Title: Biomarker Confirmation, Selection, Modelling, Prediction, and
Validation
Description: There are diverse purposes such as biomarker confirmation, novel biomarker discovery, constructing predictive models, model-based prediction, and validation.
It handles binary, continuous, and time-to-event outcomes at the sample or patient level.
- Biomarker confirmation utilizes established functions like glm() from 'stats', coxph() from 'survival', surv_fit(), and ggsurvplot() from 'survminer'.
- Biomarker discovery and variable selection are facilitated by three LASSO-related functions LASSO2(), LASSO_plus(), and LASSO2plus(), leveraging the 'glmnet' R package with additional steps.
- Eight versatile modeling functions are offered, each designed for predictive models across various outcomes and data types.
1) LASSO2(), LASSO_plus(), LASSO2plus(), and LASSO2_reg() perform variable selection using LASSO methods and construct predictive models based on selected variables.
2) XGBtraining() employs 'XGBoost' for model building and is the only function not involving variable selection.
3 [...truncated...]
Author: Aixiang Jiang [aut, cre, cph]
Maintainer: Aixiang Jiang <aijiang@bccrc.ca>
Diff between csmpv versions 1.0.3 dated 2024-03-01 and 1.0.5 dated 2025-12-11
DESCRIPTION | 20 LICENSE | 2 MD5 | 42 NAMESPACE | 4 R/XGBtraining.R | 253 - R/XGBtraining_predict.R | 135 R/XGpred.R | 419 +- R/XGpred_predict.R | 144 R/confirmVars.R | 10 R/coxTimeToEvent.R | 7 R/create_consistent_matrix.R |only R/create_model_matrix.R |only R/validation.R | 8 build/vignette.rds |binary inst/doc/csmpv_vignette.R | 997 ++--- inst/doc/csmpv_vignette.html | 7789 +++++++++++++++++++++---------------------- inst/doc/csmpv_vignette.rmd | 2321 ++++++------ man/XGBtraining_predict.Rd | 6 man/XGpred.Rd | 16 man/XGpred_predict.Rd | 2 man/confirmVars.Rd | 7 man/validation.Rd | 8 vignettes/csmpv_vignette.rmd | 2321 ++++++------ 23 files changed, 7352 insertions(+), 7159 deletions(-)
Title: Double Machine Learning for Static Panel Models with Fixed
Effects
Description: The 'xtdml' package implements partially linear panel regression (PLPR) models with high-dimensional confounding variables and an exogenous treatment variable within the double machine learning framework. The package is used to estimate the structural parameter (treatment effect) in static panel data models with fixed effects using the approaches established in Clarke and Polselli (2025) <doi:10.1093/ectj/utaf011>. 'xtdml' is built on the object-oriented package 'DoubleML' (Bach et al., 2024) <doi:10.18637/jss.v108.i03> using the 'mlr3' ecosystem.
Author: Annalivia Polselli [aut, cre]
Maintainer: Annalivia Polselli <apolselli.econ@gmail.com>
Diff between xtdml versions 0.1.10 dated 2025-12-10 and 0.1.11 dated 2025-12-11
DESCRIPTION | 12 MD5 | 10 R/helper.R | 888 +++++++++++++++++++++++++++---------------------------- R/xtdml_plr.R | 2 R/zzz.R | 39 +- man/xtdml_plr.Rd | 2 6 files changed, 476 insertions(+), 477 deletions(-)
Title: Transcription Elongation Profiling
Description: The general principle relies on calculating the cumulative signal of nascent
RNA sequencing over the gene body of any given gene or transcription unit.
'tepr' can identify transcription attenuation sites by comparing profile to
a null model which assumes uniform read density over the entirety of the
transcription unit. It can also identify increased or diminished
transcription attenuation by comparing two conditions. Besides rigorous
statistical testing and high sensitivity, a major feature of 'tepr' is its
ability to provide the elongation pattern of each individual gene, including
the position of the main attenuation point when such a phenomenon occurs.
Using 'tepr', users can visualize and refine genome-wide aggregated analyses
of elongation patterns to robustly identify effects specific to subsets of
genes. These metrics are suitable for internal comparisons (between genes in
each condition) and for studying elongation of the same gene in different
conditions or comparing it to a p [...truncated...]
Author: Nicolas Descostes [cre],
Victor Billon [aut],
Gael Cristofari [aut]
Maintainer: Nicolas Descostes <nicolas.descostes@gmail.com>
Diff between tepr versions 1.1.12 dated 2025-11-04 and 1.1.13 dated 2025-12-11
DESCRIPTION | 6 MD5 | 102 +- NEWS | 13 R/allauc.R | 16 R/attenuation.R | 10 R/averageandfilterexprs.R | 12 R/countna.R | 7 R/genesECDF.R | 19 R/kneeid.R | 8 R/meandifference.R | 26 R/plotauc.R | 16 R/plotecdf.R | 21 R/plothistoknee.R | 7 R/plotmetagenes.R | 21 R/plotmulti.R | 56 - R/preprocessing-blacklisthighmap-utils.R | 27 R/preprocessing-blacklisthighmap.R | 28 R/preprocessing-createtablescores.R | 10 R/preprocessing-makewindows.R | 7 R/preprocessing.R | 18 R/tepr.R | 101 +- R/universegroup.R | 2 R/utils.R | 67 - build/vignette.rds |binary inst/doc/tepr.R | 2 inst/doc/tepr.Rmd | 28 inst/doc/tepr.html | 652 +++++++++--------- man/allauc.Rd | 2 man/attenuation.Rd | 2 man/genesECDF.Rd | 7 man/kneeid.Rd | 2 man/meandifference.Rd | 2 man/plotauc.Rd | 2 man/plotecdf.Rd | 2 man/plothistoknee.Rd | 2 man/plotmetagenes.Rd | 2 man/teprmulti.Rd | 14 man/universegroup.Rd | 2 tests/testthat/test-allauc.R | 6 tests/testthat/test-attenuation.R | 8 tests/testthat/test-averageandfilterexprs.R | 16 tests/testthat/test-checkexptab.R | 12 tests/testthat/test-countna.R | 9 tests/testthat/test-genesECDF.R | 9 tests/testthat/test-kneeid.R | 2 tests/testthat/test-meandifference.R | 10 tests/testthat/test-preprocessing-blacklisthighmap.R | 15 tests/testthat/test-preprocessing-createtablescores.R | 7 tests/testthat/test-preprocessing.R | 11 tests/testthat/test-tepr.R | 11 tests/testthat/test-universegroup.R | 2 vignettes/tepr.Rmd | 28 52 files changed, 778 insertions(+), 689 deletions(-)
Title: Geographic Tools for Studying Gerrymandering
Description: A compilation of tools to complete common tasks for studying gerrymandering.
This focuses on the geographic tool side of common problems, such as linking
different levels of spatial units or estimating how to break up units. Functions
exist for creating redistricting-focused data for the US.
Author: Christopher T. Kenny [aut, cre] ,
Cory McCartan [ctb]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
This is a re-admission after prior archival of version 2.5.0 dated 2025-09-01
Diff between geomander versions 2.5.0 dated 2025-09-01 and 2.5.2 dated 2025-12-11
DESCRIPTION | 8 MD5 | 32 NEWS.md | 9 R/RcppExports.R | 12 R/alarm.R | 2 R/datatables.R | 4 R/lewis.R | 1898 +++++++++++++-------------- build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 6 inst/doc/Merging_Election_Data.html | 2 inst/doc/Redistricting_School_Districts.html | 22 man/block2prec.Rd | 2 man/get_heda.Rd | 2 man/get_lewis.Rd | 9 src/RcppExports.cpp | 39 src/contiguity.cpp | 137 + 17 files changed, 1161 insertions(+), 1023 deletions(-)
Title: Building and Managing Local Databases from 'Google Earth Engine'
Description: Simplifies the creation, management, and updating of local databases using data extracted from 'Google Earth Engine' ('GEE'). It integrates with 'GEE' to store, aggregate, and process spatio-temporal data, leveraging 'SQLite' for efficient, serverless storage. The 'geeLite' package provides utilities for data transformation and supports real-time monitoring and analysis of geospatial features, making it suitable for researchers and practitioners in geospatial science. For details, see Kurbucz and Andrée (2025) "Building and Managing Local Databases from Google Earth Engine with the geeLite R Package" <https://hdl.handle.net/10986/43165>.
Author: Marcell T. Kurbucz [aut, cre],
Bo Pieter Johannes Andree [aut]
Maintainer: Marcell T. Kurbucz <m.kurbucz@ucl.ac.uk>
Diff between geeLite versions 1.0.5 dated 2025-12-09 and 1.0.6 dated 2025-12-11
DESCRIPTION | 6 - MD5 | 22 ++-- NAMESPACE | 2 R/access_db.R | 241 +++++++++++++++++++++++++++++++++++++------------ R/run_geelite.R | 4 R/utils.R | 17 ++- man/aggr_by_freq.Rd | 29 +++++ man/fetch_vars.Rd | 3 man/init_postp.Rd | 13 +- man/read_db.Rd | 44 +++++--- man/read_variables.Rd | 35 ++++++- man/validate_params.Rd | 2 12 files changed, 301 insertions(+), 117 deletions(-)
Title: Double/Debiased Machine Learning
Description: Estimate common causal parameters using double/debiased machine
learning as proposed by Chernozhukov et al. (2018) <doi:10.1111/ectj.12097>.
'ddml' simplifies estimation based on (short-)stacking as discussed in
Ahrens et al. (2024) <doi:10.1002/jae.3103>, which leverages multiple base
learners to increase robustness to the underlying data generating process.
Author: Achim Ahrens [aut],
Christian B Hansen [aut],
Mark E Schaffer [aut],
Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <thomas.wiemann@chicagobooth.edu>
Diff between ddml versions 0.3.0 dated 2024-10-02 and 0.3.1 dated 2025-12-11
ddml-0.3.0/ddml/man/ddml.Rd |only ddml-0.3.1/ddml/DESCRIPTION | 18 ddml-0.3.1/ddml/MD5 | 119 - ddml-0.3.1/ddml/NAMESPACE | 62 ddml-0.3.1/ddml/NEWS.md | 65 ddml-0.3.1/ddml/R/AE98.R | 60 ddml-0.3.1/ddml/R/crosspred.R | 594 ++++---- ddml-0.3.1/ddml/R/crossval.R | 276 +-- ddml-0.3.1/ddml/R/ddml.R | 31 ddml-0.3.1/ddml/R/ddml_ate.R | 613 ++++---- ddml-0.3.1/ddml/R/ddml_att.R | 290 +-- ddml-0.3.1/ddml/R/ddml_fpliv.R | 702 ++++----- ddml-0.3.1/ddml/R/ddml_late.R | 704 ++++----- ddml-0.3.1/ddml/R/ddml_pliv.R | 574 +++---- ddml-0.3.1/ddml/R/ddml_plm.R | 730 +++++----- ddml-0.3.1/ddml/R/ensemble.R | 355 ++-- ddml-0.3.1/ddml/R/get_CEF.R | 150 +- ddml-0.3.1/ddml/R/help_functions.R | 100 - ddml-0.3.1/ddml/R/inference_functions.R | 206 +- ddml-0.3.1/ddml/R/ml_wrappers.R | 436 ++--- ddml-0.3.1/ddml/R/ols.R | 130 - ddml-0.3.1/ddml/R/shortstacking.R | 336 ++-- ddml-0.3.1/ddml/R/subsample_functions.R | 416 ++--- ddml-0.3.1/ddml/README.md | 310 ++-- ddml-0.3.1/ddml/build/partial.rdb |only ddml-0.3.1/ddml/build/vignette.rds |binary ddml-0.3.1/ddml/inst/doc/ddml.Rmd | 318 ++-- ddml-0.3.1/ddml/inst/doc/ddml.html | 1020 ++++++-------- ddml-0.3.1/ddml/man/AE98.Rd | 82 - ddml-0.3.1/ddml/man/crosspred.Rd | 334 ++-- ddml-0.3.1/ddml/man/crossval.Rd | 178 +- ddml-0.3.1/ddml/man/ddml-package.Rd |only ddml-0.3.1/ddml/man/ddml_ate.Rd | 455 +++--- ddml-0.3.1/ddml/man/ddml_fpliv.Rd | 372 ++--- ddml-0.3.1/ddml/man/ddml_late.Rd | 444 +++--- ddml-0.3.1/ddml/man/ddml_pliv.Rd | 370 ++--- ddml-0.3.1/ddml/man/ddml_plm.Rd | 370 ++--- ddml-0.3.1/ddml/man/mdl_glmnet.Rd | 100 - ddml-0.3.1/ddml/man/mdl_ranger.Rd | 2 ddml-0.3.1/ddml/man/mdl_xgboost.Rd | 103 - ddml-0.3.1/ddml/man/ols.Rd | 86 - ddml-0.3.1/ddml/man/print.summary.ddml_ate.Rd | 88 - ddml-0.3.1/ddml/man/print.summary.ddml_plm.Rd | 88 - ddml-0.3.1/ddml/man/shortstacking.Rd | 316 ++-- ddml-0.3.1/ddml/man/summary.ddml_ate.Rd | 88 - ddml-0.3.1/ddml/man/summary.ddml_plm.Rd | 122 - ddml-0.3.1/ddml/tests/testthat.R | 8 ddml-0.3.1/ddml/tests/testthat/test-crosspred.R | 262 +-- ddml-0.3.1/ddml/tests/testthat/test-crossval.R | 168 +- ddml-0.3.1/ddml/tests/testthat/test-ddml_ate.R | 390 ++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_att.R | 396 ++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_fpliv.R | 754 +++++----- ddml-0.3.1/ddml/tests/testthat/test-ddml_late.R | 476 +++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_pliv.R | 492 +++--- ddml-0.3.1/ddml/tests/testthat/test-ddml_plm.R | 590 ++++---- ddml-0.3.1/ddml/tests/testthat/test-ensemble.R | 241 +-- ddml-0.3.1/ddml/tests/testthat/test-help_functions.R | 18 ddml-0.3.1/ddml/tests/testthat/test-ml_wrappers.R | 151 +- ddml-0.3.1/ddml/tests/testthat/test-ols.R | 58 ddml-0.3.1/ddml/tests/testthat/test-shortstacking.R | 48 ddml-0.3.1/ddml/tests/testthat/test-subsample_functions.R | 216 +- ddml-0.3.1/ddml/vignettes/ddml.Rmd | 318 ++-- 62 files changed, 8423 insertions(+), 8376 deletions(-)
Title: "Nested Partially Latent Class Models"
Description: Provides functions to specify, fit and visualize
nested partially-latent class models (
Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>;
Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>;
Wu and Chen (2021) <doi:10.1002/sim.8804>) for
inference of population disease etiology and individual diagnosis. In the motivating
Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities
of interest sum to one hundred percent, the PERCH scientists frequently refer to
them as population etiology pie and individual etiology pie, hence the name of the package.
