127 ++++++++++++++----- NAMESPACE | 6 NEWS.md | 12 + R/aaa-shared.R | 5 R/github_api.R | 3 R/last_tuesday.R | 2 R/tt_available.R | 26 +-- R/tt_check_date.R | 16 ++ R/tt_clean.R |only R/tt_curate_data.R |only R/tt_curate_utils.R |only R/tt_download.R | 2 R/tt_download_file.R | 2 R/tt_intro.R |only R/tt_load.R | 3 R/tt_load_gh.R | 3 R/tt_master_file.R | 4 R/tt_meta.R |only R/tt_save_dataset.R |only R/tt_submit.R |only R/use_tidytemplate.R | 31 ++-- R/utils-pipe.R | 28 ++-- R/utils.R | 7 - build |only inst/doc |only inst/templates/cleaning.R |only inst/templates/intro.md |only inst/templates/meta.yaml |only inst/templates/tidytemplate.Rmd | 3 inst/templates/tt_curation.R |only man/figures |only man/gh_get.Rd | 2 man/prep_tt_curate.Rd |only man/printing.Rd | 2 man/shared-params.Rd | 8 - man/should_update_tt_master_file.Rd | 2 man/tt_clean.Rd |only man/tt_compile.Rd | 2 man/tt_curate_data.Rd |only man/tt_intro.Rd |only man/tt_master_file.Rd | 2 man/tt_meta.Rd |only man/tt_save_dataset.Rd |only man/tt_submit.Rd |only man/use_tidytemplate.Rd | 25 ++- tests/testthat/_snaps/tt_clean |only tests/testthat/_snaps/tt_intro |only tests/testthat/_snaps/tt_meta |only tests/testthat/_snaps/tt_meta.md |only tests/testthat/_snaps/tt_save_dataset |only tests/testthat/_snaps/tt_submit.md |only tests/testthat/fixtures/tt_submission |only tests/testthat/fixtures/tt_submission_extra |only tests/testthat/fixtures/tt_submission_missing |only tests/testthat/fixtures/tt_submission_missing_image1 |only tests/testthat/fixtures/tt_submission_missing_image2 |only tests/testthat/fixtures/tt_submission_missing_md |only tests/testthat/test-tt_check_date.R | 21 +++ tests/testthat/test-tt_clean.R |only tests/testthat/test-tt_curate_data.R |only tests/testthat/test-tt_curate_utils.R |only tests/testthat/test-tt_intro.R |only tests/testthat/test-tt_load_gh.R | 12 + tests/testthat/test-tt_meta.R |only tests/testthat/test-tt_save_dataset.R |only tests/testthat/test-tt_submit.R |only tests/testthat/test-use_tidytemplate.R | 1 vignettes |only 69 files changed, 271 insertions(+), 104 deletions(-)
Title: Run Allometric Trophic Networks Models
Description: Implements the differential equations associated to different versions of Allometric Trophic Models (ATN) to estimate the temporal dynamics of species biomasses in food webs. It offers several features to generate synthetic food webs and to parametrise models as well as a wrapper to the ODE solver deSolve.
Author: Benoit Gauzens [cre, aut],
Emilio Berti [aut]
Maintainer: Benoit Gauzens <benoit.gauzens@gmail.com>
Diff between ATNr versions 1.1.0 dated 2023-09-04 and 1.1.1 dated 2025-04-28
DESCRIPTION | 6 MD5 | 18 - NEWS.md | 3 R/default_initialisations.R | 2 build/vignette.rds |binary inst/doc/ATNr.R | 12 inst/doc/ATNr.Rmd | 2 inst/doc/ATNr.html | 668 ++++++++++++++++++++-------------------- inst/doc/model_descriptions.pdf |binary vignettes/ATNr.Rmd | 2 10 files changed, 362 insertions(+), 351 deletions(-)
Title: Bayesian Methods for Change Points Analysis
Description: Perform change points detection on univariate and multivariate time series according to the methods presented by Asael Fabian Martínez and Ramsés H. Mena (2014) <doi:10.1214/14-BA878> and Corradin, Danese and Ongaro (2022) <doi:10.1016/j.ijar.2021.12.019>. It also clusters different types of time dependent data with common change points, see "Model-based clustering of time-dependent observations with common structural changes" (Corradin,Danese,KhudaBukhsh and Ongaro, 2024) <doi:10.48550/arXiv.2410.09552> for details.
Author: Luca Danese [aut, cre, cph] ,
Riccardo Corradin [aut],
Andrea Ongaro [aut]
Maintainer: Luca Danese <l.danese1@campus.unimib.it>
Diff between BayesChange versions 2.0.0 dated 2025-03-12 and 2.1.0 dated 2025-04-28
DESCRIPTION | 6 MD5 | 81 +-- NAMESPACE | 1 NEWS.md | 7 R/BayesChange-package.R | 24 - R/ClustCpObj.R | 48 +- R/DetectCpObj.R | 370 +++++++++++------ R/RcppExports.R | 126 ++++- R/clust_cp.R | 209 +++------ R/detect_cp.R | 323 +++++++++----- README.md | 364 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/tutorial.R | 43 + inst/doc/tutorial.Rmd | 68 ++- inst/doc/tutorial.html | 452 +++++++++++--------- man/ClustCpObj.Rd | 101 ++-- man/DetectCpObj.Rd | 104 ++-- man/clust_cp.Rd | 357 ++++++++-------- man/clust_cp_epi.Rd | 25 - man/clust_cp_multi.Rd | 10 man/clust_cp_uni.Rd | 8 man/detect_cp.Rd | 250 ++++++----- man/detect_cp_epi.Rd |only man/detect_cp_multi.Rd | 134 +++--- man/detect_cp_uni.Rd | 119 ++--- man/plot.ClustCpObj.Rd | 174 ++++---- man/plot.DetectCpObj.Rd | 110 ++--- man/posterior_estimate.ClustCpObj.Rd | 116 ++--- man/posterior_estimate.DetectCpObj.Rd | 106 ++-- man/posterior_estimate.Rd | 24 - man/print.ClustCpObj.Rd | 64 +- man/print.DetectCpObj.Rd | 60 +- man/sim_epi_data.Rd | 13 man/summary.ClustCpObj.Rd | 64 +- man/summary.DetectCpObj.Rd | 62 +- src/RcppExports.cpp | 86 ++- src/code.cpp | 737 +++++++++++++++------------------- tests/testthat/test-test-clust_cp.R | 41 - tests/testthat/test-test-detect_cp.R | 5 vignettes/references.bib | 104 ++-- vignettes/tutorial.Rmd | 68 ++- 42 files changed, 2723 insertions(+), 2341 deletions(-)
Title: Structure Optimized Proximity Scaling
Description: Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of diss [...truncated...]
Author: Thomas Rusch [aut, cre] ,
Patrick Mair [aut] ,
Kurt Hornik [ctb]
Maintainer: Thomas Rusch <thomas.rusch@wu.ac.at>
Diff between stops versions 1.8-2 dated 2024-09-22 and 1.9-1 dated 2025-04-28
DESCRIPTION | 17 MD5 | 21 - NAMESPACE | 2 NEWS | 4 R/stops-package.R | 9 R/stops.R | 11 build/vignette.rds |binary inst/doc/stops.html | 842 ++++++++++++++++--------------------------------- man/stops-package.Rd | 9 man/stops.Rd | 6 vignettes/stops.Rmd | 223 ++---------- vignettes/stopsOLD.Rmd |only 12 files changed, 365 insertions(+), 779 deletions(-)
Title: Bayesian Age-Depth Modelling of Cores Dated by Pb-210
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for 210Pb-dated deposits using prior information. It can combine 210Pb, radiocarbon, and other dates in the chronologies. See Aquino et al. (2018) <doi:10.1007/s13253-018-0328-7>. Note that parts of the code underlying 'rplum' are derived from the 'rbacon' package by the same authors, and there remains a degree of overlap between the two packages.
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph]
,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rplum versions 0.5.1 dated 2024-09-29 and 0.5.2 dated 2025-04-28
DESCRIPTION | 10 MD5 | 26 + NAMESPACE | 22 + NEWS.md | 10 R/fromrbacon.R | 652 +++++++++++++++++++++++++++++++++++++++++++++++++ R/read_write_plum.R | 34 +- R/rplum-package.R | 7 R/rplum.R | 71 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rplum.R | 8 inst/doc/rplum.html | 12 man/Plum.Rd | 6 man/agedepth.Rd |only man/draw.pbmodelled.Rd |only 15 files changed, 793 insertions(+), 65 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source
package. 'pkgdown' converts your documentation, vignettes, 'README',
and more to 'HTML' making it easy to share information about your
package online.
Author: Hadley Wickham [aut, cre] ,
Jay Hesselberth [aut] ,
Maelle Salmon [aut] ,
Olivier Roy [aut],
Salim Brueggemann [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between pkgdown versions 2.1.1 dated 2024-09-17 and 2.1.2 dated 2025-04-28
DESCRIPTION | 27 + MD5 | 303 +++++++++++----------- NEWS.md | 25 + R/build-404.R | 9 R/build-article.R | 100 ++++--- R/build-articles.R | 36 +- R/build-favicons.R | 15 - R/build-footer.R | 15 - R/build-github.R | 30 +- R/build-home-authors.R | 74 ++++- R/build-home-community.R | 4 R/build-home-index.R | 63 +++- R/build-home-license.R | 4 R/build-home-md.R | 4 R/build-home.R | 23 - R/build-news.R | 52 ++- R/build-quarto-articles.R | 62 +++- R/build-redirects.R | 10 R/build-reference-index.R | 48 ++- R/build-reference.R | 89 ++++-- R/build-search-docs.R | 90 ++++-- R/build-tutorials.R | 11 R/build.R | 116 ++++---- R/check-built.R | 1 R/check.R | 1 R/clean.R | 16 - R/config.R | 179 +++++++----- R/context.R | 25 + R/deploy-site.R | 85 ++++-- R/development.R | 27 + R/external-deps.R | 38 -- R/figure.R | 33 +- R/highlight.R | 8 R/html-build.R | 6 R/init.R | 17 - R/markdown.R | 13 R/navbar-menu.R | 41 ++ R/navbar.R | 23 + R/package.R | 95 +++++- R/preview.R | 8 R/rd-example.R | 32 +- R/rd-html.R | 96 +++--- R/rd.R | 6 R/render.R | 54 ++- R/repo.R | 42 ++- R/test.R | 30 ++ R/theme.R | 64 ++-- R/topics-external.R | 4 R/topics.R | 79 +++-- R/tweak-homepage.R | 50 ++- R/tweak-navbar.R | 21 + R/tweak-page.R | 13 R/tweak-reference.R | 15 - R/tweak-tabset.R | 27 + R/tweak-tags.R | 49 ++- R/usage.R | 46 ++- R/utils-fs.R | 43 +-- R/utils-io.R | 7 R/utils-pdf.R | 4 R/utils.R | 42 +-- build/stage23.rdb |binary build/vignette.rds |binary inst/BS3/templates/head.html | 11 inst/BS5/assets/pkgdown.scss | 36 +- inst/BS5/templates/content-authors.html | 2 inst/BS5/templates/content-citation-authors.html | 2 inst/BS5/templates/head.html | 32 +- inst/doc/customise.Rmd | 15 - inst/doc/customise.html | 145 +++++----- inst/doc/how-to-update-released-site.Rmd | 16 - inst/doc/how-to-update-released-site.html | 20 + inst/doc/pkgdown.R | 14 - inst/doc/quarto.html | 182 ------------- inst/doc/quarto.qmd | 2 inst/doc/translations.R | 14 - man/build_home.Rd | 11 man/build_site.Rd | 21 - man/clean.Rd | 4 man/index.Rd | 1 man/pkgdown-package.Rd | 2 man/test-crayon.Rd | 1 man/test-dont.Rd | 1 man/test-figures.Rd | 1 man/test-links.Rd | 1 man/test-lists.Rd | 1 man/test-long-lines.Rd | 1 man/test-math-examples.Rd |only man/test-output-styles.Rd | 1 man/test-params.Rd | 1 man/test-sexpr-title.Rd | 1 man/test-tables.Rd | 1 man/test-verbatim.Rd | 1 tests/testthat/_snaps/build-article.md | 49 --- tests/testthat/_snaps/build-home-authors.md | 10 tests/testthat/_snaps/build-home-index.md | 6 tests/testthat/_snaps/build-reference-index.md | 2 tests/testthat/_snaps/check.md | 2 tests/testthat/_snaps/init.md | 24 - tests/testthat/_snaps/markdown.md | 9 tests/testthat/_snaps/navbar.md | 2 tests/testthat/_snaps/not-in-rcmcheck |only tests/testthat/_snaps/rcmdcheck |only tests/testthat/_snaps/render.md | 1 tests/testthat/assets/reference-fail/R/f.R | 1 tests/testthat/assets/reference-language |only tests/testthat/assets/reference-selector/R/funs.R | 6 tests/testthat/assets/reference/R/funs.R | 16 - tests/testthat/helper.R | 31 +- tests/testthat/test-build-article.R | 267 +++++++++++++------ tests/testthat/test-build-articles.R | 62 +++- tests/testthat/test-build-favicons.R | 3 tests/testthat/test-build-footer.R | 53 ++- tests/testthat/test-build-home-authors.R | 211 ++++++++++----- tests/testthat/test-build-home-index.R | 72 +++-- tests/testthat/test-build-home-license.R | 1 tests/testthat/test-build-home-md.R | 3 tests/testthat/test-build-home.R | 12 tests/testthat/test-build-logo.R | 1 tests/testthat/test-build-news.R | 92 ++++-- tests/testthat/test-build-quarto-articles.R | 70 +++-- tests/testthat/test-build-reference-index.R | 25 + tests/testthat/test-build-reference.R | 28 +- tests/testthat/test-build-search-docs.R | 36 +- tests/testthat/test-build-tutorials.R | 46 ++- tests/testthat/test-check.R | 22 - tests/testthat/test-config.R | 1 tests/testthat/test-development.R | 2 tests/testthat/test-figure.R | 6 tests/testthat/test-highlight.R | 12 tests/testthat/test-init.R | 9 tests/testthat/test-markdown.R | 8 tests/testthat/test-navbar-menu.R | 10 tests/testthat/test-navbar.R | 95 ++++-- tests/testthat/test-package.R | 57 +++- tests/testthat/test-preview.R | 2 tests/testthat/test-rd-data.R | 6 tests/testthat/test-rd-example.R | 5 tests/testthat/test-rd-html.R | 73 +++-- tests/testthat/test-render.R | 23 + tests/testthat/test-repo.R | 81 ++++- tests/testthat/test-templates.R | 102 ++++--- tests/testthat/test-topics.R | 28 +- tests/testthat/test-tweak-homepage.R | 60 ++-- tests/testthat/test-tweak-navbar.R | 12 tests/testthat/test-tweak-page.R | 120 ++++++-- tests/testthat/test-tweak-reference.R | 61 +++- tests/testthat/test-tweak-tabset.R | 28 +- tests/testthat/test-tweak-tags.R | 125 ++++++--- tests/testthat/test-usage.R | 3 tests/testthat/test-utils.R | 12 vignettes/customise.Rmd | 15 - vignettes/how-to-update-released-site.Rmd | 16 - vignettes/quarto.qmd | 2 vignettes/test/jss.log | 2 154 files changed, 3281 insertions(+), 1949 deletions(-)
Title: Parametric Bootstrap, Kenward-Roger and Satterthwaite Based
Methods for Test in Mixed Models
Description: Computes p-values based on (a) Satterthwaite or
Kenward-Rogers degree of freedom methods and (b) parametric bootstrap
for mixed effects models as implemented in the 'lme4'
package. Implements parametric bootstrap test for generalized linear
mixed models as implemented in 'lme4' and generalized linear
models. The package is documented in the paper by Halekoh and
Højsgaard, (2012, <doi:10.18637/jss.v059.i09>). Please see
'citation("pbkrtest")' for citation details.
Author: Ulrich Halekoh [aut, cph],
Soeren Hoejsgaard [aut, cre, cph]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between pbkrtest versions 0.5.3 dated 2024-06-26 and 0.5.4 dated 2025-04-28
pbkrtest-0.5.3/pbkrtest/man/kr_modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/man/pb_modcomp.Rd |only pbkrtest-0.5.3/pbkrtest/man/sat_modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/DESCRIPTION | 9 pbkrtest-0.5.4/pbkrtest/MD5 | 49 +- pbkrtest-0.5.4/pbkrtest/NAMESPACE | 17 pbkrtest-0.5.4/pbkrtest/NEWS | 15 pbkrtest-0.5.4/pbkrtest/R/KR_modcomp.R | 35 - pbkrtest-0.5.4/pbkrtest/R/PB_modcomp.R | 490 ++++++++++++--------- pbkrtest-0.5.4/pbkrtest/R/PB_refdist.R | 110 ++++ pbkrtest-0.5.4/pbkrtest/R/SAT_modcomp.R | 96 ++-- pbkrtest-0.5.4/pbkrtest/R/X2_modcomp.R |only pbkrtest-0.5.4/pbkrtest/R/anovax.R |only pbkrtest-0.5.4/pbkrtest/R/handle_models.r |only pbkrtest-0.5.4/pbkrtest/R/init_modcomp.R | 13 pbkrtest-0.5.4/pbkrtest/R/xx_modcomp_new.R |only pbkrtest-0.5.4/pbkrtest/build/vignette.rds |binary pbkrtest-0.5.4/pbkrtest/inst/doc/a01-pbkrtest.html | 267 +++++------ pbkrtest-0.5.4/pbkrtest/inst/doc/a01-pbkrtest.rmd | 29 + pbkrtest-0.5.4/pbkrtest/inst/doc/a02-coercion.html | 200 +++----- pbkrtest-0.5.4/pbkrtest/man/anovax.Rd |only pbkrtest-0.5.4/pbkrtest/man/anovax_list.Rd |only pbkrtest-0.5.4/pbkrtest/man/any_modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/man/comodex.Rd |only pbkrtest-0.5.4/pbkrtest/man/devfun_vp.Rd | 7 pbkrtest-0.5.4/pbkrtest/man/get_Fstat_ddf.Rd | 11 pbkrtest-0.5.4/pbkrtest/man/get_covbeta.Rd | 8 pbkrtest-0.5.4/pbkrtest/man/kr__modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/man/pb-refdist.Rd | 10 pbkrtest-0.5.4/pbkrtest/man/pb__modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/man/sat__modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/man/x2__modcomp.Rd |only pbkrtest-0.5.4/pbkrtest/vignettes/a01-pbkrtest.rmd | 29 + 33 files changed, 821 insertions(+), 574 deletions(-)
Title: Functions and Datasets for "Methods of Statistical Model
Estimation"
Description: Functions and datasets from Hilbe, J.M., and Robinson, A.P. 2013. Methods of Statistical Model Estimation. Chapman & Hall / CRC.
Author: Joseph Hilbe [aut],
Andrew Robinson [aut, cre]
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between msme versions 0.5.3 dated 2018-03-18 and 0.5.4 dated 2025-04-28
ChangeLog | 10 ++++++++++ DESCRIPTION | 18 +++++++++++++----- MD5 | 22 +++++++++++----------- R/watson.R | 18 +++++++++--------- data/doll.rda |binary data/heart.rda |binary data/medpar.rda |binary data/rwm5yr.rda |binary data/titanic.rda |binary data/ufc.rda |binary man/P__disp.Rd | 2 +- man/ml_g.Rd | 2 +- 12 files changed, 45 insertions(+), 27 deletions(-)
Title: Multinomial Logit Models
Description: Maximum likelihood estimation of random utility discrete
choice models. The software is described in Croissant (2020)
<doi:10.18637/jss.v095.i11> and the underlying methods in
Train (2009) <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.1-1 dated 2020-10-02 and 1.1-2 dated 2025-04-28
DESCRIPTION | 13 MD5 | 132 ++++----- NEWS.md | 4 R/lnl.rlogit.R | 4 R/methods.R | 2 R/mlogit.R | 2 R/test.R | 2 build/partial.rdb |binary build/vignette.rds |binary data/Car.rda |binary data/Catsup.rda |binary data/Cracker.rda |binary data/Electricity.rda |binary data/Fishing.rda |binary data/Game.rda |binary data/Game2.rda |binary data/HC.rda |binary data/Heating.rda |binary data/JapaneseFDI.rda |binary data/Mode.rda |binary data/ModeCanada.rda |binary data/NOx.rda |binary data/RiskyTransport.rda |binary data/Train.rda |binary inst/REFERENCES.bib | 41 -- inst/doc/c2.formula.data.html | 487 ++++++++++++++++++++++++++------- inst/doc/c3.rum.html | 513 ++++++++++++++++++++++++++--------- inst/doc/c4.relaxiid.html | 507 ++++++++++++++++++++++++++--------- inst/doc/c5.mxl.R | 14 inst/doc/c5.mxl.html | 559 ++++++++++++++++++++++++++++----------- inst/doc/c6.mprobit.html | 418 +++++++++++++++++++++++------ inst/doc/c7.miscmodels.html | 409 +++++++++++++++++++++++----- inst/doc/e1mlogit.html | 475 +++++++++++++++++++++++++-------- inst/doc/e2nlogit.html | 439 ++++++++++++++++++++++++------ inst/doc/e3mxlogit.R | 28 - inst/doc/e3mxlogit.html | 459 +++++++++++++++++++++++++------- inst/doc/e4mprobit.html | 395 ++++++++++++++++++++++----- inst/doc/mlogit.html | 250 ++++++++++++++++- man/Car.Rd | 35 +- man/Catsup.Rd | 15 - man/Cracker.Rd | 15 - man/Electricity.Rd | 21 - man/Fishing.Rd | 23 - man/Game.Rd | 23 - man/HC.Rd | 25 - man/Heating.Rd | 21 - man/JapaneseFDI.Rd | 37 +- man/Mode.Rd | 11 man/ModeCanada.Rd | 23 - man/NOx.Rd | 31 +- man/RiskyTransport.Rd | 52 +-- man/Train.Rd | 19 - man/cor.mlogit.Rd | 9 man/distribution.Rd | 36 +- man/effects.mlogit.Rd | 8 man/hmftest.Rd | 14 man/logsum.Rd | 44 +-- man/miscmethods.mlogit.Rd | 30 +- man/mlogit-deprecated.Rd | 46 +-- man/mlogit-package.Rd | 14 man/mlogit.Rd | 111 +++---- man/mlogit.optim.Rd | 60 ++-- man/model.matrix.dfidx_mlogit.Rd | 2 man/plot.mlogit.Rd | 24 - man/rpar.Rd | 35 +- man/scoretest.Rd | 26 - man/vcov.mlogit.Rd | 18 - 67 files changed, 4393 insertions(+), 1588 deletions(-)
Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from
'Hub'Eau' the free and public French National APIs on water
<https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] ,
Pascal Irz [ctb] ,
Sebastien Grall [ctb],
Philippe Amiotte Suchet [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between hubeau versions 0.5.1 dated 2025-01-13 and 0.5.2 dated 2025-04-28
DESCRIPTION | 6 - MD5 | 22 +++--- NEWS.md | 9 ++ R/doApiQuery.R | 4 - R/get_ecoulement.R | 14 ++-- R/get_hydrometrie.R | 37 ++++++----- R/sysdata.rda |binary inst/doc/data_extraction_naiades.html | 60 +++++++++--------- inst/doc/example_ecoulement_api.html | 10 +-- inst/doc/example_niveaux_nappes_api.html | 11 +-- man/get_ecoulement.Rd | 14 ++-- tests/testthat/test-get_hydrometrie_observations_tr.R | 15 +++- 12 files changed, 112 insertions(+), 90 deletions(-)
Title: Functions, Data and Code for Count Data
Description: Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).
Author: Joseph M Hilbe [aut],
Andrew Robinson [cre]
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between COUNT versions 1.3.4 dated 2016-10-19 and 1.3.5 dated 2025-04-28
DESCRIPTION | 21 +++++++++++++------ MD5 | 56 +++++++++++++++++++++++++-------------------------- data/affairs.rda |binary data/azcabgptca.rda |binary data/azdrg112.rda |binary data/azpro.rda |binary data/azprocedure.rda |binary data/badhealth.rda |binary data/fasttrakg.rda |binary data/fishing.rda |binary data/lbw.rda |binary data/lbwgrp.rda |binary data/loomis.rda |binary data/mdvis.rda |binary data/medpar.rda |binary data/nuts.rda |binary data/rwm.rda |binary data/rwm1984.rda |binary data/rwm5yr.rda |binary data/ships.rda |binary data/smoking.rda |binary data/titanic.rda |binary data/titanicgrp.rda |binary man/fasttrakg.Rd | 2 - man/ml.nb1.Rd | 2 - man/ml.nb2.Rd | 2 - man/ml.nbc.Rd | 2 - man/ml.pois.Rd | 2 - man/modelfit.Rd | 2 - 29 files changed, 49 insertions(+), 40 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with [...truncated...]
Author: Mary Meyer [aut],
Xiyue Liao [aut, cre]
Maintainer: Xiyue Liao <xliao@sdsu.edu>
Diff between cgam versions 1.25 dated 2025-04-23 and 1.26 dated 2025-04-28
ChangeLog | 5 ++- DESCRIPTION | 8 ++--- MD5 | 6 ++-- R/cgam.R | 89 +++++++++++++++++++++++++++++++++++++----------------------- 4 files changed, 67 insertions(+), 41 deletions(-)
Title: R Commander Plug-in for Case 2 Best-Worst Scaling
Description: Adds menu items for case 2 (profile case) best-worst scaling (BWS2) to the R Commander. BWS2 is a question-based survey method that constructs profiles (combinations of attribute levels) using an orthogonal array, asks respondents to select the best and worst levels in each profile, and measures preferences for attribute levels by analyzing the responses. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki [aut, cre]
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS2 versions 0.2-2 dated 2024-05-21 and 0.3-0 dated 2025-04-28
DESCRIPTION | 16 + MD5 | 13 - NEWS | 7 R/RcmdrPlugin.BWS2.R | 353 ++++++++++++++++++++++++++++++++++++++-- inst/CITATION | 11 - inst/etc/menus.txt | 1 man/RcmdrPlugin.BWS2-package.Rd | 29 +-- man/bws1Response.Rd |only 8 files changed, 390 insertions(+), 40 deletions(-)
More information about RcmdrPlugin.BWS2 at CRAN
Permanent link
Title: Empirical Distribution Ordering Inference Framework (EDOIF)
Description: A non-parametric framework based on estimation statistics principle. Its main purpose is to infer orders of empirical distributions from different categories based on a probability of finding a value in one distribution that is greater than an expectation of another distribution. Given a set of ordered-pair of real-category values the framework is capable of 1) inferring orders of domination of categories and representing orders in the form of a graph; 2) estimating magnitude of difference between a pair of categories in forms of mean-difference confidence intervals; and 3) visualizing domination orders and magnitudes of difference of categories. The publication of this package is at Chainarong Amornbunchornvej, Navaporn Surasvadi, Anon Plangprasopchok, and Suttipong Thajchayapong (2020) <doi:10.1016/j.heliyon.2020.e05435>.
Author: Chainarong Amornbunchornvej [aut, cre]
Maintainer: Chainarong Amornbunchornvej <grandca@gmail.com>
Diff between EDOIF versions 0.1.3 dated 2021-03-28 and 0.1.4 dated 2025-04-28
DESCRIPTION | 9 LICENSE | 6 MD5 | 80 ++-- NAMESPACE | 60 +-- NEWS.md | 18 R/EDOIF.R | 290 +++++++-------- R/SimNonNormalDist.R | 356 +++++++++---------- R/getBootMeanDiff.R | 192 +++++----- R/getConfInv.R | 100 ++--- R/getDominantNet.R | 226 ++++++------ R/getOrder.R | 74 ++-- R/graphOperation.R | 180 ++++----- R/plotGraphphics.R | 558 +++++++++++++++--------------- R/plotText.R | 166 ++++----- README.md | 311 ++++++++--------- build/vignette.rds |binary inst/CITATION | 39 +- inst/doc/EDOIF_demo.R | 160 ++++---- inst/doc/EDOIF_demo.Rmd | 216 +++++------ inst/doc/EDOIF_demo.html | 781 ++++++++++++++++++------------------------- man/EDOIF.Rd | 182 +++++----- man/SimMixDist.Rd | 74 ++-- man/SimNonNormalDist.Rd | 72 +-- man/bootDiffmeanFunc.Rd | 64 +-- man/checkSim3Res.Rd | 68 +-- man/getADJNetDen.Rd | 62 +-- man/getConfInv.Rd | 66 +-- man/getDominantRADJ.Rd | 46 +- man/getMegDiffConfInv.Rd | 76 ++-- man/getOrder.Rd | 64 +-- man/getWilcoxDominantRADJ.Rd | 54 +- man/getiGraphNetDen.Rd | 62 +-- man/getiGraphOBJ.Rd | 66 +-- man/getttestDominantRADJ.Rd | 54 +- man/meanBoot.Rd | 40 +- man/plot.EDOIF.Rd | 80 ++-- man/plotGraph.Rd | 70 +-- man/plotMeanCIs.Rd | 82 ++-- man/plotMeanDiffCIs.Rd | 86 ++-- man/print.EDOIF.Rd | 62 +-- vignettes/EDOIF_demo.Rmd | 216 +++++------ 41 files changed, 2677 insertions(+), 2791 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-09-16 1.1.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-27 0.8.0
2021-04-21 0.7.1
2021-01-28 0.7.0
2016-09-22 0.1.0
Title: Visualize Simon's Two-Stage Design
Description: To visualize the probabilities of early termination,
fail and success of Simon's two-stage design. To evaluate
and visualize the operating characteristics of Simon's
two-stage design.
Author: Tingting Zhan [aut, cre]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between VisualizeSimon2Stage versions 0.2.1 dated 2025-04-13 and 0.2.2 dated 2025-04-27
DESCRIPTION | 24 +++++----- MD5 | 16 +++---- NAMESPACE | 1 R/Sprintf.R | 12 ++--- R/autoplot.R | 50 ++++++++++++++-------- inst/doc/intro.R | 9 +--- inst/doc/intro.html | 114 +++++++++++++++++++++++----------------------------- inst/doc/intro.qmd | 17 +++---- vignettes/intro.qmd | 17 +++---- 9 files changed, 129 insertions(+), 131 deletions(-)
More information about VisualizeSimon2Stage at CRAN
Permanent link
Title: Simplify 'ggplot2' Visualisation
Description: Simplify 'ggplot2' visualisation with 'ggblanket' wrapper
functions.
Author: David Hodge [aut, cre, cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between ggblanket versions 12.2.0 dated 2025-03-10 and 12.3.0 dated 2025-04-27
ggblanket-12.2.0/ggblanket/man/aes_colour_contrast.Rd |only ggblanket-12.3.0/ggblanket/DESCRIPTION | 6 ggblanket-12.3.0/ggblanket/MD5 | 316 +- ggblanket-12.3.0/ggblanket/NAMESPACE | 6 ggblanket-12.3.0/ggblanket/NEWS.md | 11 ggblanket-12.3.0/ggblanket/R/aes.R | 12 ggblanket-12.3.0/ggblanket/R/annotate_axis_line.R | 18 ggblanket-12.3.0/ggblanket/R/gg_blanket.R | 36 ggblanket-12.3.0/ggblanket/R/guides.R |only ggblanket-12.3.0/ggblanket/R/mode_defaults.R | 5 ggblanket-12.3.0/ggblanket/R/set.R | 2 ggblanket-12.3.0/ggblanket/build/vignette.rds |binary ggblanket-12.3.0/ggblanket/inst/doc/ggblanket.R | 2 ggblanket-12.3.0/ggblanket/inst/doc/ggblanket.Rmd | 2 ggblanket-12.3.0/ggblanket/inst/doc/ggblanket.html | 12 ggblanket-12.3.0/ggblanket/man/aes_contrast.Rd |only ggblanket-12.3.0/ggblanket/man/annotate_axis_line.Rd | 18 ggblanket-12.3.0/ggblanket/man/gg_area.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_bar.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_bin_2d.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_blanket.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_boxplot.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_col.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_contour.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_contour_filled.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_crossbar.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_density.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_density_2d.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_density_2d_filled.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_errorbar.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_freqpoly.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_function.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_hex.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_histogram.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_jitter.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_label.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_line.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_linerange.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_path.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_point.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_pointrange.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_polygon.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_qq.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_quantile.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_raster.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_rect.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_ribbon.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_ribbon_line.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_rug.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_segment.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_sf.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_smooth.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_step.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_text.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_tile.Rd | 2 ggblanket-12.3.0/ggblanket/man/gg_violin.Rd | 2 ggblanket-12.3.0/ggblanket/man/guides_shape_grey.Rd |only ggblanket-12.3.0/ggblanket/man/lightness.Rd | 3 ggblanket-12.3.0/ggblanket/man/set_blanket.Rd | 2 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-area.svg | 55 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-bar.svg | 73 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-bin-2d.svg | 675 ++--- ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-blanket.svg | 93 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-boxplot.svg | 91 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-col.svg | 65 ggblanket-12.3.0/ggblanket/tests/testthat/_snaps/article-demo-light/gg-contour-filled.svg | 145 - 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Title: Cross-Validation Model Averaging for Partial Linear Functional
Additive Models
Description: Produce an averaging estimate/prediction by combining all candidate models for partial linear functional additive models, using multi-fold cross-validation criterion. More details can be referred to arXiv e-Prints via <doi:10.48550/arXiv.2105.00966>.
