Title: Request Scheduler
Description: Offers classes and functions to contact web servers while enforcing scheduling rules required by the sites. The URL class makes it easy to construct a URL by providing parameters as a vector. The Request class allows to describes SOAP (Simple Object Access Protocol) or standard requests: URL, method (POST or GET), header, body. The Scheduler class controls the request frequency for each server address by mean of rules (Rule class). The RequestResult class permits to get the request status to handle error cases and the content.
Author: Pierrick Roger [aut, cre]
Maintainer: Pierrick Roger <pierrick.roger@cea.fr>
Diff between sched versions 1.0.2 dated 2024-08-20 and 1.0.3 dated 2024-10-02
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/Rule.R | 2 +- build/vignette.rds |binary inst/doc/fcts.html | 4 ++-- inst/doc/intro.html | 2 +- tests/testthat/test_010_rule.R | 4 ++-- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Kriging Models using the 'libKriging' Library
Description: Interface to 'libKriging' 'C++' library <https://github.com/libKriging> that should
provide most standard Kriging / Gaussian process regression features
(like in 'DiceKriging', 'kergp' or 'RobustGaSP' packages).
'libKriging' relies on Armadillo linear algebra library (Apache 2 license) by Conrad Sanderson,
'lbfgsb_cpp' is a 'C++' port around 'lbfgsb' library (BSD-3 license) by
Ciyou Zhu, Richard Byrd, Jorge Nocedal and Jose Luis Morales used for hyperparameters optimization.
Author: Yann Richet [aut, cre] ,
Pascal Have [aut],
Yves Deville [aut],
Conrad Sanderson [ctb],
Ciyou Zhu [ctb],
Richard Byrd [ctb],
Jorge Nocedal [ctb],
Jose Luis Morales [ctb],
Mike Smith [ctb]
Maintainer: Yann Richet <yann.richet@irsn.fr>
Diff between rlibkriging versions 0.9-0.1 dated 2024-08-27 and 0.9-0.4 dated 2024-10-02
DESCRIPTION | 8 MD5 | 20 +- src/libK/cmake/update_version.sh | 2 src/libK/src/lib/include/libKriging/Kriging.hpp | 20 +- src/libK/src/lib/include/libKriging/LinearRegressionOptim.hpp | 2 src/libK/src/lib/include/libKriging/NoiseKriging.hpp | 20 +- src/libK/src/lib/include/libKriging/NuggetKriging.hpp | 92 ++++++++-- src/libK/travis-ci/common/before_script.sh | 2 src/libK/travis-ci/linux-macos/install.sh | 2 src/libK/travis-ci/linux-macos/loadenv.sh | 2 src/libK/travis-ci/linux-macos/test.sh | 2 11 files changed, 117 insertions(+), 55 deletions(-)
Title: Non-Normal Repeated Measurements Models
Description: Various functions to fit models for non-normal repeated
measurements, such as Binary Random Effects Models with Two Levels of Nesting,
Bivariate Beta-binomial Regression Models, Marginal Bivariate Binomial Regression Models,
Cormack capture-recapture models, Continuous-time Hidden Markov Chain Models,
Discrete-time Hidden Markov Chain Models,
Changepoint Location Models using a Continuous-time Two-state Hidden Markov Chain,
generalized nonlinear autoregression models, multivariate Gaussian copula models,
generalized non-linear mixed models with one random effect,
generalized non-linear mixed models using h-likelihood for one random effect,
Repeated Measurements Models for Counts with Frailty or Serial Dependence,
Repeated Measurements Models for Continuous Variables with Frailty or Serial Dependence,
Ordinal Random Effects Models with Dropouts, marginal homogeneity models for square
contingency tables, correlated negative binomial models with Kalman update.
References include Lindsey's [...truncated...]
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] ,
T.R. Ten Have [ctb, cph] .),
Richard Cook [ctb, cph] ,
Iain MacDonald [ctb, cph] ,
Walter Zucchini [ctb, cph] ,
Burton Garbow [ctb, cph] ,
Euginia Zharichenko [ctb, cph]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between repeated versions 1.1.9 dated 2024-09-20 and 1.1.10 dated 2024-10-02
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 7 src/binnest.f | 22 - src/chidden.f | 698 ++++++++++++++++++++++++++++++++++++++++++++++----------- src/cphidden.f | 698 ++++++++++++++++++++++++++++++++++++++++++++++----------- src/eigen.f | 32 +- src/hidden.f | 573 ++++++++++++++++++++++++++++++++++++---------- 8 files changed, 1625 insertions(+), 425 deletions(-)
Title: Multiple Imputation for Proteomics
Description: A framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) <doi:10.1371/journal.pcbi.1010420>. It is dedicated to dealing with multiple imputation for proteomics.
Author: Marie Chion [aut] ,
Christine Carapito [aut] ,
Frederic Bertrand [cre, aut] ,
Gordon Smyth [ctb],
Davis McCarthy [ctb],
Helene Borges [ctb],
Thomas Burger [ctb],
Quentin Giai-Gianetto [ctb],
Samuel Wieczorek [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between mi4p versions 1.1 dated 2023-03-23 and 1.2 dated 2024-10-02
DESCRIPTION | 15 MD5 | 83 - NAMESPACE | 1 NEWS.md | 4 R/MVgen.R | 2 R/datasets.R | 4 R/hid_ebayes.R | 11 R/meanImp_emmeans.R | 4 R/mi4limma.R | 2 R/mi4p-package.R | 38 R/proj_matrix.R | 4 R/protdatasim.R | 2 R/rubin1_all.R | 2 R/rubin2_all.R | 4 R/rubin2bt_all.R | 2 R/rubin2bt_one.R | 4 R/rubin2wt_all.R | 2 R/rubin2wt_one.R | 2 R/within_variance_comp_emmeans.R | 2 README.md | 126 -- build/partial.rdb |only build/vignette.rds |binary inst/doc/Intromi4p.R | 97 - inst/doc/Intromi4p.Rmd | 6 inst/doc/Intromi4p.html | 1875 +++++++----------------------- man/MVgen.Rd | 2 man/datasim.Rd | 2 man/figures/README-unnamed-chunk-24-1.png |binary man/hid.ebayes.Rd | 5 man/meanImp_emmeans.Rd | 2 man/mi4limma.Rd | 2 man/mi4p-package.Rd | 57 man/norm.200.m100.sd1.vs.m200.sd1.list.Rd | 2 man/proj_matrix.Rd | 2 man/protdatasim.Rd | 2 man/rubin1.all.Rd | 2 man/rubin2.all.Rd | 2 man/rubin2bt.all.Rd | 2 man/rubin2bt.one.Rd | 2 man/rubin2wt.all.Rd | 2 man/rubin2wt.one.Rd | 2 man/within_variance_comp_emmeans.Rd | 2 vignettes/Intromi4p.Rmd | 6 43 files changed, 671 insertions(+), 1717 deletions(-)
Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature
Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection
algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning.
In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf>
with a sparse matrix support.
Author: Zygmunt Zawadzki [aut, cre],
Marcin Kosinski [aut],
Krzysztof Slomczynski [ctb],
Damian Skrzypiec [ctb],
Patrick Schratz [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>
Diff between FSelectorRcpp versions 0.3.11 dated 2023-04-28 and 0.3.13 dated 2024-10-02
DESCRIPTION | 12 - MD5 | 46 +++--- R/feature_search.R | 8 - R/information_gain.R | 27 ++- R/utils.R | 4 build/vignette.rds |binary inst/doc/benchmarks_discretize.R | 10 - inst/doc/benchmarks_discretize.Rmd | 4 inst/doc/benchmarks_discretize.html | 260 +++++++++++++++++++----------------- inst/doc/get_started.R | 2 inst/doc/get_started.Rmd | 4 inst/doc/get_started.html | 136 ++++++++++-------- inst/doc/integer-variables.Rmd | 2 inst/doc/integer-variables.html | 203 +++++++++++++++------------- man/dot-information_gain.Rd | 4 man/feature_search.Rd | 8 - man/information_gain.Rd | 23 +-- man/to_formula.Rd | 4 tests/testthat.R | 21 +- tests/testthat/test-param-search.R | 136 +++++++++--------- vignettes/RJreferences.bib | 1 vignettes/benchmarks_discretize.Rmd | 4 vignettes/get_started.Rmd | 4 vignettes/integer-variables.Rmd | 2 24 files changed, 487 insertions(+), 438 deletions(-)
Title: Reads Mass Spectrometry Data in Bruker *flex Format
Description: Reads data files acquired by Bruker Daltonics' matrix-assisted
laser desorption/ionization-time-of-flight mass spectrometer of the *flex
series.
Author: Sebastian Gibb [aut, cre] ,
Samuel Granjeaud [ctb],
Alan Race [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readBrukerFlexData versions 1.9.2 dated 2024-01-22 and 1.9.3 dated 2024-10-02
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 4 ++++ R/ntbcal-functions.R | 2 +- tests/testthat/test_ntbcal-functions.R | 5 +++++ tests/testthat/test_sampleName.R | 2 +- 6 files changed, 21 insertions(+), 12 deletions(-)
More information about readBrukerFlexData at CRAN
Permanent link
Title: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality
Description: Programmatic interface to the 'SNOTEL' snow data
(<https://www.nrcs.usda.gov/programs-initiatives/sswsf-snow-survey-and-water-supply-forecasting-program>). Provides easy downloads of snow
data into your R work space or a local directory. Additional post-processing
routines to extract snow season indexes are provided.
Author: Koen Hufkens [aut, cre] ,
BlueGreen Labs [cph, fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between snotelr versions 1.5 dated 2024-09-30 and 1.5.1 dated 2024-10-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/snotel_metric.r | 1 + inst/doc/snotelr-vignette.html | 4 ++-- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Reproducible Data Science Environments with 'Nix'
Description: Simplifies the creation of reproducible data science environments
using the 'Nix' package manager, as described in
Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()`
function generates a complete description of the environment as a
`default.nix` file, which can then be built using 'Nix'. This results in
project specific software environments with pinned versions of R, packages,
linked system dependencies, and other tools. Additional helpers make it easy
to run R code in 'Nix' software environments for testing and production.
Author: Bruno Rodrigues [aut, cre] ,
Philipp Baumann [aut] ,
David Watkins [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/625>),
Jacob Wujiciak-Jens [rev] for rOpenSci, see
<https://github.com/ropensci/software-review/issues/62 [...truncated...]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Diff between rix versions 0.12.3 dated 2024-09-26 and 0.12.4 dated 2024-10-02
DESCRIPTION | 6 MD5 | 17 - NEWS.md | 6 R/rix_init.R | 45 +++- README.md | 12 + inst/doc/z-advanced-topic-reproducible-analytical-pipelines-with-nix.html | 2 inst/doc/z-advanced-topic-running-r-or-shell-code-in-nix-from-r.html | 18 - inst/extdata/default.nix | 8 tests/testthat/_snaps/rix_init/append_Rprofile.txt |only tests/testthat/test-rix_init.R | 101 +++++++++- 10 files changed, 180 insertions(+), 35 deletions(-)
Title: Pharmacokinetic Bioanalysis Experiments Design and Exploration
Description: Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations.
The package impose regulatory constrains and sanity checking for common bioanalytical procedures.
Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.
Author: Omar Elashkar [aut, cre]
Maintainer: Omar Elashkar <omar.i.elashkar@gmail.com>
Diff between PKbioanalysis versions 0.1.0 dated 2024-09-18 and 0.2.0 dated 2024-10-02
PKbioanalysis-0.1.0/PKbioanalysis/man/dot-add_every_n.Rd |only PKbioanalysis-0.1.0/PKbioanalysis/man/dot-get_plates_db.Rd |only PKbioanalysis-0.1.0/PKbioanalysis/man/dot-injecList.Rd |only PKbioanalysis-0.1.0/PKbioanalysis/man/dot-is_registered.Rd |only PKbioanalysis-0.1.0/PKbioanalysis/man/dot-plate_id.Rd |only PKbioanalysis-0.1.0/PKbioanalysis/man/dot-plate_subid.Rd |only PKbioanalysis-0.2.0/PKbioanalysis/DESCRIPTION | 12 PKbioanalysis-0.2.0/PKbioanalysis/MD5 | 48 - PKbioanalysis-0.2.0/PKbioanalysis/NAMESPACE | 4 PKbioanalysis-0.2.0/PKbioanalysis/NEWS.md |only PKbioanalysis-0.2.0/PKbioanalysis/R/PKbioanalysis-package.R | 93 +- PKbioanalysis-0.2.0/PKbioanalysis/R/dil_map.R | 8 PKbioanalysis-0.2.0/PKbioanalysis/R/injec_list.R | 224 +----- PKbioanalysis-0.2.0/PKbioanalysis/R/method_file.R |only PKbioanalysis-0.2.0/PKbioanalysis/R/plate.R | 65 + PKbioanalysis-0.2.0/PKbioanalysis/R/plate_app.R | 356 +++++----- PKbioanalysis-0.2.0/PKbioanalysis/R/utils.R |only PKbioanalysis-0.2.0/PKbioanalysis/R/zzz.R |only PKbioanalysis-0.2.0/PKbioanalysis/README.md | 12 PKbioanalysis-0.2.0/PKbioanalysis/inst/cmpds.yaml |only PKbioanalysis-0.2.0/PKbioanalysis/inst/doc/PKbioanalysis_overview.R | 18 PKbioanalysis-0.2.0/PKbioanalysis/inst/doc/PKbioanalysis_overview.Rmd | 24 PKbioanalysis-0.2.0/PKbioanalysis/inst/doc/PKbioanalysis_overview.html | 97 +- PKbioanalysis-0.2.0/PKbioanalysis/man/build_injec_seq.Rd | 4 PKbioanalysis-0.2.0/PKbioanalysis/man/download_sample_list.Rd | 4 PKbioanalysis-0.2.0/PKbioanalysis/man/plot.PlateObj.Rd | 12 PKbioanalysis-0.2.0/PKbioanalysis/tests/testthat/test-dil_map.R | 3 PKbioanalysis-0.2.0/PKbioanalysis/tests/testthat/test-injec_list.R | 13 PKbioanalysis-0.2.0/PKbioanalysis/tests/testthat/test-plate.R | 8 PKbioanalysis-0.2.0/PKbioanalysis/tests/testthat/test_methodsfile.R |only PKbioanalysis-0.2.0/PKbioanalysis/vignettes/PKbioanalysis_overview.Rmd | 24 31 files changed, 468 insertions(+), 561 deletions(-)
Title: Ensemble Methods for Combining Hub Model Outputs
Description: Functions for combining model outputs (e.g. predictions or
estimates) from multiple models into an aggregated ensemble model
output.
Author: Evan L Ray [aut],
Li Shandross [aut, cre] ,
Emily Howerton [aut] ,
Anna Krystalli [ctb] ,
Zhian N. Kamvar [ctb] ,
Nicholas G. Reich [ctb] ,
Consortium of Infectious Disease Modeling Hubs [cph]
Maintainer: Li Shandross <lshandross@umass.edu>
Diff between hubEnsembles versions 0.1.8 dated 2024-09-26 and 0.1.9 dated 2024-10-02
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 50 ++++++++++++++++++---------------- R/simple_ensemble.R | 2 - tests/testthat/test-simple_ensemble.R | 14 +++++++++ 5 files changed, 49 insertions(+), 31 deletions(-)
Title: Generalized Linear Models with Truncated Lasso Penalty
Description: Extremely efficient procedures for fitting regularization path with l0, l1, and truncated lasso penalty for linear regression and logistic regression models. This version is a completely new version compared with our previous version, which was mainly based on R. New core algorithms are developed and are now written in C++ and highly optimized.
