Title: Calculates Microbial Lag Duration (on the Population Level) from
Provided Growth Curve Data
Description: Microbial growth is often measured by growth curves i.e. a table of population sizes and times of measurements.
This package allows to use such growth curve data to determine the duration of "microbial lag phase" i.e. the time needed for microbes to restart divisions.
It implements the most commonly used methods to calculate the lag duration, these methods are discussed and described in Opalek et.al. 2022.
Citation: Smug, B. J., Opalek, M., Necki, M., & Wloch-Salamon, D. (2024). Microbial lag calculator: A shiny-based application and an R package for calculating the duration of microbial lag phase. Methods in Ecology and Evolution, 15, 301–307 <doi:10.1111/2041-210X.14269>.
Author: Bogna Smug [aut, cre]
Maintainer: Bogna Smug <bogna.smug@uj.edu.pl>
Diff between miLAG versions 1.0.4 dated 2024-10-05 and 1.0.5 dated 2025-01-17
DESCRIPTION | 10 MD5 | 80 - NAMESPACE | 40 R/globals.R | 24 R/milags_functions.R | 2340 +++++++++++++++---------------- README.md | 380 ++--- build/vignette.rds |binary inst/doc/calculating_lag.R | 76 - inst/doc/calculating_lag.html | 944 ++++++------ inst/doc/choosing_lag.R | 76 - inst/doc/choosing_lag.html | 948 ++++++------ inst/doc/getting_lag.R | 76 - inst/doc/getting_lag.html | 940 ++++++------ inst/doc/plotting_lag.R | 80 - inst/doc/plotting_lag.html | 866 +++++------ man/calc_baranyi_fit_lag.Rd | 70 man/calc_lag.Rd | 74 man/calc_lag_fit_to_baranyi_with_lag.Rd | 80 - man/calc_lag_fit_to_logistic_with_lag.Rd | 80 - man/calc_lagistic_fit_lag.Rd | 94 - man/choose_lag_fit_algorithm_baranyi.Rd | 74 man/choose_lag_fit_algorithm_logistic.Rd | 74 man/compare_algorithms.Rd | 42 man/cut_the_data.Rd | 44 man/fit_exp_lag.Rd | 52 man/fit_exp_lag_to_curve.Rd | 58 man/fit_max_infl_lag.Rd | 38 man/get_all_methods_lag.Rd | 78 - man/get_def_pars.Rd | 32 man/get_init_pars_baranyi.Rd | 70 man/get_init_pars_logistic.Rd | 76 - man/get_lag.Rd | 76 - man/get_n0.Rd | 46 man/get_theme.Rd | 36 man/lag_biomass_incr.Rd | 44 man/make_grwoth_curve_df.Rd | 42 man/plot_data.Rd | 38 man/plot_lag_fit.Rd | 42 man/smooth_data.Rd | 44 tests/testthat.R | 24 vignettes/example | 2 41 files changed, 4155 insertions(+), 4155 deletions(-)
Title: Relationship-Based Mixed-Effects Models
Description: Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the
'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between lme4breeding versions 1.0.40 dated 2024-10-16 and 1.0.50 dated 2025-01-17
lme4breeding-1.0.40/lme4breeding/R/spatial.R |only lme4breeding-1.0.40/lme4breeding/inst/doc/lmebreed.gxe.pdf |only lme4breeding-1.0.40/lme4breeding/inst/doc/lmebreed.qg.pdf |only lme4breeding-1.0.40/lme4breeding/man/spl2Dmats.Rd |only lme4breeding-1.0.40/lme4breeding/vignettes/lmebreed.gxe.html |only lme4breeding-1.0.40/lme4breeding/vignettes/lmebreed.qg.html |only lme4breeding-1.0.50/lme4breeding/ChangeLog | 2 lme4breeding-1.0.50/lme4breeding/DESCRIPTION | 8 +- lme4breeding-1.0.50/lme4breeding/MD5 | 31 ++++------ lme4breeding-1.0.50/lme4breeding/NAMESPACE | 4 - lme4breeding-1.0.50/lme4breeding/R/funs.R | 15 ++++ lme4breeding-1.0.50/lme4breeding/R/utils.R | 34 ++++++++++- lme4breeding-1.0.50/lme4breeding/build/vignette.rds |binary lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.gxe.Rmd | 2 lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.gxe.html |only lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.qg.Rmd | 2 lme4breeding-1.0.50/lme4breeding/inst/doc/lmebreed.qg.html |only lme4breeding-1.0.50/lme4breeding/man/fillData.Rd |only lme4breeding-1.0.50/lme4breeding/man/lmebreed.Rd | 2 lme4breeding-1.0.50/lme4breeding/vignettes/lmebreed.gxe.Rmd | 2 lme4breeding-1.0.50/lme4breeding/vignettes/lmebreed.qg.Rmd | 2 21 files changed, 73 insertions(+), 31 deletions(-)
Title: Utilities for Data Analysis in Agriculture
Description: Utilities designed to make the analysis of field trials easier and
more accessible for everyone working in plant breeding. It provides a simple
and intuitive interface for conducting single and multi-environmental trial
analysis, with minimal coding required. Whether you're a beginner or an
experienced user, 'agriutilities' will help you quickly and easily carry out
complex analyses with confidence. With built-in functions for fitting Linear
Mixed Models, 'agriutilities' is the ideal choice for anyone who wants to save
time and focus on interpreting their results.
Some of the functions require the R package 'asreml' for the 'ASReml' software,
this can be obtained upon purchase from 'VSN' international <https://vsni.co.uk/software/asreml-r/>.
Author: Johan Aparicio [aut, cre],
Alexia Bornhorst [aut],
The Alliance of Bioversity International and CIAT [cph]
Maintainer: Johan Aparicio <johanstevenapa@gmail.com>
Diff between agriutilities versions 1.2.0 dated 2024-01-20 and 1.2.1 dated 2025-01-17
DESCRIPTION | 12 MD5 | 66 + NAMESPACE | 3 R/SpATS.R | 90 ++ R/checkDesign.R | 10 R/extractRcov.R | 102 ++- R/fitSingle.R | 6 R/icREML.R |only R/lme4.R | 2 README.md | 117 +-- build/vignette.rds |binary inst/doc/how-to-start.R | 6 inst/doc/how-to-start.Rmd | 9 inst/doc/how-to-start.html | 200 +++--- inst/doc/repeated_measurements.R | 312 ++++++++- inst/doc/repeated_measurements.Rmd | 369 +++++++++-- inst/doc/repeated_measurements.html | 995 ++++++++++++++++++++++-------- man/extract_rcov.Rd | 45 - man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-10-2.png |binary man/figures/README-unnamed-chunk-11-1.png |only man/figures/README-unnamed-chunk-11-2.png |only man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary man/figures/logo.png |binary man/h_cullis_spt.Rd |only man/ic_reml_asr.Rd |only man/ic_reml_spt.Rd |only man/single_trial_analysis.Rd | 4 vignettes/how-to-start.Rmd | 9 vignettes/repeated_measurements.Rmd | 369 +++++++++-- 37 files changed, 2095 insertions(+), 631 deletions(-)
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Author: Abigail G. Keller [aut, cre],
Ryan P. Kelly [ctb],
Chitra M. Saraswati [rev],
Saras M. Windecker [rev]
Maintainer: Abigail G. Keller <agkeller@berkeley.edu>
Diff between eDNAjoint versions 0.2 dated 2024-10-08 and 0.3 dated 2025-01-17
eDNAjoint-0.2/eDNAjoint/R/detectionCalculate.R |only eDNAjoint-0.2/eDNAjoint/R/detectionPlot.R |only eDNAjoint-0.2/eDNAjoint/R/gobyData.R |only eDNAjoint-0.2/eDNAjoint/R/greencrabData.R |only eDNAjoint-0.2/eDNAjoint/R/jointModel.R |only eDNAjoint-0.2/eDNAjoint/R/jointSelect.R |only eDNAjoint-0.2/eDNAjoint/R/jointSummarize.R |only eDNAjoint-0.2/eDNAjoint/R/muCritical.R |only eDNAjoint-0.2/eDNAjoint/R/traditionalModel.R |only eDNAjoint-0.2/eDNAjoint/data/gobyData.rda |only eDNAjoint-0.2/eDNAjoint/data/greencrabData.rda |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_cov_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/joint_binary_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_catchability_pois.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_gamma.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_negbin.stan |only eDNAjoint-0.2/eDNAjoint/inst/stan/traditional_pois.stan |only eDNAjoint-0.2/eDNAjoint/man/detectionCalculate.Rd |only eDNAjoint-0.2/eDNAjoint/man/detectionPlot.Rd |only eDNAjoint-0.2/eDNAjoint/man/gobyData.Rd |only eDNAjoint-0.2/eDNAjoint/man/greencrabData.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointModel.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointSelect.Rd |only eDNAjoint-0.2/eDNAjoint/man/jointSummarize.Rd |only eDNAjoint-0.2/eDNAjoint/man/muCritical.Rd |only eDNAjoint-0.2/eDNAjoint/man/traditionalModel.Rd |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_cov_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_joint_binary_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_catchability_pois.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_gamma.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_gamma.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_negbin.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_negbin.h |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_pois.cc |only eDNAjoint-0.2/eDNAjoint/src/stanExports_traditional_pois.h |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-detectionCalculate.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-detectionPlot.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointModel.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointSelect.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-jointSummarize.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-muCritical.R |only eDNAjoint-0.2/eDNAjoint/tests/testthat/test-traditionalModel.R |only eDNAjoint-0.3/eDNAjoint/DESCRIPTION | 18 - eDNAjoint-0.3/eDNAjoint/MD5 | 155 +++------- eDNAjoint-0.3/eDNAjoint/NAMESPACE | 14 eDNAjoint-0.3/eDNAjoint/NEWS.md | 16 + eDNAjoint-0.3/eDNAjoint/R/detection_calculate.R |only eDNAjoint-0.3/eDNAjoint/R/detection_plot.R |only eDNAjoint-0.3/eDNAjoint/R/eDNAjoint-package.R | 23 - eDNAjoint-0.3/eDNAjoint/R/globals.R | 3 eDNAjoint-0.3/eDNAjoint/R/goby_data.R |only eDNAjoint-0.3/eDNAjoint/R/green_crab_data.R |only eDNAjoint-0.3/eDNAjoint/R/joint_model.R |only eDNAjoint-0.3/eDNAjoint/R/joint_select.R |only eDNAjoint-0.3/eDNAjoint/R/joint_summarize.R |only eDNAjoint-0.3/eDNAjoint/R/mu_critical.R |only eDNAjoint-0.3/eDNAjoint/R/srr-stats-standards.R | 10 eDNAjoint-0.3/eDNAjoint/R/stanmodels.R | 39 -- eDNAjoint-0.3/eDNAjoint/R/traditional_model.R |only eDNAjoint-0.3/eDNAjoint/R/utils-joint.R |only eDNAjoint-0.3/eDNAjoint/R/utils-traditional.R |only eDNAjoint-0.3/eDNAjoint/README.md | 45 +- eDNAjoint-0.3/eDNAjoint/build/partial.rdb |binary eDNAjoint-0.3/eDNAjoint/configure | 5 eDNAjoint-0.3/eDNAjoint/configure.win | 4 eDNAjoint-0.3/eDNAjoint/data/goby_data.rda |only eDNAjoint-0.3/eDNAjoint/data/green_crab_data.rda |only eDNAjoint-0.3/eDNAjoint/inst/README.Rmd | 35 +- eDNAjoint-0.3/eDNAjoint/inst/README.md | 152 ++++----- eDNAjoint-0.3/eDNAjoint/inst/stan/functions |only eDNAjoint-0.3/eDNAjoint/inst/stan/joint_continuous.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/joint_count.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/traditional_continuous.stan |only eDNAjoint-0.3/eDNAjoint/inst/stan/traditional_count.stan |only eDNAjoint-0.3/eDNAjoint/man/detection_calculate.Rd |only eDNAjoint-0.3/eDNAjoint/man/detection_plot.Rd |only eDNAjoint-0.3/eDNAjoint/man/eDNAjoint-package.Rd | 22 - eDNAjoint-0.3/eDNAjoint/man/goby_data.Rd |only eDNAjoint-0.3/eDNAjoint/man/green_crab_data.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_model.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_select.Rd |only eDNAjoint-0.3/eDNAjoint/man/joint_summarize.Rd |only eDNAjoint-0.3/eDNAjoint/man/mu_critical.Rd |only eDNAjoint-0.3/eDNAjoint/man/traditional_model.Rd |only eDNAjoint-0.3/eDNAjoint/src/RcppExports.cpp | 44 -- eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_continuous.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_continuous.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_count.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_joint_count.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_continuous.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_continuous.h |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_count.cc |only eDNAjoint-0.3/eDNAjoint/src/stanExports_traditional_count.h |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-detection_calculate.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-detection_plot.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_model.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_select.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-joint_summarize.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-mu_critical.R |only eDNAjoint-0.3/eDNAjoint/tests/testthat/test-traditional_model.R |only 139 files changed, 272 insertions(+), 313 deletions(-)
Title: Time Dependent Shared Frailty Cox Model
Description: Fits time-dependent shared frailty Cox model (specifically the adapted Paik et al.'s Model) based on the paper "Centre-Effect on Survival After Bone Marrow Transplantation: Application of Time-Dependent Frailty Models", by C.M. Wintrebert, H. Putter, A.H. Zwinderman and J.C. van Houwelingen (2004) <doi:10.1002/bimj.200310051>.
