Title: Distance and Similarity Measures
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre],
Christian Buchta [aut]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between proxy versions 0.4-25 dated 2021-03-05 and 0.4-26 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/similarities.R | 14 +++++++------- build/vignette.rds |binary inst/NEWS.Rd | 12 ++++++++++++ inst/doc/overview.pdf |binary 6 files changed, 27 insertions(+), 15 deletions(-)
Title: Transformed Additive Gaussian Processes
Description: Implement the transformed additive Gaussian (TAG) process and the transformed approximately additive Gaussian (TAAG) process proposed in Lin and Joseph (2020) <DOI:10.1080/00401706.2019.1665592>. These functions can be used to model deterministic computer experiments, obtain predictions at new inputs, and quantify the uncertainty of the predictions. This research is supported by a U.S. National Science Foundation grant DMS-1712642 and a U.S. Army Research Office grant W911NF-17-1-0007.
Author: Li-Hsiang Lin and V. Roshan Joseph
Maintainer: Li-Hsiang Lin <llin79@gatech.edu>
Diff between TAG versions 0.2.1 dated 2020-08-27 and 0.5.1 dated 2021-06-07
DESCRIPTION | 8 ++++---- MD5 | 24 +++++++++++++----------- NAMESPACE | 5 +++++ R/Initial_TAG.R | 38 ++++++++++++++++++++++++++++---------- R/TAG1step.R |only man/Initial.TAG.Rd | 14 +++++++++++++- man/TAAG.Rd | 5 +++-- man/TAG.Rd | 2 +- man/TAG1step.Rd |only man/check.TAAG.Rd | 2 +- man/loocv.TAAG.Rd | 2 +- man/plot.TAG.Rd | 2 +- man/pred.TAAG.Rd | 5 +++-- man/pred.TAG.Rd | 2 +- 14 files changed, 74 insertions(+), 35 deletions(-)
Title: Miscellaneous Functions 'T. Yanagida'
Description: Miscellaneous functions for descriptive statistics (e.g., frequency table, cross tabulation, multilevel descriptive statistics, coefficient alpha and omega, and various effect size measures), missing data (e.g., descriptive statistics for missing data, missing data pattern and auxiliary variable analysis), data management (e.g., grand-mean and group-mean centering, recode variables and reverse code items, scale and group scores, reading and writing SPSS and Excel files), and statistical analysis (e.g., confidence intervals, collinearity diagnostics, Levene's test, t-test, z-test, and sample size determination).
Author: Takuya Yanagida [aut, cre]
Maintainer: Takuya Yanagida <takuya.yanagida@univie.ac.at>
Diff between misty versions 0.4.0 dated 2021-05-13 and 0.4.1 dated 2021-06-07
DESCRIPTION | 10 +- MD5 | 20 ++-- NEWS.md | 16 +++ R/as.na.R | 6 - R/cohens.d.R | 226 ++++++++++++++++++++++++++++++++++++------------- R/print.misty.object.R | 8 - R/test.welch.R | 23 ++-- R/write.mplus.R | 160 +++++++++++++++++++++++++--------- man/cohens.d.Rd | 63 ++++++------- man/test.welch.Rd | 24 ++--- man/write.mplus.Rd | 115 ++++++++++++------------ 11 files changed, 439 insertions(+), 232 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 3.1.7 dated 2021-04-08 and 3.1.8 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/00-endpoint.R | 4 ++-- R/distribution.R | 2 +- R/load_taxa.R | 15 ++++++++++++--- inst/WORDLIST | 1 + man/load_taxa.Rd | 4 ++++ tests/testthat.R | 2 +- 9 files changed, 37 insertions(+), 18 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://wikidata.org/> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] (<https://orcid.org/0000-0002-0515-9542>),
EDJNet [fnd]
Maintainer: Giorgio Comai <g@giorgiocomai.eu>
Diff between tidywikidatar versions 0.2.0 dated 2021-04-19 and 0.3.0 dated 2021-06-07
tidywikidatar-0.2.0/tidywikidatar/tests/testthat/test-cache_with_more_than_one_item.R |only tidywikidatar-0.2.0/tidywikidatar/tests/testthat/test-search.R |only tidywikidatar-0.3.0/tidywikidatar/DESCRIPTION | 11 tidywikidatar-0.3.0/tidywikidatar/MD5 | 104 - tidywikidatar-0.3.0/tidywikidatar/NAMESPACE | 10 tidywikidatar-0.3.0/tidywikidatar/NEWS.md | 9 tidywikidatar-0.3.0/tidywikidatar/R/tw_caching.R | 36 tidywikidatar-0.3.0/tidywikidatar/R/tw_check.R | 35 tidywikidatar-0.3.0/tidywikidatar/R/tw_connect_to_cache.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_filter.R | 74 tidywikidatar-0.3.0/tidywikidatar/R/tw_get.R | 988 ++-------- tidywikidatar-0.3.0/tidywikidatar/R/tw_get_cached_item.R | 132 - tidywikidatar-0.3.0/tidywikidatar/R/tw_get_cached_search.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_get_others.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_get_property.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_get_property_label_description.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_get_qualifiers.R | 517 +++-- tidywikidatar-0.3.0/tidywikidatar/R/tw_label.R | 26 tidywikidatar-0.3.0/tidywikidatar/R/tw_language_settings.R |only tidywikidatar-0.3.0/tidywikidatar/R/tw_search.R | 326 ++- tidywikidatar-0.3.0/tidywikidatar/R/tw_write_item_to_cache.R | 68 tidywikidatar-0.3.0/tidywikidatar/R/tw_write_search_to_cache.R |only tidywikidatar-0.3.0/tidywikidatar/README.md | 98 tidywikidatar-0.3.0/tidywikidatar/build |only tidywikidatar-0.3.0/tidywikidatar/inst/WORDLIST | 7 tidywikidatar-0.3.0/tidywikidatar/inst/doc |only tidywikidatar-0.3.0/tidywikidatar/man/tw_check_cached_items.Rd | 13 tidywikidatar-0.3.0/tidywikidatar/man/tw_check_search.Rd | 31 tidywikidatar-0.3.0/tidywikidatar/man/tw_connect_to_cache.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_disconnect_from_cache.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_filter.Rd | 26 tidywikidatar-0.3.0/tidywikidatar/man/tw_get.Rd | 19 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_cache_file.Rd | 4 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_cache_table_name.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_get_cached_item.Rd | 13 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_cached_qualifiers.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_cached_search.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_get_description.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_image.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_label.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_property.Rd | 19 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_property_description.Rd | 9 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_property_label.Rd | 12 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_qualifiers.Rd | 10 tidywikidatar-0.3.0/tidywikidatar/man/tw_get_qualifiers_single.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_get_single.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_get_wikipedia.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_label.Rd | 11 tidywikidatar-0.3.0/tidywikidatar/man/tw_search.Rd | 21 tidywikidatar-0.3.0/tidywikidatar/man/tw_search_item.Rd | 12 tidywikidatar-0.3.0/tidywikidatar/man/tw_search_property.Rd | 15 tidywikidatar-0.3.0/tidywikidatar/man/tw_search_single.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_set_language.Rd |only tidywikidatar-0.3.0/tidywikidatar/man/tw_write_item_to_cache.Rd | 18 tidywikidatar-0.3.0/tidywikidatar/man/tw_write_qualifiers_to_cache.Rd | 24 tidywikidatar-0.3.0/tidywikidatar/man/tw_write_search_to_cache.Rd |only tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-cache.R | 42 tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-get.R | 69 tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-get_many.R | 101 - tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-get_others.R |only tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-get_properties.R | 55 tidywikidatar-0.3.0/tidywikidatar/tests/testthat/test-get_qualifiers.R | 30 tidywikidatar-0.3.0/tidywikidatar/vignettes |only 63 files changed, 1631 insertions(+), 1439 deletions(-)
Title: Ridge Estimation of Precision Matrices from High-Dimensional
Data
Description: Proper L2-penalized maximum likelihood estimators for precision
matrices and supporting functions to employ these estimators in a graphical
modeling setting. For details see van Wieringen & Peeters (2016)
<doi:10.1016/j.csda.2016.05.012> and associated publications.