Author: Zhenke Wu [cre, aut, cph] ,
Scott Zeger [aut] ,
John Muschelli [ctb] ,
Irena Chen [ctb]
Maintainer: Zhenke Wu <zhenkewu@gmail.com>
This is a re-admission after prior archival of version 1.0.3 dated 2024-01-30
Diff between baker versions 1.0.3 dated 2024-01-30 and 1.0.4 dated 2025-12-11
baker-1.0.3/baker/man/baker.Rd |only baker-1.0.4/baker/DESCRIPTION | 19 - baker-1.0.4/baker/LICENSE | 2 baker-1.0.4/baker/MD5 | 102 ++++---- baker-1.0.4/baker/NEWS.md | 2 baker-1.0.4/baker/R/baker.R | 5 baker-1.0.4/baker/R/nplcm-read-folder.R | 22 + baker-1.0.4/baker/R/nplcm.R | 34 ++ baker-1.0.4/baker/R/plot-model-check.R | 32 +- baker-1.0.4/baker/R/utils.R | 13 - baker-1.0.4/baker/README.md | 89 ++++--- baker-1.0.4/baker/build/vignette.rds |binary baker-1.0.4/baker/inst/CITATION | 4 baker-1.0.4/baker/inst/WORDLIST | 116 ++++----- baker-1.0.4/baker/inst/doc/baker_demo.R | 120 +++++----- baker-1.0.4/baker/inst/doc/baker_demo.html | 9 baker-1.0.4/baker/man/add_meas_BrS_case_Nest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_Nest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_Nest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_Nest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_Slice.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_Slice_jags.Rd | 12 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_reg_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags.Rd | 16 - baker-1.0.4/baker/man/add_meas_BrS_subclass_Nest_Slice.Rd | 16 - baker-1.0.4/baker/man/add_meas_SS_case.Rd | 16 - baker-1.0.4/baker/man/add_meas_SS_param.Rd | 16 - baker-1.0.4/baker/man/baker-package.Rd |only baker-1.0.4/baker/man/beta_parms_from_quantiles.Rd | 3 baker-1.0.4/baker/man/check_dir_create.Rd | 10 baker-1.0.4/baker/man/get_individual_prediction.Rd | 11 baker-1.0.4/baker/man/jags2_baker.Rd | 2 baker-1.0.4/baker/man/make_list.Rd | 2 baker-1.0.4/baker/man/nplcm.Rd | 15 - baker-1.0.4/baker/man/nplcm_read_folder.Rd | 11 baker-1.0.4/baker/man/plot_check_common_pattern.Rd | 10 baker-1.0.4/baker/man/plot_check_pairwise_SLORD.Rd | 12 - baker-1.0.4/baker/man/print.nplcm.Rd | 4 baker-1.0.4/baker/man/print.summary.nplcm.no_reg.Rd | 4 baker-1.0.4/baker/man/print.summary.nplcm.reg_nest.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nest_strat.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nonest.Rd | 2 baker-1.0.4/baker/man/print.summary.nplcm.reg_nonest_strat.Rd | 2 baker-1.0.4/baker/man/summary.nplcm.Rd | 6 53 files changed, 523 insertions(+), 432 deletions(-)
Title: Estimating Infection Rates from Serological Data
Description: Translates antibody levels measured in cross-sectional
population samples into estimates of the frequency with which
seroconversions (infections) occur in the sampled populations.
Replaces the previous `seroincidence` package.
Author: Kristina Lai [aut, cre],
Chris Orwa [aut],
Kwan Ho Lee [ctb],
Peter Teunis [aut, cph] ,
Kristen Aiemjoy [aut],
Douglas Ezra Morrison [aut]
Maintainer: Kristina Lai <kwlai@ucdavis.edu>
Diff between serocalculator versions 1.3.0 dated 2025-01-25 and 1.4.0 dated 2025-12-11
serocalculator-1.3.0/serocalculator/R/as_curve_params.R |only serocalculator-1.3.0/serocalculator/R/est.incidence.R |only serocalculator-1.3.0/serocalculator/R/est.incidence.by.R |only serocalculator-1.3.0/serocalculator/R/graph.decay.curves.R |only serocalculator-1.3.0/serocalculator/R/load_curve_params.R |only serocalculator-1.3.0/serocalculator/R/rho-funcs.R |only serocalculator-1.3.0/serocalculator/R/sim.cs.R |only serocalculator-1.3.0/serocalculator/R/sim.cs.multi.R |only serocalculator-1.3.0/serocalculator/R/strata.seroincidence.ests.R |only serocalculator-1.3.0/serocalculator/R/tau-funcs.R |only serocalculator-1.3.0/serocalculator/man/mkbaseline.Rd |only serocalculator-1.3.0/serocalculator/man/row_longitudinal_parameter.Rd |only serocalculator-1.3.0/serocalculator/man/serocalculator.Rd |only serocalculator-1.3.0/serocalculator/man/strata.seroincidence.by.Rd |only serocalculator-1.3.0/serocalculator/man/warn.missing.strata.Rd |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/as_curve_params |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/as_curve_params.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/class_attributes.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/est.incidence.by.md |only serocalculator-1.3.0/serocalculator/tests/testthat/_snaps/est.incidence.md |only serocalculator-1.3.0/serocalculator/tests/testthat/test-as_curve_params.R |only serocalculator-1.3.0/serocalculator/tests/testthat/test-est.incidence.R |only serocalculator-1.3.0/serocalculator/tests/testthat/test-est.incidence.by.R |only serocalculator-1.4.0/serocalculator/DESCRIPTION | 39 serocalculator-1.4.0/serocalculator/MD5 | 338 ++-- serocalculator-1.4.0/serocalculator/NAMESPACE | 32 serocalculator-1.4.0/serocalculator/NEWS.md | 91 + serocalculator-1.4.0/serocalculator/R/ab.R | 46 serocalculator-1.4.0/serocalculator/R/ab1.R |only serocalculator-1.4.0/serocalculator/R/age_scatter.R |only serocalculator-1.4.0/serocalculator/R/analyze_sims.R |only serocalculator-1.4.0/serocalculator/R/as_pop_data.R | 16 serocalculator-1.4.0/serocalculator/R/as_sr_params.R |only serocalculator-1.4.0/serocalculator/R/autoplot.curve_params.R | 70 serocalculator-1.4.0/serocalculator/R/autoplot.pop_data.R | 133 - serocalculator-1.4.0/serocalculator/R/autoplot.seroincidence.R | 19 serocalculator-1.4.0/serocalculator/R/autoplot.seroincidence.by.R | 17 serocalculator-1.4.0/serocalculator/R/autoplot.sim_results.R |only serocalculator-1.4.0/serocalculator/R/autoplot.summary.seroincidence.by.R | 82 - serocalculator-1.4.0/serocalculator/R/baseline.R |only serocalculator-1.4.0/serocalculator/R/check_parallel_cores.R | 17 serocalculator-1.4.0/serocalculator/R/check_pop_data.R | 16 serocalculator-1.4.0/serocalculator/R/check_strata.R | 45 serocalculator-1.4.0/serocalculator/R/class_attributes.R | 131 - serocalculator-1.4.0/serocalculator/R/count_strata.R | 48 serocalculator-1.4.0/serocalculator/R/density_plot.R |only serocalculator-1.4.0/serocalculator/R/df_to_array.R | 4 serocalculator-1.4.0/serocalculator/R/est_seroincidence.R |only serocalculator-1.4.0/serocalculator/R/est_seroincidence_by.R |only serocalculator-1.4.0/serocalculator/R/example_noise_params_pk.R | 31 serocalculator-1.4.0/serocalculator/R/example_typhoid_curves_nostrat.R | 2 serocalculator-1.4.0/serocalculator/R/expect_snapshot_data.R |only serocalculator-1.4.0/serocalculator/R/f_dev.r | 109 - serocalculator-1.4.0/serocalculator/R/get_biomarker_names.R |only serocalculator-1.4.0/serocalculator/R/get_biomarker_names_var.R |only serocalculator-1.4.0/serocalculator/R/get_ids.R |only serocalculator-1.4.0/serocalculator/R/graph.curve.params.R | 320 ++-- serocalculator-1.4.0/serocalculator/R/graph_seroresponse_model_1.R |only serocalculator-1.4.0/serocalculator/R/ldpar.R |only serocalculator-1.4.0/serocalculator/R/load_sr_params.R |only serocalculator-1.4.0/serocalculator/R/nlm_exit_codes.R | 17 serocalculator-1.4.0/serocalculator/R/plot_curve_params_one_ab.R |only serocalculator-1.4.0/serocalculator/R/print.seroincidence.R | 44 serocalculator-1.4.0/serocalculator/R/print.seroincidence.by.R | 57 serocalculator-1.4.0/serocalculator/R/print.summary.seroincidence.by.R | 53 serocalculator-1.4.0/serocalculator/R/sees_pop_data_pakistan_100.R | 24 serocalculator-1.4.0/serocalculator/R/sees_typhoid_ests_strat.R |only serocalculator-1.4.0/serocalculator/R/serocalculator-package.R | 135 - serocalculator-1.4.0/serocalculator/R/set_id.R |only serocalculator-1.4.0/serocalculator/R/sim.cs-utils.r | 100 - serocalculator-1.4.0/serocalculator/R/sim_pop_data.R |only serocalculator-1.4.0/serocalculator/R/sim_pop_data_multi.R |only serocalculator-1.4.0/serocalculator/R/simcs.tinf.R | 93 - serocalculator-1.4.0/serocalculator/R/simpar.R | 5 serocalculator-1.4.0/serocalculator/R/simresp.tinf.R | 192 +- serocalculator-1.4.0/serocalculator/R/strat_ests_barplot.R |only serocalculator-1.4.0/serocalculator/R/strat_ests_scatterplot.R |only serocalculator-1.4.0/serocalculator/R/strata.R |only serocalculator-1.4.0/serocalculator/R/stratify_data.R | 139 - serocalculator-1.4.0/serocalculator/R/subset.seroincidence.ests.R | 1 serocalculator-1.4.0/serocalculator/R/summary.pop_data.R | 36 serocalculator-1.4.0/serocalculator/R/summary.seroincidence.R | 84 - serocalculator-1.4.0/serocalculator/R/summary.seroincidence.by.R | 79 - serocalculator-1.4.0/serocalculator/R/utils.R | 42 serocalculator-1.4.0/serocalculator/R/warn_missing_strata.R | 83 - serocalculator-1.4.0/serocalculator/README.md | 139 - serocalculator-1.4.0/serocalculator/data/example_noise_params_pk.rda |binary serocalculator-1.4.0/serocalculator/data/example_noise_params_sees.rda |only serocalculator-1.4.0/serocalculator/data/sees_pop_data_100.rda |only serocalculator-1.4.0/serocalculator/data/sees_pop_data_pk_100.rda |binary serocalculator-1.4.0/serocalculator/data/sees_pop_data_pk_100_old_names.rda |binary serocalculator-1.4.0/serocalculator/data/sees_typhoid_ests_strat.rda |only serocalculator-1.4.0/serocalculator/inst/WORDLIST | 87 - serocalculator-1.4.0/serocalculator/inst/examples |only serocalculator-1.4.0/serocalculator/man/ab.Rd | 45 serocalculator-1.4.0/serocalculator/man/analyze_sims.Rd |only serocalculator-1.4.0/serocalculator/man/as_curve_params.Rd | 27 serocalculator-1.4.0/serocalculator/man/as_pop_data.Rd | 4 serocalculator-1.4.0/serocalculator/man/as_sr_params.Rd |only serocalculator-1.4.0/serocalculator/man/autoplot.curve_params.Rd | 63 serocalculator-1.4.0/serocalculator/man/autoplot.pop_data.Rd | 8 serocalculator-1.4.0/serocalculator/man/autoplot.seroincidence.Rd | 9 serocalculator-1.4.0/serocalculator/man/autoplot.seroincidence.by.Rd | 13 serocalculator-1.4.0/serocalculator/man/autoplot.sim_results.Rd |only serocalculator-1.4.0/serocalculator/man/autoplot.summary.seroincidence.by.Rd | 67 serocalculator-1.4.0/serocalculator/man/baseline.Rd |only serocalculator-1.4.0/serocalculator/man/check_pop_data.Rd | 4 serocalculator-1.4.0/serocalculator/man/count_strata.Rd |only serocalculator-1.4.0/serocalculator/man/df_to_array.Rd |only serocalculator-1.4.0/serocalculator/man/est.incidence.Rd | 119 - 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serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/summary.seroincidence.by.md |only serocalculator-1.4.0/serocalculator/tests/testthat/_snaps/warn_missing_strata.md |only serocalculator-1.4.0/serocalculator/tests/testthat/fixtures |only serocalculator-1.4.0/serocalculator/tests/testthat/helper-noise_ymax.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-ab.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-ab0.R | 6 serocalculator-1.4.0/serocalculator/tests/testthat/test-ab1.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-analyze_sims.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-as_pop_data.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-as_sr_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.curve_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.pop_data.R | 22 serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.sim_results.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-autoplot.summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-check_parallel_cores.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-check_strata.R | 27 serocalculator-1.4.0/serocalculator/tests/testthat/test-class_attributes.R | 24 serocalculator-1.4.0/serocalculator/tests/testthat/test-count_strata.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-df_to_array.R | 12 serocalculator-1.4.0/serocalculator/tests/testthat/test-est_seroincidence.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-est_seroincidence_by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-f_dev.R | 126 + serocalculator-1.4.0/serocalculator/tests/testthat/test-get_biomarker_names.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-get_biomarker_names_var.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-get_ids.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-graph.curve.params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-load_sr_params.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-plot_curve_params_one_ab.R | 3 serocalculator-1.4.0/serocalculator/tests/testthat/test-print.seroincidence.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-print.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-print.summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-serocalculator_example.R | 4 serocalculator-1.4.0/serocalculator/tests/testthat/test-set_id.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-sim_pop_data.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-sim_pop_data_multi.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-strata.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-stratify_data.R | 112 - serocalculator-1.4.0/serocalculator/tests/testthat/test-summary.seroincidence.by.R |only serocalculator-1.4.0/serocalculator/tests/testthat/test-warn_missing_strata.R | 33 230 files changed, 3727 insertions(+), 3009 deletions(-)
More information about serocalculator at CRAN
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Title: Predictors of Resilience to a Stressor in a Single-Arm Study
Description: Studies of resilience in older adults employ a single-arm design where everyone experiences the stressor. The simplistic approach of regressing change versus baseline yields biased estimates due to regression-to-the-mean. This package provides a method to correct the bias. It also allows covariates to be included. The method implemented in the package is described in Varadhan, R., Zhu, J., and Bandeen-Roche, K (2024), Biostatistics 25(4): 1094-1111.