Author: Chunlin Li [aut, cph] ,
Yu Yang [aut, cre, cph] ,
Chong Wu [aut, cph] ,
Xiaotong Shen [ths, cph],
Wei Pan [ths, cph]
Maintainer: Yu Yang <yuyang.stat@gmail.com>
Diff between glmtlp versions 2.0.1 dated 2021-12-17 and 2.0.2 dated 2024-10-02
glmtlp-2.0.1/glmtlp/R/glmtlp_package.R |only glmtlp-2.0.1/glmtlp/inst/doc/glmtlp.pdf |only glmtlp-2.0.2/glmtlp/DESCRIPTION | 32 ++- glmtlp-2.0.2/glmtlp/MD5 | 39 ++-- glmtlp-2.0.2/glmtlp/NEWS.md | 7 glmtlp-2.0.2/glmtlp/R/glmtlp-package.R |only glmtlp-2.0.2/glmtlp/README.md | 168 +++++++++++------- glmtlp-2.0.2/glmtlp/build/vignette.rds |binary glmtlp-2.0.2/glmtlp/inst/doc/glmtlp.R | 3 glmtlp-2.0.2/glmtlp/inst/doc/glmtlp.Rmd | 25 +- glmtlp-2.0.2/glmtlp/inst/doc/glmtlp.html |only glmtlp-2.0.2/glmtlp/man/figures/README-GLMTLP.png |only glmtlp-2.0.2/glmtlp/man/figures/README-example1-1.png |binary glmtlp-2.0.2/glmtlp/man/figures/README-example2-1.png |binary glmtlp-2.0.2/glmtlp/man/figures/README-example3-1.png |binary glmtlp-2.0.2/glmtlp/man/figures/README-example4-1.png |binary glmtlp-2.0.2/glmtlp/man/figures/README-example5-1.png |binary glmtlp-2.0.2/glmtlp/man/figures/README-example6-1.png |binary glmtlp-2.0.2/glmtlp/man/glmtlp.Rd | 33 +++ glmtlp-2.0.2/glmtlp/man/predict.glmtlp.Rd | 6 glmtlp-2.0.2/glmtlp/src/glmtlp_r_init.cc | 58 +++--- glmtlp-2.0.2/glmtlp/src/utils.h | 1 glmtlp-2.0.2/glmtlp/vignettes/glmtlp.Rmd | 25 +- 23 files changed, 245 insertions(+), 152 deletions(-)
Title: Simulation and Plots for Fossil and Taxonomy Data
Description: Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph],
Ugnė Stolz [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.4.0 dated 2024-09-05 and 2.4.1 dated 2024-10-02
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 2 +- NEWS.md | 3 +++ R/plot.fbdrange.R | 5 +++-- inst/doc/SAtree.html | 29 ++++++++++++++++------------- inst/doc/fossils.html | 38 +++++++++++++++++++------------------- inst/doc/intro.html | 10 +++++----- inst/doc/paleotree.html | 4 ++-- inst/doc/simfbd.html | 12 ++++++------ inst/doc/taxonomy.html | 14 +++++++------- 11 files changed, 76 insertions(+), 69 deletions(-)
Title: Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
Description: Estimates the time-varying reproduction number,
rate of spread, and doubling time using a range of open-source tools
(Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and
current best practices (Gostic et al. (2020)
<doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some
of the limitations of naive implementations in a framework that is
informed by community feedback and is actively supported.
Author: Sam Abbott [aut] ,
Joel Hellewell [aut] ,
Katharine Sherratt [aut],
Katelyn Gostic [aut],
Joe Hickson [aut],
Hamada S. Badr [aut] ,
Michael DeWitt [aut] ,
James M. Azam [aut] ,
Robin Thompson [ctb],
Sophie Meakin [ctb],
James Munday [ctb],
Nikos Boss [...truncated...]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between EpiNow2 versions 1.5.2 dated 2024-05-16 and 1.6.0 dated 2024-10-02
EpiNow2-1.5.2/EpiNow2/man/get_dist_spec_id.Rd |only EpiNow2-1.5.2/EpiNow2/man/sd_dist.Rd |only EpiNow2-1.5.2/EpiNow2/tests/testthat/test-adjust_infection_to_report.R |only EpiNow2-1.5.2/EpiNow2/tests/testthat/test-get_dist.R |only EpiNow2-1.5.2/EpiNow2/tests/testthat/test-opts.R |only EpiNow2-1.5.2/EpiNow2/tests/testthat/test-report_cases.R |only EpiNow2-1.5.2/EpiNow2/vignettes/EpiNow2-unnamed-chunk-11-1.png |only EpiNow2-1.5.2/EpiNow2/vignettes/EpiNow2-unnamed-chunk-15-1.png |only EpiNow2-1.6.0/EpiNow2/DESCRIPTION | 30 EpiNow2-1.6.0/EpiNow2/MD5 | 358 EpiNow2-1.6.0/EpiNow2/NAMESPACE | 36 EpiNow2-1.6.0/EpiNow2/NEWS.md | 52 EpiNow2-1.6.0/EpiNow2/R/checks.R | 122 EpiNow2-1.6.0/EpiNow2/R/create.R | 150 EpiNow2-1.6.0/EpiNow2/R/deprecated.R | 968 - EpiNow2-1.6.0/EpiNow2/R/dist_spec.R | 1144 +- EpiNow2-1.6.0/EpiNow2/R/epinow.R | 26 EpiNow2-1.6.0/EpiNow2/R/estimate_delay.R | 73 EpiNow2-1.6.0/EpiNow2/R/estimate_infections.R | 24 EpiNow2-1.6.0/EpiNow2/R/estimate_secondary.R | 34 EpiNow2-1.6.0/EpiNow2/R/estimate_truncation.R | 87 EpiNow2-1.6.0/EpiNow2/R/extract.R | 6 EpiNow2-1.6.0/EpiNow2/R/fit.R | 15 EpiNow2-1.6.0/EpiNow2/R/get.R | 128 EpiNow2-1.6.0/EpiNow2/R/opts.R | 580 - EpiNow2-1.6.0/EpiNow2/R/regional_epinow.R | 56 EpiNow2-1.6.0/EpiNow2/R/setup.R | 47 EpiNow2-1.6.0/EpiNow2/R/simulate_infections.R | 108 EpiNow2-1.6.0/EpiNow2/R/simulate_secondary.R | 30 EpiNow2-1.6.0/EpiNow2/R/stan.R | 16 EpiNow2-1.6.0/EpiNow2/R/summarise.R | 57 EpiNow2-1.6.0/EpiNow2/R/utilities.R | 22 EpiNow2-1.6.0/EpiNow2/README.md | 64 EpiNow2-1.6.0/EpiNow2/build/partial.rdb |binary EpiNow2-1.6.0/EpiNow2/build/vignette.rds |binary EpiNow2-1.6.0/EpiNow2/data/example_generation_time.rda |binary EpiNow2-1.6.0/EpiNow2/data/example_incubation_period.rda |binary EpiNow2-1.6.0/EpiNow2/data/example_reporting_delay.rda |binary EpiNow2-1.6.0/EpiNow2/inst/WORDLIST | 57 EpiNow2-1.6.0/EpiNow2/inst/doc/EpiNow2.Rmd | 149 EpiNow2-1.6.0/EpiNow2/inst/doc/EpiNow2.html | 449 EpiNow2-1.6.0/EpiNow2/inst/doc/case-studies.html | 80 EpiNow2-1.6.0/EpiNow2/inst/doc/epinow.Rmd | 136 EpiNow2-1.6.0/EpiNow2/inst/doc/epinow.html | 305 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_infections.html | 369 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_infections_options.Rmd | 272 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_infections_options.html | 949 - EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_infections_workflow.Rmd | 94 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_infections_workflow.html | 502 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_secondary.html | 74 EpiNow2-1.6.0/EpiNow2/inst/doc/estimate_truncation.html | 54 EpiNow2-1.6.0/EpiNow2/inst/doc/gaussian_process_implementation_details.Rmd | 21 EpiNow2-1.6.0/EpiNow2/inst/doc/gaussian_process_implementation_details.html | 169 EpiNow2-1.6.0/EpiNow2/inst/stan/data/gaussian_process.stan | 5 EpiNow2-1.6.0/EpiNow2/inst/stan/estimate_infections.stan | 69 EpiNow2-1.6.0/EpiNow2/inst/stan/estimate_secondary.stan | 2 EpiNow2-1.6.0/EpiNow2/inst/stan/estimate_truncation.stan | 6 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/convolve.stan | 114 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/delays.stan | 19 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/gaussian_process.stan | 227 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/observation_model.stan | 119 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/pmfs.stan | 33 EpiNow2-1.6.0/EpiNow2/inst/stan/functions/rt.stan | 68 EpiNow2-1.6.0/EpiNow2/inst/stan/simulate_infections.stan | 2 EpiNow2-1.6.0/EpiNow2/inst/stan/simulate_secondary.stan | 2 EpiNow2-1.6.0/EpiNow2/man/Distributions.Rd | 14 EpiNow2-1.6.0/EpiNow2/man/EpiNow2-package.Rd | 1 EpiNow2-1.6.0/EpiNow2/man/adjust_infection_to_report.Rd | 39 EpiNow2-1.6.0/EpiNow2/man/apply_default_cdf_cutoff.Rd |only EpiNow2-1.6.0/EpiNow2/man/apply_tolerance.Rd | 16 EpiNow2-1.6.0/EpiNow2/man/bootstrapped_dist_fit.Rd | 11 EpiNow2-1.6.0/EpiNow2/man/bound_dist.Rd |only EpiNow2-1.6.0/EpiNow2/man/c.dist_spec.Rd | 5 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Title: Disaggregation Modelling
Description: Fits disaggregation regression models using 'TMB' ('Template Model
Builder'). When the response data are aggregated to polygon level but
the predictor variables are at a higher resolution, these models can be
useful. Regression models with spatial random fields. The package is
described in detail in Nandi et al. (2023) <doi:10.18637/jss.v106.i11>.
Author: Anita Nandi [aut] ,
Tim Lucas [aut, cre] ,
Rohan Arambepola [aut],
Andre Python [aut] ,
Simon Smart [ctb]
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between disaggregation versions 0.3.0 dated 2023-11-08 and 0.4.0 dated 2024-10-02
disaggregation-0.3.0/disaggregation/R/deprecated.R |only disaggregation-0.3.0/disaggregation/man/disaggregation-deprecated.Rd |only disaggregation-0.3.0/disaggregation/man/fit_model.Rd |only disaggregation-0.3.0/disaggregation/tests/testthat/Rplots.pdf |only disaggregation-0.4.0/disaggregation/DESCRIPTION | 13 disaggregation-0.4.0/disaggregation/MD5 | 64 +-- disaggregation-0.4.0/disaggregation/NAMESPACE | 2 disaggregation-0.4.0/disaggregation/R/build_mesh.R | 32 + disaggregation-0.4.0/disaggregation/R/fit_model.R | 67 +--- disaggregation-0.4.0/disaggregation/R/plotting.R | 111 ++++-- disaggregation-0.4.0/disaggregation/R/predict.R | 113 +++--- disaggregation-0.4.0/disaggregation/R/prepare_data.R | 166 +++++++--- disaggregation-0.4.0/disaggregation/R/summary.R | 8 disaggregation-0.4.0/disaggregation/build/vignette.rds |binary disaggregation-0.4.0/disaggregation/inst/doc/disaggregation.R | 23 - disaggregation-0.4.0/disaggregation/inst/doc/disaggregation.Rmd | 20 - disaggregation-0.4.0/disaggregation/inst/doc/disaggregation.html | 22 - disaggregation-0.4.0/disaggregation/man/as.disag_data.Rd | 29 + disaggregation-0.4.0/disaggregation/man/build_mesh.Rd | 17 - disaggregation-0.4.0/disaggregation/man/disag_model.Rd |only disaggregation-0.4.0/disaggregation/man/plot.disag_model.Rd | 5 disaggregation-0.4.0/disaggregation/man/plot_disag_model_data.Rd |only disaggregation-0.4.0/disaggregation/man/predict.disag_model.Rd | 20 - disaggregation-0.4.0/disaggregation/man/predict_model.Rd | 15 disaggregation-0.4.0/disaggregation/man/predict_uncertainty.Rd | 15 disaggregation-0.4.0/disaggregation/man/prepare_data.Rd | 27 + disaggregation-0.4.0/disaggregation/src/disaggregation.cpp | 116 +++--- disaggregation-0.4.0/disaggregation/tests/testthat/helper_data.R | 7 disaggregation-0.4.0/disaggregation/tests/testthat/test-build-mesh.R | 7 disaggregation-0.4.0/disaggregation/tests/testthat/test-extract.R | 6 disaggregation-0.4.0/disaggregation/tests/testthat/test-fit-model.R | 43 -- disaggregation-0.4.0/disaggregation/tests/testthat/test-plotting.R | 38 -- disaggregation-0.4.0/disaggregation/tests/testthat/test-predict-model.R | 115 +----- disaggregation-0.4.0/disaggregation/tests/testthat/test-prepare-data.R | 102 +++--- disaggregation-0.4.0/disaggregation/tests/testthat/test-summary.R | 46 -- disaggregation-0.4.0/disaggregation/vignettes/disaggregation.Rmd | 20 - 36 files changed, 647 insertions(+), 622 deletions(-)
More information about disaggregation at CRAN
Permanent link
Title: Double/Debiased Machine Learning
Description: Estimate common causal parameters using double/debiased machine
learning as proposed by Chernozhukov et al. (2018) <doi:10.1111/ectj.12097>.
'ddml' simplifies estimation based on (short-)stacking as discussed in
Ahrens et al. (2024) <doi:10.1177/1536867X241233641>, which leverages multiple base
learners to increase robustness to the underlying data generating process.
Author: Achim Ahrens [aut],
Christian B Hansen [aut],
Mark E Schaffer [aut],
Thomas Wiemann [aut, cre]
Maintainer: Thomas Wiemann <wiemann@uchicago.edu>
Diff between ddml versions 0.2.2 dated 2024-06-26 and 0.3.0 dated 2024-10-02
DESCRIPTION | 8 - MD5 | 67 +++++----- NEWS.md | 8 + R/crosspred.R | 28 ++-- R/ddml_ate.R | 141 ++++++++-------------- R/ddml_att.R | 106 +++++------------ R/ddml_fpliv.R | 59 ++++----- R/ddml_late.R | 185 +++++++++++------------------- R/ddml_pliv.R | 47 +++---- R/ddml_plm.R | 63 +++++----- R/get_CEF.R | 31 ++++- R/help_functions.R | 95 --------------- R/inference_functions.R |only R/shortstacking.R | 18 +- R/subsample_functions.R |only README.md | 5 man/crosspred.Rd | 8 - man/ddml_ate.Rd | 42 +++--- man/ddml_fpliv.Rd | 12 + man/ddml_late.Rd | 37 +++--- man/ddml_pliv.Rd | 12 + man/ddml_plm.Rd | 14 +- man/ols.Rd | 3 man/print.summary.ddml_ate.Rd | 2 man/print.summary.ddml_plm.Rd | 2 man/shortstacking.Rd | 8 - man/summary.ddml_ate.Rd | 5 man/summary.ddml_plm.Rd | 12 + tests/testthat/test-crosspred.R | 4 tests/testthat/test-ddml_ate.R | 55 ++++++++ tests/testthat/test-ddml_att.R | 57 +++++++++ tests/testthat/test-ddml_fpliv.R | 25 ++++ tests/testthat/test-ddml_late.R | 59 +++++++++ tests/testthat/test-ddml_pliv.R | 25 ++++ tests/testthat/test-ddml_plm.R | 44 +++++++ tests/testthat/test-subsample_functions.R |only 36 files changed, 692 insertions(+), 595 deletions(-)
Title: Bayesian MMRMs using 'brms'
Description: The mixed model for repeated measures (MMRM) is a popular
model for longitudinal clinical trial data with continuous endpoints,
and 'brms' is a powerful and versatile package for fitting Bayesian
regression models. The 'brms.mmrm' R package leverages 'brms' to run
MMRMs, and it supports a simplified interfaced to reduce difficulty
and align with the best practices of the life sciences. References:
Bürkner (2017) <doi:10.18637/jss.v080.i01>, Mallinckrodt (2008)
<doi:10.1177/009286150804200402>.
