Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso (2008)
<doi:10.1177/009286150804200402> for a review. This package implements
MMRM based on the marginal linear model without random effects using
Template Model Builder ('TMB') which enables fast and robust model
fitting. Users can specify a variety of covariance matrices, weight
observations, fit models with restricted or standard maximum
likelihood inference, perform hypothesis testing with Satterthwaite or
Kenward-Roger adjustment, and extract least square means estimates by
using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre],
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Liming Li [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leibov [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Diff between mmrm versions 0.3.6 dated 2023-11-17 and 0.3.7 dated 2023-12-08
DESCRIPTION | 8 MD5 | 40 NEWS.md | 7 R/fit.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/WORDLIST | 97 inst/doc/algorithm.html | 318 -- inst/doc/between_within.html | 415 +-- inst/doc/coef_vcov.html | 139 - inst/doc/covariance.html | 310 -- inst/doc/empirical_wls.html | 232 - inst/doc/introduction.html | 3801 ++++++++++++++---------------- inst/doc/kenward.html | 379 -- inst/doc/methodological_introduction.html | 281 -- inst/doc/mmrm_review_methods.html | 324 -- inst/doc/package_structure.html | 282 -- inst/doc/predict.html | 284 -- inst/doc/satterthwaite.html | 262 -- man/mmrm_control.Rd | 2 src/covariance.h | 4 21 files changed, 2739 insertions(+), 4448 deletions(-)
Title: An Interface to the 'fastText' Library
Description: An interface to the 'fastText' library
<https://github.com/facebookresearch/fastText>. The package
can be used for text classification and to learn word vectors.
An example how to use 'fastTextR' can be found in the 'README' file.
Author: Florian Schwendinger [aut],
Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between fastTextR versions 2.0.1 dated 2022-10-31 and 2.1.0 dated 2023-12-08
DESCRIPTION | 9 +-- MD5 | 44 ++++++++------- NAMESPACE | 1 NEWS.md |only R/RcppExports.R | 4 + R/fasttext.R | 106 +++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/Cheatsheet.Rmd | 1 inst/doc/Cheatsheet.html | 6 +- inst/doc/Text_classification.R | 20 +++--- inst/doc/Text_classification.Rmd | 2 inst/doc/Text_classification.html | 2 inst/doc/Word_representations.R | 13 ++-- inst/doc/Word_representations.Rmd | 10 +++ inst/doc/Word_representations.html | 5 + man/ft_control.Rd | 6 +- man/ft_sentence_vectors.Rd |only man/ft_train.Rd | 4 - man/predict.supervised_model.Rd | 12 ++-- src/RcppExports.cpp | 13 ++++ src/interface.cc | 39 ++++++++++--- vignettes/Cheatsheet.Rmd | 1 vignettes/Text_classification.Rmd | 2 vignettes/Word_representations.Rmd | 10 +++ 24 files changed, 205 insertions(+), 105 deletions(-)
Title: Use of Interval Algebra to Create New Cohort(s) from Existing
Cohorts
Description: This software tool is designed to generate new cohorts utilizing data from
previously instantiated cohorts. It employs interval algebra operators such as UNION,
INTERSECT, and MINUS to manipulate the data within the instantiated cohorts and
create new cohorts.
Author: Gowtham Rao [aut, cre],
Observational Health Data Science and Informatics [cph]
Maintainer: Gowtham Rao <rao@ohdsi.org>
Diff between CohortAlgebra versions 0.0.4 dated 2023-09-13 and 0.1.0 dated 2023-12-08
DESCRIPTION | 10 +++++----- MD5 | 22 ++++++++++++++-------- NEWS.md | 5 +++++ R/AppendCohortTables.R | 12 +++++++++--- R/ReindexCohortsByDays.R |only R/UploadTempTable.R |only inst/doc/HowToUseCohortAlgebraRPackage.R | 2 +- inst/doc/HowToUseCohortAlgebraRPackage.html | 4 ++-- inst/sql/sql_server/ReindexCohorts.sql |only man/reindexCohortsByDays.Rd |only tests/testthat/test-appendCohortTables.R |only tests/testthat/test-eraFyCohorts.R | 17 +++++++++++++++++ tests/testthat/test-minusCohorts.R | 12 ++++++++++++ tests/testthat/test-reindexCohortsByDays.R |only tests/testthat/test-unionCohorts.R | 17 +++++++++++++++++ 15 files changed, 82 insertions(+), 19 deletions(-)
Title: Tools for General Maximum Likelihood Estimation
Description: Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.
Author: Ben Bolker [aut, cre] ,
R Development Core Team [aut],
Iago Gine-Vazquez [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between bbmle versions 1.0.25 dated 2022-05-11 and 1.0.25.1 dated 2023-12-08
bbmle-1.0.25.1/bbmle/DESCRIPTION | 11 +++++---- bbmle-1.0.25.1/bbmle/MD5 | 18 ++++++--------- bbmle-1.0.25.1/bbmle/build/vignette.rds |binary bbmle-1.0.25.1/bbmle/inst/NEWS.Rd | 8 ++++++ bbmle-1.0.25.1/bbmle/inst/doc/mle2.R | 35 ++++++++++-------------------- bbmle-1.0.25.1/bbmle/inst/doc/mle2.Rnw | 36 +++++++++++++++++++++---------- bbmle-1.0.25.1/bbmle/inst/doc/mle2.pdf |binary bbmle-1.0.25.1/bbmle/inst/doc/quasi.pdf |binary bbmle-1.0.25.1/bbmle/vignettes/mle2.Rnw | 36 +++++++++++++++++++++---------- bbmle-1.0.25/bbmle/tests/binomtest1.Rout |only bbmle-1.0.25/bbmle/tests/testbounds.Rout |only 11 files changed, 84 insertions(+), 60 deletions(-)
Title: Access and Analyze eBird Status and Trends Data Products
Description: Tools for accessing and analyzing eBird Status and
Trends Data Products
(<https://science.ebird.org/en/status-and-trends>). eBird
(<https://ebird.org/home>) is a global database of bird observations
collected by member of the public. eBird Status and Trends uses these
data to model global bird distributions, abundances, and population trends
at a high spatial and temporal resolution.
Author: Matthew Strimas-Mackey [aut, cre]
,
Shawn Ligocki [aut],
Tom Auer [aut] ,
Daniel Fink [aut] ,
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between ebirdst versions 3.2022.0 dated 2023-11-15 and 3.2022.1 dated 2023-12-08
DESCRIPTION | 6 ++-- MD5 | 53 +++++++++++++++++++----------------- NAMESPACE | 15 ++++++++++ NEWS.md | 7 ++++ R/data.R | 4 +- R/download.R | 6 ++-- R/ebirdst-defunct.R |only R/ebirdst-deprecated.R |only R/utils.R | 26 ++++++++++++----- R/zzz.R | 2 - build/vignette.rds |binary data/ebirdst_predictors.rda |binary data/ebirdst_runs.rda |binary inst/doc/applications.Rmd | 7 ---- inst/doc/applications.html | 10 ------ inst/doc/product-changelog.Rmd | 4 +- inst/doc/product-changelog.html | 4 +- inst/doc/status.Rmd | 9 ------ inst/doc/status.html | 11 ------- man/abundance_palette-deprecated.Rd |only man/date_to_st_week.Rd | 6 +++- man/ebirdst-defunct.Rd |only man/ebirdst-deprecated.Rd |only man/ebirdst_download_status.Rd | 2 - man/ebirdst_download_trends.Rd | 2 - man/ebirdst_runs.Rd | 4 +- tests/testthat/test_palette.R | 5 +++ vignettes/applications.Rmd | 7 ---- vignettes/product-changelog.Rmd | 4 +- vignettes/status.Rmd | 9 ------ 30 files changed, 102 insertions(+), 101 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18 [...truncated...]
Author: Maximilian Boeck [aut, cre] ,
Martin Feldkircher [aut] ,
Florian Huber [aut] ,
Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@unibocconi.it>
Diff between BGVAR versions 2.5.2 dated 2022-10-26 and 2.5.3 dated 2023-12-08
DESCRIPTION | 14 MD5 | 74 +-- NEWS | 9 R/BGVAR.R | 131 +++-- R/RcppExports.R | 2 R/bgvar-package.R | 46 - R/fevd.R | 4 R/hd.R | 2 R/helpers.R | 4 R/irf.R | 8 R/plot.R | 43 + R/predict.R | 8 R/utils.R | 566 +++++++++++++---------- R/zzz.R | 6 inst/CITATION | 21 inst/doc/examples.R | 64 +- inst/doc/examples.html | 1184 ++++++++++++++++++++++++------------------------- man/bgvar.Rd | 22 man/conv.diag.Rd | 2 man/dic.Rd | 2 man/eerData.Rd | 4 man/fevd.Rd | 2 man/gfevd.Rd | 2 man/hd.Rd | 2 man/irf.Rd | 8 man/monthlyData.Rd | 30 - man/pesaranData.Rd | 6 man/predict.Rd | 2 man/resid.corr.test.Rd | 2 man/residuals.Rd | 2 man/testdata.Rd | 6 src/BVAR_linear.cpp | 16 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 2 src/gvar_stacking.cpp | 18 src/helper.cpp | 2 src/irf.cpp | 20 38 files changed, 1253 insertions(+), 1085 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [ctb] ,
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.5.0 dated 2023-05-22 and 0.5.0-2 dated 2023-12-08
mlr3pipelines-0.5.0-2/mlr3pipelines/DESCRIPTION | 6 mlr3pipelines-0.5.0-2/mlr3pipelines/MD5 | 82 - mlr3pipelines-0.5.0-2/mlr3pipelines/NEWS.md | 9 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOp.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOpColRoles.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOpFilter.R | 1 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOpLearnerCV.R | 7 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOpMissingIndicators.R | 1 mlr3pipelines-0.5.0-2/mlr3pipelines/R/PipeOpTuneThreshold.R | 16 mlr3pipelines-0.5.0-2/mlr3pipelines/R/pipeline_robustify.R | 10 mlr3pipelines-0.5.0-2/mlr3pipelines/README.md | 9 mlr3pipelines-0.5.0-2/mlr3pipelines/build/partial.rdb |binary mlr3pipelines-0.5.0-2/mlr3pipelines/build/vignette.rds |binary mlr3pipelines-0.5.0-2/mlr3pipelines/inst/doc/extending.html | 681 ++++++++-- mlr3pipelines-0.5.0-2/mlr3pipelines/man/mlr_pipeops_colroles.Rd | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/man/mlr_pipeops_filter.Rd | 1 mlr3pipelines-0.5.0-2/mlr3pipelines/man/mlr_pipeops_missind.Rd | 1 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/setup.R | 9 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_GraphLearner.R | 8 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_learner_weightedaverage.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_mlr_graphs_bagging.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_mlr_graphs_branching.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_mlr_graphs_robustify.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_mlr_graphs_targettrafo.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_encode.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_encodeimpact.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_encodelmer.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_filter.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_fixfactors.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_learnercv.R | 22 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_removeconstants.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_scale.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_select.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_subsample.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_targetmutate.R | 8 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_targettrafoscalerange.R | 4 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_task_preproc.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_tunethreshold.R | 21 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_updatetarget.R | 6 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_pipeop_vtreat.R | 2 mlr3pipelines-0.5.0-2/mlr3pipelines/tests/testthat/test_selector.R | 2 mlr3pipelines-0.5.0/mlr3pipelines/inst/doc/comparison_mlr3pipelines_mlr_sklearn.html |only mlr3pipelines-0.5.0/mlr3pipelines/inst/doc/introduction.html |only 43 files changed, 738 insertions(+), 214 deletions(-)
Title: Map Pages of Memory
Description: R interface to POSIX mmap and Window's MapViewOfFile.
Author: Jeffrey A. Ryan
Maintainer: Jeffrey A. Ryan <jeff.a.ryan@gmail.com>
Diff between mmap versions 0.6-21 dated 2023-01-29 and 0.6-22 dated 2023-12-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + build/vignette.rds |binary inst/doc/mmap.pdf |binary src/mmap.c | 46 +++++++++++++++++++++++----------------------- 6 files changed, 33 insertions(+), 32 deletions(-)
Title: Automated Uncertainty Analysis
Description: Methods and tools for model selection and multi-model inference (Burnham and Anderson (2002) <doi:10.1007/b97636>, among others).
'SUR' (for parameter estimation), 'logit'/'probit' (for binary classification), and 'VARMA' (for time-series forecasting) are implemented.
Evaluations are both in-sample and out-of-sample.
It is designed to be efficient in terms of CPU usage and memory consumption.
Author: Ramin Mojab [aut, cre],
Stephen Becker [cph] by Ciyou Zhu . L-BFGS-B Version 3.0 is an
algorithmic update from 2011, with coding changes by J. L. Morales)
Maintainer: Ramin Mojab <rmojab63@gmail.com>
Diff between ldt versions 0.5.0 dated 2023-11-07 and 0.5.1 dated 2023-12-08
DESCRIPTION | 6 +-- MD5 | 48 ++++++++++++------------ NEWS.md | 5 ++ R/data.R | 34 ++++++++--------- R/g.plots.R | 2 - R/search.R | 83 +++++++++++++++++++++++++++++++++++++----- R/varma.R | 26 ++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/bin.R | 2 - inst/doc/bin.html | 2 - inst/doc/sur.R | 2 - inst/doc/sur.html | 2 - inst/doc/varma.R | 2 - inst/doc/varma.html | 33 +++++++++------- man/boxCoxTransform.Rd | 6 +-- man/get.search.modelchecks.Rd | 8 ++-- man/search.varma.Rd | 5 +- src/array.cpp | 2 - src/r_ldt.cpp | 17 +++++++- src/searchers.h | 11 +++-- src/summary.cpp | 7 --- src/varma.h | 9 ---- src/varma_modelset.cpp | 79 +++++++++++++-------------------------- tests/testthat/test-varma.R | 67 +++++++++++++++++++++------------ 25 files changed, 266 insertions(+), 192 deletions(-)
Title: Handwriting Analysis in R
Description: Perform statistical writership analysis of scanned handwritten documents.
Webpage provided at: <https://csafe-isu.github.io/handwriter/index.html>.
Author: Iowa State University of Science and Technology on behalf of its Center
for Statistics and Applications in Forensic Evidence [aut, cph,
fnd],
Nick Berry [aut],
Stephanie Reinders [aut, cre],
James Taylor [aut],
Felix Baez-Santiago [ctb],
Jon Gonzalez [...truncated...]
Maintainer: Stephanie Reinders <srein@iastate.edu>
Diff between handwriter versions 2.0.2 dated 2023-10-13 and 2.0.3 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/BatchProcessing.R | 2 ++ README.md | 3 ++- inst/doc/handwriter.R | 1 + inst/doc/handwriter.Rmd | 3 ++- inst/doc/handwriter.html | 7 ++++--- man/process_batch_dir.Rd | 14 +++++++------- man/process_batch_list.Rd | 14 +++++++------- src/ThinImageCpp.cpp | 2 +- vignettes/handwriter.Rmd | 3 ++- 12 files changed, 46 insertions(+), 35 deletions(-)
Title: Computes Numeric Fourier Integrals
Description: Computes Fourier integrals of functions of one and two variables using the Fast Fourier transform. The Fourier transforms must be evaluated on a regular grid for fast evaluation.
Author: Guillermo Basulto-Elias
Maintainer: Guillermo Basulto-Elias <guillermobasulto@gmail.com>
Diff between fourierin versions 0.2.4 dated 2019-04-07 and 0.2.5 dated 2023-12-08
fourierin-0.2.4/fourierin/R/mvfourierin.R |only fourierin-0.2.4/fourierin/src/fourierin_cx_nd.cpp |only fourierin-0.2.5/fourierin/DESCRIPTION | 18 fourierin-0.2.5/fourierin/MD5 | 37 fourierin-0.2.5/fourierin/NEWS.md | 3 fourierin-0.2.5/fourierin/R/RcppExports.R | 2 fourierin-0.2.5/fourierin/R/fourierin.R | 980 +++++------ fourierin-0.2.5/fourierin/README.md | 52 fourierin-0.2.5/fourierin/build/vignette.rds |binary fourierin-0.2.5/fourierin/inst/WORDLIST |only fourierin-0.2.5/fourierin/inst/doc/fourierin_details.R | 592 +++---- fourierin-0.2.5/fourierin/inst/doc/fourierin_details.Rmd | 746 ++++---- fourierin-0.2.5/fourierin/inst/doc/fourierin_details.html | 1170 ++++++++------ fourierin-0.2.5/fourierin/man/fourierin.Rd | 15 fourierin-0.2.5/fourierin/man/fourierin_1d.Rd | 15 fourierin-0.2.5/fourierin/man/fourierin_2d.Rd | 15 fourierin-0.2.5/fourierin/src/RcppExports.cpp | 21 fourierin-0.2.5/fourierin/src/fourierin_cx_1d.cpp | 4 fourierin-0.2.5/fourierin/tests |only fourierin-0.2.5/fourierin/vignettes/fourierin_details.Rmd | 746 ++++---- 20 files changed, 2388 insertions(+), 2028 deletions(-)
Title: Evaluates the Empirical Characteristic Function for Multivariate
Samples
Description: Evaluates the empirical characteristic function of univariate and multivariate samples.
This package uses 'RcppArmadillo' for fast evaluation. It is also possible to export the code to be used in other packages at 'C++' level.
Author: Guillermo Basulto-Elias [aut, cre]
Maintainer: Guillermo Basulto-Elias <guillermobasulto@gmail.com>
Diff between empichar versions 1.0.0 dated 2019-05-08 and 1.0.1 dated 2023-12-08
DESCRIPTION | 11 ++++++----- MD5 | 23 ++++++++++++----------- NEWS.md | 4 ++++ R/wrappers.R | 16 ++++++++-------- README.md | 34 +++++++++++++++++++++------------- inst/WORDLIST |only man/ecf.Rd | 4 ++-- man/ecf_imag.Rd | 4 ++-- man/ecf_mod.Rd | 4 ++-- man/ecf_real.Rd | 4 ++-- src/Makevars | 1 - src/Makevars.win | 1 - src/RcppExports.cpp | 13 +++++++++---- 13 files changed, 68 insertions(+), 51 deletions(-)
Title: High-Throughput Toxicokinetics
Description: Pre-made models that can be rapidly tailored to various chemicals
and species using chemical-specific in vitro data and physiological
information. These tools allow incorporation of chemical
toxicokinetics ("TK") and in vitro-in vivo extrapolation ("IVIVE")
into bioinformatics, as described by Pearce et al. (2017)
(<doi:10.18637/jss.v079.i04>). Chemical-specific
in vitro data characterizing toxicokinetics have been obtained
from relatively high-throughput experiments. The
chemical-independent ("generic") physiologically-based ("PBTK") and empirical
(for example, one compartment) "TK" models included here can be
parameterized with in vitro data or in silico predictions which are
provided for thousands of chemicals, multiple exposure routes,
and various species. High throughput toxicokinetics ("HTTK") is the
combination of in vitro data and generic models. We establish the
expected accuracy of HTTK for chemicals without in vivo data
through statistical evaluation of HTTK predicti [...truncated...]
Author: John Wambaugh [aut, cre] ,
Sarah Davidson-Fritz [aut] ,
Robert Pearce [aut] ,
Caroline Ring [aut] ,
Greg Honda [aut] ,
Mark Sfeir [aut],
Matt Linakis [aut] ,
Dustin Kapraun [aut] ,
Nathan Pollesch [ctb] ,
Miyuki Breen [ctb] ,
Shannon Bell [ctb] ,
Xia [...truncated...]
