Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame
like objects, both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 1.0.6 dated 2021-05-05 and 1.0.7 dated 2021-06-18
DESCRIPTION | 6 MD5 | 50 - NEWS.md | 10 R/across.R | 67 +- R/filter.R | 6 R/summarise.R | 10 R/utils.r | 5 build/dplyr.pdf |binary build/vignette.rds |binary inst/doc/base.html | 1087 ++++++++++++++----------------------- inst/doc/colwise.html | 685 ++++++++--------------- inst/doc/compatibility.html | 431 +++----------- inst/doc/dplyr.html | 975 +++++++++++++-------------------- inst/doc/grouping.html | 899 +++++++++++------------------- inst/doc/programming.html | 487 ++++------------ inst/doc/rowwise.html | 968 ++++++++++++-------------------- inst/doc/two-table.R | 2 inst/doc/two-table.Rmd | 4 inst/doc/two-table.html | 551 +++++------------- inst/doc/window-functions.html | 445 ++++----------- man/across.Rd | 4 man/reexports.Rd | 2 tests/testthat/_snaps/summarise.md | 2 tests/testthat/test-across.R | 150 ++++- tests/testthat/test-bind.R | 6 vignettes/two-table.Rmd | 4 26 files changed, 2571 insertions(+), 4285 deletions(-)
Title: Clustering and Classification Inference with U-Statistics
Description: Clustering and classification inference for high dimension low sample size (HDLSS)
data with U-statistics. The package contains implementations of nonparametric statistical
tests for sample homogeneity, group separation, clustering, and classification of
multivariate data. The methods have high statistical power and are tailored for data
in which the dimension L is much larger than sample size n. See Gabriela B. Cybis,
Marcio Valk and Sílvia RC Lopes (2018) <doi:10.1080/00949655.2017.1374387>, Marcio
Valk and Gabriela B. Cybis (2020) <doi:10.1080/10618600.2020.1796398>, Debora Z. Bello, Marcio
Valk and Gabriela B. Cybis (2021) <arXiv:2106.09115>.
Author: Gabriela Cybis [aut, cre],
Marcio Valk [aut],
Kazuki Yokoyama [ctb],
Debora Zava Bello [ctb]
Maintainer: Gabriela Cybis <gcybis@gmail.com>
Diff between uclust versions 0.2.0 dated 2020-01-20 and 1.0.0 dated 2021-06-18
DESCRIPTION | 20 +++++++++++--------- MD5 | 37 +++++++++++++++++++++++-------------- NAMESPACE | 5 +++++ NEWS.md | 6 ++++++ R/3functions.R |only R/Bn.R | 2 +- R/BnClustSig.R | 6 ++---- R/bn3.R |only R/boot_sigma.R | 2 +- R/is_homo.R | 6 ++---- R/is_homo3.R |only R/uclust3.R |only R/uhclust.R | 6 ++---- R/utest3.R |only README.md | 6 +++--- man/bn.Rd | 2 +- man/bn3.Rd |only man/is_homo.Rd | 6 ++---- man/is_homo3.Rd |only man/uclust.Rd | 6 ++---- man/uclust3.Rd |only man/uhclust.Rd | 6 ++---- man/utest3.Rd |only man/var_bn.Rd | 2 +- 24 files changed, 64 insertions(+), 54 deletions(-)
Title: Wavelet Approaches to Studies of Synchrony in Ecology and Other
Fields
Description: Tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. Some tools will be useful for studying community synchrony. See, for instance, Sheppard et al (2016) <doi: 10.1038/NCLIMATE2991>, Sheppard et al (2017) <doi: 10.1051/epjnbp/2017000>, Sheppard et al (2019) <doi: 10.1371/journal.pcbi.1006744>.
Author: Daniel C. Reuman [aut, cre],
Thomas L. Anderson [aut],
Jonathan A. Walter [aut],
Lei Zhao [aut],
Lawrence W. Sheppard [aut]
Maintainer: Daniel C. Reuman <reuman@ku.edu>
Diff between wsyn versions 1.0.3 dated 2021-01-11 and 1.0.4 dated 2021-06-18
DESCRIPTION | 7 MD5 | 82 +++++----- inst/doc/wsynvignette.pdf |binary tests/testthat/tests_coh.R | 2 vignettes/wsynvignette_files/figure-latex/abuse_cor-1.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-1.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-2.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-3.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-4.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-5.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-6.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-7.pdf |binary vignettes/wsynvignette_files/figure-latex/clust_demo-8.pdf |binary vignettes/wsynvignette_files/figure-latex/coh_example_call_fast-1.pdf |binary vignettes/wsynvignette_files/figure-latex/coh_plot-1.pdf |binary vignettes/wsynvignette_files/figure-latex/detect_tsspecific_sync-1.pdf |binary vignettes/wsynvignette_files/figure-latex/detect_tsspecific_sync-2.pdf |binary vignettes/wsynvignette_files/figure-latex/display_p_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd1_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd1_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd2_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropd2_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/dropdirrel_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/dropdirrel_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_1-2.pdf |binary vignettes/wsynvignette_files/figure-latex/examp_predsync_2-1.pdf |binary vignettes/wsynvignette_files/figure-latex/pearson_synmat-1.pdf |binary vignettes/wsynvignette_files/figure-latex/plotphase_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/plotrank_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmf_example_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-2.pdf |binary vignettes/wsynvignette_files/figure-latex/wmfs_wlmexample-3.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1_cors-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wpmf_example_1_plotts-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_plot-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_plotphase-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_1_power-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_2-1.pdf |binary vignettes/wsynvignette_files/figure-latex/wt_example_2-2.pdf |binary 42 files changed, 45 insertions(+), 46 deletions(-)
Title: Global Sensitivity Analysis in Physiologically Based Kinetic
Modeling
Description: Applying the global sensitivity analysis workflow to investigate
the parameter uncertainty and sensitivity in physiologically based
kinetic (PK) models, especially the physiologically based
pharmacokinetic/toxicokinetic model with multivariate outputs.
The package also provides some functions to check the convergence
and sensitivity of model parameters. The workflow was first mentioned
in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further
refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).
Author: Nan-Hung Hsieh [aut, cre] (<https://orcid.org/0000-0003-0163-2766>),
Brad Reisfeld [ctb] (<https://orcid.org/0000-0003-1310-1495>),
Weihsueh A. Chiu [ctb] (<https://orcid.org/0000-0002-7575-2368>)
Maintainer: Nan-Hung Hsieh <d99622005@ntu.edu.tw>
Diff between pksensi versions 1.2.0 dated 2020-06-15 and 1.2.1 dated 2021-06-18
DESCRIPTION | 57 + MD5 | 37 - NAMESPACE | 1 NEWS.md | 266 ++++----- R/compile.R | 37 + R/install.R | 411 +++++++------ R/pksim.R | 154 ++--- build/vignette.rds |binary inst/CITATION |only inst/doc/pbpk_apap.R | 352 +++++------ inst/doc/pbpk_apap.html | 766 ++++++++++--------------- inst/doc/pbtk1cpt.R | 372 ++++++------ inst/doc/pbtk1cpt.Rmd | 662 +++++++++++----------- inst/doc/pbtk1cpt.html | 915 +++++++++++++------------------ inst/mcsim |only man/compile_model.Rd | 4 man/figures/README-unnamed-chunk-8-1.png |only man/figures/README-unnamed-chunk-9-1.png |only man/mcsim.Rd | 11 tests/testthat/test-models.R |only tests/testthat/test-rfast99.R | 262 ++++---- vignettes/pbtk1cpt.Rmd | 662 +++++++++++----------- 22 files changed, 2411 insertions(+), 2558 deletions(-)
Title: Read EPUB File Metadata and Text
Description: Provides functions supporting the reading and parsing of internal e-book content from EPUB files.
The 'epubr' package provides functions supporting the reading and parsing of internal e-book content from EPUB files.
E-book metadata and text content are parsed separately and joined together in a tidy, nested tibble data frame.
E-book formatting is not completely standardized across all literature.
It can be challenging to curate parsed e-book content across an arbitrary collection of e-books
perfectly and in completely general form, to yield a singular, consistently formatted output.
Many EPUB files do not even contain all the same pieces of information in their respective metadata.
EPUB file parsing functionality in this package is intended for relatively general application to arbitrary EPUB e-books.
However, poorly formatted e-books or e-books with highly uncommon formatting may not work with this package.
There may even be cases where an EPUB file has DRM or some other property that makes it impossible to read with 'epubr'.
Text is read 'as is' for the most part. The only nominal changes are minor substitutions, for example curly quotes changed to straight quotes.
Substantive changes are expected to be performed subsequently by the user as part of their text analysis.
