Title: An R Autograding Extension for Otter-Grader
Description: An R autograding extension for Otter-Grader (<https://otter-grader.readthedocs.io>). It supports
grading R scripts, R Markdown documents, and R Jupyter Notebooks.
Author: Christopher Pyles [aut, cre] ,
UC Berkeley Data Science Education Program [cph]
Maintainer: Christopher Pyles <cpyles@berkeley.edu>
Diff between ottr versions 1.5.1 dated 2024-11-10 and 1.5.2 dated 2025-07-01
DESCRIPTION | 9 LICENSE | 6 MD5 | 137 +-- NAMESPACE | 18 R/GradingResults.R | 108 +-- R/TestCase.R | 166 ++-- R/TestCaseResult.R | 170 ++-- R/TestFileResult.R | 188 ++--- R/check.R | 130 +-- R/check_collector.R | 94 +- R/execute_script.R | 80 +- R/export.R | 225 +++--- R/grade_script.R | 88 +- R/load_test_cases.R | 74 +- R/run_autograder.R | 56 - R/save_notebook.R | 86 +- R/update_ast_check_calls.R | 78 +- R/utils.R | 96 +- R/valid_syntax.R | 66 - README.md | 20 man/CheckCollector.Rd | 164 ++-- man/GradingResults.Rd | 196 ++--- man/TestCase.Rd | 248 +++--- man/TestCaseResult.Rd | 250 +++---- man/TestFileResult.Rd | 246 +++--- man/check.Rd | 54 - man/collector_env.Rd | 36 - man/collector_varname.Rd | 32 man/execute_script.Rd | 50 - man/export.Rd | 82 +- man/get_collector.Rd | 22 man/grade_script.Rd | 46 - man/initialize_collector.Rd | 22 man/load_test_cases.Rd | 36 - man/run_autograder.Rd | 54 - man/running_on_jupyter.Rd | 40 - man/save_notebook.Rd | 54 - man/update_ast_check_calls.Rd | 46 - man/valid_syntax.Rd | 110 +-- tests/testthat.R | 24 tests/testthat/files/example_test_file.R | 78 +- tests/testthat/files/integration_expected_results/fails_2_hidden.json | 186 ++--- tests/testthat/files/integration_expected_results/fails_3.json | 186 ++--- tests/testthat/files/integration_expected_results/passes_all.json | 186 ++--- tests/testthat/files/integration_expected_results_rounding/fails_2_hidden.json | 186 ++--- tests/testthat/files/integration_expected_results_rounding/fails_3.json | 186 ++--- tests/testthat/files/integration_expected_results_rounding/passes_all.json | 186 ++--- tests/testthat/files/integration_test_cases/q1.R | 38 - tests/testthat/files/integration_test_cases/q2.R | 44 - tests/testthat/files/integration_test_cases/q3.R | 42 - tests/testthat/helper_make_test_cases.R | 92 +- tests/testthat/helper_make_test_file_results.R | 72 +- tests/testthat/helper_make_test_file_results_list.R | 12 tests/testthat/test_GradingResults.R | 52 - tests/testthat/test_TestCase.R | 162 ++-- tests/testthat/test_TestCaseResult.R | 152 ++-- tests/testthat/test_TestFileResult.R | 214 ++--- tests/testthat/test_check.R | 112 +-- tests/testthat/test_check_collector.R | 50 - tests/testthat/test_execute_script.R | 90 +- tests/testthat/test_export.R | 357 +++++----- tests/testthat/test_grade_script.R | 76 +- tests/testthat/test_integration.R | 110 +-- tests/testthat/test_load_test_cases.R | 64 - tests/testthat/test_run_autograder.R | 34 tests/testthat/test_running_on_jupyter.R | 20 tests/testthat/test_save_notebook.R | 88 +- tests/testthat/test_update_ast_check_calls.R | 54 - tests/testthat/test_valid_syntax.R | 34 tests/testthat/testthat-problems.rds |only 70 files changed, 3437 insertions(+), 3433 deletions(-)
Title: Spatial Interpolation using Bayesian Maximum Entropy (BME)
Description: Provides an accessible and robust implementation of core BME
methodologies for spatial prediction. It enables the systematic integration
of heterogeneous data sources including both hard data (precise
measurements) and soft interval data (bounded or uncertain observations)
while incorporating prior knowledge and supporting variogram-based spatial
modeling. The BME methodology is described in Christakos (1990)
<doi:10.1007/BF00890661> and Serre and Christakos (1999)
<doi:10.1007/s004770050029>.
Author: Kinspride Duah [aut, cre, cph] ,
Yan Sun [aut]
Maintainer: Kinspride Duah <kinspride2020@gmail.com>
Diff between BMEmapping versions 0.3.0 dated 2025-05-13 and 1.0.0 dated 2025-07-01
DESCRIPTION | 6 MD5 | 45 ++--- NAMESPACE | 1 NEWS.md | 21 ++ R/bme_cv.R | 16 - R/bme_estimate.R | 12 - R/bme_predict.R | 34 ++- R/clean_input.R |only R/covmat.R | 15 - R/distant.R | 32 --- R/exponential.R | 2 R/extended_range.R |only R/gaussian.R | 2 R/prob_zk.R | 27 +-- R/spherical.R | 2 inst/doc/Introduction_to_BMEmapping.R | 155 ++++++++--------- inst/doc/Introduction_to_BMEmapping.Rmd | 155 ++++++++--------- inst/doc/Introduction_to_BMEmapping.html | 276 +++++++++++++++---------------- man/bme_cv.Rd | 14 - man/bme_predict.Rd | 22 +- man/extended_range.Rd |only man/prob_zk.Rd | 10 - tests/testthat/test-bme_predict.R | 16 - tests/testthat/test-covmat.R | 10 - vignettes/Introduction_to_BMEmapping.Rmd | 155 ++++++++--------- 25 files changed, 512 insertions(+), 516 deletions(-)
Title: Data Access and Analytical Tools for 'VectorSurv' Users
Description: Allows registered 'VectorSurv' <https://vectorsurv.org/> users access to data through the 'VectorSurv API' <https://api.vectorsurv.org/>. Additionally provides functions for analysis and visualization.
Author: Christina De Cesaris [aut, cre]
Maintainer: Christina De Cesaris <cmdecesaris@ucdavis.edu>
Diff between vectorsurvR versions 1.4.0 dated 2025-06-02 and 1.5.0 dated 2025-07-01
vectorsurvR-1.4.0/vectorsurvR/R/getAbundanceMapData.R |only vectorsurvR-1.4.0/vectorsurvR/man/getAbundanceMapData.Rd |only vectorsurvR-1.5.0/vectorsurvR/DESCRIPTION | 8 vectorsurvR-1.5.0/vectorsurvR/MD5 | 42 - vectorsurvR-1.5.0/vectorsurvR/NAMESPACE | 10 vectorsurvR-1.5.0/vectorsurvR/R/data.R | 1 vectorsurvR-1.5.0/vectorsurvR/R/getAbundance.R | 30 vectorsurvR-1.5.0/vectorsurvR/R/getAbundanceAnomaly.R | 10 vectorsurvR-1.5.0/vectorsurvR/R/getArthroCollections.R | 435 +++++++++----- vectorsurvR-1.5.0/vectorsurvR/R/getInfectionRate.R | 17 vectorsurvR-1.5.0/vectorsurvR/R/getVectorIndex.R | 15 vectorsurvR-1.5.0/vectorsurvR/R/globals.R | 3 vectorsurvR-1.5.0/vectorsurvR/README.md | 2 vectorsurvR-1.5.0/vectorsurvR/data/sample_collections.rda |binary vectorsurvR-1.5.0/vectorsurvR/inst/doc/vectorsurvR.R | 5 vectorsurvR-1.5.0/vectorsurvR/inst/doc/vectorsurvR.Rmd | 9 vectorsurvR-1.5.0/vectorsurvR/inst/doc/vectorsurvR.html | 148 +--- vectorsurvR-1.5.0/vectorsurvR/man/getAbundance.Rd | 4 vectorsurvR-1.5.0/vectorsurvR/man/getAbundanceAnomaly.Rd | 2 vectorsurvR-1.5.0/vectorsurvR/man/getInfectionRate.Rd | 7 vectorsurvR-1.5.0/vectorsurvR/man/getVectorIndex.Rd | 10 vectorsurvR-1.5.0/vectorsurvR/man/sample_collections.Rd | 1 vectorsurvR-1.5.0/vectorsurvR/vignettes/vectorsurvR.Rmd | 9 23 files changed, 426 insertions(+), 342 deletions(-)
Title: Predictive Information Index ('PII')
Description: A simple implementation of the Predictive Information Index ('PII').
Author: Kevin E. Wells [aut, cre]
Maintainer: Kevin E. Wells <kevin.e.wells@usm.edu>
Diff between piiR versions 0.2.1 dated 2025-05-07 and 0.3.0 dated 2025-07-01
piiR-0.2.1/piiR/NEWS.md |only piiR-0.2.1/piiR/R/compare_scores.R |only piiR-0.2.1/piiR/R/pii_batch.R |only piiR-0.2.1/piiR/R/pii_classification.R |only piiR-0.2.1/piiR/R/pii_compare.R |only piiR-0.2.1/piiR/R/pii_test.R |only piiR-0.2.1/piiR/README.md |only piiR-0.2.1/piiR/man/compare_scores.Rd |only piiR-0.2.1/piiR/man/pii_batch.Rd |only piiR-0.2.1/piiR/man/pii_classification.Rd |only piiR-0.2.1/piiR/man/pii_compare.Rd |only piiR-0.2.1/piiR/man/pii_test.Rd |only piiR-0.3.0/piiR/DESCRIPTION | 13 ++++++------- piiR-0.3.0/piiR/MD5 | 18 +++--------------- piiR-0.3.0/piiR/NAMESPACE | 7 ------- piiR-0.3.0/piiR/R/pii.R | 1 - 16 files changed, 9 insertions(+), 30 deletions(-)
Title: Isolation Forest-Based Presence-Only Species Distribution
Modeling
Description: Collection of R functions to do purely presence-only species
distribution modeling with isolation forest (iForest) and its
variations such as Extended isolation forest and SCiForest. See the
details of these methods in references: Liu, F.T., Ting, K.M. and
Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C.
and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T.,
Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>,
Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016)
<https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021)
<doi:10.48550/arXiv.2110.13402>.
Additionally, Shapley values are used to explain
model inputs and outputs. See details in references: Shapley, L.S.
(1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I.
