Title: Methods and Data for Spatial Epidemiology
Description: Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb],
Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>),
Michelle Ross [ctb],
Jon Wakefield [aut],
Mikael Moise [aut] (<https://orcid.org/0000-0002-3608-1178>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between SpatialEpi versions 1.2.4 dated 2021-07-27 and 1.2.5 dated 2021-08-02
DESCRIPTION | 12 - MD5 | 96 ++++++------ NEWS.md | 12 + R/EBpostthresh.R | 2 R/NYleukemia.R | 10 - R/NYleukemia_sf.R | 12 - R/bayes_cluster.R | 18 +- R/besag_newell.R | 32 ++-- R/circle.R | 6 R/create_geo_objects.R | 14 - R/eBayes.R | 10 - R/estimate_lambda.R | 4 R/expected.R | 4 R/grid2latlong.R | 2 R/kulldorff.R | 38 ++--- R/latlong2grid.R | 2 R/mapvariable.R | 8 - R/pennLC.R | 4 R/plotmap.R | 4 R/polygon2spatial_polygon.R | 10 - R/process_MCMC_sample.R | 8 - R/scotland.R | 10 - R/scotland_sf.R | 11 - R/sf_objects.R | 6 R/zones.R | 14 - data/NYleukemia_sf.rda |binary data/pennLC_sf.rda |binary inst/doc/install_geo_libraries.html | 4 man/EBpostthresh.Rd | 2 man/NYleukemia.Rd | 4 man/NYleukemia_sf.Rd | 6 man/bayes_cluster.Rd | 6 man/besag_newell.Rd | 4 man/circle.Rd | 2 man/create_geo_objects.Rd | 12 - man/eBayes.Rd | 4 man/estimate_lambda.Rd | 4 man/grid2latlong.Rd | 2 man/kulldorff.Rd | 6 man/latlong2grid.Rd | 2 man/mapvariable.Rd | 4 man/pennLC_sf.Rd | 2 man/plotmap.Rd | 2 man/polygon2spatial_polygon.Rd | 6 man/process_MCMC_sample.Rd | 2 man/scotland.Rd | 8 - man/scotland_sf.Rd | 9 - man/zones.Rd | 10 - vignettes/Manuscript/Manuscript.Rmd | 267 ++++++++++++------------------------ 49 files changed, 328 insertions(+), 389 deletions(-)
Title: Expand Tidy Output for Categorical Parameter Estimates
Description: Create additional rows and columns on broom::tidy() output to allow for easier control on categorical parameter estimates.
Author: Guy J. Abel [aut, cre] (<https://orcid.org/0000-0002-4893-5687>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between tidycat versions 0.1.1 dated 2020-06-05 and 0.1.2 dated 2021-08-02
DESCRIPTION | 14 MD5 | 11 NEWS.md | 11 R/tidy_categorical.R | 2 build/vignette.rds |binary inst/doc/intro.html | 1504 ++++----------------------------------------------- tests |only 7 files changed, 143 insertions(+), 1399 deletions(-)
Title: Create Summary Tables for Statistical Reports
Description: Contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>
Diff between tab versions 4.1.1 dated 2019-06-17 and 5.1.1 dated 2021-08-02
DESCRIPTION | 14 MD5 | 94 +++- NAMESPACE | 6 R/archived |only R/glm_v.R |only R/tab.R | 8 R/tabcoxph.R | 90 +--- R/tabfreq.R | 86 ---- R/tabfreq_svy.R | 61 --- R/tabgee.R | 100 +---- R/tabglm.R | 110 +---- R/tabmeans.R | 58 -- R/tabmeans_svy.R | 41 -- R/tabmedians.R | 58 -- R/tabmedians_svy.R | 49 -- R/tabmulti.R | 97 +--- R/tabmulti_svy.R | 73 --- R/tabreg.R | 48 -- R/toviewer.R |only build/vignette.rds |binary inst/doc/tab.R | 73 +-- inst/doc/tab.Rmd | 139 +------ inst/doc/tab.html | 878 ++++++++++++++++----------------------------- man/formatp.Rd | 10 man/glm_v.Rd |only man/tab.Rd | 5 man/tabcoxph.Rd | 60 +-- man/tabfreq.Rd | 71 +-- man/tabfreq.svy.Rd | 47 +- man/tabgee.Rd | 61 +-- man/tabglm.Rd | 66 +-- man/tabmeans.Rd | 54 +- man/tabmeans.svy.Rd | 35 - man/tabmedians.Rd | 53 +- man/tabmedians.svy.Rd | 35 - man/tabmulti.Rd | 59 +-- man/tabmulti.svy.Rd | 52 +- man/tabreg.Rd | 28 - man/toviewer.Rd |only vignettes/bibliography.bib | 67 --- vignettes/logistic.PNG |only vignettes/tab.Rmd | 139 +------ vignettes/tabmulti.PNG |only 43 files changed, 1015 insertions(+), 1910 deletions(-)
Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre],
Juan Francisco Gomez [ctb],
Matba Rofex [cph]
Maintainer: Augusto Hassel <mpi-augusto@primary.com.ar>
Diff between rRofex versions 2.0.5 dated 2021-04-28 and 2.0.6 dated 2021-08-02
DESCRIPTION | 6 +- MD5 | 10 ++-- NEWS.md | 108 +++++++++++++++++++++++++++---------------------- R/functions.R | 88 ++++++++++++++++++++++++---------------- README.md | 120 +++++++++++++++++++++++++++++++------------------------ build/rRofex.pdf |binary 6 files changed, 189 insertions(+), 143 deletions(-)
Title: Assign Treatments, Power Calculations, Balances, Impact
Evaluation of Experiments
Description: Assists in the whole process of designing and evaluating Randomized Control Trials.
Robust treatment assignment by strata/blocks, that handles misfits;
Power calculations of the minimum detectable treatment effect or minimum populations;
Balance tables of T-test of covariates;
Balance Regression: (treatment ~ all x variables) with F-test of null model;
Impact_evaluation: Impact evaluation regressions. This function
gives you the option to include control_vars, fixed effect variables,
cluster variables (for robust SE), multiple endogenous variables and
multiple heterogeneous variables (to test treatment effect heterogeneity)
summary_statistics: Function that creates a summary statistics table with statistics
rank observations in n groups: Creates a factor variable with n groups. Each group has
a min and max label attach to each category.
Athey, Susan, and Guido W. Imbens (2017) <arXiv:1607.00698>.
Author: Isidoro Garcia-Urquieta [aut, cre]
Maintainer: Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>
Diff between RCT versions 1.1 dated 2021-02-01 and 1.1.1 dated 2021-08-02
DESCRIPTION | 7 +++---- MD5 | 16 ++++++++-------- NEWS.md | 5 ++++- R/summary_statistics.R | 2 ++ R/treatment_assign.R | 9 +++++++++ inst/doc/my-vignette.html | 10 ++++++++++ man/RCT.Rd | 2 +- man/tau_min_probability.Rd | 4 ++-- tests/testthat/test_treatment_assign.R | 12 ++++++------ 9 files changed, 45 insertions(+), 22 deletions(-)
Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions
and use them to create shells (skeletons which must be manually
completed by the user) of test files to be tested with the 'testthat'
package. Sort of like python 'doctests' for R.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Thomas Quinn [rev] (<https://orcid.org/0000-0003-0286-6329>),
Laurent Gatto [rev] (<https://orcid.org/0000-0002-1520-2268>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between exampletestr versions 1.6.3 dated 2021-04-24 and 1.6.4 dated 2021-08-02
exampletestr-1.6.3/exampletestr/tests/testthat/no-files-in-r-dir.txt |only exampletestr-1.6.4/exampletestr/DESCRIPTION | 27 exampletestr-1.6.4/exampletestr/MD5 | 25 exampletestr-1.6.4/exampletestr/NEWS.md | 6 exampletestr-1.6.4/exampletestr/R/example-extraction.R | 6 exampletestr-1.6.4/exampletestr/R/utils.R | 2 exampletestr-1.6.4/exampletestr/inst/doc/one-file-at-a-time.html | 353 ++-------- exampletestr-1.6.4/exampletestr/inst/doc/one-function-at-a-time.html | 347 ++------- exampletestr-1.6.4/exampletestr/inst/doc/whole-package.html | 341 ++------- exampletestr-1.6.4/exampletestr/tests/testthat/test-example-extraction.R | 2 exampletestr-1.6.4/exampletestr/tests/testthat/test-files.R | 21 exampletestr-1.6.4/exampletestr/tests/testthat/test-functions.R | 10 exampletestr-1.6.4/exampletestr/tests/testthat/test-shell-creation.R | 1 exampletestr-1.6.4/exampletestr/tests/testthat/test-utils.R | 4 14 files changed, 312 insertions(+), 833 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.1.4 dated 2020-07-13 and 1.1.6.2 dated 2021-08-02
DESCRIPTION | 10 +++++----- MD5 | 26 ++++++++++++++------------ NEWS.md | 7 +++++++ R/ardlDlmForecast.main.R | 4 ++-- R/koyckDlm.R | 2 +- R/koyckDlm.default.R | 4 ++-- R/koyckDlm.main.R | 8 ++++++-- data/grainProduction.RData |only man/dLagM-package.Rd | 4 ++-- man/grainProduction.Rd |only man/koyckDlm.Rd | 5 ++++- man/seaLevelTempSOI.Rd | 8 ++++---- man/sunspotTemp.Rd | 4 ++-- man/warming.Rd | 4 ++-- man/wheat.Rd | 8 +++++--- 15 files changed, 56 insertions(+), 38 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre],
R Core Team [cph] (Traceback function sources.)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.14 dated 2021-04-30 and 1.4.15 dated 2021-08-01
unitizer-1.4.14/unitizer/tests/aunitizer.R |only unitizer-1.4.14/unitizer/tests/interactive |only unitizer-1.4.14/unitizer/tests/runtt.R |only unitizer-1.4.14/unitizer/tests/test_pkgs |only unitizer-1.4.14/unitizer/tests/testpkg1.R |only unitizer-1.4.14/unitizer/tests/testthat/helper |only unitizer-1.4.14/unitizer/tests/testthat/testthat.browse.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.capture.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.change.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.demo.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.error.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.exec.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.get.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.global.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.handledruns.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.inpkg.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.ischecks.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.item.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.list.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.misc.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.options.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.parse.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.prompt.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.random.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.rrename.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.rrepairenvs.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.search.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.section.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.shim.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.state.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.text.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.translate.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.upgrade.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.utz1.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.utz2.R |only unitizer-1.4.14/unitizer/tests/testthat/testthat.zzrunlast.R |only unitizer-1.4.14/unitizer/tests/unitizer |only unitizer-1.4.15/unitizer/DESCRIPTION | 10 unitizer-1.4.15/unitizer/MD5 | 395 +++------- unitizer-1.4.15/unitizer/NEWS.md | 18 unitizer-1.4.15/unitizer/R/browse.R | 92 +- unitizer-1.4.15/unitizer/R/browse.struct.R | 19 unitizer-1.4.15/unitizer/R/exec.R | 11 unitizer-1.4.15/unitizer/R/faux_prompt.R | 55 + unitizer-1.4.15/unitizer/R/get.R | 5 unitizer-1.4.15/unitizer/R/load.R | 162 ---- unitizer-1.4.15/unitizer/R/misc.R | 4 unitizer-1.4.15/unitizer/R/options.R | 28 unitizer-1.4.15/unitizer/R/prompt.R | 31 unitizer-1.4.15/unitizer/R/rename.R | 10 unitizer-1.4.15/unitizer/R/repairenvs.R | 5 unitizer-1.4.15/unitizer/R/translate.R | 174 ++-- unitizer-1.4.15/unitizer/R/unitize.R | 25 unitizer-1.4.15/unitizer/R/unitize.core.R | 287 +++---- unitizer-1.4.15/unitizer/R/unitizer.R | 20 unitizer-1.4.15/unitizer/R/unitizer.add.R | 6 unitizer-1.4.15/unitizer/R/upgrade.R | 46 + unitizer-1.4.15/unitizer/README.md | 7 unitizer-1.4.15/unitizer/build/vignette.rds |binary unitizer-1.4.15/unitizer/demo/unitizer.R | 2 unitizer-1.4.15/unitizer/inst/doc/u0_unitizer_index.html | 40 - unitizer-1.4.15/unitizer/inst/doc/u1_intro.html | 49 - unitizer-1.4.15/unitizer/inst/doc/u2_tests.html | 40 - unitizer-1.4.15/unitizer/inst/doc/u3_interactive-env.Rmd | 6 unitizer-1.4.15/unitizer/inst/doc/u3_interactive-env.html | 42 - unitizer-1.4.15/unitizer/inst/doc/u4_reproducible-tests.html | 40 - unitizer-1.4.15/unitizer/inst/doc/u5_miscellaneous.html | 40 - unitizer-1.4.15/unitizer/man/editCalls.Rd | 13 unitizer-1.4.15/unitizer/man/infer_unitizer_location.Rd | 5 unitizer-1.4.15/unitizer/man/repair_environments.Rd | 6 unitizer-1.4.15/unitizer/man/testthat_transcribe_file.Rd | 5 unitizer-1.4.15/unitizer/man/testthat_translate_file.Rd | 58 - unitizer-1.4.15/unitizer/man/unitize.Rd | 16 unitizer-1.4.15/unitizer/man/unitizer.opts.Rd | 3 unitizer-1.4.15/unitizer/man/unitizer_prompt.Rd | 6 unitizer-1.4.15/unitizer/tests/_helper |only unitizer-1.4.15/unitizer/tests/aammrtf |only unitizer-1.4.15/unitizer/tests/t-browser.R |only unitizer-1.4.15/unitizer/tests/t-browser.Rout.save |only unitizer-1.4.15/unitizer/tests/t-capture.R |only unitizer-1.4.15/unitizer/tests/t-capture.Rout.save |only unitizer-1.4.15/unitizer/tests/t-change.R |only unitizer-1.4.15/unitizer/tests/t-change.Rout.save |only unitizer-1.4.15/unitizer/tests/t-demo.R |only unitizer-1.4.15/unitizer/tests/t-demo.Rout.save |only unitizer-1.4.15/unitizer/tests/t-error.R |only unitizer-1.4.15/unitizer/tests/t-error.Rout.save |only unitizer-1.4.15/unitizer/tests/t-exec.R |only unitizer-1.4.15/unitizer/tests/t-exec.Rout.save |only unitizer-1.4.15/unitizer/tests/t-get.R |only unitizer-1.4.15/unitizer/tests/t-get.Rout.save |only unitizer-1.4.15/unitizer/tests/t-global.R |only unitizer-1.4.15/unitizer/tests/t-global.Rout.save |only unitizer-1.4.15/unitizer/tests/t-handledruns.R |only unitizer-1.4.15/unitizer/tests/t-handledruns.Rout.save |only unitizer-1.4.15/unitizer/tests/t-ischecks.R |only unitizer-1.4.15/unitizer/tests/t-ischecks.Rout.save |only unitizer-1.4.15/unitizer/tests/t-item.R |only unitizer-1.4.15/unitizer/tests/t-item.Rout.save |only unitizer-1.4.15/unitizer/tests/t-list.R |only unitizer-1.4.15/unitizer/tests/t-list.Rout.save |only unitizer-1.4.15/unitizer/tests/t-misc.R |only unitizer-1.4.15/unitizer/tests/t-misc.Rout.save |only unitizer-1.4.15/unitizer/tests/t-nav.R |only unitizer-1.4.15/unitizer/tests/t-nav.Rout.save |only unitizer-1.4.15/unitizer/tests/t-parse.R |only unitizer-1.4.15/unitizer/tests/t-parse.Rout.save |only unitizer-1.4.15/unitizer/tests/t-prompt.R |only unitizer-1.4.15/unitizer/tests/t-prompt.Rout.save |only unitizer-1.4.15/unitizer/tests/t-random.R |only unitizer-1.4.15/unitizer/tests/t-random.Rout.save |only unitizer-1.4.15/unitizer/tests/t-rename.R |only unitizer-1.4.15/unitizer/tests/t-rename.Rout.save |only unitizer-1.4.15/unitizer/tests/t-repairenvs.R |only unitizer-1.4.15/unitizer/tests/t-repairenvs.Rout.save |only unitizer-1.4.15/unitizer/tests/t-search.R |only unitizer-1.4.15/unitizer/tests/t-search.Rout.save |only unitizer-1.4.15/unitizer/tests/t-section.R |only unitizer-1.4.15/unitizer/tests/t-section.Rout.save |only unitizer-1.4.15/unitizer/tests/t-shim.R |only unitizer-1.4.15/unitizer/tests/t-shim.Rout.save |only unitizer-1.4.15/unitizer/tests/t-state.R |only unitizer-1.4.15/unitizer/tests/t-state.Rout.save |only unitizer-1.4.15/unitizer/tests/t-text.R |only unitizer-1.4.15/unitizer/tests/t-text.Rout.save |only unitizer-1.4.15/unitizer/tests/t-translate.R |only unitizer-1.4.15/unitizer/tests/t-translate.Rout.save |only unitizer-1.4.15/unitizer/tests/t-upgrade.R |only unitizer-1.4.15/unitizer/tests/t-upgrade.Rout.save |only unitizer-1.4.15/unitizer/tests/t-utz1.R |only unitizer-1.4.15/unitizer/tests/t-utz1.Rout.save |only unitizer-1.4.15/unitizer/tests/t-utz2.R |only unitizer-1.4.15/unitizer/tests/t-utz2.Rout.save |only unitizer-1.4.15/unitizer/tests/testthat/README |only unitizer-1.4.15/unitizer/tests/zz-check.R |only unitizer-1.4.15/unitizer/vignettes/u3_interactive-env.Rmd | 6 136 files changed, 795 insertions(+), 992 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 1.0.0.1 dated 2021-07-26 and 1.0.1 dated 2021-08-01
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++--------- R/Merge_methylation.R | 14 +++++++++++- R/RNA_seq.R | 31 ++++++++++++++++++++++------ R/zzz.R | 9 +++++++- README.md | 8 +++---- inst/doc/GeoTcgaData.R | 33 ++++++++++++++++++++++++------ inst/doc/GeoTcgaData.Rmd | 38 ++++++++++++++++++++++++++-------- inst/doc/GeoTcgaData.html | 50 ++++++++++++++++++++++++++++++++++------------ man/diff_RNA.Rd | 31 ++++++++++++++++++++++------ vignettes/GeoTcgaData.Rmd | 38 ++++++++++++++++++++++++++-------- 11 files changed, 207 insertions(+), 71 deletions(-)
Title: Fast Wild Cluster Bootstrap Inference for Linear Regression
Models
Description: Implementation of the fast algorithm for wild cluster bootstrap
inference developed in Roodman et al (2019, STATA Journal) for
linear regression models
<https://journals.sagepub.com/doi/full/10.1177/1536867X19830877>,
which makes it feasible to quickly calculate bootstrap test
statistics based on a large number of bootstrap draws even for
large samples - as long as the number of bootstrapping clusters
is not too large. Multiway clustering, regression weights,
bootstrap weights, fixed effects and subcluster bootstrapping
are supported. Further, both restricted (WCR) and unrestricted
(WCU) bootstrap are supported. Methods are provided for a variety
of fitted models, including 'lm()', 'feols()'
(from package 'fixest') and 'felm()' (from package 'lfe').
Author: Alexander Fischer [aut, cre],
David Roodman [aut],
Achim Zeileis [ctb] (Author of included sandwich fragments),
Nathaniel Graham [ctb] (Contributor to included sandwich fragments),
Susanne Koell [ctb] (Contributor to included sandwich fragments),
Laurent Berge [ctb] (Author of included fixest fragments),
Sebastian Krantz [ctb]
Maintainer: Alexander Fischer <alexander-fischer1801@t-online.de>
Diff between fwildclusterboot versions 0.3.5 dated 2021-06-20 and 0.3.6 dated 2021-08-01
DESCRIPTION | 8 MD5 | 54 +++--- NEWS.md | 8 R/boottest_felm.R | 3 R/boottest_fixest.R | 2 README.md | 1 inst/doc/fwildclusterboot.R | 82 ++++------ inst/doc/fwildclusterboot.Rmd | 84 ++++------ inst/doc/fwildclusterboot.html | 202 +++++++++++-------------- inst/tinytest/test_bootcluster.R | 52 +++--- inst/tinytest/test_crosstab.R | 35 ++-- inst/tinytest/test_deterministic_alpha_beta0.R | 12 - inst/tinytest/test_deterministic_default.R | 52 +++--- inst/tinytest/test_deterministic_weights.R | 52 +++--- inst/tinytest/test_error_warning.R | 20 +- inst/tinytest/test_impose_null.R | 36 ++-- inst/tinytest/test_nthreads.R | 12 - inst/tinytest/test_p_val_type.R | 8 inst/tinytest/test_small_n_cluster.R | 2 inst/tinytest/test_stata.R | 4 inst/tinytest/test_tidy.R | 14 - inst/tinytest/test_tol_maxiter.R | 12 - inst/tinytest/test_type.R | 12 - man/boottest.felm.Rd | 3 man/boottest.fixest.Rd | 2 src/RcppExports.cpp | 5 tests/tinytest.R | 7 vignettes/fwildclusterboot.Rmd | 84 ++++------ 28 files changed, 424 insertions(+), 444 deletions(-)
More information about fwildclusterboot at CRAN
Permanent link
Title: Colour Vision Models
Description: Colour vision models, colour spaces and colour thresholds. Provides flexibility to build user-defined colour vision models for n number of photoreceptor types. Also includes Vorobyev & Osorio (1998) Receptor Noise Limited models <doi:10.1098/rspb.1998.0302>, Chittka (1992) colour hexagon <doi:10.1007/BF00199331>, and Endler & Mielke (2005) model <doi:10.1111/j.1095-8312.2005.00540.x>. Models have been extended to accept any number of photoreceptor types.
Author: Felipe M. Gawryszewski
Maintainer: Felipe Malheiros Gawrysewski <f.gawry@gmail.com>
Diff between colourvision versions 2.0.3 dated 2021-01-31 and 2.0.4 dated 2021-08-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ R/colourvision_package.R | 6 +++--- build/partial.rdb |binary inst/doc/colourvision-vignette.html | 33 +++++++++++++++++++++++++-------- man/EMtetrahedron.Rd | 4 +--- 7 files changed, 45 insertions(+), 24 deletions(-)
Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny' apps and R markdown documents. A tree allows to represent hierarchical data (e.g. the contents of a directory). Similar to the 'shinyTree' package but offers more features and options, such as the grid extension, restricting the drag-and-drop behavior, and settings for the search functionality. It is possible to attach some data to the nodes of a tree and then to get these data in 'Shiny' when a node is selected. Also provides a 'Shiny' gadget allowing to manipulate one or more folders.
Author: Stéphane Laurent [aut, cre],
jQuery contributors [ctb, cph] (jQuery),
Ivan Bozhanov [ctb, cph] (jsTree),
Vedran Opacic [ctb, cph] (jsTree bootstrap theme),
Avi Deitcher [ctb, cph] (jsTreeGrid),
Philip Hutchison [ctb, cph] (PDFObject),
Terence Eden [ctb, cph] (SuperTinyIcons)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between jsTreeR versions 1.2.0 dated 2021-01-16 and 1.3.0 dated 2021-08-01
jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/jstree.js |only jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/jstree.yaml |only jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/lib/bootstrap-theme/style.css |only jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/lib/jquery |only jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/lib/jstree/dist/themes/default-dark/style.css |only jsTreeR-1.2.0/jsTreeR/inst/htmlwidgets/lib/jstree/dist/themes/default/style.css |only jsTreeR-1.3.0/jsTreeR/DESCRIPTION | 8 jsTreeR-1.3.0/jsTreeR/MD5 | 51 jsTreeR-1.3.0/jsTreeR/NAMESPACE | 6 jsTreeR-1.3.0/jsTreeR/NEWS.md | 80 jsTreeR-1.3.0/jsTreeR/R/folderGadget.R | 1548 +++++----- jsTreeR-1.3.0/jsTreeR/R/internal.R |only jsTreeR-1.3.0/jsTreeR/R/jstree-shiny.R |only jsTreeR-1.3.0/jsTreeR/R/jstree.R | 1339 ++------ jsTreeR-1.3.0/jsTreeR/R/jstreeExamples.R |only jsTreeR-1.3.0/jsTreeR/inst/examples |only jsTreeR-1.3.0/jsTreeR/inst/htmlwidgets/jstreer.js |only jsTreeR-1.3.0/jsTreeR/inst/htmlwidgets/jstreer.yaml |only jsTreeR-1.3.0/jsTreeR/inst/htmlwidgets/lib/jstree/dist/jstree.min.js | 12 jsTreeR-1.3.0/jsTreeR/man/folderGadget.Rd | 3 jsTreeR-1.3.0/jsTreeR/man/jsTreeR-imports.Rd | 2 jsTreeR-1.3.0/jsTreeR/man/jstree-shiny.Rd | 543 --- jsTreeR-1.3.0/jsTreeR/man/jstree.Rd | 22 jsTreeR-1.3.0/jsTreeR/man/jstreeExample.Rd |only jsTreeR-1.3.0/jsTreeR/man/jstreeExamples.Rd |only 25 files changed, 1302 insertions(+), 2312 deletions(-)
Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for
Analysis and Visualization
Description: Provides a consistent API to pull United States Department of
Agriculture census and survey data from the National Agricultural
Statistics Service (NASS) QuickStats service.
Author: Brad Lindblad [aut, cre],
Michael Thomas [ctb],
Alex Mindeman [ctb]
Maintainer: Brad Lindblad <me@bradlindblad.com>
Diff between tidyUSDA versions 0.3.1 dated 2021-03-12 and 0.3.2 dated 2021-08-01
DESCRIPTION | 20 - LICENSE | 4 MD5 | 16 NEWS.md | 7 R/getQuickstat.R | 115 +++++- README.md | 3 build/vignette.rds |binary inst/doc/using_tidyusda.html | 722 ++++++++++++++++++++++++------------------- man/tidyUSDA.Rd | 2 9 files changed, 526 insertions(+), 363 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'Endnote', and 'Bibentry'.
Includes a port of the 'bibutils' utilities by Chris Putnam
<https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and
modifications to bibutils' C code, conversion to Bibentry (R and C
code)),
Chris Putman [aut] (src/*, author of the bibutils libraries,
https://sourceforge.net/projects/bibutils/),
Richard Mathar [ctb] (src/addsout.c),
Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2.1 dated 2021-06-17 and 2.2.2 dated 2021-07-31
DESCRIPTION | 8 +++---- MD5 | 11 +++++----- NEWS.md | 10 +++++++++ build/partial.rdb |binary inst/bib/easyPubMedvig_no_new_lines.xml |only src/medin.c | 33 ++++++++++++++++++++++++++++++-- tests/testthat/test-convert.R | 11 ++++++++++ 7 files changed, 62 insertions(+), 11 deletions(-)
Title: Latin Hypercube Designs (LHDs)
Description: Contains different algorithms and construction methods for optimal Latin hypercube designs (LHDs) with flexible sizes. Our package is comprehensive since it is capable of generating maximin distance LHDs, maximum projection LHDs, and orthogonal and nearly orthogonal LHDs. Detailed comparisons and summary of all the algorithms and construction methods in this package can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <arXiv:2010.09154>. This package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, design of computer experiments.
Author: Hongzhi Wang [aut, cre],
Qian Xiao [aut],
Abhyuday Mandal [aut]
Maintainer: Hongzhi Wang <hw34508@uga.edu>
Diff between LHD versions 1.3.2 dated 2021-04-05 and 1.3.3 dated 2021-07-31
DESCRIPTION | 20 MD5 | 18 NEWS.md | 4 R/GA.R | 28 - R/LaPSO.R | 48 -- R/OASA.R | 32 - R/SA.R | 32 - R/SA2008.R | 32 - R/SLHD.R | 48 -- inst/doc/Vignette_for_LHD.html | 869 ++++++++++++++++++++++++++++++----------- 10 files changed, 782 insertions(+), 349 deletions(-)
Title: Setting the Critical Path
Description: Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation and Review Technique)
and LESS (Least Cost Estimating and Scheduling) methods. The package sets the critical path,
schedule and Gantt chart. In addition, it allows you to draw a graph with marked critical activities. For more information about
project management, see: Taha H. A. (2017, ISBN:978-1-292-16554-7), Konarzewska I., Jewczak M., Kucharski A. (2020, ISBN:978-83-8220-112-3),
Rama Murthy P. (2007, ISBN:978-81-224-2944-2).
Author: Adam Kucharski
Maintainer: Adam Kucharski <aqcharski@interia.pl>
Diff between critpath versions 0.1.3 dated 2021-06-27 and 0.1.4 dated 2021-07-31
DESCRIPTION | 8 +- MD5 | 22 +++-- NAMESPACE | 2 NEWS | 4 + R/criticalpath_methodsAOE.R | 130 ++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/CPMandPERT.R | 18 ++++ inst/doc/CPMandPERT.Rmd | 47 ++++++++++-- inst/doc/CPMandPERT.html | 164 ++++++++++++++++++++++++++++++-------------- inst/doc/LESS.html | 5 - man/plot_alap.Rd |only man/plot_asap.Rd |only vignettes/CPMandPERT.Rmd | 47 ++++++++++-- 13 files changed, 362 insertions(+), 85 deletions(-)
Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] (<https://orcid.org/0000-0002-0515-9542>),
EDJNet [fnd]
Maintainer: Giorgio Comai <g@giorgiocomai.eu>
Diff between tidywikidatar versions 0.3.0 dated 2021-06-07 and 0.4.0 dated 2021-07-31
DESCRIPTION | 8 - MD5 | 28 +++--- NAMESPACE | 3 NEWS.md | 6 + R/tw_get_cached_search.R | 2 R/tw_get_others.R | 30 +++++- R/tw_get_property.R | 133 ++++++++++++++++++++++++++++- R/tw_get_property_with_details.R |only R/tw_query.R | 13 +- README.md | 5 + man/tw_get_label.Rd | 10 ++ man/tw_get_property.Rd | 8 + man/tw_get_property_same_length.Rd |only man/tw_get_property_with_details.Rd |only man/tw_get_property_with_details_single.Rd |only man/tw_query.Rd | 13 +- tests/testthat/test-cache.R | 2 17 files changed, 223 insertions(+), 38 deletions(-)
Title: Supplementary Tools for R Packages Developers
Description: Supplementary utils for CRAN maintainers and R packages developers.
Validating the library or packages.
Exploring a complexity of a specific package like evaluating sizes in bytes of all its dependencies.
Assessing the life duration of a specific package version.