Additional text cleaning can be performed at the user's discretion, such as with functions from packages like 'tm' or 'qdap'.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <mfleonawicz@gmail.com>
Diff between epubr versions 0.6.2 dated 2021-02-20 and 0.6.3 dated 2021-06-18
DESCRIPTION | 7 +--- MD5 | 18 +++++----- NEWS.md | 5 ++ R/epub.R | 6 ++- README.md | 44 ++++++++++++-------------- build/vignette.rds |binary inst/doc/epubr.Rmd | 36 ++++++++++----------- inst/doc/epubr.html | 87 ++++++++++++++++++++++++++++------------------------ man/epub.Rd | 1 vignettes/epubr.Rmd | 36 ++++++++++----------- 10 files changed, 126 insertions(+), 114 deletions(-)
Title: Analyze Group Patterns using Graph Theory in Educational
Settings
Description: Analyzes group patterns using discourse analysis data with graph theory mathematics. Takes the order of which individuals talk and converts it to a network edge and weight list. Returns the density, centrality, centralization, and subgroup information for each group. Based on the analytical framework laid out in Chai et al. (2019) <doi:10.1187/cbe.18-11-0222>.
Author: Albert Chai [aut],
Andrew Lee [aut],
Joshua Le [aut, cre],
Katherine Ly [ctb],
Kevin Banh [ctb],
Priya Pahal [ctb],
Jitarth Sheth [ctb],
Stanley Lo [aut]
Maintainer: Joshua Le <jpl038@ucsd.edu>
Diff between discourseGT versions 1.1.5 dated 2021-04-02 and 1.1.6 dated 2021-06-18
DESCRIPTION | 10 + MD5 | 10 - R/plot1Att.R | 262 ++++++++++++++++++++++++------------------------- R/plot2Att.R | 198 ++++++++++++++++++------------------- data/attributeData.rda |binary data/sampleData1.rda |binary 6 files changed, 241 insertions(+), 239 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.1.3 dated 2021-03-28 and 2.1.6 dated 2021-06-18
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/df2latex.R | 41 +++++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/CITATION | 6 +++--- inst/NEWS.Rd | 16 +++++++++++++++- inst/doc/factor.pdf |binary inst/doc/mediation.pdf |binary inst/doc/omega.pdf |binary inst/doc/overview.pdf |binary man/df2latex.Rd | 4 ++-- man/spi.Rd | 5 +++++ 12 files changed, 75 insertions(+), 27 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psych versions 2.1.3 dated 2021-03-27 and 2.1.6 dated 2021-06-18
DESCRIPTION | 8 +- MD5 | 102 ++++++++++++++++++----------------- NAMESPACE | 5 + R/bassAckward.diagram.r | 11 ++- R/cohen.d.R | 6 +- R/corr.test.R | 21 +++++-- R/diagram.R | 19 ++++++ R/error.bars.R | 25 +++++--- R/error.bars.by.R | 19 ++++-- R/error.dots.r | 13 ++++ R/fa.R | 3 - R/fa.diagram.R | 7 +- R/make.keys.R | 21 +++++++ R/mediate.r | 116 ++++++++++++++++++++++++++++++++-------- R/misc.R | 37 +++++++++++- R/multi.hist.R | 74 ++++++++++++++++++++----- R/omega.R | 4 - R/partial.r.R | 3 - R/plot.psych.R | 6 +- R/predict.principal.R | 11 ++- R/print.psych.R | 19 ++++-- R/reliability.R |only R/scatter.hist.R | 137 +++++++++++++++++++++++++++++++++++++----------- R/schmid.R | 4 - R/sim.hierarchical.R | 11 +++ R/sim.item.R | 15 +++++ R/skew.R | 6 +- R/summary.psych.R | 55 ++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 6 +- inst/News.Rd | 47 +++++++++++++++- inst/doc/intro.pdf |binary inst/doc/scoring.Rnw | 4 - inst/doc/scoring.pdf |binary man/cohen.d.Rd | 21 ++++++- man/corr.test.Rd | 4 + man/fa.Rd | 3 + man/make.keys.Rd | 9 ++- man/mediate.Rd | 4 - man/multi.hist.Rd | 7 ++ man/omega.Rd | 7 ++ man/plot.psych.Rd | 4 - man/reliability.Rd |only man/scatter.hist.Rd | 43 ++++++++++----- man/schmid.Rd | 3 - man/score.irt.Rd | 1 man/sim.hierarchical.Rd | 6 +- man/sim.irt.Rd | 1 man/simulation.circ.Rd | 1 man/skew.Rd | 1 man/tetrachor.Rd | 8 ++ vignettes/scoring.Rnw | 4 - 53 files changed, 713 insertions(+), 229 deletions(-)
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture
hidden Markov models for social sequence data and other categorical time series.
Also some more restricted versions of these type of models are available: Markov
models, mixture Markov models, and latent class models. The package supports
models for one or multiple subjects with one or multiple parallel sequences
(channels). External covariates can be added to explain cluster membership in
mixture models. The package provides functions for evaluating and comparing
models, as well as functions for visualizing of multichannel sequence data and
hidden Markov models. Models are estimated using maximum likelihood via the EM
algorithm and/or direct numerical maximization with analytical gradients. All
main algorithms are written in C++ with support for parallel computation.
Documentation is available via several vignettes in this page, and the
paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Satu Helske [aut] (<https://orcid.org/0000-0003-0532-0153>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 1.0.14 dated 2019-10-22 and 1.1.0 dated 2021-06-18
DESCRIPTION | 10 MD5 | 85 NEWS | 7 R/biofam3c.R | 4 R/colorpalette.R | 2 R/fit_model.R | 185 R/isColor.R | 2 R/plot.hmm.R | 21 R/zzz.R |only build/vignette.rds |binary inst/doc/seqHMM.pdf |10105 +++++++++++++++++--------------------- inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.R | 4 inst/doc/seqHMM_visualization.pdf |binary man/biofam3c.Rd | 10 man/build_hmm.Rd | 12 man/build_lcm.Rd | 12 man/build_mhmm.Rd | 17 man/build_mmm.Rd | 13 man/colorpalette.Rd | 6 man/fit_model.Rd | 64 man/forward_backward.Rd | 3 man/gridplot.Rd | 20 man/hmm_biofam.Rd | 6 man/hmm_mvad.Rd | 6 man/logLik.hmm.Rd | 3 man/logLik.mhmm.Rd | 3 man/mhmm_biofam.Rd | 6 man/mhmm_mvad.Rd | 6 man/mssplot.Rd | 46 man/plot.hmm.Rd | 69 man/plot.mhmm.Rd | 55 man/seqHMM-deprecated.Rd | 47 man/seqHMM.Rd | 1 man/simulate_hmm.Rd | 9 man/simulate_mhmm.Rd | 12 man/simulate_pars.Rd | 8 man/ssp.Rd | 46 man/ssplot.Rd | 44 man/summary.mhmm.Rd | 9 man/trim_model.Rd | 10 man/vcov.mhmm.Rd | 3 vignettes/references.bib | 16 44 files changed, 5413 insertions(+), 5574 deletions(-)
Title: Drug Ontology Parsing Engine
Description: Provides information on drug names (brand,
generic and street) for drugs tracked by the DEA. There are functions that
will search synonyms and return the drug names and types. The vignettes
have extensive information on the work done to create the data for the package.