Author: Shishi Liu [aut, cre],
Jingxiao Zhang [aut]
Maintainer: Shishi Liu <liushishi_644@163.com>
Diff between cvmaPLFAM versions 0.1.0 dated 2023-06-09 and 0.1.1 dated 2025-04-27
cvmaPLFAM-0.1.0/cvmaPLFAM/R/predRisk.R |only cvmaPLFAM-0.1.0/cvmaPLFAM/man/predRisk.Rd |only cvmaPLFAM-0.1.1/cvmaPLFAM/DESCRIPTION | 12 +- cvmaPLFAM-0.1.1/cvmaPLFAM/MD5 | 34 +++-- cvmaPLFAM-0.1.1/cvmaPLFAM/NAMESPACE | 3 cvmaPLFAM-0.1.1/cvmaPLFAM/NEWS.md |only cvmaPLFAM-0.1.1/cvmaPLFAM/R/cvfolds.R | 1 cvmaPLFAM-0.1.1/cvmaPLFAM/R/cvmaPLFAM.R | 158 +++++++------------------- cvmaPLFAM-0.1.1/cvmaPLFAM/R/cvpredRisk.R |only cvmaPLFAM-0.1.1/cvmaPLFAM/R/data_gen.R | 154 ++++++++++++++++--------- cvmaPLFAM-0.1.1/cvmaPLFAM/R/fpcscore.R | 9 - cvmaPLFAM-0.1.1/cvmaPLFAM/R/modelspec.R | 114 ++++++++++++------- cvmaPLFAM-0.1.1/cvmaPLFAM/R/plam.fit.R | 116 +++++++++++++++---- cvmaPLFAM-0.1.1/cvmaPLFAM/R/simu_funs.R | 47 ++++--- cvmaPLFAM-0.1.1/cvmaPLFAM/man/cvfolds.Rd | 70 +++++------ cvmaPLFAM-0.1.1/cvmaPLFAM/man/cvmaPLFAM.Rd | 168 +++++++++++++--------------- cvmaPLFAM-0.1.1/cvmaPLFAM/man/cvpredRisk.Rd |only cvmaPLFAM-0.1.1/cvmaPLFAM/man/data_gen.Rd | 98 +++++++++------- cvmaPLFAM-0.1.1/cvmaPLFAM/man/fpcscore.Rd | 79 +++++-------- cvmaPLFAM-0.1.1/cvmaPLFAM/man/modelspec.Rd | 109 +++++++++++------- cvmaPLFAM-0.1.1/cvmaPLFAM/man/plam.fit.Rd |only 21 files changed, 634 insertions(+), 538 deletions(-)
Title: Extracting Signals from Wavelet Spectra
Description: The continuous wavelet transform enables the observation of transient/non-stationary cyclicity in time-series. The goal of cyclostratigraphic studies is to define frequency/period in the depth/time domain. By conducting the continuous wavelet transform on cyclostratigraphic data series one can observe and extract cyclic signals/signatures from signals. These results can then be visualized and interpreted enabling one to identify/interpret cyclicity in the geological record, which can be used to construct astrochronological age-models and identify and interpret cyclicity in past and present climate systems. The 'WaverideR' R package builds upon existing literature and existing codebase. The list of articles which are relevant can be grouped in four subjects; cyclostratigraphic data analysis,example data sets,the (continuous) wavelet transform and astronomical solutions. References for the cyclostratigraphic data analysis articles are: Stephen Meyers (2019) <doi:10.1016/j.earscirev.20 [...truncated...]
Author: Michiel Arts [aut, cre]
Maintainer: Michiel Arts <michiel.arts@stratigraphy.eu>
Diff between WaverideR versions 0.4.0 dated 2025-04-25 and 0.4.1 dated 2025-04-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/track_period_wavelet.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Models for Correlation Matrices Based on Graphs
Description: Implement some models for
correlation/covariance matrices including two approaches
to model correlation matrices from a graphical structure.
One use latent parent variables as proposed in
Sterrantino et. al. (2024) <doi:10.48550/arXiv.2312.06289>.
The other uses a graph to specify conditional
relations between the variables.
The graphical structure makes correlation matrices
interpretable and avoids the quadratic increase of
parameters as a function of the dimension.
In the first approach a natural sequence of simpler
models along with a complexity penalization is used.
The second penalizes deviations from a base model.
These can be used as prior for model parameters,
considering C code through the 'cgeneric' interface
for the 'INLA' package (<https://www.r-inla.org>).
This allows one to use these models as building
blocks combined and to other latent Gaussian models
in order to build complex data models.
Author: Elias Krainski [cre, aut, cph]
,
Denis Rustand [aut, cph] ,
Anna Freni-Sterrantino [aut, cph]
,
Janet van Niekerk [aut, cph] ,
Haavard Rue’ [aut]
Maintainer: Elias Krainski <eliaskrainski@gmail.com>
Diff between graphpcor versions 0.1.11 dated 2025-04-19 and 0.1.12 dated 2025-04-27
graphpcor-0.1.11/graphpcor/src/cgeneric_get.c |only graphpcor-0.1.11/graphpcor/src/cgeneric_kronecker.c |only graphpcor-0.1.12/graphpcor/DESCRIPTION | 10 +++++----- graphpcor-0.1.12/graphpcor/MD5 | 12 +++++------- graphpcor-0.1.12/graphpcor/R/kronecker.R | 6 +++++- graphpcor-0.1.12/graphpcor/R/param_prec.R | 10 ++++++++-- graphpcor-0.1.12/graphpcor/man/prec.Rd | 5 +++++ graphpcor-0.1.12/graphpcor/src/Makevars | 2 +- 8 files changed, 29 insertions(+), 16 deletions(-)
Title: Provides Tests and Graphics for Assessing Tests of Equivalence
Description: Provides statistical tests and graphics for assessing tests
of equivalence. Such tests have similarity as the alternative
hypothesis instead of the null. Sample data sets are included.
Author: Andrew Robinson [aut, cre]
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between equivalence versions 0.7.2 dated 2016-05-13 and 0.8.2 dated 2025-04-27
ChangeLog | 19 +++++++++++++++++++ DESCRIPTION | 18 +++++++++++------- MD5 | 23 ++++++++++++----------- R/equiv.boot.R | 13 ++++++------- R/equivalence.xyplot.R | 8 ++++---- R/tost.R | 14 -------------- data/pref.4PG.rda |binary data/pref.LAI.rda |binary data/ufc.rda |binary man/equiv.boot.Rd | 2 +- man/equivalence.xyplot.Rd | 6 +++--- man/rtost.Rd | 8 ++++---- src/equivalence_init.c |only 13 files changed, 60 insertions(+), 51 deletions(-)
Title: Difference-in-Differences with Unpoolable Data
Description: A framework for estimating difference-in-differences with
unpoolable data, based on Karim, Webb, Austin, and Strumpf (2024)
<doi:10.48550/arXiv.2403.15910>. Supports common or staggered adoption, multiple
groups, and the inclusion of covariates. Also computes p-values for the
aggregate average treatment effect on the treated via the
randomization inference procedure described in MacKinnon and Webb (2020)
<doi:10.1016/j.jeconom.2020.04.024>.
Author: Eric Jamieson [aut, cre, cph]
Maintainer: Eric Jamieson <ericbrucejamieson@gmail.com>
Diff between undidR versions 1.0.1 dated 2025-02-24 and 1.0.2 dated 2025-04-27
DESCRIPTION | 6 ++-- MD5 | 18 +++++++------- NEWS.md | 4 +++ R/create_diff_df.r | 37 ++++++++++++++++++++---------- R/helpers.R | 23 +++++++++--------- R/plot_parallel_trends.r | 28 ++++++++++++++--------- R/undid_stage_three.r | 7 +++-- R/undid_stage_two.r | 51 +++++++++++++++++++++++++----------------- inst/doc/undidR.html | 32 +++++++++++++------------- tests/testthat/test-helpers.R | 18 +++++++++----- 10 files changed, 132 insertions(+), 92 deletions(-)
Title: Fast Likelihood Calculation for Phylogenetic Comparative Models
Description: Provides a C++ backend for multivariate phylogenetic comparative
models implemented in the R-package 'PCMBase'. Can be used in combination
with 'PCMBase' to enable fast and parallel likelihood calculation. Implements
the pruning likelihood calculation algorithm described in Mitov et al. (2020)
<doi:10.1016/j.tpb.2019.11.005>. Uses the 'SPLITT' C++ library for parallel tree traversal
described in Mitov and Stadler (2018) <doi:10.1111/2041-210X.13136>.
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBaseCpp versions 0.1.9 dated 2020-03-22 and 0.1.10 dated 2025-04-27
DESCRIPTION | 12 MD5 | 34 - NEWS.md | 54 +-- R/BenchmarkRvsCpp.R | 648 ++++++++++++++++++------------------- R/Generic.R | 550 +++++++++++++++---------------- README.md | 72 +--- build/vignette.rds |binary inst/CITATION | 15 inst/doc/PCMBaseCpp.R | 10 inst/doc/PCMBaseCpp.html | 386 ++++++++++++---------- man/BenchmarkRvsCpp.Rd | 24 - man/MiniBenchmarkRvsCpp.Rd | 18 - man/PCMInfoCpp.Rd | 16 man/benchmarkData.Rd | 6 man/benchmarkResults.Rd | 4 man/benchmarkResultsNoTransform.Rd | 4 src/Makevars | 3 vignettes/REFERENCES-R.bib | 114 ++++-- 18 files changed, 1050 insertions(+), 920 deletions(-)
Title: R Interface to 'Redatam' Library
Description: Provides an API to work with 'Redatam' (see <https://redatam.org>)
databases in both formats: 'RXDB' (new format) and 'DICX' (old format) and running
'Redatam' programs written in 'SPC' language. It's a wrapper around 'Redatam'
core and provides functions to open/close a database (redatam_open()/redatam_close()),
list entities and variables from the database (redatam_entities(), redatam_variables())
and execute a 'SPC' program and gets the results as data frames
(redatam_query(), redatam_run()).
Author: Jaime Salvador [aut, cre] ,
CELADE [cph]
Maintainer: Jaime Salvador <jaime.salvador@ideasybits.com>
Diff between redatamx versions 1.1.2 dated 2025-04-05 and 1.1.3 dated 2025-04-27
DESCRIPTION | 6 MD5 | 68 +++--- NAMESPACE | 30 +-- NEWS.md | 70 +++---- R/output-env.R | 82 ++++---- R/redatam-api.R | 414 +++++++++++++++++++++--------------------- R/redatam-package.R | 16 - R/redatam-plugins.R | 76 +++---- R/redatam-query.R | 206 ++++++++++---------- R/redatam-run.R | 200 ++++++++++---------- R/zzz.R | 34 +-- README.md | 236 +++++++++++------------ configure | 9 configure.win | 83 ++++---- inst/COPYRIGHTS | 16 - inst/License.txt | 40 ++-- man/outputs.Rd | 62 +++--- man/redatam_close.Rd | 56 ++--- man/redatam_create.Rd | 54 ++--- man/redatam_destroy_.Rd | 48 ++-- man/redatam_entities.Rd | 52 ++--- man/redatam_info.Rd | 40 ++-- man/redatam_init_.Rd | 54 ++--- man/redatam_internal_query.Rd | 58 ++--- man/redatam_internal_run.Rd | 58 ++--- man/redatam_load_plugin.Rd | 58 ++--- man/redatam_open.Rd | 52 ++--- man/redatam_query.Rd | 70 +++---- man/redatam_run.Rd | 70 +++---- man/redatam_save.Rd | 60 +++--- man/redatam_variables.Rd | 56 ++--- man/redatam_version.Rd | 40 ++-- man/redatamx-package.Rd | 58 ++--- src/dylib.hpp | 2 src/red_initialize.cpp | 3 35 files changed, 1273 insertions(+), 1264 deletions(-)
Title: Micro-Macro Analysis for Social Networks
Description: Estimates micro effects on macro structures (MEMS) and average micro mediated effects (AMME).
URL: <https://github.com/sduxbury/netmediate>.
BugReports: <https://github.com/sduxbury/netmediate/issues>.
Robins, Garry, Phillipa Pattison, and Jodie Woolcock (2005) <doi:10.1086/427322>.
Snijders, Tom A. B., and Christian E. G. Steglich (2015) <doi:10.1177/0049124113494573>.
Imai, Kosuke, Luke Keele, and Dustin Tingley (2010) <doi:10.1037/a0020761>.
Duxbury, Scott (2023) <doi:10.1177/00811750231209040>.
Duxbury, Scott (2024) <doi:10.1177/00811750231220950>.
Author: Scott Duxbury [aut, cre, cph],
Xin Zhao [ctb]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Diff between netmediate versions 1.0.1 dated 2024-06-19 and 1.1.0 dated 2025-04-27
DESCRIPTION | 15 +-- MD5 | 51 +++++----- NAMESPACE | 2 NEWS |only R/AMME.R | 10 +- R/AMME_nonparam.R | 65 +++++++++++++ R/AMME_param.R | 66 +++++++++++++ R/MEMS.R | 30 +++--- R/MEMS_QAP.R | 55 +++++++++++ R/MEMS_ergm.R | 12 +- R/MEMS_ergm_nonparam.R | 54 ++++++++++- R/MEMS_ergm_param.R | 65 +++++++++++++ R/MEMS_glm.R | 9 + R/MEMS_glm_nonparam.R | 48 +++++++++- R/MEMS_glm_param.R | 48 +++++++++- R/MEMS_pooled_ergm.R | 9 + R/MEMS_pooled_ergm_nonparam.R | 56 +++++++++++ R/MEMS_pooled_ergm_param.R | 58 +++++++++++- R/MEMS_pooled_saom.R | 59 +++++++++++- R/MEMS_rem.R | 10 +- R/MEMS_rem_param.R | 60 +++++++++++- R/MEMS_saom.R | 56 +++++++++++ R/compare_MEMS.R | 167 ++++++++++++++++++++++------------- R/mediate_MEMS.R |only man/AMME.Rd | 10 +- man/MEMS.Rd | 14 ++ man/compare_MEMS.Rd | 200 ++++++++++++++++++++++++++++++++++++++++-- man/mediate_MEMS.Rd |only 28 files changed, 1071 insertions(+), 158 deletions(-)
Title: Useful Functions for Programming and Generating Documents
Description: Tools to help developers and producers manipulate R objects
and outputs. It includes tools for displaying results and objects, and
for formatting them in the correct format.
Author: Tanguy Barthelemy [aut, cre]
Maintainer: Tanguy Barthelemy <tanguy.barthelemy@insee.fr>
Diff between TBox versions 0.1.2 dated 2024-06-14 and 0.2.2 dated 2025-04-27
DESCRIPTION | 23 - MD5 | 48 ++ NAMESPACE | 13 NEWS.md | 74 ++++ R/TBox-package.R | 5 R/format_code.R | 439 +++++++++++++++++++++------ R/manage_file.R |only README.md | 4 inst/extdata/file.csv |only inst/extdata/style.css |only inst/extdata/template.docx |only man/create_preamble_tex.Rd |only man/generate_chunk_header.Rd |only man/generate_rmd_file.Rd |only man/get_data.Rd |only man/get_fira_path.Rd |only man/get_latex_engine.Rd |only man/get_word_template_path.Rd |only man/render_code.Rd | 50 ++- man/write_data.Rd |only tests/testthat.R | 4 tests/testthat/helper.R |only tests/testthat/output_data |only tests/testthat/template_rmd |only tests/testthat/test-generate_chunk_header.R | 10 tests/testthat/test-generate_rmd_file.R | 245 ++++++++------- tests/testthat/test-get_fira_path.R |only tests/testthat/test-get_word_template_path.R |only tests/testthat/test-render_code.R |only 29 files changed, 669 insertions(+), 246 deletions(-)
Title: Functions and Datasets for "Introduction to Scientific
Programming and Simulation Using R"
Description: Provides functions and datasets from Jones, O.D., R. Maillardet, and A.P. Robinson. 2014. An Introduction to Scientific Programming and Simulation, Using R. 2nd Ed. Chapman And Hall/CRC.
Author: Owen Jones [aut],
Robert Maillardet [aut],
Andrew Robinson [aut, cre],
Olga Borovkova [aut],
Steven Carnie [aut]
Maintainer: Andrew Robinson <apro@unimelb.edu.au>
Diff between spuRs versions 2.0.2 dated 2018-05-21 and 2.0.3 dated 2025-04-27
DESCRIPTION | 30 +++++++++++++++++++++++++----- MD5 | 20 ++++++++++---------- data/kew.rda |binary data/treeg.rda |binary data/trees.rda |binary data/ufc.plots.rda |binary data/ufc.rda |binary inst/resources/errata.pdf |binary man/fitDistances.Rd | 2 +- man/kew.Rd | 2 +- man/vol.m3.Rd | 2 +- 11 files changed, 38 insertions(+), 18 deletions(-)
Title: 1d Goodness of Fit Tests
Description: Routines that allow the user to run a large number of goodness-of-fit tests.
It allows for data to be continuous or discrete. It includes routines to estimate
the power of the tests and display them as a power graph.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between Rgof versions 3.1.0 dated 2025-03-13 and 3.2.0 dated 2025-04-27
Rgof-3.1.0/Rgof/R/gof_power_cont.R |only Rgof-3.1.0/Rgof/R/gof_power_disc.R |only Rgof-3.1.0/Rgof/R/gof_test_cont.R |only Rgof-3.1.0/Rgof/R/gof_test_cont_adj.R |only Rgof-3.1.0/Rgof/R/gof_test_disc.R |only Rgof-3.1.0/Rgof/R/gof_test_disc_adj.R |only Rgof-3.1.0/Rgof/R/power_cont_R.R |only Rgof-3.1.0/Rgof/R/power_disc_R.R |only Rgof-3.1.0/Rgof/man/gof_cont.Rd |only Rgof-3.1.0/Rgof/man/gof_disc.Rd |only Rgof-3.1.0/Rgof/man/gof_power_cont.Rd |only Rgof-3.1.0/Rgof/man/gof_power_disc.Rd |only Rgof-3.1.0/Rgof/man/gof_test_cont.Rd |only Rgof-3.1.0/Rgof/man/gof_test_cont_adj.Rd |only Rgof-3.1.0/Rgof/man/gof_test_disc.Rd |only Rgof-3.1.0/Rgof/man/gof_test_disc_adj.Rd |only Rgof-3.1.0/Rgof/man/power_cont.Rd |only Rgof-3.1.0/Rgof/man/power_cont_R.Rd |only Rgof-3.1.0/Rgof/man/power_disc.Rd |only Rgof-3.1.0/Rgof/man/power_disc_R.Rd |only Rgof-3.1.0/Rgof/src/gof_cont.cpp |only Rgof-3.1.0/Rgof/src/gof_cont.h |only Rgof-3.1.0/Rgof/src/gof_disc.cpp |only Rgof-3.1.0/Rgof/src/gof_disc.h |only Rgof-3.1.0/Rgof/src/power_cont.cpp |only Rgof-3.1.0/Rgof/src/power_disc.cpp |only Rgof-3.1.0/Rgof/src/teststatistics.cpp |only Rgof-3.1.0/Rgof/src/teststatistics.h |only Rgof-3.2.0/Rgof/DESCRIPTION | 6 Rgof-3.2.0/Rgof/MD5 | 73 +-- Rgof-3.2.0/Rgof/NEWS.md | 3 Rgof-3.2.0/Rgof/R/RcppExports.R | 112 ++-- Rgof-3.2.0/Rgof/R/gof_power.R | 186 +++++-- Rgof-3.2.0/Rgof/R/gof_test.R | 138 ++++- Rgof-3.2.0/Rgof/R/gof_test_adjusted_pvalue.R | 192 ++++++- Rgof-3.2.0/Rgof/R/run.studies.R | 14 Rgof-3.2.0/Rgof/R/timecheck.R | 12 Rgof-3.2.0/Rgof/inst/doc/Rgof.R | 5 Rgof-3.2.0/Rgof/inst/doc/Rgof.Rmd | 10 Rgof-3.2.0/Rgof/inst/doc/Rgof.html | 580 ++++++++++++++++-------- Rgof-3.2.0/Rgof/man/calcTS.Rd | 12 Rgof-3.2.0/Rgof/man/gof_adj_C1.Rd |only Rgof-3.2.0/Rgof/man/gof_adj_C2.Rd |only Rgof-3.2.0/Rgof/man/gof_power.Rd | 12 Rgof-3.2.0/Rgof/man/gof_power_C.Rd |only Rgof-3.2.0/Rgof/man/gof_test.Rd | 2 Rgof-3.2.0/Rgof/man/gof_test_C.Rd |only Rgof-3.2.0/Rgof/man/gof_test_adjusted_pvalue.Rd | 24 Rgof-3.2.0/Rgof/man/timecheck.Rd | 10 Rgof-3.2.0/Rgof/src/RcppExports.cpp | 104 +--- Rgof-3.2.0/Rgof/src/calcTS.cpp |only Rgof-3.2.0/Rgof/src/calcTS.h |only Rgof-3.2.0/Rgof/src/gof_adj_C.cpp |only Rgof-3.2.0/Rgof/src/gof_power_C.cpp |only Rgof-3.2.0/Rgof/src/gof_test_C.cpp |only Rgof-3.2.0/Rgof/vignettes/Rgof.Rmd | 10 56 files changed, 1003 insertions(+), 502 deletions(-)
Title: Various Methods for the Two Sample Problem
Description: The routine twosample_test() in this package runs the
two sample test using various test statistic. The p values are
found via permutation or large sample theory. The routine twosample_power() allows the
calculation of the power in various cases, and plot_power() draws the corresponding power graphs.
The routine run.studies allows a user to quickly study the power of a new method and
how it compares to some of the standard ones.
Author: Wolfgang Rolke [aut, cre]
Maintainer: Wolfgang Rolke <wolfgang.rolke@upr.edu>
Diff between R2sample versions 3.1.1 dated 2025-03-16 and 4.0.0 dated 2025-04-27
R2sample-3.1.1/R2sample/R/power_cont_R.R |only R2sample-3.1.1/R2sample/R/power_disc_R.R |only R2sample-3.1.1/R2sample/man/perm_test_cont.Rd |only R2sample-3.1.1/R2sample/man/perm_test_disc.Rd |only R2sample-3.1.1/R2sample/man/permute_disc.Rd |only R2sample-3.1.1/R2sample/man/power_cont.Rd |only R2sample-3.1.1/R2sample/man/power_cont_R.Rd |only R2sample-3.1.1/R2sample/man/power_disc.Rd |only R2sample-3.1.1/R2sample/man/power_disc_R.Rd |only R2sample-3.1.1/R2sample/man/ts_C.Rd |only R2sample-3.1.1/R2sample/man/ts_D.Rd |only R2sample-3.1.1/R2sample/src/perm_test_cont.cpp |only R2sample-3.1.1/R2sample/src/perm_test_disc.cpp |only R2sample-3.1.1/R2sample/src/permute_disc.cpp |only R2sample-3.1.1/R2sample/src/permute_disc.h |only R2sample-3.1.1/R2sample/src/power_cont.cpp |only R2sample-3.1.1/R2sample/src/power_disc.cpp |only R2sample-3.1.1/R2sample/src/teststatistics.cpp |only R2sample-3.1.1/R2sample/src/teststatistics.h |only R2sample-4.0.0/R2sample/DESCRIPTION | 6 R2sample-4.0.0/R2sample/MD5 | 76 +- R2sample-4.0.0/R2sample/NAMESPACE | 3 R2sample-4.0.0/R2sample/NEWS.md | 5 R2sample-4.0.0/R2sample/R/RcppExports.R | 170 ++---- R2sample-4.0.0/R2sample/R/case.studies.R | 8 R2sample-4.0.0/R2sample/R/powerR.R |only R2sample-4.0.0/R2sample/R/run.studies.R | 8 R2sample-4.0.0/R2sample/R/twosample_power.R | 188 +++---- R2sample-4.0.0/R2sample/R/twosample_test.R | 115 ++-- R2sample-4.0.0/R2sample/R/twosample_test_adjusted_pvalue.R | 165 ++---- R2sample-4.0.0/R2sample/data/power_studies_results.rda |binary R2sample-4.0.0/R2sample/inst/doc/R2sample.R | 15 R2sample-4.0.0/R2sample/inst/doc/R2sample.Rmd | 67 +- R2sample-4.0.0/R2sample/inst/doc/R2sample.html | 265 +++++----- R2sample-4.0.0/R2sample/man/TSw_disc.Rd | 18 R2sample-4.0.0/R2sample/man/gen_cont_noweights.Rd |only R2sample-4.0.0/R2sample/man/gen_cont_weights.Rd |only R2sample-4.0.0/R2sample/man/gen_disc.Rd |only R2sample-4.0.0/R2sample/man/gen_sim_data.Rd |only R2sample-4.0.0/R2sample/man/powerC.Rd |only R2sample-4.0.0/R2sample/man/powerR.Rd |only R2sample-4.0.0/R2sample/man/run.studies.Rd | 3 R2sample-4.0.0/R2sample/man/testC.Rd |only R2sample-4.0.0/R2sample/man/twosample_power.Rd | 6 R2sample-4.0.0/R2sample/man/twosample_test.Rd | 8 R2sample-4.0.0/R2sample/man/twosample_test_adjusted_pvalue.Rd | 8 R2sample-4.0.0/R2sample/src/RcppExports.cpp | 186 +++---- R2sample-4.0.0/R2sample/src/TSw_disc.cpp | 118 ++-- R2sample-4.0.0/R2sample/src/calcTS.cpp |only R2sample-4.0.0/R2sample/src/calcTS.h |only R2sample-4.0.0/R2sample/src/gen_sim_data.cpp |only R2sample-4.0.0/R2sample/src/gen_sim_data.h |only R2sample-4.0.0/R2sample/src/powerC.cpp |only R2sample-4.0.0/R2sample/src/test.cpp |only R2sample-4.0.0/R2sample/src/testC.cpp |only R2sample-4.0.0/R2sample/vignettes/R2sample.Rmd | 67 +- 56 files changed, 788 insertions(+), 717 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-07-18 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-29 0.9.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-21 1.0.2
2020-04-09 1.0.1
2019-05-12 1.0.0
2016-10-24 0.2.0
2015-09-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-01 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-14 1.4-1
2014-09-15 1.4-0
2014-08-11 1.3-9
2014-06-02 1.3-8
2013-04-18 1.3-7.1
2012-09-25 1.3-7
2012-02-22 1.3-6
2011-10-11 1.3-5
2011-03-07 1.3-4
2010-11-03 1.3-3
2010-09-08 1.3-2
2010-08-19 1.3-1
2010-08-16 1.3-0
2010-07-26 1.2-9
2010-06-18 1.2-8
2010-05-03 1.2-7
2010-03-01 1.2-6
2010-02-19 1.2-5
2010-01-26 1.2-4
2009-11-06 1.2-3
2009-09-21 1.2-2
2009-08-13 1.2-1
2009-07-21 1.2-0
2009-03-27 1.1-8
2008-12-16 1.1-7
2008-08-20 1.1-5
2008-06-09 1.1-3
2008-05-14 1.1-1
2008-02-11 1.0-6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-21 1.1.0
2017-09-08 1.0.5
2017-01-20 1.0.4
2017-01-06 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-11-12 1.1.2
2022-09-18 1.1.1
2021-05-11 1.1.0
2019-03-07 1.0.3
Title: Distributed Trimmed Scores Regression for Handling Missing Data
Description: Provides functions for handling missing data using Distributed Trimmed Scores Regression and other imputation methods. It includes facilities for data imputation, evaluation metrics, and clustering analysis. It is designed to work in distributed computing environments to handle large datasets efficiently. The philosophy of the package is described in Guo G. (2024) <doi:10.1080/03610918.2022.2091779>.
Author: Guangbao Guo [aut, cre, cph] ,
Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between DTSR versions 0.1.0 dated 2024-11-08 and 0.2.0 dated 2025-04-27
DESCRIPTION | 8 ++++---- MD5 | 7 ++++++- data |only man/Frogs.Rd |only man/abalone.Rd |only 5 files changed, 10 insertions(+), 5 deletions(-)
Title: Fast Computation of Pairwise Hamming Distances
Description: Pairwise Hamming distances are computed between the rows of a binary (0/1) matrix using highly optimized 'C' code. The input is an integer matrix where each row represents a binary feature vector and returns a symmetric integer matrix of pairwise distances. Internally, rows are bit-packed into 64-bit words for fast XOR-based comparisons, with hardware-accelerated popcount operations to count differences. 'OpenMP' parallelization ensures efficient performance for large matrices.
Author: Ravi Varadhan [aut, cre]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between FastHamming versions 1.1 dated 2025-04-25 and 1.2 dated 2025-04-26
DESCRIPTION | 8 ++--- MD5 | 8 ++--- src/FastHamming.c | 79 ++++++++++++++++++++++++++++++------------------------ src/Makevars | 1 src/Makevars.win | 4 -- 5 files changed, 55 insertions(+), 45 deletions(-)
Title: Extreme Risk Measures
Description: A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations. The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2022) <doi:10.3150/21-BEJ1375>, Davison et al. (2023) <doi:10.1080/07350015.2022.2078332>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6> [...truncated...]
Author: Simone Padoan [cre, aut],
Gilles Stupfler [aut],
Bocconi Institute for Data Science and Analytics [fnd],
French National Research [fnd]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremeRisks versions 0.0.4 dated 2020-08-27 and 0.0.4-1 dated 2025-04-26
DESCRIPTION | 14 +++++++------- MD5 | 42 +++++++++++++++++++++--------------------- man/EBTailIndex.Rd | 10 +++++----- man/ExpectMES.Rd | 8 ++++---- man/HTailIndex.Rd | 8 ++++---- man/HypoTesting.Rd | 9 ++++----- man/MLTailIndex.Rd | 8 ++++---- man/MomTailIndex.Rd | 6 +++--- man/MultiHTailIndex.Rd | 9 ++++----- man/QuantMES.Rd | 9 +++++---- man/estExpectiles.Rd | 8 ++++---- man/estExtLevel.Rd | 8 ++++---- man/estMultiExpectiles.Rd | 11 +++++------ man/expectiles.Rd | 9 ++++----- man/extMultiQuantile.Rd | 13 ++++++------- man/extQuantile.Rd | 9 +++++---- man/predExpectiles.Rd | 8 ++++---- man/predMultiExpectiles.Rd | 11 +++++------ man/rbtimeseries.Rd | 8 ++++---- man/rmdata.Rd | 9 ++++----- man/rtimeseries.Rd | 8 ++++---- man/sp500.Rd | 2 +- 22 files changed, 111 insertions(+), 116 deletions(-)
Title: 'R' 'Markdown' Themes for 'UIUC' Documents and Presentations
Description: A set of custom 'R' 'Markdown' templates for documents and
presentations with the University of Illinois at Urbana-Champaign (UIUC)
color scheme and identity standards.
Author: James Balamuta [aut, cre] ,
Steven Andrew Culpepper [ctb] ,
David Dalpiaz [ctb] ,
Jose Luis Rodriguez [ctb]
Beamer Theme)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between uiucthemes versions 0.3.1 dated 2020-07-25 and 0.3.3 dated 2025-04-26
uiucthemes-0.3.1/uiucthemes/DESCRIPTION |only uiucthemes-0.3.1/uiucthemes/README.md |only uiucthemes-0.3.1/uiucthemes/build |only uiucthemes-0.3.1/uiucthemes/inst/COPYRIGHTS |only uiucthemes-0.3.1/uiucthemes/inst/rmarkdown/templates/html_imetropolis/resources |only uiucthemes-0.3.1/uiucthemes/man |only uiucthemes-0.3.1/uiucthemes/tools |only uiucthemes-0.3.3/uiucthemes/MD5 | 42 +-- uiucthemes-0.3.3/uiucthemes/NEWS.md | 26 ++ uiucthemes-0.3.3/uiucthemes/R/html_templates.R | 12 - uiucthemes-0.3.3/uiucthemes/R/latex_templates.R | 6 uiucthemes-0.3.3/uiucthemes/inst/doc/pkg-templates.Rmd | 4 uiucthemes-0.3.3/uiucthemes/inst/doc/pkg-templates.html | 120 +++------- uiucthemes-0.3.3/uiucthemes/inst/rmarkdown/templates/html_imetropolis/skeleton/fonts-imtheme.css |only uiucthemes-0.3.3/uiucthemes/inst/rmarkdown/templates/html_imetropolis/skeleton/horizontal-o-illinois.png |only uiucthemes-0.3.3/uiucthemes/inst/rmarkdown/templates/html_imetropolis/skeleton/horizontal-rb-illinois.png |only uiucthemes-0.3.3/uiucthemes/inst/rmarkdown/templates/html_imetropolis/skeleton/imtheme.css |only uiucthemes-0.3.3/uiucthemes/inst/rmarkdown/templates/html_imetropolis/skeleton/macros.js |only uiucthemes-0.3.3/uiucthemes/vignettes/pkg-templates.Rmd | 4 19 files changed, 105 insertions(+), 109 deletions(-)
Title: Extracts Environmental Data from 'ERDDAP™' Web Services
Description: Contains three functions that access
environmental data from any 'ERDDAP™' data web service. The rxtracto() function extracts
data along a trajectory for a given "radius" around the point. The
rxtracto_3D() function extracts data in a box. The rxtractogon() function
extracts data in a polygon. All of those three function use the 'rerddap' package
to extract the data, and should work with any 'ERDDAP™' server.
There are also two functions, plotBBox() and plotTrack() that use the 'plotdap'
package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre],
Marie Auger-Methe [ctb],
Sunny Bak-Hospital [ctb]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>
Diff between rerddapXtracto versions 1.2.2 dated 2025-02-25 and 1.2.3 dated 2025-04-26
DESCRIPTION | 10 ++--- MD5 | 20 +++++----- NEWS.md | 6 +++ R/interp.R | 2 - R/rxtracto.R | 2 - R/tidy_grid.R | 70 +++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/UsingrerddapXtracto.Rmd | 2 - inst/doc/UsingrerddapXtracto.html | 6 +-- man/tidy_grid.Rd | 4 +- vignettes/UsingrerddapXtracto.Rmd | 2 - 11 files changed, 75 insertions(+), 49 deletions(-)
More information about rerddapXtracto at CRAN
Permanent link
Title: Biomarker Threshold Models
Description: Contains tools to fit both predictive and prognostic biomarker effects using biomarker threshold models and continuous threshold models. Evaluate the treatment effect, biomarker effect and treatment-biomarker interaction using probability index measurement. Test for treatment-biomarker interaction using residual bootstrap method.
Author: Bingshu E. Chen [aut, cre]
Maintainer: Bingshu E. Chen <bingshu.chen@queensu.ca>
Diff between bhm versions 1.18 dated 2022-08-31 and 1.19 dated 2025-04-26
DESCRIPTION | 13 ++-- MD5 | 41 ++++++++------ NAMESPACE | 6 +- R/ars.R |only R/bhm.R | 2 R/bhm_lib.R | 155 +++++++++++++++++++++++++++++++++++++++++++++++++++++ R/ggkm.R |only R/glmpLRT.R | 20 +++--- R/llm.R | 8 ++ R/picexp.R | 6 +- R/resboot.R | 3 - man/ars.Rd |only man/bhm-package.Rd | 5 - man/bhm.Rd | 8 ++ man/brm.Rd | 2 man/control.Rd | 2 man/ggkm.Rd |only man/glmpLRT.Rd | 7 +- man/llm.Rd | 4 - man/mpl.Rd | 2 man/multiRoot.Rd |only man/numHessian.Rd |only man/numScore.Rd |only man/picexp.Rd | 3 - man/resboot.Rd | 2 25 files changed, 232 insertions(+), 57 deletions(-)
Title: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra
Description: Raman and (FT)IR spectral analysis tool for plastic particles and
other environmental samples (Cowger et al. 2021,
<doi:10.1021/acs.analchem.1c00123>). With read_any(), Open Specy provides a
single function for reading individual, batch, or map spectral data files
like .asp, .csv, .jdx, .spc, .spa, .0, and .zip. process_spec() simplifies
processing spectra, including smoothing, baseline correction,
range restriction and flattening, intensity conversions, wavenumber
alignment, and min-max normalization. Spectra can be identified in batch
using an onboard reference library (Cowger et al. 2020,
<doi:10.1177/0003702820929064>) using match_spec(). A Shiny app is available
via run_app() or online at <https://www.openanalysis.org/openspecy/>.