Checking a package CRAN check page status for any errors and warnings.
Retrieving a DESCRIPTION file for any package version.
Getting a list of all releases for a specific package.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between pacs versions 0.2.5 dated 2021-07-29 and 0.2.8 dated 2021-07-31
pacs-0.2.5/pacs/man/pacs_checkred.Rd |only pacs-0.2.5/pacs/man/pacs_deps.Rd |only pacs-0.2.5/pacs/man/pacs_description.Rd |only pacs-0.2.5/pacs/man/pacs_health.Rd |only pacs-0.2.5/pacs/man/pacs_lifeduration.Rd |only pacs-0.2.5/pacs/man/pacs_size.Rd |only pacs-0.2.5/pacs/man/pacs_timemachine.Rd |only pacs-0.2.5/pacs/man/pacs_validate.Rd |only pacs-0.2.8/pacs/DESCRIPTION | 14 +- pacs-0.2.8/pacs/MD5 | 62 +++++------- pacs-0.2.8/pacs/NAMESPACE | 14 +- pacs-0.2.8/pacs/NEWS.md | 23 ++++ pacs-0.2.8/pacs/R/comapre.R | 12 ++ pacs-0.2.8/pacs/R/deps.R | 74 +-------------- pacs-0.2.8/pacs/R/deps_timemachine.R | 5 - pacs-0.2.8/pacs/R/description.R | 71 ++++---------- pacs-0.2.8/pacs/R/lifeduration.R | 124 +++++++++---------------- pacs-0.2.8/pacs/R/pacs.R |only pacs-0.2.8/pacs/R/size.R | 43 +------- pacs-0.2.8/pacs/R/timemachine.R | 46 +++------ pacs-0.2.8/pacs/R/utils.R | 125 ++++++++++++-------------- pacs-0.2.8/pacs/R/valid.R | 134 +++++++++------------------- pacs-0.2.8/pacs/README.md | 131 ++++++++++++--------------- pacs-0.2.8/pacs/man/lib_validate.Rd | 21 ++-- pacs-0.2.8/pacs/man/pac_checkred.Rd | 10 +- pacs-0.2.8/pacs/man/pac_compare_versions.Rd | 9 + pacs-0.2.8/pacs/man/pac_deps.Rd | 4 pacs-0.2.8/pacs/man/pac_deps_timemachine.Rd | 4 pacs-0.2.8/pacs/man/pac_description.Rd | 15 ++- pacs-0.2.8/pacs/man/pac_health.Rd | 15 ++- pacs-0.2.8/pacs/man/pac_last.Rd |only pacs-0.2.8/pacs/man/pac_lifeduration.Rd | 17 ++- pacs-0.2.8/pacs/man/pac_size.Rd | 2 pacs-0.2.8/pacs/man/pac_timemachine.Rd | 11 ++ pacs-0.2.8/pacs/man/pac_true_size.Rd | 7 - pacs-0.2.8/pacs/man/pac_validate.Rd | 15 ++- pacs-0.2.8/pacs/tests/testthat/test-base.R | 98 +++++--------------- 37 files changed, 474 insertions(+), 632 deletions(-)
Title: Adaptive Best Subset Selection in Polynomial Time
Description: Extremely efficient toolkit for solving the best subset selection problem in linear regression, logistic regression, Poisson regression, Cox proportional hazard model, multiple-response regression, multinomial logistic regression, and (sequential) principal component analysis. It implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times.
Author: Jin Zhu [aut, cre] (<https://orcid.org/0000-0001-8550-5822>),
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] (<https://orcid.org/0000-0002-0688-4076>),
Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>),
spectra contributors [cph] (Spectra implementation)
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between abess versions 0.1.0 dated 2021-04-21 and 0.2.0 dated 2021-07-31
abess-0.1.0/abess/inst/doc/abess-guide.R |only abess-0.1.0/abess/inst/doc/abess-guide.Rmd |only abess-0.1.0/abess/inst/doc/abess-guide.html |only abess-0.1.0/abess/src/powell.cpp |only abess-0.1.0/abess/src/tmp |only abess-0.1.0/abess/vignettes/abess-guide.Rmd |only abess-0.1.0/abess/vignettes/crime.jpg |only abess-0.2.0/abess/DESCRIPTION | 23 abess-0.2.0/abess/LICENSE |only abess-0.2.0/abess/MD5 | 170 - abess-0.2.0/abess/NAMESPACE | 65 abess-0.2.0/abess/NEWS.md | 20 abess-0.2.0/abess/R/RcppExports.R | 14 abess-0.2.0/abess/R/abess-package.R | 94 abess-0.2.0/abess/R/abess.R | 1856 ++++++----- abess-0.2.0/abess/R/abesspca.R |only abess-0.2.0/abess/R/coef.abess.R | 138 abess-0.2.0/abess/R/coef.abesspca.R |only abess-0.2.0/abess/R/deviance.abess.R | 98 abess-0.2.0/abess/R/extract.abess.R | 198 - abess-0.2.0/abess/R/omit |only abess-0.2.0/abess/R/plot.abess.R | 307 - abess-0.2.0/abess/R/predict.abess.R | 193 - abess-0.2.0/abess/R/print.abess.R | 64 abess-0.2.0/abess/R/print.abesspca.R |only abess-0.2.0/abess/R/tmp |only abess-0.2.0/abess/R/utility.R | 774 ++-- abess-0.2.0/abess/README.md | 93 abess-0.2.0/abess/build/vignette.rds |binary abess-0.2.0/abess/inst/CITATION | 32 abess-0.2.0/abess/inst/doc/v01-abess-guide.R |only abess-0.2.0/abess/inst/doc/v01-abess-guide.Rmd |only abess-0.2.0/abess/inst/doc/v01-abess-guide.html |only abess-0.2.0/abess/inst/include |only abess-0.2.0/abess/man/abess-package.Rd | 77 abess-0.2.0/abess/man/abess.Rd | 586 +-- abess-0.2.0/abess/man/abesspca.Rd |only abess-0.2.0/abess/man/coef.abess.Rd | 76 abess-0.2.0/abess/man/coef.abesspca.Rd |only abess-0.2.0/abess/man/deviance.abess.Rd | 66 abess-0.2.0/abess/man/extract.abess.Rd | 94 abess-0.2.0/abess/man/generate.data.Rd | 267 - abess-0.2.0/abess/man/plot.abess.Rd | 114 abess-0.2.0/abess/man/predict.abess.Rd | 88 abess-0.2.0/abess/man/print.abess.Rd | 70 abess-0.2.0/abess/man/print.abesspca.Rd |only abess-0.2.0/abess/man/trim32.Rd | 52 abess-0.2.0/abess/src/Algorithm.cpp | 10 abess-0.2.0/abess/src/Algorithm.h | 3260 ++++++-------------- abess-0.2.0/abess/src/Data.h | 22 abess-0.2.0/abess/src/Makevars | 2 abess-0.2.0/abess/src/Makevars.win | 2 abess-0.2.0/abess/src/Metric.h | 817 ----- abess-0.2.0/abess/src/RcppExports.cpp | 13 abess-0.2.0/abess/src/abess.cpp | 608 ++- abess-0.2.0/abess/src/abess.h | 22 abess-0.2.0/abess/src/model_fit.cpp | 944 ----- abess-0.2.0/abess/src/model_fit.h | 865 +++++ abess-0.2.0/abess/src/normalize.cpp | 12 abess-0.2.0/abess/src/normalize.h | 5 abess-0.2.0/abess/src/path.cpp | 814 +--- abess-0.2.0/abess/src/path.h | 461 ++ abess-0.2.0/abess/src/screening.cpp | 210 - abess-0.2.0/abess/src/screening.h | 211 + abess-0.2.0/abess/src/utilities.cpp | 514 +-- abess-0.2.0/abess/src/utilities.h | 133 abess-0.2.0/abess/tests/testthat/Rplots.pdf |only abess-0.2.0/abess/tests/testthat/test-abess-group.R |only abess-0.2.0/abess/tests/testthat/test-abess.R | 662 ++-- abess-0.2.0/abess/tests/testthat/test-abesspca.R |only abess-0.2.0/abess/tests/testthat/test-exception.R |only abess-0.2.0/abess/tests/testthat/test-generic.R | 225 - abess-0.2.0/abess/tests/testthat/test-screening.R | 304 - abess-0.2.0/abess/tests/testthat/test-sparse.R |only abess-0.2.0/abess/tests/testthat/utility.R |only abess-0.2.0/abess/vignettes/Hitters.csv |only abess-0.2.0/abess/vignettes/communities.data |only abess-0.2.0/abess/vignettes/lung.csv |only abess-0.2.0/abess/vignettes/readmeTiming.png |only abess-0.2.0/abess/vignettes/sgsplicing.png |only abess-0.2.0/abess/vignettes/train.csv |only abess-0.2.0/abess/vignettes/v01-abess-guide.Rmd |only 82 files changed, 7461 insertions(+), 8284 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 2.2.0 dated 2021-07-26 and 2.2.1 dated 2021-07-31
DESCRIPTION | 12 ++++++------ MD5 | 23 +++++++++++++---------- NEWS.md | 5 +++++ R/convert_umlauts_to_tex.R | 6 +----- R/paths.R | 9 +++++++-- inst/NEWS.rd | 7 +++++++ inst/runit_tests/runit-csv.R | 7 ++----- inst/runit_tests/runit-memory_hogs.R | 10 +++++----- inst/runit_tests/runit-paths.R | 3 +-- inst/runit_tests/runit-with_dir.R | 5 ++--- inst/tinytest |only tests/testthat/test-csv.R |only tests/testthat/test-throw.R | 1 - tests/tinytest.R |only 14 files changed, 49 insertions(+), 39 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb],
Dominik Schneider [ctb],
Gerold Hepp [ctb],
Zunaira Jamile [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.10.1 dated 2021-02-08 and 0.10.2 dated 2021-07-31
DESCRIPTION | 19 - MD5 | 28 - NAMESPACE | 2 NEWS.md | 13 R/cache.R | 10 R/load.project.R | 2 build/partial.rdb |binary inst/defaults/templates/full/config/global.dcf | 2 inst/defaults/templates/minimal/config/global.dcf | 2 man/cache.Rd | 2 tests/testthat/test-cache.R | 318 +++++++++++----------- tests/testthat/test-list.R | 2 tests/testthat/test-load.R | 40 +- tests/testthat/test-qs.R | 26 + tests/testthat/test-readers.R | 34 ++ 15 files changed, 297 insertions(+), 203 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy
to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>
Diff between postcards versions 0.2.1 dated 2021-07-30 and 0.2.2 dated 2021-07-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ inst/pandoc_templates/solana.html | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024>
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>).
WARNING: This package is NOT under active development anymore, no further improvements are to be expected, and the package is at risk of being removed from CRAN.
Author: Simen Gaure [aut] (<https://orcid.org/0000-0001-7251-8747>),
Grant McDermott [ctb],
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb, cre] (<https://orcid.org/0000-0002-6802-4290>),
Daniel Lüdecke [ctb]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between lfe versions 2.8-6 dated 2021-01-11 and 2.8-7 dated 2021-07-31
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 7 ++++++- inst/devtools_internal.R | 6 ++++++ inst/doc/biascorrection.pdf |binary inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary src/utils.c | 11 +---------- tests/degenerate.Rout.save | 8 ++++---- 12 files changed, 32 insertions(+), 30 deletions(-)
Title: Isotope Calculations in R
Description: Perform common calculations based on published stable isotope theory, such as calculating carbon isotope discrimination and intrinsic water use efficiency from wood or leaf carbon isotope composition. See Farquhar, O'Leary, and Berry (1982) <doi:10.1071/PP9820121>.
Author: Justin Mathias
Maintainer: Justin Mathias <justin.m.mathias@gmail.com>
Diff between isocalcR versions 0.0.1 dated 2021-07-08 and 0.0.2 dated 2021-07-31
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/CO2data.R | 2 +- R/d13C.to.Ci.R | 2 +- R/d13C.to.CiCa.R | 2 +- R/d13C.to.diffCaCi.R | 2 +- R/d13C.to.iWUE.R | 2 +- README.md | 40 ++++++++++++++++++++++++++++++++++++++-- data/CO2data.rda |binary man/CO2data.Rd | 2 +- 11 files changed, 62 insertions(+), 22 deletions(-)
Title: Work with Datasets in the Ecological Community Design Pattern
Description: Tools to create, use, and convert 'ecocomDP' datasets. 'ecocomDP' is a dataset design pattern for harmonizing ecological community surveys in a research question agnostic format, from source datasets published across multiple repositories, and with methods that keep the derived datasets up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.
Author: Colin Smith [aut, cre, cph] (<https://orcid.org/0000-0003-2261-9931>),
Eric Sokol [aut] (<https://orcid.org/0000-0001-5923-0917>),
Margaret O'Brien [aut] (<https://orcid.org/0000-0002-1693-8322>),
Matt Bitters [ctb],
Melissa Chen [ctb],
Savannah Gonzales [ctb],
Matt Helmus [ctb],
Brendan Hobart [ctb],
Ruvi Jaimes [ctb],
Lara Janson [ctb],
Marta Jarzyna [ctb],
Michael Just [ctb],
Daijiang Li [ctb],
Wynne Moss [ctb],
Kari Norman [ctb],
Stephanie Parker [ctb],
Natalie Robinson [ctb],
Thilina Surasinghe [ctb]
Maintainer: Colin Smith <colin.smith@wisc.edu>
Diff between ecocomDP versions 1.0.0 dated 2021-06-10 and 1.1.0 dated 2021-07-31
DESCRIPTION | 21 LICENSE | 2 MD5 | 284 NAMESPACE | 66 NEWS.md | 32 R/EAL_make_eml.R | 2796 +++--- R/EAL_template_arguments.R | 896 +- R/EAL_validate.R | 1680 ++-- R/convert_to_dwca.R | 1491 +-- R/create_dataset_summary.R | 320 R/create_eml.R | 1377 +-- R/create_location.R | 376 R/create_location_ancillary.R | 125 R/create_observation.R | 138 R/create_observation_ancillary.R | 114 R/create_taxon.R | 126 R/create_taxon_ancillary.R | 145 R/create_variable_mapping.R | 258 R/data.R | 153 R/flatten_data.R | 806 + R/map_neon.ecocomdp.10003.001.001.R | 384 R/map_neon.ecocomdp.10022.001.001.R | 662 - R/map_neon.ecocomdp.10022.001.002.R | 758 - R/map_neon.ecocomdp.10043.001.001.R | 710 - R/map_neon.ecocomdp.10058.001.001.R | 472 - R/map_neon.ecocomdp.10072.001.001.R | 560 - R/map_neon.ecocomdp.10092.001.001.R | 730 - R/map_neon.ecocomdp.10093.001.001.R | 1368 +-- R/map_neon.ecocomdp.20107.001.001.R | 794 - R/map_neon.ecocomdp.20120.001.001.R | 484 - R/map_neon.ecocomdp.20166.001.001.R | 554 - R/map_neon.ecocomdp.20219.001.001.R | 374 R/map_neon_data_to_ecocomDP.r | 390 R/neon_helper_functions.r | 358 R/plot_taxa.R | 848 +- R/read_data.R | 981 +- R/save_data.R | 150 R/search_data.R | 812 +- R/taxonomyCleanr.R | 2856 +++---- R/utilities.R | 4048 +++++----- R/validate_arguments.R | 981 +- R/validate_data.R | 1620 ++-- R/zzz.R | 120 README.md | 122 build/vignette.rds |binary data/ants_L0_flat.rda |binary data/ants_L1.rda |binary inst/doc/convert.R | 142 inst/doc/convert.Rmd | 178 inst/doc/convert.html | 647 - inst/doc/create.R | 1155 +- inst/doc/create.Rmd | 1201 +- inst/doc/create.html | 1670 +--- inst/doc/use.R | 487 - inst/doc/use.Rmd | 632 - inst/doc/use.html | 1149 +- inst/extdata/L1_versions.txt | 26 inst/extdata/create_ecocomDP.R | 869 +- inst/extdata/dwca_event_core/annotations.txt | 58 inst/extdata/dwca_event_core/attributes_event.txt | 18 inst/extdata/dwca_event_core/attributes_extendedmeasurementorfact.txt | 16 inst/extdata/dwca_event_core/attributes_occurrence.txt | 18 inst/extdata/dwca_event_core/keywords.txt | 18 inst/extdata/dwca_event_core/meta.xml | 102 inst/extdata/eal_templates/annotation_defaults.txt | 14 inst/extdata/eal_templates/annotations.txt | 2 inst/extdata/eal_templates/arguments.txt | 88 inst/extdata/eal_templates/bounding_boxes.txt | 2 inst/extdata/eal_templates/custom_units.txt | 2 inst/extdata/eal_templates/geographic_coverage.txt | 2 inst/extdata/eal_templates/intellectual_rights_cc0.txt | 2 inst/extdata/eal_templates/intellectual_rights_ccby4.0.txt | 2 inst/extdata/eal_templates/keywords.txt | 2 inst/extdata/eal_templates/personnel.txt | 2 inst/extdata/eal_templates/provenance.txt | 2 inst/extdata/eal_templates/taxonomic_coverage.txt | 2 inst/extdata/eal_templates/template_characteristics.txt | 32 inst/extdata/ecocomDP/annotations.txt | 124 inst/extdata/ecocomDP/attributes_dataset_summary.txt | 16 inst/extdata/ecocomDP/attributes_location.txt | 14 inst/extdata/ecocomDP/attributes_location_ancillary.txt | 14 inst/extdata/ecocomDP/attributes_observation.txt | 20 inst/extdata/ecocomDP/attributes_observation_ancillary.txt | 12 inst/extdata/ecocomDP/attributes_taxon.txt | 12 inst/extdata/ecocomDP/attributes_taxon_ancillary.txt | 16 inst/extdata/ecocomDP/attributes_variable_mapping.txt | 14 inst/extdata/ecocomDP/keywords.txt | 18 inst/extdata/neon-field-sites.csv | 164 inst/extdata/neon_data_products_for_ecocomDP.txt | 26 inst/extdata/table_descriptions.txt | 18 inst/extdata/template_characteristics.txt | 32 inst/extdata/validation_criteria.txt | 120 man/ants_L0_flat.Rd | 133 man/ants_L1.Rd | 54 man/calc_geo_extent_bounding_box_m2.Rd | 46 man/calc_length_of_survey_years.Rd | 34 man/calc_number_of_years_sampled.Rd | 34 man/calc_std_dev_interval_betw_years.Rd | 34 man/convert_to_dwca.Rd | 124 man/create_dataset_summary.Rd | 122 man/create_eml.Rd | 242 man/create_location.Rd | 115 man/create_location_ancillary.Rd | 94 man/create_observation.Rd | 138 man/create_observation_ancillary.Rd | 88 man/create_taxon.Rd | 110 man/create_taxon_ancillary.Rd | 110 man/create_variable_mapping.Rd | 158 man/flatten_data.Rd | 64 man/plot_taxa_accum_sites.Rd | 56 man/plot_taxa_accum_time.Rd | 56 man/plot_taxa_diversity.Rd | 56 man/plot_taxa_sample_time.Rd | 56 man/plot_taxa_shared_sites.Rd | 52 man/read_data.Rd | 274 man/save_data.Rd | 104 man/search_data.Rd | 150 man/validate_data.Rd | 124 man/view_descriptions.Rd | 40 man/view_diagram.Rd | 40 man/write_tables.Rd | 170 tests/testthat.R | 8 tests/testthat/test_convert_to_dwca.R | 68 tests/testthat/test_create_dataset_summary.R | 216 tests/testthat/test_create_eml.R | 108 tests/testthat/test_create_location.R | 94 tests/testthat/test_create_location_ancillary.R | 60 tests/testthat/test_create_observation.R | 74 tests/testthat/test_create_observation_ancillary.R | 60 tests/testthat/test_create_taxon.R | 66 tests/testthat/test_create_taxon_ancillary.R | 70 tests/testthat/test_create_variable_mapping.R | 122 tests/testthat/test_flatten_data.R | 308 tests/testthat/test_plot_taxa.R | 60 tests/testthat/test_read_data.R | 360 tests/testthat/test_save_data.R | 104 tests/testthat/test_search_data.R | 396 tests/testthat/test_utilities.R | 191 tests/testthat/test_validate_arguments.R | 1002 +- tests/testthat/test_validate_data.R | 1020 +- vignettes/convert.Rmd | 178 vignettes/create.Rmd | 1201 +- vignettes/use.Rmd | 632 - 143 files changed, 25463 insertions(+), 25315 deletions(-)
Title: Testing 'DBI' 'Backends'
Description: A helper that tests 'DBI' back ends for conformity
to the interface.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph],
R Consortium [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between DBItest versions 1.7.0 dated 2019-12-16 and 1.7.1 dated 2021-07-31
DESCRIPTION | 19 MD5 | 160 ++-- NAMESPACE | 1 NEWS.md | 31 R/context.R | 2 R/expectations.R | 9 R/import-testthat.R | 2 R/run.R | 88 +- R/s4.R | 9 R/spec-compliance-methods.R | 32 R/spec-compliance.R | 2 R/spec-connection-data-type.R | 8 R/spec-connection-disconnect.R | 16 R/spec-connection-get-info.R | 63 - R/spec-driver-connect.R | 67 - R/spec-driver-constructor.R | 11 R/spec-driver-data-type.R | 31 R/spec-driver-get-info.R | 5 R/spec-getting-started.R | 7 R/spec-meta-bind-.R | 36 - R/spec-meta-bind-runner.R | 22 R/spec-meta-bind-tester-extra.R | 2 R/spec-meta-bind.R | 336 ++++----- R/spec-meta-column-info.R | 194 ++--- R/spec-meta-get-info-result.R | 63 - R/spec-meta-get-row-count.R | 172 ++-- R/spec-meta-get-rows-affected.R | 104 +- R/spec-meta-get-statement.R | 76 -- R/spec-meta-has-completed.R | 126 +-- R/spec-meta-is-valid.R | 68 - R/spec-result-clear-result.R | 47 - R/spec-result-create-table-with-data-type.R | 48 - R/spec-result-execute.R | 95 +- R/spec-result-fetch.R | 373 ++++------ R/spec-result-get-query.R | 235 ++---- R/spec-result-roundtrip.R | 312 +++----- R/spec-result-send-query.R | 141 +-- R/spec-result-send-statement.R | 160 +--- R/spec-result.R | 4 R/spec-sql-append-table.R | 676 ++++++++---------- R/spec-sql-create-table.R | 320 +++----- R/spec-sql-exists-table.R | 140 +-- R/spec-sql-list-fields.R | 139 +-- R/spec-sql-list-objects.R | 242 +++--- R/spec-sql-list-tables.R | 117 +-- R/spec-sql-quote-identifier.R | 276 +++---- R/spec-sql-quote-literal.R | 240 +++--- R/spec-sql-quote-string.R | 274 +++---- R/spec-sql-read-table.R | 361 ++++------ R/spec-sql-remove-table.R | 221 ++---- R/spec-sql-unquote-identifier.R | 254 +++---- R/spec-sql-write-table.R | 1006 ++++++++++++---------------- R/spec-transaction-begin-commit-rollback.R | 234 ++---- R/spec-transaction-with-transaction.R | 145 +--- R/spec-transaction.R | 2 R/test-all.R | 19 R/tweaks.R | 39 - R/utils.R | 134 +-- R/zzz.R | 2 README.md | 7 build/vignette.rds |binary inst/WORDLIST |only inst/doc/DBItest.R | 10 inst/doc/DBItest.Rmd | 37 - inst/doc/DBItest.html | 380 ++-------- man/context.Rd | 2 man/spec_compliance_methods.Rd |only man/spec_driver_constructor.Rd |only man/spec_getting_started.Rd |only man/spec_meta_bind.Rd | 7 man/spec_result_roundtrip.Rd | 2 man/spec_sql_append_table.Rd | 3 man/spec_sql_create_table.Rd | 3 man/spec_sql_exists_table.Rd | 1 man/spec_sql_list_objects.Rd | 5 man/spec_sql_list_tables.Rd | 5 man/spec_sql_read_table.Rd | 2 man/spec_sql_write_table.Rd | 1 man/test_all.Rd | 8 man/tweaks.Rd | 8 tests/testthat/test-consistency.R | 15 tests/testthat/test-lint.R | 2 vignettes/DBItest.Rmd | 37 - 83 files changed, 3908 insertions(+), 4645 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds
has developed flexible code for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
<http://www.ApolloChoiceModelling.com>. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess,
S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview
of the field.
Author: Stephane Hess [aut],
David Palma [aut, cre],
Thomas Hancock [ctb]
Maintainer: David Palma <D.Palma@leeds.ac.uk>
Diff between apollo versions 0.2.4 dated 2021-02-25 and 0.2.5 dated 2021-07-31
apollo-0.2.4/apollo/R/apollo_cppScript.R |only apollo-0.2.4/apollo/R/apollo_lcUnconditionals.r |only apollo-0.2.4/apollo/man/apollo_cppScript.Rd |only apollo-0.2.5/apollo/DESCRIPTION | 14 apollo-0.2.5/apollo/MD5 | 134 +- apollo-0.2.5/apollo/NAMESPACE | 9 apollo-0.2.5/apollo/R/apollo_attach.R | 13 apollo-0.2.5/apollo/R/apollo_avgInterDraws.R | 8 apollo-0.2.5/apollo/R/apollo_avgIntraDraws.R | 8 apollo-0.2.5/apollo/R/apollo_basTest.R | 27 apollo-0.2.5/apollo/R/apollo_bootstrap.R | 21 apollo-0.2.5/apollo/R/apollo_choiceAnalysis.R | 23 apollo-0.2.5/apollo/R/apollo_classAlloc.R |only apollo-0.2.5/apollo/R/apollo_combineModels.R | 2 apollo-0.2.5/apollo/R/apollo_combineResults.R | 147 +- apollo-0.2.5/apollo/R/apollo_compareInputs.R | 8 apollo-0.2.5/apollo/R/apollo_dVdB.R | 53 apollo-0.2.5/apollo/R/apollo_estimate.R | 156 +- apollo-0.2.5/apollo/R/apollo_estimateHB.R | 35 apollo-0.2.5/apollo/R/apollo_expandLoop.R |only apollo-0.2.5/apollo/R/apollo_fmnl.R |only apollo-0.2.5/apollo/R/apollo_insertFunc.R | 244 ++- apollo-0.2.5/apollo/R/apollo_lc.R | 60 apollo-0.2.5/apollo/R/apollo_lcUnconditionals.R |only apollo-0.2.5/apollo/R/apollo_lrTest.R | 31 apollo-0.2.5/apollo/R/apollo_makeCluster.R | 2 apollo-0.2.5/apollo/R/apollo_makeDraws.R | 4 apollo-0.2.5/apollo/R/apollo_makeGrad.R | 28 apollo-0.2.5/apollo/R/apollo_makeLogLike.R | 74 - apollo-0.2.5/apollo/R/apollo_mdcev.R | 73 - apollo-0.2.5/apollo/R/apollo_mdcev2.R |only apollo-0.2.5/apollo/R/apollo_mdcnev.R | 3 apollo-0.2.5/apollo/R/apollo_mnl.R | 28 apollo-0.2.5/apollo/R/apollo_modelOutput.R | 21 apollo-0.2.5/apollo/R/apollo_nl.R | 6 apollo-0.2.5/apollo/R/apollo_normalDensity.R | 6 apollo-0.2.5/apollo/R/apollo_ol.R | 2 apollo-0.2.5/apollo/R/apollo_outOfSample.R | 9 apollo-0.2.5/apollo/R/apollo_panelProd.R | 12 apollo-0.2.5/apollo/R/apollo_prediction.R | 529 ++++---- apollo-0.2.5/apollo/R/apollo_prepareProb.R | 303 ++-- apollo-0.2.5/apollo/R/apollo_preprocess.R | 133 +- apollo-0.2.5/apollo/R/apollo_readBeta.R | 24 apollo-0.2.5/apollo/R/apollo_saveOutput.R | 44 apollo-0.2.5/apollo/R/apollo_searchStart.R | 3 apollo-0.2.5/apollo/R/apollo_validate.R | 109 + apollo-0.2.5/apollo/R/apollo_validateControl.R | 12 apollo-0.2.5/apollo/R/apollo_validateInputs.R | 5 apollo-0.2.5/apollo/R/apollo_varList.R | 312 ++-- apollo-0.2.5/apollo/R/apollo_varcov.R | 14 apollo-0.2.5/apollo/R/apollo_writeF12.R | 4 apollo-0.2.5/apollo/R/apollo_writeTheta.R | 20 apollo-0.2.5/apollo/inst/doc/apollofirstexample.R | 12 apollo-0.2.5/apollo/inst/doc/apollofirstexample.Rmd | 812 ++++++------ apollo-0.2.5/apollo/inst/doc/apollofirstexample.html | 1240 ++++++++----------- apollo-0.2.5/apollo/man/apollo_bootstrap.Rd | 9 apollo-0.2.5/apollo/man/apollo_choiceAnalysis.Rd | 1 apollo-0.2.5/apollo/man/apollo_classAlloc.Rd |only apollo-0.2.5/apollo/man/apollo_combineResults.Rd | 2 apollo-0.2.5/apollo/man/apollo_estimate.Rd | 4 apollo-0.2.5/apollo/man/apollo_expandLoop.Rd |only apollo-0.2.5/apollo/man/apollo_fmnl.Rd |only apollo-0.2.5/apollo/man/apollo_insertFunc.Rd | 4 apollo-0.2.5/apollo/man/apollo_lcUnconditionals.Rd | 2 apollo-0.2.5/apollo/man/apollo_makeLogLike.Rd | 2 apollo-0.2.5/apollo/man/apollo_mdcev.Rd | 3 apollo-0.2.5/apollo/man/apollo_mdcev2.Rd |only apollo-0.2.5/apollo/man/apollo_nl.Rd | 2 apollo-0.2.5/apollo/man/apollo_prediction.Rd | 1 apollo-0.2.5/apollo/man/apollo_saveOutput.Rd | 4 apollo-0.2.5/apollo/man/apollo_validateControl.Rd | 1 apollo-0.2.5/apollo/man/apollo_varList.Rd | 28 apollo-0.2.5/apollo/man/apollo_varcov.Rd | 2 apollo-0.2.5/apollo/vignettes/apollofirstexample.Rmd | 812 ++++++------ 74 files changed, 3079 insertions(+), 2635 deletions(-)
Title: Pretty Notifications for 'Shiny'
Description: This is a wrapper of the 'React' library 'React-Toastify'. It allows to show some notifications (toasts) in 'Shiny' applications. There are options for the style, the position, the transition effect, and more.
