Title: Additive Information & Details of Evidence Synthesis
Description: A supportive collection of functions for pooled analysis of aggregate data. The current version supports users to test assumptions before relevant analysis of bias from study size and sequential analysis such as mentioned by Wetterslev, J., Jakobsen, J. C., & Gluud, C. (2017) <doi:10.1186/s12874-017-0315-7>.
Author: Enoch Kang [aut, cre]
Maintainer: Enoch Kang <y.enoch.kang@gmail.com>
Diff between aides versions 1.1.0 dated 2023-08-11 and 1.2.0 dated 2023-10-25
aides-1.1.0/aides/inst/doc/aides_vignette.R |only aides-1.1.0/aides/inst/doc/aides_vignette.Rmd |only aides-1.1.0/aides/inst/doc/aides_vignette.html |only aides-1.1.0/aides/vignettes/aides_vignette.Rmd |only aides-1.2.0/aides/DESCRIPTION | 13 aides-1.2.0/aides/MD5 | 47 aides-1.2.0/aides/NAMESPACE | 9 aides-1.2.0/aides/NEWS.md | 124 + aides-1.2.0/aides/R/aides-package.R | 15 aides-1.2.0/aides/R/do_observed_sequential_analysis.R |only aides-1.2.0/aides/R/do_sequential_analysis.R | 233 ++- aides-1.2.0/aides/R/plot_disparity.R | 830 +++++++---- aides-1.2.0/aides/R/plot_distribution_of_study_sizes.R |only aides-1.2.0/aides/R/plot_observed_sequential_analysis.R |only aides-1.2.0/aides/R/test_discordance.R | 84 - aides-1.2.0/aides/R/test_disparity.R | 541 ++++--- aides-1.2.0/aides/README.md | 326 +++- aides-1.2.0/aides/build/vignette.rds |binary aides-1.2.0/aides/inst/doc/An_overview_on_pakcage_aides.R |only aides-1.2.0/aides/inst/doc/An_overview_on_pakcage_aides.Rmd |only aides-1.2.0/aides/inst/doc/An_overview_on_pakcage_aides.html |only aides-1.2.0/aides/man/DoOSA.Rd |only aides-1.2.0/aides/man/DoSA.Rd | 74 aides-1.2.0/aides/man/PlotDisparity.Rd | 41 aides-1.2.0/aides/man/PlotDistrSS.Rd |only aides-1.2.0/aides/man/PlotOSA.Rd |only aides-1.2.0/aides/man/TestDisparity.Rd | 36 aides-1.2.0/aides/man/aides-package.Rd | 9 aides-1.2.0/aides/tests/testthat/test-DoOSA.R |only aides-1.2.0/aides/tests/testthat/test-PlotDisparity.R | 6 aides-1.2.0/aides/tests/testthat/test-PlotDistrSS.R |only aides-1.2.0/aides/tests/testthat/test-PlotOSA.R |only aides-1.2.0/aides/vignettes/An_overview_on_pakcage_aides.Rmd |only 33 files changed, 1692 insertions(+), 696 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.6.3 dated 2023-08-25 and 2.7.0 dated 2023-10-25
TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/jrf-vm-matchzeros-false.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/mst-example-plot.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/rf-collapse-a-node.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/rf-collapse-and-change.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/rf-vm-single-splits-plainedges.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/test-vm.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/test-vmr.svg |only TreeDist-2.6.3/TreeDist/tests/testthat/_snaps/plot/visualize-mci-matching.svg |only TreeDist-2.7.0/TreeDist/DESCRIPTION | 12 TreeDist-2.7.0/TreeDist/MD5 | 70 +- TreeDist-2.7.0/TreeDist/NEWS.md | 14 TreeDist-2.7.0/TreeDist/R/MSTSegments.R |only TreeDist-2.7.0/TreeDist/R/VisualizeMatching.R |only TreeDist-2.7.0/TreeDist/R/plot.R | 297 ---------- TreeDist-2.7.0/TreeDist/R/tree_distance_info.R | 18 TreeDist-2.7.0/TreeDist/build/partial.rdb |binary TreeDist-2.7.0/TreeDist/inst/REFERENCES.bib | 2 TreeDist-2.7.0/TreeDist/inst/WORDLIST | 1 TreeDist-2.7.0/TreeDist/inst/doc/Using-TreeDist.html | 6 TreeDist-2.7.0/TreeDist/inst/doc/landscapes.html | 4 TreeDist-2.7.0/TreeDist/inst/doc/treespace.R | 4 TreeDist-2.7.0/TreeDist/inst/doc/treespace.Rmd | 4 TreeDist-2.7.0/TreeDist/inst/doc/treespace.html | 6 TreeDist-2.7.0/TreeDist/inst/doc/using-distances.R | 3 TreeDist-2.7.0/TreeDist/inst/doc/using-distances.Rmd | 3 TreeDist-2.7.0/TreeDist/inst/doc/using-distances.html | 25 TreeDist-2.7.0/TreeDist/inst/treespace/app.R | 19 TreeDist-2.7.0/TreeDist/man/MSTSegments.Rd | 2 TreeDist-2.7.0/TreeDist/man/TreeDistance.Rd | 18 TreeDist-2.7.0/TreeDist/man/VisualizeMatching.Rd | 2 TreeDist-2.7.0/TreeDist/src/ints.h | 3 TreeDist-2.7.0/TreeDist/src/tree_distance_functions.cpp | 37 - TreeDist-2.7.0/TreeDist/tests/testthat/_snaps/MSTSegments |only TreeDist-2.7.0/TreeDist/tests/testthat/_snaps/VisualizeMatching |only TreeDist-2.7.0/TreeDist/tests/testthat/test-MSTSegments.R |only TreeDist-2.7.0/TreeDist/tests/testthat/test-VisualizeMatching.R |only TreeDist-2.7.0/TreeDist/tests/testthat/test-plot.R | 169 ----- TreeDist-2.7.0/TreeDist/vignettes/treespace.Rmd | 4 TreeDist-2.7.0/TreeDist/vignettes/using-distances.Rmd | 3 39 files changed, 206 insertions(+), 520 deletions(-)
Title: Bootstrap Landing Home Pages for Shiny Applications
Description: Provides functions that wrap HTML Bootstrap
components code to enable the design and layout of informative landing home
pages for Shiny applications. This can lead to a better user experience for
the users and writing less HTML for the developer.
Author: Jasmine Daly [aut, cre]
Maintainer: Jasmine Daly <jasmine.dumas@gmail.com>
Diff between shinyLP versions 1.1.2 dated 2018-04-25 and 1.1.3 dated 2023-10-25
DESCRIPTION | 15 ++++++-------- MD5 | 38 ++++++++++++++++++------------------- NEWS.md | 4 +++ R/iframe.R | 2 - R/jumbotron.R | 2 - R/list_group.R | 2 - R/list_item.R | 2 - R/panel_div.R | 2 - R/thumbnail_label.R | 2 - R/wells.R | 2 - README.md | 10 ++++----- inst/shiny-examples/LPExample/ui.R | 2 - man/iframe.Rd | 2 - man/jumbotron.Rd | 2 - man/list_group.Rd | 2 - man/list_item.Rd | 2 - man/panel_div.Rd | 2 - man/shinyLP.Rd | 1 man/thumbnail_label.Rd | 2 - man/wells.Rd | 2 - 20 files changed, 50 insertions(+), 48 deletions(-)
Title: Processing METAR Weather Reports
Description: Allows to download current and historical METAR weather reports
extract and parse basic parameters and present main weather information.
Current reports are downloaded from Aviation Weather Center
<https://aviationweather.gov/data/metar/> and historical reports from
Iowa Environmental Mesonet web page of Iowa State University
ASOS-AWOS-METAR <http://mesonet.agron.iastate.edu/AWOS/>.
Author: Pawel Cwiek [aut, cre],
David Megginson [ctb] ,
Greg Thompson [ctb]
Maintainer: Pawel Cwiek <prc.altodato@gmail.com>
Diff between pmetar versions 0.4.1 dated 2023-05-07 and 0.5.0 dated 2023-10-25
pmetar-0.4.1/pmetar/man/pmetar.Rd |only pmetar-0.5.0/pmetar/DESCRIPTION | 12 pmetar-0.5.0/pmetar/MD5 | 32 pmetar-0.5.0/pmetar/R/metar_get.R | 17 pmetar-0.5.0/pmetar/R/metar_location.R | 2 pmetar-0.5.0/pmetar/R/pmetar-package.R | 16 pmetar-0.5.0/pmetar/README.md | 6 pmetar-0.5.0/pmetar/build/vignette.rds |binary pmetar-0.5.0/pmetar/data/ourairports.rda |binary pmetar-0.5.0/pmetar/inst/doc/pmetar.Rmd | 2 pmetar-0.5.0/pmetar/inst/doc/pmetar.html | 568 +++++++-------- pmetar-0.5.0/pmetar/man/metar_get.Rd | 2 pmetar-0.5.0/pmetar/man/metar_location.Rd | 2 pmetar-0.5.0/pmetar/man/mst.Rd | 4 pmetar-0.5.0/pmetar/man/ourairports.Rd | 3 pmetar-0.5.0/pmetar/man/pmetar-package.Rd |only pmetar-0.5.0/pmetar/tests/testthat/test_metar_location.R | 2 pmetar-0.5.0/pmetar/vignettes/pmetar.Rmd | 2 18 files changed, 336 insertions(+), 334 deletions(-)
Title: Leveraging Experiment Lines to Data Analytics
Description: The natural increase in the complexity of current research experiments and data demands better tools to enhance productivity in Data Analytics. The package is a framework designed to address the modern challenges in data analytics workflows. The package is inspired by Experiment Line concepts. It aims to provide seamless support for users in developing their data mining workflows by offering a uniform data model and method API. It enables the integration of various data mining activities, including data preprocessing, classification, regression, clustering, and time series prediction. It also offers options for hyper-parameter tuning and supports integration with existing libraries and languages. Overall, the package provides researchers with a comprehensive set of functionalities for data science, promoting ease of use, extensibility, and integration with various tools and libraries. Information on Experiment Line is based on Ogasawara et al. (2009) <doi:10.1007/978-3-642-02279-1_2 [...truncated...]
