Title: Multivariate (Dynamic) Generalized Additive Models
Description: Fit Bayesian Dynamic Generalized Additive Models to sets of time series. Users can build dynamic nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2022) <doi:10.1111/2041-210X.13974>.
Author: Nicholas J Clark [aut, cre]
Maintainer: Nicholas J Clark <nicholas.j.clark1214@gmail.com>
Diff between mvgam versions 1.1.2 dated 2024-07-01 and 1.1.3 dated 2024-09-03
mvgam-1.1.2/mvgam/R/ti.R |only mvgam-1.1.2/mvgam/man/ti.Rd |only mvgam-1.1.3/mvgam/DESCRIPTION | 19 mvgam-1.1.3/mvgam/MD5 | 318 - mvgam-1.1.3/mvgam/NAMESPACE | 610 +- mvgam-1.1.3/mvgam/NEWS.md | 57 mvgam-1.1.3/mvgam/R/RW.R | 258 mvgam-1.1.3/mvgam/R/add_MACor.R | 2386 ++++---- mvgam-1.1.3/mvgam/R/add_base_dgam_lines.R | 8 mvgam-1.1.3/mvgam/R/add_binomial.R | 462 - mvgam-1.1.3/mvgam/R/add_nmixture.R | 1446 ++--- mvgam-1.1.3/mvgam/R/add_residuals.R | 44 mvgam-1.1.3/mvgam/R/add_stan_data.R | 1442 ++--- mvgam-1.1.3/mvgam/R/add_trend_lines.R | 88 mvgam-1.1.3/mvgam/R/add_tweedie_lines.R | 120 mvgam-1.1.3/mvgam/R/as.data.frame.mvgam.R | 1026 +-- mvgam-1.1.3/mvgam/R/backends.R | 378 - mvgam-1.1.3/mvgam/R/compute_edf.R | 252 mvgam-1.1.3/mvgam/R/conditional_effects.R | 635 +- mvgam-1.1.3/mvgam/R/data_grids.R | 186 mvgam-1.1.3/mvgam/R/dynamic.R | 284 - mvgam-1.1.3/mvgam/R/ensemble.R |only mvgam-1.1.3/mvgam/R/evaluate_mvgams.R | 1728 +++--- mvgam-1.1.3/mvgam/R/families.R | 3201 ++++++------ mvgam-1.1.3/mvgam/R/forecast.mvgam.R | 2 mvgam-1.1.3/mvgam/R/get_linear_predictors.R | 2 mvgam-1.1.3/mvgam/R/get_monitor_pars.R | 70 mvgam-1.1.3/mvgam/R/get_mvgam_priors.R | 2681 +++++----- mvgam-1.1.3/mvgam/R/globals.R | 2 mvgam-1.1.3/mvgam/R/gp.R | 1 mvgam-1.1.3/mvgam/R/gratia_methods.R |only mvgam-1.1.3/mvgam/R/hindcast.mvgam.R | 406 - 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mvgam-1.1.3/mvgam/tests/testthat/test-offset.R | 214 mvgam-1.1.3/mvgam/tests/testthat/test-piecewise.R | 344 - mvgam-1.1.3/mvgam/tests/testthat/test-sim_mvgam.R | 92 mvgam-1.1.3/mvgam/tests/testthat/test-update.R | 84 mvgam-1.1.3/mvgam/vignettes/SS_model.svg | 485 - mvgam-1.1.3/mvgam/vignettes/data_in_mvgam.Rmd | 13 mvgam-1.1.3/mvgam/vignettes/forecast_evaluation.Rmd | 8 mvgam-1.1.3/mvgam/vignettes/mvgam_overview.Rmd | 8 mvgam-1.1.3/mvgam/vignettes/nmixtures.Rmd | 20 mvgam-1.1.3/mvgam/vignettes/shared_states.Rmd | 12 mvgam-1.1.3/mvgam/vignettes/time_varying_effects.Rmd | 8 mvgam-1.1.3/mvgam/vignettes/trend_formulas.Rmd | 55 mvgam-1.1.3/mvgam/vignettes/trend_formulas.html |only 167 files changed, 24766 insertions(+), 24079 deletions(-)
Title: Graph/Network Analysis Based on L1 Centrality
Description: Analyze graph/network data using L1 centrality and prestige. Functions for deriving global, local, and group L1 centrality/prestige are provided. Routines for visual inspection of a graph/network are also provided. Details are in Kang and Oh (2024a) <doi:10.48550/arXiv.2404.13233> and Kang and Oh (2024b) <doi:10.48550/arXiv.2408.12078>.
Author: Seungwoo Kang [aut, cre] ,
Hee-Seok Oh [aut]
Maintainer: Seungwoo Kang <kangsw0401@snu.ac.kr>
Diff between L1centrality versions 0.2.0 dated 2024-08-20 and 0.2.1 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 8 +++++++- R/L1cent.R | 8 ++++---- R/L1centEDGE.R | 14 ++++++++------ R/L1centLOC.R | 22 +++++++++++++--------- R/L1centMDS.R | 9 +++++---- R/L1centNB.R | 13 +++++++------ man/L1cent.Rd | 8 ++++---- man/L1centEDGE.Rd | 14 ++++++++------ man/L1centLOC.Rd | 22 +++++++++++++--------- man/L1centMDS.Rd | 9 +++++---- man/L1centNB.Rd | 13 +++++++------ 13 files changed, 97 insertions(+), 75 deletions(-)
Title: Generalized Linear Models Extended
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses,
including parametric links and heteroscedastic latent variables.
Author: Achim Zeileis [aut, cre] ,
Roger Koenker [aut] ,
Philipp Doebler [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between glmx versions 0.2-0 dated 2023-03-27 and 0.2-1 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 5 +++++ build/partial.rdb |binary tests/Examples/glmx-Ex.Rout.save | 16 ++++++++-------- 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Random Forests for Multiple Imputation Based on 'ranger'
Description: An updated implementation of R package 'ranger' by Wright et al,
(2017) <doi:10.18637/jss.v077.i01> for training and predicting from random
forests, particularly suited to high-dimensional data, and for embedding in
'Multiple Imputation by Chained Equations' (MICE) by van Buuren (2007)
<doi:10.1177/0962280206074463>. Ensembles of classification and regression
trees are currently supported. Sparse data of class 'dgCMatrix' (R package
'Matrix') can be directly analyzed. Conventional bagged predictions are
available alongside an efficient prediction for MICE via the algorithm
proposed by Doove et al (2014) <doi:10.1016/j.csda.2013.10.025>. Survival
and probability forests are not supported in the update, nor is data of
class 'gwaa.data' (R package 'GenABEL'); use the original 'ranger' package
for these analyses.
Author: Stephen Wade [aut, cre] ,
Marvin N Wright [ctb]
Maintainer: Stephen Wade <stephematician@gmail.com>
Diff between literanger versions 0.0.2 dated 2023-07-13 and 0.1.0 dated 2024-09-03
COPYING | 2 DESCRIPTION | 14 ++-- MD5 | 118 ++++++++++++++++++----------------- NAMESPACE | 2 NEWS.md | 106 ++++++++++++++++++++----------- R/cpp11.R | 8 ++ R/io.R |only R/literanger-package.R | 23 +++--- R/predict.R | 22 ++++-- R/train.R | 23 ++++-- R/utility.R | 9 +- README.md | 103 +++++++++++++++++------------- build/partial.rdb |binary man/literanger-package.Rd | 16 ++-- man/predict.literanger.Rd | 2 man/read_literanger.Rd |only man/train.Rd | 2 man/write_literanger.Rd |only src/Data.decl.h | 2 src/Data.defn.h | 8 +- src/Data.h | 2 src/DataR.h | 9 +- src/DataSparse.h | 11 +-- src/Forest.decl.h | 2 src/Forest.defn.h | 2 src/ForestBase.decl.h | 13 +++ src/ForestBase.defn.h | 32 +++++++++ src/ForestClassification.decl.h | 25 ++++++- src/ForestClassification.defn.h | 71 ++++++++++++++++++++- src/ForestClassification.h | 2 src/ForestRegression.decl.h | 24 ++++++- src/ForestRegression.defn.h | 50 ++++++++++++++ src/ForestRegression.h | 2 src/Tree.decl.h | 10 +- src/Tree.defn.h | 28 ++++---- src/TreeBase.decl.h | 23 ++++++ src/TreeBase.defn.h | 53 +++++++++++++++ src/TreeClassification.decl.h | 35 +++++++++- src/TreeClassification.defn.h | 98 ++++++++++++++++++++++++++--- src/TreeClassification.h | 2 src/TreeParameters.h | 28 +++++++- src/TreeRegression.decl.h | 31 ++++++++- src/TreeRegression.defn.h | 112 +++++++++++++++++++++++++++++---- src/TreeRegression.h | 2 src/cpp11.cpp | 20 +++++ src/cpp11_io.cpp |only src/cpp11_io.decl.h |only src/cpp11_predict.cpp | 14 ++-- src/cpp11_predict.decl.h | 10 +- src/cpp11_train.cpp | 10 +- src/cpp11_train.decl.h | 9 +- src/cpp11_utility.h | 9 +- src/enum_types.h | 63 ++++++++++++++++++ src/globals.h | 2 src/utility.h | 7 +- src/utility_draw.h | 8 +- src/utility_interrupt.h | 2 src/utility_lgamma.h | 2 src/utility_math.h | 2 tests/testthat/test-char.R | 9 ++ tests/testthat/test-classification.R | 44 ++++++++++--- tests/testthat/test-interface.R | 46 +++++++++++++ tests/testthat/test-io.R |only 63 files changed, 1062 insertions(+), 322 deletions(-)
Title: Genome-Wide Identity-by-Descent
Description: Methods and tools for the analysis of Genome Wide
Identity-by-Descent ('gwid') mapping data, focusing on testing whether there
is a higher occurrence of Identity-By-Descent (IBD) segments around potential causal variants
in cases compared to controls, which is crucial for identifying rare
variants. To enhance its analytical power, 'gwid' incorporates a Sliding
Window Approach, allowing for the detection and analysis of signals from
multiple Single Nucleotide Polymorphisms (SNPs).
Author: Soroush Mahmoudiandehkordi [aut, cre],
Steven J Schrodi [aut],
Mehdi Maadooliat [aut]
Maintainer: Soroush Mahmoudiandehkordi <soroushmdg@gmail.com>
Diff between gwid versions 0.2.0 dated 2024-06-10 and 0.3.0 dated 2024-09-03
gwid-0.2.0/gwid/build |only gwid-0.2.0/gwid/inst/doc |only gwid-0.2.0/gwid/vignettes |only gwid-0.3.0/gwid/DESCRIPTION | 7 gwid-0.3.0/gwid/LICENSE | 4 gwid-0.3.0/gwid/MD5 | 115 gwid-0.3.0/gwid/NAMESPACE | 110 gwid-0.3.0/gwid/NEWS.md | 2 gwid-0.3.0/gwid/R/case_control.R | 108 gwid-0.3.0/gwid/R/extract.R | 948 ++--- gwid-0.3.0/gwid/R/haplotype_structure.R | 910 ++--- gwid-0.3.0/gwid/R/launch_app.R | 1586 +++++----- gwid-0.3.0/gwid/R/plot.R | 1 gwid-0.3.0/gwid/R/roh.R | 384 +- gwid-0.3.0/gwid/README.md | 621 ++- gwid-0.3.0/gwid/man/build_gwas.Rd | 48 gwid-0.3.0/gwid/man/build_gwid.Rd | 54 gwid-0.3.0/gwid/man/build_phase.Rd | 40 gwid-0.3.0/gwid/man/case_control.Rd | 44 gwid-0.3.0/gwid/man/extract.Rd | 38 gwid-0.3.0/gwid/man/extract.gwas.Rd | 142 gwid-0.3.0/gwid/man/extract.gwid.Rd | 136 gwid-0.3.0/gwid/man/extract_window.Rd | 40 gwid-0.3.0/gwid/man/extract_window.gwid.Rd | 142 gwid-0.3.0/gwid/man/figures/README-unnamed-chunk-7-1.png |binary gwid-0.3.0/gwid/man/figures/README-unnamed-chunk-7-2.png |only gwid-0.3.0/gwid/man/figures/README-unnamed-chunk-8-1.png |only gwid-0.3.0/gwid/man/fisher_test.Rd | 42 gwid-0.3.0/gwid/man/fisher_test.gwas.Rd | 164 - gwid-0.3.0/gwid/man/fisher_test.gwid.Rd | 168 - gwid-0.3.0/gwid/man/fisher_test.result_snps.Rd | 160 - gwid-0.3.0/gwid/man/gtest.Rd | 42 gwid-0.3.0/gwid/man/gtest.haplotype_structure.Rd | 48 gwid-0.3.0/gwid/man/haplotype_frequency.Rd | 128 gwid-0.3.0/gwid/man/haplotype_frequency.haplotype_structure.Rd | 130 gwid-0.3.0/gwid/man/haplotype_structure.Rd | 40 gwid-0.3.0/gwid/man/haplotype_structure.gwas.Rd | 144 gwid-0.3.0/gwid/man/haplotype_structure.gwid.Rd | 144 gwid-0.3.0/gwid/man/launch_app.Rd | 42 gwid-0.3.0/gwid/man/mcnemar_test.Rd | 42 gwid-0.3.0/gwid/man/mcnemar_test.result_snps.Rd | 60 gwid-0.3.0/gwid/man/mcnemar_test_permut.Rd | 42 gwid-0.3.0/gwid/man/mcnemar_test_permut.result_snps.Rd | 78 gwid-0.3.0/gwid/man/permutation_test.Rd | 42 gwid-0.3.0/gwid/man/permutation_test.gwas.Rd | 164 - gwid-0.3.0/gwid/man/permutation_test.gwid.Rd | 170 - gwid-0.3.0/gwid/man/permutation_test.haplotype_structure.Rd | 142 gwid-0.3.0/gwid/man/plot.gwas.Rd | 136 gwid-0.3.0/gwid/man/plot.gwid.Rd | 162 - gwid-0.3.0/gwid/man/plot.haplotype_frequency.Rd | 186 - gwid-0.3.0/gwid/man/plot.haplotype_structure_frequency.Rd | 166 - gwid-0.3.0/gwid/man/plot.result_snps.Rd | 154 gwid-0.3.0/gwid/man/plot.test_snps.Rd | 184 - gwid-0.3.0/gwid/man/print.gwas.Rd | 128 gwid-0.3.0/gwid/man/roh.Rd | 38 gwid-0.3.0/gwid/man/roh.phase.Rd | 82 gwid-0.3.0/gwid/man/subset.Rd | 40 gwid-0.3.0/gwid/man/subset.gwid.Rd | 136 58 files changed, 4447 insertions(+), 4437 deletions(-)
Title: Object Oriented Implementation of Probability Models
Description: Implements S4 classes for probability models based on packages 'distr' and
'distrEx'.
Author: Matthias Kohl [aut, cph],
Peter Ruckdeschel [cre, cph],
R Core Team [ctb, cph]
Maintainer: Peter Ruckdeschel <peter.ruckdeschel@uni-oldenburg.de>
Diff between distrMod versions 2.9.3 dated 2024-08-30 and 2.9.4 dated 2024-09-03
DESCRIPTION | 18 ++++++++--------- MD5 | 10 ++++----- inst/NEWS | 8 +++++++ inst/doc/distrMod.pdf |binary man/0distrMod-package.Rd | 6 ++--- tests/Examples/distrMod-Ex.Rout.save | 36 +++++++++++++++++------------------ 6 files changed, 43 insertions(+), 35 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre],
Rasmus Munk Larsen [ctb, cph],
Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.5.5 dated 2023-11-28 and 0.5.6 dated 2024-09-03
DESCRIPTION | 20 ++++++++++++--- MD5 | 29 ++++++++++++---------- src/extmat.c | 8 +++--- src/propack/propack_svd.c | 9 +++---- src/trlan/restart.c | 1 src/trlan/trl_comm_none.c | 1 src/trlan/trlan.c | 59 +++++++++++++++++++++++----------------------- src/trlan/trlan_R.c | 21 ++++++++-------- src/trlan/trlaux.c | 12 ++++----- src/trlan/trlcore.c | 6 ++-- src/trlan/ztrlan.c | 28 ++++++++++----------- src/trlan/ztrlan_R.c | 29 +++++++++++----------- src/trlan/ztrlaux.c | 4 +-- src/trlan/ztrlcore.c | 44 +++++++++++++++++----------------- tests |only 15 files changed, 146 insertions(+), 125 deletions(-)
Title: Interact with Data on 'SurveyCTO'
Description: 'SurveyCTO' is a platform for mobile data collection in offline settings.
The 'rsurveycto' R package uses the 'SurveyCTO' REST API
<https://docs.surveycto.com/05-exporting-and-publishing-data/05-api-access/01.api-access.html>
to read datasets and forms from a 'SurveyCTO' server into R as 'data.table's
and to download file attachments. The package also has limited support to
write datasets to a server.