Author: Win Cowger [cre, aut, dtc] ,
Zacharias Steinmetz [aut] ,
Hazel Vaquero [aut] ,
Nick Leong [aut] ,
Andrea Faltynkova [aut, dtc] ,
Hannah Sherrod [aut] ,
Andrew B Gray [ctb] ,
Hannah Hapich [ctb] ,
Jennifer Lynch [ctb, dtc] ,
Hannah De Frond [ctb, dtc] [...truncated...]
Maintainer: Win Cowger <wincowger@gmail.com>
Diff between OpenSpecy versions 1.4.0 dated 2024-11-04 and 1.5.3 dated 2025-04-26
DESCRIPTION | 16 MD5 | 60 NAMESPACE | 8 NEWS.md | 13 R/as_OpenSpecy.R | 40 R/conform_spec.R | 18 R/gen_OpenSpecy.R | 138 + R/manage_lib.R | 140 + R/process_spec.R | 10 R/read_ext.R | 125 - R/read_multi.R | 15 R/subtr_baseline.R | 320 ++- README.md | 25 inst/doc/sop.R | 245 +- inst/doc/sop.Rmd | 325 +-- inst/doc/sop.html | 2951 +++++------------------------------ man/OpenSpecy-package.Rd | 4 man/as_OpenSpecy.Rd | 3 man/gen_OpenSpecy.Rd | 32 man/manage_lib.Rd | 12 man/process_spec.Rd | 4 man/read_ext.Rd | 3 man/read_multi.Rd | 9 man/subtr_baseline.Rd | 95 - tests/testthat/Rplots.pdf |binary tests/testthat/test-as_OpenSpecy.R | 24 tests/testthat/test-manage_lib.R | 17 tests/testthat/test-match_spec.R | 4 tests/testthat/test-read_multi.R | 10 tests/testthat/test-subtr_baseline.R | 30 vignettes/sop.Rmd | 325 +-- 31 files changed, 1761 insertions(+), 3260 deletions(-)
Title: Accessing a Geometallurgical Database with R
Description: A template for a geometallurgical database and a fast and easy
interface for accessing it.
Author: K. Gerald van den Boogaart [aut, cre],
Stephan Matos Camacho [aut]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmDatabase versions 0.5.0 dated 2016-06-16 and 0.5.1 dated 2025-04-26
gmDatabase-0.5.0/gmDatabase/inst/doc |only gmDatabase-0.5.1/gmDatabase/DESCRIPTION | 18 gmDatabase-0.5.1/gmDatabase/MD5 | 15 gmDatabase-0.5.1/gmDatabase/R/DBinterface.R | 871 ++--- gmDatabase-0.5.1/gmDatabase/R/Database.R | 3377 ++++++++++---------- gmDatabase-0.5.1/gmDatabase/man/gmChangePassword.Rd | 74 gmDatabase-0.5.1/gmDatabase/man/gmConnectServer.Rd | 211 - gmDatabase-0.5.1/gmDatabase/man/gmSQL.Rd | 246 - gmDatabase-0.5.1/gmDatabase/man/gmSQLValues.Rd | 98 9 files changed, 2455 insertions(+), 2455 deletions(-)
Title: Behavior-Driven Development for R
Description: Write executable specifications in a natural language that describes how your code should behave.
Write specifications in feature files using 'Gherkin' language and execute them using functions implemented in R.
Use them as an extension to your 'testthat' tests to provide a high level description of how your code works.
Author: Jakub Sobolewski [aut, cre]
Maintainer: Jakub Sobolewski <jakupsob@gmail.com>
Diff between cucumber versions 2.0.0 dated 2025-04-04 and 2.0.1 dated 2025-04-26
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 +++++- build/vignette.rds |binary inst/doc/bdd.R | 2 -- inst/doc/bdd.html | 6 +++--- tests/testthat/test-examples.R | 1 + 7 files changed, 19 insertions(+), 16 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-09-03 0.2.2
2016-02-10 0.2
2014-02-23 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-11 5.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-07 0.1.1
2019-06-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-04 1.3.0
2021-06-10 1.2.0
2020-12-08 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-13 0.2.21
2016-03-27 0.2.20
2016-03-07 0.2.19
2015-12-24 0.2.18
2015-02-11 0.2.9
2015-01-31 0.2.8.3
2014-12-08 0.2.7.1
2014-11-19 0.2.7
2014-08-13 0.2.2
2014-05-06 0.1.26
2014-04-07 0.1.24
2014-03-31 0.1.23
2014-02-21 0.1.17
2014-01-20 0.1.13
2014-01-10 0.1.12
2013-12-10 0.1.11
2013-12-02 0.1.10
2013-09-27 0.1.8
2013-08-03 0.1.6
2013-06-04 0.1.5.2
2013-05-21 0.1.5
2013-05-16 0.1.3
Title: A Toolbox for Computing Efficient Designs of Experiments
Description: Algorithms for D-, A-, I-, and c-optimal designs. Some of the functions in this package require the 'gurobi' software and its accompanying R package. For their installation, please follow the instructions at <https://www.gurobi.com> and the file gurobi_inst.txt, respectively.
Author: Radoslav Harman [aut],
Lenka Filova [aut, cre]
Maintainer: Lenka Filova <optimaldesignr@gmail.com>
Diff between OptimalDesign versions 1.0.1 dated 2019-12-02 and 1.0.2.1 dated 2025-04-26
DESCRIPTION | 21 ++++++++++++++------- MD5 | 11 ++++++----- NAMESPACE | 2 +- NEWS.md |only R/Fx_glm.R | 2 +- R/od_D_DEL.R | 1 - R/od_RC.R | 2 +- 7 files changed, 23 insertions(+), 16 deletions(-)
Title: Evolutionary Algorithm
Description: Runs an evolutionary algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> .
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.4 dated 2025-01-18 and 1.0.5 dated 2025-04-25
evola-1.0.4/evola/man/fitnessf.Rd |only evola-1.0.4/evola/man/varM.Rd |only evola-1.0.5/evola/ChangeLog | 15 evola-1.0.5/evola/DESCRIPTION | 10 evola-1.0.5/evola/MD5 | 50 +- evola-1.0.5/evola/NAMESPACE | 12 evola-1.0.5/evola/R/AllClass.R |only evola-1.0.5/evola/R/evolafit.R | 493 +++++++++++++++++---------- evola-1.0.5/evola/R/methods.R |only evola-1.0.5/evola/R/plotting_funs.R | 57 +-- evola-1.0.5/evola/R/utlis.R | 214 +++++++++--- evola-1.0.5/evola/inst/doc/evola_intro.R | 339 +++++++++++++------ evola-1.0.5/evola/inst/doc/evola_intro.Rmd | 368 +++++++++++++++----- evola-1.0.5/evola/inst/doc/evola_intro.html | 499 +++++++++++++++++++--------- evola-1.0.5/evola/man/DT_cpdata.Rd | 22 - evola-1.0.5/evola/man/DT_technow.Rd | 22 - evola-1.0.5/evola/man/DT_wheat.Rd | 15 evola-1.0.5/evola/man/addZeros.Rd |only evola-1.0.5/evola/man/bestSol.Rd | 11 evola-1.0.5/evola/man/evolaPop-class.Rd |only evola-1.0.5/evola/man/evolafit.Rd | 171 ++++++--- evola-1.0.5/evola/man/importHaploSparse.Rd |only evola-1.0.5/evola/man/inbFun.Rd |only evola-1.0.5/evola/man/logspace.Rd |only evola-1.0.5/evola/man/nQtl.Rd |only evola-1.0.5/evola/man/ocsFun.Rd |only evola-1.0.5/evola/man/plot.monitor.Rd | 13 evola-1.0.5/evola/man/plot.pareto.Rd | 2 evola-1.0.5/evola/man/regFun.Rd |only evola-1.0.5/evola/man/stan.Rd | 10 evola-1.0.5/evola/man/update.method.Rd |only evola-1.0.5/evola/man/varQ.Rd |only evola-1.0.5/evola/vignettes/evola_intro.Rmd | 368 +++++++++++++++----- 33 files changed, 1911 insertions(+), 780 deletions(-)
Title: Model-Based Geostatistics
Description: Modern model-based geostatistics for point-referenced data. This package provides a
simple interface to run spatial machine learning models and geostatistical models
that estimate a continuous (raster) surface from point-referenced outcomes and,
optionally, a set of raster covariates. The package also includes functions to
summarize raster outcomes by (polygon) region while preserving uncertainty.
Author: Nathaniel Henry [aut, cre] ,
Benjamin Mayala [aut]
Maintainer: Nathaniel Henry <nat@henryspatialanalysis.com>
Diff between mbg versions 1.0.0 dated 2025-04-02 and 1.1.0 dated 2025-04-25
DESCRIPTION | 6 ++--- MD5 | 9 ++++---- R/generate_cell_draws_and_summarize.R | 2 - R/prepare_inla_data_stack.R | 4 ++- README.md | 38 +++++++++++++++++++--------------- man/figures |only 6 files changed, 34 insertions(+), 25 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.2.1 dated 2025-04-24 and 0.2.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ R/lib.R | 6 ++---- R/models.r | 8 +++++++- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel [aut, cre] ,
Romain Francois [aut] ,
Doug Bates [aut] ,
Binxiang Ni [aut],
Conrad Sanderson [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 14.4.1-1 dated 2025-03-28 and 14.4.2-1 dated 2025-04-25
ChangeLog | 26 +++++ DESCRIPTION | 8 - MD5 | 40 ++++----- build/partial.rdb |binary build/vignette.rds |binary configure | 18 ++-- configure.ac | 2 inst/NEWS.Rd | 9 ++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/config.hpp | 12 ++ inst/include/armadillo_bits/def_superlu.hpp | 24 ++--- inst/include/armadillo_bits/glue_times_meat.hpp | 34 +++++++ inst/include/armadillo_bits/include_superlu.hpp | 97 +++++++++++----------- inst/include/armadillo_bits/op_expmat_meat.hpp | 25 ++++- inst/include/armadillo_bits/op_sp_sum_bones.hpp | 8 - inst/include/armadillo_bits/op_sp_sum_meat.hpp | 12 +- inst/include/armadillo_bits/sp_auxlib_meat.hpp | 30 +++--- inst/include/armadillo_bits/translate_superlu.hpp | 12 +- inst/tinytest/test_sparse.R | 5 - 21 files changed, 236 insertions(+), 128 deletions(-)
Title: Oblique Decision Random Forest for Classification and Regression
Description: The oblique decision tree (ODT) uses linear combinations of predictors as partitioning variables in a decision tree. Oblique Decision Random Forest (ODRF) is an ensemble of multiple ODTs generated by feature bagging. Oblique Decision Boosting Tree (ODBT) applies feature bagging during the training process of ODT-based boosting trees to ensemble multiple boosting trees. All three methods can be used for classification and regression, and ODT and ODRF serve as supplements to the classical CART of Breiman (1984) <DOI:10.1201/9781315139470> and Random Forest of Breiman (2001) <DOI:10.1023/A:1010933404324> respectively.
Author: Yu Liu [aut, cre, cph],
Yingcun Xia [aut]
Maintainer: Yu Liu <liuyuchina123@gmail.com>
Diff between ODRF versions 0.0.4 dated 2023-05-28 and 0.0.5 dated 2025-04-25
DESCRIPTION | 18 - MD5 | 114 +++++------ NAMESPACE | 11 + NEWS.md | 9 R/Accuracy.R | 14 - R/ODBT.R |only R/ODRF.R | 49 ++-- R/ODT.R | 268 ++++++++++++++++++--------- R/PPO.R | 6 R/RcppExports.R | 4 R/RotMat.R | 8 R/VarImp.R | 144 +++++++------- R/as_party_ODT.R | 10 - R/best_cut_node.R | 67 +++++- R/body_fat.R | 4 R/defaults.R | 2 R/linear_split.R |only R/online_ODRF.R | 38 +-- R/online_ODT.R | 39 +-- R/plot_Accuracy.R | 22 +- R/plot_ODT.R | 16 - R/plot_ODT_depth.R | 22 +- R/plot_VarImp.R | 28 +- R/plot_prune_ODT.R | 22 +- R/predictTree.R | 21 +- R/predict_ODRF.R | 48 ++-- R/predict_ODT.R | 101 ++++++++-- R/print_ODRF.R | 2 R/print_ODT.R | 26 +- R/prune_ODRF.R | 32 +-- R/prune_ODT.R | 17 - README.md | 106 ++++++---- inst/CITATION | 7 inst/WORDLIST | 8 inst/doc/Oblique-Decision-Random-Forest.R | 37 ++- inst/doc/Oblique-Decision-Random-Forest.Rmd | 37 ++- inst/doc/Oblique-Decision-Random-Forest.html | 265 +++++++++++++------------- man/Accuracy.Rd | 6 man/ODBT.Rd |only man/ODRF.Rd | 4 man/ODT.Rd | 60 +++++- man/PPO.Rd | 4 man/RotMatMake.Rd | 2 man/VarImp.Rd | 16 - man/as.party.ODT.Rd | 2 man/best.cut.node.Rd | 41 +++- man/figures/README-plot-1.png |binary man/plot.Accuracy.Rd | 6 man/plot.ODT.Rd | 2 man/plot.VarImp.Rd | 6 man/predict.ODRF.Rd | 8 man/predict.ODT.Rd | 54 ++++- man/prune.ODRF.Rd | 2 src/BODT.cpp |only src/RcppExports.cpp | 23 ++ tests/spelling.R | 9 tests/testthat/test-ODRF.R | 28 +- tests/testthat/test-ODT.R | 14 - tests/testthat/test-predict_ODT.R | 4 vignettes/Oblique-Decision-Random-Forest.Rmd | 37 ++- 60 files changed, 1204 insertions(+), 746 deletions(-)
Title: Exporting 'flextable' to 'xlsx' Files
Description: Exports 'flextable' objects to 'xlsx' files,
utilizing functionalities provided by 'flextable' and 'openxlsx2'.
Author: Tobias Heidler [aut, cre, cph]
Maintainer: Tobias Heidler <flexlsx@heidler.ovh>
Diff between flexlsx versions 0.3.4 dated 2025-02-26 and 0.3.5 dated 2025-04-25
flexlsx-0.3.4/flexlsx/tests/testthat/test-RcppExports.R |only flexlsx-0.3.5/flexlsx/DESCRIPTION | 10 +++++----- flexlsx-0.3.5/flexlsx/MD5 | 7 +++---- flexlsx-0.3.5/flexlsx/NEWS.md | 5 +++++ flexlsx-0.3.5/flexlsx/R/wb_apply_cell_styles.R | 4 ++-- 5 files changed, 15 insertions(+), 11 deletions(-)
Title: R Interface for the GPlates Web Service and Desktop Application
Description: Query functions to the GPlates <https://www.gplates.org/> Desktop Application and the GPlates Web Service <https://gws.gplates.org/> allow users to reconstruct past positions of geographic entities based on user-selected rotation models without leaving the R running environment. The online method (GPlates Web Service) makes the rotation of static plates, coastlines, and a low number of geographic coordinates available using nothing but an internet connection. The offline method requires an external installation of the GPlates Desktop Application, but allows the efficient batch rotation of thousands of coordinates, Simple Features (sf) and Spatial (sp) objects with custom reconstruction trees and partitioning polygons. Examples of such plate tectonic models are accessible via the chronosphere <https://cran.r-project.org/package=chronosphere>. This R extension is developed under the umbrella of the DFG (Deutsche Forschungsgemeinschaft) Research Unit TERSANE2 (For 2332, [...truncated...]
Author: Adam T. Kocsis [cre, aut] ,
Nussaibah B. Raja [ctb] ,
Simon Williams [ctb] ,
Elizabeth M. Dowding [ctb] ,
Deutsche Forschungsgemeinschaft [fnd],
FAU GeoZentrum Nordbayern [fnd]
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between rgplates versions 0.5.0 dated 2024-09-06 and 0.6.0 dated 2025-04-25
DESCRIPTION | 8 - MD5 | 29 ++++-- NAMESPACE | 6 + NEWS.md | 27 ++++++ R/data.R | 2 R/front_end.R | 4 R/offline.R | 155 +++++++++++++++++++++++++++++++++++-- R/online.R | 46 +++++++++- R/platemodel.R | 15 +++ R/plot_utils.R |only R/plots.R |only R/zzz.R | 7 + data/gws.RData |binary man/figures/subduction_example.png |only man/gws.Rd | 2 man/sawteeth.Rd |only man/subductionlines.Rd |only man/velocities.Rd | 4 18 files changed, 268 insertions(+), 37 deletions(-)
Title: Performs Quality Control, Data Normalization, and Batch Effect
Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch
effect correction operations for 'NanoString nCounter' data, Talhouk
et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are
used to determine which samples passed or failed QC. Gene expression
should first be normalized to housekeeping genes, before a
reference-based approach is used to adjust for batch effects. Raw
NanoString data can be imported in the form of Reporter Code Count
(RCC) files.
Author: Derek Chiu [aut, cre] ,
Aline Talhouk [aut] ,
Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between nanostringr versions 0.5.0 dated 2025-02-05 and 0.6.0 dated 2025-04-25
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++-------- NAMESPACE | 1 NEWS.md | 5 +++ R/HKnorm.R | 2 - R/NanoStringQC.R | 46 ++++++++++++++------------------ R/nanostringr-package.R | 1 R/normalize_pools.R | 27 +++++++++---------- R/normalize_random.R | 12 ++++---- R/read_rcc.R | 68 +++++++++++++++++++++++++++++------------------- R/utils.R | 29 +++++++++----------- inst/doc/Overview.html | 8 ++--- man/rcc.Rd | 1 13 files changed, 124 insertions(+), 110 deletions(-)
Title: Analysis of Geostatistical Data
Description: Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Author: Paulo Justiniano Ribeiro Jr [aut, cre],
Peter Diggle [aut],
Ole Christensen [ctb],
Martin Schlather [ctb],
Roger Bivand [ctb],
Brian Ripley [ctb]
Maintainer: Paulo Justiniano Ribeiro Jr <paulojus@ufpr.br>
Diff between geoR versions 1.9-4 dated 2024-02-15 and 1.9-5 dated 2025-04-25
DESCRIPTION | 42 +++++++++++++++++++++++++++++++----------- MD5 | 4 ++-- man/SIC.Rd | 3 ++- 3 files changed, 35 insertions(+), 14 deletions(-)
Title: Causal Inference Modeling for Estimation of Causal Effects
Description: Provides an array of statistical models common in causal inference such as
standardization, IP weighting, propensity matching, outcome regression, and doubly-robust
estimators. Estimates of the average treatment effects from each model are given with the
standard error and a 95% Wald confidence interval (Hernan, Robins (2020) <https://miguelhernan.org/whatifbook/>).
Author: Joshua Anderson [aut, cre, cph],
Cyril Rakovski [rev],
Yesha Patel [rev],
Erin Lee [rev]
Maintainer: Joshua Anderson <jwanderson198@gmail.com>
Diff between CausalModels versions 0.2.0 dated 2022-11-23 and 0.2.1 dated 2025-04-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/outcome_regression.R | 19 ++++++++++++++----- README.md | 46 +++++++++++++++++++++++++++------------------- 5 files changed, 55 insertions(+), 32 deletions(-)
Title: Working with United States ZIP Code and ZIP Code Tabulation Area
Data
Description: Provides a set of functions for working with American postal codes,
which are known as ZIP Codes. These include accessing ZIP Code to ZIP Code
Tabulation Area (ZCTA) crosswalks, retrieving demographic data for ZCTAs, and
tabulating demographic data for three-digit ZCTAs.
Author: Christopher Prener [aut, cre] ,
Timothy Wiemken [aut] ,
Angela Cook [aut]
Maintainer: Christopher Prener <Christopher.Prener@pfizer.com>
Diff between zippeR versions 0.1.1 dated 2025-02-25 and 0.1.2 dated 2025-04-25
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 4 R/zi_aggregate.R | 182 ++++++++++++++++++++++-------------------- R/zi_crosswalk.R | 4 R/zi_get_demographics.R | 33 ++++--- R/zi_get_geometry.R | 18 ---- R/zi_utils.R | 64 ++++++++++++++ build/vignette.rds |binary inst/doc/converting-zips.Rmd | 2 inst/doc/converting-zips.html | 2 vignettes/converting-zips.Rmd | 2 12 files changed, 204 insertions(+), 135 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals. Based on the
'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but
with a focus on efficiency and simplicity at a cost of flexibility.
Author: Tim Taylor [aut, cre] ,
Jim Hester [aut] ,
Jennifer Bryan [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between super versions 0.1.0 dated 2025-03-11 and 0.1.1 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/glue.R | 2 -- README.md | 2 +- inst/doc/super.Rmd | 2 +- inst/doc/super.html | 34 +++++++++++++++++----------------- src/glue.c | 20 +------------------- src/init.c | 2 -- vignettes/super.Rmd | 2 +- 10 files changed, 37 insertions(+), 55 deletions(-)
Title: Functions for Working with 'Eprime' Text Files
Description: 'Eprime' is a set of programs for administering
psychological experiments by computer. This package provides functions
for loading, parsing, filtering and exporting data in the text files
produced by 'Eprime' experiments.
Author: Tristan Mahr [aut, cre]
Maintainer: Tristan Mahr <tristan.mahr@wisc.edu>
Diff between rprime versions 0.1.2 dated 2020-09-24 and 0.1.3 dated 2025-04-25
DESCRIPTION | 11 MD5 | 28 - NEWS.md | 4 R/to_data_frame.R | 7 build/vignette.rds |binary inst/doc/multiple-files.R | 2 inst/doc/multiple-files.html | 323 +++++++++------- inst/doc/parsing-summary.R | 2 inst/doc/parsing-summary.Rmd | 9 inst/doc/parsing-summary.html | 447 ++++++++++++++-------- inst/doc/quick-start-demo.R | 6 inst/doc/quick-start-demo.html | 810 ++++++++++++++++++++++------------------- man/rprime.Rd | 7 man/to_data_frame.Rd | 8 vignettes/parsing-summary.Rmd | 9 15 files changed, 949 insertions(+), 724 deletions(-)
Title: Synthetic Control Methods with Micro- And Meso-Level Data
Description: A generalization of the 'Synth' package that is
designed for data at a more granular level (e.g., micro-level).
Provides functions to construct weights (including propensity
score-type weights) and run analyses for synthetic control methods
with micro- and meso-level data; see Robbins, Saunders, and Kilmer
(2017) <doi:10.1080/01621459.2016.1213634> and Robbins and Davenport
(2021) <doi:10.18637/jss.v097.i02>.
Author: Michael Robbins [aut, cre],
Steven Davenport [aut]
Maintainer: Michael Robbins <mrobbins@rand.org>
Diff between microsynth versions 2.0.44 dated 2023-06-30 and 2.0.51 dated 2025-04-25
DESCRIPTION | 44 MD5 | 36 NEWS.md | 28 R/microsynth-class.R | 263 -- R/microsynth.R | 2968 +++++++++++++------------- R/miscellaneous.R | 27 R/plot_microsynth.R | 56 R/results.r | 1588 +++++++------ R/weights.r | 2293 ++++++++++---------- build/vignette.rds |binary data/seattledmi.rda |binary inst/doc/aggregating_variables_over_time.html | 642 ++--- inst/doc/ensuring_model_feasibility.html | 718 +++--- inst/doc/introduction.R | 366 +-- inst/doc/introduction.html | 2871 ++++++++++++------------- man/microsynth.Rd | 35 man/plot_microsynth.Rd | 9 man/print.microsynth.Rd | 28 man/summary.microsynth.Rd | 30 19 files changed, 6057 insertions(+), 5945 deletions(-)
Title: Discontinuous Hamiltonian Monte Carlo with Varying Trajectory
Length
Description: Hamiltonian Monte Carlo for both continuous and discontinuous
posterior distributions with customisable trajectory length
termination criterion. See Nishimura et al. (2020) <doi:10.1093/biomet/asz083> for
the original Discontinuous Hamiltonian Monte Carlo,
Hoffman et al. (2014) <doi:10.48550/arXiv.1111.4246> and Betancourt (2016)
<doi:10.48550/arXiv.1601.00225> for the definition of possible Hamiltonian
Monte Carlo termination criteria.
Author: Paolo Manildo [aut, cre]
Maintainer: Paolo Manildo <paolo.manildo@phd.unipd.it>
Diff between XDNUTS versions 1.5.6 dated 2025-01-28 and 1.6 dated 2025-04-25
DESCRIPTION | 8 MD5 | 17 R/RcppExports.R | 35 R/interface.R | 39 build/partial.rdb |binary inst/doc/Tutorial_for_main_functions.R | 4 man/print.XDNUTS.Rd | 2 man/trajectories.Rd |only src/RcppExports.cpp | 20 src/dnuts.cpp | 1458 +++++++++++++++++++++++++++++++++ 10 files changed, 1565 insertions(+), 18 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 1.7.1 dated 2024-03-25 and 1.8.2 dated 2025-04-25
skpr-1.7.1/skpr/R/gen_momentsmatrix.R |only skpr-1.7.1/skpr/R/parallel_search_progress.R |only skpr-1.7.1/skpr/R/shiny_server_code.R |only skpr-1.7.1/skpr/R/shiny_ui_code.R |only skpr-1.7.1/skpr/man/gen_momentsmatrix.Rd |only skpr-1.8.2/skpr/DESCRIPTION | 14 skpr-1.8.2/skpr/MD5 | 144 skpr-1.8.2/skpr/R/add_ci_bounds_mc_power.R | 10 skpr-1.8.2/skpr/R/anticoef_from_delta.R | 43 skpr-1.8.2/skpr/R/anticoef_from_delta_surv.R | 33 skpr-1.8.2/skpr/R/calc_conservative_anticoef.R | 4 skpr-1.8.2/skpr/R/calc_interaction_degrees.R | 99 skpr-1.8.2/skpr/R/calcnoncentralparam.R | 17 skpr-1.8.2/skpr/R/calculate_block_nesting.R | 14 skpr-1.8.2/skpr/R/calculate_convex_hull_moment_matrix.R |only skpr-1.8.2/skpr/R/calculate_degrees_of_freedom.R | 177 skpr-1.8.2/skpr/R/calculate_gefficiency.R | 88 skpr-1.8.2/skpr/R/calculate_level_vector.R | 21 skpr-1.8.2/skpr/R/calculate_power_curves.R | 631 +- skpr-1.8.2/skpr/R/calculate_split_columns.R | 27 skpr-1.8.2/skpr/R/calculate_v_from_blocks.R | 25 skpr-1.8.2/skpr/R/calculatepower.R | 11 skpr-1.8.2/skpr/R/check_for_suggest_packages.R | 18 skpr-1.8.2/skpr/R/constructRunMatrix.R | 2 skpr-1.8.2/skpr/R/contr.simplex.R | 8 skpr-1.8.2/skpr/R/convert_blockcolumn_rownames.R | 142 skpr-1.8.2/skpr/R/convert_model_dots.R | 98 skpr-1.8.2/skpr/R/convert_rownames_to_covariance.R | 48 skpr-1.8.2/skpr/R/disallowed_combinations.R | 26 skpr-1.8.2/skpr/R/effectpower.R | 45 skpr-1.8.2/skpr/R/effectpowermc.R | 136 skpr-1.8.2/skpr/R/eval_design.R | 835 +- skpr-1.8.2/skpr/R/eval_design_custom_mc.R | 287 skpr-1.8.2/skpr/R/eval_design_mc.R | 1330 ++-- skpr-1.8.2/skpr/R/eval_design_survival_mc.R | 358 - skpr-1.8.2/skpr/R/extractPvalues.R | 6 skpr-1.8.2/skpr/R/gen_anticoef.R | 7 skpr-1.8.2/skpr/R/gen_binomial_anticoef.R | 4 skpr-1.8.2/skpr/R/gen_design.R | 1642 +++-- skpr-1.8.2/skpr/R/gen_exponential_anticoef.R | 8 skpr-1.8.2/skpr/R/gen_momentsmatrix_ideal.R |only skpr-1.8.2/skpr/R/gen_poisson_anticoef.R | 6 skpr-1.8.2/skpr/R/generate_noise_block.R | 11 skpr-1.8.2/skpr/R/genparammatrix.R | 4 skpr-1.8.2/skpr/R/get_attribute.R | 54 skpr-1.8.2/skpr/R/get_block_groups.R | 4 skpr-1.8.2/skpr/R/get_moment_matrix.R |only skpr-1.8.2/skpr/R/get_optimality.R | 89 skpr-1.8.2/skpr/R/input_validation.R | 9 skpr-1.8.2/skpr/R/is_intralayer_interaction.R | 51 skpr-1.8.2/skpr/R/methods.R | 364 - skpr-1.8.2/skpr/R/normalize_design.R | 24 skpr-1.8.2/skpr/R/normalize_numeric_runmatrix.R | 13 skpr-1.8.2/skpr/R/parameterpower.R | 48 skpr-1.8.2/skpr/R/permutation_functions.R | 22 skpr-1.8.2/skpr/R/plot_correlations.R | 124 skpr-1.8.2/skpr/R/plot_fds.R | 114 skpr-1.8.2/skpr/R/quad.R | 19 skpr-1.8.2/skpr/R/rearrange_formula_by_order.R | 24 skpr-1.8.2/skpr/R/reduceRunMatrix.R | 29 skpr-1.8.2/skpr/R/remove_skpr_blockcols.R | 2 skpr-1.8.2/skpr/R/set_up_progressr_handler.R | 34 skpr-1.8.2/skpr/R/skprGUI.R | 4973 +++++++++------- skpr-1.8.2/skpr/R/skprGUI_dynamic_ui_elements.R | 293 skpr-1.8.2/skpr/R/startupmessage.R | 4 skpr-1.8.2/skpr/R/zzz.R | 17 skpr-1.8.2/skpr/man/convhull_halfspace.Rd |only skpr-1.8.2/skpr/man/detect_disallowed_combinations.Rd |only skpr-1.8.2/skpr/man/eval_design.Rd | 13 skpr-1.8.2/skpr/man/eval_design_mc.Rd | 14 skpr-1.8.2/skpr/man/gen_design.Rd | 11 skpr-1.8.2/skpr/man/gen_exponential_anticoef.Rd | 2 skpr-1.8.2/skpr/man/gen_momentsmatrix_constrained.Rd |only skpr-1.8.2/skpr/man/gen_momentsmatrix_ideal.Rd |only skpr-1.8.2/skpr/man/get_moment_matrix.Rd |only skpr-1.8.2/skpr/man/interpolate_convex_hull.Rd |only skpr-1.8.2/skpr/src/RcppExports.cpp | 2 skpr-1.8.2/skpr/src/genOptimalDesign.cpp | 20 skpr-1.8.2/skpr/src/genSplitPlotOptimalDesign.cpp | 4 skpr-1.8.2/skpr/src/getBlockedOptimalDesign.cpp | 6 80 files changed, 8421 insertions(+), 4341 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19>
for details on applying this package while Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> explain details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Lukas A. Widmer [ctb] ,
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.8-1 dated 2025-01-21 and 1.8-2 dated 2025-04-25
DESCRIPTION | 12 MD5 | 233 +++++---- NAMESPACE | 6 NEWS.md | 13 R/AS.R | 2 R/BinaryExactCI.R | 7 R/EM_bmm_ab.R | 101 +++- R/EM_bmm_mun.R | 81 ++- R/EM_gmm.R | 79 ++- R/EM_mnmm.R | 128 ++++- R/EM_msmm.R | 70 ++ R/EM_plot.R | 112 +++- R/KLdivmix.R | 12 R/RBesT-package.R | 58 +- R/SimSum.R | 10 R/automixfit.R | 39 + R/colVars.R | 10 R/colitis.R | 2 R/crohn.R | 2 R/dBetaBinomial.R | 11 R/decision1S.R | 18 R/decision1S_boundary.R | 41 + R/decision2S.R | 57 +- R/decision2S_boundary.R | 131 ++++- R/dlink.R | 38 + R/forest_plot.R | 84 ++- R/gMAP.R | 506 ++++++++++++++------- R/get_color.R | 10 R/integrate_logit_log.R | 104 +++- R/knn.R | 24 - R/likelihood.R | 4 R/lodds.R | 12 R/mix.R | 183 +++++-- R/mixbeta.R | 17 R/mixcombine.R | 12 R/mixdiff.R | 72 ++- R/mixess.R | 123 +++-- R/mixfit.R | 68 +- R/mixgamma.R | 32 - R/mixjson.R |only R/mixmode.R | 7 R/mixmvnorm.R | 208 +++++++- R/mixnorm.R | 23 R/mixplot.R | 68 ++ R/mixstanvar.R | 164 ++++-- R/oc1S.R | 12 R/oc2S.R | 85 ++- R/plot_gMAP.R | 131 ++++- R/pos1S.R | 10 R/pos2S.R | 79 ++- R/postmix.R | 57 +- R/preddist.R | 11 R/predict_gMAP.R | 64 ++ R/robustify.R | 61 +- R/support.R | 3 R/sysdata.rda |binary R/transplant.R | 2 R/uniroot_int.R | 19 R/zzz.R | 10 data/AS.rda |binary data/colitis.rda |binary data/crohn.rda |binary data/transplant.rda |binary inst/doc/RBesT.pdf |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 98 ++-- inst/doc/settings-knitr.txt | 2 inst/sbc/sbc_report.html | 927 ++++++++++++++++----------------------- man/AS.Rd | 8 man/BinaryExactCI.Rd | 4 man/RBesT-package.Rd | 20 man/SimSum.Rd | 2 man/automixfit.Rd | 2 man/colitis.Rd | 6 man/crohn.Rd | 6 man/decision1S.Rd | 4 man/decision1S_boundary.Rd | 2 man/ess.Rd | 20 man/figures |only man/forest_plot.Rd | 8 man/gMAP.Rd | 15 man/likelihood.Rd | 4 man/lodds.Rd | 12 man/mix.Rd | 13 man/mixbeta.Rd | 1 man/mixcombine.Rd | 3 man/mixdiff.Rd | 4 man/mixfit.Rd | 8 man/mixgamma.Rd | 1 man/mixjson.Rd |only man/mixmvnorm.Rd | 65 +- man/mixnorm.Rd | 1 man/mixplot.Rd | 7 man/mixstanvar.Rd | 54 +- man/oc1S.Rd | 4 man/oc2S.Rd | 4 man/plot.EM.Rd | 6 man/plot.gMAP.Rd | 8 man/pos2S.Rd | 4 man/postmix.Rd | 6 man/preddist.Rd | 4 man/predict.gMAP.Rd | 4 man/robustify.Rd | 4 man/transplant.Rd | 6 src/stanExports_gMAP.cc | 34 - tests/testthat/helper-utils.R | 24 - tests/testthat/test-EM.R | 102 ++-- tests/testthat/test-gMAP.R | 302 ++++++++---- tests/testthat/test-mixdiff.R | 49 +- tests/testthat/test-mixdist.R | 419 +++++++++++++++++ tests/testthat/test-mixjson.R |only tests/testthat/test-mixstanvar.R | 240 ++++++++-- tests/testthat/test-oc1S.R | 22 tests/testthat/test-oc2S.R | 328 +++++++++++-- tests/testthat/test-pos2S.R | 84 ++- tests/testthat/test-preddist.R | 18 tests/testthat/test-utils.R | 359 ++++++++++++--- vignettes/settings-knitr.txt | 2 118 files changed, 4842 insertions(+), 2028 deletions(-)
Title: Adaptive, Sine-Multitaper Power Spectral Density and Cross
Spectrum Estimation
Description: Produces power spectral density estimates through iterative
refinement of the optimal number of sine-tapers at each frequency. This
optimization procedure is based on the method of Riedel and Sidorenko
(1995), which minimizes the Mean Square Error (sum of variance and bias)
at each frequency, but modified for computational stability. The same
procedure can now be used to calculate the cross spectrum (multivariate
analyses).