Author: Carel F.W. Peeters [aut, cre, cph]
(<https://orcid.org/0000-0001-5766-9969>),
Anders Ellern Bilgrau [aut, cph]
(<https://orcid.org/0000-0001-9875-2902>),
Wessel N. van Wieringen [aut] (<https://orcid.org/0000-0002-5100-9123>)
Maintainer: Carel F.W. Peeters <carel.peeters@wur.nl>
Diff between rags2ridges versions 2.2.4 dated 2020-12-08 and 2.2.5 dated 2021-06-07
rags2ridges-2.2.4/rags2ridges/inst/NEWS.Rd |only rags2ridges-2.2.4/rags2ridges/inst/RAGS.png |only rags2ridges-2.2.5/rags2ridges/DESCRIPTION | 41 ++- rags2ridges-2.2.5/rags2ridges/MD5 | 131 +++++----- rags2ridges-2.2.5/rags2ridges/NEWS.md |only rags2ridges-2.2.5/rags2ridges/R/rags2ridges-package.R | 4 rags2ridges-2.2.5/rags2ridges/R/rags2ridges.R | 72 ++--- rags2ridges-2.2.5/rags2ridges/R/rags2ridgesDepr.R | 8 rags2ridges-2.2.5/rags2ridges/R/rags2ridgesFused.R | 36 +- rags2ridges-2.2.5/rags2ridges/README.md | 22 - rags2ridges-2.2.5/rags2ridges/build |only rags2ridges-2.2.5/rags2ridges/inst/convert_news.R |only rags2ridges-2.2.5/rags2ridges/inst/doc |only rags2ridges-2.2.5/rags2ridges/inst/pkgdown |only rags2ridges-2.2.5/rags2ridges/man/ADdata.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/CNplot.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/Communities.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/DiffGraph.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMblockNullPenalty.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMblockTest.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMmutualInfo.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMnetworkStats.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMnetworkStats.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMpathStats.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/GGMpathStats.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/KLdiv.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/KLdiv.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/Ugraph.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/Union.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/adjacentMat.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/conditionNumberPlot.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/covML.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/covMLknown.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/createS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/default.penalty.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/default.target.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/default.target.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/edgeHeat.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/evaluateS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/evaluateSfit.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/figures |only rags2ridges-2.2.5/rags2ridges/man/fullMontyS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/fused.test.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/getKEGGPathway.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/is.Xlist.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/isSymmetricPD.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/kegg.target.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/loss.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.LOOCV.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.LOOCVauto.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.aLOOCV.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.kCV.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/optPenalty.kCVauto.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/pcor.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/plot.ptest.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/pooledS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/print.optPenaltyFusedGrid.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/print.ptest.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/pruneMatrix.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/rags2ridges-package.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/ridgeP.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/ridgeP.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/ridgePathS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/ridgeS.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/sparsify.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/sparsify.fused.Rd | 2 rags2ridges-2.2.5/rags2ridges/man/symm.Rd | 2 rags2ridges-2.2.5/rags2ridges/vignettes |only 69 files changed, 222 insertions(+), 198 deletions(-)
Title: Ordinal Relations
Description: Functions to handle ordinal relations reflected within the feature space. Those function allow to search for ordinal relations in multi-class datasets. One can check whether proposed relations are reflected in a specific feature representation. Furthermore, it provides functions to filter, organize and further analyze those ordinal relations.
Author: L Lausser, LM Schaefer, HA Kestler
Maintainer: HA Kestler <hans.kestler@uni-ulm.de>
Diff between ORION versions 1.0.1 dated 2020-05-15 and 1.0.2 dated 2021-06-07
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- R/esl-data.R | 2 +- R/esl_org-data.R | 2 +- R/tunePareto.occ.R | 2 +- build/vignette.rds |binary inst/NEWS.Rd |only inst/doc/ORION.html | 47 ++++++++++++++++++++++++++++++++++++++++------- man/esl.Rd | 2 +- man/esl_org.Rd | 2 +- 10 files changed, 59 insertions(+), 25 deletions(-)
Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists.
They include commands for measures of association and impact for case control studies and cohort studies.
They may be particularly useful for outbreak investigations and include univariate and stratified analyses.
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.
Author: Jean Pierre Decorps [aut, cre]
Maintainer: Jean Pierre Decorps <jean.pierre.decorps@gmail.com>
Diff between EpiStats versions 1.4-1 dated 2020-04-15 and 1.5-1 dated 2021-06-07
DESCRIPTION | 8 +++--- MD5 | 16 ++++++------- R/01_EpiFuns.R | 3 +- R/CCInter_.R | 20 +++++++++++----- R/CC_.R | 4 +-- R/CSInter_.R | 10 +++----- README.md | 4 +++ inst/doc/EpiStats.R | 60 +++++++++++++++++++++++++------------------------- inst/doc/EpiStats.pdf |binary 9 files changed, 68 insertions(+), 57 deletions(-)
Title: Closed Testing with Globaltest for Pathway Analysis
Description: A shortcut procedure is proposed to implement closed testing for large-scale multiple testings, especially with the global test. This shortcut is asymptotically equivalent to closed testing and post hoc. Users could detect any possible sets of features or pathways with family-wise error rate controlled. The global test is powerful to detect associations between a group of features and an outcome of interest.
Author: Ningning Xu
Maintainer: Ningning Xu <n.xu@lumc.nl>
Diff between ctgt versions 1.0 dated 2020-03-08 and 2.0 dated 2021-06-07
ctgt-1.0/ctgt/src/Makevars.win |only ctgt-2.0/ctgt/DESCRIPTION | 8 ++++---- ctgt-2.0/ctgt/MD5 | 11 +++++------ ctgt-2.0/ctgt/R/gt2.R | 2 +- ctgt-2.0/ctgt/man/actgt.Rd | 10 +++++----- ctgt-2.0/ctgt/man/discoveries.Rd | 8 ++++---- ctgt-2.0/ctgt/man/gt2.Rd | 4 ++-- 7 files changed, 21 insertions(+), 22 deletions(-)
Title: Teaching Hydrological Modelling with the GR Rainfall-Runoff
Models ('Shiny' Interface Included)
Description: Add-on package to the 'airGR' package that simplifies its use and is aimed at being used for teaching hydrology. The package provides 1) three functions that allow to complete very simply a hydrological modelling exercise 2) plotting functions to help students to explore observed data and to interpret the results of calibration and simulation of the GR ('Génie rural') models 3) a 'Shiny' graphical interface that allows for displaying the impact of model parameters on hydrographs and models internal variables.
Author: Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Laurent Coron [aut] (<https://orcid.org/0000-0002-1503-6204>),
Pierre Brigode [aut] (<https://orcid.org/0000-0001-8257-0741>),
Guillaume Thirel [ctb] (<https://orcid.org/0000-0002-1444-1830>)
Maintainer: Olivier Delaigue <airGR@inrae.fr>
Diff between airGRteaching versions 0.2.10.112 dated 2021-02-01 and 0.2.11 dated 2021-06-07
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Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>
Diff between twang versions 2.1 dated 2021-05-25 and 2.2 dated 2021-06-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/pairwiseComparison.R | 8 ++++---- R/plot.mnps.R | 2 +- inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.pdf |binary man/twang-package.Rd | 28 ++++++++++++++-------------- 8 files changed, 30 insertions(+), 30 deletions(-)
Title: Structural Exploration of the Gene Ontology (GO) Knowledge Base
Description: It provides an effective, efficient, and fast way to explore the Gene Ontology (GO).
Given a set of genes, the package contains functions to assess the GO and obtain the
terms associated with the genes and the levels of the GO terms. The package provides
functions for the three different GO ontology. We discussed the methods explicitly in
the following article <doi:10.1038/s41598-020-73326-3>.
Author: Kalifa Manjang, Frank Emmert-Streib, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer
Maintainer: Kalifa Manjang <kalifamanjang1@gmail.com>
Diff between GOxploreR versions 1.2.0 dated 2021-05-17 and 1.2.1 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + R/drawGraph.R | 5 +++-- R/drawGraph4vis.R | 7 ++++--- inst/doc/GOxploreR.pdf |binary 6 files changed, 16 insertions(+), 13 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets)
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.2.1 dated 2021-02-17 and 1.3.0 dated 2021-06-07
cvms-1.2.1/cvms/tests/testthat/test_validate_fold.R |only cvms-1.3.0/cvms/DESCRIPTION | 29 cvms-1.3.0/cvms/MD5 | 94 - cvms-1.3.0/cvms/NEWS.md | 10 cvms-1.3.0/cvms/R/confusion_matrix.R | 6 cvms-1.3.0/cvms/R/cross_validate.R | 13 cvms-1.3.0/cvms/R/cross_validate_fn.R | 2 cvms-1.3.0/cvms/R/evaluate_predictions_multinomial.R | 25 cvms-1.3.0/cvms/R/get_nested_model_coefficients.R | 70 cvms-1.3.0/cvms/R/helpers.R | 23 cvms-1.3.0/cvms/R/internal_evaluate_model.R | 3 cvms-1.3.0/cvms/R/multiclass_probability_tibble.R | 3 cvms-1.3.0/cvms/R/plot_probabilities.R | 14 cvms-1.3.0/cvms/R/run_prediction_process.R | 80 cvms-1.3.0/cvms/R/run_quietly.R |only cvms-1.3.0/cvms/R/validate_fn.R | 2 cvms-1.3.0/cvms/build/cvms.pdf |binary cvms-1.3.0/cvms/build/vignette.rds |binary cvms-1.3.0/cvms/inst/doc/Creating_a_confusion_matrix.R | 3 cvms-1.3.0/cvms/inst/doc/Creating_a_confusion_matrix.Rmd | 9 cvms-1.3.0/cvms/inst/doc/Creating_a_confusion_matrix.html | 71 cvms-1.3.0/cvms/inst/doc/available_metrics.html | 4 cvms-1.3.0/cvms/inst/doc/cross_validating_custom_functions.R | 4 cvms-1.3.0/cvms/inst/doc/cross_validating_custom_functions.Rmd | 6 cvms-1.3.0/cvms/inst/doc/cross_validating_custom_functions.html | 208 +- cvms-1.3.0/cvms/inst/doc/evaluate_by_id.html | 52 cvms-1.3.0/cvms/inst/doc/picking_the_number_of_folds_for_cross-validation.R |only cvms-1.3.0/cvms/inst/doc/picking_the_number_of_folds_for_cross-validation.Rmd |only cvms-1.3.0/cvms/inst/doc/picking_the_number_of_folds_for_cross-validation.html |only cvms-1.3.0/cvms/inst/vignette_data |only cvms-1.3.0/cvms/man/confusion_matrix.Rd | 2 cvms-1.3.0/cvms/man/cross_validate.Rd | 6 cvms-1.3.0/cvms/man/cross_validate_fn.Rd | 4 cvms-1.3.0/cvms/man/multiclass_probability_tibble.Rd | 3 cvms-1.3.0/cvms/man/validate.Rd | 4 cvms-1.3.0/cvms/man/validate_fn.Rd | 2 cvms-1.3.0/cvms/tests/testthat/test_baseline.R | 84 - cvms-1.3.0/cvms/tests/testthat/test_choosing_metrics.R | 3 cvms-1.3.0/cvms/tests/testthat/test_combine_predictors.R | 4 cvms-1.3.0/cvms/tests/testthat/test_cross_validate.R | 827 ++++++---- cvms-1.3.0/cvms/tests/testthat/test_cross_validate_fn.R | 253 ++- cvms-1.3.0/cvms/tests/testthat/test_evaluate.R | 30 cvms-1.3.0/cvms/tests/testthat/test_metrics.R | 1 cvms-1.3.0/cvms/tests/testthat/test_validate_fn.R | 231 ++ cvms-1.3.0/cvms/vignettes/Creating_a_confusion_matrix.Rmd | 9 cvms-1.3.0/cvms/vignettes/cross_validating_custom_functions.Rmd | 6 cvms-1.3.0/cvms/vignettes/man/figures/vignette_cv_custom_fn-unnamed-chunk-35-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-27-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-28-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-3-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-30-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-32-1.png |only cvms-1.3.0/cvms/vignettes/man/figures/vignette_pick_k-unnamed-chunk-5-1.png |only cvms-1.3.0/cvms/vignettes/picking_the_number_of_folds_for_cross-validation.Rmd |only 54 files changed, 1402 insertions(+), 798 deletions(-)
Title: Access Finnish Geospatial Data
Description: Tools for reading Finnish open geospatial data in R.