Author: Alessandra Ragni [aut, cre] ,
Giulia Romani [aut],
Chiara Masci [aut]
Maintainer: Alessandra Ragni <alessandra.ragni@polimi.it>
Diff between TimeDepFrail versions 0.0.0.9 dated 2024-11-21 and 0.0.1 dated 2025-01-17
TimeDepFrail-0.0.0.9/TimeDepFrail/R/bas_hazard.R |only TimeDepFrail-0.0.1/TimeDepFrail/DESCRIPTION | 13 - TimeDepFrail-0.0.1/TimeDepFrail/MD5 | 49 ++-- TimeDepFrail-0.0.1/TimeDepFrail/NAMESPACE | 5 TimeDepFrail-0.0.1/TimeDepFrail/R/AdPaikModel.R | 73 +++--- TimeDepFrail-0.0.1/TimeDepFrail/R/base_hazard.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/extractors.R |only TimeDepFrail-0.0.1/TimeDepFrail/R/frailty_sd.R | 32 -- TimeDepFrail-0.0.1/TimeDepFrail/R/params_se.R | 15 + TimeDepFrail-0.0.1/TimeDepFrail/R/plot.R | 117 ++++++---- TimeDepFrail-0.0.1/TimeDepFrail/R/posterior_frailty.R | 19 + TimeDepFrail-0.0.1/TimeDepFrail/R/summary.R | 6 TimeDepFrail-0.0.1/TimeDepFrail/R/survival.R |only TimeDepFrail-0.0.1/TimeDepFrail/README.md | 31 +- TimeDepFrail-0.0.1/TimeDepFrail/man/AdPaikModel.Rd | 33 +- TimeDepFrail-0.0.1/TimeDepFrail/man/AdPaik_1D.Rd | 35 +- TimeDepFrail-0.0.1/TimeDepFrail/man/bas_hazard.Rd | 2 TimeDepFrail-0.0.1/TimeDepFrail/man/coef.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/coefse.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/confint.AdPaik.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/frailty_sd.AdPaik.Rd | 6 TimeDepFrail-0.0.1/TimeDepFrail/man/frailty_sd.Rd | 4 TimeDepFrail-0.0.1/TimeDepFrail/man/params_CI.Rd | 4 TimeDepFrail-0.0.1/TimeDepFrail/man/plot_bas_hazard.Rd | 14 - TimeDepFrail-0.0.1/TimeDepFrail/man/plot_frailty_sd.Rd | 26 +- TimeDepFrail-0.0.1/TimeDepFrail/man/plot_post_frailty_est.Rd | 24 -- TimeDepFrail-0.0.1/TimeDepFrail/man/plot_survival.Rd |only TimeDepFrail-0.0.1/TimeDepFrail/man/post_frailty_CI.AdPaik.Rd | 7 TimeDepFrail-0.0.1/TimeDepFrail/man/summary.AdPaik.Rd | 2 TimeDepFrail-0.0.1/TimeDepFrail/man/survival.Rd |only 30 files changed, 298 insertions(+), 219 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.16 dated 2025-01-06 and 1.3.17 dated 2025-01-17
DESCRIPTION | 6 ++-- MD5 | 22 ++++++++-------- NEWS.md | 8 ++++++ R/zzz.R | 4 +-- configure | 2 - configure.ac | 2 - inst/doc/WebGL.html | 26 +++++++++---------- inst/doc/demos.html | 60 ++++++++++++++++++++++----------------------- inst/doc/deprecation.html | 2 - inst/doc/pkgdown.html | 6 ++-- inst/doc/rgl.html | 36 +++++++++++++-------------- inst/doc/transparency.html | 18 ++++++------- 12 files changed, 100 insertions(+), 92 deletions(-)
Title: High Dimensional Geometry, Set Operations, Projection, and
Inference Using Kernel Density Estimation, Support Vector
Machines, and Convex Hulls
Description: Estimates the shape and volume of high-dimensional datasets and performs set operations: intersection / overlap, union, unique components, inclusion test, and hole detection. Uses stochastic geometry approach to high-dimensional kernel density estimation, support vector machine delineation, and convex hull generation. Applications include modeling trait and niche hypervolumes and species distribution modeling.
Author: Benjamin Blonder [aut, cre],
Cecina Babich Morrow [aut],
Stuart Brown [aut],
Gregoire Butruille [aut],
Daniel Chen [aut],
Alex Laini [aut],
David J. Harris [aut],
Clement Violet [aut]
Maintainer: Benjamin Blonder <benjamin.blonder@berkeley.edu>
Diff between hypervolume versions 3.1.4 dated 2024-05-01 and 3.1.5 dated 2025-01-17
DESCRIPTION | 44 ++++++++++++++++++++++++++++++----- MD5 | 21 ++++++++++------ NAMESPACE | 2 + R/hypervolume_distance_point.R |only R/hypervolume_set_n_union.R |only R/ignore_unused_imports.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Hypervolume-Resampling.R | 18 +++++++------- inst/doc/Hypervolume-Resampling.html | 18 +++++++------- inst/doc/occupancy.html | 14 +++++------ man/hypervolume_distance_point.Rd |only man/hypervolume_set.Rd | 2 - man/hypervolume_set_n_union.Rd |only 14 files changed, 79 insertions(+), 40 deletions(-)
Title: Animal Sounds for Bioacustic Analysis
Description: Collection of example animal sounds for bioacoustic analysis.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between NatureSounds versions 1.0.4 dated 2021-04-23 and 1.0.5 dated 2025-01-17
NatureSounds-1.0.4/NatureSounds/R/Phae.long.est-data.R |only NatureSounds-1.0.4/NatureSounds/data/Phae.long.est.rda |only NatureSounds-1.0.4/NatureSounds/man/Phae.long.est.Rd |only NatureSounds-1.0.5/NatureSounds/DESCRIPTION | 9 NatureSounds-1.0.5/NatureSounds/MD5 | 48 - NatureSounds-1.0.5/NatureSounds/NAMESPACE | 1 NatureSounds-1.0.5/NatureSounds/NEWS.md | 4 NatureSounds-1.0.5/NatureSounds/R/NatureSounds-package.R | 5 NatureSounds-1.0.5/NatureSounds/R/lbh.est-data.R | 3 NatureSounds-1.0.5/NatureSounds/README.md | 50 - NatureSounds-1.0.5/NatureSounds/build/vignette.rds |binary NatureSounds-1.0.5/NatureSounds/data/Cryp.soui.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long1.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long2.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long3.rda |binary NatureSounds-1.0.5/NatureSounds/data/Phae.long4.rda |binary NatureSounds-1.0.5/NatureSounds/data/lbh.est.rda |binary NatureSounds-1.0.5/NatureSounds/data/monk.parakeet.est.rda |binary NatureSounds-1.0.5/NatureSounds/data/thyroptera.est.rda |binary NatureSounds-1.0.5/NatureSounds/inst/CITATION | 9 NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.R | 118 +-- NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.Rmd | 9 NatureSounds-1.0.5/NatureSounds/inst/doc/Acoustic_data_sets_in_NatureSounds.html | 368 +++++----- NatureSounds-1.0.5/NatureSounds/man/NatureSounds.Rd | 11 NatureSounds-1.0.5/NatureSounds/man/lbh.est.Rd | 3 NatureSounds-1.0.5/NatureSounds/vignettes/Acoustic_data_sets_in_NatureSounds.Rmd | 9 NatureSounds-1.0.5/NatureSounds/vignettes/NatureSounds_sticker.png |only 27 files changed, 354 insertions(+), 293 deletions(-)
Title: TH's Data Archive
Description: Contains data sets used in other packages Torsten Hothorn
maintains.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between TH.data versions 1.1-2 dated 2023-04-17 and 1.1-3 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- build/partial.rdb |binary build/vignette.rds |binary data/geyser.rda |binary data/mammoexp.rda |binary inst/doc/blood_loss_report.R | 22 +++++++++++----------- inst/doc/blood_loss_report.pdf |binary inst/rda/Primary_endpoint_data.rda |binary inst/rda/bloodloss.rda |binary man/wpbc.Rd | 3 +-- 12 files changed, 28 insertions(+), 29 deletions(-)
Title: Estimation of the Structural Topic and Sentiment-Discourse Model
for Text Analysis
Description: The Structural Topic and Sentiment-Discourse (STS) model allows researchers to estimate topic models with document-level metadata that determines both topic prevalence and sentiment-discourse. The sentiment-discourse is modeled as a document-level latent variable for each topic that modulates the word frequency within a topic. These latent topic sentiment-discourse variables are controlled by the document-level metadata. The STS model can be useful for regression analysis with text data in addition to topic modeling’s traditional use of descriptive analysis. The method was developed in Chen and Mankad (2024) <doi:10.1287/mnsc.2022.00261>.