Author: Eduardo Ogasawara [aut, ths, cre]
,
Antonio Castro [aut, ctb],
Heraldo Borges [aut, ths],
Diego Carvalho [aut, ths],
Joel Santos [aut, ths],
Eduardo Bezerra [aut, ths],
Rafaelli Coutinho [aut, ths],
Federal Center for Technological Education of Rio d [...truncated...]
Maintainer: Eduardo Ogasawara <eogasawara@ieee.org>
Diff between daltoolbox versions 1.0.717 dated 2023-07-22 and 1.0.727 dated 2023-10-25
daltoolbox-1.0.717/daltoolbox/R/dal_categ_mapping.R |only daltoolbox-1.0.717/daltoolbox/R/dal_fit_curvature_max.R |only daltoolbox-1.0.717/daltoolbox/R/dal_fit_curvature_min.R |only daltoolbox-1.0.717/daltoolbox/R/dal_norm_minmax.R |only daltoolbox-1.0.717/daltoolbox/R/dal_norm_zscore.R |only daltoolbox-1.0.717/daltoolbox/R/dal_outliers.R |only daltoolbox-1.0.717/daltoolbox/R/dal_pca.R |only daltoolbox-1.0.717/daltoolbox/R/dal_sample.R |only daltoolbox-1.0.717/daltoolbox/R/dal_sample_random.R |only daltoolbox-1.0.717/daltoolbox/R/dal_sample_strat.R |only daltoolbox-1.0.717/daltoolbox/R/dal_smoothing.R |only daltoolbox-1.0.717/daltoolbox/R/dal_smoothing_cluster.R |only daltoolbox-1.0.717/daltoolbox/R/dal_smoothing_freq.R |only daltoolbox-1.0.717/daltoolbox/R/dal_smoothing_inter.R |only daltoolbox-1.0.717/daltoolbox/R/dal_transform.R |only daltoolbox-1.0.717/daltoolbox/inst/python/python_basics.py |only daltoolbox-1.0.727/daltoolbox/DESCRIPTION | 12 - daltoolbox-1.0.727/daltoolbox/MD5 | 98 +++++----- daltoolbox-1.0.727/daltoolbox/NAMESPACE | 6 daltoolbox-1.0.727/daltoolbox/R/globals.R | 3 daltoolbox-1.0.727/daltoolbox/R/reg_tune.R | 2 daltoolbox-1.0.727/daltoolbox/R/trans_autoenc_encode.R |only daltoolbox-1.0.727/daltoolbox/R/trans_autoenc_encode_decode.R |only daltoolbox-1.0.727/daltoolbox/R/trans_categ_mapping.R |only daltoolbox-1.0.727/daltoolbox/R/trans_dt_pca.R |only daltoolbox-1.0.727/daltoolbox/R/trans_fit_curvature_max.R |only daltoolbox-1.0.727/daltoolbox/R/trans_fit_curvature_min.R |only daltoolbox-1.0.727/daltoolbox/R/trans_norm_minmax.R |only daltoolbox-1.0.727/daltoolbox/R/trans_norm_zscore.R |only daltoolbox-1.0.727/daltoolbox/R/trans_outliers.R |only daltoolbox-1.0.727/daltoolbox/R/trans_sample.R |only daltoolbox-1.0.727/daltoolbox/R/trans_sample_random.R |only daltoolbox-1.0.727/daltoolbox/R/trans_sample_strat.R |only daltoolbox-1.0.727/daltoolbox/R/trans_smoothing.R |only daltoolbox-1.0.727/daltoolbox/R/trans_smoothing_cluster.R |only daltoolbox-1.0.727/daltoolbox/R/trans_smoothing_freq.R |only daltoolbox-1.0.727/daltoolbox/R/trans_smoothing_inter.R |only daltoolbox-1.0.727/daltoolbox/R/trans_transform.R |only daltoolbox-1.0.727/daltoolbox/R/ts_lstm.R | 1 daltoolbox-1.0.727/daltoolbox/README.md | 11 - daltoolbox-1.0.727/daltoolbox/data/Boston.RData |binary daltoolbox-1.0.727/daltoolbox/data/sin_data.RData |binary daltoolbox-1.0.727/daltoolbox/inst/logo.png |only daltoolbox-1.0.727/daltoolbox/inst/logo.pptx |only daltoolbox-1.0.727/daltoolbox/inst/python/autoencoder.py |only daltoolbox-1.0.727/daltoolbox/man/action.dal_transform.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/autoenc_encode.Rd |only daltoolbox-1.0.727/daltoolbox/man/autoenc_encode_decode.Rd |only daltoolbox-1.0.727/daltoolbox/man/categ_mapping.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/dal_transform.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/data_sample.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/dt_pca.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/fit_curvature_max.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/fit_curvature_min.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/inverse_transform.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/k_fold.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/minmax.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/outliers.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/reg_tune.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/sample_random.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/sample_stratified.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/smoothing.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/smoothing_cluster.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/smoothing_freq.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/smoothing_inter.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/train_test.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/train_test_from_folds.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/transform.Rd | 2 daltoolbox-1.0.727/daltoolbox/man/zscore.Rd | 2 69 files changed, 97 insertions(+), 80 deletions(-)
Title: Workflow for Open Reproducible Code in Science
Description: Create reproducible and transparent research projects in 'R'.
This package is based on the Workflow for Open
Reproducible Code in Science (WORCS), a step-by-step procedure based on best
practices for
Open Science. It includes an 'RStudio' project template, several
convenience functions, and all dependencies required to make your project
reproducible and transparent. WORCS is explained in the tutorial paper
by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021).
<doi:10.3233/DS-210031>.
Author: Caspar J. Van Lissa [aut, cre]
,
Aaron Peikert [aut] ,
Andreas M. Brandmaier [aut]
Maintainer: Caspar J. Van Lissa <c.j.vanlissa@tilburguniversity.edu>
Diff between worcs versions 0.1.13 dated 2023-10-04 and 0.1.14 dated 2023-10-25
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/check_installation.R | 5 ++--- R/codebook.R | 23 +++++++++++++++-------- R/endpoint.R | 3 ++- R/save_load.R | 28 ++++++++++++++-------------- R/worcs_project.R | 4 ++-- man/add_manuscript.Rd | 2 +- man/add_preregistration.Rd | 2 +- man/codebook.Rd | 12 ++++++------ tests/testthat/test-checksum_markdown.R |only 12 files changed, 59 insertions(+), 50 deletions(-)
Title: Spatial Statistical Modeling and Prediction
Description: Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Author: Michael Dumelle [aut, cre] ,
Matt Higham [aut],
Jay M. Ver Hoef [aut]
Maintainer: Michael Dumelle <Dumelle.Michael@epa.gov>
Diff between spmodel versions 0.4.0 dated 2023-05-26 and 0.5.0 dated 2023-10-25