Author: Ravi Varadhan [aut, cre],
Jiafeng Zhu [ctb]
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between resilience versions 2024.1.2 dated 2024-08-22 and 2025.1.0 dated 2025-12-11
resilience-2024.1.2/resilience/data/tkr.RData |only resilience-2024.1.2/resilience/man/resilience-package.Rd |only resilience-2025.1.0/resilience/DESCRIPTION | 16 resilience-2025.1.0/resilience/MD5 | 19 resilience-2025.1.0/resilience/NAMESPACE | 38 + resilience-2025.1.0/resilience/R/pre-post-regression.R | 124 +++++ resilience-2025.1.0/resilience/R/prepost_mi_list.R |only resilience-2025.1.0/resilience/R/tkr-dat.R |only resilience-2025.1.0/resilience/data/tkr.dat.rda |only resilience-2025.1.0/resilience/man/plot.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/prepost.Rd | 214 +++++----- resilience-2025.1.0/resilience/man/prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/print.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/summary.prepost_resilience_mi_list.Rd |only resilience-2025.1.0/resilience/man/tkr.dat.Rd | 51 +- 15 files changed, 332 insertions(+), 130 deletions(-)
Title: Stochastic Tree Ensembles (XBART and BART) for Supervised
Learning and Causal Inference
Description: Flexible stochastic tree ensemble software.
Robust implementations of Bayesian Additive Regression Trees (BART)
Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285>
for supervised learning and Bayesian Causal Forests (BCF)
Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195>
for causal inference. Enables model serialization and parallel sampling
and provides a low-level interface for custom stochastic forest samplers.
Author: Drew Herren [aut, cre] ,
Richard Hahn [aut],
Jared Murray [aut],
Carlos Carvalho [aut],
Jingyu He [aut],
Pedro Lima [ctb],
stochtree contributors [cph],
Eigen contributors [cph] ,
xgboost contributors [cph] ,
treelite contributors [cph] ,
Microsoft C [...truncated...]
Maintainer: Drew Herren <drewherrenopensource@gmail.com>
Diff between stochtree versions 0.2.0 dated 2025-11-22 and 0.2.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 17 +- NEWS.md | 10 + R/bart.R | 17 ++ R/bcf.R | 68 +++++---- R/posterior_transformation.R | 108 +++++++++----- configure | 18 +- configure.ac | 2 tests/testthat/test-api-combinations.R |only tests/testthat/test-predict.R | 238 +++++++++++++++++++++++++++++++++ 10 files changed, 392 insertions(+), 92 deletions(-)
Title: Tree Guided Machine Learning for Personalized Predictions and
Precision Diagnostics
Description: Generalization of the classification and regression tree (CART) model that partitions subjects into terminal nodes and tailors machine learning model to each terminal node.
Author: Yunro Chung [aut, cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between tgml versions 0.2.0 dated 2025-09-24 and 0.3.0 dated 2025-12-11
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/05b.combML_mse.R | 22 ++++++++++++++-------- R/05c.combML_bs.R | 26 ++++++++++++++++---------- R/tgml.R | 2 ++ 5 files changed, 41 insertions(+), 27 deletions(-)
Title: Genomic Mediation Analysis with Adaptive Confounding Adjustment
Description: Performs genomic mediation
analysis with adaptive confounding adjustment (GMAC) proposed by Yang et al. (2017) <doi:10.1101/gr.216754.116>. It implements large scale
mediation analysis and adaptively selects potential confounding variables to
adjust for each mediation test from a pool of candidate confounders. The package
is tailored for but not limited to genomic mediation analysis (e.g., cis-gene
mediating trans-gene regulation pattern where an eQTL, its cis-linking gene
transcript, and its trans-gene transcript play the roles as treatment, mediator
and the outcome, respectively), restricting to scenarios with the presence of
cis-association (i.e., treatment-mediator association) and random eQTL (i.e.,
treatment).
Author: Fan Yang [aut],
Jiebiao Wang [aut, cre],
Lin Chen [aut]
Maintainer: Jiebiao Wang <randel.wang@gmail.com>
Diff between GMAC versions 3.1 dated 2022-03-17 and 3.2 dated 2025-12-11
DESCRIPTION | 26 +++++++++++++++++++------- MD5 | 9 +++++---- R/GMAC.R | 2 +- build/partial.rdb |binary man/figures/Thumbs.db |only man/gmac.Rd | 2 +- 6 files changed, 26 insertions(+), 13 deletions(-)
Title: Perpendicular Line Transects for Geosciences
Description: Toolset to create perpendicular profile graphs and swath
profiles. Method are based on coordinate rotation algorithm by
Schaeben et al. (2024) <doi:10.1002/mma.9823>.
Author: Tobias Stephan [aut, cre]
Maintainer: Tobias Stephan <tobias.stephan1@yahoo.com>
Diff between geoprofiler versions 0.0.2 dated 2025-04-10 and 0.0.3 dated 2025-12-11
DESCRIPTION | 11 MD5 | 31 +- NAMESPACE | 17 - NEWS.md |only R/swath.R | 588 ++++++++++++++++++++++++++++------------------ README.md | 18 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/A_Distances.R | 4 inst/doc/A_Distances.Rmd | 6 inst/doc/A_Distances.html | 12 inst/doc/B_Swath.R | 2 inst/doc/B_Swath.Rmd | 292 +++++++++++----------- inst/doc/B_Swath.html | 12 man/swath_stats.Rd | 4 vignettes/A_Distances.Rmd | 6 vignettes/B_Swath.Rmd | 292 +++++++++++----------- 17 files changed, 733 insertions(+), 562 deletions(-)
Title: Bayesian Whole-Genome Regression
Description: Whole-genome regression methods on Bayesian framework fitted via EM
or Gibbs sampling, single step (<doi:10.1534/g3.119.400728>),
univariate and multivariate (<doi:10.1186/s12711-022-00730-w>, <doi:10.1093/genetics/iyae179>),
with optional kernel term and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
Author: Alencar Xavier [aut, cre] ,
William Muir [aut],
David Habier [aut],
Kyle Kocak [aut],
Shizhong Xu [aut],
Katy Rainey [aut]
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 2.2.15 dated 2025-11-05 and 2.2.17 dated 2025-12-11
bWGR-2.2.15/bWGR/src/RcppEigenX20251103.cpp |only bWGR-2.2.17/bWGR/DESCRIPTION | 8 - bWGR-2.2.17/bWGR/MD5 | 16 +- bWGR-2.2.17/bWGR/R/RcppExports.R | 24 +++- bWGR-2.2.17/bWGR/demo/multivariates.R | 3 bWGR-2.2.17/bWGR/man/bWGR.Rd | 4 bWGR-2.2.17/bWGR/man/mvr.Rd | 11 + bWGR-2.2.17/bWGR/src/RcppEigen20230423.cpp | 155 ---------------------------- bWGR-2.2.17/bWGR/src/RcppEigenX20251203.cpp |only bWGR-2.2.17/bWGR/src/RcppExports.cpp | 104 ++++++++++++++---- 10 files changed, 128 insertions(+), 197 deletions(-)
Title: Workflows for Health Technology Assessments in R using Discrete
EveNts
Description: Toolkit to support and perform discrete event simulations with and without
resource constraints in the context of health technology assessments (HTA).
The package focuses on cost-effectiveness modelling and aims to be submission-ready
to relevant HTA bodies in alignment with 'NICE TSD 15'
<https://sheffield.ac.uk/nice-dsu/tsds/patient-level-simulation>.
More details an examples can be found in the package website <https://jsanchezalv.github.io/WARDEN/>.
Author: Javier Sanchez Alvarez [aut, cre],
Gabriel Lemyre [ctb],
Valerie Aponte Ribero [ctb]
Maintainer: Javier Sanchez Alvarez <javiersanchezeco@gmail.com>
Diff between WARDEN versions 2.0.0 dated 2025-10-13 and 2.0.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 22 +-- NEWS.md | 17 +- R/engine_helper_f.R | 1 R/input_f.R | 24 ++- build/vignette.rds |binary inst/doc/example_ssd.html | 292 ++++++++++++++++++++---------------------- man/adj_val.Rd | 18 ++ man/ast_as_list.Rd | 126 +++++++++--------- man/qgamma_mse.Rd | 54 +++---- man/with_write_flags_lang.Rd | 122 ++++++++--------- tests/testthat/test-input_f.R | 1 12 files changed, 352 insertions(+), 331 deletions(-)
Title: Structural Equation Modeling with Deep Neural Network and
Machine Learning Algorithms
Description: Training and validation of a custom (or data-driven) Structural
Equation Models using Deep Neural Networks or Machine Learning algorithms, which
extend the fitting procedures of the 'SEMgraph' R package <doi:10.32614/CRAN.package.SEMgraph>.
Author: Mario Grassi [aut],
Barbara Tarantino [cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMdeep versions 1.1.0 dated 2025-11-10 and 1.1.1 dated 2025-12-11
DESCRIPTION | 13 +-- MD5 | 31 ++++---- NAMESPACE | 3 NEWS.md | 8 ++ R/SEMdnn.R | 20 ++--- R/SEMhelp.R | 160 +++++++++++++++++++++++++++++++++++++++++-- R/SEMml.R | 54 +++++++------- man/SEMdnn.Rd | 6 - man/SEMml.Rd | 5 - man/crossValidation.Rd | 13 +-- man/getConnectionWeight.Rd | 2 man/getGradientWeight.Rd | 2 man/getSignificanceTest.Rd | 2 man/getVariableImportance.Rd | 4 - man/predict.DNN.Rd | 4 - man/predict.ML.Rd | 5 - man/trainingReport.Rd |only 17 files changed, 248 insertions(+), 84 deletions(-)
Title: Geometric Single Cell Deconvolution
Description: Deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology.
Author: Myles Lewis [aut, cre] ,
Rachel Lau [ctb]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between cellGeometry versions 0.5.4 dated 2025-09-15 and 0.5.7 dated 2025-12-11
cellGeometry-0.5.4/cellGeometry/R/subMarkers.R |only cellGeometry-0.5.7/cellGeometry/DESCRIPTION | 7 - cellGeometry-0.5.7/cellGeometry/MD5 | 35 ++++---- cellGeometry-0.5.7/cellGeometry/NAMESPACE | 3 cellGeometry-0.5.7/cellGeometry/NEWS.md | 13 +++ cellGeometry-0.5.7/cellGeometry/R/cellMarkers.R | 5 - cellGeometry-0.5.7/cellGeometry/R/deconvolute.R | 37 +++++--- cellGeometry-0.5.7/cellGeometry/R/mergeMarkers.R | 67 +++++++++++++--- cellGeometry-0.5.7/cellGeometry/R/rstudent.R | 40 +++++++++ cellGeometry-0.5.7/cellGeometry/R/scedasticity.R | 1 cellGeometry-0.5.7/cellGeometry/R/specificity_plot.R | 6 - cellGeometry-0.5.7/cellGeometry/R/stack_plot.R | 3 cellGeometry-0.5.7/cellGeometry/README.md | 2 cellGeometry-0.5.7/cellGeometry/inst/doc/intro.Rmd | 7 + cellGeometry-0.5.7/cellGeometry/inst/doc/intro.html | 7 + cellGeometry-0.5.7/cellGeometry/man/cellMarkers.Rd | 5 - cellGeometry-0.5.7/cellGeometry/man/deconvolute.Rd | 17 ++-- cellGeometry-0.5.7/cellGeometry/man/fix_group.Rd |only cellGeometry-0.5.7/cellGeometry/man/residuals.deconv.Rd |only cellGeometry-0.5.7/cellGeometry/vignettes/intro.Rmd | 7 + 20 files changed, 205 insertions(+), 57 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] ,
Jonas Lindblad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 1.2.0 dated 2025-09-25 and 1.2.3 dated 2025-12-11
DESCRIPTION | 10 - MD5 | 34 ++-- NAMESPACE | 2 NEWS.md | 48 ++++++ R/GaussSuppressionFromData.R | 126 ++++++++++++++- R/MagnitudeRule.R | 142 +++++++++++++----- R/Singleton.R | 11 + R/SuppressDominantCells.R | 34 ++++ inst/doc/Linked_table_suppression.html | 5 inst/doc/Magnitude_table_suppression.html | 17 +- inst/doc/Small_count_frequency_table_suppression.html | 5 inst/doc/define_tables.html | 5 man/GaussSuppressionFromData.Rd | 32 +++- man/MagnitudeRule.Rd | 21 ++ man/SingletonUniqueContributor.Rd | 3 man/SuppressDominantCells.Rd | 34 ++++ man/figures/logo.png |binary tests/testthat/test-Wrappers.R | 41 +++++ 18 files changed, 482 insertions(+), 88 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Access the Felt API
Description: Upload, download, and edit internet maps with the Felt API
(<https://developers.felt.com/rest-api/getting-started>).