Author: Shawn Mankad [aut, cre],
Li Chen [aut]
Maintainer: Shawn Mankad <smankad@ncsu.edu>
Diff between sts versions 1.2 dated 2024-11-25 and 1.3 dated 2025-01-17
sts-1.2/sts/R/findRepresentativeDocs.R |only sts-1.2/sts/R/printTopWords.R |only sts-1.3/sts/DESCRIPTION | 15 +++---- sts-1.3/sts/MD5 | 55 ++++++++++++++------------ sts-1.3/sts/NAMESPACE | 43 +++++++++++--------- sts-1.3/sts/R/estimateRegns.R | 2 sts-1.3/sts/R/findRepresentativeDocs.STS.R |only sts-1.3/sts/R/heldoutLikelihood.R | 2 sts-1.3/sts/R/plot.STS.R | 1 sts-1.3/sts/R/plotRepresentativeDocs.R | 2 sts-1.3/sts/R/printRegnTables.R | 2 sts-1.3/sts/R/printTopWords.STS.R |only sts-1.3/sts/R/sts-package.R | 21 ++++++++- sts-1.3/sts/R/sts.R | 4 - sts-1.3/sts/R/topicExclusivity.R | 2 sts-1.3/sts/R/topicSemanticCoherence.R | 2 sts-1.3/sts/build |only sts-1.3/sts/inst |only sts-1.3/sts/man/estimateRegns.Rd | 12 ++--- sts-1.3/sts/man/findRepresentativeDocs.Rd | 22 ++-------- sts-1.3/sts/man/findRepresentativeDocs.STS.Rd |only sts-1.3/sts/man/heldoutLikelihood.Rd | 4 - sts-1.3/sts/man/plot.STS.Rd | 4 - sts-1.3/sts/man/plotRepresentativeDocs.Rd | 2 sts-1.3/sts/man/printRegnTables.Rd | 6 +- sts-1.3/sts/man/printTopWords.Rd | 22 +++------- sts-1.3/sts/man/printTopWords.STS.Rd |only sts-1.3/sts/man/sts-package.Rd | 28 ++++++------- sts-1.3/sts/man/sts.Rd | 54 ++++++++++++------------- sts-1.3/sts/man/topicExclusivity.Rd | 28 ++++++------- sts-1.3/sts/man/topicSemanticCoherence.Rd | 4 - sts-1.3/sts/vignettes |only 32 files changed, 174 insertions(+), 163 deletions(-)
Title: Assess Study Cohorts Using a Common Data Model
Description: Phenotype study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model. Diagnostics
are run at the database, code list, cohort, and population level to assess
whether study cohorts are ready for research.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Xihang Chen [aut] ,
Marta Alcalde-Herraiz [aut] ,
Albert Prats-Uribe [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between PhenotypeR versions 0.1.0 dated 2024-12-06 and 0.1.1 dated 2025-01-17
DESCRIPTION | 8 MD5 | 84 +- NAMESPACE | 1 R/addCodelistAttribute.R | 12 R/codelistDiagnostics.R | 22 R/cohortDiagnostics.R | 39 - R/databaseDiagnostics.R | 22 R/matchedDiagnostics.R | 28 R/mockPhenotypeR.R |only R/phenotypeDiagnostics.R | 23 R/phenotypeR-package.R | 16 R/populationDiagnostics.R | 21 R/shinyDiagnostics.R | 26 R/utils-pipe.R | 28 README.md | 30 build/vignette.rds |binary inst/doc/a02_CodelistDiagnostics.R | 12 inst/doc/a02_CodelistDiagnostics.Rmd | 12 inst/doc/a02_CodelistDiagnostics.html | 579 ---------------- inst/doc/a03_CohortDiagnostics.R | 10 inst/doc/a03_CohortDiagnostics.Rmd | 10 inst/doc/a03_CohortDiagnostics.html | 240 +++--- inst/doc/a04_MatchedDiagnostics.html | 2 inst/shiny/global.R | 115 ++- inst/shiny/scripts/preprocess.R | 23 inst/shiny/server.R | 412 ++++++----- inst/shiny/ui.R | 971 ++++++++++++++-------------- man/PhenotypeR-package.Rd | 64 - man/addCodelistAttribute.Rd | 12 man/codelistDiagnostics.Rd | 22 man/cohortDiagnostics.Rd | 23 man/databaseDiagnostics.Rd | 22 man/matchedDiagnostics.Rd | 23 man/mockPhenotypeR.Rd |only man/phenotypeDiagnostics.Rd | 23 man/pipe.Rd | 40 - man/populationDiagnostics.Rd | 21 man/shinyDiagnostics.Rd | 25 tests/testthat/test-addCodelistAttribute.R | 6 tests/testthat/test-cohortDiagnostics.R | 9 tests/testthat/test-dbms.R | 10 tests/testthat/test-populationDiagnostics.R | 4 vignettes/a02_CodelistDiagnostics.Rmd | 12 vignettes/a03_CohortDiagnostics.Rmd | 10 44 files changed, 1289 insertions(+), 1783 deletions(-)
Title: Handwriting Analysis in R
Description: Perform statistical writership analysis of scanned handwritten documents.
Webpage provided at: <https://github.com/CSAFE-ISU/handwriter>.
Author: Iowa State University of Science and Technology on behalf of its Center
for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Nick Berry [aut],
Stephanie Reinders [aut, cre],
James Taylor [aut],
Felix Baez-Santiago [ctb],
Jon Gonzalez [...truncated...]
Maintainer: Stephanie Reinders <srein@iastate.edu>
Diff between handwriter versions 3.2.3 dated 2024-11-26 and 3.2.4 dated 2025-01-17
DESCRIPTION | 6 MD5 | 32 +++- NAMESPACE | 3 NEWS.md | 16 ++ R/cluster_assignment.R | 5 R/cluster_format.R | 38 ----- R/cluster_plot.R | 65 ++++++++++ R/cluster_profiles.R |only R/data.R | 40 ++++++ R/globals.R |only README.md | 2 data/templateK40.rda |only man/get_cluster_fill_counts.Rd | 13 +- man/get_cluster_fill_rates.Rd |only man/get_writer_profiles.Rd |only man/plot_writer_profiles.Rd |only man/templateK40.Rd |only tests/testthat/fixtures/processHandwriting/make_fixtures.R | 14 ++ tests/testthat/fixtures/processHandwriting/rates.rds |only tests/testthat/fixtures/processHandwriting/rates_wo_indices.rds |only tests/testthat/test-cluster-format.R | 24 --- tests/testthat/test-cluster_profiles.R |only 22 files changed, 175 insertions(+), 83 deletions(-)
Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It
provides a framework for development and use of innovative methods for
visualization, statistical analysis, and clinical interpretation of
visual-field loss and its change over time. It is intended to be a tool for
collaborative research. The package is described in Marin-Franch and Swanson
(2013) <doi:10.1167/13.4.10> and is part of the Open Perimetry Initiative
(OPI) [Turpin, Artes, and McKendrick (2012) <doi:10.1167/12.11.22>].
Author: Ivan Marin-Franch [cre, aut, rev, cph],
William H Swanson [fnd, dtc],
Michael Wall [fnd, dtc],
Andrew Turpin [ctb],
Paul H Artes [ctb, dtc],
Cord Huchzermeyer [ctb],
Giovanni Montesano [ctb],
Mitchell W Dul [dtc]
Maintainer: Ivan Marin-Franch <imarinfr@optocom.es>
Diff between visualFields versions 1.0.5 dated 2024-09-21 and 1.0.7 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/vfreports.R | 14 +++++++++++--- data/drasdolut.rda |binary data/gpars.rda |binary data/locmaps.rda |binary data/normvals.rda |binary data/vfctrIowaPC26.rda |binary data/vfctrIowaPeri.rda |binary data/vfctrSunyiu10d2.rda |binary data/vfctrSunyiu24d2.rda |binary data/vfpwgRetest24d2.rda |binary data/vfpwgSunyiu24d2.rda |binary 13 files changed, 27 insertions(+), 19 deletions(-)
Title: An Implementation of Matrix Mathematics that Respects Row and
Column Names
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsbyname versions 0.6.10 dated 2024-02-12 and 0.6.11 dated 2025-01-17
DESCRIPTION | 12 - LICENSE | 2 MD5 | 54 ++++--- NAMESPACE | 4 NEWS.md | 32 ++++ R/Unary.R | 3 R/Utilities.R | 193 +++++++++++++++++++++++++--- R/aggregates.R | 4 R/named_triplet.R |only R/reallocate.R |only build/vignette.rds |binary inst/CITATION | 8 - inst/WORDLIST | 4 inst/doc/about-vector-arguments.html | 4 inst/doc/aggregation-vignette.R | 4 inst/doc/aggregation-vignette.html | 8 - inst/doc/applybyname-vignette.html | 8 - inst/doc/matsbyname.html | 8 - inst/doc/using-summarise-in-matsbyname.html | 4 man/aggregation_map_helpers.Rd | 4 man/create_triplet.Rd |only man/get_row_col_index_maps.Rd |only man/iszero_byname.Rd | 8 + man/reallocate_byname.Rd |only man/select_cols_byname.Rd | 8 - man/select_rowcol_piece_byname.Rd | 24 ++- man/select_rows_byname.Rd | 7 - man/select_rows_cols_byname.Rd |only man/structure_index_map.Rd |only man/to_named_triplet.Rd |only tests/testthat/test-Utilities.R | 45 ++++++ tests/testthat/test-named_triplet.R |only tests/testthat/test-reallocate.R |only 33 files changed, 360 insertions(+), 88 deletions(-)
Title: Data for Package 'Qindex'
Description: Example data used in package 'Qindex'.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [ctb]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex.data versions 0.1.1 dated 2024-04-24 and 0.1.2 dated 2025-01-17
DESCRIPTION | 24 +++++++++---------- MD5 | 12 ++++----- R/Ki67.R | 56 ++++++++++++++++++++++++++++++++------------- build/partial.rdb |binary data/Ki67.rda |binary man/Qindex.data-package.Rd | 6 ++++ man/celldata.Rd | 30 ++++++++++++------------ 7 files changed, 79 insertions(+), 49 deletions(-)
Title: Code-Logics to Handle Ontologies
Description: Provides tools to build and work with an ontology of linked (open)
data in a tidy workflow. It is inspired by the Food and Agrilculture
Organizations (FAO) caliper platform
<https://www.fao.org/statistics/caliper/web/> and
makes use of the Simple Knowledge Organisation System (SKOS).