(2017) <https://dm-gatech.github.io/CS8803-Fall2018-DML-Papers/shapley.pdf>, Molnar,
C. (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononen [...truncated...]
Author: Lei Song [aut, cre] ,
Lyndon Estes [ths]
Maintainer: Lei Song <lsong@clarku.edu>
Diff between itsdm versions 0.2.1 dated 2023-06-10 and 0.2.2 dated 2025-07-01
DESCRIPTION | 16 +++--- MD5 | 90 ++++++++++++++++++------------------ NEWS.md | 4 + R/cmcc_bioclim.R | 13 ++--- R/data.R | 4 - R/detect_envi_change.R | 14 +++-- R/dim_reduce.R | 6 +- R/future_cmcc_bioclim.R | 12 ++-- R/future_worldclim2.R | 12 ++-- R/independent_response.R | 4 - R/isotree_po.R | 18 +++---- R/itsdm-package.R | 5 +- R/marginal_response.R | 4 - R/plot.R | 4 - R/shap_dependence.R | 10 ++-- R/shap_spatial_response.R | 8 +-- R/spatial_response.R | 8 +-- R/suspicious_env_outliers.R | 18 +++---- R/variable_analysis.R | 10 ++-- R/variable_contrib.R | 6 +- R/worldclim2.R | 14 ++--- README.md | 8 ++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction_of_itsdm.html | 28 +++++------ inst/doc/itsdm_example.html | 20 ++++---- inst/doc/shap_application.html | 14 ++--- man/cmcc_bioclim.Rd | 7 +- man/detect_envi_change.Rd | 14 +++-- man/dim_reduce.Rd | 6 +- man/future_cmcc_bioclim.Rd | 6 +- man/future_worldclim2.Rd | 6 +- man/independent_response.Rd | 4 - man/isotree_po.Rd | 18 +++---- man/itsdm-package.Rd | 3 - man/mainland_africa.Rd | 4 - man/marginal_response.Rd | 4 - man/plot.EnvironmentalOutlier.Rd | 2 man/plot.ShapDependence.Rd | 2 man/shap_dependence.Rd | 10 ++-- man/shap_spatial_response.Rd | 8 +-- man/spatial_response.Rd | 8 +-- man/suspicious_env_outliers.Rd | 18 +++---- man/variable_analysis.Rd | 10 ++-- man/variable_contrib.Rd | 6 +- man/worldclim2.Rd | 6 +- 46 files changed, 251 insertions(+), 241 deletions(-)
Title: Regression Analysis Linear and Nonlinear for Agriculture
Description: Linear and nonlinear regression analysis common in agricultural science articles (Archontoulis & Miguez (2015). <doi:10.2134/agronj2012.0506>). The package includes polynomial, exponential, gaussian, logistic, logarithmic, segmented, non-parametric models, among others. The functions return the model coefficients and their respective p values, coefficient of determination, root mean square error, AIC, BIC, as well as graphs with the equations automatically.
Author: Gabriel Danilo Shimizu [aut, cre] ,
Leandro Simoes Azeredo Goncalves [aut, ctb]
Maintainer: Gabriel Danilo Shimizu <gabrield.shimizu@gmail.com>
Diff between AgroReg versions 1.2.10 dated 2024-01-16 and 1.2.11 dated 2025-07-01
DESCRIPTION | 18 +-- MD5 | 214 +++++++++++++++++++++--------------------- NEWS.md | 4 R/AM_analysis.R | 21 +++- R/BC_analysis.R | 20 ++- R/BIEXP_analysis.R | 20 ++- R/CD_analysis.R | 16 ++- R/IC_analysis.R | 2 R/LL_analysis.R | 20 ++- R/LM13_analysis.R | 20 ++- R/LM13i_analysis.R | 20 ++- R/LM23_analysis.R | 20 ++- R/LM23i_analysis.R | 20 ++- R/LM2i3_analysis.R | 20 ++- R/LM_analysis.R | 28 +++-- R/LM_i_analysis.R | 28 +++-- R/LNplt_analysis.R | 20 ++- R/LOG2_analysis.R | 21 ++-- R/LOG_analysis.R | 20 ++- R/MM_analysis.R | 20 ++- R/N_analysis.R | 20 ++- R/PAGE_analysis.R | 20 ++- R/SH_function.R | 20 ++- R/VB_analysis.R | 20 ++- R/VG_analysis.R | 20 ++- R/adjust_scale.R | 2 R/adjust_scale_x.R | 2 R/adjust_scale_y.R | 2 R/asymptotic_analysis.R | 18 ++- R/asymptotic_i_analysis.R | 20 ++- R/asymptotic_i_sup_analysis.R | 20 ++- R/asymptotic_sup_analysis.R | 20 ++- R/beta_analysis.R | 20 ++- R/comparative_function.R | 10 - R/extractmodel_analysis.R | 10 - R/gaussian_analysis.R | 16 ++- R/gompertz_analysis.R | 20 ++- R/hill_analysis.R | 20 ++- R/linearlinear_analysis.R | 20 ++- R/loess_analysis.R | 20 ++- R/logistic_analysis.R | 20 ++- R/lorentz_analysis.R | 20 ++- R/midilli_analysis.R | 20 ++- R/midillim_analysis.R | 20 ++- R/mitscherlich_analysis.R | 20 ++- R/newton_analysis.R | 20 ++- R/peleg_analysis.R | 20 ++- R/plot_arrange.R | 77 +++++++-------- R/pltLN_analysis.R | 20 ++- R/pltQD_analysis.R | 21 ++-- R/potential_analysis.R | 20 ++- R/quadraticplateau_analysis.R | 20 ++- R/regression.R | 172 +++++++++++++++++---------------- R/stat_param.R | 4 R/thompson_analysis.R | 20 ++- R/valcam_analysis.R | 20 ++- R/weibull_analysis.R | 20 ++- R/yieldloss_analysis.R | 20 ++- build/partial.rdb |binary man/AM.Rd | 5 man/BC.Rd | 5 man/CD.Rd | 5 man/GP.Rd | 5 man/LL.Rd | 5 man/LM.Rd | 5 man/LM13.Rd | 5 man/LM13i.Rd | 5 man/LM23.Rd | 5 man/LM23i.Rd | 5 man/LM2i3.Rd | 5 man/LM_i.Rd | 5 man/LOG.Rd | 5 man/LOG2.Rd | 5 man/MM.Rd | 5 man/Nreg.Rd | 5 man/PAGE.Rd | 5 man/SH.Rd | 5 man/VB.Rd | 5 man/VG.Rd | 5 man/asymptotic.Rd | 5 man/asymptotic_i.Rd | 5 man/asymptotic_ineg.Rd | 5 man/asymptotic_neg.Rd | 5 man/beta_reg.Rd | 5 man/biexponential.Rd | 5 man/comparative_model.Rd | 16 +++ man/gaussianreg.Rd | 5 man/hill.Rd | 5 man/linear.linear.Rd | 5 man/linear.plateau.Rd | 5 man/loessreg.Rd | 5 man/logistic.Rd | 5 man/lorentz.Rd | 5 man/midilli.Rd | 5 man/midillim.Rd | 5 man/mitscherlich.Rd | 5 man/newton.Rd | 5 man/peleg.Rd | 5 man/plateau.linear.Rd | 5 man/plateau.quadratic.Rd | 5 man/plot_arrange.Rd | 4 man/potential.Rd | 5 man/quadratic.plateau.Rd | 5 man/regression.Rd | 5 man/thompson.Rd | 5 man/valcam.Rd | 5 man/weibull.Rd | 5 man/yieldloss.Rd | 5 108 files changed, 1163 insertions(+), 538 deletions(-)
Title: Client for Delphi's 'COVIDcast Epidata' API
Description: Tools for Delphi's 'COVIDcast Epidata' API: data access, maps and
time series plotting, and basic signal processing. The API includes a
collection of numerous indicators relevant to the COVID-19 pandemic in the
United States, including official reports, de-identified aggregated medical
claims data, large-scale surveys of symptoms and public behavior, and
mobility data, typically updated daily and at the county level. All data
sources are documented at
<https://cmu-delphi.github.io/delphi-epidata/api/covidcast.html>.