Maintainer: John Wambaugh <wambaugh.john@epa.gov>
Diff between httk versions 2.2.2 dated 2023-02-20 and 2.3.0 dated 2023-12-08
httk-2.2.2/httk/R/get_Wetmore_Css.R |only httk-2.2.2/httk/R/get_Wetmore_Oral_Equiv.R |only httk-2.2.2/httk/R/get_Wetmore_cheminfo.R |only httk-2.2.2/httk/R/modelinfo_Schmitt.R |only httk-2.2.2/httk/R/vLiverPBPKfetus_inits.R |only httk-2.2.2/httk/inst/doc/Vc_Frank2018.R |only httk-2.2.2/httk/inst/doc/Vc_Frank2018.Rmd |only httk-2.2.2/httk/inst/doc/Vc_Frank2018.html |only httk-2.2.2/httk/inst/doc/Vd_Wambaugh2018.R |only httk-2.2.2/httk/inst/doc/Vd_Wambaugh2018.Rmd |only httk-2.2.2/httk/inst/doc/Vd_Wambaugh2018.html |only httk-2.2.2/httk/inst/doc/Ve_Honda2019.R |only httk-2.2.2/httk/inst/doc/Ve_Honda2019.Rmd |only httk-2.2.2/httk/inst/doc/Ve_Honda2019.html |only httk-2.2.2/httk/inst/doc/Vf_Wambaugh2019.R |only httk-2.2.2/httk/inst/doc/Vf_Wambaugh2019.Rmd |only httk-2.2.2/httk/inst/doc/Vf_Wambaugh2019.html |only httk-2.2.2/httk/inst/doc/Vg_Linakis2020.R |only httk-2.2.2/httk/inst/doc/Vg_Linakis2020.Rmd |only httk-2.2.2/httk/inst/doc/Vg_Linakis2020.html |only httk-2.2.2/httk/inst/doc/Vh_Kapraun2022.R |only httk-2.2.2/httk/inst/doc/Vh_Kapraun2022.Rmd |only httk-2.2.2/httk/inst/doc/Vh_Kapraun2022.html |only httk-2.2.2/httk/src/modelfetalpbtk.c |only httk-2.2.2/httk/vignettes/Vc_Frank2018.Rmd |only httk-2.2.2/httk/vignettes/Vd_Wambaugh2018.Rmd |only httk-2.2.2/httk/vignettes/Ve_Honda2019.Rmd |only httk-2.2.2/httk/vignettes/Vf_Wambaugh2019.Rmd |only httk-2.2.2/httk/vignettes/Vg_Linakis2020.Rmd |only httk-2.2.2/httk/vignettes/Vh_Kapraun2022.Rmd |only httk-2.3.0/httk/DESCRIPTION | 39 httk-2.3.0/httk/MD5 | 591 httk-2.3.0/httk/NAMESPACE | 16 httk-2.3.0/httk/NEWS.md | 194 httk-2.3.0/httk/R/add_chemtable.R | 12 httk-2.3.0/httk/R/age_draw_smooth.R | 5 httk-2.3.0/httk/R/apply_clint_adjustment.R | 10 httk-2.3.0/httk/R/apply_fup_adjustment.R | 11 httk-2.3.0/httk/R/armitage.R | 244 httk-2.3.0/httk/R/benchmark_httk.R |only httk-2.3.0/httk/R/calc_analytic_css.R | 105 httk-2.3.0/httk/R/calc_analytic_css_1comp.R | 16 httk-2.3.0/httk/R/calc_analytic_css_3comp.R | 19 httk-2.3.0/httk/R/calc_analytic_css_3compss.R | 27 httk-2.3.0/httk/R/calc_analytic_css_pbtk.R | 18 httk-2.3.0/httk/R/calc_css.R | 3 httk-2.3.0/httk/R/calc_elimination_rate.R | 13 httk-2.3.0/httk/R/calc_fetal_phys.R | 10 httk-2.3.0/httk/R/calc_fup_correction.R | 22 httk-2.3.0/httk/R/calc_half_life.R | 2 httk-2.3.0/httk/R/calc_hep_bioavailability.R | 63 httk-2.3.0/httk/R/calc_hep_clearance.R | 12 httk-2.3.0/httk/R/calc_hep_fu.R | 10 httk-2.3.0/httk/R/calc_maternal_bw.R | 6 httk-2.3.0/httk/R/calc_mc_css.R | 53 httk-2.3.0/httk/R/calc_mc_oral_equiv.R | 98 httk-2.3.0/httk/R/calc_mc_tk.R | 9 httk-2.3.0/httk/R/calc_oral_bioavailability.R |only httk-2.3.0/httk/R/calc_tkstats.R | 11 httk-2.3.0/httk/R/calc_volume_of_distribution.R | 10 httk-2.3.0/httk/R/ckd_epi_eq.R | 6 httk-2.3.0/httk/R/convert_httkpop_1comp.R | 5 httk-2.3.0/httk/R/convert_solve_x.R | 91 httk-2.3.0/httk/R/convert_units.R | 403 httk-2.3.0/httk/R/create_mc_samples.R | 184 httk-2.3.0/httk/R/data.R | 240 httk-2.3.0/httk/R/do_initial_dose_pbtk.R |only httk-2.3.0/httk/R/estimate_gfr.R | 5 httk-2.3.0/httk/R/estimate_gfr_ped.R | 5 httk-2.3.0/httk/R/estimate_hematocrit.R | 5 httk-2.3.0/httk/R/gen_age_height_weight.R | 5 httk-2.3.0/httk/R/gen_height_weight.R | 5 httk-2.3.0/httk/R/gen_serum_creatinine.R | 5 httk-2.3.0/httk/R/get_caco2.R |only httk-2.3.0/httk/R/get_cheminfo.R | 125 httk-2.3.0/httk/R/get_clint.R | 30 httk-2.3.0/httk/R/get_fabsgut.R |only httk-2.3.0/httk/R/get_gfr_category.R | 5 httk-2.3.0/httk/R/get_invitroPK_param.R | 107 httk-2.3.0/httk/R/get_lit_cheminfo.R |only httk-2.3.0/httk/R/get_lit_css.R |only httk-2.3.0/httk/R/get_lit_oral_equiv.R |only httk-2.3.0/httk/R/get_physchem_param.R | 231 httk-2.3.0/httk/R/get_weight_class.R | 4 httk-2.3.0/httk/R/hematocrit_infants.R | 5 httk-2.3.0/httk/R/honda.ivive.R | 44 httk-2.3.0/httk/R/httk-package.R | 134 httk-2.3.0/httk/R/httkpop_biotophys_default.R | 5 httk-2.3.0/httk/R/httkpop_direct_resample.R | 5 httk-2.3.0/httk/R/httkpop_direct_resample_inner.R | 5 httk-2.3.0/httk/R/httkpop_generate.R | 5 httk-2.3.0/httk/R/httkpop_mc.R | 11 httk-2.3.0/httk/R/httkpop_virtual_indiv.R | 5 httk-2.3.0/httk/R/invitro_mc.R | 170 httk-2.3.0/httk/R/ionization_functions.R | 2 httk-2.3.0/httk/R/load_dawson2021.R | 79 httk-2.3.0/httk/R/load_honda2023.R |only httk-2.3.0/httk/R/load_pradeep2020.R | 82 httk-2.3.0/httk/R/load_sipes2017.R | 76 httk-2.3.0/httk/R/lump_tissues.R | 1 httk-2.3.0/httk/R/modelinfo_1comp.R | 16 httk-2.3.0/httk/R/modelinfo_3comp.R | 8 httk-2.3.0/httk/R/modelinfo_3compss.R | 36 httk-2.3.0/httk/R/modelinfo_fetal_pbtk.R | 28 httk-2.3.0/httk/R/modelinfo_gas_pbtk.R | 44 httk-2.3.0/httk/R/modelinfo_pbtk.R | 15 httk-2.3.0/httk/R/modelinfo_schmitt.R |only httk-2.3.0/httk/R/parameterize_1comp.R | 96 httk-2.3.0/httk/R/parameterize_3comp.R | 37 httk-2.3.0/httk/R/parameterize_fetal_pbtk.R | 18 httk-2.3.0/httk/R/parameterize_gas_pbtk.R | 137 httk-2.3.0/httk/R/parameterize_pbtk.R | 107 httk-2.3.0/httk/R/parameterize_schmitt.R | 43 httk-2.3.0/httk/R/parameterize_steadystate.R | 98 httk-2.3.0/httk/R/predict_partitioning_schmitt.R | 8 httk-2.3.0/httk/R/rmed0non0u95.R | 3 httk-2.3.0/httk/R/scale_dosing.R | 12 httk-2.3.0/httk/R/solve_1comp.R | 15 httk-2.3.0/httk/R/solve_3comp.R | 24 httk-2.3.0/httk/R/solve_fetal_pbtk.R | 2 httk-2.3.0/httk/R/solve_model.R | 55 httk-2.3.0/httk/R/solve_pbtk.R | 19 httk-2.3.0/httk/R/sysdata.rda |binary httk-2.3.0/httk/R/tissue_mass_functions.R | 52 httk-2.3.0/httk/R/tissue_masses_flows.R | 4 httk-2.3.0/httk/R/tissue_scale.R | 7 httk-2.3.0/httk/R/utils.R | 10 httk-2.3.0/httk/R/zzz.R | 3 httk-2.3.0/httk/README.md | 21 httk-2.3.0/httk/build/httk.pdf |38313 ++++++++++-------- httk-2.3.0/httk/build/partial.rdb |binary httk-2.3.0/httk/build/stage23.rdb |only httk-2.3.0/httk/build/vignette.rds |binary httk-2.3.0/httk/data/Frank2018.RData |binary httk-2.3.0/httk/data/Kapraun2022Vignette.RData |binary httk-2.3.0/httk/data/Linakis2020.RData |binary httk-2.3.0/httk/data/Tables.RData |binary httk-2.3.0/httk/data/armitage_input.RData |binary httk-2.3.0/httk/data/httkpop.RData |binary httk-2.3.0/httk/data/introtoivive-toxcast.RData |binary httk-2.3.0/httk/data/vignettes.RData |binary httk-2.3.0/httk/data/wambaugh2019.RData |binary httk-2.3.0/httk/data/well_param.RData |binary httk-2.3.0/httk/inst/REFERENCES.bib | 255 httk-2.3.0/httk/inst/doc/V1_IntroToHTTK.Rmd | 2 httk-2.3.0/httk/inst/doc/V1_IntroToHTTK.html | 160 httk-2.3.0/httk/inst/doc/V2_IntrotoIVIVE.Rmd | 12 httk-2.3.0/httk/inst/doc/V2_IntrotoIVIVE.html | 186 httk-2.3.0/httk/inst/doc/Va_Pearce2017.R | 5 httk-2.3.0/httk/inst/doc/Va_Pearce2017.Rmd | 9 httk-2.3.0/httk/inst/doc/Va_Pearce2017.html | 484 httk-2.3.0/httk/inst/doc/Vb_Ring2017.html | 4 httk-2.3.0/httk/inst/doc/Vc_Pearce2017.R |only httk-2.3.0/httk/inst/doc/Vc_Pearce2017.Rmd |only httk-2.3.0/httk/inst/doc/Vc_Pearce2017.html |only httk-2.3.0/httk/inst/doc/Vd_Frank2019.R |only httk-2.3.0/httk/inst/doc/Vd_Frank2019.Rmd |only httk-2.3.0/httk/inst/doc/Vd_Frank2019.html |only httk-2.3.0/httk/inst/doc/Ve_Wambaugh2018.R |only httk-2.3.0/httk/inst/doc/Ve_Wambaugh2018.Rmd |only httk-2.3.0/httk/inst/doc/Ve_Wambaugh2018.html |only httk-2.3.0/httk/inst/doc/Vf_Honda2019.R |only httk-2.3.0/httk/inst/doc/Vf_Honda2019.Rmd |only httk-2.3.0/httk/inst/doc/Vf_Honda2019.html |only httk-2.3.0/httk/inst/doc/Vg_Wambaugh2019.R |only httk-2.3.0/httk/inst/doc/Vg_Wambaugh2019.Rmd |only httk-2.3.0/httk/inst/doc/Vg_Wambaugh2019.html |only httk-2.3.0/httk/inst/doc/Vh_Linakis2020.R |only httk-2.3.0/httk/inst/doc/Vh_Linakis2020.Rmd |only httk-2.3.0/httk/inst/doc/Vh_Linakis2020.html |only httk-2.3.0/httk/inst/doc/Vi_Kapraun2022.R |only httk-2.3.0/httk/inst/doc/Vi_Kapraun2022.Rmd |only httk-2.3.0/httk/inst/doc/Vi_Kapraun2022.html |only httk-2.3.0/httk/man/add_chemtable.Rd | 4 httk-2.3.0/httk/man/age_draw_smooth.Rd | 4 httk-2.3.0/httk/man/apply_clint_adjustment.Rd | 10 httk-2.3.0/httk/man/apply_fup_adjustment.Rd | 10 httk-2.3.0/httk/man/armitage_estimate_sarea.Rd | 4 httk-2.3.0/httk/man/armitage_eval.Rd | 167 httk-2.3.0/httk/man/armitage_input.Rd | 4 httk-2.3.0/httk/man/aylward2014.Rd | 2 httk-2.3.0/httk/man/benchmark_httk.Rd |only httk-2.3.0/httk/man/blood_mass_correct.Rd | 4 httk-2.3.0/httk/man/blood_weight.Rd | 4 httk-2.3.0/httk/man/bmiage.Rd | 4 httk-2.3.0/httk/man/body_surface_area.Rd | 4 httk-2.3.0/httk/man/bone_mass_age.Rd | 4 httk-2.3.0/httk/man/brain_mass.Rd | 4 httk-2.3.0/httk/man/calc_analytic_css.Rd | 42 httk-2.3.0/httk/man/calc_analytic_css_1comp.Rd | 9 httk-2.3.0/httk/man/calc_analytic_css_3comp.Rd | 12 httk-2.3.0/httk/man/calc_analytic_css_3compss.Rd | 12 httk-2.3.0/httk/man/calc_analytic_css_pbtk.Rd | 12 httk-2.3.0/httk/man/calc_elimination_rate.Rd | 13 httk-2.3.0/httk/man/calc_fbio.oral.Rd |only httk-2.3.0/httk/man/calc_fetal_phys.Rd | 4 httk-2.3.0/httk/man/calc_fup_correction.Rd | 21 httk-2.3.0/httk/man/calc_half_life.Rd | 2 httk-2.3.0/httk/man/calc_hep_bioavailability.Rd | 18 httk-2.3.0/httk/man/calc_hep_clearance.Rd | 12 httk-2.3.0/httk/man/calc_hep_fu.Rd | 9 httk-2.3.0/httk/man/calc_maternal_bw.Rd | 4 httk-2.3.0/httk/man/calc_mc_css.Rd | 41 httk-2.3.0/httk/man/calc_mc_oral_equiv.Rd | 50 httk-2.3.0/httk/man/calc_mc_tk.Rd | 9 httk-2.3.0/httk/man/calc_tkstats.Rd | 6 httk-2.3.0/httk/man/calc_vdist.Rd | 8 httk-2.3.0/httk/man/chem.invivo.PK.aggregate.data.Rd | 2 httk-2.3.0/httk/man/chem.physical_and_invitro.data.Rd | 52 httk-2.3.0/httk/man/ckd_epi_eq.Rd | 4 httk-2.3.0/httk/man/convert_httkpop_1comp.Rd | 4 httk-2.3.0/httk/man/convert_solve_x.Rd | 2 httk-2.3.0/httk/man/convert_units.Rd | 17 httk-2.3.0/httk/man/create_mc_samples.Rd | 54 httk-2.3.0/httk/man/dawson2021.Rd | 10 httk-2.3.0/httk/man/estimate_gfr.Rd | 4 httk-2.3.0/httk/man/estimate_gfr_ped.Rd | 4 httk-2.3.0/httk/man/estimate_hematocrit.Rd | 4 httk-2.3.0/httk/man/example.seem.Rd | 3 httk-2.3.0/httk/man/fetalpcs.Rd | 2 httk-2.3.0/httk/man/figures/httk-logo.png |binary httk-2.3.0/httk/man/gen_age_height_weight.Rd | 4 httk-2.3.0/httk/man/gen_height_weight.Rd | 4 httk-2.3.0/httk/man/gen_serum_creatinine.Rd | 4 httk-2.3.0/httk/man/get_caco2.Rd |only httk-2.3.0/httk/man/get_cheminfo.Rd | 33 httk-2.3.0/httk/man/get_fabsgut.Rd |only httk-2.3.0/httk/man/get_gfr_category.Rd | 4 httk-2.3.0/httk/man/get_invitroPK_param.Rd | 59 httk-2.3.0/httk/man/get_lit_cheminfo.Rd | 2 httk-2.3.0/httk/man/get_lit_css.Rd | 2 httk-2.3.0/httk/man/get_lit_oral_equiv.Rd | 2 httk-2.3.0/httk/man/get_physchem_param.Rd | 53 httk-2.3.0/httk/man/get_weight_class.Rd | 4 httk-2.3.0/httk/man/get_wetmore_cheminfo.Rd | 2 httk-2.3.0/httk/man/get_wetmore_css.Rd | 2 httk-2.3.0/httk/man/get_wetmore_oral_equiv.Rd | 2 httk-2.3.0/httk/man/hct_h.Rd | 4 httk-2.3.0/httk/man/hematocrit_infants.Rd | 4 httk-2.3.0/httk/man/honda.ivive.Rd | 40 httk-2.3.0/httk/man/honda2023.data.Rd |only httk-2.3.0/httk/man/honda2023.qspr.Rd |only httk-2.3.0/httk/man/httk-package.Rd | 107 httk-2.3.0/httk/man/httk.performance.Rd |only httk-2.3.0/httk/man/httkpop.Rd | 5 httk-2.3.0/httk/man/httkpop_biotophys_default.Rd | 4 httk-2.3.0/httk/man/httkpop_direct_resample.Rd | 4 httk-2.3.0/httk/man/httkpop_direct_resample_inner.Rd | 4 httk-2.3.0/httk/man/httkpop_generate.Rd | 4 httk-2.3.0/httk/man/httkpop_mc.Rd | 10 httk-2.3.0/httk/man/httkpop_virtual_indiv.Rd | 4 httk-2.3.0/httk/man/hw_H.Rd | 4 httk-2.3.0/httk/man/invitro_mc.Rd | 45 httk-2.3.0/httk/man/is_in_inclusive.Rd | 4 httk-2.3.0/httk/man/kapraun2019.Rd | 2 httk-2.3.0/httk/man/kidney_mass_children.Rd | 4 httk-2.3.0/httk/man/liver_mass_children.Rd | 4 httk-2.3.0/httk/man/load_dawson2021.Rd | 54 httk-2.3.0/httk/man/load_honda2023.Rd |only httk-2.3.0/httk/man/load_pradeep2020.Rd | 54 httk-2.3.0/httk/man/load_sipes2017.Rd | 47 httk-2.3.0/httk/man/lump_tissues.Rd | 15 httk-2.3.0/httk/man/lung_mass_children.Rd | 4 httk-2.3.0/httk/man/mcnally_dt.Rd | 4 httk-2.3.0/httk/man/mecdt.Rd | 4 httk-2.3.0/httk/man/pancreas_mass_children.Rd | 4 httk-2.3.0/httk/man/parameterize_1comp.Rd | 33 httk-2.3.0/httk/man/parameterize_3comp.Rd | 30 httk-2.3.0/httk/man/parameterize_fetal_pbtk.Rd | 9 httk-2.3.0/httk/man/parameterize_gas_pbtk.Rd | 33 httk-2.3.0/httk/man/parameterize_pbtk.Rd | 57 httk-2.3.0/httk/man/parameterize_schmitt.Rd | 19 httk-2.3.0/httk/man/parameterize_steadystate.Rd | 48 httk-2.3.0/httk/man/pearce2017regression.Rd | 3 httk-2.3.0/httk/man/pksim.pcs.Rd | 2 httk-2.3.0/httk/man/pradeep2020.Rd | 6 httk-2.3.0/httk/man/predict_partitioning_schmitt.Rd | 16 httk-2.3.0/httk/man/pregnonpregaucs.Rd | 2 httk-2.3.0/httk/man/rfun.Rd | 4 httk-2.3.0/httk/man/rmed0non0u95.Rd | 2 httk-2.3.0/httk/man/scale_dosing.Rd | 2 httk-2.3.0/httk/man/scr_h.Rd | 4 httk-2.3.0/httk/man/sipes2017.Rd |only httk-2.3.0/httk/man/skeletal_muscle_mass.Rd | 4 httk-2.3.0/httk/man/skeletal_muscle_mass_children.Rd | 4 httk-2.3.0/httk/man/skin_mass_bosgra.Rd | 4 httk-2.3.0/httk/man/solve_1comp.Rd | 12 httk-2.3.0/httk/man/solve_3comp.Rd | 16 httk-2.3.0/httk/man/solve_fetal_pbtk.Rd | 2 httk-2.3.0/httk/man/solve_gas_pbtk.Rd | 2 httk-2.3.0/httk/man/solve_model.Rd | 9 httk-2.3.0/httk/man/solve_pbtk.Rd | 16 httk-2.3.0/httk/man/spleen_mass_children.Rd | 4 httk-2.3.0/httk/man/tissue.data.Rd | 9 httk-2.3.0/httk/man/tissue_masses_flows.Rd | 4 httk-2.3.0/httk/man/tissue_scale.Rd | 6 httk-2.3.0/httk/man/wambaugh2019.nhanes.Rd | 4 httk-2.3.0/httk/man/wambaugh2019.tox21.Rd | 2 httk-2.3.0/httk/man/wang2018.Rd | 2 httk-2.3.0/httk/man/well_param.Rd | 4 httk-2.3.0/httk/src/model_fetal_pbtk.c |only httk-2.3.0/httk/tests/1comp_test.R | 6 httk-2.3.0/httk/tests/1comp_test.Rout.save | 457 httk-2.3.0/httk/tests/3comp_test.R | 55 httk-2.3.0/httk/tests/3comp_test.Rout.save | 208 httk-2.3.0/httk/tests/3compss_test.R | 50 httk-2.3.0/httk/tests/3compss_test.Rout.save | 138 httk-2.3.0/httk/tests/adddata_test.R | 6 httk-2.3.0/httk/tests/adddata_test.Rout.save | 212 httk-2.3.0/httk/tests/caco2_test.R |only httk-2.3.0/httk/tests/caco2_test.Rout.save |only httk-2.3.0/httk/tests/cheminfo_test.R | 3 httk-2.3.0/httk/tests/cheminfo_test.Rout.save | 490 httk-2.3.0/httk/tests/fetal_pbtk_testing.R | 7 httk-2.3.0/httk/tests/fetal_pbtk_testing.Rout.save | 263 httk-2.3.0/httk/tests/ivive_test.R | 161 httk-2.3.0/httk/tests/ivive_test.Rout.save | 367 httk-2.3.0/httk/tests/montecarlo_tests.R | 37 httk-2.3.0/httk/tests/montecarlo_tests.Rout.save | 545 httk-2.3.0/httk/tests/other_tests.R | 6 httk-2.3.0/httk/tests/other_tests.Rout.save | 434 httk-2.3.0/httk/tests/pbtk_test.R | 53 httk-2.3.0/httk/tests/pbtk_test.Rout.save | 199 httk-2.3.0/httk/tests/solve_gas_test.R | 14 httk-2.3.0/httk/tests/solve_gas_test.Rout.save | 485 httk-2.3.0/httk/tests/unit_test.R | 37 httk-2.3.0/httk/tests/unit_test.Rout.save | 106 httk-2.3.0/httk/vignettes/V1_IntroToHTTK.Rmd | 2 httk-2.3.0/httk/vignettes/V2_IntrotoIVIVE.Rmd | 12 httk-2.3.0/httk/vignettes/Va_Pearce2017.Rmd | 9 httk-2.3.0/httk/vignettes/Vc_Pearce2017.Rmd |only httk-2.3.0/httk/vignettes/Vd_Frank2019.Rmd |only httk-2.3.0/httk/vignettes/Ve_Wambaugh2018.Rmd |only httk-2.3.0/httk/vignettes/Vf_Honda2019.Rmd |only httk-2.3.0/httk/vignettes/Vg_Wambaugh2019.Rmd |only httk-2.3.0/httk/vignettes/Vh_Linakis2020.Rmd |only httk-2.3.0/httk/vignettes/Vi_Kapraun2022.Rmd |only 337 files changed, 28219 insertions(+), 21875 deletions(-)
Title: Bayesian Latent Variable Models
Description: Estimation of latent variable models using Bayesian methods. Currently estimates the loglinear cognitive diagnosis model of Henson, Templin, and Willse (2009) <doi:10.1007/s11336-008-9089-5>.