Author: Markus Kainu [aut, cre] (<https://orcid.org/0000-0003-1376-503X>),
Joona Lehtomaki [aut] (<https://orcid.org/0000-0002-7891-0843>),
Juuso Parkkinen [ctb] (<https://orcid.org/0000-0002-7818-5901>),
Jani Miettinen [ctb],
Pyry Kantanen [ctb],
Leo Lahti [aut] (<https://orcid.org/0000-0001-5537-637X>)
Maintainer: Markus Kainu <markus.kainu@kapsi.fi>
Diff between geofi versions 1.0.1 dated 2021-03-29 and 1.0.2 dated 2021-06-07
DESCRIPTION | 10 ++-- MD5 | 51 +++++++++++---------- NEWS.md | 46 +++++++++++-------- R/data.R | 2 R/get_population_grid.R | 6 +- R/get_statistical_grid.R | 2 build/vignette.rds |binary data/grid_sairaanhoitop.rda |binary inst/doc/geofi_datasets.R | 4 - inst/doc/geofi_datasets.Rmd | 4 - inst/doc/geofi_datasets.html | 21 ++++---- inst/doc/geofi_joining_attribute_data.R | 6 +- inst/doc/geofi_joining_attribute_data.Rmd | 6 +- inst/doc/geofi_joining_attribute_data.html | 59 +++++++++++++------------ inst/doc/geofi_making_maps.html | 43 +++++++++--------- inst/doc/geofi_spatial_analysis.html | 31 ++++++------- inst/doc/tricolore_tutorial.R | 11 ++-- inst/doc/tricolore_tutorial.Rmd | 16 ++++-- inst/doc/tricolore_tutorial.html | 68 ++++++++++++++--------------- man/figures/logo.png |binary man/figures/logo.svg |only man/get_population_grid.Rd | 9 ++- man/get_statistical_grid.Rd | 2 man/grid_sairaanhoitop.Rd | 2 vignettes/geofi_datasets.Rmd | 4 - vignettes/geofi_joining_attribute_data.Rmd | 6 +- vignettes/tricolore_tutorial.Rmd | 16 ++++-- 27 files changed, 230 insertions(+), 195 deletions(-)
Title: Hypothesis Matrix Translation
Description: Translation between experimental null hypotheses, hypothesis matrices, and contrast matrices as used in linear regression models. The package is based on the method described in Schad, Vasishth, Hohenstein, and Kliegl (2019) <doi:10.1016/j.jml.2019.104038> and Rabe, Vasishth, Hohenstein, Kliegl, and Schad (2020) <doi:10.21105/joss.02134>.
Author: Maximilian M. Rabe [aut, cre] (<https://orcid.org/0000-0002-2556-5644>),
Shravan Vasishth [aut] (<https://orcid.org/0000-0003-2027-1994>),
Sven Hohenstein [aut] (<https://orcid.org/0000-0002-9708-1593>),
Reinhold Kliegl [aut] (<https://orcid.org/0000-0002-0180-8488>),
Daniel J. Schad [aut] (<https://orcid.org/0000-0003-2586-6823>)
Maintainer: Maximilian M. Rabe <maximilian.rabe@uni-potsdam.de>
Diff between hypr versions 0.2.0 dated 2021-05-21 and 0.2.1 dated 2021-06-07
DESCRIPTION | 10 +- MD5 | 16 +-- NAMESPACE | 6 + R/hypr.R | 71 +++++++++++---- README.md | 196 ++++++++++++++++++++++-------------------- inst/doc/hypr-contrasts.html | 18 +-- inst/doc/hypr-intro.html | 38 ++++---- inst/doc/hypr-regression.html | 18 +-- man/is_intercept.Rd | 18 +++ 9 files changed, 227 insertions(+), 164 deletions(-)
Title: Data Only: The Correlates of State Policy Project Dataset
Description: Contains the Correlates of State Policy Project dataset (+ codebook) assembled by Marty P. Jordan and Matt Grossmann (2020) <http://ippsr.msu.edu/public-policy/correlates-state-policy> used by the 'cspp' package. The Correlates data contains over 2000 variables across more than 100 years that pertain to state politics and policy in the United States.
Author: Caleb Lucas (https://caleblucas.com/) and Joshua McCrain (http://joshuamccrain.com/)
Maintainer: Caleb Lucas <calebjlucas@gmail.com>
Diff between csppData versions 0.1.2 dated 2021-03-28 and 0.1.3 dated 2021-06-07
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/zzz.R | 6 +++--- README.md | 36 ++++++++++++++++++------------------ data/codebook.rda |binary data/correlates.rda |binary man/codebook.Rd | 2 +- man/correlates.Rd | 2 +- 8 files changed, 35 insertions(+), 35 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 0.5-0 dated 2021-05-11 and 1.0-0 dated 2021-06-07
DESCRIPTION | 6 MD5 | 43 +-- NEWS.md | 8 R/memoiR.R | 141 +++++++++- README.md | 7 build/vignette.rds |binary inst/doc/memoiR.Rmd | 35 +- inst/doc/memoiR.html | 27 + inst/rmarkdown/templates/beamer_presentation/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/memoir/skeleton/81-getting_started.Rmd | 53 ++- inst/rmarkdown/templates/memoir/skeleton/82-syntax.Rmd | 48 ++- inst/rmarkdown/templates/memoir/skeleton/index.Rmd | 73 +++-- inst/rmarkdown/templates/memoir/skeleton/latex/preamble.tex | 38 ++ inst/rmarkdown/templates/memoir/skeleton/latex/template.tex | 109 ++++--- inst/rmarkdown/templates/memoir/skeleton/style.css | 4 inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 4 inst/rstudio |only man/add_font.Rd |only man/add_hyphen.Rd |only man/build_ghworkflow.Rd | 112 +++---- man/draft_memoir.Rd |only tests/testthat/test_build.R | 3 vignettes/memoiR.Rmd | 35 +- 24 files changed, 517 insertions(+), 237 deletions(-)
Title: Visualise and Explore the Deep Dependencies of R Packages
Description: Provides tools for exploration of R package dependencies.
The main deepdep() function allows to acquire deep dependencies of any package and plot them in an elegant way.
It also adds some popularity measures for the packages e.g. in the form of download count through the 'cranlogs' package.
Uses the CRAN metadata database <http://crandb.r-pkg.org> and Bioconductor metadata <http://bioconductor.org>.
Other data acquire functions are: get_dependencies(), get_downloads() and get_description().
The deepdep_shiny() function runs shiny application that helps to produce a nice 'deepdep' plot.