Author: Raymond Balise [aut, cre] (<https://orcid.org/0000-0002-9856-5901>),
Layla Bouzoubaa [aut] (<https://orcid.org/0000-0002-6616-0950>),
Gabriel Odom [aut] (<https://orcid.org/0000-0003-1341-4555>),
Nathaniel Castor [aut]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between DOPE versions 2.0.1 dated 2021-05-12 and 2.1.0 dated 2021-06-18
DESCRIPTION | 20 LICENSE | 4 MD5 | 156 ++-- NAMESPACE | 26 NEWS.md | 116 +-- R/compress_lookup.R | 84 +- R/dea_brands.R | 30 R/dea_controlled.R | 34 - R/dea_factsheets.R | 32 R/dea_street_names.R | 32 R/drug_df.R | 32 R/drug_stop_words.R | 26 R/iqvia.R | 32 R/lookup.R | 160 ++-- R/lookup_df.R | 28 R/lookup_syn.R | 123 +-- R/noslang_raw.R | 32 R/noslang_street_names.R | 32 R/parse.R | 186 +++-- README.md | 132 ++- build/vignette.rds |binary data/lookup_df.rda |binary inst/doc/Intro.R | 120 +-- inst/doc/Intro.Rmd | 272 ++++---- inst/doc/Intro.html | 577 +++++------------ inst/doc/controlled.R | 302 ++++----- inst/doc/controlled.Rmd | 426 ++++++------ inst/doc/controlled.html | 908 ++++++++++----------------- inst/doc/dea_scrape.R | 138 ++-- inst/doc/dea_scrape.Rmd | 232 +++--- inst/doc/dea_scrape.html | 659 ++++++------------- inst/doc/dea_street_names.R | 76 +- inst/doc/dea_street_names.Rmd | 132 +-- inst/doc/dea_street_names.html | 585 +++++------------ inst/doc/make_lookup_df.R | 335 +++++----- inst/doc/make_lookup_df.Rmd | 473 +++++++------- inst/doc/make_lookup_df.html | 987 ++++++++++++----------------- inst/doc/noslang_street_names.R | 460 ++++++------- inst/doc/noslang_street_names.Rmd | 510 +++++++-------- inst/doc/noslang_street_names.html | 971 +++++++++++------------------ inst/doc/parse_lookup.R | 110 +-- inst/doc/parse_lookup.Rmd | 280 ++++---- inst/doc/parse_lookup.html | 1028 ++++++++++++------------------- inst/extdata/Difficult.csv |only inst/extdata/Difficult_Edited.csv |only inst/extdata/IQVIA/classify_iqvia.R | 272 ++++---- inst/extdata/README.md | 54 - inst/extdata/controlled.Rmd | 392 +++++------ inst/extdata/ontology.Rmd | 220 +++--- inst/extdata/slangUE.txt | 52 - inst/extdata/test_parse/make_test_data.R | 36 - inst/scripts/make_drug_stop_words.R | 34 - inst/scripts/processNoSlang.R | 372 +++++------ inst/scripts/studyStructure.R | 158 ++-- man/compress_lookup.Rd | 86 +- man/dea_brands.Rd | 40 - man/dea_controlled.Rd | 46 - man/dea_factsheets.Rd | 48 - man/dea_street_names.Rd | 42 - man/drug_df.Rd | 42 - man/drug_stop_words.Rd | 36 - man/iqvia.Rd | 42 - man/lookup.Rd | 78 +- man/lookup_df.Rd | 42 - man/lookup_syn.Rd | 44 - man/noslang_raw.Rd | 46 - man/noslang_street_names.Rd | 46 - man/parse.Rd | 45 - tests/testthat.R | 8 tests/testthat/test-compress_lookup.R | 46 - tests/testthat/test-lookup.R | 110 +-- tests/testthat/test-lookup_syn.R | 60 - tests/testthat/test-parse.R | 144 +++- vignettes/Intro.Rmd | 272 ++++---- vignettes/controlled.Rmd | 426 ++++++------ vignettes/dea_scrape.Rmd | 232 +++--- vignettes/dea_street_names.Rmd | 132 +-- vignettes/make_lookup_df.Rmd | 473 +++++++------- vignettes/noslang_street_names.Rmd | 510 +++++++-------- vignettes/parse_lookup.Rmd | 280 ++++---- 80 files changed, 7389 insertions(+), 8475 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of fitted probabilities and percentiles. For multiple experts, a weighted
linear pool can be calculated. Also includes functions for eliciting beliefs
about population distributions, eliciting multivariate distributions using a
Gaussian copula, eliciting a Dirichlet distribution, and eliciting distributions
for variance parameters in a random effects meta-analysis model. R Shiny apps
for most of the methods are included.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.7.0 dated 2020-02-08 and 1.8.0 dated 2021-06-18
SHELF-1.7.0/SHELF/R/shinyplotgroup.R |only SHELF-1.7.0/SHELF/R/shinyplotsingle.R |only SHELF-1.8.0/SHELF/DESCRIPTION | 10 SHELF-1.8.0/SHELF/MD5 | 105 +- SHELF-1.8.0/SHELF/NAMESPACE | 2 SHELF-1.8.0/SHELF/R/SHELF-package.R | 21 SHELF-1.8.0/SHELF/R/elicit.R | 470 +++++---- SHELF-1.8.0/SHELF/R/elicitBivariate.R | 20 SHELF-1.8.0/SHELF/R/elicitConcProb.R | 4 SHELF-1.8.0/SHELF/R/elicitCopula.R | 3 SHELF-1.8.0/SHELF/R/elicitDirichlet.R | 2 SHELF-1.8.0/SHELF/R/elicitExtension.R | 123 +- SHELF-1.8.0/SHELF/R/elicitHeterogeneity.R | 2 SHELF-1.8.0/SHELF/R/elicitMarginalsModule.R | 27 SHELF-1.8.0/SHELF/R/elicitMixture.R | 25 SHELF-1.8.0/SHELF/R/elicitMultipleExperts.R | 194 ++- SHELF-1.8.0/SHELF/R/expertdensity.R | 50 SHELF-1.8.0/SHELF/R/expertprobs.R | 48 SHELF-1.8.0/SHELF/R/expertquantiles.R | 50 SHELF-1.8.0/SHELF/R/feedbackgroup.R | 15 SHELF-1.8.0/SHELF/R/feedbacksingle.R | 74 + SHELF-1.8.0/SHELF/R/fitdist.R | 515 ++++++---- SHELF-1.8.0/SHELF/R/makeCDFPlot.R | 95 + SHELF-1.8.0/SHELF/R/makeGroupPlot.R | 10 SHELF-1.8.0/SHELF/R/makeLinearPoolPlot.R | 32 SHELF-1.8.0/SHELF/R/makeSingleExpertPlot.R | 126 ++ SHELF-1.8.0/SHELF/R/plinearpool.R | 10 SHELF-1.8.0/SHELF/R/plotQuartiles.R | 24 SHELF-1.8.0/SHELF/R/plotTertiles.R | 23 SHELF-1.8.0/SHELF/R/plotfit.R | 69 - SHELF-1.8.0/SHELF/R/plotsingle.R | 18 SHELF-1.8.0/SHELF/R/qlinearpool.R | 2 SHELF-1.8.0/SHELF/R/rlinearpool.R |only SHELF-1.8.0/SHELF/R/sampleFit.R | 22 SHELF-1.8.0/SHELF/build/vignette.rds |binary SHELF-1.8.0/SHELF/inst/NEWS.md | 27 SHELF-1.8.0/SHELF/inst/doc/Dirichlet-elicitation.pdf |binary SHELF-1.8.0/SHELF/inst/doc/Multivariate-normal-copula.pdf |binary SHELF-1.8.0/SHELF/inst/doc/SHELF-overview.pdf |binary SHELF-1.8.0/SHELF/inst/elicitationReportFile/elicitationSummary.Rmd | 198 +++ SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummary.Rmd | 210 ++++ SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummaryBivariate.Rmd | 406 +++++++ SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummaryExtension.Rmd | 499 ++++++++- SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummaryExtensionUploadedYsample.Rmd |only SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummaryGroup.Rmd | 112 ++ SHELF-1.8.0/SHELF/inst/shinyAppFiles/elicitationShinySummaryMixture.Rmd | 73 + SHELF-1.8.0/SHELF/man/SHELF-package.Rd | 21 SHELF-1.8.0/SHELF/man/elicitConcProb.Rd | 4 SHELF-1.8.0/SHELF/man/fitdist.Rd | 14 SHELF-1.8.0/SHELF/man/makeCDFPlot.Rd | 3 SHELF-1.8.0/SHELF/man/plinearpool.Rd | 8 SHELF-1.8.0/SHELF/man/plotQuartiles.Rd | 16 SHELF-1.8.0/SHELF/man/plotTertiles.Rd | 17 SHELF-1.8.0/SHELF/man/plotfit.Rd | 22 SHELF-1.8.0/SHELF/tests/testthat/test-fitting.R | 65 + SHELF-1.8.0/SHELF/tests/testthat/test-linearpool.R |only 56 files changed, 3087 insertions(+), 799 deletions(-)
Title: Mediterranean Forest Simulation
Description: Functions to simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Author: Miquel De Cáceres [aut, cre],
Shengli Huang [aut],
Víctor Granda [aut],
Antoine Cabon [aut],
Jordi Martínez-Vilalta [ctb],
Maurizio Mencuccini [ctb],
Nicolas Martin-StPaul [ctb]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between medfate versions 2.2.1 dated 2021-06-11 and 2.2.3 dated 2021-06-18
medfate-2.2.1/medfate/R/forest_mapWoodyTables.R |only medfate-2.2.1/medfate/R/soilgridsParams.R |only medfate-2.2.1/medfate/man/forest_mapWoodyTables.Rd |only medfate-2.2.1/medfate/man/soilgridsParams.Rd |only medfate-2.2.3/medfate/DESCRIPTION | 16 medfate-2.2.3/medfate/MD5 | 32 - medfate-2.2.3/medfate/NAMESPACE | 6 medfate-2.2.3/medfate/inst/doc/AdvancedWaterEnergyBalance.html | 252 +++++----- medfate-2.2.3/medfate/inst/doc/BasicWaterBalance.html | 6 medfate-2.2.3/medfate/inst/doc/ForestDynamics.html | 4 medfate-2.2.3/medfate/inst/doc/ForestGrowth.html | 4 medfate-2.2.3/medfate/inst/doc/PackageOverview.html | 4 medfate-2.2.3/medfate/inst/doc/PreparingInputs.Rmd | 4 medfate-2.2.3/medfate/inst/doc/PreparingInputs.html | 8 medfate-2.2.3/medfate/man/defaultSoilParams.Rd | 2 medfate-2.2.3/medfate/man/forest.Rd | 2 medfate-2.2.3/medfate/man/wind.Rd | 5 medfate-2.2.3/medfate/src/windKatul.cpp | 91 ++- medfate-2.2.3/medfate/vignettes/PreparingInputs.Rmd | 4 19 files changed, 226 insertions(+), 214 deletions(-)
Title: Integrative Analysis of RNA-Seq and ChIP-Seq Data
Description: Integrative analysis of gene expression (RNA-Seq data), and histone
modification data for user-defined sets of histone marks (ChIP-Seq data) to
discover consistent changes in genes between biological conditions.