Author: Andrew J. Barbour [aut, cre] ,
Jonathan Kennel [aut] ,
Robert L. Parker [aut]
Maintainer: Andrew J. Barbour <andy.barbour@gmail.com>
Diff between psd versions 2.1.1 dated 2022-01-31 and 2.1.2 dated 2025-04-25
DESCRIPTION | 15 ++-- MD5 | 41 ++++++----- R/func_riedsid.R | 2 R/func_tapers.R | 2 R/psd-package.R | 5 - README.md | 12 ++- build/partial.rdb |only build/vignette.rds |binary inst/NEWS.Rd | 18 ++--- inst/doc/fftw.R | 152 ++++++++++++++++++++++---------------------- inst/doc/fftw.pdf |binary inst/doc/multivariate.pdf |binary inst/doc/normalization.Rnw | 2 inst/doc/normalization.pdf |binary inst/doc/psd_overview.R | 2 inst/doc/psd_overview.pdf |binary man/psd-package.Rd | 17 ++++ man/riedsid.Rd | 2 man/wipp30.Rd | 3 src/resample_fft.cpp | 5 - tests/testthat/Rplots.pdf |binary vignettes/normalization.Rnw | 2 22 files changed, 151 insertions(+), 129 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.5 dated 2024-06-24 and 1.6 dated 2025-04-25
DESCRIPTION | 10 +++--- MD5 | 52 ++++++++++++++++++------------------ NAMESPACE | 3 ++ NEWS.md | 6 +++- R/SampStop.R |only build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.popA.RData |binary data/TPV.RData |binary data/Test_Data_US.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Design-effects.html | 8 ++--- inst/doc/Distance-and-MOS-PSUs.html | 14 ++++----- inst/doc/Select-samsize-fcns.html | 2 - inst/doc/Singlestage-samsize.html | 8 ++--- inst/doc/Varcomps-multistage.html | 6 ++-- man/BW2stageSRS.Rd | 4 +- man/SampStop.Rd |only man/nAuditAttr.Rd | 4 +- man/smho.N874.Rd | 2 - 28 files changed, 64 insertions(+), 55 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.9-2 dated 2025-04-07 and 0.9-3 dated 2025-04-25
DESCRIPTION | 8 MD5 | 78 NEWS.md | 9 R/blrm_exnex.R | 847 ++- R/blrm_formula_linear.R | 80 R/blrm_formula_saturating.R | 108 R/blrm_trial.R | 611 ++ R/critical_quantile.R | 148 R/diagnostics.R | 5 R/example_model.R | 5 R/lodds.R | 8 R/nsamples.R | 5 R/plot_blrm.R | 618 +- R/posterior.R | 272 - R/posterior_linpred.R | 32 R/posterior_predict.R | 24 R/pp_data.R | 56 R/predictive_interval.R | 22 R/prior_summary.R | 188 R/summary.R | 182 R/sysdata.rda |binary R/update.R | 31 R/zzz.R | 10 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.html | 12 inst/doc/map_approach.html | 12 man/blrm_exnex.Rd | 2 man/lodds.Rd | 8 tests/testthat/helper-load_gold.R | 10 tests/testthat/helper-sampling.R | 120 tests/testthat/helper-trial_examples.R | 5 tests/testthat/test-blrm_exnex.R | 3938 ++++++++++++------ tests/testthat/test-blrm_trial.R | 1068 +++- tests/testthat/test-critical_quantile.R | 104 tests/testthat/test-examples.R | 46 tests/testthat/test-plot_toxicity_curve.R | 379 - tests/testthat/test-plot_toxicity_intervals.R | 217 tests/testthat/test-plot_toxicity_intervals_stacked.R | 473 +- tests/testthat/test-posterior.R | 195 tests/testthat/test-sbc.R | 32 40 files changed, 6923 insertions(+), 3045 deletions(-)
Title: Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Description: Processing of large-in-memory/large-on disk rasters and spatial
vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in
the 'terra' package are recreated. Processing of medium-sized and smaller
spatial objects will nearly always be faster using 'terra' or 'sf', but
for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster.
To use most of the functions, you must have the stand-alone version (not
the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Author: Adam B. Smith [cre, aut]
Maintainer: Adam B. Smith <adam.smith@mobot.org>
Diff between fasterRaster versions 8.4.0.5 dated 2025-02-25 and 8.4.0.7 dated 2025-04-25
DESCRIPTION | 12 +++++----- MD5 | 44 +++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md | 10 +++++++- R/03_options.r | 1 R/dim.r | 11 +++++++++ R/extract.r | 2 - R/fast.r | 11 +++++---- R/mow.r | 8 +++--- R/plot.r | 9 +++---- R/plotRGB.r | 7 +++--- R/subset_single_bracket.r | 3 +- README.md | 4 +-- inst/doc/GRasters.html | 4 +-- inst/doc/addons.html | 4 +-- inst/doc/fasterRaster.html | 23 ++++++++++--------- inst/doc/faster_fasterRaster.html | 4 +-- inst/doc/hidden_functions.html | 4 +-- inst/doc/projects_mapsets.html | 4 +-- inst/doc/regions.html | 4 +-- inst/doc/three_d_objects.html | 4 +-- inst/pkgdown.yml | 4 +-- man/mow.Rd | 7 +++--- 23 files changed, 104 insertions(+), 81 deletions(-)
Title: Small Area Estimation for Key Health and Demographic Indicators
from Household Surveys
Description: Enables small area estimation (SAE) of health and demographic indicators in low- and middle-income countries (LMICs). It powers an R 'shiny' application that helps public health analysts, policymakers, and researchers generate subnational estimates and prevalence maps for 150+ binary indicators from Demographic and Health Surveys (DHS). Basing its core SAE analysis workflow on the 'surveyPrev' package, the app ensures methodological rigor through guided model selection, automated fitting, and interactive visualization. For more details, visit <https://sae4health.stat.uw.edu/>.
Author: Yunhan Wu [cre, aut],
Qianyu Dong [aut],
Zehang R Li [aut],
Jon Wakefield [aut]
Maintainer: Yunhan Wu <wu-thomas@outlook.com>
Diff between sae4health versions 1.2.1 dated 2025-04-01 and 1.2.2 dated 2025-04-25
DESCRIPTION | 6 MD5 | 26 +- R/app_server.R | 182 ++++++++-------- R/fct_analysis_helpers.R | 12 - R/fct_dat_input_helpers.R | 6 R/fct_helpers.R | 7 R/mod_landing_page.R | 196 ++++++++++++++--- R/mod_model_selection.R | 300 +++++++++++++++++++++++++- R/mod_survey_dat_input.R | 498 ++++++++++++++++++++++++++++++++------------ R/prepare_preload_dat.R | 41 +-- data/DHS_api_est.rda |binary data/indicator_list_all.rda |binary data/indicator_list_new.rda |binary data/match_all_result.rda |binary 14 files changed, 969 insertions(+), 305 deletions(-)
Title: Risk Calculator for Cardiovascular Disease in Japan
Description: A calculation tool to obtain the 10-year risk of cardiovascular disease from various risk models (Hisayama, Suita, EPOCH Japan).
Author: Hiroshi Okumiyama [aut, cre],
Ryosuke Fujii [aut]
Maintainer: Hiroshi Okumiyama <xzxz2019@iCloud.com>
Diff between Jcvrisk versions 0.1.1 dated 2025-04-18 and 0.1.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/02_suita_wECG.R | 2 +- R/03_suita_woECG.R | 2 +- 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre],
Xiaoqiao Xu [aut],
Prajkta Kallurkar [aut],
Ana Patricia Balbon [aut],
Maria T Secara [aut],
Adam Taback [aut],
Denise Sabac [aut],
Nicholas Chan [aut],
Shihao Ma [aut],
Bo Wang [aut],
Daniel Felsky [aut],
Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Diff between metasnf versions 2.0.6 dated 2025-03-25 and 2.1.1 dated 2025-04-25
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metasnf-2.1.1/metasnf/R/feature_plots.R | 28 metasnf-2.1.1/metasnf/R/features.R | 4 metasnf-2.1.1/metasnf/R/get_representative_solutions.R | 2 metasnf-2.1.1/metasnf/R/heatmaps.R | 1350 +++------- metasnf-2.1.1/metasnf/R/label_propagation.R | 6 metasnf-2.1.1/metasnf/R/manhattan_plot.R | 4 metasnf-2.1.1/metasnf/R/merge.R | 237 + metasnf-2.1.1/metasnf/R/n_features.R | 2 metasnf-2.1.1/metasnf/R/n_observations.R | 2 metasnf-2.1.1/metasnf/R/nclust_estimation.R | 5 metasnf-2.1.1/metasnf/R/nmi.R | 174 - metasnf-2.1.1/metasnf/R/plot.R |only metasnf-2.1.1/metasnf/R/print.R | 658 ++-- metasnf-2.1.1/metasnf/R/quality_measures.R | 40 metasnf-2.1.1/metasnf/R/rbind.R | 68 metasnf-2.1.1/metasnf/R/settings_df.R | 27 metasnf-2.1.1/metasnf/R/signal.R | 8 metasnf-2.1.1/metasnf/R/snf_config.R | 2 metasnf-2.1.1/metasnf/R/solutions_df.R | 2 metasnf-2.1.1/metasnf/R/str.R |only metasnf-2.1.1/metasnf/R/summary.R | 260 + metasnf-2.1.1/metasnf/R/summary_features.R | 2 metasnf-2.1.1/metasnf/R/t.R | 138 - 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metasnf-2.1.1/metasnf/man/generate_distance_metrics_list.Rd | 1 metasnf-2.1.1/metasnf/man/generate_settings_matrix.Rd | 1 metasnf-2.1.1/metasnf/man/get_cluster_df.Rd | 1 metasnf-2.1.1/metasnf/man/get_cluster_solutions.Rd | 8 metasnf-2.1.1/metasnf/man/get_clusters.Rd | 1 metasnf-2.1.1/metasnf/man/get_dl_uids.Rd | 1 metasnf-2.1.1/metasnf/man/get_matrix_order.Rd | 2 metasnf-2.1.1/metasnf/man/gselect.Rd | 4 metasnf-2.1.1/metasnf/man/income.Rd | 4 metasnf-2.1.1/metasnf/man/label_propagate.Rd | 6 metasnf-2.1.1/metasnf/man/mc_manhattan_plot.Rd | 2 metasnf-2.1.1/metasnf/man/merge.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/merge.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/merge.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.settings_df.Rd |only metasnf-2.1.1/metasnf/man/merge.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/merge.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/merge.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/metasnf_defunct.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_deprecated.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_error.Rd | 4 metasnf-2.1.1/metasnf/man/metasnf_warning.Rd | 4 metasnf-2.1.1/metasnf/man/mock_ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/mock_clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/mock_data_list.Rd |only metasnf-2.1.1/metasnf/man/mock_dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/mock_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_mc_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_rep_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_settings_df.Rd |only metasnf-2.1.1/metasnf/man/mock_snf_config.Rd |only metasnf-2.1.1/metasnf/man/mock_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/mock_weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/n_features.Rd | 1 metasnf-2.1.1/metasnf/man/n_observations.Rd | 1 metasnf-2.1.1/metasnf/man/not_shown_message.Rd | 4 metasnf-2.1.1/metasnf/man/ord_reg_pval.Rd | 2 metasnf-2.1.1/metasnf/man/pl.Rd |only metasnf-2.1.1/metasnf/man/plot.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/plot.data_list.Rd |only metasnf-2.1.1/metasnf/man/plot.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/plot.snf_config.Rd |only metasnf-2.1.1/metasnf/man/plot.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/prefix_dll_uid.Rd | 2 metasnf-2.1.1/metasnf/man/print.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/pubertal.Rd | 2 metasnf-2.1.1/metasnf/man/quality_measures.Rd | 2 metasnf-2.1.1/metasnf/man/random_removal.Rd | 3 metasnf-2.1.1/metasnf/man/rbind.ext_solutions_df.Rd | 4 metasnf-2.1.1/metasnf/man/rbind.solutions_df.Rd | 4 metasnf-2.1.1/metasnf/man/rbind.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/rbind.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/remove_dll_incomplete.Rd | 3 metasnf-2.1.1/metasnf/man/rename_dl.Rd | 2 metasnf-2.1.1/metasnf/man/resample.Rd | 2 metasnf-2.1.1/metasnf/man/settings_df.Rd | 4 metasnf-2.1.1/metasnf/man/snf_config.Rd | 4 metasnf-2.1.1/metasnf/man/snf_scheme.Rd | 2 metasnf-2.1.1/metasnf/man/str.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/str.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/str.data_list.Rd |only metasnf-2.1.1/metasnf/man/str.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/str.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.settings_df.Rd |only metasnf-2.1.1/metasnf/man/str.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/str.snf_config.Rd |only metasnf-2.1.1/metasnf/man/str.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/str.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/subc_v.Rd | 2 metasnf-2.1.1/metasnf/man/subsample_dl.Rd | 24 metasnf-2.1.1/metasnf/man/subsample_pairwise_aris.Rd | 75 metasnf-2.1.1/metasnf/man/summarize_clust_fns_list.Rd | 5 metasnf-2.1.1/metasnf/man/summarize_dfl.Rd | 11 metasnf-2.1.1/metasnf/man/summarize_dl.Rd | 1 metasnf-2.1.1/metasnf/man/summary.ari_matrix.Rd |only metasnf-2.1.1/metasnf/man/summary.clust_fns_list.Rd |only metasnf-2.1.1/metasnf/man/summary.dist_fns_list.Rd |only metasnf-2.1.1/metasnf/man/summary.ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.settings_df.Rd |only metasnf-2.1.1/metasnf/man/summary.sim_mats_list.Rd |only metasnf-2.1.1/metasnf/man/summary.snf_config.Rd |only metasnf-2.1.1/metasnf/man/summary.solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.t_ext_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.t_solutions_df.Rd |only metasnf-2.1.1/metasnf/man/summary.weights_matrix.Rd |only metasnf-2.1.1/metasnf/man/summary_features.Rd | 1 metasnf-2.1.1/metasnf/tests/testthat/test-batch_snf.R | 5 metasnf-2.1.1/metasnf/vignettes/a_complete_example.Rmd | 43 metasnf-2.1.1/metasnf/vignettes/clustering_algorithms.Rmd | 13 metasnf-2.1.1/metasnf/vignettes/label_propagation.Rmd | 121 metasnf-2.1.1/metasnf/vignettes/nmi_scores.Rmd | 4 233 files changed, 4212 insertions(+), 3916 deletions(-)
Title: Standardized Git Repository Data
Description: Obtain standardized data from multiple 'Git' services, including 'GitHub' and 'GitLab'.
Designed to be 'Git' service-agnostic, this package assists teams with activities spread across various
'Git' platforms by providing a unified way to access repository data.
Author: Maciej Banas [aut, cre],
Kamil Koziej [aut],
Karolina Marcinkowska [aut],
Matt Secrest [aut]
Maintainer: Maciej Banas <banasmaciek@gmail.com>
Diff between GitStats versions 2.3.0 dated 2025-04-03 and 2.3.1 dated 2025-04-25
DESCRIPTION | 6 MD5 | 78 ++--- NEWS.md | 8 R/EngineGraphQLGitHub.R | 52 ++- R/EngineGraphQLGitLab.R | 136 +++++---- R/EngineRestGitLab.R | 264 +++++++++++------- R/GQLQueryGitLab.R | 5 R/GitHost.R | 184 ++++++++---- R/GitHostGitHub.R | 5 R/GitHostGitLab.R | 85 +++++ R/GitStats.R | 120 ++++---- R/error_handlers.R |only inst/get_orgs_workflow.R | 6 inst/roche/roche_get_issues.R |only inst/roche/roche_get_orgs.R | 3 inst/roche/roche_get_repos_with_R_package.R | 25 + inst/roche/roche_get_repos_workflow.R | 11 tests/testthat/_snaps/00-get_orgs-GitLab.md | 66 ++++ tests/testthat/_snaps/01-get_repos-GitLab.md | 30 ++ tests/testthat/_snaps/01-get_repos-GitStats.md | 8 tests/testthat/_snaps/02-get_commits-GitStats.md | 9 tests/testthat/_snaps/04-get_files_content-GitLab.md | 2 tests/testthat/_snaps/06-get_issues-GitStats.md | 9 tests/testthat/_snaps/get_release-GitStats.md | 9 tests/testthat/_snaps/get_repos_with_R_packages.md | 12 tests/testthat/helper-fixtures.R | 71 ++++ tests/testthat/test-00-get_orgs-GitLab.R | 262 ++++++++++++++++++ tests/testthat/test-01-get_repos-GitHub.R | 11 tests/testthat/test-01-get_repos-GitLab.R | 274 +++++++++++++++++-- tests/testthat/test-01-get_repos-GitStats.R | 15 + tests/testthat/test-02-get_commits-GitLab.R | 7 tests/testthat/test-02-get_commits-GitStats.R | 17 + tests/testthat/test-03-get_files_structure-GitHub.R | 5 tests/testthat/test-03-get_files_structure-GitLab.R | 4 tests/testthat/test-04-get_files_content-GitHub.R | 1 tests/testthat/test-04-get_files_content-GitLab.R | 8 tests/testthat/test-06-get_issues-GitStats.R | 29 +- tests/testthat/test-get_release-GitStats.R | 17 + tests/testthat/test-get_repos_with_R_packages.R | 34 -- tests/testthat/test-get_urls_repos-GitLab.R | 6 tests/testthat/test-helpers.R | 4 41 files changed, 1458 insertions(+), 440 deletions(-)
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large)
Data Analysis
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) (fast) simulation of random fields, b) inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Flexible covariance models for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. Se [...truncated...]
Author: Moreno Bevilacqua [aut, cre, cph],
Victor Morales-Onate [ctb],
Francisco Cuevas-Pacheco [ctb],
Christian Caamano-Carrillo [ctb]
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Diff between GeoModels versions 2.1.1 dated 2025-04-13 and 2.1.2 dated 2025-04-25
DESCRIPTION | 8 MD5 | 74 - R/GeoCV.R | 442 +++++--- R/GeoCovariogram.r | 2 R/GeoCovmatrix.r | 4 R/GeoDoScores.R | 2 R/GeoFit.r | 51 R/GeoFit2.R | 8 R/GeoKrig.r | 24 R/GeoKrigloc.R | 146 +- R/GeoLik.r | 322 +++--- R/GeoNA.R | 171 ++- R/GeoNeighIndex.R | 359 +++--- R/GeoNeighbSelect.R | 32 R/GeoNeighborhood.R | 218 +++- R/GeoResiduals.r | 23 R/GeoScatterplot.R | 28 R/GeoSim.r | 3 R/GeoSimapprox.r | 1 R/GeoWls.r | 2 R/Geovarestbootstrap.R | 360 +++--- R/Utility.r | 76 + data/Jamaicatemp.RData |binary data/anomalies.rda |binary data/austemp.rda |binary data/madagascartemp.rda |binary data/spanish_wind.rda |binary data/winds.coords.rda |binary data/winds.rda |binary man/GeoNeighborhood.Rd | 6 man/GeoResiduals.Rd | 2 src/CompositeLikelihood2.c | 2136 +++++++++++++++++++++++++++-------------- src/CompositeLikelihoodCond2.c | 2087 ++++++++++++++++++++++++---------------- src/Distributions.c | 1914 ++++++++++++++++++++---------------- src/GeoModels_init.c | 15 src/Utility.c | 8 src/header.h | 2 src/weightedleastsquare.c | 6 38 files changed, 5224 insertions(+), 3308 deletions(-)
Title: NCA Calculations and Population Model Diagnosis
Description: A flexible tool that can perform
(i) traditional non-compartmental analysis (NCA) and
(ii) Simulation-based posterior predictive checks for population
pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using
NCA metrics. The methods are described in Acharya et al. (2016)
<doi:10.1016/j.cmpb.2016.01.013>.
Author: Chayan Acharya [aut],
Gulbeyaz Y. Turkyilmaz [aut],
Siv Jonsson [aut],
Mats O. Karlsson [aut],
Andrew C. Hooker [aut, cre]
Maintainer: Andrew C. Hooker <andrew.hooker@uu.se>
Diff between ncappc versions 0.3.0 dated 2018-08-24 and 1.0.0 dated 2025-04-25
DESCRIPTION | 41 - MD5 | 68 +- NAMESPACE | 3 NEWS.md | 17 R/est.nca.R | 4 R/estimate_nca_tidy.R | 32 + R/hist_mean_var.R | 39 + R/hist_mean_var_plot.R | 43 + R/nca.check.obs.R | 4 R/nca_ind_data.R | 2 R/ncappc.R | 4 R/read_nm_table.R | 55 +- R/zzz.R | 7 README.md | 86 ++- build/vignette.rds |binary inst/CITATION | 28 - inst/doc/ncappc-vignette.R | 12 inst/doc/ncappc-vignette.html | 896 +++++++++++++++++++++++++++-------- inst/misc/ncappcReport-NCA-NOPPC.Rnw | 4 inst/misc/ncappcReport-NCA-PPC.Rnw | 4 inst/misc/ncappcReport-NCA.Rnw | 4 man/dv.plot.Rd | 32 - man/est.nca.Rd | 30 - man/histobs.plot.Rd | 11 man/histpop.plot.Rd | 12 man/nca.check.obs.Rd | 42 + man/nca.check.sim.Rd | 28 - man/nca.deviation.plot.Rd | 11 man/nca.ind.data.Rd | 18 man/nca.npde.plot.Rd | 10 man/nca.pde.deviation.outlier.Rd | 18 man/nca_ind_data.Rd | 17 man/ncappc.Rd | 83 ++- man/read_nm_table.Rd | 13 tests/testthat/test-ncappc.R | 46 - 35 files changed, 1310 insertions(+), 414 deletions(-)
Title: Automatic Replication Tools for Meta-Analysis
Description: Provides a unified and straightforward interface for performing a variety of meta-analysis methods directly from user data. Users can input a data frame, specify key parameters, and effortlessly execute and compare multiple common meta-analytic models. Designed for immediate usability, the package facilitates transparent, reproducible research without manual implementation of each analytical method. Ideal for researchers aiming for efficiency and reproducibility, it streamlines workflows from data preparation to results interpretation.
Author: Petr Čala [aut, cre]
Maintainer: Petr Čala <61505008@fsv.cuni.cz>
Diff between artma versions 0.1.19 dated 2025-04-12 and 0.2.1 dated 2025-04-25
artma-0.1.19/artma/R/setup.R |only artma-0.1.19/artma/inst/artma/data/clean.R |only artma-0.1.19/artma/inst/artma/libs/logs |only artma-0.1.19/artma/inst/artma/testing/test_const.R |only artma-0.1.19/artma/inst/artma/testing/test_utils.R |only artma-0.1.19/artma/man/artma.setup.Rd |only artma-0.1.19/artma/man/ensure_valid_boxpath.Rd |only artma-0.1.19/artma/man/static_setup.Rd |only artma-0.1.19/artma/tests/E2E/test_installation.R |only artma-0.2.1/artma/DESCRIPTION | 14 artma-0.2.1/artma/MD5 | 123 ++-- artma-0.2.1/artma/NAMESPACE | 3 artma-0.2.1/artma/NEWS.md |only artma-0.2.1/artma/R/aaa.R | 50 - artma-0.2.1/artma/R/data_config.R |only artma-0.2.1/artma/R/dummy_functions.R | 10 artma-0.2.1/artma/R/globals.R | 30 - artma-0.2.1/artma/R/main.R | 16 artma-0.2.1/artma/R/methods.R | 6 artma-0.2.1/artma/R/options.R | 167 +++-- artma-0.2.1/artma/R/run.R | 29 - artma-0.2.1/artma/R/zzz.R |only artma-0.2.1/artma/build/vignette.rds |binary artma-0.2.1/artma/inst/artma/calc/dof.R | 3 artma-0.2.1/artma/inst/artma/calc/index.R |only artma-0.2.1/artma/inst/artma/calc/meta.R |only artma-0.2.1/artma/inst/artma/calc/pcc.R | 21 artma-0.2.1/artma/inst/artma/const.R | 50 + artma-0.2.1/artma/inst/artma/data/compute.R |only artma-0.2.1/artma/inst/artma/data/fill.R | 65 -- artma-0.2.1/artma/inst/artma/data/index.R | 21 artma-0.2.1/artma/inst/artma/data/preprocess.R | 244 +++++--- artma-0.2.1/artma/inst/artma/data/read.R | 36 - artma-0.2.1/artma/inst/artma/data/utils.R | 122 +++- artma-0.2.1/artma/inst/artma/data_config |only artma-0.2.1/artma/inst/artma/libs/ask.R |only artma-0.2.1/artma/inst/artma/libs/file_utils.R | 10 artma-0.2.1/artma/inst/artma/libs/modules.R | 17 artma-0.2.1/artma/inst/artma/libs/number_utils.R | 23 artma-0.2.1/artma/inst/artma/libs/path.R | 9 artma-0.2.1/artma/inst/artma/libs/string.R | 53 + artma-0.2.1/artma/inst/artma/libs/utils.R | 26 artma-0.2.1/artma/inst/artma/libs/validation.R | 45 + artma-0.2.1/artma/inst/artma/methods/variable_summary_stats.R | 2 artma-0.2.1/artma/inst/artma/options/ask.R | 5 artma-0.2.1/artma/inst/artma/options/prompts.R |only artma-0.2.1/artma/inst/artma/options/template.R | 289 ++++++---- artma-0.2.1/artma/inst/artma/options/templates/options_template.yaml | 211 ++++--- artma-0.2.1/artma/inst/artma/options/utils.R | 71 +- artma-0.2.1/artma/inst/artma/paths.R | 38 - artma-0.2.1/artma/inst/artma/testing/fixtures |only artma-0.2.1/artma/inst/artma/testing/load_test_modules.R |only artma-0.2.1/artma/inst/artma/testing/mocks/index.R |only artma-0.2.1/artma/inst/artma/testing/mocks/mock_df.R | 86 ++ artma-0.2.1/artma/inst/artma/testing/mocks/mock_options.R |only artma-0.2.1/artma/inst/artma/testing/mocks/mock_utils.R | 2 artma-0.2.1/artma/man/config.fix.Rd |only artma-0.2.1/artma/man/dot-onLoad.Rd |only artma-0.2.1/artma/man/dot-onUnload.Rd |only artma-0.2.1/artma/man/get_valid_boxpath.Rd |only artma-0.2.1/artma/man/is_devtools_load.Rd |only artma-0.2.1/artma/man/main.Rd | 8 artma-0.2.1/artma/man/methods.list.Rd | 2 artma-0.2.1/artma/man/options.copy.Rd | 5 artma-0.2.1/artma/man/options.create.Rd | 2 artma-0.2.1/artma/man/options.help.Rd | 2 artma-0.2.1/artma/man/options.load.Rd | 6 artma-0.2.1/artma/man/options.modify.Rd | 2 artma-0.2.1/artma/man/options.open.Rd |only artma-0.2.1/artma/man/run.Rd | 4 artma-0.2.1/artma/man/runtime_setup.Rd | 2 artma-0.2.1/artma/tests/E2E/test-installation.R |only artma-0.2.1/artma/tests/testthat/helper.R |only artma-0.2.1/artma/tests/testthat/setup.R |only artma-0.2.1/artma/tests/testthat/test-data-utils.R |only artma-0.2.1/artma/tests/testthat/test-dir_create_linter.R | 2 76 files changed, 1236 insertions(+), 696 deletions(-)
Title: Extracting Signals from Wavelet Spectra
Description: The continuous wavelet transform enables the observation of transient/non-stationary cyclicity in time-series. The goal of cyclostratigraphic studies is to define frequency/period in the depth/time domain. By conducting the continuous wavelet transform on cyclostratigraphic data series one can observe and extract cyclic signals/signatures from signals. These results can then be visualized and interpreted enabling one to identify/interpret cyclicity in the geological record, which can be used to construct astrochronological age-models and identify and interpret cyclicity in past and present climate systems. The 'WaverideR' R package builds upon existing literature and existing codebase. The list of articles which are relevant can be grouped in four subjects; cyclostratigraphic data analysis,example data sets,the (continuous) wavelet transform and astronomical solutions. References for the cyclostratigraphic data analysis articles are: Stephen Meyers (2019) <doi:10.1016/j.earscirev.20 [...truncated...]
Author: Michiel Arts [aut, cre]
Maintainer: Michiel Arts <michiel.arts@stratigraphy.eu>
Diff between WaverideR versions 0.3.2 dated 2023-09-06 and 0.4.0 dated 2025-04-25
DESCRIPTION | 18 MD5 | 132 +-- NAMESPACE | 17 NEWS.md | 10 R/Hilbert_transform.R | 4 R/WaverideR.R | 3 R/WaverideR_Datasets.R | 18 R/add_wavelet.R | 35 R/add_wavelet_avg.R | 7 R/analyze_wavelet.R | 513 ++++++++++++- R/anchor2time.R | 54 + R/astro_anchor.R | 3 R/curve2time_unc_anchor.R | 1214 +++++++++++++++++++++++-------- R/curve2tune.R | 8 R/dur_gaps.R | 77 + R/dynamic_extraction.R |only R/extract_amplitude.R | 6 R/extract_power.R | 3 R/extract_power_stable.R | 3 R/extract_signal.R | 2 R/extract_signal_stable.R | 3 R/extract_signal_stable_V2.R | 3 R/extract_signal_standard_deviation.R | 8 R/flmw.R | 4 R/lag_1.R |only R/loess_auto.R | 4 R/model_red_noise_wt.R | 13 R/plot_wavelet.R | 665 +++++++++++++--- R/plot_win_timeOpt.R |only R/retrack_wt_MC.R | 62 + R/sum_power_sedrate.R | 8 R/track_period_wavelet.R | 743 ++++++++++++------ R/wavelet_uncertainty.R | 17 R/win_fft.R | 37 R/win_timeOpt.R |only build/partial.rdb |binary man/Hilbert_transform.Rd | 2 man/WaverideR.Rd | 3 man/WaverideR_Datasets.Rd | 16 man/add_wavelet.Rd | 7 man/add_wavelet_avg.Rd | 7 man/analyze_wavelet.Rd | 284 ++++--- man/anchor2time.Rd | 2 man/anchor_points_grey.Rd | 2 man/astro_anchor.Rd | 2 man/completed_series.Rd | 200 ++--- man/curve2sedrate.Rd | 130 +-- man/curve2time.Rd | 174 ++-- man/curve2time_unc_anchor.Rd | 385 ++++++--- man/curve2tune.Rd | 196 ++--- man/dur_gaps.Rd | 4 man/dynamic_extraction.Rd |only man/extract_amplitude.Rd | 5 man/extract_power.Rd | 244 +++--- man/extract_power_stable.Rd | 2 man/extract_signal.Rd | 238 +++--- man/extract_signal_stable.Rd | 2 man/extract_signal_stable_V2.Rd | 2 man/extract_signal_standard_deviation.Rd | 383 ++++----- man/lag_1.Rd |only man/loess_auto.Rd | 164 ++-- man/model_red_noise_wt.Rd | 7 man/percentile_from_red_noise.Rd | 108 +- man/plot_avg_wavelet.Rd | 172 ++-- man/plot_wavelet.Rd | 593 +++++++-------- man/plot_win_timeOpt.Rd |only man/retrack_wt_MC.Rd | 17 man/track_period_wavelet.Rd | 59 + man/wavelet_uncertainty.Rd | 379 ++++----- man/win_fft.Rd | 6 man/win_timeOpt.Rd |only 71 files changed, 4773 insertions(+), 2716 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.5.1 dated 2025-04-24 and 0.5.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ build/vignette.rds |binary inst/doc/measures.html | 4 ++-- tests/testthat/test-crossprod.R | 4 ++-- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Processing of Accelerometry Data with 'GGIR' in mMARCH
Description: Mobile Motor Activity Research Consortium for Health (mMARCH) is a collaborative network of studies of clinical and community samples that employ common clinical, biological, and digital mobile measures across involved studies. One of the main scientific goals of mMARCH sites is developing a better understanding of the inter-relationships between accelerometry-measured physical activity (PA), sleep (SL), and circadian rhythmicity (CR) and mental and physical health in children, adolescents, and adults. Currently, there is no consensus on a standard procedure for a data processing pipeline of raw accelerometry data, and few open-source tools to facilitate their development. The R package 'GGIR' is the most prominent open-source software package that offers great functionality and tremendous user flexibility to process raw accelerometry data. However, even with 'GGIR', processing done in a harmonized and reproducible fashion requires a non-trivial amount of expertise combined with a care [...truncated...]
Author: Wei Guo [aut, cre],
Andrew Leroux [aut],
Vadim Zipunnikov [aut],
Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>
Diff between mMARCH.AC versions 3.2.0.0 dated 2025-04-23 and 3.2.0.1 dated 2025-04-25
DESCRIPTION | 6 +- MD5 | 12 ++-- inst/doc/features.dictionary.xlsx |binary inst/doc/mMARCH.AC.html | 4 - inst/template/features.dictionary.xlsx |binary inst/template/module7a_calculate_newfeatures.Rmd | 4 - inst/template/module7b_merge_GGIRfeatures.Rmd | 62 +++++++++++++++++------ 7 files changed, 61 insertions(+), 27 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [aut, cph]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.5.0 dated 2025-04-24 and 0.5.1 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Bayesian Treed Distributed Lag Models
Description: Estimation of distributed lag models (DLMs) based on a Bayesian additive regression trees framework. Includes several extensions of DLMs: treed DLMs and distributed lag mixture models (Mork and Wilson, 2023) <doi:10.1111/biom.13568>; treed distributed lag nonlinear models (Mork and Wilson, 2022) <doi:10.1093/biostatistics/kxaa051>; heterogeneous DLMs (Mork, et. al., 2024) <doi:10.1080/01621459.2023.2258595>; monotone DLMs (Mork and Wilson, 2024) <doi:10.1214/23-BA1412>. The package also includes visualization tools and a 'shiny' interface to check model convergence and to help interpret results.