Author: Stéphane Laurent [aut, cre],
Fadi Khadra [cph] ('React-Toastify' library
(https://fkhadra.github.io/react-toastify/introduction))
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between shinyToastify versions 1.0.0 dated 2021-07-15 and 2.0.0 dated 2021-07-31
DESCRIPTION | 8 MD5 | 21 +- NAMESPACE | 3 NEWS.md | 17 ++ R/toastify.R | 197 ++++++++++++++++++++++-- README.md | 4 inst/examples/icons |only inst/examples/toastUpdate |only inst/www/shinyToastify/toastify/toastify.js | 49 +++++ inst/www/shinyToastify/toastify/toastify.js.map | 2 man/showToast.Rd | 23 ++ man/toastUpdate.Rd |only 12 files changed, 294 insertions(+), 30 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible,
giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.6.3 dated 2021-06-22 and 0.6.4 dated 2021-07-31
tidytable-0.6.3/tidytable/tests/testthat/test-arrange_across.R |only tidytable-0.6.3/tidytable/tests/testthat/test-mutate_across.R |only tidytable-0.6.3/tidytable/tests/testthat/test-summarize_across.R |only tidytable-0.6.4/tidytable/DESCRIPTION | 6 tidytable-0.6.4/tidytable/MD5 | 94 +++++----- tidytable-0.6.4/tidytable/NAMESPACE | 11 - tidytable-0.6.4/tidytable/NEWS.md | 22 ++ tidytable-0.6.4/tidytable/R/arrange_across.R | 2 tidytable-0.6.4/tidytable/R/between.R | 15 - tidytable-0.6.4/tidytable/R/bind.R | 4 tidytable-0.6.4/tidytable/R/case_when.R | 2 tidytable-0.6.4/tidytable/R/fill.R | 24 -- tidytable-0.6.4/tidytable/R/filter.R | 21 ++ tidytable-0.6.4/tidytable/R/get_dummies.R | 19 -- tidytable-0.6.4/tidytable/R/mutate.R | 16 + tidytable-0.6.4/tidytable/R/mutate_across.R | 2 tidytable-0.6.4/tidytable/R/n_distinct.R | 20 +- tidytable-0.6.4/tidytable/R/pivot_longer.R | 23 -- tidytable-0.6.4/tidytable/R/pivot_wider.R | 48 ++--- tidytable-0.6.4/tidytable/R/pull.R | 16 + tidytable-0.6.4/tidytable/R/separate.R | 17 + tidytable-0.6.4/tidytable/R/separate_rows.R | 8 tidytable-0.6.4/tidytable/R/summarize_across.R | 2 tidytable-0.6.4/tidytable/R/tidytable-package.R | 7 tidytable-0.6.4/tidytable/R/tidytable.R | 11 - tidytable-0.6.4/tidytable/R/unite.R | 4 tidytable-0.6.4/tidytable/R/unnest.R | 70 +++++-- tidytable-0.6.4/tidytable/R/unnest_longer.R |only tidytable-0.6.4/tidytable/R/unnest_wider.R |only tidytable-0.6.4/tidytable/R/utils-general.R | 52 +++++ tidytable-0.6.4/tidytable/R/utils-prep_exprs.R | 42 +++- tidytable-0.6.4/tidytable/man/between..Rd | 15 - tidytable-0.6.4/tidytable/man/mutate..Rd | 9 tidytable-0.6.4/tidytable/man/pivot_wider..Rd | 11 - tidytable-0.6.4/tidytable/man/pull..Rd | 4 tidytable-0.6.4/tidytable/man/reexports.Rd | 3 tidytable-0.6.4/tidytable/man/separate..Rd | 3 tidytable-0.6.4/tidytable/man/unnest..Rd | 17 + tidytable-0.6.4/tidytable/man/unnest_longer..Rd |only tidytable-0.6.4/tidytable/man/unnest_wider..Rd |only tidytable-0.6.4/tidytable/tests/testthat/test-bind.R | 28 ++ tidytable-0.6.4/tidytable/tests/testthat/test-deprec-across.R |only tidytable-0.6.4/tidytable/tests/testthat/test-filter.R | 6 tidytable-0.6.4/tidytable/tests/testthat/test-mutate.R | 9 tidytable-0.6.4/tidytable/tests/testthat/test-n_distinct.R | 14 - tidytable-0.6.4/tidytable/tests/testthat/test-pivot_longer.R | 4 tidytable-0.6.4/tidytable/tests/testthat/test-pivot_wider.R | 2 tidytable-0.6.4/tidytable/tests/testthat/test-pull.R | 11 + tidytable-0.6.4/tidytable/tests/testthat/test-separate.R | 10 + tidytable-0.6.4/tidytable/tests/testthat/test-tidytable.R | 9 tidytable-0.6.4/tidytable/tests/testthat/test-unnest.R | 20 ++ tidytable-0.6.4/tidytable/tests/testthat/test-unnest_longer.R |only tidytable-0.6.4/tidytable/tests/testthat/test-unnest_wider.R |only 53 files changed, 499 insertions(+), 234 deletions(-)
Title: Monotonic Optimal Binning
Description: Generate the monotonic binning and
perform the woe (weight of evidence) transformation for the logistic regression
used in the consumer credit scorecard development. The woe transformation is a piecewise
transformation that is linear to the log odds. For a numeric variable, all of its monotonic
functional transformations will converge to the same woe transformation.
Author: WenSui Liu
Maintainer: WenSui Liu <liuwensui@gmail.com>
Diff between mob versions 0.4.1 dated 2021-04-05 and 0.4.2 dated 2021-07-31
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/pool_bin.R | 11 ++++++++--- man/pool_bin.Rd | 6 ++++-- 4 files changed, 18 insertions(+), 11 deletions(-)
Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Geomas: geom_table(), geom_plot() and geom_grob() add insets to
plots using native data coordinates, while geom_table_npc(), geom_plot_npc()
and geom_grob_npc() do the same using "npc" coordinates through new
aesthetics "npcx" and "npcy". Statistics: select observations based on 2D
density. Positions: radial nudging away from a center point and nudging away
from a line or curve.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpp versions 0.4.1 dated 2021-07-14 and 0.4.2 dated 2021-07-31
DESCRIPTION | 10 MD5 | 48 +-- NAMESPACE | 4 NEWS.md | 46 ++- R/geom-text-linked.r | 23 + R/geom-text-npc.r | 1 R/stat-apply.R | 531 ++++++++++++++++++++++++++------------- R/stat-dens1d-filter.r | 20 - R/stat-dens1d-labels.r | 85 +++--- R/stat-dens2d-filter.r | 20 - R/stat-dens2d-labels.r | 61 ++-- R/stat-quadrant-counts.R | 20 - inst/doc/grammar-extensions.R | 91 +++--- inst/doc/grammar-extensions.Rmd | 132 ++++----- inst/doc/grammar-extensions.html | 34 +- man/geom_text_linked.Rd | 2 man/geom_text_npc.Rd | 1 man/ggpp-ggproto.Rd | 148 +++++----- man/stat_apply.Rd | 448 ++++++++++++++++++-------------- man/stat_dens1d_filter.Rd | 20 - man/stat_dens1d_labels.Rd | 85 +++--- man/stat_dens2d_filter.Rd | 20 - man/stat_dens2d_labels.Rd | 61 ++-- man/stat_quadrant_counts.Rd | 20 - vignettes/grammar-extensions.Rmd | 132 ++++----- 25 files changed, 1218 insertions(+), 845 deletions(-)
Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest
Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the 'Rcpp' package,
exposing the same interface as the original Python wrapper to 'Annoy'. See
<https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released
under Version 2.0 of the Apache License. Also included is a small Windows
port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAnnoy versions 0.0.18 dated 2020-12-15 and 0.0.19 dated 2021-07-30
ChangeLog | 10 ++++++++++ DESCRIPTION | 11 +++++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/UsingAnnoyInCcppWrapper.pdf |binary 6 files changed, 28 insertions(+), 9 deletions(-)
Title: Bounding Omitted Variable Bias Using Auxiliary Data
Description: Functions to implement a Hwang(2021) <doi:10.2139/ssrn.3866876> estimator, which bounds an omitted variable bias using auxiliary data.
Author: Yujung Hwang [aut, cre] (<https://orcid.org/0000-0002-8136-8987>)
Maintainer: Yujung Hwang <yujungghwang@gmail.com>
Diff between bndovb versions 1.0 dated 2021-06-21 and 1.1 dated 2021-07-30
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/bndovbme.R | 35 +++++++++++++++++++++++++++-------- build/partial.rdb |binary inst/doc/bndovb.html | 14 +++++++------- 5 files changed, 41 insertions(+), 22 deletions(-)
Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy
to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>
Diff between postcards versions 0.2.0 dated 2021-01-06 and 0.2.1 dated 2021-07-30
DESCRIPTION | 9 +--- MD5 | 34 +++++++++------ NAMESPACE | 1 NEWS.md | 4 + R/create.R | 11 ++-- R/postcards.R | 8 +++ README.md | 60 +++++++++++++++++++++++++-- inst/img/sigridur.jpg |only inst/pandoc_templates/solana.html |only inst/rmarkdown/templates/solana |only inst/rstudio/templates/project/postcards.dcf | 2 man/create_postcard.Rd | 3 - man/figures/solana-preview.png |only man/figures/trestles-preview.png |binary man/jolla.Rd | 5 +- man/jolla_blue.Rd | 5 +- man/onofre.Rd | 5 +- man/solana.Rd |only man/trestles.Rd | 5 +- tests/testthat/test-postcards.R | 1 20 files changed, 120 insertions(+), 33 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.6.0 dated 2019-07-09 and 1.7.0 dated 2021-07-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/mice.impute.2l.glm.bin.R | 7 +++---- R/mice.impute.2l.glm.norm.R | 4 ++-- R/mice.impute.2l.glm.pois.R | 7 +++---- R/overimpute.R | 10 +++++----- man/mice.par.Rd | 2 +- man/overimpute.Rd | 2 +- 8 files changed, 26 insertions(+), 28 deletions(-)
Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<http://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre]
(<https://orcid.org/0000-0003-3506-5376>),
Manuel Leiva [aut] (<https://orcid.org/0000-0001-8891-0399>),
Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>
Diff between AtmChile versions 0.1.1 dated 2021-07-13 and 0.1.2 dated 2021-07-30
DESCRIPTION | 6 +-- MD5 | 10 +++--- R/ChileAirQuality.R | 74 ++++++++++++------------------------------------ R/ChileClimateData.R | 8 ++--- man/ChileAirQuality.Rd | 2 - man/ChileClimateData.Rd | 6 +-- 6 files changed, 35 insertions(+), 71 deletions(-)
Title: Distance Sampling Survey Design
Description: Creates survey designs for distance sampling surveys. These
designs can be assessed for various effort and coverage statistics.
Once the user is satisfied with the design characteristics they can
generate a set of transects to use in their distance sampling survey.
Many of the designs implemented in this R package were first made
available in our 'Distance' for Windows software and are detailed in
Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008,
ISBN-13: 978-0199225873). Find out more about estimating animal/plant
abundance with distance sampling at <http://distancesampling.org/>.
Author: Laura Marshall [aut, cre],
Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between dssd versions 0.2.2 dated 2021-02-25 and 0.3.0 dated 2021-07-30
dssd-0.2.2/dssd/inst/extdata/TrackExample.prj |only dssd-0.2.2/dssd/tests/testthat/test-SegmentedDesign.r |only dssd-0.2.2/dssd/tests/testthat/test-UserInput.r |only dssd-0.2.2/dssd/tests/testthat/test-xdonttest.R |only dssd-0.3.0/dssd/DESCRIPTION | 38 - dssd-0.3.0/dssd/MD5 | 66 +- dssd-0.3.0/dssd/NAMESPACE | 12 dssd-0.3.0/dssd/NEWS | 18 dssd-0.3.0/dssd/R/Class.Constructors.R | 100 +-- dssd-0.3.0/dssd/R/Line.Transect.Design.R | 4 dssd-0.3.0/dssd/R/Point.Transect.Design.R | 3 dssd-0.3.0/dssd/R/Region.R | 262 +++----- dssd-0.3.0/dssd/R/calculate.effort.R |only dssd-0.3.0/dssd/R/calculate.trackline.segl.R | 3 dssd-0.3.0/dssd/R/check.design.R |only dssd-0.3.0/dssd/R/check.line.design.R | 393 +++++++----- dssd-0.3.0/dssd/R/check.point.design.R | 254 ++++--- dssd-0.3.0/dssd/R/dssd-package.R | 2 dssd-0.3.0/dssd/README.md |only dssd-0.3.0/dssd/build/vignette.rds |binary dssd-0.3.0/dssd/inst/doc/GettingStarted.R | 12 dssd-0.3.0/dssd/inst/doc/GettingStarted.Rmd | 21 dssd-0.3.0/dssd/inst/doc/GettingStarted.html | 338 +++------- dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.R | 10 dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.Rmd | 14 dssd-0.3.0/dssd/inst/doc/MultiStrataVignette.html | 484 +++++---------- dssd-0.3.0/dssd/man/Line.Transect.Design-class.Rd | 2 dssd-0.3.0/dssd/man/calculate.effort.Rd |only dssd-0.3.0/dssd/man/dssd-package.Rd | 2 dssd-0.3.0/dssd/man/make.coverage.Rd | 16 dssd-0.3.0/dssd/man/make.design.Rd | 48 + dssd-0.3.0/dssd/man/plot.Region-methods.Rd | 48 + dssd-0.3.0/dssd/tests/test-that.R | 2 dssd-0.3.0/dssd/tests/testthat/test-check_CalcEffort.R |only dssd-0.3.0/dssd/tests/testthat/test-check_DesignParams.R |only dssd-0.3.0/dssd/tests/testthat/test-check_Designs.R |only dssd-0.3.0/dssd/tests/testthat/test-check_SegDesign.R |only dssd-0.3.0/dssd/tests/testthat/test-check_UserInput.R |only dssd-0.3.0/dssd/tests/testthat/test-x_seed_tests.R |only dssd-0.3.0/dssd/vignettes/GettingStarted.Rmd | 21 dssd-0.3.0/dssd/vignettes/MultiStrataVignette.Rmd | 14 41 files changed, 1077 insertions(+), 1110 deletions(-)
Title: Retrieval Functions for USGS and EPA Hydrologic and Water
Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey
(USGS) and U.S. Environmental Protection Agency (EPA) water quality and
hydrology data from web services. USGS web services are discovered from
National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>.
Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>),
David Lorenz [aut],
Jordan Read [ctb],
Jordan Walker [ctb],
Lindsay Carr [ctb],
David Watkins [aut] (<https://orcid.org/0000-0002-7544-0700>),
David Blodgett [ctb],
Mike Johnson [aut] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between dataRetrieval versions 2.7.8 dated 2021-06-26 and 2.7.9 dated 2021-07-30
dataRetrieval-2.7.8/dataRetrieval/vignettes/QW_changes_cache |only dataRetrieval-2.7.8/dataRetrieval/vignettes/atascadero-creek-nldi.png |only dataRetrieval-2.7.8/dataRetrieval/vignettes/ucsb.png |only dataRetrieval-2.7.9/dataRetrieval/DESCRIPTION | 8 dataRetrieval-2.7.9/dataRetrieval/MD5 | 55 -- dataRetrieval-2.7.9/dataRetrieval/NEWS | 6 dataRetrieval-2.7.9/dataRetrieval/R/findNLDI.R | 274 +++++----- dataRetrieval-2.7.9/dataRetrieval/R/getWebServiceData.R | 7 dataRetrieval-2.7.9/dataRetrieval/R/importRDB1.r | 27 dataRetrieval-2.7.9/dataRetrieval/R/readNWISdata.r | 15 dataRetrieval-2.7.9/dataRetrieval/R/readNWISqw.r | 24 dataRetrieval-2.7.9/dataRetrieval/R/whatNWISData.r | 7 dataRetrieval-2.7.9/dataRetrieval/build/vignette.rds |binary dataRetrieval-2.7.9/dataRetrieval/inst/CITATION | 2 dataRetrieval-2.7.9/dataRetrieval/inst/doc/dataRetrieval.html | 2 dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.R |only dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.Rmd |only dataRetrieval-2.7.9/dataRetrieval/inst/doc/qwdata_changes.html |only dataRetrieval-2.7.9/dataRetrieval/man/findNLDI.Rd | 6 dataRetrieval-2.7.9/dataRetrieval/man/readNWISdata.Rd | 4 dataRetrieval-2.7.9/dataRetrieval/man/readNWISqw.Rd | 21 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_general.R | 13 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_nldi.R | 2 dataRetrieval-2.7.9/dataRetrieval/tests/testthat/tests_userFriendly_fxns.R | 53 - dataRetrieval-2.7.9/dataRetrieval/vignettes/nwisData.rds |only dataRetrieval-2.7.9/dataRetrieval/vignettes/qwdata_changes.Rmd |only dataRetrieval-2.7.9/dataRetrieval/vignettes/wqpData.rds |only 27 files changed, 253 insertions(+), 273 deletions(-)
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre],
Pascal Obstétar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Diff between lidaRtRee versions 3.0.2 dated 2021-04-10 and 3.1.0 dated 2021-07-30
lidaRtRee-3.0.2/lidaRtRee/R/chmchablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/gap.detection.R |only lidaRtRee-3.0.2/lidaRtRee/R/laschablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/optical.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/quatremontagnes-data.R |only lidaRtRee-3.0.2/lidaRtRee/R/raster.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.detection.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.match.R |only lidaRtRee-3.0.2/lidaRtRee/R/tree.metrics.R |only lidaRtRee-3.0.2/lidaRtRee/R/treeinventorychablais3-data.R |only lidaRtRee-3.0.2/lidaRtRee/data/chmchablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/data/laschablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/data/quatremontagnes.rda |only lidaRtRee-3.0.2/lidaRtRee/data/treeinventorychablais3.rda |only lidaRtRee-3.0.2/lidaRtRee/man/ABAinference.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodel.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelCombineStrata.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABAmodelPlot.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/ABApredict.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/AddVegetationIndices.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/BoxcoxTr.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/chmchablais3.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cleanRaster.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cloudMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/cloudTreeMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/createDisk.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/demFiltering.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/edgeDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/gapDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/heightRegression.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/histDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/histStack.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/iBoxcoxTr.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/iBoxcoxTrBiasCor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/laschablais3.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/lmaCheck.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/maximaDetection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/maximaSelection.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/plot2Dmatched.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/plotTreeInventory.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/points2terrainStats.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/quatremontagnes.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterChullMask.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterLocalmax.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterXYMask.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rasterZonalStats.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/rastersMovingCor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/segAdjust.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/speciesColor.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/stdTreeMetrics.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeExtraction.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeMatching.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeSegmentation.Rd |only lidaRtRee-3.0.2/lidaRtRee/man/treeinventorychablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/DESCRIPTION | 18 lidaRtRee-3.1.0/lidaRtRee/MD5 | 159 - lidaRtRee-3.1.0/lidaRtRee/NAMESPACE | 78 lidaRtRee-3.1.0/lidaRtRee/R/aba.R | 1342 +++++++----- lidaRtRee-3.1.0/lidaRtRee/R/chm_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/common.R | 668 +++-- lidaRtRee-3.1.0/lidaRtRee/R/coregistration.R | 479 ++-- lidaRtRee-3.1.0/lidaRtRee/R/gap_detection.R |only lidaRtRee-3.1.0/lidaRtRee/R/las_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/metrics.R | 496 ++-- lidaRtRee-3.1.0/lidaRtRee/R/optical_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/R/quatre_montagnes-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/raster_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_detection.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_inventory_chablais3-data.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_match.R |only lidaRtRee-3.1.0/lidaRtRee/R/tree_metrics.R |only lidaRtRee-3.1.0/lidaRtRee/build/partial.rdb |binary lidaRtRee-3.1.0/lidaRtRee/data/chm_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/data/las_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/data/quatre_montagnes.rda |only lidaRtRee-3.1.0/lidaRtRee/data/tree_inventory_chablais3.rda |only lidaRtRee-3.1.0/lidaRtRee/man/aba_build_model.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_combine_strata.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_inference.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_plot.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/aba_predict.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/add_vegetation_indices.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_itr.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_itr_bias_cor.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/boxcox_tr.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/chm_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/cimg2Raster.Rd | 25 lidaRtRee-3.1.0/lidaRtRee/man/circle2Raster.Rd | 3 lidaRtRee-3.1.0/lidaRtRee/man/clean_raster.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/clouds_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/clouds_tree_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/coregistration.Rd | 61 lidaRtRee-3.1.0/lidaRtRee/man/create_disk.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/dem_filtering.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/edge_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/ellipses4Crown.Rd | 25 lidaRtRee-3.1.0/lidaRtRee/man/gap_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/height_regression.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/hist_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/hist_stack.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/las_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/lma_check.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/maxima_detection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/maxima_selection.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/plot_matched.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/plot_tree_inventory.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/pointList2SPDF.Rd | 23 lidaRtRee-3.1.0/lidaRtRee/man/points2DSM.Rd | 11 lidaRtRee-3.1.0/lidaRtRee/man/points2DTM.Rd | 18 lidaRtRee-3.1.0/lidaRtRee/man/polar2Projected.Rd | 38 lidaRtRee-3.1.0/lidaRtRee/man/quatre_montagnes.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster2Cimg.Rd | 24 lidaRtRee-3.1.0/lidaRtRee/man/raster_chull_mask.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_local_max.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_xy_mask.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/raster_zonal_stats.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/rasters2Cor.Rd | 45 lidaRtRee-3.1.0/lidaRtRee/man/rasters_moving_cor.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/seg_adjust.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/segmentation.Rd | 42 lidaRtRee-3.1.0/lidaRtRee/man/species_color.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/std_tree_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/terrain_points_metrics.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_extraction.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_inventory_chablais3.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_matching.Rd |only lidaRtRee-3.1.0/lidaRtRee/man/tree_segmentation.Rd |only lidaRtRee-3.1.0/lidaRtRee/tests |only 132 files changed, 2022 insertions(+), 1533 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04>.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.8.3 dated 2020-09-28 and 2.9.0 dated 2021-07-30
ThresholdROC-2.8.3/ThresholdROC/data/AD.txt |only ThresholdROC-2.8.3/ThresholdROC/data/chemo.txt |only ThresholdROC-2.9.0/ThresholdROC/DESCRIPTION | 14 ThresholdROC-2.9.0/ThresholdROC/MD5 | 20 ThresholdROC-2.9.0/ThresholdROC/NAMESPACE | 5 ThresholdROC-2.9.0/ThresholdROC/R/ThresholdROC-2states.R | 282 +++++++++++- ThresholdROC-2.9.0/ThresholdROC/data/AD.txt.gz |only ThresholdROC-2.9.0/ThresholdROC/data/chemo.txt.gz |only ThresholdROC-2.9.0/ThresholdROC/man/SS.Rd | 9 ThresholdROC-2.9.0/ThresholdROC/man/ThresholdROC-package.Rd | 4 ThresholdROC-2.9.0/ThresholdROC/man/plotCostROC.Rd | 2 ThresholdROC-2.9.0/ThresholdROC/man/thres2.Rd | 27 + ThresholdROC-2.9.0/ThresholdROC/man/thresTH2.Rd | 7 13 files changed, 319 insertions(+), 51 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download (and re-arrange, in the
case of NDVI3g.v0) the half-monthly data sets; import downloaded files from
ENVI binary (NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based
on the widespread 'raster' package; conduct quality control; and generate
monthly composites (e.g., maximum values) from the half-monthly input data.
As a special gimmick, a method is included to conveniently apply the
Mann-Kendall trend test upon 'Raster*' images, optionally featuring
trend-free pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between gimms versions 1.2.0 dated 2021-04-16 and 1.2.1 dated 2021-07-30
DESCRIPTION | 7 -- MD5 | 30 ++++----- NEWS.md | 11 +++ R/gimmsControls.R | 16 +++- R/significantTau.R | 4 - R/updateInventory.R | 127 +++++++++++++++++++++++++++++++++++++-- README.md | 6 + build/partial.rdb |binary data/bale3g.v1.rda |binary data/kili3g.v0.rda |binary inst/extdata/poles.html |only inst/tinytest/test-getPolesFTP.R |only inst/tinytest/tests.R | 8 ++ man/downloadGimms.Rd | 6 - man/gimms-package.Rd | 20 +++--- man/significantTau.Rd | 4 - man/updateInventory.Rd | 18 ++--- 17 files changed, 206 insertions(+), 51 deletions(-)
Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics
and geometries echoing their data argument. Layer manipulation: deletion,
insertion, extraction and reordering of layers. Deletion of unused variables
from the data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between gginnards versions 0.1.0 dated 2021-05-27 and 0.1.0-1 dated 2021-07-30
DESCRIPTION | 14 ++-- MD5 | 40 +++++------ NEWS.md | 7 ++ R/data-manip.R | 14 ++-- R/geom-debug.R | 19 +++-- R/layer-manip.R | 58 ++++++++-------- README.md | 6 - inst/doc/user-guide-1.html | 6 - inst/doc/user-guide-2.R | 10 +- inst/doc/user-guide-2.Rmd | 14 ++-- inst/doc/user-guide-2.html | 106 +++++++++++++++++-------------- man/delete_layers.Rd | 56 ++++++++-------- man/drop_vars.Rd | 12 ++- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/geom_debug.Rd | 10 +- man/geom_null.Rd | 9 +- man/gginnards-package.Rd | 2 vignettes/user-guide-2.Rmd | 14 ++-- 21 files changed, 223 insertions(+), 174 deletions(-)
Title: Adoption Probability, Triers and Users Rate of a New Product
Description: Calculate users prevalence of a product based on the prevalence of triers in the population. The measurement of triers is relatively easy. It is just a question of whether a person tried a product even once in his life or not. On the other hand, The measurement of people who also adopt it as part of their life is more complicated since adopting an innovative product is a subjective view of the individual. Mickey Kislev and Shira Kislev developed a formula to calculate the prevalence of a product's users to overcome this difficulty. The current package assists in calculating the users prevalence of a product based on the prevalence of triers in the population. See for: Kislev, M. M., and S. Kislev (2020) <doi:10.5539/ijms.v12n4p63>.
Author: Mickey Kislev [cre],
Shira Kislev [aut]
Maintainer: Mickey Kislev <mickeykislev@researchgap.ac>
Diff between ADP versions 0.1.3 dated 2021-07-28 and 0.1.5 dated 2021-07-30
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/ADP.R | 14 ++++++-------- man/ADP.Rd | 2 +- man/adp.t.Rd | 2 +- man/adp.u.Rd | 2 +- man/ptriers.Rd | 2 +- man/pusers.Rd | 4 ++-- 8 files changed, 24 insertions(+), 26 deletions(-)
Title: An R Package to Retrieve, Analyze and Visualize Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation
data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows
retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala, Daniel Ayala, David Ruiz, Aleix Sellés, Lara Sellés Vidal
Maintainer: Rafael Ayala <rafael.ayala@oist.jp>
Diff between openSkies versions 1.1.1 dated 2021-04-17 and 1.1.2 dated 2021-07-30
DESCRIPTION | 10 - MD5 | 21 +- NAMESPACE | 1 NEWS | 4 R/openSkies_classDefinitions.R | 8 + R/openSkies_formatResponseFunctions.R | 2 R/openSkies_getStateVectorsFunctions.R | 50 ++++++ R/openSkies_otherSupportFunctions.R | 31 +++ build/vignette.rds |binary inst/doc/openSkies.html | 262 +++++++++++++++------------------ man/getIntervalFlights.Rd | 2 man/getIntervalStateVectors.Rd |only 12 files changed, 233 insertions(+), 158 deletions(-)
Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [aut, cre],
Michael A. Black [aut, ths],
Robrecht Cannoodt [ctb],
Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between graphsim versions 1.0.1 dated 2020-07-17 and 1.0.2 dated 2021-07-30
graphsim-1.0.1/graphsim/inst/doc/plots_directed.html |only graphsim-1.0.1/graphsim/inst/doc/plots_directed.html.asis |only graphsim-1.0.1/graphsim/vignettes/plots_directed.html.asis |only graphsim-1.0.2/graphsim/DESCRIPTION | 17 graphsim-1.0.2/graphsim/MD5 | 27 graphsim-1.0.2/graphsim/NEWS.md | 8 graphsim-1.0.2/graphsim/R/graphsim-package.R | 7 graphsim-1.0.2/graphsim/R/plot_directed.R | 1 graphsim-1.0.2/graphsim/README.md | 13 graphsim-1.0.2/graphsim/build/partial.rdb |only graphsim-1.0.2/graphsim/build/vignette.rds |binary graphsim-1.0.2/graphsim/inst/CITATION | 2 graphsim-1.0.2/graphsim/inst/doc/simulate_expression.html | 1711 ++++++------- graphsim-1.0.2/graphsim/man/graphsim-package.Rd | 7 graphsim-1.0.2/graphsim/vignettes/import_reactome.html |only graphsim-1.0.2/graphsim/vignettes/plots_directed.Rmd | 3 graphsim-1.0.2/graphsim/vignettes/simulate_expression.Rmd | 22 17 files changed, 923 insertions(+), 895 deletions(-)
Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization,
Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the
product of two low-dimensional matrices aided with secondary information matrices about rows
and/or columns of 'X' which are also factorized using the same latent components.
The intended usage is for recommender systems, dimensionality reduction, and missing value imputation.
Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce
different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky,
(2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model,
(Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>),
or the enhanced model with 'implicit features' (Rendle, Zhang,
Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based
procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009)
<doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver
(Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative
coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>),
providing efficient methods for sparse and dense data, and mixtures thereof.