spmodel-0.4.0/spmodel/R/pseudoR2.R |only spmodel-0.4.0/spmodel/R/pseudoR2_glm.R |only spmodel-0.4.0/spmodel/inst/doc/basics.R |only spmodel-0.4.0/spmodel/inst/doc/basics.Rmd |only spmodel-0.4.0/spmodel/inst/doc/basics.pdf |only spmodel-0.4.0/spmodel/inst/doc/guide.R |only spmodel-0.4.0/spmodel/inst/doc/guide.Rmd |only spmodel-0.4.0/spmodel/inst/doc/guide.pdf |only spmodel-0.4.0/spmodel/inst/doc/technical.R |only spmodel-0.4.0/spmodel/inst/doc/technical.Rmd |only spmodel-0.4.0/spmodel/inst/doc/technical.pdf |only spmodel-0.4.0/spmodel/vignettes/basics.Rmd |only spmodel-0.4.0/spmodel/vignettes/guide.Rmd |only spmodel-0.4.0/spmodel/vignettes/technical.Rmd |only spmodel-0.5.0/spmodel/DESCRIPTION | 8 spmodel-0.5.0/spmodel/MD5 | 255 +-- spmodel-0.5.0/spmodel/NEWS.md | 212 +- spmodel-0.5.0/spmodel/R/AIC.R | 454 ++--- spmodel-0.5.0/spmodel/R/AIC_glm.R | 46 spmodel-0.5.0/spmodel/R/PseudoR2.R |only spmodel-0.5.0/spmodel/R/PseudoR2_glm.R |only spmodel-0.5.0/spmodel/R/anova.R | 452 ++--- spmodel-0.5.0/spmodel/R/anova_glm.R | 46 spmodel-0.5.0/spmodel/R/augment.R | 534 +++--- spmodel-0.5.0/spmodel/R/coef.R | 114 - spmodel-0.5.0/spmodel/R/coef_glm.R | 72 spmodel-0.5.0/spmodel/R/confint.R | 104 - spmodel-0.5.0/spmodel/R/confint_glm.R | 22 spmodel-0.5.0/spmodel/R/cooks.distance.R | 76 spmodel-0.5.0/spmodel/R/cooks.distance_glm.R | 22 spmodel-0.5.0/spmodel/R/cov_estimate_sv.R | 2 spmodel-0.5.0/spmodel/R/cov_initial_search.R | 6 spmodel-0.5.0/spmodel/R/cov_matrix.R | 120 - spmodel-0.5.0/spmodel/R/covmatrix.R | 330 +-- spmodel-0.5.0/spmodel/R/covmatrix_glm.R | 22 spmodel-0.5.0/spmodel/R/data.R | 88 - spmodel-0.5.0/spmodel/R/deviance.R | 78 spmodel-0.5.0/spmodel/R/deviance_glm.R | 22 spmodel-0.5.0/spmodel/R/dispersion_initial.R | 178 +- spmodel-0.5.0/spmodel/R/dispersion_orig2optim.R | 32 spmodel-0.5.0/spmodel/R/dispersion_params.R | 116 - spmodel-0.5.0/spmodel/R/esv.R | 358 ++-- spmodel-0.5.0/spmodel/R/fitted.R | 123 - spmodel-0.5.0/spmodel/R/fitted_glm.R | 64 spmodel-0.5.0/spmodel/R/formula.R | 58 spmodel-0.5.0/spmodel/R/formula_glm.R | 22 spmodel-0.5.0/spmodel/R/get_cooks_distance.R | 24 spmodel-0.5.0/spmodel/R/get_cooks_distance_glm.R | 6 spmodel-0.5.0/spmodel/R/get_cov_matrix_list.R | 44 spmodel-0.5.0/spmodel/R/get_data_object_glm.R | 1162 +++++++------- spmodel-0.5.0/spmodel/R/get_deviance_glm.R | 62 spmodel-0.5.0/spmodel/R/get_fitted.R | 340 ++-- spmodel-0.5.0/spmodel/R/get_local_list.R | 8 spmodel-0.5.0/spmodel/R/get_model_stats.R | 506 +++--- spmodel-0.5.0/spmodel/R/get_randcov_list.R | 13 spmodel-0.5.0/spmodel/R/get_vcov.R | 34 spmodel-0.5.0/spmodel/R/glance.R | 18 spmodel-0.5.0/spmodel/R/glance_glm.R | 22 spmodel-0.5.0/spmodel/R/glances.R | 164 - spmodel-0.5.0/spmodel/R/glances_glm.R | 76 spmodel-0.5.0/spmodel/R/hatvalues.R | 78 spmodel-0.5.0/spmodel/R/hatvalues_glm.R | 22 spmodel-0.5.0/spmodel/R/influence.R | 86 - spmodel-0.5.0/spmodel/R/influence_glm.R | 22 spmodel-0.5.0/spmodel/R/labels.R | 60 spmodel-0.5.0/spmodel/R/labels_glm.R | 22 spmodel-0.5.0/spmodel/R/logLik.R | 74 spmodel-0.5.0/spmodel/R/logLik_glm.R | 22 spmodel-0.5.0/spmodel/R/loocv.R | 466 ++--- spmodel-0.5.0/spmodel/R/loocv_glm.R | 416 ++--- spmodel-0.5.0/spmodel/R/model.frame.R | 70 spmodel-0.5.0/spmodel/R/model.frame_glm.R | 22 spmodel-0.5.0/spmodel/R/model.matrix.R | 66 spmodel-0.5.0/spmodel/R/model.matrix_glm.R | 22 spmodel-0.5.0/spmodel/R/partition_vector.R | 6 spmodel-0.5.0/spmodel/R/plot.R | 664 ++++---- spmodel-0.5.0/spmodel/R/plot_glm.R | 22 spmodel-0.5.0/spmodel/R/predict.R | 62 spmodel-0.5.0/spmodel/R/predict_glm.R | 1733 ++++++++++----------- spmodel-0.5.0/spmodel/R/randcov_initial.R | 98 - spmodel-0.5.0/spmodel/R/randcov_orig2optim.R | 112 - spmodel-0.5.0/spmodel/R/randcov_params.R | 100 - spmodel-0.5.0/spmodel/R/randcov_vector.R | 4 spmodel-0.5.0/spmodel/R/residuals.R | 168 +- spmodel-0.5.0/spmodel/R/residuals_glm.R | 98 - spmodel-0.5.0/spmodel/R/spautor.R | 12 spmodel-0.5.0/spmodel/R/spcov_initial.R | 42 spmodel-0.5.0/spmodel/R/spcov_matrix.R | 418 ++--- spmodel-0.5.0/spmodel/R/spcov_vector.R | 296 +-- spmodel-0.5.0/spmodel/R/spgautor.R | 732 ++++---- spmodel-0.5.0/spmodel/R/spgautor_checks.R | 68 spmodel-0.5.0/spmodel/R/spglm.R | 940 +++++------ spmodel-0.5.0/spmodel/R/splm.R | 74 spmodel-0.5.0/spmodel/R/spmodel-package.R | 34 spmodel-0.5.0/spmodel/R/sprbinom.R | 1 spmodel-0.5.0/spmodel/R/sprnorm.R | 714 ++++---- spmodel-0.5.0/spmodel/R/summary.R | 120 - spmodel-0.5.0/spmodel/R/tidy.R | 32 spmodel-0.5.0/spmodel/R/tidy_glm.R | 34 spmodel-0.5.0/spmodel/R/use_gloglik.R | 248 +-- spmodel-0.5.0/spmodel/R/varcomp_glm.R | 22 spmodel-0.5.0/spmodel/R/vcov.R | 72 spmodel-0.5.0/spmodel/R/vcov_glm.R | 40 spmodel-0.5.0/spmodel/README.md | 13 spmodel-0.5.0/spmodel/build/partial.rdb |only spmodel-0.5.0/spmodel/build/vignette.rds |binary spmodel-0.5.0/spmodel/inst/doc/introduction.R |only spmodel-0.5.0/spmodel/inst/doc/introduction.Rmd |only spmodel-0.5.0/spmodel/inst/doc/introduction.html |only spmodel-0.5.0/spmodel/inst/references.bib | 1316 ++++++++------- spmodel-0.5.0/spmodel/man/augment.spmodel.Rd | 20 spmodel-0.5.0/spmodel/man/caribou.Rd | 14 spmodel-0.5.0/spmodel/man/dispersion_initial.Rd | 130 - spmodel-0.5.0/spmodel/man/dispersion_params.Rd | 104 - spmodel-0.5.0/spmodel/man/fitted.spmodel.Rd | 3 spmodel-0.5.0/spmodel/man/glance.spmodel.Rd | 18 spmodel-0.5.0/spmodel/man/moose.Rd | 58 spmodel-0.5.0/spmodel/man/moose_preds.Rd | 52 spmodel-0.5.0/spmodel/man/moss.Rd | 26 spmodel-0.5.0/spmodel/man/plot.spmodel.Rd | 16 spmodel-0.5.0/spmodel/man/predict.spmodel.Rd | 24 spmodel-0.5.0/spmodel/man/pseudoR2.Rd | 2 spmodel-0.5.0/spmodel/man/seal.Rd | 8 spmodel-0.5.0/spmodel/man/spautor.Rd | 12 spmodel-0.5.0/spmodel/man/spcov_initial.Rd | 42 spmodel-0.5.0/spmodel/man/spgautor.Rd | 522 +++--- spmodel-0.5.0/spmodel/man/spglm.Rd | 678 ++++---- spmodel-0.5.0/spmodel/man/splm.Rd | 74 spmodel-0.5.0/spmodel/man/spmodel-package.Rd | 2 spmodel-0.5.0/spmodel/man/sprbeta.Rd | 116 - spmodel-0.5.0/spmodel/man/sprbinom.Rd | 118 - spmodel-0.5.0/spmodel/man/sprgamma.Rd | 116 - spmodel-0.5.0/spmodel/man/sprinvgauss.Rd | 116 - spmodel-0.5.0/spmodel/man/sprnbinom.Rd | 116 - spmodel-0.5.0/spmodel/man/sprpois.Rd | 110 - spmodel-0.5.0/spmodel/man/sulfate.Rd | 8 spmodel-0.5.0/spmodel/man/sulfate_preds.Rd | 6 spmodel-0.5.0/spmodel/tests/testthat/test-extras.R | 16 spmodel-0.5.0/spmodel/vignettes/introduction.Rmd |only 139 files changed, 9514 insertions(+), 9271 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.0.9 dated 2023-09-18 and 1.1.0 dated 2023-10-25
DESCRIPTION | 6 MD5 | 19 +- NAMESPACE | 1 NEWS.md | 5 R/other_functions.R | 211 +++++++++++++++++++++++++++++++ inst/doc/common.Rmd | 115 ++++++++++++++++ inst/doc/common.html | 106 ++++++++++++++- man/changed.Rd |only tests/testthat/test-other_functions.R | 185 +++++++++++++++++++++++++++ tests/testthat/test-override_functions.R | 20 ++ vignettes/common.Rmd | 115 ++++++++++++++++ 11 files changed, 759 insertions(+), 24 deletions(-)
Title: Pull Spatial Layers from 'WDNR ArcGIS REST API'
Description: Functions for finding and pulling data from the
'Wisconsin Department of Natural Resources ArcGIS REST APIs'
<https://dnrmaps.wi.gov/arcgis/rest/services> and
<https://dnrmaps.wi.gov/arcgis2/rest/services>.