Author: Taylor Arnold [aut],
Jacob Bien [aut],
Logan Brooks [aut],
Sarah Colquhoun [aut],
David Farrow [aut],
Jed Grabman [ctb],
Pedrito Maynard-Zhang [ctb],
Kathryn Mazaitis [aut],
Alex Reinhart [aut, cre] ,
Ryan Tibshirani [aut]
Maintainer: Alex Reinhart <areinhar@stat.cmu.edu>
Diff between covidcast versions 0.5.2 dated 2023-07-12 and 0.5.3 dated 2025-07-01
covidcast-0.5.2/covidcast/inst/doc/covidcast.R |only covidcast-0.5.2/covidcast/inst/doc/external-data.R |only covidcast-0.5.2/covidcast/inst/doc/multi-signals.R |only covidcast-0.5.2/covidcast/inst/doc/plotting-signals.R |only covidcast-0.5.3/covidcast/DESCRIPTION | 15 covidcast-0.5.3/covidcast/MD5 | 110 covidcast-0.5.3/covidcast/NEWS.md | 8 covidcast-0.5.3/covidcast/R/plot.R | 98 covidcast-0.5.3/covidcast/build/partial.rdb |binary covidcast-0.5.3/covidcast/build/vignette.rds |binary covidcast-0.5.3/covidcast/inst/doc/correlation-utils.Rmd | 12 covidcast-0.5.3/covidcast/inst/doc/correlation-utils.html | 10 covidcast-0.5.3/covidcast/inst/doc/covidcast.Rmd | 194 covidcast-0.5.3/covidcast/inst/doc/covidcast.html | 200 covidcast-0.5.3/covidcast/inst/doc/external-data.Rmd | 74 covidcast-0.5.3/covidcast/inst/doc/external-data.html | 46 covidcast-0.5.3/covidcast/inst/doc/multi-signals.Rmd | 293 covidcast-0.5.3/covidcast/inst/doc/multi-signals.html | 430 covidcast-0.5.3/covidcast/inst/doc/plotting-signals.Rmd | 116 covidcast-0.5.3/covidcast/inst/doc/plotting-signals.html | 72 covidcast-0.5.3/covidcast/inst/shapefiles/county.geojson.bz2 |binary covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/bubble-plot-with-0-and-missing.svg | 156 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-county-choropleth-with-alaska.svg | 66 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-county-choropleth-with-include.svg | 222 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-county-choropleth.svg | 1312 +- covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-hrr-choropleth-with-include.svg | 166 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-hrr-choropleth.svg | 828 - covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-msa-choropleth-with-include.svg | 168 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-msa-choropleth.svg | 966 - covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-state-choropleth-with-include.svg | 76 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-state-choropleth-with-range.svg | 288 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-state-choropleth.svg | 288 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/default-state-line-graph.svg | 480 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/simple-county-bubble-plot.svg | 6500 +++++----- covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/simple-line-graph.svg | 10 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/state-choropleth-with-no-metadata.svg | 288 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/state-line-graph-with-range.svg | 480 covidcast-0.5.3/covidcast/tests/testthat/_snaps/plot/state-line-graph-with-stderrs.svg | 26 covidcast-0.5.3/covidcast/vignettes/correlation-utils.Rmd | 12 covidcast-0.5.3/covidcast/vignettes/correlation-utils.Rmd.orig | 2 covidcast-0.5.3/covidcast/vignettes/covidcast.Rmd | 194 covidcast-0.5.3/covidcast/vignettes/covidcast.Rmd.orig |only covidcast-0.5.3/covidcast/vignettes/external-data.Rmd | 74 covidcast-0.5.3/covidcast/vignettes/external-data.Rmd.orig |only covidcast-0.5.3/covidcast/vignettes/figures/corr-unnamed-chunk-3-1.png |binary covidcast-0.5.3/covidcast/vignettes/figures/corr-unnamed-chunk-4-1.png |binary covidcast-0.5.3/covidcast/vignettes/figures/corr-unnamed-chunk-5-1.png |binary covidcast-0.5.3/covidcast/vignettes/figures/corr-unnamed-chunk-6-1.png |binary covidcast-0.5.3/covidcast/vignettes/figures/corr-unnamed-chunk-7-1.png |binary covidcast-0.5.3/covidcast/vignettes/figures/covidcast-unnamed-chunk-5-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/ext-unnamed-chunk-3-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-10-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-12-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-12-2.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-13-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-3-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-4-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-5-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-6-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-7-1.png |only covidcast-0.5.3/covidcast/vignettes/figures/plot-unnamed-chunk-8-1.png |only covidcast-0.5.3/covidcast/vignettes/multi-signals.Rmd | 293 covidcast-0.5.3/covidcast/vignettes/multi-signals.Rmd.orig |only covidcast-0.5.3/covidcast/vignettes/plotting-signals.Rmd | 116 covidcast-0.5.3/covidcast/vignettes/plotting-signals.Rmd.orig |only covidcast-0.5.3/covidcast/vignettes/precompile.R | 7 66 files changed, 8047 insertions(+), 6649 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.8 dated 2025-03-13 and 0.0.9 dated 2025-07-01
DESCRIPTION | 12 ++++++---- MD5 | 14 ++++++------ NEWS.md | 11 ++++++++++ R/reaggregate_counts.R | 10 +++++---- R/reaggregate_rates.R | 2 - README.md | 24 ++++++++------------- tests/testthat/helpers.R | 2 - tests/testthat/test-reaggregate_counts.R | 34 +++++++++++++++++++++++++++++++ 8 files changed, 76 insertions(+), 33 deletions(-)
Title: Generalized Linear Regression with DDM
Description: Drift-Diffusion Model (DDM) has been widely used to model binary
decision-making tasks, and many research studies the relationship between
DDM parameters and other characteristics of the subject. This package uses
'RStan' to perform generalized liner regression analysis over DDM parameters
via a single Bayesian Hierarchical model. Compared to estimating DDM
parameters followed by a separate regression model, 'RegDDM' reduces bias
and improves statistical power.
Author: Zekai Jin [aut, cre]
Maintainer: Zekai Jin <Jin.Zekai@nyspi.columbia.edu>
Diff between RegDDM versions 1.0 dated 2024-12-05 and 1.1 dated 2025-07-01
RegDDM-1.0/RegDDM/data/regddm_tutorial.rda |only RegDDM-1.0/RegDDM/man/regddm_tutorial.Rd |only RegDDM-1.1/RegDDM/DESCRIPTION | 8 RegDDM-1.1/RegDDM/MD5 | 38 - RegDDM-1.1/RegDDM/NAMESPACE | 18 RegDDM-1.1/RegDDM/R/RegDDM.R | 34 - RegDDM-1.1/RegDDM/R/check_error.R | 324 +++++------ RegDDM-1.1/RegDDM/R/data.R | 21 RegDDM-1.1/RegDDM/R/generate_model.R | 736 ++++++++++++------------- RegDDM-1.1/RegDDM/R/generate_sim_data.R | 304 +++++----- RegDDM-1.1/RegDDM/R/regddmfit_class.R | 18 RegDDM-1.1/RegDDM/R/summary_results.R | 138 ++-- RegDDM-1.1/RegDDM/README.md | 318 +++++----- RegDDM-1.1/RegDDM/data/regddm_data.rda |only RegDDM-1.1/RegDDM/man/generate_sim_data.Rd | 132 ++-- RegDDM-1.1/RegDDM/man/get_stan_fit.Rd | 36 - RegDDM-1.1/RegDDM/man/print.regddmfit.Rd | 50 - RegDDM-1.1/RegDDM/man/regddm.Rd | 32 - RegDDM-1.1/RegDDM/man/regddm_data.Rd |only RegDDM-1.1/RegDDM/man/regddmfit.Rd | 58 - RegDDM-1.1/RegDDM/man/summary.regddmfit.Rd | 56 - RegDDM-1.1/RegDDM/tests/testthat/test-RegDDM.R | 198 ++++-- 22 files changed, 1300 insertions(+), 1219 deletions(-)
Title: Discovery, Retrieval, and Analysis of Water Isotope Data
Description: The wiDB...() functions provide an interface to the public API
of the wiDB <https://github.com/SPATIAL-Lab/isoWater/blob/master/Protocol.md>:
build, check and submit queries, and receive and
unpack responses. Data analysis functions support Bayesian
inference of the source and source isotope composition of water
samples that may have experienced evaporation. Algorithms
adapted from Bowen et al. (2018, <doi:10.1007/s00442-018-4192-5>).
Author: Gabe Bowen [aut, cre]
Maintainer: Gabe Bowen <gabe.bowen@utah.edu>
Diff between isoWater versions 1.2.0 dated 2024-07-23 and 1.2.1 dated 2025-07-01
DESCRIPTION | 6 +-- MD5 | 14 ++++---- NEWS.md | 3 + R/wiDBfunctions.R | 20 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/isoWater.html | 84 ++++++++++++++++++++++++------------------------- man/wiDB_data.Rd | 2 - 8 files changed, 66 insertions(+), 63 deletions(-)
Title: Connect to Your 'Zendesk' Data
Description: Facilitates making a connection to the
'Zendesk' API and executing various queries. You can use it to
get ticket, ticket metrics, and user data. The 'Zendesk' documentation is
available at <https://developer.zendesk.com/rest_api
/docs/support/introduction>. This package is not supported by
'Zendesk' (owner of the software).
Author: Chris Umphlett [aut, cre],
Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between zdeskR versions 0.5.0 dated 2025-06-12 and 0.6.0 dated 2025-07-01
DESCRIPTION | 6 - MD5 | 12 +-- NAMESPACE | 1 R/get_ticket_audits.R |only R/ticket_search.R | 4 - man/get_satisfaction_ratings.Rd | 142 ++++++++++++++++++++-------------------- man/get_ticket_audits.Rd |only man/ticket_search.Rd | 84 +++++++++++------------ 8 files changed, 126 insertions(+), 123 deletions(-)
Title: Dynamic and Interactive Maps
Description: Dynamic and Interactive Maps with R, powered by 'leaflet' <https://leafletjs.com>. 'evolMap' generates a web page with interactive and dynamic maps to which you can add geometric entities (points, lines or colored geographic areas), and/or markers with optional links between them. The dynamic ability of these maps allows their components to evolve over a continuous period of time or by periods.
Author: Modesto Escobar [cre, aut, cph] ,
Carlos Prieto [aut] ,
David Barrios [aut]
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between evolMap versions 1.3.8 dated 2025-01-15 and 1.3.14 dated 2025-07-01
DESCRIPTION | 20 LICENSE | 2 LICENSE.note | 2416 ++++++++++++++++---------------- MD5 | 55 R/create_map.R | 16 R/get_location.R | 60 R/utils.R | 628 ++++---- README.md | 20 build |only inst/doc |only inst/extdata/ukr-civharm-2023-02-27.csv |only inst/www/ca.js | 2 inst/www/create_map.js | 129 + inst/www/create_map2.js | 408 ++++- inst/www/d3.layout.cloud.js | 998 ++++++------- inst/www/d3.min.js | 4 inst/www/en.js | 2 inst/www/es.js | 2 inst/www/iro.min.js | 14 inst/www/jszip.min.js | 28 inst/www/leaflet.js | 10 inst/www/leaflet.markercluster.js | 4 inst/www/leaflet.minichart.min.js |only inst/www/styles.css | 25 inst/www/styles2.css | 106 + inst/www/tutorial_ca.js | 84 - man/add_tutorial.Rd | 62 vignettes |only 28 files changed, 2763 insertions(+), 2332 deletions(-)
Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package 'glmnet' in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver,
a wide range of matrix classes that can exploit special structure
to allow large-scale inputs, and an assortment of
generalized linear model classes for fitting various types of data.
The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph],
Trevor Hastie [aut, cph, cre],
Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between adelie versions 1.0.7 dated 2025-02-28 and 1.0.8 dated 2025-07-01
DESCRIPTION | 14 MD5 | 12 R/solver.R | 6 R/utilities.R | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/adelie.html | 2176 +++++++++++++++++++++++++++++---------------------- 7 files changed, 1297 insertions(+), 915 deletions(-)
Title: Tools for Outbreak Investigation/Infectious Disease Surveillance
Description: Create epicurves, epigantt charts, and diverging bar charts
using 'ggplot2'. Prepare data for visualisation or other reporting for
infectious disease surveillance and outbreak investigation (time
series data). Includes tidy functions to solve date based
transformations for common reporting tasks, like (A) seasonal date
alignment for respiratory disease surveillance, (B) date-based case
binning based on specified time intervals like isoweek, epiweek, month
and more, (C) automated detection and marking of the new year based on
the date/datetime axis of the 'ggplot2', (D) labelling of the last
value of a time-series. An introduction on how to use epicurves can
be found on the US CDC website (2012,
<https://www.cdc.gov/training/quicklearns/epimode/index.html>).