Additionally, Pareto optimization is used to prioritize genes based on the
level of consistent changes in both RNA-Seq and ChIP-Seq data.
Method is described in Cao, Y. et al. (2020) <doi:10.1186/s12864-020-07205-6>.
Author: Yingying Cao [aut, cre]
Maintainer: Yingying Cao <yingying.cao@uni-due.de>
Diff between intePareto versions 0.1.1 dated 2021-06-11 and 0.1.2 dated 2021-06-18
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/doc/intePareto.Rmd | 1 + inst/doc/intePareto.html | 3 +++ vignettes/intePareto.Rmd | 1 + 5 files changed, 14 insertions(+), 9 deletions(-)
Title: Easy Access to the Canadian Open Government Portal
Description: Allows to search for existing resources, including datasets, on
the Canadian Open Government portal (<https://open.canada.ca/en>). It is
also designed to allow users to easily download a range of files directly
from the portal in a reproducible manner.
Author: Valentin Lucet [aut, cre],
Kevin Cazelles [ctb] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Valentin Lucet <valentin.lucet@gmail.com>
Diff between rgovcan versions 1.0.2 dated 2021-06-14 and 1.0.3 dated 2021-06-18
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only R/govcan_setup.R | 14 +++++++++++--- README.md | 13 +++++++++++-- 5 files changed, 29 insertions(+), 11 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [ctb],
David R. Hunter [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Diff between ergm.count versions 3.4.0 dated 2019-05-15 and 4.0.2 dated 2021-06-18
DESCRIPTION | 22 ++++---- LICENSE | 4 - MD5 | 52 +++++++++++------- NAMESPACE | 9 +-- R/InitErgmReference.R | 10 +-- R/InitWtErgmProposal.R | 10 +-- R/InitWtErgmTerm.R | 25 ++++++--- R/data.R |only R/ergm.count-package.R |only R/zzz.R | 21 ++++--- build |only inst/CITATION | 41 +++++++++----- inst/NEWS.Rd | 22 ++++++-- inst/doc |only man/ergm-references.Rd | 12 ++-- man/ergm-terms.Rd | 36 ++++++++++--- man/ergm.count-package.Rd | 91 ++++++++++++++------------------- man/zach.Rd | 115 ++++++++++++++++++----------------------- src/include_stubs.c | 8 +- src/init.c | 8 +- src/wtMHproposals.c | 126 +++++++++++++++++++++++----------------------- src/wtMHproposals.h | 10 +-- src/wtchangestats.c | 24 +++++--- src/wtchangestats.h | 12 ++-- tests/valued_fit.R | 14 ++--- tests/valued_sim.R | 10 +-- vignettes |only 27 files changed, 368 insertions(+), 314 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 1.17.0 dated 2021-05-08 and 1.18.0 dated 2021-06-18
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-model-h2o.R | 14 +------------- 3 files changed, 6 insertions(+), 18 deletions(-)
Title: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses
Description: A set of wrappers around 'rjags' functions to run Bayesian analyses in 'JAGS' (specifically, via 'libjags'). A single function call can control adaptive, burn-in, and sampling MCMC phases, with MCMC chains run in sequence or in parallel. Posterior distributions are automatically summarized (with the ability to exclude some monitored nodes if desired) and functions are available to generate figures based on the posteriors (e.g., predictive check plots, traceplots). Function inputs, argument syntax, and output format are nearly identical to the 'R2WinBUGS'/'R2OpenBUGS' packages to allow easy switching between MCMC samplers.
Author: Ken Kellner [cre, aut],
Mike Meredith [ctb]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between jagsUI versions 1.5.1 dated 2019-07-30 and 1.5.2 dated 2021-06-18
jagsUI-1.5.1/jagsUI/R/View.R |only jagsUI-1.5.1/jagsUI/R/xyplot.R |only jagsUI-1.5.1/jagsUI/man/View.Rd |only jagsUI-1.5.2/jagsUI/DESCRIPTION | 21 +++++---- jagsUI-1.5.2/jagsUI/MD5 | 37 ++++++++-------- jagsUI-1.5.2/jagsUI/NAMESPACE | 15 ++---- jagsUI-1.5.2/jagsUI/NEWS | 7 +++ jagsUI-1.5.2/jagsUI/R/densityplot.R | 66 ++++++++++++++++++++++++++++- jagsUI-1.5.2/jagsUI/R/geninits.R | 3 - jagsUI-1.5.2/jagsUI/R/get_plot_info.R |only jagsUI-1.5.2/jagsUI/R/jags_View.R |only jagsUI-1.5.2/jagsUI/R/mcmc_tools.R |only jagsUI-1.5.2/jagsUI/R/plot.R | 27 +++++++++--- jagsUI-1.5.2/jagsUI/R/ppcheck.R | 40 ++++++----------- jagsUI-1.5.2/jagsUI/R/processinput.R | 56 ++++++++++++------------ jagsUI-1.5.2/jagsUI/R/traceplot.R | 74 +++++++++++++++++---------------- jagsUI-1.5.2/jagsUI/R/update.R | 10 ++++ jagsUI-1.5.2/jagsUI/R/utils.R |only jagsUI-1.5.2/jagsUI/R/whiskerplot.R | 74 +++++++++++++++++---------------- jagsUI-1.5.2/jagsUI/man/densityplot.Rd |only jagsUI-1.5.2/jagsUI/man/jags_View.Rd |only jagsUI-1.5.2/jagsUI/man/ppcheck.Rd | 10 ++-- jagsUI-1.5.2/jagsUI/man/traceplot.Rd | 17 +++---- jagsUI-1.5.2/jagsUI/man/whiskerplot.Rd | 7 +-- 24 files changed, 281 insertions(+), 183 deletions(-)
Title: Two-Steps Benchmarks for Time Series Disaggregation
Description: The twoStepsBenchmark() and threeRuleSmooth() functions allow you to
disaggregate a low-frequency time-serie with time-series of higher frequency,
using the French National Accounts methodology. The aggregated sum of the
resulting time-serie is strictly equal to the low-frequency serie within the
benchmarking window. Typically, the low-frequency serie is an annual one,
unknown for the last year, and the high frequency one is either quarterly or
mensual. See "Methodology of quarterly national accounts", Insee Méthodes
N°126, by Insee (2012, ISBN:978-2-11-068613-8).
Author: Arnaud Feldmann [aut, cre] (<https://orcid.org/0000-0003-0109-7505>),
Franck Arnaud [ctb] (barplot base graphics method for the mts class),
Institut national de la statistique et des études économiques [cph]
(https://www.insee.fr/)
Maintainer: Arnaud Feldmann <arnaud.feldmann@insee.fr>
Diff between disaggR versions 0.2.1 dated 2021-05-03 and 1.0.0 dated 2021-06-18
disaggR-0.2.1/disaggR/tests/figs |only disaggR-1.0.0/disaggR/DESCRIPTION | 15 disaggR-1.0.0/disaggR/MD5 | 445 +++----- disaggR-1.0.0/disaggR/NAMESPACE | 5 disaggR-1.0.0/disaggR/NEWS.md | 5 disaggR-1.0.0/disaggR/R/bflSmooth.R | 5 disaggR-1.0.0/disaggR/R/in.R | 192 ++- disaggR-1.0.0/disaggR/R/methods.R | 37 disaggR-1.0.0/disaggR/R/plot.R | 21 disaggR-1.0.0/disaggR/R/praislm.R | 5 disaggR-1.0.0/disaggR/R/reView.R | 116 +- disaggR-1.0.0/disaggR/R/threeRuleSmooth.R | 39 disaggR-1.0.0/disaggR/R/twoStepsBenchmark.R | 242 +++- disaggR-1.0.0/disaggR/R/utils.R | 69 + disaggR-1.0.0/disaggR/inst/rmd/report.Rmd | 7 disaggR-1.0.0/disaggR/inst/rmd/report_nocompare.Rmd | 5 disaggR-1.0.0/disaggR/man/extend_tsp.Rd |only disaggR-1.0.0/disaggR/man/outliers.Rd |only disaggR-1.0.0/disaggR/man/se.Rd | 2 disaggR-1.0.0/disaggR/man/twoStepsBenchmark.Rd | 33 disaggR-1.0.0/disaggR/tests/testthat/_snaps/in.md | 506 ++++++++++ disaggR-1.0.0/disaggR/tests/testthat/_snaps/methods |only disaggR-1.0.0/disaggR/tests/testthat/_snaps/plot |only disaggR-1.0.0/disaggR/tests/testthat/_snaps/twoStepsBenchmark.md | 109 ++ disaggR-1.0.0/disaggR/tests/testthat/shiny-outliers |only disaggR-1.0.0/disaggR/tests/testthat/shiny-outlierssetcoef |only disaggR-1.0.0/disaggR/tests/testthat/test-in.R | 220 ++++ disaggR-1.0.0/disaggR/tests/testthat/test-methods.R | 52 - disaggR-1.0.0/disaggR/tests/testthat/test-plot.R | 83 + disaggR-1.0.0/disaggR/tests/testthat/test-reView.R | 214 ++++ disaggR-1.0.0/disaggR/tests/testthat/test-threeRuleSmooth.R | 6 disaggR-1.0.0/disaggR/tests/testthat/test-twoStepsBenchmark.R | 436 +++++--- 32 files changed, 2217 insertions(+), 652 deletions(-)
Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Author: Lionel Henry [cre, aut],
Thomas Lin Pedersen [aut] (<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph],
T Jake Luciani [aut] (svglite),
Matthieu Decorde [aut] (svglite),
Vaudor Lise [aut] (svglite),
Tony Plate [ctb] (svglite: Early line dashing code),
David Gohel [ctb] (svglite: Line dashing code and raster code),
Yixuan Qiu [ctb] (svglite: Improved styles; polypath implementation),
Håkon Malmedal [ctb] (svglite: Opacity code)
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vdiffr versions 1.0.1 dated 2021-06-17 and 1.0.2 dated 2021-06-18
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 +- R/expect-doppelganger.R | 4 ++-- tests/testthat/test-expect-doppelganger.R | 2 +- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Load Census TIGER/Line Shapefiles
Description: Download TIGER/Line shapefiles from the United States Census Bureau
(<https://www.census.gov/geographies/mapping-files/time-series/geo/tiger-line-file.html>)
and load into R as 'sf' objects.