Allows users to create new maps, edit existing maps, and extract data.
Provides tools for working with layers, which represent geographic data, and elements,
which are interactive annotations. Spatial data accessed from the API is
transformed to work with 'sf'.
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <ctkenny@proton.me>
Diff between feltr versions 0.0.4 dated 2023-11-05 and 0.1.0 dated 2025-12-11
feltr-0.0.4/feltr/R/finish_upload.R |only feltr-0.0.4/feltr/man/felt_finish_upload.Rd |only feltr-0.0.4/feltr/man/felt_get_style.Rd |only feltr-0.0.4/feltr/tests/testthat/t/create/felt.com |only feltr-0.0.4/feltr/tests/testthat/t/get_elements/felt.com |only feltr-0.0.4/feltr/tests/testthat/t/user/felt.com |only feltr-0.1.0/feltr/DESCRIPTION | 23 feltr-0.1.0/feltr/MD5 | 83 +- feltr-0.1.0/feltr/NAMESPACE | 19 feltr-0.1.0/feltr/NEWS.md | 15 feltr-0.1.0/feltr/R/add.R | 283 ++++++---- feltr-0.1.0/feltr/R/api_url.R | 2 feltr-0.1.0/feltr/R/comments.R | 15 feltr-0.1.0/feltr/R/create.R | 26 feltr-0.1.0/feltr/R/delete.R | 138 +++- feltr-0.1.0/feltr/R/details.R |only feltr-0.1.0/feltr/R/felt_key.R | 209 +++---- feltr-0.1.0/feltr/R/feltr-package.R |only feltr-0.1.0/feltr/R/library.R |only feltr-0.1.0/feltr/R/map.R | 186 ++++-- feltr-0.1.0/feltr/R/map_elements.R | 75 ++ feltr-0.1.0/feltr/R/proc.R | 92 +-- feltr-0.1.0/feltr/R/refresh.R |only feltr-0.1.0/feltr/R/roxygen.R |only feltr-0.1.0/feltr/R/style.R | 61 -- feltr-0.1.0/feltr/R/user.R | 56 + feltr-0.1.0/feltr/R/utils.R |only feltr-0.1.0/feltr/inst/bbox.geojson |only feltr-0.1.0/feltr/inst/httptest2/redact.R | 3 feltr-0.1.0/feltr/man/felt_add_library_layer.Rd |only feltr-0.1.0/feltr/man/felt_add_library_layer_group.Rd |only feltr-0.1.0/feltr/man/felt_add_map_elements.Rd |only feltr-0.1.0/feltr/man/felt_add_map_layers.Rd | 28 feltr-0.1.0/feltr/man/felt_add_map_layers_url.Rd | 16 feltr-0.1.0/feltr/man/felt_create_map.Rd | 19 feltr-0.1.0/feltr/man/felt_delete_map.Rd | 4 feltr-0.1.0/feltr/man/felt_delete_map_elements.Rd |only feltr-0.1.0/feltr/man/felt_delete_map_layer.Rd | 26 feltr-0.1.0/feltr/man/felt_get_comments.Rd | 8 feltr-0.1.0/feltr/man/felt_get_library.Rd |only feltr-0.1.0/feltr/man/felt_get_map.Rd | 17 feltr-0.1.0/feltr/man/felt_get_map_elements.Rd | 18 feltr-0.1.0/feltr/man/felt_get_map_layer_group.Rd |only feltr-0.1.0/feltr/man/felt_get_user.Rd | 7 feltr-0.1.0/feltr/man/felt_patch_style.Rd | 25 feltr-0.1.0/feltr/man/felt_refresh_layer.Rd |only feltr-0.1.0/feltr/man/felt_update_layer_details.Rd |only feltr-0.1.0/feltr/man/felt_update_layer_group_details.Rd |only feltr-0.1.0/feltr/man/felt_update_map_details.Rd |only feltr-0.1.0/feltr/man/feltr-package.Rd |only feltr-0.1.0/feltr/man/key.Rd | 6 feltr-0.1.0/feltr/man/set_felt_key.Rd | 3 feltr-0.1.0/feltr/tests/testthat/t/create/maps-b1286e-POST.json |only feltr-0.1.0/feltr/tests/testthat/t/get_elements/maps |only feltr-0.1.0/feltr/tests/testthat/t/user/user.json |only feltr-0.1.0/feltr/tests/testthat/test-comments.R | 14 56 files changed, 929 insertions(+), 548 deletions(-)
Title: Exponential-Family Models for Signed Networks
Description: Extends the 'ergm.multi' packages from the Statnet suite to fit (temporal) exponential-family random graph models for signed networks. The framework models positive and negative ties as interdependent, which allows estimation and testing of structural balance theory. The package also includes options for descriptive summaries, visualization, and simulation of signed networks. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Fritz, C., Mehrl, M., Thurner, P. W., & Kauermann, G. (2025) <doi:10.1017/pan.2024.21>.
Author: Marc Schalberger [cre],
Cornelius Fritz [aut],
Pavel Krivitsky [ctb]
Maintainer: Marc Schalberger <m.schalberger@fu-berlin.de>
Diff between ergm.sign versions 0.1.0 dated 2025-11-21 and 0.1.1 dated 2025-12-11
ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.delese.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.delesf.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.gwdelese.Rd |only ergm.sign-0.1.0/ergm.sign/man/InitErgmTerm.gwdelesf.Rd |only ergm.sign-0.1.1/ergm.sign/DESCRIPTION | 6 ergm.sign-0.1.1/ergm.sign/MD5 | 42 - ergm.sign-0.1.1/ergm.sign/NAMESPACE | 2 ergm.sign-0.1.1/ergm.sign/R/InitErgmTerm.sign.R | 596 +++++---------- ergm.sign-0.1.1/ergm.sign/R/UnLayer.R | 10 ergm.sign-0.1.1/ergm.sign/R/ergm.sign-package.R | 2 ergm.sign-0.1.1/ergm.sign/R/mple_sign.R | 6 ergm.sign-0.1.1/ergm.sign/R/network.sign.R | 40 - ergm.sign-0.1.1/ergm.sign/R/networks.sign.R | 1 ergm.sign-0.1.1/ergm.sign/R/path_sampler.R |only ergm.sign-0.1.1/ergm.sign/build/partial.rdb |binary ergm.sign-0.1.1/ergm.sign/build/stage23.rdb |binary ergm.sign-0.1.1/ergm.sign/data/sponsor.rda |binary ergm.sign-0.1.1/ergm.sign/inst/doc/tribes.html | 24 ergm.sign-0.1.1/ergm.sign/man/ese-ergmTerm-8531b67b.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/esf-ergmTerm-c450f580.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/eval_loglik.Rd |only ergm.sign-0.1.1/ergm.sign/man/gwese-ergmTerm-0e3a2475.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/gwesf-ergmTerm-81ee6379.Rd | 2 ergm.sign-0.1.1/ergm.sign/man/mple_sign.Rd | 10 ergm.sign-0.1.1/ergm.sign/tests/testthat/test-delayed.R | 16 25 files changed, 322 insertions(+), 441 deletions(-)
Title: Genome Polarization via Diagnostic Index Expectation
Maximization
Description: Implements a likelihood-based method for genome polarization, identifying
which alleles of SNV markers belong to either side of a barrier to gene flow. The
approach co-estimates individual assignment, barrier strength, and divergence between
sides, with direct application to studies of hybridization. Includes VCF-to-diem
conversion and input checks, support for mixed ploidy and parallelization, and tools
for visualization and diagnostic outputs. Based on diagnostic index expectation
maximization as described in Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.5.1 dated 2025-10-09 and 1.5.2 dated 2025-12-11
DESCRIPTION | 6 MD5 | 56 ++-- NAMESPACE | 1 NEWS.md | 12 + R/CheckDiemFormat.r | 14 - R/hybridIndex.r | 114 +++++++--- R/importPolarized.r | 47 ++-- R/internal.r | 41 +-- R/rank2map.r | 54 ++-- R/readIncludedSites.r |only R/smoothPolarizedGenotypes.r | 85 +++---- R/vcf2diem.r | 86 +++++-- README.md | 23 +- build/vignette.rds |binary inst/doc/Importing-data-for-genome-polarisation.html | 4 inst/doc/Understanding-genome-polarisation-output-files.html | 4 inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 4 inst/extdata/myotis.vcf |binary man/CheckDiemFormat.Rd | 4 man/hybridIndex.Rd | 89 +++++-- man/importPolarized.Rd | 12 - man/rank2map.Rd | 12 - man/readIncludedSites.Rd | 14 - man/resolveChosenInds.Rd |only man/smoothPolarizedGenotypes.Rd | 26 +- man/variantSites.Rd | 2 man/vcf2diem.Rd | 34 ++ tests/testthat/test_hybridIndex.r | 105 +++++++++ tests/testthat/test_importPolarized.r | 34 ++ tests/testthat/test_internal.r | 43 +++ 30 files changed, 666 insertions(+), 260 deletions(-)
Title: Transformation-Free Linear Regression for Compositional Outcomes
and Predictors
Description: Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2022) <doi:10.1111/biom.13465>
for transformation-free linear regression for compositional outcomes and predictors.
Author: Jacob Fiksel [aut] ,
Abhirup Datta [ctb],
Sandipan Pramanik [cre, ctb]
Maintainer: Sandipan Pramanik <sandy.pramanik@gmail.com>
Diff between codalm versions 0.1.2 dated 2021-07-26 and 0.1.3 dated 2025-12-11
codalm-0.1.2/codalm/R/data.R |only codalm-0.1.2/codalm/data |only codalm-0.1.2/codalm/man/educFM.Rd |only codalm-0.1.2/codalm/man/predict_codalm.Rd |only codalm-0.1.3/codalm/DESCRIPTION | 46 - codalm-0.1.3/codalm/MD5 | 39 - codalm-0.1.3/codalm/NAMESPACE | 1 codalm-0.1.3/codalm/NEWS.md | 4 codalm-0.1.3/codalm/R/codalm_em.R | 56 - codalm-0.1.3/codalm/R/independence_test.R | 17 codalm-0.1.3/codalm/README.md | 5 codalm-0.1.3/codalm/build/partial.rdb |only codalm-0.1.3/codalm/build/vignette.rds |binary codalm-0.1.3/codalm/inst/doc/codalm_quickstart.R | 30 codalm-0.1.3/codalm/inst/doc/codalm_quickstart.Rmd | 39 - codalm-0.1.3/codalm/inst/doc/codalm_quickstart.html | 462 ++++++++---- codalm-0.1.3/codalm/man/codalm.Rd | 17 codalm-0.1.3/codalm/man/codalm_ci.Rd | 13 codalm-0.1.3/codalm/man/codalm_indep_test.Rd | 15 codalm-0.1.3/codalm/tests/testthat/test-codalm.R | 2 codalm-0.1.3/codalm/tests/testthat/test-codalm_ci.R | 12 codalm-0.1.3/codalm/tests/testthat/test-independence_test.R | 4 codalm-0.1.3/codalm/vignettes/codalm_quickstart.Rmd | 39 - 23 files changed, 514 insertions(+), 287 deletions(-)
Title: Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and
Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>.
'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS',
'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions'
(<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>),
and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut, cph] ,
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 5.2.0 dated 2025-11-08 and 5.2.1 dated 2025-12-11
bibliometrix-5.2.0/bibliometrix/inst/biblioshiny/utils_old.R |only bibliometrix-5.2.1/bibliometrix/DESCRIPTION | 6 bibliometrix-5.2.1/bibliometrix/MD5 | 21 bibliometrix-5.2.1/bibliometrix/NEWS | 8 bibliometrix-5.2.1/bibliometrix/build/partial.rdb |binary bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/biblioAI.R | 8 bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/biblioShot.R | 192 ++++---- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/helpContent.R | 198 ++++++++ bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/libraries.R | 103 +++- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/server.R | 165 +++---- bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/ui.R | 63 ++ bibliometrix-5.2.1/bibliometrix/inst/biblioshiny/utils.R | 227 +++++++++- 12 files changed, 763 insertions(+), 228 deletions(-)
Title: Bayesian Analysis of Non-Stationary Gaussian Process Models
Description: Enables off-the-shelf functionality for fully Bayesian, nonstationary Gaussian process modeling. The approach to nonstationary modeling involves a closed-form, convolution-based covariance function with spatially-varying parameters; these parameter processes can be specified either deterministically (using covariates or basis functions) or stochastically (using approximate Gaussian processes). Stationary Gaussian processes are a special case of our methodology, and we furthermore implement approximate Gaussian process inference to account for very large spatial data sets (Finley, et al (2017) <doi:10.48550/arXiv.1702.00434>). Bayesian inference is carried out using Markov chain Monte Carlo methods via the "nimble" package, and posterior prediction for the Gaussian process at unobserved locations is provided as a post-processing step.