Author: Paul Frater [aut, cre] ,
Zac Driscoll [aut]
Maintainer: Paul Frater <paul.frater@wisconsin.gov>
Diff between wdnr.gis versions 0.1.4 dated 2022-09-23 and 0.1.5 dated 2023-10-25
DESCRIPTION | 10 +- MD5 | 16 +-- R/get_layer_functions.R | 42 +++++--- data/service_urls.rda |binary inst/doc/wdnr.gis-intro.html | 171 +++++++++++++++++------------------- man/get_hydro_layer.Rd | 2 man/get_wis_raster_layer.Rd | 152 ++++++++++++++++---------------- tests/testthat/test-get-functions.R | 8 + tests/testthat/test-utils.R | 33 +++--- 9 files changed, 223 insertions(+), 211 deletions(-)
Title: Functional Input Validation
Description: A set of basic tools to transform functions into functions with
input validation checks, in a manner suitable for both programmatic and
interactive use.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between valaddin versions 1.0.1 dated 2021-01-08 and 1.0.2 dated 2023-10-25
valaddin-1.0.1/valaddin/R/valaddin.R |only valaddin-1.0.1/valaddin/man/valaddin.Rd |only valaddin-1.0.2/valaddin/DESCRIPTION | 11 valaddin-1.0.2/valaddin/MD5 | 18 valaddin-1.0.2/valaddin/NEWS.md | 6 valaddin-1.0.2/valaddin/R/valaddin-package.R |only valaddin-1.0.2/valaddin/README.md | 200 +- valaddin-1.0.2/valaddin/build/vignette.rds |binary valaddin-1.0.2/valaddin/inst/doc/valaddin.html | 1358 +++++++++-------- valaddin-1.0.2/valaddin/man/firmly.Rd | 36 valaddin-1.0.2/valaddin/man/valaddin-package.Rd |only valaddin-1.0.2/valaddin/tests/testthat/test-checkers.R | 6 12 files changed, 870 insertions(+), 765 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Mike FC [aut] ,
Trevor L Davis [aut, cre] ,
Thomas Lin Pedersen [ctb] copied from ggplot2)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 1.1.0 dated 2023-10-03 and 1.1.1 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/pattern-both-text.R | 22 ++++++++++++---------- R/utils-misc.R | 26 ++++++++++++++++++++++++++ man/grid.pattern_text.Rd | 22 ++++++++++++---------- 6 files changed, 64 insertions(+), 28 deletions(-)
Title: Floating Percentile Model
Description: Floating Percentile Model with additional functions for optimizing inputs and evaluating outputs and assumptions.
Author: Brian Church [aut, cre] ,
Claire Detering [aut]
Maintainer: Brian Church <brianc@windwardenv.com>
Diff between RFPM versions 1.0 dated 2022-11-14 and 1.1 dated 2023-10-25
DESCRIPTION | 14 - MD5 | 58 ++-- NAMESPACE | 7 R/FPM.R | 266 ++++++++++++++-------- R/RFPM.R | 10 R/chemSig.R | 102 +++++--- R/chemSigSelect.R | 10 R/chemVI.R | 61 +++-- R/colorGradient.R | 4 R/cvFPM.R | 512 +++++++++++++++++++++++++++---------------- R/optimFPM.R | 349 ++++++++++++++++++----------- R/plot.chemSigSelect.R | 20 + R/predict.FPM.R |only R/toxCRM.R | 10 build/vignette.rds |binary inst/CITATION | 8 inst/doc/RFPM.R | 20 - inst/doc/RFPM.Rmd | 91 ++++--- inst/doc/RFPM.html | 546 +++++++++++++++++++++++----------------------- man/FPM.Rd | 34 ++ man/RFPM.Rd | 10 man/chemSig.Rd | 25 +- man/chemSigSelect.Rd | 4 man/chemVI.Rd | 9 man/colorGradient.Rd | 2 man/cvFPM.Rd | 75 +++--- man/optimFPM.Rd | 59 ++-- man/plot.chemSigSelect.Rd | 3 man/predict.FPM.Rd |only man/toxCRM.Rd | 10 vignettes/RFPM.Rmd | 91 ++++--- 31 files changed, 1408 insertions(+), 1002 deletions(-)
Title: Reproducible and Flexible Label Design
Description: An open-source R package to deploys reproducible and flexible labels using layers.
The 'huito' package is part of the 'inkaverse' project for developing different procedures and
tools used in plant science and experimental designs.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>
Diff between huito versions 0.2.3 dated 2023-07-03 and 0.2.4 dated 2023-10-25
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/image_import.R | 35 +++++++++++++++++------------------ inst/doc/germinar.R | 6 +++--- inst/doc/germinar.html | 2 +- inst/doc/huito.R | 6 +++--- inst/doc/labels.R | 4 ++-- inst/doc/labels.html | 16 +++++++++------- inst/doc/stickers.R | 6 +++--- inst/doc/stickers.html | 2 +- 11 files changed, 57 insertions(+), 52 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-23 0.9.0
2023-02-19 0.8.95.5
2023-01-12 0.8.95.4
2022-01-26 0.8.95.3
2021-11-05 0.8.95.2
2020-07-13 0.8.95.1
2020-07-01 0.8.95
2020-02-29 0.8.9
2019-12-18 0.8.8.1
2019-06-05 0.8.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-11 0.0.7
2023-06-08 0.0.6
2022-09-13 0.0.5
Title: Fast Permutation Computation
Description: Implements the algorithm of Christensen (2023) <doi:10.1214/22-BA1353> for estimating marginal likelihoods via permutation counting.
Author: Per August Jarval Moen [cre, aut]
,
Dennis Christensen [aut] ,
Yann Collet [cph]
Maintainer: Per August Jarval Moen <pamoen@math.uio.no>
Diff between perms versions 1.11 dated 2023-08-31 and 1.13 dated 2023-10-25
DESCRIPTION | 10 ++-- MD5 | 30 ++++++------ R/get_log_ML.R | 75 +++++++++++++++--------------- R/get_logpermanents.R | 71 ++++++++++++++++------------ R/get_logpermanents_bioassay.R | 102 +++++++++++++++++------------------------ R/log_sum_exp.R | 4 - man/get_log_ML.Rd | 23 +++++---- man/get_log_ML_bioassay.Rd | 31 ++++-------- man/get_log_perms.Rd | 19 +++---- man/get_log_perms_bioassay.Rd | 26 ++-------- man/log_sum_exp.Rd | 2 src/C_get_log_permanent.c | 8 +-- src/get_alphabetagamma.c | 2 src/get_log_ML.c | 34 ++++++++----- src/help_functions.c | 24 ++++++--- src/xxhash.h | 9 ++- 16 files changed, 238 insertions(+), 232 deletions(-)
Title: Finds Binary Outcome Designs Using Stochastic Curtailment
Description: Finds single- and two-arm designs using stochastic curtailment, as described by Law et al. (2022) <doi:10.1080/10543406.2021.2009498> and Law et al. (2021) <doi:10.1002/pst.2067> respectively. Designs can be single-stage or multi-stage. Non-stochastic curtailment is possible as a special case. Desired error-rates, maximum sample size and lower and upper anticipated response rates are inputted and suitable designs are returned with operating characteristics. Stopping boundaries and visualisations are also available. The package can find designs using other approaches, for example designs by Simon (1989) <doi:10.1016/0197-2456(89)90015-9> and Mander and Thompson (2010) <doi:10.1016/j.cct.2010.07.008>. Other features: compare and visualise designs using a weighted sum of expected sample sizes under the null and alternative hypotheses and maximum sample size; visualise any binary outcome design.
Author: Martin Law [aut, cre]
Maintainer: Martin Law <martin.law@mrc-bsu.cam.ac.uk>
Diff between curtailment versions 0.2.0 dated 2022-08-05 and 0.2.6 dated 2023-10-25
DESCRIPTION | 12 +++++++----- MD5 | 23 +++++++++++++---------- NEWS.md | 24 ++++++++++++++++++++++++ R/find2stageDesigns.R | 9 +++++---- R/findDesignsGivenCohortStage.R | 17 +++++++++-------- R/findSingleSimonDesign.R | 4 ++-- R/print.curtailment_simon.R |only R/simonEfficacy.R | 21 ++++++++------------- R/simonEfficacy_alternative.R |only R/simonEfficacy_deprecated.R |only README.md | 20 ++++++++++++++++++++ build/partial.rdb |binary man/find2stageDesigns.Rd | 8 ++++---- man/findSingleSimonDesign.Rd | 4 ++-- 14 files changed, 94 insertions(+), 48 deletions(-)
Title: A Wrapper to the 'BambooHR' API
Description: Enables a user to consume the 'BambooHR' API endpoints using R. The
actual URL of the API will depend on your company domain, and will be handled
by the package automatically once you setup the config file. The API documentation
can be found here <https://documentation.bamboohr.com/docs>.