Author: Kyle Walker [aut, cre],
Bob Rudis [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tigris versions 1.4 dated 2021-05-16 and 1.4.1 dated 2021-06-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/helpers.R | 6 +++++- R/shift_geometry.R | 6 +++++- data/fips_codes.rda |binary 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Sparse Tables
Description: Fast Multiplication and Marginalization of Sparse Tables.
Author: Mads Lindskou [aut, cre]
Maintainer: Mads Lindskou <mads@math.aau.dk>
Diff between sparta versions 0.7.3 dated 2021-04-22 and 0.8.0 dated 2021-06-18
DESCRIPTION | 8 +-- MD5 | 39 ++++++++-------- NAMESPACE | 10 +++- NEWS.md | 18 +++++-- R/RcppExports.R | 4 + R/api_converters.R | 12 ++++ R/api_sparta.R | 125 +++++++++++++++++++++++++++++++++++++--------------- R/helpers_misc.R | 5 ++ R/helpers_sparta.R | 66 ++++++++++++++++++++------- README.md | 6 +- man/as_array.Rd | 3 + man/getter.Rd | 6 ++ man/marg.Rd | 4 - man/merge.Rd | 29 +++++++----- man/slice.Rd | 3 + man/sparsity.Rd | 3 + man/table_size.Rd |only src/RcppExports.cpp | 18 +++++++ src/merge.cpp | 75 +++++++++++++++++++++++++++++-- src/misc_utils.cpp | 15 ++++++ src/misc_utils.h | 1 21 files changed, 348 insertions(+), 102 deletions(-)
Title: Mediation Analysis Using Joint Significance
Description: A set of helper functions to conduct joint-significance tests
for mediation analysis, as recommended by Yzerbyt, Muller, Batailler,
& Judd. (2018) <doi:10.1037/pspa0000132>.
Author: Cédric Batailler [aut, cre] (<https://orcid.org/0000-0003-0553-6827>),
Dominique Muller [aut] (<https://orcid.org/0000-0001-9544-5317>),
Vincent Yzerbyt [aut],
Charles Judd [aut],
Arnold Ho [dtc],
Nour Kteily [dtc],
Jacqueline Chen [dtc],
Simone Dohle [dtc],
Michael Siegrist [dtc]
Maintainer: Cédric Batailler <cedric.batailler@gmail.com>
Diff between JSmediation versions 0.1.1 dated 2020-01-30 and 0.1.2 dated 2021-06-18
DESCRIPTION | 80 ++- MD5 | 46 +- NEWS.md | 13 R/mdt_moderated_index.R | 3 R/utils-tidy-eval.R | 2 README.md | 9 build/vignette.rds |binary inst/doc/jsmediation.html | 590 +++++++++----------------- man/dohle_siegrist.Rd | 6 man/dohle_siegrist_wide.Rd | 6 man/figures/logo.png |binary man/ho_et_al.Rd | 6 man/tidyeval.Rd | 4 tests/testthat/test-apastylr.R | 2 tests/testthat/test-build_contrast.R | 2 tests/testthat/test-display_models.R | 2 tests/testthat/test-extract_models.R | 2 tests/testthat/test-indirect_effect-methods.R | 2 tests/testthat/test-mdt_moderated.R | 4 tests/testthat/test-mdt_moderated_index.R |only tests/testthat/test-mdt_simple.R | 2 tests/testthat/test-mdt_simple_index.R | 27 + tests/testthat/test-mdt_within.R | 2 tests/testthat/test-mdt_within_index.R |only tests/testthat/test-mdt_within_wide.R | 2 25 files changed, 347 insertions(+), 465 deletions(-)
Title: High Throughput Phenotyping (HTP) Data Analysis
Description: Phenotypic analysis of data coming from high throughput
phenotyping (HTP) platforms, including different types of outlier detection,
spatial analysis, and parameter estimation. The package is being developed
within the EPPN2020 project (<https://eppn2020.plant-phenotyping.eu/>).
Some functions have been created to be used in conjunction with the R
package 'asreml' for the 'ASReml' software, which can be obtained upon
purchase from 'VSN' international (<https://www.vsni.co.uk/software/asreml>).
Author: Emilie J Millet [aut] (<https://orcid.org/0000-0002-2913-4892>),
Maria Xose Rodriguez Alvarez [aut]
(<https://orcid.org/0000-0002-1329-9238>),
Diana Marcela Perez Valencia [aut]
(<https://orcid.org/0000-0002-9053-2929>),
Isabelle Sanchez [aut],
Nadine Hilgert [aut],
Bart-Jan van Rossum [aut, cre]
(<https://orcid.org/0000-0002-8673-2514>),
Fred van Eeuwijk [aut] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [aut]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenHTP versions 1.0.2 dated 2021-06-10 and 1.0.3 dated 2021-06-18
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 +++++- build/partial.rdb |binary data/PhenoarchDat1.rda |binary data/spatCorrectedArch.rda |binary data/spatPredArch.rda |binary inst/doc/Overview_HTP.html | 8 +++++--- inst/tinytest/test_detectSerieOut.R | 2 +- inst/tinytest/test_detectSingleOut.R | 2 +- 10 files changed, 25 insertions(+), 19 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.8 dated 2020-07-03 and 0.3.10 dated 2021-06-18
DESCRIPTION | 8 ++-- MD5 | 56 +++++++++++++++++----------------- R/SplashDams.R | 2 - R/alaska.R | 2 - R/cycle_hire.R | 2 - R/cycle_hire_osm.R | 2 - R/hawaii.R | 2 - R/seine.R | 2 - R/state.vbm.R | 2 - R/us_states.R | 2 - R/world.R | 4 +- R/worldbank_df.R | 2 - README.md | 79 ++++++++++++++++++++++++------------------------- data/world.rda |binary inst/shapes/world.dbf |binary inst/shapes/world.gpkg |binary inst/shapes/world.prj | 2 - inst/shapes/world.shp |binary inst/shapes/world.shx |binary man/SplashDams.Rd | 2 - man/alaska.Rd | 2 - man/cycle_hire.Rd | 2 - man/cycle_hire_osm.Rd | 2 - man/hawaii.Rd | 2 - man/seine.Rd | 2 - man/state.vbm.Rd | 2 - man/us_states.Rd | 2 - man/world.Rd | 4 +- man/worldbank_df.Rd | 2 - 29 files changed, 95 insertions(+), 94 deletions(-)
Title: A Multiscale Framework for Data Analysis of Global Precipitation
Description: An open-access tool/framework to download, validate, visualize, and analyze multi-source precipitation data across various spatio-temporal scales. Ultimately providing the hydrology science community with the tools for consistent and reproducible analysis regarding precipitation.