Author: Jake Hughey [aut, cre],
Robert On [aut]
Maintainer: Jake Hughey <jake@agency.fund>
Diff between rsurveycto versions 0.2.0 dated 2024-08-17 and 0.2.1 dated 2024-09-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/scto_get_form_metadata.R | 19 ++++++++++++++----- R/scto_meta.R | 13 +++++++------ tests/testthat/scto_auth.txt | 2 +- 5 files changed, 29 insertions(+), 19 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), this package implements
features like bootstrapping or simulating of parameters and models,
feature reduction (feature extraction and variable selection) as well
as functions to describe data and variable characteristics (e.g.
skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut] ,
Mattan S. Ben-Shachar [aut] ,
Indrajeet Patil [aut] ,
Soeren Hoejsgaard [aut],
Brenton M. Wiernik [aut] ,
Zen J. Lau [ctb],
Vincent Arel-Bundock [ctb] ,
Jeffrey Girard [ctb] ,
Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between parameters versions 0.22.1 dated 2024-07-21 and 0.22.2 dated 2024-09-03
parameters-0.22.1/parameters/R/methods_serp.R |only parameters-0.22.1/parameters/R/methods_tseries.R |only parameters-0.22.2/parameters/DESCRIPTION | 33 - parameters-0.22.2/parameters/MD5 | 203 +++---- parameters-0.22.2/parameters/NAMESPACE | 83 +-- parameters-0.22.2/parameters/NEWS.md | 22 parameters-0.22.2/parameters/R/1_model_parameters.R | 131 ++++ parameters-0.22.2/parameters/R/2_ci.R | 7 parameters-0.22.2/parameters/R/3_p_value.R | 54 -- parameters-0.22.2/parameters/R/4_standard_error.R | 59 +- parameters-0.22.2/parameters/R/ci_generic.R | 15 parameters-0.22.2/parameters/R/compare_parameters.R | 16 parameters-0.22.2/parameters/R/dof.R | 269 +--------- parameters-0.22.2/parameters/R/equivalence_test.R | 122 +++- parameters-0.22.2/parameters/R/extract_parameters.R | 38 - parameters-0.22.2/parameters/R/format.R | 16 parameters-0.22.2/parameters/R/format_parameters.R | 2 parameters-0.22.2/parameters/R/methods_BBMM.R | 15 parameters-0.22.2/parameters/R/methods_base.R | 31 - parameters-0.22.2/parameters/R/methods_bfsl.R | 17 parameters-0.22.2/parameters/R/methods_biglm.R | 9 parameters-0.22.2/parameters/R/methods_brglm2.R | 13 parameters-0.22.2/parameters/R/methods_cgam.R | 35 - parameters-0.22.2/parameters/R/methods_effect_size.R | 14 parameters-0.22.2/parameters/R/methods_emmeans.R | 107 +-- parameters-0.22.2/parameters/R/methods_fixest.R | 44 - parameters-0.22.2/parameters/R/methods_flexsurvreg.R | 2 parameters-0.22.2/parameters/R/methods_gee.R | 6 parameters-0.22.2/parameters/R/methods_glmgee.R | 6 parameters-0.22.2/parameters/R/methods_hglm.R | 9 parameters-0.22.2/parameters/R/methods_ivfixed.R | 21 parameters-0.22.2/parameters/R/methods_ivprobit.R | 5 parameters-0.22.2/parameters/R/methods_lm.R | 8 parameters-0.22.2/parameters/R/methods_lme4.R | 16 parameters-0.22.2/parameters/R/methods_lmtest.R | 5 parameters-0.22.2/parameters/R/methods_lqmm.R | 11 parameters-0.22.2/parameters/R/methods_lrm.R | 8 parameters-0.22.2/parameters/R/methods_mass.R | 24 parameters-0.22.2/parameters/R/methods_mediate.R | 6 parameters-0.22.2/parameters/R/methods_merTools.R | 7 parameters-0.22.2/parameters/R/methods_mfx.R | 44 - parameters-0.22.2/parameters/R/methods_mhurdle.R | 6 parameters-0.22.2/parameters/R/methods_mice.R | 59 -- parameters-0.22.2/parameters/R/methods_mmrm.R | 15 parameters-0.22.2/parameters/R/methods_model_fit.R | 10 parameters-0.22.2/parameters/R/methods_multcomp.R | 6 parameters-0.22.2/parameters/R/methods_nestedLogit.R | 34 - parameters-0.22.2/parameters/R/methods_nlme.R | 10 parameters-0.22.2/parameters/R/methods_other.R | 7 parameters-0.22.2/parameters/R/methods_plm.R | 10 parameters-0.22.2/parameters/R/methods_posterior.R | 4 parameters-0.22.2/parameters/R/methods_quantreg.R | 33 - parameters-0.22.2/parameters/R/methods_selection.R | 8 parameters-0.22.2/parameters/R/methods_survey.R | 2 parameters-0.22.2/parameters/R/methods_svy2lme.R | 6 parameters-0.22.2/parameters/R/methods_systemfit.R | 22 parameters-0.22.2/parameters/R/methods_truncreg.R | 4 parameters-0.22.2/parameters/R/methods_vgam.R | 11 parameters-0.22.2/parameters/R/methods_weightit.R |only parameters-0.22.2/parameters/R/p_significance.R |only parameters-0.22.2/parameters/R/print.compare_parameters.R | 3 parameters-0.22.2/parameters/R/print.parameters_model.R | 6 parameters-0.22.2/parameters/R/utils_format.R | 27 - parameters-0.22.2/parameters/README.md | 160 +++++ parameters-0.22.2/parameters/inst/WORDLIST | 9 parameters-0.22.2/parameters/man/ci.default.Rd | 7 parameters-0.22.2/parameters/man/degrees_of_freedom.Rd | 76 +- parameters-0.22.2/parameters/man/display.parameters_model.Rd | 3 parameters-0.22.2/parameters/man/equivalence_test.lm.Rd | 90 +++ parameters-0.22.2/parameters/man/format_parameters.Rd | 2 parameters-0.22.2/parameters/man/model_parameters.Rd | 80 ++ parameters-0.22.2/parameters/man/model_parameters.averaging.Rd | 15 parameters-0.22.2/parameters/man/model_parameters.cgam.Rd | 15 parameters-0.22.2/parameters/man/model_parameters.default.Rd | 39 + parameters-0.22.2/parameters/man/model_parameters.glht.Rd | 15 parameters-0.22.2/parameters/man/model_parameters.htest.Rd | 15 parameters-0.22.2/parameters/man/model_parameters.merMod.Rd | 26 parameters-0.22.2/parameters/man/model_parameters.mira.Rd | 44 - parameters-0.22.2/parameters/man/model_parameters.mlm.Rd | 26 parameters-0.22.2/parameters/man/model_parameters.rma.Rd | 15 parameters-0.22.2/parameters/man/model_parameters.stanreg.Rd | 35 - parameters-0.22.2/parameters/man/model_parameters.zcpglm.Rd | 15 parameters-0.22.2/parameters/man/n_clusters.Rd | 15 parameters-0.22.2/parameters/man/p_significance.lm.Rd |only parameters-0.22.2/parameters/man/p_value.Rd | 18 parameters-0.22.2/parameters/man/print.compare_parameters.Rd | 6 parameters-0.22.2/parameters/man/print.parameters_model.Rd | 8 parameters-0.22.2/parameters/man/reexports.Rd | 5 parameters-0.22.2/parameters/man/standard_error.Rd | 27 - parameters-0.22.2/parameters/tests/testthat/_snaps/brms.md |only parameters-0.22.2/parameters/tests/testthat/_snaps/equivalence_test.md | 34 - parameters-0.22.2/parameters/tests/testthat/_snaps/model_parameters.glmgee.md |only parameters-0.22.2/parameters/tests/testthat/_snaps/p_significance.md |only parameters-0.22.2/parameters/tests/testthat/_snaps/weightit.md |only parameters-0.22.2/parameters/tests/testthat/test-base.R | 6 parameters-0.22.2/parameters/tests/testthat/test-bootstrap_emmeans.R | 2 parameters-0.22.2/parameters/tests/testthat/test-brms.R |only parameters-0.22.2/parameters/tests/testthat/test-compare_parameters.R | 2 parameters-0.22.2/parameters/tests/testthat/test-equivalence_test.R | 26 parameters-0.22.2/parameters/tests/testthat/test-model_parameters.aov.R | 2 parameters-0.22.2/parameters/tests/testthat/test-model_parameters.glmgee.R |only parameters-0.22.2/parameters/tests/testthat/test-p_significance.R |only parameters-0.22.2/parameters/tests/testthat/test-p_value.R | 2 parameters-0.22.2/parameters/tests/testthat/test-printing-stan.R | 2 parameters-0.22.2/parameters/tests/testthat/test-printing2.R | 2 parameters-0.22.2/parameters/tests/testthat/test-rank_deficienty.R | 2 parameters-0.22.2/parameters/tests/testthat/test-robust.R | 6 parameters-0.22.2/parameters/tests/testthat/test-serp.R | 2 parameters-0.22.2/parameters/tests/testthat/test-weightit.R |only 109 files changed, 1333 insertions(+), 1337 deletions(-)
Title: Read 'Blackrock-Microsystems' Files ('NEV', 'NSx')
Description: Loads 'Blackrock' <https://blackrockneurotech.com> neural signal
data files into the memory, provides utility tools to extract the data into
common formats such as plain-text 'tsv' and 'HDF5'.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between readNSx versions 0.0.4 dated 2024-02-24 and 0.0.5 dated 2024-09-03
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ build/vignette.rds |binary src/rawToSEXP.cpp | 4 ++-- src/readBCI.h | 33 +++++++++++++++++++++++++++------ 6 files changed, 44 insertions(+), 18 deletions(-)
Title: Penalized Multivariate Analysis
Description: Performs Penalized Multivariate Analysis: a penalized
matrix decomposition, sparse principal components analysis,
and sparse canonical correlation analysis, described in
Witten, Tibshirani and Hastie (2009)
<doi:10.1093/biostatistics/kxp008> and Witten and Tibshirani
(2009) Extensions of sparse canonical correlation analysis,
with applications to genomic data
<doi:10.2202/1544-6115.1470>.
Author: Daniela Witten [aut],
Rob Tibshirani [aut],
Sam Gross [aut],
Balasubramanian Narasimhan [cre, aut]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between PMA versions 1.2-3 dated 2024-02-06 and 1.2-4 dated 2024-09-03
DESCRIPTION | 10 +++---- MD5 | 23 +++++++++-------- NAMESPACE | 1 NEWS.md | 6 ++++ R/MultiCCA.R | 2 + R/PMA-package.R | 5 +-- build/partial.rdb |binary cleanup |only man/PMA-package.Rd | 21 +++++++++++++++- src/FLSA.cc | 40 +++++++++++++++--------------- src/FLSAGeneral.cc | 2 - src/FLSAGeneralMain.cc | 4 +-- src/Groups.cc | 64 ++++++++++++++++++++++++------------------------- 13 files changed, 103 insertions(+), 75 deletions(-)
Title: Supplementary Distributions
Description: Ten distributions supplementing those built into R.
Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi
squared, Spearman's rho, maximum F ratio, the Pearson product
moment correlation coefficient, Johnson distributions, normal
scores and generalized hypergeometric distributions.
Author: Bob Wheeler [aut],
Thorsten Pohlert [ctb, cre]
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between SuppDists versions 1.1-9.7 dated 2022-01-03 and 1.1-9.8 dated 2024-09-03
SuppDists-1.1-9.7/SuppDists/src/Makevars |only SuppDists-1.1-9.8/SuppDists/DESCRIPTION | 8 ++--- SuppDists-1.1-9.8/SuppDists/MD5 | 7 +--- SuppDists-1.1-9.8/SuppDists/inst/NEWS.Rd | 9 +++++ SuppDists-1.1-9.8/SuppDists/src/dists.cpp | 48 ++++++++++++++++-------------- 5 files changed, 42 insertions(+), 30 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.1.7 dated 2024-07-17 and 0.1.8 dated 2024-09-03
DESCRIPTION | 6 - MD5 | 34 +++---- NAMESPACE | 7 + NEWS.md | 8 + R/RcppExports.R | 4 R/filter-fftfilt.R |only R/filter-filtfilt.R | 85 +++++++++++++++++- R/filter-fir-design.R | 6 - R/filter-utils.R | 158 +++++++++++++++++++++++++---------- R/filter.R | 7 + R/misc.R | 23 +++-- R/pwelch.R | 145 +++++++++++++++++++++++--------- inst/include/ravetools_RcppExports.h | 21 ++++ man/filter-window.Rd |only man/pwelch.Rd | 34 ++++++- src/RcppExports.cpp | 40 ++++++++ src/fftw-wrapper.cpp | 59 ++++++++++++- tests/testthat/test-filter.R | 38 ++++++++ tests/testthat/test-pwelch.R | 9 + 19 files changed, 553 insertions(+), 131 deletions(-)
Title: A 'Bootstrap 4' Version of 'shinydashboard'
Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power
of 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
<https://github.com/ColorlibHQ/AdminLTE>.
Author: David Granjon [aut, cre],
RinteRface [cph],
Almasaeed Studio [ctb, cph] ,
Winston Chang [ctb, cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Diff between bs4Dash versions 2.3.3 dated 2024-01-23 and 2.3.4 dated 2024-09-03
bs4Dash-2.3.3/bs4Dash/build/bs4Dash.pdf |only bs4Dash-2.3.3/bs4Dash/inst/bs4Dash-2.3.3 |only bs4Dash-2.3.3/bs4Dash/inst/jquery-ui-1.12.1 |only bs4Dash-2.3.4/bs4Dash/DESCRIPTION | 13 bs4Dash-2.3.4/bs4Dash/MD5 | 73 +- bs4Dash-2.3.4/bs4Dash/NEWS.md | 8 bs4Dash-2.3.4/bs4Dash/R/deps.R | 4 bs4Dash-2.3.4/bs4Dash/R/sysdata.rda |only bs4Dash-2.3.4/bs4Dash/R/tabs.R | 6 bs4Dash-2.3.4/bs4Dash/R/utils.R | 14 bs4Dash-2.3.4/bs4Dash/README.md | 16 bs4Dash-2.3.4/bs4Dash/build/stage23.rdb |binary bs4Dash-2.3.4/bs4Dash/build/vignette.rds |binary bs4Dash-2.3.4/bs4Dash/inst/bs4Dash-2.3.4 |only bs4Dash-2.3.4/bs4Dash/inst/doc/bs4Dash.R | 35 - bs4Dash-2.3.4/bs4Dash/inst/doc/bs4Dash.Rmd | 34 bs4Dash-2.3.4/bs4Dash/inst/doc/bs4Dash.html | 516 +++++++++++--- bs4Dash-2.3.4/bs4Dash/inst/doc/css-preloader.R | 31 bs4Dash-2.3.4/bs4Dash/inst/doc/css-preloader.Rmd | 30 bs4Dash-2.3.4/bs4Dash/inst/doc/css-preloader.html | 514 +++++++++++--- bs4Dash-2.3.4/bs4Dash/inst/doc/extra-elements.R | 165 ---- bs4Dash-2.3.4/bs4Dash/inst/doc/extra-elements.Rmd | 166 ---- bs4Dash-2.3.4/bs4Dash/inst/doc/extra-elements.html | 579 +++++++++++----- bs4Dash-2.3.4/bs4Dash/inst/doc/improved-boxes.R | 326 --------- bs4Dash-2.3.4/bs4Dash/inst/doc/improved-boxes.Rmd | 328 --------- bs4Dash-2.3.4/bs4Dash/inst/doc/improved-boxes.html | 734 ++++++++++++--------- bs4Dash-2.3.4/bs4Dash/inst/doc/more-skins.R | 130 --- bs4Dash-2.3.4/bs4Dash/inst/doc/more-skins.Rmd | 128 --- bs4Dash-2.3.4/bs4Dash/inst/doc/more-skins.html | 611 +++++++++++------ bs4Dash-2.3.4/bs4Dash/inst/doc/step-by-step.html | 12 bs4Dash-2.3.4/bs4Dash/inst/jquery-ui-1.13.2 |only bs4Dash-2.3.4/bs4Dash/inst/shinylive |only bs4Dash-2.3.4/bs4Dash/man/insertTab.Rd | 8 bs4Dash-2.3.4/bs4Dash/vignettes/bs4Dash.Rmd | 34 bs4Dash-2.3.4/bs4Dash/vignettes/css-preloader.Rmd | 30 bs4Dash-2.3.4/bs4Dash/vignettes/extra-elements.Rmd | 166 ---- bs4Dash-2.3.4/bs4Dash/vignettes/improved-boxes.Rmd | 328 --------- bs4Dash-2.3.4/bs4Dash/vignettes/more-skins.Rmd | 128 --- 38 files changed, 2333 insertions(+), 2834 deletions(-)
Title: Interface to the iDigBio Data API
Description: An interface to iDigBio's search API that allows downloading
specimen records. Searches are returned as a data.frame. Other functions
such as the metadata end points return lists of information. iDigBio is a US
project focused on digitizing and serving museum specimen collections on the
web. See <https://www.idigbio.org> for information on iDigBio.
