Title: Computation and Visualization of Package Download Counts and
Percentiles
Description: Compute and visualize the cross-sectional and longitudinal number
and rank percentile of package downloads from Posit/RStudio's CRAN mirror.
Author: Peter Li [aut, cre]
Maintainer: Peter Li <lindbrook@gmail.com>
Diff between packageRank versions 0.8.3 dated 2023-11-09 and 0.9.0 dated 2024-04-23
packageRank-0.8.3/packageRank/man/archivePackages.Rd |only packageRank-0.8.3/packageRank/man/cranPackages.Rd |only packageRank-0.8.3/packageRank/man/extractArchiveDate.Rd |only packageRank-0.8.3/packageRank/man/fetchCranLog.Rd |only packageRank-0.8.3/packageRank/man/fetchRLog.Rd |only packageRank-0.8.3/packageRank/man/ipFilter.Rd |only packageRank-0.8.3/packageRank/man/packageArchive.Rd |only packageRank-0.8.3/packageRank/man/packageCRAN.Rd |only packageRank-0.8.3/packageRank/man/packages_in_Archive.Rd |only packageRank-0.8.3/packageRank/man/packages_observed_in_logs.Rd |only packageRank-0.8.3/packageRank/man/packages_on_CRAN.Rd |only packageRank-0.8.3/packageRank/man/packages_partitioned.Rd |only packageRank-0.8.3/packageRank/man/sequenceFilter.Rd |only packageRank-0.8.3/packageRank/man/sizeFilter.Rd |only packageRank-0.8.3/packageRank/man/smallFilter.Rd |only packageRank-0.8.3/packageRank/man/tripletFilter.Rd |only packageRank-0.9.0/packageRank/DESCRIPTION | 13 packageRank-0.9.0/packageRank/MD5 | 155 - 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packageRank-0.9.0/packageRank/R/ipPackage.R | 99 packageRank-0.9.0/packageRank/R/logInfo.R | 40 packageRank-0.9.0/packageRank/R/packageCountry.R | 20 packageRank-0.9.0/packageRank/R/packageDistribution.R | 54 packageRank-0.9.0/packageRank/R/packageHistory.R | 151 - packageRank-0.9.0/packageRank/R/packageLog.R | 109 packageRank-0.9.0/packageRank/R/packageRank-package.R |only packageRank-0.9.0/packageRank/R/packageRank.R | 142 - packageRank-0.9.0/packageRank/R/packageSample.R | 4 packageRank-0.9.0/packageRank/R/packageVersionPercent.R | 79 packageRank-0.9.0/packageRank/R/packagesFunctions.R | 17 packageRank-0.9.0/packageRank/R/populationPlot.R | 45 packageRank-0.9.0/packageRank/R/rLog.R |only packageRank-0.9.0/packageRank/R/resolveDate.R | 20 packageRank-0.9.0/packageRank/R/sequenceFilter.R | 187 - packageRank-0.9.0/packageRank/R/sizeFilter.R | 146 - packageRank-0.9.0/packageRank/R/smallFilter.R | 31 packageRank-0.9.0/packageRank/R/topCountry.R | 78 packageRank-0.9.0/packageRank/R/tripletFilter.R | 19 packageRank-0.9.0/packageRank/R/utilities.R | 26 packageRank-0.9.0/packageRank/R/validatePackage.R | 14 packageRank-0.9.0/packageRank/R/versionPlot.R | 27 packageRank-0.9.0/packageRank/R/weeklyDownloads.R | 34 packageRank-0.9.0/packageRank/README.md | 442 +-- packageRank-0.9.0/packageRank/man/annualDownloads.Rd | 5 packageRank-0.9.0/packageRank/man/countryDistribution.Rd | 9 packageRank-0.9.0/packageRank/man/countryPackage.Rd | 15 packageRank-0.9.0/packageRank/man/downloadsCountry.Rd | 2 packageRank-0.9.0/packageRank/man/figures/README-annualDownloads-1.png |only packageRank-0.9.0/packageRank/man/filteredDownloads.Rd | 10 packageRank-0.9.0/packageRank/man/ipCount.Rd | 4 packageRank-0.9.0/packageRank/man/ipPackage.Rd | 13 packageRank-0.9.0/packageRank/man/logInfo.Rd | 7 packageRank-0.9.0/packageRank/man/packageCountry.Rd | 13 packageRank-0.9.0/packageRank/man/packageDistribution.Rd | 7 packageRank-0.9.0/packageRank/man/packageHistory.Rd | 2 packageRank-0.9.0/packageRank/man/packageLog.Rd | 14 packageRank-0.9.0/packageRank/man/packageRank-package.Rd |only packageRank-0.9.0/packageRank/man/packageRank.Rd | 7 packageRank-0.9.0/packageRank/man/packageVersionPercent.Rd | 2 packageRank-0.9.0/packageRank/man/plot.annualDownloads.Rd | 16 packageRank-0.9.0/packageRank/man/plot.bioconductorRank.Rd | 4 packageRank-0.9.0/packageRank/man/plot.countryDistribution.Rd | 6 packageRank-0.9.0/packageRank/man/plot.cranDownloads.Rd | 2 packageRank-0.9.0/packageRank/man/plot.packageRank.Rd | 4 packageRank-0.9.0/packageRank/man/plot.packageVersionPercent.Rd | 2 packageRank-0.9.0/packageRank/man/print.countryDistribution.Rd |only packageRank-0.9.0/packageRank/man/rLog.Rd |only packageRank-0.9.0/packageRank/man/topCountryCodes.Rd | 2 packageRank-0.9.0/packageRank/man/weeklyDownloads.Rd | 2 90 files changed, 2248 insertions(+), 2188 deletions(-)
Title: NHANES Data Retrieval
Description: Utility to retrieve data from the National Health and Nutrition
Examination Survey (NHANES) website <https://www.cdc.gov/nchs/nhanes/index.htm>.
Author: Christopher Endres [aut, cre],
Laha Ale [aut] ,
Robert Gentleman [aut],
Deepayan Sarkar [aut]
Maintainer: Christopher Endres <cjendres1@gmail.com>
Diff between nhanesA versions 1.0 dated 2024-01-09 and 1.1 dated 2024-04-23
DESCRIPTION | 10 ++--- MD5 | 23 ++++++----- R/nhanes.R | 10 ++--- R/nhanes_codebook.R | 4 +- R/nhanes_constants.R | 1 R/nhanes_search.R | 33 +++------------- R/nhanes_tables.R | 75 +++++++++++++++++++++++++++++++++++--- R/nhanes_translate.R | 15 +++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/Introducing_nhanesA.html | 4 +- inst/doc/UsingSurveyWeights.html | 8 ++-- man/nhanesManifest.Rd | 5 ++ 13 files changed, 127 insertions(+), 61 deletions(-)
Title: Causal Moderated Mediation Analysis
Description: Causal moderated mediation analysis using the methods proposed by Qin and Wang (2023) <doi:10.3758/s13428-023-02095-4>. Causal moderated mediation analysis is crucial for investigating how, for whom, and where a treatment is effective by assessing the heterogeneity of mediation mechanism across individuals and contexts. This package enables researchers to estimate and test the conditional and moderated mediation effects, assess their sensitivity to unmeasured pre-treatment confounding, and visualize the results. The package is built based on the quasi-Bayesian Monte Carlo method, because it has relatively better performance at small sample sizes, and its running speed is the fastest. The package is applicable to a treatment of any scale, a binary or continuous mediator, a binary or continuous outcome, and one or more moderators of any scale.
Author: Xu Qin [aut, cre, cph],
Lijuan Wang [ctb]
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between moderate.mediation versions 0.0.8 dated 2024-02-29 and 0.0.9 dated 2024-04-23
DESCRIPTION | 8 +++---- MD5 | 8 +++---- R/moderate.mediation.R | 54 +++++++++++++++++++++++++++++++++++++------------ man/modmed.Rd | 2 - man/modmed.sens.Rd | 2 - 5 files changed, 51 insertions(+), 23 deletions(-)
More information about moderate.mediation at CRAN
Permanent link
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi:10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootech [...truncated...]
Author: Gabriel Danilo Shimizu [aut, cre]
,
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
,
Leandro Simoes Azeredo Goncalves [aut, ctb]
Maintainer: Gabriel Danilo Shimizu <gabrield.shimizu@gmail.com>
Diff between AgroR versions 1.3.5 dated 2023-09-13 and 1.3.6 dated 2024-04-23
DESCRIPTION | 8 MD5 | 84 +++++----- NAMESPACE | 3 NEWS.md | 14 + R/DBCglm_function.R | 4 R/DICglm_function.R | 4 R/FAT2DBC_function.R | 18 +- R/FAT2DBCad_function.R | 25 +-- R/FAT2DIC_function.R | 18 +- R/FAT2DICad_function.R | 25 +-- R/FAT3DBC_function.R | 8 R/FAT3DBCad_function.R | 10 - R/FAT3DIC_function.R | 8 R/FAT3DICad_function.R | 10 - R/PSUBDBC_function.R | 25 +-- R/PSUBDIC_function.R | 27 +-- R/bargraph_function.R | 10 - R/conjdbc_function.R | 9 - R/conjdic_function.R | 33 ++-- R/correlation_function.R | 34 ++-- R/dbc_function.R | 12 - R/dic_function.R | 16 + R/dql_function.R | 12 - R/dunnet_function.R | 11 - R/fat2_table.R |only R/grid_onefactor.R |only R/polynomial2color_function.R | 2 R/seggraph2_function.R | 6 R/seggraph_function.R | 8 R/sk_graph_function.R | 56 +++--- R/summarise_conj.R |only R/summarise_function.R | 337 +++++++++++++++++++++++++++++++++++------- R/tabledesc_function.R | 2 README.md | 4 build/partial.rdb |binary man/DBC.Rd | 3 man/DIC.Rd | 3 man/DQL.Rd | 3 man/bar_graph.Rd | 10 + man/corgraph.Rd | 20 ++ man/fat2_table.Rd |only man/grid.onefactor.Rd |only man/polynomial2_color.Rd | 2 man/sk_graph.Rd | 4 man/summarise_anova.Rd | 3 man/summarise_conj.Rd |only 46 files changed, 628 insertions(+), 263 deletions(-)
Title: Pediatric Blood Pressure
Description: Data and utilities for estimating pediatric blood pressure
percentiles by sex, age, and optionally height (stature) as described in
Martin et.al. (2022) <doi:10.1001/jamanetworkopen.2022.36918>.
Blood pressure percentiles for children under one year of age come from Gemelli
et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure
percentiles for children at least one year of age are informed by
data from the National Heart, Lung, and Blood Institute (NHLBI) and the
Centers for Disease Control and Prevention (CDC)
<doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013)
<doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing
data source comes from Martin et.al. (2022)
<doi:10.1542/hpeds.2021-005998>.
Author: Peter DeWitt [aut, cre] ,
Blake Martin [ctb] ,
David Albers [ctb] ,
Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between pedbp versions 1.0.2 dated 2022-11-23 and 2.0.0 dated 2024-04-23
pedbp-1.0.2/pedbp/man/pediatric_vital_sign_distributions.Rd |only pedbp-1.0.2/pedbp/tests/test-head_circ_for_age.R |only pedbp-1.0.2/pedbp/tests/test-length_for_age_inf.R |only pedbp-1.0.2/pedbp/tests/test-stature_for_age.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_age_inf.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_length_inf.R |only pedbp-1.0.2/pedbp/tests/test-weight_for_stature.R |only pedbp-2.0.0/pedbp/DESCRIPTION | 21 pedbp-2.0.0/pedbp/MD5 | 143 + pedbp-2.0.0/pedbp/NAMESPACE | 37 pedbp-2.0.0/pedbp/NEWS.md | 52 pedbp-2.0.0/pedbp/R/RcppExports.R |only pedbp-2.0.0/pedbp/R/bmi_for_age.R |only pedbp-2.0.0/pedbp/R/bp_cdf_plot.R | 137 + pedbp-2.0.0/pedbp/R/bp_charts.R |only pedbp-2.0.0/pedbp/R/bp_distribution.R | 282 +-- pedbp-2.0.0/pedbp/R/datasets.R | 12 pedbp-2.0.0/pedbp/R/est_norm.R | 35 pedbp-2.0.0/pedbp/R/growth-standard-charts.R |only pedbp-2.0.0/pedbp/R/growth-standards.R |only pedbp-2.0.0/pedbp/R/gs_cdf.R |only pedbp-2.0.0/pedbp/R/head_circumference_for_age.R |only pedbp-2.0.0/pedbp/R/lms.R | 532 +------ pedbp-2.0.0/pedbp/R/pedbp-defunct.R |only pedbp-2.0.0/pedbp/R/pedbp-package.R |only pedbp-2.0.0/pedbp/R/stature_for_age.R |only pedbp-2.0.0/pedbp/R/sysdata.rda |binary pedbp-2.0.0/pedbp/R/weight_for_age.R |only pedbp-2.0.0/pedbp/R/weight_for_stature.R |only pedbp-2.0.0/pedbp/R/zzz.R |only pedbp-2.0.0/pedbp/README.md | 177 +- pedbp-2.0.0/pedbp/build/partial.rdb |only pedbp-2.0.0/pedbp/build/vignette.rds |binary pedbp-2.0.0/pedbp/data/bp_parameters.rda |binary pedbp-2.0.0/pedbp/data/flynn2017.rda |only pedbp-2.0.0/pedbp/data/gemelli1990.rda |binary pedbp-2.0.0/pedbp/data/lo2013.rda |binary pedbp-2.0.0/pedbp/data/nhlbi_bp_norms.rda |binary pedbp-2.0.0/pedbp/inst/CITATION | 11 pedbp-2.0.0/pedbp/inst/WORDLIST | 36 pedbp-2.0.0/pedbp/inst/doc/bp-distributions.R | 365 ---- pedbp-2.0.0/pedbp/inst/doc/bp-distributions.Rmd | 731 +--------- pedbp-2.0.0/pedbp/inst/doc/bp-distributions.html | 693 ++------- pedbp-2.0.0/pedbp/inst/doc/growth-standards.R |only pedbp-2.0.0/pedbp/inst/doc/growth-standards.Rmd |only pedbp-2.0.0/pedbp/inst/doc/growth-standards.html |only pedbp-2.0.0/pedbp/inst/images/bp_cdf_example-1.png |binary pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/overview.md | 33 pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/server.R | 731 +++++++++- pedbp-2.0.0/pedbp/inst/shinyapps/pedbp/ui.R | 656 +++++++- pedbp-2.0.0/pedbp/man/bmi_for_age.Rd |only pedbp-2.0.0/pedbp/man/bp_cdf.Rd | 60 pedbp-2.0.0/pedbp/man/bp_chart.Rd |only pedbp-2.0.0/pedbp/man/bp_distribution.Rd | 176 ++ pedbp-2.0.0/pedbp/man/bpdata.Rd | 17 pedbp-2.0.0/pedbp/man/cppBP.Rd |only pedbp-2.0.0/pedbp/man/cppPGSF.Rd |only pedbp-2.0.0/pedbp/man/distribution-quantile-zscores-by-lms.Rd |only pedbp-2.0.0/pedbp/man/est_norm.Rd | 19 pedbp-2.0.0/pedbp/man/figures |only pedbp-2.0.0/pedbp/man/growth-standards.Rd |only pedbp-2.0.0/pedbp/man/gs_cdf.Rd |only pedbp-2.0.0/pedbp/man/gs_chart.Rd |only pedbp-2.0.0/pedbp/man/head_circumference_for_age.Rd |only pedbp-2.0.0/pedbp/man/pedbp-defunct.Rd |only pedbp-2.0.0/pedbp/man/pedbp-package.Rd |only pedbp-2.0.0/pedbp/man/stature_for_age.Rd |only pedbp-2.0.0/pedbp/man/weight_for_age.Rd |only pedbp-2.0.0/pedbp/man/weight_for_stature.Rd |only pedbp-2.0.0/pedbp/src |only pedbp-2.0.0/pedbp/tests/test-bmi_for_age.R | 350 +--- pedbp-2.0.0/pedbp/tests/test-bp-by-source.R |only pedbp-2.0.0/pedbp/tests/test-bp_cdf.R |only pedbp-2.0.0/pedbp/tests/test-bp_chart.R |only pedbp-2.0.0/pedbp/tests/test-bp_distributions.R | 453 ++++-- pedbp-2.0.0/pedbp/tests/test-bp_parameters.R | 28 pedbp-2.0.0/pedbp/tests/test-cppBP.R |only pedbp-2.0.0/pedbp/tests/test-cppPGSF.R |only pedbp-2.0.0/pedbp/tests/test-est_norm.R | 93 + pedbp-2.0.0/pedbp/tests/test-gemelli1990.R | 13 pedbp-2.0.0/pedbp/tests/test-gs_chart.R |only pedbp-2.0.0/pedbp/tests/test-head_circumference_for_age.R |only pedbp-2.0.0/pedbp/tests/test-height_for_age.R |only pedbp-2.0.0/pedbp/tests/test-internal-data.R |only pedbp-2.0.0/pedbp/tests/test-length_for_age.R |only pedbp-2.0.0/pedbp/tests/test-lms.R |only pedbp-2.0.0/pedbp/tests/test-lo2013.R | 16 pedbp-2.0.0/pedbp/tests/test-nhlbi_bp_norms.R | 12 pedbp-2.0.0/pedbp/tests/test-weight_for_age.R | 353 +--- pedbp-2.0.0/pedbp/tests/test-weight_for_height.R |only pedbp-2.0.0/pedbp/tests/test-weight_for_length.R |only pedbp-2.0.0/pedbp/vignettes/bp-distributions.Rmd | 731 +--------- pedbp-2.0.0/pedbp/vignettes/growth-standards.Rmd |only pedbp-2.0.0/pedbp/vignettes/references.bib | 41 94 files changed, 3328 insertions(+), 3718 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
function [...truncated...]
Author: Stefan Widgren [aut, cre] ,
Robin Eriksson [aut] ,
Stefan Engblom [aut] ,
Pavol Bauer [aut] ,
Thomas Rosendal [ctb] ,
Ivana Rodriguez Ewerloef [ctb] ,
Attractive Chaos [cph]
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 9.6.0 dated 2023-12-20 and 9.7.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 93 ++--- NAMESPACE | 2 NEWS.md | 23 + R/C-generator.R | 144 +++++++- R/SimInf.R | 6 R/SimInf_indiv_events.R | 396 +++++++++++++++++++++-- R/check_arguments.R | 57 +++ R/distance.R | 15 R/mparse.R | 453 ++++++++++++++++++++------ R/prevalence.R | 26 + R/u0.R | 115 ++++-- R/v0.R | 15 README.md | 22 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/SimInf.pdf |binary inst/doc/post-process-data.R |only inst/doc/post-process-data.Rmd |only inst/doc/post-process-data.html |only inst/doc/scheduled-events.R | 39 ++ inst/doc/scheduled-events.Rmd | 96 +++++ inst/doc/scheduled-events.html | 102 +++++- man/SEIR.Rd | 8 man/SIR.Rd | 8 man/SIS.Rd | 8 man/SISe.Rd | 8 man/SISe3.Rd | 8 man/SISe3_sp.Rd | 8 man/SISe_sp.Rd | 8 man/SimInf.Rd | 28 + man/distance_matrix.Rd | 11 man/events.Rd | 22 - man/figures |only man/individual_events.Rd | 3 man/mparse.Rd | 89 +++-- man/node_events.Rd |only man/prevalence-SimInf_pfilter-method.Rd |only man/u0.Rd | 24 - man/v0-set.Rd | 13 src/init.c | 6 src/misc/SimInf_clean_indiv_events.c | 38 +- src/misc/SimInf_distance_matrix.c | 37 +- tests/SimInf_model.R | 4 tests/indiv_events.R | 540 +++++++++++++++++++++++++++++++- tests/ldata_sp.R | 23 + tests/mparse.R | 167 +++++++++ tests/pfilter.R | 12 tests/v0.R | 9 vignettes/post-process-data.Rmd |only vignettes/scheduled-events.Rmd | 96 +++++ 51 files changed, 2368 insertions(+), 422 deletions(-)
Title: Get Silhouettes of Organisms from PhyloPic
Description: Work with the PhyloPic Web Service (<http://api-docs.phylopic.org/v2/>)
to fetch silhouette images of organisms. Includes functions for adding
silhouettes to both base R plots and ggplot2 plots.
Author: William Gearty [aut, cre] ,
Lewis A. Jones [aut] ,
Scott Chamberlain [aut] ,
David Miller [ctb]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between rphylopic versions 1.3.0 dated 2023-12-20 and 1.4.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 94 ++++----- NAMESPACE | 4 NEWS.md | 5 R/add_phylopic_legend.R |only R/get_attribution.R | 103 +++++++--- R/pick_phylopic.R | 16 + R/zzz.r | 20 + build/vignette.rds |binary inst/doc/a-getting-started.Rmd | 27 +- inst/doc/a-getting-started.html | 27 +- inst/doc/b-advanced-ggplot.Rmd | 36 ++- inst/doc/b-advanced-ggplot.html | 73 +++---- inst/doc/c-advanced-base.Rmd | 2 inst/doc/c-advanced-base.html | 16 - man/add_phylopic_legend.Rd |only man/get_attribution.Rd | 13 + man/pick_phylopic.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/add_phylopic_base/phylopic-in-background.svg | 11 - tests/testthat/_snaps/add_phylopic_legend |only tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-img.svg | 13 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-larger-glyphs.svg | 26 +- tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph-with-uuid.svg | 13 - tests/testthat/_snaps/geom_phylopic/phylopic-key-glyph.svg | 24 +- tests/testthat/test-add_phylopic_legend.R |only tests/testthat/test-get_attribution.R | 11 - tests/testthat/test-pick_phylo.R | 5 tests/testthat/test-resolve_phylopic.R | 6 vignettes/a-getting-started.Rmd | 27 +- vignettes/b-advanced-ggplot.Rmd | 36 ++- vignettes/base-geog-plot-2-1.png |binary vignettes/base-penguin-plot-2-1.png |binary vignettes/base-penguin-plot-3-1.png |binary vignettes/base-penguin-plot-4-1.png |binary vignettes/base-penguin-plot-5-1.png |binary vignettes/base-phylo-plot-3-1.png |binary vignettes/base-phylo-plot-4-1.png |binary vignettes/c-advanced-base.Rmd | 2 vignettes/ggplot-geog-plot-2-1.png |binary vignettes/ggplot-geog-plot-3-1.png |binary vignettes/ggplot-penguin-plot-2-1.png |binary vignettes/ggplot-penguin-plot-3-1.png |binary vignettes/ggplot-penguin-plot-4-1.png |binary vignettes/ggplot-penguin-plot-5-1.png |binary vignettes/ggplot-penguin-plot-6-1.png |binary vignettes/ggplot-phylo-plot-2-1.png |binary vignettes/ggplot-phylo-plot-3-1.png |binary vignettes/ggplot-phylo-plot-4-1.png |binary 49 files changed, 391 insertions(+), 233 deletions(-)
Title: Infrastructure for Partially Observable Markov Decision
Processes (POMDP)
Description: Provides the infrastructure to define and analyze the solutions of Partially Observable Markov Decision Process (POMDP) models. Interfaces for various exact and approximate solution algorithms are available including value iteration, point-based value iteration and SARSOP. Smallwood and Sondik (1973) <doi:10.1287/opre.21.5.1071>.
Author: Michael Hahsler [aut, cph, cre]
,
Hossein Kamalzadeh [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between pomdp versions 1.2.1 dated 2024-04-09 and 1.2.2 dated 2024-04-23
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS.md | 7 +++++++ R/round_stochchastic.R | 5 ++--- R/simulate_MDP.R | 2 +- R/simulate_POMDP.R | 7 +++++-- inst/doc/gridworlds.html | 46 +++++++++++++++++++++++----------------------- inst/doc/pomdp.Rmd | 2 +- inst/doc/pomdp.html | 14 +++++++------- man/round_stochastic.Rd | 6 ++---- man/simulate_MDP.Rd | 2 +- man/simulate_POMDP.Rd | 1 + src/POMDP.cpp | 20 ++++++++++++++++---- src/math.cpp | 3 --- tests/testthat/test-cpp.R | 1 + vignettes/pomdp.Rmd | 2 +- 16 files changed, 87 insertions(+), 69 deletions(-)
Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse
set of pipelining operators ('PipeOps') that can be composed into graphs.
Operations exist for data preprocessing, model fitting, and ensemble
learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can
therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre],
Florian Pfisterer [aut] ,
Lennart Schneider [aut] ,
Bernd Bischl [aut] ,
Michel Lang [aut] ,
Sebastian Fischer [ctb] ,
Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>
Diff between mlr3pipelines versions 0.5.1 dated 2024-03-26 and 0.5.2 dated 2024-04-23
mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_compat.R |only mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_functions.R |only mlr3pipelines-0.5.1/mlr3pipelines/tests/testthat/helper_test_pipeops.R |only mlr3pipelines-0.5.2/mlr3pipelines/DESCRIPTION | 18 mlr3pipelines-0.5.2/mlr3pipelines/MD5 | 320 +++++----- mlr3pipelines-0.5.2/mlr3pipelines/NAMESPACE | 1 mlr3pipelines-0.5.2/mlr3pipelines/NEWS.md | 8 mlr3pipelines-0.5.2/mlr3pipelines/R/GraphLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpBoxCox.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpClassifAvg.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpEncode.R | 14 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpEncodeLmer.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpFilter.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpICA.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpImputeLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpKernelPCA.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpLearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpLearnerCV.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpNMF.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpOVR.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpProxy.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpRandomResponse.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpRegrAvg.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpSmote.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTextVectorizer.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpThreshold.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTrafo.R | 6 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpTuneThreshold.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpVtreat.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/PipeOpYeoJohnson.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/mlr_graphs.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/mlr_pipeops.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_bagging.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_convert_types.R |only mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_ovr.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_robustify.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_stacking.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/pipeline_targettrafo.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/po.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/R/ppl.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/inst/testthat |only mlr3pipelines-0.5.2/mlr3pipelines/man/Graph.Rd | 8 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOp.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpEnsemble.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpImpute.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTargetTrafo.Rd | 20 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTaskPreproc.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/PipeOpTaskPreprocSimple.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs.Rd | 10 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_bagging.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_convert_types.Rd |only mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_ovr.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_robustify.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_stacking.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_graphs_targettrafo.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_learners_graph.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_boxcox.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_branch.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_chunk.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classbalancing.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classifavg.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_classweights.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_colapply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_collapsefactors.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_colroles.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_copy.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_datefeatures.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encode.Rd | 24 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encodeimpact.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_encodelmer.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_featureunion.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_filter.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_fixfactors.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_histbin.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ica.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputeconstant.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputehist.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputelearner.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemean.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemedian.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputemode.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputeoor.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_imputesample.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_kernelpca.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_learner.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_learner_cv.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_missind.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_modelmatrix.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_multiplicityexply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_multiplicityimply.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_mutate.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_nmf.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_nop.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ovrsplit.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_ovrunite.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_pca.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_proxy.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_quantilebin.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_randomprojection.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_randomresponse.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_regravg.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_removeconstants.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_renamecolumns.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_replicate.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scale.Rd | 10 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scalemaxabs.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_scalerange.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_select.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_smote.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_spatialsign.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_subsample.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targetinvert.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targetmutate.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_targettrafoscalerange.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_textvectorizer.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_threshold.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_tunethreshold.Rd | 16 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_unbranch.Rd | 12 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_updatetarget.Rd | 18 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_vtreat.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/mlr_pipeops_yeojohnson.Rd | 14 mlr3pipelines-0.5.2/mlr3pipelines/man/po.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/man/ppl.Rd | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/helper_mlr3pipelines.R |only mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_Graph.R | 5 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_GraphLearner.R | 9 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_conversion.R | 7 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_dictionary.R | 4 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_learner_weightedaverage.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_bagging.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_branching.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_convert_types.R |only mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_ovr.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_robustify.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_stacking.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_mlr_graphs_targettrafo.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_multichannels.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_multiplicities.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_boxcox.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_encodelmer.R | 8 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_featureunion.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_filter.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_ica.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_imputelearner.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_learner.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_learnercv.R | 5 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_missind.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_ovr.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_proxy.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_randomresponse.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_smote.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_targetmutate.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_targettrafoscalerange.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_textvectorizer.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_threshold.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_tunethreshold.R | 3 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_updatetarget.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_pipeop_yeojohnson.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_po.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_ppl.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_resample.R | 1 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_typecheck.R | 2 mlr3pipelines-0.5.2/mlr3pipelines/tests/testthat/test_usecases.R | 11 164 files changed, 912 insertions(+), 615 deletions(-)
Title: Download Flight and Airport Data from Brazil
Description: Download flight and airport data from Brazil’s Civil Aviation Agency
(ANAC) <https://www.gov.br/anac>. The data includes detailed
information on all aircrafts, aerodromes, airports, and airport
movements registered in ANAC, on airfares and on every international
flight to and from Brazil, as well as domestic flights within the country.
Author: Rafael H. M. Pereira [aut, cre]
,
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between flightsbr versions 0.4.0 dated 2023-12-04 and 0.4.1 dated 2024-04-23
DESCRIPTION | 8 +- MD5 | 46 ++++++------- NAMESPACE | 36 +++++----- NEWS.md | 8 ++ R/utils.R | 8 +- README.md | 4 - man/download_aircrafts_data.Rd | 64 +++++++++--------- man/download_airfares_data.Rd | 70 ++++++++++---------- man/download_airport_movement_data.Rd | 70 ++++++++++---------- man/download_flightsbr_file.Rd | 76 ++++++++++----------- man/flightsbr.Rd | 75 ++++++++++----------- man/get_aircrafts_dates_available.Rd | 42 ++++++------ man/get_aircrafts_url.Rd | 52 +++++++------- man/get_airfares_dates_available.Rd | 52 +++++++------- man/get_airfares_url.Rd | 60 ++++++++--------- man/get_airport_movement_dates_available.Rd | 52 +++++++------- man/get_airport_movements_url.Rd | 52 +++++++------- man/get_flight_dates_available.Rd | 42 ++++++------ man/get_flights_url.Rd | 60 ++++++++--------- man/latest_flights_date.Rd | 44 ++++++------ man/read_aircrafts.Rd | 74 ++++++++++----------- man/read_airfares.Rd | 98 ++++++++++++++-------------- man/read_airport_movements.Rd | 78 +++++++++++----------- man/read_airports.Rd | 74 ++++++++++----------- 24 files changed, 628 insertions(+), 617 deletions(-)
Title: Collapsed Latent Position Cluster Model for Social Networks
Description: Markov chain Monte Carlo based inference routines for collapsed latent position cluster models or social networks, which includes searches over the model space (number of clusters in the latent position cluster model). The label switching algorithm used is that of Nobile and Fearnside (2007) <doi:10.1007/s11222-006-9014-7> which relies on the algorithm of Carpaneto and Toth (1980) <doi:10.1145/355873.355883>.