Author: Alexander Bartel [aut, cre]
Maintainer: Alexander Bartel <alexander.bartel@fu-berlin.de>
Diff between ggsurveillance versions 0.4.0 dated 2025-05-09 and 0.5.0 dated 2025-07-01
DESCRIPTION | 33 - MD5 | 111 ++-- NAMESPACE | 5 NEWS.md | 14 R/align_dates_seasonal.R | 98 --- R/bin_by_date.R |only R/create_agegroups.R | 22 R/data.R | 4 R/geom_bar_diverging.R | 26 R/geom_epicurve.R | 267 +++++----- R/geom_epigantt.R | 3 R/geom_vline_year.R | 122 +--- R/geometric_mean.R | 15 R/ggplot_theme_helpers.R | 2 R/guide_axis_nested_date.R |only R/label.R |only R/label_skip.R | 10 R/scale_cases_5er.R | 12 R/scale_continuous_diverging.R | 9 R/scale_date_limit_days.R | 56 -- R/stat_last_value.R | 2 R/themes.R |only README.md | 39 - inst/WORDLIST | 1 inst/doc/Epicurves_with_ggsurveillance.html | 2 man/align_dates_seasonal.Rd | 27 - man/bin_by_date.Rd |only man/create_agegroups.Rd | 26 man/figures/epicurve_readme.png |binary man/figures/epicurve_readme.svg | 5 man/figures/ggsurveillance.png |only man/figures/seasonal_plot_readme.png |binary man/geom_bar_diverging.Rd | 24 man/geom_epicurve.Rd | 86 ++- man/geom_epigantt.Rd | 3 man/geom_vline_year.Rd | 203 +++---- man/geometric_mean.Rd | 3 man/guide_axis_nested_date.Rd |only man/influenza_germany.Rd | 2 man/label_date.Rd | 146 ++--- man/label_power10.Rd |only man/label_skip.Rd | 84 +-- man/population_german_states.Rd | 86 +-- man/scale_continuous_diverging.Rd | 210 +++---- man/scale_y_cases_5er.Rd | 22 man/stat_last_value.Rd | 2 tests/testthat/_snaps/geom_epicurve/1-geom-epicurve-basic-date-warn.svg |only tests/testthat/_snaps/geom_epicurve/1-geom-epicurve-basic-date.svg | 24 tests/testthat/_snaps/geom_epicurve/2-geom-epicurve-date-resolutionna.svg | 120 ++-- tests/testthat/_snaps/geom_epicurve/3-geom-epicurve-facet.svg |only tests/testthat/_snaps/geom_epicurve/3-geom-epicurve-flipped-aes-back.svg |only tests/testthat/_snaps/geom_epicurve/3-geom-epicurve-flipped-aes.svg | 131 +++- tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-base-new.svg |only tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-base.svg |only tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-epiyear.svg |only tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-fill-gaps.svg |only tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-isoyear.svg |only tests/testthat/_snaps/geom_epicurve/8-stat-bin-date-year.svg |only tests/testthat/test-align_and_bin_dates_seasonal.R | 37 + tests/testthat/test-align_dates_seasonal.R | 15 tests/testthat/test-bin_by_date.R |only tests/testthat/test-geom_epicurve.R | 87 +++ tests/testthat/test-geom_vline_year.R | 108 +--- tests/testthat/test-label_power10.R |only tests/testthat/test-label_skip.R | 2 tests/testthat/test_extras.R | 2 66 files changed, 1267 insertions(+), 1041 deletions(-)
More information about ggsurveillance at CRAN
Permanent link
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothee Giraud [cre, aut] ,
Hugues Pecout [ctb] ,
Ronan Ysebaert [ctb] ,
Elina Marveaux [ctb] ,
Ian Fellows [cph] ,
Jim Lemon [cph]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 0.12.0 dated 2024-10-22 and 1.0.0 dated 2025-07-01
mapsf-0.12.0/mapsf/R/mf_leg_c.R |only mapsf-0.12.0/mapsf/R/mf_leg_gl.R |only mapsf-0.12.0/mapsf/R/mf_leg_p.R |only mapsf-0.12.0/mapsf/R/mf_leg_pl.R |only mapsf-0.12.0/mapsf/R/mf_leg_s.R |only mapsf-0.12.0/mapsf/R/mf_leg_t.R |only mapsf-0.12.0/mapsf/inst/tinytest/test_pkg_utils.R |only mapsf-0.12.0/mapsf/man/figures/features.png |only mapsf-0.12.0/mapsf/man/figures/mtq.png |only mapsf-0.12.0/mapsf/man/figures/website.png |only mapsf-0.12.0/mapsf/man/mf_legend_c.Rd |only mapsf-0.12.0/mapsf/man/mf_legend_gl.Rd |only mapsf-0.12.0/mapsf/man/mf_legend_p.Rd |only mapsf-0.12.0/mapsf/man/mf_legend_pl.Rd |only mapsf-0.12.0/mapsf/man/mf_legend_s.Rd |only mapsf-0.12.0/mapsf/man/mf_legend_t.Rd |only mapsf-0.12.0/mapsf/vignettes/dt.RData |only mapsf-0.12.0/mapsf/vignettes/fig/deco.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line_c.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line_g.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line_p.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line_pt.svg |only mapsf-0.12.0/mapsf/vignettes/fig/line_t.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_c.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_g.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_p.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_pc.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_pt.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_s.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_sc.svg |only mapsf-0.12.0/mapsf/vignettes/fig/point_t.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_c.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_g.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_p.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_pc.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_pt.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_s.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_sc.svg |only mapsf-0.12.0/mapsf/vignettes/fig/poly_t.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_agolalight.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_brutal.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_candy.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_dark.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_darkula.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_default.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_green.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_iceberg.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_ink.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_jsk.svg |only mapsf-0.12.0/mapsf/vignettes/fig/th_nevermind.svg |only mapsf-1.0.0/mapsf/DESCRIPTION | 24 mapsf-1.0.0/mapsf/MD5 | 239 ++-- mapsf-1.0.0/mapsf/NAMESPACE | 10 mapsf-1.0.0/mapsf/NEWS.md | 40 mapsf-1.0.0/mapsf/R/mf_annotation.R | 84 - mapsf-1.0.0/mapsf/R/mf_arrow.R | 43 mapsf-1.0.0/mapsf/R/mf_background.R | 26 mapsf-1.0.0/mapsf/R/mf_base.R | 65 + mapsf-1.0.0/mapsf/R/mf_choro.R | 29 mapsf-1.0.0/mapsf/R/mf_credits.R | 30 mapsf-1.0.0/mapsf/R/mf_distr.R | 103 +- mapsf-1.0.0/mapsf/R/mf_doc_utils.R | 9 mapsf-1.0.0/mapsf/R/mf_export.R | 35 mapsf-1.0.0/mapsf/R/mf_frame.R |only mapsf-1.0.0/mapsf/R/mf_get_leg_pos.R | 9 mapsf-1.0.0/mapsf/R/mf_get_pal.R | 214 +++- mapsf-1.0.0/mapsf/R/mf_get_ratio.R | 81 + mapsf-1.0.0/mapsf/R/mf_grad.R | 26 mapsf-1.0.0/mapsf/R/mf_graticule.R | 7 mapsf-1.0.0/mapsf/R/mf_init.R | 46 mapsf-1.0.0/mapsf/R/mf_inset.R | 2 mapsf-1.0.0/mapsf/R/mf_label.R | 10 mapsf-1.0.0/mapsf/R/mf_layout.R | 5 mapsf-1.0.0/mapsf/R/mf_legend.R | 42 mapsf-1.0.0/mapsf/R/mf_map.R | 31 mapsf-1.0.0/mapsf/R/mf_map_utils.R | 35 mapsf-1.0.0/mapsf/R/mf_pkg_utils.R | 168 --- mapsf-1.0.0/mapsf/R/mf_png.R |only mapsf-1.0.0/mapsf/R/mf_prop.R | 77 + mapsf-1.0.0/mapsf/R/mf_prop_choro.R | 43 mapsf-1.0.0/mapsf/R/mf_prop_typo.R | 53 - mapsf-1.0.0/mapsf/R/mf_raster.R | 33 mapsf-1.0.0/mapsf/R/mf_raster_utils.R | 29 mapsf-1.0.0/mapsf/R/mf_scale.R | 111 +- mapsf-1.0.0/mapsf/R/mf_shadow.R | 3 mapsf-1.0.0/mapsf/R/mf_svg.R |only mapsf-1.0.0/mapsf/R/mf_symb.R | 25 mapsf-1.0.0/mapsf/R/mf_symb_choro.R | 44 mapsf-1.0.0/mapsf/R/mf_theme.R | 263 +++-- mapsf-1.0.0/mapsf/R/mf_theme_utils.R |only mapsf-1.0.0/mapsf/R/mf_title.R | 71 + mapsf-1.0.0/mapsf/R/mf_typo.R | 28 mapsf-1.0.0/mapsf/R/mf_worldmap.R | 3 mapsf-1.0.0/mapsf/R/package.R | 3 mapsf-1.0.0/mapsf/README.md | 118 -- mapsf-1.0.0/mapsf/build/vignette.rds |binary mapsf-1.0.0/mapsf/inst/CITATION |only mapsf-1.0.0/mapsf/inst/doc/mapsf.R | 195 +-- mapsf-1.0.0/mapsf/inst/doc/mapsf.Rmd | 362 ++----- mapsf-1.0.0/mapsf/inst/doc/mapsf.html | 1025 ++++++++------------- mapsf-1.0.0/mapsf/inst/tinytest/test_annotation.R | 2 mapsf-1.0.0/mapsf/inst/tinytest/test_arrow.R | 2 mapsf-1.0.0/mapsf/inst/tinytest/test_export.R | 44 mapsf-1.0.0/mapsf/inst/tinytest/test_frame.R |only mapsf-1.0.0/mapsf/inst/tinytest/test_get_ratio.R | 2 mapsf-1.0.0/mapsf/inst/tinytest/test_init.R | 4 mapsf-1.0.0/mapsf/inst/tinytest/test_legend.R | 17 mapsf-1.0.0/mapsf/inst/tinytest/test_map.R | 11 mapsf-1.0.0/mapsf/inst/tinytest/test_pal.R | 17 mapsf-1.0.0/mapsf/inst/tinytest/test_raster.R | 24 mapsf-1.0.0/mapsf/inst/tinytest/test_scale.R | 3 mapsf-1.0.0/mapsf/inst/tinytest/test_theme.R | 3 mapsf-1.0.0/mapsf/man/figures/example1-1.png |binary mapsf-1.0.0/mapsf/man/figures/mapsf_cheatsheet.png |binary mapsf-1.0.0/mapsf/man/mapsf.Rd | 4 mapsf-1.0.0/mapsf/man/mf_annotation.Rd | 2 mapsf-1.0.0/mapsf/man/mf_arrow.Rd | 11 mapsf-1.0.0/mapsf/man/mf_background.Rd | 3 mapsf-1.0.0/mapsf/man/mf_base.Rd | 10 mapsf-1.0.0/mapsf/man/mf_choro.Rd | 18 mapsf-1.0.0/mapsf/man/mf_export.Rd | 13 mapsf-1.0.0/mapsf/man/mf_frame.Rd |only mapsf-1.0.0/mapsf/man/mf_get_pal.Rd | 70 - mapsf-1.0.0/mapsf/man/mf_get_ratio.Rd | 11 mapsf-1.0.0/mapsf/man/mf_grad.Rd | 13 mapsf-1.0.0/mapsf/man/mf_graticule.Rd | 2 mapsf-1.0.0/mapsf/man/mf_init.Rd | 4 mapsf-1.0.0/mapsf/man/mf_legend.Rd | 14 mapsf-1.0.0/mapsf/man/mf_map.Rd | 37 mapsf-1.0.0/mapsf/man/mf_png.Rd |only mapsf-1.0.0/mapsf/man/mf_prop.Rd | 13 mapsf-1.0.0/mapsf/man/mf_prop_choro.Rd | 16 mapsf-1.0.0/mapsf/man/mf_prop_typo.Rd | 16 mapsf-1.0.0/mapsf/man/mf_raster.Rd | 12 mapsf-1.0.0/mapsf/man/mf_scale.Rd | 11 mapsf-1.0.0/mapsf/man/mf_shadow.Rd | 2 mapsf-1.0.0/mapsf/man/mf_svg.Rd |only mapsf-1.0.0/mapsf/man/mf_symb.Rd | 18 mapsf-1.0.0/mapsf/man/mf_symb_choro.Rd | 22 mapsf-1.0.0/mapsf/man/mf_theme.Rd | 143 +- mapsf-1.0.0/mapsf/man/mf_title.Rd | 8 mapsf-1.0.0/mapsf/man/mf_typo.Rd | 18 mapsf-1.0.0/mapsf/vignettes/fig/maplayout.png |only mapsf-1.0.0/mapsf/vignettes/fig/mf_base.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_choro.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_grad.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_prop.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_prop_choro.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_prop_typo.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_raster.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_symb.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_symb_choro.svg |only mapsf-1.0.0/mapsf/vignettes/fig/mf_typo.svg |only mapsf-1.0.0/mapsf/vignettes/mapsf.Rmd | 362 ++----- 157 files changed, 2450 insertions(+), 2431 deletions(-)
Title: Produces an Odds Ratio Plot from a Logistic Regression Model
Description: Produces an Odds Ratio (OR) Plot to visualise the result of a
logistic regression analysis.