Author: Jonathan Templin [aut, cre]
Maintainer: Jonathan Templin <jonathan-templin@uiowa.edu>
Diff between blatent versions 0.1.1 dated 2020-12-15 and 0.1.2 dated 2023-12-08
DESCRIPTION | 12 ++-- MD5 | 38 ++++++++------- NAMESPACE | 1 R/QmatrixToBlatentSyntax.R |only R/blatent.R | 1 R/blatentControl.R | 1 R/blatentEstimate.R | 1 R/blatentPPMC.R | 10 ++-- R/chainSummary.R | 2 R/classBlatentModel.R | 103 ++++++++++++++++++++++++++++++++++++++++-- R/convertSyntaxToFormula.R | 4 + R/createModelData.R | 7 ++ R/initializeSpecs.R | 14 +++++ README.md | 12 ++++ man/QmatrixToBlatentSyntax.Rd |only man/blatent.Rd | 1 src/Makevars | 2 src/Makevars.win | 1 src/RcppExports.cpp | 9 ++- src/bin2dec_Rcpp.cpp | 1 src/rks_Rcpp.cpp | 2 21 files changed, 185 insertions(+), 37 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'DDIwR', 'QCA' and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts
information (set names, set values) from those expressions. Other functions
perform various other checks if possibly numeric (even if all numbers reside
in a character vector) and coerce to numeric, or check if the numbers are
whole. It also offers, among many others, a highly versatile recoding
routine and some more flexible alternatives to the base functions 'with()'
and 'within()'.
SOP simplification functions in this package use related minimization from
package 'QCA', which is recommended to be installed despite not being listed
in the Imports field, due to circular dependency issues.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.33 dated 2023-06-30 and 0.34 dated 2023-12-08
admisc-0.33/admisc/R/dashes.R |only admisc-0.33/admisc/R/tildae.R |only admisc-0.33/admisc/man/tildae.Rd |only admisc-0.34/admisc/DESCRIPTION | 6 ++-- admisc-0.34/admisc/MD5 | 44 ++++++++++++++++-------------- admisc-0.34/admisc/NAMESPACE | 9 +++++- admisc-0.34/admisc/R/change.R |only admisc-0.34/admisc/R/expand.R | 1 admisc-0.34/admisc/R/getInfo.R | 13 +++++--- admisc-0.34/admisc/R/getLevels.R | 6 ++-- admisc-0.34/admisc/R/inside.R | 24 ++++++++++++++-- admisc-0.34/admisc/R/overwrite.R |only admisc-0.34/admisc/R/recreate.R | 10 +++++- admisc-0.34/admisc/R/simplify.R | 4 +- admisc-0.34/admisc/R/stopError.R | 3 -- admisc-0.34/admisc/R/tilde.R |only admisc-0.34/admisc/R/translate.R | 13 ++++---- admisc-0.34/admisc/R/unicode.R |only admisc-0.34/admisc/R/verify.R | 5 +-- admisc-0.34/admisc/R/wholeNumeric.R | 2 - admisc-0.34/admisc/build/partial.rdb |binary admisc-0.34/admisc/inst/ChangeLog | 32 ++++++++++++--------- admisc-0.34/admisc/man/admisc_internal.Rd | 3 ++ admisc-0.34/admisc/man/admisc_package.Rd | 6 ++-- admisc-0.34/admisc/man/change.Rd |only admisc-0.34/admisc/man/getName.Rd | 2 - admisc-0.34/admisc/man/overwrite.Rd |only admisc-0.34/admisc/man/tilde.Rd |only 28 files changed, 114 insertions(+), 69 deletions(-)
Title: Interface to the 'C++' Library 'Pf'
Description: Builds and runs 'c++' code for classes that encapsulate state space model, particle filtering algorithm pairs.
Algorithms include the Bootstrap Filter from Gordon et al. (1993) <doi:10.1049/ip-f-2.1993.0015>, the generic SISR filter,
the Auxiliary Particle Filter from Pitt et al (1999) <doi:10.2307/2670179>, and a variety of Rao-Blackwellized
particle filters inspired by Andrieu et al. (2002) <doi:10.1111/1467-9868.00363>. For more details on the 'c++' library
'pf', see Brown (2020) <doi:10.21105/joss.02599>.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>
Diff between pfr versions 1.0.0 dated 2023-08-15 and 1.0.1 dated 2023-12-08
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 build/vignette.rds |binary inst/doc/my-vignette.R | 24 +- inst/doc/my-vignette.Rmd | 2 inst/doc/my-vignette.html | 416 ++++++++++++++++++++++++++++------------------ vignettes/my-vignette.Rmd | 2 8 files changed, 286 insertions(+), 182 deletions(-)
Title: Facilitation of Data Preparation and Plotting Procedures for RDA
and PCA Analyses
Description: Help to the occasional R user for synthesis and enhanced graphical visualization of redundancy analysis (RDA) and principal component analysis (PCA) methods and objects.
Inputs are : data frame, RDA (package 'vegan') and PCA (package 'FactoMineR') objects.
Outputs are : synthesized results of RDA, displayed in console and saved in tables ; displayed and saved objects of PCA graphic visualization of individuals and variables projections with multiple graphic parameters.
Author: Gregoire Bianchetti [aut, cre]
Maintainer: Gregoire Bianchetti <auguste.blam@gmail.com>
Diff between GABB versions 0.3.5 dated 2023-11-27 and 0.3.7 dated 2023-12-08
DESCRIPTION | 9 MD5 | 10 R/PCA_RDA_graphics.R | 4024 +++++++++++++++++++++---------------------- R/RDA_outputs_synthesis.R | 225 +- man/PCA_RDA_graphics.Rd | 3 man/RDA_outputs_synthesis.Rd | 2 6 files changed, 2148 insertions(+), 2125 deletions(-)
Title: Create Common TLGs Used in Clinical Trials
Description: Table, Listings, and Graphs (TLG) library for common outputs
used in clinical trials.
Author: Joe Zhu [aut, cre],
Daniel Sabanes Bove [aut],
Jana Stoilova [aut],
Heng Wang [aut],
Francois Collin [aut],
Adrian Waddell [aut],
Pawel Rucki [aut],
Chendi Liao [aut],
Jennifer Li [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between tern versions 0.9.0 dated 2023-09-01 and 0.9.3 dated 2023-12-08
tern-0.9.0/tern/R/summary_stats.R |only tern-0.9.0/tern/man/a_summary_internal.Rd |only tern-0.9.0/tern/man/figures/tern.png |only tern-0.9.0/tern/man/summary_stats.Rd |only tern-0.9.0/tern/tests/testthat/_snaps/summary_stats.md |only tern-0.9.0/tern/tests/testthat/test-summary_stats.R |only tern-0.9.3/tern/DESCRIPTION | 51 - tern-0.9.3/tern/MD5 | 413 +++++----- tern-0.9.3/tern/NAMESPACE | 24 tern-0.9.3/tern/NEWS.md | 135 ++- tern-0.9.3/tern/R/abnormal.R | 45 - tern-0.9.3/tern/R/abnormal_by_baseline.R | 39 tern-0.9.3/tern/R/abnormal_by_marked.R | 92 +- tern-0.9.3/tern/R/abnormal_by_worst_grade.R | 162 ++- tern-0.9.3/tern/R/abnormal_by_worst_grade_worsen.R | 65 - tern-0.9.3/tern/R/analyze_variables.R | 342 +++----- tern-0.9.3/tern/R/analyze_vars_in_cols.R | 133 ++- tern-0.9.3/tern/R/argument_convention.R | 20 tern-0.9.3/tern/R/compare_variables.R | 20 tern-0.9.3/tern/R/count_cumulative.R | 18 tern-0.9.3/tern/R/count_missed_doses.R | 21 tern-0.9.3/tern/R/count_occurrences.R | 205 +++- tern-0.9.3/tern/R/count_occurrences_by_grade.R | 59 - tern-0.9.3/tern/R/count_patients_events_in_cols.R | 50 - tern-0.9.3/tern/R/count_patients_with_event.R | 28 tern-0.9.3/tern/R/count_patients_with_flags.R | 53 - tern-0.9.3/tern/R/count_values.R | 12 tern-0.9.3/tern/R/decorate_grob.R | 35 tern-0.9.3/tern/R/desctools_binom_diff.R | 158 +-- tern-0.9.3/tern/R/estimate_multinomial_rsp.R | 18 tern-0.9.3/tern/R/estimate_proportion.R | 36 tern-0.9.3/tern/R/formatting_functions.R | 195 ++++ tern-0.9.3/tern/R/g_forest.R | 5 tern-0.9.3/tern/R/g_lineplot.R | 116 +- tern-0.9.3/tern/R/h_biomarkers_subgroups.R | 14 tern-0.9.3/tern/R/h_map_for_count_abnormal.R | 16 tern-0.9.3/tern/R/h_response_biomarkers_subgroups.R | 4 tern-0.9.3/tern/R/h_stack_by_baskets.R | 18 tern-0.9.3/tern/R/h_survival_biomarkers_subgroups.R | 10 tern-0.9.3/tern/R/imputation_rule.R |only tern-0.9.3/tern/R/incidence_rate.R | 37 tern-0.9.3/tern/R/kaplan_meier_plot.R | 116 ++ tern-0.9.3/tern/R/logistic_regression.R | 6 tern-0.9.3/tern/R/odds_ratio.R | 27 tern-0.9.3/tern/R/package.R | 4 tern-0.9.3/tern/R/prop_diff.R | 53 - tern-0.9.3/tern/R/prop_diff_test.R | 25 tern-0.9.3/tern/R/response_biomarkers_subgroups.R | 4 tern-0.9.3/tern/R/response_subgroups.R | 157 +-- tern-0.9.3/tern/R/riskdiff.R | 48 - tern-0.9.3/tern/R/summarize_ancova.R | 39 tern-0.9.3/tern/R/summarize_change.R | 28 tern-0.9.3/tern/R/summarize_colvars.R | 11 tern-0.9.3/tern/R/summarize_coxreg.R | 79 + tern-0.9.3/tern/R/summarize_functions.R | 1 tern-0.9.3/tern/R/summarize_glm_count.R | 29 tern-0.9.3/tern/R/summarize_num_patients.R | 56 - tern-0.9.3/tern/R/summarize_patients_exposure_in_cols.R | 118 +- tern-0.9.3/tern/R/survival_biomarkers_subgroups.R | 111 +- tern-0.9.3/tern/R/survival_coxph_pairwise.R | 31 tern-0.9.3/tern/R/survival_duration_subgroups.R | 142 +-- tern-0.9.3/tern/R/survival_time.R | 146 ++- tern-0.9.3/tern/R/survival_timepoint.R | 78 - tern-0.9.3/tern/R/utils_default_stats_formats_labels.R |only tern-0.9.3/tern/R/utils_factor.R | 4 tern-0.9.3/tern/R/utils_ggplot.R |only tern-0.9.3/tern/R/utils_rtables.R | 143 +++ tern-0.9.3/tern/R/utils_split_funs.R |only tern-0.9.3/tern/README.md | 54 - tern-0.9.3/tern/build/partial.rdb |binary tern-0.9.3/tern/inst/WORDLIST | 4 tern-0.9.3/tern/inst/doc/tables.html | 46 - tern-0.9.3/tern/inst/doc/tern.html | 4 tern-0.9.3/tern/man/abnormal.Rd | 65 - tern-0.9.3/tern/man/abnormal_by_baseline.Rd | 78 + tern-0.9.3/tern/man/abnormal_by_marked.Rd | 69 - tern-0.9.3/tern/man/abnormal_by_worst_grade.Rd | 123 +- tern-0.9.3/tern/man/abnormal_by_worst_grade_worsen.Rd | 64 - tern-0.9.3/tern/man/add_riskdiff.Rd | 12 tern-0.9.3/tern/man/add_rowcounts.Rd | 5 tern-0.9.3/tern/man/afun_riskdiff.Rd | 12 tern-0.9.3/tern/man/analyze_variables.Rd | 301 +++---- tern-0.9.3/tern/man/analyze_vars_in_cols.Rd | 33 tern-0.9.3/tern/man/apply_auto_formatting.Rd |only tern-0.9.3/tern/man/argument_convention.Rd | 31 tern-0.9.3/tern/man/c_label_n.Rd | 10 tern-0.9.3/tern/man/c_label_n_alt.Rd |only tern-0.9.3/tern/man/compare_variables.Rd | 156 +-- tern-0.9.3/tern/man/control_analyze_vars.Rd | 2 tern-0.9.3/tern/man/control_lineplot_vars.Rd | 17 tern-0.9.3/tern/man/count_cumulative.Rd | 77 + tern-0.9.3/tern/man/count_missed_doses.Rd | 55 - tern-0.9.3/tern/man/count_occurrences.Rd | 196 ++-- tern-0.9.3/tern/man/count_occurrences_by_grade.Rd | 156 ++- tern-0.9.3/tern/man/count_patients_events_in_cols.Rd | 65 - tern-0.9.3/tern/man/count_patients_with_event.Rd | 155 +-- tern-0.9.3/tern/man/count_patients_with_flags.Rd | 144 +-- tern-0.9.3/tern/man/count_values_funs.Rd | 105 +- tern-0.9.3/tern/man/cox_regression.Rd | 215 ++--- tern-0.9.3/tern/man/create_afun_compare.Rd | 3 tern-0.9.3/tern/man/create_afun_summary.Rd | 3 tern-0.9.3/tern/man/decorate_grob.Rd | 4 tern-0.9.3/tern/man/default_na_str.Rd |only tern-0.9.3/tern/man/default_stats_formats_labels.Rd |only tern-0.9.3/tern/man/estimate_multinomial_rsp.Rd | 69 - tern-0.9.3/tern/man/estimate_proportions.Rd | 108 +- tern-0.9.3/tern/man/extract_rsp_subgroups.Rd | 47 - tern-0.9.3/tern/man/extract_survival_biomarkers.Rd | 55 - tern-0.9.3/tern/man/extract_survival_subgroups.Rd | 56 - tern-0.9.3/tern/man/extreme_format.Rd | 3 tern-0.9.3/tern/man/figures/logo.png |only tern-0.9.3/tern/man/format_auto.Rd |only tern-0.9.3/tern/man/format_count_fraction.Rd | 3 tern-0.9.3/tern/man/format_count_fraction_fixed_dp.Rd | 3 tern-0.9.3/tern/man/format_count_fraction_lt10.Rd |only tern-0.9.3/tern/man/format_extreme_values.Rd | 3 tern-0.9.3/tern/man/format_extreme_values_ci.Rd | 3 tern-0.9.3/tern/man/format_fraction.Rd | 3 tern-0.9.3/tern/man/format_fraction_fixed_dp.Rd | 3 tern-0.9.3/tern/man/format_fraction_threshold.Rd | 3 tern-0.9.3/tern/man/format_sigfig.Rd |only tern-0.9.3/tern/man/format_xx.Rd | 3 tern-0.9.3/tern/man/formatting_functions.Rd | 3 tern-0.9.3/tern/man/g_forest.Rd | 7 tern-0.9.3/tern/man/g_km.Rd | 15 tern-0.9.3/tern/man/g_lineplot.Rd | 27 tern-0.9.3/tern/man/h_adlb_abnormal_by_worst_grade.Rd |only tern-0.9.3/tern/man/h_count_cumulative.Rd | 4 tern-0.9.3/tern/man/h_grob_tbl_at_risk.Rd | 17 tern-0.9.3/tern/man/h_km_layout.Rd | 12 tern-0.9.3/tern/man/h_map_for_count_abnormal.Rd | 11 tern-0.9.3/tern/man/h_prop_diff.Rd | 4 tern-0.9.3/tern/man/h_response_biomarkers_subgroups.Rd | 4 tern-0.9.3/tern/man/h_stack_by_baskets.Rd | 9 tern-0.9.3/tern/man/h_survival_biomarkers_subgroups.Rd | 13 tern-0.9.3/tern/man/h_tab_one_biomarker.Rd | 13 tern-0.9.3/tern/man/h_tbl_coxph_pairwise.Rd | 14 tern-0.9.3/tern/man/imputation_rule.Rd |only tern-0.9.3/tern/man/incidence_rate.Rd | 73 - tern-0.9.3/tern/man/labels_or_names.Rd | 2 tern-0.9.3/tern/man/labels_use_control.Rd |only tern-0.9.3/tern/man/logistic_summary_by_flag.Rd | 8 tern-0.9.3/tern/man/odds_ratio.Rd | 369 ++++---- tern-0.9.3/tern/man/prop_diff.Rd | 104 +- tern-0.9.3/tern/man/prop_diff_test.Rd | 81 + tern-0.9.3/tern/man/response_biomarkers_subgroups.Rd | 3 tern-0.9.3/tern/man/response_subgroups.Rd | 58 + tern-0.9.3/tern/man/rtable2gg.Rd |only tern-0.9.3/tern/man/strata_normal_quantile.Rd | 1 tern-0.9.3/tern/man/summarize_ancova.Rd | 104 +- tern-0.9.3/tern/man/summarize_change.Rd | 75 - tern-0.9.3/tern/man/summarize_colvars.Rd | 10 tern-0.9.3/tern/man/summarize_functions.Rd | 1 tern-0.9.3/tern/man/summarize_glm_count.Rd | 102 +- tern-0.9.3/tern/man/summarize_num_patients.Rd | 172 ++-- tern-0.9.3/tern/man/summarize_patients_exposure_in_cols.Rd | 204 ++-- tern-0.9.3/tern/man/survival_biomarkers_subgroups.Rd | 40 tern-0.9.3/tern/man/survival_coxph_pairwise.Rd | 110 +- tern-0.9.3/tern/man/survival_duration_subgroups.Rd | 60 + tern-0.9.3/tern/man/survival_time.Rd | 87 +- tern-0.9.3/tern/man/survival_timepoint.Rd | 109 +- tern-0.9.3/tern/man/to_string_matrix.Rd | 43 - tern-0.9.3/tern/man/ungroup_stats.Rd | 5 tern-0.9.3/tern/man/utils_split_funs.Rd |only tern-0.9.3/tern/tests/testthat/_snaps/analyze_variables.md | 162 ++- tern-0.9.3/tern/tests/testthat/_snaps/analyze_vars_in_cols.md | 76 + tern-0.9.3/tern/tests/testthat/_snaps/compare_variables.md | 6 tern-0.9.3/tern/tests/testthat/_snaps/count_occurrences.md | 117 ++ tern-0.9.3/tern/tests/testthat/_snaps/decorate_grob |only tern-0.9.3/tern/tests/testthat/_snaps/formats.md | 35 tern-0.9.3/tern/tests/testthat/_snaps/g_forest |only tern-0.9.3/tern/tests/testthat/_snaps/g_km/g-km-at-risk-title.svg |only tern-0.9.3/tern/tests/testthat/_snaps/g_km/g-km-ref-group-coxph.svg |only tern-0.9.3/tern/tests/testthat/_snaps/g_km/grob-tmp-ci.svg |only tern-0.9.3/tern/tests/testthat/_snaps/g_km/grob-tmp.svg |only tern-0.9.3/tern/tests/testthat/_snaps/g_lineplot |only tern-0.9.3/tern/tests/testthat/_snaps/g_step |only tern-0.9.3/tern/tests/testthat/_snaps/g_waterfall |only tern-0.9.3/tern/tests/testthat/_snaps/imputation_rule.md |only tern-0.9.3/tern/tests/testthat/_snaps/response_biomarkers_subgroups.md | 26 tern-0.9.3/tern/tests/testthat/_snaps/response_subgroups.md | 32 tern-0.9.3/tern/tests/testthat/_snaps/summarize_coxreg.md | 2 tern-0.9.3/tern/tests/testthat/_snaps/summarize_glm_count.md | 78 + tern-0.9.3/tern/tests/testthat/_snaps/summarize_num_patients.md | 34 tern-0.9.3/tern/tests/testthat/_snaps/survival_biomarkers_subgroups.md | 26 tern-0.9.3/tern/tests/testthat/_snaps/survival_duration_subgroups.md | 41 tern-0.9.3/tern/tests/testthat/_snaps/survival_time.md | 51 + tern-0.9.3/tern/tests/testthat/_snaps/utils_default_stats_formats_labels.md |only tern-0.9.3/tern/tests/testthat/_snaps/utils_ggplot |only tern-0.9.3/tern/tests/testthat/_snaps/utils_rtables.md | 107 +- tern-0.9.3/tern/tests/testthat/_snaps/utils_split_fun.md |only tern-0.9.3/tern/tests/testthat/test-abnormal_by_marked.R | 17 tern-0.9.3/tern/tests/testthat/test-abnormal_by_worst_grade.R | 27 tern-0.9.3/tern/tests/testthat/test-analyze_variables.R | 77 + tern-0.9.3/tern/tests/testthat/test-analyze_vars_in_cols.R | 183 ++++ tern-0.9.3/tern/tests/testthat/test-compare_variables.R | 14 tern-0.9.3/tern/tests/testthat/test-count_occurrences.R | 135 +++ tern-0.9.3/tern/tests/testthat/test-count_occurrences_by_grade.R | 7 tern-0.9.3/tern/tests/testthat/test-decorate_grob.R | 20 tern-0.9.3/tern/tests/testthat/test-formats.R | 76 + tern-0.9.3/tern/tests/testthat/test-g_forest.R | 16 tern-0.9.3/tern/tests/testthat/test-g_km.R | 58 + tern-0.9.3/tern/tests/testthat/test-g_lineplot.R | 29 tern-0.9.3/tern/tests/testthat/test-g_step.R | 8 tern-0.9.3/tern/tests/testthat/test-g_waterfall.R | 18 tern-0.9.3/tern/tests/testthat/test-imputation_rule.R |only tern-0.9.3/tern/tests/testthat/test-odds_ratio.R | 2 tern-0.9.3/tern/tests/testthat/test-prop_diff.R | 6 tern-0.9.3/tern/tests/testthat/test-response_biomarkers_subgroups.R | 19 tern-0.9.3/tern/tests/testthat/test-response_subgroups.R | 22 tern-0.9.3/tern/tests/testthat/test-split_cols_by_groups.R | 2 tern-0.9.3/tern/tests/testthat/test-summarize_ancova.R | 2 tern-0.9.3/tern/tests/testthat/test-summarize_coxreg.R | 15 tern-0.9.3/tern/tests/testthat/test-summarize_glm_count.R | 43 - tern-0.9.3/tern/tests/testthat/test-summarize_num_patients.R | 21 tern-0.9.3/tern/tests/testthat/test-survival_biomarkers_subgroups.R | 24 tern-0.9.3/tern/tests/testthat/test-survival_duration_subgroups.R | 24 tern-0.9.3/tern/tests/testthat/test-survival_time.R | 72 + tern-0.9.3/tern/tests/testthat/test-test_proportion_diff.R | 10 tern-0.9.3/tern/tests/testthat/test-utils_default_stats_formats_labels.R |only tern-0.9.3/tern/tests/testthat/test-utils_ggplot.R |only tern-0.9.3/tern/tests/testthat/test-utils_rtables.R | 54 + tern-0.9.3/tern/tests/testthat/test-utils_split_fun.R |only 223 files changed, 6591 insertions(+), 3908 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector
Graphics'. 'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Thomas Lin Pedersen [cre, aut]
,
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] ,
David Gohel [ctb] ,
Yixuan Qiu [ctb] ,
Hakon Malmedal [ctb] ,
Posit, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between svglite versions 2.1.2 dated 2023-10-11 and 2.1.3 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/fonts.html | 4 ++-- inst/doc/scaling.html | 4 ++-- src/devSVG.cpp | 1 - 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library,
from <https://spacy.io>.