Author: Daniel Turek [aut, cre],
Mark Risser [aut]
Maintainer: Daniel Turek <danielturek@gmail.com>
Diff between BayesNSGP versions 0.1.2 dated 2022-01-08 and 0.2.0 dated 2025-12-11
DESCRIPTION | 17 MD5 | 43 - NAMESPACE | 12 R/SGV.R | 32 - R/core.R | 1178 +++++++++++++++++++++++++++--------------- R/gp2Scale.R |only man/Cy_sm.Rd |only man/R_sparse_cholesky.Rd |only man/R_sparse_solveMat.Rd |only man/crossCy_sm.Rd |only man/determineNeighbors.Rd | 8 man/dmnorm_gp2Scale.Rd |only man/inverseEigen.Rd | 6 man/matern_corr.Rd | 12 man/nimble_sparse_cholesky.Rd |only man/nimble_sparse_solveMat.Rd |only man/nsCorr.Rd | 18 man/nsCrosscorr.Rd | 26 man/nsCrossdist.Rd | 4 man/nsCrossdist3d.Rd | 2 man/nsDist.Rd | 2 man/nsDist3d.Rd | 2 man/nsgpModel.Rd | 36 - man/nsgpPredict.Rd | 28 man/orderCoordinatesMMD.Rd | 8 man/rmnorm_gp2Scale.Rd |only man/sgvSetup.Rd | 5 27 files changed, 929 insertions(+), 510 deletions(-)
Title: Causal Inference using Bayesian Additive Regression Trees
Description: Contains a variety of methods to generate typical causal inference estimates using Bayesian Additive Regression Trees (BART) as the underlying regression model (Hill (2012) <doi:10.1198/jcgs.2010.08162>).
Author: Vincent Dorie [aut, cre] ,
Jennifer Hill [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between bartCause versions 1.0-9 dated 2024-09-16 and 1.0-10 dated 2025-12-11
DESCRIPTION | 13 ++++++------ MD5 | 20 +++++++++---------- R/generics.R | 8 +++++-- R/responseFit.R | 5 +++- R/utility.R | 37 +++++++++++++++++++++++++++++++++++- build/partial.rdb |binary inst/NEWS.Rd | 9 ++++++++ tests/testthat/test-04-bartc.R | 22 +++++++++++++++------ tests/testthat/test-05-generics.R | 7 ++++++ tests/testthat/test-06-regression.R | 4 ++- tests/testthat/test-11-stan4bart.R | 6 ++--- 11 files changed, 101 insertions(+), 30 deletions(-)
Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre] ,
Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between proxy versions 0.4-27 dated 2022-06-09 and 0.4-28 dated 2025-12-11
DESCRIPTION | 14 +++++++------ MD5 | 28 +++++++++++++-------------- NAMESPACE | 5 ++-- R/registry.R | 8 +++---- R/util.R | 16 +++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 13 ++++++++++++ inst/doc/overview.pdf |binary man/dist.Rd | 2 - src/apply.c | 36 ++++++++++++++++++++--------------- src/arrayIndex.c | 35 ++++++++++++++++++++++++++++++++-- src/distance.c | 20 ++++++++++--------- src/util.c | 38 +++++++++++++++++++++---------------- tests/util.R | 6 +++-- tests/util.Rout.save | 51 +++++++++++++++++++++++++++++++++----------------- 15 files changed, 182 insertions(+), 90 deletions(-)
Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to
explain why the model should be trusted. While global measures such as
accuracy are useful, they cannot be used for explaining why a model
made a specific prediction. 'lime' (a port of the 'lime' 'Python'
package) is a method for explaining the outcome of black box models by
fitting a local model around the point in question an perturbations of
this point. The approach is described in more detail in the article by
Ribeiro et al. (2016) <doi:10.48550/arXiv.1602.04938>.
Author: Emil Hvitfeldt [aut, cre] ,
Thomas Lin Pedersen [aut] ,
Michael Benesty [aut]
Maintainer: Emil Hvitfeldt <emil.hvitfeldt@posit.co>
Diff between lime versions 0.5.3 dated 2022-08-19 and 0.5.4 dated 2025-12-11
lime-0.5.3/lime/demo |only lime-0.5.4/lime/DESCRIPTION | 79 +- lime-0.5.4/lime/LICENSE | 4 lime-0.5.4/lime/MD5 | 68 - lime-0.5.4/lime/NAMESPACE | 6 lime-0.5.4/lime/NEWS.md | 4 lime-0.5.4/lime/R/a_dataframe.R | 316 +++++--- lime-0.5.4/lime/R/character.R | 109 ++ lime-0.5.4/lime/R/explain.R | 21 lime-0.5.4/lime/R/image.R | 188 +++-- lime-0.5.4/lime/R/import-standalone-purrr.R |only lime-0.5.4/lime/R/lime-package.r | 36 lime-0.5.4/lime/R/lime.R | 132 +++ lime-0.5.4/lime/R/models.R | 84 +- lime-0.5.4/lime/R/permute_cases.R | 177 +++- lime-0.5.4/lime/R/plot.R | 81 +- lime-0.5.4/lime/R/plot_image.R | 202 +++-- lime-0.5.4/lime/R/plot_text.R | 43 - lime-0.5.4/lime/R/shiny.R | 126 ++- lime-0.5.4/lime/README.md | 48 - lime-0.5.4/lime/build/partial.rdb |only lime-0.5.4/lime/build/vignette.rds |binary lime-0.5.4/lime/inst/doc/Understanding_lime.R | 88 +- lime-0.5.4/lime/inst/doc/Understanding_lime.Rmd | 94 +- lime-0.5.4/lime/inst/doc/Understanding_lime.html | 548 ++++++++------- lime-0.5.4/lime/man/figures/README-unnamed-chunk-2-1.png |binary lime-0.5.4/lime/man/figures/README-unnamed-chunk-3-1.png |binary lime-0.5.4/lime/man/figures/lifecycle-deprecated.svg |only lime-0.5.4/lime/man/figures/lifecycle-experimental.svg |only lime-0.5.4/lime/man/figures/lifecycle-stable.svg |only lime-0.5.4/lime/man/figures/lifecycle-superseded.svg |only lime-0.5.4/lime/man/lime-package.Rd | 11 lime-0.5.4/lime/tests/testthat.R | 8 lime-0.5.4/lime/tests/testthat/test-data.frame.R | 9 lime-0.5.4/lime/tests/testthat/test-h2o.R | 182 ++-- lime-0.5.4/lime/tests/testthat/test-permutations.R | 32 lime-0.5.4/lime/tests/testthat/test-text.R | 46 - lime-0.5.4/lime/vignettes/Understanding_lime.Rmd | 94 +- 38 files changed, 1922 insertions(+), 914 deletions(-)
Title: Less Code with More Comprehensive Results
Description: Each function replaces multiple standard R functions. For example,
two function calls, Read() and CountAll(), generate summary statistics for
all variables in the data frame, plus histograms and bar charts. Other
functions provide data aggregation via pivot tables; comprehensive
regression, ANOVA, and t-test; visualizations including integrated
Violin/Box/Scatter plot for a numerical variable, bar chart, histogram,
box plot, density curves, calibrated power curve; reading multiple data
formats with the same call; variable labels; time series with aggregation
and forecasting; color themes; and Trellis (facet) graphics. Also includes
a confirmatory factor analysis of multiple-indicator measurement models,
pedagogical routines for data simulation (e.g., Central Limit Theorem),
generation and rendering of regression instructions for interpretative output,
and both interactive construction of visualizations and interactive
visualizations with plotly.
Author: David W. Gerbing [aut, cre]
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 4.4.5 dated 2025-08-22 and 4.5 dated 2025-12-11
lessR-4.4.5/lessR/R/BarChart.R |only lessR-4.4.5/lessR/R/BoxPlot.R |only lessR-4.4.5/lessR/R/Histogram.R |only lessR-4.4.5/lessR/R/PieChart.R |only lessR-4.4.5/lessR/R/Plot.R |only lessR-4.4.5/lessR/R/Read2.R |only lessR-4.4.5/lessR/R/ScatterPlot.R |only lessR-4.4.5/lessR/R/av.R |only lessR-4.4.5/lessR/R/av_brief.R |only lessR-4.4.5/lessR/R/bc.R |only lessR-4.4.5/lessR/R/bc.stat.R |only lessR-4.4.5/lessR/R/bx.R |only lessR-4.4.5/lessR/R/ca.R |only lessR-4.4.5/lessR/R/cfa.R |only lessR-4.4.5/lessR/R/cp.R |only lessR-4.4.5/lessR/R/cr.R |only lessR-4.4.5/lessR/R/cr_brief.R |only lessR-4.4.5/lessR/R/db.R |only lessR-4.4.5/lessR/R/efa.R |only lessR-4.4.5/lessR/R/hs.R |only lessR-4.4.5/lessR/R/lr.R |only lessR-4.4.5/lessR/R/model2.R |only lessR-4.4.5/lessR/R/mrg.R |only lessR-4.4.5/lessR/R/nt.R |only lessR-4.4.5/lessR/R/pc.R |only lessR-4.4.5/lessR/R/pc.main.R |only lessR-4.4.5/lessR/R/prop.R |only lessR-4.4.5/lessR/R/rd.R |only lessR-4.4.5/lessR/R/rd.cor.R |only lessR-4.4.5/lessR/R/rd_lbl.R |only lessR-4.4.5/lessR/R/reflect.R |only lessR-4.4.5/lessR/R/reg.R |only lessR-4.4.5/lessR/R/reg.brief.R |only lessR-4.4.5/lessR/R/reg_brief.R |only lessR-4.4.5/lessR/R/reord.R |only lessR-4.4.5/lessR/R/set.R |only lessR-4.4.5/lessR/R/sp.R |only lessR-4.4.5/lessR/R/ss.R |only lessR-4.4.5/lessR/R/tt.R |only lessR-4.4.5/lessR/R/tt_brief.R |only lessR-4.4.5/lessR/R/ttp.R |only lessR-4.4.5/lessR/R/vl.R |only lessR-4.4.5/lessR/R/vp.R |only lessR-4.4.5/lessR/R/wrt.R |only lessR-4.4.5/lessR/R/wrt_r.R |only lessR-4.4.5/lessR/R/wrt_x.R |only lessR-4.4.5/lessR/inst/shiny_apps/PieChart |only lessR-4.4.5/lessR/inst/shiny_apps/Trellis |only lessR-4.4.5/lessR/inst/shiny_apps/help/PieChart.html |only lessR-4.4.5/lessR/inst/shiny_apps/help/Trellis.html |only lessR-4.4.5/lessR/man/BarChart.Rd |only lessR-4.4.5/lessR/man/Histogram.Rd |only lessR-4.4.5/lessR/man/PieChart.Rd |only lessR-4.4.5/lessR/man/Plot.Rd |only lessR-4.5/lessR/DESCRIPTION | 45 lessR-4.5/lessR/MD5 | 201 -- lessR-4.5/lessR/NAMESPACE | 13 lessR-4.5/lessR/NEWS.md | 48 lessR-4.5/lessR/R/ANOVA.R | 6 lessR-4.5/lessR/R/ANOVAz2.R | 38 lessR-4.5/lessR/R/Chart.R |only lessR-4.5/lessR/R/CountAll.R | 5 lessR-4.5/lessR/R/Flows.R |only lessR-4.5/lessR/R/Regression.R | 15 lessR-4.5/lessR/R/X.R |only lessR-4.5/lessR/R/XY.R |only lessR-4.5/lessR/R/aliases.R |only lessR-4.5/lessR/R/bc.ParamValid.R | 13 lessR-4.5/lessR/R/bc.data.frame.R | 6 lessR-4.5/lessR/R/bc.main.R | 199 +- lessR-4.5/lessR/R/bc.plotly.R |only lessR-4.5/lessR/R/bubble.plotly.R |only lessR-4.5/lessR/R/corScree.R | 3 lessR-4.5/lessR/R/dn.main.R | 164 + lessR-4.5/lessR/R/dn.plotly.R |only lessR-4.5/lessR/R/do.plotly.R |only lessR-4.5/lessR/R/dpmat.main.R | 15 lessR-4.5/lessR/R/hier.plotly.R |only lessR-4.5/lessR/R/hs.plotly.R |only lessR-4.5/lessR/R/hst.main.R | 282 +-- lessR-4.5/lessR/R/hst.stats.R | 8 lessR-4.5/lessR/R/interact.R | 7 lessR-4.5/lessR/R/param.VBS.R | 19 lessR-4.5/lessR/R/param.old.R | 3 lessR-4.5/lessR/R/piechart.plotly.R |only lessR-4.5/lessR/R/plt.bck.R | 6 lessR-4.5/lessR/R/plt.bins.R | 4 lessR-4.5/lessR/R/plt.bubble.R | 6 lessR-4.5/lessR/R/plt.colors.R | 5 lessR-4.5/lessR/R/plt.contour.R | 169 - lessR-4.5/lessR/R/plt.fit.R | 6 lessR-4.5/lessR/R/plt.forecast.R | 24 lessR-4.5/lessR/R/plt.lattice.R | 27 lessR-4.5/lessR/R/plt.main.R | 399 ++-- lessR-4.5/lessR/R/plt.plotly.R |only lessR-4.5/lessR/R/plt.sym.legend.R | 6 lessR-4.5/lessR/R/plt.txt.R | 143 - lessR-4.5/lessR/R/prob_znorm.R | 29 lessR-4.5/lessR/R/radar.plotly.R |only lessR-4.5/lessR/R/reg.1ancova.R | 7 lessR-4.5/lessR/R/reg.3dnResidual.R | 4 lessR-4.5/lessR/R/savePlotly.R |only lessR-4.5/lessR/R/simCImean.R | 31 lessR-4.5/lessR/R/simCLT.R | 65 lessR-4.5/lessR/R/simFlips.R | 26 lessR-4.5/lessR/R/simMeans.R | 29 lessR-4.5/lessR/R/ss.factor.R | 61 lessR-4.5/lessR/R/ss.pivot.R |only lessR-4.5/lessR/R/ss.real.R | 5 lessR-4.5/lessR/R/stats.R |only lessR-4.5/lessR/R/style.R | 22 lessR-4.5/lessR/R/tt.1group.R | 3 lessR-4.5/lessR/R/tt.2graph.R | 11 lessR-4.5/lessR/R/tt.2group.R | 5 lessR-4.5/lessR/R/ttest.R | 3 lessR-4.5/lessR/R/zzz.R | 595 ++++-- lessR-4.5/lessR/R/zzz_plotly.R |only lessR-4.5/lessR/build/vignette.rds |binary lessR-4.5/lessR/inst/CITATION | 43 lessR-4.5/lessR/inst/doc/intro.R | 19 lessR-4.5/lessR/inst/doc/intro.Rmd | 39 lessR-4.5/lessR/inst/doc/intro.html | 1723 ++++++++++--------- lessR-4.5/lessR/inst/shiny_apps/BarChart/app.R | 605 ++++-- lessR-4.5/lessR/inst/shiny_apps/Histogram/app.R | 313 +-- lessR-4.5/lessR/inst/shiny_apps/ScatterPlot/app.R | 359 ++- lessR-4.5/lessR/man/ANOVA.Rd | 3 lessR-4.5/lessR/man/Chart.Rd |only lessR-4.5/lessR/man/Correlation.Rd | 30 lessR-4.5/lessR/man/Flows.Rd |only lessR-4.5/lessR/man/Logit.Rd | 14 lessR-4.5/lessR/man/Read.Rd | 68 lessR-4.5/lessR/man/Regression.Rd | 25 lessR-4.5/lessR/man/X.Rd |only lessR-4.5/lessR/man/XY.Rd |only lessR-4.5/lessR/man/getColors.Rd | 12 lessR-4.5/lessR/man/interact.Rd | 2 lessR-4.5/lessR/man/savePlotly.Rd |only lessR-4.5/lessR/man/simCLT.Rd | 6 lessR-4.5/lessR/man/style.Rd | 22 lessR-4.5/lessR/vignettes/intro.Rmd | 39 140 files changed, 3536 insertions(+), 2567 deletions(-)
Title: Accelerated Oblique Random Forests
Description: Fit, interpret, and compute predictions with oblique random
forests. Includes support for partial dependence, variable importance,
passing customized functions for variable importance and identification
of linear combinations of features. Methods for the oblique random
survival forest are described in Jaeger et al., (2023)
<DOI:10.1080/10618600.2023.2231048>.