Supports L1 and L2 regularization in the main models,
offers alternative most-popular and content-based models, and implements functionality
for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph],
Jorge Nocedal [cph] (Copyright holder of included LBFGS library),
Naoaki Okazaki [cph] (Copyright holder of included LBFGS library),
David Blackman [cph] (Copyright holder of original Xoshiro code),
Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between cmfrec versions 3.2.1 dated 2021-07-29 and 3.2.2 dated 2021-07-30
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/helpers.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Machine Learning Time Series Forecasting
Description: Compute both static and recursive time series forecasts of machine learning models.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iForecast versions 1.0.2 dated 2021-02-21 and 1.0.3 dated 2021-07-30
DESCRIPTION | 8 ++++---- MD5 | 8 +++++--- R/rollingWindows.R |only man/iForecast.Rd | 2 +- man/rollingWindows.Rd |only man/ttsCaret.Rd | 6 +++--- 6 files changed, 13 insertions(+), 11 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.4.12 dated 2021-07-13 and 0.4.15 dated 2021-07-30
DESCRIPTION | 13 ++++--------- MD5 | 24 ++++++++++++------------ NEWS.md | 17 ++++++++++++++++- R/attachment.R | 4 ++-- R/body.R | 12 +++++++++++- R/server.R | 4 +++- README.md | 8 ++++---- man/attachment.Rd | 11 +++++++++-- man/html.Rd | 6 +++++- tests/testthat/setup-files.R | 9 +++++++-- tests/testthat/teardown-files.R | 2 +- tests/testthat/test-body.R | 9 +++++++++ tests/testthat/test-server.R | 2 +- 13 files changed, 84 insertions(+), 37 deletions(-)
Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading,
analyzing and visualizing datasets from UCSC Xena
(<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public
databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 1.1.0 dated 2021-07-16 and 1.1.1 dated 2021-07-30
DESCRIPTION | 6 MD5 | 288 NAMESPACE | 150 NEWS.md | 41 R/GeomSplitViolin.R | 110 R/analyze_gene_drug_response.R | 908 R/ccle.R | 288 R/data.R | 244 R/ezcor.R | 870 R/get_pancan_value.R | 758 R/get_pcawg_value.R | 254 R/globalVariables.R | 34 R/load_data.R | 134 R/ope_pancan_value.R | 122 R/query_custom_value.R | 20 R/query_toil_value_df.R | 122 R/query_value.R | 392 R/run.R | 50 R/tcga_surv.R | 412 R/utils-pipe.R | 36 R/utils.R | 116 R/vis_analyze_gene_drug_response.R | 224 R/vis_ccle_value.R | 332 R/vis_identifier.R | 748 R/vis_pancan_value.R | 2588 - R/vis_pcawg_value.R | 928 R/xenashiny.R | 18 R/zzz.R |only README.md | 534 build/vignette.rds |binary inst/doc/api.R | 108 inst/doc/api.Rmd | 254 inst/doc/api.html | 898 inst/extdata/ccle_drug_response_extend.rda |only inst/modules_apps/app.R | 38 inst/modules_apps/simple_module_from_rstudio.R | 66 inst/modules_apps/xx_modules.R | 98 inst/shinyapp/App.R | 670 inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R | 124 inst/shinyapp/modules/home-pancan-search.R | 178 inst/shinyapp/modules/modules-ccle-gene-drug-respose-df.R | 352 inst/shinyapp/modules/modules-ccle-gene-drug-target.R | 358 inst/shinyapp/modules/modules-ccle-genecor.R | 516 inst/shinyapp/modules/modules-ccle-search.R | 328 inst/shinyapp/modules/modules-file-upload.R | 238 inst/shinyapp/modules/modules-ga-group-comparison.R | 1496 inst/shinyapp/modules/modules-ga-matrix-correlation.R | 778 inst/shinyapp/modules/modules-ga-scatter-correlation.R | 762 inst/shinyapp/modules/modules-ga-surv-analysis.R | 1420 inst/shinyapp/modules/modules-pancan-anatomy.R | 340 inst/shinyapp/modules/modules-pancan-genecor.R | 498 inst/shinyapp/modules/modules-pancan-immune.R | 352 inst/shinyapp/modules/modules-pancan-radar.R | 402 inst/shinyapp/modules/modules-pancan-search-cancer.R | 380 inst/shinyapp/modules/modules-pancan-search.R | 378 inst/shinyapp/modules/modules-pancan-til.R | 376 inst/shinyapp/modules/modules-pancan-unicox.R | 350 inst/shinyapp/modules/modules-pcawg-genecor.R | 590 inst/shinyapp/modules/modules-pcawg-search.R | 432 inst/shinyapp/modules/modules-pcawg-survival-analysis.R | 692 inst/shinyapp/modules/modules-pcawg-unicox.R | 384 inst/shinyapp/modules/modules-survival-analysis.R | 792 inst/shinyapp/server/general-analysis.R | 384 inst/shinyapp/server/global.R | 32 inst/shinyapp/server/home.R | 170 inst/shinyapp/server/modules.R | 36 inst/shinyapp/server/repository.R | 832 inst/shinyapp/shiny-doc/citation.md | 83 inst/shinyapp/shiny-doc/terms.md | 324 inst/shinyapp/shiny-doc/usage.md | 324 inst/shinyapp/ui/chooser.R | 94 inst/shinyapp/ui/developers.R | 244 inst/shinyapp/ui/footer.R | 32 inst/shinyapp/ui/general-analysis.R | 187 inst/shinyapp/ui/global.R | 22 inst/shinyapp/ui/help.R | 64 inst/shinyapp/ui/home.R | 284 inst/shinyapp/ui/pancan-analysis.R | 156 inst/shinyapp/ui/repository.R | 238 inst/shinyapp/www/bootstrap4.css | 704 inst/shinyapp/www/chooser-binding.js | 168 inst/shinyapp/www/css/bootstrap-grid.css | 4098 +- inst/shinyapp/www/css/bootstrap-grid.min.css | 12 inst/shinyapp/www/css/bootstrap-reboot.css | 658 inst/shinyapp/www/css/bootstrap-reboot.min.css | 14 inst/shinyapp/www/css/bootstrap.css |17948 +++++----- inst/shinyapp/www/css/bootstrap.min.css | 12 inst/shinyapp/www/js/bootstrap.bundle.js |12656 +++---- inst/shinyapp/www/js/bootstrap.bundle.min.js | 12 inst/shinyapp/www/js/bootstrap.js | 7788 ++-- inst/shinyapp/www/js/bootstrap.min.js | 12 man/TCGA.organ.Rd | 30 man/UCSCXenaShiny.Rd | 18 man/analyze_gene_drug_response_asso.Rd | 74 man/analyze_gene_drug_response_diff.Rd | 130 man/app_run.Rd | 48 man/available_hosts.Rd | 34 man/ccle_absolute.Rd | 36 man/ccle_info.Rd | 36 man/ezcor.Rd | 98 man/ezcor_batch.Rd | 104 man/ezcor_partial_cor.Rd | 98 man/get_pancan_value.Rd | 298 man/keep_cat_cols.Rd | 44 man/load_data.Rd | 82 man/pcawg_info.Rd | 36 man/pcawg_purity.Rd | 36 man/pipe.Rd | 24 man/query_molecule_value.Rd | 76 man/query_pancan_value.Rd | 120 man/query_toil_value_df.Rd | 68 man/tcga_clinical.Rd | 36 man/tcga_genome_instability.Rd | 36 man/tcga_gtex.Rd | 30 man/tcga_purity.Rd | 36 man/tcga_subtypes.Rd | 36 man/tcga_surv.Rd | 36 man/tcga_surv_analysis.Rd | 154 man/tcga_tmb.Rd | 36 man/toil_info.Rd | 36 man/vis_ccle_gene_cor.Rd | 108 man/vis_ccle_tpm.Rd | 44 man/vis_gene_TIL_cor.Rd | 74 man/vis_gene_cor.Rd | 84 man/vis_gene_cor_cancer.Rd | 96 man/vis_gene_drug_response_asso.Rd | 52 man/vis_gene_drug_response_diff.Rd | 70 man/vis_gene_immune_cor.Rd | 72 man/vis_gene_msi_cor.Rd | 66 man/vis_gene_stemness_cor.Rd | 66 man/vis_gene_tmb_cor.Rd | 66 man/vis_identifier_cor.Rd | 136 man/vis_identifier_grp_comparison.Rd | 210 man/vis_identifier_grp_surv.Rd | 144 man/vis_identifier_multi_cor.Rd | 146 man/vis_pancan_anatomy.Rd | 62 man/vis_pcawg_dist.Rd | 102 man/vis_pcawg_gene_cor.Rd | 120 man/vis_pcawg_unicox_tree.Rd | 74 man/vis_toil_TvsN.Rd | 110 man/vis_toil_TvsN_cancer.Rd | 92 man/vis_unicox_tree.Rd | 74 tests/testthat.R | 8 tests/testthat/test-run_app.R | 2 tests/testthat/test-vis_pancan_value.R | 10 vignettes/api.Rmd | 254 146 files changed, 38638 insertions(+), 38593 deletions(-)
Title: Raw Data Quality Control Tool for LC-MS System
Description: Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between RawHummus versions 0.1.0 dated 2021-07-19 and 0.1.5 dated 2021-07-30
DESCRIPTION | 11 MD5 | 25 - NAMESPACE | 3 R/runGui.R | 39 - README.md |only inst/shiny/Gui/Report.Rmd | 329 +++++++++++---- inst/shiny/Gui/logo.png |only inst/shiny/Gui/mds/landing.md | 64 +- inst/shiny/Gui/rsconnect/shinyapps.io/dong/RawHummus.dcf | 6 inst/shiny/Gui/server-convert.R | 101 ++-- inst/shiny/Gui/server-evaluate.R | 4 inst/shiny/Gui/server.R | 6 inst/shiny/Gui/style.css |only inst/shiny/Gui/ui-tab-evaluate.R | 2 inst/shiny/Gui/ui.R | 119 ++--- 15 files changed, 445 insertions(+), 264 deletions(-)
Title: Creates Log Files
Description: Contains functions to help create log files. The
package aims to overcome the difficulty of the base R sink() command. The
log_print() function will print to both the console and the file log,
without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between logr versions 1.2.4 dated 2021-06-16 and 1.2.5 dated 2021-07-30
DESCRIPTION | 10 - MD5 | 36 +++-- NAMESPACE | 2 NEWS.md | 20 +-- R/logr.R | 203 ++++++++++++++++++++++++------- R/unicode.R |only README.md | 2 build/vignette.rds |binary inst/doc/logr-globals.R | 8 + inst/doc/logr-globals.Rmd | 19 ++ inst/doc/logr-globals.html | 6 inst/doc/logr-put.Rmd | 2 inst/doc/logr-put.html | 2 man/log_path.Rd |only man/log_status.Rd |only tests/testthat/log |only tests/testthat/test-logr.R | 294 +++++++++++++++++++++++++++++++++++++++++++++ vignettes/logr-globals.Rmd | 19 ++ vignettes/logr-put.Rmd | 2 19 files changed, 549 insertions(+), 76 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay, Charles Reynard, Allison Cheung and Nagendra Singanallur.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.31 dated 2021-07-19 and 2.0.33 dated 2021-07-30
DESCRIPTION | 10 MD5 | 71 +- NEWS | 20 R/epi.bohning.R | 12 R/epi.descriptives.R | 117 ++-- R/epi.ssclus1estb.R | 5 R/epi.ssclus1estc.R | 6 R/epi.ssclus2estb.R | 7 R/epi.ssclus2estc.R | 4 R/epi.sssimpleestb.R | 5 R/epi.sssimpleestc.R | 4 R/epi.ssstrataestb.R | 5 R/epi.ssstrataestc.R | 4 inst/doc/epiR_RSurveillance.html | 4 inst/doc/epiR_descriptive.html | 48 - inst/doc/epiR_measures_of_association.R | 51 + inst/doc/epiR_measures_of_association.Rmd | 139 ++++- inst/doc/epiR_measures_of_association.html | 690 ++++++++++++++++++++++--- inst/doc/epiR_sample_size.R | 22 inst/doc/epiR_sample_size.Rmd | 24 inst/doc/epiR_sample_size.html | 28 - inst/doc/epiR_surveillance.html | 4 man/epi.descriptives.Rd | 27 man/epi.edr.Rd | 2 man/epi.ssclus1estb.Rd | 14 man/epi.ssclus1estc.Rd | 10 man/epi.ssclus2estb.Rd | 10 man/epi.ssclus2estc.Rd | 10 man/epi.sssimpleestb.Rd | 36 + man/epi.sssimpleestc.Rd | 17 man/epi.ssstrataestb.Rd | 12 man/epi.ssstrataestc.Rd | 11 vignettes/attributable_fraction.png |only vignettes/attributable_risk.png |only vignettes/epiR_measures_of_association.Rmd | 139 ++++- vignettes/epiR_sample_size.Rmd | 24 vignettes/population_attributable_fraction.png |only vignettes/population_attributable_risk.png |only vignettes/risk_ratio.png |only 39 files changed, 1269 insertions(+), 323 deletions(-)
Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: The goal is to deliver the full functionality of 'ECharts' with minimal overhead. 'ECharts' is based on data structures and 'echarty' users build R lists for these same data structures. One to three 'echarty' commands are usually sufficient to produce any chart.
Author: Larry Helgason [aut, cre, cph],
John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>
Diff between echarty versions 0.2.0 dated 2021-06-13 and 0.3.1 dated 2021-07-30
echarty-0.2.0/echarty/man/ec.timegrp.Rd |only echarty-0.3.1/echarty/DESCRIPTION | 8 echarty-0.3.1/echarty/MD5 | 34 echarty-0.3.1/echarty/NAMESPACE | 2 echarty-0.3.1/echarty/NEWS.md | 63 + echarty-0.3.1/echarty/R/echarty.R | 599 ++++++++++------ echarty-0.3.1/echarty/R/examples.R | 167 +--- echarty-0.3.1/echarty/demo/eshiny.R | 797 +++++++++++----------- echarty-0.3.1/echarty/inst/htmlwidgets/echarty.js | 85 +- echarty-0.3.1/echarty/inst/js/echarts.min.js | 4 echarty-0.3.1/echarty/inst/js/renderers.js | 4 echarty-0.3.1/echarty/man/ec.clmn.Rd |only echarty-0.3.1/echarty/man/ec.data.Rd | 5 echarty-0.3.1/echarty/man/ec.examples.Rd | 167 +--- echarty-0.3.1/echarty/man/ec.init.Rd | 71 + echarty-0.3.1/echarty/man/ec.inspect.Rd | 6 echarty-0.3.1/echarty/man/ec.plugjs.Rd | 8 echarty-0.3.1/echarty/man/ecr.band.Rd | 50 - echarty-0.3.1/echarty/man/ecr.ebars.Rd | 33 19 files changed, 1155 insertions(+), 948 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.4.5 dated 2021-05-29 and 0.5.0 dated 2021-07-30
dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-Bold.ttf |only dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-BoldItalic.ttf |only dlookr-0.4.5/dlookr/inst/fonts/LiberationSansNarrow/LiberationSansNarrow-Italic.ttf |only dlookr-0.4.5/dlookr/vignettes/img/diag_intro_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diag_outlier_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diagn_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/diagn_title_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_anova_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_intro_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_lm_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_normality_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/eda_title_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_agenda_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_content_pdf.png |only dlookr-0.4.5/dlookr/vignettes/img/trans_title_pdf.png |only dlookr-0.5.0/dlookr/DESCRIPTION | 18 dlookr-0.5.0/dlookr/MD5 | 155 +- dlookr-0.5.0/dlookr/NAMESPACE | 50 dlookr-0.5.0/dlookr/NEWS | 57 dlookr-0.5.0/dlookr/R/EDA.R | 7 dlookr-0.5.0/dlookr/R/aggregate.R | 277 ++++ dlookr-0.5.0/dlookr/R/binning.R | 49 dlookr-0.5.0/dlookr/R/compare.R | 14 dlookr-0.5.0/dlookr/R/correlate.R | 84 - dlookr-0.5.0/dlookr/R/diagnose.R | 22 dlookr-0.5.0/dlookr/R/discribe.R | 181 --- dlookr-0.5.0/dlookr/R/dlookr.R | 9 dlookr-0.5.0/dlookr/R/dlookr_templ_html.R |only dlookr-0.5.0/dlookr/R/dlookr_templ_paged.R |only dlookr-0.5.0/dlookr/R/html_diagnose.R |only dlookr-0.5.0/dlookr/R/html_eda.R |only dlookr-0.5.0/dlookr/R/html_transformation.R |only dlookr-0.5.0/dlookr/R/missing.R | 7 dlookr-0.5.0/dlookr/R/overview.R | 250 +++- dlookr-0.5.0/dlookr/R/paged.R |only dlookr-0.5.0/dlookr/R/report.R |only dlookr-0.5.0/dlookr/R/report_tbl_dbi.R |only dlookr-0.5.0/dlookr/R/tbl_dbi.R | 30 dlookr-0.5.0/dlookr/R/transform.R | 9 dlookr-0.5.0/dlookr/R/utils.R | 217 +++ dlookr-0.5.0/dlookr/inst/doc/EDA.R | 136 -- dlookr-0.5.0/dlookr/inst/doc/EDA.Rmd | 289 ++--- dlookr-0.5.0/dlookr/inst/doc/EDA.html | 413 ++++--- dlookr-0.5.0/dlookr/inst/doc/diagonosis.R | 92 - dlookr-0.5.0/dlookr/inst/doc/diagonosis.Rmd | 240 ++-- dlookr-0.5.0/dlookr/inst/doc/diagonosis.html | 573 ++++++---- dlookr-0.5.0/dlookr/inst/doc/introduce.Rmd | 9 dlookr-0.5.0/dlookr/inst/doc/introduce.html | 54 dlookr-0.5.0/dlookr/inst/doc/transformation.R | 33 dlookr-0.5.0/dlookr/inst/doc/transformation.Rmd | 163 ++ dlookr-0.5.0/dlookr/inst/doc/transformation.html | 271 +++- dlookr-0.5.0/dlookr/inst/report/R_logo_html.svg |only dlookr-0.5.0/dlookr/inst/report/cover1.jpg |only dlookr-0.5.0/dlookr/inst/report/cover2.jpg |only dlookr-0.5.0/dlookr/inst/report/cover3.jpg |only dlookr-0.5.0/dlookr/inst/report/diagnosis_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/diagnosis_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/dlookr.svg |only dlookr-0.5.0/dlookr/inst/report/dlookr_html.svg |only dlookr-0.5.0/dlookr/inst/report/eda_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/eda_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/header_temp.html |only dlookr-0.5.0/dlookr/inst/report/transformation_paged_temp.Rmd |only dlookr-0.5.0/dlookr/inst/report/transformation_temp.Rmd |only dlookr-0.5.0/dlookr/inst/resources |only dlookr-0.5.0/dlookr/man/describe.data.frame.Rd | 12 dlookr-0.5.0/dlookr/man/describe.tbl_dbi.Rd | 18 dlookr-0.5.0/dlookr/man/diagnose_category.data.frame.Rd | 6 dlookr-0.5.0/dlookr/man/diagnose_paged_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/diagnose_paged_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/diagnose_web_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/diagnose_web_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/dlookr_orange_paged.Rd |only dlookr-0.5.0/dlookr/man/dlookr_templ_html.Rd |only dlookr-0.5.0/dlookr/man/eda_paged_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/eda_paged_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/eda_web_report.data.frame.Rd |only dlookr-0.5.0/dlookr/man/eda_web_report.tbl_dbi.Rd |only dlookr-0.5.0/dlookr/man/find_class.Rd | 7 dlookr-0.5.0/dlookr/man/overview.Rd | 15 dlookr-0.5.0/dlookr/man/plot.optimal_bins.Rd | 8 dlookr-0.5.0/dlookr/man/plot_box_numeric.data.frame.Rd | 6 dlookr-0.5.0/dlookr/man/plot_hist_numeric.data.frame.Rd |only dlookr-0.5.0/dlookr/man/plot_na_pareto.Rd | 4 dlookr-0.5.0/dlookr/man/summary.overview.Rd | 5 dlookr-0.5.0/dlookr/man/transformation_paged_report.Rd |only dlookr-0.5.0/dlookr/man/transformation_web_report.Rd |only dlookr-0.5.0/dlookr/vignettes/EDA.Rmd | 289 ++--- dlookr-0.5.0/dlookr/vignettes/diagonosis.Rmd | 240 ++-- dlookr-0.5.0/dlookr/vignettes/img/diag_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_web_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/diag_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/eda_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_paged_content.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_paged_cover.jpg |only dlookr-0.5.0/dlookr/vignettes/img/transformation_web_title.jpg |only dlookr-0.5.0/dlookr/vignettes/introduce.Rmd | 9 dlookr-0.5.0/dlookr/vignettes/transformation.Rmd | 163 ++ 102 files changed, 3022 insertions(+), 1469 deletions(-)
Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to
help quantify their robustness.
Author: R Validation Hub [aut],
Doug Kelkhoff [aut, cre],
Marly Gotti [aut],
Eli Miller [aut],
Kevin K [aut],
Yilong Zhang [aut],
Eric Milliman [aut],
Juliane Manitz [aut],
Mark Padgham [ctb],
PSI special interest group Application and Implementation of
Methodologies in Statistics [cph]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between riskmetric versions 0.1.0 dated 2021-05-13 and 0.1.1 dated 2021-07-29
riskmetric-0.1.0/riskmetric/man/as_pkg_ref.Rd |only riskmetric-0.1.1/riskmetric/DESCRIPTION | 8 riskmetric-0.1.1/riskmetric/MD5 | 44 +- riskmetric-0.1.1/riskmetric/NAMESPACE | 1 riskmetric-0.1.1/riskmetric/NEWS.md | 5 riskmetric-0.1.1/riskmetric/R/pkg_cohort.R |only riskmetric-0.1.1/riskmetric/R/pkg_ref_cache_remote_checks.R | 25 - riskmetric-0.1.1/riskmetric/R/pkg_ref_class.R | 188 ++++++---- riskmetric-0.1.1/riskmetric/R/utils.R | 15 riskmetric-0.1.1/riskmetric/build/vignette.rds |binary riskmetric-0.1.1/riskmetric/inst/doc/extending-riskmetric.html | 69 +-- riskmetric-0.1.1/riskmetric/inst/doc/riskmetric.R | 7 riskmetric-0.1.1/riskmetric/inst/doc/riskmetric.Rmd | 7 riskmetric-0.1.1/riskmetric/inst/doc/riskmetric.html | 56 +- riskmetric-0.1.1/riskmetric/man/figures |only riskmetric-0.1.1/riskmetric/man/firstS3method.Rd | 2 riskmetric-0.1.1/riskmetric/man/get_pkg_ref_classes.Rd |only riskmetric-0.1.1/riskmetric/man/pkg_ref.Rd | 39 +- riskmetric-0.1.1/riskmetric/man/pkg_ref_class_hierarchy.Rd |only riskmetric-0.1.1/riskmetric/tests/testthat/setup_mock_web_requests.R | 19 - riskmetric-0.1.1/riskmetric/tests/testthat/setup_test_packages.R | 25 + riskmetric-0.1.1/riskmetric/tests/testthat/test_packages/pkgsourcegood/man/hello_world_test.Rd | 2 riskmetric-0.1.1/riskmetric/tests/testthat/test_pkg_ref.R | 89 ++-- riskmetric-0.1.1/riskmetric/tests/testthat/test_webmocks/data/cran_package_checks.html |only riskmetric-0.1.1/riskmetric/tests/testthat/test_webmocks/rebuild_webmocks.R | 4 riskmetric-0.1.1/riskmetric/vignettes/riskmetric.Rmd | 7 26 files changed, 392 insertions(+), 220 deletions(-)
Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre],
David Zimmermann [ctb]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Diff between solitude versions 1.1.1 dated 2020-09-17 and 1.1.3 dated 2021-07-29
solitude-1.1.1/solitude/README.md |only solitude-1.1.3/solitude/DESCRIPTION | 16 +++-- solitude-1.1.3/solitude/MD5 | 9 +-- solitude-1.1.3/solitude/NEWS.md | 4 + solitude-1.1.3/solitude/R/isolationForest_r6.R | 75 +++++++++++++++++-------- solitude-1.1.3/solitude/man/isolationForest.Rd | 59 +++++++++++++++---- 6 files changed, 116 insertions(+), 47 deletions(-)
Title: R Interface to 'Bloomberg Data License'
Description: R interface to access prices and market data with the
'Bloomberg Data License' service from
<https://www.bloomberg.com/professional/product/data-license/>.
As a prerequisite, a valid Data License from 'Bloomberg' is needed
together with the corresponding SFTP credentials and whitelisting
of the IP from which accessing the service.
This software and its author are in no way affiliated,
endorsed, or approved by 'Bloomberg' or any of its affiliates.
'Bloomberg' is a registered trademark.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between RblDataLicense versions 0.2.3 dated 2020-09-20 and 0.2.4 dated 2021-07-29
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/core.R | 2 +- README.md | 4 ++-- inst/doc/RblDataLicense.Rmd | 2 +- inst/doc/RblDataLicense.html | 41 +++++++++++++++++++++++++++++++++++++---- man/RblConnect.Rd | 4 ++-- vignettes/RblDataLicense.Rmd | 2 +- 9 files changed, 60 insertions(+), 23 deletions(-)
More information about RblDataLicense at CRAN
Permanent link
Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization,
Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the
product of two low-dimensional matrices aided with secondary information matrices about rows
and/or columns of 'X' which are also factorized using the same latent components.
The intended usage is for recommender systems, dimensionality reduction, and missing value imputation.
Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce
different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky,
(2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model,
(Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>),
or the enhanced model with 'implicit features' (Rendle, Zhang,
Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based
procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009)
<doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver
(Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative
coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>),
providing efficient methods for sparse and dense data, and mixtures thereof.
Supports L1 and L2 regularization in the main models,
offers alternative most-popular and content-based models, and implements functionality
for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph],
Jorge Nocedal [cph] (Copyright holder of included LBFGS library),
Naoaki Okazaki [cph] (Copyright holder of included LBFGS library),
David Blackman [cph] (Copyright holder of original Xoshiro code),
Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between cmfrec versions 3.1.2 dated 2021-06-28 and 3.2.1 dated 2021-07-29
DESCRIPTION | 25 + LICENSE | 2 MD5 | 55 +- R/factors.R | 3 R/factors_single.R | 2 R/fit.R | 117 ++++- R/helpers.R | 170 +++++--- R/impute.R | 17 R/items.R | 11 R/other.R | 2 R/predict.R | 20 - R/predict_new.R | 8 R/topN.R | 10 inst/COPYRIGHTS |only inst/doc/cmfrec_vignette.R | 12 inst/doc/cmfrec_vignette.Rmd | 12 inst/doc/cmfrec_vignette.html | 51 +- man/factors.Rd | 3 man/factors_single.Rd | 4 man/fit.Rd | 34 + man/imputeX.Rd | 13 src/Rwrapper.c | 60 ++- src/arithmetic_ansi.h | 2 src/cmfrec.h | 120 +++--- src/collective.c | 826 ++++++++++++++++++++++++++++-------------- src/common.c | 292 ++++++++++---- src/helpers.c | 551 +++++++++++++++++++++++----- src/offsets.c | 137 +++++- vignettes/cmfrec_vignette.Rmd | 12 29 files changed, 1801 insertions(+), 770 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.1.3 dated 2021-04-05 and 4.1.4 dated 2021-07-29
CHANGELOG | 25 +++ DESCRIPTION | 10 - MD5 | 68 +++++----- R/FUN_utils.R | 28 ++-- R/FUN_vsgvs.R | 29 +++- R/GWAS.R | 5 R/RcppExports.R | 4 R/mmer.R | 17 ++ R/vpredict.R | 8 - inst/doc/v1.sommer.quick.start.R | 4 inst/doc/v1.sommer.quick.start.Rmd | 92 +++++++------- inst/doc/v1.sommer.quick.start.pdf |binary inst/doc/v2.sommer.changes.and.faqs.R | 2 inst/doc/v2.sommer.changes.and.faqs.Rmd | 118 +++++++++--------- inst/doc/v2.sommer.changes.and.faqs.pdf |binary inst/doc/v3.sommer.qg.R | 10 - inst/doc/v3.sommer.qg.Rmd | 90 +++++++------- inst/doc/v3.sommer.qg.pdf |binary inst/doc/v4.sommer.gxe.pdf |binary inst/doc/v5.sommer.vs.lme4.pdf |binary man/DT_cpdata.Rd | 31 +++- man/GWAS.Rd | 5 man/build.HMM.Rd | 10 - man/mmer.Rd | 8 - man/vs.Rd | 19 ++ src/MNR.cpp | 191 ++++++++++++++++++++---------- src/RcppExports.cpp | 10 - vignettes/v1.sommer.quick.start.Rmd | 92 +++++++------- vignettes/v1.sommer.quick.start.html | 97 ++++++++------- vignettes/v2.sommer.changes.and.faqs.Rmd | 118 +++++++++--------- vignettes/v2.sommer.changes.and.faqs.html | 117 ++++++++++-------- vignettes/v3.sommer.qg.Rmd | 90 +++++++------- vignettes/v3.sommer.qg.html | 168 +++++++++----------------- vignettes/v4.sommer.gxe.html | 4 vignettes/v5.sommer.vs.lme4.html | 4 35 files changed, 807 insertions(+), 667 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>),
Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.19.3 dated 2019-05-12 and 1.20 dated 2021-07-29
DESCRIPTION | 14 ++-- MD5 | 92 ++++++++++++++--------------- NAMESPACE | 3 NEWS | 35 ++++++++++- R/binPeaks-functions.R | 13 ++-- R/determineWarpingFunctions-functions.R | 2 R/grouper-functions.R | 17 +++-- R/referencePeaks-functions.R | 2 build/vignette.rds |binary inst/CITATION | 4 - inst/doc/MALDIquant-intro.R | 50 +++++++-------- inst/doc/MALDIquant-intro.pdf |binary man/AbstractMassObject-class.Rd | 2 man/MALDIquant-package.Rd | 8 +- man/MALDIquant-parallel.Rd | 3 man/MassPeaks-class.Rd | 2 man/MassSpectrum-class.Rd | 2 man/alignSpectra-functions.Rd | 2 man/averageMassSpectra-functions.Rd | 2 man/binPeaks-functions.Rd | 27 ++++++-- man/calibrateIntensity-methods.Rd | 2 man/createMassPeaks-functions.Rd | 2 man/createMassSpectrum-functions.Rd | 2 man/detectPeaks-methods.Rd | 2 man/determineWarpingFunctions-functions.Rd | 2 man/estimateBaseline-methods.Rd | 2 man/estimateNoise-methods.Rd | 2 man/fiedler2009subset.Rd | 6 - man/filterPeaks-functions.Rd | 2 man/findEmptyMassObjects-functions.Rd | 2 man/intensityMatrix-functions.Rd | 2 man/isMassObject-functions.Rd | 2 man/isMassObjectList-functions.Rd | 2 man/labelPeaks-methods.Rd | 2 man/mergeMassPeaks-functions.Rd | 2 man/monoisotopicPeaks-methods.Rd | 2 man/msiSlices-functions.Rd | 2 man/plot-methods.Rd | 2 man/plotMsiSlice-methods.Rd | 2 man/referencePeaks-functions.Rd | 2 man/removeBaseline-methods.Rd | 2 man/smoothIntensity-methods.Rd | 2 man/transformIntensity-methods.Rd | 2 man/trim-methods.Rd | 2 man/warp-functions.Rd | 2 tests/testthat/test_binPeaks-functions.R | 9 ++ tests/testthat/test_grouper-functions.R | 11 ++- 47 files changed, 214 insertions(+), 140 deletions(-)
Title: Maps, Data and Methods Related to Guerry (1833) "Moral
Statistics of France"
Description: Maps of France in 1830, multivariate datasets from A.-M. Guerry and others, and statistical and
graphic methods related to Guerry's "Moral Statistics of France". The goal is to facilitate the exploration and
development of statistical and graphic methods for multivariate data in a geo-spatial context of historical interest.