Author: Dominik Rafacz [aut, cre] (<https://orcid.org/0000-0003-0925-1909>),
Hubert Baniecki [aut],
Szymon Maksymiuk [aut],
Mateusz Bakala [aut]
Maintainer: Dominik Rafacz <dominikrafacz@gmail.com>
Diff between deepdep versions 0.2.5.2 dated 2021-05-21 and 0.2.5.3 dated 2021-06-07
deepdep-0.2.5.2/deepdep/tests/fixtures/deepdep-3.yml |only deepdep-0.2.5.2/deepdep/tests/fixtures/get_available_packages-1.yml |only deepdep-0.2.5.2/deepdep/tests/fixtures/get_available_packages-2.yml |only deepdep-0.2.5.2/deepdep/tests/fixtures/get_available_packages-3.yml |only deepdep-0.2.5.3/deepdep/DESCRIPTION | 6 deepdep-0.2.5.3/deepdep/MD5 | 22 deepdep-0.2.5.3/deepdep/NEWS.md | 1 deepdep-0.2.5.3/deepdep/tests/fixtures/deepdep-1.yml |89152 ++++++++++ deepdep-0.2.5.3/deepdep/tests/fixtures/deepdep-2.yml |85243 --------- deepdep-0.2.5.3/deepdep/tests/fixtures/plot-1.yml | 292 deepdep-0.2.5.3/deepdep/tests/fixtures/plot-2.yml | 49 deepdep-0.2.5.3/deepdep/tests/testthat/test-deepdep.R | 19 deepdep-0.2.5.3/deepdep/tests/testthat/test-get_available_packages.R | 20 deepdep-0.2.5.3/deepdep/tests/testthat/test-plot.R | 7 14 files changed, 89436 insertions(+), 85375 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] (<https://orcid.org/0000-0002-6294-8185>),
Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>),
Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.1-1 dated 2020-06-09 and 1.1-2 dated 2021-06-07
DESCRIPTION | 12 MD5 | 28 +- R/mvt.R | 88 +++--- R/tvpack.R | 6 build/vignette.rds |binary inst/NEWS | 26 + inst/doc/MVT_Rnews.pdf |binary man/algorithms.Rd | 30 +- man/pmvnorm.Rd | 39 +- man/pmvt.Rd | 8 src/miwa.c | 544 ++++++++++++++++------------------------- src/tvpack.f | 334 ++++++++----------------- tests/bugfix-tests.Rout.save | 11 tests/regtest-TVPACK.R | 57 ++++ tests/regtest-TVPACK.Rout.save | 74 +++++ 15 files changed, 612 insertions(+), 645 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible framework for
statistical inference of a broad class of time series and other data. KFAS
includes computationally efficient functions for Kalman filtering, smoothing,
forecasting, and simulation of multivariate exponential family state space models,
with observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.4.5 dated 2021-05-10 and 1.4.6 dated 2021-06-07
KFAS-1.4.5/KFAS/src/approx.f95 |only KFAS-1.4.5/KFAS/src/approxloop.f95 |only KFAS-1.4.5/KFAS/src/artransform.f95 |only KFAS-1.4.5/KFAS/src/covmeanw.f95 |only KFAS-1.4.5/KFAS/src/filter1step.f95 |only KFAS-1.4.5/KFAS/src/filter1stepnovar.f95 |only KFAS-1.4.5/KFAS/src/filtersimfast.f95 |only KFAS-1.4.5/KFAS/src/gloglik.f95 |only KFAS-1.4.5/KFAS/src/gsmoothall.f95 |only KFAS-1.4.5/KFAS/src/isample.f95 |only KFAS-1.4.5/KFAS/src/isamplefilter.f95 |only KFAS-1.4.5/KFAS/src/kfilter.f95 |only KFAS-1.4.5/KFAS/src/kfilter2.f95 |only KFAS-1.4.5/KFAS/src/kfstheta.f95 |only KFAS-1.4.5/KFAS/src/ldl.f95 |only KFAS-1.4.5/KFAS/src/ldlssm.f95 |only KFAS-1.4.5/KFAS/src/marginalxx.f95 |only KFAS-1.4.5/KFAS/src/mvfilter.f95 |only KFAS-1.4.5/KFAS/src/ngfilter.f95 |only KFAS-1.4.5/KFAS/src/ngloglik.f95 |only KFAS-1.4.5/KFAS/src/ngsmooth.f95 |only KFAS-1.4.5/KFAS/src/predict.f95 |only KFAS-1.4.5/KFAS/src/ptheta.f95 |only KFAS-1.4.5/KFAS/src/pytheta.f95 |only KFAS-1.4.5/KFAS/src/simfilter.f95 |only KFAS-1.4.5/KFAS/src/simgaussian.f95 |only KFAS-1.4.5/KFAS/src/simgaussianuncond.f95 |only KFAS-1.4.5/KFAS/src/smoothonestep.f95 |only KFAS-1.4.5/KFAS/src/smoothsim.f95 |only KFAS-1.4.5/KFAS/src/smoothsimfast.f95 |only KFAS-1.4.6/KFAS/ChangeLog | 4 + KFAS-1.4.6/KFAS/DESCRIPTION | 8 +-- KFAS-1.4.6/KFAS/MD5 | 74 +++++++++++++++--------------- KFAS-1.4.6/KFAS/R/KFAS-package.R | 4 - KFAS-1.4.6/KFAS/R/fitSSM.R | 62 ++++++++++++++++++++++++- KFAS-1.4.6/KFAS/inst/doc/KFAS.pdf |binary KFAS-1.4.6/KFAS/man/KFAS.Rd | 4 - KFAS-1.4.6/KFAS/man/fitSSM.Rd | 61 ++++++++++++++++++++++++ KFAS-1.4.6/KFAS/src/approx.f90 |only KFAS-1.4.6/KFAS/src/approxloop.f90 |only KFAS-1.4.6/KFAS/src/artransform.f90 |only KFAS-1.4.6/KFAS/src/covmeanw.f90 |only KFAS-1.4.6/KFAS/src/filter1step.f90 |only KFAS-1.4.6/KFAS/src/filter1stepnovar.f90 |only KFAS-1.4.6/KFAS/src/filtersimfast.f90 |only KFAS-1.4.6/KFAS/src/gloglik.f90 |only KFAS-1.4.6/KFAS/src/gsmoothall.f90 |only KFAS-1.4.6/KFAS/src/isample.f90 |only KFAS-1.4.6/KFAS/src/isamplefilter.f90 |only KFAS-1.4.6/KFAS/src/kfilter.f90 |only KFAS-1.4.6/KFAS/src/kfilter2.f90 |only KFAS-1.4.6/KFAS/src/kfstheta.f90 |only KFAS-1.4.6/KFAS/src/ldl.f90 |only KFAS-1.4.6/KFAS/src/ldlssm.f90 |only KFAS-1.4.6/KFAS/src/marginalxx.f90 |only KFAS-1.4.6/KFAS/src/mvfilter.f90 |only KFAS-1.4.6/KFAS/src/ngfilter.f90 |only KFAS-1.4.6/KFAS/src/ngloglik.f90 |only KFAS-1.4.6/KFAS/src/ngsmooth.f90 |only KFAS-1.4.6/KFAS/src/predict.f90 |only KFAS-1.4.6/KFAS/src/ptheta.f90 |only KFAS-1.4.6/KFAS/src/pytheta.f90 |only KFAS-1.4.6/KFAS/src/simfilter.f90 |only KFAS-1.4.6/KFAS/src/simgaussian.f90 |only KFAS-1.4.6/KFAS/src/simgaussianuncond.f90 |only KFAS-1.4.6/KFAS/src/smoothonestep.f90 |only KFAS-1.4.6/KFAS/src/smoothsim.f90 |only KFAS-1.4.6/KFAS/src/smoothsimfast.f90 |only 68 files changed, 171 insertions(+), 46 deletions(-)
Title: Using the Docker Container to Create R Workers on Local or Cloud
Platform
Description: This is the core package that provides both the user API and developer API to deploy
the parallel cluster on the cloud using the container service. The user can call
clusterPreset() to define the cloud service provider and container and makeDockerCluster()
to create the cluster. The developer should see "developer's cookbook" on how to define
the cloud provider and container.