Author: Jason Wyse [aut, cre],
Caitriona Ryan [aut],
Nial Friel [ths]
Maintainer: Jason Wyse <wyseja@tcd.ie>
Diff between collpcm versions 1.3 dated 2024-01-09 and 1.4 dated 2024-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/collpcm.undo.label.switching.R | 19 +++++++++++-------- build/vignette.rds |binary inst/doc/collpcm.pdf |binary 6 files changed, 26 insertions(+), 17 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.1.4 dated 2023-01-06 and 0.1.5 dated 2024-04-23
DESCRIPTION | 10 MD5 | 81 R/compareTables.R | 90 R/data.R | 61 R/loadDataADaMSDTM.R | 13 R/plots-palettes.R | 1 R/plots-palettesCDISC.R | 36 R/plots-utility.R | 13 R/roundHalfUp.R | 8 R/table-getClinDT.R | 30 build/vignette.rds |binary data/dataADaMCDISCP01.RData |binary data/dataSDTMCDISCP01.RData |binary inst/NEWS | 6 inst/doc/clinUtils-vignette.html |90262 ++++++++++++++++++------------ inst/extdata/cdiscpilot01/SDTM/ae.xpt |binary inst/extdata/cdiscpilot01/SDTM/cm.xpt |binary inst/extdata/cdiscpilot01/SDTM/dm.xpt |binary inst/extdata/cdiscpilot01/SDTM/ds.xpt |only inst/extdata/cdiscpilot01/SDTM/ex.xpt |binary inst/extdata/cdiscpilot01/SDTM/lb.xpt |binary inst/extdata/cdiscpilot01/SDTM/mh.xpt |binary inst/extdata/cdiscpilot01/SDTM/qs.xpt |only inst/extdata/cdiscpilot01/SDTM/suppdm.xpt |only inst/extdata/cdiscpilot01/SDTM/sv.xpt |binary inst/extdata/cdiscpilot01/SDTM/vs.xpt |binary man/clinColors.Rd | 13 man/colorPaletteNRIND.Rd | 12 man/compareDiff.Rd | 40 man/compareTables.Rd | 38 man/comparisonTables-common-args.Rd | 22 man/dataADaMCDISCP01.Rd | 32 man/dataSDTMCDISCP01.Rd | 29 man/exportDiffData.Rd | 16 man/formatDTBarVar.Rd | 12 man/formatVarForPlotLabel.Rd | 13 man/getClinDT.Rd | 24 man/getClinDTButtons.Rd | 6 man/getLabelVar.Rd | 13 man/getPaletteCDISC.Rd | 12 man/mergeDiffWithData.Rd | 12 man/roundHalfUpTextFormat.Rd | 8 man/shapePaletteNRIND.Rd | 12 43 files changed, 56895 insertions(+), 34030 deletions(-)
Title: A Program for Missing Data
Description: A tool that "multiply imputes" missing data in a single cross-section
(such as a survey), from a time series (like variables collected for
each year in a country), or from a time-series-cross-sectional data
set (such as collected by years for each of several countries).
Amelia II implements our bootstrapping-based algorithm that gives
essentially the same answers as the standard IP or EMis approaches,
is usually considerably faster than existing approaches and can
handle many more variables. Unlike Amelia I and other statistically
rigorous imputation software, it virtually never crashes (but please
let us know if you find to the contrary!). The program also
generalizes existing approaches by allowing for trends in time series
across observations within a cross-sectional unit, as well as priors
that allow experts to incorporate beliefs they have about the values
of missing cells in their data. Amelia II also includes useful
diagnostics of the fit of multiple imputation models. The p [...truncated...]
Author: James Honaker [aut],
Gary King [aut],
Matthew Blackwell [aut, cre]
Maintainer: Matthew Blackwell <mblackwell@gov.harvard.edu>
Diff between Amelia versions 1.8.1 dated 2022-11-19 and 1.8.2 dated 2024-04-23
Amelia-1.8.1/Amelia/man/amelia.package.Rd |only Amelia-1.8.2/Amelia/DESCRIPTION | 10 Amelia-1.8.2/Amelia/MD5 | 37 +- Amelia-1.8.2/Amelia/R/amelia-package.R |only Amelia-1.8.2/Amelia/R/ameliagui.r | 10 Amelia-1.8.2/Amelia/R/diag.r | 8 Amelia-1.8.2/Amelia/R/emb.r | 6 Amelia-1.8.2/Amelia/R/prep.r | 2 Amelia-1.8.2/Amelia/build/partial.rdb |binary Amelia-1.8.2/Amelia/build/vignette.rds |binary Amelia-1.8.2/Amelia/inst/doc/ameliaview.html | 183 +++++------ Amelia-1.8.2/Amelia/inst/doc/diagnostics.html | 175 +++++------ Amelia-1.8.2/Amelia/inst/doc/intro-mi.Rmd | 2 Amelia-1.8.2/Amelia/inst/doc/intro-mi.html | 86 ++--- Amelia-1.8.2/Amelia/inst/doc/using-amelia.Rmd | 4 Amelia-1.8.2/Amelia/inst/doc/using-amelia.html | 387 ++++++++++++------------- Amelia-1.8.2/Amelia/man/Amelia-package.Rd |only Amelia-1.8.2/Amelia/src/Makevars | 1 Amelia-1.8.2/Amelia/src/Makevars.win | 1 Amelia-1.8.2/Amelia/vignettes/intro-mi.Rmd | 2 Amelia-1.8.2/Amelia/vignettes/using-amelia.Rmd | 4 21 files changed, 455 insertions(+), 463 deletions(-)
Title: Dynamic OpenAPI/Swagger Client
Description: Access services specified in OpenAPI (formerly Swagger) format.
It is not a code generator. Client is generated dynamically as a list of R
functions.
Author: Darko Bergant [aut, cre],
Marcel Ramos [ctb],
Sean Davis [ctb],
Martin Morgan [ctb]
Maintainer: Darko Bergant <darko.bergant@gmail.com>
Diff between rapiclient versions 0.1.3 dated 2020-01-17 and 0.1.4 dated 2024-04-23
DESCRIPTION | 25 ++++++++++++++++--------- MD5 | 26 +++++++++++++------------- R/operations.R | 12 +++++++++--- R/print.R | 6 +++--- R/rapiclient.R | 3 +-- man/get_operation_definitions.Rd | 2 +- man/get_operations.Rd | 3 +-- man/get_parameters.Rd | 2 -- man/get_schema_graphviz_dot.Rd | 9 +++++++-- man/print.rapi_api.Rd | 2 +- man/print.rapi_operation.Rd | 2 +- man/print.rapi_schema_function.Rd | 2 +- man/rapiclient-package.Rd | 19 +++++++++++++++++++ man/result_handlers.Rd | 6 +++--- 14 files changed, 76 insertions(+), 43 deletions(-)
Title: Interfaces to Phylogenetic Software in R
Description: Functions that wrap popular phylogenetic software for sequence
alignment, masking of sequence alignments, and estimation of phylogenies and
ancestral character states.
Author: Christoph Heibl [aut, cre],
Natalie Cusimano [aut],
Franz-Sebastian Krah [aut]
Maintainer: Christoph Heibl <christoph.heibl@gmx.net>
Diff between ips versions 0.0.11 dated 2019-07-04 and 0.0.12 dated 2024-04-23
ips-0.0.11/ips/inst/NEWS.Rd |only ips-0.0.11/ips/man/deleteEmptyCells.Rd |only ips-0.0.12/ips/DESCRIPTION | 15 - ips-0.0.12/ips/MD5 | 132 ++++++++------- ips-0.0.12/ips/NAMESPACE | 19 ++ ips-0.0.12/ips/NEWS.md |only ips-0.0.12/ips/R/EmptyCells.R |only ips-0.0.12/ips/R/aliscore.R | 2 ips-0.0.12/ips/R/assembleDataNode.R | 29 ++- ips-0.0.12/ips/R/assembleDistributionNode.R | 115 ------------- ips-0.0.12/ips/R/assembleInitNode.R | 64 +++++-- ips-0.0.12/ips/R/assembleLikelihoodNode.R |only ips-0.0.12/ips/R/assembleLoggers.R | 189 ++++++++++++++++------ ips-0.0.12/ips/R/assembleOperators.R | 237 ++++++++++++++++++---------- ips-0.0.12/ips/R/assemblePriorNode.R |only ips-0.0.12/ips/R/assembleStateNode.R | 160 +++++++++++++++--- ips-0.0.12/ips/R/assembleTaxonSetPrior.R |only ips-0.0.12/ips/R/assembleTreeNode.R |only ips-0.0.12/ips/R/beastLog.R |only ips-0.0.12/ips/R/blastn.R |only ips-0.0.12/ips/R/combMyTree.R |only ips-0.0.12/ips/R/deleteEmptyCells.R | 37 ---- ips-0.0.12/ips/R/descendants.R | 1 ips-0.0.12/ips/R/extractBEASTstats.R | 1 ips-0.0.12/ips/R/gammaPrior.R |only ips-0.0.12/ips/R/gblocks.R | 4 ips-0.0.12/ips/R/identifyEmptyCells.R |only ips-0.0.12/ips/R/mafft.R | 18 +- ips-0.0.12/ips/R/mrbayes.R | 59 ++++++ ips-0.0.12/ips/R/multistateML.R | 6 ips-0.0.12/ips/R/operator.R |only ips-0.0.12/ips/R/parameter.R |only ips-0.0.12/ips/R/phylo2mafft.R | 2 ips-0.0.12/ips/R/pis.R | 30 +++ ips-0.0.12/ips/R/prank.R | 4 ips-0.0.12/ips/R/raxml.R | 6 ips-0.0.12/ips/R/rbeauti.R | 200 +++++++++++++++++++---- ips-0.0.12/ips/R/rbeauti.taxonset.R | 10 - ips-0.0.12/ips/R/rc.R | 90 +++++++--- ips-0.0.12/ips/R/read.beast.R | 176 ++++++++++---------- ips-0.0.12/ips/R/read.beast.table.R | 2 ips-0.0.12/ips/R/read.fas.R | 3 ips-0.0.12/ips/R/sister.R | 2 ips-0.0.12/ips/R/trimEnds.R | 26 ++- ips-0.0.12/ips/R/write.nex.R | 1 ips-0.0.12/ips/README.md | 2 ips-0.0.12/ips/data/log_list.rda |only ips-0.0.12/ips/data/operator_list.rda |only ips-0.0.12/ips/inst/CITATION | 11 - ips-0.0.12/ips/man/EmptyCells.Rd |only ips-0.0.12/ips/man/aliscore.Rd | 2 ips-0.0.12/ips/man/beastLog.Rd |only ips-0.0.12/ips/man/blastn.Rd |only ips-0.0.12/ips/man/combMyTree.Rd |only ips-0.0.12/ips/man/gblocks.Rd | 16 + ips-0.0.12/ips/man/ips-internal.Rd | 6 ips-0.0.12/ips/man/ips-package.Rd | 4 ips-0.0.12/ips/man/ips.16S.Rd | 2 ips-0.0.12/ips/man/ips.28S.Rd | 2 ips-0.0.12/ips/man/ips.cox1.Rd | 2 ips-0.0.12/ips/man/ips.tree.Rd | 2 ips-0.0.12/ips/man/mafft.Rd | 24 ++ ips-0.0.12/ips/man/mafft.merge.Rd | 3 ips-0.0.12/ips/man/mrbayes.Rd | 130 ++++++++------- ips-0.0.12/ips/man/mrbayes.lset.Rd | 4 ips-0.0.12/ips/man/mrbayes.mcmc.Rd | 2 ips-0.0.12/ips/man/mrbayes.prset.Rd | 2 ips-0.0.12/ips/man/multistate.Rd | 6 ips-0.0.12/ips/man/oi.Rd | 3 ips-0.0.12/ips/man/partitionfinder.Rd | 12 + ips-0.0.12/ips/man/phylo2mafft.Rd | 2 ips-0.0.12/ips/man/pis.Rd | 46 ++--- ips-0.0.12/ips/man/prank.Rd | 2 ips-0.0.12/ips/man/raxml.Rd | 24 ++ ips-0.0.12/ips/man/rbeauti.Rd | 112 +++++++------ ips-0.0.12/ips/man/rc.Rd |only ips-0.0.12/ips/man/read.beast.Rd | 12 - ips-0.0.12/ips/man/read.beast.table.Rd | 2 78 files changed, 1310 insertions(+), 765 deletions(-)
Title: 'R' Bindings for 'TMB'
Description: Native 'R' interface to 'TMB' (Template Model Builder) so models can be written entirely in 'R' rather than 'C++'. Automatic differentiation, to any order, is available for a rich subset of 'R' features, including linear algebra for dense and sparse matrices, complex arithmetic, Fast Fourier Transform, probability distributions and special functions. 'RTMB' provides easy access to model fitting and validation following the principles of Kristensen, K., Nielsen, A., Berg, C. W., Skaug, H., & Bell, B. M. (2016) <DOI:10.18637/jss.v070.i05> and Thygesen, U.H., Albertsen, C.M., Berg, C.W. et al. (2017) <DOI:10.1007/s10651-017-0372-4>.
Author: Kasper Kristensen [aut, cre]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between RTMB versions 1.4 dated 2023-12-01 and 1.5 dated 2024-04-23
DESCRIPTION | 8 MD5 | 64 +++--- NAMESPACE | 5 R/00roxygen.R | 18 + R/RcppExports.R | 36 ++- R/adjoint.R |only R/advector.R | 101 ++++++--- R/methods.R | 75 ++++++- R/mvgauss.R | 15 + build/vignette.rds |binary inst/doc/RTMB-advanced.R | 46 ++++ inst/doc/RTMB-advanced.html | 207 +++++++++++++------- inst/doc/RTMB-advanced.rmd | 92 ++++++++ inst/doc/RTMB-introduction.html | 6 inst/include |only inst/tinytest/test-distributions.R | 27 ++ inst/tinytest/test-tape.R | 50 ++++ man/ADapply.Rd | 6 man/ADconstruct.Rd | 5 man/ADjoint.Rd |only man/ADmatrix.Rd | 7 man/ADvector.Rd | 10 man/Distributions.Rd | 24 ++ man/RTMB-package.Rd | 8 man/TMB-interface.Rd | 3 man/Tape.Rd | 28 ++ src/RTMB.cpp | 382 ------------------------------------- src/RTMB.h | 11 - src/RTMB_tape.cpp |only src/RcppExports.cpp | 103 +++++++-- src/math.cpp | 20 + src/misc.cpp | 76 ++++++- vignettes/RTMB-advanced.rmd | 92 ++++++++ 33 files changed, 940 insertions(+), 585 deletions(-)
Title: Routines for L1 Estimation
Description: L1 estimation for linear regression using Barrodale and Roberts' method
<doi:10.1145/355616.361024> and the EM algorithm <doi:10.1023/A:1020759012226>.
Estimation of mean and covariance matrix using the multivariate Laplace distribution,
density, distribution function, quantile function and random number generation
for univariate and multivariate Laplace distribution <doi:10.1080/03610929808832115>.
Author: Felipe Osorio [aut, cre] ,
Tymoteusz Wolodzko [aut]
Maintainer: Felipe Osorio <felipe.osorios@usm.cl>
Diff between L1pack versions 0.41-24 dated 2023-05-18 and 0.41-245 dated 2024-04-23
ChangeLog | 17 +++++++++++++---- DESCRIPTION | 15 ++++++++------- MD5 | 46 +++++++++++++++++++++++++++------------------- NAMESPACE | 9 +++++---- R/LaplaceFit.R |only R/distn.R | 21 +++++++++++++-------- R/lad.R | 16 +++++++++------- R/wilson_hilferty.R |only data |only inst/CITATION | 8 ++++---- man/Laplace.Rd | 19 ++++++++----------- man/LaplaceFit.Rd |only man/confint.lad.Rd | 4 ++-- man/ereturns.Rd |only man/l1fit.Rd | 4 ++-- man/lad.Rd | 18 +++++++++--------- man/mLaplace.Rd | 16 ++++++++++------ man/vcov.lad.Rd | 2 +- man/wilson.hilferty.Rd |only src/R_init_L1pack.c | 30 ++++++++++++++++++++---------- src/base.h | 5 +++-- src/distn.c | 33 ++++++++++++++++++++++++++++++++- src/interface.c | 46 +++++++++++++++++++++++++++++++++++++++++++++- src/interface.h | 12 +++++++++++- src/lad.h | 6 ++---- src/lad_EM.c | 15 ++++++++++----- src/laplace_fitter.c |only src/wilson-hilferty.c |only 28 files changed, 234 insertions(+), 108 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre, cph],
Matt Dennis [ctb],
Antoine Bichat [ctb] ,
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb],
Swechhya Bista [ctb],
Colin Fay [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.7.18 dated 2023-08-30 and 0.8.0 dated 2024-04-23
emayili-0.7.18/emayili/inst/shiny/send-message/rsconnect |only emayili-0.8.0/emayili/DESCRIPTION | 8 +-- emayili-0.8.0/emayili/MD5 | 13 ++--- emayili-0.8.0/emayili/NAMESPACE | 3 + emayili-0.8.0/emayili/R/encodable.R | 1 emayili-0.8.0/emayili/R/header.R | 1 emayili-0.8.0/emayili/R/server.R | 39 +++++++++++++-- emayili-0.8.0/emayili/man/server.Rd | 15 +++++ 8 files changed, 64 insertions(+), 16 deletions(-)
Title: Testing Randomness in R
Description: Provides several non parametric randomness tests for numeric sequences.
Author: Frederico Caeiro [aut, cre] ,
Ayana Mateus [aut]
Maintainer: Frederico Caeiro <fac@fct.unl.pt>
Diff between randtests versions 1.0.1 dated 2022-06-20 and 1.0.2 dated 2024-04-23
randtests-1.0.1/randtests/NEWS |only randtests-1.0.2/randtests/Changes |only randtests-1.0.2/randtests/DESCRIPTION | 8 +-- randtests-1.0.2/randtests/MD5 | 6 +- randtests-1.0.2/randtests/man/randtests-package.Rd | 56 ++++++++++----------- 5 files changed, 35 insertions(+), 35 deletions(-)
Title: Support Technical Processes Following 'Maelstrom Research'
Standards
Description: Functions to support rigorous processes in data cleaning,
evaluation, and documentation across datasets from different studies based
on Maelstrom Research guidelines. The package includes the core functions
to evaluate and format the main inputs that define the process, diagnose
errors, and summarize and evaluate datasets and their associated
data dictionaries. The main outputs are clean datasets and associated
metadata, and tabular and visual summary reports. As described in
Maelstrom Research guidelines for rigorous retrospective data
harmonization (Fortier I and al. (2017) <doi:10.1093/ije/dyw075>).
Author: Guillaume Fabre [aut, cre] ,
Maelstrom-research group [cph, fnd]
Maintainer: Guillaume Fabre <guijoseph.fabre@gmail.com>
Diff between madshapR versions 1.0.3 dated 2023-12-19 and 1.1.0 dated 2024-04-23
madshapR-1.0.3/madshapR/R/07-data_summarise.R |only madshapR-1.0.3/madshapR/man/madshapR_help.Rd |only madshapR-1.1.0/madshapR/DESCRIPTION | 6 madshapR-1.1.0/madshapR/MD5 | 78 - madshapR-1.1.0/madshapR/NAMESPACE | 1 madshapR-1.1.0/madshapR/NEWS.md | 516 ++++++----- madshapR-1.1.0/madshapR/R/01-utils.R | 4 madshapR-1.1.0/madshapR/R/02-dictionaries_functions.R | 60 - madshapR-1.1.0/madshapR/R/03-dataset_functions.R | 13 madshapR-1.1.0/madshapR/R/04-catalogue_functions.R | 302 ++++-- madshapR-1.1.0/madshapR/R/05-unit_checks.R | 230 +--- madshapR-1.1.0/madshapR/R/06-data_evaluate.R | 118 +- madshapR-1.1.0/madshapR/R/07-data_summarize.R |only madshapR-1.1.0/madshapR/R/08-data_visualize.R | 199 ++-- madshapR-1.1.0/madshapR/R/deprecated.R | 23 madshapR-1.1.0/madshapR/README.md | 2 madshapR-1.1.0/madshapR/build/partial.rdb |binary madshapR-1.1.0/madshapR/build/vignette.rds |binary madshapR-1.1.0/madshapR/data/madshapR_DEMO.rda |binary madshapR-1.1.0/madshapR/data/valueType_list.rda |binary madshapR-1.1.0/madshapR/inst/WORDLIST | 14 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.R | 2 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.Rmd | 2 madshapR-1.1.0/madshapR/inst/doc/madshapR-vignette.html | 2 madshapR-1.1.0/madshapR/man/check_dataset_categories.Rd | 13 madshapR-1.1.0/madshapR/man/data_dict_evaluate.Rd | 3 madshapR-1.1.0/madshapR/man/dataset_evaluate.Rd | 19 madshapR-1.1.0/madshapR/man/dataset_preprocess.Rd | 4 madshapR-1.1.0/madshapR/man/dataset_summarize.Rd | 5 madshapR-1.1.0/madshapR/man/dataset_visualize.Rd | 8 madshapR-1.1.0/madshapR/man/deprecated.Rd | 7 madshapR-1.1.0/madshapR/man/dossier_evaluate.Rd | 12 madshapR-1.1.0/madshapR/man/dossier_summarize.Rd | 2 madshapR-1.1.0/madshapR/man/madshapR_website.Rd |only madshapR-1.1.0/madshapR/man/summary_variables.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_categorical.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_date.Rd | 19 madshapR-1.1.0/madshapR/man/summary_variables_datetime.Rd | 10 madshapR-1.1.0/madshapR/man/summary_variables_numeric.Rd | 12 madshapR-1.1.0/madshapR/man/summary_variables_text.Rd | 12 madshapR-1.1.0/madshapR/man/variable_visualize.Rd | 7 madshapR-1.1.0/madshapR/vignettes/madshapR-vignette.Rmd | 2 42 files changed, 1029 insertions(+), 702 deletions(-)
Title: Nonparametric Change Point Detection for Multivariate Time
Series
Description: Implements the nonparametric moving sum procedure for detecting
changes in the joint characteristic function (NP-MOJO) for multiple change
point detection in multivariate time series. See McGonigle, E. T., Cho, H.
(2023) <doi:10.48550/arXiv.2305.07581> for description of the NP-MOJO methodology.
Author: Euan T. McGonigle [aut, cre],
Haeran Cho [aut]
Maintainer: Euan T. McGonigle <e.t.mcgonigle@soton.ac.uk>
Diff between CptNonPar versions 0.1.1 dated 2023-06-13 and 0.2.1 dated 2024-04-23
DESCRIPTION | 10 - MD5 | 29 ++- NAMESPACE | 1 NEWS.md | 13 + R/multilag.cpts.merge.R | 14 + R/multiscale.np.mojo.R |only R/np.mojo.R | 45 +++-- R/np.mojo.multilag.R | 52 +++--- R/utils.R | 2 man/multilag.cpts.merge.Rd | 8 - man/multiscale.np.mojo.Rd |only man/np.mojo.Rd | 41 ++--- man/np.mojo.multilag.Rd | 46 +++-- tests/testthat/test-multilag.R | 22 +- tests/testthat/test-multiscale.np.mojo.R |only tests/testthat/test-np.R | 240 ++++++++++++++++++------------- tests/testthat/test-np.mojo.R | 28 ++- 17 files changed, 318 insertions(+), 233 deletions(-)
Title: Multiple Data Analysis Tools for Property Listing Tasks
Description: Application to estimate statistical values using properties provided by a group of individuals to describe
concepts using 'shiny'. It estimates the underlying distribution to generate new descriptive words
Canessa et al. (2023) <doi:10.3758/s13428-022-01811-w>, applies a new clustering model, and uses simulations to estimate
the probability that two persons describe the same words based on their descriptions
Canessa et al. (2022) <doi:10.3758/s13428-022-02030-z>.
Author: Sebastian Moreno [aut, cre],
Cristobal Heredia [aut],
Enrique Canessa [ths],
Sergio Chaigneau [ths]
Maintainer: Sebastian Moreno <sebastian.moreno.araya@gmail.com>
Diff between WordListsAnalytics versions 0.2.0 dated 2024-04-18 and 0.2.1 dated 2024-04-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/PLT_server.R | 9 +++++---- 3 files changed, 10 insertions(+), 9 deletions(-)
More information about WordListsAnalytics at CRAN
Permanent link
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] ,
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
Francois Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.12.0 dated 2023-06-21 and 2.13.0 dated 2024-04-23
DESCRIPTION | 13 - MD5 | 105 +++++------ NAMESPACE | 5 NEWS.md | 18 + R/copy_labels.R | 49 +++-- R/is_prefixed.R | 3 R/lookfor.R | 115 +++++++----- R/na_values.R | 77 +++++--- R/recode.R | 32 +-- R/recode_if.R | 14 - R/remove_attributes.R | 3 R/remove_labels.R | 30 +-- R/retrocompatibility.R | 12 - R/tagged_na.R | 44 +++- R/to_character.R | 46 ++-- R/to_factor.R | 146 ++++++++------- R/to_labelled.R | 117 +++++++----- R/to_na.R | 6 R/update_with.R |only R/val_labels.R | 347 +++++++++++++++++++++++++------------ R/var_label.R | 35 ++- README.md | 2 build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/intro_labelled.R | 46 ++-- inst/doc/intro_labelled.Rmd | 42 ++-- inst/doc/intro_labelled.html | 40 ++-- inst/doc/look_for.R | 2 inst/doc/look_for.html | 292 +++++++++++++------------------ inst/doc/missing_values.R | 2 inst/doc/packed_columns.Rmd | 2 inst/doc/packed_columns.html | 4 man/copy_labels.Rd | 12 - man/look_for.Rd | 4 man/na_values.Rd | 5 man/recode.haven_labelled.Rd | 7 man/recode_if.Rd | 2 man/remove_attributes.Rd | 3 man/sort_val_labels.Rd | 4 man/to_character.Rd | 5 man/to_factor.Rd | 15 - man/to_labelled.Rd | 32 +-- man/update_variable_labels_with.Rd |only man/val_labels.Rd | 51 ++++- man/var_label.Rd | 15 - tests/spelling.R | 3 tests/testthat/test-copy_labels.r | 4 tests/testthat/test-labelled.r | 50 ++++- tests/testthat/test-miscellanous.R | 2 tests/testthat/test-na_values.R | 21 +- tests/testthat/test-to_labelled.r | 35 +-- tests/testthat/test-update_with.r |only tests/testthat/test_lookfor.R | 13 - vignettes/intro_labelled.Rmd | 42 ++-- vignettes/packed_columns.Rmd | 2 55 files changed, 1148 insertions(+), 829 deletions(-)
Title: Inflators for Australian Policy Analysis
Description: Using Australian Bureau of Statistics indices, provides functions
that convert historical, nominal statistics to real, contemporary values
without worrying about date input quality, performance, or the ABS catalogue.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between grattanInflators versions 0.5.1 dated 2024-03-26 and 0.5.3 dated 2024-04-23
grattanInflators-0.5.1/grattanInflators/src/C_fastIDate.c |only grattanInflators-0.5.3/grattanInflators/DESCRIPTION | 6 grattanInflators-0.5.3/grattanInflators/MD5 | 22 - grattanInflators-0.5.3/grattanInflators/NEWS.md | 7 grattanInflators-0.5.3/grattanInflators/R/fast_as_idate.R | 16 grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_cpi_inflator.R | 2 grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_guess_format.R |only grattanInflators-0.5.3/grattanInflators/inst/tinytest/test_lf_inflator.R | 43 +- grattanInflators-0.5.3/grattanInflators/man/fast_as_idate.Rd | 79 ++- grattanInflators-0.5.3/grattanInflators/src/check_input.c | 2 grattanInflators-0.5.3/grattanInflators/src/grattanInflator.h | 1 grattanInflators-0.5.3/grattanInflators/src/idate_YearMonth.c | 203 +++++++++- grattanInflators-0.5.3/grattanInflators/src/init.c | 24 - 13 files changed, 303 insertions(+), 102 deletions(-)
More information about grattanInflators at CRAN
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Title: Estimation in Difference-in-Difference Designs with Multiple
Groups and Periods
Description: Estimation of event-study Difference-in-Difference (DID) estimators in designs with multiple groups and periods, and with a potentially non-binary treatment that may increase or decrease multiple times.
Author: Diego Ciccia [aut, cre],
Felix Knau [aut],
Melitine Malezieux [aut],
Doulo Sow [aut],
Clement de Chaisemartin [aut]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between DIDmultiplegtDYN versions 1.0.5 dated 2024-03-01 and 1.0.8 dated 2024-04-23
DESCRIPTION | 8 +- MD5 | 27 +++--- NAMESPACE | 3 NEWS.md | 18 ++++ R/did_multiplegt_bootstrap.R | 13 ++- R/did_multiplegt_by_path.R |only R/did_multiplegt_dyn.R | 89 +++++++++++++++++----- R/did_multiplegt_dyn_core.R | 10 ++ R/did_multiplegt_dyn_design.R | 1 R/did_multiplegt_dyn_graph.R | 60 +++++++++------ R/did_multiplegt_main.R | 155 ++++++++++++++++++++++++++++++++------- R/print.R | 18 +++- R/progressBar.R | 7 + R/rnames.R |only man/did_multiplegt_dyn.Rd | 41 ++++++---- man/rnames.did_multiplegt_dyn.Rd |only 16 files changed, 338 insertions(+), 112 deletions(-)
More information about DIDmultiplegtDYN at CRAN
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Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Description: Facilities for constructing variance dispersion graphs, fraction-
of-design-space plots and similar graphics for exploring the properties of
experimental designs. The design region is explored via random sampling, which
allows for more flexibility than traditional variance dispersion graphs. A
formula interface is leveraged to provide access to complex model formulae.