Author: Mijael R. Vargas G. [aut, cre],
Yannis Markonis [aut, ths],
Rajani K. Pradhan [ctb]
Maintainer: Mijael R. Vargas G. <mirovago@gmail.com>
Diff between pRecipe versions 0.0.1 dated 2021-06-10 and 0.1.0 dated 2021-06-18
pRecipe-0.0.1/pRecipe/man/download_cmorph.Rd |only pRecipe-0.0.1/pRecipe/man/download_persiann_cdr.Rd |only pRecipe-0.0.1/pRecipe/man/reformat_cmorph.Rd |only pRecipe-0.0.1/pRecipe/man/reformat_persiann_cdr.Rd |only pRecipe-0.1.0/pRecipe/DESCRIPTION | 8 pRecipe-0.1.0/pRecipe/MD5 | 55 +-- pRecipe-0.1.0/pRecipe/NAMESPACE | 7 pRecipe-0.1.0/pRecipe/NEWS.md |only pRecipe-0.1.0/pRecipe/R/aux_functions.R | 14 pRecipe-0.1.0/pRecipe/R/downloaders.R | 341 +++++++++------------ pRecipe-0.1.0/pRecipe/R/pRecipe.R | 31 - pRecipe-0.1.0/pRecipe/R/reformatters.R | 84 ----- pRecipe-0.1.0/pRecipe/man/download_20cr.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_all.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_cmap.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_cpc.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_cru_ts.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_data.Rd | 2 pRecipe-0.1.0/pRecipe/man/download_ghcn.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_gpcc.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_gpcp.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_gpm_imergm.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_ncep_doe.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_ncep_ncar.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_precl.Rd | 4 pRecipe-0.1.0/pRecipe/man/download_trmm_3b43.Rd | 8 pRecipe-0.1.0/pRecipe/man/download_udel.Rd | 4 pRecipe-0.1.0/pRecipe/man/import_full_data.Rd | 2 pRecipe-0.1.0/pRecipe/man/import_subset_data.Rd | 2 pRecipe-0.1.0/pRecipe/man/merge_time.Rd | 2 pRecipe-0.1.0/pRecipe/man/reformat_data.Rd | 2 31 files changed, 238 insertions(+), 372 deletions(-)
Title: Assessing the Partial Association Between Ordinal Variables
Description: An implementation of the unified framework for assessing partial association
between ordinal variables after adjusting for a set of covariates (Dungang Liu, Shaobo
Li, Yan Yu and Irini Moustaki (2020), accepted by the Journal of the American
Statistical Association). This package provides a set of tools to quantify, visualize,
and test partial associations between multiple ordinal variables. It can produce a number
of $phi$ measures, partial regression plots, 3-D plots, and $p$-values for testing
$H_0: phi=0$ or $H_0: phi <= delta$.
Author: Xiaorui (Jeremy) Zhu [aut, cre],
Shaobo Li [aut],
Dungang Liu [ctb, aut],
Yuejie Chen [ctb]
Maintainer: Xiaorui (Jeremy) Zhu <zhuxiaorui1989@gmail.com>
Diff between PAsso versions 0.1.9 dated 2021-05-07 and 0.1.10 dated 2021-06-18
DESCRIPTION | 6 +- MD5 | 41 +++++++++--------- NAMESPACE | 1 NEWS.md | 14 ++++++ R/PAsso.R | 24 +++++----- R/data.R | 10 ++-- R/plot.R | 15 +++++- R/plot3D.R | 94 ++++++++++++++++++++++++++++++++----------- R/residuals.R | 21 +++++---- R/surrogate.R | 16 ++++--- R/test.R | 5 +- README.md | 11 +---- build/partial.rdb |binary man/ANES2016.Rd | 10 ++-- man/PAsso.Rd | 24 +++++----- man/plot.Rd | 13 +++++ man/plot3D.Rd | 17 ++++--- man/plot3D_one.Rd |only man/residuals.Rd | 21 +++++---- man/surrogate.Rd | 16 ++++--- tests/testthat/Rplots.pdf |binary tests/testthat/test-plot3D.R | 30 +++++++++++++ 22 files changed, 253 insertions(+), 136 deletions(-)
Title: An Alternative to the Hodrick-Prescott Filter
Description: In the working paper titled "Why You Should Never Use the Hodrick-Prescott
Filter", James D. Hamilton proposes a new alternative to economic time series
filtering. The neverhpfilter package provides functions and data for reproducing his work. Hamilton (2017) <doi:10.3386/w23429>.
Author: Justin M. Shea [aut, cre]
Maintainer: Justin M. Shea <jshea@roosevelt.edu>
Diff between neverhpfilter versions 0.3-1 dated 2020-02-09 and 0.4-0 dated 2021-06-18
DESCRIPTION | 10 - MD5 | 96 +++++------ NEWS.md | 16 + R/EXPGSC1.R | 4 R/FEDFUNDS.R | 4 R/GCEC1.R | 4 R/GDPC1.R | 6 R/GDPDEF.R | 4 R/GPDIC1.R | 4 R/GS10.R | 4 R/IMPGSC1.R | 4 R/PAYEMS.R | 4 R/PCECC96.R | 4 R/SP500.R | 24 +- R/UNRATENSA.R | 4 R/USREC.R | 4 build/vignette.rds |binary data/EXPGSC1.RData |binary data/FEDFUNDS.RData |binary data/GCEC1.RData |binary data/GDPC1.RData |binary data/GDPDEF.RData |binary data/GPDIC1.RData |binary data/GS10.RData |binary data/IMPGSC1.RData |binary data/PAYEMS.RData |binary data/PCECC96.RData |binary data/SP500.RData |binary data/UNRATENSA.RData |binary data/USREC.RData |binary inst/doc/Getting-started.html | 321 +++++++------------------------------ inst/doc/Reproducing-Hamilton.Rmd | 5 inst/doc/Reproducing-Hamilton.html | 286 +++++--------------------------- man/EXPGSC1.Rd | 10 - man/FEDFUNDS.Rd | 10 - man/GCEC1.Rd | 10 - man/GDPC1.Rd | 12 - man/GDPDEF.Rd | 10 - man/GPDIC1.Rd | 10 - man/GS10.Rd | 10 - man/Hamilton_table_2.Rd | 6 man/IMPGSC1.Rd | 10 - man/PAYEMS.Rd | 10 - man/PCECC96.Rd | 10 - man/SP500.Rd | 30 ++- man/UNRATENSA.Rd | 10 - man/USREC.Rd | 10 - man/yth_filter.Rd | 3 vignettes/Reproducing-Hamilton.Rmd | 5 49 files changed, 316 insertions(+), 658 deletions(-)
Title: Statistics for Matrix Distributions
Description: Tools for homogeneous and in-homogeneous phase-type distributions.
Methods for functional evaluation, simulation and estimation using the
expectation-maximization (EM) algorithm are provided.
The methods of this package are based on the following references.
Asmussen, S., Nerman, O., & Olsson, M. (1996) <https://www.jstor.org/stable/4616418>,
Olsson, M. (1996) <https://www.jstor.org/stable/4616419>.
Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>
Albrecher, H., Bladt, M., & Yslas, J. (2020) <doi:10.1111/sjos.12505>
Bladt, M., & Yslas, J. (2020) <arXiv:2011.03219>.
Author: Martin Bladt [aut, cre],
Jorge Yslas [aut]
Maintainer: Martin Bladt <martinbladt@gmail.com>
Diff between matrixdist versions 1.1.0 dated 2021-06-17 and 1.1.2 dated 2021-06-18
DESCRIPTION | 8 +++---- MD5 | 4 +-- src/EM_LL_PADE.cpp | 60 ++++++++++++++++++++++++++--------------------------- 3 files changed, 36 insertions(+), 36 deletions(-)
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 3.0.6 dated 2020-09-10 and 3.0.7 dated 2021-06-18
DESCRIPTION | 8 MD5 | 32 - NAMESPACE | 1 NEWS.md | 4 R/CCAMLRGIS.R | 2 R/CCAMLRGIS_DataDescription.R | 2 R/add_RefGrid.R | 2 R/cGrid.r | 21 R/create.R | 11 README.md | 78 -- build/vignette.rds |binary inst/doc/CCAMLRGIS.R | 98 --- inst/doc/CCAMLRGIS.Rmd | 116 --- inst/doc/CCAMLRGIS.html | 1336 ++++++++++++++++-------------------------- man/CCAMLRp.Rd | 2 man/create_PolyGrids.Rd | 11 vignettes/CCAMLRGIS.Rmd | 116 --- 17 files changed, 676 insertions(+), 1164 deletions(-)
Title: The Acute COPD Exacerbation Prediction Tool (ACCEPT)
Description: Allows clinicians to predict the rate and severity of future acute exacerbation in Chronic Obstructive Pulmonary Disease (COPD) patients, based on the clinical prediction model published in Adibi et al. (2020) <doi:10.1016/S2213-2600(19)30397-2>.
Author: Amin Adibi [aut, cre],
Mohsen Sadatsafavi [aut, cph],
Abdollah Safari [aut],
Ainsleigh Hill [aut]
Maintainer: Amin Adibi <adibi@alumni.ubc.ca>
Diff between accept versions 0.8.2 dated 2021-06-15 and 0.8.3 dated 2021-06-18
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ R/predict.R | 36 ++++++++++++++++++++++++------------ 4 files changed, 35 insertions(+), 18 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-03 0.9.0.40
2021-04-02 0.9.0.4
Title: Client for 'Mapzen' and Related Map APIs
Description: Provides an interface to 'Mapzen'-based APIs (including
geocode.earth, Nextzen, and NYC GeoSearch) for geographic search
and geocoding, isochrone calculation, and vector data to draw map tiles.
See <https://www.mapzen.com/documentation/> for more information. The original
Mapzen has gone out of business, but 'rmapzen' can be set up to work with
any provider who implements the Mapzen API.