Provide it with a binomial regression model produced by 'glm()' and it will
convert the estimates to odds ratios with a 95% confidence interval and
plot the results using 'ggplot2'.
Author: Craig Parylo [aut, cre, cph]
Maintainer: Craig Parylo <craig.parylo2@nhs.net>
Diff between plotor versions 0.6.0 dated 2025-05-28 and 0.7.0 dated 2025-07-01
plotor-0.6.0/plotor/tests/testthat/_snaps |only plotor-0.7.0/plotor/DESCRIPTION | 10 plotor-0.7.0/plotor/MD5 | 26 plotor-0.7.0/plotor/NAMESPACE | 1 plotor-0.7.0/plotor/NEWS.md | 154 ++- plotor-0.7.0/plotor/R/gt_extras.R |only plotor-0.7.0/plotor/R/plot_or.R | 469 +++++++++- plotor-0.7.0/plotor/README.md | 25 plotor-0.7.0/plotor/inst/doc/using_plotor.html | 183 ++- plotor-0.7.0/plotor/inst/img/table_or.png |binary plotor-0.7.0/plotor/man/check_or.Rd |only plotor-0.7.0/plotor/man/plot_or.Rd | 25 plotor-0.7.0/plotor/man/table_or.Rd | 40 plotor-0.7.0/plotor/tests/testthat/test-plot_or.R | 137 +- plotor-0.7.0/plotor/tests/testthat/test_data/make_test_data.R | 166 +-- 15 files changed, 911 insertions(+), 325 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph] ,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.6 dated 2023-11-29 and 2.1.7 dated 2025-07-01
DESCRIPTION | 12 MD5 | 26 NEWS.md | 25 R/Rogue-package.R | 4 R/SPIC.R | 2 R/stability.R | 12 build/partial.rdb |binary build/vignette.rds |binary inst/apa-old-doi-prefix.csl | 1672 ++++++++++++++++++++++++++++++---------- inst/doc/Bayesian.html | 146 +-- man/Rogue-package.Rd | 3 man/RogueTaxa.Rd | 3 src/rnr/RogueNaRok.c | 2 tests/testthat/test-stability.R | 11 14 files changed, 1408 insertions(+), 510 deletions(-)
Title: Dimension Reduction Techniques for Conditional Quantiles
Description: An implementation of dimension reduction techniques
for conditional quantiles. Nonparametric estimation of
conditional quantiles is also available.
Author: Eliana Christou [aut, cre]
Maintainer: Eliana Christou <echris15@uncc.edu>
Diff between quantdr versions 1.2.2 dated 2022-05-10 and 1.3.2 dated 2025-07-01
DESCRIPTION | 17 MD5 | 27 NEWS.md | 6 R/cqs.R | 6 R/dr.R |only R/llqr.R | 3 README.md | 28 build/vignette.rds |binary inst/doc/quantdr.R | 88 +- inst/doc/quantdr.html | 1088 +++++++++++++++++++------------ man/cqs.Rd | 35 man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/llqr.Rd | 19 man/llqrcv.Rd | 4 15 files changed, 818 insertions(+), 503 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes ADAM (Svetunkov, 2023, <https://openforecast.org/adam/>),
Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>)
and several simulation functions. It also allows dealing with intermittent demand based on the
iETS framework (Svetunkov & Boylan, 2019, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre]
Maintainer: Ivan Svetunkov <ivan@svetunkov.com>
Diff between smooth versions 4.2.0 dated 2025-04-02 and 4.3.0 dated 2025-07-01
smooth-4.2.0/smooth/man/auto.ssarima.Rd |only smooth-4.3.0/smooth/DESCRIPTION | 8 smooth-4.3.0/smooth/MD5 | 104 +-- smooth-4.3.0/smooth/NAMESPACE | 3 smooth-4.3.0/smooth/NEWS | 22 smooth-4.3.0/smooth/R/RcppExports.R | 4 smooth-4.3.0/smooth/R/adam-ces.R | 294 ++++---- smooth-4.3.0/smooth/R/adam-es.R | 21 smooth-4.3.0/smooth/R/adam-gum.R | 191 +++-- smooth-4.3.0/smooth/R/adam-msarima.R | 16 smooth-4.3.0/smooth/R/adam-ssarima.R |only smooth-4.3.0/smooth/R/adam.R | 601 +++++++++--------- smooth-4.3.0/smooth/R/adamGeneral.R | 228 +++--- smooth-4.3.0/smooth/R/autoadam.R | 72 +- smooth-4.3.0/smooth/R/autoces.R | 46 - smooth-4.3.0/smooth/R/autogum.R | 60 - smooth-4.3.0/smooth/R/automsarima.R | 3 smooth-4.3.0/smooth/R/autossarima.R | 319 +++------ smooth-4.3.0/smooth/R/ces.R | 6 smooth-4.3.0/smooth/R/gum.R | 7 smooth-4.3.0/smooth/R/methods.R | 53 + smooth-4.3.0/smooth/R/smoothCombine.R | 149 +--- smooth-4.3.0/smooth/R/ssarima.R | 56 - smooth-4.3.0/smooth/build/partial.rdb |binary smooth-4.3.0/smooth/build/vignette.rds |binary smooth-4.3.0/smooth/inst/doc/adam.html | 732 ++++++++++------------ smooth-4.3.0/smooth/inst/doc/ces.html | 52 - smooth-4.3.0/smooth/inst/doc/es.html | 198 ++--- smooth-4.3.0/smooth/inst/doc/gum.html | 44 - smooth-4.3.0/smooth/inst/doc/oes.html | 106 +-- smooth-4.3.0/smooth/inst/doc/simulate.html | 50 - smooth-4.3.0/smooth/inst/doc/sma.html | 12 smooth-4.3.0/smooth/inst/doc/smooth.html | 4 smooth-4.3.0/smooth/inst/doc/ssarima.html | 174 ++--- smooth-4.3.0/smooth/man/adam.Rd | 36 - smooth-4.3.0/smooth/man/ces.Rd | 143 +--- smooth-4.3.0/smooth/man/es.Rd | 55 - smooth-4.3.0/smooth/man/gum.Rd | 141 +--- smooth-4.3.0/smooth/man/msarima.Rd | 43 - smooth-4.3.0/smooth/man/oes.Rd | 11 smooth-4.3.0/smooth/man/sim.es.Rd | 2 smooth-4.3.0/smooth/man/sim.oes.Rd | 2 smooth-4.3.0/smooth/man/sim.sma.Rd | 2 smooth-4.3.0/smooth/man/sim.ssarima.Rd | 2 smooth-4.3.0/smooth/man/sma.Rd | 12 smooth-4.3.0/smooth/man/smooth.Rd | 13 smooth-4.3.0/smooth/man/smoothCombine.Rd | 41 - smooth-4.3.0/smooth/man/ssarima.Rd | 282 +++++--- smooth-4.3.0/smooth/src/RcppExports.cpp | 8 smooth-4.3.0/smooth/src/adamGeneral.cpp | 39 - smooth-4.3.0/smooth/src/adamRefitter.cpp | 186 +++-- smooth-4.3.0/smooth/tests/testthat/test_adam.R | 4 smooth-4.3.0/smooth/tests/testthat/test_ces.R | 3 smooth-4.3.0/smooth/tests/testthat/test_ssarima.R | 18 54 files changed, 2404 insertions(+), 2274 deletions(-)
Title: Ecological Restoration Planning
Description: Flexible framework for ecological restoration planning. It aims to identify priority areas for restoration efforts using optimization algorithms (based on Justeau-Allaire et al. 2021 <doi:10.1111/1365-2664.13803>). Priority areas can be identified by maximizing landscape indices, such as the effective mesh size (Jaeger 2000 <doi:10.1023/A:1008129329289>), or the integral index of connectivity (Pascual-Hortal & Saura 2006 <doi:10.1007/s10980-006-0013-z>). Additionally, constraints can be used to ensure that priority areas exhibit particular characteristics (e.g., ensure that particular places are not selected for restoration, ensure that priority areas form a single contiguous network). Furthermore, multiple near-optimal solutions can be generated to explore multiple options in restoration planning. The package leverages the 'Choco-solver' software to perform optimization using constraint programming (CP) techniques (<https://choco-solver.org/>).