Author: Kenneth Benoit [cre, aut, cph]
,
Akitaka Matsuo [aut] ,
Johannes Gruber [ctb] ,
European Research Council [fnd]
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>
Diff between spacyr versions 1.2.1 dated 2020-03-04 and 1.3.0 dated 2023-12-08
spacyr-1.2.1/spacyr/man/find_spacy_env.Rd |only spacyr-1.3.0/spacyr/DESCRIPTION | 13 spacyr-1.3.0/spacyr/MD5 | 93 spacyr-1.3.0/spacyr/NAMESPACE | 1 spacyr-1.3.0/spacyr/NEWS.md | 4 spacyr-1.3.0/spacyr/R/data.R | 4 spacyr-1.3.0/spacyr/R/entity-functions.R | 29 spacyr-1.3.0/spacyr/R/nounphrase-functions.R | 23 spacyr-1.3.0/spacyr/R/parse-extractor-functions.R | 26 spacyr-1.3.0/spacyr/R/spacy_extract_entity.R | 36 spacyr-1.3.0/spacyr/R/spacy_extract_nounphrases.R | 34 spacyr-1.3.0/spacyr/R/spacy_initialize.R | 361 --- spacyr-1.3.0/spacyr/R/spacy_install.R | 813 +------- spacyr-1.3.0/spacyr/R/spacy_langmodel_functions.R | 114 - spacyr-1.3.0/spacyr/R/spacy_parse.R | 46 spacyr-1.3.0/spacyr/R/spacy_tokenize.R | 20 spacyr-1.3.0/spacyr/R/utils.R | 17 spacyr-1.3.0/spacyr/README.md | 263 +- spacyr-1.3.0/spacyr/build/vignette.rds |binary spacyr-1.3.0/spacyr/inst/WORDLIST | 5 spacyr-1.3.0/spacyr/inst/doc/using_spacyr.html | 1006 +++++----- spacyr-1.3.0/spacyr/man/data_char_paragraph.Rd | 4 spacyr-1.3.0/spacyr/man/data_char_sentences.Rd | 4 spacyr-1.3.0/spacyr/man/entity_extract.Rd | 37 spacyr-1.3.0/spacyr/man/find_spacy.Rd | 6 spacyr-1.3.0/spacyr/man/get-functions.Rd | 12 spacyr-1.3.0/spacyr/man/nounphrase_extract.Rd | 29 spacyr-1.3.0/spacyr/man/process_document.Rd | 12 spacyr-1.3.0/spacyr/man/spacy_download_langmodel.Rd | 49 spacyr-1.3.0/spacyr/man/spacy_download_langmodel_virtualenv.Rd |only spacyr-1.3.0/spacyr/man/spacy_extract_entity.Rd | 26 spacyr-1.3.0/spacyr/man/spacy_extract_nounphrases.Rd | 6 spacyr-1.3.0/spacyr/man/spacy_initialize.Rd | 39 spacyr-1.3.0/spacyr/man/spacy_install.Rd | 124 - spacyr-1.3.0/spacyr/man/spacy_install_virtualenv.Rd |only spacyr-1.3.0/spacyr/man/spacy_parse.Rd | 6 spacyr-1.3.0/spacyr/man/spacy_tokenize.Rd | 16 spacyr-1.3.0/spacyr/man/spacy_uninstall.Rd | 13 spacyr-1.3.0/spacyr/man/spacy_upgrade.Rd | 82 spacyr-1.3.0/spacyr/man/spacyr-package.Rd | 2 spacyr-1.3.0/spacyr/tests/testthat/test-1-spacy_initialize.R | 39 spacyr-1.3.0/spacyr/tests/testthat/test-2-spacy_parse.R | 26 spacyr-1.3.0/spacyr/tests/testthat/test-3-spacy_tokenize.R | 423 ++-- spacyr-1.3.0/spacyr/tests/testthat/test-4-entity-functions.R | 487 ++-- spacyr-1.3.0/spacyr/tests/testthat/test-5-nounphrase-functions.R | 567 ++--- spacyr-1.3.0/spacyr/tests/testthat/test-6-quanteda-methods.R | 3 spacyr-1.3.0/spacyr/tests/testthat/test-7-spacy-install.R | 143 - spacyr-1.3.0/spacyr/tests/testthat/utils.R | 11 spacyr-1.3.0/spacyr/vignettes/using_spacyr.Rmd | 40 49 files changed, 2234 insertions(+), 2880 deletions(-)
Title: Create Data Frames that are Easier to Exchange and Reuse
Description: The aim of the 'dataset' package is to make tidy datasets easier to release,
exchange and reuse. It organizes and formats data frame 'R' objects into well-referenced,
well-described, interoperable datasets into release and reuse ready form. A subjective
interpretation of the W3C DataSet recommendation and the datacube model <https://www.w3.org/TR/vocab-data-cube/>,
which is also used in the global Statistical Data and Metadata eXchange standards,
the application of the connected Dublin Core <https://www.dublincore.org/specifications/dublin-core/dcmi-terms/>
and DataCite <https://support.datacite.org/docs/datacite-metadata-schema-44/> standards
preferred by European open science repositories to improve the findability, accessibility,
interoperability and reusability of the datasets.
Author: Daniel Antal [aut, cre] ,
Marcelo Perlin [rev]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Diff between dataset versions 0.2.1 dated 2023-03-18 and 0.2.7 dated 2023-12-08
dataset-0.2.1/dataset/R/bibentry.R |only dataset-0.2.1/dataset/R/dataset_export.R |only dataset-0.2.1/dataset/R/dataset_local_id.R |only dataset-0.2.1/dataset/R/dataset_uri.R |only dataset-0.2.1/dataset/R/resource_type.R |only dataset-0.2.1/dataset/R/resource_type_general.R |only dataset-0.2.1/dataset/R/source.R |only dataset-0.2.1/dataset/inst/doc/dataspice.R |only dataset-0.2.1/dataset/inst/doc/dataspice.Rmd |only dataset-0.2.1/dataset/inst/doc/dataspice.html |only dataset-0.2.1/dataset/inst/doc/metadata.R |only dataset-0.2.1/dataset/inst/doc/metadata.Rmd |only dataset-0.2.1/dataset/inst/doc/metadata.html |only dataset-0.2.1/dataset/inst/doc/publish.R |only dataset-0.2.1/dataset/inst/doc/publish.Rmd |only dataset-0.2.1/dataset/inst/doc/publish.html |only dataset-0.2.1/dataset/inst/doc/reproducible.R |only dataset-0.2.1/dataset/inst/doc/reproducible.Rmd |only dataset-0.2.1/dataset/inst/doc/reproducible.html |only dataset-0.2.1/dataset/man/attributes_measures.Rd |only dataset-0.2.1/dataset/man/bibentry_dataset.Rd |only dataset-0.2.1/dataset/man/dataset_export.Rd |only dataset-0.2.1/dataset/man/dataset_local_id.Rd |only dataset-0.2.1/dataset/man/dataset_source.Rd |only dataset-0.2.1/dataset/man/dataset_uri.Rd |only dataset-0.2.1/dataset/man/dimensions.Rd |only dataset-0.2.1/dataset/man/measures.Rd |only dataset-0.2.1/dataset/man/resource_type.Rd |only dataset-0.2.1/dataset/man/resource_type_general.Rd |only dataset-0.2.1/dataset/tests/testthat/test-bibentry.R |only dataset-0.2.1/dataset/tests/testthat/test-dataset_export.R |only dataset-0.2.1/dataset/tests/testthat/test-dataset_local_id.R |only dataset-0.2.1/dataset/tests/testthat/test-dataset_uri.R |only dataset-0.2.1/dataset/tests/testthat/test-resource_type.R |only dataset-0.2.1/dataset/tests/testthat/test-resource_type_general.R |only dataset-0.2.1/dataset/vignettes/dataspice.Rmd |only dataset-0.2.1/dataset/vignettes/metadata.Rmd |only dataset-0.2.1/dataset/vignettes/publish.Rmd |only dataset-0.2.1/dataset/vignettes/reproducible.Rmd |only dataset-0.2.7/dataset/DESCRIPTION | 8 dataset-0.2.7/dataset/MD5 | 235 - dataset-0.2.7/dataset/NAMESPACE | 130 dataset-0.2.7/dataset/NEWS.md | 122 dataset-0.2.7/dataset/R/DataStructure.R |only dataset-0.2.7/dataset/R/as_bibentry.R |only dataset-0.2.7/dataset/R/as_dataset.R |only dataset-0.2.7/dataset/R/creator.R | 114 dataset-0.2.7/dataset/R/datacite.R | 531 +-- dataset-0.2.7/dataset/R/dataset.R | 605 --- dataset-0.2.7/dataset/R/dataset_bibentry.R |only dataset-0.2.7/dataset/R/dataset_download.R | 156 dataset-0.2.7/dataset/R/dataset_title.R | 179 - dataset-0.2.7/dataset/R/datasource.R |only dataset-0.2.7/dataset/R/describe.R |only dataset-0.2.7/dataset/R/description.R | 93 dataset-0.2.7/dataset/R/dublincore.R | 640 +-- dataset-0.2.7/dataset/R/geolocation.R | 87 dataset-0.2.7/dataset/R/identifier.R | 111 dataset-0.2.7/dataset/R/iris_dataset.R | 52 dataset-0.2.7/dataset/R/language.R | 137 dataset-0.2.7/dataset/R/publication_year.R | 92 dataset-0.2.7/dataset/R/publisher.R | 115 dataset-0.2.7/dataset/R/related_item.R | 181 - dataset-0.2.7/dataset/R/rights.R | 104 dataset-0.2.7/dataset/R/size.R | 80 dataset-0.2.7/dataset/R/subject.R | 247 - dataset-0.2.7/dataset/R/var_labels.R |only dataset-0.2.7/dataset/R/version.R | 92 dataset-0.2.7/dataset/README.md | 470 -- dataset-0.2.7/dataset/build/vignette.rds |binary dataset-0.2.7/dataset/data/iris_dataset.rda |binary dataset-0.2.7/dataset/inst/CITATION | 20 dataset-0.2.7/dataset/inst/WORDLIST | 281 - dataset-0.2.7/dataset/inst/doc/RDF.R | 147 dataset-0.2.7/dataset/inst/doc/RDF.Rmd | 239 - dataset-0.2.7/dataset/inst/doc/RDF.html | 1021 ++--- dataset-0.2.7/dataset/inst/doc/datacite.R |only dataset-0.2.7/dataset/inst/doc/datacite.Rmd |only dataset-0.2.7/dataset/inst/doc/datacite.html |only dataset-0.2.7/dataset/inst/doc/dataset.R | 122 dataset-0.2.7/dataset/inst/doc/dataset.Rmd | 302 - dataset-0.2.7/dataset/inst/doc/dataset.html | 1225 +++---- dataset-0.2.7/dataset/inst/doc/dublincore.R |only dataset-0.2.7/dataset/inst/doc/dublincore.Rmd |only dataset-0.2.7/dataset/inst/doc/dublincore.html |only dataset-0.2.7/dataset/inst/doc/motivation.R | 128 dataset-0.2.7/dataset/inst/doc/motivation.Rmd | 460 +- dataset-0.2.7/dataset/inst/doc/motivation.html | 1721 ++++------ dataset-0.2.7/dataset/inst/doc/survey.R | 185 - dataset-0.2.7/dataset/inst/doc/survey.Rmd | 272 - dataset-0.2.7/dataset/inst/doc/survey.html | 996 ++--- dataset-0.2.7/dataset/man/DataStructure.Rd |only dataset-0.2.7/dataset/man/creator.Rd | 26 dataset-0.2.7/dataset/man/datacite.Rd | 85 dataset-0.2.7/dataset/man/dataset.Rd | 203 - dataset-0.2.7/dataset/man/dataset_bibentry.Rd |only dataset-0.2.7/dataset/man/dataset_download.Rd | 90 dataset-0.2.7/dataset/man/dataset_title.Rd | 49 dataset-0.2.7/dataset/man/datasource.Rd |only dataset-0.2.7/dataset/man/describe.Rd |only dataset-0.2.7/dataset/man/description.Rd | 13 dataset-0.2.7/dataset/man/dublincore.Rd | 169 dataset-0.2.7/dataset/man/geolocation.Rd | 9 dataset-0.2.7/dataset/man/identifier.Rd | 5 dataset-0.2.7/dataset/man/initialise_dsd.Rd |only dataset-0.2.7/dataset/man/language.Rd | 16 dataset-0.2.7/dataset/man/publication_year.Rd | 12 dataset-0.2.7/dataset/man/publisher.Rd | 12 dataset-0.2.7/dataset/man/related_item.Rd | 8 dataset-0.2.7/dataset/man/related_item_identifier.Rd | 3 dataset-0.2.7/dataset/man/rights.Rd | 10 dataset-0.2.7/dataset/man/size.Rd | 34 dataset-0.2.7/dataset/man/subject.Rd | 86 dataset-0.2.7/dataset/man/var_labels.Rd |only dataset-0.2.7/dataset/man/version.Rd | 6 dataset-0.2.7/dataset/tests/spelling.R | 6 dataset-0.2.7/dataset/tests/testthat.R | 24 dataset-0.2.7/dataset/tests/testthat/test-DataStructure.R |only dataset-0.2.7/dataset/tests/testthat/test-as_bibentry.R |only dataset-0.2.7/dataset/tests/testthat/test-as_dataset.R |only dataset-0.2.7/dataset/tests/testthat/test-creator.R | 37 dataset-0.2.7/dataset/tests/testthat/test-datacite.R | 49 dataset-0.2.7/dataset/tests/testthat/test-datacube.R | 32 dataset-0.2.7/dataset/tests/testthat/test-dataset.R | 123 dataset-0.2.7/dataset/tests/testthat/test-dataset_bibentry.R |only dataset-0.2.7/dataset/tests/testthat/test-dataset_download.R | 44 dataset-0.2.7/dataset/tests/testthat/test-dataset_title.R | 49 dataset-0.2.7/dataset/tests/testthat/test-datasource.R |only dataset-0.2.7/dataset/tests/testthat/test-describe.R |only dataset-0.2.7/dataset/tests/testthat/test-description.R | 30 dataset-0.2.7/dataset/tests/testthat/test-dublincore.R | 82 dataset-0.2.7/dataset/tests/testthat/test-geolocation.R | 32 dataset-0.2.7/dataset/tests/testthat/test-identifier.R | 21 dataset-0.2.7/dataset/tests/testthat/test-language.R | 48 dataset-0.2.7/dataset/tests/testthat/test-publication_year.R | 28 dataset-0.2.7/dataset/tests/testthat/test-publisher.R | 46 dataset-0.2.7/dataset/tests/testthat/test-related_item.R | 36 dataset-0.2.7/dataset/tests/testthat/test-rights.R | 38 dataset-0.2.7/dataset/tests/testthat/test-size.R | 18 dataset-0.2.7/dataset/tests/testthat/test-source.R | 17 dataset-0.2.7/dataset/tests/testthat/test-subject.R | 87 dataset-0.2.7/dataset/tests/testthat/test-use_function.R | 48 dataset-0.2.7/dataset/tests/testthat/test-var_labels.R |only dataset-0.2.7/dataset/tests/testthat/test-version.R | 14 dataset-0.2.7/dataset/vignettes/RDF.Rmd | 239 - dataset-0.2.7/dataset/vignettes/datacite.Rmd |only dataset-0.2.7/dataset/vignettes/dataset.Rmd | 302 - dataset-0.2.7/dataset/vignettes/dublincore.Rmd |only dataset-0.2.7/dataset/vignettes/motivation.Rmd | 460 +- dataset-0.2.7/dataset/vignettes/survey.Rmd | 272 - dataset-0.2.7/dataset/vignettes/triple_file.csv | 34 dataset-0.2.7/dataset/vignettes/triple_file.nq | 32 152 files changed, 6874 insertions(+), 7910 deletions(-)
Title: Bayesian Additive Regression Trees with Stan-Sampled Parametric
Extensions
Description: Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) components and Stan (Stan Development Team (2021) <https://mc-stan.org/>) sampled parametric ones. Multilevel models can be expressed using 'lme4' syntax (Bates, Maechler, Bolker, and Walker (2015) <doi:10.18637/jss.v067.i01>).
Author: Vincent Dorie [aut, cre] ,
Ben Goodrich [ctb] ,
Jonah Gabry [ctb] ,
Imad Ali [ctb] ,
Sam Brilleman [ctb] ,
Paul-Christian Burkner [ctb] ,
Joshua Pritikin [ctb] ,
Andrew Gelman [ctb] ,
Bob Carpenter [ctb] ,
Matt Hoffman [ctb] ,
Daniel Lee [ctb] ,
Mich [...truncated...]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between stan4bart versions 0.0-6 dated 2023-02-03 and 0.0-7 dated 2023-12-08
DESCRIPTION | 8 +++--- MD5 | 22 +++++++++--------- R/generics.R | 12 +++++++-- R/lme4_functions.R | 18 +++++++++----- R/misc.R | 25 ++++++++++++++++++++ R/stan4bart.R | 8 ++++-- R/test_data.R | 26 +++++++++++++++++++-- inst/NEWS.Rd | 10 ++++++++ src/include/rstan/io/r_ostream.hpp | 4 +-- src/init.cpp | 36 +++++++++++++++-------------- src/stan_sampler.cpp | 44 ++++++++++++++++++++++-------------- tests/testthat/test-01-continuous.R | 24 +++++++++++++++++++ 12 files changed, 172 insertions(+), 65 deletions(-)
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization
for biological sequence (DNA and protein) data. Seqinr includes
utilities for sequence data management under the ACNUC system
described in Gouy, M. et al. (1984) Nucleic Acids Res.