Author: Daniel Mork [aut, cre, cph] ,
Seongwon Im [aut] ,
Ander Wilson [aut]
Maintainer: Daniel Mork <dmork@hsph.harvard.edu>
Diff between dlmtree versions 1.0.0 dated 2024-05-31 and 1.1.0 dated 2025-04-25
dlmtree-1.0.0/dlmtree/R/tdlmm.R |only dlmtree-1.0.0/dlmtree/R/tdlnm.R |only dlmtree-1.0.0/dlmtree/man/predict.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/predict.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.summary.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/print.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/shiny.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/shiny.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.hdlm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.hdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.monotone.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/summary.tdlnm.Rd |only dlmtree-1.0.0/dlmtree/man/tdlmm.Rd |only dlmtree-1.0.0/dlmtree/man/tdlnm.Rd |only dlmtree-1.1.0/dlmtree/DESCRIPTION | 12 dlmtree-1.1.0/dlmtree/MD5 | 145 +++---- dlmtree-1.1.0/dlmtree/NAMESPACE | 23 - dlmtree-1.1.0/dlmtree/NEWS.md | 51 ++ dlmtree-1.1.0/dlmtree/R/adj_coexposure.R | 27 - dlmtree-1.1.0/dlmtree/R/combine.models.R | 22 - dlmtree-1.1.0/dlmtree/R/control.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.hdlm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.hdlmm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.monotone.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlmm.R |only dlmtree-1.1.0/dlmtree/R/diagnose.summary.tdlnm.R |only dlmtree-1.1.0/dlmtree/R/dlmtree.R | 245 ++++-------- dlmtree-1.1.0/dlmtree/R/drawTree.R | 3 dlmtree-1.1.0/dlmtree/R/estDLM.R | 92 +--- dlmtree-1.1.0/dlmtree/R/generic.R | 118 +++++ dlmtree-1.1.0/dlmtree/R/get_sbd_dlmtree.R | 10 dlmtree-1.1.0/dlmtree/R/pip.R | 5 dlmtree-1.1.0/dlmtree/R/plot.summary.monotone.R | 10 dlmtree-1.1.0/dlmtree/R/plot.summary.tdlm.R | 47 -- dlmtree-1.1.0/dlmtree/R/plot.summary.tdlmm.R | 29 - dlmtree-1.1.0/dlmtree/R/plot.summary.tdlnm.R | 19 dlmtree-1.1.0/dlmtree/R/predict.hdlm.R | 109 +---- dlmtree-1.1.0/dlmtree/R/predict.hdlmm.R | 146 ++----- dlmtree-1.1.0/dlmtree/R/print.dlmtree.R | 57 -- dlmtree-1.1.0/dlmtree/R/print.summary.hdlm.R | 92 ---- dlmtree-1.1.0/dlmtree/R/print.summary.hdlmm.R | 101 ----- dlmtree-1.1.0/dlmtree/R/print.summary.monotone.R | 73 --- dlmtree-1.1.0/dlmtree/R/print.summary.tdlm.R | 19 dlmtree-1.1.0/dlmtree/R/print.summary.tdlmm.R | 63 +-- dlmtree-1.1.0/dlmtree/R/print.summary.tdlnm.R | 28 - dlmtree-1.1.0/dlmtree/R/shiny.hdlm.R | 54 +- dlmtree-1.1.0/dlmtree/R/shiny.hdlmm.R | 48 -- dlmtree-1.1.0/dlmtree/R/splitpoints.R | 2 dlmtree-1.1.0/dlmtree/R/summary.hdlm.R | 90 +++- dlmtree-1.1.0/dlmtree/R/summary.hdlmm.R | 110 +++-- dlmtree-1.1.0/dlmtree/R/summary.monotone.R | 133 +++--- dlmtree-1.1.0/dlmtree/R/summary.tdlm.R | 135 ++++-- dlmtree-1.1.0/dlmtree/R/summary.tdlmm.R | 362 ++++++++---------- dlmtree-1.1.0/dlmtree/R/summary.tdlnm.R | 135 +++--- dlmtree-1.1.0/dlmtree/README.md | 12 dlmtree-1.1.0/dlmtree/inst/examples/dlmtree_example.R | 8 dlmtree-1.1.0/dlmtree/man/adj_coexposure.Rd | 13 dlmtree-1.1.0/dlmtree/man/diagnose.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree-package.Rd | 2 dlmtree-1.1.0/dlmtree/man/dlmtree.Rd | 139 +----- dlmtree-1.1.0/dlmtree/man/dlmtree.control.diagnose.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.family.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.het.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.hyper.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.mcmc.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.mix.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.monotone.Rd |only dlmtree-1.1.0/dlmtree/man/dlmtree.control.tdlnm.Rd |only dlmtree-1.1.0/dlmtree/man/drawTree.Rd | 2 dlmtree-1.1.0/dlmtree/man/estDLM.Rd | 21 - dlmtree-1.1.0/dlmtree/man/get_sbd_dlmtree.Rd | 10 dlmtree-1.1.0/dlmtree/man/pip.Rd | 5 dlmtree-1.1.0/dlmtree/man/plot.summary.tdlm.Rd | 4 dlmtree-1.1.0/dlmtree/man/plot.summary.tdlnm.Rd | 9 dlmtree-1.1.0/dlmtree/man/predict.Rd |only dlmtree-1.1.0/dlmtree/man/print.Rd |only dlmtree-1.1.0/dlmtree/man/shiny.Rd | 14 dlmtree-1.1.0/dlmtree/man/splitpoints.Rd | 2 dlmtree-1.1.0/dlmtree/man/summary.Rd |only dlmtree-1.1.0/dlmtree/src/dlmtreeHDLMGaussian.cpp | 21 - dlmtree-1.1.0/dlmtree/src/dlmtreeHDLMMGaussian.cpp | 38 + dlmtree-1.1.0/dlmtree/src/tdlmm_Cpp.cpp | 27 - dlmtree-1.1.0/dlmtree/src/tdlnm_Cpp.cpp | 9 96 files changed, 1314 insertions(+), 1637 deletions(-)
More information about branchingprocess at CRAN
Permanent link
Title: Import 'Stata' Data Files
Description: Function to read and write the 'Stata' file format.
Author: Jan Marvin Garbuszus [aut],
Sebastian Jeworutzki [aut, cre]
,
R Core Team [cph],
Magnus Thor Torfason [ctb],
Luke M. Olson [ctb],
Giovanni Righi [ctb],
Kevin Jin [ctb]
Maintainer: Sebastian Jeworutzki <Sebastian.Jeworutzki@ruhr-uni-bochum.de>
Diff between readstata13 versions 0.10.1 dated 2023-02-21 and 0.11.0 dated 2025-04-25
readstata13-0.10.1/readstata13/src/Makevars.win |only readstata13-0.11.0/readstata13/DESCRIPTION | 11 readstata13-0.11.0/readstata13/MD5 | 72 ++- readstata13-0.11.0/readstata13/NAMESPACE | 3 readstata13-0.11.0/readstata13/NEWS | 200 +++++------ readstata13-0.11.0/readstata13/NEWS.md |only readstata13-0.11.0/readstata13/R/RcppExports.R | 4 readstata13-0.11.0/readstata13/R/convert.R | 12 readstata13-0.11.0/readstata13/R/dbcal.R | 2 readstata13-0.11.0/readstata13/R/read.R | 37 +- readstata13-0.11.0/readstata13/R/readstata13.R | 4 readstata13-0.11.0/readstata13/R/save.R | 17 readstata13-0.11.0/readstata13/R/tools.R | 92 +++++ readstata13-0.11.0/readstata13/README.md | 154 +++----- readstata13-0.11.0/readstata13/build |only readstata13-0.11.0/readstata13/inst/doc |only readstata13-0.11.0/readstata13/inst/extdata/myproject2.dtas |only readstata13-0.11.0/readstata13/inst/include/read_dta.h | 3 readstata13-0.11.0/readstata13/inst/include/read_pre13_dta.h | 3 readstata13-0.11.0/readstata13/inst/include/readstata.h | 21 - readstata13-0.11.0/readstata13/inst/include/statadefines.h | 3 readstata13-0.11.0/readstata13/man/get.frames.Rd |only readstata13-0.11.0/readstata13/man/read.dta13.Rd | 16 readstata13-0.11.0/readstata13/man/read.dtas.Rd |only readstata13-0.11.0/readstata13/man/readstata13.Rd | 1 readstata13-0.11.0/readstata13/man/save.dta13.Rd | 8 readstata13-0.11.0/readstata13/src/Makevars | 3 readstata13-0.11.0/readstata13/src/RcppExports.cpp | 11 readstata13-0.11.0/readstata13/src/read.cpp | 11 readstata13-0.11.0/readstata13/src/read_data.cpp | 15 readstata13-0.11.0/readstata13/src/read_dta.cpp | 67 ++- readstata13-0.11.0/readstata13/src/read_pre13_dta.cpp | 27 + readstata13-0.11.0/readstata13/src/save_dta.cpp | 22 - readstata13-0.11.0/readstata13/src/save_pre13_dta.cpp | 2 readstata13-0.11.0/readstata13/tests/testthat/data |only readstata13-0.11.0/readstata13/tests/testthat/test_read.R | 127 ++++++ readstata13-0.11.0/readstata13/tests/testthat/test_save.R | 182 +++++++++- readstata13-0.11.0/readstata13/vignettes |only 38 files changed, 785 insertions(+), 345 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).
Author: Maarten Blaauw [aut, cre] ,
J. Andres Christen [aut, ctb, cph]
,
Marco A. Aquino Lopez [aut] ,
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 3.3.1 dated 2024-09-28 and 3.4.1 dated 2025-04-25
DESCRIPTION | 10 +- MD5 | 68 ++++++++--------- NAMESPACE | 9 ++ NEWS.md | 16 +++- R/MCMC.R | 4 - R/accrate.R | 54 ++++++++------ R/agedepth.R | 68 ++++++++++++----- R/calc.R | 21 ++--- R/calibrate.R | 46 +++++++----- R/forplum.R | 14 +-- R/internal_plots.R | 69 ++++++++++++++++-- R/plots.R | 29 ++++--- R/rbacon-package.R | 8 +- R/rbacon.R | 60 +++++++++++---- R/read_write.R | 24 +++++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rbacon.R | 92 ++++++++++++------------ inst/doc/rbacon.Rmd | 31 ++++---- inst/doc/rbacon.html | 193 +++++++++++++++++++++++++-------------------------- man/Bacon.Rd | 8 +- man/Bacon.hist.Rd | 2 man/accrate.depth.Rd | 10 ++ man/add.dates.Rd | 6 - man/agedepth.Rd | 10 ++ man/agemodel.it.Rd | 2 man/calib.plot.Rd | 3 man/scissors.Rd | 2 man/thinner.Rd | 7 + src/bacon.cpp | 95 +------------------------ src/bacon.h | 11 ++ src/input.cpp | 2 src/ranfun.cpp | 8 +- src/ranfun.h | 2 vignettes/rbacon.Rmd | 31 ++++---- 35 files changed, 572 insertions(+), 443 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.2-0 dated 2025-02-20 and 3.2-6 dated 2025-04-25
DESCRIPTION | 8 MD5 | 177 ++-- NAMESPACE | 4 NEWS.md | 93 ++ R/CalcSleepRegularityIndex.R | 32 R/GGIR.R | 134 ++- R/HASIB.R | 75 + R/HASPT.R | 286 +++++++ R/addSplitNames.R |only R/appendRecords.R | 16 R/check_params.R | 142 +-- R/convertEpochData.R | 909 ++++++++++++++--------- R/extract_params.R | 16 R/g.analyse.R | 16 R/g.analyse.avday.R | 25 R/g.analyse.perday.R | 126 ++- R/g.analyse.perfile.R | 36 R/g.calibrate.R | 4 R/g.dotorcomma.R | 2 R/g.fragmentation.R | 2 R/g.getM5L5.R | 18 R/g.getmeta.R | 1 R/g.impute.R | 24 R/g.inspectfile.R | 25 R/g.loadlog.R | 7 R/g.part1.R | 2 R/g.part2.R | 4 R/g.part3.R | 4 R/g.part4.R | 38 - R/g.part5.R | 27 R/g.part5.addfirstwake.R | 17 R/g.part5.analyseRest.R | 10 R/g.part5.definedays.R | 12 R/g.part5.savetimeseries.R | 21 R/g.part5_analyseSegment.R | 18 R/g.part5_initialise_ts.R | 6 R/g.part6.R | 34 R/g.readaccfile.R | 18 R/g.report.part2.R | 13 R/g.report.part4.R | 103 +- R/g.report.part5.R | 13 R/g.report.part6.R | 23 R/g.sib.det.R | 84 +- R/g.sibreport.R | 17 R/g.weardec.R | 3 R/getPart1BasicInfo.R |only R/getSplitNames.R |only R/get_nw_clip_block_params.R | 1 R/inspect_binFile_brand.R |only R/isfilelist.R | 3 R/load_params.R | 18 R/markerButtonForRest.R |only R/monitor_types.R | 2 R/splitRecords.R |only R/visualReport.R | 35 README.md | 3 build/vignette.rds |binary inst/doc/CutPoints.Rmd | 106 +- inst/doc/CutPoints.html | 911 ++++++++++-------------- inst/doc/GGIR.R | 44 - inst/doc/GGIR.Rmd | 215 ----- inst/doc/GGIR.html | 261 ------ inst/doc/GGIRParameters.Rmd | 20 inst/doc/GGIRParameters.html | 458 ++++++++---- inst/doc/GGIRoutput.Rmd | 11 inst/doc/GGIRoutput.html | 98 +- man/CalcSleepRegularityIndex.Rd | 12 man/GGIR-package.Rd | 4 man/GGIR.Rd | 437 +++++++---- man/HASIB.Rd | 12 man/HASPT.Rd | 17 man/addSplitNames.Rd |only man/convertEpochData.Rd | 9 man/g.analyse.perday.Rd | 14 man/g.getM5L5.Rd | 5 man/g.part5.analyseRest.Rd | 1 man/g.weardec.Rd | 6 man/getPart1BasicInfo.Rd |only man/getSplitNames.Rd |only man/inspect_binFile_brand.Rd |only man/markerButtonForRest.Rd |only man/splitRecords.Rd |only tests/testthat/test_HASIB.R | 7 tests/testthat/test_HASPT.R |only tests/testthat/test_convertExtEpochData.R | 75 + tests/testthat/test_greadaccfile.R | 24 tests/testthat/test_gweardec.R | 24 tests/testthat/test_lightPart5.R | 4 tests/testthat/test_load_check_params.R | 56 - tests/testthat/test_part5_fixmissingnight.R | 2 tests/testthat/test_part5_markerButtonForRest.R |only tests/testthat/test_part6.R | 9 tests/testthat/test_splitRecords.R |only vignettes/CutPoints.Rmd | 106 +- vignettes/GGIR.Rmd | 215 ----- vignettes/GGIRParameters.Rmd | 20 vignettes/GGIRoutput.Rmd | 11 97 files changed, 3251 insertions(+), 2650 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-15 0.11.3
2019-04-25 0.11.2
2019-03-14 0.11.1
2018-05-23 0.11.0
2018-02-05 0.10.1
2017-11-27 0.10.0
2017-06-30 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-07 0.4.5
2014-08-06 0.4.2
2012-11-06 0.4.1
2012-07-10 0.4.0
2011-11-29 0.3.3
2011-10-20 0.3.2
2011-09-19 0.3.1
2011-07-06 0.3.0
2011-02-08 0.2.6
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.5 dated 2025-04-23 and 0.1.6 dated 2025-04-25
DESCRIPTION | 8 +++---- MD5 | 6 ++--- NEWS.md | 4 +++ src/survival_analysis.cpp | 48 ++++++++++++++++++++++++++-------------------- 4 files changed, 39 insertions(+), 27 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut],
Sungho Choi [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.11 dated 2025-04-04 and 1.3.12 dated 2025-04-25
DESCRIPTION | 10 MD5 | 31 NAMESPACE | 6 NEWS.md | 6 R/CreateTableOneJS.R | 11 R/forestcox.R | 737 ++++++--------- R/forestglm.R | 1237 +++++++++++++++----------- R/utils.R |only inst/doc/jstable.html | 28 inst/doc/jstable_competing_risk_analysis.html | 4 inst/doc/jstable_options.html | 12 man/TableSubgroupGLM.Rd | 8 man/TableSubgroupMultiGLM.Rd | 8 man/collapse_counts.Rd |only man/count_event_by.Rd | 2 man/count_event_by_glm.Rd |only tests/testthat/test-CreateTableOneJS.R | 1 tests/testthat/test-forestglm.R | 24 18 files changed, 1152 insertions(+), 973 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obspy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian.sharer@earthscope.org>
Diff between IRISSeismic versions 1.6.7 dated 2024-12-10 and 1.7.0 dated 2025-04-25
DESCRIPTION | 12 MD5 | 57 +- R/Class-IrisClient.R | 865 ++++++++++++++++++++++++++-------------- R/Class-Stream.R | 2 R/Class-Trace.R | 2 R/spectralUtils.R | 9 R/zzz.R |only build/vignette.rds |binary inst/doc/IRISSeismic-intro.Rmd | 23 - inst/doc/IRISSeismic-intro.html | 20 man/IRISSeismic-package.Rd | 53 +- man/IrisClient-class.Rd | 13 man/Stream-class.Rd | 2 man/butterworth.Rd | 2 man/getDataAvailability.Rd | 2 man/getDataselect.Rd | 7 man/getEvent.Rd | 4 man/getSNCL.Rd | 2 man/getTimeseries.Rd | 10 man/getUnavailability.Rd | 2 src/Makevars | 2 src/Makevars.win | 2 src/libmseed/fileutils.c | 50 +- src/libmseed/genutils.c | 47 -- src/libmseed/libmseed.def | 6 src/libmseed/libmseed.h | 11 src/libmseed/logging.c | 9 src/libmseed/parseutils.c | 2 src/libmseed/unpack.c | 4 vignettes/IRISSeismic-intro.Rmd | 23 - 30 files changed, 751 insertions(+), 492 deletions(-)
Title: Apply Functions to All Combinations of List Elements
Description: Provides an extension to the 'purrr' family of mapping
functions to apply a function to each combination of elements in a
list of inputs. Also includes functions for automatically detecting
output type in mapping functions, finding every combination of
elements of lists or rows of data frames, and applying multiple models
to multiple subsets of a dataset.
Author: Alexander Rossell Hayes [aut, cre, cph]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Diff between crossmap versions 0.4.1 dated 2025-04-21 and 0.4.2 dated 2025-04-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ tests/testthat/test-errors.R | 2 ++ tests/testthat/test-future_xmap.R | 34 ++++------------------------------ 5 files changed, 17 insertions(+), 37 deletions(-)
Title: Alternating Optimization
Description: An iterative process that optimizes a function by alternately
performing restricted optimization over parameter subsets. Instead of joint
optimization, it breaks the optimization problem down into simpler
sub-problems. This approach can make optimization feasible when joint
optimization is too difficult.
Author: Lennart Oelschlaeger [aut, cre]
,
Siddhartha Chib [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between ao versions 1.1.0 dated 2024-07-13 and 1.2.0 dated 2025-04-25
ao-1.1.0/ao/R/procedure.R |only ao-1.1.0/ao/man/Procedure.Rd |only ao-1.1.0/ao/man/ao_input_check.Rd |only ao-1.1.0/ao/tests/testthat/test-procedure.R |only ao-1.2.0/ao/DESCRIPTION | 24 ao-1.2.0/ao/MD5 | 40 ao-1.2.0/ao/NAMESPACE | 44 ao-1.2.0/ao/NEWS.md | 276 +- ao-1.2.0/ao/R/ao-package.R | 85 ao-1.2.0/ao/R/ao.R | 1104 ++++----- ao-1.2.0/ao/R/process.R |only ao-1.2.0/ao/README.md | 277 +- ao-1.2.0/ao/build/vignette.rds |binary ao-1.2.0/ao/inst/doc/ao.R | 328 +- ao-1.2.0/ao/inst/doc/ao.Rmd | 779 +++--- ao-1.2.0/ao/inst/doc/ao.html | 1905 ++++++++-------- ao-1.2.0/ao/man/Process.Rd |only ao-1.2.0/ao/man/ao-package.Rd | 60 ao-1.2.0/ao/man/ao.Rd | 585 ++-- ao-1.2.0/ao/man/figures/README-rosenbrock_ao_path-1.png |binary ao-1.2.0/ao/tests/testthat.R | 8 ao-1.2.0/ao/tests/testthat/test-ao.R | 146 - ao-1.2.0/ao/vignettes/ao.Rmd | 779 +++--- ao-1.2.0/ao/vignettes/ref.bib | 108 24 files changed, 3324 insertions(+), 3224 deletions(-)
Title: Read, Write and Edit 'xlsx' Files
Description: Simplifies the creation of 'xlsx' files by
providing a high level interface to writing, styling and editing
worksheets.
Author: Jordan Mark Barbone [aut] ,
Jan Marvin Garbuszus [aut, cre],
Olivier Roy [ctb],
openxlsx authors [cph] ,
Arseny Kapoulkine [ctb, cph]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx2 versions 1.14 dated 2025-03-20 and 1.15 dated 2025-04-25
DESCRIPTION | 6 MD5 | 155 +++++++++--------- NEWS.md | 33 ++++ R/RcppExports.R | 25 ++- R/class-comment.R | 23 -- R/class-style_mgr.R | 66 ++++---- R/class-workbook-wrappers.R | 19 +- R/class-workbook.R | 153 +++++++++--------- R/class-worksheet.R | 33 +--- R/dates.R | 96 ++++------- R/deprecate.R | 20 ++ R/helper-functions.R | 77 +++++++-- R/openxlsx2-package.R | 20 ++ R/read.R | 187 ++++++++++++++++------ R/utils.R | 38 ---- R/wb_functions.R | 50 +----- R/wb_load.R | 7 R/wb_styles.R | 11 - R/write.R | 34 ++-- R/write_xlsx.R | 10 + README.md | 44 ++--- build/vignette.rds |binary inst/WORDLIST | 10 - inst/doc/Update-from-openxlsx.html | 22 +- inst/doc/conditional-formatting.html | 109 +++++-------- inst/doc/openxlsx2_charts_manual.html | 6 inst/doc/openxlsx2_read_to_df.html | 132 ++++++++-------- inst/doc/openxlsx2_style_manual.R | 6 inst/doc/openxlsx2_style_manual.Rmd | 6 inst/doc/openxlsx2_style_manual.html | 14 - man/create_cell_style.Rd | 6 man/create_comment.Rd | 2 man/create_numfmt.Rd | 2 man/openxlsx2-package.Rd | 21 ++ man/wb_add_data.Rd | 13 + man/wb_add_data_table.Rd | 13 + man/wb_cell_style.Rd | 2 man/wb_to_df.Rd | 13 + man/write_datatable.Rd | 13 + src/RcppExports.cpp | 61 +++++-- src/date.cpp |only src/helper_functions.cpp | 207 ++++++++++++++++++++++--- src/load_workbook.cpp | 45 ++--- src/openxlsx2.h | 58 +++---- src/strings_xml.cpp | 58 +------ src/styles_xml.cpp | 51 ++---- src/write_file.cpp | 2 src/xlsb.cpp | 4 tests/testthat/test-base_font.R | 2 tests/testthat/test-class-color.R | 12 - tests/testthat/test-class-comment.R | 83 +++++++--- tests/testthat/test-class-hyperlink.R | 14 - tests/testthat/test-class-workbook-wrappers.R | 22 +- tests/testthat/test-class-workbook.R | 22 +- tests/testthat/test-class-worksheet.R | 6 tests/testthat/test-clean_sheet.R | 2 tests/testthat/test-cloneWorksheet.R | 6 tests/testthat/test-conditional_formatting.R | 214 ++++++++++---------------- tests/testthat/test-date_time_conversion.R | 143 ++++++++++++++++- tests/testthat/test-fill_merged_cells.R | 52 +++--- tests/testthat/test-form_control.R | 12 - tests/testthat/test-formulas.R | 90 ++++++++++ tests/testthat/test-freeze_pane.R | 28 +-- tests/testthat/test-helper-functions.R | 17 ++ tests/testthat/test-loading_workbook.R | 20 +- tests/testthat/test-named_regions.R | 2 tests/testthat/test-outlines.R | 19 +- tests/testthat/test-protect-workbook.R | 4 tests/testthat/test-read_from_created_wb.R | 2 tests/testthat/test-read_sources.R | 8 tests/testthat/test-read_write_logicals.R | 2 tests/testthat/test-save.R | 111 ++++++++----- tests/testthat/test-strings_xml.R | 14 - tests/testthat/test-utils.R | 27 +++ tests/testthat/test-wb_functions.R | 16 - tests/testthat/test-wb_styles.R | 116 ++++++-------- tests/testthat/test-write.R | 42 ++++- tests/testthat/test-writing_posixct.R | 4 vignettes/openxlsx2_style_manual.Rmd | 6 79 files changed, 1867 insertions(+), 1234 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut] ,
Hyungwoo Jo [aut],
Jeongmin Seo [aut],
Hojun LEE [aut],
Sungho Choi [aut],
Yeji Ka [...truncated...]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.6.4 dated 2025-03-10 and 1.6.8 dated 2025-04-25
DESCRIPTION | 20 ++-- MD5 | 49 ++++++---- NAMESPACE | 5 + NEWS.md | 18 +++ R/coxph.R | 59 ++++--------- R/gee.R | 121 +++++++++++++++++++------- R/jsBasicGadget.R | 12 +- R/jsPropensityGadget.R | 68 +++++++++------ R/jsRepeatedGadget.R | 35 +++++-- R/jsSurveyGadget.R | 38 +++++--- R/kaplan.R | 12 +- R/regress.R | 149 ++++++++++++++++++++++++++++----- R/roc.R | 18 ++- R/templateGenerator.R |only R/theme.R |only build/vignette.rds |binary inst/assets |only inst/doc/jsmodule.html | 4 inst/doc/jsmodule_subgroup_cmprsk.html | 4 inst/rstudio/addins.dcf | 7 + inst/www/style_basic.css |only inst/www/style_ps.css |only inst/www/style_repeated.css |only inst/www/style_survey.css |only man/GEEModuleLinear.Rd | 5 - man/GEEModuleLogistic.Rd | 5 - man/logisticModule2.Rd | 5 - man/regressModule2.Rd | 5 - man/templateGenerator.Rd |only man/use_jsmodule_style.Rd |only 30 files changed, 437 insertions(+), 202 deletions(-)
Title: Functions to Estimate Tree Volume and Phytomass in the Italian
Forest Inventory 2005
Description: Tabacchi et al. (2011) published a very detailed study producing a uniform system of functions to estimate tree volume and
phytomass components (stem, branches, stool). The estimates of the 2005 Italian forest inventory (<https://www.inventarioforestale.org/it/>)
are based on these functions. The study documents the domain of applicability of each function and the equations to quantify estimates
accuracies for individual estimates as well as for aggregated estimates. This package makes the functions available in the R environment.
Version 2 exposes two distinct functions for individual and summary estimates. To facilitate access to the functions, tree species
identification is now based on EPPO species codes (<https://data.eppo.int/>).
Author: Nicola Puletti [aut, cre] ,
Mirko Grotti [aut],
Roberto Scotti [aut]
Maintainer: Nicola Puletti <nicola.puletti@gmail.com>
Diff between ForIT versions 2.4.0 dated 2023-09-26 and 2.5.0 dated 2025-04-25
ForIT-2.4.0/ForIT/man/ForIT.Rd |only ForIT-2.5.0/ForIT/DESCRIPTION | 16 ++++++++-------- ForIT-2.5.0/ForIT/MD5 | 16 ++++++++-------- ForIT-2.5.0/ForIT/NAMESPACE | 1 + ForIT-2.5.0/ForIT/NEWS.md | 6 ++---- ForIT-2.5.0/ForIT/R/ForIT.R | 6 ++---- ForIT-2.5.0/ForIT/R/INFCaccuracyPlot.R | 4 ++-- ForIT-2.5.0/ForIT/R/INFCvpeSUM.R | 8 +++++--- ForIT-2.5.0/ForIT/man/ForIT-package.Rd |only ForIT-2.5.0/ForIT/man/PlottingINFCaccuracy.Rd | 4 ++-- 10 files changed, 30 insertions(+), 31 deletions(-)
Title: Fast Change Point Detection via Sequential Gradient Descent
Description: Implements fast change point detection algorithm based on the
paper "Sequential Gradient Descent and Quasi-Newton's Method for
Change-Point Analysis" by Xianyang Zhang, Trisha Dawn
<https://proceedings.mlr.press/v206/zhang23b.html>. The algorithm is
based on dynamic programming with pruning and sequential gradient
descent. It is able to detect change points a magnitude faster than
the vanilla Pruned Exact Linear Time(PELT). The package includes
examples of linear regression, logistic regression, Poisson
regression, penalized linear regression data, and whole lot more
examples with custom cost function in case the user wants to use their
own cost function.
Author: Xingchi Li [aut, cre, cph] ,
Xianyang Zhang [aut, cph]
Maintainer: Xingchi Li <anthony.li.stat.tamu.edu@lixingchi.com>
Diff between fastcpd versions 0.16.1 dated 2025-03-20 and 0.16.2 dated 2025-04-25
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 6 + R/fastcpd.R | 4 build/vignette.rds |binary man/fastcpd.Rd | 2 src/fastcpd_classes.cc | 59 +++++----- src/ref_r_family.c | 5 tests/testthat/test-vignettes-comparison-pelt-logistic-regression.R | 2 tests/testthat/test-vignettes-comparison-pelt-poisson-regression.R | 2 10 files changed, 58 insertions(+), 46 deletions(-)
Title: Simulated Sampling Procedure for Community Ecology
Description: The Simulation-based Sampling Protocol (SSP) is an R package designed to estimate sampling effort in studies of ecological communities. It is based on the concept of pseudo-multivariate standard error (MultSE) (Anderson & Santana-Garcon, 2015, <doi:10.1111/ele.12385>) and the simulation of ecological data. The theoretical background is described in Guerra-Castro et al. (2020, <doi:10.1111/ecog.05284>).
Author: Edlin Guerra-Castro [aut, cre],
Maite Mascaro [aut],
Nuno Simoes [aut],
Juan Cruz-Motta [aut],
Juan Cajas [aut]
Maintainer: Edlin Guerra-Castro <edlinguerra@gmail.com>
Diff between SSP versions 1.0.1 dated 2020-03-28 and 1.0.2 dated 2025-04-24
DESCRIPTION | 15 - MD5 | 49 +-- NAMESPACE | 3 NEWS.md |only R/assempar.R | 99 +++++- R/datquality.R | 56 +++ R/ioptimum.R | 64 ++++ R/plot_ssp.R | 219 +++++++++------ R/sampsd.R | 68 ++++ R/simdata.R | 59 +++- R/summary_ssp.R | 51 +++ README.md | 43 +-- build/partial.rdb |only build/vignette.rds |binary inst/doc/SSP-guide.R | 12 inst/doc/SSP-guide.Rmd | 6 inst/doc/SSP-guide.html | 687 ++++++++++++++++++++++++++++++++++-------------- man/SSP-package.Rd | 11 man/assempar.Rd | 88 ++---- man/datquality.Rd | 120 ++------ man/figures |only man/ioptimum.Rd | 146 +++------- man/plot_ssp.Rd | 132 ++------- man/sampsd.Rd | 143 +++------ man/simdata.Rd | 102 ++----- man/summary_ssp.Rd | 116 ++------ vignettes/SSP-guide.Rmd | 6 27 files changed, 1367 insertions(+), 928 deletions(-)
Title: Forest Estimations and Dendrometric Computations
Description: Computation of dendrometric and structural
parameters from forest inventory data. The objective is to provide an
user-friendly R package for researchers, ecologists, foresters,
statisticians, loggers and others persons who deal with forest inventory
data. Useful conversion of angle value from degree to radian, conversion from
angle to slope (in percentage) and their reciprocals as well as principal
angle determination are also included. Position and dispersion parameters
usually found in forest studies are implemented. The package contains
Fibonacci series, its extensions and the Golden Number computation.
Useful references are Arcadius Y. J. Akossou, Soufianou Arzouma,
Eloi Y. Attakpa, Noël H. Fonton and Kouami Kokou (2013) <doi:10.3390/d5010099>
and W. Bonou, R. Glele Kakaï, A.E. Assogbadjo, H.N. Fonton, B. Sinsin (2009)
<doi:10.1016/j.foreco.2009.05.032> .
Author: Narcisse Yehouenou [aut, cre],
Information and Communication Technology for you ONG [fnd]
Maintainer: Narcisse Yehouenou <narcisstar211@gmail.com>
Diff between dendrometry versions 0.0.2 dated 2023-02-07 and 0.0.3 dated 2025-04-24
dendrometry-0.0.2/dendrometry/man/circum.Rd |only dendrometry-0.0.2/dendrometry/man/principal.Rd |only dendrometry-0.0.2/dendrometry/man/rad.Rd |only dendrometry-0.0.2/dendrometry/man/slope2angle.Rd |only dendrometry-0.0.3/dendrometry/DESCRIPTION | 12 dendrometry-0.0.3/dendrometry/MD5 | 84 dendrometry-0.0.3/dendrometry/NAMESPACE | 13 dendrometry-0.0.3/dendrometry/NEWS.md | 12 dendrometry-0.0.3/dendrometry/R/dendrometry.R | 1811 ++++++++++----- dendrometry-0.0.3/dendrometry/build/partial.rdb |binary dendrometry-0.0.3/dendrometry/build/vignette.rds |binary dendrometry-0.0.3/dendrometry/demo/dendro.R | 18 dendrometry-0.0.3/dendrometry/demo/volume.R | 54 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.R | 102 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.Rmd | 103 dendrometry-0.0.3/dendrometry/inst/doc/dendrometry.html | 293 +- dendrometry-0.0.3/dendrometry/man/Logging.Rd | 6 dendrometry-0.0.3/dendrometry/man/Tree.Rd | 13 dendrometry-0.0.3/dendrometry/man/adjWeibull.Rd |only dendrometry-0.0.3/dendrometry/man/angle2slope.Rd | 52 dendrometry-0.0.3/dendrometry/man/barkFactor.Rd |only dendrometry-0.0.3/dendrometry/man/basal.Rd | 40 dendrometry-0.0.3/dendrometry/man/basalContribution.Rd |only dendrometry-0.0.3/dendrometry/man/basal_i.Rd | 18 dendrometry-0.0.3/dendrometry/man/blackman.Rd | 2 dendrometry-0.0.3/dendrometry/man/dbh.Rd | 25 dendrometry-0.0.3/dendrometry/man/deg.Rd | 23 dendrometry-0.0.3/dendrometry/man/dendrometry-package.Rd | 8 dendrometry-0.0.3/dendrometry/man/densityRegen.Rd |only dendrometry-0.0.3/dendrometry/man/densityTree.Rd | 26 dendrometry-0.0.3/dendrometry/man/diameterMean.Rd | 10 dendrometry-0.0.3/dendrometry/man/distanceH.Rd | 18 dendrometry-0.0.3/dendrometry/man/factorize.Rd | 3 dendrometry-0.0.3/dendrometry/man/fiboRate.Rd | 78 dendrometry-0.0.3/dendrometry/man/fibonacci.Rd | 4 dendrometry-0.0.3/dendrometry/man/girard.Rd |only dendrometry-0.0.3/dendrometry/man/green.Rd | 2 dendrometry-0.0.3/dendrometry/man/height.Rd | 44 dendrometry-0.0.3/dendrometry/man/loreyHeight.Rd | 15 dendrometry-0.0.3/dendrometry/man/makedata.Rd | 17 dendrometry-0.0.3/dendrometry/man/param_i.Rd |only dendrometry-0.0.3/dendrometry/man/print.angle.Rd |only dendrometry-0.0.3/dendrometry/man/print.slope.Rd |only dendrometry-0.0.3/dendrometry/man/rfreq.Rd |only dendrometry-0.0.3/dendrometry/man/sampleSize.Rd | 21 dendrometry-0.0.3/dendrometry/man/skewness.Rd | 2 dendrometry-0.0.3/dendrometry/man/spNmReduce.Rd |only dendrometry-0.0.3/dendrometry/man/stacking.Rd | 3 dendrometry-0.0.3/dendrometry/man/volume.Rd | 8 dendrometry-0.0.3/dendrometry/vignettes/dendrometry.Rmd | 103 50 files changed, 1992 insertions(+), 1051 deletions(-)
Title: Nonparametric Bootstrap Test for Regression Monotonicity
Description: Implements nonparametric bootstrap tests for detecting monotonicity
in regression functions from Hall, P. and Heckman, N. (2000) <doi:10.1214/aos/1016120363>
Includes tools for visualizing results using Nadaraya-Watson kernel regression and supports
efficient computation with 'C++'.