Author: William Michael Landau [aut, cre]
,
Kevin Kunzmann [aut] ,
Yoni Sidi [aut],
Christian Stock [aut] ,
Eli Lilly and Company [cph, fnd],
Boehringer Ingelheim Pharma GmbH & Co. KG [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between brms.mmrm versions 1.1.0 dated 2024-07-29 and 1.1.1 dated 2024-10-02
DESCRIPTION | 6 MD5 | 85 - NEWS.md | 8 R/brm_formula.R | 41 R/brm_formula_sigma.R | 2 README.md | 28 inst/WORDLIST | 1 inst/doc/archetypes.Rmd | 6 inst/doc/archetypes.html | 24 inst/doc/inference.Rmd | 2 inst/doc/inference.html | 41 inst/doc/model.Rmd | 12 inst/doc/model.html | 18 inst/doc/sbc.html | 182 +- inst/doc/simulation.Rmd | 216 +- inst/doc/simulation.html | 246 +-- inst/doc/usage.Rmd | 991 +++++------- inst/doc/usage.html | 1225 +++++++--------- man/brm_formula.Rd | 29 man/brm_formula_sigma.Rd | 2 vignettes/archetypes.Rmd | 6 vignettes/archetypes.Rmd.source | 6 vignettes/inference.Rmd | 2 vignettes/model.Rmd | 12 vignettes/sbc/_targets.R | 5 vignettes/sbc/renv.lock | 84 - vignettes/sbc/renv/activate.R |only vignettes/sbc/results/autoregressive.fst |binary vignettes/sbc/results/autoregressive_moving_average.fst |binary vignettes/sbc/results/compound_symmetry.fst |binary vignettes/sbc/results/diagonal.fst |binary vignettes/sbc/results/moving_average.fst |binary vignettes/sbc/results/subgroup.fst |binary vignettes/sbc/results/unstructured.fst |binary vignettes/sbc/run.sh |only vignettes/simulation.Rmd | 216 +- vignettes/simulation.Rmd.source | 2 vignettes/usage.Rmd | 991 +++++------- vignettes/usage.Rmd.source | 390 ++--- vignettes/usage/difference-1.png |binary vignettes/usage/differencecustom-1.png |binary vignettes/usage/draws-1.png |binary vignettes/usage/drawscustom-1.png |binary vignettes/usage/priorvsposterior-1.png |only vignettes/usage/response-1.png |binary 45 files changed, 2398 insertions(+), 2481 deletions(-)
Title: Query 'Snowflake' Databases with 'SQL'
Description: A wrapper allowing 'SQL' queries to be run on a 'Snowflake' instance directly from an 'R' script, by using the 'snowflake-connector-python' package in the background.
Author: Dani Mermelstein [aut, cre, cph]
Maintainer: Dani Mermelstein <dmermelstein@hey.com>
Diff between snowquery versions 1.2.0 dated 2024-05-08 and 1.2.1 dated 2024-10-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/queryDB.R | 17 +++++++++++++---- 3 files changed, 19 insertions(+), 10 deletions(-)
Title: Further Capabilities in Geographic Information Science
Description: Mapping and spatial data manipulation tools - in particular
drawing thematic maps with nice looking legends, and aggregation of point
data to polygons.
Author: Chris Brunsdon [aut],
Binbin Lu [aut, cre],
Hongyan Chen [aut]
Maintainer: Binbin Lu <binbinlu@whu.edu.cn>
Diff between GISTools versions 1.0-1 dated 2024-09-19 and 1.0-2 dated 2024-10-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/thematic.map.R | 18 ++++++++++++++---- man/GISTools-package.Rd | 4 ++-- man/thematic.map.Rd | 16 +++++++++++++--- 5 files changed, 37 insertions(+), 17 deletions(-)
Title: Adaptive Optimal Two-Stage Designs
Description: Optimize one or two-arm, two-stage designs for clinical trials with
respect to several implemented objective criteria or custom objectives.
Optimization under uncertainty and conditional (given stage-one outcome)
constraints are supported.
See Pilz et al. (2019) <doi:10.1002/sim.8291> and
Kunzmann et al. (2021) <doi:10.18637/jss.v098.i09> for details.
Author: Kevin Kunzmann [aut, cph] ,
Maximilian Pilz [aut, cre] ,
Jan Meis [aut] ,
Nico Bruder [aut]
Maintainer: Maximilian Pilz <maximilian.pilz@itwm.fraunhofer.de>
Diff between adoptr versions 1.1.0 dated 2024-08-19 and 1.1.1 dated 2024-10-02
DESCRIPTION | 10 +- MD5 | 24 ++-- NEWS.md | 190 +++++++++++++++++++------------------- R/CompositeScore.R | 2 build/vignette.rds |binary inst/doc/adoptr.html | 12 +- inst/doc/adoptr_jss.html | 11 +- inst/doc/composite-scores.html | 4 inst/doc/conditional-scores.html | 8 - inst/doc/defining-new-scores.html | 6 - inst/doc/other-endpoints.html | 6 - inst/doc/working-with-priors.html | 4 man/adoptr.Rd | 2 13 files changed, 142 insertions(+), 137 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines
Description: Pipeline tools coordinate the pieces of computationally
demanding analysis projects.
The 'targets' package is a 'Make'-like pipeline tool for statistics and
data science in R. The package skips costly runtime for tasks
that are already up to date,
orchestrates the necessary computation with implicit parallel computing,
and abstracts files as R objects. If all the current output matches
the current upstream code and data, then the whole pipeline is up
to date, and the results are more trustworthy than otherwise.
The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
,
Matthew T. Warkentin [ctb],
Mark Edmondson [ctb] ,
Samantha Oliver [rev] ,
Tristan Mahr [rev] ,
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between targets versions 1.7.1 dated 2024-06-20 and 1.8.0 dated 2024-10-02
targets-1.7.1/targets/R/class_store_custom.R |only targets-1.7.1/targets/R/class_store_file_fast.R |only targets-1.7.1/targets/man/tar_branch_names_raw.Rd |only targets-1.7.1/targets/man/tar_deps_raw.Rd |only targets-1.7.1/targets/man/tar_helper_raw.Rd |only targets-1.7.1/targets/man/tar_load_raw.Rd |only targets-1.7.1/targets/man/tar_read_raw.Rd |only targets-1.7.1/targets/man/tar_target_raw.Rd |only targets-1.7.1/targets/man/tar_timestamp_raw.Rd |only targets-1.7.1/targets/tests/testthat/test-class_store_custom.R |only targets-1.7.1/targets/tests/testthat/test-class_store_file_fast.R |only targets-1.8.0/targets/DESCRIPTION | 27 targets-1.8.0/targets/MD5 | 571 +++++----- targets-1.8.0/targets/NAMESPACE | 54 targets-1.8.0/targets/NEWS.md | 22 targets-1.8.0/targets/R/class_active.R | 4 targets-1.8.0/targets/R/class_auto.R |only targets-1.8.0/targets/R/class_aws.R | 2 targets-1.8.0/targets/R/class_aws_file.R | 1 targets-1.8.0/targets/R/class_builder.R | 23 targets-1.8.0/targets/R/class_cloud.R | 5 targets-1.8.0/targets/R/class_counter.R | 9 targets-1.8.0/targets/R/class_cue.R | 7 targets-1.8.0/targets/R/class_external.R | 5 targets-1.8.0/targets/R/class_file.R | 43 targets-1.8.0/targets/R/class_gcp.R | 2 targets-1.8.0/targets/R/class_gcp_file.R | 1 targets-1.8.0/targets/R/class_null.R |only targets-1.8.0/targets/R/class_options.R | 85 - targets-1.8.0/targets/R/class_pattern.R | 2 targets-1.8.0/targets/R/class_pipeline.R | 1 targets-1.8.0/targets/R/class_record.R | 2 targets-1.8.0/targets/R/class_resources_repository_cas.R |only targets-1.8.0/targets/R/class_runtime.R | 29 targets-1.8.0/targets/R/class_scheduler.R | 22 targets-1.8.0/targets/R/class_stem.R | 8 targets-1.8.0/targets/R/class_store.R | 123 +- targets-1.8.0/targets/R/class_store_file.R | 4 targets-1.8.0/targets/R/class_store_format_custom.R |only targets-1.8.0/targets/R/class_store_format_custom_methods.R |only targets-1.8.0/targets/R/class_store_repository_cas.R |only targets-1.8.0/targets/R/class_store_repository_cas_file.R |only targets-1.8.0/targets/R/class_store_repository_cas_methods.R |only targets-1.8.0/targets/R/class_target.R | 17 targets-1.8.0/targets/R/class_verbose.R | 1 targets-1.8.0/targets/R/tar_active.R | 2 targets-1.8.0/targets/R/tar_branch_index.R | 2 targets-1.8.0/targets/R/tar_branch_names.R | 14 targets-1.8.0/targets/R/tar_branch_names_raw.R | 26 targets-1.8.0/targets/R/tar_branches.R | 36 targets-1.8.0/targets/R/tar_built.R | 2 targets-1.8.0/targets/R/tar_call.R | 2 targets-1.8.0/targets/R/tar_canceled.R | 2 targets-1.8.0/targets/R/tar_completed.R | 2 targets-1.8.0/targets/R/tar_crew.R | 2 targets-1.8.0/targets/R/tar_definition.R | 8 targets-1.8.0/targets/R/tar_delete.R | 2 targets-1.8.0/targets/R/tar_deps.R | 13 targets-1.8.0/targets/R/tar_deps_raw.R | 16 targets-1.8.0/targets/R/tar_described_as.R | 2 targets-1.8.0/targets/R/tar_destroy.R | 8 targets-1.8.0/targets/R/tar_dir.R | 4 targets-1.8.0/targets/R/tar_dispatched.R | 2 targets-1.8.0/targets/R/tar_errored.R | 2 targets-1.8.0/targets/R/tar_format.R | 30 targets-1.8.0/targets/R/tar_format_get.R |only targets-1.8.0/targets/R/tar_glimpse.R | 2 targets-1.8.0/targets/R/tar_group.R | 2 targets-1.8.0/targets/R/tar_helper.R | 14 targets-1.8.0/targets/R/tar_helper_raw.R | 18 targets-1.8.0/targets/R/tar_invalidate.R | 2 targets-1.8.0/targets/R/tar_load.R | 36 targets-1.8.0/targets/R/tar_load_everything.R | 4 targets-1.8.0/targets/R/tar_load_globals.R | 4 targets-1.8.0/targets/R/tar_load_raw.R | 44 targets-1.8.0/targets/R/tar_make.R | 5 targets-1.8.0/targets/R/tar_make_clustermq.R | 2 targets-1.8.0/targets/R/tar_make_future.R | 2 targets-1.8.0/targets/R/tar_make_interactive.R | 5 targets-1.8.0/targets/R/tar_manifest.R | 2 targets-1.8.0/targets/R/tar_mermaid.R | 2 targets-1.8.0/targets/R/tar_meta.R | 2 targets-1.8.0/targets/R/tar_meta_delete.R | 30 targets-1.8.0/targets/R/tar_meta_download.R | 30 targets-1.8.0/targets/R/tar_meta_sync.R | 28 targets-1.8.0/targets/R/tar_meta_upload.R | 28 targets-1.8.0/targets/R/tar_network.R | 2 targets-1.8.0/targets/R/tar_newer.R | 2 targets-1.8.0/targets/R/tar_objects.R | 4 targets-1.8.0/targets/R/tar_older.R | 2 targets-1.8.0/targets/R/tar_option_get.R | 11 targets-1.8.0/targets/R/tar_option_reset.R | 2 targets-1.8.0/targets/R/tar_option_set.R | 40 targets-1.8.0/targets/R/tar_outdated.R | 2 targets-1.8.0/targets/R/tar_package.R | 8 targets-1.8.0/targets/R/tar_process.R | 2 targets-1.8.0/targets/R/tar_progress.R | 2 targets-1.8.0/targets/R/tar_progress_branches.R | 4 targets-1.8.0/targets/R/tar_progress_summary.R | 2 targets-1.8.0/targets/R/tar_prune.R | 4 targets-1.8.0/targets/R/tar_prune_list.R | 2 targets-1.8.0/targets/R/tar_read.R | 28 targets-1.8.0/targets/R/tar_read_raw.R | 31 targets-1.8.0/targets/R/tar_renv.R | 3 targets-1.8.0/targets/R/tar_repository_cas.R |only targets-1.8.0/targets/R/tar_repository_cas_local.R |only targets-1.8.0/targets/R/tar_repository_cas_local_gc.R |only targets-1.8.0/targets/R/tar_resources.R | 4 targets-1.8.0/targets/R/tar_resources_aws.R | 7 targets-1.8.0/targets/R/tar_resources_gcp.R | 7 targets-1.8.0/targets/R/tar_resources_network.R | 5 targets-1.8.0/targets/R/tar_resources_repository_cas.R |only targets-1.8.0/targets/R/tar_script.R | 2 targets-1.8.0/targets/R/tar_seed.R | 6 targets-1.8.0/targets/R/tar_source.R | 4 targets-1.8.0/targets/R/tar_target.R | 126 +- targets-1.8.0/targets/R/tar_target_raw.R | 78 - targets-1.8.0/targets/R/tar_timestamp.R | 17 targets-1.8.0/targets/R/tar_timestamp_raw.R | 42 targets-1.8.0/targets/R/tar_traceback.R | 2 targets-1.8.0/targets/R/tar_visnetwork.R | 2 targets-1.8.0/targets/R/tar_watch.R | 70 - targets-1.8.0/targets/R/tar_watch_ui.R | 26 targets-1.8.0/targets/R/tar_workspace.R | 8 targets-1.8.0/targets/R/tar_workspaces.R | 2 targets-1.8.0/targets/R/utils_assert.R | 17 targets-1.8.0/targets/R/utils_callr.R | 88 + targets-1.8.0/targets/R/utils_cli.R | 21 targets-1.8.0/targets/R/utils_files.R | 76 + targets-1.8.0/targets/R/utils_imports.R | 2 targets-1.8.0/targets/R/utils_language.R | 10 targets-1.8.0/targets/R/utils_path.R | 8 targets-1.8.0/targets/R/utils_script.R |only targets-1.8.0/targets/R/utils_url.R | 15 targets-1.8.0/targets/inst/WORDLIST | 2 targets-1.8.0/targets/man/tar_active.Rd | 3 targets-1.8.0/targets/man/tar_backoff.Rd | 1 targets-1.8.0/targets/man/tar_branch_index.Rd | 3 targets-1.8.0/targets/man/tar_branch_names.Rd | 26 targets-1.8.0/targets/man/tar_branches.Rd | 30 targets-1.8.0/targets/man/tar_built.Rd | 2 targets-1.8.0/targets/man/tar_call.Rd | 3 targets-1.8.0/targets/man/tar_cancel.Rd | 1 targets-1.8.0/targets/man/tar_canceled.Rd | 2 targets-1.8.0/targets/man/tar_cas_d.Rd |only targets-1.8.0/targets/man/tar_cas_e.Rd |only targets-1.8.0/targets/man/tar_cas_u.Rd |only targets-1.8.0/targets/man/tar_completed.Rd | 2 targets-1.8.0/targets/man/tar_crew.Rd | 10 targets-1.8.0/targets/man/tar_cue.Rd | 4 targets-1.8.0/targets/man/tar_definition.Rd | 1 targets-1.8.0/targets/man/tar_delete.Rd | 2 targets-1.8.0/targets/man/tar_deps.Rd | 19 targets-1.8.0/targets/man/tar_described_as.Rd | 3 targets-1.8.0/targets/man/tar_destroy.Rd | 6 targets-1.8.0/targets/man/tar_dispatched.Rd | 2 targets-1.8.0/targets/man/tar_edit.Rd | 1 targets-1.8.0/targets/man/tar_envir.Rd | 1 targets-1.8.0/targets/man/tar_errored.Rd | 2 targets-1.8.0/targets/man/tar_format.Rd | 36 targets-1.8.0/targets/man/tar_format_get.Rd |only targets-1.8.0/targets/man/tar_github_actions.Rd | 1 targets-1.8.0/targets/man/tar_glimpse.Rd | 2 targets-1.8.0/targets/man/tar_group.Rd | 3 targets-1.8.0/targets/man/tar_helper.Rd | 22 targets-1.8.0/targets/man/tar_invalidate.Rd | 2 targets-1.8.0/targets/man/tar_load.Rd | 59 - 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targets-1.8.0/targets/tests/aws/test-deprecated.R | 2 targets-1.8.0/targets/tests/aws/test-utils_aws.R | 6 targets-1.8.0/targets/tests/gcp/test-class_gcp_file.R | 8 targets-1.8.0/targets/tests/gcp/test-utils_gcp.R | 6 targets-1.8.0/targets/tests/interactive/test-class_url.R | 2 targets-1.8.0/targets/tests/interactive/test-file.R | 18 targets-1.8.0/targets/tests/testthat/test-class_auto.R |only targets-1.8.0/targets/tests/testthat/test-class_aws.R | 22 targets-1.8.0/targets/tests/testthat/test-class_aws_file.R | 32 targets-1.8.0/targets/tests/testthat/test-class_build.R | 2 targets-1.8.0/targets/tests/testthat/test-class_builder.R | 108 + targets-1.8.0/targets/tests/testthat/test-class_command.R | 2 targets-1.8.0/targets/tests/testthat/test-class_cue.R | 21 targets-1.8.0/targets/tests/testthat/test-class_database.R | 5 targets-1.8.0/targets/tests/testthat/test-class_file.R | 29 targets-1.8.0/targets/tests/testthat/test-class_frames.R | 4 targets-1.8.0/targets/tests/testthat/test-class_fst.R | 18 targets-1.8.0/targets/tests/testthat/test-class_gcp.R | 18 targets-1.8.0/targets/tests/testthat/test-class_gcp_file.R | 28 targets-1.8.0/targets/tests/testthat/test-class_glimpse.R | 4 targets-1.8.0/targets/tests/testthat/test-class_group.R | 2 targets-1.8.0/targets/tests/testthat/test-class_imports.R | 2 targets-1.8.0/targets/tests/testthat/test-class_inspection.R | 10 targets-1.8.0/targets/tests/testthat/test-class_memory.R | 4 targets-1.8.0/targets/tests/testthat/test-class_meta.R | 8 targets-1.8.0/targets/tests/testthat/test-class_null.R |only targets-1.8.0/targets/tests/testthat/test-class_options.R | 56 targets-1.8.0/targets/tests/testthat/test-class_outdated.R | 6 targets-1.8.0/targets/tests/testthat/test-class_parallel.R | 2 targets-1.8.0/targets/tests/testthat/test-class_pattern.R | 22 targets-1.8.0/targets/tests/testthat/test-class_qs.R | 18 targets-1.8.0/targets/tests/testthat/test-class_rds.R | 16 targets-1.8.0/targets/tests/testthat/test-class_record.R | 2 targets-1.8.0/targets/tests/testthat/test-class_resources_repository_cas.R |only targets-1.8.0/targets/tests/testthat/test-class_stem.R | 16 targets-1.8.0/targets/tests/testthat/test-class_store_file.R | 16 targets-1.8.0/targets/tests/testthat/test-class_store_format_custom.R |only targets-1.8.0/targets/tests/testthat/test-class_target.R | 14 targets-1.8.0/targets/tests/testthat/test-class_torch.R | 2 targets-1.8.0/targets/tests/testthat/test-class_vector.R | 2 targets-1.8.0/targets/tests/testthat/test-tar_branches.R | 16 targets-1.8.0/targets/tests/testthat/test-tar_config_set.R | 32 targets-1.8.0/targets/tests/testthat/test-tar_deduplicate.R | 4 targets-1.8.0/targets/tests/testthat/test-tar_format.R | 76 - 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Title: Spatial Resampling Infrastructure
Description: Functions and classes for spatial resampling to use with the
'rsample' package, such as spatial cross-validation (Brenning, 2012)
<doi:10.1109/IGARSS.2012.6352393>. The scope of 'rsample' and
'spatialsample' is to provide the basic building blocks for creating
and analyzing resamples of a spatial data set, but neither package
includes functions for modeling or computing statistics. The resampled
spatial data sets created by 'spatialsample' do not contain much
overhead in memory.