Graphics can be constructed simultaneously for multiple experimental designs
and/or multiple model formulae. Instead of using pointwise optimization to
find the minimum and maximum scaled prediction variance curves, which can be
inaccurate and time consuming, this package uses quantile regression as an
alternative.
Author: Pieter Schoonees [aut, cre, cph],
Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Diff between vdg versions 1.2.2 dated 2022-07-07 and 1.2.3 dated 2024-04-23
vdg-1.2.2/vdg/R/vdg-package.R |only vdg-1.2.3/vdg/DESCRIPTION | 14 +++++++------- vdg-1.2.3/vdg/MD5 | 11 +++++------ vdg-1.2.3/vdg/build/partial.rdb |binary vdg-1.2.3/vdg/build/vignette.rds |binary vdg-1.2.3/vdg/inst/doc/vdg.pdf |binary vdg-1.2.3/vdg/man/vdg-package.Rd | 7 +------ 7 files changed, 13 insertions(+), 19 deletions(-)
More information about bayesMeanScale at CRAN
Permanent link
Title: Available Light Within the Water Column and Seafloor of Arctic
Fjords
Description: Satellite data collected between 2003 and 2022,
in conjunction with gridded bathymetric data (50-150 m resolution),
are used to estimate the irradiance reaching the bottom of a series of representative EU Arctic fjords.
An Earth System Science Data (ESSD) manuscript, Schlegel et al. (2023, in review),
that provides a detailed explanation of the methodology is currently in review.
Author: Bernard Gentili [aut],
Jean-Pierre Gattuso [aut] ,
Robert W. Schlegel [aut, cre]
Maintainer: Robert W. Schlegel <robert.schlegel@imev-mer.fr>
Diff between FjordLight versions 0.7.0 dated 2023-12-02 and 0.8 dated 2024-04-23
DESCRIPTION | 16 MD5 | 57 +-- NAMESPACE | 1 NEWS.md | 39 ++ R/fl_DownloadFjord.R | 40 +- R/fl_ListFjords.R | 15 R/fl_LoadFjord.R | 24 + R/flget_KPARMonthlyTS.R |only R/flget_PARbottomMonthlyTS.R | 90 ++-- R/flplot_KPARMonthlyTS.R |only R/flplot_PARbottomMonthlyTS.R | 2 R/flplot_climatology.R | 4 README.md | 11 build/vignette.rds |binary inst/CITATION |only inst/doc/fl_example.R | 114 +++++- inst/doc/fl_example.Rmd | 150 +++++++- inst/doc/fl_example.html | 455 +++++++++++++++++++------ inst/extdata/test_ClimSD.nc |only inst/extdata/test_MonthlyKpar.nc |only inst/extdata/test_YearlySD.nc |only man/fl_DownloadFjord.Rd | 19 - man/fl_ListFjords.Rd | 4 man/fl_LoadFjord.Rd | 16 man/flget_KPARMonthlyTS.Rd |only man/flplot_KPARMonthlyTS.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test-fl_DownloadFjord.R | 38 +- tests/testthat/test-fl_LoadFjord.R | 27 + tests/testthat/test-flget_KPARMonthlyTS.R |only tests/testthat/test-flget_PARbottomMonthlyTS.R | 2 tests/testthat/test-flget_Pfunction.R | 2 tests/testthat/test-flget_climatology.R | 2 vignettes/fl_example.Rmd | 150 +++++++- 34 files changed, 1031 insertions(+), 247 deletions(-)
Title: Modules for 'ShinyItemAnalysis'
Description: Package including additional modules for interactive
'ShinyItemAnalysis' application for the psychometric analysis of
educational tests, psychological assessments, health-related and other
types of multi-item measurements, or ratings from multiple raters.
Author: Patricia Martinkova [aut, cre]
,
Jan Netik [aut]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between SIAmodules versions 0.1.0 dated 2023-03-29 and 0.1.1 dated 2024-04-23
SIAmodules-0.1.0/SIAmodules/inst/modules |only SIAmodules-0.1.1/SIAmodules/DESCRIPTION | 15 +- SIAmodules-0.1.1/SIAmodules/MD5 | 54 +------- SIAmodules-0.1.1/SIAmodules/NAMESPACE | 2 SIAmodules-0.1.1/SIAmodules/NEWS.md |only SIAmodules-0.1.1/SIAmodules/R/sm_cat.R | 115 +++++++++++++----- SIAmodules-0.1.1/SIAmodules/R/sm_dif_c.R | 10 - SIAmodules-0.1.1/SIAmodules/R/sm_irr.R | 6 SIAmodules-0.1.1/SIAmodules/README.md | 5 SIAmodules-0.1.1/SIAmodules/build/partial.rdb |binary SIAmodules-0.1.1/SIAmodules/inst/sc/cat.R |only SIAmodules-0.1.1/SIAmodules/man/SIAmodules-package.Rd | 2 12 files changed, 121 insertions(+), 88 deletions(-)
Title: Marker-Based Cell Type Purification for Single-Cell Sequencing
Data
Description: A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of s [...truncated...]
Author: Massimo Andreatta [aut, cre] ,
Ariel Berenstein [aut] ,
Josep Garnica [aut],
Santiago Carmona [aut]
Maintainer: Massimo Andreatta <massimo.andreatta@unil.ch>
Diff between scGate versions 1.6.0 dated 2023-11-06 and 1.6.2 dated 2024-04-23
DESCRIPTION | 12 ++-- MD5 | 16 +++--- NAMESPACE | 1 R/main.R | 35 ++++++++++--- R/utils.R | 100 +++++++++++++++++++++++++++++++++++++-- build/vignette.rds |binary inst/NEWS.Rd | 8 +++ man/combine_scGate_multiclass.Rd | 2 man/scGate.Rd | 8 ++- 9 files changed, 153 insertions(+), 29 deletions(-)
Title: Multivariate Polynomials with Rational Coefficients
Description: Symbolic calculation and evaluation of multivariate
polynomials with rational coefficients. This package is strongly
inspired by the 'spray' package. It provides a function to
compute Gröbner bases (reference <doi:10.1007/978-3-319-16721-3>).
The header file of the C++ code can be used by other packages. It
provides the templated class 'Qspray' that can be used to represent and
to deal with multivariate polynomials with another type of coefficients.
Author: Stephane Laurent [aut, cre],
Robin Hankin [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between qspray versions 2.1.1 dated 2023-09-07 and 3.0.0 dated 2024-04-23
DESCRIPTION | 24 - MD5 | 113 ++++- NAMESPACE | 45 ++ NEWS.md | 33 + R/RcppExports.R | 20 - R/characteristicPolynomial.R |only R/creation.R |only R/evaluation.R |only R/groebner.R | 266 +++++++------ R/integrateOnSimplex.R |only R/internal.R | 96 ++++ R/qspray.R | 576 ++++++++--------------------- R/qsprayDivision.R |only R/queries.R |only R/show.R |only R/symmetricPolynomials.R |only R/transformation.R |only R/yacas.R | 48 +- README.md | 370 +++++++++++++++++-- configure | 12 inst/include |only man/ESFpoly.Rd | 4 man/HallInnerProduct.Rd |only man/MSFpoly.Rd | 2 man/MSPcombination.Rd |only man/PSFpoly.Rd |only man/PSPexpression.Rd |only man/as.function.qspray.Rd | 17 man/as.qspray.Rd | 3 man/changeVariables.Rd |only man/characteristicPolynomial.Rd |only man/collinearQsprays.Rd |only man/compactSymmetricQspray.Rd |only man/composeQspray.Rd |only man/dQspray.Rd | 9 man/derivQspray.Rd | 9 man/evalQspray.Rd | 6 man/getCoefficient.Rd |only man/getConstantTerm.Rd |only man/integratePolynomialOnSimplex.Rd | 2 man/isConstant.Rd |only man/isPolynomialOf.Rd |only man/isQone.Rd |only man/isQzero.Rd |only man/isSymmetricQspray.Rd |only man/isUnivariate.Rd |only man/numberOfTerms.Rd |only man/numberOfVariables.Rd |only man/orderedQspray.Rd |only man/permuteVariables.Rd |only man/qdivision.Rd | 12 man/qlone.Rd | 11 man/qone.Rd | 6 man/qsprayDivision.Rd |only man/qsprayMaker.Rd | 4 man/qspray_from_list.Rd |only man/qzero.Rd | 6 man/rQspray.Rd |only man/showMonomialOld.Rd |only man/showMonomialX1X2X3.Rd |only man/showMonomialXYZ.Rd |only man/showQspray.Rd |only man/showQsprayOption-set.Rd |only man/showQsprayX1X2X3.Rd |only man/showQsprayXYZ.Rd |only man/substituteQspray.Rd |only man/swapVariables.Rd |only src/Makevars.in | 2 src/Makevars.win | 3 src/RcppExports.cpp | 70 ++- src/division.cpp |only src/evaluation.cpp |only src/qspray.cpp | 577 ++---------------------------- tests/testthat/helper-00.R |only tests/testthat/test-HallInnerProduct.R |only tests/testthat/test-basic.R | 7 tests/testthat/test-collinear.R |only tests/testthat/test-composeQspray.R |only tests/testthat/test-division.R | 3 tests/testthat/test-getCoefficient.R |only tests/testthat/test-groebner.R |only tests/testthat/test-permuteVariables.R |only tests/testthat/test-show.R |only tests/testthat/test-substitute.R |only tests/testthat/test-symmetricPolynomial.R |only 85 files changed, 1119 insertions(+), 1237 deletions(-)
Title: Preparation, Checking and Post-Processing Data for PK/PD
Modeling
Description: Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Author: Philip Delff [aut, cre],
Eric Anderson [ctb]
Maintainer: Philip Delff <philip@delff.dk>
Diff between NMdata versions 0.1.5 dated 2024-02-21 and 0.1.6 dated 2024-04-23
DESCRIPTION | 16 ++-- MD5 | 71 +++++++++++------- NAMESPACE | 5 + NEWS.md | 102 ++++++++++++++++---------- R/NMcheckData.R | 72 ++++++++++-------- R/NMexpandDoses.R | 21 +++-- R/NMextractDataFile.R | 1 R/NMinfo.R | 12 +-- R/NMreadExt.R | 16 ++-- R/NMreadShk.R |only R/NMreadTab.R | 2 R/NMreadTabSlow.R |only R/NMscanData.R | 17 ---- R/NMwriteSection.R | 22 ++--- R/addOmegaCorr.R |only R/addTAPD.R | 45 ++++++----- R/colLabels.R | 1 R/dt2mat.R |only R/flagsAssign.R | 5 - R/fnAppend.R | 12 ++- R/mat2dt.R |only R/uniquePresent.R | 27 +++++- man/NMcheckData.Rd | 59 +++++++-------- man/NMinfo.Rd | 12 +-- man/NMreadExt.Rd | 14 +-- man/NMreadShk.Rd |only man/NMreadTabSlow.Rd |only man/NMwriteSection.Rd | 22 ++--- man/addOmegaCorr.Rd |only man/addTAPD.Rd | 30 +++---- man/colLabels.Rd | 3 man/dt2mat.Rd |only man/fnAppend.Rd | 2 man/mat2dt.Rd |only man/uniquePresent.Rd |only tests/testthat/testReference/NMreadExt_01.rds |only tests/testthat/testReference/NMreadExt_03.rds |only tests/testthat/testReference/NMreadExt_04.rds |only tests/testthat/testReference/NMreadShk_01.rds |only tests/testthat/testReference/addTAPD_04.rds |only tests/testthat/testReference/fnAppend_02.rds |only tests/testthat/test_NMreadShk.R |only tests/testthat/test_NMscanData.R | 11 +- tests/testthat/test_addTAPD.R | 40 +++++++++- tests/testthat/test_fnAppend.R | 14 +++ tests/testthat/test_uniquePresent.R |only 46 files changed, 394 insertions(+), 260 deletions(-)
More information about GregoryQuadrature at CRAN
Permanent link
Title: Functions for Extreme Value Distributions
Description: Extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme
value distributions, and provides fitting functions which
calculate maximum likelihood estimates for univariate and
bivariate maxima models, and for univariate and bivariate
threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between evd versions 2.3-6.1 dated 2022-07-04 and 2.3-7 dated 2024-04-23
DESCRIPTION | 8 +-- MD5 | 14 ++--- R/mvdist.R | 91 ++++++++++++++++++++----------------- build/vignette.rds |binary inst/CHANGES | 16 ++++++ inst/CITATION | 15 ++---- inst/doc/Multivariate_Extremes.pdf |binary man/uccle.Rd | 4 - 8 files changed, 85 insertions(+), 63 deletions(-)
Title: Young Tableaux
Description: Deals with Young tableaux (field of combinatorics). For standard
Young tabeaux, performs enumeration, counting, random generation, the
Robinson-Schensted correspondence, and conversion to and from paths on
the Young lattice. Also performs enumeration and counting of
semistandard Young tableaux, enumeration of skew semistandard Young
tableaux, and computation of Kostka numbers.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between syt versions 0.3.0 dated 2023-12-06 and 0.4.0 dated 2024-04-23
DESCRIPTION | 19 ++++----- MD5 | 51 ++++++++++++++++-------- NAMESPACE | 15 +++++++ NEWS.md | 15 +++++-- R/Kostka.R |only R/ballot.R | 10 ++-- R/dualsyt.R | 2 R/enumeration.R | 3 - R/hooks.R | 2 R/internal.R | 37 ++++++++++++----- R/isSYT.R |only R/skewTableaux.R |only R/ssyt.R | 78 ++++++++++++++----------------------- R/syt2matrix.R | 41 ++++++++++++++++--- R/tableaux.R |only man/KostkaNumber.Rd |only man/all_ssSkewTableaux.Rd |only man/all_ssytx.Rd | 3 - man/all_sytx.Rd | 3 - man/dualSkewTableau.Rd |only man/dualTableau.Rd |only man/isSSYT.Rd |only man/isSYT.Rd |only man/isSemistandardSkewTableau.Rd |only man/isSkewTableau.Rd |only man/isStandardSkewTableau.Rd |only man/prettySkewTableau.Rd |only man/prettyTableau.Rd |only man/syt2matrix.Rd | 4 + man/tableau2matrix.Rd |only man/tableauShape.Rd |only tests/testthat/test-Kostka.R |only tests/testthat/test-dual.R | 10 +++- tests/testthat/test-enumeration.R | 1 tests/testthat/test-skewTableaux.R |only tests/testthat/test-ssyt.R | 10 ++++ 36 files changed, 198 insertions(+), 106 deletions(-)
Title: Some Datetime Pickers for 'Shiny'
Description: Provides three types of datetime pickers for usage in a
'Shiny' UI. A datetime picker is an input field for selecting both a
date and a time.
Author: Stephane Laurent [aut, cre],
Wojciech Maj [cph] ),
Porinn [cph] ),
Dmitriy Kovalenko [cph] )
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between shinyDatetimePickers versions 1.1.0 dated 2023-08-07 and 1.2.0 dated 2024-04-23
DESCRIPTION | 8 MD5 | 19 NAMESPACE | 3 NEWS.md | 5 R/datetimeMaterialPicker.R | 24 - R/datetimePicker.R | 24 - R/datetimeSliderPicker.R | 24 - inst/www/datetimePicker/datetimePicker.js | 573 +++++++++++++++++++++++--- inst/www/datetimePicker/datetimePicker.js.map | 2 man/updateDatetimeMaterialPickerInput.Rd |only man/updateDatetimePickerInput.Rd |only man/updateDatetimeSliderPickerInput.Rd |only 12 files changed, 576 insertions(+), 106 deletions(-)
More information about shinyDatetimePickers at CRAN
Permanent link
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.3.2 dated 2023-11-17 and 1.4.0 dated 2024-04-23
DESCRIPTION | 8 - MD5 | 32 ++--- R/glmm.gei.R | 261 +++++++++++++++++++++++------------------ R/glmm.gei.meta.R | 36 ++--- inst/doc/MAGEE.Rnw | 25 +++ inst/doc/MAGEE.pdf |binary inst/extdata/meta1.txt | 2 inst/extdata/meta2.txt | 2 inst/extdata/meta3.txt | 2 inst/extdata/meta4.txt | 2 inst/extdata/meta5.txt | 2 inst/extdata/readme | 2 man/MAGEE-package.Rd | 4 man/glmm.gei.Rd | 22 ++- src/fitglmm.cpp | 257 ++++++++++++++-------------------------- tests/testthat/test_glmm.gei.R | 72 +++++------ vignettes/MAGEE.Rnw | 25 +++ 17 files changed, 380 insertions(+), 374 deletions(-)
Title: Kantorovich Distance Between Probability Measures
Description: Computes the Kantorovich distance between two probability
measures on a finite set. The Kantorovich distance is also known as
the Monge-Kantorovich distance or the first Wasserstein distance.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between kantorovich versions 3.1.0 dated 2023-08-22 and 3.2.0 dated 2024-04-23
DESCRIPTION | 10 ++--- MD5 | 32 +++++++++--------- NEWS.md | 7 ++++ R/kantorovich_CVX.R | 27 +++++++-------- R/kantorovich_glpk.R | 33 +++++++++---------- R/kantorovich_lpsolve.R | 26 +++++++-------- R/kantorovich_ompr.R | 37 ++++++++++----------- inst/doc/kantorovich.R | 6 +-- inst/doc/kantorovich.html | 4 +- man/kantorovich_CVX.Rd | 14 ++++---- man/kantorovich_glpk.Rd | 21 ++++-------- man/kantorovich_lp.Rd | 14 ++++---- man/kantorovich_ompr.Rd | 72 +++++++++++++++++++++--------------------- tests/testthat/test-CVX.R | 2 - tests/testthat/test-glpk.R | 2 - tests/testthat/test-lpSolve.R | 4 +- tests/testthat/test-ompr.R | 2 - 17 files changed, 157 insertions(+), 156 deletions(-)
Title: Sensitivities of Prices of Financial Options and Implied
Volatilities
Description: Methods to calculate sensitivities of financial option prices for
European, geometric and arithmetic Asian, and American options, with various
payoff functions in the Black Scholes model, and in more general jump diffusion
models. A shiny app to interactively plot the results is included. Furthermore,
methods to compute implied volatilities are provided for a wide range of option
types and custom payoff functions. Classical formulas are implemented for
European options in the Black Scholes Model, as is presented in Hull, J. C.
(2017), Options, Futures, and Other Derivatives.
In the case of Asian options, Malliavin Monte Carlo Greeks are implemented, see
Hudde, A. & Rüschendorf, L. (2023). European and Asian Greeks for exponential
Lévy processes. <doi:10.1007/s11009-023-10014-5>. For American
options, the Binomial Tree Method is implemented, as is presented in Hull,
J. C. (2017).
Author: Anselm Hudde [aut, cre]
Maintainer: Anselm Hudde <anselmhudde@gmx.de>
Diff between greeks versions 1.3.5 dated 2024-03-03 and 1.4.2 dated 2024-04-23
DESCRIPTION | 6 - MD5 | 14 +- NEWS.md | 33 ++++-- R/Malliavin_Geometric_Asian_Greeks.R | 32 ++---- README.md | 2 tests/testthat/test-Binomial_American_Greeks.R | 9 + tests/testthat/test-Malliavin_European_Greeks.R | 29 +++--- tests/testthat/test-Malliavin_Geometric_Asian_Greeks.R | 81 +++++++---------- 8 files changed, 103 insertions(+), 103 deletions(-)
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Description: A system for 'declaratively' creating graphics, based on "The
Grammar of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.
Author: Hadley Wickham [aut] ,
Winston Chang [aut] ,
Lionel Henry [aut],
Thomas Lin Pedersen [aut, cre]
,
Kohske Takahashi [aut],
Claus Wilke [aut] ,
Kara Woo [aut] ,
Hiroaki Yutani [aut] ,
Dewey Dunnington [aut] ,
Teun van den Brand [aut] ,
Posit, PBC [cph, [...truncated...]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between ggplot2 versions 3.5.0 dated 2024-02-23 and 3.5.1 dated 2024-04-23
DESCRIPTION | 32 - MD5 | 432 +++++++++++++------------- NEWS.md | 48 ++ R/aes.R | 2 R/annotation.R | 17 - R/autolayer.R | 2 R/autoplot.R | 114 ++++++ R/axis-secondary.R | 10 R/bin.R | 8 R/coord-.R | 2 R/coord-flip.R | 13 R/coord-map.R | 20 + R/coord-polar.R | 12 R/coord-radial.R | 58 ++- R/coord-transform.R | 2 R/data.R | 2 R/docs_layer.R |only R/facet-.R | 4 R/facet-grid-.R | 6 R/facet-wrap.R | 6 R/fortify.R | 1 R/geom-.R | 2 R/geom-bar.R | 3 R/geom-bin2d.R | 4 R/geom-blank.R | 1 R/geom-boxplot.R | 6 R/geom-count.R | 4 R/geom-density.R | 4 R/geom-density2d.R | 4 R/geom-dotplot.R | 2 R/geom-errorbar.R | 2 R/geom-errorbarh.R | 2 R/geom-function.R | 16 R/geom-hex.R | 7 R/geom-histogram.R | 4 R/geom-path.R | 9 R/geom-point.R | 30 + R/geom-quantile.R | 4 R/geom-raster.R | 4 R/geom-sf.R | 8 R/geom-smooth.R | 4 R/geom-text.R | 15 R/geom-tile.R | 4 R/geom-violin.R | 6 R/ggproto.R | 12 R/guide-axis-logticks.R | 59 ++- R/guide-bins.R | 12 R/guide-colorbar.R | 2 R/guide-colorsteps.R | 55 +-- R/guide-legend.R | 18 + R/labels.R | 3 R/layer.R | 48 ++ R/plot-build.R | 18 - R/plot.R | 2 R/position-.R | 2 R/position-jitter.R | 4 R/position-jitterdodge.R | 2 R/save.R | 3 R/scale-.R | 25 + R/scale-alpha.R | 9 R/scale-binned.R | 2 R/scale-brewer.R | 2 R/scale-colour.R | 2 R/scale-continuous.R | 2 R/scale-date.R | 4 R/scale-discrete-.R | 4 R/scale-gradient.R | 2 R/scale-grey.R | 4 R/scale-hue.R | 6 R/scale-identity.R | 2 R/scale-linetype.R | 4 R/scale-linewidth.R | 2 R/scale-manual.R | 4 R/scale-shape.R | 4 R/scale-size.R | 12 R/scale-steps.R | 11 R/stat-.R | 5 R/stat-boxplot.R | 2 R/stat-contour.R | 8 R/stat-count.R | 2 R/stat-smooth.R | 5 R/stat-summary-bin.R | 2 R/theme-defaults.R | 3 R/theme-elements.R | 5 R/theme.R | 11 R/utilities-help.R | 10 R/utilities-resolution.R | 10 R/utilities.R | 6 README.md | 4 inst/doc/extending-ggplot2.R | 8 inst/doc/extending-ggplot2.Rmd | 8 inst/doc/extending-ggplot2.html | 21 - inst/doc/ggplot2-in-packages.R | 24 - inst/doc/ggplot2-in-packages.Rmd | 24 - inst/doc/ggplot2-in-packages.html | 24 - inst/doc/ggplot2-specs.Rmd | 3 inst/doc/ggplot2-specs.html | 14 man/aes_colour_fill_alpha.Rd | 4 man/aes_group_order.Rd | 4 man/aes_linetype_size_shape.Rd | 4 man/aes_position.Rd | 4 man/annotate.Rd | 34 +- man/autolayer.Rd | 6 man/automatic_plotting.Rd |only man/autoplot.Rd | 6 man/binned_scale.Rd | 10 man/borders.Rd | 32 + man/continuous_scale.Rd | 4 man/coord_flip.Rd | 14 man/coord_map.Rd | 3 man/coord_polar.Rd | 17 - man/coord_trans.Rd | 3 man/discrete_scale.Rd | 6 man/facet_grid.Rd | 3 man/facet_wrap.Rd | 3 man/fortify.Rd | 6 man/geom_abline.Rd | 31 + man/geom_bar.Rd | 52 ++- man/geom_bin_2d.Rd | 53 ++- man/geom_blank.Rd | 63 +++ man/geom_boxplot.Rd | 53 ++- man/geom_contour.Rd | 82 +++- man/geom_count.Rd | 53 ++- man/geom_density.Rd | 53 ++- man/geom_density_2d.Rd | 20 - man/geom_dotplot.Rd | 47 ++ man/geom_errorbarh.Rd | 63 +++ man/geom_function.Rd | 98 ++++- man/geom_hex.Rd | 52 ++- man/geom_histogram.Rd | 53 ++- man/geom_jitter.Rd | 63 +++ man/geom_linerange.Rd | 63 +++ man/geom_map.Rd | 47 ++ man/geom_path.Rd | 63 +++ man/geom_point.Rd | 63 +++ man/geom_polygon.Rd | 63 +++ man/geom_qq.Rd | 62 +++ man/geom_quantile.Rd | 53 ++- man/geom_ribbon.Rd | 82 +++- man/geom_rug.Rd | 63 +++ man/geom_segment.Rd | 63 +++ man/geom_smooth.Rd | 58 ++- man/geom_spoke.Rd | 63 +++ man/geom_text.Rd | 69 +++- man/geom_tile.Rd | 63 +++ man/geom_violin.Rd | 53 ++- man/ggplot.Rd | 3 man/ggplot2-ggproto.Rd | 15 man/ggplot_build.Rd | 2 man/ggplot_gtable.Rd | 2 man/ggproto.Rd | 15 man/ggsave.Rd | 3 man/ggsf.Rd | 82 +++- man/ggtheme.Rd | 3 man/guide_axis_logticks.Rd | 29 + man/guide_colourbar.Rd | 2 man/guide_coloursteps.Rd | 2 man/guide_legend.Rd | 2 man/labs.Rd | 3 man/layer.Rd | 58 ++- man/layer_geoms.Rd |only man/layer_positions.Rd |only man/layer_sf.Rd | 49 ++ man/layer_stats.Rd |only man/position_dodge.Rd | 2 man/position_identity.Rd | 2 man/position_nudge.Rd | 2 man/position_stack.Rd | 2 man/register_theme_elements.Rd | 3 man/resolution.Rd | 5 man/scale_alpha.Rd | 9 man/scale_binned.Rd | 9 man/scale_brewer.Rd | 2 man/scale_colour_continuous.Rd | 2 man/scale_colour_discrete.Rd | 3 man/scale_continuous.Rd | 3 man/scale_date.Rd | 4 man/scale_discrete.Rd | 7 man/scale_gradient.Rd | 9 man/scale_grey.Rd | 15 man/scale_hue.Rd | 15 man/scale_identity.Rd | 2 man/scale_linetype.Rd | 7 man/scale_linewidth.Rd | 3 man/scale_manual.Rd | 10 man/scale_shape.Rd | 7 man/scale_size.Rd | 16 man/scale_steps.Rd | 35 -- man/sec_axis.Rd | 2 man/stat_ecdf.Rd | 62 +++ man/stat_ellipse.Rd | 62 +++ man/stat_identity.Rd | 62 +++ man/stat_sf_coordinates.Rd | 64 +++ man/stat_summary.Rd | 71 +++- man/stat_summary_2d.Rd | 62 +++ man/stat_unique.Rd | 62 +++ man/theme.Rd | 7 man/txhousing.Rd | 2 tests/testthat/_snaps/annotate.md | 4 tests/testthat/_snaps/coord-map.md | 4 tests/testthat/_snaps/coord-polar.md | 4 tests/testthat/_snaps/guides.md | 2 tests/testthat/_snaps/layer.md | 2 tests/testthat/_snaps/prohibited-functions.md |only tests/testthat/_snaps/sec-axis.md | 2 tests/testthat/test-annotate.R | 6 tests/testthat/test-coord-map.R | 6 tests/testthat/test-coord-polar.R | 22 + tests/testthat/test-coord-train.R | 2 tests/testthat/test-coord_sf.R | 2 tests/testthat/test-draw-key.R | 5 tests/testthat/test-guides.R | 51 ++- tests/testthat/test-prohibited-functions.R | 27 + tests/testthat/test-scales.R | 14 tests/testthat/test-stat-bin.R | 7 tests/testthat/test-theme.R | 2 tests/testthat/test-utilities.R | 3 vignettes/extending-ggplot2.Rmd | 8 vignettes/ggplot2-in-packages.Rmd | 24 - vignettes/ggplot2-specs.Rmd | 3 220 files changed, 3395 insertions(+), 1108 deletions(-)
Title: Interpret Tree Ensembles
Description: For tree ensembles such as random forests, regularized random forests and gradient boosted trees, this package provides functions for: extracting, measuring and pruning rules; selecting a compact rule set; summarizing rules into a learner; calculating frequent variable interactions; formatting rules in latex code. Reference: Interpreting tree ensembles with inTrees (Houtao Deng, 2019, <doi:10.1007/s41060-018-0144-8>).