Author: Steffen Ehrmann [aut, cre] ,
Arne Ruemmler [aut, ctb] ,
Carsten Meyer [ctb]
Maintainer: Steffen Ehrmann <steffen.ehrmann@posteo.de>
Diff between ontologics versions 0.7.0 dated 2023-05-10 and 0.7.4 dated 2025-01-17
DESCRIPTION | 12 MD5 | 100 - NAMESPACE | 5 NEWS.md | 209 +- R/1onto.R | 503 +++---- R/edit_matches.R | 831 ++++++----- R/export_as_rdf.R | 902 ++++++------ R/get_class.R | 182 +- R/get_concept.R | 215 +-- R/get_source.R | 154 +- R/imports.R | 30 R/load_ontology.R | 70 - R/makeTreeMap.R | 132 - R/make_tree.R | 146 +- R/new_class.R | 184 +- R/new_concept.R | 512 +++---- R/new_mapping.R | 584 ++++---- R/new_source.R | 246 +-- R/start_ontology.R | 180 +- R/zzz.R | 34 README.md | 38 build/vignette.rds |binary inst/doc/conversion_to_rdf.R | 36 inst/doc/conversion_to_rdf.Rmd | 310 ++-- inst/doc/conversion_to_rdf.html | 1270 +++++++++--------- inst/doc/create_an_ontology.R | 192 +- inst/doc/create_an_ontology.Rmd | 278 +-- inst/doc/create_an_ontology.html | 1956 ++++++++++++++-------------- inst/doc/map_new_concepts.R | 180 +- inst/doc/map_new_concepts.Rmd | 252 +-- inst/doc/map_new_concepts.html | 1492 ++++++++++----------- inst/doc/ontology_database_description.Rmd | 220 +-- inst/doc/ontology_database_description.html | 1006 +++++++------- man/edit_matches.Rd | 136 + man/export_as_rdf.Rd | 66 man/figures/logo.svg | 744 +++++----- man/get_class.Rd | 94 - man/get_concept.Rd | 91 - man/get_source.Rd | 80 - man/make_tree.Rd | 42 man/new_class.Rd | 68 man/new_mapping.Rd | 184 +- man/new_source.Rd | 162 +- man/onto-class.Rd | 40 man/pipe.Rd | 40 man/show-onto-method.Rd | 28 vignettes/conversion_to_rdf.Rmd | 310 ++-- vignettes/create_an_ontology.Rmd | 278 +-- vignettes/map_new_concepts.Rmd | 252 +-- vignettes/ontology_database_description.Rmd | 220 +-- vignettes/skos.rdf | 936 ++++++------- 51 files changed, 8192 insertions(+), 8040 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.1-4 dated 2023-05-16 and 1.2-1 dated 2025-01-17
DESCRIPTION | 8 +++---- MD5 | 20 ++++++++++--------- NAMESPACE | 5 ++-- R/cyclic.R | 50 +++++++++++++++++++++++++++++++++++++++++------- R/formula.R | 7 +++--- build |only inst/NEWS.Rd | 14 ++++++++++++- man/Bernstein_basis.Rd | 4 +-- man/Legendre_basis.Rd | 4 +-- man/as.basis.formula.Rd | 3 +- man/cyclic_basis.Rd |only tests/bases-Ex.R | 7 ++++++ 12 files changed, 91 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-10-16 0.2.0
2020-07-13 0.1.2
2020-04-07 0.1.1
2020-01-29 0.1.0
2019-07-23 0.0.2
2019-07-11 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-29 0.1.2
2020-11-01 0.1.1
2020-05-04 0.1.0
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.8.3 dated 2024-01-22 and 0.9 dated 2025-01-17
DESCRIPTION | 14 ++- MD5 | 85 ++++++++++++--------- R/Pfit.R |only R/RcppExports.R | 4 + R/SAPA.R | 35 ++++++-- R/SlpAsp.R | 159 ++++++++++++++++------------------------ README.md | 5 - build/vignette.rds |binary inst/doc/README.R | 2 inst/doc/README.html | 51 ++++++------ inst/testdata |only man/Pfit.Rd |only man/SAPA.Rd | 8 +- man/figures/README-AdjSD-1.png |binary man/figures/README-BPI-1.png |binary man/figures/README-DMV-1.png |binary man/figures/README-RIE-1.png |binary man/figures/README-RP-1.png |binary man/figures/README-SAPA-1.png |binary man/figures/README-SlpAsp-1.png |binary man/figures/README-TPI-1.png |binary man/figures/README-Topo-1.png |binary man/figures/README-VRM-1.png |binary man/figures/SlpAsp.png |binary man/figures/qmetrics.jpg |binary man/figures/sub_qfit01.png |binary man/figures/sub_qfit02.png |binary man/figures/sub_qfit03.png |binary man/figures/sub_qfit04.png |binary man/figures/sub_qfit05.png |binary man/figures/sub_qfit06.png |binary man/figures/sub_qfit07.png |binary man/figures/sub_qfit08.png |binary man/figures/sub_qfit09.png |binary man/figures/sub_qfit10.png |binary man/figures/sub_qfit11.png |binary man/fragments/README_Frag.Rmd | 2 src/RcppExports.cpp | 18 ++++ src/cpp_code.cpp | 29 +++++++ tests |only 40 files changed, 238 insertions(+), 174 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.4.0 dated 2025-01-16 and 1.4.1 dated 2025-01-17
DESCRIPTION | 10 +++---- MD5 | 18 ++++++------- NEWS.md | 4 ++ cleanup | 2 - configure | 26 +++++++++---------- configure.ac | 8 ++--- src/gsl_nls.h | 5 ++- src/nls.c | 2 - src/nls_irls.c | 2 - src/nls_utils.c | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++--- 10 files changed, 114 insertions(+), 38 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 1.3.0 dated 2024-11-20 and 1.4.0 dated 2025-01-17
DESCRIPTION | 6 +- MD5 | 23 ++++++----- NEWS.md | 10 ++++ R/scale-epiweek.R | 13 ++++-- R/scale-isoweek.R | 13 ++++-- R/scale-yearweek.R | 9 +++- inst/doc/grates.html | 6 +- man/scale_x_grates_epiweek.Rd | 6 +- man/scale_x_grates_isoweek.Rd | 6 +- man/scale_x_grates_yearweek.Rd | 4 + tests/testthat/_snaps/plots/epiweek_weeks.png |only tests/testthat/_snaps/plots/isoweek_weeks.png |only tests/testthat/_snaps/plots/yearweek_thursday_weeks_only.png |only tests/testthat/test-plots.R | 9 ++++ 14 files changed, 74 insertions(+), 31 deletions(-)
Title: Solve Least Squares with GMRES(k)
Description: Solves a least squares system Ax~=b (dim(A)=(m,n) with m >= n) with a precondition matrix B: BAx=Bb (dim(B)=(n,m)). Implemented method is based on GMRES (Saad, Youcef; Schultz, Martin H. (1986). "GMRES: A Generalized Minimal Residual Algorithm for Solving Nonsymmetric Linear Systems" <doi:10.1137/0907058>) with callback functions, i.e. no explicit A, B or b are required.
Author: Serguei Sokol [aut, cre]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between gmresls versions 0.2.2 dated 2024-10-18 and 0.2.3 dated 2025-01-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/gmresls.R | 15 +++++++++++---- inst/COPYRIGHTS | 2 +- inst/unitTests/runit.gmresls.R | 2 ++ man/gmresls.Rd | 4 +++- 7 files changed, 32 insertions(+), 16 deletions(-)
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest,
using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
Author: Jelle Goeman [aut, cre],
Aldo Solari [aut],
Rosa Meijer [aut]
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between cherry versions 0.6-14 dated 2021-05-07 and 0.6-15 dated 2025-01-17
ChangeLog | 5 +++++ DESCRIPTION | 22 +++++++++++++++++----- MD5 | 20 ++++++++++---------- build/vignette.rds |binary inst/CITATION | 33 +++++++++------------------------ inst/doc/cherry.pdf |binary man/adjusted.Rd | 45 +++++++++++++++++++++++---------------------- man/closed.Rd | 47 ++++++++++++++++++++++++----------------------- man/closure-class.Rd | 45 +++++++++++++++++++++++---------------------- man/hommelFast.Rd | 2 +- man/select.Rd | 39 ++++++++++++++++++++------------------- 11 files changed, 132 insertions(+), 126 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.
Author: Dominique Makowski [aut, cre] ,
Daniel Luedecke [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Micah K. Wilson [aut] ,
Brenton M. Wiernik [aut] ,
Paul-Christian Buerkner [rev],
Tristan Mahr [rev] ,
Henrik Singmann [ctb] ,
Quentin F. Gron [...truncated...]