Author: Michael Mahoney [aut, cre] ,
Julia Silge [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between spatialsample versions 0.5.1 dated 2023-11-07 and 0.6.0 dated 2024-10-02
DESCRIPTION | 8 - MD5 | 48 +++++----- NEWS.md | 5 + R/spatial_block_cv.R | 11 +- R/spatial_nndm_cv.R | 10 +- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/spatialsample.html | 14 +- man/figures/README-2022-06-12_boston-anim-.gif |binary man/figures/README-2022-06-12_boston_static-1.png |binary tests/testthat/_snaps/autoplot/block-split-plots.svg | 4 tests/testthat/_snaps/autoplot/buffered-llo-split-plot.svg | 4 tests/testthat/_snaps/autoplot/buffered-rsample-plot.svg | 10 +- tests/testthat/_snaps/autoplot/buffered-rset-plot.svg | 10 +- tests/testthat/_snaps/autoplot/buffered-vfold-plot.svg | 2 tests/testthat/_snaps/autoplot/buffered-vfold-split.svg | 10 +- tests/testthat/_snaps/autoplot/cluster-split-plots.svg | 4 tests/testthat/_snaps/autoplot/repeated-block-cv.svg | 2 tests/testthat/_snaps/autoplot/repeated-llo.svg | 4 tests/testthat/_snaps/autoplot/repeated-vfold.svg | 10 +- tests/testthat/_snaps/autoplot/snake-flips-rows-the-right-way.svg | 10 +- tests/testthat/test-autoplot.R | 1 tests/testthat/test-buffer.R | 3 tests/testthat/test-spatial_nndm_cv.R | 22 ++++ 25 files changed, 114 insertions(+), 80 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.
Author: Robert J. Hijmans [cre, aut] ,
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ct [...truncated...]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.6-26 dated 2023-10-14 and 3.6-30 dated 2024-10-02
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++---------- R/coerce.R | 3 ++ R/getData.R | 18 +++++++++----- R/netCDFwriteCD.R | 8 +++++- R/raster.R | 10 +++---- R/rasterFromGDAL.R | 8 ++++++ R/writeStartStop.R | 6 ++-- build/partial.rdb |binary man/extract.Rd | 2 - man/getData.Rd | 63 ++------------------------------------------------ man/hillShade.Rd | 11 -------- man/raster-package.Rd | 1 man/terrain.Rd | 18 -------------- 14 files changed, 58 insertions(+), 124 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre] ,
John Fox [aut] ,
Phil Chalmers [aut] ,
Georges Monette [ctb] ,
Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.9.8 dated 2024-07-25 and 1.0.0 dated 2024-10-02
matlib-0.9.8/matlib/vignettes/file75fc193c2d21.html |only matlib-0.9.8/matlib/vignettes/file75fc2d985765.html |only matlib-0.9.8/matlib/vignettes/file75fc37d71f65.html |only matlib-0.9.8/matlib/vignettes/file75fc68d870a4.html |only matlib-0.9.8/matlib/vignettes/file75fc756d1ecc.html |only matlib-0.9.8/matlib/vignettes/plotEqn1snapshot.png |only matlib-0.9.8/matlib/vignettes/webgl298c61ce23cc.html |only matlib-1.0.0/matlib/DESCRIPTION | 13 - matlib-1.0.0/matlib/MD5 | 149 ++++++----- matlib-1.0.0/matlib/NAMESPACE | 60 ++++ matlib-1.0.0/matlib/NEWS.md | 12 matlib-1.0.0/matlib/R/Eqn.R |only matlib-1.0.0/matlib/R/latexMatrix.R |only matlib-1.0.0/matlib/R/latexMatrixOperations.R |only matlib-1.0.0/matlib/R/matrix2latex.R | 36 ++ matlib-1.0.0/matlib/R/plotEqn.R | 2 matlib-1.0.0/matlib/R/rowops.R | 9 matlib-1.0.0/matlib/R/showEqn.R | 22 + matlib-1.0.0/matlib/R/util.R | 4 matlib-1.0.0/matlib/build/vignette.rds |binary matlib-1.0.0/matlib/inst/WORDLIST | 32 ++ matlib-1.0.0/matlib/inst/doc/data-beta.R | 2 matlib-1.0.0/matlib/inst/doc/data-beta.Rmd | 8 matlib-1.0.0/matlib/inst/doc/data-beta.html | 51 ++-- matlib-1.0.0/matlib/inst/doc/det-ex1.R | 6 matlib-1.0.0/matlib/inst/doc/det-ex1.Rmd | 9 matlib-1.0.0/matlib/inst/doc/det-ex1.html | 12 matlib-1.0.0/matlib/inst/doc/det-ex2.html | 6 matlib-1.0.0/matlib/inst/doc/eigen-ex1.R | 16 - matlib-1.0.0/matlib/inst/doc/eigen-ex1.Rmd | 24 - matlib-1.0.0/matlib/inst/doc/eigen-ex1.html | 20 - matlib-1.0.0/matlib/inst/doc/eigen-ex2.html | 6 matlib-1.0.0/matlib/inst/doc/ginv.R | 22 - matlib-1.0.0/matlib/inst/doc/ginv.Rmd | 22 - matlib-1.0.0/matlib/inst/doc/ginv.html | 6 matlib-1.0.0/matlib/inst/doc/gramreg.html | 42 +-- matlib-1.0.0/matlib/inst/doc/inv-3d.R |only matlib-1.0.0/matlib/inst/doc/inv-3d.Rmd |only matlib-1.0.0/matlib/inst/doc/inv-3d.html |only matlib-1.0.0/matlib/inst/doc/inv-ex1.html | 12 matlib-1.0.0/matlib/inst/doc/inv-ex2.R | 14 - matlib-1.0.0/matlib/inst/doc/inv-ex2.Rmd | 14 - matlib-1.0.0/matlib/inst/doc/inv-ex2.html | 46 +-- matlib-1.0.0/matlib/inst/doc/latex-equations.R |only matlib-1.0.0/matlib/inst/doc/latex-equations.Rmd |only matlib-1.0.0/matlib/inst/doc/latex-equations.html |only matlib-1.0.0/matlib/inst/doc/linear-equations.R | 40 ++- matlib-1.0.0/matlib/inst/doc/linear-equations.Rmd | 115 +++++++-- matlib-1.0.0/matlib/inst/doc/linear-equations.html | 242 +++++++++++-------- matlib-1.0.0/matlib/man/Eqn.Rd |only matlib-1.0.0/matlib/man/J.Rd | 70 ++--- matlib-1.0.0/matlib/man/LU.Rd | 124 ++++----- matlib-1.0.0/matlib/man/MoorePenrose.Rd | 72 ++--- matlib-1.0.0/matlib/man/QR.Rd | 98 +++---- matlib-1.0.0/matlib/man/R.Rd | 76 ++--- matlib-1.0.0/matlib/man/angle.Rd | 116 ++++----- matlib-1.0.0/matlib/man/buildTmat.Rd | 134 +++++----- matlib-1.0.0/matlib/man/cholesky.Rd | 76 ++--- matlib-1.0.0/matlib/man/circle.Rd | 144 +++++------ matlib-1.0.0/matlib/man/cone3d.Rd | 74 ++--- matlib-1.0.0/matlib/man/echelon.Rd | 118 ++++----- matlib-1.0.0/matlib/man/figures/symbMat-Lambda.png |only matlib-1.0.0/matlib/man/figures/symbMat-SVD.png |only matlib-1.0.0/matlib/man/figures/symbMat-x.png |only matlib-1.0.0/matlib/man/getYmult.Rd | 44 +-- matlib-1.0.0/matlib/man/gsorth.Rd | 76 ++--- matlib-1.0.0/matlib/man/latexMatrix.Rd |only matlib-1.0.0/matlib/man/latexMatrixOperations.Rd |only matlib-1.0.0/matlib/man/len.Rd | 56 ++-- matlib-1.0.0/matlib/man/matrix2latex.Rd | 15 + matlib-1.0.0/matlib/man/mpower.Rd | 76 ++--- matlib-1.0.0/matlib/man/plotEqn.Rd | 2 matlib-1.0.0/matlib/man/powerMethod.Rd | 142 +++++------ matlib-1.0.0/matlib/man/printMatrix.Rd | 4 matlib-1.0.0/matlib/man/rowadd.Rd | 9 matlib-1.0.0/matlib/man/showEqn.Rd | 15 - matlib-1.0.0/matlib/man/symMat.Rd | 70 ++--- matlib-1.0.0/matlib/man/xprod.Rd | 78 +++--- matlib-1.0.0/matlib/vignettes/CanvasMatrix.js | 2 matlib-1.0.0/matlib/vignettes/data-beta.Rmd | 8 matlib-1.0.0/matlib/vignettes/det-ex1.Rmd | 9 matlib-1.0.0/matlib/vignettes/eigen-ex1.Rmd | 24 - matlib-1.0.0/matlib/vignettes/ginv.Rmd | 22 - matlib-1.0.0/matlib/vignettes/inv-3d.Rmd |only matlib-1.0.0/matlib/vignettes/inv-ex2.Rmd | 14 - matlib-1.0.0/matlib/vignettes/latex-equations.Rmd |only matlib-1.0.0/matlib/vignettes/linear-equations.Rmd | 115 +++++++-- matlib-1.0.0/matlib/vignettes/references.bib |only 88 files changed, 1698 insertions(+), 1259 deletions(-)
Title: Pre-Compiled 'CmdStan' Models in R Packages
Description: Similar to 'rstantools' for 'rstan',
the 'instantiate' package builds pre-compiled
'CmdStan' models into CRAN-ready statistical modeling R packages.
The models compile once during installation,
the executables live inside the file systems of their respective packages,
and users have the full power and convenience of
'cmdstanr' without any additional compilation after package installation.
This approach saves time and helps R package developers
migrate from 'rstan' to the more modern 'cmdstanr'.
Packages 'rstantools', 'cmdstanr', 'stannis', and
'stanapi' are similar Stan clients with different objectives.
Author: William Michael Landau [aut, cre]
,
Eli Lilly and Company [cph, fnd]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Diff between instantiate versions 0.2.2 dated 2024-03-20 and 0.2.3 dated 2024-10-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/stan_package_model.R | 13 +++++++++++-- inst/configuration/install.libs.R | 4 +++- man/stan_package_model.Rd | 12 +++++++++++- 6 files changed, 39 insertions(+), 13 deletions(-)
Title: Graphs for Correspondence Analysis
Description: Readable, complete and pretty graphs for correspondence analysis made
with 'FactoMineR'. They can be rendered as interactive 'HTML' plots, showing useful
informations at mouse hover. The interest is not mainly visual but statistical:
it helps the reader to keep in mind the data contained in the cross-table or Burt
table while reading the correspondence analysis, thus preventing over-interpretation.
Most graphs are made with 'ggplot2', which means that you can use the + syntax to
manually add as many graphical pieces you want, or change theme elements. 3D
graphs are made with 'plotly'.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>
Diff between ggfacto versions 0.3.1 dated 2024-08-30 and 0.3.2 dated 2024-10-02
DESCRIPTION | 8 ++-- MD5 | 6 +-- NEWS.md | 78 ++++++++++++++++++++++-------------------- R/geometrical_data_analysis.R | 41 ++++++++++++++++------ 4 files changed, 80 insertions(+), 53 deletions(-)
More information about microinverterdata at CRAN
Permanent link
Title: Bayesian Adaptive Trial Simulator Software (BATSS) for
Generalised Linear Models
Description: Defines operating characteristics of Bayesian Adaptive Trials considering a generalised linear model response via Monte Carlo simulations of Bayesian GLM fitted via integrated Laplace approximations (INLA).