12:121-127 <doi:10.1093/nar/12.1Part1.121>.
Author: Delphine Charif [aut],
Olivier Clerc [ctb],
Carolin Frank [ctb],
Jean R. Lobry [aut, cph],
Anamaria Necsulea [ctb],
Leonor Palmeira [ctb],
Simon Penel [cre],
Guy Perriere [ctb]
Maintainer: Simon Penel <simon.penel@univ-lyon1.fr>
Diff between seqinr versions 4.2-30 dated 2023-04-05 and 4.2-36 dated 2023-12-08
DESCRIPTION | 41 +--- MD5 | 236 ++++++++++++------------ NEWS | 3 R/AAstat.R | 58 ++--- R/ClassSeq.R | 76 +++---- R/GC.R | 308 +++++++++++++++---------------- R/PI.R | 72 +++---- R/R_socket.R | 30 +-- R/acnucclose.R | 40 ++-- R/acnucopen.R | 98 +++++----- R/al2bp.R | 14 - R/allistranks.R | 92 ++++----- R/amb.R | 56 ++--- R/as.alignment.R | 6 R/as.matrix.alignment.R | 12 - R/autosocket.R | 70 +++---- R/baselineabif.R | 34 +-- R/bma.R | 34 +-- R/cai.R | 18 - R/choosebank.R | 244 ++++++++++++------------- R/circle.R | 16 - R/clfcd.R | 168 ++++++++--------- R/clientid.R | 28 +- R/closebank.R | 44 ++-- R/col2alpha.R | 4 R/comp.R | 74 +++---- R/consensus.R | 76 +++---- R/count.R | 70 +++---- R/countfreelists.R | 40 ++-- R/countsubseqs.R | 54 ++--- R/db.growth.R | 164 ++++++++-------- R/dia.bactgensize.R | 372 +++++++++++++++++++------------------- R/dist.alignment.R | 60 +++--- R/dotPlot.R | 64 +++--- R/dotchart.uco.R | 156 ++++++++-------- R/draw.oriloc.R | 140 +++++++------- R/draw.rearranged.oriloc.R | 110 +++++------ R/draw.recstat.R | 72 +++---- R/extract.breakpoints.R | 180 +++++++++--------- R/extractseqs.R | 178 +++++++++--------- R/fastacc.R | 44 ++-- R/gb2fasta.R | 52 ++--- R/gbk2g2.R | 138 +++++++------- R/gbk2g2.euk.R | 284 ++++++++++++++--------------- R/getAnnot.R | 50 ++--- R/getFrag.R | 42 ++-- R/getKeyword.R | 70 +++---- R/getLength.R | 22 +- R/getLocation.R | 78 ++++---- R/getName.R | 4 R/getSequence.R | 92 ++++----- R/getTrans.R | 22 +- R/getType.R | 40 ++-- R/getlistrank.R | 64 +++--- R/getliststate.R | 50 ++--- R/gfrag.R | 66 +++--- R/ghelp.R | 50 ++--- R/isenum.R | 106 +++++----- R/kaks.R | 64 +++--- R/knowndbs.R | 68 +++---- R/lseqinr.R | 2 R/modifylist.R | 126 ++++++------- R/move.R | 10 - R/oriloc.R | 436 ++++++++++++++++++++++----------------------- R/parser.socket.R | 30 +-- R/peakabif.R | 132 ++++++------- R/permutation.R | 76 +++---- R/plot.SeqAcnucWeb.R | 200 ++++++++++---------- R/plotPanels.R | 40 ++-- R/plotabif.R | 102 +++++----- R/plotladder.R | 66 +++--- R/pmw.R | 61 ++++++ R/prepgetannots.R | 106 +++++----- R/prettyseq.R | 70 +++---- R/query.r | 226 +++++++++++------------ R/quitacnuc.R | 10 - R/read.abif.R | 302 +++++++++++++++---------------- R/read.alignment.R | 172 +++++++++++++---- R/read.fasta.R | 298 +++++++++++++++--------------- R/readBins.R | 68 +++---- R/readPanels.R | 76 +++---- R/readfirstrec.R | 58 ++--- R/readsmj.R | 142 +++++++------- R/rearranged.oriloc.R | 60 +++--- R/recstat.R | 130 ++++++------- R/residuecount.R | 46 ++-- R/reverse.align.R | 146 +++++++-------- R/rho.R | 26 +- R/rot13.R | 8 R/s2n.R | 30 +-- R/savelist.R | 110 +++++------ R/setlistname.R | 42 ++-- R/splitseq.R | 26 +- R/stresc.R | 36 +-- R/stutterabif.R | 212 ++++++++++----------- R/swap.R | 12 - R/synonymous.R | 44 ++-- R/tablecode.R | 248 ++++++++++++------------- R/test.co.recstat.R | 194 ++++++++++---------- R/test.li.recstat.R | 18 - R/translate.R | 138 +++++++------- R/trimSpace.R | 18 - R/uco.R | 62 +++--- R/util.R | 86 ++++---- R/where.is.this.acc.R | 100 +++++----- R/words.R | 8 R/words.pos.R | 16 - R/write.fasta.R | 70 +++---- R/zscore.R | 112 +++++------ man/choosebank.Rd | 5 man/dotPlot.Rd | 6 man/get.db.growth.Rd | 2 man/kaks.Rd | 4 man/query.Rd | 2 man/read.alignment.Rd | 5 man/rot13.Rd | 3 man/uco.Rd | 2 man/zscore.Rd | 2 src/getzlibsock.c | 2 119 files changed, 5007 insertions(+), 4851 deletions(-)
Title: Wrapper for 'SUNDIALS' Solving ODE and Sensitivity Problem
Description: Wrapper for widely used 'SUNDIALS' software (SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers) and more precisely to its 'CVODES' solver. It is aiming to solve ordinary differential equations (ODE) and optionally pending forward sensitivity problem. The wrapper is made 'R' friendly by allowing to pass custom parameters to user's callback functions. Such functions can be both written in 'R' and in 'C++' ('RcppArmadillo' flavor). In case of 'C++', performance is greatly improved so this option is highly advisable when performance matters. If provided, Jacobian matrix can be calculated either in dense or sparse format. In the latter case 'rmumps' package is used to solve corresponding linear systems. Root finding and pending event management are optional and can be specified as 'R' or 'C++' functions too. This makes them a very flexible tool for controlling the ODE system during the time course simulation. 'SUNDIALS' library was published in Hindmarsh et al. (2005) <doi:1 [...truncated...]
Author: Serguei Sokol [cre, aut],
Carol S. Woodward [ctb],
Daniel R. Reynolds [ctb],
Alan C. Hindmarsh [ctb],
David J. Gardner [ctb],
Cody J. Balos [ctb],
Radu Serban [ctb],
Scott D. Cohen [ctb],
Peter N. Brown [ctb],
George Byrne [ctb],
Allan G. Taylor [ctb [...truncated...]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between r2sundials versions 6.5.0-3 dated 2023-03-24 and 6.5.0-4 dated 2023-12-08
DESCRIPTION | 10 ++-- MD5 | 97 +++++++++++++++++++++++++++++++++++++++++++---- NEWS | 8 +++ R/RcppExports.R | 14 +++--- build/partial.rdb |binary cleanup | 2 man/r2cvodes.Rd | 14 +++--- src/Makevars | 2 src/lib-5.0.0 |only src/lib/cvodes/README.md |only src/r2sundials.cpp | 14 +++--- 11 files changed, 125 insertions(+), 36 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models
Description: Algorithms to speed up the Bayesian Lasso Cox model (Lee et al., Int J Biostat, 2011 <doi:10.2202/1557-4679.1301>) and the Bayesian Lasso Cox with mandatory variables (Zucknick et al. Biometrical J, 2015 <doi:10.1002/bimj.201400160>).
Author: Zhi Zhao [aut, cre],
Manuela Zucknick [aut],
Maral Saadati [aut],
Axel Benner [aut]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Diff between psbcSpeedUp versions 2.0.4 dated 2023-10-12 and 2.0.5 dated 2023-12-08
psbcSpeedUp-2.0.4/psbcSpeedUp/src/drive-e758d6e6.o.tmp |only psbcSpeedUp-2.0.5/psbcSpeedUp/DESCRIPTION | 13 psbcSpeedUp-2.0.5/psbcSpeedUp/MD5 | 51 - psbcSpeedUp-2.0.5/psbcSpeedUp/NAMESPACE | 12 psbcSpeedUp-2.0.5/psbcSpeedUp/NEWS.md | 6 psbcSpeedUp-2.0.5/psbcSpeedUp/R/coef.psbcSpeedUp.R | 9 psbcSpeedUp-2.0.5/psbcSpeedUp/R/plot.psbcSpeedUp.R | 15 psbcSpeedUp-2.0.5/psbcSpeedUp/R/plotBrier.R |only psbcSpeedUp-2.0.5/psbcSpeedUp/R/predict.psbcSpeedUp.R |only psbcSpeedUp-2.0.5/psbcSpeedUp/R/psbcSpeedUp.R | 51 - psbcSpeedUp-2.0.5/psbcSpeedUp/README.md | 38 psbcSpeedUp-2.0.5/psbcSpeedUp/build |only psbcSpeedUp-2.0.5/psbcSpeedUp/cleanup | 4 psbcSpeedUp-2.0.5/psbcSpeedUp/inst |only psbcSpeedUp-2.0.5/psbcSpeedUp/man/coef.psbcSpeedUp.Rd | 7 psbcSpeedUp-2.0.5/psbcSpeedUp/man/figures/README_plot_brier.png |only psbcSpeedUp-2.0.5/psbcSpeedUp/man/plot.psbcSpeedUp.Rd | 7 psbcSpeedUp-2.0.5/psbcSpeedUp/man/plotBrier.Rd |only psbcSpeedUp-2.0.5/psbcSpeedUp/man/predict.psbcSpeedUp.Rd |only psbcSpeedUp-2.0.5/psbcSpeedUp/man/psbcSpeedUp.Rd | 13 psbcSpeedUp-2.0.5/psbcSpeedUp/src/drive.cpp | 297 +++--- psbcSpeedUp-2.0.5/psbcSpeedUp/src/drive.h | 16 psbcSpeedUp-2.0.5/psbcSpeedUp/src/global.cpp | 2 psbcSpeedUp-2.0.5/psbcSpeedUp/src/global.h | 25 psbcSpeedUp-2.0.5/psbcSpeedUp/src/init.c | 5 psbcSpeedUp-2.0.5/psbcSpeedUp/src/psbc.cpp | 449 ++++------ psbcSpeedUp-2.0.5/psbcSpeedUp/src/psbc.h | 42 psbcSpeedUp-2.0.5/psbcSpeedUp/src/utils.cpp | 130 +- psbcSpeedUp-2.0.5/psbcSpeedUp/src/utils.h | 141 +-- psbcSpeedUp-2.0.5/psbcSpeedUp/vignettes |only 30 files changed, 683 insertions(+), 650 deletions(-)
Title: My Utilities for Developing Data Science Software
Description: Some general utilities (helper functions) that I and maybe others
find useful when developing data science software. Functionality includes
argument validation, density calculation, sampling, matrix printing,
user interaction, storage helpers and more. The vignettes illustrate use
cases.
Author: Lennart Oelschlaeger [aut, cre]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Diff between oeli versions 0.3.0 dated 2023-12-02 and 0.3.1 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/storage_helpers.html | 8 ++++---- src/RcppExports.cpp | 2 +- 5 files changed, 16 insertions(+), 12 deletions(-)
Title: Sensitivity Analysis with 'mrgsolve'
Description: Perform sensitivity analysis on ordinary differential equation
based models, including ad-hoc graphical analyses based on structured
sequences of parameters as well as local sensitivity analysis. Functions
are provided for creating inputs, simulating scenarios and plotting outputs.
Author: Kyle Baron [aut, cre]
Maintainer: Kyle Baron <kylebtwin@imap.cc>
Diff between mrgsim.sa versions 0.1.0 dated 2020-11-30 and 0.2.0 dated 2023-12-08
DESCRIPTION | 11 - MD5 | 89 ++++++----- NAMESPACE | 8 - NEWS.md |only R/AAA.R | 10 + R/lsa.R | 92 ++++++----- R/parseq.R | 137 ++++++++++++----- R/sens.R | 18 +- R/sens_each.R | 145 ++++++++++++------ R/sens_grid.R | 18 +- R/sens_plot.R | 232 ++++++++++++++++++++++++------ R/sens_run.R | 18 +- R/seq.R | 62 +++++--- R/utils.R | 25 +-- build |only inst/WORDLIST | 1 inst/doc |only man/as.data.frame.sens_each.Rd | 8 - man/denest.Rd | 6 man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/lsa.Rd | 16 +- man/mrgsim.sa.Rd | 8 + man/parseq_cv.Rd | 12 - man/parseq_fct.Rd | 12 - man/parseq_manual.Rd | 7 man/parseq_range.Rd | 17 +- man/parseq_reference.Rd | 4 man/plot.lsa.Rd | 11 - man/select_par.Rd | 4 man/select_sens.Rd | 14 + man/sens_fun.Rd | 18 +- man/sens_plot.Rd | 58 +++++-- man/sens_run.Rd | 17 +- man/seq_cv.Rd | 14 + man/seq_even.Rd | 8 - man/seq_fct.Rd | 14 + man/seq_geo.Rd | 10 - tests/testthat/test-lsa.R | 6 tests/testthat/test-parseq.R |only tests/testthat/test-select-sens.R |only tests/testthat/test-sens-plot.R |only tests/testthat/test-sens_grid.R | 9 - vignettes |only 48 files changed, 756 insertions(+), 383 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting, originating from Japan and now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.4.10 dated 2023-10-28 and 1.4.11 dated 2023-12-08
DESCRIPTION | 8 ++--- MD5 | 58 +++++++++++++++++++++--------------------- NEWS.md | 7 +++++ R/ichimoku.R | 28 ++++++++++---------- R/iplot.R | 6 ++-- R/methods.R | 6 ++-- R/mltools.R | 8 ++--- R/oanda.R | 47 +++++++++++++++++++--------------- R/plot.R | 4 +- R/strat.R | 20 +++++++++----- R/switch.R | 13 ++++----- R/utils.R | 30 +++++++-------------- build/vignette.rds |binary inst/doc/xoanda.Rmd | 6 ++-- inst/doc/xoanda.html | 16 +++++++---- man/as.data.frame.ichimoku.Rd | 4 +- man/ichimoku.Rd | 16 +++++------ man/look.Rd | 2 - man/matrix_df.Rd | 4 +- man/oanda.Rd | 5 ++- man/oanda_chart.Rd | 5 ++- man/oanda_instruments.Rd | 5 ++- man/oanda_orders.Rd | 5 ++- man/oanda_positions.Rd | 5 ++- man/oanda_quote.Rd | 5 ++- man/oanda_stream.Rd | 10 ++++--- man/oanda_studio.Rd | 5 ++- man/oanda_view.Rd | 5 ++- man/xts_df.Rd | 4 +- vignettes/xoanda.Rmd | 6 ++-- 30 files changed, 186 insertions(+), 157 deletions(-)
Title: Homomorphic Encryption Polynomials
Description: Homomorphic encryption (Brakerski and Vaikuntanathan (2014) <doi:10.1137/120868669>) using Ring Learning with Errors (Lyubashevsky et al. (2012) <https://eprint.iacr.org/2012/230>) is a form of Learning with Errors (Regev (2005) <doi:10.1145/1060590.1060603>) using polynomial rings over finite fields. Functions to generate the required polynomials (using 'polynom'), with various distributions of coefficients are provided. Additionally, functions to generate and take coefficient modulo are provided.
Author: Bastiaan Quast [aut, cre]
Maintainer: Bastiaan Quast <bquast@gmail.com>
Diff between HEtools versions 0.2.0 dated 2023-11-11 and 1.0.0 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/GenDiscrGauss.R | 2 +- README.md | 4 ++-- man/GenDiscrGauss.Rd | 2 +- tests/testthat/tests.R | 17 ++++++++++++++--- 7 files changed, 32 insertions(+), 16 deletions(-)
Title: Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC
Description: A set of functions to allow analysis of count data (such
as faecal egg count data) using Bayesian MCMC methods. Returns
information on the possible values for mean count, coefficient
of variation and zero inflation (true prevalence) present in
the data. A complete faecal egg count reduction test (FECRT)
model is implemented, which returns inference on the true
efficacy of the drug from the pre- and post-treatment data
provided, using non-parametric bootstrapping as well as using
Bayesian MCMC. Functions to perform power analyses for faecal
egg counts (including FECRT) are also provided.
Author: Matthew Denwood [aut, cre]
Maintainer: Matthew Denwood <md@sund.ku.dk>
Diff between bayescount versions 0.9.99-8 dated 2022-05-07 and 0.9.99-9 dated 2023-12-08
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- src/power.c | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-)
Title: Dynamic Multi-Species Size Spectrum Modelling
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Gustav Delius [cre, aut, cph] ,
Finlay Scott [aut, cph],
Julia Blanchard [aut, cph] ,
Ken Andersen [aut, cph] ,
Richard Southwell [ctb, cph]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 2.4.1 dated 2023-04-26 and 2.5.0 dated 2023-12-08
mizer-2.4.1/mizer/tests/testthat/Rplots.pdf |only mizer-2.5.0/mizer/DESCRIPTION | 14 mizer-2.5.0/mizer/MD5 | 90 +-- mizer-2.5.0/mizer/NAMESPACE | 8 mizer-2.5.0/mizer/NEWS.md | 59 ++ mizer-2.5.0/mizer/R/MizerParams-class.R | 29 - mizer-2.5.0/mizer/R/age_mat.R | 2 mizer-2.5.0/mizer/R/manipulate_species.R | 26 - mizer-2.5.0/mizer/R/newMultispeciesParams.R | 22 mizer-2.5.0/mizer/R/project.R | 15 mizer-2.5.0/mizer/R/project_methods.R | 4 mizer-2.5.0/mizer/R/setBevertonHolt.R | 8 mizer-2.5.0/mizer/R/setExtEncounter.R |only mizer-2.5.0/mizer/R/setFishing.R | 6 mizer-2.5.0/mizer/R/setMetabolicRate.R | 2 mizer-2.5.0/mizer/R/setPredKernel.R | 14 mizer-2.5.0/mizer/R/setReproduction.R | 1 mizer-2.5.0/mizer/R/setSearchVolume.R | 3 mizer-2.5.0/mizer/R/species_params.R | 311 +++++++++---- mizer-2.5.0/mizer/R/upgrade.R | 20 mizer-2.5.0/mizer/README.md | 2 mizer-2.5.0/mizer/data/NS_params.rda |binary mizer-2.5.0/mizer/data/NS_sim.rda |binary mizer-2.5.0/mizer/inst/shiny/selectivity_effects/rsconnect |only mizer-2.5.0/mizer/man/MizerParams-class.Rd | 8 mizer-2.5.0/mizer/man/completeSpeciesParams.Rd |only mizer-2.5.0/mizer/man/gear_params.Rd | 5 mizer-2.5.0/mizer/man/get_h_default.Rd | 3 mizer-2.5.0/mizer/man/newMultispeciesParams.Rd | 14 mizer-2.5.0/mizer/man/project.Rd | 15 mizer-2.5.0/mizer/man/setExtEncounter.Rd |only mizer-2.5.0/mizer/man/setExtMort.Rd | 1 mizer-2.5.0/mizer/man/setFishing.Rd | 1 mizer-2.5.0/mizer/man/setInitialValues.Rd | 1 mizer-2.5.0/mizer/man/setInteraction.Rd | 1 mizer-2.5.0/mizer/man/setMaxIntakeRate.Rd | 1 mizer-2.5.0/mizer/man/setMetabolicRate.Rd | 1 mizer-2.5.0/mizer/man/setParams.Rd | 11 mizer-2.5.0/mizer/man/setPredKernel.Rd | 1 mizer-2.5.0/mizer/man/setReproduction.Rd | 1 mizer-2.5.0/mizer/man/setSearchVolume.Rd | 1 mizer-2.5.0/mizer/man/species_params.Rd | 73 +-- mizer-2.5.0/mizer/man/validSpeciesParams.Rd | 13 mizer-2.5.0/mizer/tests/testthat/test-manipulate_species.R | 2 mizer-2.5.0/mizer/tests/testthat/test-project_methods.R | 8 mizer-2.5.0/mizer/tests/testthat/test-setExtEncounter.R |only mizer-2.5.0/mizer/tests/testthat/test-setFishing.R | 2 mizer-2.5.0/mizer/tests/testthat/test-setPredKernel.R | 9 mizer-2.5.0/mizer/tests/testthat/test-species_params.R | 70 ++ 49 files changed, 633 insertions(+), 245 deletions(-)
Title: Local Polynomial (Ridge) Regression
Description: Local Polynomial Regression with Ridging.