Author: Francois Michonneau [aut, cph] ,
Matthew Collins [aut] ,
Scott Chamberlain [ctb],
Kevin Love [ctb],
Hem Nalini Morzaria-Luna [ctb],
Michelle L. Gaynor [ctb, aut],
Jesse Bennett [cre]
Maintainer: Jesse Bennett <j3553@ufl.edu>
Diff between ridigbio versions 0.3.9 dated 2024-08-20 and 0.4.0 dated 2024-09-03
DESCRIPTION | 8 +- MD5 | 88 +++++++++++++++--------------- NEWS.md | 5 + R/base.R | 30 +++++++--- README.md | 1 inst/doc/BadCoordinateID.R | 35 +++++++++-- inst/doc/BadCoordinateID.Rmd | 37 +++++++++--- inst/doc/BadCoordinateID.html | 9 +-- inst/doc/BasicUsage.R | 36 +++++++++--- inst/doc/BasicUsage.Rmd | 40 +++++++++---- inst/doc/BasicUsage.html | 18 +++--- inst/doc/Fields.R | 36 ++++++++---- inst/doc/Fields.Rmd | 35 ++++++++--- inst/doc/Fields.html | 6 +- inst/doc/FindTissue.R | 35 +++++++++-- inst/doc/FindTissue.Rmd | 43 ++++++++++---- inst/doc/FindTissue.html | 15 +++-- inst/doc/IDDataFlags.R | 24 +++++++- inst/doc/IDDataFlags.Rmd | 23 ++++++- inst/doc/MediaAPIDemo.R | 43 ++++++++++++-- inst/doc/MediaAPIDemo.Rmd | 44 ++++++++++++--- inst/doc/MediaAPIDemo.html | 6 -- inst/doc/ModifiedDataID.R | 44 ++++++++++++--- inst/doc/ModifiedDataID.Rmd | 43 ++++++++++++-- inst/doc/RecordAPIDemo.R | 43 +++++++++++--- inst/doc/RecordAPIDemo.Rmd | 42 +++++++++++--- tests/testthat/test-base.R | 3 + tests/testthat/test-idig_build_attrib.R | 2 tests/testthat/test-idig_count_media.R | 6 ++ tests/testthat/test-idig_count_records.R | 4 + tests/testthat/test-idig_meta_fields.R | 12 ++++ tests/testthat/test-idig_search_media.R | 8 ++ tests/testthat/test-idig_search_records.R | 16 +++++ tests/testthat/test-idig_top_media.R | 6 ++ tests/testthat/test-idig_top_records.R | 8 ++ tests/testthat/test-idig_view_media.R | 2 tests/testthat/test-idig_view_records.R | 2 vignettes/BadCoordinateID.Rmd | 37 +++++++++--- vignettes/BasicUsage.Rmd | 40 +++++++++---- vignettes/Fields.Rmd | 35 ++++++++--- vignettes/FindTissue.Rmd | 43 ++++++++++---- vignettes/IDDataFlags.Rmd | 23 ++++++- vignettes/MediaAPIDemo.Rmd | 44 ++++++++++++--- vignettes/ModifiedDataID.Rmd | 43 ++++++++++++-- vignettes/RecordAPIDemo.Rmd | 42 +++++++++++--- 45 files changed, 895 insertions(+), 270 deletions(-)
Title: Read-Write Support for 'NumPy' Files via 'Rcpp'
Description: The 'cnpy' library written by Carl Rogers provides read and write
facilities for files created with (or for) the 'NumPy' extension for 'Python'.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with as C++11 which should be the default on
all platforms since the release of R 3.3.0.
Author: Dirk Eddelbuettel [aut, cre] ,
Wush Wu [aut] ,
Carl Rogers [aut]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCNPy versions 0.2.12 dated 2023-11-27 and 0.2.13 dated 2024-09-03
ChangeLog | 24 ++++++++++++++++++++++++ DESCRIPTION | 18 ++++++++++++------ MD5 | 18 +++++++++--------- README.md | 6 +++--- build/vignette.rds |binary inst/NEWS.Rd | 11 ++++++++++- inst/doc/RcppCNPy-intro.pdf |binary inst/doc/UsingReticulate.pdf |binary tests/saveAndLoad.R | 16 ++++++++-------- tests/saveAndLoad.Rout.save | 24 ++++++++++++------------ 10 files changed, 78 insertions(+), 39 deletions(-)
Title: Computer Experiment Designs
Description: In computer experiments space-filling designs are having great impact. Most popularly used space-filling designs are Uniform designs (UDs), Latin hypercube designs (LHDs) etc. For further references one can see Mckay (1979) <DOI:10.1080/00401706.1979.10489755> and Fang (1980) <https://cir.nii.ac.jp/crid/1570291225616774784>. In this package, we have provided algorithms for generate efficient LHDs and UDs. Here, generated LHDs are efficient as they possess lower value of Maxpro measure, Phi_p value and Maximum Absolute Correlation (MAC) value based on the weightage given to each criterion. On the other hand, the produced UDs are having good space-filling property as they attained the lower bound of Discrete Discrepancy measure.
Author: Ashutosh Dalal [aut, cre],
Cini Varghese [aut, ctb],
Rajender Parsad [aut, ctb],
Mohd Harun [aut, ctb]
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Diff between CompExpDes versions 1.0.2 dated 2024-08-21 and 1.0.3 dated 2024-09-03
CompExpDes-1.0.2/CompExpDes/R/UDesigns_1.R |only CompExpDes-1.0.2/CompExpDes/R/UDesigns_2.R |only CompExpDes-1.0.2/CompExpDes/man/UDesigns_1.Rd |only CompExpDes-1.0.2/CompExpDes/man/UDesigns_2.Rd |only CompExpDes-1.0.3/CompExpDes/DESCRIPTION | 8 +++---- CompExpDes-1.0.3/CompExpDes/MD5 | 16 ++++++++------ CompExpDes-1.0.3/CompExpDes/NAMESPACE | 5 ++-- CompExpDes-1.0.3/CompExpDes/R/UDesigns_I.R |only CompExpDes-1.0.3/CompExpDes/R/UDesigns_II.R |only CompExpDes-1.0.3/CompExpDes/R/UDesigns_III.R |only CompExpDes-1.0.3/CompExpDes/R/max_coincidence_number.R |only CompExpDes-1.0.3/CompExpDes/man/UDesigns_I.Rd |only CompExpDes-1.0.3/CompExpDes/man/UDesigns_II.Rd |only CompExpDes-1.0.3/CompExpDes/man/UDesigns_III.Rd |only CompExpDes-1.0.3/CompExpDes/man/max_coincidence_number.Rd |only 15 files changed, 17 insertions(+), 12 deletions(-)
Title: File-Backed Array for Out-of-Memory Computation
Description: Stores large arrays in files to avoid occupying large
memories. Implemented with super fast gigabyte-level multi-threaded
reading/writing via 'OpenMP'. Supports multiple non-character data
types (double, float, complex, integer, logical, and raw).
Author: Zhengjia Wang [aut, cre, cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between filearray versions 0.1.7 dated 2024-07-16 and 0.1.8 dated 2024-09-03
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 4 +++ build/vignette.rds |binary src/load.cpp | 10 ++++++- src/mapreduce.cpp | 69 ++++++++++++++++++++++++++++++++++++----------------- 6 files changed, 68 insertions(+), 31 deletions(-)
Title: 'Java' Environments for R Projects
Description: Quickly install 'Java Development Kit (JDK)' without
administrative privileges and set environment variables in current R
session or project to solve common issues with 'Java' environment
management in 'R'. Recommended to users of 'Java'/'rJava'-dependent
'R' packages such as 'r5r', 'opentripplanner', 'xlsx', 'openNLP',
'rWeka', 'RJDBC', 'tabulapdf', and many more. 'rJavaEnv' prevents
common problems like 'Java' not found, 'Java' version conflicts,
missing 'Java' installations, and the inability to install 'Java' due
to lack of administrative privileges. 'rJavaEnv' automates the
download, installation, and setup of the 'Java' on a per-project basis
by setting the relevant 'JAVA_HOME' in the current 'R' session or the
current working directory (via '.Rprofile', with the user's consent).
Similar to what 'renv' does for 'R' packages, 'rJavaEnv' allows
different 'Java' versions to be used across different projects, but
can also be configured to allow multiple versions within the same
proj [...truncated...]
Author: Egor Kotov [aut, cre, cph] ,
Mauricio Vargas [ctb] ,
Hadley Wickham [ctb]
Maintainer: Egor Kotov <kotov.egor@gmail.com>
Diff between rJavaEnv versions 0.1.2 dated 2024-08-26 and 0.2.1 dated 2024-09-03
rJavaEnv-0.1.2/rJavaEnv/inst/figures |only rJavaEnv-0.2.1/rJavaEnv/DESCRIPTION | 50 +- rJavaEnv-0.2.1/rJavaEnv/MD5 | 69 ++-- rJavaEnv-0.2.1/rJavaEnv/NAMESPACE | 2 rJavaEnv-0.2.1/rJavaEnv/NEWS.md | 16 rJavaEnv-0.2.1/rJavaEnv/R/java_download.R | 14 rJavaEnv-0.2.1/rJavaEnv/R/java_env.R | 99 +++-- rJavaEnv-0.2.1/rJavaEnv/R/java_install.R | 77 ---- rJavaEnv-0.2.1/rJavaEnv/R/java_unpack.R |only rJavaEnv-0.2.1/rJavaEnv/R/onLoad.R | 3 rJavaEnv-0.2.1/rJavaEnv/R/use_java.R |only rJavaEnv-0.2.1/rJavaEnv/README.md | 167 ++++------ rJavaEnv-0.2.1/rJavaEnv/build/vignette.rds |binary rJavaEnv-0.2.1/rJavaEnv/inst/CITATION | 2 rJavaEnv-0.2.1/rJavaEnv/inst/doc/multiple-java-with-targets-callr.R |only rJavaEnv-0.2.1/rJavaEnv/inst/doc/multiple-java-with-targets-callr.html |only rJavaEnv-0.2.1/rJavaEnv/inst/doc/multiple-java-with-targets-callr.qmd |only rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv-step-by-step.R | 22 + rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv-step-by-step.html | 65 ++- rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv-step-by-step.qmd | 51 ++- rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv.R | 20 - rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv.html | 20 - rJavaEnv-0.2.1/rJavaEnv/inst/doc/rJavaEnv.qmd | 40 +- rJavaEnv-0.2.1/rJavaEnv/inst/schemaorg.json | 34 +- rJavaEnv-0.2.1/rJavaEnv/man/figures/logo.png |binary rJavaEnv-0.2.1/rJavaEnv/man/java_check_version_cmd.Rd | 6 rJavaEnv-0.2.1/rJavaEnv/man/java_check_version_rjava.Rd | 12 rJavaEnv-0.2.1/rJavaEnv/man/java_check_version_system.Rd | 9 rJavaEnv-0.2.1/rJavaEnv/man/java_download.Rd | 4 rJavaEnv-0.2.1/rJavaEnv/man/java_env_set.Rd | 2 rJavaEnv-0.2.1/rJavaEnv/man/java_env_set_rprofile.Rd | 2 rJavaEnv-0.2.1/rJavaEnv/man/java_env_unset.Rd | 2 rJavaEnv-0.2.1/rJavaEnv/man/java_install.Rd | 8 rJavaEnv-0.2.1/rJavaEnv/man/java_quick_install.Rd | 6 rJavaEnv-0.2.1/rJavaEnv/man/java_unpack.Rd |only rJavaEnv-0.2.1/rJavaEnv/man/rJavaEnv-package.Rd | 3 rJavaEnv-0.2.1/rJavaEnv/man/use_java.Rd |only rJavaEnv-0.2.1/rJavaEnv/vignettes/multiple-java-with-targets-callr.qmd |only rJavaEnv-0.2.1/rJavaEnv/vignettes/rJavaEnv-step-by-step.qmd | 51 ++- rJavaEnv-0.2.1/rJavaEnv/vignettes/rJavaEnv.qmd | 40 +- 40 files changed, 554 insertions(+), 342 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and technical writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.5 dated 2024-05-16 and 0.6.6 dated 2024-09-03
DESCRIPTION | 14 ++++----- MD5 | 62 +++++++++++++++++++++------------------ NAMESPACE | 3 + NEWS.md | 17 ++++++++++ R/design_noreps.R | 29 +++++++++++++----- R/design_repblock.R | 23 ++++++++++++-- R/figure2qmd.R | 4 +- R/gdoc2qmd.R | 61 +++++++++++++++++---------------------- R/outliers_remove.R | 6 +-- R/plot_diag.R | 17 ++++++---- R/plot_diagnostic.R |only R/remove_outliers.R |only R/table2qmd.R | 2 - R/tarpuy_design.R | 13 ++++++-- R/tarpuy_plex.R | 76 ++++++++++++++++++++++++++++++------------------- R/tarpuy_traits.R | 63 ++++++++++++++++++++++------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/apps.html | 2 - inst/doc/policy.Rmd | 2 - inst/doc/policy.html | 4 +- inst/doc/rticles.html | 2 - inst/tarpuy/pkgs.R | 1 man/design_noreps.Rd | 5 ++- man/design_repblock.Rd | 6 +++ man/include_pdf.Rd | 42 +++++++++++++-------------- man/outliers_remove.Rd | 6 +-- man/plot_diag.Rd | 6 +-- man/plot_diagnostic.Rd |only man/remove_outliers.Rd |only man/tarpuy_design.Rd | 7 +++- man/tarpuy_plex.Rd | 5 ++- man/tarpuy_traits.Rd | 16 +++++----- vignettes/policy.Rmd | 2 - 34 files changed, 294 insertions(+), 202 deletions(-)
Title: Interior Point Conic Optimization Solver
Description: A versatile interior point solver that solves linear programs (LPs), quadratic programs (QPs), second-order cone programs (SOCPs), semidefinite programs (SDPs), and problems with exponential and power cone constraints (<https://clarabel.org/stable/>). For quadratic objectives, unlike interior point solvers based on the standard homogeneous self-dual embedding (HSDE) model, Clarabel handles quadratic objective without requiring any epigraphical reformulation of its objective function. It can therefore be significantly faster than other HSDE-based solvers for problems with quadratic objective functions. Infeasible problems are detected using using a homogeneous embedding technique.
Author: Balasubramanian Narasimhan [aut, cre],
Paul Goulart [aut, cph],
Yuwen Chen [aut],
Hiroaki Yutani [ctb] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stanford.edu>
Diff between clarabel versions 0.9.0 dated 2024-06-22 and 0.9.0.1 dated 2024-09-03
DESCRIPTION | 11 +-- MD5 | 10 +-- NEWS.md | 8 ++ inst/doc/clarabel.html | 154 ++++++++++++++++++++++++------------------------- src/Makevars.in | 4 - src/Makevars.win | 4 - 6 files changed, 102 insertions(+), 89 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-05 1.0.4
2023-12-17 1.0.3
2023-11-19 1.0.2
2023-11-12 1.0.1
2023-11-01 1.0.0
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands of trees (Silva and Wilkinson 2021)
<doi:10.1093/sysbio/syab015>,
for calculating the median [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.8.0 dated 2024-07-26 and 2.9.0 dated 2024-09-03
TreeDist-2.8.0/TreeDist/inst/doc/tree-islands.R |only TreeDist-2.8.0/TreeDist/inst/doc/tree-islands.Rmd |only TreeDist-2.8.0/TreeDist/inst/doc/tree-islands.html |only TreeDist-2.8.0/TreeDist/vignettes/tree-islands.Rmd |only TreeDist-2.9.0/TreeDist/DESCRIPTION | 8 TreeDist-2.9.0/TreeDist/MD5 | 96 TreeDist-2.9.0/TreeDist/NEWS.md | 476 +- TreeDist-2.9.0/TreeDist/R/VisualizeMatching.R | 408 +- TreeDist-2.9.0/TreeDist/R/cluster_stats.R | 51 TreeDist-2.9.0/TreeDist/R/spectral_clustering.R | 153 TreeDist-2.9.0/TreeDist/R/tree_distance.R | 341 - TreeDist-2.9.0/TreeDist/R/tree_distance_msd.R | 126 TreeDist-2.9.0/TreeDist/R/tree_distance_utilities.R | 1244 +++--- TreeDist-2.9.0/TreeDist/build/partial.rdb |binary TreeDist-2.9.0/TreeDist/build/vignette.rds |binary TreeDist-2.9.0/TreeDist/inst/doc/Robinson-Foulds.html | 19 TreeDist-2.9.0/TreeDist/inst/doc/Using-TreeDist.Rmd | 298 - TreeDist-2.9.0/TreeDist/inst/doc/Using-TreeDist.html | 28 TreeDist-2.9.0/TreeDist/inst/doc/landscapes.html | 1949 ---------- TreeDist-2.9.0/TreeDist/inst/doc/treespace.html | 16 TreeDist-2.9.0/TreeDist/inst/doc/using-distances.R | 6 TreeDist-2.9.0/TreeDist/inst/doc/using-distances.Rmd | 850 ++-- TreeDist-2.9.0/TreeDist/inst/doc/using-distances.html | 255 - TreeDist-2.9.0/TreeDist/man/GeneralizedRF.Rd | 121 TreeDist-2.9.0/TreeDist/man/VisualizeMatching.Rd | 152 TreeDist-2.9.0/TreeDist/man/cluster-statistics.Rd | 16 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/MSTSegments/mst-example-plot.svg | 622 +-- TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/Plot3/plotting-order.svg | 134 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/Plot3/simple-plot.svg | 134 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/hidden-edge-labels.svg |only TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/jrf-vm-matchzeros-false.svg | 348 - TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/rf-collapse-a-node.svg | 566 +- TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/rf-collapse-and-change.svg | 554 +- TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/rf-vm-single-splits-plainedges.svg | 352 - TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/test-vm.svg | 396 +- TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/test-vmr.svg | 368 - TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 566 +- TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/vm-one-rooted.svg | 196 - TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/VisualizeMatching/vm-unrooted.svg | 186 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/plot/test-lc-letters.svg | 162 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/plot/test-uc-letters.svg | 162 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/plot/test-with-space.svg | 162 TreeDist-2.9.0/TreeDist/tests/testthat/_snaps/plot/test-without-space.svg | 162 TreeDist-2.9.0/TreeDist/tests/testthat/test-Reduce.R | 130 TreeDist-2.9.0/TreeDist/tests/testthat/test-VisualizeMatching.R | 289 - TreeDist-2.9.0/TreeDist/tests/testthat/test-cluster_stats.R | 6 TreeDist-2.9.0/TreeDist/tests/testthat/test-different-tips.R | 164 TreeDist-2.9.0/TreeDist/tests/testthat/test-spectral_clustering.R |only TreeDist-2.9.0/TreeDist/tests/testthat/test-tree_distance.R | 81 TreeDist-2.9.0/TreeDist/tests/testthat/test-tree_distance_utilities.R | 705 +-- TreeDist-2.9.0/TreeDist/vignettes/Using-TreeDist.Rmd | 298 - TreeDist-2.9.0/TreeDist/vignettes/using-distances.Rmd | 850 ++-- 52 files changed, 6199 insertions(+), 8007 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of linear
regression, GLM, and Cox regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge. For more
information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>,
Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang
(2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015)
<doi:10.1111/biom.12300>, or visit the package homepage
<https://pbreheny.github.io/grpreg/>.