Author: Dominique-Laurent Couturier [aut, cre]
,
Liz Ryan [aut] ,
Rainer Puhr [aut],
Thomas Jaki [aut] ,
Stephane Heritier [aut]
Maintainer: Dominique-Laurent Couturier <dominique.couturier@mrc-bsu.cam.ac.uk>
Diff between BATSS versions 0.7.14 dated 2024-07-14 and 1.0.0 dated 2024-10-02
DESCRIPTION | 6 +- MD5 | 12 ++--- R/example_functions.R | 2 R/glm.R | 4 - R/glm_generic.R | 2 R/glm_internal.R | 18 ++++--- R/summary.batss.R | 116 +++++++++++++++++++++++++++++++++++++++++++------- 7 files changed, 124 insertions(+), 36 deletions(-)
Title: Clustering of Weighted Data
Description: Clusters state sequences and weighted data. It provides an optimized weighted PAM algorithm as well as functions for aggregating replicated cases, computing cluster quality measures for a range of clustering solutions and plotting (fuzzy) clusters of state sequences. Parametric bootstraps methods to validate typology of sequences are also provided. Finally, it provides a fuzzy and crisp CLARA algorithm to cluster large database with sequence analysis.
Author: Matthias Studer [aut, cre]
Maintainer: Matthias Studer <matthias.studer@unige.ch>
Diff between WeightedCluster versions 1.6-4 dated 2023-07-07 and 1.8-0 dated 2024-10-02
DESCRIPTION | 12 - MD5 | 70 +++++----- NAMESPACE | 145 +++++++++++---------- NEWS | 162 +++++++++++++----------- R/aggregatecases.R | 102 +++++++-------- R/as.seqtree.R | 240 ++++++++++++++++++------------------ R/bootclustrange.R |only R/clara_clustrange.R |only R/davies_bouldin.R |only R/plot.seqclararange.R |only R/seqnullcqi.R | 24 +-- R/wfcmdd.r |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 10 + inst/doc/WeightedCluster.pdf |binary inst/doc/WeightedClusterFR.pdf |binary inst/doc/WeightedClusterPreview.pdf |binary man/as.clustrange.Rd | 2 man/as.seqtree.Rd | 2 man/bootclustrange.Rd |only man/clustassoc.Rd | 4 man/fuzzyseqplot.Rd | 8 - man/kmedoids.Rd | 2 man/plot.seqclararange.Rd |only man/seqclararange.Rd |only man/seqclustname.Rd | 2 man/seqnull.Rd | 2 man/seqnullcqi.Rd | 15 +- man/seqpropclust.Rd | 18 +- man/wcAggregateCases.Rd | 2 man/wcCmpCluster.Rd | 4 man/wcSilhouetteObs.Rd | 2 src/PAM.cpp | 2 src/cluster.cpp | 6 src/cluster.h | 1 src/clusterquality.cpp | 68 +++++----- src/init.c | 1 src/kmedoidbase.cpp | 8 - src/kmedoidbasebody.cpp | 2 40 files changed, 482 insertions(+), 434 deletions(-)
More information about WeightedCluster at CRAN
Permanent link
Title: Efficiently Retrieve and Process Satellite Imagery
Description: Downloads spatial data from spatiotemporal asset catalogs
('STAC'), computes standard spectral indices from the Awesome Spectral
Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>)
against raster data, and glues the outputs together into predictor bricks.
Methods focus on interoperability with the broader spatial ecosystem;
function arguments and outputs use classes from 'sf' and 'terra', and data
downloading functions support complex 'CQL2' queries using 'rstac'.
Author: Michael Mahoney [aut, cre] ,
Felipe Carvalho [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/636>),
Michael Sumner [rev] for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/636>),
Permian Global [cph, f [...truncated...]
Maintainer: Michael Mahoney <mike.mahoney.218@gmail.com>
Diff between rsi versions 0.2.1 dated 2024-06-27 and 0.3.0 dated 2024-10-02
DESCRIPTION | 18 +- MD5 | 50 +++--- NAMESPACE | 2 NEWS.md | 19 ++ R/calculate_indices.R | 24 +++ R/download.R | 14 + R/get_stac_data.R | 224 +++++++++++-------------------- R/mask_functions.R | 87 ++++++++++-- R/misc.R | 38 +++++ R/query_and_sign.R | 27 +++ README.md | 108 +++++++++++++- build/partial.rdb |binary build/vignette.rds |binary man/alos_palsar_mask_function.Rd | 7 man/calculate_indices.Rd | 24 +++ man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |only man/get_stac_data.Rd | 130 +++++++++++------ man/landsat_mask_function.Rd | 47 ++++++ man/rsi-package.Rd | 2 man/rsi_download_rasters.Rd | 6 man/rsi_gdal_options.Rd |only man/rsi_query_api.Rd | 7 tests/testthat/test-mask_functions.R | 15 ++ tests/testthat/test-query_and_sign.R |only 28 files changed, 597 insertions(+), 252 deletions(-)
Title: Canonical Correlations and Tests of Independence
Description: A simple interface for multivariate correlation analysis that unifies various classical
statistical procedures including t-tests, tests in univariate and multivariate linear models,
parametric and nonparametric tests for correlation, Kruskal-Wallis tests, common approximate
versions of Wilcoxon rank-sum and signed rank tests, chi-squared tests of independence, score
tests of particular hypotheses in generalized linear models, canonical correlation analysis and
linear discriminant analysis.
Author: Robert Schlicht [aut, cre]
Maintainer: Robert Schlicht <robert.schlicht@tu-dresden.de>
Diff between cctest versions 1.0.0 dated 2024-08-27 and 1.1.0 dated 2024-10-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cctest.R | 5 +++-- man/cctest.Rd | 37 ++++++++++++++++++------------------- 4 files changed, 28 insertions(+), 28 deletions(-)
Title: Comparing Two Diagnostic Tests with Dichotomous Results using
Paired Data
Description: Provides a method for comparing the results of two binary diagnostic tests using paired data.
Users can rapidly perform descriptive and inferential statistics in a single function call. Options permit users to select which parameters they are interested in comparing and methods for correction for multiple comparisons.
Confidence intervals are calculated using the methods with the best coverage. Hypothesis tests use the methods with the best asymptotic performance. A summary of the methods is available in Roldán-Nofuentes (2020) <doi:10.1186/s12874-020-00988-y>.
This package is targeted at clinical researchers who want to rapidly and effectively compare results from binary diagnostic tests.
Author: Kyle J. Wilson [cre, aut] ,
Marc Henrion [aut] ,
Jose Antonio Roldan Nofuentes [aut]
Maintainer: Kyle J. Wilson <kyle.jordan.wilson@googlemail.com>
Diff between testCompareR versions 1.0.4 dated 2024-09-17 and 1.1.0 dated 2024-10-02
DESCRIPTION | 6 MD5 | 28 - NAMESPACE | 7 NEWS.md | 9 R/compareR.R | 18 R/compareR_internal.R | 140 +++++++ R/generics.R |only R/methods.R |only R/validatR.R |only inst/doc/using_testCompareR.R | 3 inst/doc/using_testCompareR.Rmd | 3 inst/doc/using_testCompareR.html | 719 +++++++++++++-------------------------- man/compareR.Rd | 14 man/plot.compareR.Rd |only man/print.compareR.Rd |only man/summary.compareR.Rd |only tests/testthat/test_compareR.R | 10 vignettes/using_testCompareR.Rmd | 3 18 files changed, 454 insertions(+), 506 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding / decoding. Hashes strings and raw vectors directly. Stream hashes
files potentially larger than memory, as well as in-memory objects through
R's serialization mechanism. Implementations include the SHA-256, SHA-3 and
'Keccak' cryptographic hash functions, SHAKE256 extendable-output function
(XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.2 dated 2024-09-09 and 1.0.3 dated 2024-10-02
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/base.R | 3 ++- R/secret.R | 38 ++++++++++++++++++++++---------------- README.md | 14 +++++++------- man/base64dec.Rd | 3 ++- man/keccak.Rd | 12 +++++++----- man/sha256.Rd | 20 +++++++++++--------- man/sha3.Rd | 12 +++++++----- man/shake256.Rd | 16 +++++++++------- man/siphash13.Rd | 14 ++++++++------ src/base.c | 21 +++++++++++---------- tests/tests.R | 30 ++++++++++++++++-------------- 14 files changed, 122 insertions(+), 97 deletions(-)
Title: Correct Mass Isotopologue Distribution Vectors
Description: In metabolic flux experiments tracer molecules (often glucose
containing labelled carbon) are incorporated in compounds measured
using mass spectrometry. The mass isotopologue distributions of these
compounds needs to be corrected for natural abundance of labelled
carbon and other effects, which are specific on the compound and
ionization technique applied. This package provides functions to
correct such effects in gas chromatography atmospheric pressure
chemical ionization mass spectrometry analyses.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between CorMID versions 0.1.9 dated 2023-08-10 and 0.2.1 dated 2024-10-02
CorMID-0.1.9/CorMID/R/calc_mid_error.R |only CorMID-0.1.9/CorMID/R/poss_local.R |only CorMID-0.1.9/CorMID/R/prep.R |only CorMID-0.1.9/CorMID/R/weight_errors.R |only CorMID-0.2.1/CorMID/DESCRIPTION | 15 CorMID-0.2.1/CorMID/MD5 | 48 +- CorMID-0.2.1/CorMID/NAMESPACE | 6 CorMID-0.2.1/CorMID/R/CalcTheoreticalMDV.R | 41 + CorMID-0.2.1/CorMID/R/CorMID.R | 262 +++++------ CorMID-0.2.1/CorMID/R/FitMID.R | 62 +- CorMID-0.2.1/CorMID/R/data.R |only CorMID-0.2.1/CorMID/R/getMID.R |only CorMID-0.2.1/CorMID/R/recMID.R | 7 CorMID-0.2.1/CorMID/R/utils.R |only CorMID-0.2.1/CorMID/README.md | 112 +++- CorMID-0.2.1/CorMID/build/vignette.rds |binary CorMID-0.2.1/CorMID/data/isotopes.rda |only CorMID-0.2.1/CorMID/data/precalc_idx.rda |only CorMID-0.2.1/CorMID/inst/doc/CorMID.R | 4 CorMID-0.2.1/CorMID/inst/doc/CorMID.html | 76 +-- CorMID-0.2.1/CorMID/man/CalcTheoreticalMDV.Rd | 14 CorMID-0.2.1/CorMID/man/CorMID.Rd | 87 ++- CorMID-0.2.1/CorMID/man/figures |only CorMID-0.2.1/CorMID/man/getMID.Rd |only CorMID-0.2.1/CorMID/man/isotopes.Rd |only CorMID-0.2.1/CorMID/man/precalc_idx.Rd |only CorMID-0.2.1/CorMID/man/prep.Rd | 2 CorMID-0.2.1/CorMID/man/recMID.Rd | 10 CorMID-0.2.1/CorMID/tests/testthat/test-CalcTheoreticalMDV.R | 2 CorMID-0.2.1/CorMID/tests/testthat/test-CorMID.R | 4 CorMID-0.2.1/CorMID/tests/testthat/test-recMID.R | 8 31 files changed, 435 insertions(+), 325 deletions(-)
More information about CompositionalRF at CRAN
Permanent link
Title: Multivariate Morphometric Analysis
Description: Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.
Author: Marek Slenker [aut, cre] ,
Petr Koutecky [ctb] ,
Karol Marhold [ctb]
Maintainer: Marek Slenker <marek.slenker@savba.sk>
Diff between MorphoTools2 versions 1.0.2.0 dated 2024-09-30 and 1.0.2.1 dated 2024-10-02
DESCRIPTION | 4 ++-- MD5 | 4 ++-- R/plot.biplot.R | 10 +++++----- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing
Parents
Description: Parentage assignment package.
Parentage assignment is performed based on observed average Mendelian transmission probability distributions or Exclusion.
The main functions of this package are the function APIS_2n(), APIS_3n() and launch_APIShiny(), which perform parentage assignment.
Author: Julien Roche [aut, cre],
Ronan Griot [aut],
Mathieu Besson [aut],
Francois Allal [aut],
Marc Vandeputte [aut],
Jonathan D'Ambrosio [aut],
Romain Morvezin [aut],
Florence Phocas [aut],
Sophie Brard-Fudulea [aut],
Pierrick Haffray [aut]
Maintainer: Julien Roche <julien.roche@inrae.fr>
Diff between APIS versions 2.0.4 dated 2023-11-30 and 2.0.7 dated 2024-10-02
DESCRIPTION | 12 MD5 | 18 R/App_APIS_Shiny.R | 3079 ++++++++++++++++++++++------------------------ R/functions_APIS_2n.R | 682 +++++----- R/functions_APIS_3n.R | 744 +++++------ R/functions_check.R | 358 ++--- data/APIS_dam.rda |binary data/APIS_offspring.rda |binary data/APIS_offspring3n.rda |binary data/APIS_sire.rda |binary 10 files changed, 2441 insertions(+), 2452 deletions(-)
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Samra Goumri [aut],
Zauad Shahreer Abeer [aut],
Eduard Szoecs [ctb]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.5.2 dated 2024-09-05 and 1.5.3 dated 2024-10-02
DESCRIPTION | 6 - MD5 | 24 +++---- NEWS.md | 5 + R/update-variables.R | 162 +++++++++++++++++++++++------------------------- inst/doc/datamods.R | 151 -------------------------------------------- inst/doc/datamods.Rmd | 22 +++--- inst/doc/datamods.html | 22 +++--- inst/doc/i18n.R | 29 -------- inst/doc/i18n.Rmd | 8 +- inst/doc/i18n.html | 30 ++++---- man/update-variables.Rd | 17 ++++- vignettes/datamods.Rmd | 22 +++--- vignettes/i18n.Rmd | 8 +- 13 files changed, 170 insertions(+), 336 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.9.3 dated 2024-07-29 and 0.9.8 dated 2024-10-02
cheapr-0.9.3/cheapr/R/cast.R |only cheapr-0.9.3/cheapr/src/altrep_utils.cpp |only cheapr-0.9.8/cheapr/DESCRIPTION | 8 cheapr-0.9.8/cheapr/MD5 | 98 +- cheapr-0.9.8/cheapr/NAMESPACE | 43 cheapr-0.9.8/cheapr/NEWS.md | 43 cheapr-0.9.8/cheapr/R/as_discrete.R |only cheapr-0.9.8/cheapr/R/bin.R |only cheapr-0.9.8/cheapr/R/comparison.R | 65 + cheapr-0.9.8/cheapr/R/cpp11.R | 76 + cheapr-0.9.8/cheapr/R/dots.R |only cheapr-0.9.8/cheapr/R/extras.R | 92 +- cheapr-0.9.8/cheapr/R/factors.R | 171 +++ cheapr-0.9.8/cheapr/R/gcd.R | 21 cheapr-0.9.8/cheapr/R/get_breaks.R |only cheapr-0.9.8/cheapr/R/int64.R |only cheapr-0.9.8/cheapr/R/lists.R | 3 cheapr-0.9.8/cheapr/R/nas.R | 36 cheapr-0.9.8/cheapr/R/new_df.R |only cheapr-0.9.8/cheapr/R/overview.R | 57 - cheapr-0.9.8/cheapr/R/scalars.R | 117 ++ cheapr-0.9.8/cheapr/R/sset.R | 2 cheapr-0.9.8/cheapr/R/utils.R | 64 - cheapr-0.9.8/cheapr/README.md | 313 ++----- cheapr-0.9.8/cheapr/man/as_discrete.Rd |only cheapr-0.9.8/cheapr/man/bin.Rd |only cheapr-0.9.8/cheapr/man/dots.Rd |only cheapr-0.9.8/cheapr/man/extras.Rd | 30 cheapr-0.9.8/cheapr/man/factors.Rd | 51 + cheapr-0.9.8/cheapr/man/figures |only cheapr-0.9.8/cheapr/man/gcd.Rd | 21 cheapr-0.9.8/cheapr/man/get_breaks.Rd |only cheapr-0.9.8/cheapr/man/lists.Rd | 3 cheapr-0.9.8/cheapr/man/new_df.Rd |only cheapr-0.9.8/cheapr/man/overview.Rd | 6 cheapr-0.9.8/cheapr/man/scalars.Rd | 91 +- cheapr-0.9.8/cheapr/src/altrep.cpp |only cheapr-0.9.8/cheapr/src/attrs.cpp | 58 - cheapr-0.9.8/cheapr/src/cheapr_cpp.h | 52 + cheapr-0.9.8/cheapr/src/comparison.cpp | 612 +++++++++++++ cheapr-0.9.8/cheapr/src/cpp11.cpp | 263 +++-- cheapr-0.9.8/cheapr/src/gcd.cpp | 302 ++++-- cheapr-0.9.8/cheapr/src/int64.cpp |only cheapr-0.9.8/cheapr/src/lag.cpp | 498 +++++------ cheapr-0.9.8/cheapr/src/lists.cpp | 167 +-- cheapr-0.9.8/cheapr/src/nas.cpp | 923 +++++++++------------ cheapr-0.9.8/cheapr/src/scalars.cpp | 282 ++++-- cheapr-0.9.8/cheapr/src/set_math.cpp | 193 ++-- cheapr-0.9.8/cheapr/src/sset.cpp | 3 cheapr-0.9.8/cheapr/src/utils.cpp | 193 ++++ cheapr-0.9.8/cheapr/src/which.cpp | 429 ++++++++- cheapr-0.9.8/cheapr/tests/testthat/test-factors.R | 6 cheapr-0.9.8/cheapr/tests/testthat/test-gcd.R | 10 cheapr-0.9.8/cheapr/tests/testthat/test-lag.R | 30 cheapr-0.9.8/cheapr/tests/testthat/test-nas.R | 26 cheapr-0.9.8/cheapr/tests/testthat/test-set_math.R | 56 + cheapr-0.9.8/cheapr/tests/testthat/test-sset.R | 3 cheapr-0.9.8/cheapr/tests/testthat/test-which.R | 2 58 files changed, 3759 insertions(+), 1760 deletions(-)
Title: Unbiased Central Moment Estimates
Description: Calculates one-sample unbiased central moment estimates and
two-sample pooled estimates up to 6th order, including estimates of
powers and products of central moments. Provides the machinery for
obtaining unbiased central moment estimators beyond 6th order by generating
expressions for expectations of raw sample moments and their powers and
products.