Author: Michael Friendly [aut, cre],
Stephane Dray [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between Guerry versions 1.7.0 dated 2020-01-29 and 1.7.1 dated 2021-07-29
DESCRIPTION | 13 +++++++---- MD5 | 22 ++++++++++++++----- build/partial.rdb |binary build/vignette.rds |only inst |only man/Guerry-package.Rd | 4 +-- man/Guerry.Rd | 57 ++++++++++++++++++++++++++++++++++++++++++-------- man/gfrance.Rd | 3 +- vignettes |only 9 files changed, 77 insertions(+), 22 deletions(-)
Title: Analyzing the Opinions in a Big Text Document
Description: Designed for performing impact analysis of
opinions in a digital text document (DTD). The
package allows a user to assess the extent to which a theme
or subject within a document impacts the overall opinion
expressed in the document. The package can be applied to a wide
range of opinion-based DTD, including commentaries on social media
platforms (such as 'Facebook', 'Twitter' and 'Youtube'),
online products reviews, and so on.
The utility of 'opitools' was originally demonstrated
in Adepeju and Jimoh (2021) <doi:10.31235/osf.io/c32qh> in the
assessment of COVID-19 impacts on neighbourhood policing using
Twitter data. Further examples can be found in the vignette of
the package.
Author: Monsuru Adepeju [cre, aut],
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>
Diff between opitools versions 1.0.2 dated 2021-03-05 and 1.8.0 dated 2021-07-29
opitools-1.0.2/opitools/R/covid_keys.R |only opitools-1.0.2/opitools/R/osd_data.R |only opitools-1.0.2/opitools/R/policing_otd.R |only opitools-1.0.2/opitools/R/tweets.R |only opitools-1.0.2/opitools/data/covid_keys.rda |only opitools-1.0.2/opitools/data/policing_otd.rda |only opitools-1.0.2/opitools/man/covid_keys.Rd |only opitools-1.0.2/opitools/man/policing_otd.Rd |only opitools-1.8.0/opitools/DESCRIPTION | 34 opitools-1.8.0/opitools/MD5 | 67 - opitools-1.8.0/opitools/NAMESPACE | 123 + opitools-1.8.0/opitools/NEWS.md | 16 opitools-1.8.0/opitools/R/data.R |only opitools-1.8.0/opitools/R/opi_impact.R | 78 - opitools-1.8.0/opitools/R/opi_score.R | 24 opitools-1.8.0/opitools/R/opi_sim.R | 16 opitools-1.8.0/opitools/R/word_distrib.R | 4 opitools-1.8.0/opitools/R/word_imp.R |only opitools-1.8.0/opitools/README.md | 98 - opitools-1.8.0/opitools/build/vignette.rds |binary opitools-1.8.0/opitools/data/covid_theme.rda |only opitools-1.8.0/opitools/data/debate_dtd.rda |only opitools-1.8.0/opitools/data/policing_dtd.rda |only opitools-1.8.0/opitools/data/refreshment_theme.rda |only opitools-1.8.0/opitools/data/reviews_dtd.rda |only opitools-1.8.0/opitools/data/signage_theme.rda |only opitools-1.8.0/opitools/inst/doc/opitools-vignette.R | 309 ++--- opitools-1.8.0/opitools/inst/doc/opitools-vignette.Rmd | 401 +++--- opitools-1.8.0/opitools/inst/doc/opitools-vignette.html | 986 ++++++++++++---- opitools-1.8.0/opitools/man/covid_theme.Rd |only opitools-1.8.0/opitools/man/debate_dtd.Rd |only opitools-1.8.0/opitools/man/opi_impact.Rd | 53 opitools-1.8.0/opitools/man/opi_score.Rd | 24 opitools-1.8.0/opitools/man/opi_sim.Rd | 16 opitools-1.8.0/opitools/man/osd_data.Rd | 23 opitools-1.8.0/opitools/man/policing_dtd.Rd |only opitools-1.8.0/opitools/man/refreshment_theme.Rd |only opitools-1.8.0/opitools/man/reviews_dtd.Rd |only opitools-1.8.0/opitools/man/signage_theme.Rd |only opitools-1.8.0/opitools/man/tweets.Rd | 20 opitools-1.8.0/opitools/man/word_distrib.Rd | 4 opitools-1.8.0/opitools/man/word_imp.Rd |only opitools-1.8.0/opitools/vignettes/likert.png |binary opitools-1.8.0/opitools/vignettes/opitools-vignette.Rmd | 401 +++--- opitools-1.8.0/opitools/vignettes/references.bib | 19 opitools-1.8.0/opitools/vignettes/wordcloud.png |binary 46 files changed, 1640 insertions(+), 1076 deletions(-)
Title: Locally Stationary Time Series
Description: A set of functions that allow stationary analysis and locally stationary time series analysis.
Author: Ricardo Olea [aut, cph],
Wilfredo Palma [aut, cph],
Pilar Rubio [aut],
Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Mauricio Vargas <mavargas11@uc.cl>
Diff between LSTS versions 2.0 dated 2021-04-18 and 2.1 dated 2021-07-29
DESCRIPTION | 25 ++++++----------------- MD5 | 36 +++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 6 +++++ R/box_ljung_test.R | 2 - R/ls_kalman.R | 8 +++---- R/ls_whittle.R | 18 ++++++++--------- R/ls_whittle_loglik.R | 1 R/ls_whittle_loglik_sd.R | 1 R/ls_whittle_loglik_theta.R | 1 R/ts_diag.R | 12 +++++++---- build/partial.rdb |binary inst/REFERENCES.bib | 43 +++++++++++++++++------------------------ man/LS.kalman.Rd | 8 +++---- man/LS.whittle.Rd | 18 ++++++++--------- man/LS.whittle.loglik.Rd | 3 -- man/LS.whittle.loglik.sd.Rd | 3 -- man/LS.whittle.loglik.theta.Rd | 3 -- man/ts.diag.Rd | 6 ++++- 19 files changed, 90 insertions(+), 105 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
Author: Stefan Lenz [aut, cre] (<https://orcid.org/0000-0001-9135-1743>),
Harald Binder [aut] (<https://orcid.org/0000-0002-5666-8662>)
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 0.6.3 dated 2021-03-27 and 1.0.0 dated 2021-07-29
JuliaConnectoR-0.6.3/JuliaConnectoR/inst/examples/iris-example/project_1_0 |only JuliaConnectoR-0.6.3/JuliaConnectoR/inst/examples/iris-example/project_1_4 |only JuliaConnectoR-1.0.0/JuliaConnectoR/DESCRIPTION | 8 JuliaConnectoR-1.0.0/JuliaConnectoR/MD5 | 44 JuliaConnectoR-1.0.0/JuliaConnectoR/NAMESPACE | 2 JuliaConnectoR-1.0.0/JuliaConnectoR/R/JuliaConnectoR-package.R | 38 JuliaConnectoR-1.0.0/JuliaConnectoR/R/connecting.R | 136 ++ JuliaConnectoR-1.0.0/JuliaConnectoR/R/handling_dataframes.R | 5 JuliaConnectoR-1.0.0/JuliaConnectoR/R/main.R | 11 JuliaConnectoR-1.0.0/JuliaConnectoR/R/reading.R | 626 +++++----- JuliaConnectoR-1.0.0/JuliaConnectoR/inst/CITATION |only JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/RConnector.jl | 2 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/communicating.jl | 113 + JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/evaluating.jl | 28 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/main.jl | 13 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/sharing.jl | 88 - JuliaConnectoR-1.0.0/JuliaConnectoR/inst/Julia/writing.jl | 35 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/examples/iris-example/iris-example.R | 3 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/examples/iris-example/iris-example.jl | 7 JuliaConnectoR-1.0.0/JuliaConnectoR/inst/examples/iris-example/project_1_6 |only JuliaConnectoR-1.0.0/JuliaConnectoR/man/EnvVars-JuliaConnectoR.Rd |only JuliaConnectoR-1.0.0/JuliaConnectoR/man/startJuliaServer.Rd |only JuliaConnectoR-1.0.0/JuliaConnectoR/man/stopJulia.Rd |only JuliaConnectoR-1.0.0/JuliaConnectoR/tests/testthat.R | 3 JuliaConnectoR-1.0.0/JuliaConnectoR/tests/testthat/test.R | 100 + 25 files changed, 791 insertions(+), 471 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut],
Martin Studer [cre],
The Apache Software Foundation [ctb, cph] (Apache POI),
Graph Builder [ctb, cph] (Curvesapi Java library),
Brett Woolridge [ctb, cph] (SparseBitSet Java library)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>
Diff between XLConnect versions 1.0.3 dated 2021-04-11 and 1.0.4 dated 2021-07-29
DESCRIPTION | 15 ++-- MD5 | 23 +++---- NEWS | 6 + R/onLoad.R | 37 ++++++++---- build/vignette.rds |binary inst/COPYRIGHTS | 8 ++ inst/doc/XLConnect.pdf |binary inst/doc/XLConnectImpatient.pdf |binary inst/unitTests/resources/testReadWorksheetSparseBitSet.xlsx |only inst/unitTests/runit.workbook.readWorksheet.R | 4 + java/README | 5 + man/setDataFormat-methods.Rd | 2 man/setDataFormatForType-methods.Rd | 2 13 files changed, 73 insertions(+), 29 deletions(-)
Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical
models and returns the result as tidy data frames. These data frames are
ready to use with the 'ggplot2'-package. Effects and predictions can be
calculated for many different models. Interaction terms, splines and
polynomial terms are also supported. The main functions are ggpredict(),
ggemmeans() and ggeffect(). There is a generic plot()-method to plot the
results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>),
Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 1.1.0 dated 2021-04-30 and 1.1.1 dated 2021-07-29
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Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.0.2 dated 2021-07-28 and 1.0.3 dated 2021-07-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 5 +++++ R/founderPop.R | 2 +- inst/doc/intro.html | 6 +++--- inst/doc/traits.pdf |binary 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Peter Kochunov [aut],
Si Gao [aut, cre],
Fatima Talib [aut]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Diff between RVIpkg versions 0.2.5 dated 2021-07-20 and 0.2.6 dated 2021-07-29
DESCRIPTION | 6 - MD5 | 24 ++--- R/EP.GM.R | 29 +++--- R/EP.Subcortical.R | 29 +++--- R/RVI_func.R | 214 ++++++++++++++++++++++++------------------------ R/sysdata.rda |binary build/partial.rdb |binary data/EP.GM.rda |binary data/EP.Subcortical.rda |binary data/EP.WM.rda |binary man/EP.GM.Rd | 1 man/EP.Subcortical.Rd | 1 man/RVI_func.Rd | 6 - 13 files changed, 157 insertions(+), 153 deletions(-)
Title: Find Free Versions of Scholarly Publications via Unpaywall
Description: This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly
oaDOI, a service finding free full-texts of academic papers by linking DOIs with
open access journals and repositories. It provides unified access to various data sources
for open access full-text links including Crossref and the Directory of Open Access
Journals (DOAJ). API usage is free and no registration is required.
Author: Najko Jahn [aut, cre],
Tuija Sonkkila [rev] (Tuija Sonkkila reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-6892-9305>),
Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/115,
<https://orcid.org/0000-0002-3520-2046>),
Anne Hobert [ctb] (<https://orcid.org/0000-0003-2429-2995>),
Delwen Franzen [ctb]
Maintainer: Najko Jahn <najko.jahn@gmail.com>
Diff between roadoi versions 0.7 dated 2021-01-20 and 0.7.1 dated 2021-07-29
DESCRIPTION | 10 MD5 | 16 - README.md | 344 ++++---------------------------- build/vignette.rds |binary inst/doc/intro.R | 30 -- inst/doc/intro.Rmd | 70 ------ inst/doc/intro.html | 404 +++++--------------------------------- tests/testthat/test_oadoi_fetch.r | 2 vignettes/intro.Rmd | 70 ------ 9 files changed, 120 insertions(+), 826 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and
multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kamiński [cph],
Dropbox, Inc. [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>
Diff between gdalcubes versions 0.4.0 dated 2021-07-13 and 0.4.1 dated 2021-07-29
DESCRIPTION | 13 +++++++++---- MD5 | 17 +++++++++-------- NEWS.md | 5 +++++ configure | 21 ++++++++++----------- configure.ac | 5 ++--- inst/doc/MODIS.html | 12 ++++++------ src/Makevars.ucrt |only src/Makevars.win | 22 ++++++++++++---------- src/RcppExports.cpp | 5 +++++ tools/winlibs.R | 3 +-- 10 files changed, 59 insertions(+), 44 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre],
Ian Cook [aut],
Nic Crane [aut],
Jonathan Keane [aut],
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 4.0.1 dated 2021-05-28 and 5.0.0 dated 2021-07-29
arrow-4.0.1/arrow/src/runtimeinfo.cpp |only arrow-5.0.0/arrow/DESCRIPTION | 33 arrow-5.0.0/arrow/MD5 | 305 +-- arrow-5.0.0/arrow/NAMESPACE | 33 arrow-5.0.0/arrow/NEWS.md | 39 arrow-5.0.0/arrow/R/array-data.R | 10 arrow-5.0.0/arrow/R/array.R | 32 arrow-5.0.0/arrow/R/arrow-datum.R | 121 + arrow-5.0.0/arrow/R/arrow-package.R | 41 arrow-5.0.0/arrow/R/arrow-tabular.R | 23 arrow-5.0.0/arrow/R/arrowExports.R | 180 + arrow-5.0.0/arrow/R/buffer.R | 14 arrow-5.0.0/arrow/R/chunked-array.R | 32 arrow-5.0.0/arrow/R/compression.R | 6 arrow-5.0.0/arrow/R/compute.R | 114 - arrow-5.0.0/arrow/R/config.R | 14 arrow-5.0.0/arrow/R/csv.R | 66 arrow-5.0.0/arrow/R/dataset-format.R | 19 arrow-5.0.0/arrow/R/dataset-partition.R | 30 arrow-5.0.0/arrow/R/dataset-scan.R | 34 arrow-5.0.0/arrow/R/dataset-write.R | 10 arrow-5.0.0/arrow/R/dataset.R | 90 arrow-5.0.0/arrow/R/dplyr-arrange.R |only arrow-5.0.0/arrow/R/dplyr-collect.R |only arrow-5.0.0/arrow/R/dplyr-eval.R |only arrow-5.0.0/arrow/R/dplyr-filter.R |only arrow-5.0.0/arrow/R/dplyr-functions.R |only arrow-5.0.0/arrow/R/dplyr-group-by.R |only arrow-5.0.0/arrow/R/dplyr-mutate.R |only arrow-5.0.0/arrow/R/dplyr-select.R |only arrow-5.0.0/arrow/R/dplyr-summarize.R |only arrow-5.0.0/arrow/R/dplyr.R | 945 ---------- arrow-5.0.0/arrow/R/enums.R | 12 arrow-5.0.0/arrow/R/expression.R | 305 +-- arrow-5.0.0/arrow/R/feather.R | 11 arrow-5.0.0/arrow/R/field.R | 9 arrow-5.0.0/arrow/R/filesystem.R | 12 arrow-5.0.0/arrow/R/flight.R | 2 arrow-5.0.0/arrow/R/ipc_stream.R | 9 arrow-5.0.0/arrow/R/json.R | 4 arrow-5.0.0/arrow/R/metadata.R | 47 arrow-5.0.0/arrow/R/parquet.R | 21 arrow-5.0.0/arrow/R/python.R | 77 arrow-5.0.0/arrow/R/record-batch-reader.R | 22 arrow-5.0.0/arrow/R/record-batch-writer.R | 4 arrow-5.0.0/arrow/R/record-batch.R | 21 arrow-5.0.0/arrow/R/scalar.R | 30 arrow-5.0.0/arrow/R/schema.R | 17 arrow-5.0.0/arrow/R/table.R | 20 arrow-5.0.0/arrow/R/type.R | 66 arrow-5.0.0/arrow/R/util.R | 74 arrow-5.0.0/arrow/README.md | 8 arrow-5.0.0/arrow/configure | 7 arrow-5.0.0/arrow/inst/build_arrow_static.sh | 2 arrow-5.0.0/arrow/inst/doc/arrow.html | 648 +++--- arrow-5.0.0/arrow/inst/doc/dataset.html | 704 ++----- arrow-5.0.0/arrow/inst/doc/developing.R | 5 arrow-5.0.0/arrow/inst/doc/developing.Rmd | 16 arrow-5.0.0/arrow/inst/doc/developing.html | 812 +++----- arrow-5.0.0/arrow/inst/doc/flight.html | 392 +--- arrow-5.0.0/arrow/inst/doc/fs.html | 423 +--- arrow-5.0.0/arrow/inst/doc/install.html | 689 ++----- arrow-5.0.0/arrow/inst/doc/python.html | 460 +--- arrow-5.0.0/arrow/man/ArrayData.Rd | 10 arrow-5.0.0/arrow/man/ChunkedArray.Rd | 30 arrow-5.0.0/arrow/man/CsvReadOptions.Rd | 7 arrow-5.0.0/arrow/man/Field.Rd | 4 arrow-5.0.0/arrow/man/FileFormat.Rd | 15 arrow-5.0.0/arrow/man/ParquetFileReader.Rd | 4 arrow-5.0.0/arrow/man/RecordBatch.Rd | 4 arrow-5.0.0/arrow/man/RecordBatchReader.Rd | 6 arrow-5.0.0/arrow/man/RecordBatchWriter.Rd | 4 arrow-5.0.0/arrow/man/Scalar.Rd | 29 arrow-5.0.0/arrow/man/Scanner.Rd | 3 arrow-5.0.0/arrow/man/Schema.Rd | 4 arrow-5.0.0/arrow/man/Table.Rd | 4 arrow-5.0.0/arrow/man/array.Rd | 29 arrow-5.0.0/arrow/man/arrow-package.Rd | 1 arrow-5.0.0/arrow/man/buffer.Rd | 17 arrow-5.0.0/arrow/man/call_function.Rd | 8 arrow-5.0.0/arrow/man/codec_is_available.Rd | 5 arrow-5.0.0/arrow/man/contains_regex.Rd |only arrow-5.0.0/arrow/man/copy_files.Rd | 4 arrow-5.0.0/arrow/man/data-type.Rd | 4 arrow-5.0.0/arrow/man/enums.Rd | 5 arrow-5.0.0/arrow/man/get_stringr_pattern_options.Rd |only arrow-5.0.0/arrow/man/hive_partition.Rd | 9 arrow-5.0.0/arrow/man/io_thread_count.Rd |only arrow-5.0.0/arrow/man/list_compute_functions.Rd | 7 arrow-5.0.0/arrow/man/load_flight_server.Rd | 5 arrow-5.0.0/arrow/man/match_arrow.Rd | 35 arrow-5.0.0/arrow/man/open_dataset.Rd | 65 arrow-5.0.0/arrow/man/read_delim_arrow.Rd | 4 arrow-5.0.0/arrow/man/read_feather.Rd | 4 arrow-5.0.0/arrow/man/read_json_arrow.Rd | 4 arrow-5.0.0/arrow/man/read_parquet.Rd | 4 arrow-5.0.0/arrow/man/recycle_scalars.Rd |only arrow-5.0.0/arrow/man/repeat_value_as_array.Rd |only arrow-5.0.0/arrow/man/s3_bucket.Rd | 6 arrow-5.0.0/arrow/man/type.Rd | 10 arrow-5.0.0/arrow/man/unify_schemas.Rd | 7 arrow-5.0.0/arrow/man/value_counts.Rd | 6 arrow-5.0.0/arrow/man/write_csv_arrow.Rd |only arrow-5.0.0/arrow/man/write_dataset.Rd | 2 arrow-5.0.0/arrow/man/write_feather.Rd | 4 arrow-5.0.0/arrow/man/write_ipc_stream.Rd | 7 arrow-5.0.0/arrow/man/write_parquet.Rd | 4 arrow-5.0.0/arrow/man/write_to_raw.Rd | 7 arrow-5.0.0/arrow/src/RTasks.cpp |only arrow-5.0.0/arrow/src/altrep.cpp |only arrow-5.0.0/arrow/src/array_to_vector.cpp | 401 +--- arrow-5.0.0/arrow/src/arrowExports.cpp | 695 +++++-- arrow-5.0.0/arrow/src/arrow_cpp11.h | 1 arrow-5.0.0/arrow/src/arrow_types.h | 24 arrow-5.0.0/arrow/src/compute.cpp | 124 + arrow-5.0.0/arrow/src/config.cpp |only arrow-5.0.0/arrow/src/csv.cpp | 30 arrow-5.0.0/arrow/src/dataset.cpp | 71 arrow-5.0.0/arrow/src/expression.cpp | 71 arrow-5.0.0/arrow/src/py-to-r.cpp | 48 arrow-5.0.0/arrow/src/r_task_group.h |only arrow-5.0.0/arrow/src/r_to_arrow.cpp | 804 ++++++-- arrow-5.0.0/arrow/src/recordbatch.cpp | 21 arrow-5.0.0/arrow/src/recordbatchreader.cpp | 40 arrow-5.0.0/arrow/src/scalar.cpp | 4 arrow-5.0.0/arrow/src/symbols.cpp | 9 arrow-5.0.0/arrow/src/table.cpp | 64 arrow-5.0.0/arrow/src/threadpool.cpp | 8 arrow-5.0.0/arrow/src/type_infer.cpp | 2 arrow-5.0.0/arrow/tests/testthat/helper-arrow.R | 8 arrow-5.0.0/arrow/tests/testthat/helper-data.R | 2 arrow-5.0.0/arrow/tests/testthat/helper-expectation.R | 143 + arrow-5.0.0/arrow/tests/testthat/test-Array.R | 85 arrow-5.0.0/arrow/tests/testthat/test-RecordBatch.R | 154 + arrow-5.0.0/arrow/tests/testthat/test-Table.R | 106 - arrow-5.0.0/arrow/tests/testthat/test-altrep.R |only arrow-5.0.0/arrow/tests/testthat/test-chunked-array.R | 54 arrow-5.0.0/arrow/tests/testthat/test-compute-aggregate.R | 91 arrow-5.0.0/arrow/tests/testthat/test-compute-arith.R | 5 arrow-5.0.0/arrow/tests/testthat/test-compute-sort.R | 18 arrow-5.0.0/arrow/tests/testthat/test-csv.R | 77 arrow-5.0.0/arrow/tests/testthat/test-data-type.R | 15 arrow-5.0.0/arrow/tests/testthat/test-dataset.R | 566 ++--- arrow-5.0.0/arrow/tests/testthat/test-dplyr-arrange.R | 23 arrow-5.0.0/arrow/tests/testthat/test-dplyr-filter.R | 67 arrow-5.0.0/arrow/tests/testthat/test-dplyr-group-by.R | 2 arrow-5.0.0/arrow/tests/testthat/test-dplyr-lubridate.R |only arrow-5.0.0/arrow/tests/testthat/test-dplyr-mutate.R | 176 + arrow-5.0.0/arrow/tests/testthat/test-dplyr-string-functions.R | 782 +++++++- arrow-5.0.0/arrow/tests/testthat/test-dplyr.R | 942 +++++++++ arrow-5.0.0/arrow/tests/testthat/test-expression.R | 115 - arrow-5.0.0/arrow/tests/testthat/test-feather.R | 8 arrow-5.0.0/arrow/tests/testthat/test-field.R | 15 arrow-5.0.0/arrow/tests/testthat/test-filesystem.R | 4 arrow-5.0.0/arrow/tests/testthat/test-metadata.R | 42 arrow-5.0.0/arrow/tests/testthat/test-na-omit.R |only arrow-5.0.0/arrow/tests/testthat/test-parquet.R | 8 arrow-5.0.0/arrow/tests/testthat/test-python.R | 57 arrow-5.0.0/arrow/tests/testthat/test-scalar.R | 2 arrow-5.0.0/arrow/tests/testthat/test-schema.R | 28 arrow-5.0.0/arrow/tests/testthat/test-thread-pool.R | 8 arrow-5.0.0/arrow/tests/testthat/test-type.R | 107 + arrow-5.0.0/arrow/tools/nixlibs.R | 46 arrow-5.0.0/arrow/tools/winlibs.R | 6 arrow-5.0.0/arrow/vignettes/developing.Rmd | 16 165 files changed, 8035 insertions(+), 5667 deletions(-)
Title: Class-Agnostic Time Series
Description: Time series toolkit with identical behavior for all
time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo',
'timeSeries', 'tsibble', 'tis' or 'irts'. Also converts reliably between these classes.