Author: Jiefei Wang [aut, cre]
Maintainer: Jiefei Wang <szwjf08@gmail.com>
Diff between DockerParallel versions 1.0.0 dated 2021-05-04 and 1.0.3 dated 2021-06-07
DockerParallel-1.0.0/DockerParallel/R/all-generics.R |only DockerParallel-1.0.0/DockerParallel/R/method-developer-accessors.R |only DockerParallel-1.0.0/DockerParallel/R/utils.R |only DockerParallel-1.0.0/DockerParallel/man/getDockerInstanceIps.Rd |only DockerParallel-1.0.0/DockerParallel/man/initializeProvider.Rd |only DockerParallel-1.0.0/DockerParallel/man/instanceStatus.Rd |only DockerParallel-1.0.0/DockerParallel/man/killDockerInstances.Rd |only DockerParallel-1.0.0/DockerParallel/man/runDockerServer.Rd |only DockerParallel-1.0.0/DockerParallel/man/runDockerWorkers.Rd |only DockerParallel-1.0.0/DockerParallel/man/waitInstanceUntilRunning.Rd |only DockerParallel-1.0.0/DockerParallel/vignettes/vignette.md |only DockerParallel-1.0.3/DockerParallel/DESCRIPTION | 12 DockerParallel-1.0.3/DockerParallel/MD5 | 132 +- DockerParallel-1.0.3/DockerParallel/NAMESPACE | 73 - DockerParallel-1.0.3/DockerParallel/NEWS | 23 DockerParallel-1.0.3/DockerParallel/R/AAA.R | 94 - DockerParallel-1.0.3/DockerParallel/R/accessors.R |only DockerParallel-1.0.3/DockerParallel/R/all-generics-CloudProvider.R |only DockerParallel-1.0.3/DockerParallel/R/all-generics-ContainerProvider.R |only DockerParallel-1.0.3/DockerParallel/R/all-generics-base.R |only DockerParallel-1.0.3/DockerParallel/R/all-utils.R |only DockerParallel-1.0.3/DockerParallel/R/class-CloudConfig.R | 48 DockerParallel-1.0.3/DockerParallel/R/class-CloudRuntime.R | 65 - DockerParallel-1.0.3/DockerParallel/R/class-DockerCluster.R |only DockerParallel-1.0.3/DockerParallel/R/class-DockerHardware.R | 19 DockerParallel-1.0.3/DockerParallel/R/dummyContainer.R |only DockerParallel-1.0.3/DockerParallel/R/dummyProvider.R |only DockerParallel-1.0.3/DockerParallel/R/method-DockerCluster-utils.R | 274 ++--- DockerParallel-1.0.3/DockerParallel/R/method-DockerCluster.R | 540 ++++------ DockerParallel-1.0.3/DockerParallel/R/method-DockerContainer.R | 36 DockerParallel-1.0.3/DockerParallel/R/method-default.R | 68 - DockerParallel-1.0.3/DockerParallel/R/method-export.R | 124 +- DockerParallel-1.0.3/DockerParallel/R/testthat.R | 217 +--- DockerParallel-1.0.3/DockerParallel/R/zzz.R | 1 DockerParallel-1.0.3/DockerParallel/README.md | 199 ++- DockerParallel-1.0.3/DockerParallel/build/vignette.rds |binary DockerParallel-1.0.3/DockerParallel/inst/doc/developer-cookbook.R | 130 +- DockerParallel-1.0.3/DockerParallel/inst/doc/developer-cookbook.Rmd | 195 +-- DockerParallel-1.0.3/DockerParallel/inst/doc/developer-cookbook.html | 361 ++++-- DockerParallel-1.0.3/DockerParallel/man/CloudConfig-class.Rd | 24 DockerParallel-1.0.3/DockerParallel/man/CloudPrivateServer.Rd |only DockerParallel-1.0.3/DockerParallel/man/CloudRuntime-class.Rd | 20 DockerParallel-1.0.3/DockerParallel/man/DockerCluster-class.Rd | 3 DockerParallel-1.0.3/DockerParallel/man/DockerContainer-class.Rd | 10 DockerParallel-1.0.3/DockerParallel/man/DockerHardware-class.Rd | 10 DockerParallel-1.0.3/DockerParallel/man/DockerHardware.Rd |only DockerParallel-1.0.3/DockerParallel/man/DockerServerManagement.Rd |only DockerParallel-1.0.3/DockerParallel/man/DockerStaticData.Rd |only DockerParallel-1.0.3/DockerParallel/man/DummyContainer.Rd |only DockerParallel-1.0.3/DockerParallel/man/DummyProvider.Rd |only DockerParallel-1.0.3/DockerParallel/man/accessors.Rd | 92 + DockerParallel-1.0.3/DockerParallel/man/cleanupDockerCluster-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/cleanupDockerCluster.Rd |only DockerParallel-1.0.3/DockerParallel/man/clusterPreset.Rd | 6 DockerParallel-1.0.3/DockerParallel/man/configServerContainerEnv.Rd | 11 DockerParallel-1.0.3/DockerParallel/man/configWorkerContainerEnv.Rd | 11 DockerParallel-1.0.3/DockerParallel/man/containerParallelBackend.Rd | 17 DockerParallel-1.0.3/DockerParallel/man/dockerClusterExists-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/dockerClusterExists.Rd | 3 DockerParallel-1.0.3/DockerParallel/man/exported-apis.Rd | 2 DockerParallel-1.0.3/DockerParallel/man/generalDockerClusterTest.Rd | 15 DockerParallel-1.0.3/DockerParallel/man/generics-commonParams.Rd | 2 DockerParallel-1.0.3/DockerParallel/man/getDockerServerIp-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/getDockerServerIp.Rd |only DockerParallel-1.0.3/DockerParallel/man/getDockerWorkerNumbers-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/getDockerWorkerNumbers.Rd |only DockerParallel-1.0.3/DockerParallel/man/getServerContainer.Rd | 10 DockerParallel-1.0.3/DockerParallel/man/getServerStatus-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/getServerStatus.Rd |only DockerParallel-1.0.3/DockerParallel/man/initializeCloudProvider-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/initializeCloudProvider.Rd |only DockerParallel-1.0.3/DockerParallel/man/makeDockerCluster.Rd | 30 DockerParallel-1.0.3/DockerParallel/man/reconnectDockerCluster-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/reconnectDockerCluster.Rd | 3 DockerParallel-1.0.3/DockerParallel/man/resetDummyProvider.Rd |only DockerParallel-1.0.3/DockerParallel/man/runDockerServer-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/setDockerWorkerNumber-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/setDockerWorkerNumber.Rd |only DockerParallel-1.0.3/DockerParallel/man/show-CloudConfig-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/show-CloudRuntime-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/show-DockerContainer-method.Rd |only DockerParallel-1.0.3/DockerParallel/man/show-DockerHardware-method.Rd | 4 DockerParallel-1.0.3/DockerParallel/man/stopDockerServer-DummyProvider-method.Rd |only DockerParallel-1.0.3/DockerParallel/tests |only DockerParallel-1.0.3/DockerParallel/vignettes/components.jpg |binary DockerParallel-1.0.3/DockerParallel/vignettes/developer-cookbook.Rmd | 195 +-- DockerParallel-1.0.3/DockerParallel/vignettes/package-structure.jpg |binary 87 files changed, 1678 insertions(+), 1401 deletions(-)
More information about DockerParallel at CRAN
Permanent link
Title: Wrapper for the National Bank of Poland API
Description: Use the <http://api.nbp.pl/> API through R. Retrieve
currency exchange rates and gold prices data published by the
National Bank of Poland in form of convenient R objects.
Author: Ryszard Szymanski [aut, cre]
Maintainer: Ryszard Szymanski <ryszard.szymanski@outlook.com>
Diff between rnbp versions 0.2.0 dated 2020-06-29 and 0.2.1 dated 2021-06-07
DESCRIPTION | 7 +- MD5 | 40 ++++++++-------- NEWS.md | 8 ++- R/endpoint_goldprice.R | 66 ++++++++++++++++----------- R/endpoint_rates.R | 66 ++++++++++++++++----------- R/endpoint_tables.R | 65 ++++++++++++++++---------- man/get_current_exchangerate.Rd | 14 +++-- man/get_current_exchangerate_table.Rd | 14 +++-- man/get_current_goldprice.Rd | 14 +++-- man/get_exchangerate_from.Rd | 13 +++-- man/get_exchangerate_from_interval.Rd | 13 +++-- man/get_exchangerate_table_from.Rd | 12 +++- man/get_exchangerate_tables_from_interval.Rd | 13 +++-- man/get_goldprice_from.Rd | 13 +++-- man/get_goldprice_from_interval.Rd | 13 +++-- man/get_last_n_exchangerate_tables.Rd | 13 +++-- man/get_last_n_exchangerates.Rd | 13 +++-- man/get_last_n_goldprices.Rd | 13 +++-- man/get_todays_exchangerate.Rd | 13 +++-- man/get_todays_exchangerate_table.Rd | 13 +++-- man/get_todays_goldprice.Rd | 13 +++-- 21 files changed, 270 insertions(+), 179 deletions(-)
Title: Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait
data associated with the tips of a phylogenetic tree. Examples of such models
are Gaussian continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the
tips of the tree as an observed (final) state of a Markov process starting from
an initial state at the root and evolving along the branches of the tree. The
PCMBase R package provides a general framework for manipulating such models.