Author: Dimitri Justeau-Allaire [aut, cre] ,
Jeffrey O Hanson [aut] ,
Ghislain Vieilledent [aut] ,
Philippe Vismara [aut],
Xavier Lorca [aut],
Philippe Birnbaum [aut]
Maintainer: Dimitri Justeau-Allaire <dimitri.justeau@gmail.com>
Diff between restoptr versions 1.0.6 dated 2023-08-18 and 1.1.0 dated 2025-07-01
restoptr-1.0.6/restoptr/inst/java/restopt-2.0.1.jar |only restoptr-1.1.0/restoptr/DESCRIPTION | 24 restoptr-1.1.0/restoptr/MD5 | 153 +++-- restoptr-1.1.0/restoptr/NAMESPACE | 4 restoptr-1.1.0/restoptr/NEWS.md | 8 restoptr-1.1.0/restoptr/R/add_available_areas_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_compactness_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_components_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_connected_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_locked_out_constraint.R | 4 restoptr-1.1.0/restoptr/R/add_min_iic_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_min_mesh_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_nb_patches_constraint.R |only restoptr-1.1.0/restoptr/R/add_no_new_patch_constraint.R |only restoptr-1.1.0/restoptr/R/add_restorable_constraint.R | 2 restoptr-1.1.0/restoptr/R/add_settings.R | 2 restoptr-1.1.0/restoptr/R/package.R | 2 restoptr-1.1.0/restoptr/R/preprocessing.R | 2 restoptr-1.1.0/restoptr/R/restopt_problem.R | 201 +++++-- restoptr-1.1.0/restoptr/R/set_max_iic_objective.R | 6 restoptr-1.1.0/restoptr/R/set_max_mesh_objective.R | 6 restoptr-1.1.0/restoptr/R/set_max_nb_pus_objective.R | 6 restoptr-1.1.0/restoptr/R/set_max_restore_objective.R | 6 restoptr-1.1.0/restoptr/R/set_min_nb_patches_objective.R |only restoptr-1.1.0/restoptr/R/set_min_nb_pus_objective.R | 6 restoptr-1.1.0/restoptr/R/set_min_restore_objective.R | 6 restoptr-1.1.0/restoptr/R/set_no_objective.R | 6 restoptr-1.1.0/restoptr/R/solve.R | 45 + restoptr-1.1.0/restoptr/R/terra_utils.R | 12 restoptr-1.1.0/restoptr/R/zzz.R | 5 restoptr-1.1.0/restoptr/README.md | 16 restoptr-1.1.0/restoptr/build/vignette.rds |binary restoptr-1.1.0/restoptr/inst/doc/case_study.html | 104 +-- restoptr-1.1.0/restoptr/inst/doc/restoptr.html | 265 +++++----- restoptr-1.1.0/restoptr/inst/java/restopt-2.1.0.jar |only restoptr-1.1.0/restoptr/man/add_available_areas_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_compactness_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_components_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_connected_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_locked_out_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_min_iic_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_min_mesh_constraint.Rd | 4 restoptr-1.1.0/restoptr/man/add_nb_patches_constraint.Rd |only restoptr-1.1.0/restoptr/man/add_no_new_patch_constraint.Rd |only restoptr-1.1.0/restoptr/man/add_restorable_constraint.Rd | 6 restoptr-1.1.0/restoptr/man/add_settings.Rd | 2 restoptr-1.1.0/restoptr/man/area_to_nb_cells.Rd | 2 restoptr-1.1.0/restoptr/man/cell_area.Rd | 2 restoptr-1.1.0/restoptr/man/cell_width.Rd | 2 restoptr-1.1.0/restoptr/man/figures/README-habitat_data-1.png |binary restoptr-1.1.0/restoptr/man/figures/README-locked_out_data-1.png |binary restoptr-1.1.0/restoptr/man/figures/README-solution-1.png |binary restoptr-1.1.0/restoptr/man/figures/logo.tif |only restoptr-1.1.0/restoptr/man/get_aggregation_factor.Rd | 2 restoptr-1.1.0/restoptr/man/get_aggregation_method.Rd |only restoptr-1.1.0/restoptr/man/get_cell_area.Rd | 2 restoptr-1.1.0/restoptr/man/get_constraints.Rd | 2 restoptr-1.1.0/restoptr/man/get_existing_habitat.Rd | 2 restoptr-1.1.0/restoptr/man/get_habitat_threshold.Rd | 2 restoptr-1.1.0/restoptr/man/get_locked_out_areas.Rd | 2 restoptr-1.1.0/restoptr/man/get_objective.Rd | 2 restoptr-1.1.0/restoptr/man/get_original_habitat.Rd | 2 restoptr-1.1.0/restoptr/man/get_restorable_habitat.Rd | 2 restoptr-1.1.0/restoptr/man/get_settings.Rd | 2 restoptr-1.1.0/restoptr/man/invert_vector.Rd | 4 restoptr-1.1.0/restoptr/man/nb_cell_to_area.Rd | 2 restoptr-1.1.0/restoptr/man/preprocess_input.Rd | 2 restoptr-1.1.0/restoptr/man/print.RestoptProblem.Rd | 2 restoptr-1.1.0/restoptr/man/restopt_problem.Rd | 13 restoptr-1.1.0/restoptr/man/restoptr.Rd | 22 restoptr-1.1.0/restoptr/man/set_max_iic_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_max_mesh_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_max_nb_pus_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_max_restore_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_min_nb_patches_objective.Rd |only restoptr-1.1.0/restoptr/man/set_min_nb_pus_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_min_restore_objective.Rd | 3 restoptr-1.1.0/restoptr/man/set_no_objective.Rd | 3 restoptr-1.1.0/restoptr/man/solve.RestoptProblem.Rd | 24 restoptr-1.1.0/restoptr/tests/testthat/test_add_nb_patches_constraint.R |only restoptr-1.1.0/restoptr/tests/testthat/test_add_no_new_patch_constraint.R |only restoptr-1.1.0/restoptr/tests/testthat/test_restopt_problem.R | 1 restoptr-1.1.0/restoptr/tests/testthat/test_set_min_nb_patches_objective.R |only restoptr-1.1.0/restoptr/tests/testthat/test_solve.R | 66 ++ 84 files changed, 708 insertions(+), 414 deletions(-)
Title: Meta-Analysis of Generalized Additive Models
Description: Meta-analysis of generalized additive
models and generalized additive mixed models. A typical use case is
when data cannot be shared across locations, and an overall meta-analytic
fit is sought. 'metagam' provides functionality for removing individual
participant data from models computed using the 'mgcv' and 'gamm4' packages such
that the model objects can be shared without exposing individual data.
Furthermore, methods for meta-analysing these fits are provided. The implemented
methods are described in Sorensen et al. (2020), <doi:10.1016/j.neuroimage.2020.117416>,
extending previous works by Schwartz and Zanobetti (2000)
and Crippa et al. (2018) <doi:10.6000/1929-6029.2018.07.02.1>.
Author: Oystein Sorensen [aut, cre] ,
Andreas M. Brandmaier [aut] ,
Athanasia Mo Mowinckel [aut]
Maintainer: Oystein Sorensen <oystein.sorensen@psykologi.uio.no>
Diff between metagam versions 0.4.0 dated 2023-05-05 and 0.4.1 dated 2025-07-01
DESCRIPTION | 17 +- MD5 | 32 +-- R/metagam_package.R | 5 R/misc.R | 6 R/plot_metagam.R | 10 - README.md | 16 + build/vignette.rds |binary inst/doc/dominance.html | 59 ++++--- inst/doc/heterogeneity.R | 2 inst/doc/heterogeneity.html | 57 +++---- inst/doc/introduction.R | 4 inst/doc/introduction.html | 141 ++++++++--------- inst/doc/multivariate.R | 2 inst/doc/multivariate.html | 143 ++++++++--------- inst/doc/pvals.R | 104 ++++++------ inst/doc/pvals.html | 353 ++++++++++++++++++++++---------------------- man/metagam-package.Rd | 19 ++ 17 files changed, 505 insertions(+), 465 deletions(-)
Title: Help to Fit of a Parametric Distribution to Non-Censored or
Censored Data
Description: Extends the fitdistr() function (of the MASS package) with several functions
to help the fit of a parametric distribution to non-censored or censored data.
Censored data may contain left censored, right censored and interval censored values,
with several lower and upper bounds. In addition to maximum likelihood estimation (MLE),
the package provides moment matching (MME), quantile matching (QME), maximum goodness-of-fit
estimation (MGE) and maximum spacing estimation (MSE) methods (available only for
non-censored data). Weighted versions of MLE, MME, QME and MSE are available. See e.g.
Casella & Berger (2002), Statistical inference, Pacific Grove, for a general introduction
to parametric estimation.
Author: Marie-Laure Delignette-Muller [aut] ,
Christophe Dutang [aut] ,
Regis Pouillot [ctb],
Jean-Baptiste Denis [ctb],
Aurelie Siberchicot [aut, cre]
Maintainer: Aurelie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between fitdistrplus versions 1.2-2 dated 2025-01-07 and 1.2-3 dated 2025-07-01
DESCRIPTION | 17 MD5 | 111 NEWS.md | 16 R/cdfcomp.R | 8 R/cdfcompcens.R | 6 R/denscomp.R | 13 R/logLik-surface.R | 87 R/mledist.R | 28 R/ppcomp.R | 8 R/ppcompcens.R | 2 R/qqcomp.R | 8 R/qqcompcens.R | 2 R/util-startarg.R | 30 README.md | 16 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ.R | 99 inst/doc/FAQ.Rmd | 126 inst/doc/FAQ.html | 4590 ++++----------------------- inst/doc/Optimalgo.html | 558 +-- inst/doc/fitdistrplus_vignette.html | 902 ++--- inst/doc/starting-values.Rmd | 10 inst/doc/starting-values.html | 222 - man/CIcdfplot.Rd | 2 man/Surv2fitdistcens.Rd | 2 man/bootdist.Rd | 1 man/bootdistcens.Rd | 2 man/descdist.Rd | 4 man/detectbound.Rd | 4 man/fitdist.Rd | 2 man/fitdistcens.Rd | 2 man/fitdistrplus.Rd | 11 man/gofstat.Rd | 4 man/graphcomp.Rd | 2 man/graphcompcens.Rd | 4 man/logLik-plot.Rd | 2 man/logLik-surface.Rd | 2 man/mgedist.Rd | 4 man/mledist.Rd | 8 man/mmedist.Rd | 4 man/msedist.Rd | 4 man/plotdist.Rd | 5 man/plotdistcens.Rd | 4 man/qmedist.Rd | 4 man/quantile.Rd | 5 tests/t-denscomp.R | 11 tests/t-fitdist-burr.R |only tests/t-llplot.R | 18 tests/t-mledist-cens.R | 10 tests/t-mledist-cvg-NelderMead.R |only tests/t-ppcomp.R | 12 tests/t-qmedist-cvg-NelderMead.R |only tests/t-qqcomp.R | 14 tests/t-qqcompcens.R | 2 tests/t-startingvalues-fellerpareto-family.R | 2 tests/t-startingvalues-inv-family.R |only tests/t-startingvalues-invBurr-family.R |only vignettes/FAQ.Rmd | 126 vignettes/starting-values.Rmd | 10 59 files changed, 2130 insertions(+), 5016 deletions(-)
Title: Comprehensive Automatized Evaluation of Distribution Models for
Count Data
Description: A large number of measurements generate count data. This is a statistical data type
that only assumes non-negative integer values and is generated by counting. Typically, counting
data can be found in biomedical applications, such as the analysis of DNA double-strand breaks.