Author: Burkhardt Seifert <seifert@ifspm.unizh.ch> ;
Packaged for R by Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between lpridge versions 1.0-8 dated 2018-06-12 and 1.1-0 dated 2023-12-08
ChangeLog | 25 +++++++++++++++++++++++++ DESCRIPTION | 13 +++++++++---- MD5 | 8 ++++---- man/lpepa.Rd | 16 +++++++++------- man/lpridge.Rd | 6 +++--- 5 files changed, 50 insertions(+), 18 deletions(-)
More information about rgeoboundaries at CRAN
Permanent link
More information about MadanTextNetwork at CRAN
Permanent link
Title: Light Gradient Boosting Machine
Description: Tree based algorithms can be improved by introducing boosting frameworks.
'LightGBM' is one such framework, based on Ke, Guolin et al. (2017) <https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision>.
This package offers an R interface to work with it.
It is designed to be distributed and efficient with the following advantages:
1. Faster training speed and higher efficiency.
2. Lower memory usage.
3. Better accuracy.
4. Parallel learning supported.
5. Capable of handling large-scale data.
In recognition of these advantages, 'LightGBM' has been widely-used in many winning solutions of machine learning competitions.
Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple m [...truncated...]
Author: Yu Shi [aut],
Guolin Ke [aut],
Damien Soukhavong [aut],
James Lamb [aut, cre],
Qi Meng [aut],
Thomas Finley [aut],
Taifeng Wang [aut],
Wei Chen [aut],
Weidong Ma [aut],
Qiwei Ye [aut],
Tie-Yan Liu [aut],
Nikita Titov [aut],
Yachen Yan [ctb],
Microsof [...truncated...]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between lightgbm versions 3.3.5 dated 2023-01-16 and 4.2.0 dated 2023-12-08
lightgbm-3.3.5/lightgbm/R/lgb.unloader.R |only lightgbm-3.3.5/lightgbm/man/getinfo.Rd |only lightgbm-3.3.5/lightgbm/man/lgb.unloader.Rd |only lightgbm-3.3.5/lightgbm/man/setinfo.Rd |only lightgbm-3.3.5/lightgbm/src/include/Eigen/src/Geometry/arch/Geometry_SSE.h |only lightgbm-3.3.5/lightgbm/src/include/Eigen/src/LU/arch/Inverse_SSE.h |only lightgbm-3.3.5/lightgbm/src/include/LightGBM/cuda/cuda_utils.h |only lightgbm-3.3.5/lightgbm/src/include/LightGBM/fmt/locale.h |only lightgbm-3.3.5/lightgbm/src/include/LightGBM/fmt/posix.h |only lightgbm-3.3.5/lightgbm/src/include/LightGBM/utils/common_legacy_solaris.h |only lightgbm-3.3.5/lightgbm/src/network/ifaddrs_patch.cpp |only lightgbm-3.3.5/lightgbm/src/network/ifaddrs_patch.h |only lightgbm-3.3.5/lightgbm/src/treelearner/cuda_kernel_launcher.cu |only lightgbm-3.3.5/lightgbm/src/treelearner/cuda_kernel_launcher.h |only lightgbm-3.3.5/lightgbm/src/treelearner/cuda_tree_learner.cpp |only lightgbm-3.3.5/lightgbm/src/treelearner/cuda_tree_learner.h |only lightgbm-3.3.5/lightgbm/tests/testthat/test_lgb.unloader.R |only lightgbm-4.2.0/lightgbm/DESCRIPTION | 45 lightgbm-4.2.0/lightgbm/MD5 | 736 - lightgbm-4.2.0/lightgbm/NAMESPACE | 21 lightgbm-4.2.0/lightgbm/R/aliases.R | 172 lightgbm-4.2.0/lightgbm/R/callback.R | 133 lightgbm-4.2.0/lightgbm/R/lgb.Booster.R | 760 - lightgbm-4.2.0/lightgbm/R/lgb.DataProcessor.R |only lightgbm-4.2.0/lightgbm/R/lgb.Dataset.R | 432 lightgbm-4.2.0/lightgbm/R/lgb.Predictor.R | 363 lightgbm-4.2.0/lightgbm/R/lgb.convert_with_rules.R | 19 lightgbm-4.2.0/lightgbm/R/lgb.cv.R | 155 lightgbm-4.2.0/lightgbm/R/lgb.drop_serialized.R |only lightgbm-4.2.0/lightgbm/R/lgb.importance.R | 5 lightgbm-4.2.0/lightgbm/R/lgb.interprete.R | 15 lightgbm-4.2.0/lightgbm/R/lgb.make_serializable.R |only lightgbm-4.2.0/lightgbm/R/lgb.model.dt.tree.R | 10 lightgbm-4.2.0/lightgbm/R/lgb.plot.importance.R | 5 lightgbm-4.2.0/lightgbm/R/lgb.plot.interpretation.R | 11 lightgbm-4.2.0/lightgbm/R/lgb.restore_handle.R |only lightgbm-4.2.0/lightgbm/R/lgb.train.R | 110 lightgbm-4.2.0/lightgbm/R/lightgbm.R | 145 lightgbm-4.2.0/lightgbm/R/multithreading.R |only lightgbm-4.2.0/lightgbm/R/readRDS.lgb.Booster.R | 36 lightgbm-4.2.0/lightgbm/R/saveRDS.lgb.Booster.R | 57 lightgbm-4.2.0/lightgbm/R/utils.R | 151 lightgbm-4.2.0/lightgbm/README.md | 102 lightgbm-4.2.0/lightgbm/build |only lightgbm-4.2.0/lightgbm/configure | 738 - lightgbm-4.2.0/lightgbm/configure.ac | 12 lightgbm-4.2.0/lightgbm/configure.win | 38 lightgbm-4.2.0/lightgbm/demo/basic_walkthrough.R | 1 lightgbm-4.2.0/lightgbm/demo/boost_from_prediction.R | 5 lightgbm-4.2.0/lightgbm/demo/early_stopping.R | 1 lightgbm-4.2.0/lightgbm/demo/leaf_stability.R | 6 lightgbm-4.2.0/lightgbm/demo/multiclass.R | 14 lightgbm-4.2.0/lightgbm/demo/multiclass_custom_objective.R | 4 lightgbm-4.2.0/lightgbm/demo/weight_param.R | 25 lightgbm-4.2.0/lightgbm/inst |only lightgbm-4.2.0/lightgbm/man/dim.Rd | 6 lightgbm-4.2.0/lightgbm/man/dimnames.lgb.Dataset.Rd | 2 lightgbm-4.2.0/lightgbm/man/getLGBMThreads.Rd |only lightgbm-4.2.0/lightgbm/man/get_field.Rd | 2 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.Rd | 12 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.construct.Rd | 2 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.create.valid.Rd | 13 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.save.Rd | 2 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.set.categorical.Rd | 2 lightgbm-4.2.0/lightgbm/man/lgb.Dataset.set.reference.Rd | 2 lightgbm-4.2.0/lightgbm/man/lgb.configure_fast_predict.Rd |only lightgbm-4.2.0/lightgbm/man/lgb.cv.Rd | 31 lightgbm-4.2.0/lightgbm/man/lgb.drop_serialized.Rd |only lightgbm-4.2.0/lightgbm/man/lgb.dump.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.get.eval.result.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.importance.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.interprete.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.load.Rd | 5 lightgbm-4.2.0/lightgbm/man/lgb.make_serializable.Rd |only lightgbm-4.2.0/lightgbm/man/lgb.model.dt.tree.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.plot.importance.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.plot.interpretation.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.restore_handle.Rd |only lightgbm-4.2.0/lightgbm/man/lgb.save.Rd | 3 lightgbm-4.2.0/lightgbm/man/lgb.train.Rd | 31 lightgbm-4.2.0/lightgbm/man/lgb_shared_dataset_params.Rd | 4 lightgbm-4.2.0/lightgbm/man/lgb_shared_params.Rd | 30 lightgbm-4.2.0/lightgbm/man/lightgbm.Rd | 78 lightgbm-4.2.0/lightgbm/man/predict.lgb.Booster.Rd | 110 lightgbm-4.2.0/lightgbm/man/print.lgb.Booster.Rd |only lightgbm-4.2.0/lightgbm/man/readRDS.lgb.Booster.Rd | 10 lightgbm-4.2.0/lightgbm/man/saveRDS.lgb.Booster.Rd | 11 lightgbm-4.2.0/lightgbm/man/setLGBMThreads.Rd |only lightgbm-4.2.0/lightgbm/man/set_field.Rd | 2 lightgbm-4.2.0/lightgbm/man/slice.Rd | 8 lightgbm-4.2.0/lightgbm/man/summary.lgb.Booster.Rd |only lightgbm-4.2.0/lightgbm/src/Makevars.in | 6 lightgbm-4.2.0/lightgbm/src/Makevars.win.in | 8 lightgbm-4.2.0/lightgbm/src/application/predictor.hpp | 8 lightgbm-4.2.0/lightgbm/src/boosting/bagging.hpp |only lightgbm-4.2.0/lightgbm/src/boosting/boosting.cpp | 5 lightgbm-4.2.0/lightgbm/src/boosting/cuda |only lightgbm-4.2.0/lightgbm/src/boosting/gbdt.cpp | 413 lightgbm-4.2.0/lightgbm/src/boosting/gbdt.h | 125 lightgbm-4.2.0/lightgbm/src/boosting/gbdt_model_text.cpp | 35 lightgbm-4.2.0/lightgbm/src/boosting/goss.hpp | 168 lightgbm-4.2.0/lightgbm/src/boosting/rf.hpp | 45 lightgbm-4.2.0/lightgbm/src/boosting/sample_strategy.cpp |only lightgbm-4.2.0/lightgbm/src/boosting/score_updater.hpp | 22 lightgbm-4.2.0/lightgbm/src/c_api.cpp | 525 lightgbm-4.2.0/lightgbm/src/cuda |only lightgbm-4.2.0/lightgbm/src/include/Eigen/Cholesky | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/Core | 19 lightgbm-4.2.0/lightgbm/src/include/Eigen/Eigenvalues | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/Geometry | 5 lightgbm-4.2.0/lightgbm/src/include/Eigen/Householder | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/Jacobi | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/LU | 7 lightgbm-4.2.0/lightgbm/src/include/Eigen/QR | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/SVD | 1 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Cholesky/LDLT.h | 10 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Cholesky/LLT.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Array.h | 32 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/ArrayWrapper.h | 42 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/AssignEvaluator.h | 120 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/BandMatrix.h | 32 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Block.h | 72 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/BooleanRedux.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/CoreEvaluators.h | 253 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/CwiseBinaryOp.h | 24 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/CwiseNullaryOp.h | 89 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/CwiseUnaryOp.h | 12 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/CwiseUnaryView.h | 20 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/DenseBase.h | 82 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/DenseCoeffsBase.h | 34 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/DenseStorage.h | 158 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Diagonal.h | 34 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Dot.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/EigenBase.h | 16 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/ForceAlignedAccess.h | 12 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/GeneralProduct.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/GenericPacketMath.h | 629 - lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/GlobalFunctions.h | 5 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Inverse.h | 16 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Map.h | 8 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/MapBase.h | 8 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/MathFunctions.h | 477 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/MathFunctionsImpl.h | 98 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Matrix.h | 36 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/NestByValue.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/NumTraits.h | 94 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/PartialReduxEvaluator.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/PlainObjectBase.h | 61 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Product.h | 44 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/ProductEvaluators.h | 167 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Random.h | 36 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Redux.h | 22 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Ref.h | 137 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Replicate.h | 12 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Reshaped.h | 7 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/ReturnByValue.h | 10 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Reverse.h | 14 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Select.h | 14 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/SelfAdjointView.h | 36 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Solve.h | 24 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/SolveTriangular.h | 24 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/StableNorm.h | 57 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/StlIterators.h | 19 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Stride.h | 13 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Transpose.h | 12 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Transpositions.h | 32 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/TriangularMatrix.h | 112 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/VectorwiseOp.h | 26 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/Visitor.h | 150 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX/Complex.h | 102 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX/MathFunctions.h | 79 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX/PacketMath.h | 390 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX/TypeCasting.h | 48 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX512/Complex.h | 70 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 237 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 401 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AVX512/TypeCasting.h | 16 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AltiVec/Complex.h | 235 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AltiVec/MatrixProduct.h | 3080 ++++- lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 484 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/CUDA/Complex.h | 315 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/Default/BFloat16.h | 150 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/Default/ConjHelper.h | 116 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h | 1140 + lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h | 51 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/Default/Half.h | 510 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/GPU/PacketMath.h | 459 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/MSA/Complex.h | 72 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/MSA/PacketMath.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/NEON/Complex.h | 109 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/NEON/GeneralBlockPanelKernel.h |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/NEON/MathFunctions.h | 24 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/NEON/PacketMath.h | 1758 ++ lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/NEON/TypeCasting.h | 8 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SSE/Complex.h | 178 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SSE/MathFunctions.h | 33 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SSE/PacketMath.h | 389 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SSE/TypeCasting.h | 7 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SVE |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SYCL/InteropHeaders.h | 3 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/SYCL/MathFunctions.h | 18 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/ZVector/Complex.h | 124 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/ZVector/MathFunctions.h | 10 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/arch/ZVector/PacketMath.h | 56 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/functors/BinaryFunctors.h | 173 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/functors/NullaryFunctors.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/functors/StlFunctors.h | 34 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/functors/UnaryFunctors.h | 62 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 201 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/products/Parallelizer.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/products/SelfadjointRank2Update.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/BlasUtil.h | 201 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/ConfigureVectorization.h | 62 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/Constants.h | 21 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/DisableStupidWarnings.h | 3 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/ForwardDeclarations.h | 4 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/IndexedViewHelper.h | 12 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/IntegralConstant.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/Macros.h | 287 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/Memory.h | 59 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/Meta.h | 255 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/StaticAssert.h | 5 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/SymbolicIndex.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Core/util/XprHelper.h | 50 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 97 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Eigenvalues/Tridiagonalization.h | 30 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/AlignedBox.h | 102 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/AngleAxis.h | 8 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/EulerAngles.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/Homogeneous.h | 26 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/ParametrizedLine.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/Quaternion.h | 22 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/Rotation2D.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/Scaling.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/Transform.h | 82 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Geometry/arch/Geometry_SIMD.h |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Householder/HouseholderSequence.h | 28 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/Jacobi/Jacobi.h | 2 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/LU/FullPivLU.h | 6 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/LU/InverseImpl.h | 31 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/LU/PartialPivLU.h | 13 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/LU/arch/InverseSize4.h |only lightgbm-4.2.0/lightgbm/src/include/Eigen/src/SVD/BDCSVD.h | 34 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/SVD/JacobiSVD.h | 33 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/SVD/SVDBase.h | 42 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 52 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/plugins/BlockMethods.h | 3 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/plugins/CommonCwiseUnaryOps.h | 43 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h | 8 lightgbm-4.2.0/lightgbm/src/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h | 10 lightgbm-4.2.0/lightgbm/src/include/LightGBM/arrow.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/arrow.tpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/bin.h | 160 lightgbm-4.2.0/lightgbm/src/include/LightGBM/boosting.h | 4 lightgbm-4.2.0/lightgbm/src/include/LightGBM/c_api.h | 267 lightgbm-4.2.0/lightgbm/src/include/LightGBM/config.h | 156 lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_algorithms.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_column_data.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_metadata.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_metric.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_objective_function.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_random.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_row_data.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_split_info.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_tree.hpp |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/cuda_utils.hu |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/cuda/vector_cudahost.h | 4 lightgbm-4.2.0/lightgbm/src/include/LightGBM/dataset.h | 390 lightgbm-4.2.0/lightgbm/src/include/LightGBM/dataset_loader.h | 23 lightgbm-4.2.0/lightgbm/src/include/LightGBM/fast_double_parser.h | 74 lightgbm-4.2.0/lightgbm/src/include/LightGBM/feature_group.h | 175 lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/args.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/chrono.h | 1682 ++ lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/color.h | 273 lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/compile.h | 731 - lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/core.h | 2958 +++- lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/format-inl.h | 3675 ++---- lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/format.h | 6100 +++++----- lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/os.h | 355 lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/ostream.h | 240 lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/printf.h | 642 - lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/ranges.h | 738 - lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/std.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/fmt/xchar.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/meta.h | 2 lightgbm-4.2.0/lightgbm/src/include/LightGBM/metric.h | 5 lightgbm-4.2.0/lightgbm/src/include/LightGBM/objective_function.h | 20 lightgbm-4.2.0/lightgbm/src/include/LightGBM/sample_strategy.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/train_share_states.h | 198 lightgbm-4.2.0/lightgbm/src/include/LightGBM/tree.h | 28 lightgbm-4.2.0/lightgbm/src/include/LightGBM/tree_learner.h | 13 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/binary_writer.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/byte_buffer.h |only lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/common.h | 38 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/file_io.h | 30 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/json11.h | 4 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/openmp_wrapper.h | 39 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/text_reader.h | 11 lightgbm-4.2.0/lightgbm/src/include/LightGBM/utils/threading.h | 2 lightgbm-4.2.0/lightgbm/src/io/bin.cpp | 418 lightgbm-4.2.0/lightgbm/src/io/config.cpp | 137 lightgbm-4.2.0/lightgbm/src/io/config_auto.cpp | 316 lightgbm-4.2.0/lightgbm/src/io/cuda |only lightgbm-4.2.0/lightgbm/src/io/dataset.cpp | 751 - lightgbm-4.2.0/lightgbm/src/io/dataset_loader.cpp | 501 lightgbm-4.2.0/lightgbm/src/io/dense_bin.hpp | 146 lightgbm-4.2.0/lightgbm/src/io/file_io.cpp | 2 lightgbm-4.2.0/lightgbm/src/io/json11.cpp | 6 lightgbm-4.2.0/lightgbm/src/io/metadata.cpp | 473 lightgbm-4.2.0/lightgbm/src/io/multi_val_dense_bin.hpp | 129 lightgbm-4.2.0/lightgbm/src/io/multi_val_sparse_bin.hpp | 133 lightgbm-4.2.0/lightgbm/src/io/parser.cpp | 56 lightgbm-4.2.0/lightgbm/src/io/sparse_bin.hpp | 191 lightgbm-4.2.0/lightgbm/src/io/train_share_states.cpp | 166 lightgbm-4.2.0/lightgbm/src/io/tree.cpp | 43 lightgbm-4.2.0/lightgbm/src/lightgbm_R.cpp | 519 lightgbm-4.2.0/lightgbm/src/lightgbm_R.h | 286 lightgbm-4.2.0/lightgbm/src/metric/binary_metric.hpp | 10 lightgbm-4.2.0/lightgbm/src/metric/cuda |only lightgbm-4.2.0/lightgbm/src/metric/map_metric.hpp | 4 lightgbm-4.2.0/lightgbm/src/metric/metric.cpp | 160 lightgbm-4.2.0/lightgbm/src/metric/multiclass_metric.hpp | 8 lightgbm-4.2.0/lightgbm/src/metric/rank_metric.hpp | 6 lightgbm-4.2.0/lightgbm/src/metric/regression_metric.hpp | 10 lightgbm-4.2.0/lightgbm/src/metric/xentropy_metric.hpp | 24 lightgbm-4.2.0/lightgbm/src/network/linker_topo.cpp | 4 lightgbm-4.2.0/lightgbm/src/network/linkers_socket.cpp | 2 lightgbm-4.2.0/lightgbm/src/network/socket_wrapper.hpp | 9 lightgbm-4.2.0/lightgbm/src/objective/binary_objective.hpp | 18 lightgbm-4.2.0/lightgbm/src/objective/cuda |only lightgbm-4.2.0/lightgbm/src/objective/multiclass_objective.hpp | 10 lightgbm-4.2.0/lightgbm/src/objective/objective_function.cpp | 123 lightgbm-4.2.0/lightgbm/src/objective/rank_objective.hpp | 99 lightgbm-4.2.0/lightgbm/src/objective/regression_objective.hpp | 109 lightgbm-4.2.0/lightgbm/src/objective/xentropy_objective.hpp | 20 lightgbm-4.2.0/lightgbm/src/treelearner/col_sampler.hpp | 6 lightgbm-4.2.0/lightgbm/src/treelearner/cost_effective_gradient_boosting.hpp | 16 lightgbm-4.2.0/lightgbm/src/treelearner/cuda |only lightgbm-4.2.0/lightgbm/src/treelearner/data_parallel_tree_learner.cpp | 344 lightgbm-4.2.0/lightgbm/src/treelearner/data_partition.hpp | 2 lightgbm-4.2.0/lightgbm/src/treelearner/feature_histogram.hpp | 683 + lightgbm-4.2.0/lightgbm/src/treelearner/feature_parallel_tree_learner.cpp | 1 lightgbm-4.2.0/lightgbm/src/treelearner/gpu_tree_learner.cpp | 74 lightgbm-4.2.0/lightgbm/src/treelearner/gpu_tree_learner.h | 2 lightgbm-4.2.0/lightgbm/src/treelearner/gradient_discretizer.cpp |only lightgbm-4.2.0/lightgbm/src/treelearner/gradient_discretizer.hpp |only lightgbm-4.2.0/lightgbm/src/treelearner/leaf_splits.hpp | 107 lightgbm-4.2.0/lightgbm/src/treelearner/linear_tree_learner.cpp | 22 lightgbm-4.2.0/lightgbm/src/treelearner/linear_tree_learner.h | 10 lightgbm-4.2.0/lightgbm/src/treelearner/monotone_constraints.hpp | 2 lightgbm-4.2.0/lightgbm/src/treelearner/parallel_tree_learner.h | 24 lightgbm-4.2.0/lightgbm/src/treelearner/serial_tree_learner.cpp | 436 lightgbm-4.2.0/lightgbm/src/treelearner/serial_tree_learner.h | 21 lightgbm-4.2.0/lightgbm/src/treelearner/split_info.hpp | 12 lightgbm-4.2.0/lightgbm/src/treelearner/tree_learner.cpp | 18 lightgbm-4.2.0/lightgbm/src/treelearner/voting_parallel_tree_learner.cpp | 9 lightgbm-4.2.0/lightgbm/src/utils |only lightgbm-4.2.0/lightgbm/tests/testthat.R | 2 lightgbm-4.2.0/lightgbm/tests/testthat/helper.R |only lightgbm-4.2.0/lightgbm/tests/testthat/test_Predictor.R | 632 + lightgbm-4.2.0/lightgbm/tests/testthat/test_basic.R | 1894 ++- lightgbm-4.2.0/lightgbm/tests/testthat/test_custom_objective.R | 28 lightgbm-4.2.0/lightgbm/tests/testthat/test_dataset.R | 201 lightgbm-4.2.0/lightgbm/tests/testthat/test_learning_to_rank.R | 63 lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.Booster.R | 842 + lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.convert_with_rules.R | 10 lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.importance.R | 2 lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.interprete.R | 8 lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.plot.importance.R | 4 lightgbm-4.2.0/lightgbm/tests/testthat/test_lgb.plot.interpretation.R | 8 lightgbm-4.2.0/lightgbm/tests/testthat/test_metrics.R | 4 lightgbm-4.2.0/lightgbm/tests/testthat/test_multithreading.R |only lightgbm-4.2.0/lightgbm/tests/testthat/test_parameters.R | 71 lightgbm-4.2.0/lightgbm/tests/testthat/test_utils.R | 75 lightgbm-4.2.0/lightgbm/tests/testthat/test_weighted_loss.R | 12 lightgbm-4.2.0/lightgbm/vignettes |only 381 files changed, 35011 insertions(+), 16964 deletions(-)
Title: Australian Tax Policy Analysis
Description: Utilities to cost and evaluate Australian tax policy, including fast
projections of personal income tax collections, high-performance tax and
transfer calculators, and an interface to common indices from the Australian
Bureau of Statistics. Written to support Grattan Institute's Australian
Perspectives program, and related projects. Access to the Australian Taxation
Office's sample files of personal income tax returns is assumed.