Author: Tarak Shah [aut, cre],
Daniel Possenriede [ctb]
Maintainer: Tarak Shah <tarak.shah@gmail.com>
Diff between rmapzen versions 0.4.2 dated 2019-08-19 and 0.4.3 dated 2021-06-18
DESCRIPTION | 12 - MD5 | 68 +++---- NEWS.md | 5 R/as-sf.R | 1 R/costing-models.R | 4 R/data.R | 2 R/geocode.R | 2 R/isochrone.R | 2 R/mz-place.R | 2 R/mz-references.R | 2 R/mz-search.R | 4 R/rmapzen.R | 10 - R/structured-search.R | 2 R/vector-tiles.R | 2 README.md | 32 ++- build/vignette.rds |binary inst/doc/rmapzen-introduction.R | 14 - inst/doc/rmapzen-introduction.Rmd | 14 - inst/doc/rmapzen-introduction.html | 351 ++++++++++++++++++++++--------------- man/ca_tiles.Rd | 4 man/costing_models.Rd | 10 - man/mapzen_references.Rd | 10 - man/marina_walks.Rd | 4 man/marina_walks_polygons.Rd | 4 man/mz_geocode_structured.Rd | 16 + man/mz_isochrone.Rd | 16 + man/mz_place.Rd | 5 man/mz_structured_search.Rd | 17 + man/mz_tile_coordinates.Rd | 3 man/mz_vector_tiles.Rd | 2 man/oakland_public.Rd | 6 man/rmapzen.Rd | 11 - man/search.Rd | 44 +++- tests/testthat.R | 2 vignettes/rmapzen-introduction.Rmd | 14 - 35 files changed, 425 insertions(+), 272 deletions(-)
More information about RFpredInterval at CRAN
Permanent link
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.
Author: Carson Sievert [aut, cre] (<https://orcid.org/0000-0002-4958-2844>),
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut] (<https://orcid.org/0000-0002-1994-3581>),
Pedro Despouy [aut],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>),
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.9.4 dated 2021-06-08 and 4.9.4.1 dated 2021-06-18
plotly-4.9.4.1/plotly/DESCRIPTION | 12 plotly-4.9.4.1/plotly/MD5 | 30 - plotly-4.9.4.1/plotly/NEWS.md | 8 plotly-4.9.4.1/plotly/R/ggplotly.R | 9 plotly-4.9.4.1/plotly/tests/testthat/Rplots.pdf |binary plotly-4.9.4.1/plotly/tests/testthat/test-api.R | 300 +++++----- plotly-4.9.4.1/plotly/tests/testthat/test-ggplot-bar.R | 2 plotly-4.9.4.1/plotly/tests/testthat/test-ggplot-quantile.R | 6 plotly-4.9.4.1/plotly/tests/testthat/test-plotly-data.R | 2 plotly-4.9.4.1/plotly/tests/testthat/test-plotly-filename.R | 2 plotly-4.9.4.1/plotly/tests/testthat/test-plotly-getfigure.R | 14 plotly-4.9.4.1/plotly/tests/testthat/test-plotly-shiny.R | 72 +- plotly-4.9.4/plotly/inst/examples/shiny/event_data/tests/shinytest/mytest-current |only 13 files changed, 231 insertions(+), 226 deletions(-)
Title: An Imputation Approach to Estimating Path-Specific Causal
Effects
Description: In causal mediation analysis with multiple causally ordered mediators, a set of path-specific
effects are identified under standard ignorability assumptions. This package implements an imputation
approach to estimating these effects along with a set of bias formulas for conducting sensitivity analysis
(Zhou and Yamamoto <doi:10.31235/osf.io/2rx6p>). It contains two main functions: paths() for estimating
path-specific effects and sens() for conducting sensitivity analysis. Estimation uncertainty is quantified
using the nonparametric bootstrap.
Author: Minh Trinh [cre],
Teppei Yamamoto [aut],
Xiang Zhou [aut]
Maintainer: Minh Trinh <mdtrinh@mit.edu>
Diff between paths versions 0.1.0 dated 2020-05-06 and 0.1.1 dated 2021-06-18
ChangeLog |only DESCRIPTION | 13 ++++++------- MD5 | 6 ++++-- NEWS.md |only R/print.paths.R | 3 +-- 5 files changed, 11 insertions(+), 11 deletions(-)
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a unified
interface for model fitting, prediction, performance assessment, and
presentation of results. Approaches for model fitting and prediction of
numerical, categorical, or censored time-to-event outcomes include
traditional regression models, regularization methods, tree-based methods,
support vector machines, neural networks, ensembles, data preprocessing,
filtering, and model tuning and selection. Performance metrics are provided
for model assessment and can be estimated with independent test sets, split
sampling, cross-validation, or bootstrap resampling. Resample estimation
can be executed in parallel for faster processing and nested in cases of
model tuning and selection. Modeling results can be summarized with
descriptive statistics; calibration curves; variable importance; partial
dependence plots; confusion matrices; and ROC, lift, and other performance
curves.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 2.8.0 dated 2021-04-16 and 2.9.0 dated 2021-06-18
DESCRIPTION | 35 MD5 | 249 +-- NAMESPACE | 8 NEWS.md | 40 R/MLControl.R | 68 R/MLModel.R | 28 R/ML_AdaBagModel.R | 6 R/ML_AdaBoostModel.R | 12 R/ML_BARTMachineModel.R | 6 R/ML_BARTModel.R | 11 R/ML_BlackBoostModel.R | 8 R/ML_C50Model.R | 2 R/ML_CForestModel.R | 6 R/ML_CoxModel.R | 4 R/ML_EarthModel.R | 4 R/ML_FDAModel.R | 4 R/ML_GAMBoostModel.R | 6 R/ML_GBMModel.R | 12 R/ML_GLMBoostModel.R | 6 R/ML_GLMModel.R | 2 R/ML_GLMNetModel.R | 10 R/ML_KNNModel.R | 13 R/ML_LARSModel.R | 2 R/ML_LDAModel.R | 4 R/ML_LMModel.R | 2 R/ML_MDAModel.R | 4 R/ML_NNetModel.R | 8 R/ML_NaiveBayesModel.R | 4 R/ML_NullModel.R | 2 R/ML_PLSModel.R | 10 R/ML_QDAModel.R | 2 R/ML_RFSRCModel.R | 10 R/ML_RPartModel.R | 6 R/ML_RandomForestModel.R | 10 R/ML_RangerModel.R | 24 R/ML_SVMModel.R | 13 R/ML_StackedModel.R | 14 R/ML_SuperModel.R | 14 R/ML_SurvRegModel.R | 8 R/ML_TreeModel.R | 4 R/ML_XGBModel.R | 15 R/ModelFrame.R | 46 R/ModelRecipe.R | 47 R/ModeledInput.R | 8 R/RcppExports.R |only R/TrainedInputs.R | 69 R/TrainedModels.R | 31 R/calibration.R | 58 R/case_components.R |only R/classes.R | 127 + R/coerce.R | 4 R/combine.R | 45 R/conditions.R |only R/confusion.R | 7 R/convert.R | 24 R/dependence.R | 10 R/diff.R | 4 R/expand.R | 83 - R/extract.R | 12 R/fit.R | 10 R/grid.R | 131 - R/metricinfo.R | 2 R/metrics.R | 29 R/metrics_factor.R | 30 R/metrics_numeric.R | 18 R/modelinfo.R | 4 R/performance.R | 30 R/performance_curve.R | 20 R/plot.R | 13 R/predict.R | 11 R/print.R | 134 + R/recipe_roles.R | 16 R/resample.R | 132 - R/response.R | 27 R/settings.R | 173 -- R/step_kmedoids.R | 7 R/step_lincomp.R | 8 R/step_sbf.R | 7 R/step_spca.R | 2 R/summary.R | 4 R/survival.R | 307 ++- R/utils.R | 194 +- R/varimp.R | 2 build/vignette.rds |binary inst/doc/MLModels.html | 4 inst/doc/UsersGuide.R | 234 +- inst/doc/UsersGuide.Rmd | 277 +-- inst/doc/UsersGuide.html | 757 ++++----- man/AdaBoostModel.Rd | 2 man/EarthModel.Rd | 2 man/FDAModel.Rd | 2 man/GBMModel.Rd | 2 man/GLMNetModel.Rd | 2 man/Grid.Rd | 13 man/KNNModel.Rd | 2 man/MLControl.Rd | 34 man/MLModel.Rd | 11 man/ModelFrame-methods.Rd | 3 man/ParameterGrid.Rd | 16 man/RFSRCModel.Rd | 2 man/RandomForestModel.Rd | 2 man/RangerModel.Rd | 4 man/SelectedInput.Rd | 8 man/SelectedModel.Rd | 2 man/SurvMatrix.Rd | 7 man/TunedInput.Rd | 2 man/TunedModel.Rd | 6 man/XGBModel.Rd | 2 man/calibration.Rd | 15 man/extract-methods.Rd | 3 man/metrics.Rd | 15 man/performance.Rd | 4 man/plot-methods.Rd | 2 man/predict.Rd | 7 man/print-methods.Rd | 36 man/recipe_roles.Rd | 12 man/resample-methods.Rd | 18 man/settings.Rd | 31 src |only tests/testthat/Rplots.pdf |binary tests/testthat/test-settings.R | 60 tests/testthat/test-survival.R | 16 tests/testthat/test-survival.txt | 1992 +++++++++++++++---------- vignettes/UsersGuide.Rmd | 277 +-- vignettes/bibliography.bib | 10 vignettes/img/using_strategies_tune_plot-1.png |binary vignettes/setup.R | 4 127 files changed, 3666 insertions(+), 2814 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2020) <arXiv:2004.02653> and Sigrist (2021) <arXiv:2105.08966> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the included version of Eigen [ctb, cph],