Author: Houtao Deng [aut, cre],
Xin Guan [aut],
Vadim Khotilovich [aut]
Maintainer: Houtao Deng <softwaredeng@gmail.com>
Diff between inTrees versions 1.3 dated 2022-05-31 and 1.4 dated 2024-04-23
inTrees-1.3/inTrees/R/XGB2List.R |only inTrees-1.4/inTrees/DESCRIPTION | 8 ++++---- inTrees-1.4/inTrees/MD5 | 8 ++++---- inTrees-1.4/inTrees/NEWS | 5 ++++- inTrees-1.4/inTrees/R/XGB2LIST.R |only inTrees-1.4/inTrees/man/selectRuleRRF.Rd | 1 + 6 files changed, 13 insertions(+), 9 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 4.0.7 dated 2024-02-05 and 4.0.8 dated 2024-04-23
DESCRIPTION | 8 - MD5 | 58 ++++---- NAMESPACE | 2 NEWS.md | 5 R/CCAMLRGIS-package.R | 1 R/add_Cscale.R | 2 R/add_Legend.R |only R/add_RefGrid.R | 2 R/add_col.R | 3 R/add_labels.R | 2 R/create.R | 11 - R/create_Arrow.R | 3 R/create_Hashes.R |only R/get_iso_polys.R | 111 +++++++++------- README.md | 317 +++++++++++++++++++++++++++++++++++++++-------- build/vignette.rds |binary inst/doc/CCAMLRGIS.html | 4 man/CCAMLRGIS-package.Rd | 1 man/add_Cscale.Rd | 2 man/add_Legend.Rd |only man/add_RefGrid.Rd | 2 man/add_col.Rd | 3 man/add_labels.Rd | 2 man/create_Arrow.Rd | 3 man/create_Hashes.Rd |only man/create_Lines.Rd | 2 man/create_Points.Rd | 2 man/create_PolyGrids.Rd | 3 man/create_Polys.Rd | 2 man/create_Stations.Rd | 2 man/figures |only man/get_iso_polys.Rd | 46 ++++-- 32 files changed, 428 insertions(+), 171 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-01-08 0.7.3
Title: Visualize Simon's Two-Stage Design
Description: To visualize the probabilities of early
termination, fail and success of Simon's two-stage
design. To evaluate and visualize the operating
characteristics of Simon's two-stage design.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between VisualizeSimon2Stage versions 0.1.3 dated 2024-03-20 and 0.1.4 dated 2024-04-22
VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/R/0info.R |only VisualizeSimon2Stage-0.1.3/VisualizeSimon2Stage/inst |only VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/DESCRIPTION | 21 +- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/MD5 | 37 +-- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/NAMESPACE | 3 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/NEWS.md | 2 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/0PACKAGE.R |only VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/Simon_oc.R | 45 ++-- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/Simon_pr.R | 72 ------- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/autoplot.ph2simon.R |only VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/ph2simon_etc.R | 99 ---------- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/R/r_simon.R |only VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/Simon_oc.Rd | 25 +- VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/Simon_pr.Rd | 19 - VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/Sprintf.Simon_oc.Rd | 1 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/Sprintf.ph2simon.Rd | 3 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/VisualizeSimon2Stage-package.Rd | 11 - VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/autoplot.ph2simon.Rd | 32 +++ VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/print_ph2simon.Rd | 2 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/r_simon.Rd | 16 - VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/show-Simon_oc-method.Rd | 1 VisualizeSimon2Stage-0.1.4/VisualizeSimon2Stage/man/show-Simon_pr-method.Rd | 1 22 files changed, 135 insertions(+), 255 deletions(-)
More information about VisualizeSimon2Stage at CRAN
Permanent link
Title: Soil Database Interface
Description: A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.8.1 dated 2024-01-09 and 2.8.2 dated 2024-04-22
soilDB-2.8.1/soilDB/man/dot-get_SRI_gdb_names.Rd |only soilDB-2.8.2/soilDB/DESCRIPTION | 8 soilDB-2.8.2/soilDB/MD5 | 81 soilDB-2.8.2/soilDB/NAMESPACE | 3 soilDB-2.8.2/soilDB/NEWS.md | 24 soilDB-2.8.2/soilDB/R/ISSR800.R | 9 soilDB-2.8.2/soilDB/R/ROSETTA.R | 16 soilDB-2.8.2/soilDB/R/SDA-spatial.R | 236 - soilDB-2.8.2/soilDB/R/WCS-utils.R | 10 soilDB-2.8.2/soilDB/R/fetchLDM.R | 2 soilDB-2.8.2/soilDB/R/fetchSDA_spatial.R | 36 soilDB-2.8.2/soilDB/R/fetchSRI.R | 3 soilDB-2.8.2/soilDB/R/fetchSoilGrids.R | 66 soilDB-2.8.2/soilDB/R/get_SDA_coecoclass.R | 2 soilDB-2.8.2/soilDB/R/get_ecosite_history_from_NASIS_db.R | 5 soilDB-2.8.2/soilDB/R/get_mapunit_from_NASIS.R | 15 soilDB-2.8.2/soilDB/R/get_site_data_from_NASIS_db.R | 44 soilDB-2.8.2/soilDB/R/get_soilseries_from_NASIS.R | 33 soilDB-2.8.2/soilDB/R/mukey-WCS.R | 22 soilDB-2.8.2/soilDB/R/seriesExtent.R | 2 soilDB-2.8.2/soilDB/R/simplifyArtifactData.R | 15 soilDB-2.8.2/soilDB/R/simplifyFragmentData.R | 11 soilDB-2.8.2/soilDB/R/soilColorWCS.R | 13 soilDB-2.8.2/soilDB/R/soilDB-package.R | 6 soilDB-2.8.2/soilDB/R/utils.R | 8 soilDB-2.8.2/soilDB/build/partial.rdb |binary soilDB-2.8.2/soilDB/build/vignette.rds |binary soilDB-2.8.2/soilDB/inst/doc/fetchNASIS.R | 2 soilDB-2.8.2/soilDB/inst/doc/fetchNASIS.html | 144 + soilDB-2.8.2/soilDB/inst/doc/wcs-ssurgo.R | 29 soilDB-2.8.2/soilDB/inst/doc/wcs-ssurgo.Rmd | 23 soilDB-2.8.2/soilDB/inst/doc/wcs-ssurgo.html | 1361 +++++------ soilDB-2.8.2/soilDB/man/ROSETTA.Rd | 4 soilDB-2.8.2/soilDB/man/SDA_spatialQuery.Rd | 5 soilDB-2.8.2/soilDB/man/fetchSoilGrids.Rd | 12 soilDB-2.8.2/soilDB/man/get_ecosite_history_from_NASIS_db.Rd | 9 soilDB-2.8.2/soilDB/man/get_soilseries_from_NASIS.Rd | 12 soilDB-2.8.2/soilDB/man/soilColor.wcs.Rd | 2 soilDB-2.8.2/soilDB/man/soilDB-package.Rd | 1 soilDB-2.8.2/soilDB/tests/testthat/test-fetchSDA_spatial.R | 1 soilDB-2.8.2/soilDB/tests/testthat/test-fetchSoilGrids.R | 2 soilDB-2.8.2/soilDB/vignettes/wcs-ssurgo.Rmd | 23 42 files changed, 1242 insertions(+), 1058 deletions(-)
Title: Weighted Confusion Matrix
Description: Allows users to create weighted confusion matrices and accuracy
metrics that help with the model selection process for classification
problems, where distance from the correct category is important. The
package includes several weighting schemes which can be parameterized, as
well as custom configuration options. Furthermore, users can decide
whether they wish to positively or negatively affect the accuracy score
as a result of applying weights to the confusion matrix. Functions are
included to calculate accuracy metrics for imbalanced data. Finally,
'wconf' integrates well with the 'caret' package, but it can also work
standalone when provided data in matrix form.
References:
Kuhn, M. (2008) "Building Perspective Models in R Using the caret Package"
<doi:10.18637/jss.v028.i05>
Monahov, A. (2021) "Model Evaluation with Weighted Threshold Optimization
(and the mewto R package)" <doi:10.2139/ssrn.3805911>
Starovoitov, V., Golub, Y. (2020). New Function for Estimating Imbalanc [...truncated...]
Author: Alexandru Monahov [aut, cre, cph]
Maintainer: Alexandru Monahov <alexandru.monahov@proton.me>
Diff between wconf versions 1.0.0 dated 2023-12-12 and 1.1.0 dated 2024-04-22
DESCRIPTION | 17 +- MD5 | 30 ++-- NAMESPACE | 1 NEWS.md | 17 ++ R/balancedaccuracy.R |only R/wconf-package.R | 9 + R/wconfusionmatrix.R | 58 +++++++- R/weightmatrix.R | 75 +++++++++- README.md | 22 +++ inst/doc/wconf_guide.R | 35 +++++ inst/doc/wconf_guide.Rmd | 201 ++++++++++++++++++++++++++++ inst/doc/wconf_guide.html | 320 +++++++++++++++++++++++++++++++++++++++++----- man/balancedaccuracy.Rd |only man/wconf-package.Rd | 10 + man/wconfusionmatrix.Rd | 19 ++ man/weightmatrix.Rd | 25 +++ vignettes/wconf_guide.Rmd | 201 ++++++++++++++++++++++++++++ 17 files changed, 965 insertions(+), 75 deletions(-)
Title: 'tidyverse' Methods and 'ggplot2' Helpers for 'terra' Objects
Description: Extension of the 'tidyverse' for 'SpatRaster' and
'SpatVector' objects of the 'terra' package. It includes also new
'geom_' functions that provide a convenient way of visualizing 'terra'
objects with 'ggplot2'.
Author: Diego Hernangomez [aut, cre, cph]
,
Dewey Dunnington [ctb] ,
ggplot2 authors [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between tidyterra versions 0.5.2 dated 2024-01-19 and 0.6.0 dated 2024-04-22
tidyterra-0.5.2/tidyterra/man/drop_na.SpatRaster.Rd |only tidyterra-0.5.2/tidyterra/man/drop_na.SpatVector.Rd |only tidyterra-0.6.0/tidyterra/DESCRIPTION | 18 tidyterra-0.6.0/tidyterra/MD5 | 264 - tidyterra-0.6.0/tidyterra/NAMESPACE | 13 tidyterra-0.6.0/tidyterra/NEWS.md | 72 tidyterra-0.6.0/tidyterra/R/arrange-SpatVector.R | 20 tidyterra-0.6.0/tidyterra/R/as_coordinates.R | 16 tidyterra-0.6.0/tidyterra/R/as_sf.R | 20 tidyterra-0.6.0/tidyterra/R/as_spatraster.R | 56 tidyterra-0.6.0/tidyterra/R/as_spatvector.R | 41 tidyterra-0.6.0/tidyterra/R/as_tibble-Spat.R | 71 tidyterra-0.6.0/tidyterra/R/autoplot-Spat.R | 19 tidyterra-0.6.0/tidyterra/R/bind-cols-SpatVector.R | 38 tidyterra-0.6.0/tidyterra/R/bind-rows-SpatVector.R | 32 tidyterra-0.6.0/tidyterra/R/compare_spatrasters.R | 26 tidyterra-0.6.0/tidyterra/R/count-tally-SpatVector.R | 18 tidyterra-0.6.0/tidyterra/R/data.R | 61 tidyterra-0.6.0/tidyterra/R/distinct-SpatVector.R | 16 tidyterra-0.6.0/tidyterra/R/drop_na-Spat.R | 122 tidyterra-0.6.0/tidyterra/R/fill-SpatVector.R |only tidyterra-0.6.0/tidyterra/R/filter-Spat.R | 39 tidyterra-0.6.0/tidyterra/R/fortify-Spat.R | 104 tidyterra-0.6.0/tidyterra/R/geom_spat_contour.R | 94 tidyterra-0.6.0/tidyterra/R/geom_spat_contour_fill.R | 1 tidyterra-0.6.0/tidyterra/R/geom_spat_contour_text.R |only tidyterra-0.6.0/tidyterra/R/geom_spatraster.R | 78 tidyterra-0.6.0/tidyterra/R/geom_spatraster_rgb.R | 595 +-- tidyterra-0.6.0/tidyterra/R/geom_spatvector.R | 20 tidyterra-0.6.0/tidyterra/R/glimpse-Spat.R | 428 +- tidyterra-0.6.0/tidyterra/R/group-by-SpatVector.R | 30 tidyterra-0.6.0/tidyterra/R/group-data-SpatVector.R | 10 tidyterra-0.6.0/tidyterra/R/grouped-SpatVector.R | 12 tidyterra-0.6.0/tidyterra/R/join-SpatVector.R | 23 tidyterra-0.6.0/tidyterra/R/mutate-Spat.R | 35 tidyterra-0.6.0/tidyterra/R/pivot-long-SpatVector.R |only tidyterra-0.6.0/tidyterra/R/pivot-wide-SpatVector.R |only tidyterra-0.6.0/tidyterra/R/pull-Spat.R | 26 tidyterra-0.6.0/tidyterra/R/pull_crs.R | 31 tidyterra-0.6.0/tidyterra/R/relocate-Spat.R | 22 tidyterra-0.6.0/tidyterra/R/rename-Spat.R | 25 tidyterra-0.6.0/tidyterra/R/replace_na-Spat.R | 11 tidyterra-0.6.0/tidyterra/R/rowwise-SpatVector.R | 34 tidyterra-0.6.0/tidyterra/R/scales_coltab.R | 28 tidyterra-0.6.0/tidyterra/R/scales_cross_blended.R | 1510 +++++----- tidyterra-0.6.0/tidyterra/R/scales_hypso.R | 1484 ++++----- tidyterra-0.6.0/tidyterra/R/scales_terrain.R | 509 +-- tidyterra-0.6.0/tidyterra/R/scales_whitebox.R | 711 ++-- tidyterra-0.6.0/tidyterra/R/scales_wiki.R | 604 ++-- tidyterra-0.6.0/tidyterra/R/select-Spat.R | 31 tidyterra-0.6.0/tidyterra/R/slice-Spat.R | 56 tidyterra-0.6.0/tidyterra/R/stat_spat_coordinates.R | 6 tidyterra-0.6.0/tidyterra/R/stat_spatraster.R | 16 tidyterra-0.6.0/tidyterra/R/summarise-SpatVector.R | 21 tidyterra-0.6.0/tidyterra/R/sysdata.rda |binary tidyterra-0.6.0/tidyterra/R/tidyterra-package.R | 5 tidyterra-0.6.0/tidyterra/README.md | 174 - 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tidyterra-0.6.0/tidyterra/tests/testthat/test-as_spatvector.R | 1252 ++++---- tidyterra-0.6.0/tidyterra/tests/testthat/test-fill-SpatVector.R |only tidyterra-0.6.0/tidyterra/tests/testthat/test-fortify-Spat.R | 48 tidyterra-0.6.0/tidyterra/tests/testthat/test-geom_spat_contour_text.R |only tidyterra-0.6.0/tidyterra/tests/testthat/test-geom_spatraster_1lyr_coltab.R | 16 tidyterra-0.6.0/tidyterra/tests/testthat/test-glimpse-Spat.R | 41 tidyterra-0.6.0/tidyterra/tests/testthat/test-pivot-long-SpatVector.R |only tidyterra-0.6.0/tidyterra/tests/testthat/test-pivot-wide-SpatVector.R |only tidyterra-0.6.0/tidyterra/vignettes/aggregate-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/aggregate-2.png |binary tidyterra-0.6.0/tidyterra/vignettes/contourfilled-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/contourlines-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/faceted-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/hypso-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/lux_ggplot-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/paper.bib | 512 +-- tidyterra-0.6.0/tidyterra/vignettes/rgb-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/spatraster-example1-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/spatraster-example2-1.png |binary tidyterra-0.6.0/tidyterra/vignettes/tidyterra.Rmd | 165 - 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Title: Analyses of Text using Transformers Models from HuggingFace,
Natural Language Processing and Machine Learning
Description: Link R with Transformers from Hugging Face to transform text variables to word embeddings; where the word embeddings are used to statistically test the mean difference between set of texts, compute semantic similarity scores between texts, predict numerical variables, and visual statistically significant words according to various dimensions etc. For more information see <https://www.r-text.org>.
Author: Oscar Kjell [aut, cre] ,
Salvatore Giorgi [aut] ,
Andrew Schwartz [aut]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Diff between text versions 1.2.0 dated 2024-02-13 and 1.2.1 dated 2024-04-22
text-1.2.0/text/tests/testthat/notrun/test_6_finetune.R |only text-1.2.0/text/tests/testthat/test_1_Analyses_flow.R |only text-1.2.0/text/tests/testthat/test_2_1_textTrain_strata.R |only text-1.2.0/text/tests/testthat/test_2_textTrain.R |only text-1.2.0/text/tests/testthat/test_99_textEmbed.R |only text-1.2.1/text/DESCRIPTION | 8 text-1.2.1/text/MD5 | 104 +-- text-1.2.1/text/NAMESPACE | 3 text-1.2.1/text/NEWS.md | 5 text-1.2.1/text/R/0_0_text_install.R | 234 +++---- text-1.2.1/text/R/0_1_globals.R | 4 text-1.2.1/text/R/0_2_privateFunctions.R | 324 ++++++---- text-1.2.1/text/R/0_3_textModels.R | 18 text-1.2.1/text/R/1_1_textEmbed.R | 269 +++++--- text-1.2.1/text/R/2_1_textTrain.R | 13 text-1.2.1/text/R/2_2_textTrainRegression.R | 142 ++-- text-1.2.1/text/R/2_3_textTrainRandomForest.R | 199 ++++-- text-1.2.1/text/R/2_4_textPredict.R | 288 +++++--- text-1.2.1/text/R/2_5_textTrainN.R | 226 +++--- text-1.2.1/text/R/3_1_textSimilarity.R | 2 text-1.2.1/text/R/4_0_textPlot.R | 5 text-1.2.1/text/R/4_1_textPlotCentrality.R | 2 text-1.2.1/text/R/4_3_textPlotProjection.R | 2 text-1.2.1/text/R/6_1_textFineTune.R | 10 text-1.2.1/text/R/6_2_textFineTuneDomain.R | 3 text-1.2.1/text/R/7_1_textTopics.R | 114 +++ text-1.2.1/text/R/7_2_textTopicsAnalysis.R | 4 text-1.2.1/text/R/zzz.R | 2 text-1.2.1/text/build/vignette.rds |binary text-1.2.1/text/inst/doc/pre_trained_models.R |only text-1.2.1/text/inst/doc/pre_trained_models.Rmd |only text-1.2.1/text/inst/doc/pre_trained_models.html |only text-1.2.1/text/inst/extdata/text_models_info.csv |only text-1.2.1/text/inst/python/__pycache__/run_mlm.cpython-39.pyc |binary text-1.2.1/text/inst/python/bert_topic.py | 56 + text-1.2.1/text/inst/python/huggingface_Interface3.py | 109 ++- text-1.2.1/text/inst/python/huggingface_Interface4.py | 11 text-1.2.1/text/man/textEmbed.Rd | 18 text-1.2.1/text/man/textEmbedLayerAggregation.Rd | 6 text-1.2.1/text/man/textEmbedRawLayers.Rd | 9 text-1.2.1/text/man/textFineTuneTask.Rd | 6 text-1.2.1/text/man/textModelLayers.Rd | 13 text-1.2.1/text/man/textPredict.Rd | 50 + text-1.2.1/text/man/textTopics.Rd | 3 text-1.2.1/text/man/textTopicsReduce.Rd |only text-1.2.1/text/man/textTopicsTree.Rd |only text-1.2.1/text/man/textTrainNPlot.Rd | 45 - text-1.2.1/text/man/textTrainRandomForest.Rd | 3 text-1.2.1/text/man/textTrainRegression.Rd | 9 text-1.2.1/text/man/textrpp_install.Rd | 9 text-1.2.1/text/tests/testthat/test_0_install_test.R | 32 text-1.2.1/text/tests/testthat/test_1_1_Analyses_flow.R |only text-1.2.1/text/tests/testthat/test_1_2_textEmbed.R |only text-1.2.1/text/tests/testthat/test_2_1_textTrainRegression.R |only text-1.2.1/text/tests/testthat/test_2_2_textTrainRandomForest.R |only text-1.2.1/text/tests/testthat/test_2_3_textTrain_strata.R |only text-1.2.1/text/tests/testthat/test_2_4_textTrainN.R |only text-1.2.1/text/tests/testthat/test_2_5_textPredict.R |only text-1.2.1/text/tests/testthat/test_4_textPlot.R | 19 text-1.2.1/text/tests/testthat/test_6_textFineTune.R |only text-1.2.1/text/tests/testthat/test_7_textTopics.R | 15 text-1.2.1/text/tests/testthat/test_zz_UNinstall_test.R |only text-1.2.1/text/tests/testthat/test_zzz_install_virtualenv_test.R |only text-1.2.1/text/vignettes/pre_trained_models.Rmd |only 64 files changed, 1637 insertions(+), 757 deletions(-)
Title: Topic Inference to Identify Tissue Architecture in Multiplexed
Images
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. 'SpaTopic' is scalable to large-scale image datasets without extracting neighborhood information for every single cell. For more details on the methodology, see <https://xiyupeng.github.io/SpaTopic/>.
Author: Xiyu Peng [aut, cre]
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Diff between SpaTopic versions 1.0.1 dated 2024-01-17 and 1.1.0 dated 2024-04-22
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 2 ++ R/Gibbs_sampler.R | 28 +++++++++++++++++++++++----- README.md | 40 ++++++++++++++++++++++++++++++---------- inst/doc/Intro_SpaTopic.Rmd | 2 +- inst/doc/Intro_SpaTopic.html | 28 +++++++++++++++++++++------- vignettes/Intro_SpaTopic.Rmd | 2 +- 8 files changed, 90 insertions(+), 36 deletions(-)
Title: Standard and Nonstandard Statistical Models and Methods for Test
Equating
Description: Contains functions to perform various models and
methods for test equating (Kolen and Brennan, 2014
<doi:10.1007/978-1-4939-0317-7> ; Gonzalez and Wiberg, 2017
<doi:10.1007/978-3-319-51824-4> ; von Davier et. al, 2004
<doi:10.1007/b97446>). It currently implements the traditional mean, linear
and equipercentile equating methods. Both IRT observed-score and true-score
equating are also supported, as well as the mean-mean, mean-sigma, Haebara
and Stocking-Lord IRT linking methods. It also supports newest methods such
that local equating, kernel equating (using Gaussian, logistic,
Epanechnikov, uniform and adaptive kernels) with presmoothing, and IRT
parameter linking methods based on asymmetric item characteristic functions.
Functions to obtain both standard error of equating (SEE) and standard error
of equating differences between two equating functions (SEED) are also
implemented for the kernel method of equating.
Author: Jorge Gonzalez [cre, aut],
Daniel Leon Acuna [ctb]
Maintainer: Jorge Gonzalez <jorge.gonzalez@mat.uc.cl>
Diff between SNSequate versions 1.3-4 dated 2022-12-20 and 1.3-5 dated 2024-04-22
DESCRIPTION | 35 MD5 | 30 NAMESPACE | 141 +- R/BB.smooth.R |only R/bandwidth.R | 652 +++++----- R/discrete.smooth.R |only R/epan.R | 22 R/irt.eq.R | 8 R/kefJG.R |only R/ker.eq.R | 2978 +++++++++++++++++++++++------------------------ R/kpmfeJG.R |only R/loglin.smooth.R | 903 +++++++------- build/partial.rdb |binary inst/CITATION | 24 man/BB.smooth.Rd |only man/SNSequate-package.Rd | 160 +- man/bandwidth.Rd | 4 man/discrete.smooth.Rd |only man/ker.eq.Rd | 6 19 files changed, 2510 insertions(+), 2453 deletions(-)
Title: Web Interface to 'R' Functions
Description: Web front end for your 'R' functions producing plots or tables.
If you have a function or set of related functions, you can make them
available over the internet through a web browser. This is the same
motivation as the 'shiny' package, but note that the development of
'shinylight' is not in any way linked to that of 'shiny' (beyond the use of
the 'httpuv' package). You might prefer 'shinylight' to 'shiny' if you want
a lighter weight deployment with easier horizontal scaling, or if you want
to develop your front end yourself in JavaScript and HTML just using
a lightweight remote procedure call interface to your R code on the
server.
Author: Pieter Vermeesch [aut],
Tim Band [aut, cre]
Maintainer: Tim Band <t.band@ucl.ac.uk>
Diff between shinylight versions 1.1.2 dated 2022-11-30 and 1.2 dated 2024-04-22
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/shinylight.R | 22 +++++++++------------- README.md | 3 +-- inst/www/js/dataentrygrid.min.js | 2 +- inst/www/js/shinylight-framework.js | 26 ++++++++++++++++++++++++-- inst/www/locales/en/framework.json | 4 ++++ 7 files changed, 50 insertions(+), 29 deletions(-)
Title: Technical Data Sets by Ruijter et al. (2013)
Description: The real-time quantitative polymerase chain reaction
(qPCR) technical data sets by Ruijter et al. (2013)
<doi:10.1016/j.ymeth.2012.08.011>: (i) the four-point 10-fold dilution
series; (ii) 380 replicates; and (iii) the competimer data set. These
three data sets can be used to benchmark qPCR methods. Original data set
is available at
<https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip>.
This package fixes incorrect annotations in the original data sets.
Author: Ramiro Magno [aut, cre] ,
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between ruijter versions 0.1.2 dated 2023-02-08 and 0.1.3 dated 2024-04-22
.aspell |only DESCRIPTION | 23 ++++++++++++----------- MD5 | 16 ++++++++++------ NAMESPACE | 1 + NEWS.md |only R/ruijter-package.R |only README.md | 20 +++++++++++++++++--- build |only man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/ruijter-package.Rd |only 12 files changed, 40 insertions(+), 20 deletions(-)
Title: Biomarker Data Set by Vermeulen et al. (2009)
Description: The biomarker data set by Vermeulen et al. (2009)
<doi:10.1016/S1470-2045(09)70154-8> is provided. The data
source, however, is by Ruijter et al. (2013)
<doi:10.1016/j.ymeth.2012.08.011>. The original data set may
be downloaded from
<https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip>.
This data set is for a real-time quantitative polymerase chain reaction
(PCR) experiment that comprises the raw fluorescence data of 24,576
amplification curves. This data set comprises 59 genes of interest and 5
reference genes. Each gene was assessed on 366 neuroblastoma complementary
DNA (cDNA) samples and on 18 standard dilution series samples (10-fold
5-point dilution series x 3 replicates + no template controls (NTC) x 3
replicates).
Author: Ramiro Magno [aut, cre] ,
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between vermeulen versions 0.1.1 dated 2022-11-10 and 0.1.2 dated 2024-04-22
.aspell |only DESCRIPTION | 22 +++++++++++----------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 36 ++++++++++++++++++------------------ build/partial.rdb |binary inst/WORDLIST | 17 ++++++----------- man/vermeulen-package.Rd | 6 +++--- 8 files changed, 48 insertions(+), 49 deletions(-)
Title: Real-Time PCR Data Sets by Rutledge et al. (2004)
Description: Real-time quantitative polymerase chain reaction (qPCR) data
by Rutledge et al. (2004) <doi:10.1093/nar/gnh177> in tidy format. The
data comprises a six-point, ten-fold dilution series, repeated in five
independent runs, for two different amplicons. In each run, each standard
concentration is replicated four times. For the original raw data file see
the Supplementary Data section:
<https://academic.oup.com/nar/article/32/22/e178/2375678#supplementary-data>.
Author: Ramiro Magno [aut, cre] ,
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between rutledge versions 0.1.0 dated 2023-02-27 and 0.1.1 dated 2024-04-22
rutledge-0.1.0/rutledge/R/utils-pipe.R |only rutledge-0.1.0/rutledge/man/pipe.Rd |only rutledge-0.1.1/rutledge/DESCRIPTION | 22 +++++----- rutledge-0.1.1/rutledge/MD5 | 15 +++--- rutledge-0.1.1/rutledge/NAMESPACE | 2 rutledge-0.1.1/rutledge/NEWS.md |only rutledge-0.1.1/rutledge/README.md | 15 ++++-- rutledge-0.1.1/rutledge/build/partial.rdb |binary rutledge-0.1.1/rutledge/man/figures/README-unnamed-chunk-3-1.png |binary rutledge-0.1.1/rutledge/man/rutledge-package.Rd | 6 +- 10 files changed, 31 insertions(+), 29 deletions(-)
Title: Retrieve Global River Gauge Data
Description: Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.
Author: Ryan Riggs [aut, cre] ,
Simon Moulds [aut] ,
Michel Wortmann [aut] ,
Louise Slater [aut] ,
George Allen [aut]
Maintainer: Ryan Riggs <ryanriggs7@gmail.com>
Diff between RivRetrieve versions 0.1.4 dated 2024-03-02 and 0.1.5 dated 2024-04-22
DESCRIPTION | 10 ++++----- MD5 | 16 +++++++-------- NEWS.md | 4 +++ build/vignette.rds |binary inst/doc/my-vignette.html | 14 ++++++------- man/RivRetrieve-package.Rd | 2 - man/get_timeseries_id.Rd | 48 ++++++++++++++++++++++----------------------- man/make_bom_request.Rd | 44 ++++++++++++++++++++--------------------- tests/testthat.R | 24 +++++++++++----------- 9 files changed, 83 insertions(+), 79 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Tomasz Kalinowski [ctb, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] ,
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph]
Maintainer: Tomasz Kalinowski <tomasz@posit.co>
Diff between reticulate versions 1.36.0 dated 2024-04-15 and 1.36.1 dated 2024-04-22
DESCRIPTION | 6 - MD5 | 22 ++--- NEWS.md | 16 +++- R/conda.R | 45 ++++++++--- R/conversion.R | 6 - inst/doc/python_dependencies.Rmd | 113 ++++++++++++++--------------- inst/doc/python_dependencies.html | 137 ++++++++++++++++++------------------ inst/doc/python_primer.html | 28 +++---- man/conda-tools.Rd | 11 ++ src/python.cpp | 4 - tests/testthat/test-python-pandas.R | 26 ++++++ vignettes/python_dependencies.Rmd | 113 ++++++++++++++--------------- 12 files changed, 300 insertions(+), 227 deletions(-)
Title: Real-Time PCR Data Sets by Batsch et al. (2008)
Description: Real-time quantitative polymerase chain reaction (qPCR) data
sets by Batsch et al. (2008) <doi:10.1186/1471-2105-9-95>. This package
provides five data sets, one for each PCR target: (i) rat SLC6A14,
(ii) human SLC22A13, (iii) pig EMT, (iv) chicken ETT, and (v) human
GAPDH. Each data set comprises a five-point, four-fold dilution series.
For each concentration there are three replicates. Each amplification curve
is 45 cycles long. Original raw data file:
<https://static-content.springer.com/esm/art%3A10.1186%2F1471-2105-9-95/MediaObjects/12859_2007_2080_MOESM5_ESM.xls>.