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.15.0 dated 2024-10-17 and 0.15.1 dated 2025-01-17
DESCRIPTION | 12 +-- MD5 | 112 ++++++++++++++--------------- NEWS.md | 10 ++ R/bayesfactor.R | 11 +- R/bayesfactor_parameters.R | 1 R/bci.R | 11 -- R/check_prior.R | 3 R/contr.equalprior.R | 1 R/convert_pd_to_p.R | 1 R/describe_posterior.R | 22 +---- R/describe_prior.R | 1 R/distribution.R | 7 - R/equivalence_test.R | 5 - R/estimate_density.R | 4 - R/eti.R | 7 - R/format.R | 4 - R/hdi.R | 2 R/map_estimate.R | 3 R/mcse.R | 1 R/mediation.R | 5 - R/p_direction.R | 5 - R/p_map.R | 17 ---- R/p_rope.R | 1 R/p_significance.R | 1 R/p_to_bf.R | 1 R/print.R | 2 R/print_html.R | 7 - R/print_md.R | 5 - R/rope.R | 28 +++++-- R/rope_range.R | 1 R/sensitivity_to_prior.R | 5 - R/sexit.R | 3 R/sexit_thresholds.R | 2 R/si.R | 2 R/simulate_data.R | 1 R/simulate_priors.R | 6 - R/spi.R | 2 R/unupdate.R | 2 R/utils.R | 9 +- R/utils_bayesfactor.R | 1 R/utils_hdi_ci.R | 3 build/partial.rdb |binary build/vignette.rds |binary man/bayesfactor.Rd | 11 +- man/describe_posterior.Rd | 10 +- man/diagnostic_posterior.Rd | 32 +++++--- man/equivalence_test.Rd | 10 +- man/p_rope.Rd | 10 +- man/rope.Rd | 26 ++++-- tests/testthat/_snaps/windows/print.md | 106 ++++++++++++++++++--------- tests/testthat/test-data.frame-with-rvar.R | 8 +- tests/testthat/test-describe_posterior.R | 1 tests/testthat/test-emmGrid.R | 32 +++++--- tests/testthat/test-marginaleffects.R | 33 +++++++- tests/testthat/test-p_map.R | 1 tests/testthat/test-rope.R | 1 tests/testthat/test-rope_range.R | 1 57 files changed, 298 insertions(+), 311 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to optimal and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2024;
<doi:10.1111/bmsp.12315>). The optimal algorithms require that an
integer linear programming solver is installed. This package will install
'lpSolve' (<https://cran.r-project.org/p [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb] ,
Hannah Hengelbrock [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.7 dated 2024-10-01 and 0.8.9 dated 2025-01-17
DESCRIPTION | 15 MD5 | 39 - NAMESPACE | 2 R/categories_to_binary.R | 42 + R/input-validation.R | 9 R/must-link-anticlustering.R | 285 +++++++++- R/wrapper-anticlustering.R | 10 R/wrapper-three-phase-search-dynamic-population-size.R |only build/vignette.rds |binary inst/doc/Categorical_vars.Rmd | 2 inst/doc/Categorical_vars.html | 34 - inst/doc/Speeding_up_anticlustering.html | 28 inst/tinytest/test-2pml.R |only inst/tinytest/test-three-phase-search-dynamic-population-size.R |only man/anticlustering.Rd | 10 man/categories_to_binary.Rd | 32 - man/figures/clustering-1.png |binary man/figures/matching-1.png |binary man/three_phase_search_anticlustering.Rd |only src/anticlust_init.c | 4 src/three-phase-dispersion.c |only src/three-phase-header.h |only src/three_phase_search_dynamic_population_size.c |only vignettes/Categorical_vars.Rmd | 2 24 files changed, 421 insertions(+), 93 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: Functions aiming to facilitate the analysis of the structure of animal acoustic signals in 'R'. 'warbleR' makes use of the basic sound analysis tools from the packages 'tuneR' and 'seewave', and offers new tools for explore and quantify acoustic signal structure. The package allows to organize and manipulate multiple sound files, create spectrograms of complete recordings or individual signals in different formats, run several measures of acoustic structure, and characterize different structural levels in acoustic signals.
Author: Marcelo Araya-Salas [aut, cre]
,
Grace Smith-Vidaurre [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between warbleR versions 1.1.33 dated 2024-12-11 and 1.1.34 dated 2025-01-17
DESCRIPTION | 6 MD5 | 47 build/vignette.rds |binary data/comp_matrix.rda |binary data/lbh_selec_table.rda |binary data/sim_coor_sing.rda |binary data/sth_annotations.rda |binary inst/doc/a_warbleR.Rmd | 10 inst/doc/a_warbleR.html | 1753 ++++++++++++++++++++++---- inst/doc/b_annotation_data_format.R | 71 - inst/doc/b_annotation_data_format.Rmd | 30 inst/doc/b_annotation_data_format.html | 2164 +++++++++++++++++++++++++-------- inst/doc/c_warbleR_workflow_02.Rmd | 10 inst/doc/c_warbleR_workflow_02.html | 1903 +++++++++++++++++++++++------ inst/doc/d_warbleR_workflow_03.Rmd | 10 inst/doc/d_warbleR_workflow_03.html | 2093 +++++++++++++++++++++++++------ man/compare_methods.Rd | 2 man/freq_ts.Rd | 2 man/overlapping_sels.Rd | 2 man/sth_annotations.Rd | 2 vignettes/a_warbleR.Rmd | 10 vignettes/b_annotation_data_format.Rmd | 30 vignettes/by_song.png |only vignettes/c_warbleR_workflow_02.Rmd | 10 vignettes/d_warbleR_workflow_03.Rmd | 10 25 files changed, 6544 insertions(+), 1621 deletions(-)
Title: Shape Constrained Additive Models
Description: Generalized additive models under shape
constraints on the component functions of the linear predictor.
Models can include multiple shape-constrained (univariate
and bivariate) and unconstrained terms. Routines of the
package 'mgcv' are used to set up the model matrix, print,
and plot the results. Multiple smoothing parameter
estimation by the Generalized Cross Validation or similar.
See Pya and Wood (2015) <doi:10.1007/s11222-013-9448-7>
for an overview. A broad selection of shape-constrained
smoothers, linear functionals of smooths with shape constraints,
and Gaussian models with AR1 residuals.
Author: Natalya Pya [aut, cre]
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-17 dated 2024-06-19 and 1.2-18 dated 2025-01-17
ChangeLog | 16 - DESCRIPTION | 14 MD5 | 90 +++--- NAMESPACE | 22 + R/bfgs.r | 8 R/bivar.smooth.const.R | 90 ++---- R/estimate.scam.R | 2 R/plot.r | 91 ++++-- R/predict.scam.R | 94 ++++-- R/scam.r | 93 +++--- R/uni.smooth.const-lscop.r | 146 ++++++++++ R/uni.smooth.const-with-po.r | 417 +++++++++++++++++++++++++---- build/partial.rdb |binary man/Predict.matrix.mpi.smooth.Rd | 8 man/anova.scam.Rd | 3 man/linear.functional.terms.Rd | 6 man/plot.scam.Rd | 6 man/predict.scam.Rd | 1 man/scam.Rd | 121 ++++---- man/scam.check.Rd | 3 man/shape.constrained.smooth.terms.Rd | 6 man/smooth.construct.cv.smooth.spec.rd | 2 man/smooth.construct.lmpi.smooth.spec.Rd | 22 + man/smooth.construct.mdcv.smooth.spec.Rd | 37 +- man/smooth.construct.mdcx.smooth.spec.Rd | 4 man/smooth.construct.miso.smooth.spec.Rd | 4 man/smooth.construct.mpi.smooth.spec.Rd | 7 man/smooth.construct.po.smooth.spec.Rd | 34 ++ man/smooth.construct.tecvcv.smooth.spec.Rd | 51 +-- man/smooth.construct.tecxcv.smooth.spec.Rd | 52 +-- man/smooth.construct.tecxcx.smooth.spec.Rd | 52 +-- man/smooth.construct.tedecv.smooth.spec.Rd | 51 +-- man/smooth.construct.tedecx.smooth.spec.Rd | 53 +-- man/smooth.construct.tedmd.smooth.spec.Rd | 43 +- man/smooth.construct.tedmi.smooth.spec.Rd | 42 +- man/smooth.construct.temicv.smooth.spec.Rd | 51 +-- man/smooth.construct.temicx.smooth.spec.Rd | 51 +-- man/smooth.construct.tescv.smooth.spec.Rd | 53 +-- man/smooth.construct.tescx.smooth.spec.Rd | 55 +-- man/smooth.construct.tesmd1.smooth.spec.Rd | 85 ++--- man/smooth.construct.tesmd2.smooth.spec.Rd | 87 ++---- man/smooth.construct.tesmi1.smooth.spec.Rd | 88 ++---- man/smooth.construct.tesmi2.smooth.spec.Rd | 83 ++--- man/smooth.construct.tismd.smooth.spec.Rd | 2 man/smooth.construct.tismi.smooth.spec.Rd | 1 man/summary.scam.Rd | 3 46 files changed, 1381 insertions(+), 869 deletions(-)
Title: Self-Adapting Mixture (SAM) Priors
Description: Implementation of the SAM prior and generation of its
operating characteristics for dynamically borrowing information
from historical data. For details, please refer to Yang et al. (2023)
<doi:10.1111/biom.13927>.
Author: Peng Yang [aut, cre] ,
Ying Yuan [aut]
Maintainer: Peng Yang <py11@rice.edu>
Diff between SAMprior versions 1.1.1 dated 2023-09-27 and 2.0.0 dated 2025-01-17
DESCRIPTION | 12 +++++--- MD5 | 33 +++++++++++++---------- NAMESPACE | 5 +++ NEWS.md | 6 +++- R/PS_SAM_data.R |only R/PS_prior.R |only R/SAM_prior.R | 3 -- R/SAM_weight.R | 3 -- R/get_OC.R | 7 ++--- R/support.R | 1 data |only inst/doc/Example_binary.R | 14 +++++----- inst/doc/Example_binary.html | 54 ++++++++++++++++++--------------------- inst/doc/Example_continuous.R | 18 ++++++------- inst/doc/Example_continuous.html | 54 ++++++++++++++++++--------------------- man/PS_SAM_data.Rd |only man/PS_prior.Rd |only man/SAM_prior.Rd | 3 -- man/SAM_weight.Rd | 3 -- man/get_OC.Rd | 7 ++--- 20 files changed, 115 insertions(+), 108 deletions(-)
Title: Functions for Base Types and Core R and 'Tidyverse' Features
Description: A toolbox for working with base types, core R features
like the condition system, and core 'Tidyverse' features like tidy
evaluation.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
mikefc [cph] ,
Yann Collet [cph] ,
Posit, PBC [cph, fnd]
Maintainer: Lionel Henry <lionel@posit.co>
Diff between rlang versions 1.1.4 dated 2024-06-04 and 1.1.5 dated 2025-01-17
DESCRIPTION | 8 +++--- MD5 | 40 ++++++++++++++++----------------- NEWS.md | 5 ++++ R/cnd-abort.R | 4 --- man/cnd_inherits.Rd | 8 +----- man/glue-operators.Rd | 10 -------- man/missing_arg.Rd | 8 +----- man/qq_show.Rd | 2 - man/rmd/topic-condition-formatting.Rmd | 2 - man/splice-operator.Rd | 4 --- man/topic-condition-formatting.Rd | 2 - man/topic-data-mask-ambiguity.Rd | 2 - man/topic-data-mask-programming.Rd | 8 ------ man/topic-data-mask.Rd | 6 ---- man/topic-defuse.Rd | 4 --- man/topic-error-call.Rd | 4 +-- man/topic-inject-out-of-context.Rd | 12 --------- man/topic-inject.Rd | 2 - man/topic-metaprogramming.Rd | 6 ---- man/topic-multiple-columns.Rd | 2 - src/version.c | 2 - 21 files changed, 39 insertions(+), 102 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators for models and (robust) covariance matrices, and tests for panel data
econometrics, including within/fixed effects, random effects, between, first-difference,
nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models,
panel generalized method of moments (GMM) and general FGLS models,
mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators
with common factors, variable coefficients and limited dependent variables models.
Test functions include model specification, serial correlation, cross-sectional dependence,
panel unit root and panel Granger (non-)causality. Typical references are general econometrics
text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>),
Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018),
Panel Data Econometrics with R (<doi:10.1002/9781119504641>).