Author: Patrick Breheny [aut, cre] ,
Yaohui Zeng [ctb],
Ryan Kurth [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.4.0 dated 2021-07-26 and 3.5.0 dated 2024-09-03
grpreg-3.4.0/grpreg/R/calcNullDev.R |only grpreg-3.4.0/grpreg/R/print.R |only grpreg-3.4.0/grpreg/inst/tinytest/basic-functionality.R |only grpreg-3.4.0/grpreg/man/auc.Rd |only grpreg-3.4.0/grpreg/man/birthwt-grpreg.Rd |only grpreg-3.4.0/grpreg/man/cv-grpreg.Rd |only grpreg-3.4.0/grpreg/man/logLik-grpreg.Rd |only grpreg-3.4.0/grpreg/man/plot-cv-grpreg.Rd |only grpreg-3.4.0/grpreg/man/plot-grpreg.Rd |only grpreg-3.4.0/grpreg/man/plot-grpsurv-func.Rd |only grpreg-3.4.0/grpreg/man/predict.Rd |only grpreg-3.4.0/grpreg/man/select-grpreg.Rd |only grpreg-3.4.0/grpreg/man/summary-cv-grpreg.Rd |only grpreg-3.4.0/grpreg/vignettes/web |only grpreg-3.5.0/grpreg/DESCRIPTION | 10 grpreg-3.5.0/grpreg/MD5 | 145 ++-- grpreg-3.5.0/grpreg/NAMESPACE | 44 - grpreg-3.5.0/grpreg/NEWS.md | 16 grpreg-3.5.0/grpreg/R/auc.R | 49 + grpreg-3.5.0/grpreg/R/calc_null_dev.R |only grpreg-3.5.0/grpreg/R/cv-grpreg.R | 117 +++- grpreg-3.5.0/grpreg/R/cv-grpsurv.R | 19 grpreg-3.5.0/grpreg/R/data.R |only grpreg-3.5.0/grpreg/R/expand_spline.R | 2 grpreg-3.5.0/grpreg/R/gBridge.R | 80 ++ grpreg-3.5.0/grpreg/R/gen_nonlinear_data.R | 10 grpreg-3.5.0/grpreg/R/grpreg-package.R |only grpreg-3.5.0/grpreg/R/grpreg.R | 239 ++++++++ grpreg-3.5.0/grpreg/R/grpsurv.R | 145 ++++ grpreg-3.5.0/grpreg/R/logLik.R | 54 + grpreg-3.5.0/grpreg/R/loss.R | 6 grpreg-3.5.0/grpreg/R/plot-cv.R | 60 +- grpreg-3.5.0/grpreg/R/plot-grpsurv-func.R | 32 + grpreg-3.5.0/grpreg/R/plot.R | 43 + grpreg-3.5.0/grpreg/R/plot_spline.R | 8 grpreg-3.5.0/grpreg/R/predict-cv.R | 7 grpreg-3.5.0/grpreg/R/predict-surv.R | 1 grpreg-3.5.0/grpreg/R/predict.R | 66 ++ grpreg-3.5.0/grpreg/R/se-grpsurv.R | 4 grpreg-3.5.0/grpreg/R/select.R | 63 ++ grpreg-3.5.0/grpreg/R/summary-cv-grpreg.R | 57 + grpreg-3.5.0/grpreg/README.md | 6 grpreg-3.5.0/grpreg/build/partial.rdb |binary grpreg-3.5.0/grpreg/build/vignette.rds |binary grpreg-3.5.0/grpreg/inst/CITATION | 64 +- grpreg-3.5.0/grpreg/inst/doc/getting-started.html | 465 +++++++++++----- grpreg-3.5.0/grpreg/inst/doc/getting-started.rmd | 2 grpreg-3.5.0/grpreg/inst/tinytest/additive-models.R | 27 grpreg-3.5.0/grpreg/inst/tinytest/agreement.R | 5 grpreg-3.5.0/grpreg/inst/tinytest/auc.R |only grpreg-3.5.0/grpreg/inst/tinytest/binomial.R |only grpreg-3.5.0/grpreg/inst/tinytest/cv-grpsurv.R | 2 grpreg-3.5.0/grpreg/inst/tinytest/cv.R | 43 + grpreg-3.5.0/grpreg/inst/tinytest/extra-features.R | 24 grpreg-3.5.0/grpreg/inst/tinytest/gaussian.R |only grpreg-3.5.0/grpreg/inst/tinytest/grpsurv.R | 4 grpreg-3.5.0/grpreg/inst/tinytest/poisson.R |only grpreg-3.5.0/grpreg/inst/tinytest/select.R |only grpreg-3.5.0/grpreg/man/AUC.cv.grpsurv.Rd |only grpreg-3.5.0/grpreg/man/Birthwt.Rd | 90 +-- grpreg-3.5.0/grpreg/man/Lung.Rd | 85 +- grpreg-3.5.0/grpreg/man/birthwt.grpreg.Rd |only grpreg-3.5.0/grpreg/man/cv.grpreg.Rd |only grpreg-3.5.0/grpreg/man/expand_spline.Rd | 1 grpreg-3.5.0/grpreg/man/gBridge.Rd | 170 +++-- grpreg-3.5.0/grpreg/man/gen_nonlinear_data.Rd | 4 grpreg-3.5.0/grpreg/man/grpreg-package.Rd | 116 +-- grpreg-3.5.0/grpreg/man/grpreg.Rd | 435 +++++++------- grpreg-3.5.0/grpreg/man/grpsurv.Rd | 310 +++++----- grpreg-3.5.0/grpreg/man/logLik.grpreg.Rd |only grpreg-3.5.0/grpreg/man/plot.cv.grpreg.Rd |only grpreg-3.5.0/grpreg/man/plot.grpreg.Rd |only grpreg-3.5.0/grpreg/man/plot.grpsurv.func.Rd |only grpreg-3.5.0/grpreg/man/plot_spline.Rd | 4 grpreg-3.5.0/grpreg/man/predict.grpreg.Rd |only grpreg-3.5.0/grpreg/man/select.Rd |only grpreg-3.5.0/grpreg/man/summary.cv.grpreg.Rd |only grpreg-3.5.0/grpreg/src/gdfit_cox.c | 32 - grpreg-3.5.0/grpreg/src/gdfit_gaussian.c | 80 +- grpreg-3.5.0/grpreg/src/gdfit_glm.c | 20 grpreg-3.5.0/grpreg/src/lcdfit_cox.c | 36 - grpreg-3.5.0/grpreg/src/lcdfit_gaussian.c | 14 grpreg-3.5.0/grpreg/src/lcdfit_glm.c | 16 grpreg-3.5.0/grpreg/src/maxprod.c | 4 grpreg-3.5.0/grpreg/tests/test.R | 2 grpreg-3.5.0/grpreg/vignettes/articles |only grpreg-3.5.0/grpreg/vignettes/getting-started.rmd | 2 87 files changed, 2326 insertions(+), 1014 deletions(-)
Title: Measuring Morphological Diversity and Evolutionary Tempo
Description: Measures morphological diversity from discrete character data and
estimates evolutionary tempo on phylogenetic trees. Imports morphological
data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>)
format with read_nexus_matrix(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are test_rates(), which implements AIC and likelihood
ratio tests for discrete character rates introduced across Lloyd et al.
(2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014)
<doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)
<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>,
and calculate_morphological_distances(), which implements multiple discrete
character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills
(1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>,
and Hopkins and St John (2018) [...truncated...]
Author: Graeme T. Lloyd [aut, cre, cph],
Thomas Guillerme [aut, cph],
Jen Hoyal Cuthill [aut, cph],
Emma Sherratt [aut, cph],
Steve C. Wang [aut, cph]
Maintainer: Graeme T. Lloyd <graemetlloyd@gmail.com>
Diff between Claddis versions 0.6.3 dated 2020-09-26 and 0.7.0 dated 2024-09-03
Claddis-0.6.3/Claddis/R/compactify_matrix.R |only Claddis-0.6.3/Claddis/R/constructors.r |only Claddis-0.6.3/Claddis/R/map_stochastic_changes.R |only Claddis-0.6.3/Claddis/man/compactify_matrix.Rd |only Claddis-0.6.3/Claddis/man/map_stochastic_changes.Rd |only Claddis-0.7.0/Claddis/CHANGELOG | 81 +++ Claddis-0.7.0/Claddis/DESCRIPTION | 29 - Claddis-0.7.0/Claddis/MD5 | 243 +++++++-- Claddis-0.7.0/Claddis/NAMESPACE | 66 ++ Claddis-0.7.0/Claddis/R/Claddis-package.R | 2 Claddis-0.7.0/Claddis/R/add_polymorphisms_to_costmatrix.R |only Claddis-0.7.0/Claddis/R/add_uncertainties_to_costmatrix.R |only Claddis-0.7.0/Claddis/R/assign_taxa_to_bins.R | 28 - Claddis-0.7.0/Claddis/R/bin_changes.R | 25 - Claddis-0.7.0/Claddis/R/bin_character_completeness.R | 56 +- Claddis-0.7.0/Claddis/R/bin_edge_lengths.R | 36 - Claddis-0.7.0/Claddis/R/build_cladistic_matrix.R | 37 - Claddis-0.7.0/Claddis/R/calculate_MPD.R |only Claddis-0.7.0/Claddis/R/calculate_WMPD.R |only Claddis-0.7.0/Claddis/R/calculate_g.r |only Claddis-0.7.0/Claddis/R/calculate_gmax.r |only Claddis-0.7.0/Claddis/R/calculate_kardashian_index.R |only Claddis-0.7.0/Claddis/R/calculate_morphological_distances.R | 27 - Claddis-0.7.0/Claddis/R/calculate_tree_length.r |only Claddis-0.7.0/Claddis/R/check_cladisticMatrix.R |only Claddis-0.7.0/Claddis/R/check_costMatrix.R |only Claddis-0.7.0/Claddis/R/check_stateGraph.R |only Claddis-0.7.0/Claddis/R/check_taxonGroups.R |only Claddis-0.7.0/Claddis/R/check_timeBins.R |only Claddis-0.7.0/Claddis/R/classify_costmatrix.R |only Claddis-0.7.0/Claddis/R/compactify_cladistic_matrix.R |only Claddis-0.7.0/Claddis/R/convert_adjacency_matrix_to_costmatrix.r |only Claddis-0.7.0/Claddis/R/convert_costmatrix_to_stategraph.r |only Claddis-0.7.0/Claddis/R/convert_state_tree_to_adjacency_matrix.r |only Claddis-0.7.0/Claddis/R/convert_stategraph_to_costmatrix.r |only Claddis-0.7.0/Claddis/R/count_cherries.R |only Claddis-0.7.0/Claddis/R/drop_time_tip.R |only Claddis-0.7.0/Claddis/R/estimate_ancestral_states.R | 34 - Claddis-0.7.0/Claddis/R/estimate_squared_change_ancestors.r |only Claddis-0.7.0/Claddis/R/find_costmatrix_minimum_span.r |only Claddis-0.7.0/Claddis/R/find_minimum_spanning_edges.R | 2 Claddis-0.7.0/Claddis/R/find_shortest_costmatrix_path.r |only Claddis-0.7.0/Claddis/R/find_stategraph_minimum_span.r |only Claddis-0.7.0/Claddis/R/find_time_bin_midpoints.R |only Claddis-0.7.0/Claddis/R/find_unique_trees.r |only Claddis-0.7.0/Claddis/R/fix_costmatrix.R |only Claddis-0.7.0/Claddis/R/fix_root_time.R | 8 Claddis-0.7.0/Claddis/R/is.cladisticMatrix.R |only Claddis-0.7.0/Claddis/R/is.costMatrix.R |only Claddis-0.7.0/Claddis/R/is.stateGraph.R |only Claddis-0.7.0/Claddis/R/is.taxonGroups.R |only Claddis-0.7.0/Claddis/R/is.timeBins.R |only Claddis-0.7.0/Claddis/R/is_graph_connected.R |only Claddis-0.7.0/Claddis/R/locate_bracket_positions.r |only Claddis-0.7.0/Claddis/R/make_costmatrix.r |only Claddis-0.7.0/Claddis/R/make_labels.r |only Claddis-0.7.0/Claddis/R/map_dollo_changes.R | 9 Claddis-0.7.0/Claddis/R/ordinate_cladistic_matrix.R | 14 Claddis-0.7.0/Claddis/R/partition_time_bins.R | 4 Claddis-0.7.0/Claddis/R/permute_all_polymorphisms.r |only Claddis-0.7.0/Claddis/R/permute_all_treeshape_labellings.r |only Claddis-0.7.0/Claddis/R/permute_all_uncertainties.r |only Claddis-0.7.0/Claddis/R/permute_connected_graphs.r |only Claddis-0.7.0/Claddis/R/permute_costmatrices.r |only Claddis-0.7.0/Claddis/R/permute_graph_splits.r |only Claddis-0.7.0/Claddis/R/permute_restricted_compositions.r |only Claddis-0.7.0/Claddis/R/permute_tipstates.r |only Claddis-0.7.0/Claddis/R/permute_treeshapes.r |only Claddis-0.7.0/Claddis/R/plot_changes_on_tree.R | 21 Claddis-0.7.0/Claddis/R/plot_chronophylomorphospace.R | 8 Claddis-0.7.0/Claddis/R/plot_morphospace.R | 189 +++++++ Claddis-0.7.0/Claddis/R/plot_morphospace_stack.R | 24 Claddis-0.7.0/Claddis/R/plot_multi_morphospace.R | 6 Claddis-0.7.0/Claddis/R/plot_rates_character.R | 12 Claddis-0.7.0/Claddis/R/plot_rates_time.R | 32 - Claddis-0.7.0/Claddis/R/plot_rates_tree.R | 12 Claddis-0.7.0/Claddis/R/print.cladisticMatrix.r | 33 - Claddis-0.7.0/Claddis/R/print.costMatrix.r |only Claddis-0.7.0/Claddis/R/print.stateGraph.r |only Claddis-0.7.0/Claddis/R/print.taxonGroups.r |only Claddis-0.7.0/Claddis/R/print.timeBins.r |only Claddis-0.7.0/Claddis/R/prune_cladistic_matrix.R | 4 Claddis-0.7.0/Claddis/R/read_nexus_matrix.R | 245 ++++++---- Claddis-0.7.0/Claddis/R/reconstruct_ancestral_states.r |only Claddis-0.7.0/Claddis/R/safe_taxonomic_reduction.R | 4 Claddis-0.7.0/Claddis/R/safe_taxonomic_reinsertion.R | 2 Claddis-0.7.0/Claddis/R/split_out_subgraphs.R |only Claddis-0.7.0/Claddis/R/test_rates.R | 152 +++--- Claddis-0.7.0/Claddis/R/trim_matrix.R | 9 Claddis-0.7.0/Claddis/R/write_nexus_matrix.R | 78 ++- Claddis-0.7.0/Claddis/R/write_tnt_matrix.R | 80 +-- Claddis-0.7.0/Claddis/README.md | 12 Claddis-0.7.0/Claddis/build |only Claddis-0.7.0/Claddis/data/day_2016.RData |binary Claddis-0.7.0/Claddis/data/gauthier_1986.RData |binary Claddis-0.7.0/Claddis/data/michaux_1989.RData |binary Claddis-0.7.0/Claddis/inst/CITATION | 29 + Claddis-0.7.0/Claddis/man/Claddis-package.Rd | 8 Claddis-0.7.0/Claddis/man/add_polymorphisms_to_costmatrix.Rd |only Claddis-0.7.0/Claddis/man/add_uncertainties_to_costmatrix.Rd |only Claddis-0.7.0/Claddis/man/assign_taxa_to_bins.Rd | 15 Claddis-0.7.0/Claddis/man/bin_changes.Rd | 11 Claddis-0.7.0/Claddis/man/bin_character_completeness.Rd | 27 - 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Title: Scaling Models and Classifiers for Textual Data
Description: Scaling models and classifiers for sparse matrix objects representing
textual data in the form of a document-feature matrix. Includes original
implementations of 'Laver', 'Benoit', and Garry's (2003) <doi:10.1017/S0003055403000698>,
'Wordscores' model, the Perry and 'Benoit' (2017) <doi:10.48550/arXiv.1710.08963> class affinity scaling model,
and the 'Slapin' and 'Proksch' (2008) <doi:10.1111/j.1540-5907.2008.00338.x> 'wordfish'
model, as well as methods for correspondence analysis, latent semantic analysis,
and fast Naive Bayes and linear 'SVMs' specially designed for sparse textual data.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Patrick O. Perry [aut] ,
Benjamin Lauderdale [aut] ,
Johannes Gruber [aut] ,
William Lowe [aut] ,
Vikas Sindhwani [cph] ,
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textmodels versions 0.9.8 dated 2024-08-29 and 0.9.9 dated 2024-09-03
quanteda.textmodels-0.9.8/quanteda.textmodels/tests/spelling.Rout.save |only quanteda.textmodels-0.9.9/quanteda.textmodels/DESCRIPTION | 6 +- quanteda.textmodels-0.9.9/quanteda.textmodels/MD5 | 15 ++--- quanteda.textmodels-0.9.9/quanteda.textmodels/NEWS.md | 5 + quanteda.textmodels-0.9.9/quanteda.textmodels/inst/WORDLIST | 2 quanteda.textmodels-0.9.9/quanteda.textmodels/inst/doc/textmodel_performance.html | 30 +++++----- quanteda.textmodels-0.9.9/quanteda.textmodels/src/ca.cpp | 3 - quanteda.textmodels-0.9.9/quanteda.textmodels/src/wordfish.cpp | 1 quanteda.textmodels-0.9.9/quanteda.textmodels/tests/testthat.R | 6 +- 9 files changed, 39 insertions(+), 29 deletions(-)
More information about quanteda.textmodels at CRAN
Permanent link
Title: Sourcing Archaeological Materials by Chemical Composition
Description: Exploration and analysis of compositional data in the
framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package
provides tools for chemical fingerprinting and source tracking of
ancient materials.