Author: Christoph Sax [aut, cre] (<https://orcid.org/0000-0002-7192-7044>)
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between tsbox versions 0.2.1 dated 2020-04-29 and 0.3.0 dated 2021-07-29
tsbox-0.2.1/tsbox/tests/testthat/test_arithmetic.R |only tsbox-0.2.1/tsbox/tests/testthat/test_auto.R |only tsbox-0.2.1/tsbox/tests/testthat/test_date_utils.R |only tsbox-0.2.1/tsbox/tests/testthat/test_defects.R |only tsbox-0.2.1/tsbox/tests/testthat/test_dirty.R |only tsbox-0.2.1/tsbox/tests/testthat/test_non_heuristic.R |only tsbox-0.2.1/tsbox/tests/testthat/test_nonstandard_cnames.R |only tsbox-0.2.1/tsbox/tests/testthat/test_nyc_flights.R |only tsbox-0.2.1/tsbox/tests/testthat/test_object_conversion.R |only tsbox-0.2.1/tsbox/tests/testthat/test_readme.R |only tsbox-0.2.1/tsbox/tests/testthat/test_subannual.R |only tsbox-0.2.1/tsbox/tests/testthat/test_time_conversion.R |only tsbox-0.2.1/tsbox/tests/testthat/test_tricky.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_bind.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_chain.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_default.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_frequency.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_high_freq.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_index.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_irregular.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_lag.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_long_wide.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_low_freq.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_pc.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_pick.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_plot.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_regular.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_scale.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_span.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_summary.R |only tsbox-0.2.1/tsbox/tests/testthat/test_ts_tzone.R |only tsbox-0.2.1/tsbox/tests/testthat/test_tsibble.R |only tsbox-0.2.1/tsbox/tests/testthat/test_tslist.R |only tsbox-0.3.0/tsbox/DESCRIPTION | 15 tsbox-0.3.0/tsbox/MD5 | 227 ++++----- tsbox-0.3.0/tsbox/NAMESPACE | 17 tsbox-0.3.0/tsbox/NEWS.md | 37 + tsbox-0.3.0/tsbox/R/0_convert_data.R | 104 +--- tsbox-0.3.0/tsbox/R/convert_exact.R | 4 tsbox-0.3.0/tsbox/R/convert_heuristic.R | 18 tsbox-0.3.0/tsbox/R/date_helpers.R | 5 tsbox-0.3.0/tsbox/R/date_utils.R | 18 tsbox-0.3.0/tsbox/R/dts.R | 4 tsbox-0.3.0/tsbox/R/dts_helpers.R | 27 - tsbox-0.3.0/tsbox/R/guess_dts.R | 9 tsbox-0.3.0/tsbox/R/guess_time_var_value.R | 12 tsbox-0.3.0/tsbox/R/sysdata.rda |only tsbox-0.3.0/tsbox/R/to_from_all.R | 18 tsbox-0.3.0/tsbox/R/to_from_ts.R | 47 + tsbox-0.3.0/tsbox/R/to_from_tsibble.R | 18 tsbox-0.3.0/tsbox/R/to_from_tslist.R | 7 tsbox-0.3.0/tsbox/R/to_from_xts.R | 8 tsbox-0.3.0/tsbox/R/ts_.R | 16 tsbox-0.3.0/tsbox/R/ts_apply.R | 1 tsbox-0.3.0/tsbox/R/ts_arithmetic.R | 8 tsbox-0.3.0/tsbox/R/ts_bind.R | 13 tsbox-0.3.0/tsbox/R/ts_c.R | 25 tsbox-0.3.0/tsbox/R/ts_chain.R | 6 tsbox-0.3.0/tsbox/R/ts_default.R | 4 tsbox-0.3.0/tsbox/R/ts_examples.R | 24 tsbox-0.3.0/tsbox/R/ts_first_of_period.R | 34 - tsbox-0.3.0/tsbox/R/ts_frequency.R | 121 +++- tsbox-0.3.0/tsbox/R/ts_ggplot.R | 82 ++- tsbox-0.3.0/tsbox/R/ts_index.R | 69 +- tsbox-0.3.0/tsbox/R/ts_lag.R | 3 tsbox-0.3.0/tsbox/R/ts_long_wide.R | 25 tsbox-0.3.0/tsbox/R/ts_na_omit.R | 3 tsbox-0.3.0/tsbox/R/ts_pc.R | 5 tsbox-0.3.0/tsbox/R/ts_pick.R | 10 tsbox-0.3.0/tsbox/R/ts_plot.R | 23 tsbox-0.3.0/tsbox/R/ts_regular.R | 12 tsbox-0.3.0/tsbox/R/ts_span.R | 36 + tsbox-0.3.0/tsbox/R/ts_summary.R | 22 tsbox-0.3.0/tsbox/R/ts_trend.R | 6 tsbox-0.3.0/tsbox/R/tsbox-package.R | 26 - tsbox-0.3.0/tsbox/README.md | 72 +- tsbox-0.3.0/tsbox/build/vignette.rds |binary tsbox-0.3.0/tsbox/inst/CITATION |only tsbox-0.3.0/tsbox/inst/WORDLIST | 22 tsbox-0.3.0/tsbox/inst/doc/convert.Rmd | 2 tsbox-0.3.0/tsbox/inst/doc/convert.html | 310 ++---------- tsbox-0.3.0/tsbox/inst/doc/ts-functions.Rmd | 2 tsbox-0.3.0/tsbox/inst/doc/ts-functions.html | 298 ++--------- tsbox-0.3.0/tsbox/inst/doc/tsbox.html | 326 +++---------- tsbox-0.3.0/tsbox/inst/upd_meta_freq_data.R |only tsbox-0.3.0/tsbox/man/copy_class.Rd | 17 tsbox-0.3.0/tsbox/man/relevant_class.Rd | 4 tsbox-0.3.0/tsbox/man/ts_.Rd | 15 tsbox-0.3.0/tsbox/man/ts_arithmetic.Rd | 8 tsbox-0.3.0/tsbox/man/ts_bind.Rd | 4 tsbox-0.3.0/tsbox/man/ts_boxable.Rd | 4 tsbox-0.3.0/tsbox/man/ts_c.Rd | 4 tsbox-0.3.0/tsbox/man/ts_default.Rd | 4 tsbox-0.3.0/tsbox/man/ts_dts.Rd | 4 tsbox-0.3.0/tsbox/man/ts_examples.Rd | 15 tsbox-0.3.0/tsbox/man/ts_first_of_period.Rd |only tsbox-0.3.0/tsbox/man/ts_frequency.Rd | 19 tsbox-0.3.0/tsbox/man/ts_ggplot.Rd | 14 tsbox-0.3.0/tsbox/man/ts_index.Rd | 18 tsbox-0.3.0/tsbox/man/ts_lag.Rd | 6 tsbox-0.3.0/tsbox/man/ts_long.Rd | 8 tsbox-0.3.0/tsbox/man/ts_na_omit.Rd | 7 tsbox-0.3.0/tsbox/man/ts_pc.Rd | 4 tsbox-0.3.0/tsbox/man/ts_pick.Rd | 8 tsbox-0.3.0/tsbox/man/ts_plot.Rd | 15 tsbox-0.3.0/tsbox/man/ts_regular.Rd | 4 tsbox-0.3.0/tsbox/man/ts_span.Rd | 11 tsbox-0.3.0/tsbox/man/ts_summary.Rd | 8 tsbox-0.3.0/tsbox/man/ts_trend.Rd | 7 tsbox-0.3.0/tsbox/man/ts_ts.Rd | 34 - tsbox-0.3.0/tsbox/man/tsbox-deprecated.Rd | 4 tsbox-0.3.0/tsbox/man/tsbox-package.Rd | 26 - tsbox-0.3.0/tsbox/tests/spelling.R |only tsbox-0.3.0/tsbox/tests/testthat/test-arithmetic.R |only tsbox-0.3.0/tsbox/tests/testthat/test-auto.R |only tsbox-0.3.0/tsbox/tests/testthat/test-date_utils.R |only tsbox-0.3.0/tsbox/tests/testthat/test-defects.R |only tsbox-0.3.0/tsbox/tests/testthat/test-dirty.R |only tsbox-0.3.0/tsbox/tests/testthat/test-issues.R |only tsbox-0.3.0/tsbox/tests/testthat/test-non_heuristic.R |only tsbox-0.3.0/tsbox/tests/testthat/test-nonstandard_cnames.R |only tsbox-0.3.0/tsbox/tests/testthat/test-nyc_flights.R |only tsbox-0.3.0/tsbox/tests/testthat/test-object_conversion.R |only tsbox-0.3.0/tsbox/tests/testthat/test-readme.R |only tsbox-0.3.0/tsbox/tests/testthat/test-subannual.R |only tsbox-0.3.0/tsbox/tests/testthat/test-time_conversion.R |only tsbox-0.3.0/tsbox/tests/testthat/test-tricky.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_bind.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_chain.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_default.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_first_of_period.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_frequency.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_high_freq.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_index.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_irregular.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_lag.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_long_wide.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_low_freq.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_pc.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_pick.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_plot.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_regular.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_scale.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_span.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_summary.R |only tsbox-0.3.0/tsbox/tests/testthat/test-ts_tzone.R |only tsbox-0.3.0/tsbox/tests/testthat/test-tsibble.R |only tsbox-0.3.0/tsbox/tests/testthat/test-tslist.R |only tsbox-0.3.0/tsbox/vignettes/convert.Rmd | 2 tsbox-0.3.0/tsbox/vignettes/ts-functions.Rmd | 2 152 files changed, 1215 insertions(+), 1262 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
(<https://orcid.org/0000-0002-8673-2514>),
Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>),
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.6 dated 2021-07-26 and 1.0.7 dated 2021-07-29
statgenGWAS-1.0.6/statgenGWAS/R/sysdata.rda |only statgenGWAS-1.0.7/statgenGWAS/DESCRIPTION | 8 statgenGWAS-1.0.7/statgenGWAS/MD5 | 33 +- statgenGWAS-1.0.7/statgenGWAS/NEWS.md | 4 statgenGWAS-1.0.7/statgenGWAS/build/partial.rdb |binary statgenGWAS-1.0.7/statgenGWAS/inst/doc/GWAS.html | 40 +- statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/result1_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/result2_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/result3_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/resultM1_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/resultM2_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/resultM3_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/stg0_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/stg1_GWARes_ph2 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/stgM0_GWARes_ph1 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/stgM1_GWARes_ph2 |only statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_GWAS.R | 16 statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_STG.R | 163 +--------- statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_STGHelper.R | 27 - statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_STGoptions.R | 20 - statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_plots.R | 8 statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/test_utils.R | 5 statgenGWAS-1.0.7/statgenGWAS/inst/tinytest/testdata.rda |binary 23 files changed, 118 insertions(+), 206 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.6.1 dated 2021-05-16 and 1.6.2 dated 2021-07-29
pillar-1.6.1/pillar/R/tibble-opt.R |only pillar-1.6.1/pillar/tests/testthat/test-tibble-opt.R |only pillar-1.6.2/pillar/DESCRIPTION | 10 pillar-1.6.2/pillar/MD5 | 182 ++-- pillar-1.6.2/pillar/NAMESPACE | 3 pillar-1.6.2/pillar/NEWS.md | 38 pillar-1.6.2/pillar/R/aaa-options.R |only pillar-1.6.2/pillar/R/char.R | 8 pillar-1.6.2/pillar/R/continuation-data.R | 4 pillar-1.6.2/pillar/R/ctl_colonnade.R | 123 +- pillar-1.6.2/pillar/R/ctl_new_pillar.R | 2 pillar-1.6.2/pillar/R/ctl_pillar.R | 2 pillar-1.6.2/pillar/R/ctl_pillar_component.R | 19 pillar-1.6.2/pillar/R/deprecated.R | 16 pillar-1.6.2/pillar/R/extent.R | 4 pillar-1.6.2/pillar/R/glimpse.R | 11 pillar-1.6.2/pillar/R/multi.R | 137 ++- pillar-1.6.2/pillar/R/num.R | 54 - pillar-1.6.2/pillar/R/options.R |only pillar-1.6.2/pillar/R/ornament.R | 3 pillar-1.6.2/pillar/R/pillar-package.R | 31 pillar-1.6.2/pillar/R/pillar.R | 2 pillar-1.6.2/pillar/R/shaft-.R | 33 pillar-1.6.2/pillar/R/shaft-simple.R | 8 pillar-1.6.2/pillar/R/sigfig.R | 16 pillar-1.6.2/pillar/R/styles.R | 22 pillar-1.6.2/pillar/R/tbl-format-body.R | 2 pillar-1.6.2/pillar/R/tbl-format-footer.R | 88 + pillar-1.6.2/pillar/R/tbl-format-header.R | 2 pillar-1.6.2/pillar/R/tbl-format-setup.R | 35 pillar-1.6.2/pillar/R/tbl-format.R | 72 + pillar-1.6.2/pillar/R/title.R | 2 pillar-1.6.2/pillar/R/type-sum.R | 10 pillar-1.6.2/pillar/R/type.R | 6 pillar-1.6.2/pillar/R/utils.R | 12 pillar-1.6.2/pillar/R/vctr.R | 2 pillar-1.6.2/pillar/R/vctrs.R | 2 pillar-1.6.2/pillar/R/width.R | 4 pillar-1.6.2/pillar/R/zzz.R | 9 pillar-1.6.2/pillar/build/vignette.rds |binary pillar-1.6.2/pillar/inst/doc/debugme.html | 1 pillar-1.6.2/pillar/inst/doc/digits.Rmd | 14 pillar-1.6.2/pillar/inst/doc/digits.html | 22 pillar-1.6.2/pillar/inst/doc/extending.html | 1 pillar-1.6.2/pillar/inst/doc/numbers.R | 14 pillar-1.6.2/pillar/inst/doc/numbers.Rmd | 17 pillar-1.6.2/pillar/inst/doc/numbers.html | 191 ++-- pillar-1.6.2/pillar/inst/doc/printing.R | 38 pillar-1.6.2/pillar/inst/doc/printing.html | 75 - pillar-1.6.2/pillar/man/colonnade.Rd | 22 pillar-1.6.2/pillar/man/ctl_new_pillar.Rd | 2 pillar-1.6.2/pillar/man/deprecated.Rd | 10 pillar-1.6.2/pillar/man/format_tbl.Rd | 38 pillar-1.6.2/pillar/man/format_type_sum.Rd | 1 pillar-1.6.2/pillar/man/glimpse.Rd | 7 pillar-1.6.2/pillar/man/new_tbl_format_setup.Rd | 5 pillar-1.6.2/pillar/man/num.Rd | 23 pillar-1.6.2/pillar/man/pillar-package.Rd | 39 pillar-1.6.2/pillar/man/pillar_options.Rd |only pillar-1.6.2/pillar/man/style_subtle.Rd | 12 pillar-1.6.2/pillar/man/tbl_format_body.Rd | 2 pillar-1.6.2/pillar/man/tbl_format_footer.Rd | 2 pillar-1.6.2/pillar/man/tbl_format_header.Rd | 2 pillar-1.6.2/pillar/man/tbl_format_setup.Rd | 23 pillar-1.6.2/pillar/man/type_sum.Rd | 7 pillar-1.6.2/pillar/tests/testthat.R | 10 pillar-1.6.2/pillar/tests/testthat/_snaps/ctl_colonnade.md | 21 pillar-1.6.2/pillar/tests/testthat/_snaps/ctl_colonnade_1.md | 442 +++++----- pillar-1.6.2/pillar/tests/testthat/_snaps/ctl_colonnade_2.md | 442 +++++----- pillar-1.6.2/pillar/tests/testthat/_snaps/format_character.md | 12 pillar-1.6.2/pillar/tests/testthat/_snaps/format_integer64.md | 36 pillar-1.6.2/pillar/tests/testthat/_snaps/format_list_of.md | 10 pillar-1.6.2/pillar/tests/testthat/_snaps/format_multi.md | 31 pillar-1.6.2/pillar/tests/testthat/_snaps/format_multi_fuzz.md | 352 +++---- pillar-1.6.2/pillar/tests/testthat/_snaps/format_multi_fuzz_2.md | 352 +++---- pillar-1.6.2/pillar/tests/testthat/_snaps/format_survival.md | 28 pillar-1.6.2/pillar/tests/testthat/_snaps/format_unspecified.md | 8 pillar-1.6.2/pillar/tests/testthat/_snaps/multi.md |only pillar-1.6.2/pillar/tests/testthat/_snaps/num.md | 11 pillar-1.6.2/pillar/tests/testthat/_snaps/tbl-format-footer.md | 152 +++ pillar-1.6.2/pillar/tests/testthat/_snaps/tbl-format-setup.md | 56 - pillar-1.6.2/pillar/tests/testthat/_snaps/tbl-format.md | 58 + pillar-1.6.2/pillar/tests/testthat/_snaps/type_sum.md | 10 pillar-1.6.2/pillar/tests/testthat/setup.R | 2 pillar-1.6.2/pillar/tests/testthat/test-ctl_colonnade.R | 43 pillar-1.6.2/pillar/tests/testthat/test-ctl_colonnade_1.R | 63 - pillar-1.6.2/pillar/tests/testthat/test-ctl_colonnade_2.R | 59 - pillar-1.6.2/pillar/tests/testthat/test-format_integer64.R | 3 pillar-1.6.2/pillar/tests/testthat/test-format_multi.R | 1 pillar-1.6.2/pillar/tests/testthat/test-multi.R |only pillar-1.6.2/pillar/tests/testthat/test-num.R | 8 pillar-1.6.2/pillar/tests/testthat/test-options.R |only pillar-1.6.2/pillar/tests/testthat/test-tbl-format-footer.R | 59 + pillar-1.6.2/pillar/tests/testthat/test-tbl-format.R | 6 pillar-1.6.2/pillar/vignettes/digits.Rmd | 14 pillar-1.6.2/pillar/vignettes/numbers.Rmd | 17 96 files changed, 2302 insertions(+), 1546 deletions(-)
Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between param6 versions 0.2.0 dated 2021-07-26 and 0.2.1 dated 2021-07-29
DESCRIPTION | 6 LICENSE | 2 MD5 | 70 - NAMESPACE | 55 - NEWS.md | 52 - R/ParameterSet.R | 871 ++++++++++---------- R/ParameterSet_S3methods.R | 417 ++++----- R/ParameterSet_helpers.R | 680 +++++++-------- R/ParameterSet_methods.R | 975 +++++++++++----------- R/cnd.R | 188 ++-- R/helpers.R | 258 +++--- R/prm.R | 250 ++--- R/support_dictionary.R | 116 +- R/tools.R | 67 + R/zzz.R | 30 README.md | 434 +++++----- man/ParameterSet.Rd | 1340 +++++++++++++++---------------- man/as.ParameterSet.Rd | 52 - man/as.data.table.ParameterSet.Rd | 42 man/as.prm.Rd | 44 - man/c.ParameterSet.Rd | 44 - man/cnd.Rd | 114 +- man/cpset.Rd | 50 - man/expect_equal_ps.Rd | 28 man/length.ParameterSet.Rd | 28 man/param6-package.Rd | 50 - man/prm.Rd | 122 +- man/pset.Rd | 106 +- man/rep.ParameterSet.Rd | 68 - man/sub-.ParameterSet.Rd | 34 man/support_dictionary.Rd | 32 tests/testthat.R | 4 tests/testthat/helpers.R | 6 tests/testthat/test-helpers.R | 218 ++--- tests/testthat/test-paramset.R | 1631 ++++++++++++++++++++------------------ tests/testthat/test-prm.R | 164 +-- 36 files changed, 4406 insertions(+), 4242 deletions(-)
Title: Fit Repeated Linear Regressions
Description: When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz/regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Author: Lijun Wang [aut, cre, cph]
Maintainer: Lijun Wang <szcfweiya@gmail.com>
Diff between fRLR versions 1.2 dated 2021-07-28 and 1.2.1 dated 2021-07-29
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/doc/fRLR.html | 24 ++++++++++++------------ src/Makevars.in | 7 +------ 4 files changed, 21 insertions(+), 26 deletions(-)
Title: Automated Analysis of Multiplex Digital PCR Data
Description: The automated clustering and quantification of the digital PCR
data is based on the combination of 'DBSCAN' (Hahsler et al. (2019)
<doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et al. (1981)
<doi:10.1007/978-1-4757-0450-1>) algorithms.
The analysis is independent of multiplexing geometry, dPCR system,
and input amount.
The details about input data and parameters are available in the
vignette.
Author: Alfonso De Falco [aut, cre] (<https://orcid.org/0000-0001-9985-9920>),
Michel Mittelbronn [ctb],
Christophe Olinger [ctb],
Daniel Stieber [ctb],
Laboratoire national de santé [cph]
Maintainer: Alfonso De Falco <alfonsodefalco90@gmail.com>
Diff between dPCP versions 1.0.3 dated 2020-09-25 and 1.0.4 dated 2021-07-29
DESCRIPTION | 13 - MD5 | 10 - build/vignette.rds |binary inst/doc/dPCP_vignette.Rmd | 4 inst/doc/dPCP_vignette.html | 340 +++++++++++--------------------------------- vignettes/dPCP_vignette.Rmd | 4 6 files changed, 105 insertions(+), 266 deletions(-)
Title: Income Concentration Analysis with Complex Survey Samples
Description: Variance estimation on indicators of income concentration and
poverty using complex sample survey designs. Wrapper around the
'survey' package.
Author: Djalma Pessoa [aut],
Anthony Damico [aut, cre],
Guilherme Jacob [aut]
Maintainer: Anthony Damico <ajdamico@gmail.com>
Diff between convey versions 0.2.3 dated 2021-03-18 and 0.2.4 dated 2021-07-29
convey-0.2.3/convey/R/svyafc.R |only convey-0.2.3/convey/R/svyafcdec.R |only convey-0.2.3/convey/R/svyamato.R |only convey-0.2.3/convey/R/svybcc.R |only convey-0.2.3/convey/R/svybmi.R |only convey-0.2.3/convey/R/svyrenyi.R |only convey-0.2.3/convey/R/svysen.R |only convey-0.2.3/convey/R/svysst.R |only convey-0.2.3/convey/R/svyzenga.R |only convey-0.2.3/convey/R/svyzengacurve.R |only convey-0.2.3/convey/man/svyafc.Rd |only convey-0.2.3/convey/man/svyafcdec.Rd |only convey-0.2.3/convey/man/svyamato.Rd |only convey-0.2.3/convey/man/svybcc.Rd |only convey-0.2.3/convey/man/svybmi.Rd |only convey-0.2.3/convey/man/svyrenyi.Rd |only convey-0.2.3/convey/man/svysen.Rd |only convey-0.2.3/convey/man/svysst.Rd |only convey-0.2.3/convey/man/svyzenga.Rd |only convey-0.2.3/convey/man/svyzengacurve.Rd |only convey-0.2.3/convey/tests/testthat/test-extract_renyi-pos.R |only convey-0.2.3/convey/tests/testthat/test-extract_svyafc.R |only convey-0.2.3/convey/tests/testthat/test-extract_svyafcdec.R |only convey-0.2.3/convey/tests/testthat/test-extract_svyamato-pos.R |only convey-0.2.3/convey/tests/testthat/test-extract_svybcc.R |only convey-0.2.3/convey/tests/testthat/test-extract_svybmi.R |only convey-0.2.3/convey/tests/testthat/test-extract_svysen.R |only convey-0.2.3/convey/tests/testthat/test-extract_svysst.R |only convey-0.2.3/convey/tests/testthat/test-extract_svyzenga-pos.R |only convey-0.2.3/convey/tests/testthat/test-extract_svyzengacurve.R |only convey-0.2.4/convey/DESCRIPTION | 11 convey-0.2.4/convey/MD5 | 64 -- convey-0.2.4/convey/NAMESPACE | 40 - convey-0.2.4/convey/R/svyarpt.R | 4 convey-0.2.4/convey/R/svyiqalpha.R | 4 convey-0.2.4/convey/R/svyisq.R | 4 convey-0.2.4/convey/R/svylorenz.R | 14 convey-0.2.4/convey/R/svypoormed.R | 4 convey-0.2.4/convey/R/svyrmir.R | 6 convey-0.2.4/convey/man/svyarpt.Rd | 2 convey-0.2.4/convey/man/svyiqalpha.Rd | 2 convey-0.2.4/convey/man/svyisq.Rd | 2 convey-0.2.4/convey/man/svylorenz.Rd | 4 convey-0.2.4/convey/man/svypoormed.Rd | 2 convey-0.2.4/convey/man/svyrmir.Rd | 2 convey-0.2.4/convey/tests/testthat/Rplots.pdf |binary convey-0.2.4/convey/tests/testthat/test-matrix.R | 248 +++------ convey-0.2.4/convey/tests/testthat/test-skewed_distributions.R | 249 ++++------ 48 files changed, 232 insertions(+), 430 deletions(-)
Title: Binary Classification Using Extensions of Discriminant Analysis
Description: Implements methods for sample size
reduction within Linear and Quadratic Discriminant Analysis in Lapanowski and Gaynanova (2020) <arXiv:2005.03858>.
Also includes methods for non-linear discriminant analysis with simultaneous sparse feature selection in Lapanowski and Gaynanova (2019) PMLR 89:1704-1713.
Author: Alexander F. Lapanowski [aut, cre],
Irina Gaynanova [aut]
Maintainer: Alexander F. Lapanowski <aflapan@gmail.com>
Diff between biClassify versions 1.1 dated 2021-07-27 and 1.2 dated 2021-07-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/RcppExports.R | 4 ---- inst/doc/biClassify.pdf |binary src/RcppExports.cpp | 16 ---------------- src/sparseKOS.cpp | 14 -------------- 6 files changed, 9 insertions(+), 43 deletions(-)
Title: ILO Open Data via Ilostat Bulk Download Facility or SDMX Web
Service
Description: Tools to download data from the ilostat database
<https://ilostat.ilo.org> together with search and
manipulation utilities.
Author: ILO Department of Statistics [cph, fnd],
David Bescond [aut, cre] (<https://orcid.org/0000-0002-1642-0304>),
Mabelin Villarreal-Fuentes [ctb]
(<https://orcid.org/0000-0001-5644-5760>)
Maintainer: David Bescond <bescond@ilo.org>
Diff between Rilostat versions 1.1.7 dated 2021-03-16 and 1.1.8 dated 2021-07-29
DESCRIPTION | 14 +++++----- MD5 | 16 ++++++------ NAMESPACE | 6 ++++ NEWS.md | 4 +++ R/Rilostat.R | 5 +++ R/distribution_ilostat.r |only R/get_ilostat.R | 58 +++++++++++++++++++++++++++++++++++++------- README.md | 2 - man/distribution_ilostat.Rd |only man/get_ilostat.Rd | 20 +++++++++++++++ 10 files changed, 101 insertions(+), 24 deletions(-)
Title: Disease-Drived Differential Proteins Co-Expression Network
Analysis
Description: Functions designed to connect disease-related differential proteins and
co-expression network. It provides the basic statics analysis included t test, ANOVA analysis.
The network construction is not offered by the package, you can used 'WGCNA' package which you
can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis
included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and
hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>
Diff between DDPNA versions 0.2.7 dated 2021-04-28 and 0.3.0 dated 2021-07-29
DDPNA-0.2.7/DDPNA/data/datalist |only DDPNA-0.3.0/DDPNA/DESCRIPTION | 8 - DDPNA-0.3.0/DDPNA/MD5 | 9 - DDPNA-0.3.0/DDPNA/R/MaxquantDataconvert.R | 12 - DDPNA-0.3.0/DDPNA/R/missing_value_impute.R | 178 +++++++++----------------- DDPNA-0.3.0/DDPNA/man/missing_value_impute.Rd | 9 + 6 files changed, 82 insertions(+), 134 deletions(-)
Title: Dynamical Systems Approach to Immune Response Modeling
Description: Simulation models (apps) of various within-host immune response scenarios.
The purpose of the package is to help individuals learn
about within-host infection and immune response modeling from a dynamical systems perspective.
All apps include explanations of the underlying models and instructions on what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>),
Cody Dailey [ctb],
Yang Ge [ctb],
Spencer Hall [ctb],
Brian McKay [ctb],
Sina Solaimanpour [ctb],
Alexis Vittengl [ctb],
Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>
Diff between DSAIRM versions 0.8.7 dated 2021-03-20 and 0.9.3 dated 2021-07-28
DSAIRM-0.8.7/DSAIRM/R/generate_equations.R |only DSAIRM-0.8.7/DSAIRM/R/simulate_basicvirus_ode.R |only DSAIRM-0.8.7/DSAIRM/R/simulate_basicvirus_stochastic.R |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/bacteriaexploration_documentation.Rmd |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/bacteriaexploration_documentation.html |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/references.bib |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/virusexploration_documentation.Rmd |only DSAIRM-0.8.7/DSAIRM/inst/appinformation/virusexploration_documentation.html |only DSAIRM-0.8.7/DSAIRM/inst/docsfordevelopers |only DSAIRM-0.8.7/DSAIRM/inst/helperfunctions |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/Environmental_Transmission_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SEIRSd_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SIRSd_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/SIR_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/mbmodels/Vector_transmission_model.rds |only DSAIRM-0.8.7/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_ode.R |only DSAIRM-0.8.7/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_stochastic.R |only DSAIRM-0.8.7/DSAIRM/man/generate_equations.Rd |only DSAIRM-0.8.7/DSAIRM/man/simulate_basicvirus_ode.Rd |only DSAIRM-0.8.7/DSAIRM/man/simulate_basicvirus_stochastic.Rd |only DSAIRM-0.8.7/DSAIRM/tests/testthat/test-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/DESCRIPTION | 15 DSAIRM-0.9.3/DSAIRM/MD5 | 230 ++-- DSAIRM-0.9.3/DSAIRM/NAMESPACE | 5 DSAIRM-0.9.3/DSAIRM/NEWS.md | 11 DSAIRM-0.9.3/DSAIRM/R/DSAIRM.R | 31 DSAIRM-0.9.3/DSAIRM/R/generate_documentation.R | 4 DSAIRM-0.9.3/DSAIRM/R/generate_fctcall.R | 101 + DSAIRM-0.9.3/DSAIRM/R/generate_ggplot.R | 26 DSAIRM-0.9.3/DSAIRM/R/generate_shinyinput.R | 21 DSAIRM-0.9.3/DSAIRM/R/run_model.R | 106 +- DSAIRM-0.9.3/DSAIRM/R/simulate_Basic_Virus_Model_ode.R |only DSAIRM-0.9.3/DSAIRM/R/simulate_Basic_Virus_Model_stochastic.R |only DSAIRM-0.9.3/DSAIRM/R/simulate_basicbacteria_modelexploration.R | 224 ++-- DSAIRM-0.9.3/DSAIRM/R/simulate_basicbacteria_ode.R | 4 DSAIRM-0.9.3/DSAIRM/R/simulate_basicvirus_fit.R | 373 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_basicvirus_modelexploration.R | 245 ++-- DSAIRM-0.9.3/DSAIRM/R/simulate_confint_fit.R | 399 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_drugresistance_stochastic.R | 6 DSAIRM-0.9.3/DSAIRM/R/simulate_fludrug_fit.R | 405 +++---- DSAIRM-0.9.3/DSAIRM/R/simulate_modelcomparison_fit.R | 463 ++++---- DSAIRM-0.9.3/DSAIRM/R/simulate_pkpdmodel_ode.R | 12 DSAIRM-0.9.3/DSAIRM/R/simulate_usanalysis.R | 8 DSAIRM-0.9.3/DSAIRM/R/simulate_virusandtx_ode.R | 2 DSAIRM-0.9.3/DSAIRM/build/vignette.rds |binary DSAIRM-0.9.3/DSAIRM/inst/DSAIRM/app.R | 43 DSAIRM-0.9.3/DSAIRM/inst/appinformation/apptable.tsv | 32 DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_documentation.Rmd | 515 ++++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_documentation.html | 208 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteria_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_documentation.Rmd |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_documentation.html |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicbacteriaexploration_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_documentation.Rmd | 446 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_documentation.html | 111 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirus_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_documentation.Rmd |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_documentation.html |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusexploration_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.Rmd | 432 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_documentation.html | 131 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/basicvirusstochastic_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_documentation.Rmd | 405 +++++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_documentation.html | 160 +-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/drugresistance_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/dsairm_references.bib |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_documentation.Rmd | 529 ++++++---- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_documentation.html | 183 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitbasicmodel_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_documentation.Rmd | 304 +++-- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_documentation.html | 116 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitconfint_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/fitfludrug_documentation.Rmd | 358 ++++-- 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DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_documentation.Rmd | 460 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_documentation.html | 157 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/usanalysis_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_documentation.Rmd | 453 +++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_documentation.html | 143 +- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandir_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_documentation.Rmd | 502 ++++++--- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_documentation.html | 180 ++- DSAIRM-0.9.3/DSAIRM/inst/appinformation/virusandtx_tasktable.tsv |only DSAIRM-0.9.3/DSAIRM/inst/doc/DSAIRM.Rmd | 21 DSAIRM-0.9.3/DSAIRM/inst/doc/DSAIRM.html | 59 - DSAIRM-0.9.3/DSAIRM/inst/mbmodels/Basic_Bacteria_model.Rds |only DSAIRM-0.9.3/DSAIRM/inst/mbmodels/Basic_Virus_model.Rds |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_Basic_Virus_Model_ode.R |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_Basic_Virus_Model_stochastic.R |only DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_modelexploration.R | 224 ++-- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicbacteria_ode.R | 4 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_fit.R | 373 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_basicvirus_modelexploration.R | 245 ++-- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_confint_fit.R | 399 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_drugresistance_stochastic.R | 6 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_fludrug_fit.R | 405 +++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_modelcomparison_fit.R | 463 ++++---- DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_pkpdmodel_ode.R | 12 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_usanalysis.R | 8 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulate_virusandtx_ode.R | 2 DSAIRM-0.9.3/DSAIRM/inst/simulatorfunctions/simulatorfunctions.zip |binary DSAIRM-0.9.3/DSAIRM/man/DSAIRM.Rd | 67 - DSAIRM-0.9.3/DSAIRM/man/generate_fctcall.Rd | 46 DSAIRM-0.9.3/DSAIRM/man/generate_ggplot.Rd | 4 DSAIRM-0.9.3/DSAIRM/man/simulate_Basic_Virus_Model_ode.Rd |only DSAIRM-0.9.3/DSAIRM/man/simulate_Basic_Virus_Model_stochastic.Rd |only DSAIRM-0.9.3/DSAIRM/man/simulate_basicbacteria_ode.Rd | 2 DSAIRM-0.9.3/DSAIRM/man/simulate_basicvirus_fit.Rd | 234 ++-- DSAIRM-0.9.3/DSAIRM/man/simulate_confint_fit.Rd | 188 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_drugresistance_stochastic.Rd | 188 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_fludrug_fit.Rd | 194 +-- DSAIRM-0.9.3/DSAIRM/man/simulate_modelcomparison_fit.Rd | 228 ++-- DSAIRM-0.9.3/DSAIRM/man/simulate_usanalysis.Rd | 28 DSAIRM-0.9.3/DSAIRM/man/simulate_virusandtx_ode.Rd | 200 +-- DSAIRM-0.9.3/DSAIRM/tests/testthat/Rplots.pdf |binary DSAIRM-0.9.3/DSAIRM/tests/testthat/test-basicbacteria-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-basicvirus-modelexploration.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-fit-apps.R | 83 + DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_documentation.R | 4 DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_ggplot.R | 61 - DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_plotly.R | 61 - DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_shinyinput.R | 21 DSAIRM-0.9.3/DSAIRM/tests/testthat/test-generate_usplot.R | 124 +- DSAIRM-0.9.3/DSAIRM/tests/testthat/test-individual-apps.R |only DSAIRM-0.9.3/DSAIRM/tests/testthat/test-run_model.R | 156 ++ DSAIRM-0.9.3/DSAIRM/tests/testthat/test-stochastic-virus-app.R | 120 +- DSAIRM-0.9.3/DSAIRM/vignettes/DSAIRM.Rmd | 21 DSAIRM-0.9.3/DSAIRM/vignettes/mainmenu.png |binary DSAIRM-0.9.3/DSAIRM/vignettes/modelexample.png |binary 140 files changed, 8792 insertions(+), 5975 deletions(-)
Title: Safe, Multiple, Simultaneous String Substitution
Description: Designed to enable simultaneous substitution in strings in a safe fashion.