Author: Ramiro Magno [aut, cre] ,
Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Diff between batsch versions 0.1.0 dated 2023-02-14 and 0.1.1 dated 2024-04-22
batsch-0.1.0/batsch/R/utils-pipe.R |only batsch-0.1.0/batsch/man/pipe.Rd |only batsch-0.1.1/batsch/DESCRIPTION | 16 +++---- batsch-0.1.1/batsch/MD5 | 23 +++++------ batsch-0.1.1/batsch/NAMESPACE | 2 batsch-0.1.1/batsch/NEWS.md |only batsch-0.1.1/batsch/README.md | 11 ++--- batsch-0.1.1/batsch/build/partial.rdb |binary batsch-0.1.1/batsch/man/batsch-package.Rd | 4 - batsch-0.1.1/batsch/man/figures/README-unnamed-chunk-2-1.png |binary batsch-0.1.1/batsch/man/figures/README-unnamed-chunk-3-1.png |binary batsch-0.1.1/batsch/man/figures/README-unnamed-chunk-4-1.png |binary batsch-0.1.1/batsch/man/figures/README-unnamed-chunk-5-1.png |binary batsch-0.1.1/batsch/man/figures/README-unnamed-chunk-6-1.png |binary 14 files changed, 27 insertions(+), 29 deletions(-)
Title: Exploratory Graph Analysis – a Framework for Estimating the
Number of Dimensions in Multivariate Data using Network
Psychometrics
Description: Implements the Exploratory Graph Analysis (EGA) framework for dimensionality
and psychometric assessment. EGA estimates the number of dimensions in
psychological data using network estimation methods and community detection
algorithms. A bootstrap method is provided to assess the stability of dimensions
and items. Fit is evaluated using the Entropy Fit family of indices. Unique
Variable Analysis evaluates the extent to which items are locally dependent (or
redundant). Network loadings provide similar information to factor loadings and
can be used to compute network scores. A bootstrap and permutation approach are
available to assess configural and metric invariance. Hierarchical structures
can be detected using Hierarchical EGA. Time series and intensive longitudinal
data can be analyzed using Dynamic EGA, supporting individual, group, and
population level assessments.
Author: Hudson Golino [aut, cre] ,
Alexander Christensen [aut] ,
Robert Moulder [ctb] ,
Luis E. Garrido [ctb] ,
Laura Jamison [ctb] ,
Dingjing Shi [ctb]
Maintainer: Hudson Golino <hfg9s@virginia.edu>
Diff between EGAnet versions 2.0.5 dated 2024-03-15 and 2.0.6 dated 2024-04-22
DESCRIPTION | 16 - MD5 | 30 +-- NEWS | 19 ++ R/EBICglasso.qgraph.R | 8 R/TMFG.R | 231 ++++++++++++------------ R/auto.correlate.R | 33 ++- R/bootEGA.R | 83 +++++--- R/helpers.R | 24 +- R/invariance.R | 53 +++-- R/itemStability.R | 427 ++++++++++++++++++++++++--------------------- R/net.loads.R | 67 ++----- R/network.predictability.R | 10 - man/TMFG.Rd | 6 man/invariance.Rd | 2 man/itemStability.Rd | 14 - man/net.loads.Rd | 7 16 files changed, 574 insertions(+), 456 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.3.7 dated 2023-08-19 and 1.3.8 dated 2024-04-22
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 5 + R/ScatterHist.R | 6 +- inst/doc/WVPlots_concept.html | 113 +++++++++++++++++++---------------------- inst/doc/WVPlots_examples.html | 29 +++++----- 6 files changed, 85 insertions(+), 86 deletions(-)
Title: Variable Selection in Partial Least Squares
Description: Interfaces and methods for variable selection in Partial Least
Squares. The methods include filter methods, wrapper methods and embedded
methods. Both regression and classification is supported.
Author: Kristian Hovde Liland [aut, cre]
,
Tahir Mehmood [ctb],
Solve Saeboe [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between plsVarSel versions 0.9.10 dated 2023-01-12 and 0.9.11 dated 2024-04-22
DESCRIPTION | 12 ++--- MD5 | 16 +++---- NAMESPACE | 9 +++- NEWS | 4 + R/T2.R | 7 ++- R/mvrV.R | 26 ++++++----- R/utilities.R | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 44 +++++++++++++++++++- inst/CITATION | 7 ++- 9 files changed, 220 insertions(+), 32 deletions(-)
Title: Analytics & Machine Learning Sidekick
Description: Auxiliary package for better/faster analytics, visualization, data mining, and machine
learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling,
Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust
results, without the need of repetitive coding or extensive R programming skills.
Author: Bernardo Lares [aut, cre]
Maintainer: Bernardo Lares <laresbernardo@gmail.com>
Diff between lares versions 5.2.5 dated 2024-01-22 and 5.2.7 dated 2024-04-22
DESCRIPTION | 6 - MD5 | 92 +++++++++++++-------------- R/chatgpt.R | 4 - R/correlations.R | 9 +- R/credentials.R | 2 R/currency.R | 2 R/dalex_explainers.R | 10 +-- R/dim_reduction.R | 4 - R/facebook.R | 6 - R/gemini.R | 2 R/lares.R | 2 R/mails.R | 2 R/maze.R | 6 - R/onehotencoding.R | 2 R/other_functions.R | 150 +++++++++++++++++++++++---------------------- R/robyn.R | 48 +++++++------- R/stocks.R | 10 +-- R/text_mining.R | 2 R/theme_lares.R | 18 +++-- R/tictoc.R | 4 - R/trees.R | 2 R/wordle.R | 2 R/wrangling.R | 100 +++++++++++++++++++----------- R/zzz.R | 2 man/categ_reducer.Rd | 2 man/corr_cross.Rd | 2 man/daily_stocks.Rd | 2 man/dalex_variable.Rd | 4 - man/etf_sector.Rd | 2 man/fb_accounts.Rd | 2 man/fb_ads.Rd | 2 man/fb_insights.Rd | 2 man/font_exists.Rd | 8 +- man/gemini_ask.Rd | 2 man/get_currency.Rd | 2 man/gpt_ask.Rd | 2 man/num_abbr.Rd | 14 +++- man/ohse.Rd | 2 man/reduce_pca.Rd | 2 man/reduce_tsne.Rd | 2 man/robyn_hypsbuilder.Rd | 14 ++-- man/robyn_modelselector.Rd | 4 - man/stocks_hist.Rd | 4 - man/theme_lares.Rd | 2 man/try_require.Rd | 2 man/weighted_value.Rd | 2 man/wordle.Rd | 2 47 files changed, 311 insertions(+), 258 deletions(-)
Title: Arrange 'Grobs' in Tables
Description: Tools to make it easier to work with "tables" of 'grobs'. The
'gtable' package defines a 'gtable' grob class that specifies a grid
along with a list of grobs and their placement in the grid. Further
the package makes it easy to manipulate and combine 'gtable' objects
so that complex compositions can be built up sequentially.
Author: Hadley Wickham [aut],
Thomas Lin Pedersen [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@posit.co>
Diff between gtable versions 0.3.4 dated 2023-08-21 and 0.3.5 dated 2024-04-22
DESCRIPTION | 44 +++++++++++++++-------------------- LICENSE | 2 - MD5 | 28 +++++++++++----------- NEWS.md | 2 + R/gtable.R | 2 - README.md | 44 +++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/profiling.R | 2 - inst/doc/profiling.html | 17 +++++++++---- man/figures/lifecycle-superseded.svg | 2 - man/gtable-package.Rd | 3 -- man/gtable_col.Rd | 4 +-- man/gtable_matrix.Rd | 4 +-- man/gtable_row.Rd | 4 +-- man/gtable_spacer.Rd | 4 +-- 15 files changed, 84 insertions(+), 78 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>;
Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>;
Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings
and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank mo [...truncated...]
Author: Oystein Sorensen [aut, cre] ,
Waldir Leoncio [aut],
Valeria Vitelli [aut] ,
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut],
Anja Stein [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 2.2.0 dated 2024-04-19 and 2.2.1 dated 2024-04-22
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ build/partial.rdb |binary tests/testthat/test-smc_update_correctness.R | 1 + 5 files changed, 12 insertions(+), 7 deletions(-)
Title: Import, Manipulate and Explore the Results of an 'Antares'
Simulation
Description: Import, manipulate and explore results generated by 'Antares', a
powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems
(more information about 'Antares' here : <https://antares-simulator.org/>).
Author: Tatiana Vargas [aut, cre],
Jalal-Edine ZAWAM [aut],
Frederic Breant [ctb],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Victor Perrier [ctb],
Etienne Sanchez [ctb],
Assil Mansouri [ctb],
Clement Berthet [ctb],
Kamel Kemiha [c [...truncated...]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Diff between antaresRead versions 2.6.0 dated 2023-08-30 and 2.6.1 dated 2024-04-22
antaresRead-2.6.0/antaresRead/man/aggregatate_mc_all_old.Rd |only antaresRead-2.6.1/antaresRead/DESCRIPTION | 13 - antaresRead-2.6.1/antaresRead/MD5 | 43 ++-- antaresRead-2.6.1/antaresRead/NEWS.md | 17 + antaresRead-2.6.1/antaresRead/R/API-methods.R | 21 +- antaresRead-2.6.1/antaresRead/R/aggregateResult.R | 18 - antaresRead-2.6.1/antaresRead/R/giveSize.R | 2 antaresRead-2.6.1/antaresRead/R/importOutput.R | 96 +++++++--- antaresRead-2.6.1/antaresRead/R/readAntaresClusters.R | 2 antaresRead-2.6.1/antaresRead/R/readClusterDesc.R | 50 +++-- antaresRead-2.6.1/antaresRead/R/readIniFile.R | 24 +- antaresRead-2.6.1/antaresRead/R/readInputClusters.R | 4 antaresRead-2.6.1/antaresRead/R/setSimulationPath.R | 9 antaresRead-2.6.1/antaresRead/R/utils_api.R | 32 ++- antaresRead-2.6.1/antaresRead/build/vignette.rds |binary antaresRead-2.6.1/antaresRead/inst/doc/antaresH5.Rmd | 1 antaresRead-2.6.1/antaresRead/inst/doc/antaresH5.html | 6 antaresRead-2.6.1/antaresRead/inst/doc/antaresRead.html | 4 antaresRead-2.6.1/antaresRead/man/API-methods.Rd | 23 +- antaresRead-2.6.1/antaresRead/man/aggregatate_mc_all.Rd | 6 antaresRead-2.6.1/antaresRead/tests/testthat/test-readAntares.R | 10 + antaresRead-2.6.1/antaresRead/tests/testthat/test-readClusterDesc.R | 40 +++- antaresRead-2.6.1/antaresRead/vignettes/antaresH5.Rmd | 1 23 files changed, 294 insertions(+), 128 deletions(-)
Title: Worldwide or Coordinates-Based Heat Maps
Description: Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.
Author: Luigi Annicchiarico [cre, aut]
Maintainer: Luigi Annicchiarico <luigi.annic@gmail.com>
Diff between WorldMapR versions 0.1.0 dated 2024-02-13 and 0.1.1 dated 2024-04-22
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 3 +++ NEWS.md | 7 +++++++ R/geometries_data.R | 13 ++++++++++--- R/worldplot.R | 12 ++++++++++-- R/worldplotCat.R | 27 ++++++++++++++++++++++----- man/worldplotCat.Rd | 2 +- tests/testthat/testCat2.R | 24 ++++++++++++++++++++++++ 9 files changed, 89 insertions(+), 23 deletions(-)
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.3.5 dated 2024-01-29 and 0.3.6 dated 2024-04-22
DESCRIPTION | 10 - MD5 | 60 ++++----- NEWS.md | 227 ++++++++++++++++------------------- R/bde_check_access.R | 120 +++++++++--------- R/catalogs.R | 46 ++++--- R/indicators.R | 2 R/scales.R | 15 -- R/series.R | 13 +- R/theme_tidybde.R | 4 R/utils.R | 2 README.md | 13 -- build/vignette.rds |binary inst/WORDLIST | 2 inst/doc/tidyBdE.Rmd | 9 - inst/doc/tidyBdE.html | 18 +- inst/schemaorg.json | 4 man/bde_catalog_load.Rd | 14 +- man/bde_catalog_search.Rd | 2 man/bde_catalog_update.Rd | 12 - man/bde_check_access.Rd | 2 man/bde_indicators.Rd | 2 man/bde_parse_dates.Rd | 2 man/bde_series_load.Rd | 13 +- man/figures/README-chart-1.png |binary man/figures/README-macroseries-1.png |binary man/scales_bde.Rd | 7 - man/theme_tidybde.Rd | 4 tests/testthat/test-series.R | 2 vignettes/chart-1.png |binary vignettes/macroseries-1.png |binary vignettes/tidyBdE.Rmd | 9 - 31 files changed, 314 insertions(+), 300 deletions(-)
Title: Simple Functions to Save Time and Memory
Description: Fast and memory-efficient (or 'cheap') tools to facilitate
efficient programming, saving time and memory. It aims to provide
'cheaper' alternatives to common base R functions, as well as some
additional functions.
Author: Nick Christofides [aut, cre]
Maintainer: Nick Christofides <nick.christofides.r@gmail.com>
Diff between cheapr versions 0.8.0 dated 2024-04-12 and 0.9.0 dated 2024-04-22
DESCRIPTION | 6 - MD5 | 38 ++++---- NAMESPACE | 1 NEWS.md | 8 + R/cpp11.R | 8 + R/lag.R |only R/sset.R | 14 --- README.md | 179 +++++++++++++++++++++++++++-------------- man/lag_.Rd |only src/attrs.cpp | 2 src/cheapr_cpp.h | 22 +---- src/cpp11.cpp | 16 +++ src/gcd.cpp | 2 src/lag.cpp |only src/nas.cpp | 2 src/sequences.cpp | 2 src/set_math.cpp | 58 ++++++------- src/sset.cpp | 2 src/utils.cpp | 7 + src/which.cpp | 2 tests/testthat/test-lag.R |only tests/testthat/test-set_math.R | 172 +++++++++++++++++++-------------------- 22 files changed, 302 insertions(+), 239 deletions(-)
Title: Genome Interval Arithmetic
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R, enabling
interactive analysis and visualization of genome-scale data. Riemondy
et al. (2017) <doi:10.12688/f1000research.11997.1>.
Author: Jay Hesselberth [aut] ,
Kent Riemondy [aut, cre] ,
RNA Bioscience Initiative [fnd, cph]
Maintainer: Kent Riemondy <kent.riemondy@cuanschutz.edu>
Diff between valr versions 0.8.0 dated 2024-04-04 and 0.8.1 dated 2024-04-22
DESCRIPTION | 7 ++++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ inst/doc/valr.html | 4 ++-- tests/testthat.R | 1 - 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Asymptotic Timing
Description: Computing and visualizing comparative
asymptotic timings of different algorithms and code versions.
Also includes functionality for comparing empirical timings with
expected references such as linear or quadratic,
<https://en.wikipedia.org/wiki/Asymptotic_computational_complexity>
Also includes functionality for measuring asymptotic memory and other
quantities.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between atime versions 2024.4.12 dated 2024-04-13 and 2024.4.17 dated 2024-04-22
DESCRIPTION | 6 MD5 | 78 +- NAMESPACE | 38 - NEWS | 203 +++---- R/atime.R | 475 +++++++++-------- R/predict.R | 233 ++++---- R/references.R | 355 ++++++------ R/versions.R | 745 +++++++++++++-------------- build/vignette.rds |binary inst/doc/Custom_Plots.R | 144 ++--- inst/doc/Custom_Plots.Rmd | 202 +++---- inst/doc/Custom_Plots.html | 506 +++++++++--------- inst/doc/Custom_References.R | 114 ++-- inst/doc/Custom_References.Rmd | 248 ++++----- inst/doc/Custom_References.html | 545 +++++++++---------- inst/doc/Custom_Units.R | 123 ++-- inst/doc/Custom_Units.Rmd | 270 +++++---- inst/doc/Custom_Units.html | 578 +++++++++++---------- inst/doc/cum_median.R | 62 +- inst/doc/cum_median.Rmd | 106 +-- inst/doc/cum_median.html | 406 +++++++------- inst/doc/regex.R | 128 ++-- inst/doc/regex.Rmd | 194 +++---- inst/doc/regex.html | 523 +++++++++---------- man/atime.Rd | 135 ++-- man/atime_grid.Rd | 172 +++--- man/atime_pkg.Rd | 116 ++-- man/atime_versions.Rd | 172 +++--- man/atime_versions_exprs.Rd | 174 +++--- man/atime_versions_remove.Rd | 26 man/glob_find_replace.Rd | 38 - man/references_best.Rd | 86 +-- tests/testthat.R | 2 tests/testthat/test-CRAN.R | 770 ++++++++++++++-------------- vignettes/Custom_Plots.Rmd | 202 +++---- vignettes/Custom_References.Rmd | 248 ++++----- vignettes/Custom_Units.Rmd | 270 +++++---- vignettes/binseg.html |only vignettes/compare-data.table-tidyverse.html |only vignettes/cum_median.Rmd | 106 +-- vignettes/regex.Rmd | 194 +++---- 41 files changed, 4628 insertions(+), 4365 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-16 0.3.0
2017-02-19 0.2.1
2017-01-01 0.1.1
Title: Create Native 'Excel' Charts and Work with Microsoft 'Excel'
Files
Description: An R interface to the 'OpenPyXL' 'Python' library to create
native 'Excel' charts and work with Microsoft 'Excel' files.
Author: Felix Luginbuhl [aut, cre, cph]
,
Eric Gazoni [ctb, cph] ),
Charlie Clark [ctb, cph] ),
openpyxl authors [ctb, cph] )
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between xlcharts versions 0.0.1 dated 2024-04-18 and 0.0.2 dated 2024-04-22
DESCRIPTION | 10 ++++++---- MD5 | 6 ++++-- NEWS.md |only README.md | 22 +++++++++++++++++----- man/figures/logo.png |only 5 files changed, 27 insertions(+), 11 deletions(-)
Title: Statistical Inference for Box-Cox Based Receiver Operating
Characteristic Curves
Description: Generation of Box-Cox based ROC curves and several aspects of inferences and hypothesis testing. Can be used when inferences for one biomarker (Bantis LE, Nakas CT, Reiser B. (2018)<doi:10.1002/bimj.201700107>) are of interest or when comparisons of two correlated biomarkers (Bantis LE, Nakas CT, Reiser B. (2021)<doi:10.1002/bimj.202000128>) are of interest. Provides inferences and comparisons around the AUC, the Youden index, the sensitivity at a given specificity level (and vice versa), the optimal operating point of the ROC curve (in the Youden sense), and the Youden based cutoff.
Author: Leonidas Bantis [aut],
Benjamin Brewer [cre, ctb],
Christos Nakas [ctb],
Benjamin Reiser [ctb]
Maintainer: Benjamin Brewer <tennisbenj@gmail.com>
Diff between rocbc versions 3.0.0 dated 2024-03-25 and 3.1.0 dated 2024-04-22
DESCRIPTION | 8 MD5 | 18 R/threerocs.R | 6 R/threerocs2.R |only build/vignette.rds |binary inst/doc/documentation_rocbc.R | 256 ++++++-- inst/doc/documentation_rocbc.Rmd | 278 +++++++- inst/doc/documentation_rocbc.html | 1206 +++++++++++++++++++++----------------- man/threerocs.Rd | 4 man/threerocs2.Rd |only vignettes/documentation_rocbc.Rmd | 278 +++++++- 11 files changed, 1386 insertions(+), 668 deletions(-)
Title: Adaptive Parallel Tempering for 'NIMBLE'
Description: Functions for adaptive parallel tempering (APT) with NIMBLE models. Adapted from 'Lacki' & 'Miasojedow' (2016) <DOI:10.1007/s11222-015-9579-0> and 'Miasojedow, Moulines and Vihola' (2013) <DOI:10.1080/10618600.2013.778779>.
Author: David Pleydell [aut, cre, cph] ,
Daniel Turek [cph] ,
Perry de Valpine [cph] ,
Christopher Paciorek [cph] ,
Nick Michaud [cph]
Maintainer: David Pleydell <david.pleydell@inrae.fr>
Diff between nimbleAPT versions 1.0.4 dated 2021-11-22 and 1.0.5 dated 2024-04-22
DESCRIPTION | 10 - MD5 | 20 +-- R/APT_functions.R | 52 +++++---- R/nimbleAPT-package.r | 8 - build/vignette.rds |binary inst/CITATION | 2 inst/NEWS | 7 + inst/doc/nimbleAPT-vignette.R | 2 inst/doc/nimbleAPT-vignette.html | 203 ++++++++++++++++++++------------------- man/buildAPT.Rd | 7 + man/nimbleAPT.Rd | 2 11 files changed, 173 insertions(+), 140 deletions(-)
Title: Evidential Regression
Description: An implementation of the 'Evidential Neural Network for Regression' model recently introduced in Denoeux (2023) <doi:10.1109/TFUZZ.2023.3268200>. In this model, prediction uncertainty is quantified by Gaussian random fuzzy numbers as introduced in Denoeux (2023) <doi:10.1016/j.fss.2022.06.004>. The package contains functions for training the network, tuning hyperparameters by cross-validation or the hold-out method, and making predictions. It also contains utilities for making calculations with Gaussian random fuzzy numbers (such as, e.g., computing the degrees of belief and plausibility of an interval, or combining Gaussian random fuzzy numbers).
Author: Thierry Denoeux [aut, cre]
Maintainer: Thierry Denoeux <tdenoeux@utc.fr>
Diff between evreg versions 1.0.3 dated 2023-11-09 and 1.0.4 dated 2024-04-22
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NEWS | 7 +++++++ R/ENNreg.R | 9 +++------ R/ENNreg_cv.R | 2 +- R/ENNreg_holdout.R | 2 +- R/ENNreg_init.R | 2 +- R/combination_GRFN.R | 2 +- R/evreg.R | 4 ++-- inst/doc/Introduction.R | 14 +++++++------- inst/doc/Introduction.html | 37 +++++++++++++++++++------------------ man/ENNreg.Rd | 2 +- man/ENNreg_cv.Rd | 2 +- man/ENNreg_holdout.Rd | 2 +- man/combination_GRFN.Rd | 2 +- man/evreg.Rd | 5 +++-- vignettes/tdenoeux.bib | 7 ++++--- 17 files changed, 74 insertions(+), 67 deletions(-)
Title: Feature Stores for the 'diseasy' Framework
Description: Simple feature stores and tools for creating personalised feature stores.
'diseasystore' powers feature stores which can automatically link and aggregate features to a given stratification
level. These feature stores are automatically time-versioned (powered by the 'SCDB' package) and allows you to easily
and dynamically compute features as part of your continuous integration.
Author: Rasmus Skytte Randloev [aut, cre]
,
Marcus Munch Gruenewald [ctb] ,
Kaare Graesboell [rev] ,
Kasper Schou Telkamp [rev] ,
Lasse Engbo Christiansen [rev]
,
Sofia Myrup Otero [rev],
Statens Serum Institut, SSI [cph, fnd]
Maintainer: Rasmus Skytte Randloev <rske@ssi.dk>
Diff between diseasystore versions 0.2.0 dated 2024-03-20 and 0.2.1 dated 2024-04-22
DESCRIPTION | 12 MD5 | 38 NAMESPACE | 1 NEWS.md | 4 R/0_locks.R | 8 R/DiseasystoreBase.R | 96 - R/drop_diseasystore.R | 169 --- R/test_diseasystore.R | 978 +++++++++----------- R/truncate_interlace.R | 7 README.md | 2 build/vignette.rds |binary inst/doc/diseasystore-ecdc-respiratory-viruses.Rmd | 5 inst/doc/diseasystore-ecdc-respiratory-viruses.html | 9 inst/doc/diseasystore-google-covid-19.html | 4 inst/doc/diseasystore.html | 81 + tests/testthat/helper-setup.R | 10 tests/testthat/test-0_linters.R | 8 tests/testthat/test-DiseasystoreBase.R | 525 +++++----- tests/testthat/test-drop_diseasystore.R | 79 - vignettes/diseasystore-ecdc-respiratory-viruses.Rmd | 5 20 files changed, 944 insertions(+), 1097 deletions(-)
More information about ConfidenceEllipse at CRAN
Permanent link
Title: Sparse-Group Boosting
Description: Sparse-group boosting to be used in conjunction with the 'mboost' for modeling grouped data.
Applicable to all sparse-group lasso type problems where within-group and between-group sparsity is desired.
Interprets and visualizes individual variables and groups.
Author: Fabian Obster [aut, cre, cph]
Maintainer: Fabian Obster <fabian.obster@unibw.de>
Diff between sgboost versions 0.1.0 dated 2024-04-11 and 0.1.2 dated 2024-04-22
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 2 inst/doc/sgboost.R | 3 inst/doc/sgboost.Rmd | 39 ++--- inst/doc/sgboost.html | 302 ++++++++++++++++++++--------------------- tests/testthat/test-get_coef.R | 12 - vignettes/sgboost.Rmd | 39 ++--- 8 files changed, 213 insertions(+), 204 deletions(-)
Title: The Rainfall-Runoff Erosivity Factor
Description: Determination of rainfall-runoff erosivity factor.
Author: Dione Pereira Cardoso [aut, cre], Edilson Marcelino Silva [aut], Paulo Cesar Ossani [aut], Marx Leandro Naves Silva [ctb],
Joel Augusto Muniz [ctb], Daniel Furtado Ferreira [ctb], Junior Cesar Avanzi [ctb]
Maintainer: Dione Pereira Cardoso <cardoso.dione@gmail.com>
Diff between RainfallErosivityFactor versions 0.1.0 dated 2018-11-18 and 1.0.0 dated 2024-04-22
DESCRIPTION | 8 - MD5 | 6 R/RainfallErosivityFactor.R | 291 ++++++++++++++++++++++------------------- man/RainfallErosivityFactor.Rd | 7 4 files changed, 168 insertions(+), 144 deletions(-)
More information about RainfallErosivityFactor at CRAN
Permanent link
Title: Power and Sample Size Calculation for Non-Proportional Hazards
and Beyond
Description: Performs power and sample size calculation for non-proportional hazards model using the Fleming-Harrington family of weighted log-rank tests. The sequentially calculated log-rank test score statistics are assumed to have independent increments as characterized in Anastasios A. Tsiatis (1982) <doi:10.1080/01621459.1982.10477898>. The mean and variance of log-rank test score statistics are calculated based on Kaifeng Lu (2021) <doi:10.1002/pst.2069>. The boundary crossing probabilities are calculated using the recursive integration algorithm described in Christopher Jennison and Bruce W. Turnbull (2000, ISBN:0849303168). The package can also be used for continuous, binary, and count data. For continuous data, it can handle missing data through mixed-model for repeated measures (MMRM). In crossover designs, it can estimate direct treatment effects while accounting for carryover effects. For binary data, it can design Simon's 2-stage, modified toxicity probability-2 (mTPI-2), a [...truncated...]
Author: Kaifeng Lu
Maintainer: Kaifeng Lu <kaifenglu@gmail.com>
Diff between lrstat versions 0.2.4 dated 2024-03-19 and 0.2.5 dated 2024-04-22
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Title: Effective Reproduction Number Estimation
Description: Estimate the effective reproduction number from wastewater
and clinical data sources.
Author: David Champredon [aut, cre] ,
Warsame Yusuf [aut] ,
Irena Papst [aut]
Maintainer: David Champredon <david.champredon@canada.ca>
Diff between ern versions 1.3.1 dated 2024-01-29 and 2.0.0 dated 2024-04-22
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Title: Elegant Tools for Processing and Visualization of Lipidomics
Data
Description: An elegant tool for processing and visualizing lipidomics data generated by mass spectrometry. 'LipidomicsR' simplifies channel and replicate handling while providing thorough lipid species annotation. Its visualization capabilities encompass principal components analysis plots, heatmaps, volcano plots, and radar plots, enabling concise data summarization and quality assessment. Additionally, it can generate bar plots and line plots to visualize the abundance of each lipid species.
Author: Mingshi Li [aut, com],
Hengyu Zhu [aut, cre]
Maintainer: Hengyu Zhu <hengyu.21@intl.zju.edu.cn>
Diff between LipidomicsR versions 0.1.6 dated 2024-03-16 and 0.3.6 dated 2024-04-22
LipidomicsR-0.1.6/LipidomicsR/R/lineplot.R |only LipidomicsR-0.1.6/LipidomicsR/man/cleanXpert.Rd |only LipidomicsR-0.1.6/LipidomicsR/man/paramWizard.Rd |only LipidomicsR-0.3.6/LipidomicsR/DESCRIPTION | 16 LipidomicsR-0.3.6/LipidomicsR/LICENSE | 4 LipidomicsR-0.3.6/LipidomicsR/MD5 | 70 LipidomicsR-0.3.6/LipidomicsR/NAMESPACE | 128 - LipidomicsR-0.3.6/LipidomicsR/R/abundance.R | 187 ++ LipidomicsR-0.3.6/LipidomicsR/R/channel_cleaner.R |only LipidomicsR-0.3.6/LipidomicsR/R/data_cleaner.R | 732 +++------- LipidomicsR-0.3.6/LipidomicsR/R/delRep.R | 123 + LipidomicsR-0.3.6/LipidomicsR/R/extract.R | 160 +- LipidomicsR-0.3.6/LipidomicsR/R/heatmap.R | 69 LipidomicsR-0.3.6/LipidomicsR/R/importer_group.R |only LipidomicsR-0.3.6/LipidomicsR/R/qc.R | 583 +++---- LipidomicsR-0.3.6/LipidomicsR/R/rsd_del.R |only LipidomicsR-0.3.6/LipidomicsR/R/volcano_master.R | 45 LipidomicsR-0.3.6/LipidomicsR/README.md |only LipidomicsR-0.3.6/LipidomicsR/data |only LipidomicsR-0.3.6/LipidomicsR/man/QCplot.Rd | 10 LipidomicsR-0.3.6/LipidomicsR/man/absolute.calculator.Rd | 4 LipidomicsR-0.3.6/LipidomicsR/man/abundance.lineplot.Rd | 28 LipidomicsR-0.3.6/LipidomicsR/man/abundance.signif.Rd | 3 LipidomicsR-0.3.6/LipidomicsR/man/abundance.summary.Rd | 3 LipidomicsR-0.3.6/LipidomicsR/man/channel.delete.Rd | 13 LipidomicsR-0.3.6/LipidomicsR/man/delRep.Rd | 13 LipidomicsR-0.3.6/LipidomicsR/man/groupXpert.Rd |only LipidomicsR-0.3.6/LipidomicsR/man/heatmap.Rd | 18 LipidomicsR-0.3.6/LipidomicsR/man/importer.Rd | 4 LipidomicsR-0.3.6/LipidomicsR/man/lEa.Rd | 9 LipidomicsR-0.3.6/LipidomicsR/man/lEr.Rd | 2 LipidomicsR-0.3.6/LipidomicsR/man/nor.absolute.Rd | 6 LipidomicsR-0.3.6/LipidomicsR/man/nor.relative.Rd | 6 LipidomicsR-0.3.6/LipidomicsR/man/noridx.Rd | 17 LipidomicsR-0.3.6/LipidomicsR/man/normalization_calculator.Rd | 57 LipidomicsR-0.3.6/LipidomicsR/man/percent.calculator.Rd | 12 LipidomicsR-0.3.6/LipidomicsR/man/relative_calculator.Rd | 4 LipidomicsR-0.3.6/LipidomicsR/man/rsd_calculator.Rd |only LipidomicsR-0.3.6/LipidomicsR/man/sepclass.Rd | 7 LipidomicsR-0.3.6/LipidomicsR/man/toGroup.calculator.Rd |only LipidomicsR-0.3.6/LipidomicsR/man/total.abundance.Rd |only LipidomicsR-0.3.6/LipidomicsR/man/volcano.Rd | 9 42 files changed, 1215 insertions(+), 1127 deletions(-)
Title: Core Tools for Packages in the 'fable' Framework
Description: Provides tools, helpers and data structures for
developing models and time series functions for 'fable' and extension
packages. These tools support a consistent and tidy interface for time
series modelling and analysis.