This framework consists of an application programming interface for specifying
data and model parameters, and efficient algorithms for simulating trait evolution
under a model and calculating the likelihood of model parameters for an assumed
model and trait data. The package implements a growing collection of models,
which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed
Gaussian models, in which different types of the above models can be associated
with different branches of the tree. The PCMBase package is limited to
trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic
models. The PCMFit package provides functionality for inference of
these models to tree and trait data. The package web-site
<https://venelin.github.io/PCMBase/>
provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph] (<a
href="https://venelin.github.io">venelin.github.io</a>),
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBase versions 1.2.11 dated 2019-12-12 and 1.2.12 dated 2021-06-07
DESCRIPTION | 10 MD5 | 373 NAMESPACE | 2500 +- NEWS.md | 138 R/AutoGeneratedModelTypes.R |20972 ++++++++++++------------ R/BM.R | 234 R/BMdrift.R | 268 R/DOU.R | 348 R/DefaultModelTypes.R | 321 R/GaussianPCM.R | 2521 +- R/JOU.R | 354 R/LatexTools.R | 204 R/MixedGaussian.R | 692 R/OU.R | 392 R/PCM.R | 4388 ++--- R/PCMBaseTestObjects.R | 144 R/PCMParam.R | 2953 +-- R/PCMTable.R | 394 R/PCMTree.R | 5107 +++-- R/Utilities.R | 882 - R/White.R | 228 R/matrixparametrizations.R | 1224 - R/zzz.R | 46 README.md | 472 build/vignette.rds |binary inst/CITATION | 118 inst/doc/PCMBase.R | 328 inst/doc/PCMBase.Rmd | 656 inst/doc/PCMBase.html | 1681 - inst/doc/PCMCreateModel.R | 474 inst/doc/PCMCreateModel.Rmd | 882 - inst/doc/PCMCreateModel.html | 1308 - inst/doc/PCMParam.R | 340 inst/doc/PCMParam.Rmd | 578 inst/doc/PCMParam.html | 1869 +- inst/doc/PCMTracePruning.R | 784 inst/doc/PCMTracePruning.Rmd | 966 - inst/doc/PCMTracePruning.html | 7935 ++++----- man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd | 48 man/Args_MixedGaussian_MGPMScalarOUType.Rd | 28 man/Args_MixedGaussian_MGPMSurfaceOUType.Rd | 28 man/FormatCellAsLatex.Rd | 36 man/FormatTableAsLatex.Rd | 60 man/MGPMScalarOUType.Rd | 28 man/MGPMSurfaceOUType.Rd | 28 man/MatchListMembers.Rd | 88 man/MixedGaussian.Rd | 158 man/MixedGaussianTemplate.Rd |only man/PCM.Rd | 263 man/PCMAbCdEf.Rd | 85 man/PCMAddToListAttribute.Rd | 90 man/PCMApplyTransformation.Rd | 58 man/PCMBaseIsADevRelease.Rd | 28 man/PCMBaseTestObjects.Rd | 108 man/PCMColorPalette.Rd | 56 man/PCMCombineListAttribute.Rd | 38 man/PCMCond.GaussianPCM.Rd | 76 man/PCMCond.Rd | 70 man/PCMCondVOU.Rd | 86 man/PCMCreateLikelihood.Rd | 124 man/PCMDefaultModelTypes.Rd | 69 man/PCMDefaultObject.Rd | 48 man/PCMDescribe.Rd | 44 man/PCMDescribeParameters.Rd | 38 man/PCMExtractDimensions.Rd | 61 man/PCMExtractRegimes.Rd | 50 man/PCMFindMethod.Rd | 44 man/PCMFixParameter.Rd | 40 man/PCMGenerateModelTypes.Rd | 77 man/PCMGenerateParameterizations.Rd | 99 man/PCMGetAttribute.Rd | 64 man/PCMGetVecParamsRegimesAndModels.Rd | 66 man/PCMInfo.Rd | 147 man/PCMLik.Rd | 220 man/PCMLikDmvNorm.Rd | 111 man/PCMLikTrace.Rd | 129 man/PCMListMembers.Rd | 63 man/PCMListParameterizations.Rd | 80 man/PCMLmr.Rd | 114 man/PCMMapModelTypesToRegimes.Rd | 58 man/PCMMean.Rd | 111 man/PCMMeanAtTime.Rd | 101 man/PCMModelTypes.Rd | 36 man/PCMModels.Rd | 58 man/PCMNumRegimes.Rd | 34 man/PCMNumTraits.Rd | 36 man/PCMOptions.Rd | 174 man/PCMPExpxMeanExp.Rd | 72 man/PCMPLambdaP_1.Rd | 50 man/PCMPairSums.Rd | 34 man/PCMParam.Rd | 46 man/PCMParamCount.Rd | 85 man/PCMParamGetShortVector.Rd | 52 man/PCMParamLoadOrStore.Rd | 70 man/PCMParamLocateInShortVector.Rd | 76 man/PCMParamLowerLimit.Rd | 50 man/PCMParamRandomVecParams.Rd | 73 man/PCMParamSetByName.Rd | 90 man/PCMParamType.Rd | 332 man/PCMParamUpperLimit.Rd | 50 man/PCMParentClasses.Rd | 44 man/PCMParseErrorMessage.Rd | 34 man/PCMPlotGaussianDensityGrid2D.Rd | 59 man/PCMPlotGaussianSample2D.Rd | 56 man/PCMPlotMath.Rd | 46 man/PCMPlotTraitData2D.Rd | 108 man/PCMPresentCoordinates.Rd | 86 man/PCMRegimes.Rd | 34 man/PCMSetAttribute.Rd | 95 man/PCMSim.Rd | 141 man/PCMSpecify.Rd | 44 man/PCMTable.Rd | 66 man/PCMTableParameterizations.Rd | 57 man/PCMTrajectory.Rd | 223 man/PCMTree.Rd | 212 man/PCMTreeBackbonePartition.Rd | 186 man/PCMTreeDropClade.Rd | 136 man/PCMTreeDtNodes.Rd | 66 man/PCMTreeEdgeTimes.Rd | 28 man/PCMTreeEvalNestedEDxOnTree.Rd | 122 man/PCMTreeExtractClade.Rd | 123 man/PCMTreeGetBranchLength.Rd | 38 man/PCMTreeGetDaughters.Rd | 38 man/PCMTreeGetLabels.Rd | 55 man/PCMTreeGetParent.Rd | 38 man/PCMTreeGetPartNames.Rd | 36 man/PCMTreeGetPartRegimes.Rd | 36 man/PCMTreeGetPartition.Rd | 62 man/PCMTreeGetPartsForNodes.Rd | 42 man/PCMTreeGetRegimesForEdges.Rd | 38 man/PCMTreeGetRegimesForNodes.Rd | 42 man/PCMTreeGetTipsInPart.Rd | 70 man/PCMTreeGetTipsInRegime.Rd | 70 man/PCMTreeInsertSingletons.Rd | 248 man/PCMTreeJumps.Rd | 36 man/PCMTreeListAllPartitions.Rd | 107 man/PCMTreeListCladePartitions.Rd | 103 man/PCMTreeListDescendants.Rd | 55 man/PCMTreeListRootPaths.Rd | 56 man/PCMTreeLocateEpochOnBranches.Rd | 42 man/PCMTreeLocateMidpointsOnBranches.Rd | 44 man/PCMTreeMatchLabels.Rd | 58 man/PCMTreeMatrixNodesInSamePart.Rd | 144 man/PCMTreeNearestNodesToEpoch.Rd | 38 man/PCMTreeNodeTimes.Rd | 42 man/PCMTreeNumNodes.Rd | 40 man/PCMTreeNumParts.Rd | 34 man/PCMTreeNumTips.Rd | 34 man/PCMTreePlot.Rd | 59 man/PCMTreePostorder.Rd | 36 man/PCMTreePreorder.Rd | 36 man/PCMTreeSetLabels.Rd | 119 man/PCMTreeSetPartRegimes.Rd | 183 man/PCMTreeSetPartition.Rd | 137 man/PCMTreeSetRegimesForEdges.Rd | 72 man/PCMTreeSplitAtNode.Rd | 110 man/PCMTreeTableAncestors.Rd | 56 man/PCMTreeToString.Rd | 42 man/PCMTreeVCV.Rd | 48 man/PCMUnfixParameter.Rd | 40 man/PCMVar.Rd | 157 man/PCMVarAtTime.Rd | 116 man/TruePositiveRate.Rd | 78 man/UpperTriFactor.Rd | 76 man/White.Rd | 26 man/as.MixedGaussian.Rd |only man/dataFig3.Rd | 34 man/is.GaussianPCM.Rd |only man/is.MixedGaussian.Rd | 34 man/is.PCM.Rd | 34 man/is.PCMTree.Rd | 34 tests/README.txt | 6 tests/testthat.R | 8 tests/testthat/test-MixedGaussian.R | 352 tests/testthat/test-PCM.R | 532 tests/testthat/test-PCMLik-BM.R | 160 tests/testthat/test-PCMLik-BMdrift.R | 282 tests/testthat/test-PCMLik-DOU.R | 154 tests/testthat/test-PCMLik-OU.R | 176 tests/testthat/test-PCMParam.R | 132 tests/testthat/test-PCMSim.R | 114 tests/testthat/test-PCMTree.R | 276 tests/testthat/test-Transformations.R | 130 vignettes/PCMBase.Rmd | 656 vignettes/PCMCreateModel.Rmd | 882 - vignettes/PCMParam.Rmd | 578 vignettes/PCMTracePruning.Rmd | 966 - vignettes/REFERENCES-R.bib | 197 vignettes/REFERENCES.bib | 652 189 files changed, 40354 insertions(+), 38958 deletions(-)
Title: FLuctuation ANalysis on Mutation Models
Description: Tools for fluctuations analysis of mutant cells counts. Main reference is A. Mazoyer, R. Drouilhet, S. Despreaux and B. Ycart (2017) <doi:10.32614/RJ-2017-029>.
Author: Adrien Mazoyer [aut, cre],
Remy Drouilhet [aut],
Stephane Despreaux [aut],
Bernard Ycart [aut]
Maintainer: Adrien Mazoyer <adrien.mazoyer@math.univ-toulouse.fr>
Diff between flan versions 0.8 dated 2020-04-29 and 0.9 dated 2021-06-07
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NAMESPACE | 2 +- R/flan.R | 30 ++++++++++++++++++++---------- man/draw.clone.Rd | 9 +++++++-- man/flan-package.Rd | 6 +++--- 6 files changed, 43 insertions(+), 28 deletions(-)
Title: Tools to Make Developing R Packages Easier
Description: Collection of package development tools.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph, fnd]
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between devtools versions 2.4.1 dated 2021-05-05 and 2.4.2 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md | 10 ++++++++++ R/active.R | 2 +- R/check-doc.R | 9 ++++++++- R/document.R | 2 +- R/sitrep.R | 2 +- README.md | 2 +- inst/doc/dependencies.html | 4 ++-- tests/testthat/test-check-doc.R |only tests/testthat/test-uninstall.R | 5 +---- 11 files changed, 38 insertions(+), 23 deletions(-)
Title: Visualization of a Correlation Matrix
Description: A graphical display of a correlation matrix or general matrix.