Author: Yves Croissant [aut],
Giovanni Millo [aut],
Kevin Tappe [aut, cre],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Kevin Tappe <kevin.tappe@bwi.uni-stuttgart.de>
Diff between plm versions 2.6-4 dated 2024-04-01 and 2.6-5 dated 2025-01-17
plm-2.6-4/plm/inst/removed |only plm-2.6-4/plm/inst/tests |only plm-2.6-5/plm/DESCRIPTION | 10 plm-2.6-5/plm/MD5 | 190 ++----------- plm-2.6-5/plm/NAMESPACE | 1 plm-2.6-5/plm/NEWS.md | 23 + plm-2.6-5/plm/R/deprecated.R | 2 plm-2.6-5/plm/R/detect_lin_dep_alias.R | 2 plm-2.6-5/plm/R/est_cce.R | 2 plm-2.6-5/plm/R/est_ggls.R | 13 plm-2.6-5/plm/R/est_gmm.R | 332 ++++++++++++----------- plm-2.6-5/plm/R/est_mg.R | 2 plm-2.6-5/plm/R/est_pi.R | 2 plm-2.6-5/plm/R/est_vcm.R | 47 +-- plm-2.6-5/plm/R/tool_argvalues.R | 6 plm-2.6-5/plm/R/tool_pdata.frame.R | 7 plm-2.6-5/plm/R/tool_ranfixef.R | 2 plm-2.6-5/plm/R/tool_transformations_collapse.R | 2 plm-2.6-5/plm/R/tool_vcovG.R | 111 +++++-- plm-2.6-5/plm/README.md | 5 plm-2.6-5/plm/build/partial.rdb |binary plm-2.6-5/plm/build/vignette.rds |binary plm-2.6-5/plm/inst/DPD98.R |only plm-2.6-5/plm/inst/DPD98.txt |only plm-2.6-5/plm/inst/REFERENCES.bib | 15 - plm-2.6-5/plm/inst/doc/A_plmPackage.R | 2 plm-2.6-5/plm/inst/doc/A_plmPackage.Rmd | 18 - plm-2.6-5/plm/inst/doc/A_plmPackage.html | 154 +++++----- plm-2.6-5/plm/inst/doc/B_plmFunction.html | 11 plm-2.6-5/plm/inst/doc/C_plmModelComponents.R | 32 +- plm-2.6-5/plm/inst/doc/C_plmModelComponents.html | 8 plm-2.6-5/plm/man/detect.lindep.Rd | 2 plm-2.6-5/plm/man/mtest.Rd | 44 ++- plm-2.6-5/plm/man/pgmm.Rd | 58 ++-- plm-2.6-5/plm/man/sargan.Rd | 96 +++--- plm-2.6-5/plm/man/vcovHC.plm.Rd | 5 plm-2.6-5/plm/man/within_intercept.Rd | 2 plm-2.6-5/plm/vignettes/A_plmPackage.Rmd | 18 - 38 files changed, 634 insertions(+), 590 deletions(-)
Title: Estimation and Use of the Generalised (Tukey) Lambda
Distribution
Description: The generalised lambda distribution, or Tukey lambda distribution,
provides a wide variety of shapes with one functional form.
This package provides random numbers, quantiles, probabilities,
densities and density quantiles for four different types of the distribution,
the FKML (Freimer et al 1988), RS (Ramberg and Schmeiser 1974), GPD (van Staden
and Loots 2009) and FM5 - see documentation for details.
It provides the density function, distribution function, and Quantile-Quantile
plots.
It implements a variety of estimation methods for the distribution,
including diagnostic plots.
Estimation methods include the starship (all 4 types),
method of L-Moments for the GPD and FKML types, and a
number of methods for only the FKML type.
These include maximum likelihood, maximum product of spacings,
Titterington's method, Moments, Trimmed L-Moments and
Distributional Least Absolutes.
Author: Robert King [aut, cre] ,
Benjamin Dean [aut],
Sigbert Klinke [aut],
Paul van Staden [aut]
Maintainer: Robert King <Robert.King.Newcastle@gmail.com>
Diff between gld versions 2.6.6 dated 2022-10-23 and 2.6.7 dated 2025-01-17
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++--------- NAMESPACE | 1 R/methods.R | 36 ++++++++++++++++++++++++++++------- TODO | 2 - build/partial.rdb |binary man/GeneralisedLambdaDistribution.Rd | 2 - man/gld.lmoments.Rd | 10 ++++----- man/gld.moments.Rd | 13 ++++++------ man/plot.starship.Rd | 6 +++-- 10 files changed, 61 insertions(+), 35 deletions(-)
Title: Build and Manipulate Study Cohorts Using a Common Data Model
Description: Create and manipulate study cohorts in data mapped to the
Observational Medical Outcomes Partnership Common Data Model.
Author: Edward Burn [aut, cre] ,
Marti Catala [aut] ,
Nuria Mercade-Besora [aut] ,
Marta Alcalde-Herraiz [aut] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Xihang Chen [aut] ,
Kim Lopez-Guell [aut] ,
Elin Rowlands [aut]
Maintainer: Edward Burn <edward.burn@ndorms.ox.ac.uk>
Diff between CohortConstructor versions 0.3.3 dated 2024-11-26 and 0.3.4 dated 2025-01-17
DESCRIPTION | 12 MD5 | 190 +-- R/collapseCohorts.R | 13 R/conceptCohort.R | 165 ++- R/exitAtColumnDate.R | 11 R/exitAtDate.R | 26 R/intersectCohorts.R | 10 R/matchCohorts.R | 35 R/measurementCohort.R | 23 R/padCohortDate.R | 11 R/requireCohortIntersect.R | 16 R/requireConceptIntersect.R | 15 R/requireDateRange.R | 32 R/requireDeathFlag.R | 9 R/requireDemographics.R | 10 R/requireIsEntry.R | 36 R/requireMinCohortCount.R | 9 R/requireTableIntersect.R | 11 R/sampleCohorts.R | 9 R/stratifyCohorts.R | 8 R/subsetCohorts.R | 8 R/trimDemographics.R | 13 R/unionCohorts.R | 4 R/validateFunctions.R | 98 - R/yearCohorts.R | 10 README.md | 45 inst/doc/a01_building_base_cohorts.R | 6 inst/doc/a01_building_base_cohorts.Rmd | 162 +-- inst/doc/a01_building_base_cohorts.html | 16 inst/doc/a02_cohort_table_requirements.R | 6 inst/doc/a02_cohort_table_requirements.Rmd | 6 inst/doc/a02_cohort_table_requirements.html | 46 inst/doc/a03_require_demographics.R | 6 inst/doc/a03_require_demographics.Rmd | 6 inst/doc/a03_require_demographics.html | 46 inst/doc/a04_require_intersections.R | 6 inst/doc/a04_require_intersections.Rmd | 6 inst/doc/a04_require_intersections.html | 46 inst/doc/a06_concatanate_cohorts.R | 6 inst/doc/a06_concatanate_cohorts.Rmd | 6 inst/doc/a06_concatanate_cohorts.html | 52 inst/doc/a07_filter_cohorts.R | 18 inst/doc/a07_filter_cohorts.Rmd | 216 ++-- inst/doc/a07_filter_cohorts.html | 30 inst/doc/a08_split_cohorts.R | 12 inst/doc/a08_split_cohorts.Rmd | 162 +-- inst/doc/a08_split_cohorts.html | 6 inst/doc/a09_combine_cohorts.R | 24 inst/doc/a09_combine_cohorts.Rmd | 294 ++--- inst/doc/a09_combine_cohorts.html | 6 inst/doc/a10_match_cohorts.R | 66 - inst/doc/a10_match_cohorts.Rmd | 20 inst/doc/a10_match_cohorts.html | 22 inst/doc/a11_benchmark.html | 521 +++++---- man/conceptCohort.Rd | 24 man/matchCohorts.Rd | 9 man/measurementCohort.Rd | 7 man/requireCohortIntersect.Rd | 2 man/requireConceptIntersect.Rd | 4 man/requireIsFirstEntry.Rd | 2 man/requireIsLastEntry.Rd | 5 man/trimToDateRange.Rd | 9 tests/testthat/test-addIndex.R | 138 +- tests/testthat/test-collapseCohorts.R | 621 +++++------ tests/testthat/test-conceptCohort.R | 582 +++++++---- tests/testthat/test-demographicsCohort.R | 13 tests/testthat/test-entryAtColumnDate.R | 18 tests/testthat/test-exitAtColumnDate.R | 12 tests/testthat/test-exitAtDate.R | 22 tests/testthat/test-intersectCohorts.R | 1356 +++++++++++++------------- tests/testthat/test-matchCohorts.R | 696 ++++++------- tests/testthat/test-measurementCohort.R | 753 ++++++++------ tests/testthat/test-padCohortDate.R | 785 +++++++-------- tests/testthat/test-requireCohortIntersect.R | 666 ++++++------ tests/testthat/test-requireConceptIntersect.R | 684 ++++++------- tests/testthat/test-requireDateRange.R | 12 tests/testthat/test-requireDeathFlag.R | 12 tests/testthat/test-requireDemographics.R | 14 tests/testthat/test-requireIsEntry.R | 16 tests/testthat/test-requireMinCohortCount.R | 32 tests/testthat/test-requireTableIntersect.R | 12 tests/testthat/test-sampleCohorts.R | 318 +++--- tests/testthat/test-stratifyCohorts.R | 324 +++--- tests/testthat/test-subsetCohorts.R | 292 ++--- tests/testthat/test-trimDemographics.R | 96 - tests/testthat/test-unionCohorts.R | 758 +++++++------- tests/testthat/test-yearCohorts.R | 12 vignettes/a01_building_base_cohorts.Rmd | 162 +-- vignettes/a02_cohort_table_requirements.Rmd | 6 vignettes/a03_require_demographics.Rmd | 6 vignettes/a04_require_intersections.Rmd | 6 vignettes/a06_concatanate_cohorts.Rmd | 6 vignettes/a07_filter_cohorts.Rmd | 216 ++-- vignettes/a08_split_cohorts.Rmd | 162 +-- vignettes/a09_combine_cohorts.Rmd | 294 ++--- vignettes/a10_match_cohorts.Rmd | 20 96 files changed, 6180 insertions(+), 5652 deletions(-)
More information about CohortConstructor at CRAN
Permanent link
Title: A Template for Creating Reproducible 'shiny' Applications
Description: Create a skeleton 'shiny' application with create_template() that is
reproducible, can be saved and meets academic standards for attribution.