Author: Tom Bowling [aut, cre],
Tim Fry [aut],
Harry Alexander [ctb],
Andrew Little [ctb],
Mark Druffel [ctb]
Maintainer: Tom Bowling <tom.bowling@ascent.io>
Diff between bambooHR versions 0.1.0 dated 2022-03-15 and 0.1.1 dated 2023-10-25
DESCRIPTION | 17 ++++++++--------- MD5 | 26 +++++++++++++------------- NAMESPACE | 4 ++++ R/build_url.r | 2 +- R/get_company_file.R | 2 ++ R/get_employee_file.R | 2 ++ R/get_report.R | 1 + R/get_request.R | 5 ++--- man/ISO_8601.Rd | 6 +++--- man/bambooHR-package.Rd | 4 ++-- man/build_url.Rd | 2 +- man/date_formats.Rd | 8 ++++---- man/get_meta.Rd | 3 +-- man/get_request.Rd | 5 +---- 14 files changed, 45 insertions(+), 42 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-19 1.0
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'PubMed', 'Endnote', and
'Bibentry'. Includes a port of the 'bibutils' utilities by Chris
Putnam <https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] ),
Chris Putman [aut] ,
Richard Mathar [ctb] ,
Johannes Wilm [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.15 dated 2023-08-21 and 2.2.16 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ build/partial.rdb |binary src/name.c | 8 +++++--- 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Kernel Change Point Detection on the Running Statistics
Description: The running statistics of interest is first extracted using a time window which is slid across the time series, and in each window, the running statistics value is computed. KCP (Kernel Change Point) detection proposed by Arlot et al. (2012) <arXiv:1202.3878> is then implemented to flag the change points on the running statistics (Cabrieto et al., 2018, <doi:10.1016/j.ins.2018.03.010>). Change points are located by minimizing a variance criterion based on the pairwise similarities between running statistics which are computed via the Gaussian kernel. KCP can locate change points for a given k number of change points. To determine the optimal k, the KCP permutation test is first carried out by comparing the variance of the running statistics extracted from the original data to that of permuted data. If this test is significant, then there is sufficient evidence for at least one change point in the data. Model selection is then used to determine the optimal k>0.
Author: Jedelyn Cabrieto [aut],
Kristof Meers [aut, cre],
Evelien Schat [ctb],
Janne Adolf [ctb],
Peter Kuppens [ctb],
Francis Tuerlinckx [ctb],
Eva Ceulemans [ctb]
Maintainer: Kristof Meers <kristof.meers+cran@kuleuven.be>
Diff between kcpRS versions 1.1.0 dated 2023-01-19 and 1.1.1 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ man/kcpRS-package.Rd | 7 ------- 4 files changed, 9 insertions(+), 13 deletions(-)
Title: Fast and Versatile Argument Checks
Description: Tests and assertions to perform frequent argument checks. A
substantial part of the package was written in C to minimize any worries
about execution time overhead.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [ctb],
Denes Toth [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between checkmate versions 2.2.0 dated 2023-04-27 and 2.3.0 dated 2023-10-25
DESCRIPTION | 6 LICENSE | 1 MD5 | 28 ++-- NEWS.md | 7 + R/checkAtomic.R | 3 R/checkPathForOutput.R | 4 R/checkScalarNA.R | 2 build/vignette.rds |binary inst/doc/checkmate.R | 4 inst/doc/checkmate.html | 236 +++++++++++++++++------------------- inst/doc/tinytest.html | 4 man/checkAtomic.Rd | 3 man/checkPathForOutput.Rd | 2 tests/testthat/test_checkAtomic.R | 4 tests/testthat/test_checkScalarNA.R | 5 15 files changed, 161 insertions(+), 148 deletions(-)
Title: Subset Partitioning via Anticlustering
Description: The method of anticlustering partitions a pool of elements
into groups (i.e., anticlusters) with the goal of maximizing
between-group similarity or within-group heterogeneity. The
anticlustering approach thereby reverses the logic of cluster analysis
that strives for high within-group homogeneity and clear separation
between groups. Computationally, anticlustering is accomplished by
maximizing instead of minimizing a clustering objective function, such
as the intra-cluster variance (used in k-means clustering) or the sum
of pairwise distances within clusters. The main function
anticlustering() gives access to exact and heuristic anticlustering
methods described in Papenberg and Klau (2021;
<doi:10.1037/met0000301>), Brusco et al. (2020;
<doi:10.1111/bmsp.12186>), and Papenberg (2023;
<doi:10.1111/bmsp.12315>). The exact algorithms require that an
integer linear programming solver is installed, either the GNU linear
programming kit (<https://www.gnu.org/software/g [...truncated...]
Author: Martin Papenberg [aut, cre] ,
Meik Michalke [ctb] ,
Gunnar W. Klau [ths],
Juliane V. Nagel [ctb] ,
Martin Breuer [ctb] ,
Marie L. Schaper [ctb] ,
Max Diekhoff [ctb]
Maintainer: Martin Papenberg <martin.papenberg@hhu.de>
Diff between anticlust versions 0.8.0 dated 2023-09-13 and 0.8.0-1 dated 2023-10-25
DESCRIPTION | 6 - MD5 | 20 ++--- inst/doc/Speeding_up_anticlustering.html | 26 +++--- src/categorical-contraints.c | 45 +++-------- src/declarations.h | 39 +++++----- src/dispersion_anticlustering.c | 32 ++++---- src/distance-anticlustering.c | 32 ++++---- src/free-memory.c | 6 - src/kmeans-anticlustering.c | 118 +++++++------------------------ src/set-up-data-structures.c | 22 ++--- src/variance-objective.c | 2 11 files changed, 135 insertions(+), 213 deletions(-)
Title: Dereplicate and Cherry-Pick Mass Spectrometry Spectra
Description: Convenient wrapper functions for the analysis of
matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF)
spectra data in order to select only representative spectra (also
called cherry-pick). The package covers the preprocessing and
dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik
(2018) <doi:10.3389/fmicb.2018.01294>) needed to cluster MALDI-TOF
spectra before the final cherry-picking step. It enables the easy
exclusion of spectra and/or clusters to accommodate complex
cherry-picking strategies. Alternatively, cherry-picking using
taxonomic identification MALDI-TOF data is made easy with functions to
import inconsistently formatted reports.
Author: Charlie Pauvert [aut, cre, cph]
,
David Wylensek [ctb] ,
Selina Nuechtern [ctb],
Thomas Clavel [ctb, fnd, cph]
Maintainer: Charlie Pauvert <cpauvert@ukaachen.de>
Diff between maldipickr versions 1.1.1 dated 2023-09-07 and 1.2.0 dated 2023-10-25
DESCRIPTION | 7 - MD5 | 43 +++++---- NEWS.md | 19 ++++ R/check_spectra.R | 25 ++++- R/delineate_with_similarity.R | 69 ++++++---------- R/import_biotyper_spectra.R | 4 R/is_a_processed_spectra_list.R | 9 -- R/is_a_rds_list.R | 4 R/merge_processed_spectra.R | 8 - R/process_spectra.R | 14 +-- README.md | 15 ++- inst/doc/dereplicate-bruker-maldi-biotyper-spectra.Rmd | 14 +-- inst/doc/dereplicate-bruker-maldi-biotyper-spectra.html | 34 ++++--- inst/doc/import-data-from-bruker-maldi-biotyper.html | 12 +- inst/three_processed_spectra_with_one_peakless.RDS |only man/check_spectra.Rd | 5 - man/delineate_with_similarity.Rd | 24 +---- tests/testthat/test-check_spectra.R | 20 ++++ tests/testthat/test-delineate_with_similarity.R | 44 ++++++---- tests/testthat/test-is_a_processed_spectra_list.R | 3 tests/testthat/test-merge_processed_spectra.R | 54 ++++++++++++ tests/testthat/test-pick_spectra.R | 18 ++++ vignettes/dereplicate-bruker-maldi-biotyper-spectra.Rmd | 14 +-- 23 files changed, 291 insertions(+), 168 deletions(-)
Title: Analyzing Data with Cellwise Outliers
Description: Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.1007/s10994-021-05960-5> (open access),
Raymaekers and Rousseeuw (2021) <doi:10.52933/jdssv.v1i3.18> (open access),
Raymaekers and Rousseeuw (2022) <arXiv:2207.13493> (open access)
Rousseeuw (2022) <doi:10.1016/j.ecosta.2023.01.007> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples",
"DI_examples", "cellMCD_examples" , "Correspondence_analysis_examples",
and "cellwise_weights_examples".