Author: Mitchell O'Hara-Wild [aut, cre]
,
Rob Hyndman [aut],
Earo Wang [aut] ,
Di Cook [ctb],
George Athanasopoulos [ctb],
David Holt [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between fabletools versions 0.4.1 dated 2024-03-02 and 0.4.2 dated 2024-04-22
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- NEWS.md | 4 ++++ R/plot.R | 2 +- build/fabletools.pdf |binary build/stage23.rdb |only build/vignette.rds |binary inst/WORDLIST | 1 + inst/doc/extension_models.html | 18 +++++++++--------- 9 files changed, 26 insertions(+), 20 deletions(-)
Title: Download and Tidy IPC and CH Data
Description: Utilities to access Integrated Food Security Phase Classification
(IPC) and Cadre Harmonisé (CH) food security data. Wrapper functions are
available for all of the 'IPC-CH' Public API (<https://docs.api.ipcinfo.org>)
simplified and advanced endpoints to easily download the data in a clean and
tidy format.
Author: Seth Caldwell [aut, cre, cph]
Maintainer: Seth Caldwell <caldwellst@gmail.com>
Diff between ripc versions 0.2.1 dated 2024-03-15 and 0.3.0 dated 2024-04-22
ripc-0.2.1/ripc/R/ripc-package.R |only ripc-0.2.1/ripc/R/utils-imports.R |only ripc-0.3.0/ripc/DESCRIPTION | 10 ripc-0.3.0/ripc/MD5 | 46 ++- ripc-0.3.0/ripc/NAMESPACE | 2 ripc-0.3.0/ripc/NEWS.md | 12 ripc-0.3.0/ripc/R/Ripc-package.R |only ripc-0.3.0/ripc/R/create_areas_df.R |only ripc-0.3.0/ripc/R/create_base_df.R |only ripc-0.3.0/ripc/R/create_groups_df.R |only ripc-0.3.0/ripc/R/ipc_get.R | 81 ++---- ripc-0.3.0/ripc/R/ipc_get_analyses.R | 30 +- ripc-0.3.0/ripc/R/ipc_get_areas.R | 113 +++------ ripc-0.3.0/ripc/R/ipc_get_country.R | 54 ---- ripc-0.3.0/ripc/R/ipc_get_icons.R | 7 ripc-0.3.0/ripc/R/ipc_get_points.R | 50 ---- ripc-0.3.0/ripc/R/ipc_get_population.R | 281 +---------------------- ripc-0.3.0/ripc/R/null_converter.R |only ripc-0.3.0/ripc/R/population_utils.R |only ripc-0.3.0/ripc/README.md | 47 ++- ripc-0.3.0/ripc/build/vignette.rds |binary ripc-0.3.0/ripc/inst/WORDLIST |only ripc-0.3.0/ripc/man/figures/README-geojson-1.png |only ripc-0.3.0/ripc/man/ipc_get.Rd | 10 ripc-0.3.0/ripc/man/ipc_get_analyses.Rd | 3 ripc-0.3.0/ripc/man/ipc_get_areas.Rd | 16 - ripc-0.3.0/ripc/man/ipc_get_country.Rd | 4 ripc-0.3.0/ripc/man/ipc_get_points.Rd | 5 ripc-0.3.0/ripc/man/ipc_get_population.Rd | 3 29 files changed, 217 insertions(+), 557 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]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.2-7 dated 2024-02-26 and 1.2-9 dated 2024-04-22
DESCRIPTION | 6 MD5 | 28 - NEWS.md | 7 R/memoiR.R | 190 +++++----- build/vignette.rds |binary inst/doc/memoiR.Rmd | 2 inst/doc/memoiR.html | 2 inst/rmarkdown/templates/memoir/skeleton/82-syntax.Rmd | 8 inst/rmarkdown/templates/simple_article/skeleton/skeleton.Rmd | 10 inst/rmarkdown/templates/stylish_article/skeleton/skeleton.Rmd | 10 man/build_ghworkflow.Rd | 2 man/build_githubpages.Rd | 10 man/build_gitignore.Rd | 2 man/build_readme.Rd | 2 vignettes/memoiR.Rmd | 2 15 files changed, 146 insertions(+), 135 deletions(-)
Title: Automated Retrieval of ACLED Conflict Event Data
Description: Access and manage the application programming interface (API) of the Armed Conflict Location & Event Data Project (ACLED) at <https://acleddata.com/>. The package makes it easy to retrieve a user-defined sample (or all of the available data) of ACLED, enabling a seamless integration of regular data updates into the research work flow. It requires a minimal number of dependencies. See the package's README file for a note on replicability when drawing on ACLED data. When using this package, you acknowledge that you have read ACLED's terms and conditions of use, and that you agree with their attribution requirements.
Author: Christoph Dworschak [aut, cre]
,
Rob Williams [ctb]
Maintainer: Christoph Dworschak <dworschak@posteo.de>
Diff between acled.api versions 1.1.7 dated 2024-01-10 and 1.1.8 dated 2024-04-22
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- NEWS.md | 11 ++++++ R/acled.api.R | 75 ++++++++++++++++++++++++++---------------- R/acled.api.internal.R | 8 +--- R/supp.fun.R | 6 +-- README.md | 77 ++++++++++++++++++++++++++++---------------- man/acled.api.Rd | 31 +++++++++++------ tests/testthat/test-acled.R | 5 +- 9 files changed, 146 insertions(+), 91 deletions(-)
Title: Functions Used for SAiVE Group Research, Collaborations, and
Publications
Description: Holds functions developed by the University of Ottawa's SAiVE
(Spatio-temporal Analysis of isotope Variations in the Environment)
research group with the intention of facilitating the re-use of code,
foster good code writing practices, and to allow others to benefit
from the work done by the SAiVE group. Contributions are welcome via
the 'GitHub' repository <https://github.com/UO-SAiVE/SAiVE> by group members as well as non-members.
Author: Ghislain de Laplante [aut, cre, cph]
Maintainer: Ghislain de Laplante <ghislain.delaplante@yukon.ca>
Diff between SAiVE versions 1.0.4 dated 2024-02-07 and 1.0.5 dated 2024-04-22
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 15 + R/createStreams.R | 16 - R/drainageBasins.R | 64 +++---- R/hydroProcess.R | 20 +- R/modelMatch.R | 6 R/spatPredict.R | 309 ++++++++++++++++++++++++----------- R/thinFeatures.R | 16 - R/wbtCheck.R | 2 man/spatPredict.Rd | 48 +++-- tests/testthat/test-createStreams.R | 2 tests/testthat/test-drainageBasins.R | 2 tests/testthat/test-hydroProcess.R | 2 14 files changed, 346 insertions(+), 188 deletions(-)
Title: Robust Rank Correlation Coefficient and Test
Description: Provides the robust gamma rank correlation coefficient as introduced by
Bodenhofer, Krone, and Klawonn (2013) <DOI:10.1016/j.ins.2012.11.026>
along with a permutation-based rank correlation test.
The rank correlation coefficient and the test are explicitly
designed for dealing with noisy numerical data.
Author: Martin Krone [aut], Ulrich Bodenhofer [aut,cre]
Maintainer: Ulrich Bodenhofer <ulrich@bodenhofer.com>
Diff between rococo versions 1.1.7 dated 2018-10-12 and 1.1.8 dated 2024-04-22
rococo-1.1.7/rococo/vignettes/JKU_EN_noName.pdf |only rococo-1.1.7/rococo/vignettes/bioinf-article.txi |only rococo-1.1.7/rococo/vignettes/bioinf-bar.png |only rococo-1.1.7/rococo/vignettes/bioinf.cls |only rococo-1.1.8/rococo/DESCRIPTION | 15 ++-- rococo-1.1.8/rococo/MD5 | 21 ++---- rococo-1.1.8/rococo/README.md | 31 ++++++--- rococo-1.1.8/rococo/build/vignette.rds |binary rococo-1.1.8/rococo/inst/CITATION | 14 ++-- rococo-1.1.8/rococo/inst/NEWS | 7 +- rococo-1.1.8/rococo/inst/doc/rococo.Rnw | 78 ++--------------------- rococo-1.1.8/rococo/inst/doc/rococo.pdf |binary rococo-1.1.8/rococo/vignettes/rococo.Rnw | 78 ++--------------------- rococo-1.1.8/rococo/vignettes/ubmanual.cls |only 14 files changed, 71 insertions(+), 173 deletions(-)
Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API <https://gwas-api.mrcieu.ac.uk/>. Includes a wrapper
to make generic calls to the API, plus convenience functions for
specific queries.
Author: Gibran Hemani [aut, cre, cph] ,
Ben Elsworth [aut] ,
Tom Palmer [aut] ,
Rita Rasteiro [aut]
Maintainer: Gibran Hemani <g.hemani@bristol.ac.uk>
Diff between ieugwasr versions 0.2.2 dated 2024-03-28 and 1.0.0 dated 2024-04-22
ieugwasr-0.2.2/ieugwasr/R/utils-pipe.R |only ieugwasr-0.2.2/ieugwasr/inst/doc/timings.R |only ieugwasr-0.2.2/ieugwasr/inst/doc/timings.Rmd |only ieugwasr-0.2.2/ieugwasr/inst/doc/timings.html |only ieugwasr-0.2.2/ieugwasr/man/dot-data.Rd |only ieugwasr-0.2.2/ieugwasr/man/get_access_token.Rd |only ieugwasr-0.2.2/ieugwasr/man/pipe.Rd |only ieugwasr-0.2.2/ieugwasr/man/revoke_access_token.Rd |only ieugwasr-0.2.2/ieugwasr/vignettes/timings.Rmd |only ieugwasr-1.0.0/ieugwasr/DESCRIPTION | 10 ieugwasr-1.0.0/ieugwasr/MD5 | 94 ++++----- ieugwasr-1.0.0/ieugwasr/NAMESPACE | 7 ieugwasr-1.0.0/ieugwasr/NEWS.md | 10 ieugwasr-1.0.0/ieugwasr/R/afl2.r | 47 +--- ieugwasr-1.0.0/ieugwasr/R/api.R | 82 +++---- ieugwasr-1.0.0/ieugwasr/R/globals.R |only ieugwasr-1.0.0/ieugwasr/R/ld_clump.R | 23 -- ieugwasr-1.0.0/ieugwasr/R/ld_matrix.R | 9 ieugwasr-1.0.0/ieugwasr/R/query.R | 120 ++++------- ieugwasr-1.0.0/ieugwasr/R/variants.R | 20 + ieugwasr-1.0.0/ieugwasr/R/zzz.R | 21 -- ieugwasr-1.0.0/ieugwasr/README.md | 19 + ieugwasr-1.0.0/ieugwasr/build/vignette.rds |binary ieugwasr-1.0.0/ieugwasr/inst/doc/guide.Rmd | 37 +-- ieugwasr-1.0.0/ieugwasr/inst/doc/guide.html | 176 +++++++++-------- ieugwasr-1.0.0/ieugwasr/man/afl2_chrpos.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/afl2_list.Rd | 7 ieugwasr-1.0.0/ieugwasr/man/afl2_rsid.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/api_query.Rd | 6 ieugwasr-1.0.0/ieugwasr/man/associations.Rd | 7 ieugwasr-1.0.0/ieugwasr/man/batches.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/check_access_token.Rd | 5 ieugwasr-1.0.0/ieugwasr/man/editcheck.Rd | 7 ieugwasr-1.0.0/ieugwasr/man/fill_n.Rd | 12 - ieugwasr-1.0.0/ieugwasr/man/get_opengwas_jwt.Rd |only ieugwasr-1.0.0/ieugwasr/man/gwasinfo.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/infer_ancestry.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/ld_clump.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/ld_clump_api.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/ld_matrix.Rd | 3 ieugwasr-1.0.0/ieugwasr/man/ld_reflookup.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/phewas.Rd | 12 - ieugwasr-1.0.0/ieugwasr/man/tophits.Rd | 9 ieugwasr-1.0.0/ieugwasr/man/user.Rd |only ieugwasr-1.0.0/ieugwasr/man/variants_chrpos.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/variants_gene.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/variants_rsid.Rd | 4 ieugwasr-1.0.0/ieugwasr/man/variants_to_rsid.Rd | 4 ieugwasr-1.0.0/ieugwasr/tests/testthat/test_afl2.r | 2 ieugwasr-1.0.0/ieugwasr/tests/testthat/test_api.r | 4 ieugwasr-1.0.0/ieugwasr/tests/testthat/test_ld.r | 4 ieugwasr-1.0.0/ieugwasr/tests/testthat/test_query.r | 32 ++- ieugwasr-1.0.0/ieugwasr/tests/testthat/test_variants.r | 2 ieugwasr-1.0.0/ieugwasr/vignettes/guide.Rmd | 37 +-- 54 files changed, 422 insertions(+), 450 deletions(-)
Title: Color Science Methods and Data
Description: Methods and data for color science - color conversions by observer,
illuminant, and gamma. Color matching functions and chromaticity diagrams.
Color indices, color differences, and spectral data conversion/analysis.
This package is deprecated and will someday be removed; for reasons and details please see the README file.
Author: Jose Gama [aut],
Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between colorscience versions 1.0.8 dated 2019-10-29 and 1.0.9 dated 2024-04-22
DESCRIPTION | 10 +- MD5 | 80 +++++++++++------------ NEWS.md | 8 ++ README.md | 2 man/CIE1931XYZ2CIE1931xyz.Rd | 4 - man/CIE1931XYZ2CIE1960uv.Rd | 4 - man/CIE1931XYZ2CIE1976uv.Rd | 4 - man/CIE1931xy2CIE1960uv.Rd | 4 - man/CIE1931xy2CIE1976uv.Rd | 4 - man/CIE1960UCS2CIE1964.Rd | 4 - man/CIE1960UCS2xy.Rd | 4 - man/CIELabtoDIN99.Rd | 4 - man/DIN99toCIELab.Rd | 4 - man/Hue.2.RGB.Rd | 4 - man/MaxChromaFromExtrapRenotationData.Rd | 4 - man/MaxChromasForStandardMunsellHuesAndValues.Rd | 4 - man/MunsellHues.Rd | 4 - man/MunsellNeutrals2sRGB.Rd | 4 - man/MunsellSpectral.Rd | 4 - man/PhotoYCC2RGB.Rd | 4 - man/RGB2PhotoYCC.Rd | 4 - man/RGB2YCbCr.Rd | 4 - man/RGB2YIQ.Rd | 4 - man/RGB2YPbPr.Rd | 4 - man/TCSdata.Rd | 4 - man/YCbCr2RGB.Rd | 4 - man/YIQ2RGB.Rd | 4 - man/YPbPr2RGB.Rd | 4 - man/compuphaseDifferenceRGB.Rd | 4 - man/createIsoTempLinesTable.Rd | 4 - man/footcandle2candela.steradian.sqmeter.Rd | 4 - man/footcandle2lux.Rd | 4 - man/footcandle2watt.sqcentimeter.Rd | 4 - man/huedegreemunsell.Rd | 4 - man/kelvin2xy.Rd | 4 - man/spectra2CCT.Rd | 4 - man/spectra2CRIGAIFSCI.Rd | 4 - man/spectra2lux.Rd | 4 - man/whitepointsRGB.Rd | 4 - man/whitepointsilluminants.Rd | 4 - man/xy2CCT.HernandezAndres.Rd | 4 - 41 files changed, 127 insertions(+), 121 deletions(-)
Title: An Implementation of the Bayesian Markov (Renewal) Mixed Models
Description: The Bayesian Markov renewal mixed models take sequentially observed categorical data with continuous duration times, being either state duration or inter-state duration. These models comprehensively analyze the stochastic dynamics of both state transitions and duration times under the influence of multiple exogenous factors and random individual effect. The default setting flexibly models the transition probabilities using Dirichlet mixtures and the duration times using gamma mixtures. It also provides the flexibility of modeling the categorical sequences using Bayesian Markov mixed models alone, either ignoring the duration times altogether or dividing duration time into multiples of an additional category in the sequence by a user-specific unit. The package allows extensive inference of the state transition probabilities and the duration times as well as relevant plots and graphs. It also includes a synthetic data set to demonstrate the desired format of input data set and the utilit [...truncated...]
Author: Yutong Wu [aut, cre],
Abhra Sarkar [aut]
Maintainer: Yutong Wu <yutong.wu@utexas.edu>
Diff between BMRMM versions 1.0.0 dated 2023-06-19 and 1.0.1 dated 2024-04-22
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/BMRMM.R | 12 +++++++----- R/model_cont_isi.R | 7 +++++-- R/model_transition.R | 6 +++++- R/print_and_plot_results.R | 12 ++++++------ R/print_and_plot_results_fn.R | 7 +++++-- man/BMRMM.Rd | 12 +++++++----- man/summary.BMRMM.Rd | 12 ++++++------ 9 files changed, 52 insertions(+), 38 deletions(-)
Title: Multiple-Scaled Clustering
Description: Model based clustering using
the multivariate multiple Scaled t (MST) and multivariate multiple
scaled contaminated normal (MSCN) distributions. The MST is an
extension of the multivariate Student-t distribution to include
flexible tail behaviors, Forbes, F. & Wraith, D. (2014) <doi:10.1007/s11222-013-9414-4>. The MSCN represents a heavy-tailed
generalization of the multivariate normal (MN) distribution to
model elliptical contoured scatters in the presence of mild outliers
(also referred to as "bad" points) and automatically detect bad points, Punzo, A. & Tortora, C. (2021) <doi:10.1177/1471082X19890935>.
Author: Cristina Tortora [aut, cre, cph]
,
Antonio Punzo [aut] ,
Louis Tran [aut]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MSclust versions 1.0.3 dated 2023-05-04 and 1.0.4 dated 2024-04-21
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PLRfactorization.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Author: Michael Hahsler [aut, cre, cph]
,
Margaret H. Dunham [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.2.0 dated 2022-06-25 and 1.2.1 dated 2024-04-21
rEMM-1.2.0/rEMM/src |only rEMM-1.2.1/rEMM/DESCRIPTION | 14 ++--- rEMM-1.2.1/rEMM/MD5 | 33 +++++------ rEMM-1.2.1/rEMM/NAMESPACE | 2 rEMM-1.2.1/rEMM/NEWS.md | 5 + rEMM-1.2.1/rEMM/R/SimpleMC.R | 5 - rEMM-1.2.1/rEMM/README.md | 50 +++++++++++++----- rEMM-1.2.1/rEMM/build/partial.rdb |binary rEMM-1.2.1/rEMM/build/vignette.rds |binary rEMM-1.2.1/rEMM/data/16S.rda |binary rEMM-1.2.1/rEMM/data/Derwent.rda |binary rEMM-1.2.1/rEMM/data/EMMTraffic.rda |binary rEMM-1.2.1/rEMM/data/EMMsim.rda |binary rEMM-1.2.1/rEMM/inst/CITATION | 39 +++++++------- rEMM-1.2.1/rEMM/inst/README_files/example_model-1.png |binary rEMM-1.2.1/rEMM/inst/doc/rEMM.pdf |binary rEMM-1.2.1/rEMM/man/plot.EMM.Rd | 6 +- 17 files changed, 88 insertions(+), 66 deletions(-)
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph]
,
Matthew Bolanos [ctb],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 2.0-1 dated 2023-02-28 and 2.0-2 dated 2024-04-21
DESCRIPTION | 14 +- MD5 | 164 ++++++++++++++++----------------- NAMESPACE | 5 + NEWS.md | 14 ++ R/AAA_stream-package.R | 17 ++- R/DSC_BIRCH.R | 2 R/DSC_DBSTREAM.R | 19 +++ R/DSC_DStream.R | 9 + R/DSC_R.R | 1 R/DSC_TwoStage.R | 4 R/DSF_Convolve.R | 2 R/DSF_FeaturesSelection.R |only R/DSF_Scale.R | 3 R/DST_Runner.R | 3 R/get_assignment.R | 6 + R/recluster.R | 1 README.md | 188 ++++---------------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/extending_stream.pdf |binary inst/doc/stream.Rnw | 2 inst/doc/stream.pdf |binary man/DSAggregate.Rd | 4 man/DSAggregate_Sample.Rd | 4 man/DSAggregate_Window.Rd | 4 man/DSC.Rd | 2 man/DSC_BIRCH.Rd | 2 man/DSC_DBSTREAM.Rd | 15 ++- man/DSC_DStream.Rd | 3 man/DSC_Macro.Rd | 2 man/DSC_Micro.Rd | 2 man/DSC_R.Rd | 2 man/DSC_SlidingWindow.Rd | 2 man/DSC_Static.Rd | 2 man/DSC_TwoStage.Rd | 2 man/DSClassifier.Rd | 2 man/DSD_BarsAndGaussians.Rd | 2 man/DSD_Benchmark.Rd | 2 man/DSD_Cubes.Rd | 2 man/DSD_Gaussians.Rd | 2 man/DSD_MG.Rd | 2 man/DSD_Memory.Rd | 2 man/DSD_Mixture.Rd | 2 man/DSD_NULL.Rd | 2 man/DSD_ReadDB.Rd | 2 man/DSD_ReadStream.Rd | 2 man/DSD_ScaleStream.Rd | 3 man/DSD_Target.Rd | 2 man/DSD_UniformNoise.Rd | 2 man/DSD_mlbenchData.Rd | 2 man/DSD_mlbenchGenerator.Rd | 2 man/DSF.Rd | 3 man/DSF_Convolve.Rd | 7 - man/DSF_Downsample.Rd | 5 - man/DSF_ExponentialMA.Rd | 5 - man/DSF_FeatureSelection.Rd |only man/DSF_Func.Rd | 5 - man/DSF_Scale.Rd | 5 - man/DSF_dplyr.Rd | 7 - man/DSOutlier.Rd | 4 man/DSRegressor.Rd | 4 man/DST.Rd | 2 man/DST_SlidingWindow.Rd | 4 man/DST_WriteStream.Rd | 4 man/animate_cluster.Rd | 6 - man/animate_data.Rd | 2 man/close_stream.Rd | 2 man/evaluate.DSC.Rd | 2 man/evaluate.Rd | 4 man/get_assignment.Rd | 2 man/get_points.Rd | 2 man/plot.DSC.Rd | 2 man/plot.DSD.Rd | 2 man/predict.Rd | 6 - man/prune_clusters.Rd | 2 man/read_saveDSC.Rd | 2 man/recluster.Rd | 2 man/reset_stream.Rd | 2 man/stream-package.Rd | 39 +++++++ man/stream_pipeline.Rd | 4 man/update.Rd | 4 tests/testthat/test-DSC_formula.R | 13 ++ tests/testthat/test-DSF.R | 20 ++++ vignettes/stream.Rnw | 2 84 files changed, 356 insertions(+), 352 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and
to carry out supervised dimensionality reduction. An implementation of
the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370>
is also provided. This is a complete re-implementation in R (and C++,
via the 'Rcpp' package): no Python installation is required. See the
uwot website (<https://github.com/jlmelville/uwot>) for more
documentation and examples.
Author: James Melville [aut, cre, cph],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb],
Dirk Eddelbuettel [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.2.1 dated 2024-04-15 and 0.2.2 dated 2024-04-21
DESCRIPTION | 10 ++++---- MD5 | 36 ++++++++++++++--------------- NEWS.md | 17 +++++++++++++- R/init.R | 40 ++++++++++++++++++++++++++++----- R/rspectra_init.R | 12 +++++++++ R/uwot.R | 2 + inst/doc/uwot.R | 1 inst/doc/uwot.Rmd | 1 inst/doc/uwot.html | 5 ++-- man/load_uwot.Rd | 2 + tests/testthat/test_errors.R | 1 tests/testthat/test_neighbors.R | 1 tests/testthat/test_normlaplacian.R | 16 ++++++++----- tests/testthat/test_output.R | 18 +++++++++----- tests/testthat/test_saveload.R | 1 tests/testthat/test_similarity_graph.R | 1 tests/testthat/test_spectral.R | 1 tests/testthat/test_transform.R | 1 vignettes/uwot.Rmd | 1 19 files changed, 123 insertions(+), 44 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 2.1.1 dated 2023-09-25 and 2.1.2 dated 2024-04-21
DESCRIPTION | 6 ++--- MD5 | 26 +++++++++++------------ NEWS | 3 ++ R/rsa.R | 11 ++++++--- build/vignette.rds |binary configure | 9 ++++++-- inst/doc/bignum.html | 32 ++++++++++++++-------------- inst/doc/crypto_hashing.R | 2 - inst/doc/crypto_hashing.html | 8 +++---- inst/doc/keys.html | 48 +++++++++++++++++++++---------------------- inst/doc/secure_rng.R | 2 - inst/doc/secure_rng.html | 18 ++++++++-------- man/rsa_encrypt.Rd | 6 +++-- src/rsa.c | 10 +++++--- 14 files changed, 98 insertions(+), 83 deletions(-)
Title: Spatial and Spatio-Temporal Models using 'INLA'
Description: Prepare objects to implement models over spatial and
spacetime domains with the 'INLA' package (<https://www.r-inla.org>).
These objects contain data to for the 'cgeneric' interface in
'INLA', enabling fast parallel computations.
We implemented the spatial barrier model, see Bakka et. al. (2019)
<doi:10.1016/j.spasta.2019.01.002>, and some of the spatio-temporal
models in Lindgren et. al. (2023) <doi:10.48550/arXiv.2006.04917>.
Details are provided in the available vignettes and from the URL bellow.
Author: Elias Teixeira Krainski [cre, aut, cph]
,
Finn Lindgren [aut] ,
Haavard Rue [aut]
Maintainer: Elias Teixeira Krainski <eliaskrainski@gmail.com>
Diff between INLAspacetime versions 0.1.7 dated 2023-08-27 and 0.1.8 dated 2024-04-21
DESCRIPTION | 18 ++--- MD5 | 85 ++++++++++++++------------- NAMESPACE | 5 + R/INLAspacetime.R | 12 +-- R/ar2cor.R | 17 ++++- R/ar2precision.R | 5 - R/barrierModel.define.R | 13 ++-- R/ghcndUtils.R | 55 ++++++++++++++---- R/mesh.dual.R | 41 +++++++++---- R/mesh2d.R | 6 + R/mesh2fem.R | 51 +++++++++++++--- R/mesh2projector.R | 10 --- R/paramsUtils.R | 107 ++++++++++++++++++----------------- R/polyUtils.R | 46 ++++++++++++--- R/spde2precision.R | 1 R/stModel.define.R | 7 +- R/stModel.matrices.R | 95 +++++++++++-------------------- R/stats.inla.R | 12 +-- R/upperPadding.R | 2 R/worldMap.R | 119 +++++++++++++++++++++++++++++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/website_examples.R | 4 - inst/examples/test4.R | 4 - man/Earth_poly.Rd |only man/INLAspacetime.Rd | 5 - man/Jmatrices.Rd | 4 + man/ar2cor.Rd | 2 man/ar2precision.Rd | 5 - man/barrierModel.define.Rd | 12 ++- man/downloadUtilFiles.Rd | 4 - man/ghcndSelect.Rd | 3 man/mesh.dual.Rd | 15 +++- man/mesh2d.Rd | 6 + man/paramsUtils.Rd | 56 +++++++++++++----- man/polyUtils.Rd | 22 +++++-- man/spde2precision.Rd | 1 man/stats.inla.Rd | 3 man/upperPadding.Rd | 2 man/worldMap.Rd | 28 ++++----- man/world_grid.Rd |only src/INLAspacetime_init.c |only src/ar2cor.c |only src/ar2cor.h |only vignettes/web/barrierExample.Rmd | 4 - vignettes/web/piemonte.Rmd | 18 ----- 46 files changed, 568 insertions(+), 337 deletions(-)
Title: Nested Cross Validation for the Relaxed Lasso and Other Machine
Learning Models
Description: Cross validation informed Relaxed LASSO, Artificial Neural Network (ANN), gradient boosting machine ('xgboost'), Random Forest ('RandomForestSRC'), Recursive Partitioning ('RPART') or step wise regression models are fit. Nested cross validation (or analogous for the random forest) is used to estimate and compare performances between these models with results presented in tabular or graphical means. Calibration plots can also be generated, again based upon (nested) cross validation.