Safe means it does not rely on placeholders (which can cause errors in same length matches).
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Diff between mgsub versions 1.7.2 dated 2020-07-22 and 1.7.3 dated 2021-07-28
DESCRIPTION | 9 ++--- MD5 | 24 +++++++------- NEWS.md | 3 + inst/doc/Safe-Censoring.R | 23 ------------- inst/doc/Safe-Censoring.Rmd | 28 ---------------- inst/doc/Safe-Censoring.html | 33 +------------------ inst/doc/Safe-Substitution.R | 46 --------------------------- inst/doc/Safe-Substitution.Rmd | 67 +--------------------------------------- inst/doc/Safe-Substitution.html | 59 +---------------------------------- man/censor_worker.Rd | 10 +---- man/mgsub_censor.Rd | 10 +---- vignettes/Safe-Censoring.Rmd | 28 ---------------- vignettes/Safe-Substitution.Rmd | 67 +--------------------------------------- 13 files changed, 32 insertions(+), 375 deletions(-)
Title: A Method to Download Department of Education College Scorecard
Data
Description: A method to download Department of Education College
Scorecard data using the public API
<https://collegescorecard.ed.gov/data/documentation/>. It is based on
the 'dplyr' model of piped commands to select and filter data in a
single chained function call. An API key from the U.S. Department of
Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between rscorecard versions 0.19.1 dated 2021-07-20 and 0.20.0 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/sysdata.rda |binary tests/testthat/test-dictionary.R | 4 ++-- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm).
Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>).
For details see Niku et al. (2019a) <doi:10.1371/journal.pone.0216129> and
Niku et al. (2019b) <doi:10.1111/2041-210X.13303>.
Author: Jenni Niku [aut, cre],
Wesley Brooks [aut],
Riki Herliansyah [aut],
Francis K.C. Hui [aut],
Sara Taskinen [aut],
David I. Warton [aut],
Bert van der Veen [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>
Diff between gllvm versions 1.3.0 dated 2021-04-30 and 1.3.1 dated 2021-07-28
gllvm-1.3.0/gllvm/build |only gllvm-1.3.0/gllvm/data/sim_bacteria.RData |only gllvm-1.3.0/gllvm/inst/doc |only gllvm-1.3.0/gllvm/man/optima.Rd |only gllvm-1.3.0/gllvm/man/sim_bacteria.Rd |only gllvm-1.3.0/gllvm/vignettes |only gllvm-1.3.1/gllvm/DESCRIPTION | 16 gllvm-1.3.1/gllvm/MD5 | 93 - gllvm-1.3.1/gllvm/NAMESPACE | 13 gllvm-1.3.1/gllvm/NEWS.md | 16 gllvm-1.3.1/gllvm/R/TMBtrait.R | 510 ++++-- gllvm-1.3.1/gllvm/R/anova.gllvm.R | 26 gllvm-1.3.1/gllvm/R/confint.gllvm.R | 106 + gllvm-1.3.1/gllvm/R/ecoCoefs.gllvm.R | 213 -- gllvm-1.3.1/gllvm/R/getLV.gllvm.R | 48 gllvm-1.3.1/gllvm/R/getPredictErr.gllvm.R | 41 gllvm-1.3.1/gllvm/R/getResidualCor.gllvm.R | 8 gllvm-1.3.1/gllvm/R/getResidualCov.gllvm.R | 152 + gllvm-1.3.1/gllvm/R/gllvm.R | 410 ++++- gllvm-1.3.1/gllvm/R/gllvm.TMB.R | 982 +++++++++--- gllvm-1.3.1/gllvm/R/gllvm.auxiliary.R | 1836 +++++++++++++++++------ gllvm-1.3.1/gllvm/R/gllvm.makeform.R |only gllvm-1.3.1/gllvm/R/logLik.gllvm.R | 8 gllvm-1.3.1/gllvm/R/ordiplot.gllvm.R | 273 ++- gllvm-1.3.1/gllvm/R/plot.gllvm.R | 5 gllvm-1.3.1/gllvm/R/predict.gllvm.R | 212 +- gllvm-1.3.1/gllvm/R/predictLVs.gllvm.R | 74 gllvm-1.3.1/gllvm/R/randomCoefplot.R | 5 gllvm-1.3.1/gllvm/R/residuals.gllvm.R | 24 gllvm-1.3.1/gllvm/R/se.gllvm.R | 266 ++- gllvm-1.3.1/gllvm/R/simulate.gllvm.R | 60 gllvm-1.3.1/gllvm/R/summary.gllvm.R | 204 ++ gllvm-1.3.1/gllvm/man/AICc.Rd | 48 gllvm-1.3.1/gllvm/man/ecoCoefs.Rd |only gllvm-1.3.1/gllvm/man/getLV.gllvm.Rd | 6 gllvm-1.3.1/gllvm/man/getPredictErr.gllvm.Rd | 2 gllvm-1.3.1/gllvm/man/getResidualCor.gllvm.Rd | 6 gllvm-1.3.1/gllvm/man/getResidualCov.gllvm.Rd | 24 gllvm-1.3.1/gllvm/man/gllvm.Rd | 99 - gllvm-1.3.1/gllvm/man/ordiplot.gllvm.Rd | 36 gllvm-1.3.1/gllvm/man/plot.gllvm.Rd | 4 gllvm-1.3.1/gllvm/man/predict.gllvm.Rd | 16 gllvm-1.3.1/gllvm/man/se.gllvm.Rd | 64 gllvm-1.3.1/gllvm/man/summary.gllvm.Rd | 33 gllvm-1.3.1/gllvm/src/gllvm.cpp | 881 ++++++++--- gllvm-1.3.1/gllvm/tests/testthat/test-fitgllvm.R | 2 46 files changed, 4983 insertions(+), 1839 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, restricted
quantile regression, and directional quantile classification. A vignette
is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and
included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code,
<https://orcid.org/0000-0002-7104-5826>),
Cinzia Viroli [ctb] (Contributions to dqc code,
<https://orcid.org/0000-0002-3278-5266>)
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>
Diff between Qtools versions 1.5.4 dated 2021-02-07 and 1.5.5 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 24 ++++++++++---------- NEWS | 8 ++++++ R/Qtools.R | 60 +++++++++++++++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/Qtools.html | 26 +++++++++++++++++++++ man/Qtools-package.Rd | 6 ++--- man/cmidecdf.Rd | 2 - man/midq2q.Rd | 14 +++++++++-- man/midrq.Rd | 9 +++++-- man/midrqControl.Rd | 2 - man/summary.midrq.Rd | 2 - man/vcov.midrq.Rd | 2 - 13 files changed, 114 insertions(+), 49 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>),
Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>),
John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>),
Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>),
David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.0.1 dated 2021-05-14 and 1.0.2 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 21 ++++++++-------- NEWS | 6 ++++ R/hybrids.R | 66 +++++++++++++++++++++++++++++++++++++++++++++------- R/pullGeno.R | 34 ++++++++++++++++++++------ README.md | 2 + build/vignette.rds |binary inst/CITATION | 2 - inst/doc/intro.html | 6 ++-- inst/doc/traits.pdf |binary man/setPhenoGCA.Rd | 39 ++++++++++++++++++++++++++---- src/OCS.cpp |only 12 files changed, 144 insertions(+), 40 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Eamon B. O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 3.4 dated 2021-05-13 and 3.5 dated 2021-07-28
pomp-3.4/pomp/R/aaa.R |only pomp-3.4/pomp/data/blowflies.csv |only pomp-3.4/pomp/data/parus.csv |only pomp-3.5/pomp/DESCRIPTION | 18 +- pomp-3.5/pomp/MD5 | 37 ++-- pomp-3.5/pomp/R/bake.R | 291 +++++++++++++++++++++++++++--------- pomp-3.5/pomp/R/bsmc2.R | 6 pomp-3.5/pomp/R/concat.R | 4 pomp-3.5/pomp/R/objfun.R | 10 + pomp-3.5/pomp/build/partial.rdb |binary pomp-3.5/pomp/data/LondonYorke.rda |binary pomp-3.5/pomp/data/blowflies.csv.xz |only pomp-3.5/pomp/data/bsflu.rda |binary pomp-3.5/pomp/data/ebolaWA2014.rda |binary pomp-3.5/pomp/data/ewcitmeas.rda |binary pomp-3.5/pomp/data/ewmeas.rda |binary pomp-3.5/pomp/data/parus.csv.gz |only pomp-3.5/pomp/inst/NEWS | 46 +++++ pomp-3.5/pomp/inst/NEWS.Rd | 27 +++ pomp-3.5/pomp/inst/doc/index.html | 86 ++++------ pomp-3.5/pomp/man/bake.Rd | 124 +++++++++++++-- pomp-3.5/pomp/man/partrans.Rd | 5 22 files changed, 492 insertions(+), 162 deletions(-)
Title: Analytic Insurance Rating Techniques
Description: Methods for insurance rating. It helps actuaries to implement GLMs within all relevant steps needed to construct
a risk premium from raw data. It provides a data driven strategy for the construction of insurance tariff classes.
This strategy is based on the work by Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>. It also provides recipes
on how to easily perform one-way, or univariate, analyses on an insurance portfolio. In addition it adds functionality
to include reference categories in the levels of the coefficients in the output of a generalized linear regression analysis.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>
Diff between insurancerating versions 0.6.6 dated 2021-05-19 and 0.6.7 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/construct_tariff_classes.R | 5 +++-- R/model_refinement.R | 24 ++++++++++++++++++++++++ R/rows_per_date.R | 6 ++++-- R/utils_refinement.R | 8 ++++++++ man/figures/normalitysim-1.png |binary man/get_data.Rd |only 10 files changed, 57 insertions(+), 15 deletions(-)
More information about insurancerating at CRAN
Permanent link
Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library
simplifies training fast and accurate neural networks
using modern best practices. It is based on research
in to deep learning best practices undertaken
at 'fast.ai', including 'out of the box' support
for vision, text, tabular, audio, time series, and
collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>
Diff between fastai versions 2.0.8 dated 2021-05-16 and 2.0.9 dated 2021-07-28
DESCRIPTION | 7 -- MD5 | 50 +++++++++------ NEWS.md | 8 ++ R/generics_mask.R | 30 --------- R/install_fastai.R | 44 ++++--------- R/package.R | 2 R/stats.R | 4 - README.md | 2 build/vignette.rds |binary inst/doc/optimizer.Rmd | 2 inst/doc/optimizer.html | 2 man/abs.fastai.torch_core.TensorMask.Rd | 11 --- man/greater-than-equals-.fastai.torch_core.TensorMask.Rd | 9 -- man/install_fastai.Rd | 4 - man/lr_find.Rd | 3 man/mask_eq.Rd | 8 -- man/max.fastai.torch_core.TensorMask.Rd | 9 -- tests/testthat/test-GAN.R |only tests/testthat/test-collab.R |only tests/testthat/test-experimental.R |only tests/testthat/test-generics-tensor.R |only tests/testthat/test-image.R |only tests/testthat/test-medical.R |only tests/testthat/test-medical_image_render.R |only tests/testthat/test-model_load.R |only tests/testthat/test-modify.R |only tests/testthat/test-nn_module.R |only tests/testthat/test-predict_medical.R |only tests/testthat/test-pretrained_in_cnn_learner.R |only tests/testthat/test-regression.R |only tests/testthat/test-tabular.R |only tests/testthat/test-text-load.R |only tests/testthat/test-text.R |only vignettes/optimizer.Rmd | 2 34 files changed, 68 insertions(+), 129 deletions(-)
Title: Deep Learning
Description: Implementation of some Deep Learning methods. Includes multilayer perceptron, different activation functions, regularisation strategies, stochastic gradient descent and dropout. Thanks go to the following references for helping to inspire and develop the package: Ian Goodfellow, Yoshua Bengio, Aaron Courville, Francis Bach (2016, ISBN:978-0262035613) Deep Learning. Terrence J. Sejnowski (2018, ISBN:978-0262038034) The Deep Learning Revolution. Grant Sanderson (3brown1blue) <https://www.youtube.com/playlist?list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi> Neural Networks YouTube playlist. Michael A. Nielsen <http://neuralnetworksanddeeplearning.com/> Neural Networks and Deep Learning.
Author: Benjamin Taylor [aut, cre]
Maintainer: Benjamin Taylor <benjamin.taylor.software@gmail.com>
Diff between deepNN versions 1.0 dated 2020-03-05 and 1.1 dated 2021-07-28
DESCRIPTION | 8 +-- MD5 | 38 +++++++++--------- R/cost_functions.R | 98 +++++++++++++++++++++++------------------------ R/miscellaneous.R | 14 ++++-- R/networks.R | 25 ----------- R/optimisation.R | 28 ++++++------- R/prediction.R | 27 +----------- R/regularisation.R | 56 +++++++++++++------------- man/L1_regularisation.Rd | 10 ---- man/L2_regularisation.Rd | 10 ---- man/NNpredict.Rd | 25 ----------- man/Qloss.Rd | 15 ------- man/deepNN-package.Rd | 4 + man/download_mnist.Rd | 6 +- man/dropoutProbs.Rd | 15 ------- man/multinomial.Rd | 13 ------ man/no_regularisation.Rd | 11 ----- man/train.Rd | 25 ----------- man/wQloss.Rd | 15 ------- man/wmultinomial.Rd | 13 ------ 20 files changed, 139 insertions(+), 317 deletions(-)
Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data
formats based on Google protocol-buffers. Currently supports 'rexp.proto' for
serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for
vector tiles. This package uses the auto-generated C++ code by protobuf-compiler,
hence the entire serialization is optimized at compile time. The 'RProtoBuf'
package on the other hand uses the protobuf runtime library to provide a general-
purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between protolite versions 2.1 dated 2020-01-13 and 2.1.1 dated 2021-07-28
DESCRIPTION | 9 ++++----- MD5 | 13 +++++++------ NEWS | 4 ++++ cleanup | 3 +-- configure | 48 ++++++++++++++++++++++++++---------------------- src/Makevars.ucrt |only src/Makevars.win | 2 +- src/RcppExports.cpp | 5 +++++ 8 files changed, 48 insertions(+), 36 deletions(-)
Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Colin Rundel [ctb],
Andy Teucher [ctb],
liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between lwgeom versions 0.2-6 dated 2021-04-02 and 0.2-7 dated 2021-07-28
DESCRIPTION | 7 ++++--- MD5 | 29 ++++++++++++++++------------- NAMESPACE | 4 ++++ R/RcppExports.R | 4 ++++ R/wrap_x.R |only configure | 20 ++++++++++++++++++-- configure.ac | 6 +++++- man/st_wrap_x.Rd |only src/Makevars.ucrt |only src/Makevars.win | 23 ++++++++++------------- src/RcppExports.cpp | 19 +++++++++++++++++++ src/lwgeom.cpp | 18 ++++++++++++++++++ tests/dist.R | 1 + tests/dist.Rout.save | 8 +++++--- tests/geod.Rout.save | 18 +++++++++++------- tests/testthat.Rout.save | 12 +++++++----- tests/testthat/test_lwgeom.R | 16 ++++++++++++++++ 17 files changed, 138 insertions(+), 47 deletions(-)
Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language
identification and the successor of 'cld2' (available from CRAN). The algorithm is still
experimental and takes a novel approach to language detection with different properties
and outcomes. It can be useful to combine this with the Bayesian classifier results
from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Google Inc [cph] (CLD3 C++ library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between cld3 versions 1.4.1 dated 2021-01-11 and 1.4.2 dated 2021-07-28
DESCRIPTION | 7 +++---- MD5 | 7 ++++--- NEWS | 3 +++ src/Makevars.ucrt |only src/Makevars.win | 2 +- 5 files changed, 11 insertions(+), 8 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] (<https://orcid.org/0000-0003-0637-3812>),
Branislav Panic [ctb] (<https://orcid.org/0000-0001-8349-8550>),
Jernej Klemenc [ctb] (<https://orcid.org/0000-0002-6778-6728>),
Simon Oman [ctb] (<https://orcid.org/0000-0001-8213-0818>)
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.13.0 dated 2021-07-14 and 2.13.1 dated 2021-07-28
rebmix-2.13.0/rebmix/data/sensorless.drive.rda |only rebmix-2.13.0/rebmix/data/steel.plates.rda |only rebmix-2.13.0/rebmix/man/sensorless.drive.Rd |only rebmix-2.13.0/rebmix/man/steel.plates.Rd |only rebmix-2.13.1/rebmix/DESCRIPTION | 6 rebmix-2.13.1/rebmix/MD5 | 98 +++++------ rebmix-2.13.1/rebmix/R/RCLRMIX.R | 2 rebmix-2.13.1/rebmix/R/RCLSMIX.R | 4 rebmix-2.13.1/rebmix/R/REBMIX.R | 2 rebmix-2.13.1/rebmix/R/RNGMIX.R | 2 rebmix-2.13.1/rebmix/build/partial.rdb |binary rebmix-2.13.1/rebmix/build/vignette.rds |binary rebmix-2.13.1/rebmix/data/adult.rda |binary rebmix-2.13.1/rebmix/data/bearings.rda |binary rebmix-2.13.1/rebmix/data/datalist | 4 rebmix-2.13.1/rebmix/data/galaxy.rda |binary rebmix-2.13.1/rebmix/data/iris.rda |binary rebmix-2.13.1/rebmix/data/sensorlessdrive.rda |only rebmix-2.13.1/rebmix/data/steelplates.rda |only rebmix-2.13.1/rebmix/data/truck.rda |binary rebmix-2.13.1/rebmix/data/weibull.rda |binary rebmix-2.13.1/rebmix/data/weibullnormal.rda |binary rebmix-2.13.1/rebmix/data/wine.rda |binary rebmix-2.13.1/rebmix/demo/rebmix.fault.detection.R | 88 ++++----- rebmix-2.13.1/rebmix/demo/rebmix.galaxy.R | 6 rebmix-2.13.1/rebmix/demo/rebmix.mixed.continuous.discrete.R | 4 rebmix-2.13.1/rebmix/demo/rebmix.multivariate.normal.R | 2 rebmix-2.13.1/rebmix/demo/rebmix.truck.R | 6 rebmix-2.13.1/rebmix/demo/rebmix.univariate.normal.R | 2 rebmix-2.13.1/rebmix/demo/rebmix.weibullnormal.R | 6 rebmix-2.13.1/rebmix/inst/NEWS.Rd | 6 rebmix-2.13.1/rebmix/inst/doc/rebmix.R | 12 - rebmix-2.13.1/rebmix/inst/doc/rebmix.Rnw | 34 +-- rebmix-2.13.1/rebmix/inst/doc/rebmix.pdf |binary rebmix-2.13.1/rebmix/man/RCLS.chunk.Rd | 2 rebmix-2.13.1/rebmix/man/RCLSMIX.Rd | 2 rebmix-2.13.1/rebmix/man/REBMIX.boot.Rd | 2 rebmix-2.13.1/rebmix/man/REBMIX.plot.Rd | 2 rebmix-2.13.1/rebmix/man/adult.Rd | 4 rebmix-2.13.1/rebmix/man/bearings.Rd | 4 rebmix-2.13.1/rebmix/man/demix.Rd | 2 rebmix-2.13.1/rebmix/man/galaxy.Rd | 2 rebmix-2.13.1/rebmix/man/iris.Rd | 4 rebmix-2.13.1/rebmix/man/sensorlessdrive.Rd |only rebmix-2.13.1/rebmix/man/split.Rd | 2 rebmix-2.13.1/rebmix/man/steelplates.Rd |only rebmix-2.13.1/rebmix/man/truck.Rd | 4 rebmix-2.13.1/rebmix/man/weibull.Rd | 4 rebmix-2.13.1/rebmix/man/weibullnormal.Rd | 4 rebmix-2.13.1/rebmix/man/wine.Rd | 4 rebmix-2.13.1/rebmix/src/emf.cpp | 21 +- rebmix-2.13.1/rebmix/src/rebmixf.cpp | 12 - rebmix-2.13.1/rebmix/src/rngmixf.cpp | 2 rebmix-2.13.1/rebmix/vignettes/rebmix.Rnw | 34 +-- 54 files changed, 196 insertions(+), 199 deletions(-)
Title: Fair Data Adaptation with Quantile Preservation
Description: An implementation of the fair data adaptation with quantile
preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>.
The adaptation procedure uses the specified causal graph to pre-process the
given training and testing data in such a way to remove the bias caused by
the protected attribute. The procedure uses tree ensembles for quantile
regression.
Author: Drago Plecko [aut, cre]
Maintainer: Drago Plecko <drago.plecko@stat.math.ethz.ch>
Diff between fairadapt versions 0.1.0 dated 2019-11-28 and 0.2.0 dated 2021-07-28
fairadapt-0.1.0/fairadapt/R/Fair_Adaptation.R |only fairadapt-0.1.0/fairadapt/R/Input_Verification.R |only fairadapt-0.1.0/fairadapt/R/utility.R |only fairadapt-0.1.0/fairadapt/man/figures |only fairadapt-0.2.0/fairadapt/DESCRIPTION | 42 ++++-- fairadapt-0.2.0/fairadapt/MD5 | 111 ++++++++++++++++- fairadapt-0.2.0/fairadapt/NAMESPACE | 48 +++++++ fairadapt-0.2.0/fairadapt/NEWS.md |only fairadapt-0.2.0/fairadapt/R/checks.R |only fairadapt-0.2.0/fairadapt/R/data.R |only fairadapt-0.2.0/fairadapt/R/fairadapt.R |only fairadapt-0.2.0/fairadapt/R/generics.R |only fairadapt-0.2.0/fairadapt/R/graphs.R |only fairadapt-0.2.0/fairadapt/R/quants.R |only fairadapt-0.2.0/fairadapt/R/utils.R |only fairadapt-0.2.0/fairadapt/README.md | 101 ++++++++++------ fairadapt-0.2.0/fairadapt/build |only fairadapt-0.2.0/fairadapt/data |only fairadapt-0.2.0/fairadapt/inst |only fairadapt-0.2.0/fairadapt/man/adaptedData.Rd |only fairadapt-0.2.0/fairadapt/man/computeQuants.Rd |only fairadapt-0.2.0/fairadapt/man/fairTwins.Rd |only fairadapt-0.2.0/fairadapt/man/fairadapt.Rd | 142 +++++++++++++---------- fairadapt-0.2.0/fairadapt/man/gov_census.Rd |only fairadapt-0.2.0/fairadapt/man/graphModel.Rd |only fairadapt-0.2.0/fairadapt/man/linearQuants.Rd |only fairadapt-0.2.0/fairadapt/man/mcqrnnQuants.Rd |only fairadapt-0.2.0/fairadapt/man/rangerQuants.Rd |only fairadapt-0.2.0/fairadapt/man/uni_admission.Rd |only fairadapt-0.2.0/fairadapt/man/visualizeGraph.Rd |only fairadapt-0.2.0/fairadapt/tests |only fairadapt-0.2.0/fairadapt/vignettes |only 32 files changed, 325 insertions(+), 119 deletions(-)
Title: Co-Clustering Package for Binary, Categorical, Contingency and
Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by
biclustering, co-clustering or block clustering, is an important technique
in two way data analysis. It consists of estimating a mixture model which
takes into account the block clustering problem on both the individual and
variables sets. The 'blockcluster' package provides a bridge between the C++
core library build on top of the 'STK++' library, and the R statistical
computing environment. This package allows to co-cluster binary
<doi:10.1016/j.csda.2007.09.007>, contingency <doi:10.1080/03610920903140197>,
continuous <doi:10.1007/s11634-013-0161-3> and categorical data-sets
<doi:10.1007/s11222-014-9472-2>. It also provides utility functions to
visualize the results. This package may be useful for various applications
in fields of Data mining, Information retrieval, Biology, computer vision
and many more. More information about the project and comprehensive tutorial
can be found on the link mentioned in URL.
Author: Serge Iovleff [aut, cre],
Parmeet Singh Bhatia [aut],
Josselin Demont [ctb],
Vincent Brault [ctb],
Vincent Kubicki [ctb],
Gerard Goavert [ctb],
Christophe Biernacki [ctb],
Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>
Diff between blockcluster versions 4.5.0 dated 2021-07-13 and 4.5.1 dated 2021-07-28
DESCRIPTION | 8 +++--- MD5 | 14 +++++------ inst/NEWS.Rd | 5 ++-- inst/doc/blockcluster_tutorial.pdf |binary src/coclust/src/Models/BinaryLBModelequalepsilon.cpp | 23 +++++++------------ src/coclust/src/Models/BinaryLBModelequalepsilon.h | 3 -- src/coclust/src/Models/CategoricalLBModel.cpp | 4 +-- src/coclust/src/Models/ContinuousLBModel.cpp | 13 +++++----- 8 files changed, 32 insertions(+), 38 deletions(-)
Title: Fit, Simulate and Diagnose Models for Network Evolution Based on
Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Mark S. Handcock [aut, ths],
David R. Hunter [ctb],
Steven M. Goodreau [ctb, ths],
Martina Morris [ctb, ths],
Nicole Bohme Carnegie [ctb],
Carter T. Butts [ctb],
Ayn Leslie-Cook [ctb],
Skye Bender-deMoll [ctb],
Li Wang [ctb],
Kirk Li [ctb],
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel+tergm@unsw.edu.au>
Diff between tergm versions 4.0.1 dated 2021-06-24 and 4.0.2 dated 2021-07-28
DESCRIPTION | 10 +-- MD5 | 63 ++++++++++++------------- R/InitErgmProposal.DynMoME.R | 11 +++- R/InitErgmTerm.netseries.R | 25 +++++---- R/control.stergm.R | 4 + R/simulate.tergm.R | 8 +-- R/stergm.R | 2 R/stergm.utils.R | 22 +++++--- R/tergm.EGMME.GD.R | 4 - R/tergm.EGMME.R | 4 - R/tergm.EGMME.SA.R | 8 +-- R/tergm.EGMME.initialfit.R | 24 ++++----- R/tergm.R | 2 R/tergm.getMCMCsample.R | 2 R/tergm.godfather.R | 2 build/partial.rdb |binary build/tergm.pdf |binary inst/CITATION | 4 - inst/NEWS.Rd | 25 +++++++++ man/control.stergm.Rd | 4 + man/stergm.Rd | 2 man/tergm.Rd | 2 src/changestats_duration.c | 9 +++ src/discordTNT.c | 13 ++--- tests/testthat/test-EGMME-initialfit.R | 14 ++--- tests/testthat/test-discord-proposals.R | 28 +++++------ tests/testthat/test-edgelist_with_lasttoggle.R |only tests/testthat/test-extract-formulae.R | 36 +++++++------- tests/testthat/test-simulate.R | 26 +++++----- tests/testthat/test-term-.SubsetStatistics.R | 18 +++---- tests/testthat/test-term-Change.R | 28 +++++------ tests/testthat/test-term-Cross.R | 50 +++++++++---------- tests/testthat/test-terms-Form-Persist-Diss.R | 48 +++++++++---------- 33 files changed, 280 insertions(+), 218 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.5 dated 2021-03-22 and 0.1.6 dated 2021-07-28
DESCRIPTION | 9 +-- MD5 | 31 +++++----- NAMESPACE | 1 NEWS.md | 11 +++ R/opq.R | 86 ++++++++++++++++++++++++++++-- R/osmdata-methods.R | 1 build/vignette.rds |binary inst/WORDLIST | 26 +++++++++ inst/doc/osm-sf-translation.html | 11 ++- inst/doc/osmdata-sc.html | 11 ++- inst/doc/osmdata.R | 50 +++-------------- inst/doc/osmdata.Rmd | 111 ++++++++++++++++----------------------- inst/doc/osmdata.html | 59 ++++++++------------ man/add_osm_features.Rd |only src/RcppExports.cpp | 5 + tests/testthat/test-osmdata.R | 1 vignettes/osmdata.Rmd | 111 ++++++++++++++++----------------------- 17 files changed, 291 insertions(+), 233 deletions(-)
Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, and to plot the curves and their underlying data, as well as functions to calibrate radiocarbon dates.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between IntCal versions 0.2.1 dated 2021-07-19 and 0.2.2 dated 2021-07-28
IntCal-0.2.1/IntCal/man/mix.curves.Rd |only IntCal-0.2.2/IntCal/DESCRIPTION | 8 IntCal-0.2.2/IntCal/MD5 | 46 ++-- IntCal-0.2.2/IntCal/NAMESPACE | 6 IntCal-0.2.2/IntCal/NEWS.md | 8 IntCal-0.2.2/IntCal/R/IntCal.R | 154 +++------------ IntCal-0.2.2/IntCal/R/calibrate.R | 243 +----------------------- IntCal-0.2.2/IntCal/R/plots.R |only IntCal-0.2.2/IntCal/build/partial.rdb |binary IntCal-0.2.2/IntCal/build/vignette.rds |binary IntCal-0.2.2/IntCal/inst/doc/calculations.R | 11 + IntCal-0.2.2/IntCal/inst/doc/calculations.Rmd | 21 ++ IntCal-0.2.2/IntCal/inst/doc/calculations.html | 240 +++++++++++++++++++++++- IntCal-0.2.2/IntCal/inst/doc/intro.R | 9 IntCal-0.2.2/IntCal/inst/doc/intro.Rmd | 23 +- IntCal-0.2.2/IntCal/inst/doc/intro.html | 244 +++++++++++++++++++++++-- IntCal-0.2.2/IntCal/inst/doc/plots.Rmd | 3 IntCal-0.2.2/IntCal/inst/doc/plots.html | 233 ++++++++++++++++++++++- IntCal-0.2.2/IntCal/man/calBP.14C.Rd |only IntCal-0.2.2/IntCal/man/calibrate.Rd | 19 + IntCal-0.2.2/IntCal/man/draw.ccurve.Rd | 2 IntCal-0.2.2/IntCal/man/draw.dates.Rd |only IntCal-0.2.2/IntCal/man/glue.ccurves.Rd |only IntCal-0.2.2/IntCal/man/mix.ccurves.Rd |only IntCal-0.2.2/IntCal/vignettes/calculations.Rmd | 21 ++ IntCal-0.2.2/IntCal/vignettes/intro.Rmd | 23 +- IntCal-0.2.2/IntCal/vignettes/plots.Rmd | 3 27 files changed, 884 insertions(+), 433 deletions(-)
Title: Fit Repeated Linear Regressions
Description: When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz//regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Author: Lijun Wang [aut, cre, cph]
Maintainer: Lijun Wang <szcfweiya@gmail.com>
Diff between fRLR versions 1.1 dated 2019-01-08 and 1.2 dated 2021-07-28
fRLR-1.1/fRLR/inst/doc/fRLR.Rnw |only fRLR-1.1/fRLR/inst/doc/fRLR.pdf |only fRLR-1.1/fRLR/man/frlr.Rd |only fRLR-1.1/fRLR/vignettes/fRLR.Rnw |only fRLR-1.2/fRLR/DESCRIPTION | 16 fRLR-1.2/fRLR/MD5 | 34 fRLR-1.2/fRLR/NAMESPACE | 9 fRLR-1.2/fRLR/R/RcppExports.R | 42 - fRLR-1.2/fRLR/R/package.R |only fRLR-1.2/fRLR/build/vignette.rds |binary fRLR-1.2/fRLR/configure | 1525 +++++++++++++++++++++++++++++++++++++- fRLR-1.2/fRLR/configure.ac | 12 fRLR-1.2/fRLR/inst/doc/fRLR.R | 48 - fRLR-1.2/fRLR/inst/doc/fRLR.Rmd |only fRLR-1.2/fRLR/inst/doc/fRLR.html |only fRLR-1.2/fRLR/man/frlr1.Rd | 40 fRLR-1.2/fRLR/man/frlr2.Rd | 52 - fRLR-1.2/fRLR/src/Makevars.in | 5 fRLR-1.2/fRLR/src/Makevars.win | 4 fRLR-1.2/fRLR/src/RcppExports.cpp | 19 fRLR-1.2/fRLR/src/frlr.cpp | 256 +----- fRLR-1.2/fRLR/vignettes/fRLR.Rmd |only 22 files changed, 1726 insertions(+), 336 deletions(-)
Title: Find Pattern in Files of All Branches of a 'git' Repository
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given 'git' repository, including all its branches. The results can also be returned in a dataframe.