Author: Jakob Raymaekers [aut, cre],
Peter Rousseeuw [aut],
Wannes Van den Bossche [ctb],
Mia Hubert [ctb]
Maintainer: Jakob Raymaekers <jakob.raymaekers@kuleuven.be>
Diff between cellWise versions 2.5.2 dated 2023-04-20 and 2.5.3 dated 2023-10-25
DESCRIPTION | 10 MD5 | 114 ++-- R/ICPCA.R | 28 - R/MacroPCA.R | 58 +- R/MacroPCApredict.R | 48 +- R/TVCN.R | 7 R/Wrap.R | 4 R/cellMCD.R | 69 +- R/cellMap.R | 528 +++++++++------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Correspondence_analysis_examples.R | 34 - inst/doc/Correspondence_analysis_examples.Rmd | 33 - inst/doc/Correspondence_analysis_examples.html | 242 ++++++---- inst/doc/DDC_examples.R | 113 +--- inst/doc/DDC_examples.Rmd | 111 +--- inst/doc/DDC_examples.html | 585 ++++++++++++++----------- inst/doc/DI_examples.R | 56 -- inst/doc/DI_examples.Rmd | 58 +- inst/doc/DI_examples.html | 256 ++++++---- inst/doc/MacroPCA_examples.R | 108 +--- inst/doc/MacroPCA_examples.Rmd | 110 +--- inst/doc/MacroPCA_examples.html | 452 +++++++++++-------- inst/doc/cellMCD_examples.R | 67 +- inst/doc/cellMCD_examples.Rmd | 96 +--- inst/doc/cellMCD_examples.html | 549 ++++++++++++++--------- inst/doc/cellwise_weights_examples.R | 13 inst/doc/cellwise_weights_examples.Rmd | 13 inst/doc/cellwise_weights_examples.html | 184 +++++-- inst/doc/transfo_examples.R | 58 +- inst/doc/transfo_examples.Rmd | 64 +- inst/doc/transfo_examples.html | 317 +++++++++---- inst/doc/wrap_examples.R | 15 inst/doc/wrap_examples.Rmd | 19 inst/doc/wrap_examples.html | 241 ++++++---- man/DDC.Rd | 5 man/DI.Rd | 62 +- man/ICPCA.Rd | 43 - man/MacroPCA.Rd | 27 - man/MacroPCApredict.Rd | 36 - man/cellHandler.Rd | 26 - man/cellMCD.Rd | 84 +-- man/cellMap.Rd | 80 +-- man/data_VOC.Rd | 2 man/plot_cellMCD.Rd | 4 man/transfo.Rd | 16 man/transfo_newdata.Rd | 8 man/transfo_transformback.Rd | 6 man/unpack.Rd | 3 man/weightedEM.Rd | 3 vignettes/Correspondence_analysis_examples.Rmd | 33 - vignettes/DDC_examples.Rmd | 111 +--- vignettes/DI_examples.Rmd | 58 +- vignettes/MacroPCA_examples.Rmd | 110 +--- vignettes/cellMCD_examples.Rmd | 96 +--- vignettes/cellwise_weights_examples.Rmd | 13 vignettes/transfo_examples.Rmd | 64 +- vignettes/wrap_examples.Rmd | 19 58 files changed, 2945 insertions(+), 2624 deletions(-)
Title: Steve's Toy Data for Teaching About a Variety of Methodological,
Social, and Political Topics
Description: This is a collection of various kinds of data with broad uses for teaching.
My students, and academics like me who teach the same topics I teach, should find
this useful if their teaching workflow is also built around the R programming
language. The applications are multiple but mostly cluster on topics of statistical
methodology, international relations, and political economy.
Author: Steve Miller [aut, cre]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevedata versions 1.0.0 dated 2023-05-30 and 1.1.0 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 39 ++++++++++++++++++++++++--------------- NEWS.md | 8 ++++++++ R/rd-GHR04.R |only R/rd-Lipset59.R |only R/rd-co2emissions.R | 16 ++++++---------- R/rd-mm_nhis.R | 2 +- R/rd-mm_randhie.R | 2 +- R/rd-scb_regions.R |only R/rd-sealevels.R | 2 +- R/rd-so2concentrations.R | 2 +- R/rd-yugo_sales.R | 11 ++++++----- build/partial.rdb |binary data/GHR04.rda |only data/Lipset59.rda |only data/scb_regions.rda |only man/GHR04.Rd |only man/Lipset59.Rd |only man/co2emissions.Rd | 16 ++++++---------- man/mm_nhis.Rd | 2 +- man/mm_randhie.Rd | 2 +- man/scb_regions.Rd |only man/sealevels.Rd | 2 +- man/so2concentrations.Rd | 2 +- man/yugo_sales.Rd | 11 ++++++----- 25 files changed, 67 insertions(+), 56 deletions(-)
Title: Hybrid FA-CFA for Controlling Acquiescence in Restricted
Factorial Solutions
Description: Performs hybrid multi-stage factor analytic procedure for controlling acquiescence in restricted solutions (Ferrando & Lorenzo-Seva, 2000 <https://www.uv.es/revispsi/articulos3.00/ferran7.pdf>).
Author: David Navarro-Gonzalez [aut, cre],
Pere J. Ferrando [aut],
Fabia Morales-Vives [aut],
Ana Hernandez-Dorado [aut]
Maintainer: David Navarro-Gonzalez <david.navarro@urv.cat>
Diff between siren versions 1.0.3 dated 2023-08-08 and 1.0.4 dated 2023-10-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/acquihybrid.R | 14 +++++++++----- build/partial.rdb |binary 4 files changed, 16 insertions(+), 12 deletions(-)
Title: Cubature over Polygonal Domains
Description: Numerical integration of continuously differentiable
functions f(x,y) over simple closed polygonal domains.
The following cubature methods are implemented:
product Gauss cubature (Sommariva and Vianello, 2007,
<doi:10.1007/s10543-007-0131-2>),
the simple two-dimensional midpoint rule
(wrapping 'spatstat.geom' functions), and
adaptive cubature for radially symmetric functions via line
integrate() along the polygon boundary (Meyer and Held, 2014,
<doi:10.1214/14-AOAS743>, Supplement B).
For simple integration along the axes, the 'cubature' package
is more appropriate.
Author: Sebastian Meyer [aut, cre, trl]
,
Leonhard Held [ths],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between polyCub versions 0.8.1 dated 2022-11-28 and 0.9.0 dated 2023-10-25
DESCRIPTION | 22 ++++++------- MD5 | 72 ++++++++++++++++++++++----------------------- NEWS.md | 14 ++++++++ R/circleCub.R | 3 - R/coerce-gpc-methods.R | 45 +++++++++++++--------------- R/coerce-sp-methods.R | 7 +--- R/plotpolyf.R | 3 - R/polyCub.SV.R | 2 - R/polyCub.exact.Gauss.R | 55 ++++++++++++++++++---------------- R/polyCub.iso.R | 2 - R/polyCub.midpoint.R | 2 - R/sfg2gpc.R | 52 +++++++++++++++----------------- R/xylist.R | 3 - R/zzz.R | 59 +++++++++++------------------------- README.md | 15 +++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 1 inst/doc/polyCub.R | 2 - inst/doc/polyCub.Rmd | 22 ++++++++----- inst/doc/polyCub.html | 40 +++++++++++++------------ man/circleCub.Gauss.Rd | 3 - man/coerce-gpc-methods.Rd | 39 ++++++++++++------------ man/coerce-sp-methods.Rd | 7 +--- man/gpclibPermit.Rd | 11 ++++-- man/plot_polyregion.Rd | 3 - man/plotpolyf.Rd | 3 - man/polyCub-package.Rd | 26 +++++----------- man/polyCub.Rd | 3 - man/polyCub.SV.Rd | 5 +-- man/polyCub.exact.Gauss.Rd | 33 ++++++++++---------- man/polyCub.iso.Rd | 5 +-- man/polyCub.midpoint.Rd | 2 - man/sfg2gpc.Rd | 52 ++++++++++++++++---------------- man/xylist.Rd | 3 - tests/test-polyCub.R | 5 +-- vignettes/polyCub.Rmd | 22 ++++++++----- 37 files changed, 311 insertions(+), 332 deletions(-)
Title: Retrieve Weather Data from the Open-Meteo API
Description: A client for the Open-Meteo API that retrieves Open-Meteo
weather data in a tidy format. No API key is required. The API specification
is located at <https://open-meteo.com/en/docs>.
Author: Tom Pisel [aut, cre, cph]
Maintainer: Tom Pisel <mail@tompisel.com>
Diff between openmeteo versions 0.2.3 dated 2023-10-17 and 0.2.4 dated 2023-10-25
openmeteo-0.2.3/openmeteo/tests/testthat/climate-api.open-meteo.com/v1/climate-e8dc3c.json |only openmeteo-0.2.4/openmeteo/DESCRIPTION | 6 openmeteo-0.2.4/openmeteo/MD5 | 76 - openmeteo-0.2.4/openmeteo/NEWS.md | 4 openmeteo-0.2.4/openmeteo/R/air_quality.R | 1 openmeteo-0.2.4/openmeteo/R/climate_forecast.R | 7 openmeteo-0.2.4/openmeteo/R/marine_forecast.R | 1 openmeteo-0.2.4/openmeteo/R/river_discharge.R | 1 openmeteo-0.2.4/openmeteo/R/utils.R | 4 openmeteo-0.2.4/openmeteo/R/weather_forecast.R | 1 openmeteo-0.2.4/openmeteo/R/weather_history.R | 1 openmeteo-0.2.4/openmeteo/man/climate_forecast.Rd | 3 openmeteo-0.2.4/openmeteo/tests/testthat/air-quality-api.open-meteo.com/v1/air-quality-28475d.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-073b9d.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-4418bd.json | 632 +++++----- openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-5c7be9.R | 12 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-7d2d21.R | 12 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-b38ace.json | 10 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-d1305e.json | 10 openmeteo-0.2.4/openmeteo/tests/testthat/api.open-meteo.com/v1/forecast-dfbcef.json | 10 openmeteo-0.2.4/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-43cae1.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-466132.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/archive-api.open-meteo.com/v1/archive-f5378f.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/climate-api.open-meteo.com/v1/climate-1f9a08.json |only openmeteo-0.2.4/openmeteo/tests/testthat/flood-api.open-meteo.com/v1/flood-da69b0.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-03439e.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-053f48.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-2728d6.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-307695.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-3581ca.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-3655a5.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-415fcc.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-4200be.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-62759c.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-83a9f2.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-93c3e8.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-d132b4.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/geocoding-api.open-meteo.com/v1/search-ecd5a0.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/marine-api.open-meteo.com/v1/marine-205c9e.json | 2 openmeteo-0.2.4/openmeteo/tests/testthat/test-utils.R | 2 40 files changed, 427 insertions(+), 406 deletions(-)
Title: Gross Flows Estimation under Complex Surveys
Description: The philosophy in the package is described in Stasny (1988) <doi:10.2307/1391558> and Gutierrez, A., Trujillo, L. & Silva, N. (2014), <ISSN:1492-0921> to estimate the gross flows under complex surveys using a Markov chain approach with non response.