Timothy A. Davis [cph],
Guolin Ke [ctb],
Damien Soukhavong [ctb],
James Lamb [ctb],
Other authors of LightGBM for the included version of LightGBM [ctb],
Microsoft Corporation [cph],
Dropbox, Inc. [cph],
Jay Loden [cph],
Dave Daeschler [cph],
Giampaolo Rodola [cph],
Alberto Ferreira [ctb],
Daniel Lemire [ctb],
Victor Zverovich [cph],
IBM Corporation [ctb],
Keith O'Hara [cph]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 0.6.1 dated 2021-05-25 and 0.6.3 dated 2021-06-18
gpboost-0.6.1/gpboost/tests/testthat/_snaps |only gpboost-0.6.3/gpboost/DESCRIPTION | 8 gpboost-0.6.3/gpboost/MD5 | 44 - gpboost-0.6.3/gpboost/R/GPModel.R | 23 gpboost-0.6.3/gpboost/R/callback.R | 8 gpboost-0.6.3/gpboost/R/gpb.Booster.R | 30 gpboost-0.6.3/gpboost/R/gpb.Dataset.R | 19 gpboost-0.6.3/gpboost/R/gpb.Predictor.R | 6 gpboost-0.6.3/gpboost/R/gpb.cv.R | 12 gpboost-0.6.3/gpboost/R/gpb.train.R | 2 gpboost-0.6.3/gpboost/R/utils.R | 32 gpboost-0.6.3/gpboost/configure.ac | 2 gpboost-0.6.3/gpboost/demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 10 gpboost-0.6.3/gpboost/man/gpb.cv.Rd | 3 gpboost-0.6.3/gpboost/src/gpboost_R.cpp | 375 ++++++---- gpboost-0.6.3/gpboost/src/gpboost_R.h | 18 gpboost-0.6.3/gpboost/src/include/GPBoost/re_model.h | 1 gpboost-0.6.3/gpboost/src/include/GPBoost/re_model_template.h | 103 ++ gpboost-0.6.3/gpboost/src/include/unconstrained/nm.hpp | 3 gpboost-0.6.3/gpboost/tests/testthat/test_GPModel_non_Gaussian_data.R | 42 - gpboost-0.6.3/gpboost/tests/testthat/test_Predictor.R | 24 gpboost-0.6.3/gpboost/tests/testthat/test_basic.R | 33 gpboost-0.6.3/gpboost/tests/testthat/test_dataset.R | 20 gpboost-0.6.3/gpboost/tests/testthat/test_gpb.Booster.R | 24 24 files changed, 550 insertions(+), 292 deletions(-)
More information about ICvectorfields at CRAN
Permanent link
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] (libphonenumber),
Vonage Holdings Corp. [ctb, cph] (libphonenumber),
Ian Galpin [ctb, cph] (libphonenumber),
Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 8.12.24 dated 2021-05-31 and 8.12.25 dated 2021-06-18
dialrjars-8.12.24/dialrjars/inst/java/carrier-1.150.jar |only dialrjars-8.12.24/dialrjars/inst/java/geocoder-2.160.jar |only dialrjars-8.12.24/dialrjars/inst/java/libphonenumber-8.12.24.jar |only dialrjars-8.12.24/dialrjars/inst/java/prefixmapper-2.160.jar |only dialrjars-8.12.25/dialrjars/DESCRIPTION | 6 ++--- dialrjars-8.12.25/dialrjars/MD5 | 12 +++++----- dialrjars-8.12.25/dialrjars/NEWS.md | 10 ++++++++ dialrjars-8.12.25/dialrjars/inst/java/carrier-1.151.jar |only dialrjars-8.12.25/dialrjars/inst/java/geocoder-2.161.jar |only dialrjars-8.12.25/dialrjars/inst/java/libphonenumber-8.12.25.jar |only dialrjars-8.12.25/dialrjars/inst/java/prefixmapper-2.161.jar |only 11 files changed, 19 insertions(+), 9 deletions(-)
Title: Calculates Demographic Indicators
Description: Calculates key indicators such as fertility rates (Total Fertility Rate (TFR), General Fertility Rate (GFR),
and Age Specific Fertility Rate (ASFR)) using Demographic and Health Survey (DHS) women/individual data,
childhood mortality probabilities and rates such as Neonatal Mortality Rate (NNMR), Post-neonatal Mortality Rate (PNNMR),
Infant Mortality Rate (IMR), Child Mortality Rate (CMR), and Under-five Mortality Rate (U5MR), and adult mortality indicators
such as the Age Specific Mortality Rate (ASMR), Age Adjusted Mortality Rate (AAMR), Age Specific Maternal Mortality Rate (ASMMR),
Age Adjusted Maternal Mortality Rate (AAMMR), Age Specific Pregnancy Related Mortality Rate (ASPRMR),
Age Adjusted Pregnancy Related Mortality Rate (AAPRMR), Maternal Mortality Ratio (MMR) and Pregnancy Related Mortality Ratio (PRMR).
In addition to the indicators, the 'DHS.rates' package estimates sampling errors indicators such as Standard Error (SE),
Design Effect (DEFT), Relative Standard Error (RSE) and Confidence Interval (CI).
The package is developed according to the DHS methodology of calculating the fertility indicators and
the childhood mortality rates outlined in the
"Guide to DHS Statistics" (Croft, Trevor N., Aileen M. J. Marshall, Courtney K. Allen, et al. 2018, <https://dhsprogram.com/Data/Guide-to-DHS-Statistics/index.cfm>)
and the DHS methodology of estimating the sampling errors indicators outlined in
the "DHS Sampling and Household Listing Manual" (ICF International 2012, <https://dhsprogram.com/pubs/pdf/DHSM4/DHS6_Sampling_Manual_Sept2012_DHSM4.pdf>).
Author: Mahmoud Elkasabi
Maintainer: Mahmoud Elkasabi <mahmoud.elkasabi@icf.com>
Diff between DHS.rates versions 0.8.0 dated 2020-10-11 and 0.9.0 dated 2021-06-18
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/ASFR.R | 11 +++++++---- R/GFR.R | 3 +++ R/TFR.R | 3 +++ R/chmort.R | 4 ++-- build/vignette.rds |binary inst/doc/DHS.rates.html | 47 ++++++++++++++++++++++++++++++++++++++++------- 8 files changed, 66 insertions(+), 24 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of spatial data. The package implements basic and high-level functions for raster data and for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Dan Baston [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
Ben Fasoli [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Kassel Hingee [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Babak Naimi [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 3.4-10 dated 2021-05-03 and 3.4-13 dated 2021-06-18
DESCRIPTION | 13 +++---- MD5 | 40 +++++++++++----------- R/AAgeneric_functions.R | 2 + R/as.character.R | 4 +- R/extend.R | 4 +- R/extractPolygons.R | 86 ++++++++++++++++++++++++++++++++++++------------ R/hillShade.R | 1 R/netCDFtoRasterCD.R | 7 ++- R/plotRGB.R | 13 +++---- build/partial.rdb |binary man/Rcpp-classes.Rd | 2 - man/autocor.Rd | 2 - man/calc.Rd | 2 - man/extend.Rd | 3 + man/extract.Rd | 7 ++- man/hillShade.Rd | 2 - man/predict.Rd | 3 - man/projectRaster.Rd | 3 - man/spEasy.Rd | 2 - man/terrain.Rd | 2 - man/writeRaster.Rd | 1 21 files changed, 123 insertions(+), 76 deletions(-)
Title: Power and Sample Size Calculation for Bulk Tissue and
Single-Cell eQTL Analysis
Description: Power and sample size calculation for bulk tissue and single-cell eQTL analysis
based on ANOVA, simple linear regression, or linear mixed effects model. It can also calculate power/sample size
for testing the association of a SNP to a continuous type phenotype.
Please see the reference: Dong X, Li X, Chang T-W, Scherzer CR, Weiss ST, Qiu W. (2021) <doi:10.1093/bioinformatics/btab385>.
Author: Xianjun Dong [aut, ctb],
Xiaoqi Li [aut, ctb],
Tzuu-Wang Chang [aut, ctb],
Scott T. Weiss [aut, ctb],
Weiliang Qiu [aut, cre]
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
Diff between powerEQTL versions 0.3.1 dated 2021-05-22 and 0.3.3 dated 2021-06-18
DESCRIPTION | 11 +-- MD5 | 10 +-- NAMESPACE | 68 +++++++++++----------- NEWS | 7 ++ R/powerEQTL.scRNAseq.sim.R | 129 ++++++++++++++++++++++-------------------- man/powerEQTL.scRNAseq.sim.Rd | 3 6 files changed, 123 insertions(+), 105 deletions(-)