Gerlovina and Hubbard (2019) <doi:10.1080/25742558.2019.1701917>.
Author: Inna Gerlovina [aut, cre],
Alan Hubbard [aut]
Maintainer: Inna Gerlovina <innager@berkeley.edu>
Diff between Umoments versions 0.1.1 dated 2020-02-12 and 1.0.1 dated 2024-10-02
DESCRIPTION | 11 ++++------ MD5 | 48 +++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/vignetteUmom.R | 1 inst/doc/vignetteUmom.pdf |binary man/uM2.Rd | 15 +++++++++----- man/uM2M3.Rd | 15 +++++++++----- man/uM2M3pool.Rd | 15 +++++++++----- man/uM2M4.Rd | 15 +++++++++----- man/uM2M4pool.Rd | 15 +++++++++----- man/uM2pool.Rd | 15 +++++++++----- man/uM2pow2.Rd | 15 +++++++++----- man/uM2pow2pool.Rd | 15 +++++++++----- man/uM2pow3.Rd | 15 +++++++++----- man/uM2pow3pool.Rd | 15 +++++++++----- man/uM3.Rd | 15 +++++++++----- man/uM3pool.Rd | 15 +++++++++----- man/uM3pow2.Rd | 15 +++++++++----- man/uM3pow2pool.Rd | 15 +++++++++----- man/uM4.Rd | 15 +++++++++----- man/uM4pool.Rd | 15 +++++++++----- man/uM5.Rd | 15 +++++++++----- man/uM5pool.Rd | 15 +++++++++----- man/uM6.Rd | 15 +++++++++----- man/uM6pool.Rd | 15 +++++++++----- 25 files changed, 229 insertions(+), 131 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ,
David Fletcher [ctb] ,
Yan Ru Choo [ctb]
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.6.10 dated 2024-08-22 and 5.0.0 dated 2024-10-02
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secr-5.0.0/secr/man/AICcompatible.Rd | 1 secr-5.0.0/secr/man/CV.Rd | 1 secr-5.0.0/secr/man/D.designdata.Rd | 1 secr-5.0.0/secr/man/DA.Rd | 1 secr-5.0.0/secr/man/DENSITY.Rd | 1 secr-5.0.0/secr/man/Dsurface.Rd | 1 secr-5.0.0/secr/man/FAQ.Rd | 1 secr-5.0.0/secr/man/LLsurface.Rd | 1 secr-5.0.0/secr/man/LRtest.Rd | 1 secr-5.0.0/secr/man/MCgof.Rd |only secr-5.0.0/secr/man/MCgof.methods.Rd |only secr-5.0.0/secr/man/OVpossum.Rd | 1 secr-5.0.0/secr/man/PG.Rd | 13 secr-5.0.0/secr/man/Parallel.Rd | 7 secr-5.0.0/secr/man/RMarkInput.Rd | 1 secr-5.0.0/secr/man/RSE.Rd | 1 secr-5.0.0/secr/man/Rsurface.Rd | 1 secr-5.0.0/secr/man/addCovariates.Rd | 1 secr-5.0.0/secr/man/addSightings.Rd | 1 secr-5.0.0/secr/man/addTelemetry.Rd | 1 secr-5.0.0/secr/man/as.data.frame.Rd | 1 secr-5.0.0/secr/man/as.mask.Rd | 1 secr-5.0.0/secr/man/as.popn.Rd | 1 secr-5.0.0/secr/man/autoini.Rd | 1 secr-5.0.0/secr/man/blackbear.Rd |only secr-5.0.0/secr/man/capthist.Rd | 1 secr-5.0.0/secr/man/capthistfn.Rd | 1 secr-5.0.0/secr/man/chat.Rd | 1 secr-5.0.0/secr/man/circular.Rd | 1 secr-5.0.0/secr/man/clone.Rd | 1 secr-5.0.0/secr/man/closedN.Rd | 2 secr-5.0.0/secr/man/closure.Rd | 1 secr-5.0.0/secr/man/cluster.Rd | 1 secr-5.0.0/secr/man/coef.secr.Rd | 5 secr-5.0.0/secr/man/confint.secr.Rd | 1 secr-5.0.0/secr/man/contour.Rd | 44 +- secr-5.0.0/secr/man/coulombe.Rd | 1 secr-5.0.0/secr/man/covariates.Rd | 1 secr-5.0.0/secr/man/deermouse.Rd | 1 secr-5.0.0/secr/man/deletemaskpoints.Rd | 1 secr-5.0.0/secr/man/derivedMS.Rd | 15 secr-5.0.0/secr/man/details.Rd | 2 secr-5.0.0/secr/man/detectfn.Rd | 6 secr-5.0.0/secr/man/detector.Rd | 1 secr-5.0.0/secr/man/deviance.secr.Rd | 1 secr-5.0.0/secr/man/discretize.Rd | 1 secr-5.0.0/secr/man/distancetotrap.Rd | 1 secr-5.0.0/secr/man/ellipse.secr.Rd | 1 secr-5.0.0/secr/man/empirical.Rd | 28 - secr-5.0.0/secr/man/esaPlot.Rd |only secr-5.0.0/secr/man/expected.n.Rd | 1 secr-5.0.0/secr/man/fxTotal.Rd |only secr-5.0.0/secr/man/fxi.Rd | 79 ++-- secr-5.0.0/secr/man/hcov.Rd | 1 secr-5.0.0/secr/man/head.Rd | 1 secr-5.0.0/secr/man/homerange.Rd | 3 secr-5.0.0/secr/man/hornedlizard.Rd | 1 secr-5.0.0/secr/man/join.Rd | 1 secr-5.0.0/secr/man/list.secr.fit.Rd | 5 secr-5.0.0/secr/man/logit.Rd | 1 secr-5.0.0/secr/man/logmultinom.Rd | 1 secr-5.0.0/secr/man/make.capthist.Rd | 1 secr-5.0.0/secr/man/make.lacework.Rd | 1 secr-5.0.0/secr/man/make.mask.Rd | 5 secr-5.0.0/secr/man/make.systematic.Rd | 1 secr-5.0.0/secr/man/make.traps.Rd | 1 secr-5.0.0/secr/man/make.tri.Rd | 1 secr-5.0.0/secr/man/makeNewData.Rd |only secr-5.0.0/secr/man/manip.Rd | 1 secr-5.0.0/secr/man/mask.Rd | 5 secr-5.0.0/secr/man/mask.check.Rd | 3 secr-5.0.0/secr/man/modelAverage.Rd | 6 secr-5.0.0/secr/man/ms.Rd | 1 secr-5.0.0/secr/man/occasionKey.Rd | 1 secr-5.0.0/secr/man/ovenbird.Rd | 2 secr-5.0.0/secr/man/ovensong.Rd | 1 secr-5.0.0/secr/man/pdot.Rd | 8 secr-5.0.0/secr/man/plot.capthist.Rd | 1 secr-5.0.0/secr/man/plot.mask.Rd | 1 secr-5.0.0/secr/man/plot.popn.Rd | 1 secr-5.0.0/secr/man/plot.secr.Rd | 1 secr-5.0.0/secr/man/plot.traps.Rd | 1 secr-5.0.0/secr/man/plotmaskedge.Rd | 1 secr-5.0.0/secr/man/pmixProfileLL.Rd | 1 secr-5.0.0/secr/man/pointsInPolygon.Rd | 1 secr-5.0.0/secr/man/polyarea.Rd | 3 secr-5.0.0/secr/man/popn.Rd | 1 secr-5.0.0/secr/man/possum.Rd | 1 secr-5.0.0/secr/man/predict.secr.Rd | 6 secr-5.0.0/secr/man/predictDsurface.Rd | 1 secr-5.0.0/secr/man/print.capthist.Rd | 1 secr-5.0.0/secr/man/print.secr.Rd | 1 secr-5.0.0/secr/man/print.traps.Rd | 1 secr-5.0.0/secr/man/randomHabitat.Rd | 1 secr-5.0.0/secr/man/raster2.Rd | 21 - secr-5.0.0/secr/man/rbind.capthist.Rd | 1 secr-5.0.0/secr/man/rbind.popn.Rd | 1 secr-5.0.0/secr/man/rbind.traps.Rd | 1 secr-5.0.0/secr/man/read.mask.Rd | 1 secr-5.0.0/secr/man/read.telemetry.Rd | 1 secr-5.0.0/secr/man/read.traps.Rd | 1 secr-5.0.0/secr/man/rectangularMask.Rd | 1 secr-5.0.0/secr/man/reduce.Rd | 1 secr-5.0.0/secr/man/reduce.capthist.Rd | 1 secr-5.0.0/secr/man/region.N.Rd | 1 secr-5.0.0/secr/man/score.test.Rd | 11 secr-5.0.0/secr/man/secr-defunct.Rd | 11 secr-5.0.0/secr/man/secr-deprecated.Rd | 76 ++-- secr-5.0.0/secr/man/secr-internal.Rd | 4 secr-5.0.0/secr/man/secr-package.Rd | 6 secr-5.0.0/secr/man/secr-version5.Rd |only secr-5.0.0/secr/man/secr.design.MS.Rd | 1 secr-5.0.0/secr/man/secr.fit.Rd | 3 secr-5.0.0/secr/man/secr.test.Rd | 12 secr-5.0.0/secr/man/secrRNG.Rd | 1 secr-5.0.0/secr/man/secrdemo.Rd | 1 secr-5.0.0/secr/man/secrtest.Rd | 1 secr-5.0.0/secr/man/session.Rd | 1 secr-5.0.0/secr/man/sharefactorlevels.Rd | 1 secr-5.0.0/secr/man/sighting.Rd | 1 secr-5.0.0/secr/man/signal.Rd | 1 secr-5.0.0/secr/man/signalmatrix.Rd | 1 secr-5.0.0/secr/man/sim.capthist.Rd | 1 secr-5.0.0/secr/man/sim.popn.Rd | 3 secr-5.0.0/secr/man/sim.secr.Rd | 3 secr-5.0.0/secr/man/skink.Rd | 1 secr-5.0.0/secr/man/smooths.Rd | 1 secr-5.0.0/secr/man/snip.Rd | 1 secr-5.0.0/secr/man/sort.Rd | 1 secr-5.0.0/secr/man/spacing.Rd | 1 secr-5.0.0/secr/man/speed.Rd | 1 secr-5.0.0/secr/man/stoatDNA.Rd | 1 secr-5.0.0/secr/man/strip.legend.Rd | 1 secr-5.0.0/secr/man/subset.capthist.Rd | 1 secr-5.0.0/secr/man/subset.mask.Rd | 1 secr-5.0.0/secr/man/subset.popn.Rd | 1 secr-5.0.0/secr/man/subset.traps.Rd | 1 secr-5.0.0/secr/man/suggest.buffer.Rd | 5 secr-5.0.0/secr/man/summary.capthist.Rd | 1 secr-5.0.0/secr/man/summary.mask.Rd | 1 secr-5.0.0/secr/man/summary.popn.Rd | 1 secr-5.0.0/secr/man/summary.traps.Rd | 1 secr-5.0.0/secr/man/timevaryingcov.Rd | 1 secr-5.0.0/secr/man/transformations.Rd | 1 secr-5.0.0/secr/man/trap.builder.Rd | 1 secr-5.0.0/secr/man/traps.Rd | 1 secr-5.0.0/secr/man/trapsfn.Rd | 1 secr-5.0.0/secr/man/trend.Rd | 1 secr-5.0.0/secr/man/trim.Rd | 1 secr-5.0.0/secr/man/troubleshooting.Rd | 1 secr-5.0.0/secr/man/turnover.Rd | 1 secr-5.0.0/secr/man/updateCH.Rd | 1 secr-5.0.0/secr/man/usage.Rd | 11 secr-5.0.0/secr/man/usagePlot.Rd | 1 secr-5.0.0/secr/man/userdist.Rd | 1 secr-5.0.0/secr/man/utility.Rd | 4 secr-5.0.0/secr/man/vcov.secr.Rd | 1 secr-5.0.0/secr/man/verify.Rd | 1 secr-5.0.0/secr/man/write.Rd | 1 secr-5.0.0/secr/man/writeGPS.Rd | 9 secr-5.0.0/secr/src/RcppExports.cpp | 133 +++---- secr-5.0.0/secr/src/autils.cpp | 466 ------------------------ secr-5.0.0/secr/src/detectfn.cpp | 432 ++++++++++------------ secr-5.0.0/secr/src/getdenom.cpp | 1 secr-5.0.0/secr/src/geth.cpp | 4 secr-5.0.0/secr/src/hdot.cpp |only secr-5.0.0/secr/src/integral1D.cpp |only secr-5.0.0/secr/src/integral2D.cpp |only secr-5.0.0/secr/src/makegk.cpp | 269 ++++++-------- secr-5.0.0/secr/src/makegkpoly.cpp | 10 secr-5.0.0/secr/src/makelookup.cpp | 1 secr-5.0.0/secr/src/nkpoint.cpp | 4 secr-5.0.0/secr/src/pdot.cpp | 156 +------- secr-5.0.0/secr/src/poly.h | 84 ++-- secr-5.0.0/secr/src/polygonNR.cpp |only secr-5.0.0/secr/src/prwifastproximity.cpp | 2 secr-5.0.0/secr/src/prwipolygonfxi.cpp | 2 secr-5.0.0/secr/src/prwisignal.cpp | 414 ++++++++++----------- secr-5.0.0/secr/src/prwisimple.cpp | 2 secr-5.0.0/secr/src/prwisimplefxi.cpp | 2 secr-5.0.0/secr/src/secr.h | 69 --- secr-5.0.0/secr/src/sighting.cpp | 1 secr-5.0.0/secr/src/sightingchat.cpp | 5 secr-5.0.0/secr/src/sightingexpectedmusk.cpp | 1 secr-5.0.0/secr/src/simsecr.cpp | 41 +- secr-5.0.0/secr/src/transectutils.cpp |only secr-5.0.0/secr/src/trapping.cpp | 49 -- secr-5.0.0/secr/tests/testthat/test-MCgof.R |only secr-5.0.0/secr/tests/testthat/test-derived.R | 2 secr-5.0.0/secr/vignettes/secr-overview.Rmd | 38 +- 261 files changed, 2184 insertions(+), 2895 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [aut, ctb]
,
Etienne Bacher [aut, ctb] ,
Ale [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between insight versions 0.20.4 dated 2024-09-01 and 0.20.5 dated 2024-10-02
DESCRIPTION | 35 - MD5 | 102 ++-- NAMESPACE | 5 NEWS.md | 16 R/compute_variances.R | 43 +- R/display.R | 4 R/export_table.R | 8 R/find_formula.R | 19 R/find_parameters_mixed.R | 5 R/format_table.R | 2 R/get_datagrid.R | 577 ++++++++++++++-------------- R/get_loglikelihood.R | 2 R/get_parameters_bayesian.R | 10 R/get_parameters_mixed.R | 12 R/get_residuals.R | 8 R/get_varcov_sandwich.R | 26 - R/get_variances.R | 3 R/get_weights.R | 32 + R/helper_functions.R | 16 R/print_parameters.R | 10 R/utilities.R | 39 + R/utils_model_info.R | 4 inst/doc/display.html | 220 +++++----- man/display.Rd | 4 man/export_table.Rd | 3 man/find_parameters.glmmTMB.Rd | 2 man/format_table.Rd | 2 man/get_datagrid.Rd | 18 man/get_variance.Rd | 3 man/get_weights.Rd | 6 man/print_parameters.Rd | 5 man/trim_ws.Rd | 8 tests/testthat/test-cgam.R | 1 tests/testthat/test-cpglmm.R | 10 tests/testthat/test-emmeans.R | 25 - tests/testthat/test-fixest.R | 1 tests/testthat/test-get_data.R | 1 tests/testthat/test-get_datagrid.R | 106 ++++- tests/testthat/test-get_predicted.R | 16 tests/testthat/test-get_variance.R | 1 tests/testthat/test-glmmTMB.R | 72 +++ tests/testthat/test-htest.R | 1 tests/testthat/test-is_converged.R | 2 tests/testthat/test-mlogit.R | 2 tests/testthat/test-mmrm.R | 1 tests/testthat/test-model_data.R | 2 tests/testthat/test-model_info.R | 1 tests/testthat/test-null_model.R | 3 tests/testthat/test-r2_nakagawa_negbin_zi.R | 16 tests/testthat/test-r2_nakagawa_tweedie.R | 12 tests/testthat/test-spatial.R | 10 tests/testthat/test-utilities.R | 4 52 files changed, 861 insertions(+), 675 deletions(-)
Title: Comparative 'Phylogenetic' Analyses of Diversification
Description: Contains a number of comparative 'phylogenetic' methods,
mostly focusing on analysing diversification and character
evolution. Contains implementations of 'BiSSE' (Binary State
'Speciation' and Extinction) and its unresolved tree extensions,
'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE',
'GeoSSE', and 'BiSSE-ness' Other included methods include Markov
models of discrete and continuous trait evolution and constant rate
'speciation' and extinction.