Author: Byron Jaeger [aut, cre] ,
Nicholas Pajewski [ctb],
Sawyer Welden [ctb],
Christopher Jackson [rev],
Marvin Wright [rev],
Lukas Burk [rev]
Maintainer: Byron Jaeger <byron.jaeger@gmail.com>
Diff between aorsf versions 0.1.5 dated 2024-05-29 and 0.1.6 dated 2025-12-11
DESCRIPTION | 15 LICENSE | 4 MD5 | 124 +-- NEWS.md | 274 ++++--- R/bibentries.R | 252 +++---- R/check.R | 47 + R/coerce_nans.R | 4 R/collapse_misc.R | 124 +-- R/data-pbc_orsf.R | 86 +- R/fctr.R | 348 +++++----- R/orsf.R | 1000 ++++++++++++++-------------- R/orsf_R6.R | 105 ++- R/orsf_control.R | 1113 +++++++++++++++----------------- R/orsf_data_prep.R | 111 +-- R/orsf_print.R | 86 +- R/orsf_vi.R | 2 R/orsf_vs.R | 20 R/prep_x.R | 4 R/ref_code.R | 270 +++---- R/roxy.R | 374 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 150 ++-- inst/doc/aorsf.R | 26 inst/doc/aorsf.Rmd | 316 ++++----- inst/doc/aorsf.html | 33 inst/doc/fast.html | 11 inst/doc/oobag.html | 57 + inst/doc/pd.R | 14 inst/doc/pd.Rmd | 1108 +++++++++++++++---------------- inst/doc/pd.html | 11 man/orsf.Rd | 50 - man/orsf_control.Rd | 28 man/orsf_control_cph.Rd | 4 man/orsf_control_custom.Rd | 4 man/orsf_control_fast.Rd | 4 man/orsf_control_net.Rd | 4 man/orsf_ice_oob.Rd | 56 - man/orsf_pd_oob.Rd | 107 ++- man/orsf_scale_cph.Rd | 112 +-- man/orsf_vs.Rd | 9 man/predict.ObliqueForest.Rd | 10 man/roxygen/meta.R | 8 src/TreeClassification.cpp | 3 tests/testthat/_snaps/verbosity.md | 66 - tests/testthat/test-compute-gini.R | 8 tests/testthat/test-fctr.R | 26 tests/testthat/test-find_cutpoints.R | 190 ++--- tests/testthat/test-find_rows_inbag.R | 56 - tests/testthat/test-impute_meanmode.R | 374 +++++----- tests/testthat/test-is_col_splittable.R | 124 +-- tests/testthat/test-orsf.R | 8 tests/testthat/test-orsf_pd.R | 632 +++++++++--------- tests/testthat/test-orsf_print.R | 16 tests/testthat/test-orsf_scale_x.R | 116 +-- tests/testthat/test-orsf_train.R | 74 +- tests/testthat/test-orsf_vi.R | 1021 ++++++++++++++--------------- tests/testthat/test-orsf_vs.R | 28 tests/testthat/test-orsf_weights.R | 130 +-- tests/testthat/test-ref_code.R | 32 tests/testthat/test-sprout_node.R | 90 +- vignettes/aorsf.Rmd | 316 ++++----- vignettes/pd.Rmd | 1108 +++++++++++++++---------------- 63 files changed, 5583 insertions(+), 5320 deletions(-)
More information about impermanentlosscalc at CRAN
Permanent link
Title: Cox Models by Likelihood Based Boosting for a Single Survival
Endpoint or Competing Risks
Description: Provides routines for fitting Cox models by likelihood based
boosting for single event survival data with right censoring or in the
presence of competing risks. The methodology is described in Binder
and Schumacher (2008) <doi:10.1186/1471-2105-9-14> and Binder et al.
(2009) <doi:10.1093/bioinformatics/btp088>.
Author: John Zobolas [cre, aut] ,
Harald Binder [aut]
Maintainer: John Zobolas <bblodfon@gmail.com>
This is a re-admission after prior archival of version 1.4 dated 2013-05-10
Diff between CoxBoost versions 1.4 dated 2013-05-10 and 1.5.1 dated 2025-12-11
CoxBoost-1.4/CoxBoost/R/optimStepSizeFactor.R |only CoxBoost-1.4/CoxBoost/changeLog |only CoxBoost-1.4/CoxBoost/man/optimStepSizeFactor.Rd |only CoxBoost-1.5.1/CoxBoost/DESCRIPTION | 39 CoxBoost-1.5.1/CoxBoost/LICENSE |only CoxBoost-1.5.1/CoxBoost/MD5 | 50 CoxBoost-1.5.1/CoxBoost/NAMESPACE | 39 CoxBoost-1.5.1/CoxBoost/NEWS.md |only CoxBoost-1.5.1/CoxBoost/R/CoxBoost.R | 2144 +++++++++++++++----- CoxBoost-1.5.1/CoxBoost/R/estimPVal.R | 105 CoxBoost-1.5.1/CoxBoost/R/iCoxBoost.R | 379 +++ CoxBoost-1.5.1/CoxBoost/R/resample.CoxBoost.R |only CoxBoost-1.5.1/CoxBoost/R/zzz.R |only CoxBoost-1.5.1/CoxBoost/README.md |only CoxBoost-1.5.1/CoxBoost/build |only CoxBoost-1.5.1/CoxBoost/inst |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost-package.Rd |only CoxBoost-1.5.1/CoxBoost/man/CoxBoost.Rd | 285 ++ CoxBoost-1.5.1/CoxBoost/man/coef.CoxBoost.Rd | 26 CoxBoost-1.5.1/CoxBoost/man/cv.CoxBoost.Rd | 150 + CoxBoost-1.5.1/CoxBoost/man/cvcb.control.Rd | 70 CoxBoost-1.5.1/CoxBoost/man/estimPVal.Rd | 101 CoxBoost-1.5.1/CoxBoost/man/figures |only CoxBoost-1.5.1/CoxBoost/man/iCoxBoost.Rd | 233 +- CoxBoost-1.5.1/CoxBoost/man/optimCoxBoostPenalty.Rd | 102 CoxBoost-1.5.1/CoxBoost/man/plot.CoxBoost.Rd | 32 CoxBoost-1.5.1/CoxBoost/man/predict.CoxBoost.Rd | 86 CoxBoost-1.5.1/CoxBoost/man/predict.iCoxBoost.Rd | 67 CoxBoost-1.5.1/CoxBoost/man/print.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/resample.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/man/stabtrajec.Rd |only CoxBoost-1.5.1/CoxBoost/man/summary.CoxBoost.Rd |only CoxBoost-1.5.1/CoxBoost/src/find_best.c | 229 -- CoxBoost-1.5.1/CoxBoost/src/init.c |only 34 files changed, 3137 insertions(+), 1000 deletions(-)
Title: Download and Process Oklahoma Mesonet Data
Description: A collection of functions to download and process weather data from
the Oklahoma Mesonet <https://mesonet.org>. Functions are available for downloading station metadata,
downloading Mesonet time series (MTS) files, importing MTS files into R, and
converting soil temperature change measurements into soil matric potential and
volumetric soil moisture.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between mesonet versions 0.0.1 dated 2025-07-28 and 0.0.2 dated 2025-12-11
DESCRIPTION | 8 ++-- MD5 | 32 ++++++++-------- NEWS.md | 8 ++++ R/mnet_concatenate.R | 3 + R/mnet_download_mts.R | 12 +++++- R/mnet_requisition_list.R | 4 +- R/mnet_retrieve.R | 4 +- R/mnet_site_info.R | 7 ++- R/mnet_summarize.R | 11 ++++- R/mnet_test_cache.R | 56 ++++++++++++++-------------- inst/tinytest/test_01_mnet_site_info.R | 2 - inst/tinytest/test_05_mnet_concatenate.R | 61 +++++++++++++++---------------- man/mnet_concatenate.Rd | 3 + man/mnet_download_mts.Rd | 6 ++- man/mnet_requisition_list.Rd | 2 - man/mnet_retrieve.Rd | 4 +- man/mnet_summarize.Rd | 4 +- 17 files changed, 133 insertions(+), 94 deletions(-)
Title: Custom Visualizations & Functions for Streamlined Analyses of
Single Cell Sequencing
Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
Author: Samuel Marsh [aut, cre] ,
Ming Tang [ctb],
Velina Kozareva [ctb],
Lucas Graybuck [ctb],
Zoe Clarke [ctb]
Maintainer: Samuel Marsh <sccustomize@gmail.com>
Diff between scCustomize versions 3.2.3 dated 2025-12-09 and 3.2.4 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 2 +- R/Utilities.R | 15 ++++++++------- 4 files changed, 16 insertions(+), 15 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] ,
Francois Guilhaumon [aut] ,
Kevin Cazelles [rev]
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 2.0.0 dated 2025-03-03 and 2.1.0 dated 2025-12-11
sars-2.0.0/sars/inst/_pkgdown.yml |only sars-2.0.0/sars/tests/testthat/Rplots.pdf |only sars-2.1.0/sars/DESCRIPTION | 22 sars-2.1.0/sars/MD5 | 97 +-- sars-2.1.0/sars/NEWS.md | 7 sars-2.1.0/sars/R/class_plot.R | 233 +++++++-- sars-2.1.0/sars/R/coleman.R | 2 sars-2.1.0/sars/R/gdm.R | 2 sars-2.1.0/sars/R/mod_linear_power.R | 2 sars-2.1.0/sars/R/sar_asymp.R | 2 sars-2.1.0/sars/R/sar_average.R | 13 sars-2.1.0/sars/R/sar_betap.R | 2 sars-2.1.0/sars/R/sar_chapman.R | 2 sars-2.1.0/sars/R/sar_countryside.R | 7 sars-2.1.0/sars/R/sar_epm1.R | 2 sars-2.1.0/sars/R/sar_epm2.R | 2 sars-2.1.0/sars/R/sar_gompertz.R | 2 sars-2.1.0/sars/R/sar_habitat.R | 4 sars-2.1.0/sars/R/sar_heleg.R | 2 sars-2.1.0/sars/R/sar_koba.R | 2 sars-2.1.0/sars/R/sar_loga.R | 2 sars-2.1.0/sars/R/sar_logistic.R | 2 sars-2.1.0/sars/R/sar_mmf.R | 2 sars-2.1.0/sars/R/sar_monod.R | 2 sars-2.1.0/sars/R/sar_negexpo.R | 2 sars-2.1.0/sars/R/sar_p1.R | 2 sars-2.1.0/sars/R/sar_p2.R | 2 sars-2.1.0/sars/R/sar_power.R | 2 sars-2.1.0/sars/R/sar_powerR.R | 2 sars-2.1.0/sars/R/sar_ratio.R | 2 sars-2.1.0/sars/R/sar_threshold.R | 2 sars-2.1.0/sars/R/sar_weibull3.R | 2 sars-2.1.0/sars/R/sar_weibull4.R | 2 sars-2.1.0/sars/README.md | 58 +- sars-2.1.0/sars/inst/REFERENCES.bib | 36 + sars-2.1.0/sars/inst/doc/sars-r-package.R | 68 ++ sars-2.1.0/sars/inst/doc/sars-r-package.Rmd | 127 ++++ sars-2.1.0/sars/inst/doc/sars-r-package.html | 385 +++++++++++++-- sars-2.1.0/sars/inst/model_factory.R | 5 sars-2.1.0/sars/man/countryside_extrap.Rd | 2 sars-2.1.0/sars/man/figures/README-unnamed-chunk-5-1.png |binary sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-1.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-2.png |only sars-2.1.0/sars/man/figures/README-unnamed-chunk-7-3.png |only sars-2.1.0/sars/man/plot.habitat.Rd | 73 ++ sars-2.1.0/sars/man/sar_countryside.Rd | 3 sars-2.1.0/sars/man/sar_habitat.Rd | 2 sars-2.1.0/sars/tests/testthat/test_countryside.R | 29 + sars-2.1.0/sars/tests/testthat/test_multi.R | 7 sars-2.1.0/sars/tests/testthat/test_power.R | 3 sars-2.1.0/sars/vignettes/REFERENCES.bib | 47 + sars-2.1.0/sars/vignettes/sars-r-package.Rmd | 127 ++++ 52 files changed, 1194 insertions(+), 209 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.8.2 dated 2025-11-10 and 0.9.0 dated 2025-12-11
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- R/boxviolinplot.R | 12 +++++++++--- R/densityplot.R | 2 +- R/dimplot.R | 18 +++++++++--------- R/heatmap.R | 8 +++++++- R/network.R | 5 +++-- R/roccurve.R | 3 ++- R/theming.R | 9 +++++---- R/velocityplot.R | 4 ++-- man/Heatmap.Rd | 3 ++- man/HeatmapAtomic.Rd | 3 ++- man/ROCCurve.Rd | 3 ++- man/theme_this.Rd | 3 ++- 14 files changed, 62 insertions(+), 43 deletions(-)
Title: Extract Event Statistics in Hydrologic Time Series
Description: Events from individual hydrologic time series are extracted, and events
are matched across multiple time series. The package has been applied in studies
such as Wasko and Guo (2022) <doi:10.1002/hyp.14563> and Mohammadpour Khoie,
Guo and Wasko (2025) <doi:10.1016/j.envsoft.2025.106521>.