Forked from 'wallace'. Code is split into modules that are loaded and linked
together automatically and each call one function. Guidance pages explain
modules to users and flexible logging informs them of any errors. Options
enable asynchronous operations, viewing of source code, interactive maps and
data tables. Use to create complex analytical applications, following best
practices in open science and software development. Includes functions for
automating repetitive development tasks and an example application at
run_shinyscholar() that requires
install.packages("shinyscholar", dependencies = TRUE). A guide to developing
applications can be found on the package website.
Author: Simon E. H. Smart [aut, cre, cph],
Tim Lucas [aut] ,
Jamie M. Kass [ctb],
Gonzalo E. Pinilla-Buitrago [ctb],
Andrea Paz [ctb],
Bethany A. Johnson [ctb],
Valentina Grisales-Betancur [ctb],
Dean Attali [ctb],
Matthew E. Aiello-Lammens [ctb],
Cory Merow [...truncated...]
Maintainer: Simon E. H. Smart <simon.smart@cantab.net>
Diff between shinyscholar versions 0.2.2 dated 2025-01-15 and 0.2.3 dated 2025-01-17
shinyscholar-0.2.2/shinyscholar/tools |only shinyscholar-0.2.3/shinyscholar/DESCRIPTION | 12 ++++--- shinyscholar-0.2.3/shinyscholar/MD5 | 17 ++++------ shinyscholar-0.2.3/shinyscholar/NEWS.md | 6 +++ shinyscholar-0.2.3/shinyscholar/R/create_template.R | 6 +-- shinyscholar-0.2.3/shinyscholar/README.md | 2 - shinyscholar-0.2.3/shinyscholar/inst/app_skeleton/global.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/inst/shiny/Rmd/text_intro_tab.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/inst/shiny/Rmd/userReport_intro.Rmd | 2 - shinyscholar-0.2.3/shinyscholar/tests/testthat/test-downloads.R | 3 + 10 files changed, 31 insertions(+), 21 deletions(-)
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu [aut, cre]
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.11 dated 2024-12-04 and 0.2.12 dated 2025-01-17
DESCRIPTION | 8 MD5 | 97 +-- NAMESPACE | 3 NEWS.md | 14 R/RcppExports.R | 896 ++++++++++++++++++------------ R/getDesignProportions.R | 209 ------- R/getDesignSurvivals.R | 277 +++++++++ R/prints.R | 312 +++++----- R/wrappers.R | 16 man/binary_tte_sim.Rd | 2 man/float_to_fraction.Rd |only man/getDesignEquiv.Rd | 144 ---- man/getDesignOddsRatioEquiv.Rd | 14 man/getDesignRiskDiffEquiv.Rd | 15 man/getDesignRiskRatioEquiv.Rd | 14 man/getDurationFromNevents.Rd | 6 man/getNeventsFromHazardRatio.Rd | 2 man/kmpower.Rd | 48 + man/kmpowerequiv.Rd | 46 + man/kmstat.Rd | 12 man/kmstat1.Rd | 12 man/logisregr.Rd | 10 man/lrpowerequiv.Rd | 2 man/lrschoenfeld.Rd |only man/natrisk.Rd | 1 man/nbpowerequiv.Rd | 31 - man/nbsamplesizeequiv.Rd | 9 man/nbstat.Rd | 5 man/nevent.Rd | 1 man/nevent2.Rd | 1 man/patrisk.Rd | 1 man/pevent.Rd | 1 man/qrcpp.Rd | 10 man/rmpower.Rd | 48 + man/rmpowerequiv.Rd | 46 + man/rmstat.Rd | 12 man/rmstat1.Rd | 12 man/svdcpp.Rd |only src/RcppExports.cpp | 435 ++------------- src/kmstat.cpp | 1128 +++++++++++++++------------------------ src/logistic_regression.cpp | 204 ++++++- src/logistic_regression.h | 10 src/lrsim.cpp | 2 src/lrstat.cpp | 279 +++------ src/misc.cpp | 5 src/nbstat.cpp | 695 ++++-------------------- src/rmstat.cpp | 546 ++++++++++++++---- src/survival_analysis.cpp | 597 ++++++++++++++++++++ src/survival_analysis.h | 10 src/utilities.cpp | 912 +++++++++++++++++++++++-------- src/utilities.h | 31 - 51 files changed, 3991 insertions(+), 3200 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust (Kuensch et al. (2011) <doi:10.3929/ethz-a-009900710>) and Gaussian (Harville (1977) <doi:10.1080/01621459.1977.10480998>) (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions (Cressie (1993) <doi:10.1002/9781119115151>), along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes (Davies and Bryant (2013) <doi:10.18637/jss.v055.i09>), unbiased back-transformation of Kriging predictions of log-transformed data (Cressie (2006) <doi:10.1007/s11004-005-9022-8>).
Author: Andreas Papritz [aut, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between georob versions 0.3-21 dated 2025-01-08 and 0.3-22 dated 2025-01-17
georob-0.3-21/georob/vignettes/fig-ash-Kriging-polygons.pdf |only georob-0.3-21/georob/vignettes/fig-ash-bKriging-plot-robust-gaussian-1.pdf |only georob-0.3-21/georob/vignettes/fig-meuse-zinc-block-Kriging-blocks.pdf |only georob-0.3-21/georob/vignettes/fig-meuse-zinc-block-Kriging-plot.pdf |only georob-0.3-22/georob/ChangeLog | 5 georob-0.3-22/georob/DESCRIPTION | 8 georob-0.3-22/georob/MD5 | 22 georob-0.3-22/georob/inst/NEWS.Rd | 14 georob-0.3-22/georob/inst/doc/georob_vignette.R | 254 +- georob-0.3-22/georob/inst/doc/georob_vignette.Rnw | 1107 +++++----- georob-0.3-22/georob/inst/doc/georob_vignette.pdf |binary georob-0.3-22/georob/vignettes/georob_vignette.Rnw | 1107 +++++----- georob-0.3-22/georob/vignettes/r_coalash_objects.RData |binary georob-0.3-22/georob/vignettes/r_meuse_zinc_objects.RData |binary 14 files changed, 1356 insertions(+), 1161 deletions(-)
More information about rtables.officer at CRAN
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More information about MonotonicityTest at CRAN
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Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr [aut, cre]
Maintainer: Frank E Harrell Jr <fh@fharrell.com>
Diff between rms versions 6.9-0 dated 2024-12-12 and 7.0-0 dated 2025-01-17
rms-6.9-0/rms/R/LRchunktest.r |only rms-6.9-0/rms/src/ormuv.f90 |only rms-6.9-0/rms/src/ratfor/ormuv.r |only rms-7.0-0/rms/DESCRIPTION | 14 rms-7.0-0/rms/MD5 | 138 +++-- rms-7.0-0/rms/NAMESPACE | 7 rms-7.0-0/rms/NEWS | 41 + rms-7.0-0/rms/R/Glm.r | 2 rms-7.0-0/rms/R/Ocens.r |only rms-7.0-0/rms/R/anova.rms.s | 187 ++++--- rms-7.0-0/rms/R/bootcov.s | 409 +++++++--------- rms-7.0-0/rms/R/calibrate.default.s | 2 rms-7.0-0/rms/R/contrast.s | 137 ++++- rms-7.0-0/rms/R/fastbw.s | 50 +- rms-7.0-0/rms/R/groupkm.s | 2 rms-7.0-0/rms/R/infoMxop.r |only rms-7.0-0/rms/R/lrm.fit.r | 287 +++++++---- rms-7.0-0/rms/R/lrm.s | 43 + rms-7.0-0/rms/R/ols.s | 4 rms-7.0-0/rms/R/orm.fit.s | 720 ++++++++++++++++------------- rms-7.0-0/rms/R/orm.s | 156 +++--- rms-7.0-0/rms/R/pentrace.s | 44 - rms-7.0-0/rms/R/plotIntercepts.r |only rms-7.0-0/rms/R/predab.resample.s | 4 rms-7.0-0/rms/R/predict.lrm.s | 3 rms-7.0-0/rms/R/predictrms.s | 4 rms-7.0-0/rms/R/quickRefit.r |only rms-7.0-0/rms/R/residuals.lrm.s | 2 rms-7.0-0/rms/R/rexVar.r | 14 rms-7.0-0/rms/R/rmsMisc.s | 266 ++++------ rms-7.0-0/rms/R/sensuc.s | 10 rms-7.0-0/rms/R/summary.rms.s | 6 rms-7.0-0/rms/R/val.prob.s | 59 +- rms-7.0-0/rms/R/validate.lrm.s | 66 +- rms-7.0-0/rms/R/validate.psm.s | 6 rms-7.0-0/rms/inst/tests/Glm.s | 3 rms-7.0-0/rms/inst/tests/Rq2.s | 2 rms-7.0-0/rms/inst/tests/bootcov.r | 3 rms-7.0-0/rms/inst/tests/lrm-orm-penalty.r |only rms-7.0-0/rms/inst/tests/lrm.s | 3 rms-7.0-0/rms/inst/tests/lrmMean.s | 4 rms-7.0-0/rms/inst/tests/modelData.r | 4 rms-7.0-0/rms/inst/tests/orm-bootcov.r | 35 - rms-7.0-0/rms/inst/tests/orm-bootcov2.r |only rms-7.0-0/rms/inst/tests/orm-quantile.r |only rms-7.0-0/rms/inst/tests/orm-residuals.r | 4 rms-7.0-0/rms/inst/tests/orm-weight.r |only rms-7.0-0/rms/inst/tests/orm.s | 50 +- rms-7.0-0/rms/inst/tests/orm2.s | 8 rms-7.0-0/rms/inst/tests/orm5.r | 6 rms-7.0-0/rms/inst/tests/orm7.r |only rms-7.0-0/rms/inst/tests/psm.s | 10 rms-7.0-0/rms/inst/tests/rexVar.r | 4 rms-7.0-0/rms/inst/tests/robcov2.r | 2 rms-7.0-0/rms/inst/tests/scale.r | 31 - rms-7.0-0/rms/man/Ocens.Rd |only rms-7.0-0/rms/man/anova.rms.Rd | 6 rms-7.0-0/rms/man/as.data.frame.Ocens.Rd |only rms-7.0-0/rms/man/bootcov.Rd | 32 + rms-7.0-0/rms/man/contrast.Rd | 52 +- rms-7.0-0/rms/man/fastbw.Rd | 5 rms-7.0-0/rms/man/infoMxop.Rd |only rms-7.0-0/rms/man/lrm.Rd | 10 rms-7.0-0/rms/man/lrm.fit.Rd | 28 - rms-7.0-0/rms/man/ols.Rd | 2 rms-7.0-0/rms/man/orm.Rd | 59 +- rms-7.0-0/rms/man/orm.fit.Rd | 65 +- rms-7.0-0/rms/man/pentrace.Rd | 8 rms-7.0-0/rms/man/plotIntercepts.Rd |only rms-7.0-0/rms/man/predab.resample.Rd | 5 rms-7.0-0/rms/man/residuals.lrm.Rd | 4 rms-7.0-0/rms/man/rexVar.Rd | 8 rms-7.0-0/rms/man/rms-internal.Rd | 1 rms-7.0-0/rms/man/sub-.Ocens.Rd |only rms-7.0-0/rms/man/summary.rms.Rd | 4 rms-7.0-0/rms/man/val.prob.Rd | 2 rms-7.0-0/rms/src/init.c | 10 rms-7.0-0/rms/src/lrmll.f90 | 62 +- rms-7.0-0/rms/src/ormll.f90 |only 79 files changed, 1842 insertions(+), 1373 deletions(-)
Title: Disproportionality Functions for Pharmacovigilance
Description: Tools for performing disproportionality analysis using the information component, proportional reporting rate and the reporting odds ratio. The anticipated use is passing data to the da() function, which executes the disproportionality analysis. See Norén et al (2011) <doi:10.1177/0962280211403604> and Montastruc et al (2011) <doi:10.1111/j.1365-2125.2011.04037.x> for further details.