Author: Acero William <wfaceror@unal.edu.co>, Gutierrez Andres <andres.gutierrez@un.org>, Trujillo Leonardo <ltrujillo@unal.edu.co>
Maintainer: Acero William <wfaceror@unal.edu.co>
Diff between GFE versions 0.1.0 dated 2018-08-02 and 0.1.1 dated 2023-10-25
DESCRIPTION | 15 MD5 | 12 R/AuxFunctions.R | 2 R/civ_models.R | 728 +++++++++++++++++++++++----------------------- man/estGF.Rd | 13 man/reSamGF.Rd | 11 man/round_preserve_sum.Rd | 2 7 files changed, 397 insertions(+), 386 deletions(-)
Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists.
The package includes commands for measures of association and impact for case control studies and cohort studies.
It may be particularly useful for outbreak investigations including univariable analysis and stratified analysis.
The functions for cohort studies include the CS(), CSTable() and CSInter() commands.
The functions for case control studies include the CC(), CCTable() and CCInter() commands.
References - Cornfield, J. 1956. A statistical problem arising from retrospective studies. In Vol. 4 of Proceedings of the Third Berkeley Symposium, ed. J. Neyman, 135-148. Berkeley, CA - University of California Press.
Woolf, B. 1955. On estimating the relation between blood group disease.
Annals of Human Genetics 19 251-253. Reprinted in Evolution of Epidemiologic Ideas Annotated Readings on Concepts and Methods, ed. S. Greenland, pp. 108-110.
Newton Lower Falls, MA Epidemiology Resources.
Gilles Desve & Peter Makary, 2007. 'CSTABLE [...truncated...]
Author: Jean Pierre Decorps [aut],
Esther Kissling [ctb],
Lore Merdrignac [cre]
Maintainer: Lore Merdrignac <l.merdrignac@epiconcept.fr>
Diff between EpiStats versions 1.6-1 dated 2023-09-19 and 1.6-2 dated 2023-10-25
EpiStats-1.6-1/EpiStats/R/CC.R |only EpiStats-1.6-2/EpiStats/DESCRIPTION | 14 EpiStats-1.6-2/EpiStats/MD5 | 49 - EpiStats-1.6-2/EpiStats/NAMESPACE | 52 - EpiStats-1.6-2/EpiStats/R/01_EpiFuns.R | 532 ++++++++--------- EpiStats-1.6-2/EpiStats/R/CCInter_.R | 775 +++++++++++++------------ EpiStats-1.6-2/EpiStats/R/CCTable_.R | 278 ++++---- EpiStats-1.6-2/EpiStats/R/CC_.R | 359 ++++++----- EpiStats-1.6-2/EpiStats/R/CSInter_.R | 621 ++++++++++---------- EpiStats-1.6-2/EpiStats/R/CSTable.R | 267 ++++---- EpiStats-1.6-2/EpiStats/R/CS_.R | 432 +++++++------ EpiStats-1.6-2/EpiStats/R/EpiStatsFun.R | 53 + EpiStats-1.6-2/EpiStats/R/crosstable.R | 278 ++++---- EpiStats-1.6-2/EpiStats/R/orderFactors.R | 36 - EpiStats-1.6-2/EpiStats/inst/doc/EpiStats.R | 12 EpiStats-1.6-2/EpiStats/inst/doc/EpiStats.Rmd | 12 EpiStats-1.6-2/EpiStats/inst/doc/EpiStats.pdf |binary EpiStats-1.6-2/EpiStats/man/CC.Rd | 164 ++--- EpiStats-1.6-2/EpiStats/man/CCInter.Rd | 148 ++-- EpiStats-1.6-2/EpiStats/man/CCTable.Rd | 154 ++-- EpiStats-1.6-2/EpiStats/man/CS.Rd | 142 ++-- EpiStats-1.6-2/EpiStats/man/CSInter.Rd | 132 ++-- EpiStats-1.6-2/EpiStats/man/CSTable.Rd | 150 ++-- EpiStats-1.6-2/EpiStats/man/crossTable.Rd | 100 +-- EpiStats-1.6-2/EpiStats/man/orderFactors.Rd | 88 +- EpiStats-1.6-2/EpiStats/vignettes/EpiStats.Rmd | 12 26 files changed, 2581 insertions(+), 2279 deletions(-)
Title: Create and Query a Local Copy of 'GenBank' in R
Description: Download large sections of
'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and generate a local
SQL-based database. A user can then query this database using 'restez'
functions or through 'rentrez' <https://CRAN.R-project.org/package=rentrez>
wrappers.
Author: Joel H. Nitta [aut, cre] ,
Dom Bennett [aut]
Maintainer: Joel H. Nitta <joelnitta@gmail.com>
Diff between restez versions 2.1.3 dated 2022-11-11 and 2.1.4 dated 2023-10-25
DESCRIPTION | 8 - MD5 | 150 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 8 + R/download-tools.R | 10 -- R/status-tools.R | 8 + README.md | 4 inst/CITATION | 46 ++++++++--- man/add_rcrd_log.Rd | 1 man/cat_line.Rd | 1 man/char.Rd | 1 man/check_connection.Rd | 1 man/cleanup.Rd | 1 man/connected.Rd | 1 man/connection_get.Rd | 1 man/db_download_intern.Rd | 1 man/db_sqlngths_get.Rd | 1 man/db_sqlngths_log.Rd | 1 man/dir_size.Rd | 1 man/dwnld_path_get.Rd | 1 man/dwnld_rcrd_log.Rd | 1 man/entrez_fasta_get.Rd | 1 man/entrez_gb_get.Rd | 1 man/extract_accession.Rd | 1 man/extract_by_patterns.Rd | 1 man/extract_clean_sequence.Rd | 1 man/extract_definition.Rd | 1 man/extract_features.Rd | 1 man/extract_inforecpart.Rd | 1 man/extract_keywords.Rd | 1 man/extract_locus.Rd | 1 man/extract_organism.Rd | 1 man/extract_seqrecpart.Rd | 1 man/extract_sequence.Rd | 1 man/extract_version.Rd | 1 man/file_download.Rd | 1 man/filename_log.Rd | 1 man/flatfile_read.Rd | 1 man/gb_build.Rd | 1 man/gb_df_create.Rd | 1 man/gb_df_generate.Rd | 1 man/gb_sql_add.Rd | 1 man/gb_sql_query.Rd | 1 man/gbrelease_check.Rd | 1 man/gbrelease_get.Rd | 1 man/gbrelease_log.Rd | 1 man/has_data.Rd | 1 man/identify_downloadable_files.Rd | 1 man/last_add_get.Rd | 1 man/last_dwnld_get.Rd | 1 man/last_entry_get.Rd | 1 man/latest_genbank_release.Rd | 1 man/latest_genbank_release_notes.Rd | 1 man/message_missing.Rd | 1 man/mock_def.Rd | 1 man/mock_gb_df_generate.Rd | 1 man/mock_org.Rd | 1 man/mock_rec.Rd | 1 man/mock_seq.Rd | 1 man/predict_datasizes.Rd | 1 man/print.status.Rd | 77 +----------------- man/readme_log.Rd | 1 man/restez_connect.Rd | 1 man/restez_disconnect.Rd | 1 man/restez_path_check.Rd | 1 man/restez_rl.Rd | 1 man/search_gz.Rd | 1 man/seshinfo_log.Rd | 1 man/setup.Rd | 1 man/slctn_get.Rd | 1 man/slctn_log.Rd | 1 man/sql_path_get.Rd | 1 man/stat.Rd | 1 man/status_class.Rd | 1 man/testdatadir_get.Rd | 1 tests/testthat/test-status-tools.R | 2 76 files changed, 140 insertions(+), 240 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <arXiv:1712.0036v1>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang and Junfang Chen
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>
Diff between BioM2 versions 1.0.1 dated 2023-09-27 and 1.0.2 dated 2023-10-25
BioM2-1.0.1/BioM2/man/VisMulti.Rd |only BioM2-1.0.2/BioM2/DESCRIPTION | 15 - BioM2-1.0.2/BioM2/MD5 | 24 + BioM2-1.0.2/BioM2/NAMESPACE | 14 BioM2-1.0.2/BioM2/NEWS | 10 BioM2-1.0.2/BioM2/R/BioM2.R | 436 ++++++++++++++++++++++++++++-- BioM2-1.0.2/BioM2/R/data.R | 35 ++ BioM2-1.0.2/BioM2/data/TransAnno.rda |only BioM2-1.0.2/BioM2/data/TransData_Test.rda |only BioM2-1.0.2/BioM2/man/MethylAnno.Rd | 4 BioM2-1.0.2/BioM2/man/MethylData_Test.Rd | 4 BioM2-1.0.2/BioM2/man/PlotCorModule.Rd |only BioM2-1.0.2/BioM2/man/PlotPathFearture.Rd |only BioM2-1.0.2/BioM2/man/PlotPathInner.Rd |only BioM2-1.0.2/BioM2/man/PlotPathNet.Rd |only BioM2-1.0.2/BioM2/man/TransAnno.Rd |only BioM2-1.0.2/BioM2/man/TransData_Test.Rd |only BioM2-1.0.2/BioM2/man/VisMultiModule.Rd |only 18 files changed, 496 insertions(+), 46 deletions(-)
Title: Easily Create Production-Ready Rich Text Format (RTF) Table and
Figure
Description: Create production-ready Rich Text Format (RTF) table and figure
with flexible format.