Author: Conrad Wasko [aut, cre],
Danlu Guo [aut],
Mohammad Masoud Mohammadpour Khoie [ctb]
Maintainer: Conrad Wasko <conrad.wasko@gmail.com>
Diff between hydroEvents versions 0.12.0 dated 2025-02-12 and 0.13.0 dated 2025-12-11
DESCRIPTION | 24 +- MD5 | 26 +- NAMESPACE | 39 +-- NEWS.md | 16 - R/calcREIC.R |only R/eventRVEIM.R |only R/plotEvents.R | 13 - R/postCorrection.R |only README.md | 534 ++++++++++++++++++++++++++++---------------------- data/hourlyQ.rda |only man/calcREIC.Rd |only man/eventBaseflow.Rd | 95 ++++---- man/eventMaxima.Rd | 121 +++++------ man/eventMinima.Rd | 121 +++++------ man/eventPOT.Rd | 109 +++++----- man/eventRVEIM.Rd |only man/hourlyQ.Rd |only man/postCorrection.Rd |only 18 files changed, 595 insertions(+), 503 deletions(-)
Title: Calculate Model-Based Metrics of Proportionality on Count-Based
Compositional Data
Description: Calculates metrics of proportionality using the logit-normal multinomial model. It can also provide empirical and plugin estimates of these metrics.
Author: Kevin McGregor [aut, cre, cph],
Nneka Okaeme [aut]
Maintainer: Kevin McGregor <kevin.mcgregor@umanitoba.ca>
Diff between countprop versions 1.0.1 dated 2023-08-18 and 1.1.1 dated 2025-12-11
DESCRIPTION | 12 +-- MD5 | 33 ++++----- NAMESPACE | 2 NEWS.md | 17 ++++ R/mle.R | 79 ++++++++++++++++------ R/proportionality.R | 155 ++++++++++++++++++++++++++------------------ README.md | 12 +++ build/vignette.rds |binary inst/doc/countprop.R | 2 inst/doc/countprop.pdf |binary man/convertSigma.Rd |only man/ebicPlot.Rd | 2 man/logLik.Rd | 6 + man/logitNormalVariation.Rd | 9 +- man/mleLR.Rd | 6 + man/mlePath.Rd | 5 + man/naiveVariation.Rd | 6 + man/pluginVariation.Rd | 2 18 files changed, 232 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-06 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-27 0.1.1
2024-06-18 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-28 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-01 2.5.0
2024-02-15 2.3.0
2023-04-16 2.2.1
2022-06-23 2.1.0
2022-03-06 2.0.3
2021-12-08 2.0.2
2021-06-16 1.0.8
2021-06-14 1.0.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-12-10 0.4.3
2025-12-02 0.4.2
2023-08-21 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-21 1.6.6
2023-12-17 1.6.1
2023-09-11 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-09-12 0.4.2
2023-11-22 0.4
2023-10-05 0.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-16 0.1.3
2023-10-09 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-10-01 1.6.8
2024-10-11 1.6.7
2024-05-15 1.6.6
2023-10-16 1.6.3
2023-09-10 1.6.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-03-10 1.6.7
2024-05-19 1.6.6
2023-09-23 1.6.1
2023-09-11 1.6.0
Title: Read the Swiss Register of Plant Protection Products
Description: Generate data objects from XML versions of the Swiss
Register of Plant Protection Products. An online version of the
register can be accessed at <https://www.psm.admin.ch/de/produkte>. There is no
guarantee of correspondence of the data read in using this package with that
online version, or with the original registration documents. Also, the
Federal Food Safety and Veterinary Office, coordinating the authorisation of
plant protection products in Switzerland, does not answer requests regarding
this package.
Author: Daniel Baumgartner [ctb] ,
Marcel Mathis [rev, ctb],
Romualdus Kasteel [rev] ,
Elisabeth Lutz [ctb],
Johannes Ranke [aut, cre] ,
Agroscope [cph]
Maintainer: Johannes Ranke <johannes.ranke@agroscope.admin.ch>
Diff between srppp versions 1.1.0 dated 2025-07-17 and 2.0.0 dated 2025-12-11
DESCRIPTION | 12 MD5 | 37 NAMESPACE | 1 NEWS.md | 9 R/resolve_cultures.R | 8 R/srppp-package.R | 1 R/srppp-xml.R | 129 README.md | 3 build/vignette.rds |binary inst/doc/srppp.html | 3314 +++++----- inst/doc/srppp_products_with_MO.html | 755 +- inst/testdata/Daten_Pflanzenschutzmittelverzeichnis_2024-12-16.zip |binary inst/testdata/PublicationData_2025_12_01.xml.xz |only man/resolve_cultures.Rd | 2 man/srppp_xml_get.Rd | 2 tests/testthat/setup.R | 13 tests/testthat/test-alternative_products.R | 23 tests/testthat/test-resolve_cultures.R | 74 tests/testthat/test-srppp_xml.R | 33 tests/testthat/test-use_rates.R | 56 20 files changed, 2354 insertions(+), 2118 deletions(-)
Title: Visualization Tool for Numerical Data on Human/Mouse Organs and
Organelles
Description: A tool for visualizing numerical data (e.g., gene expression, protein abundance) on predefined anatomical maps of human/mouse organs and subcellular organelles. It supports customization of color schemes, filtering by organ systems (for organisms) or organelle types, and generation of optional bar charts for quantitative comparison. The package integrates coordinate data for organs and organelles to plot anatomical/subcellular contours, mapping data values to specific structures for intuitive visualization of biological data distribution.The underlying method was described in the preprint by Zhou et al. (2022) <doi:10.1101/2022.09.07.506938>.
Author: Qirui Shen [aut, cre]
Maintainer: Qirui Shen <shenqr@i.smu.edu.cn>
Diff between OrgHeatmap versions 0.3.1 dated 2025-11-26 and 0.3.2 dated 2025-12-11
DESCRIPTION | 14 ++--- MD5 | 14 ++--- NAMESPACE | 106 ++++++++++++++++++++++----------------------- NEWS.md | 7 +- R/OrgHeatmap.R | 6 +- README.md | 2 data/mouse_organ_coord.rda |binary man/OrgHeatmap.Rd | 4 - 8 files changed, 78 insertions(+), 75 deletions(-)
Title: Curated Datasets and Tools for Epidemiological Data Analysis
Description: Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, 'DIVINE' makes the process more efficient, transparent, and reproducible.
Author: Natalia Pallares [aut, cre],
Joao Carmezim [aut],
Pau Satorra [aut],
Lucia Blanc [aut],
Cristian Tebe [aut]
Maintainer: Natalia Pallares <npallares@igtp.cat>
Diff between DIVINE versions 0.1.0 dated 2025-11-11 and 0.1.1 dated 2025-12-11
DESCRIPTION | 6 MD5 | 56 +- NEWS.md | 6 R/end_followup.R | 4 R/export_data.R | 8 R/icu.R | 4 R/multi_plot.R | 773 ++++++++++++++++++++------------------- build/vignette.rds |binary data/analytics.rda |binary data/comorbidities.rda |binary data/complications.rda |binary data/concomitant_medication.rda |binary data/demographic.rda |binary data/end_followup.rda |binary data/icu.rda |binary data/inhosp_antibiotics.rda |binary data/inhosp_antivirals.rda |binary data/inhosp_other_treatments.rda |binary data/scores.rda |binary data/symptoms.rda |binary data/vaccine.rda |binary data/vital_signs.rda |binary inst/doc/DIVINE.R | 16 inst/doc/DIVINE.Rmd | 668 ++++++++++++++++----------------- inst/doc/DIVINE.html | 30 - man/end_followup.Rd | 4 man/icu.Rd | 4 man/multi_plot.Rd | 63 +-- vignettes/DIVINE.Rmd | 668 ++++++++++++++++----------------- 29 files changed, 1166 insertions(+), 1144 deletions(-)
Title: 'vcd' Extensions and Additions
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre] ,
Heather Turner [ctb],
David Meyer [ctb],
Achim Zeileis [ctb] ,
Duncan Murdoch [ctb],
David Firth [ctb],
Matt Kumar [ctb],
Shuguang Sun [ctb],
Daniel Sabanes Bove [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between vcdExtra versions 0.8-6 dated 2025-07-24 and 0.8.7 dated 2025-12-11
vcdExtra-0.8-6/vcdExtra/R/vcdExtra-deprecated.R |only vcdExtra-0.8-6/vcdExtra/build/partial.rdb |only vcdExtra-0.8-6/vcdExtra/man/figures |only vcdExtra-0.8-6/vcdExtra/man/vcdExtra-deprecated.Rd |only vcdExtra-0.8.7/vcdExtra/DESCRIPTION | 27 vcdExtra-0.8.7/vcdExtra/MD5 | 241 +++--- vcdExtra-0.8.7/vcdExtra/NAMESPACE | 246 ++---- vcdExtra-0.8.7/vcdExtra/NEWS.md | 13 vcdExtra-0.8.7/vcdExtra/R/CMHtest.R | 708 ++++++++++++------ vcdExtra-0.8.7/vcdExtra/R/CrabSatellites.R |only vcdExtra-0.8.7/vcdExtra/R/Crossings.R | 76 + vcdExtra-0.8.7/vcdExtra/R/GKgamma.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/HLtest.R | 90 ++ vcdExtra-0.8.7/vcdExtra/R/Kway.R | 93 ++ vcdExtra-0.8.7/vcdExtra/R/LRstats.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/Summarise.R | 89 +- vcdExtra-0.8.7/vcdExtra/R/blogits.R | 54 + vcdExtra-0.8.7/vcdExtra/R/collapse.table.R | 94 ++ vcdExtra-0.8.7/vcdExtra/R/cutfac.R | 73 + vcdExtra-0.8.7/vcdExtra/R/data.R |only vcdExtra-0.8.7/vcdExtra/R/datasets.R | 48 + vcdExtra-0.8.7/vcdExtra/R/expand.dft.R | 48 + vcdExtra-0.8.7/vcdExtra/R/glmlist.R | 98 ++ vcdExtra-0.8.7/vcdExtra/R/logLik.loglm.R | 63 + vcdExtra-0.8.7/vcdExtra/R/loglin-utilities.R | 102 ++ vcdExtra-0.8.7/vcdExtra/R/logseries.R | 185 +++- vcdExtra-0.8.7/vcdExtra/R/mcaplot.R | 96 +- vcdExtra-0.8.7/vcdExtra/R/modFit.R | 41 + vcdExtra-0.8.7/vcdExtra/R/mosaic.glm.R | 219 +++++ vcdExtra-0.8.7/vcdExtra/R/mosaic.glmlist.R | 149 +++ vcdExtra-0.8.7/vcdExtra/R/mosaic3d.R | 184 +++- vcdExtra-0.8.7/vcdExtra/R/print.Kappa.R | 36 vcdExtra-0.8.7/vcdExtra/R/seq_loglm.R | 88 +- vcdExtra-0.8.7/vcdExtra/R/seq_mosaic.R | 80 +- vcdExtra-0.8.7/vcdExtra/R/split3d.R | 78 + vcdExtra-0.8.7/vcdExtra/R/update.xtabs.R | 39 vcdExtra-0.8.7/vcdExtra/R/vcdExtra-package.R |only vcdExtra-0.8.7/vcdExtra/R/zero.test.R | 64 + vcdExtra-0.8.7/vcdExtra/data/CrabSatellites.rda |only vcdExtra-0.8.7/vcdExtra/inst/doc/a1-creating.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a2-tests.html | 10 vcdExtra-0.8.7/vcdExtra/inst/doc/a3-loglinear.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a4-mosaics.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a5-demo-housing.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a6-mobility.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.Rmd | 1 vcdExtra-0.8.7/vcdExtra/inst/doc/a7-continuous.html | 4 vcdExtra-0.8.7/vcdExtra/inst/doc/datasets.html | 6 vcdExtra-0.8.7/vcdExtra/inst/doc/tidyCats.html | 4 vcdExtra-0.8.7/vcdExtra/man/Abortion.Rd | 78 - vcdExtra-0.8.7/vcdExtra/man/Accident.Rd | 99 +- vcdExtra-0.8.7/vcdExtra/man/AirCrash.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Alligator.Rd | 61 - vcdExtra-0.8.7/vcdExtra/man/Asbestos.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/Bartlett.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/Burt.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/CMHtest.Rd | 309 +++---- vcdExtra-0.8.7/vcdExtra/man/Caesar.Rd | 82 -- vcdExtra-0.8.7/vcdExtra/man/Cancer.Rd | 58 - vcdExtra-0.8.7/vcdExtra/man/Cormorants.Rd | 91 +- vcdExtra-0.8.7/vcdExtra/man/CrabSatellites.Rd |only vcdExtra-0.8.7/vcdExtra/man/Crossings.Rd | 79 -- vcdExtra-0.8.7/vcdExtra/man/CyclingDeaths.Rd | 54 - vcdExtra-0.8.7/vcdExtra/man/DaytonSurvey.Rd | 97 +- vcdExtra-0.8.7/vcdExtra/man/Depends.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Detergent.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Donner.Rd | 146 +-- vcdExtra-0.8.7/vcdExtra/man/Draft1970.Rd | 83 +- vcdExtra-0.8.7/vcdExtra/man/Draft1970table.Rd | 81 -- vcdExtra-0.8.7/vcdExtra/man/Dyke.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Fungicide.Rd | 71 - vcdExtra-0.8.7/vcdExtra/man/GKgamma.