Author: Nicolas Frerebeau [aut, cre] ,
Anne Philippe [aut] ,
Brice Lebrun [ctb] ,
Arthur Leck [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between nexus versions 0.2.0 dated 2024-02-26 and 0.3.0 dated 2024-09-03
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Title: Co-Data Learning for Bayesian Additive Regression Trees
Description: Estimate prior variable weights for Bayesian Additive Regression
Trees (BART). These weights correspond to the probabilities of the variables
being selected in the splitting rules of the sum-of-trees.
Weights are estimated using empirical Bayes and external information on
the explanatory variables (co-data).
BART models are fitted using the 'dbarts' 'R' package.
See Goedhart and others (2023) <doi:10.48550/arXiv.2311.09997> for details.
Author: Jeroen M. Goedhart [aut, cre, cph]
,
Thomas Klausch [aut],
Mark A. van de Wiel [aut],
Vincent Dorie [ctb] ,
Hanarth Fonds [fnd]
Maintainer: Jeroen M. Goedhart <jeroengoed@gmail.com>
Diff between EBcoBART versions 1.0.1 dated 2024-09-02 and 1.0.2 dated 2024-09-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/EBcoBART_Functions.R | 10 +++++----- README.md | 6 +++--- man/EBcoBART.Rd | 8 +++++--- 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Automatic Interpolation Package
Description: An automatic interpolation is done by automatically estimating the variogram and then calling gstat. An overview is given by Hiemstra et al (2008) <doi:10.1016/j.cageo.2008.10.011>.
Author: Paul Hiemstra [aut],
Jon Olav Skoien [aut, cre]
Maintainer: Jon Olav Skoien <jon.skoien@gmail.com>
Diff between automap versions 1.1-9 dated 2023-03-23 and 1.1-12 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- tests/autoKrige.cv.R | 3 ++- tests/autoKrige.cv.Rout.save | 3 ++- tests/automap.R | 3 ++- tests/automap.Rout.save | 4 ++-- 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Bayesian Treed Gaussian Process Models
Description: Bayesian nonstationary, semiparametric nonlinear regression
and design by treed Gaussian processes (GPs) with jumps to the limiting
linear model (LLM). Special cases also implemented include Bayesian
linear models, CART, treed linear models, stationary separable and
isotropic GPs, and GP single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided, including ALM,
ALC, and expected improvement. The latter supports derivative-free
optimization of noisy black-box functions. For details and tutorials,
see Gramacy (2007) <doi:10.18637/jss.v019.i09> and Gramacy & Taddy (2010)
<doi:10.18637/jss.v033.i06>.
Author: Robert B. Gramacy [aut, cre],
Matt A. Taddy [aut]
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between tgp versions 2.4-22.1 dated 2024-08-17 and 2.4-23 dated 2024-09-03
ChangeLog | 6 +++++ DESCRIPTION | 18 ++++++++++++----- MD5 | 56 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary data/exp2d.rda |binary inst/doc/tgp.pdf |binary inst/doc/tgp2.pdf |binary src/base.cc | 6 ++--- src/base.h | 6 ++--- src/corr.cc | 10 ++++----- src/exp.cc | 10 ++++----- src/exp_sep.cc | 10 ++++----- src/gp.cc | 12 +++++------ src/lh.c | 1 src/list.cc | 13 ++++++------ src/matern.cc | 16 +++++++-------- src/matrix.c | 10 ++++----- src/model.cc | 12 +++++------ src/mr_exp_sep.cc | 10 ++++----- src/mstructs.cc | 6 ++--- src/params.cc | 9 ++++---- src/rand_draws.c | 12 +++++------ src/randomkit.c | 4 +-- src/rhelp.h | 13 +----------- src/sim.cc | 10 ++++----- src/temper.cc | 6 ++--- src/tgp.cc | 15 +++++++------- src/tree.cc | 24 +++++++++++----------- src/twovar.cc | 10 ++++----- 29 files changed, 157 insertions(+), 148 deletions(-)
Title: Interface Between 'GRASS' Geographical Information System and
'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Author: Roger Bivand [cre, aut] ,
Rainer Krug [ctb] ,
Robin Lovelace [ctb] ,
Markus Neteler [ctb] ,
Sebastian Jeworutzki [ctb] ,
Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgrass versions 0.4-3 dated 2024-06-19 and 0.4-4 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/coerce.html | 6 +++--- tests/test_XML_xml2.R | 8 +++++--- tests/test_XML_xml2.Rout.save | 18 ++++++++---------- tests/test_terra_ptr.R | 2 +- tests/test_terra_ptr.Rout.save | 14 ++++++-------- 7 files changed, 33 insertions(+), 35 deletions(-)
More information about ProSportsDraftData at CRAN
Permanent link
Title: Continuous Cartogram
Description: Procedures for making continuous cartogram. Procedures available are:
flow based cartogram (Gastner & Newman (2004) <doi:10.1073/pnas.0400280101>),
fast flow based cartogram (Gastner, Seguy & More (2018) <doi:10.1073/pnas.1712674115>),
rubber band based cartogram (Dougenik et al. (1985)
<doi:10.1111/j.0033-0124.1985.00075.x>).
Author: Pierre-Andre Cornillon [aut, cre],
Florent Demoraes [aut],
Flow-Based-Cartograms [cph]
Maintainer: Pierre-Andre Cornillon <pierre-andre.cornillon@univ-rennes2.fr>
Diff between cartogramR versions 1.1-0 dated 2024-07-26 and 1.2-0 dated 2024-09-03
cartogramR-1.1-0/cartogramR/man/geom_cartogramR-deprecated.Rd |only cartogramR-1.2-0/cartogramR/DESCRIPTION | 11 cartogramR-1.2-0/cartogramR/MD5 | 25 - cartogramR-1.2-0/cartogramR/R/cartogramR.R | 2 cartogramR-1.2-0/cartogramR/R/cartogramR_options.R | 13 cartogramR-1.2-0/cartogramR/R/geom_cartogramR.R | 2 cartogramR-1.2-0/cartogramR/R/make_layer.R | 12 cartogramR-1.2-0/cartogramR/man/cartogramR-deprecated.Rd | 32 ++ cartogramR-1.2-0/cartogramR/man/cartogramR_options.Rd | 2 cartogramR-1.2-0/cartogramR/src/cartogram.c | 30 +- cartogramR-1.2-0/cartogramR/src/cartogram.h | 25 - cartogramR-1.2-0/cartogramR/src/cartogramR.c | 144 ++++++++-- cartogramR-1.2-0/cartogramR/src/diff_integrate.c | 48 ++- cartogramR-1.2-0/cartogramR/src/ffb_integrate.c | 102 ++++--- 14 files changed, 294 insertions(+), 154 deletions(-)
Title: R Interface to 'IGN' Web Services
Description: Automatic open data acquisition from resources of IGN
('Institut National de Information Geographique et forestiere')
(<https://www.ign.fr/>). Available datasets include various types of
raster and vector data, such as digital elevation models, state
borders, spatial databases, cadastral parcels, and more. There also
access to point clouds data ('LIDAR') and specifics API
(<https://apicarto.ign.fr/api/doc/>).
Author: Paul Carteron [aut, cre]
Maintainer: Paul Carteron <carteronpaul@gmail.com>
Diff between happign versions 0.3.0 dated 2024-05-07 and 0.3.1 dated 2024-09-03
DESCRIPTION | 10 MD5 | 49 + NAMESPACE | 9 NEWS.md | 7 R/get_apicarto_cadastre.R | 267 +++++++--- R/get_iso.R |only R/get_wms_raster.R | 12 R/get_wmts.R | 10 README.md | 2 build/vignette.rds |binary inst/doc/Getting_started.html | 2 man/build_iso_query.Rd |only man/get_apicarto_cadastre.Rd | 57 +- man/get_iso.Rd |only man/get_wms_raster.Rd | 2 man/get_wmts.Rd | 3 tests/testthat/fetch_data |only tests/testthat/fetch_data error dtolerance |only tests/testthat/fetch_data error no data |only tests/testthat/get_apicarto_cadastre |only tests/testthat/get_layers_metada_wfs/data.geopf.fr/wfs/ows-866ab9.xml | 2 tests/testthat/get_layers_metada_wms/data.geopf.fr/wms-r/wms-3fee96.R | 6 tests/testthat/get_layers_metada_wmts/data.geopf.fr/wmts-36368b.xml | 2 tests/testthat/process_responses |only tests/testthat/test-get_apicarto_cadastre.R |only tests/testthat/test-get_iso.R |only tests/testthat/test-get_layers_metadata.R | 4 27 files changed, 307 insertions(+), 137 deletions(-)
Title: Textual Statistics for the Quantitative Analysis of Textual Data
Description: Textual statistics functions formerly in the 'quanteda' package.
Textual statistics for characterizing and comparing textual data. Includes
functions for measuring term and document frequency, the co-occurrence of
words, similarity and distance between features and documents, feature entropy,
keyword occurrence, readability, and lexical diversity. These functions
extend the 'quanteda' package and are specially designed for sparse textual data.
Author: Kenneth Benoit [cre, aut, cph]
,
Kohei Watanabe [aut] ,
Haiyan Wang [aut] ,
Jiong Wei Lua [aut],
Jouni Kuha [aut] ,
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between quanteda.textstats versions 0.97.1 dated 2024-08-27 and 0.97.2 dated 2024-09-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ README.md | 2 +- src/keyness.cpp | 3 ++- 5 files changed, 14 insertions(+), 9 deletions(-)
More information about quanteda.textstats at CRAN
Permanent link
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.3-0 dated 2024-08-30 and 1.3-1 dated 2024-09-03
DESCRIPTION | 8 MD5 | 24 - R/interface.R | 4 build/partial.rdb |binary inst/NEWS.Rd | 19 inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.R | 249 ++++++------ inst/doc/lmvnorm_src.Rnw | 827 ++++++++++++++++++++-------------------- inst/doc/lmvnorm_src.pdf |binary inst/litdb.bib | 19 vignettes/litdb.bib | 19 vignettes/lmvnorm_src.Rnw | 827 ++++++++++++++++++++-------------------- vignettes/lmvnorm_src.Rout.save | 577 +++++++++++++-------------- 13 files changed, 1300 insertions(+), 1273 deletions(-)
Title: Datasets for Teaching Archaeology and Paleontology
Description: Datasets for teaching quantitative approaches and modeling in
archaeology and paleontology. This package provides several types of
data related to broad topics (cultural evolution, radiocarbon dating,
paleoenvironments, etc.), which can be used to illustrate statistical
methods in the classroom (multivariate data analysis, compositional
data analysis, diversity measurement, etc.).
Author: Nicolas Frerebeau [aut, cre] ,
Brice Lebrun [ctb] ,
Universite Bordeaux Montaigne [fnd],
CNRS [fnd]
Maintainer: Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between folio versions 1.4.0 dated 2024-02-26 and 1.5.0 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 29 ++++++++++++++++++----------- NEWS.md | 6 ++++++ R/chemical.R | 39 ++++++++++++++++++++++++++++++++++++++- R/folio-package.R | 2 +- R/spatial.R |only README.md | 40 +++++++++++++++------------------------- build/partial.rdb |binary data/bronze.rda |only data/cities.rda |only data/inrap.rda |only data/kommos.rda |binary inst/CITATION | 2 +- man/bronze.Rd |only man/cities.Rd |only man/folio-package.Rd | 2 +- man/inrap.Rd |only man/kommos.Rd | 3 ++- man/verre.Rd | 1 + 19 files changed, 87 insertions(+), 45 deletions(-)
Title: Estimation and Inference for Conditional Copula Models
Description: Provides functions for the estimation of conditional copulas models,
various estimators of conditional Kendall's tau
(proposed in Derumigny and Fermanian (2019a, 2019b, 2020)
<doi:10.1515/demo-2019-0016>,
<doi:10.1016/j.csda.2019.01.013>,
<doi:10.1016/j.jmva.2020.104610>),
and test procedures for the simplifying assumption
(proposed in Derumigny and Fermanian (2017) <doi:10.1515/demo-2017-0011>
and Derumigny, Fermanian and Min (2022) <doi:10.1002/cjs.11742>).
Author: Alexis Derumigny [aut, cre] ,
Jean-David Fermanian [ctb, ths]
,
Aleksey Min [ctb] ,
Rutger van der Spek [ctb]
Maintainer: Alexis Derumigny <a.f.f.derumigny@tudelft.nl>
Diff between CondCopulas versions 0.1.3 dated 2023-09-26 and 0.1.4.1 dated 2024-09-03
DESCRIPTION | 13 - MD5 | 66 +++--- NAMESPACE | 4 NEWS.md | 36 +++ R/CKTmatrix.kernel.R | 9 R/bCond.simpA.CKT.R | 8 R/bCond.simpA.param.R | 14 + R/bCond.tree.conversion.R | 10 - R/bCond.treeCKT.R | 44 ++++ R/estimationCKT.KendallReg.R | 66 ++++-- R/estimationCKT.R | 56 +++-- R/estimationCKT.classif.kNN.R | 15 + R/estimationCKT.datasetPairs.R | 29 +- R/estimationCKT.kernel.R | 112 +++++++---- R/estimationCKT.kernelCV.R | 84 +++++--- R/estimationCondCopulas.R | 79 ++++---- R/simpA.NP.R | 5 R/simpA.kendallReg.R | 401 ++++++++++++++++++++++++++++++++--------- R/simpA.param.R | 5 R/zzz.R |only README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/simulatedData.html | 6 man/CKT.KendallReg.LambdaCV.Rd | 25 +- man/CKT.estimate.Rd | 30 +-- man/CKT.hCV.l1out.Rd | 41 ++-- man/CKT.kendallReg.fit.Rd | 22 +- man/CKT.kernel.Rd | 43 +++- man/bCond.treeCKT.Rd | 6 man/estimateNPCondCopula.Rd | 26 +- man/estimateParCondCopula.Rd | 25 +- man/simpA.kendallReg.Rd | 107 ++++++++-- tests |only 34 files changed, 970 insertions(+), 419 deletions(-)
Title: Linters for 'box' Modules
Description: Static code analysis of 'box' modules.
The package enhances code quality by providing linters that check for common issues,
enforce best practices, and ensure consistent coding standards.
Author: Ricardo Rodrigo Basa [aut, cre],
Jakub Nowicki [aut],
Mateusz Kolomanski [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Ricardo Rodrigo Basa <opensource+rodrigo@appsilon.com>
Diff between box.linters versions 0.10.3 dated 2024-08-21 and 0.10.4 dated 2024-09-03
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 5 +++++ R/namespaced_function_calls.R | 7 ++++++- R/style_box_use.R | 7 +++++++ R/zzz.R | 13 +++++++++++-- inst/WORDLIST | 1 + tests/testthat/test-style_box_use.R | 25 +++++++++++++++++++++---- 8 files changed, 61 insertions(+), 17 deletions(-)
Title: Add Continuous Legends to Plots
Description: Annotate plots with legends for continuous variables and colour
spectra using the base graphics plotting tools; and manipulate irregular
polygons.
Author: Martin R. Smith [aut, cre, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between PlotTools versions 0.3.0 dated 2023-10-30 and 0.3.1 dated 2024-09-03
DESCRIPTION | 8 MD5 | 17 NEWS.md | 5 R/Col2Hex.R | 1 R/SpectrumLegend.R | 119 - man/Col2Hex.Rd | 59 tests/testthat/_snaps/SpectrumLegend/sizelegend-h.svg | 1150 ++++------ tests/testthat/_snaps/SpectrumLegend/spectrumlegend-log-y.svg |only tests/testthat/test-Col2Hex.R | 17 tests/testthat/test-SpectrumLegend.R | 200 - 10 files changed, 801 insertions(+), 775 deletions(-)
Title: Simulate Evapotranspiration and Soil Moisture with the SVAT
Model LWF-Brook90
Description: Provides a flexible and easy-to use interface for the soil vegetation
atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran.
The model simulates daily transpiration, interception, soil and snow evaporation,
streamflow and soil water fluxes through a soil profile covered with vegetation,
as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003)
<doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions
for model set up, execution and parallelization provides easy access to plot-level SVAT
simulations, as well as multi-run and large-scale applications.
Author: Paul Schmidt-Walter [aut, cre]
,
Volodymyr Trotsiuk [aut] ,
Klaus Hammel [aut],
Martin Kennel [aut],
Anthony Federer [aut],
Tobias Hohenbrink [aut] ,
Gisbert Hetkamp [aut],
Robert Nuske [ctb] ,
Bavarian State Institute of Forestry [cph, fnd],
Northw [...truncated...]