Author: Hugh Parsonage [aut, cre],
Tim Cameron [aut],
Brendan Coates [aut],
Matthew Katzen [aut],
William Young [aut],
Ittima Cherastidtham [dtc],
W. Karsten [ctb],
M. Enrique Garcia [ctb],
Matt Cowgill [aut]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattan versions 2023.1.1 dated 2023-09-04 and 2023.1.2 dated 2023-12-08
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/income_tax.R | 14 ++++++++++++-- R/small_business_tax_offset.R | 2 +- man/income_tax.Rd | 5 ++++- man/small_business_tax_offset.Rd | 2 +- src/Cincome_tax.c | 20 +++++++++++++++++++- src/Crebate_income.c | 2 +- src/Offset.c | 4 +++- src/grattan.h | 10 +++++----- src/init.c | 4 ++-- src/isEquiInt.c | 2 +- src/sapto.c | 9 ++++----- 14 files changed, 74 insertions(+), 38 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre],
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchi [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.14.8 dated 2023-02-17 and 1.14.10 dated 2023-12-08
data.table-1.14.10/data.table/DESCRIPTION | 16 data.table-1.14.10/data.table/MD5 | 154 data.table-1.14.10/data.table/NAMESPACE | 2 data.table-1.14.10/data.table/NEWS.md | 24 data.table-1.14.10/data.table/R/data.table.R | 2 data.table-1.14.10/data.table/R/frank.R | 2 data.table-1.14.10/data.table/R/fread.R | 2 data.table-1.14.10/data.table/R/print.data.table.R | 3 data.table-1.14.10/data.table/R/setkey.R | 2 data.table-1.14.10/data.table/README.md | 4 data.table-1.14.10/data.table/build/vignette.rds |binary data.table-1.14.10/data.table/inst/cc | 4 data.table-1.14.10/data.table/inst/doc/datatable-benchmarking.html | 370 + data.table-1.14.10/data.table/inst/doc/datatable-faq.R | 8 data.table-1.14.10/data.table/inst/doc/datatable-faq.Rmd | 4 data.table-1.14.10/data.table/inst/doc/datatable-faq.html | 1961 +++++++--- data.table-1.14.10/data.table/inst/doc/datatable-importing.html | 516 +- data.table-1.14.10/data.table/inst/doc/datatable-intro.R | 6 data.table-1.14.10/data.table/inst/doc/datatable-intro.Rmd | 4 data.table-1.14.10/data.table/inst/doc/datatable-intro.html | 1571 ++++---- data.table-1.14.10/data.table/inst/doc/datatable-keys-fast-subset.R | 6 data.table-1.14.10/data.table/inst/doc/datatable-keys-fast-subset.Rmd | 6 data.table-1.14.10/data.table/inst/doc/datatable-keys-fast-subset.html | 1107 +++-- data.table-1.14.10/data.table/inst/doc/datatable-reference-semantics.R | 6 data.table-1.14.10/data.table/inst/doc/datatable-reference-semantics.Rmd | 6 data.table-1.14.10/data.table/inst/doc/datatable-reference-semantics.html | 805 ++-- data.table-1.14.10/data.table/inst/doc/datatable-reshape.R | 6 data.table-1.14.10/data.table/inst/doc/datatable-reshape.Rmd | 4 data.table-1.14.10/data.table/inst/doc/datatable-reshape.html | 695 +-- data.table-1.14.10/data.table/inst/doc/datatable-sd-usage.R | 6 data.table-1.14.10/data.table/inst/doc/datatable-sd-usage.Rmd | 9 data.table-1.14.10/data.table/inst/doc/datatable-sd-usage.html | 1029 ++--- data.table-1.14.10/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.R | 10 data.table-1.14.10/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.Rmd | 6 data.table-1.14.10/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.html | 746 ++- data.table-1.14.10/data.table/inst/po/en@quot/LC_MESSAGES/R-data.table.mo |binary data.table-1.14.10/data.table/inst/po/en@quot/LC_MESSAGES/data.table.mo |binary data.table-1.14.10/data.table/inst/po/zh_CN/LC_MESSAGES/R-data.table.mo |binary data.table-1.14.10/data.table/inst/po/zh_CN/LC_MESSAGES/data.table.mo |binary data.table-1.14.10/data.table/inst/tests/benchmark.Rraw.bz2 |only data.table-1.14.10/data.table/inst/tests/froll.Rraw.bz2 |only data.table-1.14.10/data.table/inst/tests/nafill.Rraw.bz2 |only data.table-1.14.10/data.table/inst/tests/other.Rraw.bz2 |only data.table-1.14.10/data.table/inst/tests/tests.Rraw.bz2 |only data.table-1.14.10/data.table/inst/tests/types.Rraw.bz2 |only data.table-1.14.10/data.table/man/assign.Rd | 2 data.table-1.14.10/data.table/man/data.table.Rd | 43 data.table-1.14.10/data.table/man/fread.Rd | 16 data.table-1.14.10/data.table/man/froll.Rd | 36 data.table-1.14.10/data.table/man/fsort.Rd | 6 data.table-1.14.10/data.table/man/fwrite.Rd | 36 data.table-1.14.10/data.table/man/openmp-utils.Rd | 24 data.table-1.14.10/data.table/man/setops.Rd | 16 data.table-1.14.10/data.table/man/special-symbols.Rd | 12 data.table-1.14.10/data.table/po/R-data.table.pot | 19 data.table-1.14.10/data.table/po/R-zh_CN.po | 68 data.table-1.14.10/data.table/po/data.table.pot | 685 +-- data.table-1.14.10/data.table/po/zh_CN.po | 753 +-- data.table-1.14.10/data.table/src/assign.c | 11 data.table-1.14.10/data.table/src/chmatch.c | 3 data.table-1.14.10/data.table/src/forder.c | 2 data.table-1.14.10/data.table/src/fread.c | 12 data.table-1.14.10/data.table/src/fsort.c | 6 data.table-1.14.10/data.table/src/fwrite.c | 14 data.table-1.14.10/data.table/src/gsumm.c | 12 data.table-1.14.10/data.table/src/ijoin.c | 2 data.table-1.14.10/data.table/src/init.c | 31 data.table-1.14.10/data.table/src/rbindlist.c | 8 data.table-1.14.10/data.table/src/reorder.c | 4 data.table-1.14.10/data.table/src/snprintf.c | 2 data.table-1.14.10/data.table/src/subset.c | 2 data.table-1.14.10/data.table/vignettes/datatable-faq.Rmd | 4 data.table-1.14.10/data.table/vignettes/datatable-intro.Rmd | 4 data.table-1.14.10/data.table/vignettes/datatable-keys-fast-subset.Rmd | 6 data.table-1.14.10/data.table/vignettes/datatable-reference-semantics.Rmd | 6 data.table-1.14.10/data.table/vignettes/datatable-reshape.Rmd | 4 data.table-1.14.10/data.table/vignettes/datatable-sd-usage.Rmd | 9 data.table-1.14.10/data.table/vignettes/datatable-secondary-indices-and-auto-indexing.Rmd | 6 data.table-1.14.8/data.table/inst/tests/benchmark.Rraw |only data.table-1.14.8/data.table/inst/tests/froll.Rraw |only data.table-1.14.8/data.table/inst/tests/nafill.Rraw |only data.table-1.14.8/data.table/inst/tests/other.Rraw |only data.table-1.14.8/data.table/inst/tests/tests.Rraw |only data.table-1.14.8/data.table/inst/tests/types.Rraw |only 84 files changed, 6625 insertions(+), 4341 deletions(-)
Title: Interface to the 'SymEngine' Library
Description: Provides an R interface to 'SymEngine' <https://github.com/symengine/>,
a standalone 'C++' library for fast symbolic manipulation. The package has functionalities
for symbolic computation like calculating exact mathematical expressions, solving
systems of linear equations and code generation.
Author: Jialin Ma [cre, aut],
Isuru Fernando [aut],
Xin Chen [aut]
Maintainer: Jialin Ma <marlin@inventati.org>
Diff between symengine versions 0.2.2 dated 2022-10-23 and 0.2.3 dated 2023-12-08
symengine-0.2.2/symengine/tools/translate_to_cmake_flags.R |only symengine-0.2.3/symengine/DESCRIPTION | 8 - symengine-0.2.3/symengine/MD5 | 34 ++-- symengine-0.2.3/symengine/NAMESPACE | 2 symengine-0.2.3/symengine/R/vector.R | 29 +-- symengine-0.2.3/symengine/README.md | 2 symengine-0.2.3/symengine/build/vignette.rds |binary symengine-0.2.3/symengine/configure | 20 +- symengine-0.2.3/symengine/configure.win | 20 +- symengine-0.2.3/symengine/inst/doc/odesystem.html | 74 +++++----- symengine-0.2.3/symengine/inst/doc/quick_start.R | 2 symengine-0.2.3/symengine/inst/doc/quick_start.html | 66 ++++---- symengine-0.2.3/symengine/man/symengine.Rd | 6 symengine-0.2.3/symengine/man/vecbasic-bindings.Rd | 8 - symengine-0.2.3/symengine/src/Makevars.in | 2 symengine-0.2.3/symengine/src/rbinding.cpp | 33 +--- symengine-0.2.3/symengine/src/upstream.tar |binary symengine-0.2.3/symengine/tools/bundle_symengine_source.sh | 2 symengine-0.2.3/symengine/tools/cran_comments/cran-comments_0.2.3.md |only 19 files changed, 146 insertions(+), 162 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [ctb],
Emily de la Rua [ctb],
Abinaya Yogasekaram [ctb],
Joe Zhu [ctb, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.3 dated 2023-08-30 and 0.6.6 dated 2023-12-08
rtables-0.6.3/rtables/inst/bootstrap |only rtables-0.6.3/rtables/man/as_result_df.Rd |only rtables-0.6.3/rtables/man/export_as_pdf.Rd |only rtables-0.6.3/rtables/man/figures/rtables_logo.svg |only rtables-0.6.3/rtables/man/figures/rtables_logo_large.png |only rtables-0.6.3/rtables/man/figures/rtables_logo_small.png |only rtables-0.6.3/rtables/man/path_enriched_df.Rd |only rtables-0.6.3/rtables/man/result_df_specs.Rd |only rtables-0.6.6/rtables/DESCRIPTION | 25 rtables-0.6.6/rtables/MD5 | 398 - rtables-0.6.6/rtables/NAMESPACE | 29 rtables-0.6.6/rtables/NEWS.md | 57 rtables-0.6.6/rtables/R/00tabletrees.R | 2664 ++++---- rtables-0.6.6/rtables/R/Viewer.R | 72 rtables-0.6.6/rtables/R/argument_conventions.R | 45 rtables-0.6.6/rtables/R/as_html.R | 297 rtables-0.6.6/rtables/R/colby_constructors.R | 1918 +++--- rtables-0.6.6/rtables/R/compare_rtables.R | 372 - rtables-0.6.6/rtables/R/deprecated.R | 48 rtables-0.6.6/rtables/R/format_rcell.R | 13 rtables-0.6.6/rtables/R/indent.R | 42 rtables-0.6.6/rtables/R/index_footnotes.R | 169 rtables-0.6.6/rtables/R/make_split_fun.R | 311 - rtables-0.6.6/rtables/R/make_subset_expr.R | 364 - rtables-0.6.6/rtables/R/simple_analysis.R | 28 rtables-0.6.6/rtables/R/split_funs.R | 1328 ++-- rtables-0.6.6/rtables/R/summary.R | 481 - rtables-0.6.6/rtables/R/tree_accessors.R | 2911 ++++++--- rtables-0.6.6/rtables/R/tt_afun_utils.R | 739 +- rtables-0.6.6/rtables/R/tt_compare_tables.R | 267 rtables-0.6.6/rtables/R/tt_compatibility.R | 1440 ++-- rtables-0.6.6/rtables/R/tt_dotabulation.R | 3078 +++++----- rtables-0.6.6/rtables/R/tt_export.R | 1464 +++- rtables-0.6.6/rtables/R/tt_from_df.R | 23 rtables-0.6.6/rtables/R/tt_paginate.R | 1132 ++- rtables-0.6.6/rtables/R/tt_pos_and_access.R | 1576 ++--- rtables-0.6.6/rtables/R/tt_showmethods.R | 423 - rtables-0.6.6/rtables/R/tt_sort.R | 288 rtables-0.6.6/rtables/R/tt_test_afuns.R | 67 rtables-0.6.6/rtables/R/tt_toString.R | 856 +- rtables-0.6.6/rtables/R/utils.R | 85 rtables-0.6.6/rtables/R/validate_table_struct.R | 197 rtables-0.6.6/rtables/R/zzz_constants.R | 29 rtables-0.6.6/rtables/README.md | 12 rtables-0.6.6/rtables/build/vignette.rds |binary rtables-0.6.6/rtables/inst/doc/advanced_usage.R | 180 rtables-0.6.6/rtables/inst/doc/advanced_usage.Rmd | 184 rtables-0.6.6/rtables/inst/doc/advanced_usage.html | 238 rtables-0.6.6/rtables/inst/doc/baseline.R | 26 rtables-0.6.6/rtables/inst/doc/baseline.Rmd | 26 rtables-0.6.6/rtables/inst/doc/baseline.html | 74 rtables-0.6.6/rtables/inst/doc/clinical_trials.R | 313 - rtables-0.6.6/rtables/inst/doc/clinical_trials.Rmd | 313 - rtables-0.6.6/rtables/inst/doc/clinical_trials.html | 541 - rtables-0.6.6/rtables/inst/doc/custom_appearance.R | 67 rtables-0.6.6/rtables/inst/doc/custom_appearance.Rmd | 67 rtables-0.6.6/rtables/inst/doc/custom_appearance.html | 107 rtables-0.6.6/rtables/inst/doc/example_analysis_coxreg.R | 6 rtables-0.6.6/rtables/inst/doc/example_analysis_coxreg.Rmd | 6 rtables-0.6.6/rtables/inst/doc/example_analysis_coxreg.html | 10 rtables-0.6.6/rtables/inst/doc/exploratory_analysis.R | 60 rtables-0.6.6/rtables/inst/doc/exploratory_analysis.Rmd | 56 rtables-0.6.6/rtables/inst/doc/exploratory_analysis.html | 115 rtables-0.6.6/rtables/inst/doc/format_precedence.html | 4 rtables-0.6.6/rtables/inst/doc/introduction.R | 44 rtables-0.6.6/rtables/inst/doc/introduction.Rmd | 224 rtables-0.6.6/rtables/inst/doc/introduction.html | 536 - rtables-0.6.6/rtables/inst/doc/introspecting_tables.R |only rtables-0.6.6/rtables/inst/doc/introspecting_tables.Rmd |only rtables-0.6.6/rtables/inst/doc/introspecting_tables.html |only rtables-0.6.6/rtables/inst/doc/manual_table_construction.html | 80 rtables-0.6.6/rtables/inst/doc/sorting_pruning.R | 22 rtables-0.6.6/rtables/inst/doc/sorting_pruning.Rmd | 22 rtables-0.6.6/rtables/inst/doc/sorting_pruning.html | 42 rtables-0.6.6/rtables/inst/doc/split_functions.R | 204 rtables-0.6.6/rtables/inst/doc/split_functions.Rmd | 204 rtables-0.6.6/rtables/inst/doc/split_functions.html | 245 rtables-0.6.6/rtables/inst/doc/subsetting_tables.R | 26 rtables-0.6.6/rtables/inst/doc/subsetting_tables.Rmd | 26 rtables-0.6.6/rtables/inst/doc/subsetting_tables.html | 33 rtables-0.6.6/rtables/inst/doc/tabulation_concepts.R | 8 rtables-0.6.6/rtables/inst/doc/tabulation_concepts.Rmd | 8 rtables-0.6.6/rtables/inst/doc/tabulation_concepts.html | 8 rtables-0.6.6/rtables/inst/doc/tabulation_dplyr.R | 39 rtables-0.6.6/rtables/inst/doc/tabulation_dplyr.Rmd | 39 rtables-0.6.6/rtables/inst/doc/tabulation_dplyr.html | 53 rtables-0.6.6/rtables/inst/doc/title_footer.R | 138 rtables-0.6.6/rtables/inst/doc/title_footer.Rmd | 138 rtables-0.6.6/rtables/inst/doc/title_footer.html | 206 rtables-0.6.6/rtables/man/Viewer.Rd | 44 rtables-0.6.6/rtables/man/add_colcounts.Rd | 9 rtables-0.6.6/rtables/man/add_combo_facet.Rd | 14 rtables-0.6.6/rtables/man/add_combo_levels.Rd | 51 rtables-0.6.6/rtables/man/add_existing_table.Rd | 11 rtables-0.6.6/rtables/man/add_overall_col.Rd | 6 rtables-0.6.6/rtables/man/add_overall_level.Rd | 18 rtables-0.6.6/rtables/man/analyze.Rd | 18 rtables-0.6.6/rtables/man/analyze_colvars.Rd | 41 rtables-0.6.6/rtables/man/as_html.Rd | 29 rtables-0.6.6/rtables/man/avarspl.Rd | 14 rtables-0.6.6/rtables/man/basic_table.Rd | 26 rtables-0.6.6/rtables/man/brackets.Rd | 16 rtables-0.6.6/rtables/man/build_table.Rd | 37 rtables-0.6.6/rtables/man/cbind_rtables.Rd | 2 rtables-0.6.6/rtables/man/cell_values.Rd | 48 rtables-0.6.6/rtables/man/clear_imods.Rd | 10 rtables-0.6.6/rtables/man/compare_rtables.Rd | 94 rtables-0.6.6/rtables/man/constr_args.Rd | 12 rtables-0.6.6/rtables/man/data.frame_export.Rd |only rtables-0.6.6/rtables/man/df_to_tt.Rd | 1 rtables-0.6.6/rtables/man/do_base_split.Rd | 26 rtables-0.6.6/rtables/man/export_as_docx.Rd |only rtables-0.6.6/rtables/man/figures/logo.png |only rtables-0.6.6/rtables/man/figures/rtables-basics.png |only rtables-0.6.6/rtables/man/format_rcell.Rd | 2 rtables-0.6.6/rtables/man/formatters_methods.Rd | 2 rtables-0.6.6/rtables/man/gen_args.Rd | 3 rtables-0.6.6/rtables/man/gfc.Rd | 2 rtables-0.6.6/rtables/man/in_rows.Rd | 4 rtables-0.6.6/rtables/man/indent.Rd | 2 rtables-0.6.6/rtables/man/insert_row_at_path.Rd | 11 rtables-0.6.6/rtables/man/insert_rrow.Rd | 14 rtables-0.6.6/rtables/man/int_methods.Rd | 34 rtables-0.6.6/rtables/man/list_wrap.Rd | 2 rtables-0.6.6/rtables/man/make_afun.Rd | 73 rtables-0.6.6/rtables/man/make_col_row_df.Rd | 2 rtables-0.6.6/rtables/man/make_split_fun.Rd | 60 rtables-0.6.6/rtables/man/make_split_result.Rd | 15 rtables-0.6.6/rtables/man/manual_cols.Rd | 13 rtables-0.6.6/rtables/man/matrix_form-VTableTree-method.Rd | 7 rtables-0.6.6/rtables/man/paginate.Rd | 45 rtables-0.6.6/rtables/man/prune_table.Rd | 14 rtables-0.6.6/rtables/man/qtable_layout.Rd | 19 rtables-0.6.6/rtables/man/rbind.Rd | 46 rtables-0.6.6/rtables/man/reexports.Rd | 16 rtables-0.6.6/rtables/man/ref_fnotes.Rd | 13 rtables-0.6.6/rtables/man/row_paths_summary.Rd | 14 rtables-0.6.6/rtables/man/rowclasses.Rd | 13 rtables-0.6.6/rtables/man/rrow.Rd | 2 rtables-0.6.6/rtables/man/rrowl.Rd | 8 rtables-0.6.6/rtables/man/rtable.Rd | 18 rtables-0.6.6/rtables/man/section_div.Rd |only rtables-0.6.6/rtables/man/sort_at_path.Rd | 30 rtables-0.6.6/rtables/man/split_cols_by.Rd | 38 rtables-0.6.6/rtables/man/split_cols_by_multivar.Rd | 20 rtables-0.6.6/rtables/man/split_funcs.Rd | 10 rtables-0.6.6/rtables/man/split_rows_by.Rd | 64 rtables-0.6.6/rtables/man/split_rows_by_multivar.Rd | 8 rtables-0.6.6/rtables/man/summarize_row_groups.Rd | 35 rtables-0.6.6/rtables/man/tabclasses.Rd | 16 rtables-0.6.6/rtables/man/table_shell.Rd | 22 rtables-0.6.6/rtables/man/table_structure.Rd | 6 rtables-0.6.6/rtables/man/tostring.Rd | 32 rtables-0.6.6/rtables/man/trim_levels_to_map.Rd | 14 rtables-0.6.6/rtables/man/trim_prune_funs.Rd | 18 rtables-0.6.6/rtables/man/trim_rows.Rd | 16 rtables-0.6.6/rtables/man/tsv_io.Rd | 8 rtables-0.6.6/rtables/man/tt_to_flextable.Rd | 134 rtables-0.6.6/rtables/man/ttap.Rd | 14 rtables-0.6.6/rtables/man/validate_table_struct.Rd | 4 rtables-0.6.6/rtables/man/value_formats.Rd | 4 rtables-0.6.6/rtables/man/varcuts.Rd | 44 rtables-0.6.6/rtables/man/vil.Rd | 16 rtables-0.6.6/rtables/tests/testthat/setup-fakedata.R | 313 - rtables-0.6.6/rtables/tests/testthat/test-accessors.R | 495 + rtables-0.6.6/rtables/tests/testthat/test-binding.R | 395 - rtables-0.6.6/rtables/tests/testthat/test-compare_rtables.R | 67 rtables-0.6.6/rtables/tests/testthat/test-deprecated.R | 162 rtables-0.6.6/rtables/tests/testthat/test-exporters.R | 530 + rtables-0.6.6/rtables/tests/testthat/test-formatting.R | 322 - rtables-0.6.6/rtables/tests/testthat/test-header-footer.R | 274 rtables-0.6.6/rtables/tests/testthat/test-indent-mod.R | 398 - rtables-0.6.6/rtables/tests/testthat/test-lyt-tabulation.R | 2756 ++++---- rtables-0.6.6/rtables/tests/testthat/test-make-afun.R | 738 +- rtables-0.6.6/rtables/tests/testthat/test-pagination.R | 840 +- rtables-0.6.6/rtables/tests/testthat/test-printing.R | 1061 ++- rtables-0.6.6/rtables/tests/testthat/test-regressions.R | 870 +- rtables-0.6.6/rtables/tests/testthat/test-result_data_frame.R | 168 rtables-0.6.6/rtables/tests/testthat/test-rtables.R | 81 rtables-0.6.6/rtables/tests/testthat/test-sanitize-struct.R | 86 rtables-0.6.6/rtables/tests/testthat/test-sort-prune.R | 483 - rtables-0.6.6/rtables/tests/testthat/test-spanning.R | 47 rtables-0.6.6/rtables/tests/testthat/test-split_funs.R | 569 - rtables-0.6.6/rtables/tests/testthat/test-structure-summary.R | 107 rtables-0.6.6/rtables/tests/testthat/test-subset-access.R | 834 +- rtables-0.6.6/rtables/tests/testthat/test-tab_afun_cfun.R | 605 + rtables-0.6.6/rtables/tests/testthat/test_utils.R | 42 rtables-0.6.6/rtables/vignettes/advanced_usage.Rmd | 184 rtables-0.6.6/rtables/vignettes/baseline.Rmd | 26 rtables-0.6.6/rtables/vignettes/clinical_trials.Rmd | 313 - rtables-0.6.6/rtables/vignettes/custom_appearance.Rmd | 67 rtables-0.6.6/rtables/vignettes/example_analysis_coxreg.Rmd | 6 rtables-0.6.6/rtables/vignettes/exploratory_analysis.Rmd | 56 rtables-0.6.6/rtables/vignettes/introduction.Rmd | 224 rtables-0.6.6/rtables/vignettes/introspecting_tables.Rmd |only rtables-0.6.6/rtables/vignettes/sorting_pruning.Rmd | 22 rtables-0.6.6/rtables/vignettes/split_functions.Rmd | 204 rtables-0.6.6/rtables/vignettes/subsetting_tables.Rmd | 26 rtables-0.6.6/rtables/vignettes/tabulation_concepts.Rmd | 8 rtables-0.6.6/rtables/vignettes/tabulation_dplyr.Rmd | 39 rtables-0.6.6/rtables/vignettes/title_footer.Rmd | 138 201 files changed, 24223 insertions(+), 18853 deletions(-)
Title: Bayesian Change-Point Detection and Time Series Decomposition
Description: Interpretation of time series data is affected by model choices. Different models can give different or even contradicting estimates of patterns, trends, and mechanisms for the same data--a limitation alleviated by the Bayesian estimator of abrupt change,seasonality, and trend (BEAST) of this package. BEAST seeks to improve time series decomposition by forgoing the "single-best-model" concept and embracing all competing models into the inference via a Bayesian model averaging scheme. It is a flexible tool to uncover abrupt changes (i.e., change-points), cyclic variations (e.g., seasonality), and nonlinear trends in time-series observations. BEAST not just tells when changes occur but also quantifies how likely the detected changes are true. It detects not just piecewise linear trends but also arbitrary nonlinear trends. BEAST is applicable to real-valued time series data of all kinds, be it for remote sensing, economics, climate sciences, ecology, and hydrology. Example applications in [...truncated...]
Author: Tongxi Hu [aut],
Yang Li [aut],
Xuesong Zhang [aut],
Kaiguang Zhao [aut, cre],
Jack Dongarra [ctb],
Cleve Moler [ctb]
Maintainer: Kaiguang Zhao <zhao.1423@osu.edu>
Diff between Rbeast versions 0.9.9 dated 2023-05-14 and 1.0.0 dated 2023-12-08
DESCRIPTION | 16 MD5 | 158 +-- NEWS.md | 9 R/beast.R | 123 +- R/beast.irreg.R | 58 - R/beast.old.R | 9 R/beast123.R | 23 data/imagestack.RData |binary man/beast.Rd | 130 +- man/beast.irreg.Rd | 119 +- man/beast123.Rd | 117 +- src/_beastv2_gui_plot.c | 6 src/_beastv2_gui_winmain.c | 16 src/abc_000_macro.h | 19 src/abc_001_config.h | 13 src/abc_blas_lapack_lib.h | 2 src/abc_common.c | 293 +++++- src/abc_common.h | 7 src/abc_datatype.h | 12 src/abc_date.c | 575 ++++++++--- src/abc_date.h | 42 src/abc_dir.c | 6 src/abc_ide_util.h | 44 src/abc_ide_util_R.c | 36 src/abc_ide_util_common.c | 710 ++++++++++++-- src/abc_ide_util_matlab.c | 16 src/abc_ide_util_python.c | 159 ++- src/abc_ioFlush.c | 7 src/abc_mat.c | 80 + src/abc_mat.h | 3 src/abc_math_avx.c | 6 src/abc_math_avx512.c | 6 src/abc_mcmc.c | 2 src/abc_mem.c | 304 ++++-- src/abc_mem.h | 18 src/abc_mem_ext.c | 4 src/abc_pthread.c | 259 +++-- src/abc_pthread.h | 219 +--- src/abc_rand_pcg_local.c | 1 src/abc_rand_pcg_local.h | 7 src/abc_rand_pcg_local_avx2.c | 43 src/abc_rand_pcg_local_avx512.c | 15 src/abc_rand_pcg_local_generic.c | 10 src/abc_sort.c | 143 ++ src/abc_sort.h | 9 src/abc_timer.h | 8 src/abc_tranpose.c | 36 src/abc_tranpose.h | 2 src/abc_ts_func.c | 176 --- src/abc_ts_func.h | 48 src/abc_vec.c | 298 ++++-- src/abc_vec.h | 11 src/abc_vec_avx2.c | 144 +- src/abc_vec_avx512.c | 133 +- src/abc_vec_generic.c | 123 +- src/abc_win32_demo.h | 2 src/beastv2_COREV4.c | 89 + src/beastv2_COREV4_bic.c |only src/beastv2_COREV4_bic_mthrd.c |only src/beastv2_COREV4_gui.c | 1560 +++++++++++++++----------------- src/beastv2_COREV4_mthrd.c | 77 - src/beastv2_basis_allocinitmem.c | 18 src/beastv2_basis_computexy_q.c | 2 src/beastv2_basis_cvtKnotsToBinVec.c | 8 src/beastv2_basis_genrandbasis.c | 13 src/beastv2_basis_gensegment.c | 5 src/beastv2_basis_proposeNew_q.c | 4 src/beastv2_basis_updateKsKe_prec0123.c | 4 src/beastv2_basis_updategoodvec.c | 4 src/beastv2_date.c |only src/beastv2_func_q.c | 14 src/beastv2_header.h | 54 - src/beastv2_header_solaris.h | 83 - src/beastv2_io_in_args.c | 813 +++++++--------- src/beastv2_io_in_readts.c | 38 src/beastv2_io_out_allocmem_q.c | 8 src/beastv2_io_out_printargs.c | 226 ++-- src/beastv2_io_out_tsextractprint.c | 2 src/beastv2_model_allocinit_q.c | 18 src/beastv2_svdbasis.c |only src/beastv2_xxyy_allocmem_q.c | 58 - src/glue_code.c | 322 +++++- 82 files changed, 5100 insertions(+), 3155 deletions(-)
Title: Plug-in Kernel Density Estimation
Description: Kernel density estimation with global bandwidth selection
via "plug-in".
Author: Eva Herrmann <eherrmann@mathematik.tu-darmstadt.de> ;
R interface etc by Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between plugdensity versions 0.8-4 dated 2022-02-23 and 0.8-5 dated 2023-12-08
ChangeLog | 4 ++++ DESCRIPTION | 14 ++++++-------- MD5 | 4 ++-- 3 files changed, 12 insertions(+), 10 deletions(-)
Title: Generalized Two Arms Clinical Trial Sample Size Calculation
Description: Two arms clinical trials required sample size is calculated in the comprehensive parametric context. The calculation is based on the type of endpoints(continuous/binary/time-to-event/ordinal), design (parallel/crossover), hypothesis tests (equality/noninferiority/superiority/equivalence), trial arms noncompliance rates and expected loss of follow-up. Methods are described in: Chow SC, Shao J, Wang H, Lokhnygina Y (2017) <doi:10.1201/9781315183084>, Wittes, J (2002) <doi:10.1093/epirev/24.1.39>, Sato, T (2000) <doi:10.1002/1097-0258(20001015)19:19%3C2689::aid-sim555%3E3.0.co;2-0>, Lachin J M, Foulkes, M A (1986) <doi:10.2307/2531201>, Whitehead J(1993) <doi:10.1002/sim.4780122404>, Julious SA (2023) <doi:10.1201/9780429503658>.
Author: Mohsen Soltanifar [aut] ,
Chel Hee Lee [cre, aut]
Maintainer: Chel Hee Lee <chelhee.lee@ucalgary.ca>
Diff between GenTwoArmsTrialSize versions 0.0.4.3 dated 2023-12-07 and 0.0.4.4 dated 2023-12-08
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
More information about GenTwoArmsTrialSize at CRAN
Permanent link
Title: Read and Write FWF Files in the 'Blaise' Format
Description: Can be used to read and write a fwf with an accompanying 'Blaise' datamodel.
Blaise is the software suite built by Statistics Netherlands (CBS). It is essentially a
way to write and collect surveys and perform statistical analysis on the data. It stores its data in
fixed width format with an accompanying metadata file, this is the Blaise format. The package automatically
interprets this metadata and reads the file into an R dataframe.
When supplying a datamodel for writing, the dataframe will be automatically converted
to that format and checked for compatibility.
Supports dataframes, tibbles and LaF objects.
For more information about 'Blaise', see <https://blaise.com/products/general-information>.
Author: Sjoerd Ophof [aut, cre]
Maintainer: Sjoerd Ophof <sjoerd.ophof@gmail.com>
Diff between blaise versions 1.3.10 dated 2023-08-18 and 1.3.11 dated 2023-12-08
DESCRIPTION | 6 MD5 | 18 +- NEWS.md | 3 R/get_model.R | 2 R/write_data.R | 204 ++++++++++++++++----------------- inst/doc/introduction_to_blaise.R | 2 inst/doc/introduction_to_blaise.html | 26 ++-- tests/testthat/test_read_fwf.R | 9 - tests/testthat/test_write_datamodel.R | 37 ++++- tests/testthat/test_write_fwf_blaise.R | 16 ++ 10 files changed, 179 insertions(+), 144 deletions(-)
Title: Seamless Multicollinearity Management
Description: System for seamless management of multicollinearity in data frames
with numeric and/or categorical variables for statistical analysis and
machine learning modeling. The package combines bivariate correlation
(Pearson, Spearman, and Cramer's V) with variance inflation factor analysis,
target encoding to transform categorical variables into numeric (Micci-Barreca, D. 2001
<DOI:10.1145/507533.507538>), and a flexible
feature prioritization method, to deliver a comprehensive
multicollinearity management tool covering a wide range of use cases.
Author: Blas M. Benito [aut, cre, cph]
Maintainer: Blas M. Benito <blasbenito@gmail.com>
Diff between collinear versions 1.1.0 dated 2023-11-30 and 1.1.1 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 4 ++++ R/vif_df.R | 27 +++++++++++++++++++++------ R/vif_select.R | 10 ++++++++++ README.md | 4 ++-- man/vif_df.Rd | 13 +++++++++++-- man/vif_select.Rd | 10 ++++++++++ tests/testthat/test-vif_df.R | 9 +++++++-- tests/testthat/test-vif_select.R | 9 +++++++++ 10 files changed, 86 insertions(+), 24 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between curl versions 5.1.0 dated 2023-10-02 and 5.2.0 dated 2023-12-08
DESCRIPTION | 10 +++--- MD5 | 25 ++++++++--------- NAMESPACE | 2 + NEWS | 6 ++++ R/echo.R | 21 ++++++++++++-- build/vignette.rds |binary inst/doc/intro.R | 10 +++--- inst/doc/intro.html | 76 ++++++++++++++++++++++++++-------------------------- man/curl_echo.Rd | 7 ++++ src/Makevars.win | 2 - src/findport.c |only src/handle.c | 20 +++++++------ src/init.c | 2 + src/utils.c | 6 ++-- 14 files changed, 110 insertions(+), 77 deletions(-)
Title: Trio Data Analysis with Knockoff Statistics for FDR Control
Description: Identification of putative causal variants in genome-wide association studies with the trio design. The package implements the methods in the paper: Yang, Y., Wang, C., Liu, L., Buxbaum, J., He, Z., & Ionita-Laza, I. (2022). KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. The American Journal of Human Genetics, 109(10), 1761-1776.
Author: Yi Yang [aut, cre]
Maintainer: Yi Yang <yi.yang@cityu.edu.hk>
Diff between KnockoffTrio versions 1.0.1 dated 2022-10-17 and 1.0.2 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/create_knockoff.R | 4 ++-- man/create_knockoff.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Train and Apply a Gaussian Stochastic Process Model
Description: Train a Gaussian stochastic process model of an unknown function, possibly observed with error, via maximum likelihood or maximum a posteriori (MAP) estimation, run model diagnostics, and make predictions, following Sacks, J., Welch, W.J., Mitchell, T.J., and Wynn, H.P. (1989) "Design and Analysis of Computer Experiments", Statistical Science, <doi:10.1214/ss/1177012413>. Perform sensitivity analysis and visualize low-order effects, following Schonlau, M. and Welch, W.J. (2006), "Screening the Input Variables to a Computer Model Via Analysis of Variance and Visualization", <doi:10.1007/0-387-28014-6_14>.
Author: William J. Welch [aut, cre, cph]
,
Yilin Yang [aut]
Maintainer: William J. Welch <will@stat.ubc.ca>
Diff between GaSP versions 1.0.4 dated 2023-05-18 and 1.0.5 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- README.md | 6 ++++++ build/vignette.rds |binary inst/doc/GaSP_vignette.R | 16 ++++++++-------- inst/doc/GaSP_vignette.pdf |binary src/GaSP_init.c | 2 ++ src/RtoC.c | 3 +++ src/lib.h | 14 ++++++++------ src/libout.c | 5 +++-- src/libreg.c | 19 +++++++++---------- 11 files changed, 52 insertions(+), 39 deletions(-)
Title: Templated Reporting Workflows in Word and PowerPoint
Description: Automated reporting in Word and PowerPoint can require customization for each organizational template. This package works around this by adding standard reporting functions and an abstraction layer to facilitate automated reporting workflows that can be replicated across different organizational templates.
Author: John Harrold [aut, cre] ,
Bryan Smith [aut]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between onbrand versions 1.0.3 dated 2023-07-16 and 1.0.4 dated 2023-12-08
onbrand-1.0.3/onbrand/vignettes/onbrand_hex.png |only onbrand-1.0.4/onbrand/DESCRIPTION | 10 onbrand-1.0.4/onbrand/MD5 | 29 onbrand-1.0.4/onbrand/NEWS.md | 4 onbrand-1.0.4/onbrand/R/add_pptx_ph_content.R | 50 onbrand-1.0.4/onbrand/R/report_add_slide.R | 124 +- onbrand-1.0.4/onbrand/inst/doc/Creating_Templated_Office_Workflows.R | 36 onbrand-1.0.4/onbrand/inst/doc/Creating_Templated_Office_Workflows.Rmd | 48 onbrand-1.0.4/onbrand/inst/doc/Creating_Templated_Office_Workflows.html | 543 +++++----- onbrand-1.0.4/onbrand/inst/doc/Custom_Office_Templates.Rmd | 2 onbrand-1.0.4/onbrand/inst/doc/Custom_Office_Templates.html | 3 onbrand-1.0.4/onbrand/man/add_pptx_ph_content.Rd | 16 onbrand-1.0.4/onbrand/man/report_add_slide.Rd | 64 - onbrand-1.0.4/onbrand/vignettes/Creating_Templated_Office_Workflows.Rmd | 48 onbrand-1.0.4/onbrand/vignettes/Custom_Office_Templates.Rmd | 2 onbrand-1.0.4/onbrand/vignettes/ppt_workflow_output.png |binary 16 files changed, 647 insertions(+), 332 deletions(-)
Title: Batch Correction of Single Cell Transcriptome Data
Description: Non-linear/linear hybrid method for batch-effect correction
that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between
datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
Author: Martin Loza [aut, cre] ,
Diego Diez [aut]
Maintainer: Martin Loza <martin.loza.lopez@gmail.com>
Diff between Canek versions 0.2.4 dated 2023-11-05 and 0.2.5 dated 2023-12-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ build/partial.rdb |binary inst/doc/toy_example.html | 6 +++--- tests/testthat/test-Clustering.R | 6 +++--- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Interface to the Australian Statistical Geography Standard
Description: The Australian Statistical Geography Standard ('ASGS') is
a set of shapefiles by the Australian Bureau of Statistics. This package
provides an interface to those shapefiles, as well as methods for converting
coordinates to shapefiles.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between ASGS.foyer versions 0.3.1 dated 2021-03-21 and 0.3.3 dated 2023-12-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 ++++++++ R/install_ASGS.R | 14 +++++++++++--- README.md | 11 +++++++---- man/install_ASGS.Rd | 5 ++++- 6 files changed, 39 insertions(+), 17 deletions(-)