Author: Yilong Zhang [aut],
Siruo Wang [aut],
Simiao Ye [aut],
Fansen Kong [aut],
Brian Lang [aut],
Benjamin Wang [aut, cre],
Nan Xiao [ctb],
Madhusudhan Ginnaram [ctb],
Ruchitbhai Patel [ctb],
Huei-Ling Chen [ctb],
Peikun Wu [ctb],
Uday Preetham Palukuru [c [...truncated...]
Maintainer: Benjamin Wang <benjamin.wang@merck.com>
Diff between r2rtf versions 1.1.0 dated 2023-07-10 and 1.1.1 dated 2023-10-25
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NEWS.md | 17 ++++++++++++++--- R/conversion.R | 12 ++++++------ R/data.R | 4 ++-- R/rtf_convert_format.R | 12 ++++++------ R/rtf_rich_text.R | 4 ++-- man/r2rtf_HAMD17.Rd | 4 ++-- man/utf8Tortf.Rd | 10 +++++----- 9 files changed, 53 insertions(+), 42 deletions(-)
Title: Multipopulation Evolutionary Strategy HMS
Description: The HMS (Hierarchic Memetic Strategy) is a composite global optimization
strategy consisting of a multi-population evolutionary strategy and some
auxiliary methods. The HMS makes use of a dynamically-evolving data structure
that provides an organization among the component populations. It is a tree
with a fixed maximal height and variable internal node degree. Each component
population is governed by a particular evolutionary engine. This package
provides a simple R implementation with examples of using different genetic
algorithms as the population engines. References: J. Sawicki, M. Łoś,
M. Smołka, J. Alvarez-Aramberri (2022) <doi:10.1007/s11047-020-09836-w>.
Author: Wojciech Achtelik [aut, cre],
Marcin Kozubek [aut],
Maciej Smolka [ths, aut] ,
AGH University of Krakow [cph]
Maintainer: Wojciech Achtelik <wachtelik@gmail.com>
Diff between hmsr versions 1.0.0 dated 2023-10-12 and 1.0.1 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 +++----- R/sprouting_condition.R | 13 +++++-------- man/sc_max_metric.Rd | 6 +++--- tests/testthat/test-hms.R | 8 ++++---- 6 files changed, 23 insertions(+), 28 deletions(-)
Title: Diagnostics for OMOP Common Data Model Drug Records
Description: Ingredient specific diagnostics for drug exposure records in the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Ger Inberg [aut, cre] ,
Edward Burn [aut] ,
Yuchen Guo [ctb] ,
Marti Catala [ctb] ,
Mike Du [ctb] ,
Theresa Burkard [ctb] ,
Xintong Li [ctb] ,
Ross Williams [ctb] ,
Erasmus MC [cph]
Maintainer: Ger Inberg <g.inberg@erasmusmc.nl>
Diff between DrugExposureDiagnostics versions 0.4.7 dated 2023-10-16 and 1.0.0 dated 2023-10-25
DrugExposureDiagnostics-0.4.7/DrugExposureDiagnostics/vignettes/articles |only DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/DESCRIPTION | 6 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/MD5 | 27 +-- DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/NEWS.md | 15 +- DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/R/executeChecks.R | 4 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/R/obscureCounts.R | 6 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/inst/doc/Introduction_to_DrugExposureDiagnostics.R | 2 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/inst/doc/Introduction_to_DrugExposureDiagnostics.Rmd | 5 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/inst/doc/Introduction_to_DrugExposureDiagnostics.html | 9 - DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/inst/doc/Summary_of_checks.html | 70 +++++----- DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/man/executeChecks.Rd | 4 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/man/executeChecksSingleIngredient.Rd | 4 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/tests/testthat/test-Eunomia.R | 4 DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/tests/testthat/test-ObscureCounts.R | 33 ++-- DrugExposureDiagnostics-1.0.0/DrugExposureDiagnostics/vignettes/Introduction_to_DrugExposureDiagnostics.Rmd | 5 15 files changed, 105 insertions(+), 89 deletions(-)
More information about DrugExposureDiagnostics at CRAN
Permanent link
Title: Scrubbing and Other Data Cleaning Routines for fMRI
Description: Data-driven fMRI denoising with projection scrubbing (Pham et al
(2022) <doi:10.1016/j.neuroimage.2023.119972>). Also includes routines for
DVARS (Derivatives VARianceS) (Afyouni and Nichols (2018)
<doi:10.1016/j.neuroimage.2017.12.098>), motion scrubbing (Power et al
(2012) <doi:10.1016/j.neuroimage.2011.10.018>), aCompCor (anatomical
Components Correction) (Muschelli et al (2014)
<doi:10.1016/j.neuroimage.2014.03.028>), detrending, and nuisance
regression. Projection scrubbing is also applicable to other
outlier detection tasks involving high-dimensional data.
Author: Amanda Mejia [aut, cre],
John Muschelli [aut] ,
Damon Pham [aut] ,
Daniel McDonald [ctb],
Fatma Parlak [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between fMRIscrub versions 0.14.4 dated 2023-10-23 and 0.14.5 dated 2023-10-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- tests/testthat/test-test_all_methods.R | 9 ++------- tests/testthat/test-test_scrubbing.R | 7 ++----- 4 files changed, 10 insertions(+), 18 deletions(-)
Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for
Analysis and Visualization
Description: Provides a consistent API to pull United States Department of
Agriculture census and survey data from the National Agricultural
Statistics Service (NASS) QuickStats service.
Author: Brad Lindblad [aut, cre],
Michael Thomas [ctb],
Alex Mindeman [ctb]
Maintainer: Brad Lindblad <me@bradlindblad.com>
Diff between tidyUSDA versions 0.4.0 dated 2022-05-01 and 0.4.1 dated 2023-10-25
DESCRIPTION | 10 ++-- MD5 | 17 +++---- NEWS.md | 4 + R/getQuickstat.R | 10 ++-- R/plotting.R | 2 README.md | 24 ++++++---- build/vignette.rds |binary inst/doc/using_tidyusda.R | 8 +-- inst/doc/using_tidyusda.html | 103 ++++++++++++++++++++++--------------------- man/figures |only 10 files changed, 98 insertions(+), 80 deletions(-)
Title: Computes Proximity in Large Sparse Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large sparse matrices using the Armadillo and Intel TBB libraries.
Among several built-in similarity/distance measures, computation of correlation,
cosine similarity and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph]
,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.3.3 dated 2022-10-06 and 0.3.4 dated 2023-10-25
DESCRIPTION | 9 MD5 | 44 +- NAMESPACE | 26 - NEWS.md | 206 +++++----- R/RcppExports.R | 38 - R/proxy.R | 539 +++++++++++++------------- README.md | 238 +++++------ build/vignette.rds |binary inst/doc/measures.R | 6 inst/doc/measures.Rmd | 385 +++++++++--------- inst/doc/measures.html | 902 ++++++++++++++++++++++---------------------- man/colSds.Rd | 48 +- man/colZeros.Rd | 44 +- man/simil.Rd | 241 +++++------ src/Makevars | 3 src/Makevars.win | 1 src/pair.cpp | 15 tests/testthat.R | 6 tests/testthat/function.R | 312 +++++++-------- tests/testthat/test-dist.R | 646 +++++++++++++++---------------- tests/testthat/test-proxy.R | 378 +++++++++--------- tests/testthat/test-simil.R | 533 +++++++++++++------------- vignettes/measures.Rmd | 385 +++++++++--------- 23 files changed, 2546 insertions(+), 2459 deletions(-)
Title: Stepwise Elimination and Term Reordering for Mixed-Effects
Regression
Description: Finds the largest possible regression model that will still converge
for various types of regression analyses (including mixed models and generalized
additive models) and then optionally performs stepwise elimination similar to the
forward and backward effect-selection methods in SAS, based on the change in
log-likelihood or its significance, Akaike's Information Criterion, the Bayesian
Information Criterion, the explained deviance, or the F-test of the change in R².
Author: Cesko C. Voeten [aut, cre]
Maintainer: Cesko C. Voeten <cvoeten@gmail.com>
Diff between buildmer versions 2.10 dated 2023-09-11 and 2.11 dated 2023-10-25
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/buildmer-private.R | 3 +++ R/control.R | 6 +++--- R/directions.R | 18 +++++++----------- R/patchers.R | 2 +- inst/doc/buildmer.html | 11 ++++++++++- man/buildmerControl.Rd | 4 ++-- 9 files changed, 53 insertions(+), 29 deletions(-)