Maintainer: Paul Schmidt-Walter <paulsw@posteo.de>
Diff between LWFBrook90R versions 0.5.3 dated 2023-10-16 and 0.6.0 dated 2024-09-03
LWFBrook90R-0.5.3/LWFBrook90R/src/output_day.h |only LWFBrook90R-0.5.3/LWFBrook90R/src/output_layer.h |only LWFBrook90R-0.6.0/LWFBrook90R/DESCRIPTION | 12 LWFBrook90R-0.6.0/LWFBrook90R/MD5 | 42 - LWFBrook90R-0.6.0/LWFBrook90R/NEWS.md | 13 LWFBrook90R-0.6.0/LWFBrook90R/R/mrunLWFB90.R | 11 LWFBrook90R-0.6.0/LWFBrook90R/R/r_lwfbrook90.R | 12 LWFBrook90R-0.6.0/LWFBrook90R/R/runLWFB90.R | 8 LWFBrook90R-0.6.0/LWFBrook90R/R/setparms_LWFB90.R | 6 LWFBrook90R-0.6.0/LWFBrook90R/inst/doc/LWFBrook90R-3-Multiruns.html | 8 LWFBrook90R-0.6.0/LWFBrook90R/man/LWFBrook90R-package.Rd | 2 LWFBrook90R-0.6.0/LWFBrook90R/man/r_lwfbrook90.Rd | 4 LWFBrook90R-0.6.0/LWFBrook90R/man/run_LWFB90.Rd | 2 LWFBrook90R-0.6.0/LWFBrook90R/man/set_paramLWFB90.Rd | 3 LWFBrook90R-0.6.0/LWFBrook90R/src/Makevars | 2 LWFBrook90R-0.6.0/LWFBrook90R/src/VARDCL.h | 4 LWFBrook90R-0.6.0/LWFBrook90R/src/md_brook90.f95 | 397 ++++++++-- LWFBrook90R-0.6.0/LWFBrook90R/src/md_decl_const.f95 | 2 LWFBrook90R-0.6.0/LWFBrook90R/src/md_typedefs.f95 |only LWFBrook90R-0.6.0/LWFBrook90R/src/output_layer_pint.h | 22 LWFBrook90R-0.6.0/LWFBrook90R/src/output_pint.h | 4 LWFBrook90R-0.6.0/LWFBrook90R/src/skeleton.c | 6 LWFBrook90R-0.6.0/LWFBrook90R/tests/testthat/test-multirun.R |only LWFBrook90R-0.6.0/LWFBrook90R/tests/testthat/test-runLWFB90.R | 21 24 files changed, 477 insertions(+), 104 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.1-2 dated 2024-07-02 and 3.1-4 dated 2024-09-03
DESCRIPTION | 10 MD5 | 98 ++++---- NEWS.md | 34 +++ R/HASPT.R | 8 R/check_params.R | 8 R/create_test_sleeplog_csv.R | 5 R/g.getM5L5.R | 4 R/g.getmeta.R | 7 R/g.loadlog.R | 27 ++ R/g.part4.R | 22 + R/g.part5.addfirstwake.R | 11 R/g.part5.savetimeseries.R | 7 R/g.part5.wakesleepwindows.R | 9 R/g.report.part4.R | 18 - R/g.report.part5.R | 8 R/g.report.part5_dictionary.R | 7 R/g.sib.det.R | 5 R/get_nw_clip_block_params.R | 22 - R/load_params.R | 2 build/vignette.rds |binary inst/doc/CutPoints.Rmd | 24 +- inst/doc/CutPoints.html | 36 +-- inst/doc/GGIR.R | 6 inst/doc/GGIR.Rmd | 101 --------- inst/doc/GGIR.html | 117 ---------- inst/doc/GGIRParameters.R | 4 inst/doc/GGIRParameters.Rmd | 5 inst/doc/GGIRParameters.html | 232 +++++++++++---------- inst/doc/GGIRoutput.R | 4 inst/doc/GGIRoutput.Rmd | 12 - inst/doc/GGIRoutput.html | 23 +- inst/doc/TutorialDaySegmentAnalyses.R | 2 inst/doc/TutorialDaySegmentAnalyses.Rmd | 2 inst/doc/TutorialDaySegmentAnalyses.html | 2 inst/doc/readmyacccsv.R | 2 inst/doc/readmyacccsv.Rmd | 2 inst/doc/readmyacccsv.html | 2 man/GGIR.Rd | 22 + man/create_test_sleeplog_csv.Rd | 6 man/get_nw_clip_block_params.Rd | 22 - tests/testthat/test_chainof5parts.R | 14 - tests/testthat/test_load_check_params.R | 2 tests/testthat/test_recording.starts.at.midnight.R | 37 +++ tests/testthat/test_recordingEndSleepHour.R | 12 - vignettes/CutPoints.Rmd | 24 +- vignettes/GGIR.Rmd | 101 --------- vignettes/GGIRParameters.Rmd | 5 vignettes/GGIRoutput.Rmd | 12 - vignettes/TutorialDaySegmentAnalyses.Rmd | 2 vignettes/readmyacccsv.Rmd | 2 50 files changed, 488 insertions(+), 661 deletions(-)
Title: Paleoecology Functions for Regime Shift Analysis
Description: Contains a variety of functions, based around
regime shift analysis of paleoecological data.
Citations:
Rodionov() from Rodionov (2004) <doi:10.1029/2004GL019448>
Lanzante() from Lanzante (1996) <doi:10.1002/(SICI)1097-0088(199611)16:11%3C1197::AID-JOC89%3E3.0.CO;2-L>
Hellinger_trans from Numerical Ecology, Legendre & Legendre (ISBN 9780444538680)
rolling_autoc from Liu, Gao & Wang (2018) <doi:10.1016/j.scitotenv.2018.06.276>
Sample data sets lake_data & lake_RSI processed from Bush, Silman & Urrego (2004) <doi:10.1126/science.1090795>
Sample data set January_PDO from NOAA: <https://www.ncei.noaa.gov/access/monitoring/pdo/>.
Author: Alex H. Room [aut, cre, cph] ,
Felipe Franco-Gaviria [ctb, fnd]
,
Dunia H. Urrego [ctb, fnd] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Alex H. Room <alexhroom+cran@protonmail.com>
Diff between rshift versions 3.0.0 dated 2023-10-17 and 3.1.0 dated 2024-09-03
DESCRIPTION | 13 +++--- MD5 | 29 ++++++++------ NAMESPACE | 3 + R/RSI_graph.R | 9 +++- R/extendr-wrappers.R | 11 +++++ R/regime_means.R |only configure | 1 inst/doc/STARSmanual.ltx | 82 ++++++++++++++++++++++-------------------- inst/doc/STARSmanual.pdf |binary man/RSI_graph.Rd | 4 +- man/regime_means.Rd |only man/rust_regime_means.Rd |only src/rust/Cargo.toml | 4 +- src/rust/src/lib.rs | 38 ++++++++++++++++++- src/rust/vendor.tar.xz |binary vignettes/STARSmanual.ltx | 82 ++++++++++++++++++++++-------------------- vignettes/rshift_PDO_plot.png |binary 17 files changed, 171 insertions(+), 105 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut] ,
Marta Zaffaroni [aut] ,
Jean-Francois Rey [aut, cre] ,
Julien Papaix [aut],
Jean-Loup Gaussen [ctb],
Manon Couty [ctb]
Maintainer: Jean-Francois Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.4.0 dated 2024-03-12 and 1.5.0 dated 2024-09-03
landsepi-1.4.0/landsepi/R/landsepi.R |only landsepi-1.5.0/landsepi/DESCRIPTION | 32 landsepi-1.5.0/landsepi/MD5 | 123 landsepi-1.5.0/landsepi/NEWS.md | 58 landsepi-1.5.0/landsepi/R/Cultivars_List.R | 41 landsepi-1.5.0/landsepi/R/Methods-LandsepiParams.R | 217 landsepi-1.5.0/landsepi/R/demo_landsepi.R | 8 landsepi-1.5.0/landsepi/R/landsepi-package.R |only landsepi-1.5.0/landsepi/R/output.R | 3 landsepi-1.5.0/landsepi/R/runShiny.R | 4 landsepi-1.5.0/landsepi/build/vignette.rds |binary landsepi-1.5.0/landsepi/configure | 18 landsepi-1.5.0/landsepi/configure.ac | 2 landsepi-1.5.0/landsepi/data/dispP_a40_b7.rda |binary landsepi-1.5.0/landsepi/data/landscapesTEST.rda |binary landsepi-1.5.0/landsepi/inst/CITATION | 19 landsepi-1.5.0/landsepi/inst/doc/O1-run_simple_simul.R | 18 landsepi-1.5.0/landsepi/inst/doc/O1-run_simple_simul.Rmd | 25 landsepi-1.5.0/landsepi/inst/doc/O1-run_simple_simul.html | 2973 ++++------ landsepi-1.5.0/landsepi/inst/doc/O2-run_exp_design.R | 6 landsepi-1.5.0/landsepi/inst/doc/O2-run_exp_design.Rmd | 6 landsepi-1.5.0/landsepi/inst/doc/O2-run_exp_design.html | 602 -- landsepi-1.5.0/landsepi/inst/doc/O3-landscape_dispersal.html | 489 - landsepi-1.5.0/landsepi/inst/doc/O4-run_sex_repro.R | 6 landsepi-1.5.0/landsepi/inst/doc/O4-run_sex_repro.Rmd | 6 landsepi-1.5.0/landsepi/inst/doc/O4-run_sex_repro.html | 636 -- landsepi-1.5.0/landsepi/inst/doc/O5-bibliography.Rmd |only landsepi-1.5.0/landsepi/inst/doc/O5-bibliography.html |only landsepi-1.5.0/landsepi/inst/doc/landsepi_poster.pdf |binary landsepi-1.5.0/landsepi/inst/doc/list_of_parameters.pdf |binary landsepi-1.5.0/landsepi/inst/shiny-landsepi/Dockerfile | 11 landsepi-1.5.0/landsepi/inst/shiny-landsepi/global.R | 263 landsepi-1.5.0/landsepi/inst/shiny-landsepi/modules/editableDT.R | 61 landsepi-1.5.0/landsepi/inst/shiny-landsepi/server.R | 879 +- landsepi-1.5.0/landsepi/inst/shiny-landsepi/ui.R | 427 - landsepi-1.5.0/landsepi/inst/shiny-landsepi/www/2022_LogoSAVE_entier_court_bleu.png |only landsepi-1.5.0/landsepi/man/allocateCroptypeCultivars.Rd | 6 landsepi-1.5.0/landsepi/man/allocateCultivarGenes.Rd | 4 landsepi-1.5.0/landsepi/man/allocateLandscapeCroptypes.Rd | 6 landsepi-1.5.0/landsepi/man/compute_audpc100S.Rd | 6 landsepi-1.5.0/landsepi/man/getMatrixCroptypePatho.Rd | 8 landsepi-1.5.0/landsepi/man/getMatrixCultivarPatho.Rd | 8 landsepi-1.5.0/landsepi/man/getMatrixPolyPatho.Rd | 8 landsepi-1.5.0/landsepi/man/inoculumToMatrix.Rd | 4 landsepi-1.5.0/landsepi/man/landsepi-package.Rd | 32 landsepi-1.5.0/landsepi/man/loadCroptypes.Rd | 6 landsepi-1.5.0/landsepi/man/loadCultivar.Rd | 13 landsepi-1.5.0/landsepi/man/loadInoculum.Rd | 4 landsepi-1.5.0/landsepi/man/loadOutputs.Rd | 4 landsepi-1.5.0/landsepi/man/runSimul.Rd | 38 landsepi-1.5.0/landsepi/man/saveDeploymentStrategy.Rd | 6 landsepi-1.5.0/landsepi/man/setCroptypes.Rd | 6 landsepi-1.5.0/landsepi/man/setCultivars.Rd | 4 landsepi-1.5.0/landsepi/man/survivalProbToMatrix.Rd | 4 landsepi-1.5.0/landsepi/man/updateSurvivalProb.Rd | 4 landsepi-1.5.0/landsepi/src/Model.cpp | 26 landsepi-1.5.0/landsepi/src/Model.hpp | 4 landsepi-1.5.0/landsepi/src/initialisation.cpp | 2 landsepi-1.5.0/landsepi/src/printReadWrite.cpp | 4 landsepi-1.5.0/landsepi/tests/testthat/test-LandsepiParams-Method.R | 8 landsepi-1.5.0/landsepi/vignettes/O1-run_simple_simul.Rmd | 25 landsepi-1.5.0/landsepi/vignettes/O2-run_exp_design.Rmd | 6 landsepi-1.5.0/landsepi/vignettes/O4-run_sex_repro.Rmd | 6 landsepi-1.5.0/landsepi/vignettes/O5-bibliography.Rmd |only landsepi-1.5.0/landsepi/vignettes/landsepi.bib |only landsepi-1.5.0/landsepi/vignettes/listofparameters.pdf |binary 66 files changed, 3610 insertions(+), 3575 deletions(-)
Title: Don't Overthink Your Palette of Colors
Description: Access diverse 'ggplot2'-compatible color palettes for
simplified data visualization.
Author: Jorge Mestre [aut, cre]
Maintainer: Jorge Mestre <jorge.mestre.tomas@csic.es>
Diff between DOYPAColors versions 0.0.1 dated 2023-11-04 and 0.0.2 dated 2024-09-03
DOYPAColors-0.0.1/DOYPAColors/R/DOYPAColors_functions.R |only DOYPAColors-0.0.2/DOYPAColors/DESCRIPTION | 29 ++-- DOYPAColors-0.0.2/DOYPAColors/LICENSE | 4 DOYPAColors-0.0.2/DOYPAColors/MD5 | 38 +++-- DOYPAColors-0.0.2/DOYPAColors/NAMESPACE | 23 +-- DOYPAColors-0.0.2/DOYPAColors/NEWS.md | 22 ++- DOYPAColors-0.0.2/DOYPAColors/R/colors.R |only DOYPAColors-0.0.2/DOYPAColors/R/scales.R |only DOYPAColors-0.0.2/DOYPAColors/R/utils.R |only DOYPAColors-0.0.2/DOYPAColors/build |only DOYPAColors-0.0.2/DOYPAColors/inst |only DOYPAColors-0.0.2/DOYPAColors/man/doypa.Rd | 99 ++++++++----- DOYPAColors-0.0.2/DOYPAColors/man/doypa_palette.Rd | 70 +++++---- DOYPAColors-0.0.2/DOYPAColors/man/figures |only DOYPAColors-0.0.2/DOYPAColors/man/list_doypa_pals.Rd | 39 ++--- DOYPAColors-0.0.2/DOYPAColors/man/preview_doypa_pals.Rd | 59 ++++---- DOYPAColors-0.0.2/DOYPAColors/man/preview_pal.Rd |only DOYPAColors-0.0.2/DOYPAColors/man/scale_color_doypa.Rd | 115 ++++++++-------- DOYPAColors-0.0.2/DOYPAColors/man/scale_colour_doypa.Rd | 76 +++++----- DOYPAColors-0.0.2/DOYPAColors/man/scale_fill_doypa.Rd | 115 ++++++++-------- DOYPAColors-0.0.2/DOYPAColors/tests |only DOYPAColors-0.0.2/DOYPAColors/vignettes |only 22 files changed, 397 insertions(+), 292 deletions(-)
Title: Group Lasso and Elastic Net Solver for Generalized Linear Models
Description: Extremely efficient procedures for fitting the entire group lasso and group elastic net regularization path for GLMs, multinomial, the Cox model and multi-task Gaussian models. Similar to the R package glmnet in scope of models, and in computational speed. This package provides R bindings to the C++ code underlying the corresponding Python package 'adelie'. These bindings offer a general purpose group elastic net solver,
a wide range of matrix classes that can exploit special structure
to allow large-scale inputs, and an assortment of
generalized linear model classes for fitting various types of data. The package includes
The package is an implementation of Yang, J. and Hastie, T. (2024) <doi:10.48550/arXiv.2405.08631>.
Author: James Yang [aut, cph],
Trevor Hastie [aut, cph, cre],
Balasubramanian Narasimhan [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between adelie versions 1.0.1 dated 2024-06-20 and 1.0.2 dated 2024-09-03
adelie-1.0.1/adelie/tests |only adelie-1.0.2/adelie/DESCRIPTION | 29 adelie-1.0.2/adelie/MD5 | 102 - adelie-1.0.2/adelie/NAMESPACE | 25 adelie-1.0.2/adelie/NEWS.md | 4 adelie-1.0.2/adelie/R/adelie-package.R | 5 adelie-1.0.2/adelie/R/glm.R | 90 - adelie-1.0.2/adelie/R/matrix.R | 263 ++-- adelie-1.0.2/adelie/R/solver.R | 245 ++-- adelie-1.0.2/adelie/R/state.R | 27 adelie-1.0.2/adelie/R/utilities.R |only adelie-1.0.2/adelie/R/wrappers.R |only adelie-1.0.2/adelie/build/partial.rdb |only adelie-1.0.2/adelie/build/vignette.rds |binary adelie-1.0.2/adelie/inst/adelie/adelie/__init__.py | 2 adelie-1.0.2/adelie/inst/adelie/adelie/matrix.py | 40 adelie-1.0.2/adelie/inst/adelie/adelie/src/adelie_core.cpp | 1 adelie-1.0.2/adelie/inst/adelie/adelie/src/decl.hpp | 1 adelie-1.0.2/adelie/inst/adelie/adelie/src/include/adelie_core/matrix/utils.hpp | 27 adelie-1.0.2/adelie/inst/adelie/adelie/src/matrx_utils_blas.cpp |only adelie-1.0.2/adelie/inst/doc/adelie.R | 125 +- adelie-1.0.2/adelie/inst/doc/adelie.Rmd | 452 +++++++ adelie-1.0.2/adelie/inst/doc/adelie.html | 608 ++++++++-- adelie-1.0.2/adelie/man/cv.grpnet.Rd |only adelie-1.0.2/adelie/man/gaussian_cov.Rd | 24 adelie-1.0.2/adelie/man/glm.binomial.Rd | 14 adelie-1.0.2/adelie/man/glm.cox.Rd | 26 adelie-1.0.2/adelie/man/glm.gaussian.Rd | 12 adelie-1.0.2/adelie/man/glm.multigaussian.Rd | 14 adelie-1.0.2/adelie/man/glm.multinomial.Rd | 10 adelie-1.0.2/adelie/man/glm.poisson.Rd | 12 adelie-1.0.2/adelie/man/grpnet.Rd | 152 +- adelie-1.0.2/adelie/man/matrix.block_diag.Rd | 3 adelie-1.0.2/adelie/man/matrix.concatenate.Rd | 20 adelie-1.0.2/adelie/man/matrix.dense.Rd | 14 adelie-1.0.2/adelie/man/matrix.eager_cov.Rd |only adelie-1.0.2/adelie/man/matrix.interaction.Rd | 28 adelie-1.0.2/adelie/man/matrix.kronecker_eye.Rd | 14 adelie-1.0.2/adelie/man/matrix.lazy_cov.Rd | 8 adelie-1.0.2/adelie/man/matrix.one_hot.Rd | 10 adelie-1.0.2/adelie/man/matrix.snp_phased_ancestry.Rd | 3 adelie-1.0.2/adelie/man/matrix.snp_unphased.Rd | 4 adelie-1.0.2/adelie/man/matrix.sparse.Rd | 15 adelie-1.0.2/adelie/man/matrix.standardize.Rd | 23 adelie-1.0.2/adelie/man/matrix.subset.Rd | 16 adelie-1.0.2/adelie/man/plot.cv.grpnet.Rd |only adelie-1.0.2/adelie/man/plot.grpnet.Rd |only adelie-1.0.2/adelie/man/predict.cv.grpnet.Rd |only adelie-1.0.2/adelie/man/predict.grpnet.Rd |only adelie-1.0.2/adelie/man/print.cv.grpnet.Rd |only adelie-1.0.2/adelie/man/print.grpnet.Rd |only adelie-1.0.2/adelie/src/RcppExports.cpp | 2 adelie-1.0.2/adelie/src/rcpp_glm.cpp | 2 adelie-1.0.2/adelie/src/rcpp_matrix_utils_blas.cpp |only adelie-1.0.2/adelie/vignettes/adelie.Rmd | 452 +++++++ adelie-1.0.2/adelie/vignettes/assets |only 56 files changed, 2375 insertions(+), 549 deletions(-)
Title: Statistical Network Models for Dynamic Network Data
Description: Tools for fitting statistical network models to dynamic network data.