For some datasets, for example when the design matrix is not of full rank, 'glmnet' may have very long run times when fitting the relaxed lasso model, from our experience when fitting Cox models on data with many predictors and many patients, making it difficult to get solutions from either glmnet() or cv.glmnet(). This may be remedied with the 'path=TRUE' options when calling glmnet() and cv.glmnet(). Within the glmnetr package the approach of path=TRUE is taken by default.
When fitting not a relaxed la [...truncated...]
Author: Walter K Kremers [aut, cre] ,
Nicholas B Larson [ctb]
Maintainer: Walter K Kremers <kremers.walter@mayo.edu>
Diff between glmnetr versions 0.4-5 dated 2024-04-19 and 0.4-6 dated 2024-04-21
glmnetr-0.4-5/glmnetr/R/calplot_240409.R |only glmnetr-0.4-5/glmnetr/R/nested.glmnetr_240418.R |only glmnetr-0.4-6/glmnetr/DESCRIPTION | 8 ++++---- glmnetr-0.4-6/glmnetr/MD5 | 18 +++++++++--------- glmnetr-0.4-6/glmnetr/NAMESPACE | 1 + glmnetr-0.4-6/glmnetr/R/calplot_240420.R |only glmnetr-0.4-6/glmnetr/R/nested.glmnetr_240420.R |only glmnetr-0.4-6/glmnetr/man/calplot.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/calplot0.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/myaxis.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/myrug.Rd | 2 +- glmnetr-0.4-6/glmnetr/man/nested.glmnetr.Rd | 2 +- 12 files changed, 19 insertions(+), 18 deletions(-)
Title: Volumetric Analysis using Graphic Double Integration
Description: Tools implementing an automated version of the graphic double integration technique (GDI) for volume implementation, and some other related utilities for paleontological image-analysis. GDI was first employed by Jerison (1973) <ISBN:9780323141086> and Hurlburt (1999) <doi:10.1080/02724634.1999.10011145> and is primarily used for volume or mass estimation of (extinct) animals. The package 'gdi' aims to make this technique as convenient and versatile as possible. The core functions of 'gdi' provide utilities for automatically measuring diameters from digital silhouettes provided as image files and calculating volume via graphic double integration with simple elliptical, superelliptical (following Motani 2001 <doi:10.1666/0094-8373(2001)027%3C0735:EBMFST%3E2.0.CO;2>) or complex cross-sectional models. Additionally, the package provides functions for estimating the center of mass position (COM), the moment of inertia (I) for 3D shapes and the second moment of area (Ix, Iy [...truncated...]
Author: Darius Nau [aut, cre]
Maintainer: Darius Nau <dariusnau@gmx.at>
Diff between gdi versions 1.5.4 dated 2023-09-07 and 1.6.0 dated 2024-04-21
DESCRIPTION | 10 ++--- MD5 | 28 ++++++++-------- NAMESPACE | 5 ++ NEWS.md | 14 ++++++++ R/gdi.r | 49 ++++++++++++++++++++++++---- build/vignette.rds |binary inst/doc/estimating_COM.R | 6 +-- inst/doc/estimating_COM.Rmd | 6 +-- inst/doc/estimating_COM.html | 74 ++++++++++++++++++++++--------------------- inst/doc/misc.R | 2 - inst/doc/misc.Rmd | 2 - inst/doc/misc.html | 29 ++++++++++++++-- man/plot_sil.Rd | 31 ++++++++++++++++-- vignettes/estimating_COM.Rmd | 6 +-- vignettes/misc.Rmd | 2 - 15 files changed, 184 insertions(+), 80 deletions(-)
Title: Fully-Latent Principal Stratification
Description: Simulation and analysis of Fully-Latent Principal Stratification (FLPS) with measurement models. Lee, Adam, Kang, & Whittaker (2023). <doi:10.1007/978-3-031-27781-8_25>. This package is supported by the Institute of Education Sciences, U.S. Department of Education, through Grant R305D210036.
Author: Sooyong Lee [aut, cre],
Adam Sales [aut],
Hyeon-Ah Kang [aut],
Tiffany Whittaker [aut]
Maintainer: Sooyong Lee <sooyongl09@gmail.com>
Diff between flps versions 1.0.0 dated 2023-11-02 and 1.1.0 dated 2024-04-21
DESCRIPTION | 24 - MD5 | 72 ++- NAMESPACE | 1 NEWS.md | 7 R/data_desc.r | 101 +++++ R/flps-package.r | 2 R/load_rstan.r | 3 R/make_FLPSdata.r | 5 R/plot_function.r | 286 +++++++++++---- R/priors.r | 1 R/run_FLPS.r | 18 R/sim_utils.r |only R/summary_function.r | 336 ++++++++++++++++-- R/z_utils.r | 153 -------- R/z_validate.r | 21 + R/zzz.r | 2 README.md | 77 ++-- build/vignette.rds |binary data/example0.rda |only data/example1.rda |only data/example2.rda |only data/example3.rda |only inst/doc/flps.html | 42 +- inst/stan/singlelevel/singlelevel_GRM.stan | 7 inst/stan/singlelevel/singlelevel_IRT.stan | 7 inst/stan/singlelevel/singlelevel_LCA.stan | 104 +++-- inst/stan/singlelevel/singlelevel_LCA_threeclass.stan | 35 + inst/stan/singlelevel/singlelevel_LPA.stan | 97 +++-- inst/stan/singlelevel/singlelevel_LPA_threeclass.stan | 31 + inst/stan/singlelevel/singlelevel_RASCH.stan | 6 inst/stan/singlelevel/singlelevel_SEM.stan | 11 man/example0.Rd |only man/example1.Rd |only man/example2.Rd |only man/example3.Rd |only man/flps-package.Rd | 3 man/flps_plot.Rd | 4 man/plot.Rd | 2 man/print.Rd | 2 man/print.summary.flps.Rd |only man/runFLPS.Rd | 14 man/summary.flps.Rd | 12 42 files changed, 1014 insertions(+), 472 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data,
including the Royston-Parmar spline model, generalized gamma and
generalized F distributions. Any user-defined parametric
distribution can be fitted, given at least an R function defining
the probability density or hazard. There are also tools for
fitting and predicting from fully parametric multi-state models,
based on either cause-specific hazards or mixture models.
Author: Christopher Jackson [aut, cre],
Paul Metcalfe [ctb],
Jordan Amdahl [ctb],
Matthew T. Warkentin [ctb],
Michael Sweeting [ctb],
Kevin Kunzmann [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 2.2.2 dated 2023-02-01 and 2.3 dated 2024-04-21
DESCRIPTION | 19 MD5 | 175 + NAMESPACE | 9 NEWS.md |only R/GenF.R | 12 R/GenGamma.R | 2 R/Gompertz.R | 2 R/Llogis.R | 2 R/ajfit.R | 29 R/broom-funs.R | 2 R/custom.R | 25 R/deriv.R | 155 + R/deriv2.R |only R/distributions.R | 4 R/flexsurv-package.R | 483 ++--- R/flexsurvmix.R | 29 R/flexsurvreg.R | 376 +++- R/fracpoly.R | 2 R/hr_flexsurvreg.R | 6 R/mstate.R | 3108 +++++++++++++++++----------------- R/plot.flexsurvreg.R | 11 R/predict.flexsurvreg.R | 17 R/residuals.flexsurvreg.R | 21 R/simulate_flexsurvreg.R | 4 R/spline.R | 264 ++ R/standsurv.R | 501 +++-- R/summary.flexsurvmix.R | 23 R/summary.flexsurvreg.R | 163 - R/summary.flexsurvrtrunc.R | 218 +- R/survsplinek.R | 260 +- R/utils.R | 23 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 9 inst/doc/distributions.Rnw | 2 inst/doc/distributions.pdf |binary inst/doc/flexsurv-examples.pdf |binary inst/doc/flexsurv.pdf |binary inst/doc/multistate.Rnw | 1724 +++++++++--------- inst/doc/multistate.pdf |binary inst/doc/standsurv.R | 4 inst/doc/standsurv.Rmd | 4 inst/doc/standsurv.html | 628 +++--- man/AIC.fmsm.Rd |only man/AICc.Rd |only man/AICc.flexsurvreg.Rd |only man/BIC.flexsurvreg.Rd |only man/GenF.Rd | 3 man/GenF.orig.Rd | 7 man/Survspline.Rd | 23 man/Survsplinek.Rd | 159 + man/ajfit_fmsm.Rd | 3 man/basis.Rd | 17 man/bootci.fmsm.Rd | 10 man/figures |only man/flexsurv-package.Rd | 6 man/flexsurvmix.Rd | 22 man/flexsurvreg.Rd | 64 man/flexsurvspline.Rd | 11 man/logLik.flexsurvreg.Rd |only man/model.frame.flexsurvmix.Rd |only man/msfit.flexsurvreg.Rd | 3 man/nobs.flexsurvreg.Rd | 11 man/pmatrix.simfs.Rd | 23 man/predict.flexsurvreg.Rd | 16 man/rmst_generic.Rd | 8 man/sim.fmsm.Rd | 2 man/standsurv.Rd | 28 man/totlos.simfs.Rd | 14 man/vcov.flexsurvreg.Rd |only tests/test_base.R | 2 tests/testthat/test-broom.R | 12 tests/testthat/test_aic.R |only tests/testthat/test_contrasts.R |only tests/testthat/test_custom.R | 350 ++- tests/testthat/test_flexsurvmix.R | 6 tests/testthat/test_flexsurvmix_opt.R |only tests/testthat/test_flexsurvreg.R | 85 tests/testthat/test_fmixmsm_outputs.R |only tests/testthat/test_fmsm.R | 122 - tests/testthat/test_genf.R | 243 +- tests/testthat/test_gompertz.R | 123 - tests/testthat/test_hess.R |only tests/testthat/test_llogis.R | 70 tests/testthat/test_mstate.R | 44 tests/testthat/test_outputs.R | 5 tests/testthat/test_residuals.R |only tests/testthat/test_rtrunc.R | 124 - tests/testthat/test_spline.R | 73 tests/testthat/test_splinedist.R | 11 tests/testthat/test_standsurv.R | 223 ++ tests/testthat/test_survsplinek.R |only tests/testthat/test_utils.R | 10 vignettes/distributions.Rnw | 2 vignettes/flexsurv.Rnw | 19 vignettes/multistate.Rnw | 1724 +++++++++--------- vignettes/standsurv.Rmd | 4 97 files changed, 6664 insertions(+), 5334 deletions(-)
Title: Interpretable Discovery and Inference of Heterogeneous Treatment
Effects
Description: Provides a new method for interpretable heterogeneous
treatment effects characterization in terms of decision rules
via an extensive exploration of heterogeneity patterns by an
ensemble-of-trees approach, enforcing high stability in the
discovery. It relies on a two-stage pseudo-outcome regression, and
it is supported by theoretical convergence guarantees. Bargagli-Stoffi,
F. J., Cadei, R., Lee, K., & Dominici, F. (2023) Causal rule ensemble:
Interpretable Discovery and Inference of Heterogeneous Treatment Effects.
arXiv preprint <doi:10.48550/arXiv.2009.09036>.
Author: Naeem Khoshnevis [aut, cre] ,
Daniela Maria Garcia [aut] ,
Riccardo Cadei [aut] ,
Kwonsang Lee [aut] ,
Falco Joannes Bargagli Stoffi [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between CRE versions 0.2.5 dated 2023-12-06 and 0.2.6 dated 2024-04-21
DESCRIPTION | 10 - MD5 | 45 +++++-- NEWS.md | 8 + R/extract_rules.R | 4 R/filter_irrelevant_rules.R | 4 R/generate_rules.R | 2 R/inTrees.R |only README.md | 67 ++++------ inst/CITATION |only inst/doc/CRE.html | 158 ++++++++++++------------- inst/doc/Contribution.html | 68 +++++----- inst/doc/Testing-the-Package.html | 100 +++++++-------- tests/testthat/test-check_input_data.R |only tests/testthat/test-cre.R |only tests/testthat/test-discover_rules.R |only tests/testthat/test-estimate_cate.R |only tests/testthat/test-estimate_ite.R |only tests/testthat/test-estimate_ite_aipw.R |only tests/testthat/test-estimate_ite_bart.R |only tests/testthat/test-estimate_ite_cf.R |only tests/testthat/test-estimate_ite_poisson.R |only tests/testthat/test-estimate_ite_slearner.R |only tests/testthat/test-estimate_ite_tlearner.R |only tests/testthat/test-estimate_ite_xlearner.R |only tests/testthat/test-estimate_ps.R |only tests/testthat/test-evaluate.R |only tests/testthat/test-extract_effect_modifiers.R |only tests/testthat/test-extract_rules.R |only tests/testthat/test-filter_correlated_rules.R |only tests/testthat/test-filter_extreme_rules.R |only tests/testthat/test-filter_irrelevant_rules.R |only tests/testthat/test-generate_cre_dataset.R |only tests/testthat/test-generate_rules.R |only tests/testthat/test-generate_rules_matrix.R |only tests/testthat/test-honest_splitting.R |only tests/testthat/test-interpret_rules.R |only tests/testthat/test-predict.R |only 37 files changed, 244 insertions(+), 222 deletions(-)
Title: Structured Allometric Models for Trees
Description: Access allometric models used in forest resource analysis, such as
volume equations, taper equations, biomass models, among many others. Users
are able to efficiently find and select allometric models suitable for their
project area and use them in analysis. Additionally, 'allometric' provides a
structured framework for adding new models to an open-source models
repository.
Author: Bryce Frank [aut, cre] ,
Francisco Mauro [aut] ,
Elijah Allensworth [aut]
Maintainer: Bryce Frank <bfrank70@gmail.com>
Diff between allometric versions 2.1.0 dated 2023-11-07 and 2.3.0 dated 2024-04-21
DESCRIPTION | 6 LICENSE | 4 MD5 | 117 ++++++++-------- NAMESPACE | 3 R/install.R | 42 +++--- R/load.R | 78 +++++++++-- R/publication_processing.R | 19 ++ R/utils-pipe.R | 28 ++-- R/zzz.R | 7 - README.md | 38 ++--- inst/testdata/fixef_no_descriptors.json | 52 +++---- inst/testdata/test_parameters |only inst/testdata/test_publications |only inst/variable_defs/b.csv | 3 inst/variable_defs/e.csv | 1 inst/variable_defs/h.csv | 1 inst/variable_defs/measures.csv | 3 inst/variable_defs/n.csv | 2 inst/variable_defs/r.csv | 4 inst/variable_defs/t.csv |only inst/variable_defs/v.csv | 2 man/Publication.Rd | 100 +++++++------- man/Taxa.Rd | 60 ++++---- man/Taxon.Rd | 72 +++++----- man/add_model-Publication-FixedEffectsModel-method.Rd | 44 +++--- man/add_model-Publication-MixedEffectsModel-method.Rd | 44 +++--- man/add_model.Rd | 42 +++--- man/add_set.Rd | 46 +++--- man/aggregate_taxa.Rd | 6 man/check_args_in_predict_fn.Rd | 24 +-- man/check_descriptor_set.Rd | 28 ++-- man/check_descriptor_validity.Rd | 24 +-- man/check_models_installed.Rd | 28 ++-- man/check_parameters_in_mixed_fns.Rd | 24 +-- man/check_parameters_in_predict_fn.Rd | 24 +-- man/check_parametric_model.Rd | 24 +-- man/check_taxon_hierarchy.Rd | 24 +-- man/descriptors_to_S4.Rd | 24 +-- man/equals-Taxon-Taxon-method.Rd | 36 ++--- man/fia_trees.Rd | 58 ++++---- man/get_measure_defs.Rd | 34 ++-- man/get_params_path.Rd |only man/grapes-in-grapes-Taxa-Taxon-method.Rd | 42 +++--- man/grapes-in-grapes-Taxon-Taxa-method.Rd | 40 ++--- man/grapes-in-grapes-character-Taxa-method.Rd | 40 ++--- man/grapes-in-grapes-character-Taxon-method.Rd | 40 ++--- man/ingest_models.Rd |only man/install_models.Rd | 14 -- man/load_models.Rd | 126 +++++++++++++++--- man/load_parameter_frame.Rd | 38 ++--- man/pipe.Rd | 40 ++--- man/select_model.model_tbl.Rd | 42 +++--- man/set_params_path.Rd |only man/unnest_models.model_tbl.Rd | 42 +++--- man/unnest_taxa.Rd | 40 ++--- man/unnest_taxa.model_tbl.Rd | 40 ++--- tests/testthat.R | 22 +-- tests/testthat/test-install.R | 11 - tests/testthat/test-model-set.R | 22 +-- tests/testthat/test-model-tbl.R | 4 tests/testthat/test-publication-processing.R | 13 + tests/testthat/test-taxa.R | 17 ++ 62 files changed, 1000 insertions(+), 809 deletions(-)
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor) or analysis of variance (for cases where more than two levels or factors exist) to calculate the fold change or relative expression. The functions also provide standard deviations and confidence limits for means and apply statistical mean comparisons. To facilitate using 'rtpcr', diffe [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 1.0.4 dated 2024-04-20 and 1.0.5 dated 2024-04-21
DESCRIPTION | 6 - MD5 | 28 ++++---- R/oneFACTORplot.r | 4 - R/qpcrANCOVA.r | 162 ++++++++++++++++++++++++++++++++++++------------- R/qpcrANOVA.r | 102 ++++++++++++++++++++++++++---- R/qpcrhlpr.r | 64 ------------------- R/threeFACTORplot.r | 6 - R/twoFACTORplot.r | 10 +-- inst/doc/vignette.R | 62 +++++++++--------- inst/doc/vignette.Rmd | 26 +++---- inst/doc/vignette.html | 83 ++++++++++++++----------- man/qpcrANCOVA.Rd | 22 ++++-- man/threeFACTORplot.Rd | 2 man/twoFACTORplot.Rd | 6 - vignettes/vignette.Rmd | 26 +++---- 15 files changed, 361 insertions(+), 248 deletions(-)
Title: Tagging and Validating Epidemiological Data
Description: Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
Author: Hugo Gruson [aut, cre] ,
Thibaut Jombart [aut, ccp],
Tim Taylor [ctb],
Chris Hartgerink [rev]
Maintainer: Hugo Gruson <hugo@data.org>
Diff between linelist versions 1.1.2 dated 2024-04-19 and 1.1.3 dated 2024-04-21
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/linelist-package.R | 4 ++-- inst/CITATION | 2 +- inst/doc/compat-dplyr.html | 20 ++++++++++---------- inst/doc/linelist.R | 1 - inst/doc/linelist.Rmd | 1 - inst/doc/linelist.html | 45 ++++++++++++++++++++++----------------------- man/linelist-package.Rd | 4 ++-- vignettes/linelist.Rmd | 1 - 11 files changed, 57 insertions(+), 55 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] ,
Jasper Cooper [aut] ,
Alexander Coppock [aut] ,
Macartan Humphreys [aut] ,
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Diff between DeclareDesign versions 1.0.8 dated 2024-03-07 and 1.0.10 dated 2024-04-21
DESCRIPTION | 8 - MD5 | 80 ++++++------ NEWS.md | 5 R/compare_designs.R | 18 +- R/declare_estimator.R | 105 +++++++++-------- R/declare_measurement.R | 40 +++--- R/declare_model.R | 22 ++- R/declare_test.R | 46 ++++--- R/design_helper_functions.R | 3 R/diagnose_design.R | 16 +- R/simulate_design.R | 12 + R/utilities.R | 10 + man/compare_functions.Rd | 18 +- man/declare_estimator.Rd | 105 +++++++++-------- man/declare_measurement.Rd | 40 +++--- man/declare_model.Rd | 22 ++- man/declare_test.Rd | 46 ++++--- man/diagnose_design.Rd | 14 +- man/simulate_design.Rd | 14 +- tests/testthat/test-allow-custom-functions.R | 16 +- tests/testthat/test-alternative-df-compatibility.R | 4 tests/testthat/test-assignment.R | 36 ++--- tests/testthat/test-citation.R | 5 tests/testthat/test-compare-designs.R | 2 tests/testthat/test-declare-design.R | 44 +++++-- tests/testthat/test-demo.R | 14 +- tests/testthat/test-design-library.R | 2 tests/testthat/test-design-summary.R | 44 +++++-- tests/testthat/test-diagnosands.R | 8 - tests/testthat/test-diagnose-design.R | 30 +++- tests/testthat/test-estimators.R | 28 ++-- tests/testthat/test-factorial.R | 10 - tests/testthat/test-model.R | 11 + tests/testthat/test-modify-design.R | 19 +-- tests/testthat/test-multiple-coefficients.R | 4 tests/testthat/test-multiple-estimands-one-estimator.R | 1 tests/testthat/test-population.R | 6 tests/testthat/test-potential-outcomes.R | 39 ++++-- tests/testthat/test-reshape-diagnosis.R | 2 tests/testthat/test-sims-independent.R | 11 + tests/testthat/test-subset.R | 2 41 files changed, 579 insertions(+), 383 deletions(-)
Title: Quantifying (Animal) Sound Degradation
Description: Intended to facilitate acoustic analysis of (animal) sound transmission experiments, which typically aim to quantify changes in signal structure when transmitted in a given habitat by broadcasting and re-recording animal sounds at increasing distances. The package offers a workflow with functions to prepare the data set for analysis as well as to calculate and visualize several degradation metrics, including blur ratio, signal-to-noise ratio, excess attenuation and envelope correlation among others (Dabelsteen et al 1993 <doi:10.1121/1.406682>).
Author: Marcelo Araya-Salas [aut, cre]
,
Michael Mahoney [rev] ,
Dena Clink [rev]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between baRulho versions 1.0.6 dated 2022-03-01 and 2.1.0 dated 2024-04-21
baRulho-1.0.6/baRulho/R/atmospheric_attenuation.R |only baRulho-1.0.6/baRulho/R/find_peaks_bRlo_int.R |only baRulho-1.0.6/baRulho/R/playback_est-data.R |only baRulho-1.0.6/baRulho/R/playback_est_unaligned-data.R |only baRulho-1.0.6/baRulho/R/prep_X_bRlo_int.R |only baRulho-1.0.6/baRulho/R/search_templates.R |only baRulho-1.0.6/baRulho/R/spcc_align.R |only baRulho-1.0.6/baRulho/R/spectral_blur_ratio.R |only baRulho-1.0.6/baRulho/R/spectral_correlation.R |only baRulho-1.0.6/baRulho/data/playback_est.rda |only baRulho-1.0.6/baRulho/data/playback_est_unaligned.rda |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.R |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.Rmd |only baRulho-1.0.6/baRulho/inst/doc/baRulho_quantifying_sound_degradation.html |only baRulho-1.0.6/baRulho/man/atmospheric_attenuation.Rd |only baRulho-1.0.6/baRulho/man/baRulho.Rd |only baRulho-1.0.6/baRulho/man/playback_est.Rd |only baRulho-1.0.6/baRulho/man/playback_est_unaligned.Rd |only baRulho-1.0.6/baRulho/man/search_templates.Rd |only baRulho-1.0.6/baRulho/man/spcc_align.Rd |only baRulho-1.0.6/baRulho/man/spectral_blur_ratio.Rd |only baRulho-1.0.6/baRulho/man/spectral_correlation.Rd |only baRulho-1.0.6/baRulho/vignettes/analysis_workflow.jpg |only baRulho-1.0.6/baRulho/vignettes/baRulho_quantifying_sound_degradation.Rmd |only baRulho-1.0.6/baRulho/vignettes/example_master.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/example_test1.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/example_test2.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/spcc_align_results.gif |only baRulho-1.0.6/baRulho/vignettes/spectral_blur_ratio_example.gif |only baRulho-1.0.6/baRulho/vignettes/spectro_synth_song.png |only baRulho-1.0.6/baRulho/vignettes/synthetic_master.wav.jpeg |only baRulho-1.0.6/baRulho/vignettes/tlalpan_playback.jpeg |only baRulho-2.1.0/baRulho/DESCRIPTION | 49 baRulho-2.1.0/baRulho/MD5 | 132 +- baRulho-2.1.0/baRulho/NAMESPACE | 49 baRulho-2.1.0/baRulho/NEWS.md | 68 + baRulho-2.1.0/baRulho/R/add_noise.R |only baRulho-2.1.0/baRulho/R/align_test_files.R | 346 +++--- baRulho-2.1.0/baRulho/R/attenuation.R |only baRulho-2.1.0/baRulho/R/auto_realign.R |only baRulho-2.1.0/baRulho/R/baRulho-package.R | 34 baRulho-2.1.0/baRulho/R/blur_ratio.R | 538 +++------- baRulho-2.1.0/baRulho/R/detection_distance.R |only baRulho-2.1.0/baRulho/R/envelope_correlation.R | 294 ++--- baRulho-2.1.0/baRulho/R/excess_attenuation.R | 392 ++----- baRulho-2.1.0/baRulho/R/find_markers.R |only baRulho-2.1.0/baRulho/R/internal_functions.R |only baRulho-2.1.0/baRulho/R/manual_realign.R |only baRulho-2.1.0/baRulho/R/master_est-data.R |only baRulho-2.1.0/baRulho/R/master_sound_file.R | 527 +++++---- baRulho-2.1.0/baRulho/R/noise_profile.R | 336 ++---- baRulho-2.1.0/baRulho/R/plot_aligned_sounds.R |only baRulho-2.1.0/baRulho/R/plot_blur_ratio.R |only baRulho-2.1.0/baRulho/R/plot_degradation.R |only baRulho-2.1.0/baRulho/R/set_reference_sounds.R |only baRulho-2.1.0/baRulho/R/signal_to_noise_ratio.R | 364 ++---- baRulho-2.1.0/baRulho/R/spcc.R | 249 ++-- baRulho-2.1.0/baRulho/R/spectrum_blur_ratio.R |only baRulho-2.1.0/baRulho/R/spectrum_correlation.R |only baRulho-2.1.0/baRulho/R/synth_sounds.R |only baRulho-2.1.0/baRulho/R/tail_to_signal_ratio.R | 340 +++--- baRulho-2.1.0/baRulho/R/template_params.R |only baRulho-2.1.0/baRulho/R/test_sounds_est-data.R |only baRulho-2.1.0/baRulho/README.md | 175 ++- baRulho-2.1.0/baRulho/build/vignette.rds |binary baRulho-2.1.0/baRulho/data/master_est.rda |only baRulho-2.1.0/baRulho/data/test_sounds_est.rda |only baRulho-2.1.0/baRulho/inst/CITATION | 11 baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.R |only baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.Rmd |only baRulho-2.1.0/baRulho/inst/doc/align_test_sounds.html |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.R |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.Rmd |only baRulho-2.1.0/baRulho/inst/doc/quantify_degradation.html |only baRulho-2.1.0/baRulho/man/add_noise.Rd |only baRulho-2.1.0/baRulho/man/align_test_files.Rd | 120 -- baRulho-2.1.0/baRulho/man/attenuation.Rd |only baRulho-2.1.0/baRulho/man/auto_realign.Rd |only baRulho-2.1.0/baRulho/man/baRulho-package.Rd |only baRulho-2.1.0/baRulho/man/blur_ratio.Rd | 111 +- baRulho-2.1.0/baRulho/man/detection_distance.Rd |only baRulho-2.1.0/baRulho/man/envelope_correlation.Rd | 78 - baRulho-2.1.0/baRulho/man/excess_attenuation.Rd | 77 - baRulho-2.1.0/baRulho/man/figures |only baRulho-2.1.0/baRulho/man/find_markers.Rd |only baRulho-2.1.0/baRulho/man/manual_realign.Rd |only baRulho-2.1.0/baRulho/man/master_est.Rd |only baRulho-2.1.0/baRulho/man/master_sound_file.Rd | 85 + baRulho-2.1.0/baRulho/man/noise_profile.Rd | 64 - baRulho-2.1.0/baRulho/man/plot_aligned_sounds.Rd |only baRulho-2.1.0/baRulho/man/plot_blur_ratio.Rd |only baRulho-2.1.0/baRulho/man/plot_degradation.Rd |only baRulho-2.1.0/baRulho/man/set_reference_sounds.Rd |only baRulho-2.1.0/baRulho/man/signal_to_noise_ratio.Rd | 94 + baRulho-2.1.0/baRulho/man/spcc.Rd | 75 - baRulho-2.1.0/baRulho/man/spectrum_blur_ratio.Rd |only baRulho-2.1.0/baRulho/man/spectrum_correlation.Rd |only baRulho-2.1.0/baRulho/man/synth_sounds.Rd |only baRulho-2.1.0/baRulho/man/tail_to_signal_ratio.Rd | 84 + baRulho-2.1.0/baRulho/man/test_sounds_est.Rd |only baRulho-2.1.0/baRulho/vignettes/align_test_sounds.Rmd |only baRulho-2.1.0/baRulho/vignettes/auto_realign_results.gif |only baRulho-2.1.0/baRulho/vignettes/baRulho_sticker.png |only baRulho-2.1.0/baRulho/vignettes/blur_ratio_example.gif |binary baRulho-2.1.0/baRulho/vignettes/manual_realign.gif |only baRulho-2.1.0/baRulho/vignettes/quantify_degradation.Rmd |only 106 files changed, 2464 insertions(+), 2228 deletions(-)
Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for ultra
high-dimensional, multi-gigabyte data sets that cannot be loaded into
memory. Designed to be more memory- and computation-efficient than existing
lasso-fitting packages like 'glmnet' and 'ncvreg', thus allowing
the user to analyze big data analysis even on an ordinary laptop.