Author: Dylan Huynh [aut, cre]
Maintainer: Dylan Huynh <dylanhuynh@utexas.edu>
Diff between MonotonicityTest versions 1.1 dated 2025-04-02 and 1.2 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 5 ++++- R/main.R | 16 ++++++---------- R/monotonicity-result.R |only man/monotonicity_test.Rd | 10 ++-------- tests/testthat/Rplots.pdf |only tests/testthat/test-main.R | 5 +++++ 8 files changed, 27 insertions(+), 27 deletions(-)
More information about MonotonicityTest at CRAN
Permanent link
Title: Modern Database Engine for Complex Data Based on
Multi-Dimensional Arrays
Description: The modern database 'TileDB' introduces a powerful on-disk
format for storing and accessing any complex data based on multi-dimensional
arrays. It supports dense and sparse arrays, dataframes and key-values stores,
cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded implementation,
supports parallel I/O, data versioning ('time travel'), metadata and groups.
It is implemented as an embeddable cross-platform C++ library with APIs from
several languages, and integrations. This package provides the R support.
Author: TileDB, Inc. [aut, cph],
Isaiah Norton [cre]
Maintainer: Isaiah Norton <isaiah@tiledb.com>
Diff between tiledb versions 0.30.2 dated 2024-10-04 and 0.31.1 dated 2025-04-24
tiledb-0.30.2/tiledb/R/Init.R |only tiledb-0.31.1/tiledb/DESCRIPTION | 11 tiledb-0.31.1/tiledb/MD5 | 446 - tiledb-0.31.1/tiledb/NAMESPACE | 6 tiledb-0.31.1/tiledb/NEWS.md | 19 tiledb-0.31.1/tiledb/R/Array.R | 227 tiledb-0.31.1/tiledb/R/ArraySchema.R | 981 ++- tiledb-0.31.1/tiledb/R/ArraySchemaEvolution.R | 187 tiledb-0.31.1/tiledb/R/ArrowIO.R | 60 tiledb-0.31.1/tiledb/R/Attribute.R | 311 - tiledb-0.31.1/tiledb/R/BatchedQuery.R | 695 +- tiledb-0.31.1/tiledb/R/Config.R | 82 tiledb-0.31.1/tiledb/R/Ctx.R | 56 tiledb-0.31.1/tiledb/R/CurrentDomain.R | 65 tiledb-0.31.1/tiledb/R/DataFrame.R | 438 - tiledb-0.31.1/tiledb/R/Dim.R | 279 tiledb-0.31.1/tiledb/R/Domain.R | 174 tiledb-0.31.1/tiledb/R/Error.R | 4 tiledb-0.31.1/tiledb/R/Filestore.R | 74 tiledb-0.31.1/tiledb/R/Filter.R | 75 tiledb-0.31.1/tiledb/R/FilterList.R | 108 tiledb-0.31.1/tiledb/R/FragmentInfo.R | 183 tiledb-0.31.1/tiledb/R/Group.R | 417 - tiledb-0.31.1/tiledb/R/Matrix.R | 98 tiledb-0.31.1/tiledb/R/Metadata.R | 51 tiledb-0.31.1/tiledb/R/NDRectangle.R | 145 tiledb-0.31.1/tiledb/R/Object.R | 54 tiledb-0.31.1/tiledb/R/Query.R | 291 - tiledb-0.31.1/tiledb/R/QueryCondition.R | 375 - tiledb-0.31.1/tiledb/R/RcppExports.R | 4 tiledb-0.31.1/tiledb/R/SparseMatrix.R | 194 tiledb-0.31.1/tiledb/R/Stats.R | 18 tiledb-0.31.1/tiledb/R/Subarray.R | 27 tiledb-0.31.1/tiledb/R/TileDB-Package.R | 2 tiledb-0.31.1/tiledb/R/TileDBArray.R | 2814 +++++----- tiledb-0.31.1/tiledb/R/Utils.R | 365 - tiledb-0.31.1/tiledb/R/VFS.R | 327 - tiledb-0.31.1/tiledb/R/Version.R | 182 tiledb-0.31.1/tiledb/R/zzz.R |only tiledb-0.31.1/tiledb/README.md | 4 tiledb-0.31.1/tiledb/build/vignette.rds |binary tiledb-0.31.1/tiledb/configure.ac | 6 tiledb-0.31.1/tiledb/inst/doc/data-ingestion-from-sql.html | 2 tiledb-0.31.1/tiledb/inst/doc/documentation.html | 2 tiledb-0.31.1/tiledb/inst/doc/installation-options.html | 2 tiledb-0.31.1/tiledb/inst/doc/introduction.html | 6 tiledb-0.31.1/tiledb/inst/doc/introduction.md | 4 tiledb-0.31.1/tiledb/inst/doc/tiledb-mariadb-examples.html | 2 tiledb-0.31.1/tiledb/inst/pkgconfigtest |only tiledb-0.31.1/tiledb/inst/tinytest/test_arrayschema.R | 7 tiledb-0.31.1/tiledb/inst/tinytest/test_querycondition.R | 30 tiledb-0.31.1/tiledb/inst/tinytest/test_tiledbarray.R | 9 tiledb-0.31.1/tiledb/inst/tinytest/test_vfs.R | 111 tiledb-0.31.1/tiledb/man/array_consolidate.Rd | 9 tiledb-0.31.1/tiledb/man/array_vacuum.Rd | 16 tiledb-0.31.1/tiledb/man/as.vector.tiledb_config.Rd | 4 tiledb-0.31.1/tiledb/man/attrs-set-tiledb_array-method.Rd | 6 tiledb-0.31.1/tiledb/man/attrs-tiledb_array-ANY-method.Rd | 4 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-ANY-method.Rd | 14 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-character-method.Rd | 14 tiledb-0.31.1/tiledb/man/attrs-tiledb_array_schema-numeric-method.Rd | 14 tiledb-0.31.1/tiledb/man/cell_order-tiledb_array_schema-method.Rd | 5 tiledb-0.31.1/tiledb/man/config-tiledb_ctx-method.Rd | 4 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insertions(+), 4709 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics
Description: A collection of functions to create spatial weights matrix
objects from polygon 'contiguities', from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial 'autocorrelation',
including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord'
(1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel'
general cross product statistic, Empirical Bayes estimates and
'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992)
<doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured
join count statistics, 'APLE' ('Li 'et al.' )
<doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C'
('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and
'Getis/Ord' G ('Ord' and 'Getis' 1995)
< [...truncated...]
Author: Roger Bivand [cre, aut] ,
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assuncao [ctb],
Anil Bera [ctb],
Olaf Berke [ctb],
F. Guillaume Blanchet [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Steph [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 1.3-10 dated 2025-01-20 and 1.3-11 dated 2025-04-24
spdep-1.3-10/spdep/inst/etc/misc/contiguity-myid.swm |only spdep-1.3-10/spdep/inst/etc/misc/contiguity-unique-id-islands.swm |only spdep-1.3-10/spdep/inst/etc/misc/contiguity-unique-id.swm |only spdep-1.3-10/spdep/inst/etc/misc/nc-contiguity-unique-id-island.swm |only spdep-1.3-10/spdep/inst/etc/misc/nc-contiguity-unique-id.swm |only spdep-1.3-11/spdep/DESCRIPTION | 8 - spdep-1.3-11/spdep/MD5 | 53 ++++------ spdep-1.3-11/spdep/NAMESPACE | 7 - spdep-1.3-11/spdep/NEWS.md | 12 +- spdep-1.3-11/spdep/R/SD.RStests.R | 21 ++- spdep-1.3-11/spdep/R/cat_durbin.R |only spdep-1.3-11/spdep/build/partial.rdb |binary spdep-1.3-11/spdep/build/vignette.rds |binary spdep-1.3-11/spdep/inst/doc/CO69.html | 6 - spdep-1.3-11/spdep/inst/doc/nb_sf.Rmd | 2 spdep-1.3-11/spdep/inst/doc/nb_sf.html | 33 +++--- spdep-1.3-11/spdep/inst/doc/sids.html | 16 +-- spdep-1.3-11/spdep/inst/doc/subgraphs.R | 13 +- spdep-1.3-11/spdep/inst/doc/subgraphs.Rmd | 13 +- spdep-1.3-11/spdep/inst/doc/subgraphs.html | 28 ++--- spdep-1.3-11/spdep/inst/tinytest/test_Durbin_factor.R |only spdep-1.3-11/spdep/man/SD.RStests.Rd | 15 ++ spdep-1.3-11/spdep/man/bhicv.Rd | 3 spdep-1.3-11/spdep/man/joincount.multi.Rd | 3 spdep-1.3-11/spdep/man/licd_multi.Rd | 3 spdep-1.3-11/spdep/man/localC.Rd | 2 spdep-1.3-11/spdep/man/mstree.Rd | 3 spdep-1.3-11/spdep/man/read.gwt2nb.Rd | 3 spdep-1.3-11/spdep/man/skater.Rd | 3 spdep-1.3-11/spdep/vignettes/nb_sf.Rmd | 2 spdep-1.3-11/spdep/vignettes/subgraphs.Rmd | 13 +- 31 files changed, 148 insertions(+), 114 deletions(-)
Title: Communicate with 'Ollama' to Run Large Language Models Locally
Description: Wraps the 'Ollama' <https://ollama.com> API, which can be used to
communicate with generative large language models locally.
Author: Johannes B. Gruber [aut, cre] ,
Maximilian Weber [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between rollama versions 0.2.0 dated 2024-12-06 and 0.2.1 dated 2025-04-24
rollama-0.2.0/rollama/tests/testthat/_snaps |only rollama-0.2.1/rollama/DESCRIPTION | 6 rollama-0.2.1/rollama/MD5 | 47 +- rollama-0.2.1/rollama/NEWS.md | 7 rollama-0.2.1/rollama/R/chat.r | 37 +- rollama-0.2.1/rollama/R/embedding.r | 3 rollama-0.2.1/rollama/R/lib.R | 128 ++++--- rollama-0.2.1/rollama/R/models.r | 8 rollama-0.2.1/rollama/R/rollama-package.R | 7 rollama-0.2.1/rollama/R/utils.r | 19 - rollama-0.2.1/rollama/README.md | 309 +++++++------------ rollama-0.2.1/rollama/build/vignette.rds |binary rollama-0.2.1/rollama/inst/WORDLIST | 1 rollama-0.2.1/rollama/inst/doc/annotation.html | 5 rollama-0.2.1/rollama/inst/doc/hf-gguf.html | 5 rollama-0.2.1/rollama/inst/doc/image-annotation.html | 5 rollama-0.2.1/rollama/inst/doc/text-embedding.html | 5 rollama-0.2.1/rollama/man/ping_ollama.Rd | 4 rollama-0.2.1/rollama/man/pull_model.Rd | 7 rollama-0.2.1/rollama/man/query.Rd | 23 + rollama-0.2.1/rollama/man/rollama-options.Rd | 7 rollama-0.2.1/rollama/man/rollama-package.Rd | 2 rollama-0.2.1/rollama/tests/testthat.R | 1 rollama-0.2.1/rollama/tests/testthat/test-chat.R | 17 + rollama-0.2.1/rollama/tests/testthat/test-models.R | 6 25 files changed, 362 insertions(+), 297 deletions(-)
Title: Copula-Based Mixed Regression Models
Description: Estimation of 2-level factor copula-based regression models for clustered data where the response variable can be either discrete or continuous.
Author: Pavel Krupskii [aut, ctb, cph],
Bouchra R. Nasri [aut, ctb, cph],
Bruno N Remillard [aut, cre, cph]
Maintainer: Bruno N Remillard <bruno.remillard@hec.ca>
Diff between CopulaGAMM versions 0.4.1 dated 2023-11-30 and 0.6.5 dated 2025-04-24
DESCRIPTION | 8 - MD5 | 48 +++++----- NAMESPACE | 2 R/EstContinuous.R | 210 ++++++++++++++++++++++++++++++++++++----------- R/EstCopulaGAMM.R |only R/EstDiscrete.R | 71 +++++++++------ R/MAP.continuous.R | 16 +-- R/MAP.discrete.R | 7 + R/SimGenCluster.R | 16 +-- R/SimMultinomial.R | 9 +- R/coplik.R | 31 ++++-- R/dcop.R | 17 ++- R/invfunc.R | 4 R/margins.R | 25 +++-- R/predictContinuous.R | 6 - R/predictCopulaGAMM.R |only R/predictDiscrete.R | 3 data/normal.rda |binary data/out.normal.rda |binary man/EstContinuous.Rd | 20 ++-- man/EstCopulaGAMM.Rd |only man/EstDiscrete.Rd | 4 man/SimGenCluster.Rd | 4 man/SimMultinomial.Rd | 6 - man/dcop.Rd | 2 man/normal.Rd | 2 man/predictCopulaGAMM.Rd |only 27 files changed, 334 insertions(+), 177 deletions(-)
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing
Data
Description: A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of s [...truncated...]
Author: Massimo Andreatta [aut, cre] ,
Ariel Berenstein [aut] ,
Josep Garnica [aut],
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>
Diff between scGate versions 1.6.2 dated 2024-04-23 and 1.7.0 dated 2025-04-24
DESCRIPTION | 16 ++++++++-------- MD5 | 14 +++++++------- R/utils.R | 11 ++++++++++- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/make.index.Rmd | 2 +- inst/doc/make.index.html | 2 +- vignettes/make.index.Rmd | 2 +- 8 files changed, 34 insertions(+), 19 deletions(-)
Title: Mating Environmental Designs
Description: In breeding experiments, mating environmental (ME) designs are very popular as mating designs are directly implemented in the field environment using block or row-column designs. Here, three functions are given related to three new methods which will generate mating diallel cross designs (Hinkelmann and Kempthorne, 1963<doi:10.2307/2333899>) or mating environmental (ME) designs along with design parameters, C matrix, eigenvalues (EVs), degree of fractionations (DF) and canonical efficiency factor (CEF). Another one function is added to check the properties of a given ME diallel cross design.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between MEDesigns versions 1.0.0 dated 2024-12-02 and 1.0.1 dated 2025-04-24
DESCRIPTION | 9 ++- MD5 | 13 +++- NAMESPACE | 3 + R/CheckME_Diallel.R | 2 R/MEBanalysis.R |only R/ME_CDC.R | 154 +++++++++++++++++----------------------------------- R/sysdata.rda |only data |only man/MEBanalysis.Rd |only man/MEdata.Rd |only 10 files changed, 70 insertions(+), 111 deletions(-)
Title: Unified Framework for Numerical Optimizers
Description: Provides a unified object-oriented framework for numerical
optimizers in R. Allows for both minimization and maximization with any
optimizer, optimization over more than one function argument, measuring of
computation time, setting a time limit for long optimization tasks.
Author: Lennart Oelschlaeger [aut, cre]
,
Marius Oetting [ctb]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between optimizeR versions 1.1.3 dated 2025-03-27 and 1.2.0 dated 2025-04-24
optimizeR-1.1.3/optimizeR/R/debug.R |only optimizeR-1.1.3/optimizeR/R/legacy.R |only optimizeR-1.1.3/optimizeR/man/apply_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/define_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/new_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/test_objective.Rd |only optimizeR-1.1.3/optimizeR/man/test_optimizer.Rd |only optimizeR-1.1.3/optimizeR/man/validate_optimizer.Rd |only optimizeR-1.1.3/optimizeR/tests/testthat/_snaps/legacy.md |only optimizeR-1.1.3/optimizeR/tests/testthat/test-debug.R |only optimizeR-1.1.3/optimizeR/tests/testthat/test-legacy.R |only optimizeR-1.2.0/optimizeR/DESCRIPTION | 14 optimizeR-1.2.0/optimizeR/MD5 | 48 optimizeR-1.2.0/optimizeR/NAMESPACE | 51 optimizeR-1.2.0/optimizeR/NEWS.md | 6 optimizeR-1.2.0/optimizeR/R/objective.R | 603 ++++- optimizeR-1.2.0/optimizeR/R/optimizeR-package.R | 59 optimizeR-1.2.0/optimizeR/R/optimizer.R | 1061 ++++++---- optimizeR-1.2.0/optimizeR/R/optimizer_dictionary.R | 202 + optimizeR-1.2.0/optimizeR/R/parameter_spaces.R | 30 optimizeR-1.2.0/optimizeR/README.md | 107 - optimizeR-1.2.0/optimizeR/man/Objective.Rd | 303 ++ optimizeR-1.2.0/optimizeR/man/Optimizer.Rd | 342 ++- optimizeR-1.2.0/optimizeR/man/ParameterSpaces.Rd | 18 optimizeR-1.2.0/optimizeR/man/figures/README-plot-ackley-1.png |binary optimizeR-1.2.0/optimizeR/man/optimizer_dictionary.Rd | 7 optimizeR-1.2.0/optimizeR/tests/testthat/_snaps/objective.md | 263 ++ optimizeR-1.2.0/optimizeR/tests/testthat/_snaps/optimizer.md |only optimizeR-1.2.0/optimizeR/tests/testthat/test-objective.R | 223 ++ optimizeR-1.2.0/optimizeR/tests/testthat/test-optimizer.R | 206 + optimizeR-1.2.0/optimizeR/tests/testthat/test-parameter_spaces.R | 8 31 files changed, 2605 insertions(+), 946 deletions(-)
Title: 'DT' Extension for CRUD (Create, Read, Update, Delete)
Applications in 'shiny'
Description: The core of this package is a function eDT() which enhances DT::datatable() such that it can be used to interactively modify data in 'shiny'. By the use of generic 'dplyr' methods it supports many types of data storage, with relational databases ('dbplyr') being the main use case.
Author: Jasper Schelfhout [aut, cre],
Maxim Nazarov [rev],
Daan Seynaeve [rev],
Lennart Tuijnder [rev],
Saar Junius [aut]
Maintainer: Jasper Schelfhout <jasper.schelfhout@openanalytics.eu>
Diff between editbl versions 1.2.0 dated 2025-03-31 and 1.3.0 dated 2025-04-24
DESCRIPTION | 12 - MD5 | 59 +++--- R/eDT.R | 195 +++++++++++++++++++-- R/utils.R | 11 - README.md | 18 + inst/NEWS | 19 +- inst/doc/howto_relational_db.R | 2 inst/doc/howto_relational_db.html | 6 inst/doc/howto_relational_db.rmd | 2 inst/doc/howto_relational_db_dm.html | 6 inst/doc/howto_row_level_access.html | 4 inst/doc/howto_switch_from_DT.html | 4 man/addButtons.Rd | 9 man/canXXXRowTemplate.Rd | 8 man/createButtons.Rd | 9 man/createCloneButtonHTML.Rd |only man/createCloneButtonHTML_shiny.Rd |only man/eDT.Rd | 11 + man/evalCanCloneRow.Rd |only man/evalCanDeleteRow.Rd | 2 man/evalCanEditRow.Rd | 2 man/initData.Rd | 13 + tests/testthat/test-utils.R | 30 +++ vignettes/howto_relational_db.rmd | 2 vignettes/screenshots/howto_relational_db_1.png |binary vignettes/screenshots/howto_relational_db_2.png |binary vignettes/screenshots/howto_relational_db_3.png |binary vignettes/screenshots/howto_relational_db_dm_1.png |binary vignettes/screenshots/howto_row_level_access_1.png |binary vignettes/screenshots/howto_row_level_access_2.png |binary vignettes/screenshots/howto_switch_from_DT_1.png |binary vignettes/screenshots/howto_switch_from_DT_2.png |binary 32 files changed, 336 insertions(+), 88 deletions(-)
Title: Generalized Propensity Score Estimation and Matching for
Multiple Groups
Description: Implements the Vector Matching algorithm to match multiple
treatment groups based on previously estimated generalized propensity
scores. The package includes tools for visualizing initial confounder
imbalances, estimating treatment assignment probabilities using various
methods, defining the common support region, performing matching across
multiple groups, and evaluating matching quality. For more details, see
Lopez and Gutman (2017) <doi:10.1214/17-STS612>.
Author: Mateusz Kolek [aut, cre, cph]
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>
Diff between vecmatch versions 1.0.3 dated 2025-03-28 and 1.1.0 dated 2025-04-24
DESCRIPTION | 9 +-- MD5 | 27 ++++++--- NEWS.md |only R/csregion.R | 30 ++++++++++ R/match_gps.R | 106 ++++++++++++++++++++++++-------------- R/methods.R | 15 +++++ README.md | 42 +++++++-------- build/vignette.rds |only inst/WORDLIST | 1 inst/doc |only man/csregion.Rd | 14 ++++- man/figures/unnamed-chunk-2-1.png |binary tests/testthat/test-csregion.R | 12 +++- tests/testthat/test-match_gps.R | 38 +++---------- vignettes |only 15 files changed, 190 insertions(+), 104 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel [aut, cre] ,
Khanh Nguyen [aut] ,
Terry Leitch [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.25 dated 2025-03-25 and 0.4.26 dated 2025-04-24
ChangeLog | 23 +++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- configure | 18 +++++++++--------- configure.ac | 2 +- data/tsQuotes.RData |binary data/vcube.RData |binary inst/NEWS.Rd | 8 ++++++++ inst/tinytest/test_schedule.R | 12 +++++++++--- src/Makevars.win | 18 ++++++++++++++---- 10 files changed, 77 insertions(+), 30 deletions(-)
Title: Search and Get Data from the I14Y Interoperability Platform of
Switzerland
Description: Search and download Swiss data and metadata from the I14Y
interoperability platform of Switzerland using its public APIs
<https://www.i14y.admin.ch/api/index.html>.
Author: Felix Luginbuhl [aut, cre, cph]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between I14Y versions 0.1.2 dated 2025-04-16 and 0.1.3 dated 2025-04-24
DESCRIPTION | 7 ++++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 10 insertions(+), 5 deletions(-)
Title: 'HiGHS' Optimization Solver
Description: R interface to 'HiGHS', an optimization solver for solving mixed integer
optimization problems with quadratic or linear objective and linear constraints.
Author: Florian Schwendinger [aut, cre],
Dirk Schumacher [aut],
Julian Hall [cph],
Ivet Galabova [cph],
Leona Gottwald [cph],
Michael Feldmeier [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between highs versions 1.9.0-1 dated 2025-01-08 and 1.10.0-1 dated 2025-04-24
highs-1.10.0-1/highs/DESCRIPTION | 7 highs-1.10.0-1/highs/MD5 | 1038 +++++----- highs-1.10.0-1/highs/NAMESPACE | 60 highs-1.10.0-1/highs/NEWS.md | 5 highs-1.10.0-1/highs/R/RcppExports.R | 92 highs-1.10.0-1/highs/R/constants.R |only highs-1.10.0-1/highs/R/examples.R |only highs-1.10.0-1/highs/R/highs.R | 62 highs-1.10.0-1/highs/R/model-api.R |only highs-1.10.0-1/highs/R/options.R | 345 +-- highs-1.10.0-1/highs/R/smat.R | 9 highs-1.10.0-1/highs/R/solver-api.R |only highs-1.10.0-1/highs/README.md | 425 ++-- highs-1.10.0-1/highs/configure | 7 highs-1.10.0-1/highs/inst/HiGHS/CMakeLists.txt | 236 +- highs-1.10.0-1/highs/inst/HiGHS/FEATURES.md | 14 highs-1.10.0-1/highs/inst/HiGHS/MODULE.bazel | 2 highs-1.10.0-1/highs/inst/HiGHS/README.md | 70 highs-1.10.0-1/highs/inst/HiGHS/Version.txt | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/FindCUDAConf.cmake |only highs-1.10.0-1/highs/inst/HiGHS/cmake/cpp-highs.cmake | 145 + highs-1.10.0-1/highs/inst/HiGHS/cmake/dotnet.cmake | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/highs-config.cmake.in |only highs-1.10.0-1/highs/inst/HiGHS/cmake/python-highs.cmake | 2 highs-1.10.0-1/highs/inst/HiGHS/cmake/sources-python.cmake | 834 ++++---- highs-1.10.0-1/highs/inst/HiGHS/cmake/sources.cmake | 61 highs-1.10.0-1/highs/inst/HiGHS/extern/filereaderlp/reader.cpp | 11 highs-1.10.0-1/highs/inst/HiGHS/highs |only highs-1.10.0-1/highs/inst/HiGHS/meson.build | 7 highs-1.10.0-1/highs/inst/HiGHS/nuget/Highs.csproj | 2 highs-1.10.0-1/highs/inst/HiGHS/nuget/README.md | 2 highs-1.10.0-1/highs/inst/HiGHS/pyproject.toml | 20 highs-1.10.0-1/highs/inst/HiGHS/tests/test_highspy.py | 32 highs-1.10.0-1/highs/inst/build_highs.sh | 108 - highs-1.10.0-1/highs/inst/tinytest/test_model-api.R |only highs-1.10.0-1/highs/inst/tinytest/test_solver-api.R |only highs-1.10.0-1/highs/man/example_model.Rd |only highs-1.10.0-1/highs/man/example_solver.Rd |only highs-1.10.0-1/highs/man/hi_model_get_ncons.Rd |only highs-1.10.0-1/highs/man/hi_model_get_nvars.Rd |only highs-1.10.0-1/highs/man/hi_model_set_constraint_matrix.Rd |only highs-1.10.0-1/highs/man/hi_model_set_hessian.Rd |only highs-1.10.0-1/highs/man/hi_model_set_lhs.Rd |only highs-1.10.0-1/highs/man/hi_model_set_lower.Rd |only highs-1.10.0-1/highs/man/hi_model_set_ncol.Rd |only highs-1.10.0-1/highs/man/hi_model_set_nrow.Rd |only highs-1.10.0-1/highs/man/hi_model_set_objective.Rd |only highs-1.10.0-1/highs/man/hi_model_set_offset.Rd |only highs-1.10.0-1/highs/man/hi_model_set_rhs.Rd |only highs-1.10.0-1/highs/man/hi_model_set_sense.Rd |only highs-1.10.0-1/highs/man/hi_model_set_upper.Rd |only highs-1.10.0-1/highs/man/hi_model_set_vartype.Rd |only highs-1.10.0-1/highs/man/hi_new_model.Rd |only highs-1.10.0-1/highs/man/hi_new_solver.Rd |only highs-1.10.0-1/highs/man/hi_reset_global_scheduler.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_cols.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_rows.Rd |only highs-1.10.0-1/highs/man/hi_solver_add_vars.Rd |only highs-1.10.0-1/highs/man/hi_solver_change_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_change_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear_model.Rd |only highs-1.10.0-1/highs/man/hi_solver_clear_solver.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_bool_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_constraint_matrix.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_dbl_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_int_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_lp_costs.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_num_col.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_num_row.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_options.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_sense.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_solution.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_str_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_get_vartype.Rd |only highs-1.10.0-1/highs/man/hi_solver_infinity.Rd |only highs-1.10.0-1/highs/man/hi_solver_info.Rd |only highs-1.10.0-1/highs/man/hi_solver_run.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_coeff.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_constraint_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_integrality.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_objective.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_offset.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_option.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_options.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_sense.Rd |only highs-1.10.0-1/highs/man/hi_solver_set_variable_bounds.Rd |only highs-1.10.0-1/highs/man/hi_solver_status.Rd |only highs-1.10.0-1/highs/man/hi_solver_status_message.Rd |only highs-1.10.0-1/highs/man/hi_solver_write_basis.Rd |only highs-1.10.0-1/highs/man/hi_solver_write_model.Rd |only highs-1.10.0-1/highs/man/highs_write_model.Rd |only highs-1.10.0-1/highs/src/Makevars.in | 1 highs-1.10.0-1/highs/src/RcppExports.cpp | 300 ++ highs-1.10.0-1/highs/src/highs_interface.cpp | 319 ++- highs-1.9.0-1/highs/R/api.R |only highs-1.9.0-1/highs/R/model.R |only highs-1.9.0-1/highs/inst/HiGHS/app |only highs-1.9.0-1/highs/inst/HiGHS/docs |only highs-1.9.0-1/highs/inst/HiGHS/examples |only highs-1.9.0-1/highs/inst/HiGHS/extern/catch.hpp |only highs-1.9.0-1/highs/inst/HiGHS/highs-config.cmake.in |only highs-1.9.0-1/highs/inst/HiGHS/src |only highs-1.9.0-1/highs/man/hapi_new_model.Rd |only 107 files changed, 2730 insertions(+), 1490 deletions(-)
Title: Non-Negative Matrix Factorization for Single-Cell Omics
Description: A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.
Author: Massimo Andreatta [aut, cre] ,
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unige.ch>
Diff between GeneNMF versions 0.6.2 dated 2024-11-12 and 0.8.0 dated 2025-04-24
DESCRIPTION | 12 ++++---- MD5 | 16 +++++------ NAMESPACE | 1 R/main.R | 69 ++++++++++++++++++++++++++++++++++++++++--------- R/utils.R | 40 ++++++++++++++++++++++++++-- README.md | 2 - inst/NEWS.Rd | 16 +++++++++++ man/getMetaPrograms.Rd | 10 ++++--- man/runGSEA.Rd | 5 +++ 9 files changed, 137 insertions(+), 34 deletions(-)
Title: Functions for Calculating Fit-Robustness of CNA-Solutions
Description: Functions for automatically performing
a reanalysis series
on a data set using CNA, and for calculating the fit-robustness
of the resulting models, as described in
Parkkinen and Baumgartner (2021) <doi:10.1177/0049124120986200>.
Author: Veli-Pekka Parkkinen [aut, cre, cph],
Michael Baumgartner [aut, cph],
Mathias Ambuehl [aut, cph]
Maintainer: Veli-Pekka Parkkinen <parkkinenv@gmail.com>
Diff between frscore versions 0.4.1 dated 2024-06-11 and 0.5.0 dated 2025-04-24
DESCRIPTION | 8 MD5 | 29 - NAMESPACE | 2 NEWS.md | 11 R/causal_submodel.R | 2 R/frscore.R | 162 ++------- R/frscored_cna.R | 41 +- R/plot_submodel_network.R |only man/causal_submodel.Rd | 6 man/frscore.Rd | 25 - man/frscored_cna.Rd | 35 -- man/plot_submodel_network.Rd |only man/rean_cna.Rd | 21 + man/submodel_adjacencies_to_igraph.Rd |only tests/testthat/_snaps/frscore.md | 12 tests/testthat/_snaps/frscored_cna.md | 576 +++++++++++++++------------------- tests/testthat/test_frscored_cna.R | 47 ++ 17 files changed, 423 insertions(+), 554 deletions(-)
Title: Flexible, Extensible, & Reproducible Processing of Pupil Data
Description: Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date unfortunately lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris', on the other hand, follows a design philosophy that provides users with an intuitive, modular, performant, and extensible pupillometry data preprocessing framework out-of-the-box. 'eyeris' introduces a Brain Imaging Data Structure (BIDS)-like organization for derivative (i.e., preprocessed) pupillometry [...truncated...]
Author: Shawn Schwartz [aut, cre, cph]
,
Stanford Wu Tsai Human Performance Alliance [fnd],
Stanford Ric Weiland Graduate Fellowship [fnd],
Stanford Center for Mind, Brain, Computation and Technology [fnd],
NIH National Institute on Aging R01 AG065255 [fnd], [...truncated...]