The number of DNA double-strand breaks can be counted in individual cells using various
bioanalytical methods. For diagnostic applications, it is relevant to record the distribution of
the number data in order to determine their biomedical significance (Roediger, S. et al., 2018.
Journal of Laboratory and Precision Medicine. <doi:10.21037/jlpm.2018.04.10>). The software
offers functions for a comprehensive automated evaluation of distribution models of count
data. In addition to programmatic interaction, a graphical user interface (web server)
is included, which enables fast and interactive data-scientific analyses. The user is supported
in selecting the most suitable counting distribution for his own data se [...truncated...]
Author: Jaroslaw Chilimoniuk [cre, ctb] ,
Alicja Gosiewska [ctb] ,
Jadwiga Slowik [ctb] ,
Michal Burdukiewicz [aut] ,
Stefan Roediger [ctb]
Maintainer: Jaroslaw Chilimoniuk <jaroslaw.chilimoniuk@gmail.com>
Diff between countfitteR versions 1.4 dated 2020-09-30 and 1.5 dated 2025-07-01
DESCRIPTION | 23 MD5 | 144 NAMESPACE | 118 R/compare_fit.R | 186 R/countfitteR-package.R | 74 R/countfitteR_gui.R | 52 R/datasets.R | 126 R/distrs.R | 130 R/fit_counts.R | 118 R/fit_counts_separate.R | 200 R/fit_counts_whole.R | 254 R/fitlist.R | 223 R/process_counts.R | 34 R/select_model.R | 58 R/utils.R | 100 R/validate_data.R | 38 README.md | 120 build/vignette.rds |binary inst/CITATION | 41 inst/WORDLIST | 46 inst/countfitteR/readmes/about.md | 64 inst/countfitteR/readmes/cmp_distr/1.md | 6 inst/countfitteR/readmes/count_data/1.md | 6 inst/countfitteR/readmes/count_data/2.md | 6 inst/countfitteR/readmes/count_data/3.md | 6 inst/countfitteR/readmes/count_data/4.md | 2 inst/countfitteR/readmes/data_upload/1.md | 16 inst/countfitteR/readmes/data_upload/2.md | 6 inst/countfitteR/readmes/manual.html | 792 inst/countfitteR/readmes/manual.md | 182 inst/countfitteR/readmes/mean_value/1.md | 6 inst/countfitteR/readmes/mean_value/2.md | 6 inst/countfitteR/readmes/mean_value/3.md | 6 inst/countfitteR/readmes/mean_value/4.md | 2 inst/countfitteR/readmes/settings/1.md | 6 inst/countfitteR/report/countfitter_report.Rmd | 158 inst/countfitteR/report/ggtheme.R | 58 inst/countfitteR/server.R | 372 inst/countfitteR/tests/mytest-expected/001.json | 52 inst/countfitteR/tests/mytest-expected/002.json | 52 inst/countfitteR/tests/mytest-expected/003.json |18274 +++++++++--------- inst/countfitteR/tests/mytest-expected/004.json |24232 ++++++++++++------------ inst/countfitteR/tests/mytest-expected/005.json |24228 +++++++++++------------ inst/countfitteR/tests/mytest-expected/006.json |24228 +++++++++++------------ inst/countfitteR/tests/mytest-expected/007.json |21452 ++++++++++----------- inst/countfitteR/tests/mytest.R | 88 inst/countfitteR/ui.R | 170 inst/countfitteR/utils.R | 28 inst/doc/countfitteR.R | 22 inst/doc/countfitteR.Rmd | 98 inst/doc/countfitteR.html | 2891 +- man/case_study.Rd | 28 man/case_study_APC.Rd | 26 man/case_study_FITC.Rd | 26 man/case_study_all.Rd | 28 man/compare_fit.Rd | 58 man/countfitteR-package.Rd | 66 man/countfitteR_gui.Rd | 54 man/decide.Rd | 54 man/fit_counts.Rd | 78 man/plot_fitcmp.Rd | 44 man/process_counts.Rd | 50 man/select_model.Rd | 56 man/sim_dat.Rd | 74 man/summary_fitlist.Rd | 63 man/validate_counts.Rd | 50 man/zinb.Rd | 70 man/zip.Rd | 62 tests/spelling.R | 6 tests/testthat.R | 6 tests/testthat/testing.R | 138 vignettes/countfitteR.Rmd | 98 vignettes/countfitteR.bib | 150 73 files changed, 60495 insertions(+), 60390 deletions(-)
Title: Interpolation and Extrapolation for Three Dimensions of
Biodiversity
Description: Biodiversity is a multifaceted concept covering different levels of organization from
genes to ecosystems. 'iNEXT.3D' extends 'iNEXT' to include three dimensions (3D)
of biodiversity, i.e., taxonomic diversity (TD), phylogenetic diversity (PD) and functional
diversity (FD). This package provides functions to compute standardized 3D diversity estimates
with a common sample size or sample coverage. A unified framework based on Hill numbers
and their generalizations (Hill-Chao numbers) are used to quantify 3D. All 3D estimates
are in the same units of species/lineage equivalents and can be meaningfully compared.
The package features size- and coverage-based rarefaction and extrapolation sampling
curves to facilitate rigorous comparison of 3D diversity across individual assemblages.
Asymptotic 3D diversity estimates are also provided. See Chao et al. (2021)
<doi:10.1111/2041-210X.13682> for more details.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb],
PoYen Chuang [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.3D versions 1.0.8 dated 2025-02-18 and 1.0.9 dated 2025-07-01
DESCRIPTION | 17 ++++++++---- MD5 | 38 ++++++++++++++--------------- NEWS | 3 +- R/FD_Fun.R | 17 +++++++++++- R/PD_Fun.R | 18 ++++++++++++- R/TD_Fun.R | 30 +++++++++++++++++++--- build/vignette.rds |binary data/Brazil_rainforest_abun_data.rda |binary data/Brazil_rainforest_distance_matrix.rda |binary data/Brazil_rainforest_phylo_tree.rda |binary data/Fish_distance_matrix.rda |binary data/Fish_incidence_data.rda |binary data/Fish_phylo_tree.rda |binary inst/doc/Introduction.Rnw | 14 +++++----- inst/doc/Introduction.pdf |binary src/FDRcpp.cpp | 12 ++++++--- src/PDRcpp.cpp | 12 +++++++-- src/TDRcpp.cpp | 29 ++++++++++++++++------ vignettes/Introduction.Rnw | 14 +++++----- vignettes/mypaper.pdf |binary 20 files changed, 142 insertions(+), 62 deletions(-)
Title: Accelerated Stability Kinetic Modelling
Description: Estimate the Šesták–Berggren kinetic model (degradation model) from experimental data.
A closed-form (analytic) solution to the degradation model is implemented as a non-linear fit,
allowing for the extrapolation of the degradation of a drug product - both in time and
temperature. Parametric bootstrap, with kinetic parameters drawn from the multivariate
t-distribution, and analytical formulae (the delta method) are available options to calculate
the confidence and prediction intervals.
The results (modelling, extrapolations and statistical intervals) can be visualised
with multiple plots. The examples illustrate the accelerated stability modelling in drugs and
vaccines development.
Author: Bernard G Franq [aut, cph],
Ben Wells [ctb],
Alex Ball [cre],
Daniel Williams [ctb]
Maintainer: Alex Ball <alex_keith_ball@hotmail.com>
Diff between AccelStab versions 2.2.1 dated 2025-05-27 and 2.3.1 dated 2025-07-01
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 2 NEWS.md | 16 R/excursion.R | 165 +++++----- R/step1_down.R | 98 +++--- R/step1_down_basic.R | 2 R/step1_sample_mvt.R | 776 +++++++++++++++++++++++++++--------------------- inst/doc/AccelStab.Rmd | 630 +++++++++++++++++++------------------- inst/doc/AccelStab.html | 315 +++++++++---------- man/excursion.Rd | 8 man/step1_sample_mvt.Rd | 5 vignettes/AccelStab.Rmd | 630 +++++++++++++++++++------------------- 13 files changed, 1406 insertions(+), 1273 deletions(-)
Title: Add Tooltips in 'Shiny' Apps with 'Hint.css'
Description: In 'Shiny' apps, it is sometimes useful to store information
on a particular item in a tooltip. 'Prompter' allows you to easily
create such tooltips, using 'Hint.css'.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between prompter versions 1.2.0 dated 2024-04-08 and 1.2.1 dated 2025-07-01
DESCRIPTION | 8 - LICENSE | 4 MD5 | 34 ++-- NAMESPACE | 8 - NEWS.md | 46 +++--- R/add_prompt.R | 296 +++++++++++++++++++-------------------- R/use_prompt.R | 32 ++-- R/zzz.R | 12 - README.md | 166 ++++++++++----------- inst/WORDLIST | 14 - inst/hint/hint.min.css | 54 +++---- man/add_prompt.Rd | 164 ++++++++++----------- man/use_prompt.Rd | 28 +-- tests/spelling.R | 6 tests/testthat.R | 8 - tests/testthat/test-add_prompt.R | 84 +++++------ tests/testthat/test-use_prompt.R | 6 tests/testthat/test-zzz.R | 6 18 files changed, 490 insertions(+), 486 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 0.16.0 dated 2025-05-20 and 0.16.1 dated 2025-07-01
DESCRIPTION | 8 ++-- MD5 | 46 +++++++++++++------------- NEWS.md | 10 +++++ R/bayesfactor_parameters.R | 2 - R/bci.R | 4 +- R/check_prior.R | 2 - R/describe_posterior.R | 70 +++++++++++++++++++++++++++++++++------- R/equivalence_test.R | 4 +- R/eti.R | 4 +- R/hdi.R | 4 +- R/map_estimate.R | 2 - R/p_direction.R | 4 +- R/p_map.R | 4 +- R/p_rope.R | 4 +- R/p_significance.R | 4 +- R/point_estimate.R | 4 +- R/rope.R | 14 ++++++-- R/sensitivity_to_prior.R | 2 - R/utils.R | 39 ++++++++++++++++++++-- R/utils_clean_stan_parameters.R | 10 +++++ build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 2 - man/sensitivity_to_prior.Rd | 2 - 24 files changed, 176 insertions(+), 69 deletions(-)
Title: Estimating Marginal Effects with Prognostic Covariate Adjustment
Description: Conduct power analyses and inference of marginal effects.