It also contains some algorithms to do matrix reordering. In addition,
corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.88 dated 2021-05-11 and 0.89 dated 2021-06-07
DESCRIPTION | 8 +- MD5 | 24 ++++---- R/cor-mtest.R | 9 ++- R/corrplot.R | 56 +++++++++++++----- R/corrplot.mixed.R | 15 +++-- inst/NEWS | 10 +++ inst/doc/corrplot-intro.R | 19 +++--- inst/doc/corrplot-intro.Rmd | 19 +++--- inst/doc/corrplot-intro.html | 123 ++++++++++++++++++++--------------------- man/cor.mtest.Rd | 5 + man/corrplot.Rd | 5 + tests/testthat/test-corrplot.R | 28 +++++---- vignettes/corrplot-intro.Rmd | 19 +++--- 13 files changed, 196 insertions(+), 144 deletions(-)
Title: Bayesian Modelling of Raman Spectroscopy
Description: Sequential Monte Carlo (SMC) algorithms for fitting a generalised additive
mixed model (GAMM) to surface-enhanced resonance Raman spectroscopy (SERRS),
using the method of Moores et al. (2016) <arXiv:1604.07299>. Multivariate
observations of SERRS are highly collinear and lend themselves to a reduced-rank
representation. The GAMM separates the SERRS signal into three components: a
sequence of Lorentzian, Gaussian, or pseudo-Voigt peaks; a smoothly-varying baseline;
and additive white noise. The parameters of each component of the model are estimated
iteratively using SMC. The posterior distributions of the parameters given the observed
spectra are represented as a population of weighted particles.
Author: Matt Moores [aut, cre] (<https://orcid.org/0000-0003-4531-3572>),
Jake Carson [aut] (<https://orcid.org/0000-0002-7896-0971>),
Benjamin Moskowitz [ctb],
Kirsten Gracie [dtc],
Karen Faulds [dtc] (<https://orcid.org/0000-0002-5567-7399>),
Mark Girolami [aut],
Engineering and Physical Sciences Research Council [fnd] (EPSRC
programme grant ref: EP/L014165/1),
University of Warwick [cph]
Maintainer: Matt Moores <mmoores@gmail.com>
Diff between serrsBayes versions 0.4-1 dated 2020-02-05 and 0.4-2 dated 2021-06-07
DESCRIPTION | 12 MD5 | 89 +-- NEWS.md | 14 R/RcppExports.R | 665 ++++++++++++------------ R/fitSpectraSMC.R | 4 R/fitVoigtIBIS.R | 2 R/fitVoigtPeaksSMC.R | 551 ++++++++++---------- R/getBsplineBasis.R | 3 R/serrsBayes.R | 4 README.md | 16 build/partial.rdb |only build/vignette.rds |binary data/result2.rda |binary inst/CITATION | 42 + inst/doc/Introduction.R | 239 ++++---- inst/doc/Introduction.Rmd | 347 ++++++------ inst/doc/Introduction.html | 1073 +++++++++++++++++++-------------------- inst/doc/Methanol.R | 243 ++++---- inst/doc/Methanol.Rmd | 399 +++++++------- inst/doc/Methanol.html | 756 ++++++++++++--------------- inst/image/README-example-1.png |binary inst/image/README-plotting-1.png |binary man/computeLogLikelihood.Rd | 14 man/fitSpectraMCMC.Rd | 3 man/fitSpectraSMC.Rd | 17 man/fitVoigtIBIS.Rd | 19 man/fitVoigtPeaksSMC.Rd | 17 man/getBsplineBasis.Rd | 3 man/getVoigtParam.Rd | 2 man/lsTamra.Rd | 6 man/marginalMetropolisUpdate.Rd | 20 man/methanol.Rd | 6 man/mhUpdateVoigt.Rd | 17 man/mixedVoigt.Rd | 2 man/reWeightParticles.Rd | 17 man/resampleParticles.Rd | 2 man/residualResampling.Rd | 5 man/result.Rd | 6 man/result2.Rd | 4 man/serrsBayes.Rd | 5 src/Makevars.win | 2 src/mixLorentz.cpp | 15 src/mixVoigt.cpp | 8 vignettes/Introduction.Rmd | 347 ++++++------ vignettes/Methanol.Rmd | 399 +++++++------- vignettes/refs.bib | 203 +++---- 46 files changed, 2824 insertions(+), 2774 deletions(-)
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre]
(<https://orcid.org/0000-0001-7890-3857>),
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.1.6 dated 2020-08-10 and 0.1.7 dated 2021-06-07
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++-------- NEWS.md | 10 +++++++ R/export_workspace.R | 20 ++++++++++----- R/ipi_c_eu.R | 5 ++- R/spec_rjd.R | 68 ++++++++++++++++++++++++++++++--------------------- R/tramoseats.R | 2 - R/x13.R | 12 ++++----- README.md | 2 - data/ipi_c_eu.rda |binary man/ipi_c_eu.Rd | 2 - man/tramoseats.Rd | 2 - 12 files changed, 92 insertions(+), 61 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE)
biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>,
geometric adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method, power law residuals
(POLAR) statistics by Doring et al. (2015)
<doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for
computing biometrical analysis such as path analysis, canonical
correlation, partial correlation, clustering analysis, and tools for
inspecting, manipulating, summarizing and plotting typical
multi-environment trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.13.0 dated 2021-03-27 and 1.14.0 dated 2021-06-07
DESCRIPTION | 6 MD5 | 56 NEWS.md | 8 R/anova_joint.R | 2 R/env_dissimilarity.R | 17 R/ge_plot.R | 6 R/get_model_data.R | 78 R/gytb.R | 5 R/mgidi.R | 9 R/mps.R | 56 R/mtsi.R | 2 R/path_coeff.R | 131 R/plot_blup.R | 8 R/resp_surf.R | 10 R/waas.R | 26 R/zzz.R | 4 build/metan.pdf |26620 +++++++++++++++++++++--------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/metan_start.Rmd | 2 inst/doc/metan_start.html | 14 man/env_dissimilarity.Rd | 4 man/figures/README-AMMI-1.png |binary man/figures/README-GGE-1.png |binary man/ge_factanal.Rd | 6 man/get_model_data.Rd | 6 man/path_coeff.Rd | 12 man/plot_blup.Rd | 7 vignettes/metan_start.Rmd | 2 29 files changed, 13639 insertions(+), 13458 deletions(-)
Title: Web Interface to 'IsoplotR'
Description: Provides a graphical user interface to the 'IsoplotR' package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the 'IsoplotR' toolbox.
Author: Pieter Vermeesch [aut, cre],
Tim Band [ctb]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotRgui versions 3.8 dated 2021-04-06 and 4.0 dated 2021-06-07
DESCRIPTION | 13 - MD5 | 67 ++++----- R/server.R | 87 +++++++---- build/docker.sh | 12 - inst/www/help/average.html | 4 inst/www/help/radial.html | 5 inst/www/home/home.js | 14 + inst/www/home/map.html | 4 inst/www/home/news.html | 37 ++-- inst/www/home/world.svg | 6 inst/www/js/IsoplotR.js | 193 +++++++++++++++----------- inst/www/js/constants.json | 4 inst/www/js/examples.js | 3 inst/www/js/js2R.js | 125 +++++++++------- inst/www/js/languages.json |only inst/www/js/settings.json | 32 +--- inst/www/locales/en/contextual_help.json | 14 - inst/www/locales/en/dictionary_id.json | 12 - inst/www/locales/en/home_id.json | 4 inst/www/locales/es/dictionary_id.json | 7 inst/www/locales/es/home_id.json | 9 - inst/www/locales/zh_Hans/contextual_help.json | 11 - inst/www/locales/zh_Hans/dictionary_id.json | 7 inst/www/locales/zh_Hans/home_id.json | 4 inst/www/options/K-Ca.html | 2 inst/www/options/KDE.html | 7 inst/www/options/MDS.html | 3 inst/www/options/Pb-Pb.html | 6 inst/www/options/Th-U.html | 26 +-- inst/www/options/U-Pb.html | 4 inst/www/options/ages.html | 7 inst/www/options/average.html | 3 inst/www/options/other.html | 2 inst/www/options/radial.html | 6 inst/www/version.txt | 2 35 files changed, 413 insertions(+), 329 deletions(-)
Title: Read and Write General Transit Feed Specification (GTFS) Files
Description: Tools for the development of packages related to General
Transit Feed Specification (GTFS) files. Establishes a standard for
representing GTFS feeds using R data types. Provides fast and flexible
functions to read and write GTFS feeds while sticking to this
standard. Defines a basic 'gtfs' class which is meant to be extended
by packages that depend on it. And offers utility functions that
support checking the structure of GTFS objects.
Author: Daniel Herszenhut [aut, cre] (<https://orcid.org/0000-0001-8066-1105>),
Flavio Poletti [aut],
Mark Padgham [rev],
Rafael H. M. Pereira [rev] (<https://orcid.org/0000-0003-2125-7465>),
Tom Buckley [rev],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>
Diff between gtfsio versions 0.1.1 dated 2021-05-26 and 0.1.2 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 8 +++++++- R/checks.R | 12 ++++++------ README.md | 15 ++++++++++----- inst/CITATION | 8 +++++--- inst/doc/gtfsio.R | 2 ++ inst/doc/gtfsio.Rmd | 2 ++ inst/doc/gtfsio.html | 5 ++++- inst/tinytest/test_checks.R | 36 ++++++++++++++++++++---------------- vignettes/gtfsio.Rmd | 2 ++ 11 files changed, 71 insertions(+), 45 deletions(-)
Title: Download Data from the CSO 'PxStat' API
Description: Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide
format. The Central Statistics Office (CSO) is the national statistical institute of Ireland
and 'PxStat' is the CSOs online database of Official Statistics. This database contains current
and historical data series compiled from CSO statistical releases and is accessed at
<http://data.cso.ie>.