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/GSS.Rd | 46 - vcdExtra-0.8.7/vcdExtra/man/Geissler.Rd | 85 +- vcdExtra-0.8.7/vcdExtra/man/Gilby.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Glass.Rd | 95 +- vcdExtra-0.8.7/vcdExtra/man/HLtest.Rd | 123 +-- vcdExtra-0.8.7/vcdExtra/man/HairEyePlace.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/Hauser79.Rd | 117 +- vcdExtra-0.8.7/vcdExtra/man/Heart.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Heckman.Rd | 90 +- vcdExtra-0.8.7/vcdExtra/man/HospVisits.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/HouseTasks.Rd | 52 - vcdExtra-0.8.7/vcdExtra/man/Hoyt.Rd | 104 +- vcdExtra-0.8.7/vcdExtra/man/ICU.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/JobSat.Rd | 44 - vcdExtra-0.8.7/vcdExtra/man/Kway.Rd | 148 +-- vcdExtra-0.8.7/vcdExtra/man/LRstats.Rd | 114 +- vcdExtra-0.8.7/vcdExtra/man/Mammograms.Rd | 43 - vcdExtra-0.8.7/vcdExtra/man/Mental.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/Mice.Rd | 62 - vcdExtra-0.8.7/vcdExtra/man/Mobility.Rd | 59 - vcdExtra-0.8.7/vcdExtra/man/PhdPubs.Rd | 69 - vcdExtra-0.8.7/vcdExtra/man/ShakeWords.Rd | 68 - vcdExtra-0.8.7/vcdExtra/man/Summarise.Rd | 105 +- vcdExtra-0.8.7/vcdExtra/man/TV.Rd | 88 +- vcdExtra-0.8.7/vcdExtra/man/Titanicp.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Toxaemia.Rd | 76 - vcdExtra-0.8.7/vcdExtra/man/Vietnam.Rd | 70 - vcdExtra-0.8.7/vcdExtra/man/Vote1980.Rd | 75 - vcdExtra-0.8.7/vcdExtra/man/WorkerSat.Rd | 45 - vcdExtra-0.8.7/vcdExtra/man/Yamaguchi87.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/blogits.Rd | 102 +- vcdExtra-0.8.7/vcdExtra/man/collapse.table.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/cutfac.Rd | 120 +-- vcdExtra-0.8.7/vcdExtra/man/datasets.Rd | 100 +- vcdExtra-0.8.7/vcdExtra/man/expand.dft.Rd | 82 +- vcdExtra-0.8.7/vcdExtra/man/glmlist.Rd | 113 +- vcdExtra-0.8.7/vcdExtra/man/logLik.loglm.Rd | 96 +- vcdExtra-0.8.7/vcdExtra/man/loglin-utilities.Rd | 296 ++----- vcdExtra-0.8.7/vcdExtra/man/logseries.Rd | 127 +-- vcdExtra-0.8.7/vcdExtra/man/mcaplot.Rd | 125 +-- vcdExtra-0.8.7/vcdExtra/man/modFit.Rd | 64 - vcdExtra-0.8.7/vcdExtra/man/mosaic.glm.Rd | 276 +++---- vcdExtra-0.8.7/vcdExtra/man/mosaic.glmlist.Rd | 214 ++--- vcdExtra-0.8.7/vcdExtra/man/mosaic3d.Rd | 281 +++---- vcdExtra-0.8.7/vcdExtra/man/print.Kappa.Rd | 65 - vcdExtra-0.8.7/vcdExtra/man/seq_loglm.Rd | 156 +-- vcdExtra-0.8.7/vcdExtra/man/seq_mosaic.Rd | 122 +-- vcdExtra-0.8.7/vcdExtra/man/split3d.Rd | 115 +- vcdExtra-0.8.7/vcdExtra/man/update.xtabs.Rd | 66 - vcdExtra-0.8.7/vcdExtra/man/vcdExtra-package.Rd | 189 ++-- vcdExtra-0.8.7/vcdExtra/man/zero.test.Rd | 98 +- vcdExtra-0.8.7/vcdExtra/tests |only vcdExtra-0.8.7/vcdExtra/vignettes/a7-continuous.Rmd | 1 125 files changed, 6175 insertions(+), 4683 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 1.1.0 dated 2025-11-06 and 1.2.0 dated 2025-12-11
DESCRIPTION | 12 ++- MD5 | 19 +++-- NAMESPACE | 5 + NEWS.md | 6 + R/aaa.R | 7 + R/mock_request.R |only R/request.R | 105 ++++++++++++++++++----------- R/response.R | 51 +++++++------- man/maybe_request.Rd |only man/mock_request.Rd |only man/random_key.Rd | 2 tests/testthat/_snaps/request_unclassed.md |only tests/testthat/test-request_unclassed.R |only 13 files changed, 133 insertions(+), 74 deletions(-)
Title: Efficient Implementation of Kendall's Correlation Coefficient
Computation
Description: The computational complexity of the implemented algorithm for
Kendall's correlation is O(n log(n)), which is faster than the base R
implementation with a computational complexity of O(n^2). For small vectors
(i.e., less than 100 observations), the time difference is negligible.
However, for larger vectors, the speed difference can be substantial and the
numerical difference is minimal. The references are
Knight (1966) <doi:10.2307/2282833>,
Abrevaya (1999) <doi:10.1016/S0165-1765(98)00255-9>,
Christensen (2005) <doi:10.1007/BF02736122> and
Emara (2024) <https://learningcpp.org/>.
This implementation is described in
Vargas Sepulveda (2025) <doi:10.1371/journal.pone.0326090>.
Author: Mauricio Vargas Sepulveda [aut, cre] ,
Loader Catherine [ctb] ),
Ross Ihaka [ctb] )
Maintainer: Mauricio Vargas Sepulveda <m.vargas.sepulveda@gmail.com>
Diff between kendallknight versions 1.0.0 dated 2025-08-31 and 1.0.1 dated 2025-12-11
kendallknight-1.0.0/kendallknight/R/cpp11.R |only kendallknight-1.0.0/kendallknight/build/vignette.rds |only kendallknight-1.0.0/kendallknight/data |only kendallknight-1.0.0/kendallknight/inst/doc |only kendallknight-1.0.0/kendallknight/man/arcade.Rd |only kendallknight-1.0.0/kendallknight/src/cpp11.cpp |only kendallknight-1.0.0/kendallknight/vignettes |only kendallknight-1.0.1/kendallknight/DESCRIPTION | 12 - kendallknight-1.0.1/kendallknight/MD5 | 30 +-- kendallknight-1.0.1/kendallknight/NEWS.md | 4 kendallknight-1.0.1/kendallknight/R/cpp4r.R |only kendallknight-1.0.1/kendallknight/R/kendallknight-package.R | 20 -- kendallknight-1.0.1/kendallknight/README.md | 30 ++- kendallknight-1.0.1/kendallknight/build/partial.rdb |binary kendallknight-1.0.1/kendallknight/inst/CITATION |only kendallknight-1.0.1/kendallknight/inst/WORDLIST | 2 kendallknight-1.0.1/kendallknight/man/figures/logo.svg | 81 ++-------- kendallknight-1.0.1/kendallknight/man/kendallknight-package.Rd | 2 kendallknight-1.0.1/kendallknight/src/cpp4r.cpp |only kendallknight-1.0.1/kendallknight/src/kendall_correlation.cpp | 8 20 files changed, 70 insertions(+), 119 deletions(-)
Title: Datastore for 'fiery' Web Servers
Description: Provides a persistent datastore for 'fiery' apps. The datastore is
build on top of the 'storr' package and can thus be based on a variety of
backends. The datastore contains both a global and session-scoped section.
Author: Thomas Lin Pedersen [aut, cre] ,
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between firesale versions 0.1.0 dated 2025-08-27 and 0.1.1 dated 2025-12-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/FireSale.R | 4 ++++ man/FireSale.Rd | 4 +++- man/firesale-package.Rd | 2 +- 6 files changed, 21 insertions(+), 11 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code, automated
reporting or use an easy to remember set of tidy functions for low
code exploratory data analysis.
Author: Roland Krasser [aut, cre]
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 1.3.6 dated 2025-10-02 and 1.4.0 dated 2025-12-11
DESCRIPTION | 8 +- MD5 | 82 ++++++++++++------------- NEWS.md | 6 + R/explain-xgboost.R | 130 ++++++++++++++++++++++++++++++++--------- R/explain.R | 25 ++++++- build/vignette.rds |binary inst/doc/abtest.html | 24 +++---- inst/doc/clean-drop.html | 6 - inst/doc/data.html | 6 - inst/doc/describe.html | 6 - inst/doc/explain.html | 52 ++++++++-------- inst/doc/explore-mtcars.html | 34 +++++----- inst/doc/explore-penguins.html | 14 ++-- inst/doc/explore-titanic.html | 24 +++---- inst/doc/explore.html | 58 +++++++++--------- inst/doc/predict.html | 10 +-- inst/doc/report-target.html | 12 +-- inst/doc/report-targetpct.html | 12 +-- inst/doc/report.html | 10 +-- inst/doc/tips-tricks.html | 16 ++--- man/check_vec_low_variance.Rd | 50 +++++++-------- man/create_data_abtest.Rd | 90 ++++++++++++++-------------- man/create_data_esoteric.Rd | 72 +++++++++++----------- man/create_notebook_explore.Rd | 2 man/cut_vec_num_avg.Rd | 38 +++++------ man/drop_obs_if.Rd | 46 +++++++------- man/drop_obs_with_na.Rd | 44 ++++++------- man/drop_var_by_names.Rd | 46 +++++++------- man/drop_var_low_variance.Rd | 46 +++++++------- man/drop_var_no_variance.Rd | 42 ++++++------- man/drop_var_not_numeric.Rd | 42 ++++++------- man/drop_var_with_na.Rd | 42 ++++++------- man/explain_forest.Rd | 2 man/explain_logreg.Rd | 2 man/explain_tree.Rd | 4 - man/explore_col.Rd | 106 ++++++++++++++++----------------- man/get_color.Rd | 72 +++++++++++----------- man/interact.Rd | 54 ++++++++--------- man/log_info_if.Rd | 38 +++++------ man/predict_target.Rd | 2 man/show_color.Rd | 42 ++++++------- man/use_data_wordle.Rd | 42 ++++++------- 42 files changed, 778 insertions(+), 681 deletions(-)
Title: Read bigWig and bigBed Files
Description: Read bigWig and bigBed files using "libBigWig"
<https://github.com/dpryan79/libBigWig>. Provides lightweight access
to the binary bigWig and bigBed formats developed by the UCSC Genome
Browser group.
Author: Jay Hesselberth [aut, cre],
RNA Bioscience Initiative [fnd, cph],
Devon Ryan [cph]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between cpp11bigwig versions 0.1.2 dated 2025-08-18 and 0.1.3 dated 2025-12-11
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/read.r | 49 +----- README.md | 8 - man/read_bigbed.Rd | 10 - src/cpp11bigwig.cpp | 333 ++++++++++++++++++++++++++++++--------------- tests/testthat/test-read.R | 33 ++++ 8 files changed, 293 insertions(+), 164 deletions(-)
Title: Statistical Methods for Phenology Analysis in Temperate Fruit
Trees
Description: The phenology of plants (i.e. the timing of their annual life
phases) depends on climatic cues. For temperate trees and many other plants,
spring phases, such as leaf emergence and flowering, have been found to result
from the effects of both cool (chilling) conditions and heat. Fruit tree
scientists (pomologists) have developed some metrics to quantify chilling
and heat (e.g. see Luedeling (2012) <doi:10.1016/j.scienta.2012.07.011>).
'chillR' contains functions for processing temperature records into
chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units
(Growing Degree Hours). Regarding chilling metrics, Chill Portions are often
considered the most promising, but they are difficult to calculate. This package
makes it easy. 'chillR' also contains procedures for conducting a PLS analysis
relating phenological dates (e.g. bloom dates) to either mean temperatures or
mean chill and heat accumulation rates, based on long-term weather and phenology
records (Lued [...truncated...]
Author: Eike Luedeling [aut, cre] ,
Lars Caspersen [aut] ,
Eduardo Fernandez [aut]
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between chillR versions 0.76 dated 2024-11-14 and 0.77 dated 2025-12-11
DESCRIPTION | 28 +- MD5 | 40 ++- NAMESPACE | 4 R/Kendall.R |only R/chillR-package.R | 10 R/download_baseline_cmip6_ecmwfr.R | 101 +++++++-- R/download_cmip6_ecmwfr.R | 150 +++++++------- R/extract_cmip6_data.R | 69 ++++-- R/plot_phenology_trends.R | 8 R/plot_scenarios.R | 8 R/print.Kendall.R |only R/summary.Kendall.R |only build/partial.rdb |only build/vignette.rds |binary inst/doc/PhenoFlex.html | 208 +++++++++---------- inst/doc/hourly_temperatures.html | 9 man/chillR-package.Rd | 32 ++- man/download_baseline_cmip6_ecmwfr.Rd | 214 ++++++++++---------- man/download_cmip6_ecmwfr.Rd | 360 +++++++++++++++++----------------- man/plot_phenology_trends.Rd | 8 man/plot_scenarios.Rd | 8 src/Kendall.f |only src/RcppExports.cpp | 10 src/init.c |only 24 files changed, 684 insertions(+), 583 deletions(-)