Author: Yaohui Zeng [aut],
Chuyi Wang [aut],
Tabitha Peter [aut],
Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between biglasso versions 1.5.2 dated 2022-10-05 and 1.6.0 dated 2024-04-21
biglasso-1.5.2/biglasso/R/cv.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.cv.biglasso.R |only biglasso-1.5.2/biglasso/R/plot.mbiglasso.R |only biglasso-1.5.2/biglasso/R/predict.cv.R |only biglasso-1.5.2/biglasso/R/summary.cv.biglasso.R |only biglasso-1.5.2/biglasso/src/Makevars.win |only biglasso-1.6.0/biglasso/DESCRIPTION | 18 biglasso-1.6.0/biglasso/MD5 | 82 +- biglasso-1.6.0/biglasso/NAMESPACE | 2 biglasso-1.6.0/biglasso/NEWS.md | 21 biglasso-1.6.0/biglasso/R/biglasso-package.R | 302 ++++----- biglasso-1.6.0/biglasso/R/biglasso.R | 117 +-- biglasso-1.6.0/biglasso/R/biglasso_fit.R |only biglasso-1.6.0/biglasso/R/biglasso_path.R |only biglasso-1.6.0/biglasso/R/cv-biglasso.R |only biglasso-1.6.0/biglasso/R/loss.R | 20 biglasso-1.6.0/biglasso/R/plot-biglasso.R |only biglasso-1.6.0/biglasso/R/plot-cv-biglasso.R |only biglasso-1.6.0/biglasso/R/plot-mbiglasso.R |only biglasso-1.6.0/biglasso/R/predict-cv.R |only biglasso-1.6.0/biglasso/R/predict.R | 56 - biglasso-1.6.0/biglasso/R/setupX.R | 48 - biglasso-1.6.0/biglasso/R/summary-cv-biglasso.R |only biglasso-1.6.0/biglasso/build/vignette.rds |binary biglasso-1.6.0/biglasso/inst/CITATION | 17 biglasso-1.6.0/biglasso/inst/doc/biglasso.R | 4 biglasso-1.6.0/biglasso/inst/doc/biglasso.Rmd | 30 biglasso-1.6.0/biglasso/inst/doc/biglasso.html | 648 +++++++++++++-------- biglasso-1.6.0/biglasso/man/biglasso-package.Rd | 306 ++++----- biglasso-1.6.0/biglasso/man/biglasso.Rd | 507 ++++++++-------- biglasso-1.6.0/biglasso/man/biglasso_fit.Rd |only biglasso-1.6.0/biglasso/man/biglasso_path.Rd |only biglasso-1.6.0/biglasso/man/colon.Rd | 82 +- biglasso-1.6.0/biglasso/man/cv.biglasso.Rd | 239 +++---- biglasso-1.6.0/biglasso/man/loss.biglasso.Rd | 76 +- biglasso-1.6.0/biglasso/man/plot.biglasso.Rd | 67 -- biglasso-1.6.0/biglasso/man/plot.cv.biglasso.Rd | 122 +-- biglasso-1.6.0/biglasso/man/plot.mbiglasso.Rd | 14 biglasso-1.6.0/biglasso/man/predict.biglasso.Rd | 207 +++--- biglasso-1.6.0/biglasso/man/predict.cv.biglasso.Rd | 168 ++--- biglasso-1.6.0/biglasso/man/setupX.Rd | 153 ++-- biglasso-1.6.0/biglasso/man/summary.cv.biglasso.Rd | 105 +-- biglasso-1.6.0/biglasso/src/Makevars | 7 biglasso-1.6.0/biglasso/src/biglasso_omp.h | 1 biglasso-1.6.0/biglasso/src/gaussian.cpp | 4 biglasso-1.6.0/biglasso/src/gaussian_simple.cpp |only biglasso-1.6.0/biglasso/src/init.c | 16 biglasso-1.6.0/biglasso/src/utilities.cpp | 208 ++++++ biglasso-1.6.0/biglasso/src/utilities.h | 35 + biglasso-1.6.0/biglasso/vignettes/biglasso.Rmd | 30 51 files changed, 2047 insertions(+), 1665 deletions(-)
Title: Explicitly Qualifying Namespaces by Automatically Adding 'pkg::'
to Functions
Description: Automatically adding 'pkg::' to a function, i.e. mutate()
becomes dplyr::mutate(). It is up to the user to determine which
packages should be used explicitly, whether to include base R packages
or use the functionality on selected text, a file, or a complete
directory. User friendly logging is provided in the 'RStudio' Markers
pane. Lives in the spirit of 'lintr' and 'styler'. Can also be used
for checking which packages are actually used in a project.
Author: Matthias Nistler
Maintainer: Matthias Nistler <m_nistler@web.de>
Diff between origin versions 1.1.1 dated 2023-09-03 and 1.1.2 dated 2024-04-21
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- NEWS.md | 8 ++++ R/fix_html_tokens.R | 74 ++++++++++++++++++++++------------------- R/run_logging.R | 2 - README.md | 4 +- build/vignette.rds |binary inst/doc/origin.R | 6 +-- tests/testthat/_snaps/print.md | 40 +++++++++++----------- tests/testthat/test-print.R | 3 + 10 files changed, 90 insertions(+), 73 deletions(-)
Title: Functions for Wayne W. Daniel's Biostatistics, Tenth Edition
Description: Functions to accompany Wayne W. Daniel's
Biostatistics: A Foundation for Analysis in the
Health Sciences, Tenth Edition.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between DanielBiostatistics10th versions 0.2.0 dated 2024-04-11 and 0.2.1 dated 2024-04-21
DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/R/chp7.power.R |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/autoplot.BooleanTable.Rd |only DanielBiostatistics10th-0.2.0/DanielBiostatistics10th/man/binom2pois.Rd |only DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/DESCRIPTION | 14 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/MD5 | 38 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/NAMESPACE | 58 --- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/NEWS.md | 3 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/BooleanTable.R | 78 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp11.R | 83 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp2.R | 35 -- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp4.R | 175 ---------- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp5.6.7.R | 35 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp7_power.R |only DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/R/chp9.R | 83 ---- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/BooleanTable.Rd | 2 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter02.Rd | 5 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter04.Rd | 32 - DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter05to07.Rd | 37 +- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter07_power.Rd | 5 DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter09.Rd | 29 - DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter11.Rd | 38 -- DanielBiostatistics10th-0.2.1/DanielBiostatistics10th/man/Chapter14.Rd | 12 22 files changed, 108 insertions(+), 654 deletions(-)
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Title: Handy Tools for TJU/TJUH Employees
Description: Functions for admin needs of employees of
Thomas Jefferson University and Thomas Jefferson
University Hospital, Philadelphia, PA.
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between ThomasJeffersonUniv versions 0.1.0 dated 2022-05-18 and 0.1.1 dated 2024-04-21
ThomasJeffersonUniv-0.1.0/ThomasJeffersonUniv/R/ThomasJeffersonUniv_info.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/DESCRIPTION | 28 - ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/MD5 | 39 ++ ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/NAMESPACE | 30 + ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/0PACKAGE.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/TJU_Cayuse.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/TJU_Fiscal_Year.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/TJU_SchoolTerm.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/TJU_Workday.R | 162 ++++++---- ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/cat_named.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/checkCount.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/checkDuplicated.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/difftime_ext.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/phone10_zip5.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/sourcePath.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/R/splitDF.R |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/inst |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/TJU_Cayuse.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/TJU_Fiscal_Year.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/TJU_SchoolTerm.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/TJU_Workday.Rd | 26 - ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/ThomasJeffersonUniv-package.Rd | 9 ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/allDates.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/asDifftime.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/checkCount.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/checkDuplicated.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/matchDF.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/mergeDF.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/phone10.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/sourcePath.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/splitDF.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/timeUnits.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/units_difftime-set.Rd |only ThomasJeffersonUniv-0.1.1/ThomasJeffersonUniv/man/zip5.Rd |only 34 files changed, 208 insertions(+), 86 deletions(-)
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Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-04-03 0.0.2
2024-01-31 0.0.1
Title: Linked Micromap Plots for U. S. and Other Geographic Areas
Description: Provides the users with the ability to quickly create
linked micromap plots for a collection of geographic areas.
Linked micromap plots are visualizations of geo-referenced data
that link statistical graphics to an organized series of small
maps or graphic images. The Help description contains examples
of how to use the 'micromapST' function. Contained in this
package are border group datasets to support creating linked
micromap plots for the 50 U.S. states and District of Columbia
(51 areas), the U. S. 20 Seer Registries, the 105 counties in
the state of Kansas, the 62 counties of New York, the 24
counties of Maryland, the 29 counties of Utah, the 32
administrative areas in China, the 218 administrative areas in
the UK and Ireland (for testing only), the 25 districts in the
city of Seoul South Korea, and the 52 counties on the Africa
continent.
A border group dataset contains the boundaries related to the
data level areas, a second layer boundaries, a top or third
layer boundary, a pa [...truncated...]
Author: Jim Pearson [aut, cre, cph],
Dan Carr [aut, cph],
Linda Pickle [ctb, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>
Diff between micromapST versions 3.0.2 dated 2024-01-10 and 3.0.3 dated 2024-04-20
DESCRIPTION | 8 MD5 | 16 - R/BuildBorderGroup.r | 17 - R/micromapDefSets.r | 4 R/micromapST.r | 409 ++++++++++++++++++++++++++-------------------- R/panelFunctions.r | 27 +-- inst/doc/NEWS | 15 + man/micromapST-package.Rd | 4 man/micromapST.Rd | 12 - 9 files changed, 302 insertions(+), 210 deletions(-)
Title: Interface for MOA Stream Clustering Algorithms
Description: Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
Author: Michael Hahsler [aut, cre, cph]
,
John Forrest [aut, cph],
Matthew Bolanos [ctb],
Matthias Carnein [ctb],
Dalibor Krleza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between streamMOA versions 1.3-0 dated 2022-09-03 and 1.3-1 dated 2024-04-20
DESCRIPTION | 12 +++--- MD5 | 62 ++++++++++++++++++------------------ NAMESPACE | 4 ++ NEWS.md | 7 ++++ R/AAA_streamMOA-package.R | 11 +----- R/DSC_CluStream.R | 2 - R/DSC_ClusTree.R | 4 +- R/DSC_DenStream.R | 10 ++--- R/DSC_MOA.R | 7 +--- R/DSC_streamkm.R | 4 +- R/DSClassifier_MOA.R | 15 ++++++-- R/DSD_MOA.R | 2 - R/DSD_RandomRBFGeneratorEvents.R | 4 +- R/DSOutlier_MCOD.R | 4 +- R/DSRegressor_MOA.R |only README.md | 17 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/README_files/plot-1.png |binary inst/doc/streamMOA.Rnw | 2 - inst/doc/streamMOA.pdf |binary man/DSC_CluStream.Rd | 2 - man/DSC_ClusTree.Rd | 4 +- man/DSC_DenStream.Rd | 10 ++--- man/DSC_MCOD.Rd | 4 +- man/DSC_MOA.Rd | 8 +--- man/DSC_StreamKM.Rd | 4 +- man/DSClassifier_MOA.Rd | 6 ++- man/DSD_MOA.Rd | 2 - man/DSD_RandomRBFGeneratorEvents.Rd | 4 +- man/DSRegressor_MOA.Rd |only man/streamMOA-package.Rd | 24 +++++++++++++ vignettes/streamMOA.Rnw | 2 - 33 files changed, 139 insertions(+), 98 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Fits regularization paths for linear regression, GLM, and Cox
regression models using lasso or nonconvex penalties, in particular the
minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD)
penalty, with options for additional L2 penalties (the "elastic net" idea).
Utilities for carrying out cross-validation as well as post-fitting
visualization, summarization, inference, and prediction are also provided.
For more information, see Breheny and Huang (2011) <doi:10.1214/10-AOAS388>
or visit the ncvreg homepage <https://pbreheny.github.io/ncvreg/>.
Author: Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.14.1 dated 2023-04-25 and 3.14.2 dated 2024-04-20
ncvreg-3.14.1/ncvreg/vignettes/web |only ncvreg-3.14.2/ncvreg/DESCRIPTION | 10 ncvreg-3.14.2/ncvreg/MD5 | 103 ++++---- ncvreg-3.14.2/ncvreg/NEWS.md | 3 ncvreg-3.14.2/ncvreg/R/auc.R | 8 ncvreg-3.14.2/ncvreg/R/cv-ncvreg.R | 135 +++++------ ncvreg-3.14.2/ncvreg/R/data.R | 2 ncvreg-3.14.2/ncvreg/R/local-mfdr.R | 8 ncvreg-3.14.2/ncvreg/R/logLik.R | 7 ncvreg-3.14.2/ncvreg/R/mfdr.R | 32 +- ncvreg-3.14.2/ncvreg/R/ncvfit.R | 11 ncvreg-3.14.2/ncvreg/R/ncvreg.R | 213 +++++++++--------- ncvreg-3.14.2/ncvreg/R/ncvsurv.R | 102 +++----- ncvreg-3.14.2/ncvreg/R/perm-ncvreg.R | 55 ++-- ncvreg-3.14.2/ncvreg/R/permres-ncvreg.R | 45 +-- ncvreg-3.14.2/ncvreg/R/plot-cv-ncvreg.R | 61 ++--- ncvreg-3.14.2/ncvreg/R/plot-mfdr.R | 47 ++-- ncvreg-3.14.2/ncvreg/R/plot-ncvreg.R | 33 +- ncvreg-3.14.2/ncvreg/R/plot-ncvsurv-func.R | 21 - ncvreg-3.14.2/ncvreg/R/predict-surv.R | 69 +++-- ncvreg-3.14.2/ncvreg/R/predict.R | 62 ++--- ncvreg-3.14.2/ncvreg/R/residuals.R | 8 ncvreg-3.14.2/ncvreg/R/std.R | 23 + ncvreg-3.14.2/ncvreg/R/summary-cv-ncvreg.R | 64 ++--- ncvreg-3.14.2/ncvreg/R/summary-ncvreg.R | 61 +++-- ncvreg-3.14.2/ncvreg/build/partial.rdb |binary ncvreg-3.14.2/ncvreg/build/vignette.rds |binary ncvreg-3.14.2/ncvreg/inst/doc/getting-started.html | 243 ++++++++++----------- ncvreg-3.14.2/ncvreg/inst/tinytest/cv-ncvreg.R | 13 + ncvreg-3.14.2/ncvreg/inst/tinytest/ncvfit.R | 1 ncvreg-3.14.2/ncvreg/man/AUC.Rd | 15 - ncvreg-3.14.2/ncvreg/man/Lung.Rd | 2 ncvreg-3.14.2/ncvreg/man/cv.ncvreg.Rd | 114 ++++----- ncvreg-3.14.2/ncvreg/man/local_mfdr.Rd | 6 ncvreg-3.14.2/ncvreg/man/logLik.ncvreg.Rd | 6 ncvreg-3.14.2/ncvreg/man/mfdr.Rd | 22 - ncvreg-3.14.2/ncvreg/man/ncvfit.Rd | 8 ncvreg-3.14.2/ncvreg/man/ncvreg.Rd | 128 +++++------ ncvreg-3.14.2/ncvreg/man/ncvsurv.Rd | 111 ++++----- ncvreg-3.14.2/ncvreg/man/perm.ncvreg.Rd | 36 +-- ncvreg-3.14.2/ncvreg/man/permres.Rd | 31 +- ncvreg-3.14.2/ncvreg/man/plot.cv.ncvreg.Rd | 52 ++-- ncvreg-3.14.2/ncvreg/man/plot.mfdr.Rd | 30 +- ncvreg-3.14.2/ncvreg/man/plot.ncvreg.Rd | 24 -- ncvreg-3.14.2/ncvreg/man/plot.ncvsurv.func.Rd | 15 - ncvreg-3.14.2/ncvreg/man/predict.ncvreg.Rd | 44 +-- ncvreg-3.14.2/ncvreg/man/predict.ncvsurv.Rd | 47 ++-- ncvreg-3.14.2/ncvreg/man/std.Rd | 19 - ncvreg-3.14.2/ncvreg/man/summary.cv.ncvreg.Rd | 46 +-- ncvreg-3.14.2/ncvreg/man/summary.ncvreg.Rd | 61 ++--- 50 files changed, 1111 insertions(+), 1146 deletions(-)
Title: Create Custom Research Compendiums
Description: Provides functions to create and manage research compendiums for data analysis. Research compendiums are a standard and intuitive folder structure for organizing the digital materials of a research project, which can significantly improve reproducibility. The package offers several compendium structure options that fit different research project as well as the ability of duplicating the folder structure of existing projects or implementing custom structures. It also simplifies the use of version control.
Author: Marcelo Araya-Salas [aut, cre]
,
Andrea Yure Arriaga Madrigal [aut]
Maintainer: Marcelo Araya-Salas <marcelo.araya@ucr.ac.cr>
Diff between sketchy versions 1.0.2 dated 2022-02-09 and 1.0.3 dated 2024-04-20
DESCRIPTION | 15 - MD5 | 34 ++-- NAMESPACE | 12 + R/add_to_gitignore.R | 51 ------ R/compendiums-data.R | 7 R/internal_functions.R |only R/load_packages.R |only R/make_compendium.R | 315 +++++++++++++++++++++++++++++++++------- R/print_skeleton.R | 4 R/sketchy-package.R | 7 R/sysdata.rda |binary README.md | 84 +++++----- data/compendiums.rda |binary inst/CITATION | 17 -- man/add_to_gitignore.Rd | 2 man/compendiums.Rd | 7 man/figures/sketchy_sticker.png |only man/load_packages.Rd |only man/make_compendium.Rd | 10 - man/sketchy.Rd | 11 + 20 files changed, 389 insertions(+), 187 deletions(-)
Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM',
with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut] ,
Christian Kleiber [aut] ,
Achim Zeileis [aut, cre] ,
Nikolas Kuschnig [ctb] ,
R Core Team [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between ivreg versions 0.6-2 dated 2023-03-17 and 0.6-3 dated 2024-04-20
DESCRIPTION | 17 MD5 | 39 - NEWS.md | 14 R/ivreg.R | 2 R/ivregMethods.R | 156 ++++ build/vignette.rds |binary inst/doc/Diagnostics-for-2SLS-Regression.Rmd | 8 inst/doc/Diagnostics-for-2SLS-Regression.html | 257 +++---- inst/doc/ivreg.R | 2 inst/doc/ivreg.Rmd | 6 inst/doc/ivreg.html | 896 +++++++++++--------------- man/figures/README-2sls.svg | 265 +++---- man/figures/README-effects-1.png |binary man/figures/README-influenceplot-1.png |binary man/figures/README-qqplot-1.png |binary man/ivreg.Rd | 2 man/ivregMethods.Rd | 27 tests/testthat/test-predict.R |only vignettes/Diagnostics-for-2SLS-Regression.Rmd | 8 vignettes/ivreg.Rmd | 6 vignettes/ivreg.bib | 9 21 files changed, 891 insertions(+), 823 deletions(-)
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2021-10-08 0.9.4
2021-06-30 0.9.3
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2021-02-17 0.9.1.2
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2020-10-13 0.9.0.1
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2016-03-11 1.0.15
2015-11-26 1.0.13
2015-02-10 1.0.11
2015-01-19 1.0.10
2015-01-12 1.0.9
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2014-08-06 1.0.5
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2018-06-28 1.6.1
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2018-03-02 1.5
2018-02-01 1.4.2
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2014-10-13 14.10-11
2014-10-10 14.10-8
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2019-10-17 2.8.6
2019-03-19 2.8.5
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2016-12-03 0.1.3
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Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] ,
Kurt Hornik [aut] ,
Artifex Software, Inc. [ctb, cph]
Maintainer: Ingo Feinerer <feinerer@logic.at>
Diff between tm versions 0.7-12 dated 2024-03-11 and 0.7-13 dated 2024-04-20
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary data/acq.rda |binary data/crude.rda |binary inst/NEWS.Rd | 7 +++++++ inst/doc/extensions.pdf |binary inst/doc/tm.pdf |binary man/TextDocument.Rd | 2 +- man/content_transformer.Rd | 2 +- man/termFreq.Rd | 4 ++-- 12 files changed, 26 insertions(+), 19 deletions(-)
Title: Concise, Lazy and Reliable Wrapper for 'chromote' and 'selenium'
Description: A user-friendly wrapper for web automation, using either
'chromote' or 'selenium'. Provides a simple and consistent API to make
web scraping and testing scripts easy to write and understand.
Elements are lazy, and automatically wait for the website to be valid,
resulting in reliable and reproducible code, with no visible impact on
the experience of the programmer.
Author: Ashby Thorpe [aut, cre, cph]
Maintainer: Ashby Thorpe <ashbythorpe@gmail.com>
Diff between selenider versions 0.3.0 dated 2024-01-27 and 0.4.0 dated 2024-04-20
selenider-0.3.0/selenider/R/flatmap.R |only selenider-0.3.0/selenider/tests/testthat/_snaps/format.md |only selenider-0.3.0/selenider/tests/testthat/test-flatmap.R |only selenider-0.3.0/selenider/tests/testthat/test-format.R |only selenider-0.4.0/selenider/DESCRIPTION | 34 +-- selenider-0.4.0/selenider/MD5 | 91 +++++----- selenider-0.4.0/selenider/NAMESPACE | 5 selenider-0.4.0/selenider/NEWS.md | 19 +- selenider-0.4.0/selenider/R/actions.R | 24 ++ selenider-0.4.0/selenider/R/cache.R | 6 selenider-0.4.0/selenider/R/children.R | 22 -- selenider-0.4.0/selenider/R/collections.R |only selenider-0.4.0/selenider/R/conditions.R | 26 ++ selenider-0.4.0/selenider/R/elem_filter.R | 9 selenider-0.4.0/selenider/R/elem_flatten.R | 3 selenider-0.4.0/selenider/R/equal.R | 10 - selenider-0.4.0/selenider/R/find_elements.R | 12 + selenider-0.4.0/selenider/R/format.R | 1 selenider-0.4.0/selenider/R/get_actual_element.R | 28 ++- selenider-0.4.0/selenider/R/global_actions.R | 61 +++++- selenider-0.4.0/selenider/R/js.R | 14 - selenider-0.4.0/selenider/R/lazy_list.R | 7 selenider-0.4.0/selenider/R/print.R | 9 selenider-0.4.0/selenider/R/print_lazy.R | 19 +- selenider-0.4.0/selenider/R/properties.R | 14 + selenider-0.4.0/selenider/R/rvest.R | 4 selenider-0.4.0/selenider/R/selector.R | 52 +++-- selenider-0.4.0/selenider/R/session-options.R | 2 selenider-0.4.0/selenider/R/session.R | 6 selenider-0.4.0/selenider/R/utils-errors.R | 21 -- selenider-0.4.0/selenider/R/utils.R | 22 ++ selenider-0.4.0/selenider/README.md | 2 selenider-0.4.0/selenider/build/vignette.rds |binary selenider-0.4.0/selenider/inst/doc/selenider.html | 4 selenider-0.4.0/selenider/inst/doc/unit-testing.html | 8 selenider-0.4.0/selenider/inst/doc/with-rvest.html | 4 selenider-0.4.0/selenider/man/as.list.selenider_elements.Rd | 88 +-------- selenider-0.4.0/selenider/man/back.Rd | 6 selenider-0.4.0/selenider/man/chromote_options.Rd | 2 selenider-0.4.0/selenider/man/elem_cache.Rd | 4 selenider-0.4.0/selenider/man/elem_flatmap.Rd |only selenider-0.4.0/selenider/man/find_each_element.Rd |only selenider-0.4.0/selenider/man/open_url.Rd | 4 selenider-0.4.0/selenider/man/print.selenider_element.Rd | 19 -- selenider-0.4.0/selenider/man/print_lazy.Rd |only selenider-0.4.0/selenider/man/reload.Rd | 6 selenider-0.4.0/selenider/man/take_screenshot.Rd | 2 selenider-0.4.0/selenider/tests/testthat/test-collections.R |only selenider-0.4.0/selenider/tests/testthat/test-global_actions.R | 2 selenider-0.4.0/selenider/tests/testthat/test-lazy_list.R | 1 selenider-0.4.0/selenider/tests/testthat/test-utils-errors.R | 12 - 51 files changed, 395 insertions(+), 290 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-19 1.0.4
2020-07-17 1.0.2
2020-07-08 0.24
2020-07-01 0.23
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-12 1.0-8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-02 0.4
2017-11-25 0.3
2017-08-06 0.2
2016-11-16 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-18 2.0
2014-09-17 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-03 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-02 1.0.1
2018-11-27 0.3.8
2018-10-04 0.3.7
2018-08-22 0.3.0
2018-07-24 0.2.6
2018-07-23 0.2.5
2018-06-12 0.2.0
2018-06-10 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-28 0.0-5
2015-06-29 0.0-4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-14 0.1.1
2019-05-20 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-05-12 1.0.4
2021-11-13 1.0.3
2021-07-06 1.0.2
2021-03-28 1.0.1
2021-02-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-20 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-12 1.0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-18 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-09-16 0.2.2
2015-04-11 0.2
2015-02-03 0.1.7
2014-12-03 0.1.6
2014-07-28 0.1.5
2014-05-19 0.1.4
2014-05-07 0.1.3
2014-04-02 0.1.2
2013-10-19 0.1.1
2013-10-17 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-21 1.0.4
2016-04-08 1.0.3
2015-09-09 1.0.2
2015-08-31 1.0.1
2015-08-26 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-30 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-19 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-27 0.1.1
2016-12-05 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-17 2.0.4
Title: qPCR Data Analysis
Description: Various methods are employed for statistical analysis and graphical presentation of real-time PCR (quantitative PCR or qPCR) data. 'rtpcr' handles amplification efficiency calculation, statistical analysis and graphical representation of real-time PCR data based on up to two reference genes. By accounting for amplification efficiency values, 'rtpcr' was developed using a general calculation method described by Ganger et al. (2017) <doi:10.1186/s12859-017-1949-5> and Taylor et al. (2019) <doi:10.1016/j.tibtech.2018.12.002>, covering both the Livak and Pfaffl methods. Based on the experimental conditions, the functions of the 'rtpcr' package use t-test (for experiments with a two-level factor) or analysis of variance (for cases where more than two levels or factors exist) to calculate the fold change or relative expression. The functions also provide standard deviations and confidence limits for means and apply statistical mean comparisons. To facilitate using 'rtpcr', diffe [...truncated...]
Author: Ghader Mirzaghaderi [aut, cre, cph]
Maintainer: Ghader Mirzaghaderi <gh.mirzaghaderi@uok.ac.ir>
Diff between rtpcr versions 1.0.3 dated 2024-04-13 and 1.0.4 dated 2024-04-20
rtpcr-1.0.3/rtpcr/data/data_ttest2.rda |only rtpcr-1.0.3/rtpcr/inst/extdata/data_ttest2.csv |only rtpcr-1.0.3/rtpcr/man/data_ttest2.Rd |only rtpcr-1.0.4/rtpcr/DESCRIPTION | 8 rtpcr-1.0.4/rtpcr/MD5 | 79 +-- rtpcr-1.0.4/rtpcr/R/efficiency.r | 7 rtpcr-1.0.4/rtpcr/R/meanTech.r | 1 rtpcr-1.0.4/rtpcr/R/multiplot.r | 2 rtpcr-1.0.4/rtpcr/R/oneFACTORplot.r | 31 - rtpcr-1.0.4/rtpcr/R/package_data.r | 11 rtpcr-1.0.4/rtpcr/R/qpcrANCOVA.r | 128 ++++- rtpcr-1.0.4/rtpcr/R/qpcrANOVA.r | 39 - rtpcr-1.0.4/rtpcr/R/qpcrTTEST.r | 43 + rtpcr-1.0.4/rtpcr/R/qpcrTTESTplot.r | 81 ++- rtpcr-1.0.4/rtpcr/R/qpcrhlpr.r | 14 rtpcr-1.0.4/rtpcr/R/threeFACTORplot.r | 30 - rtpcr-1.0.4/rtpcr/R/twoFACTORplot.r | 34 - rtpcr-1.0.4/rtpcr/data/Taylor_etal2019.rda |only rtpcr-1.0.4/rtpcr/inst/doc/vignette.R | 36 + rtpcr-1.0.4/rtpcr/inst/doc/vignette.Rmd | 111 +++-- rtpcr-1.0.4/rtpcr/inst/doc/vignette.html | 463 +++++++++------------ rtpcr-1.0.4/rtpcr/inst/extdata/Taylor_etal2019.csv |only rtpcr-1.0.4/rtpcr/man/Lee_etal2020qPCR.Rd | 58 +- rtpcr-1.0.4/rtpcr/man/Taylor_etal2019.Rd |only rtpcr-1.0.4/rtpcr/man/data_1factor.Rd | 54 +- rtpcr-1.0.4/rtpcr/man/data_2factor.Rd | 56 +- rtpcr-1.0.4/rtpcr/man/data_2factorBlock.Rd | 58 +- rtpcr-1.0.4/rtpcr/man/data_3factor.Rd | 58 +- rtpcr-1.0.4/rtpcr/man/data_efficiency.Rd | 48 +- rtpcr-1.0.4/rtpcr/man/data_ttest.Rd | 50 +- rtpcr-1.0.4/rtpcr/man/data_withTechRep.Rd | 60 +- rtpcr-1.0.4/rtpcr/man/efficiency.Rd | 7 rtpcr-1.0.4/rtpcr/man/figures |only rtpcr-1.0.4/rtpcr/man/meanTech.Rd | 1 rtpcr-1.0.4/rtpcr/man/multiplot.Rd | 2 rtpcr-1.0.4/rtpcr/man/oneFACTORplot.Rd | 18 rtpcr-1.0.4/rtpcr/man/qpcrANCOVA.Rd | 44 + rtpcr-1.0.4/rtpcr/man/qpcrANOVA.Rd | 2 rtpcr-1.0.4/rtpcr/man/qpcrTTEST.Rd | 17 rtpcr-1.0.4/rtpcr/man/qpcrTTESTplot.Rd | 13 rtpcr-1.0.4/rtpcr/man/threeFACTORplot.Rd | 16 rtpcr-1.0.4/rtpcr/man/twoFACTORplot.Rd | 14 rtpcr-1.0.4/rtpcr/vignettes/vignette.Rmd | 111 +++-- 43 files changed, 1013 insertions(+), 792 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-04-18 0.31
2017-01-21 0.30
2017-01-09 0.21
2014-02-21 0.17
2013-06-26 0.16
2013-03-30 0.13
2013-03-01 0.11
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-28 1.2
2011-06-17 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-03-17 1.2.4
2022-03-28 1.2.3
2022-03-04 1.2.2
2022-01-23 1.2.1
2021-05-09 1.1.1
2021-02-17 1.1.0
2020-05-12 0.1.0