The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides
access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>.
This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.
Author: Eoin Horgan [aut] (<https://orcid.org/0000-0002-3446-6154>),
Conor Crowley [aut, cre],
Vytas Vaiciulis [aut],
Mervyn O'Luing [aut]
Maintainer: Conor Crowley <conor.crowley@cso.ie>
Diff between csodata versions 1.1.1 dated 2020-12-17 and 1.2.0 dated 2021-06-07
DESCRIPTION | 12 - MD5 | 36 ++-- NAMESPACE | 1 R/cso_get_data.R | 38 +++- R/cso_get_geo.R | 46 +++-- R/cso_get_meta.R | 59 ++++-- R/cso_get_toc.R | 175 +++++++++++++------- build/vignette.rds |binary inst/doc/quick_start_guide.R | 14 - inst/doc/quick_start_guide.html | 346 ++++++++++------------------------------ man/cso_get_content.Rd | 11 - man/cso_get_data.Rd | 7 man/cso_get_geo.Rd | 5 man/cso_get_interval.Rd | 9 - man/cso_get_meta.Rd | 13 - man/cso_get_toc.Rd | 23 ++ man/cso_get_var_values.Rd | 10 - man/cso_get_vars.Rd | 9 - man/cso_search_toc.Rd | 11 + 19 files changed, 414 insertions(+), 411 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>,
Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.2.6 dated 2021-02-23 and 1.2.7 dated 2021-06-07
DESCRIPTION | 10 MD5 | 16 - R/impact_analysis.R | 32 +-- R/impact_misc.R | 2 R/impact_model.R | 2 build/vignette.rds |binary inst/doc/CausalImpact.html | 357 +++++++++++++++++++++++++++++++--- tests/testthat/test-impact-analysis.R | 9 tests/testthat/test-impact-model.R | 5 9 files changed, 366 insertions(+), 67 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-05 0.1.3
2019-12-16 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-29 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-12 0.6.1
2019-03-09 0.6
2018-06-05 0.5
2018-03-30 0.4
2018-03-22 0.3
2018-02-03 0.2
2017-12-07 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-12 0.1.1
2018-06-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-14 0.4.0
2018-04-17 0.3.0
2018-03-20 0.2.0
2017-09-11 0.1.0
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb],
Pavel N. Krivitsky [ctb] (<https://orcid.org/0000-0002-9101-3362>),
Brendan Knapp [ctb] (<https://orcid.org/0000-0003-3284-4972>),
Michał Bojanowski [ctb],
Chad Klumb [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.16.1 dated 2020-10-07 and 1.17.0 dated 2021-06-07
COPYING | 4 ChangeLog | 18 +- DESCRIPTION | 41 ++-- MD5 | 139 +++++++++------- NAMESPACE | 33 +++ R/access.R | 234 +++++++++++++++++---------- R/as.edgelist.R | 20 +- R/assignment.R | 2 R/coercion.R | 25 +- R/constructors.R | 39 ++-- R/dataframe.R |only R/fileio.R | 14 - R/layout.R | 6 R/misc.R | 357 ++++++++++++++++++++++++++++++------------ R/network-package.R | 20 +- R/operators.R | 60 ++++--- R/plot.R | 14 - R/printsum.R | 8 R/zzz.R | 26 --- README.md | 29 ++- build/vignette.rds |binary inst/CITATION | 12 - inst/doc/networkVignette.pdf |binary inst/network.api/networkapi.c | 1 inst/network.api/networkapi.h | 1 man/add.edges.Rd | 11 + man/as.color.Rd | 32 +-- man/as.data.frame.network.Rd |only man/as.edgelist.Rd | 31 ++- man/as.matrix.network.Rd | 27 ++- man/as.network.matrix.Rd | 18 +- man/as.sociomatrix.Rd | 9 - man/attribute.methods.Rd | 236 ++++++++++++++++++--------- man/deletion.methods.Rd | 44 ++--- man/edgeset.constructors.Rd | 90 ++++------ man/emon.Rd | 70 ++++---- man/get.edges.Rd | 21 +- man/get.neighborhood.Rd | 3 man/loading.attributes.Rd | 6 man/mixingmatrix.Rd |only man/network-internal.Rd | 24 -- man/network-operators.Rd | 14 - man/network-package.Rd | 12 - man/network.Rd | 175 +++++++++++++++++++- man/network.arrow.Rd | 21 ++ man/network.edgelabel.Rd | 14 + man/network.extraction.Rd | 5 man/network.indicators.Rd | 12 + man/network.initialize.Rd | 10 - man/network.layout.Rd | 20 +- man/network.loop.Rd | 20 ++ man/network.vertex.Rd | 14 + man/read.paj.Rd | 14 + src/Rinit.c | 2 src/access.c | 2 src/access.h | 2 src/constructors.c | 2 src/constructors.h | 2 src/layout.c | 2 src/layout.h | 2 src/utils.c | 2 src/utils.h | 2 tests |only 63 files changed, 1370 insertions(+), 704 deletions(-)
Title: Advanced Vector Toolkit
Description: Image objects/arrays, geometric objects/arrays (in 2D/3D), block matrices and matrix arrays, with related binary operators and plain text markup. Mid-level plotting/rendering functions (as building blocks for high-level plotting functions), with dual support for base and grid graphics systems. Also, sequence/set utilities, linear transformations and additional color matrix/array transformations.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between vectools versions 0.2.0 dated 2020-10-22 and 0.3.0 dated 2021-06-07
vectools-0.2.0/vectools/R/02_vm_operators.r |only vectools-0.2.0/vectools/R/05_LL.r |only vectools-0.2.0/vectools/R/06_vt.r |only vectools-0.2.0/vectools/R/10_OO_constructors.r |only vectools-0.2.0/vectools/R/15_OO_most_methods.r |only vectools-0.2.0/vectools/R/20_STR_format_methods.r |only vectools-0.2.0/vectools/R/25_STR_objtag.r |only vectools-0.2.0/vectools/R/30_M1_seq.r |only vectools-0.2.0/vectools/R/35_M1_plots.r |only vectools-0.2.0/vectools/R/36_M1_algrebra.r |only vectools-0.2.0/vectools/R/40_TAB_select.r |only vectools-0.2.0/vectools/R/45_TAB_ghead.r |only vectools-0.2.0/vectools/R/46_TAB_headt.r |only vectools-0.2.0/vectools/R/50_M2_gkron.r |only vectools-0.2.0/vectools/R/55_M2_pool.r |only vectools-0.2.0/vectools/R/56_M2_convolutions.r |only vectools-0.2.0/vectools/build |only vectools-0.2.0/vectools/inst |only vectools-0.2.0/vectools/man/10_object_arrays_and_main_subclasses.Rd |only vectools-0.2.0/vectools/man/11_other_matrix-like_objects.Rd |only vectools-0.2.0/vectools/man/12_is_functions.Rd |only vectools-0.2.0/vectools/man/13_other_conversion_functions.Rd |only vectools-0.2.0/vectools/man/20_standard_methods.Rd |only vectools-0.2.0/vectools/man/21_combine_and_replication_functions.Rd |only vectools-0.2.0/vectools/man/30_objtag_methods.Rd |only vectools-0.2.0/vectools/man/40_unique-related_functions.Rd |only vectools-0.2.0/vectools/man/41_sequence_properties.Rd |only vectools-0.2.0/vectools/man/42_optimization-related_functions.Rd |only vectools-0.2.0/vectools/man/43_other_sequence_functions.Rd |only vectools-0.2.0/vectools/man/50_SQL-like_functions.Rd |only vectools-0.2.0/vectools/man/51_grouped_head.Rd |only vectools-0.2.0/vectools/man/52_combined_head_and_tail.Rd |only vectools-0.2.0/vectools/man/60_pre-multiplication_transformation_matrices.Rd |only vectools-0.2.0/vectools/man/61_post-multiplication_transformation_matrices.Rd |only vectools-0.2.0/vectools/man/62_other_transformation_matrices.Rd |only vectools-0.2.0/vectools/man/63_test_plots.Rd |only vectools-0.2.0/vectools/man/70_outer_generalizations.Rd |only vectools-0.2.0/vectools/man/71_pooling.Rd |only vectools-0.2.0/vectools/man/72_convolutions.Rd |only vectools-0.2.0/vectools/man/73_image_filters.Rd |only vectools-0.2.0/vectools/vignettes |only vectools-0.3.0/vectools/DESCRIPTION | 14 - 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Title: Access the 'City of Vancouver' Open Data API
Description: Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data.
Functionality to list the data catalogue and access data and geographic records.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between VancouvR versions 0.1.3 dated 2021-05-10 and 0.1.4 dated 2021-06-07
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 9 ++++++++- README.md | 4 +++- build/vignette.rds |binary inst/doc/Demo.R | 7 ++++--- inst/doc/Demo.Rmd | 7 ++++--- inst/doc/Demo.html | 26 +++++++++++++------------- inst/doc/Isolines.R | 3 ++- inst/doc/Isolines.Rmd | 3 ++- vignettes/Demo.Rmd | 7 ++++--- vignettes/Isolines.Rmd | 3 ++- 12 files changed, 56 insertions(+), 41 deletions(-)