Author: Richard G. FitzJohn [aut, cre],
Emma Goldberg [aut],
Karen Magnuson-Ford [aut],
Roger Sidje [aut]
Maintainer: Richard G. FitzJohn <rich.fitzjohn@gmail.com>
Diff between diversitree versions 0.10-0 dated 2023-12-20 and 0.10-1 dated 2024-10-02
DESCRIPTION | 6 ++-- MD5 | 32 ++++++++++++------------- build/partial.rdb |binary man/find.mle.Rd | 28 ++++++++++----------- man/make.mkn.Rd | 2 - src/GslOdeR.cpp | 2 - src/TimeMachine.cpp | 8 +++--- src/asr-joint.c | 7 +---- src/continuous.c | 64 +++++++++++++++++++++++++------------------------- src/hdr.c | 3 +- src/mkn-pij.c | 20 +++++++-------- src/quasse-eqs-fftC.c | 26 ++++++++++---------- src/rfftw.c | 8 +++--- src/scm-mkn.c | 62 ++++++++++++++++++++++++------------------------ src/simulate-bisse.c | 24 +++++++++--------- src/util-splines.c | 28 ++++++++++----------- src/util.c | 38 ++++++++++++++--------------- 17 files changed, 178 insertions(+), 180 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format, METAL
Format and BGEN Format) into R
Description: Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.
Author: Xiaowei Zhan [aut, cre],
Dajiang Liu [aut],
Attractive Chaos [cph] . We removed standard IO related functions, e.g. printf,
fprintf ; also changed its un-safe pointer arithmetics.),
Broad Institute / Massachusetts Institute of Technology [cph],
Genom [...truncated...]
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 9.4 dated 2024-02-03 and 9.7 dated 2024-10-02
seqminer-9.4/seqminer/src/htslib-1.16.tar.bz2 |only seqminer-9.7/seqminer/ChangeLog | 12 seqminer-9.7/seqminer/DESCRIPTION | 8 seqminer-9.7/seqminer/MD5 | 35 seqminer-9.7/seqminer/README.md | 2 seqminer-9.7/seqminer/src/BGenIndex.h | 4 seqminer-9.7/seqminer/src/Makevars.in | 8 seqminer-9.7/seqminer/src/R_CPP_interface.cpp | 84 seqminer-9.7/seqminer/src/Rannotation.cpp | 4 seqminer-9.7/seqminer/src/bgen2genoLoader.cpp | 46 seqminer-9.7/seqminer/src/plink2genoLoader.cpp | 4 seqminer-9.7/seqminer/src/rvMetaLoader.cpp | 74 seqminer-9.7/seqminer/src/scbcf2genoLoader.cpp | 4 seqminer-9.7/seqminer/src/scvcf2genoLoader.cpp | 6 seqminer-9.7/seqminer/src/sqlite/shell.c |19272 ++++ seqminer-9.7/seqminer/src/sqlite/sqlite3.c |104339 +++++++++++++++++-------- seqminer-9.7/seqminer/src/sqlite/sqlite3.h | 4082 seqminer-9.7/seqminer/src/sqlite/sqlite3ext.h | 96 seqminer-9.7/seqminer/src/vcf2genoLoader.cpp | 44 19 files changed, 91670 insertions(+), 36454 deletions(-)
Title: 'SAS' Linear Model
Description: This is a core implementation of 'SAS' procedures for linear models - GLM, REG, ANOVA, TTEST, FREQ, and UNIVARIATE. Some R packages provide type II and type III SS. However, the results of nested and complex designs are often different from those of 'SAS.' Different results does not necessarily mean incorrectness. However, many wants the same results to SAS. This package aims to achieve that.
Reference: Littell RC, Stroup WW, Freund RJ (2002, ISBN:0-471-22174-0).
Author: Kyun-Seop Bae [aut, cre]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between sasLM versions 0.10.4 dated 2024-05-31 and 0.10.5 dated 2024-10-02
sasLM-0.10.4/sasLM/inst/doc/Report-Different-Simplest2406011131.pdf |only sasLM-0.10.4/sasLM/inst/doc/Report-NOT-OKs2406011132.pdf |only sasLM-0.10.4/sasLM/inst/doc/Validation-Report-GLM-2406011134.pdf |only sasLM-0.10.5/sasLM/DESCRIPTION | 9 ++++--- sasLM-0.10.5/sasLM/MD5 | 12 +++++----- sasLM-0.10.5/sasLM/R/RDmn1.R | 7 +++-- sasLM-0.10.5/sasLM/inst/NEWS.Rd | 6 +++++ sasLM-0.10.5/sasLM/inst/doc/Report-Different-Simplest2410021412.pdf |only sasLM-0.10.5/sasLM/inst/doc/Report-NOT-OKs2410021413.pdf |only sasLM-0.10.5/sasLM/inst/doc/Validation-Report-GLM-2410021413.pdf |only 10 files changed, 21 insertions(+), 13 deletions(-)
Title: Random Forests for Dependent Data
Description: Fits non-linear regression models on dependant data with Generalised Least Square (GLS) based Random Forest (RF-GLS) detailed in Saha, Basu and Datta (2021) <doi:10.1080/01621459.2021.1950003>.
Author: Arkajyoti Saha [aut, cre],
Sumanta Basu [aut],
Abhirup Datta [aut]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between RandomForestsGLS versions 0.1.4 dated 2022-04-28 and 0.1.5 dated 2024-10-02
DESCRIPTION | 8 +- MD5 | 16 ++--- build/vignette.rds |binary inst/doc/RandomForestsGLS_user_guide.pdf |binary src/Makevars | 4 + src/RFGLS.cpp | 90 ++++++++++++++++--------------- src/packagename_init.c | 4 + src/util.cpp | 8 ++ src/util.h | 4 + 9 files changed, 77 insertions(+), 57 deletions(-)
More information about RandomForestsGLS at CRAN
Permanent link
Title: Methods for Fitting Network Time Series Models
Description: Simulation of, and fitting models for, Generalised Network Autoregressive (GNAR) time series models which take account of network structure, potentially with exogenous variables. Such models are described in Knight et al. (2020) <doi:10.18637/jss.v096.i05> and Nason and Wei (2021) <doi:10.1111/rssa.12875>. Diagnostic tools for GNAR(X) models can be found in Nason et al. (2023) <doi:10.48550/arXiv.2312.00530>.
Author: Kathryn Leeming [aut],
Guy Nason [aut],
Matt Nunes [aut, cre],
Marina Knight [ctb],
James Wei [aut],
Daniel Salnikov [aut],
Mario Cortina Borja [ctb]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
Diff between GNAR versions 1.1.3 dated 2023-12-18 and 1.1.4 dated 2024-10-02
GNAR-1.1.3/GNAR/man/wagner_plot.Rd |only GNAR-1.1.4/GNAR/DESCRIPTION | 10 +- GNAR-1.1.4/GNAR/MD5 | 36 +++++---- GNAR-1.1.4/GNAR/NAMESPACE | 7 + GNAR-1.1.4/GNAR/R/corbit_plot_edit.r |only GNAR-1.1.4/GNAR/R/corrbit.R | 91 ++++++------------------- GNAR-1.1.4/GNAR/R/global_gnar_fitting.R |only GNAR-1.1.4/GNAR/R/nacf_dummy_models.R | 4 - GNAR-1.1.4/GNAR/R/nacf_pnacf_edited.r |only GNAR-1.1.4/GNAR/R/nacf_r.R | 4 - GNAR-1.1.4/GNAR/R/plot_corbit_line_segment.r |only GNAR-1.1.4/GNAR/R/rectangular_corbit_plot.r |only GNAR-1.1.4/GNAR/R/weight_adjustment_methods.R |only GNAR-1.1.4/GNAR/data/NHSTrustMVCAug120.net.rda |binary GNAR-1.1.4/GNAR/data/fiveNode.rda |binary GNAR-1.1.4/GNAR/data/gdp.rda |binary GNAR-1.1.4/GNAR/data/logMVbedMVC.vts.rda |binary GNAR-1.1.4/GNAR/data/vswind.rda |binary GNAR-1.1.4/GNAR/inst/CHANGES | 2 GNAR-1.1.4/GNAR/man/NHSTrustMVCAug120.net.Rd | 5 - GNAR-1.1.4/GNAR/man/corbit_plot.Rd | 37 ++++------ GNAR-1.1.4/GNAR/man/logMVbedMVC.vts.Rd | 2 GNAR-1.1.4/GNAR/man/r_corbit_plot.Rd |only 23 files changed, 83 insertions(+), 115 deletions(-)
Title: Data Sets for Psychometric Modeling
Description: Collection of data sets from various assessments that can be used to
evaluate psychometric models. These data sets have been analyzed in the
following papers that introduced new methodology as part of the application section:
Jimenez, A., Balamuta, J. J., & Culpepper, S. A. (2023) <doi:10.1111/bmsp.12307>,
Culpepper, S. A., & Balamuta, J. J. (2021) <doi:10.1080/00273171.2021.1985949>,
Yinghan Chen et al. (2021) <doi:10.1007/s11336-021-09750-9>,
Yinyin Chen et al. (2020) <doi:10.1007/s11336-019-09693-2>,
Culpepper, S. A. (2019a) <doi:10.1007/s11336-019-09683-4>,
Culpepper, S. A. (2019b) <doi:10.1007/s11336-018-9643-8>,
Culpepper, S. A., & Chen, Y. (2019) <doi:10.3102/1076998618791306>,
Culpepper, S. A., & Balamuta, J. J. (2017) <doi:10.1007/s11336-015-9484-7>,
and Culpepper, S. A. (2015) <doi:10.3102/1076998615595403>.
Author: James Joseph Balamuta [aut, cre, cph]
,
Steven Andrew Culpepper [aut, cph]
,
Jeffrey Alan Douglas [aut, cph],
Auburn Jimenez [ctb, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between edmdata versions 1.2.0 dated 2021-07-25 and 1.3.0 dated 2024-10-02
edmdata-1.2.0/edmdata/data/items_probability_part_one.rda |only edmdata-1.2.0/edmdata/man/items_probability_part_one.Rd |only edmdata-1.3.0/edmdata/DESCRIPTION | 21 edmdata-1.3.0/edmdata/MD5 | 39 + edmdata-1.3.0/edmdata/NEWS.md | 28 + edmdata-1.3.0/edmdata/R/hcp-penn-matrix.R |only edmdata-1.3.0/edmdata/R/ordered-pswc-data.R |only edmdata-1.3.0/edmdata/R/pisa12-us-math.R |only edmdata-1.3.0/edmdata/R/pisa12-us-vignette-data.R |only edmdata-1.3.0/edmdata/R/probability-data.R | 40 + edmdata-1.3.0/edmdata/R/timss15-background-data.R |only edmdata-1.3.0/edmdata/README.md | 214 ++++++---- edmdata-1.3.0/edmdata/build/partial.rdb |binary edmdata-1.3.0/edmdata/data/items_hcp_penn_matrix.rda |only edmdata-1.3.0/edmdata/data/items_hcp_penn_matrix_missing.rda |only edmdata-1.3.0/edmdata/data/items_ordered_pisa12_us_vignette.rda |only edmdata-1.3.0/edmdata/data/items_ordered_pswc_hw.rda |only edmdata-1.3.0/edmdata/data/items_ordered_timss15_background.rda |only edmdata-1.3.0/edmdata/data/items_pisa12_us_math.rda |only edmdata-1.3.0/edmdata/data/items_probability_part_one_full.rda |only edmdata-1.3.0/edmdata/data/items_probability_part_one_reduced.rda |only edmdata-1.3.0/edmdata/data/qmatrix_probability_part_one.rda |binary edmdata-1.3.0/edmdata/man/edmdata-package.Rd | 16 edmdata-1.3.0/edmdata/man/items-hcp-penn.Rd |only edmdata-1.3.0/edmdata/man/items-probability.Rd |only edmdata-1.3.0/edmdata/man/items_ordered_eclsk_atl.Rd | 2 edmdata-1.3.0/edmdata/man/items_ordered_pisa12_us_vignette.Rd |only edmdata-1.3.0/edmdata/man/items_ordered_pswc_hw.Rd |only edmdata-1.3.0/edmdata/man/items_ordered_timss15_background.Rd |only edmdata-1.3.0/edmdata/man/items_pisa12_us_math.Rd |only edmdata-1.3.0/edmdata/man/qmatrix_probability_part_one.Rd | 3 31 files changed, 244 insertions(+), 119 deletions(-)
Title: Sound Waves Onto Morphometric Data
Description: Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Author: Pedro Rocha [aut, cre]
Maintainer: Pedro Rocha <p.rocha1990@gmail.com>
Diff between SoundShape versions 1.3.0 dated 2023-08-23 and 1.3.1 dated 2024-10-02
DESCRIPTION | 10 +++---- MD5 | 48 +++++++++++++++++------------------ R/centralis.R | 56 ++++++++++++++++++++--------------------- R/cuvieri.R | 56 ++++++++++++++++++++--------------------- R/eigensound.R | 8 ++--- R/hypo.surf.R | 10 +++---- R/kroyeri.R | 56 ++++++++++++++++++++--------------------- R/raven.list.R | 4 +- R/raven.to.wave.R | 57 ++++++++++++++++++++++-------------------- R/threeDspectro.R | 18 ++++++------- README.md | 8 ++--- build/vignette.rds |binary inst/doc/Getting-started.R | 14 +++++----- inst/doc/Getting-started.Rmd | 8 ++--- inst/doc/Getting-started.html | 50 ++++++++++++++++++------------------ man/SoundShape.Rd | 2 - man/centralis.Rd | 2 - man/cuvieri.Rd | 2 - man/eigensound.Rd | 8 ++--- man/hypo.surf.Rd | 10 +++---- man/kroyeri.Rd | 2 - man/raven.list.Rd | 4 +- man/raven.to.wave.Rd | 6 ++-- man/threeDspectro.Rd | 18 ++++++------- vignettes/Getting-started.Rmd | 8 ++--- 25 files changed, 234 insertions(+), 231 deletions(-)
Title: 'Targets' Extension for 'SQL' Queries
Description: Provides an extension for 'SQL' queries as separate file
within 'targets' pipelines. The shorthand creates two targets,
the query file and the query result.