Can be used for fitting both dynamic network actor models ('DyNAMs') and
relational event models ('REMs').
Stadtfeld, Hollway, and Block (2017a) <doi:10.1177/0081175017709295>,
Stadtfeld, Hollway, and Block (2017b) <doi:10.1177/0081175017733457>,
Stadtfeld and Block (2017) <doi:10.15195/v4.a14>,
Hoffman et al. (2020) <doi:10.1017/nws.2020.3>.
Author: James Hollway [aut, dtc] ,
Christoph Stadtfeld [aut, dtc],
Marion Hoffman [aut],
Alvaro Uzaheta [cre, aut] ,
Mirko Reul [ctb],
Timon Elmer [ctb],
Kieran Mepham [ctb],
Per Block [ctb],
Xiaolei Zhang [ctb],
Weigutian Ou [ctb],
Emily Garvin [ctb],
Siwei [...truncated...]
Maintainer: Alvaro Uzaheta <ualvaro@ethz.ch>
Diff between goldfish versions 1.6.8 dated 2024-04-11 and 1.6.10 dated 2024-09-03
DESCRIPTION | 10 - MD5 | 56 +++--- NEWS.md | 12 + R/data_Social_Evolution.R | 1 R/functions_data.R | 4 R/functions_diagnostics.R | 4 README.md | 4 configure | 257 ++++++++++++++++++++++++++++++++ configure.ac | 1 inst/doc/dynami-example.Rmd | 48 ++--- inst/doc/dynami-example.html | 2 inst/doc/goldfishEffects.html | 2 inst/doc/teaching1.Rmd | 70 ++++---- inst/doc/teaching1.html | 14 - inst/doc/teaching2.Rmd | 62 +++---- inst/doc/teaching2.html | 20 +- man/Social_Evolution.Rd | 3 man/defineNodes.Rd | 4 man/examine.Rd | 4 src/Makevars.in | 3 vignettes/dynami-example.Rmd | 48 ++--- vignettes/teaching/plot-teaching1-1.png |binary vignettes/teaching/plot-teaching1-2.png |binary vignettes/teaching/plot-teaching1-3.png |binary vignettes/teaching/plot-teaching2-1.png |binary vignettes/teaching1.Rmd | 70 ++++---- vignettes/teaching1.Rmd.orig | 6 vignettes/teaching2.Rmd | 62 +++---- vignettes/teaching2.Rmd.orig | 6 29 files changed, 516 insertions(+), 257 deletions(-)
Title: ILO Open Data via Ilostat Bulk Download Facility
Description: Tools to download data from the ilostat database
<https://ilostat.ilo.org> together with search and
manipulation utilities.
Author: David Bescond [aut, cre] ,
Mabelin Villarreal-Fuentes [ctb]
,
ILO Department of Statistics [cph, fnd]
Maintainer: David Bescond <bescond@ilo.org>
Diff between Rilostat versions 2.1.0 dated 2024-05-23 and 2.2.0 dated 2024-09-03
DESCRIPTION | 17 +++++++++-------- MD5 | 18 ++++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/Rilostat.R | 4 ++-- R/dataexplorer.R |only R/get_ilostat.R | 4 ++-- R/get_ilostat_dic.R | 2 +- R/get_ilostat_toc.R | 2 +- README.md | 2 +- man/dataexplorer.Rd |only 11 files changed, 32 insertions(+), 23 deletions(-)
Title: Extra Appenders for 'lgr'
Description: Additional appenders for the logging package 'lgr' that
support logging to databases, email and push notifications.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgrExtra versions 0.0.8 dated 2023-01-06 and 0.0.9 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NEWS.md | 7 ++++++- R/AppenderDbi.R | 4 ++-- R/AppenderDigest.R | 18 +++++++++--------- R/AppenderDt.R | 8 ++++---- R/AppenderElasticSearch.R | 17 ++++++++--------- R/AppenderSyslog.R | 6 +++--- R/LayoutDbi.R | 2 +- man/AppenderDbi.Rd | 4 ++-- man/AppenderDigest.Rd | 4 ++-- man/AppenderDt.Rd | 6 +++--- man/AppenderElasticSearch.Rd | 30 ++++++++++++++---------------- man/AppenderGmail.Rd | 4 ++-- man/AppenderPushbullet.Rd | 6 +++--- man/AppenderSendmail.Rd | 4 ++-- man/AppenderSyslog.Rd | 8 ++++---- man/LayoutDbi.Rd | 2 +- tests/testthat/test_AppenderDbi.R | 3 ++- tests/testthat/test_AppenderDt.R | 2 ++ 20 files changed, 93 insertions(+), 88 deletions(-)
Title: Kinship Analysis with Linked Markers
Description: A 'shiny' application for forensic kinship testing, based on
the 'pedsuite' R packages. 'KLINK' is closely aligned with the (non-R)
software 'Familias' and 'FamLink', but offers several unique features,
including visualisations and automated report generation. The
calculation of likelihood ratios supports pairs of linked markers, and
all common mutation models.
Author: Magnus Dehli Vigeland [aut, cre]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between KLINK versions 1.0.1 dated 2024-08-19 and 1.0.2 dated 2024-09-03
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/launchApp.R | 15 ++++++--------- R/parseXML.R | 2 +- R/writeResult.R | 4 +++- README.md | 9 +++++---- inst/shiny/app.R | 6 +++--- man/figures/screenshot-klink.png |binary man/launchApp.Rd | 2 +- 10 files changed, 36 insertions(+), 31 deletions(-)
Title: High Dimensional Time Series Analysis Tools
Description: Procedures for high-dimensional time series analysis including factor analysis
proposed by Lam and Yao (2012) <doi:10.1214/12-AOS970> and Chang, Guo and Yao (2015)
<doi:10.1016/j.jeconom.2015.03.024>,martingale difference test proposed by
Chang, Jiang and Shao (2022) <doi:10.1016/j.jeconom.2022.09.001> in press,principal
component analysis proposed by Chang, Guo and Yao (2018) <doi:10.1214/17-AOS1613>,
identifying cointegration proposed by Zhang, Robinson and Yao (2019)
<doi:10.1080/01621459.2018.1458620>, unit root test proposed by Chang, Cheng and Yao (2021)
<doi:10.1093/biomet/asab034>, white noise test proposed by Chang, Yao and Zhou (2017)
<doi:10.1093/biomet/asw066>, CP-decomposition for high-dimensional matrix time
series proposed by Chang, He, Yang and Yao(2023) <doi:10.1093/jrsssb/qkac011> and
Chang, Du, Huang and Yao (2024+), and Statistical inference for high-dimensional
spectral density matrix porposed by Chang, Jiang, McElroy [...truncated...]
Author: Chen Lin [aut, cre],
Jinyuan Chang [aut],
Qiwei Yao [aut]
Maintainer: Chen Lin <linchen@smail.swufe.edu.cn>
Diff between HDTSA versions 1.0.3 dated 2024-06-04 and 1.0.4 dated 2024-09-03
DESCRIPTION | 10 - MD5 | 8 R/CP_functions_unified.R | 386 +++++++++++++++++++++++------------------------ man/CP_MTS.Rd | 2 man/DGP.CP.Rd | 2 5 files changed, 201 insertions(+), 207 deletions(-)
Title: Generating Features for a Cohort
Description: An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.
Author: Martijn Schuemie [aut],
Marc Suchard [aut],
Patrick Ryan [aut],
Jenna Reps [aut],
Anthony Sena [aut],
Ger Inberg [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between FeatureExtraction versions 3.6.0 dated 2024-07-15 and 3.7.0 dated 2024-09-03
FeatureExtraction-3.6.0/FeatureExtraction/inst/java/FeatureExtraction.jar |only FeatureExtraction-3.6.0/FeatureExtraction/man/filterCovariateDataCovariates.Rd |only FeatureExtraction-3.6.0/FeatureExtraction/tests/testthat/testthat-problems.rds |only FeatureExtraction-3.7.0/FeatureExtraction/DESCRIPTION | 12 - FeatureExtraction-3.7.0/FeatureExtraction/MD5 | 90 ++++------ FeatureExtraction-3.7.0/FeatureExtraction/R/DefaultCovariateSettings.R | 4 FeatureExtraction-3.7.0/FeatureExtraction/R/GetCovariates.R | 21 +- FeatureExtraction-3.7.0/FeatureExtraction/R/GetCovariatesFromCohortAttributes.R | 20 +- FeatureExtraction-3.7.0/FeatureExtraction/R/GetCovariatesFromOtherCohorts.R | 17 + FeatureExtraction-3.7.0/FeatureExtraction/R/GetDefaultCovariates.R | 51 ++--- FeatureExtraction-3.7.0/FeatureExtraction/R/Table1.R | 4 FeatureExtraction-3.7.0/FeatureExtraction/R/UnitTestHelperFunctions.R | 6 FeatureExtraction-3.7.0/FeatureExtraction/README.md | 1 FeatureExtraction-3.7.0/FeatureExtraction/inst/csv/jarChecksum.txt | 2 FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/CreatingCovariatesBasedOnOtherCohorts.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/CreatingCovariatesUsingCohortAttributes.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuilders.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/CreatingCustomCovariateBuildersKorean.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/UsingFeatureExtraction.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/doc/UsingFeatureExtractionKorean.pdf |binary FeatureExtraction-3.7.0/FeatureExtraction/inst/java/featureExtraction-3.7.0-SNAPSHOT.jar |only FeatureExtraction-3.7.0/FeatureExtraction/java/org/ohdsi/featureExtraction/FeatureExtraction.java | 29 ++- FeatureExtraction-3.7.0/FeatureExtraction/man/createCovariateSettings.Rd | 6 FeatureExtraction-3.7.0/FeatureExtraction/man/createTable1.Rd | 4 FeatureExtraction-3.7.0/FeatureExtraction/man/dot-getDbLooCovariateData.Rd | 6 FeatureExtraction-3.7.0/FeatureExtraction/man/getDbCohortAttrCovariatesData.Rd | 11 - FeatureExtraction-3.7.0/FeatureExtraction/man/getDbCohortBasedCovariatesData.Rd | 9 - FeatureExtraction-3.7.0/FeatureExtraction/man/getDbCovariateData.Rd | 19 +- FeatureExtraction-3.7.0/FeatureExtraction/man/getDbDefaultCovariateData.Rd | 9 - FeatureExtraction-3.7.0/FeatureExtraction/tests/testBigQuery.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testOracle.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testPostgres.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testSnowflake.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testSpark.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testSqlServer.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/setup.R | 8 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-Aggregation.R | 1 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-CompareCohorts.R | 1 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-CovariateData.R | 13 + FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-GetCohortBasedCovariates.R | 26 +- FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-GetCovariates.R | 4 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-GetCovariatesFromCohortAttributes.R | 3 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-GetCovariatesTemporalSequence.R | 1 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-GetDefaultCovariates.R | 1 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-HelperFunctions.R | 1 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-Table1.R | 2 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-query-no-fail.R | 8 FeatureExtraction-3.7.0/FeatureExtraction/tests/testthat/test-spot-checks.R | 4 48 files changed, 245 insertions(+), 161 deletions(-)
More information about FeatureExtraction at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-08-26 0.1.0
Title: Semi-Automatic Reporting of Ordinary Surveys
Description: Offers a systematic way for conditional reporting of figures and tables for many
(and bivariate combinations of) variables, typically from survey data.
Contains interactive 'ggiraph'-based
(<https://CRAN.R-project.org/package=ggiraph>) plotting functions and
data frame-based summary tables (bivariate significance tests,
frequencies/proportions, unique open ended responses, etc) with
many arguments for customization, and extensions possible. Uses a global
options() system for neatly reducing redundant code.
Also contains tools for immediate saving of objects and returning a hashed link to the object,
useful for creating download links to high resolution images upon rendering in 'Quarto'.
Suitable for highly customized reports, primarily intended for survey
research.
Author: Stephan Daus [aut, cre, cph] ,
Julia Silge [ctb] ,
David Robinson [ctb] ,
Nordic Institute for The Studies of Innovation, Research and Education
[fnd],
Kristiania University College [fnd]
Maintainer: Stephan Daus <stephus.daus@gmail.com>
Diff between saros versions 1.0.4 dated 2024-02-28 and 1.2.0 dated 2024-09-03
saros-1.0.4/saros/R/add_attributes_unfinished.R |only saros-1.0.4/saros/R/add_caption_attribute.R |only saros-1.0.4/saros/R/add_section_heading_line.R |only saros-1.0.4/saros/R/argument_validation_and_insertion.R |only saros-1.0.4/saros/R/attach_chapter_dataset2.R |only saros-1.0.4/saros/R/attach_indep.R |only saros-1.0.4/saros/R/attach_new_output_to_output.R |only saros-1.0.4/saros/R/cat_freq_plot_html.R |only saros-1.0.4/saros/R/cat_prop_plot_html.R |only saros-1.0.4/saros/R/cat_table.R |only saros-1.0.4/saros/R/check_duplicates_in_data_overview.R |only saros-1.0.4/saros/R/chr_table.R |only saros-1.0.4/saros/R/crosstable3.R |only saros-1.0.4/saros/R/data_overview.R |only saros-1.0.4/saros/R/default_draft_report_arguments_in_yaml.R |only saros-1.0.4/saros/R/draft_report.R |only saros-1.0.4/saros/R/embed_cat_freq_plot_docx.R |only saros-1.0.4/saros/R/embed_cat_prop_plot_docx.R |only saros-1.0.4/saros/R/estimate_plot_height.R |only saros-1.0.4/saros/R/filename_sanitizer.R |only 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Title: Simulate Data from a DAG and Associated Node Information
Description: Simulate complex data from a given directed acyclic graph and information about each individual node.
Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to
one of many implemented regressions, such as logistic regression, linear
regression, poisson regression and more. Also includes a comprehensive framework for discrete-time
simulation, which can generate even more complex longitudinal data.