Maintainer: Shawn Schwartz <stschwartz@stanford.edu>
Diff between eyeris versions 1.0.0 dated 2025-03-31 and 1.1.0 dated 2025-04-24
eyeris-1.0.0/eyeris/man/figures/interactive-reports-demo.gif |only eyeris-1.0.0/eyeris/man/figures/report_example_annotated-1.png |only eyeris-1.1.0/eyeris/DESCRIPTION | 55 +- eyeris-1.1.0/eyeris/LICENSE | 2 eyeris-1.1.0/eyeris/MD5 | 109 ++-- eyeris-1.1.0/eyeris/NAMESPACE | 4 eyeris-1.1.0/eyeris/NEWS.md | 49 + eyeris-1.1.0/eyeris/R/constants.R |only eyeris-1.1.0/eyeris/R/eyeris-package.R | 3 eyeris-1.1.0/eyeris/R/pipeline-bidsify.R | 11 eyeris-1.1.0/eyeris/R/pipeline-deblink.R | 35 + eyeris-1.1.0/eyeris/R/pipeline-detransient.R | 28 - eyeris-1.1.0/eyeris/R/pipeline-detrend.R | 27 - eyeris-1.1.0/eyeris/R/pipeline-epoch.R | 9 eyeris-1.1.0/eyeris/R/pipeline-glassbox.R | 268 +++++++--- eyeris-1.1.0/eyeris/R/pipeline-interpolate.R | 29 - eyeris-1.1.0/eyeris/R/pipeline-loadasc.R | 36 + eyeris-1.1.0/eyeris/R/pipeline-lpfilt.R | 30 - eyeris-1.1.0/eyeris/R/pipeline-zscore.R | 27 - eyeris-1.1.0/eyeris/R/plot.eyeris.R | 4 eyeris-1.1.0/eyeris/README.md | 76 +- eyeris-1.1.0/eyeris/build/partial.rdb |binary eyeris-1.1.0/eyeris/build/vignette.rds |binary eyeris-1.1.0/eyeris/inst/doc/anatomy.R | 1 eyeris-1.1.0/eyeris/inst/doc/anatomy.Rmd | 5 eyeris-1.1.0/eyeris/inst/doc/anatomy.html | 32 - eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.R | 8 eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.Rmd | 77 +- eyeris-1.1.0/eyeris/inst/doc/complete-pipeline.html | 131 +++- eyeris-1.1.0/eyeris/inst/doc/custom-extensions.Rmd | 2 eyeris-1.1.0/eyeris/inst/doc/custom-extensions.html | 27 - eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.R | 4 eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.Rmd | 8 eyeris-1.1.0/eyeris/inst/doc/epoching-bids-reports.html | 37 - eyeris-1.1.0/eyeris/inst/doc/reports.R | 8 eyeris-1.1.0/eyeris/inst/doc/reports.Rmd | 10 eyeris-1.1.0/eyeris/inst/doc/reports.html | 27 - eyeris-1.1.0/eyeris/man/bidsify.Rd | 11 eyeris-1.1.0/eyeris/man/deblink.Rd | 36 + eyeris-1.1.0/eyeris/man/detransient.Rd | 29 - eyeris-1.1.0/eyeris/man/detrend.Rd | 28 - eyeris-1.1.0/eyeris/man/epoch.Rd | 9 eyeris-1.1.0/eyeris/man/eyelink_asc_demo_dataset.Rd |only eyeris-1.1.0/eyeris/man/eyeris-package.Rd | 13 eyeris-1.1.0/eyeris/man/figures/README-timeseries-plot-1.png |only eyeris-1.1.0/eyeris/man/figures/README-timeseries-plot-2.png |only eyeris-1.1.0/eyeris/man/figures/README-unnamed-chunk-3-1.png |only eyeris-1.1.0/eyeris/man/figures/logo.png |binary eyeris-1.1.0/eyeris/man/glassbox.Rd | 77 +- eyeris-1.1.0/eyeris/man/interpolate.Rd | 30 - eyeris-1.1.0/eyeris/man/load_asc.Rd | 36 + eyeris-1.1.0/eyeris/man/lpfilt.Rd | 31 - eyeris-1.1.0/eyeris/man/plot.eyeris.Rd | 4 eyeris-1.1.0/eyeris/man/zscore.Rd | 28 - eyeris-1.1.0/eyeris/vignettes/anatomy.Rmd | 5 eyeris-1.1.0/eyeris/vignettes/complete-pipeline.Rmd | 77 +- eyeris-1.1.0/eyeris/vignettes/custom-extensions.Rmd | 2 eyeris-1.1.0/eyeris/vignettes/epoching-bids-reports.Rmd | 8 eyeris-1.1.0/eyeris/vignettes/reports.Rmd | 10 59 files changed, 1108 insertions(+), 505 deletions(-)
Title: Bayesian Inference for Neyman-Scott Point Processes
Description: The Bayesian MCMC estimation of parameters for Thomas-type cluster
point process with various inhomogeneities. It allows for inhomogeneity in
(i) distribution of parent points, (ii) mean number of points in a cluster,
(iii) cluster spread. The package also allows for the Bayesian MCMC
algorithm for the homogeneous generalized Thomas process. The cluster size
is allowed to have a variance that is greater or less than the expected
value (cluster sizes are over or under dispersed). Details are described in
Dvořák, Remeš, Beránek & Mrkvička (2022) <arXiv: 10.48550/arXiv.2205.07946>.
Author: Mrkvicka Tomas [aut],
Dvorak Jiri [aut],
Beranek Ladislav [aut],
Remes Radim [aut, cre],
Park Jaewoo [ctb],
Lee Sujeong [ctb]
Maintainer: Remes Radim <inrem@jcu.cz>
Diff between binspp versions 0.1.26 dated 2022-12-08 and 0.2.0 dated 2025-04-24
DESCRIPTION | 18 - MD5 | 32 +- NAMESPACE | 11 R/RcppExports.R | 39 ++ R/binspp-package.R | 114 ++++--- R/estgtp.R | 606 +++++++++++++++++++++--------------------- R/estinternsp.R |only build/partial.rdb |binary man/AuxVarGen.Rd |only man/binspp-package.Rd |only man/binspp.Rd | 7 man/coeff.Rd |only man/estinternsp.Rd |only man/pCClik2.Rd |only man/plot_conn.Rd |only man/print_outputs_internsp.Rd |only src/Makevars | 22 + src/Makevars.win |only src/RcppExports.cpp | 106 +++++++ src/STThomas.cpp |only src/header.h | 1 src/poit_updates.cpp | 3 22 files changed, 589 insertions(+), 370 deletions(-)
Title: Time Series Prediction with Integrated Tuning
Description: Time series prediction is a critical task in data analysis, requiring not only the selection of appropriate models, but also suitable data preprocessing and tuning strategies.
TSPredIT (Time Series Prediction with Integrated Tuning) is a framework that provides a seamless integration of data preprocessing, decomposition, model training, hyperparameter optimization, and evaluation.
Unlike other frameworks, TSPredIT emphasizes the co-optimization of both preprocessing and modeling steps, improving predictive performance.
It supports a variety of statistical and machine learning models, filtering techniques, outlier detection, data augmentation, and ensemble strategies.
More information is available in Salles et al. <doi:10.1007/978-3-662-68014-8_2>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Carla Pacheco [aut],
Cristiane Gea [aut],
Diogo Santos [aut],
Rebecca Salles [aut],
Vitoria Birindiba [aut],
Eduardo Bezerra [aut],
Esther Pacitti [aut],
Fabio Porto [aut],
CEFET/RJ [cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between tspredit versions 1.0.787 dated 2024-12-04 and 1.1.707 dated 2025-04-24
DESCRIPTION | 151 ++++++++++++++++++++++++------------------------- MD5 | 58 +++++++++--------- R/recursive_filter.R | 2 R/ts_aug_awareness.R | 2 R/ts_aug_awaresmooth.R | 2 R/ts_aug_flip.R | 2 R/ts_aug_jitter.R | 4 - R/ts_aug_none.R | 2 R/ts_aug_shrink.R | 2 R/ts_aug_stretch.R | 2 R/ts_aug_wormhole.R | 2 R/ts_fil_ema.R | 2 R/ts_fil_emd.R | 2 R/ts_fil_fft.R | 2 R/ts_fil_hp.R | 2 R/ts_fil_kalman.R | 2 R/ts_fil_lowess.R | 2 R/ts_fil_ma.R | 2 R/ts_fil_none.R | 2 R/ts_fil_qes.R | 2 R/ts_fil_remd.R | 2 R/ts_fil_seas_adj.R | 2 R/ts_fil_ses.R | 2 R/ts_fil_smooth.R | 2 R/ts_fil_spline.R | 2 R/ts_fil_wavelet.R | 4 - R/ts_fil_winsor.R | 2 R/ts_maintune.R | 4 - R/ts_norm_none.R | 2 README.md | 72 ++++++++++++++++------- 30 files changed, 186 insertions(+), 155 deletions(-)
Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut],
Ran Tao [aut, cre],
Joey Sherrill [prg],
Jiangmei Xiong [ctb]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>
Diff between sleev versions 1.1.1 dated 2025-04-20 and 1.1.2 dated 2025-04-24
sleev-1.1.1/sleev/inst/doc/sleev_vignette.R |only sleev-1.1.1/sleev/inst/doc/sleev_vignette.Rmd |only sleev-1.1.1/sleev/inst/doc/sleev_vignette.pdf |only sleev-1.1.1/sleev/vignettes/sleev_vignette.Rmd |only sleev-1.1.2/sleev/DESCRIPTION | 11 ++++++----- sleev-1.1.2/sleev/MD5 | 14 +++++++------- sleev-1.1.2/sleev/build/vignette.rds |binary sleev-1.1.2/sleev/inst/article/sleev_vignette.pdf |binary sleev-1.1.2/sleev/inst/doc/sleev_vignette_file.Rnw |only sleev-1.1.2/sleev/inst/doc/sleev_vignette_file.pdf |only sleev-1.1.2/sleev/vignettes/sleev_vignette.pdf |only sleev-1.1.2/sleev/vignettes/sleev_vignette_file.Rnw |only 12 files changed, 13 insertions(+), 12 deletions(-)
Title: Reconstruction of Daily Data - Precipitation
Description: Applies quality control to daily precipitation observations;
reconstructs the original series by estimating precipitation in missing values; and
creates gridded datasets of daily precipitation.
Author: Roberto Serrano-Notivoli [aut, cre]
,
Adrian Huerta [aut] ,
Abel Centella [ctb]
Maintainer: Roberto Serrano-Notivoli <roberto.serrano@unizar.es>
Diff between reddPrec versions 2.0.4 dated 2025-03-09 and 3.0.0 dated 2025-04-24
DESCRIPTION | 35 ++++++-- MD5 | 66 ++++++++++++--- NAMESPACE | 41 +++++++++ R/eqc_Plot.R |only R/eqc_PrecisionRounding-get_dec_patterns.R |only R/eqc_PrecisionRounding-get_ndec.R |only R/eqc_PrecisionRounding.R |only R/eqc_SmallGaps-get_ngaps.R |only R/eqc_SmallGaps.R |only R/eqc_Truncation-get_lenght_borderline.R |only R/eqc_Truncation-get_ts_borderline.R |only R/eqc_Truncation.R |only R/eqc_Ts.R |only R/eqc_WeeklyCycle-get_wd_fraction.R |only R/eqc_WeeklyCycle.R |only R/fillData.R | 47 ++--------- R/gapFilling.R | 13 +-- R/gridPcp.R | 120 ++++++++++++++++++++++++----- R/hmg_Ts.R |only R/hmg_adjustment_ts.R |only R/hmg_build_ts.R |only R/hmg_cleaning_trend_ar1.R |only R/hmg_detection_ts.R |only R/hmg_indices_ts.R |only R/hmg_nearby_ts.R |only R/hmg_qc_hmg_ts.R |only R/learner_glm.R |only R/learner_nn.R |only R/learner_rf.R |only R/learner_svm.R |only R/learner_xgboost.R |only R/predday.R | 47 ++++++----- R/predpoint.R | 40 ++------- R/qcFirst.R | 41 ++------- R/qcLast.R | 47 +++-------- R/qcPrec.R | 10 +- R/stand_qq.R | 8 + inst |only man/eqc_Plot.Rd |only man/eqc_PrecisionRounding.Rd |only man/eqc_SmallGaps.Rd |only man/eqc_Truncation.Rd |only man/eqc_Ts.Rd |only man/eqc_WeeklyCycle.Rd |only man/gapFilling.Rd | 3 man/gridPcp.Rd | 54 +++++++++++-- man/hmg_Ts.Rd |only man/learner_glm.Rd |only man/learner_nn.Rd |only man/learner_rf.Rd |only man/learner_svm.Rd |only man/learner_xgboost.Rd |only man/qcPrec.Rd | 3 53 files changed, 366 insertions(+), 209 deletions(-)
Title: Fast PCA for Large Pedigrees
Description: Carry out principal component analysis (PCA) of very large pedigrees such as found
in breeding populations! This package, 'randPedPCA', exploits sparse matrices and randomised
linear algebra to deliver a gazillion-times speed-up compared to naive singular value decoposition (SVD)
(and eigen decomposition).
Author: Hanbin Lee [aut],
Hannes Becher [cre],
Ros Craddock [aut],
Gregor Gorjanc [aut]
Maintainer: Hannes Becher <h.becher@ed.ac.uk>
Diff between randPedPCA versions 1.0.0 dated 2025-04-24 and 1.0.1 dated 2025-04-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/pedigree-pca.html | 12 ++++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test_rppca.R | 22 +++++++++++----------- 5 files changed, 26 insertions(+), 26 deletions(-)
Title: Retrieval-Augmented Generation (RAG) Workflows in R with Local
and Web Search
Description: Enables Retrieval-Augmented Generation (RAG) workflows in R by combining
local vector search using 'DuckDB' with optional web search via the 'Tavily' API.
Supports OpenAI- and Ollama-compatible embedding models, full-text and HNSW
(Hierarchical Navigable Small World) indexing, and modular large language model
(LLM) invocation. Designed for advanced question-answering, chat-based
applications, and production-ready AI pipelines. This package is the R
equivalent of the 'python' package 'RAGFlowChain' available at
<https://pypi.org/project/RAGFlowChain/>.
Author: Kwadwo Daddy Nyame Owusu Boakye [aut, cre]
Maintainer: Kwadwo Daddy Nyame Owusu Boakye <kwadwo.owusuboakye@outlook.com>
Diff between RAGFlowChainR versions 0.1.0 dated 2025-04-24 and 0.1.1 dated 2025-04-24
DESCRIPTION | 27 - MD5 | 14 NEWS.md |only R/create_rag_chain.R | 80 +++-- R/create_vectorstore.R | 481 ++++++++++++++----------------- man/create_vectorstore.Rd | 38 +- man/figures |only tests/testthat/test_create_rag_chain.R | 166 +++------- tests/testthat/test_create_vectorstore.R | 384 ++++++------------------ 9 files changed, 455 insertions(+), 735 deletions(-)
Title: Seamless 'Nonmem' Simulation Platform
Description: A complete and seamless 'Nonmem' simulation interface within R. Turns 'Nonmem' control streams into simulation control streams, executes them with specified simulation input data and returns the results. The simulation is performed by 'Nonmem', eliminating manual work and risks of re-implementation of models in other tools.
Author: Philip Delff [aut, cre],
Brian Reilly [ctb],
Sanaya Shroff [ctb],
Boris Grinshpun [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMsim versions 0.2.0 dated 2025-03-12 and 0.2.1 dated 2025-04-24
NMsim-0.2.0/NMsim/man/initsToExt.Rd |only NMsim-0.2.0/NMsim/tests/testthat/testReference/NMsim_VarCov_04.rds |only NMsim-0.2.1/NMsim/DESCRIPTION | 12 NMsim-0.2.1/NMsim/MD5 | 183 - NMsim-0.2.1/NMsim/NAMESPACE | 4 NMsim-0.2.1/NMsim/NEWS.md | 81 NMsim-0.2.1/NMsim/R/NMaddSamples.R |only NMsim-0.2.1/NMsim/R/NMcreateDoses.R | 6 NMsim-0.2.1/NMsim/R/NMcreateMatLines.R | 23 NMsim-0.2.1/NMsim/R/NMexec.R | 61 NMsim-0.2.1/NMsim/R/NMexecDirectory.R | 11 NMsim-0.2.1/NMsim/R/NMreadFilters.R | 1 NMsim-0.2.1/NMsim/R/NMreadInits.R | 1 NMsim-0.2.1/NMsim/R/NMreadSimModTab.R | 6 NMsim-0.2.1/NMsim/R/NMreplaceInits.R | 22 NMsim-0.2.1/NMsim/R/NMrunLin.R |only NMsim-0.2.1/NMsim/R/NMrunWin.R | 131 - NMsim-0.2.1/NMsim/R/NMsim.R | 43 NMsim-0.2.1/NMsim/R/NMsimCheckMod.R | 41 NMsim-0.2.1/NMsim/R/NMsim_EBE.R | 2 NMsim-0.2.1/NMsim/R/NMsim_NWPRI.R | 6 NMsim-0.2.1/NMsim/R/NMsim_VarCov.R | 55 NMsim-0.2.1/NMsim/R/NMsim_default.R | 2 NMsim-0.2.1/NMsim/R/NMsim_helpers.R | 31 NMsim-0.2.1/NMsim/R/NMsim_typical.R | 2 NMsim-0.2.1/NMsim/R/NMupdateSizes.R | 18 NMsim-0.2.1/NMsim/R/NMwriteInits.R | 20 NMsim-0.2.1/NMsim/R/addBlocks.R |only NMsim-0.2.1/NMsim/R/addEVID2.R | 269 -- NMsim-0.2.1/NMsim/R/callNonmemDirect.R |only NMsim-0.2.1/NMsim/R/cleaningPatterns.R |only NMsim-0.2.1/NMsim/R/completeCov.R | 2 NMsim-0.2.1/NMsim/R/expandCovs.R | 106 NMsim-0.2.1/NMsim/R/forestDefineCovs.R |only NMsim-0.2.1/NMsim/R/forestSummarize.R |only NMsim-0.2.1/NMsim/R/genPhiFile.R | 31 NMsim-0.2.1/NMsim/R/modifyModel.R | 49 NMsim-0.2.1/NMsim/R/readParsWide.R | 76 NMsim-0.2.1/NMsim/R/reportFailedRun.R | 6 NMsim-0.2.1/NMsim/R/samplePars.R |only NMsim-0.2.1/NMsim/R/sampleParsSimpar.R | 15 NMsim-0.2.1/NMsim/R/samplePars_mvrnorm.R |only NMsim-0.2.1/NMsim/R/samplePars_simpar.R |only NMsim-0.2.1/NMsim/R/simPopEtas.R | 11 NMsim-0.2.1/NMsim/R/summarizeCovs.R | 145 - NMsim-0.2.1/NMsim/R/typicalize.R | 2 NMsim-0.2.1/NMsim/README.md | 17 NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs.csv |only NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs.rds |only NMsim-0.2.1/NMsim/inst/examples/data/xgxr2covs_meta.txt |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr132.mod |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.coi |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.cor |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.cov |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.ext |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.lst |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.mod |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.phi |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134.shk |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134_etas.txt |only NMsim-0.2.1/NMsim/inst/examples/nonmem/xgxr134_res.txt |only NMsim-0.2.1/NMsim/man/NMaddSamples.Rd |only NMsim-0.2.1/NMsim/man/NMcreateMatLines.Rd | 8 NMsim-0.2.1/NMsim/man/NMreplaceInits.Rd | 2 NMsim-0.2.1/NMsim/man/NMrunLin.Rd | 2 NMsim-0.2.1/NMsim/man/NMsimCheckMod.Rd | 13 NMsim-0.2.1/NMsim/man/NMupdateSizes.Rd | 3 NMsim-0.2.1/NMsim/man/addBlocks.Rd |only NMsim-0.2.1/NMsim/man/addEVID2.Rd | 115 NMsim-0.2.1/NMsim/man/callNonmemDirect.Rd | 2 NMsim-0.2.1/NMsim/man/expandCovs.Rd | 55 NMsim-0.2.1/NMsim/man/forestDefineCovs.Rd |only NMsim-0.2.1/NMsim/man/forestSummarize.Rd |only NMsim-0.2.1/NMsim/man/genPhiFile.Rd | 12 NMsim-0.2.1/NMsim/man/modifyModel.Rd | 13 NMsim-0.2.1/NMsim/man/readParsWide.Rd | 29 NMsim-0.2.1/NMsim/man/samplePars.Rd |only NMsim-0.2.1/NMsim/man/simPopEtas.Rd | 16 NMsim-0.2.1/NMsim/man/simplePath.Rd |only NMsim-0.2.1/NMsim/man/summarizeCovs.Rd | 33 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/NMsimData_predu_sd2_NWPRI.csv | 1202 +++++----- NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/NMsimData_predu_sd2_NWPRI.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI/predu_sd2_NWPRI.mod | 12 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/predu_sd2_NWPRI_MetaData.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail/xgxr021_nmtranfail.lst | 2 NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr021_nmtranfail_MetaData.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1 |only NMsim-0.2.1/NMsim/tests/testthat/testData/nonmem/NMsim/xgxr032_VarCov_1_MetaData.rds |only NMsim-0.2.1/NMsim/tests/testthat/testData/simres/xgxr134_forest1_MetaData.rds |only NMsim-0.2.1/NMsim/tests/testthat/testData/simres/xgxr134_forest1_ResultsData.fst |only NMsim-0.2.1/NMsim/tests/testthat/testReference/NMcreateDoses_16.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/NMcreateMatLines_01.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMreadParsWide_01.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_NWPRI_02.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_NWPRI_02_OMEGAP.rds |binary NMsim-0.2.1/NMsim/tests/testthat/testReference/NMsim_VarCov_01.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/addEVID2_17.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/addEVID2_18.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/samplePars_02.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/samplePars_03.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/summarizeCovs_01.rds |only NMsim-0.2.1/NMsim/tests/testthat/testReference/summarizeCovs_02.rds |only NMsim-0.2.1/NMsim/tests/testthat/test_NMcreateDoses.R | 9 NMsim-0.2.1/NMsim/tests/testthat/test_NMcreateMatLines.R | 11 NMsim-0.2.1/NMsim/tests/testthat/test_NMreadParsWide.R | 6 NMsim-0.2.1/NMsim/tests/testthat/test_NMsimCheckMod.R |only NMsim-0.2.1/NMsim/tests/testthat/test_NMsim_NWPRI.R | 12 NMsim-0.2.1/NMsim/tests/testthat/test_NMsim_VarCov.R |only NMsim-0.2.1/NMsim/tests/testthat/test_NMupdateSizes.R | 4 NMsim-0.2.1/NMsim/tests/testthat/test_addEVID2.R | 85 NMsim-0.2.1/NMsim/tests/testthat/test_genPhiFile.R | 1 NMsim-0.2.1/NMsim/tests/testthat/test_sampleParsSimpar.R | 68 NMsim-0.2.1/NMsim/tests/testthat/test_summarizeCovs.R |only 113 files changed, 1476 insertions(+), 1730 deletions(-)
Title: Mobility Oriented-Parity Metric
Description: A set of tools to perform multiple versions of the Mobility
Oriented-Parity metric. This multivariate analysis helps to characterize
levels of dissimilarity between a set of conditions of reference and another
set of conditions of interest. If predictive models are transferred to
conditions different from those over which models were calibrated (trained),
this metric helps to identify transfer conditions that differ
substantially from those of calibration. These tools are implemented
following principles proposed in Owens et al. (2013)
<doi:10.1016/j.ecolmodel.2013.04.011>, and expanded to obtain more detailed
results that aid in interpretation as in Cobos et al. (2024)
<doi:10.21425/fob.17.132916>.
Author: Marlon E. Cobos [aut, cre] ,
Hannah L. Owens [aut] ,
Jorge Soberon [aut] ,
A. Townsend Peterson [aut]
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between mop versions 0.1.2 dated 2024-03-28 and 0.1.3 dated 2025-04-24
DESCRIPTION | 13 +++++++------ MD5 | 26 +++++++++++++------------- NEWS.md | 7 +++++++ R/helpers.R | 4 +--- R/mop.R | 9 +++++++-- README.md | 32 ++++++++++++++++++++++++++++++-- man/figures/README-load-1.png |binary man/figures/README-load-2.png |binary man/figures/README-plots-1.png |binary man/figures/README-plots-2.png |binary man/figures/README-plots-3.png |binary man/figures/README-plots-4.png |binary man/figures/README-plots-5.png |binary man/match_na_raster.Rd | 4 +--- 14 files changed, 66 insertions(+), 29 deletions(-)
Title: 'C++' Header Library for Ordinary Differential Equations
Description: A 'C++' header library for using the 'libsoda-cxx' library with R. The 'C++' header reimplements the 'lsoda' function from the 'ODEPACK' library for solving initial value problems for first order ordinary differential equations (Hindmarsh, 1982; <https://computing.llnl.gov/sites/default/files/ODEPACK_pub1_u88007.pdf>). The 'C++' header can be used by other R packages by linking against this package. The 'C++' functions can be called inline using 'Rcpp'. Finally, the package provides an 'ode' function to call from R.
Author: Mark Clements [aut, cre],
Dilawar Singh [ctb],
Heng Li [ctb],
Peter N. Brown [ctb],
George D. Byrne [ctb],
Alan C. Hindmarsh [ctb],
Cleve Moler [ctb],
Linda R. Petzold [ctb]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between lsoda versions 1.0 dated 2025-04-22 and 1.1 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/include/lsoda.h | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Lagrangian Multiplier Smoothing Splines for Smooth Function
Estimation
Description: Implements Lagrangian multiplier smoothing splines for flexible
nonparametric regression and function estimation. Provides tools for fitting,
prediction, and inference using a constrained optimization approach to
enforce smoothness.
Supports generalized linear models, Weibull accelerated failure time (AFT) models,
quadratic programming problems, and customizable arbitrary correlation structures.
Options for fitting in parallel are provided. The method builds upon the framework described
by Ezhov et al. (2018) <doi:10.1515/jag-2017-0029> using Lagrangian multipliers
to fit cubic splines. For more information on correlation structure estimation,
see Searle et al. (2009) <ISBN:978-0470009598>. For quadratic programming and
constrained optimization in general, see Nocedal & Wright (2006) <doi:10.1007/978-0-387-40065-5>.
For a comprehensive background on smoothing splines, see Wahba (1990)
<doi:10.1137/1.9781611970128> and Wood (2006) <ISBN:978-1584884743>
[...truncated...]
Author: Matthew Davis [aut, cre]
Maintainer: Matthew Davis <matthewlouisdavis@gmail.com>
Diff between lgspline versions 0.1.0 dated 2025-04-22 and 0.2.0 dated 2025-04-24
DESCRIPTION | 6 +- MD5 | 4 - tests/testthat/test-advanced.R | 83 +++++++++++++++++++++++------------------ 3 files changed, 53 insertions(+), 40 deletions(-)
Title: The Machine Learning and AI Modeling Companion to 'healthyR'
Description: Hospital machine learning and ai data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative
hospital data. Some of these include predicting length of stay, and readmits.
The aim is to provide a simple and consistent verb framework that takes the
guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ai versions 0.1.0 dated 2024-09-11 and 0.1.1 dated 2025-04-24
DESCRIPTION | 6 MD5 | 64 ++--- NEWS.md | 494 +++++++++++++++++++-------------------- R/data-prep-c50.R | 3 R/data-prep-earth.R | 113 ++++---- R/data-prep-glmnet.R | 3 R/data-prep-knn.R | 3 R/data-prep-ranger.R | 5 R/data-prep-svm_poly.R | 3 R/data-prep-svm_rbf.R | 3 R/data-prep-xgboost.R | 3 R/get-juiced-data.R | 136 +++++----- R/hai-data-scale.R | 2 R/utils-mesh-generator.R | 2 README.md | 2 inst/doc/auto-kmeans.R | 26 +- inst/doc/auto-kmeans.html | 6 inst/doc/getting-started.html | 170 ++++++------- inst/doc/kmeans-umap.html | 30 +- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/generate_mesh_data.Rd | 5 man/get_juiced_data.Rd | 6 man/hai_c50_data_prepper.Rd | 3 man/hai_data_scale.Rd | 2 man/hai_earth_data_prepper.Rd | 3 man/hai_glmnet_data_prepper.Rd | 3 man/hai_knn_data_prepper.Rd | 3 man/hai_ranger_data_prepper.Rd | 3 man/hai_svm_poly_data_prepper.Rd | 3 man/hai_svm_rbf_data_prepper.Rd | 3 man/hai_xgboost_data_prepper.Rd | 3 man/pca_your_recipe.Rd | 3 33 files changed, 588 insertions(+), 526 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4,
<doi:10.1007/978-1-4614-8456-1>).
Author: Steven P. Millard [aut],
Alexander Kowarik [ctb, cre]
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between EnvStats versions 3.0.0 dated 2024-08-24 and 3.1.0 dated 2025-04-24
EnvStats-3.0.0/EnvStats/man/htest.object.Rd |only EnvStats-3.0.0/EnvStats/man/print.htestEnvStats.Rd |only EnvStats-3.1.0/EnvStats/DESCRIPTION | 8 EnvStats-3.1.0/EnvStats/MD5 | 58 +- EnvStats-3.1.0/EnvStats/NAMESPACE | 10 EnvStats-3.1.0/EnvStats/NEWS | 25 + EnvStats-3.1.0/EnvStats/R/StatTestText.R | 49 +- EnvStats-3.1.0/EnvStats/R/chenTTest.R | 191 ++++----- EnvStats-3.1.0/EnvStats/R/geom_stripchart.R | 276 +++++++------- EnvStats-3.1.0/EnvStats/R/gofTestCensored.R | 2 EnvStats-3.1.0/EnvStats/R/print.R |only EnvStats-3.1.0/EnvStats/R/print.default.R |only EnvStats-3.1.0/EnvStats/R/print.htest.R |only EnvStats-3.1.0/EnvStats/R/print.htestEnvStats.R | 228 +++++------ EnvStats-3.1.0/EnvStats/R/signTest.R | 16 EnvStats-3.1.0/EnvStats/man/Distribution.df.Rd | 8 EnvStats-3.1.0/EnvStats/man/FcnsByCatEstDistParams.Rd | 1 EnvStats-3.1.0/EnvStats/man/chenTTest.Rd | 6 EnvStats-3.1.0/EnvStats/man/ciTableMean.Rd | 2 EnvStats-3.1.0/EnvStats/man/enparCensored.Rd | 4 EnvStats-3.1.0/EnvStats/man/geom_stripchart.Rd | 4 EnvStats-3.1.0/EnvStats/man/htest.htestEnvStats.object.Rd |only EnvStats-3.1.0/EnvStats/man/kendallSeasonalTrendTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/kendallTrendTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/print.Rd |only EnvStats-3.1.0/EnvStats/man/print.htest.htestEnvStats.Rd |only EnvStats-3.1.0/EnvStats/man/quantileTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/rosnerTest.Rd | 2 EnvStats-3.1.0/EnvStats/man/serialCorrelationTest.Rd | 11 EnvStats-3.1.0/EnvStats/man/signTest.Rd | 182 ++++++++- EnvStats-3.1.0/EnvStats/man/stripChart.Rd | 8 EnvStats-3.1.0/EnvStats/man/twoSampleLinearRankTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/varGroupTest.Rd | 8 EnvStats-3.1.0/EnvStats/man/zTestGevdShape.Rd | 8 34 files changed, 681 insertions(+), 458 deletions(-)
Title: Python-Based Extensions for Data Analytics Workflows
Description: Provides Python-based extensions to enhance data analytics workflows,
particularly for tasks involving data preprocessing and predictive modeling.
Includes tools for data sampling, transformation, feature selection,
balancing strategies (e.g., SMOTE), and model construction.
These capabilities leverage Python libraries via the reticulate interface,
enabling seamless integration with a broader machine learning ecosystem.
Supports instance selection and hybrid workflows that combine R and Python
functionalities for flexible and reproducible analytical pipelines.
The architecture is inspired by the Experiment Lines approach, which promotes
modularity, extensibility, and interoperability across tools.
More information on Experiment Lines is available in
Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_20>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Diego Salles [aut, ths],
Federal Center for Technological Education of Rio de Janeiro
[cph]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolboxdp versions 1.0.777 dated 2024-12-04 and 1.0.787 dated 2025-04-24
DESCRIPTION | 52 +++++++++++++++++++++++------------- MD5 | 35 +++++++++++++++++++++--- NAMESPACE | 5 +++ R/bal_oversampling.R | 3 -- R/bal_subsampling.R | 2 - R/globals.R |only R/sk_cla_gb.R |only README.md | 72 ++++++++++++++++++++++++++++++++++++++------------- inst/python/sklearn |only man/cla_gb.Rd |only 10 files changed, 124 insertions(+), 45 deletions(-)
Title: Scale Functions for Visualization
Description: Graphical scales map data to aesthetics, and provide methods
for automatically determining breaks and labels for axes and legends.
Author: Hadley Wickham [aut],
Thomas Lin Pedersen [cre, aut]
,
Dana Seidel [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between scales versions 1.3.0 dated 2023-11-28 and 1.4.0 dated 2025-04-24
DESCRIPTION | 24 +- LICENSE | 2 MD5 | 262 ++++++++++++++++-------------- NAMESPACE | 46 +++++ NEWS.md | 189 ++++++++++++--------- R/bounds.R | 53 ++++-- R/breaks-log.R | 88 ++++++++++ R/breaks-retired.R | 10 - R/breaks.R | 59 ++++++ R/colour-manip.R | 199 ++++++++++++++++++++-- R/colour-mapping.R | 168 ++++++++++++++----- R/colour-ramp.R | 16 - R/date-time.R | 7 R/full-seq.R | 11 + R/import-standalone-obj-type.R |only R/import-standalone-types-check.R |only R/label-bytes.R | 13 - R/label-compose.R |only R/label-currency.R | 66 +++++-- R/label-date.R | 55 ++++-- R/label-dictionary.R |only R/label-glue.R |only R/label-log.R | 53 ++++-- R/label-number-auto.R | 8 R/label-number-si.R | 8 R/label-number.R | 193 +++++++++++++++++----- R/label-ordinal.R | 27 ++- R/label-percent.R | 27 ++- R/label-pvalue.R | 25 +- R/label-scientific.R | 25 ++ R/label-wrap.R | 6 R/labels-retired.R | 45 +++-- R/pal-.R |only R/pal-area.R | 5 R/pal-brewer.R | 44 ++++- R/pal-dichromat.R | 11 - R/pal-gradient.R | 28 ++- R/pal-grey.R | 6 R/pal-hue.R | 12 + R/pal-linetype.R | 19 +- R/pal-manual.R | 31 +++ R/pal-rescale.R | 8 R/pal-shape.r | 5 R/pal-viridis.R | 11 + R/palette-registry.R |only R/range.R | 30 ++- R/scale-continuous.R | 43 ++++ R/scale-discrete.R | 27 ++- R/transform-compose.R | 15 + R/transform-date.R | 23 +- R/transform-numeric.R | 26 +- R/transform.R | 81 ++++++--- R/utils.R | 71 ++++++++ README.md | 44 ++--- build/partial.rdb |binary man/alpha.Rd | 8 man/breaks_exp.Rd |only man/breaks_extended.Rd | 6 man/breaks_log.Rd | 6 man/breaks_pretty.Rd | 6 man/breaks_timespan.Rd | 6 man/breaks_width.Rd | 6 man/col2hcl.Rd | 8 man/col_mix.Rd |only man/colour_manip.Rd |only man/comma.Rd | 27 ++- man/compose_label.Rd |only man/date_format.Rd | 6 man/dollar_format.Rd | 15 + man/figures/README-labels-1.png |binary man/figures/README-transforms-1.png |binary man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-4-1.png |only man/figures/logo.png |binary man/label_bytes.Rd | 30 ++- man/label_currency.Rd | 28 ++- man/label_date.Rd | 40 +++- man/label_dictionary.Rd |only man/label_glue.Rd |only man/label_log.Rd | 18 +- man/label_number.Rd | 29 ++- man/label_number_auto.Rd | 11 + man/label_number_si.Rd | 20 +- man/label_ordinal.Rd | 28 +-- man/label_parse.Rd | 3 man/label_percent.Rd | 24 +- man/label_pvalue.Rd | 10 - man/label_scientific.Rd | 6 man/label_wrap.Rd | 2 man/minor_breaks_log.Rd |only man/muted.Rd | 8 man/new_continuous_palette.Rd |only man/number.Rd | 27 ++- man/number_options.Rd |only man/ordinal_format.Rd | 21 -- man/pal_dichromat.Rd | 2 man/pal_div_gradient.Rd | 15 - man/pal_manual.Rd | 7 man/pal_seq_gradient.Rd | 7 man/palette-recommendations.Rd |only man/percent_format.Rd | 15 + man/pvalue_format.Rd | 11 - man/scales-package.Rd | 2 man/scientific_format.Rd | 7 man/train_continuous.Rd | 4 man/train_discrete.Rd | 11 + man/transform_boxcox.Rd | 8 man/unit_format.Rd | 11 - tests/testthat/_snaps/breaks-log.md |only tests/testthat/_snaps/colour-mapping.md | 77 ++++++++ tests/testthat/_snaps/label-bytes.md |only tests/testthat/_snaps/label-number.md | 4 tests/testthat/_snaps/pal-manual.md |only tests/testthat/_snaps/palette-registry.md |only tests/testthat/_snaps/scale-continuous.md |only tests/testthat/_snaps/trans-compose.md | 8 tests/testthat/_snaps/trans-numeric.md |only tests/testthat/_snaps/trans.md | 2 tests/testthat/_snaps/utils.md |only tests/testthat/test-bounds.R | 3 tests/testthat/test-breaks-log.R | 23 ++ tests/testthat/test-breaks.R | 18 ++ tests/testthat/test-colour-manip.R | 46 +++++ tests/testthat/test-colour-mapping.R | 88 +++++++--- tests/testthat/test-full-seq.R | 25 ++ tests/testthat/test-label-bytes.R | 12 - tests/testthat/test-label-compose.R |only tests/testthat/test-label-currency.R | 6 tests/testthat/test-label-date.R | 15 + tests/testthat/test-label-dictionary.R |only tests/testthat/test-label-glue.R |only tests/testthat/test-label-log.R | 1 tests/testthat/test-label-number.R | 60 ++++++ tests/testthat/test-label-ordinal.R | 1 tests/testthat/test-label-percent.R | 1 tests/testthat/test-label-pvalue.R | 1 tests/testthat/test-label-scientific.R | 1 tests/testthat/test-offset-by.R | 5 tests/testthat/test-pal-.R |only tests/testthat/test-pal-manual.R | 2 tests/testthat/test-palette-registry.R |only tests/testthat/test-range.R | 9 - tests/testthat/test-scale-continuous.R | 14 + tests/testthat/test-scale-discrete.R | 10 + tests/testthat/test-trans-compose.R | 5 tests/testthat/test-trans-date.R | 15 + tests/testthat/test-trans-numeric.R | 118 +++++++++---- tests/testthat/test-utils.R |only 148 files changed, 2482 insertions(+), 812 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.5.0 dated 2025-04-22 and 0.5.1 dated 2025-04-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/doc/measures.html | 4 ++-- src/linear.cpp | 6 ++++++ 5 files changed, 21 insertions(+), 9 deletions(-)
Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.science/hal-00714174/>) ; S. Karlin and S. Altschul (1990) <https://pmc.ncbi.nlm.nih.gov/articles/PMC53667/> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.science/hal-00937529v1/> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut],
Chris Verschelden [aut],
Charly Marty [aut],
David Robelin [aut, cre],
Sabine Mercier [aut],
Sebastien Dejean [aut],
The authors of Eigen the library for the included version of Eigen
[cph]
Maintainer: David Robelin <david.robelin@inrae.fr>
Diff between localScore versions 2.0.2 dated 2025-04-19 and 2.0.3 dated 2025-04-24
DESCRIPTION | 8 +- MD5 | 28 +++---- R/RcppExports.R | 21 ++++- build/vignette.rds |binary inst/doc/ExcursionsheightDocumentation.pdf |binary inst/doc/localScorePackageDocumentation.R | 3 inst/doc/localScorePackageDocumentation.Rmd | 3 inst/doc/localScorePackageDocumentation.pdf |binary man/daudin.Rd | 15 ++-- man/karlin.Rd | 11 +- man/maxPartialSumd.Rd | 8 +- man/mcc.Rd | 11 +- src/function_wrapper.cpp | 101 ++++++++++++++++++--------- tests/testthat/test-daudin.R | 49 ++++++++++++- vignettes/localScorePackageDocumentation.Rmd | 3 15 files changed, 180 insertions(+), 81 deletions(-)
Title: Client for 'LaminDB'
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data
framework for biology. This package allows you to query and download
data from 'LaminDB' instances.