Author: Oskar Gauffin [aut] ,
Michele Fusaroli [cre]
Maintainer: Michele Fusaroli <michele.fusaroli@who-umc.org>
Diff between pvda versions 0.0.3 dated 2024-03-01 and 0.0.4 dated 2025-01-17
DESCRIPTION | 21 +++++++++++-------- MD5 | 24 +++++++++++----------- NEWS.md | 3 ++ R/da_object_oriented_functions.R | 5 +++- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Disproportionality_analysis.Rmd | 8 +++---- inst/doc/Disproportionality_analysis.html | 32 +++++++++++++++--------------- man/da.Rd | 3 +- man/print.da.Rd | 2 + vignettes/Disproportionality_analysis.Rmd | 8 +++---- vignettes/print_console_printout.png |binary vignettes/summary_console_printout.png |binary 13 files changed, 59 insertions(+), 47 deletions(-)
Title: Interface for Large Language Model APIs in R
Description: A unified interface to interact with various Large Language Model (LLM) APIs such as 'OpenAI' (see <https://platform.openai.com/docs/quickstart> for details), 'Anthropic' (see <https://docs.anthropic.com/en/api/getting-started> for details), 'Groq' (see <https://console.groq.com/docs/api-reference> for details), 'Together AI' (see <https://docs.together.ai/docs/quickstart> for details), 'DeepSeek' (see <https://api-docs.deepseek.com> for details), and 'Voyage AI' (see <https://docs.voyageai.com/docs/introduction> for details). Allows users to configure API parameters, send messages, and retrieve responses seamlessly within R.
Author: Ali Sanaei [aut, cre]
Maintainer: Ali Sanaei <sanaei@uchicago.edu>
Diff between LLMR versions 0.1.1 dated 2024-10-21 and 0.1.2 dated 2025-01-17
DESCRIPTION | 8 - MD5 | 11 + NAMESPACE | 4 R/LLMR.R | 285 +++++++++++++++++++++++++++++------------------- man/call_llm.Rd | 81 +++---------- man/llm_config.Rd | 72 +++++------- man/parse_embeddings.Rd |only 7 files changed, 241 insertions(+), 220 deletions(-)
Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.2 dated 2025-01-07 and 0.2.3 dated 2025-01-17
DESCRIPTION | 12 ++++++------ MD5 | 18 ++++++++++++------ NEWS.md | 6 ++++++ R/t_dor_slide.R | 2 +- inst/WORDLIST | 2 ++ inst/doc/autoslideR.html | 8 ++++---- tests/testthat/_snaps/g_mean_slides |only tests/testthat/t_dm_output.rds |binary 8 files changed, 31 insertions(+), 17 deletions(-)
More information about autoslider.core at CRAN
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Title: CIE XYZ and some of Its Derived Color Spaces
Description: Functions for converting among CIE XYZ, xyY, Lab, and Luv.
Calculate Correlated Color Temperature (CCT) and the Planckian and daylight loci.
The XYZs of some standard illuminants and some standard linear chromatic adaptation transforms (CATs) are included.
Three standard color difference metrics are included.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between spacesXYZ versions 1.3-0 dated 2024-01-23 and 1.4-0 dated 2025-01-17
spacesXYZ-1.3-0/spacesXYZ/R/logging.R |only spacesXYZ-1.4-0/spacesXYZ/DESCRIPTION | 14 spacesXYZ-1.4-0/spacesXYZ/MD5 | 36 spacesXYZ-1.4-0/spacesXYZ/NAMESPACE | 1 spacesXYZ-1.4-0/spacesXYZ/NEWS.md | 7 spacesXYZ-1.4-0/spacesXYZ/R/CCT.R | 1618 ++++++++++----------- spacesXYZ-1.4-0/spacesXYZ/R/DeltaE.R | 4 spacesXYZ-1.4-0/spacesXYZ/R/adaptation.R | 564 +++---- spacesXYZ-1.4-0/spacesXYZ/R/basic.R | 748 ++++----- spacesXYZ-1.4-0/spacesXYZ/R/datasets.R | 5 spacesXYZ-1.4-0/spacesXYZ/R/daylight.R | 100 - spacesXYZ-1.4-0/spacesXYZ/R/hooks.R | 60 spacesXYZ-1.4-0/spacesXYZ/R/logger.R |only spacesXYZ-1.4-0/spacesXYZ/R/quintic.R | 234 +-- spacesXYZ-1.4-0/spacesXYZ/R/utils.R | 100 - spacesXYZ-1.4-0/spacesXYZ/build/vignette.rds |binary spacesXYZ-1.4-0/spacesXYZ/inst/doc/adaptation.R | 26 spacesXYZ-1.4-0/spacesXYZ/inst/doc/adaptation.html | 634 +++++--- spacesXYZ-1.4-0/spacesXYZ/inst/doc/isotherms.pdf |binary spacesXYZ-1.4-0/spacesXYZ/man/spacesXYZ-package.Rd | 36 20 files changed, 2255 insertions(+), 1932 deletions(-)
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre],
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Davide Garolini [aut],
Emily de la Rua [aut],
Abinaya Yogasekaram [aut],
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jennifer [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.6 dated 2024-09-24 and 0.9.7 dated 2025-01-17
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tern-0.9.7/tern/R/count_cumulative.R | 21 tern-0.9.7/tern/R/count_missed_doses.R | 13 tern-0.9.7/tern/R/count_occurrences.R | 67 tern-0.9.7/tern/R/count_occurrences_by_grade.R | 156 + tern-0.9.7/tern/R/count_patients_events_in_cols.R | 7 tern-0.9.7/tern/R/count_patients_with_event.R | 107 - tern-0.9.7/tern/R/count_patients_with_flags.R | 143 + tern-0.9.7/tern/R/count_values.R | 96 - tern-0.9.7/tern/R/estimate_multinomial_rsp.R | 5 tern-0.9.7/tern/R/estimate_proportion.R | 5 tern-0.9.7/tern/R/formatting_functions.R | 2 tern-0.9.7/tern/R/g_forest.R | 1 tern-0.9.7/tern/R/g_ipp.R | 2 tern-0.9.7/tern/R/g_km.R | 1 tern-0.9.7/tern/R/g_lineplot.R | 39 tern-0.9.7/tern/R/g_step.R | 1 tern-0.9.7/tern/R/g_waterfall.R | 1 tern-0.9.7/tern/R/incidence_rate.R | 5 tern-0.9.7/tern/R/odds_ratio.R | 34 tern-0.9.7/tern/R/package.R | 3 tern-0.9.7/tern/R/prop_diff.R | 5 tern-0.9.7/tern/R/prop_diff_test.R | 5 tern-0.9.7/tern/R/riskdiff.R | 3 tern-0.9.7/tern/R/summarize_ancova.R | 5 tern-0.9.7/tern/R/summarize_change.R | 150 + tern-0.9.7/tern/R/summarize_coxreg.R | 5 tern-0.9.7/tern/R/summarize_glm_count.R | 85 - 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Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Oblique Random Forest ('aorsf'), Recursive Partitioning ('RPART') or step wise regression models are fit. Cross validation leave out samples (leading to nested cross validation) or bootstrap out-of-bag samples are used to evaluate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (outer nested) cross validation or bootstrap leave out (out of bag) samples.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied by using the 'path=TRUE' option when calling [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.5-4 dated 2024-10-24 and 0.5-5 dated 2025-01-17
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glmnetr-0.5-5/glmnetr/man/boot.factor.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/calplot.Rd | 19 + glmnetr-0.5-5/glmnetr/man/cox.sat.dev.Rd | 2 glmnetr-0.5-5/glmnetr/man/devrat_.Rd | 2 glmnetr-0.5-5/glmnetr/man/diff_time.Rd | 2 glmnetr-0.5-5/glmnetr/man/diff_time1.Rd | 2 glmnetr-0.5-5/glmnetr/man/factor.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/get.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/get.id.foldid.Rd | 2 glmnetr-0.5-5/glmnetr/man/glmnetr.compcv.Rd | 24 + glmnetr-0.5-5/glmnetr/man/glmnetr.simdata.Rd | 2 glmnetr-0.5-5/glmnetr/man/glmnetr_seed.Rd | 6 glmnetr-0.5-5/glmnetr/man/nested.cis.Rd | 11 glmnetr-0.5-5/glmnetr/man/nested.compare.Rd | 8 glmnetr-0.5-5/glmnetr/man/nested.compare_0_5_1.Rd |only glmnetr-0.5-5/glmnetr/man/nested.glmnetr.Rd | 43 ++- glmnetr-0.5-5/glmnetr/man/orf_tune.Rd | 6 glmnetr-0.5-5/glmnetr/man/plot.cv.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/plot.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/plot.nested.glmnetr.Rd | 4 glmnetr-0.5-5/glmnetr/man/plot_perf_glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/print.nested.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/print.orf_tune.Rd | 2 glmnetr-0.5-5/glmnetr/man/roundperf.Rd | 2 glmnetr-0.5-5/glmnetr/man/summary.nested.glmnetr.Rd | 2 glmnetr-0.5-5/glmnetr/man/summary.orf_tune.Rd | 2 glmnetr-0.5-5/glmnetr/vignettes/An_Overview_of_glmnetr_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/An_Overview_of_glmnetr_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Calibration_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Calibration_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Ridge_and_Lasso_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Ridge_and_Lasso_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Using_ann_tab_cv_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Using_ann_tab_cv_241228.pdf.asis |only glmnetr-0.5-5/glmnetr/vignettes/Using_stepreg_241228.Rmd |only glmnetr-0.5-5/glmnetr/vignettes/Using_stepreg_241228.pdf.asis |only 99 files changed, 202 insertions(+), 117 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-28 0.2.1
2022-08-31 0.2.0
2021-01-19 0.1.0