Uses plug-in estimation and influence functions to perform robust inference,
optionally leveraging historical data to increase precision with
prognostic covariate adjustment. The methods are described in
Højbjerre-Frandsen et al. (2025) <doi:10.48550/arXiv.2503.22284>.
Author: Mathias Lerbech Jeppesen [aut, cre],
Emilie Hojbjerre-Frandsen [aut],
Novo Nordisk A/S [cph]
Maintainer: Mathias Lerbech Jeppesen <mathiasljeppesen@outlook.com>
Diff between postcard versions 1.0.0 dated 2025-04-08 and 1.0.1 dated 2025-07-01
DESCRIPTION | 6 MD5 | 37 +- NEWS.md | 5 R/power_linear.R | 30 - R/power_marginaleffect.R | 18 - README.md | 23 - inst/doc/model-fit.html | 41 +- inst/doc/postcard.Rmd | 6 inst/doc/postcard.html | 10 inst/doc/prospective-power.html | 2 man/figures |only man/power_linear.Rd | 20 - man/power_marginaleffect.Rd | 22 - tests/testthat/_snaps/fit_best_learner.md | 240 +++++++-------- tests/testthat/_snaps/power.md | 70 ++-- tests/testthat/_snaps/rctglm_prog_methods.md | 304 +++++++++---------- tests/testthat/_snaps/rctglm_with_prognosticscore.md | 234 +++++++------- tests/testthat/test-power.R | 4 vignettes/postcard.Rmd | 6 19 files changed, 546 insertions(+), 532 deletions(-)
Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent
(IBD) probabilities can be calculated using Hidden Markov Models and
inheritance vectors following Lander and Green
(<https://www.jstor.org/stable/29713>) and Huang
(<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic
packages for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre] ,
Wenhao Li [ctb] ,
Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenIBD versions 1.0.8 dated 2025-02-05 and 1.0.9 dated 2025-07-01
DESCRIPTION | 25 +++++++++++++------------ MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/pedPlot.R | 7 ++++--- R/readRABBIT.R | 26 ++++++++++++++++++-------- README.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/IBDCalculations.Rmd | 2 +- inst/doc/IBDCalculations.html | 18 +++++++++--------- inst/doc/IBDFileFormat.html | 4 ++-- vignettes/IBDCalculations.Rmd | 2 +- 12 files changed, 64 insertions(+), 47 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre] ,
Willem Kruijer [aut] ,
Fred van Eeuwijk [ctb] ,
Martin Boer [ctb] ,
Marcos Malosetti [ctb] ,
Daniela Bustos-Korts [ctb] ,
Emilie Millet [ctb] ,
Joao Paulo [ctb] ,
Maikel Verouden [ctb] ,
Ron Wehrens [ctb] ,
Choazhi Zh [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.11 dated 2025-03-31 and 1.0.12 dated 2025-07-01
DESCRIPTION | 39 ++++++++++++----------- MD5 | 37 ++++++++++++---------- NAMESPACE | 1 NEWS.md | 9 ++++- R/GWASHelp.R | 70 ++++++++++++++++++++++++++++++++++++++----- R/createGData.R | 2 - R/createGWAS.R | 2 - R/geneticMapPlot.R | 2 - R/qtlPlot.R | 3 + R/readPlink.R | 4 +- R/readVcf.R |only R/runSingleTraitGwas.R | 19 ++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/GWAS.html | 24 +++++++------- inst/tinytest/test_gData.R | 6 --- inst/tinytest/test_readVcf.R |only man/gData.Rd | 2 - man/readPLINK.Rd | 4 +- man/readVcf.Rd |only man/runSingleTraitGwas.Rd | 19 ++++++----- 21 files changed, 156 insertions(+), 87 deletions(-)
Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG,
Meteoclimatic...).
Author: Victor Granda [aut, cre] ,
Miquel de Caceres [ctb] ,
Aitor Ameztegui [ctb] ,
Luis Franco [ctb],
Ruben Fernandez-Casal [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between meteospain versions 0.2.0 dated 2024-10-17 and 0.2.1 dated 2025-07-01
DESCRIPTION | 19 MD5 | 71 +-- NAMESPACE | 1 NEWS.md | 17 R/aemet_helpers.R | 663 ++++++++++++++++++++------------- R/get_data.R | 43 -- R/meteocat_helpers.R | 467 ++++++++++++++--------- R/meteoclimatic_helpers.R | 22 + R/meteogalicia_helpers.R | 498 +++++++++++++++--------- R/ria_helpers.R | 334 ++++++++-------- R/services_options.R | 18 R/utils.R | 259 +++++++++--- R/zzz.R | 8 README.md | 99 ++-- build/vignette.rds |binary inst/doc/aemet.R | 6 inst/doc/aemet.html | 87 ++-- inst/doc/api_limits.R | 2 inst/doc/api_limits.html | 592 +++++++++++++++++------------ inst/doc/compatibility.html | 173 ++++---- inst/doc/meteocat.R | 6 inst/doc/meteocat.html | 91 ++-- inst/doc/meteoclimatic.html | 65 +-- inst/doc/meteogalicia.html | 46 +- inst/doc/ria.html | 63 +-- man/clear_meteospain_cache.Rd |only man/figures/README-plot_stations-1.png |binary man/figures/README-plot_stations-2.png |binary man/get_meteo_from.Rd | 18 man/get_quota_from.Rd | 7 man/get_stations_info_from.Rd | 17 man/services_options.Rd | 21 - tests/testthat/test-aemet.R | 45 +- tests/testthat/test-meteocat.R | 71 +-- tests/testthat/test-meteoclimatic.R | 4 tests/testthat/test-meteogalicia.R | 39 + tests/testthat/test-riaa.R | 2 37 files changed, 2293 insertions(+), 1581 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 1.3.12 dated 2025-04-25 and 1.3.13 dated 2025-07-01
DESCRIPTION | 10 ++++----- MD5 | 12 +++++------ NEWS.md | 3 ++ R/cox2.R | 7 ++++-- inst/doc/jstable.html | 28 +++++++++++++------------- inst/doc/jstable_competing_risk_analysis.html | 4 +-- inst/doc/jstable_options.html | 4 +-- 7 files changed, 37 insertions(+), 31 deletions(-)
Title: Methods for Colour Vectors and Colour Palettes
Description: Provides a comprehensive library for colour vectors and colour
palettes using a new family of colour classes (palettes_colour and
palettes_palette) that always print as hex codes with colour previews.
Capabilities include: formatting, casting and coercion, extraction and
updating of components, plotting, colour mixing arithmetic, and colour
interpolation.
Author: Michael McCarthy [aut, cre, cph]
Maintainer: Michael McCarthy <m.mccarthy1624@gmail.com>
Diff between palettes versions 0.2.1 dated 2024-07-13 and 0.2.2 dated 2025-07-01
palettes-0.2.1/palettes/R/colour.R |only palettes-0.2.1/palettes/R/data.R |only palettes-0.2.1/palettes/R/palette.R |only palettes-0.2.2/palettes/DESCRIPTION | 8 palettes-0.2.2/palettes/MD5 | 56 palettes-0.2.2/palettes/NEWS.md | 8 palettes-0.2.2/palettes/R/ggplot2-scales.R | 9 palettes-0.2.2/palettes/R/included-palettes.R |only palettes-0.2.2/palettes/R/pal_colour.R |only palettes-0.2.2/palettes/R/pal_palette.R |only palettes-0.2.2/palettes/R/plot.R | 4 palettes-0.2.2/palettes/R/sysdata.rda |binary palettes-0.2.2/palettes/README.md | 32 palettes-0.2.2/palettes/build/vignette.rds |binary palettes-0.2.2/palettes/data/discrete_palettes.rda |only palettes-0.2.2/palettes/data/diverging_palettes.rda |only palettes-0.2.2/palettes/data/penguin_palettes.rda |only palettes-0.2.2/palettes/data/performance_palettes.rda |only palettes-0.2.2/palettes/data/sequential_palettes.rda |only palettes-0.2.2/palettes/inst/doc/biscale.html | 517 +- palettes-0.2.2/palettes/inst/doc/compatibility.html | 546 ++ palettes-0.2.2/palettes/inst/doc/creating-packages.R | 226 - palettes-0.2.2/palettes/inst/doc/creating-packages.html | 660 ++- palettes-0.2.2/palettes/inst/doc/ggplot2.html | 439 +- palettes-0.2.2/palettes/inst/doc/gt.html | 3012 ++++++++-------- palettes-0.2.2/palettes/inst/doc/palettes.html | 663 ++- palettes-0.2.2/palettes/man/carto_palettes.Rd |only palettes-0.2.2/palettes/man/met_palettes.Rd | 2 palettes-0.2.2/palettes/man/nord_palettes.Rd | 2 palettes-0.2.2/palettes/man/pal_colour.Rd | 2 palettes-0.2.2/palettes/man/pal_palette.Rd | 2 palettes-0.2.2/palettes/man/penguin_palettes.Rd |only palettes-0.2.2/palettes/man/performance_palettes.Rd |only palettes-0.2.2/palettes/man/pnw_palettes.Rd | 2 palettes-0.2.2/palettes/man/scale_colour_palette_d.Rd | 6 palettes-0.2.2/palettes/man/viridis_palettes.Rd | 2 36 files changed, 3705 insertions(+), 2493 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-20 0.2.0
2019-02-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-01 2.2.1
2022-05-10 2.2.0
2022-04-26 2.1.0