Author: Robrecht Cannoodt [aut, cre] ,
Luke Zappia [aut] ,
Data Intuitive [aut],
Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@lamin.ai>
Diff between laminr versions 1.0.1 dated 2025-03-18 and 1.1.0 dated 2025-04-24
laminr-1.0.1/laminr/inst/doc/welcome.qmd |only laminr-1.0.1/laminr/vignettes/cellxgene_basic.html |only laminr-1.0.1/laminr/vignettes/example_workflow.html |only laminr-1.0.1/laminr/vignettes/introduction.Rmd |only laminr-1.0.1/laminr/vignettes/laminr.Rmd |only laminr-1.0.1/laminr/vignettes/setup.Rmd |only laminr-1.0.1/laminr/vignettes/welcome.qmd |only laminr-1.1.0/laminr/DESCRIPTION | 20 +- laminr-1.1.0/laminr/MD5 | 79 ++++++----- laminr-1.1.0/laminr/NAMESPACE | 5 laminr-1.1.0/laminr/R/Artifact.R | 27 ++-- laminr-1.1.0/laminr/R/Collection.R | 4 laminr-1.1.0/laminr/R/Registry.R | 10 - laminr-1.1.0/laminr/R/Transform.R | 4 laminr-1.1.0/laminr/R/arguments.R |only laminr-1.1.0/laminr/R/checks.R | 12 + laminr-1.1.0/laminr/R/file_loaders.R | 6 laminr-1.1.0/laminr/R/import.R | 44 ++++-- laminr-1.1.0/laminr/R/install.R | 39 ++++- laminr-1.1.0/laminr/R/lamin_cli.R | 33 +++- laminr-1.1.0/laminr/R/lamindb.R | 77 ++++++----- laminr-1.1.0/laminr/R/laminr-package.R | 6 laminr-1.1.0/laminr/R/packages.R |only laminr-1.1.0/laminr/R/require.R |only laminr-1.1.0/laminr/R/save_active_file.R | 8 - laminr-1.1.0/laminr/R/utils.R | 21 +-- laminr-1.1.0/laminr/R/view.R | 34 ++++- laminr-1.1.0/laminr/R/wrap-python.R | 135 ++++++++++++++++++-- laminr-1.1.0/laminr/R/zzz.R | 2 laminr-1.1.0/laminr/README.md | 58 -------- laminr-1.1.0/laminr/build/vignette.rds |binary laminr-1.1.0/laminr/inst/doc/welcome.Rmd |only laminr-1.1.0/laminr/inst/doc/welcome.html | 116 ++++++++++++++--- laminr-1.1.0/laminr/man/figures |only laminr-1.1.0/laminr/man/import_module.Rd | 36 ++++- laminr-1.1.0/laminr/man/install_lamindb.Rd | 16 +- laminr-1.1.0/laminr/man/laminr-package.Rd | 2 laminr-1.1.0/laminr/man/require_module.Rd |only laminr-1.1.0/laminr/tests/testthat.R | 3 laminr-1.1.0/laminr/tests/testthat/setup.R | 28 +--- laminr-1.1.0/laminr/tests/testthat/test-Artifact.R |only laminr-1.1.0/laminr/tests/testthat/test-checks.R | 4 laminr-1.1.0/laminr/tests/testthat/test-import.R | 10 + laminr-1.1.0/laminr/tests/testthat/test-install.R | 14 +- laminr-1.1.0/laminr/vignettes/welcome.Rmd |only 45 files changed, 576 insertions(+), 277 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.15.7 dated 2025-03-17 and 0.16.0 dated 2025-04-24
rix-0.15.7/rix/inst/extdata/result |only rix-0.16.0/rix/DESCRIPTION | 6 rix-0.16.0/rix/MD5 | 109 ++++---- rix-0.16.0/rix/NEWS.md | 25 +- rix-0.16.0/rix/R/fetchers.R | 3 rix-0.16.0/rix/R/nix_hash.R | 122 +++++++++- rix-0.16.0/rix/R/rix.R | 39 ++- rix-0.16.0/rix/R/rix_helpers.R | 85 ++++-- rix-0.16.0/rix/README.md | 15 - rix-0.16.0/rix/build/vignette.rds |binary rix-0.16.0/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 15 + rix-0.16.0/rix/inst/doc/b1-setting-up-and-using-rix-on-linux-and-windows.html | 12 rix-0.16.0/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.Rmd | 8 rix-0.16.0/rix/inst/doc/b2-setting-up-and-using-rix-on-macos.html | 9 rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.R | 20 + rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.Rmd | 28 ++ rix-0.16.0/rix/inst/doc/d1-installing-r-packages-in-a-nix-environment.html | 92 ++++--- rix-0.16.0/rix/inst/doc/e-configuring-ide.Rmd | 22 + rix-0.16.0/rix/inst/doc/e-configuring-ide.html | 40 ++- rix-0.16.0/rix/inst/extdata/available_df.csv | 7 rix-0.16.0/rix/inst/extdata/default.nix | 16 - rix-0.16.0/rix/inst/extdata/run-pipeline.yaml | 2 rix-0.16.0/rix/man/renv2nix.Rd | 2 rix-0.16.0/rix/man/rix.Rd | 4 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_datathin.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-14-0.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-15-5.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v0-17-3.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/renv_helpers/default_v1-0-7.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix-python/python_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/bioc-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/bleeding-edge_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/code_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/codium_default.nix | 18 - rix-0.16.0/rix/tests/testthat/_snaps/rix/date_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/frozen-edge_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/no_quarto_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/one_git_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/other_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/positron_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/r-devel-bioc-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/r-devel_default.nix | 12 rix-0.16.0/rix/tests/testthat/_snaps/rix/rstudio_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/rix/yes_quarto_default.nix | 16 - rix-0.16.0/rix/tests/testthat/_snaps/tar_nix_ga/run-pipeline.yaml | 2 rix-0.16.0/rix/tests/testthat/result | 2 rix-0.16.0/rix/tests/testthat/test-available_r.R | 3 rix-0.16.0/rix/tests/testthat/test-fetchers.R | 17 + rix-0.16.0/rix/tests/testthat/test-rix-python.R | 46 +++ rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/gen_envs.R | 11 rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/mlr3_default.nix | 12 rix-0.16.0/rix/tests/testthat/testdata/remote-pkgs/mlr3_dups_default.nix | 12 rix-0.16.0/rix/vignettes/b1-setting-up-and-using-rix-on-linux-and-windows.Rmd | 15 + rix-0.16.0/rix/vignettes/b2-setting-up-and-using-rix-on-macos.Rmd | 8 rix-0.16.0/rix/vignettes/d1-installing-r-packages-in-a-nix-environment.Rmd | 28 ++ rix-0.16.0/rix/vignettes/e-configuring-ide.Rmd | 22 + 56 files changed, 805 insertions(+), 340 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.9.6 dated 2025-03-12 and 1.0.0 dated 2025-04-24
DESCRIPTION | 10 MD5 | 40 NEWS.md | 13 R/FixRiskyIntervals.R | 8 R/GaussSuppressionFromData.R | 5 R/Intervals.R | 8 R/PackageSpecs.R | 4 build/vignette.rds |binary inst/doc/Magnitude_table_suppression.R | 26 inst/doc/Magnitude_table_suppression.Rmd | 49 inst/doc/Magnitude_table_suppression.html | 643 ++++++--- inst/doc/Small_count_frequency_table_suppression.R | 24 inst/doc/Small_count_frequency_table_suppression.Rmd | 45 inst/doc/Small_count_frequency_table_suppression.html | 622 +++++---- inst/doc/define_tables.html | 1202 +++++++++--------- man/ComputeIntervals.Rd | 2 man/GaussSuppressionFromData.Rd | 4 tests/testthat/test-FixRiskyIntervals.R | 2 vignettes/GaussKable.R | 8 vignettes/Magnitude_table_suppression.Rmd | 49 vignettes/Small_count_frequency_table_suppression.Rmd | 45 21 files changed, 1700 insertions(+), 1109 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: 'HiGHS' Plugin for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the quadratic solver 'HiGHS'. More information about
'HiGHS' can be found at <https://highs.dev>.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.highs versions 1.0-3 dated 2023-07-06 and 1.0-4 dated 2025-04-24
ROI.plugin.highs-1.0-3/ROI.plugin.highs/tests |only ROI.plugin.highs-1.0-4/ROI.plugin.highs/DESCRIPTION | 9 +++++---- ROI.plugin.highs-1.0-4/ROI.plugin.highs/MD5 | 5 +++-- ROI.plugin.highs-1.0-4/ROI.plugin.highs/inst |only 4 files changed, 8 insertions(+), 6 deletions(-)
More information about ROI.plugin.highs at CRAN
Permanent link
Title: Heuristic Capacitated Vehicle Routing Problem Solver
Description: Implements the Clarke-Wright algorithm to find a quasi-optimal solution to the Capacitated Vehicle Routing Problem. See Clarke, G. and Wright, J.R. (1964) <doi:10.1287/opre.12.4.568> for details. The implementation is accompanied by helper functions to inspect its solution.
Author: Lukas Schneiderbauer [aut, cre, cph]
Maintainer: Lukas Schneiderbauer <lukas.schneiderbauer@gmail.com>
Diff between heumilkr versions 0.2.0 dated 2024-04-01 and 0.3.0 dated 2025-04-24
heumilkr-0.2.0/heumilkr/R/plumber.R |only heumilkr-0.3.0/heumilkr/DESCRIPTION | 8 - heumilkr-0.3.0/heumilkr/MD5 | 43 +++---- heumilkr-0.3.0/heumilkr/NEWS.md | 30 ++++- heumilkr-0.3.0/heumilkr/R/autoplot.R | 50 ++++++++ heumilkr-0.3.0/heumilkr/R/clarke_wright.R | 52 ++++----- heumilkr-0.3.0/heumilkr/R/cpp11.R | 4 heumilkr-0.3.0/heumilkr/R/cvrplib.R | 49 +++++--- heumilkr-0.3.0/heumilkr/R/heumilkr_solution.R | 2 heumilkr-0.3.0/heumilkr/README.md | 3 heumilkr-0.3.0/heumilkr/build/partial.rdb |binary heumilkr-0.3.0/heumilkr/build/vignette.rds |binary heumilkr-0.3.0/heumilkr/inst/doc/clarke_wright_performance.html | 4 heumilkr-0.3.0/heumilkr/man/autoplot.heumilkr_solution.Rd |only heumilkr-0.3.0/heumilkr/man/clarke_wright.Rd | 9 + heumilkr-0.3.0/heumilkr/man/clarke_wright_cvrplib.Rd | 10 + heumilkr-0.3.0/heumilkr/man/plot.heumilkr_solution.Rd |only heumilkr-0.3.0/heumilkr/src/clarke_wright.cpp | 13 -- heumilkr-0.3.0/heumilkr/src/cpp11.cpp | 8 - heumilkr-0.3.0/heumilkr/src/routing_state.cpp | 57 ++++++++-- heumilkr-0.3.0/heumilkr/tests/testthat/helper-hedgehog.R | 4 heumilkr-0.3.0/heumilkr/tests/testthat/test-autoplot.R | 30 ++--- heumilkr-0.3.0/heumilkr/tests/testthat/test-clarke_wright.R | 50 ++++++++ heumilkr-0.3.0/heumilkr/tests/testthat/test-cvrplib.R | 1 24 files changed, 286 insertions(+), 141 deletions(-)
Title: Helpers for Model Coefficients Tibbles
Description: Provides suite of functions to work with regression model
'broom::tidy()' tibbles. The suite includes functions to group
regression model terms by variable, insert reference and header rows
for categorical variables, add variable labels, and more.
Author: Joseph Larmarange [aut, cre] ,
Daniel D. Sjoberg [aut]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between broom.helpers versions 1.20.0 dated 2025-03-06 and 1.21.0 dated 2025-04-24
DESCRIPTION | 9 MD5 | 97 +++--- NAMESPACE | 11 NEWS.md | 13 R/custom_tidiers.R | 65 ++++ R/model_get_assign.R | 6 R/model_get_coefficients_type.R | 6 R/model_get_contrasts.R | 6 R/model_get_model_frame.R | 9 R/model_get_model_matrix.R | 6 R/model_get_nlevels.R | 6 R/model_get_terms.R | 6 R/model_get_weights.R | 6 R/model_get_xlevels.R | 6 R/model_identify_variables.R | 8 R/model_list_variables.R | 2 R/tidy_add_term_labels.R | 28 + R/tidy_disambiguate_terms.R | 3 R/tidy_group_by.R | 6 R/tidy_plus_plus.R | 12 README.md | 4 build/vignette.rds |binary data/supported_models.rda |binary inst/WORDLIST | 4 inst/doc/broom-helpers.R | 12 inst/doc/broom-helpers.Rmd | 19 + inst/doc/broom-helpers.html | 530 +++++++++++++++++----------------- man/model_get_assign.Rd | 3 man/model_get_coefficients_type.Rd | 3 man/model_get_contrasts.Rd | 3 man/model_get_model_frame.Rd | 3 man/model_get_model_matrix.Rd | 3 man/model_get_nlevels.Rd | 3 man/model_get_terms.Rd | 3 man/model_get_weights.Rd | 3 man/model_get_xlevels.Rd | 3 man/model_identify_variables.Rd | 3 man/supported_models.Rd | 1 man/tidy_add_term_labels.Rd | 3 man/tidy_broom.Rd | 1 man/tidy_multgee.Rd | 1 man/tidy_parameters.Rd | 1 man/tidy_plus_plus.Rd | 3 man/tidy_svy_vglm.Rd |only man/tidy_vgam.Rd | 1 man/tidy_with_broom_or_parameters.Rd | 1 man/tidy_zeroinfl.Rd | 1 tests/testthat/test-add_term_labels.R | 15 tests/testthat/test-tidy_plus_plus.R | 22 + vignettes/broom-helpers.Rmd | 19 + 50 files changed, 639 insertions(+), 340 deletions(-)
Title: Efficient Spatial Thinning of Species Occurrences
Description: Provides efficient geospatial thinning algorithms to reduce
the density of coordinate data while maintaining spatial
relationships. Implements K-D Tree and brute-force distance-based
thinning, as well as grid-based and precision-based thinning methods.
For more information on the methods, see Elseberg et al. (2012)
<https://hdl.handle.net/10446/86202>.
Author: Jorge Mestre-Tomas [aut, cre]
Maintainer: Jorge Mestre-Tomas <jorge.mestre.tomas@csic.es>
Diff between GeoThinneR versions 1.1.0 dated 2024-10-03 and 2.0.0 dated 2025-04-24
GeoThinneR-1.1.0/GeoThinneR/R/brute_force_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/R/kd_tree_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/R/max_thinning_algorithm.R |only GeoThinneR-1.1.0/GeoThinneR/R/rounding_hashing_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/man/assign_coords_to_grid.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/brute_force_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-3-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-5-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/figures/README-unnamed-chunk-7-1.png |only GeoThinneR-1.1.0/GeoThinneR/man/kd_tree_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/long_lat_to_cartesian.Rd |only GeoThinneR-1.1.0/GeoThinneR/man/rounding_hashing_thinning.Rd |only GeoThinneR-1.1.0/GeoThinneR/src |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-brute_force_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-kd_tree_thinning.R |only GeoThinneR-1.1.0/GeoThinneR/tests/testthat/test-rounding_hashing_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/DESCRIPTION | 16 GeoThinneR-2.0.0/GeoThinneR/LICENSE | 4 GeoThinneR-2.0.0/GeoThinneR/MD5 | 86 GeoThinneR-2.0.0/GeoThinneR/NAMESPACE | 37 GeoThinneR-2.0.0/GeoThinneR/NEWS.md | 28 GeoThinneR-2.0.0/GeoThinneR/R/GeoThinned_class.R |only GeoThinneR-2.0.0/GeoThinneR/R/data.R | 68 GeoThinneR-2.0.0/GeoThinneR/R/distance_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/R/grid_thinning.R | 40 GeoThinneR-2.0.0/GeoThinneR/R/precision_thinning.R | 17 GeoThinneR-2.0.0/GeoThinneR/R/thin_points.R | 237 +- GeoThinneR-2.0.0/GeoThinneR/R/thinning_algorithm.R |only GeoThinneR-2.0.0/GeoThinneR/R/utils.R | 192 +- GeoThinneR-2.0.0/GeoThinneR/README.md | 178 - GeoThinneR-2.0.0/GeoThinneR/build/vignette.rds |binary GeoThinneR-2.0.0/GeoThinneR/data/caretta.rda |binary GeoThinneR-2.0.0/GeoThinneR/data/thunnus.rda |only GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.R | 238 +- GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.Rmd | 395 ++-- GeoThinneR-2.0.0/GeoThinneR/inst/doc/GeoThinneR.html | 948 +++++----- GeoThinneR-2.0.0/GeoThinneR/man/GeoThinned.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/calculate_spatial_coverage.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/caretta.Rd | 33 GeoThinneR-2.0.0/GeoThinneR/man/compute_nearest_neighbor_distances.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_brute.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_kdtree.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/compute_neighbors_local_kdtree.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/distance_thinning.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/estimate_k_max.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/figures/README-GeoThinneR_summary.png |only GeoThinneR-2.0.0/GeoThinneR/man/grid_thinning.Rd | 21 GeoThinneR-2.0.0/GeoThinneR/man/lon_lat_to_cartesian.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/max_thinning_algorithm.Rd | 26 GeoThinneR-2.0.0/GeoThinneR/man/precision_thinning.Rd | 12 GeoThinneR-2.0.0/GeoThinneR/man/select_target_points.Rd |only GeoThinneR-2.0.0/GeoThinneR/man/thin_points.Rd | 127 - GeoThinneR-2.0.0/GeoThinneR/man/thunnus.Rd |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-GeoThinned_class.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-distance_thinning.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-grid_thinning.R | 18 GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-precision_thinning.R | 8 GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-thin_points.R | 120 - GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-thinning_algorithm.R |only GeoThinneR-2.0.0/GeoThinneR/tests/testthat/test-utils.R | 30 GeoThinneR-2.0.0/GeoThinneR/vignettes/GeoThinneR.Rmd | 395 ++-- 61 files changed, 1983 insertions(+), 1291 deletions(-)
Title: Estimate and Manipulate Age-Depth Models
Description: Estimate age-depth models from stratigraphic and sedimentological data,
and transform data
between the time and stratigraphic domain.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between admtools versions 0.4.0 dated 2024-10-03 and 0.5.0 dated 2025-04-24
admtools-0.4.0/admtools/data/CarboCATLite_data.rda |only admtools-0.5.0/admtools/DESCRIPTION | 8 admtools-0.5.0/admtools/MD5 | 100 +++++--- admtools-0.5.0/admtools/NAMESPACE | 36 +++ admtools-0.5.0/admtools/NEWS.md | 8 admtools-0.5.0/admtools/R/T_and_L_unit_handling.R | 135 +++++++++++- admtools-0.5.0/admtools/R/adm_to_ddc.R |only admtools-0.5.0/admtools/R/flip_ddc.R |only admtools-0.5.0/admtools/R/get_total_thickness.R | 7 admtools-0.5.0/admtools/R/get_total_thicknesses.R |only admtools-0.5.0/admtools/R/plot.ddc.R |only admtools-0.5.0/admtools/R/section_names.R |only admtools-0.5.0/admtools/R/sedrate_gen_helpers.R | 63 +++++ admtools-0.5.0/admtools/R/strat_to_time.fossils.R |only admtools-0.5.0/admtools/R/strat_to_time.taxonomy.R |only admtools-0.5.0/admtools/R/summary.R | 22 + admtools-0.5.0/admtools/R/time_to_strat.fossils.R |only admtools-0.5.0/admtools/R/time_to_strat.taxonomy.R |only admtools-0.5.0/admtools/R/tp_to_ddc.R |only admtools-0.5.0/admtools/README.md | 4 admtools-0.5.0/admtools/build/vignette.rds |binary admtools-0.5.0/admtools/data/CarboCatLite_data.rda |only admtools-0.5.0/admtools/inst/CITATION | 6 admtools-0.5.0/admtools/inst/WORDLIST | 17 + admtools-0.5.0/admtools/inst/doc/FossilSim_integration.R |only admtools-0.5.0/admtools/inst/doc/FossilSim_integration.Rmd |only admtools-0.5.0/admtools/inst/doc/FossilSim_integration.html |only admtools-0.5.0/admtools/inst/doc/adm_from_sedrate.Rmd | 6 admtools-0.5.0/admtools/inst/doc/adm_from_sedrate.html | 24 +- admtools-0.5.0/admtools/inst/doc/adm_from_trace_cont.html | 12 - admtools-0.5.0/admtools/inst/doc/admtools.R | 3 admtools-0.5.0/admtools/inst/doc/admtools.Rmd | 7 admtools-0.5.0/admtools/inst/doc/admtools.html | 6 admtools-0.5.0/admtools/inst/doc/admtools_doc.Rmd | 56 ++++ admtools-0.5.0/admtools/inst/doc/admtools_doc.html | 84 +++++++ admtools-0.5.0/admtools/inst/doc/correlation.R |only admtools-0.5.0/admtools/inst/doc/correlation.Rmd |only admtools-0.5.0/admtools/inst/doc/correlation.html |only admtools-0.5.0/admtools/man/adm_to_ddc.Rd |only admtools-0.5.0/admtools/man/flip_ddc.Rd |only admtools-0.5.0/admtools/man/get_L_unit.Rd | 2 admtools-0.5.0/admtools/man/get_L_units.Rd |only admtools-0.5.0/admtools/man/get_T_unit.Rd | 4 admtools-0.5.0/admtools/man/get_section_names.Rd |only admtools-0.5.0/admtools/man/get_total_thickness.Rd | 2 admtools-0.5.0/admtools/man/get_total_thicknesses.Rd |only admtools-0.5.0/admtools/man/plot.ddc.Rd |only admtools-0.5.0/admtools/man/plot.timelist.Rd | 32 +- admtools-0.5.0/admtools/man/sed_rate_from_matrix.Rd | 8 admtools-0.5.0/admtools/man/sed_rate_gen_from_bounds.Rd | 17 + admtools-0.5.0/admtools/man/sed_rate_gen_gamma.Rd |only admtools-0.5.0/admtools/man/set_L_unit.Rd | 4 admtools-0.5.0/admtools/man/set_L_units.Rd |only admtools-0.5.0/admtools/man/set_T_unit.Rd | 6 admtools-0.5.0/admtools/man/set_section_names.Rd |only admtools-0.5.0/admtools/man/strat_to_time.fossils.Rd |only admtools-0.5.0/admtools/man/strat_to_time.taxonomy.Rd |only admtools-0.5.0/admtools/man/summary.ddc.Rd |only admtools-0.5.0/admtools/man/time_to_strat.fossils.Rd |only admtools-0.5.0/admtools/man/time_to_strat.taxonomy.Rd |only admtools-0.5.0/admtools/man/tp_to_ddc.Rd |only admtools-0.5.0/admtools/tests/testthat/test_flip_ddc.R |only admtools-0.5.0/admtools/tests/testthat/test_strat_to_time.R | 17 + admtools-0.5.0/admtools/tests/testthat/test_time_to_strat.R | 17 + admtools-0.5.0/admtools/vignettes/FossilSim_integration.Rmd |only admtools-0.5.0/admtools/vignettes/adm_from_sedrate.Rmd | 6 admtools-0.5.0/admtools/vignettes/admtools.Rmd | 7 admtools-0.5.0/admtools/vignettes/admtools_doc.Rmd | 56 ++++ admtools-0.5.0/admtools/vignettes/correlation.Rmd |only 69 files changed, 672 insertions(+), 110 deletions(-)
Title: Headless Chrome Web Browser Interface
Description: An implementation of the 'Chrome DevTools Protocol', for
controlling a headless Chrome web browser.
Author: Garrick Aden-Buie [aut, cre] ,
Winston Chang [aut],
Barret Schloerke [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Garrick Aden-Buie <garrick@posit.co>
Diff between chromote versions 0.5.0 dated 2025-03-21 and 0.5.1 dated 2025-04-23
DESCRIPTION | 14 ++-- LICENSE |only MD5 | 89 +++++++++++++-------------- NEWS.md | 8 ++ R/browser.R | 6 - R/chromote.R | 14 ++-- R/chromote_session.R | 101 +++++++++++++++++++++++++++--- R/utils.R | 13 +++ README.md | 14 +--- build/vignette.rds |binary inst/doc/chromote.html | 13 +-- inst/doc/commands-and-events.Rmd | 3 inst/doc/commands-and-events.html | 6 - inst/doc/example-authentication.Rmd | 6 - inst/doc/example-authentication.html | 6 - inst/doc/example-custom-headers.Rmd | 4 - inst/doc/example-custom-headers.html | 4 - inst/doc/example-custom-user-agent.Rmd | 4 - inst/doc/example-custom-user-agent.html | 4 - inst/doc/example-extract-text.Rmd | 13 +-- inst/doc/example-extract-text.html | 37 +++++------ inst/doc/example-loading-page.Rmd | 20 +++++- inst/doc/example-loading-page.html | 18 +++++ inst/doc/example-remote-hosts.Rmd | 18 ----- inst/doc/example-remote-hosts.html | 22 ------ inst/doc/example-screenshot.Rmd | 20 ++---- inst/doc/example-screenshot.html | 76 ++++++++++------------- inst/doc/sync-async.Rmd | 2 inst/doc/sync-async.html | 3 inst/doc/which-chrome.Rmd | 4 - inst/doc/which-chrome.html | 4 - man/Browser.Rd | 6 - man/ChromoteSession.Rd | 105 ++++++++++++++++++++++++++++---- man/chromote-package.Rd | 2 man/default_chromote_object.Rd | 8 +- man/fragments/basic-usage.Rmd | 6 - vignettes/commands-and-events.Rmd | 3 vignettes/example-authentication.Rmd | 6 - vignettes/example-custom-headers.Rmd | 4 - vignettes/example-custom-user-agent.Rmd | 4 - vignettes/example-extract-text.Rmd | 13 +-- vignettes/example-loading-page.Rmd | 20 +++++- vignettes/example-remote-hosts.Rmd | 18 ----- vignettes/example-screenshot.Rmd | 20 ++---- vignettes/sync-async.Rmd | 2 vignettes/which-chrome.Rmd | 4 - 46 files changed, 470 insertions(+), 297 deletions(-)
Title: Treatment Switching
Description: Implements rank-preserving structural failure time model (RPSFTM), iterative parameter estimation (IPE), inverse probability of censoring weights (IPCW), and two-stage estimation (TSE) methods for treatment switching in randomized clinical trials.
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between trtswitch versions 0.1.4 dated 2025-03-20 and 0.1.5 dated 2025-04-23
DESCRIPTION | 10 MD5 | 101 +++---- NAMESPACE | 1 NEWS.md | 28 ++ R/RcppExports.R | 116 +++++++- R/ipcw.R | 141 +++++++++- R/ipe.R | 65 ++++ R/liferegr.R | 10 R/logisregr.R | 7 R/phregr.R | 8 R/rpsftm.R | 44 ++- R/tsegest.R | 120 +++++++-- R/tsesimp.R | 69 ++++- inst/doc/ipcw.Rmd | 6 inst/doc/ipcw.html | 8 inst/doc/ipe.R | 11 inst/doc/ipe.Rmd | 11 inst/doc/ipe.html | 69 ++--- inst/doc/rpsftm.html | 2 inst/doc/tsegest.R | 20 + inst/doc/tsegest.Rmd | 14 - inst/doc/tsegest.html | 56 ++-- inst/doc/tsesimp.html | 16 - man/ipcw.Rd | 27 +- man/ipe.Rd | 33 +- man/liferegr.Rd | 8 man/logisregr.Rd | 8 man/phregr.Rd | 8 man/rpsftm.Rd | 19 + man/survQuantile.Rd |only man/tsegest.Rd | 64 +++- man/tsegestsim.Rd | 32 ++ man/tsesimp.Rd | 20 + src/RcppExports.cpp | 65 +++- src/ipcw.cpp | 17 - src/ipe.cpp | 18 + src/logistic_regression.cpp | 32 +- src/logistic_regression.h | 4 src/rpsftm.cpp | 20 + src/survival_analysis.cpp | 552 ++++++++++++++++++++++++++++++++++++++---- src/survival_analysis.h | 16 + src/tsegest.cpp | 161 ++++++++---- src/tsegestsim.cpp | 166 ++++++++---- src/tsesimp.cpp | 10 tests/testthat/test-ipcw.R | 58 ++-- tests/testthat/test-ipe.R | 18 - tests/testthat/test-rpsftm.R | 14 - tests/testthat/test-tsegest.R | 15 - tests/testthat/test-tsesimp.R | 21 - vignettes/ipcw.Rmd | 6 vignettes/ipe.Rmd | 11 vignettes/tsegest.Rmd | 14 - 52 files changed, 1774 insertions(+), 596 deletions(-)
Title: A Unified Time Series Event Detection Framework
Description: By analyzing time series, it is possible to observe significant changes in the behavior of observations that frequently characterize events. Events present themselves as anomalies, change points, or motifs. In the literature, there are several methods for detecting events. However, searching for a suitable time series method is a complex task, especially considering that the nature of events is often unknown. This work presents Harbinger, a framework for integrating and analyzing event detection methods. Harbinger contains several state-of-the-art methods described in Salles et al. (2020) <doi:10.5753/sbbd.2020.13626>.
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut],
Antonio Mello [aut],
Ellen Paixao [aut],
Fernando Fraga [aut],
Heraldo Borges [aut],
Janio Lima [aut],
Jessica Souza [aut],
Lais Baroni [aut],
Lucas Tavares [aut],
Rebecca Salles [aut],
Diego [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between harbinger versions 1.1.707 dated 2024-12-03 and 1.1.717 dated 2025-04-23
DESCRIPTION | 18 +++--- MD5 | 81 ++++++++++++++------------- R/han_autoencoder.R | 11 +-- R/hanc_ml.R | 4 - R/hanct_dtw.R | 4 - R/hanct_kmeans.R | 4 - R/hanr_arima.R | 4 - R/hanr_emd.R | 4 - R/hanr_fbiad.R | 2 R/hanr_fft.R | 2 R/hanr_garch.R | 2 R/hanr_hist.R | 2 R/hanr_ml.R | 4 - R/hanr_red.R | 2 R/hanr_remd.R | 2 R/hanr_wavelet.R | 2 R/har_ensemble.R | 4 - R/har_eval.R | 4 - R/har_eval_soft.R | 2 R/harbinger.R | 6 +- R/hcp_amoc.R | 2 R/hcp_binseg.R | 2 R/hcp_cf_arima.R | 4 - R/hcp_cf_ets.R | 2 R/hcp_cf_lr.R | 2 R/hcp_chow.R | 2 R/hcp_garch.R | 4 - R/hcp_gft.R | 2 R/hcp_pelt.R | 2 R/hcp_red.R | 6 +- R/hcp_scp.R | 4 - R/hdis_mp.R | 2 R/hdis_sax.R | 34 +++++------ R/hmo_mp.R | 2 R/hmo_sax.R | 28 ++++----- R/hmo_xsax.R | 2 R/hmu_pca.R | 3 - R/trans_sax.R | 2 R/trans_xsax.R | 2 README.md | 113 ++++++++++++++++++++++----------------- man/figures/README-example-1.png |only man/han_autoencoder.Rd | 12 +--- 42 files changed, 204 insertions(+), 192 deletions(-)