Author: David Ranzolin [aut, cre, cph]
Maintainer: David Ranzolin <daranzolin@gmail.com>
Diff between sqltargets versions 0.2.0 dated 2024-07-30 and 0.2.1 dated 2024-10-02
sqltargets-0.2.0/sqltargets/inst/tar_visnetwork.png |only sqltargets-0.2.1/sqltargets/DESCRIPTION | 6 ++--- sqltargets-0.2.1/sqltargets/MD5 | 12 +++++----- sqltargets-0.2.1/sqltargets/NEWS.md | 4 +++ sqltargets-0.2.1/sqltargets/R/source_sql_to_dataframe.R | 8 +++--- sqltargets-0.2.1/sqltargets/README.md | 19 ++++++++++------ sqltargets-0.2.1/sqltargets/inst/sqltargets_hex.png |only sqltargets-0.2.1/sqltargets/inst/tar_glimpse.png |only sqltargets-0.2.1/sqltargets/man/figures |only 9 files changed, 30 insertions(+), 19 deletions(-)
Title: Penalty Learning
Description: Implementations of algorithms from
Learning Sparse Penalties for Change-point Detection
using Max Margin Interval Regression, by
Hocking, Rigaill, Vert, Bach
<http://proceedings.mlr.press/v28/hocking13.html>
published in proceedings of ICML2013.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between penaltyLearning versions 2024.1.25 dated 2024-02-01 and 2024.9.3 dated 2024-10-02
DESCRIPTION | 13 ++++--- MD5 | 60 ++++++++++++++++----------------- NEWS | 6 ++- man/IntervalRegressionCV.Rd | 2 - man/IntervalRegressionCVmargin.Rd | 2 - man/IntervalRegressionInternal.Rd | 2 - man/IntervalRegressionRegularized.Rd | 2 - man/IntervalRegressionUnregularized.Rd | 2 - man/ROChange.Rd | 2 - man/changeLabel.Rd | 2 - man/check_features_targets.Rd | 2 - man/check_target_pred.Rd | 2 - man/coef.IntervalRegression.Rd | 2 - man/featureMatrix.Rd | 2 - man/featureVector.Rd | 2 - man/geom_tallrect.Rd | 2 - man/labelError.Rd | 2 - man/largestContinuousMinimumC.Rd | 2 - man/largestContinuousMinimumR.Rd | 2 - man/modelSelection.Rd | 2 - man/modelSelectionC.Rd | 2 - man/modelSelectionR.Rd | 2 - man/plot.IntervalRegression.Rd | 2 - man/predict.IntervalRegression.Rd | 2 - man/print.IntervalRegression.Rd | 2 - man/squared.hinge.Rd | 2 - man/targetIntervalROC.Rd | 2 - man/targetIntervalResidual.Rd | 2 - man/targetIntervals.Rd | 2 - man/theme_no_space.Rd | 2 - src/interface.cpp | 22 ++++++------ 31 files changed, 82 insertions(+), 73 deletions(-)
More information about penaltyLearning at CRAN
Permanent link
Title: Optimal Segmentation Subject to Up-Down Constraints
Description: Computes optimal changepoint models using the
Poisson likelihood for non-negative count data,
subject to the PeakSeg constraint:
the first change must be up, second change down, third change up, etc.
For more info about the models and algorithms,
read "Constrained Dynamic Programming and Supervised Penalty Learning
Algorithms for Peak Detection"
<https://jmlr.org/papers/v21/18-843.html> by TD Hocking et al.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegOptimal versions 2024.1.24 dated 2024-01-24 and 2024.10.1 dated 2024-10-02
DESCRIPTION | 19 MD5 | 42 - NAMESPACE | 8 NEWS | 197 ++++--- R/PeakSegFPOP.R | 460 +++++++++--------- R/PeakSegPDPA.R | 748 ++++++++++++++---------------- R/PoissonLoss.R | 78 +-- R/oracle.R | 20 man/H3K4me3_PGP_immune_chunk24.Rd | 36 - man/H3K4me3_XJ_immune_chunk1.Rd | 30 - man/PeakSegFPOP.Rd | 202 ++++---- man/PeakSegFPOPchrom.Rd | 152 +++--- man/PeakSegPDPA.Rd | 204 ++++---- man/PeakSegPDPAInf.Rd | 140 ++--- man/PeakSegPDPAchrom.Rd | 216 ++++---- man/PoissonLoss.Rd | 58 +- man/oracleModelComplexity.Rd | 38 - src/interface.cpp | 4 tests/testthat.R | 4 tests/testthat/test-CRAN-PeakSegFPOP.R | 294 +++++------ tests/testthat/test-CRAN-PeakSegPDPA.R | 360 +++++++------- tests/testthat/test-CRAN-PeakSegPDPAInf.R | 92 +-- 22 files changed, 1704 insertions(+), 1698 deletions(-)
More information about PeakSegOptimal at CRAN
Permanent link
Title: Joint Peak Detection in Several ChIP-Seq Samples
Description: Jointly segment several ChIP-seq samples to find the peaks
which are the same and different across samples. The fast approximate
maximum Poisson likelihood algorithm is described in
"PeakSegJoint: fast supervised peak detection via joint segmentation
of multiple count data samples"
<doi:10.48550/arXiv.1506.01286>
by TD Hocking and G Bourque.
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegJoint versions 2024.6.27 dated 2024-06-27 and 2024.10.1 dated 2024-10-02
DESCRIPTION | 13 ++- MD5 | 44 ++++++------- NEWS | 4 + man/ConvertModelList.Rd | 2 man/PeakErrorSamples.Rd | 2 man/PeakSegJointError.Rd | 2 man/PeakSegJointFaster.Rd | 2 man/PeakSegJointFasterOne.Rd | 2 man/PeakSegJointHeuristic.Rd | 2 man/PeakSegJointHeuristicStep1.Rd | 2 man/PeakSegJointHeuristicStep2.Rd | 2 man/PeakSegJointSeveral.Rd | 2 man/PoissonLoss.Rd | 2 man/ProfileList.Rd | 2 man/binSum.Rd | 2 man/clusterPeaks.Rd | 2 man/featureMatrixJoint.Rd | 2 man/multiClusterPeaks.Rd | 2 src/PeakSegJoint.c | 68 ++++++++++---------- src/PeakSegJointFaster.c | 128 +++++++++++++++++++------------------- src/PeakSegJoint_interface.c | 6 - src/binSum.c | 6 - tests/testthat.R | 9 +- 23 files changed, 159 insertions(+), 149 deletions(-)
Title: Disk-Based Constrained Change-Point Detection
Description: Disk-based implementation of
Functional Pruning Optimal Partitioning with up-down constraints
<doi:10.18637/jss.v101.i10> for single-sample peak calling
(independently for each sample and genomic problem),
can handle huge data sets (10^7 or more).
Author: Toby Dylan Hocking [aut, cre]
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegDisk versions 2023.11.27 dated 2023-11-28 and 2024.10.1 dated 2024-10-02
PeakSegDisk-2023.11.27/PeakSegDisk/vignettes/seconds.csv |only PeakSegDisk-2024.10.1/PeakSegDisk/DESCRIPTION | 12 PeakSegDisk-2024.10.1/PeakSegDisk/MD5 | 103 - PeakSegDisk-2024.10.1/PeakSegDisk/NAMESPACE | 40 PeakSegDisk-2024.10.1/PeakSegDisk/NEWS | 132 - PeakSegDisk-2024.10.1/PeakSegDisk/R/PeakSegFPOP_df.R | 268 +-- PeakSegDisk-2024.10.1/PeakSegDisk/R/PeakSegFPOP_dir.R | 564 +++--- PeakSegDisk-2024.10.1/PeakSegDisk/R/PeakSegFPOP_file.R | 250 +- PeakSegDisk-2024.10.1/PeakSegDisk/R/PeakSegFPOP_vec.R | 156 - PeakSegDisk-2024.10.1/PeakSegDisk/R/col.name.list.R | 88 - PeakSegDisk-2024.10.1/PeakSegDisk/R/fread.R | 242 +- PeakSegDisk-2024.10.1/PeakSegDisk/R/sequentialSearch_dir.R | 306 +-- PeakSegDisk-2024.10.1/PeakSegDisk/R/writeBedGraph.R | 118 - PeakSegDisk-2024.10.1/PeakSegDisk/build/vignette.rds |binary PeakSegDisk-2024.10.1/PeakSegDisk/inst/CITATION | 46 PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Examples.R | 266 +-- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Examples.Rnw | 810 ++++----- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Examples.pdf |binary PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Spatial_correlation.R | 370 ++-- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Spatial_correlation.Rmd | 514 ++--- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Spatial_correlation.html | 873 +++++----- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Worst_case.R | 152 - PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Worst_case.Rmd | 200 +- PeakSegDisk-2024.10.1/PeakSegDisk/inst/doc/Worst_case.html | 549 +++--- PeakSegDisk-2024.10.1/PeakSegDisk/man/ChIPreads.Rd | 72 PeakSegDisk-2024.10.1/PeakSegDisk/man/Mono27ac.Rd | 78 PeakSegDisk-2024.10.1/PeakSegDisk/man/PeakSegFPOP_df.Rd | 198 +- PeakSegDisk-2024.10.1/PeakSegDisk/man/PeakSegFPOP_dir.Rd | 298 +-- PeakSegDisk-2024.10.1/PeakSegDisk/man/PeakSegFPOP_file.Rd | 150 - PeakSegDisk-2024.10.1/PeakSegDisk/man/PeakSegFPOP_vec.Rd | 140 - PeakSegDisk-2024.10.1/PeakSegDisk/man/coef.PeakSegFPOP_df.Rd | 42 PeakSegDisk-2024.10.1/PeakSegDisk/man/coef.PeakSegFPOP_dir.Rd | 38 PeakSegDisk-2024.10.1/PeakSegDisk/man/col.name.list.Rd | 88 - PeakSegDisk-2024.10.1/PeakSegDisk/man/fread.first.Rd | 104 - PeakSegDisk-2024.10.1/PeakSegDisk/man/fread.last.Rd | 104 - PeakSegDisk-2024.10.1/PeakSegDisk/man/plot.PeakSegFPOP_df.Rd | 38 PeakSegDisk-2024.10.1/PeakSegDisk/man/plot.PeakSegFPOP_dir.Rd | 38 PeakSegDisk-2024.10.1/PeakSegDisk/man/sequentialSearch_dir.Rd | 160 - PeakSegDisk-2024.10.1/PeakSegDisk/man/summary.PeakSegFPOP_dir.Rd | 38 PeakSegDisk-2024.10.1/PeakSegDisk/man/wc2int.Rd | 34 PeakSegDisk-2024.10.1/PeakSegDisk/man/writeBedGraph.Rd | 88 - PeakSegDisk-2024.10.1/PeakSegDisk/src/interface.cpp | 24 PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat.R | 10 PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-PeakSegFPOP_dir.R | 368 ++-- PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-PeakSegFPOP_file.R | 138 - PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-PeakSegFPOP_vec.R | 32 PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-bad-paths.R | 36 PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-cpp-errors.R | 406 ++-- PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-sequentialSearch.R | 52 PeakSegDisk-2024.10.1/PeakSegDisk/tests/testthat/test-CRAN-wc2int.R | 70 PeakSegDisk-2024.10.1/PeakSegDisk/vignettes/Examples.Rnw | 810 ++++----- PeakSegDisk-2024.10.1/PeakSegDisk/vignettes/Spatial_correlation.Rmd | 514 ++--- PeakSegDisk-2024.10.1/PeakSegDisk/vignettes/Worst_case.Rmd | 200 +- 53 files changed, 5219 insertions(+), 5208 deletions(-)
Title: Interactive Exploratory Data Analysis Tool
Description: Simplify your R data analysis and data visualization workflow by turning your data frame into an interactive 'Tableau'-like interface, leveraging the 'graphic-walker' JavaScript library and the 'htmlwidgets' package.
Author: Yue Yu [aut, cre] ,
Kanaries Data Inc. [cph, fnd]
Maintainer: Yue Yu <yue.yu@connect.ust.hk>
Diff between GWalkR versions 0.1.5 dated 2024-08-25 and 0.2.0 dated 2024-10-02
DESCRIPTION | 9 +- MD5 | 14 ++- NAMESPACE | 4 + R/data_parser.R | 36 +++++---- R/duckdb_utils.R |only R/gwalkr.R | 59 ++++++++------ R/gwalkr_kernel.R |only inst/htmlwidgets/lib/gwalkr/gwalkr-app.iife.js | 100 ++++++++++++------------- man/gwalkr.Rd | 5 + 9 files changed, 129 insertions(+), 98 deletions(-)
Title: Fast Inference for Large Spatial Datasets using BRISC
Description: Fits bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using nearest neighbor Gaussian processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
Author: Arkajyoti Saha [aut, cre],
Abhirup Datta [aut],
Jorge Nocedal [ctb],
Naoaki Okazaki [ctb],
Lukas M. Weber [ctb]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between BRISC versions 1.0.5 dated 2022-04-29 and 1.0.6 dated 2024-10-02
DESCRIPTION | 6 - MD5 | 28 +++--- man/BRISC_neighbor.Rd | 2 src/BRISC.cpp | 202 ++++++++++++++++++++++---------------------- src/BRISC_Predict.cpp | 24 +++-- src/Makevars.in | 4 src/Makevars.win | 5 - src/arithmetic_ansi.h | 3 src/arithmetic_sse_double.h | 3 src/arithmetic_sse_float.h | 3 src/init.c | 3 src/lbfgs.c | 3 src/lbfgs.h | 3 src/util.cpp | 8 + src/util.h | 4 15 files changed, 171 insertions(+), 130 deletions(-)