Author: Robin Denz [aut, cre],
Katharina Meiszl [aut]
Maintainer: Robin Denz <robin.denz@rub.de>
Diff between simDAG versions 0.1.2 dated 2024-06-13 and 0.2.0 dated 2024-09-03
simDAG-0.1.2/simDAG/tests/testthat/test_node_conditional_distr.r |only simDAG-0.2.0/simDAG/DESCRIPTION | 6 simDAG-0.2.0/simDAG/MD5 | 147 ++++--- simDAG-0.2.0/simDAG/NAMESPACE | 1 simDAG-0.2.0/simDAG/NEWS.md | 22 + simDAG-0.2.0/simDAG/R/dag_from_data.r | 22 - simDAG-0.2.0/simDAG/R/distributions.r | 22 - simDAG-0.2.0/simDAG/R/formula_interface.r |only simDAG-0.2.0/simDAG/R/input_checks.r | 28 - simDAG-0.2.0/simDAG/R/node.r | 64 ++- simDAG-0.2.0/simDAG/R/node_binomial.r | 13 simDAG-0.2.0/simDAG/R/node_conditional_prob.r | 2 simDAG-0.2.0/simDAG/R/node_multinomial.r | 4 simDAG-0.2.0/simDAG/R/plot.DAG.r | 8 simDAG-0.2.0/simDAG/R/plot.simDT_data.r | 4 simDAG-0.2.0/simDAG/R/sim2long.r | 2 simDAG-0.2.0/simDAG/R/sim2start_stop.r | 2 simDAG-0.2.0/simDAG/R/sim2wide.r | 7 simDAG-0.2.0/simDAG/R/sim_discrete_time.r | 30 + simDAG-0.2.0/simDAG/R/sim_dt_helpers.r | 18 simDAG-0.2.0/simDAG/R/sim_from_dag.r | 32 + simDAG-0.2.0/simDAG/R/structural_equations.r | 77 ++-- simDAG-0.2.0/simDAG/build/vignette.rds |binary simDAG-0.2.0/simDAG/inst/doc/v_covid_example.html | 25 - simDAG-0.2.0/simDAG/inst/doc/v_sim_discrete_time.html | 2 simDAG-0.2.0/simDAG/inst/doc/v_sim_from_dag.html | 5 simDAG-0.2.0/simDAG/inst/doc/v_using_formulas.R |only simDAG-0.2.0/simDAG/inst/doc/v_using_formulas.Rmd |only simDAG-0.2.0/simDAG/inst/doc/v_using_formulas.html |only simDAG-0.2.0/simDAG/man/node.Rd | 20 - simDAG-0.2.0/simDAG/man/node_binomial.Rd | 21 - simDAG-0.2.0/simDAG/man/node_conditional_distr.Rd | 4 simDAG-0.2.0/simDAG/man/node_conditional_prob.Rd | 8 simDAG-0.2.0/simDAG/man/node_custom.Rd | 38 +- simDAG-0.2.0/simDAG/man/node_gaussian.Rd | 8 simDAG-0.2.0/simDAG/man/node_multinomial.Rd | 6 simDAG-0.2.0/simDAG/man/node_negative_binomial.Rd | 6 simDAG-0.2.0/simDAG/man/node_poisson.Rd | 4 simDAG-0.2.0/simDAG/man/plot.DAG.Rd | 12 simDAG-0.2.0/simDAG/man/plot.simDT.Rd | 3 simDAG-0.2.0/simDAG/man/rbernoulli.Rd | 10 simDAG-0.2.0/simDAG/man/rcategorical.Rd | 6 simDAG-0.2.0/simDAG/man/simDAG.Rd | 1 simDAG-0.2.0/simDAG/man/sim_discrete_time.Rd | 4 simDAG-0.2.0/simDAG/man/sim_from_dag.Rd | 4 simDAG-0.2.0/simDAG/man/sim_n_datasets.Rd | 4 simDAG-0.2.0/simDAG/tests/testthat/Rplots.pdf |binary simDAG-0.2.0/simDAG/tests/testthat/_snaps/dag.md | 13 simDAG-0.2.0/simDAG/tests/testthat/_snaps/plot.DAG.md | 8 simDAG-0.2.0/simDAG/tests/testthat/test_add_missing_parents.r | 5 simDAG-0.2.0/simDAG/tests/testthat/test_args_from_formula.r |only simDAG-0.2.0/simDAG/tests/testthat/test_clean_node_args.r | 9 simDAG-0.2.0/simDAG/tests/testthat/test_dag.r | 16 simDAG-0.2.0/simDAG/tests/testthat/test_dag_from_data.r | 32 + simDAG-0.2.0/simDAG/tests/testthat/test_data_for_formula.r |only simDAG-0.2.0/simDAG/tests/testthat/test_get_cat_col_levs.r |only simDAG-0.2.0/simDAG/tests/testthat/test_get_interaction_term_for_formula.r |only simDAG-0.2.0/simDAG/tests/testthat/test_get_right_box_labels.r | 9 simDAG-0.2.0/simDAG/tests/testthat/test_input_checks_node_time_to_event.r | 18 simDAG-0.2.0/simDAG/tests/testthat/test_node.r | 188 ++++++++-- simDAG-0.2.0/simDAG/tests/testthat/test_node_binomial.r | 25 + simDAG-0.2.0/simDAG/tests/testthat/test_node_conditional_distr.R |only simDAG-0.2.0/simDAG/tests/testthat/test_node_conditional_prob.r | 16 simDAG-0.2.0/simDAG/tests/testthat/test_node_cox.r | 18 simDAG-0.2.0/simDAG/tests/testthat/test_node_gaussian.r | 91 ++++ simDAG-0.2.0/simDAG/tests/testthat/test_node_negative_binomial.r | 14 simDAG-0.2.0/simDAG/tests/testthat/test_node_poisson.r | 14 simDAG-0.2.0/simDAG/tests/testthat/test_parse_formula.r |only simDAG-0.2.0/simDAG/tests/testthat/test_plot.DAG.r | 8 simDAG-0.2.0/simDAG/tests/testthat/test_plot.simDT.r | 6 simDAG-0.2.0/simDAG/tests/testthat/test_rbernoulli.r | 15 simDAG-0.2.0/simDAG/tests/testthat/test_rcategorical.r | 22 - simDAG-0.2.0/simDAG/tests/testthat/test_sanitize_formula.r |only simDAG-0.2.0/simDAG/tests/testthat/test_sim2data.r | 9 simDAG-0.2.0/simDAG/tests/testthat/test_sim2long.last.r | 14 simDAG-0.2.0/simDAG/tests/testthat/test_sim2start_stop.last.r | 62 ++- simDAG-0.2.0/simDAG/tests/testthat/test_sim_discrete_time.r | 67 +++ simDAG-0.2.0/simDAG/tests/testthat/test_sim_from_dag.r | 56 ++ simDAG-0.2.0/simDAG/tests/testthat/test_sim_n_datasets.r | 7 simDAG-0.2.0/simDAG/tests/testthat/test_str_eq_root.r | 11 simDAG-0.2.0/simDAG/vignettes/v_using_formulas.Rmd |only 81 files changed, 1110 insertions(+), 345 deletions(-)
Title: Hidden Hybrid Markov/Semi-Markov Model Fitting
Description: Develops algorithms for fitting, prediction, simulation
and initialization of the following models
(1)- hidden hybrid Markov/semi-Markov model,
introduced by Guedon (2005) <doi:10.1016/j.csda.2004.05.033>,
(2)- nonparametric mixture of B-splines emissions (Langrock et al., 2015
<doi:10.1111/biom.12282>),
(3)- regime switching regression model
(Kim et al., 2008 <doi:10.1016/j.jeconom.2007.10.002>) and auto-regressive
hidden hybrid Markov/semi-Markov model,
(4)- spline-based nonparametric
estimation of additive state-switching models
(Langrock et al., 2018 <doi:10.1111/stan.12133>)
(5)- robust emission model proposed by
Qin et al, 2024 <doi:10.1007/s10479-024-05989-4>
(6)- several emission distributions, including mixture of multivariate normal
(which can also handle missing data using EM algorithm) and multi-nomial emission
(for modeling polymer or DNA sequences)
(7)- tools for prediction of future state sequence, computing the score of a new sequence,
spli [...truncated...]
Author: Morteza Amini [aut, cre, cph],
Afarin Bayat [aut],
Reza Salehian [aut]
Maintainer: Morteza Amini <morteza.amini@ut.ac.ir>
Diff between hhsmm versions 0.4.0 dated 2024-05-08 and 0.4.1 dated 2024-09-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/dmixlm.R | 6 ++++-- R/predict-hhsmm.R | 6 +++--- R/predict-hhsmmspec.R | 4 ++-- man/predict.hhsmm.Rd | 8 ++++---- man/predict.hhsmmspec.Rd | 6 +++--- 7 files changed, 26 insertions(+), 24 deletions(-)
Title: A Fast Algorithm to Factorize High-Dimensional Tensor Product
Matrices
Description: Here we provide tools for the computation and factorization of high-dimensional
tensor products that are formed by smaller matrices. The methods are based on
properties of Kronecker products (Searle 1982, p. 265, ISBN-10: 0470009616).
We evaluated this methodology by benchmark testing and illustrated its use in
Gaussian Linear Models ('Lopez-Cruz et al., 2024') <doi:10.1093/g3journal/jkae001>.
Author: Marco Lopez-Cruz [aut, cre],
Gustavo de los Campos [aut],
Paulino Perez-Rodriguez [aut]
Maintainer: Marco Lopez-Cruz <maraloc@gmail.com>
Diff between tensorEVD versions 0.1.3 dated 2024-05-30 and 0.1.4 dated 2024-09-03
DESCRIPTION | 8 +++--- MD5 | 40 ++++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 5 ++++ R/Hadamard.R | 10 +++++--- R/Hadamard_cov.R | 3 +- R/Kronecker.R | 8 +++++- R/Kronecker_cov.R | 3 +- R/Sum.R |only build/vignette.rds |binary inst/doc/tensorEVD-documentation.Rmd |only inst/doc/tensorEVD-documentation.html | 2 - man/hadamard.Rd | 14 ++++++----- man/kronecker.Rd | 4 ++- man/sum.Rd |only src/Makevars | 1 src/c_hadamard.c | 20 ++++++----------- src/c_sum.c |only src/c_tensor_evd.c | 12 +++------- src/init.c | 6 +++-- src/tensorEVD.h | 2 + src/utils.c | 39 +++++++++++++++++++++++++++++++-- vignettes/tensorEVD-documentation.Rmd | 2 - 23 files changed, 118 insertions(+), 62 deletions(-)
Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Peiyuan Zhu [aut, cre],
Claude Boivin [aut]
Maintainer: Peiyuan Zhu <garyzhubc@gmail.com>
Diff between dst versions 1.7.1 dated 2024-08-26 and 1.8.0 dated 2024-09-03
DESCRIPTION | 8 +- MD5 | 73 +++++++++++++------------ NAMESPACE | 1 NEWS.md | 8 ++ R/bca.R | 61 +++++++++++++++++--- R/belplau.R | 47 +++++++++++++++- R/belplauLogsumexp.R | 46 +++++++++++++++ R/commonality.R | 41 +++++++++++--- R/mFromQQ.R | 3 - R/mFromQQRecursive.R |only inst/doc/Bayes_Rule.html | 17 ++--- inst/doc/Captain_Example.html | 27 +++------ inst/doc/Crime_Scene.html | 22 +++---- inst/doc/Crime_Scene_Commonality.R | 18 ++++++ inst/doc/Crime_Scene_Commonality.Rmd | 26 ++++++++ inst/doc/Crime_Scene_Commonality.html | 66 +++++++++++++++------- inst/doc/Evidential_Modelling.html | 6 -- inst/doc/Holmes_Burglary.html | 12 ---- inst/doc/Introduction_to_Belief_Functions.html | 64 ++++++++++----------- inst/doc/PJM_example_DSC.html | 13 ---- inst/doc/PJM_example_DSC_Multivalued_Map.html | 10 --- inst/doc/PJM_example_DSC_Simplified.html | 13 ---- inst/doc/Reliability_Proof_Machinery.html | 50 ++++++----------- inst/doc/Simple_Implication.Rmd | 1 inst/doc/Simple_Implication.html | 8 -- inst/doc/The_Monty_Hall_Game.html | 12 +--- inst/doc/The_PJM_example.html | 12 +--- inst/doc/Zadeh_Example.html | 18 ++---- inst/dst.pdf |binary man/bca.Rd | 8 ++ man/belplau.Rd | 4 + man/belplauLogsumexp.Rd | 4 + man/commonality.Rd | 4 + man/mFromQQRecursive.Rd |only tests/testthat/test_belplau.R | 12 ++++ tests/testthat/test_commonality.R | 10 +++ tests/testthat/test_mFromQQRecursive.R |only vignettes/Crime_Scene_Commonality.Rmd | 26 ++++++++ vignettes/Simple_Implication.Rmd | 1 39 files changed, 470 insertions(+), 282 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel Sjoberg [aut, cre],
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.2.0 dated 2024-07-20 and 0.2.1 dated 2024-09-03
cardx-0.2.0/cardx/tests/testthat/_snaps/ard_stats_chisq_test.md |only cardx-0.2.1/cardx/DESCRIPTION | 22 - cardx-0.2.1/cardx/MD5 | 182 +++++----- cardx-0.2.1/cardx/NAMESPACE | 4 cardx-0.2.1/cardx/NEWS.md | 18 cardx-0.2.1/cardx/R/add_total_n.survey.design.R |only cardx-0.2.1/cardx/R/ard_aod_wald_test.R | 4 cardx-0.2.1/cardx/R/ard_car_anova.R | 4 cardx-0.2.1/cardx/R/ard_car_vif.R | 5 cardx-0.2.1/cardx/R/ard_categorical.survey.design.R | 60 +-- cardx-0.2.1/cardx/R/ard_categorical_ci.R | 6 cardx-0.2.1/cardx/R/ard_categorical_ci.survey.design.R | 12 cardx-0.2.1/cardx/R/ard_continuous.survey.design.R | 8 cardx-0.2.1/cardx/R/ard_continuous_ci.R | 9 cardx-0.2.1/cardx/R/ard_continuous_ci.survey.design.R | 12 cardx-0.2.1/cardx/R/ard_dichotomous.survey.design.R | 4 cardx-0.2.1/cardx/R/ard_effectsize_cohens_d.R | 10 cardx-0.2.1/cardx/R/ard_effectsize_hedges_g.R | 11 cardx-0.2.1/cardx/R/ard_emmeans_mean_difference.R | 4 cardx-0.2.1/cardx/R/ard_missing.survey.design.R | 9 cardx-0.2.1/cardx/R/ard_regression.R | 121 ++++-- cardx-0.2.1/cardx/R/ard_smd_smd.R | 6 cardx-0.2.1/cardx/R/ard_stats_anova.R | 4 cardx-0.2.1/cardx/R/ard_stats_aov.R | 14 cardx-0.2.1/cardx/R/ard_stats_chisq_test.R | 8 cardx-0.2.1/cardx/R/ard_stats_fisher_test.R | 8 cardx-0.2.1/cardx/R/ard_stats_kruskal_test.R | 8 cardx-0.2.1/cardx/R/ard_stats_mcnemar_test.R | 11 cardx-0.2.1/cardx/R/ard_stats_mood_test.R | 7 cardx-0.2.1/cardx/R/ard_stats_oneway_test.R | 1 cardx-0.2.1/cardx/R/ard_stats_poisson_test.R |only cardx-0.2.1/cardx/R/ard_stats_prop_test.R | 5 cardx-0.2.1/cardx/R/ard_stats_t_test.R | 9 cardx-0.2.1/cardx/R/ard_stats_t_test_onesample.R | 9 cardx-0.2.1/cardx/R/ard_stats_wilcox_test.R | 9 cardx-0.2.1/cardx/R/ard_stats_wilcox_test_onesample.R | 9 cardx-0.2.1/cardx/R/ard_survey_svychisq.R | 8 cardx-0.2.1/cardx/R/ard_survey_svyranktest.R | 6 cardx-0.2.1/cardx/R/ard_survey_svyttest.R | 6 cardx-0.2.1/cardx/R/ard_survival_survdiff.R | 4 cardx-0.2.1/cardx/R/ard_survival_survfit.R | 2 cardx-0.2.1/cardx/R/ard_survival_survfit_diff.R | 4 cardx-0.2.1/cardx/R/construction_helpers.R | 29 - cardx-0.2.1/cardx/R/reexports.R | 4 cardx-0.2.1/cardx/man/ard_continuous_ci.Rd | 2 cardx-0.2.1/cardx/man/ard_stats_poisson_test.Rd |only cardx-0.2.1/cardx/man/ard_total_n.survey.design.Rd |only cardx-0.2.1/cardx/man/cardx-package.Rd | 3 cardx-0.2.1/cardx/man/construction_helpers.Rd | 15 cardx-0.2.1/cardx/man/dot-format_poissontest_results.Rd |only cardx-0.2.1/cardx/man/reexports.Rd | 3 cardx-0.2.1/cardx/tests/testthat/_snaps/ard_car_vif.md | 4 cardx-0.2.1/cardx/tests/testthat/_snaps/ard_regression.md | 126 +++--- cardx-0.2.1/cardx/tests/testthat/_snaps/ard_regression_basic.md | 26 - cardx-0.2.1/cardx/tests/testthat/_snaps/ard_stats_aov.md | 33 + cardx-0.2.1/cardx/tests/testthat/_snaps/ard_stats_poisson_test.md |only cardx-0.2.1/cardx/tests/testthat/_snaps/ard_total_n.survey.design.md |only cardx-0.2.1/cardx/tests/testthat/_snaps/construction_helpers.md | 17 cardx-0.2.1/cardx/tests/testthat/test-ard_aod_wald_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_car_anova.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_car_vif.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_categorical.survey.design.R | 34 + cardx-0.2.1/cardx/tests/testthat/test-ard_categorical_ci.survey.design.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_continuous.survey.design.R | 10 cardx-0.2.1/cardx/tests/testthat/test-ard_continuous_ci.data.frame.R | 16 cardx-0.2.1/cardx/tests/testthat/test-ard_continuous_ci.survey.design.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_dichotomous.survey.design.R | 16 cardx-0.2.1/cardx/tests/testthat/test-ard_effectsize_cohens_d.R | 23 + cardx-0.2.1/cardx/tests/testthat/test-ard_effectsize_hedges_g.R | 23 + cardx-0.2.1/cardx/tests/testthat/test-ard_emmeans_mean_difference.R | 13 cardx-0.2.1/cardx/tests/testthat/test-ard_missing.survey.design.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_proportion_ci.R | 11 cardx-0.2.1/cardx/tests/testthat/test-ard_regression.R | 23 + cardx-0.2.1/cardx/tests/testthat/test-ard_regression_basic.R | 10 cardx-0.2.1/cardx/tests/testthat/test-ard_smd_smd.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_anova.R | 11 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_aov.R | 7 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_chisq_test.R | 22 - cardx-0.2.1/cardx/tests/testthat/test-ard_stats_fisher_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_kruskal_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_mcnemar_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_mood_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_oneway_test.R | 7 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_poisson_test.R |only cardx-0.2.1/cardx/tests/testthat/test-ard_stats_prop_test.R | 8 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_t_test.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_t_test_onesample.R | 15 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_wilcox_test.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_stats_wilcox_test_onesample.R | 16 cardx-0.2.1/cardx/tests/testthat/test-ard_survey_svychisq.R | 14 cardx-0.2.1/cardx/tests/testthat/test-ard_survey_svyranktest.R | 14 cardx-0.2.1/cardx/tests/testthat/test-ard_survey_svyttest.R | 14 cardx-0.2.1/cardx/tests/testthat/test-ard_survival_survdiff.R | 7 cardx-0.2.1/cardx/tests/testthat/test-ard_survival_survfit.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_survival_survfit_diff.R | 9 cardx-0.2.1/cardx/tests/testthat/test-ard_total_n.survey.design.R |only cardx-0.2.1/cardx/tests/testthat/test-construction_helpers.R | 8 97 files changed, 957 insertions(+), 397 deletions(-)