Author: Stéphane Laurent [aut, cre],
Rob Burns [cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between findInGit versions 0.1.0 dated 2021-07-27 and 0.1.1 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 5 +++++ R/findInGit.R | 14 ++++++++++++-- R/grepInGit.R | 26 ++++++++++++++++++-------- man/findInGit-shiny.Rd | 5 +++++ man/findInGit.Rd | 5 +++++ 7 files changed, 54 insertions(+), 19 deletions(-)
Title: Partially Observed Integrated Functional Depth
Description: Integrated Depths for Partially Observed Functional Data (PoFD). Applications to visualization, outlier detection and classification. Software companion for Elías, Antonio, Jiménez, Raúl, Paganoni, Anna M. and Sangalli, Laura M., (2020), "Integrated Depth for Partially Observed Functional Data".
Author: Antonio Elías [aut, cre],
Raúl Jiménez [ctb],
Anna M. Paganoni [ctb],
Laura M. Sangalli [ctb]
Maintainer: Antonio Elías <antonioefz91@gmail.com>
Diff between fdaPOIFD versions 1.0.0 dated 2021-01-13 and 1.0.1 dated 2021-07-28
DESCRIPTION | 8 +++++--- MD5 | 13 +++++++++---- NEWS.md | 3 +++ R/gaussianPoFD.R | 27 ++++++++++++++++++++++++--- build |only inst |only man/gaussian_PoFD.Rd | 5 ++++- vignettes |only 8 files changed, 45 insertions(+), 11 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre],
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut],
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] (libsvm C++-code),
Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-7 dated 2021-05-23 and 1.7-8 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/gknn.R | 16 +++++++++------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary man/gknn.Rd | 2 +- 9 files changed, 28 insertions(+), 20 deletions(-)
Title: moDel Agnostic Language for Exploration and eXplanation
Description: Unverified black box model is the path to the failure. Opaqueness leads to distrust.
Distrust leads to ignoration. Ignoration leads to rejection.
DALEX package xrays any model and helps to explore and explain its behaviour.
Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance. But such black-box models usually lack of direct interpretability.
DALEX package contains various methods that help to understand the link between input variables
and model output. Implemented methods help to explore model on the level of a single instance
as well as a level of the whole dataset.
All model explainers are model agnostic and can be compared across different models.
DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration.
Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Szymon Maksymiuk [aut] (<https://orcid.org/0000-0002-3120-1601>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 2.2.1 dated 2021-06-01 and 2.3.0 dated 2021-07-28
DESCRIPTION | 6 +++--- MD5 | 12 +++++++----- NAMESPACE | 1 + R/misc_loss_functions.R | 16 ++++++---------- R/model_performance.R | 10 ++++------ R/plot_list.R |only R/plot_model_performance.R | 9 +++++---- man/plot.list.Rd |only 8 files changed, 26 insertions(+), 28 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in
Fleming & Calabrese et al (2014) <doi:10.1086/675504>,
Fleming et al (2014) <doi:10.1111/2041-210X.12176>,
Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>,
Fleming et al (2015) <doi:10.1890/14-2010.1>,
Fleming et al (2016) <doi:10.1890/15-1607>,
Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>,
Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>,
Péron et al (2017) <doi:10.1002/ecm.1260>,
Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>,
Fleming et al (2018) <doi:10.1002/eap.1704>,
Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>,
Fleming et al (2019) <doi:10.1111/2041-210X.13270>,
Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>,
Fleming et al (2020) <doi:10.1101/2020.06.12.130195>,
and
Noonan et al (2021) <doi:10.1111/2041-210X.13597>.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Michael J. Noonan [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc],
Rogério C. de Paula [dtc],
Thomas Akre [dtc],
Jonathan Drescher-Lehman [dtc],
Autumn-Lynn Harrison [dtc],
Ronaldo G. Morato [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.6.0 dated 2021-01-10 and 0.6.1 dated 2021-07-28
DESCRIPTION | 13 MD5 | 153 +++++------ NAMESPACE | 6 NEWS.md | 141 ++++++---- R/1.R | 12 R/QP.R | 2 R/acf.R | 2 R/animate.R |only R/circle.R |only R/cluster.R | 615 +++++++++++++++++++++++++++++----------------- R/covm.R | 10 R/ctmm.R | 30 +- R/ctpm.R |only R/export.R | 19 + R/extent.R | 43 ++- R/fit.R | 247 ++++++++++++------ R/kalman.R | 21 + R/kde.R | 1 R/krige.R | 200 ++++++++++---- R/likelihood.R | 242 +++++++++++------- R/matrix.R | 8 R/mean.R | 7 R/meta.chisq.R | 74 ++--- R/optim.R | 37 +- R/outlier.R | 16 - R/overlap.R | 4 R/parameters.R | 251 +++++++++++++----- R/plot.telemetry.R | 82 +++--- R/plot.variogram.R | 189 +++++++++----- R/projection.R | 2 R/rsf.R | 214 +++++++++++++++- R/select.R | 60 +++- R/speed.R | 18 - R/stats.R | 96 +++++-- R/str.R | 7 R/summary.ctmm.R | 20 - R/telemetry.R | 237 +++++++++++++++-- R/uere.R | 416 +++++++++++++++++++++---------- R/units.R | 217 ++++++++++------ R/variogram.R | 169 +++++++----- R/variogram.fit.R | 124 +++++---- TODO | 12 build/partial.rdb |binary build/vignette.rds |binary data/buffalo.rda |binary data/coati.rda |binary data/gazelle.rda |binary data/jaguar.rda |binary data/pelican.rda |binary data/turtle.rda |binary data/wolf.rda |binary inst/doc/akde.html | 68 +---- inst/doc/error.R | 25 + inst/doc/error.Rmd | 34 +- inst/doc/error.html | 162 ++++++------ inst/doc/periodogram.Rmd | 4 inst/doc/periodogram.html | 176 +++++-------- inst/doc/variogram.html | 220 +++++++--------- man/as.telemetry.Rd | 22 + man/cluster.Rd |only man/ctmm-FAQ.Rd | 2 man/ctmm-package.Rd | 4 man/ctmm.boot.Rd | 30 +- man/ctmm.fit.Rd | 4 man/encounter.Rd | 4 man/export.Rd | 38 +- man/meta.Rd | 7 man/outlie.Rd | 7 man/pelican.Rd | 2 man/plot.variogram.Rd | 2 man/residuals.Rd | 4 man/simulate.ctmm.Rd | 11 man/summary.UD.Rd | 3 man/summary.ctmm.Rd | 8 man/uere.Rd | 4 man/variogram.Rd | 10 man/variogram.fit.Rd | 5 man/video.Rd |only vignettes/error.Rmd | 34 +- vignettes/periodogram.Rmd | 4 80 files changed, 3186 insertions(+), 1725 deletions(-)
Title: Simulate and Estimate Close-Kin Dispersal Kernels
Description: Functions for simulating and estimating kinship-related dispersal. Based
on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A.
Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship
reveals limited intergenerational dispersal in the yellow fever mosquito".
Assumes an additive variance model of dispersal in two dimensions, compatible with
Wright's neighbourhood area. Simple and composite dispersal simulations are supplied,
as well as the functions needed to estimate parent-offspring dispersal for simulated or
empirical data, and to undertake sampling design for future field studies of dispersal.
For ease of use an integrated Shiny app is also included.
Author: Moshe-Elijah Jasper [aut, cre]
(<https://orcid.org/0000-0003-4541-3223>)
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>
Diff between kindisperse versions 0.10.1 dated 2021-07-17 and 0.10.2 dated 2021-07-28
DESCRIPTION | 6 MD5 | 27 - NAMESPACE | 3 R/app.R | 8 R/kindisperse-package.R | 1 README.md | 577 +++++++++++++------------- build/partial.rdb |binary inst/doc/using-kindisperse.R | 2 inst/doc/using-kindisperse.Rmd | 149 +++--- inst/doc/using-kindisperse.html | 441 +++++++++++-------- man/figures/README-graphical_simulation-1.png |binary man/figures/README-simgraphhist-1.png |binary man/figures/README-simgraphpin-1.png |binary vignettes/KDPackageRefs.bibtex |only vignettes/using-kindisperse.Rmd | 149 +++--- 15 files changed, 728 insertions(+), 635 deletions(-)
Title: Approximate String Matching, Fuzzy Text Search, and String
Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Also offers fuzzy text search based on various string
distance measures. Can calculate various string distances based on edits
(Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences. This package is built for speed and
runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>),
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb],
Chris Muir [ctb],
Johannes Gruber [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.6.3 dated 2020-10-09 and 0.9.7 dated 2021-07-28
DESCRIPTION | 7 +++---- MD5 | 22 ++++++++++++---------- NEWS | 12 ++++++++++++ R/stringsim.R | 4 ++-- R/utils.R | 2 +- build/vignette.rds |binary inst/doc/RJournal_6_111-122-2014.pdf |binary inst/doc/stringdist_C-Cpp_api.pdf |binary inst/tinytest/test_gh_issue_78.R |only inst/tinytest/test_gh_issue_88.R |only inst/tinytest/test_stringsim.R | 2 +- src/Rstringdist.c | 17 ++++++----------- src/utils.c | 15 ++++++++++++--- 13 files changed, 49 insertions(+), 32 deletions(-)
Title: Circular, Periodic, or Framed Data Clustering: Fast, Optimal,
and Reproducible
Description: Fast, optimal, and reproducible clustering algorithms for
circular, periodic, or framed data. The algorithms introduced here
are based on a core algorithm for optimal framed clustering the authors
have developed (Debnath & Song 2021) <doi:10.1109/TCBB.2021.3077573>.
The runtime of these algorithms is O(K N log^2 N), where K is the number
of clusters and N is the number of circular data points. On a desktop
computer using a single processor core, millions of data points can be
grouped into a few clusters within seconds. One can apply the algorithms
to characterize events along circular DNA molecules, circular RNA
molecules, and circular genomes of bacteria, chloroplast, and
mitochondria. One can also cluster climate data along any given
longitude or latitude. Periodic data clustering can be formulated as
circular clustering. The algorithms offer a general high-performance
solution to circular, periodic, or framed data clustering.
Author: Tathagata Debnath [aut] (<https://orcid.org/0000-0001-6445-275X>),
Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between OptCirClust versions 0.0.3 dated 2020-12-18 and 0.0.4 dated 2021-07-28
DESCRIPTION | 37 ++-- MD5 | 49 ++--- NAMESPACE | 1 NEWS.md | 11 + R/CirClust.R | 6 R/FramedClust.R | 9 - build/partial.rdb |only build/vignette.rds |binary inst/CITATION |only inst/REFERENCES.bib |only inst/doc/CircularGenomes.R | 5 inst/doc/CircularGenomes.Rmd | 12 - inst/doc/CircularGenomes.html | 267 +++--------------------------- inst/doc/Performance.R | 12 - inst/doc/Performance.Rmd | 20 +- inst/doc/Performance.html | 271 +++--------------------------- inst/doc/Tutorial_CirClust.Rmd | 8 inst/doc/Tutorial_CirClust.html | 328 +++++++------------------------------ inst/doc/Tutorial_FramedClust.Rmd | 8 inst/doc/Tutorial_FramedClust.html | 320 ++++++------------------------------ man/CirClust.Rd | 7 man/FramedClust.Rd | 6 src/RcppExports.cpp | 5 vignettes/CircularGenomes.Rmd | 12 - vignettes/Performance.Rmd | 20 +- vignettes/Tutorial_CirClust.Rmd | 8 vignettes/Tutorial_FramedClust.Rmd | 8 27 files changed, 345 insertions(+), 1085 deletions(-)
Title: Collection of Functions for Matrix Calculations
Description: A collection of functions to support matrix calculations
for probability, econometric and numerical analysis. There are
additional functions that are comparable to APL functions which
are useful for actuarial models such as pension mathematics.
This package is used for teaching and research purposes at the
Department of Finance and Risk Engineering, New York
University, Polytechnic Institute, Brooklyn, NY 11201.
Horn, R.A. (1990) Matrix Analysis. ISBN 978-0521386326.
Lancaster, P. (1969) Theory of Matrices. ISBN 978-0124355507.
Lay, D.C. (1995) Linear Algebra: And Its Applications. ISBN 978-0201845563.
Author: Frederick Novomestky <fnovomes@poly.edu>
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between matrixcalc versions 1.0-4 dated 2021-06-03 and 1.0-5 dated 2021-07-28
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Pulling Clean Data from Covid19india.org
Description: Pull raw and pre-cleaned versions of national and state-level
COVID-19 time-series data from covid19india.org <https://www.covid19india.org>.
Easily obtain and merge case count data, testing data, and vaccine data.
Also assists in calculating the time-varying effective reproduction number
with sensible parameters for COVID-19.
Author: Max Salvatore [aut, cre],
Michael Kleinsasser [aut]
Maintainer: Max Salvatore <mmsalva@umich.edu>
Diff between covid19india versions 0.1.2 dated 2021-07-21 and 0.1.3 dated 2021-07-28
DESCRIPTION | 17 ++++++------ MD5 | 38 ++++++++++++++------------- NAMESPACE | 7 +++-- R/check_for_data_correction.R |only R/extract_latest.R | 5 ++- R/get_all_data.R | 6 ++-- R/get_cfr.R | 6 ++-- R/get_metrics_tables.R | 34 +++++++++++++------------ R/get_nat_counts.R | 21 +++++++++++++-- R/get_nat_tests.R | 4 +- R/get_r0.R | 53 +++++++++++++++++++++++++++++++-------- R/get_state_counts.R | 27 +++++++++++++++++-- R/get_state_tests.R | 5 ++- R/get_state_vax.R | 4 -- README.md | 15 ++++++++--- man/check_for_data_correction.Rd |only man/get_all_data.Rd | 4 ++ man/get_metrics_tables.Rd | 4 ++ man/get_nat_counts.Rd | 7 +++-- man/get_r0.Rd | 5 ++- man/get_state_counts.Rd | 5 ++- 21 files changed, 184 insertions(+), 83 deletions(-)
Title: Download Data from the Wittgenstein Human Capital Data Explorer
Description: Download and plot education specific demographic data from the Wittgenstein Human Capital Data Explorer <http://dataexplorer.wittgensteincentre.org/>.
Author: Guy J. Abel [aut, cre, ctb] (<https://orcid.org/0000-0002-4893-5687>),
Samir K.C. [ctb] (<https://orcid.org/0000-0002-5213-9181>),
Michaela Potancokova [ctb],
Claudia Reiter [ctb] (<https://orcid.org/0000-0002-1485-3851>),
Andrea Tamburini [ctb],
Dilek Yildiz [ctb] (<https://orcid.org/0000-0001-6192-0634>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>
Diff between wcde versions 0.0.1 dated 2021-06-23 and 0.0.2 dated 2021-07-28
wcde-0.0.1/wcde/R/epop_ssp2.R |only wcde-0.0.1/wcde/data/epop_ssp2.rda |only wcde-0.0.1/wcde/man/epop_ssp2.Rd |only wcde-0.0.2/wcde/DESCRIPTION | 42 +++++---- wcde-0.0.2/wcde/MD5 | 47 +++++----- wcde-0.0.2/wcde/NAMESPACE | 1 wcde-0.0.2/wcde/NEWS.md | 8 + wcde-0.0.2/wcde/R/edu_group_sum.R | 4 wcde-0.0.2/wcde/R/find_indicators.R | 3 wcde-0.0.2/wcde/R/get_wcde.R | 10 +- wcde-0.0.2/wcde/R/past_epop.R |only wcde-0.0.2/wcde/R/wcde_pull.R | 11 -- wcde-0.0.2/wcde/R/wic_indicators.R | 2 wcde-0.0.2/wcde/R/wic_scenarios.R | 2 wcde-0.0.2/wcde/data/past_epop.rda |only wcde-0.0.2/wcde/data/wic_scenarios.rda |binary wcde-0.0.2/wcde/inst/doc/intro.R | 73 +++++++++++++--- wcde-0.0.2/wcde/inst/doc/intro.Rmd | 94 +++++++++++++++++--- wcde-0.0.2/wcde/inst/doc/intro.html | 127 +++++++++++++++++----------- wcde-0.0.2/wcde/man/edu_group_sum.Rd | 4 wcde-0.0.2/wcde/man/figures/world4_ssp2.gif |only wcde-0.0.2/wcde/man/find_indicator.Rd | 2 wcde-0.0.2/wcde/man/get_wcde.Rd | 8 - wcde-0.0.2/wcde/man/past_epop.Rd |only wcde-0.0.2/wcde/man/wcde_pull.Rd | 4 wcde-0.0.2/wcde/man/wic_indicators.Rd | 2 wcde-0.0.2/wcde/man/wic_scenarios.Rd | 2 wcde-0.0.2/wcde/vignettes/intro.Rmd | 94 +++++++++++++++++--- 28 files changed, 375 insertions(+), 165 deletions(-)
Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>
Diff between covid19italy versions 0.3.0 dated 2020-07-21 and 0.3.1 dated 2021-07-28
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Title: Missing Item Responses Imputation for Test and Assessment Data
Description: Functions for imputing missing item responses for dichotomous and
polytomous test and assessment data. This package enables missing imputation
methods that are suitable for test and assessment data, including:
listwise (LW) deletion (see De Ayala et al. 2001 <doi:10.1111/j.1745-3984.2001.tb01124.x>),
treating as incorrect (IN, see Lord, 1974 <doi: 10.1111/j.1745-3984.1974.tb00996.x>;
Mislevy & Wu, 1996 <doi: 10.1002/j.2333-8504.1996.tb01708.x>;
Pohl et al., 2014 <doi: 10.1177/0013164413504926>), person mean imputation (PM),
item mean imputation (IM), two-way (TW) and response function (RF) imputation
(see Sijtsma & van der Ark, 2003 <doi: 10.1207/s15327906mbr3804_4>),
logistic regression (LR) imputation, and expectation–maximization (EM)
imputation (see Finch, 2008 <doi: 10.1111/j.1745-3984.2008.00062.x>).
Author: Shenghai Dai [aut, cre],
Xiaolin Wang [aut],
Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Diff between TestDataImputation versions 1.2 dated 2020-11-16 and 2.1 dated 2021-07-28
TestDataImputation-1.2/TestDataImputation/man/LogsticReg.Rd |only TestDataImputation-2.1/TestDataImputation/DESCRIPTION | 17 TestDataImputation-2.1/TestDataImputation/MD5 | 38 +- TestDataImputation-2.1/TestDataImputation/NAMESPACE | 29 - TestDataImputation-2.1/TestDataImputation/R/EMimpute.r | 7 TestDataImputation-2.1/TestDataImputation/R/ImputeTestData.r | 81 +++- TestDataImputation-2.1/TestDataImputation/R/ItemMean.r | 2 TestDataImputation-2.1/TestDataImputation/R/Listwise.r | 2 TestDataImputation-2.1/TestDataImputation/R/LogisticReg.r | 7 TestDataImputation-2.1/TestDataImputation/R/PersonMean.r | 2 TestDataImputation-2.1/TestDataImputation/R/ResponseFun.r |only TestDataImputation-2.1/TestDataImputation/R/TreatIncorrect.r | 9 TestDataImputation-2.1/TestDataImputation/R/TwoWay.r | 5 TestDataImputation-2.1/TestDataImputation/man/EMimpute.Rd | 74 ++-- TestDataImputation-2.1/TestDataImputation/man/ImputeTestData.Rd | 171 +++++----- TestDataImputation-2.1/TestDataImputation/man/ItemMean.Rd | 58 +-- TestDataImputation-2.1/TestDataImputation/man/Listwise.Rd | 64 +-- TestDataImputation-2.1/TestDataImputation/man/LogisticReg.Rd |only TestDataImputation-2.1/TestDataImputation/man/PersonMean.Rd | 76 ++-- TestDataImputation-2.1/TestDataImputation/man/ResponseFun.Rd |only TestDataImputation-2.1/TestDataImputation/man/TreatIncorrect.Rd | 88 ++--- TestDataImputation-2.1/TestDataImputation/man/Twoway.Rd | 79 ++-- 22 files changed, 437 insertions(+), 372 deletions(-)
More information about TestDataImputation at CRAN
Permanent link
Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations,
weight-enabled frequency tables and common descriptive
(univariate) statistics in concise tables available in a
variety of formats (plain ASCII, Markdown and HTML). A good
point-of-entry for exploring data, both for experienced
and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>
Diff between summarytools versions 0.9.9 dated 2021-03-19 and 1.0.0 dated 2021-07-28
summarytools-0.9.9/summarytools/inst/doc/Introduction.R |only summarytools-0.9.9/summarytools/inst/doc/Introduction.Rmd |only summarytools-0.9.9/summarytools/inst/doc/Introduction.html |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.R |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.Rmd |only summarytools-0.9.9/summarytools/inst/doc/Recommendations-rmarkdown.html |only summarytools-0.9.9/summarytools/vignettes/Introduction.Rmd |only summarytools-0.9.9/summarytools/vignettes/Recommendations-rmarkdown.Rmd |only summarytools-0.9.9/summarytools/vignettes/define_keywords.png |only summarytools-0.9.9/summarytools/vignettes/dfSummary_in_RStudio_Viewer.png |only summarytools-0.9.9/summarytools/vignettes/dfSummary_md.png |only summarytools-1.0.0/summarytools/DESCRIPTION | 10 summarytools-1.0.0/summarytools/MD5 | 105 +- summarytools-1.0.0/summarytools/NAMESPACE | 3 summarytools-1.0.0/summarytools/NEWS.md | 61 + summarytools-1.0.0/summarytools/R/args_validation.R | 58 - summarytools-1.0.0/summarytools/R/cleartmp.R | 19 summarytools-1.0.0/summarytools/R/ctable.R | 128 +- summarytools-1.0.0/summarytools/R/define_keywords.R | 181 ++-- summarytools-1.0.0/summarytools/R/descr.R | 93 +- summarytools-1.0.0/summarytools/R/dfSummary.R | 325 ++++--- summarytools-1.0.0/summarytools/R/freq.R | 36 summarytools-1.0.0/summarytools/R/helpers.R | 40 summarytools-1.0.0/summarytools/R/label.R | 8 summarytools-1.0.0/summarytools/R/print.list.R | 2 summarytools-1.0.0/summarytools/R/print.stby.R | 34 summarytools-1.0.0/summarytools/R/print.summarytools.R | 444 ++++++---- summarytools-1.0.0/summarytools/R/st_css.R | 13 summarytools-1.0.0/summarytools/R/st_options.R | 164 +++ summarytools-1.0.0/summarytools/R/stby.R | 4 summarytools-1.0.0/summarytools/R/summarytools.R | 29 summarytools-1.0.0/summarytools/R/tabagisme.R | 2 summarytools-1.0.0/summarytools/R/use_custom_lang.R | 37 summarytools-1.0.0/summarytools/R/view.R | 19 summarytools-1.0.0/summarytools/R/zzz.R | 31 summarytools-1.0.0/summarytools/build/vignette.rds |binary summarytools-1.0.0/summarytools/inst/doc/introduction.R |only summarytools-1.0.0/summarytools/inst/doc/introduction.Rmd |only summarytools-1.0.0/summarytools/inst/doc/introduction.html |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.R |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.Rmd |only summarytools-1.0.0/summarytools/inst/doc/rmarkdown.html |only summarytools-1.0.0/summarytools/inst/includes/fig-valign.tex |only summarytools-1.0.0/summarytools/inst/includes/stylesheets/summarytools.css | 2 summarytools-1.0.0/summarytools/man/cleartmp.Rd | 7 summarytools-1.0.0/summarytools/man/ctable.Rd | 128 +- summarytools-1.0.0/summarytools/man/define_keywords.Rd | 38 summarytools-1.0.0/summarytools/man/descr.Rd | 89 +- summarytools-1.0.0/summarytools/man/dfSummary.Rd | 129 +- summarytools-1.0.0/summarytools/man/format_number.Rd |only summarytools-1.0.0/summarytools/man/freq.Rd | 29 summarytools-1.0.0/summarytools/man/print.list.Rd | 93 +- summarytools-1.0.0/summarytools/man/print.stby.Rd | 93 +- summarytools-1.0.0/summarytools/man/print.summarytools.Rd | 173 ++- summarytools-1.0.0/summarytools/man/st_css.Rd | 14 summarytools-1.0.0/summarytools/man/st_options.Rd | 85 + summarytools-1.0.0/summarytools/man/summarytools-package.Rd | 29 summarytools-1.0.0/summarytools/man/tabagisme.Rd | 2 summarytools-1.0.0/summarytools/man/view.Rd | 122 +- summarytools-1.0.0/summarytools/vignettes/assets |only summarytools-1.0.0/summarytools/vignettes/introduction.Rmd |only summarytools-1.0.0/summarytools/vignettes/rmarkdown.Rmd |only 62 files changed, 1785 insertions(+), 1094 deletions(-)
Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks.
References:
J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>
Diff between BiDAG versions 2.0.2 dated 2021-04-30 and 2.0.3 dated 2021-07-28
BiDAG-2.0.2/BiDAG/data/Asiamatrix.rda |only BiDAG-2.0.2/BiDAG/data/gsimmatrix.rda |only BiDAG-2.0.2/BiDAG/man/plotdiffs.DBN.Rd |only BiDAG-2.0.3/BiDAG/DESCRIPTION | 13 - BiDAG-2.0.3/BiDAG/MD5 | 77 ++++--- BiDAG-2.0.3/BiDAG/NAMESPACE | 6 BiDAG-2.0.3/BiDAG/R/DBNdata.R | 1 BiDAG-2.0.3/BiDAG/R/DBNfns.R | 81 ++++---- BiDAG-2.0.3/BiDAG/R/RcppExports.R | 8 BiDAG-2.0.3/BiDAG/R/corescore.R | 4 BiDAG-2.0.3/BiDAG/R/extractors.R |only BiDAG-2.0.3/BiDAG/R/graphhelpfns.R | 12 - BiDAG-2.0.3/BiDAG/R/initpar.R | 17 + BiDAG-2.0.3/BiDAG/R/main.R | 8 BiDAG-2.0.3/BiDAG/R/performanceassess.R | 28 +- BiDAG-2.0.3/BiDAG/R/plotS3.R | 24 +- BiDAG-2.0.3/BiDAG/R/plotfns.R | 22 +- BiDAG-2.0.3/BiDAG/R/plotusingrgraphviz.R | 274 +++++++++++++++++----------- BiDAG-2.0.3/BiDAG/R/printmethods.R | 72 +++---- BiDAG-2.0.3/BiDAG/R/scoreagainstdag.R | 32 ++- BiDAG-2.0.3/BiDAG/R/summary.R | 4 BiDAG-2.0.3/BiDAG/data/Asiamat.rda |only BiDAG-2.0.3/BiDAG/data/gsimmat.rda |only BiDAG-2.0.3/BiDAG/man/DBNdata.Rd | 7 BiDAG-2.0.3/BiDAG/man/compact2full.Rd | 12 - BiDAG-2.0.3/BiDAG/man/compareDBNs.Rd | 10 - BiDAG-2.0.3/BiDAG/man/full2compact.Rd | 10 - BiDAG-2.0.3/BiDAG/man/getDAG.Rd |only BiDAG-2.0.3/BiDAG/man/getMCMCscore.Rd |only BiDAG-2.0.3/BiDAG/man/getSpace.Rd |only BiDAG-2.0.3/BiDAG/man/getTrace.Rd |only BiDAG-2.0.3/BiDAG/man/iterativeMCMC.Rd | 5 BiDAG-2.0.3/BiDAG/man/iterativeMCMCclass.Rd | 4 BiDAG-2.0.3/BiDAG/man/kirc.Rd | 2 BiDAG-2.0.3/BiDAG/man/kirp.Rd | 2 BiDAG-2.0.3/BiDAG/man/orderMCMC.Rd | 5 BiDAG-2.0.3/BiDAG/man/partitionMCMC.Rd | 3 BiDAG-2.0.3/BiDAG/man/plotDBN.Rd | 10 - BiDAG-2.0.3/BiDAG/man/plotdiffsDBN.Rd |only BiDAG-2.0.3/BiDAG/man/plotpcor.Rd | 6 BiDAG-2.0.3/BiDAG/man/plotpedges.Rd | 4 BiDAG-2.0.3/BiDAG/man/scoreagainstDAG.Rd | 12 + BiDAG-2.0.3/BiDAG/man/scoreparameters.Rd | 6 BiDAG-2.0.3/BiDAG/src/RcppExports.cpp | 33 +-- BiDAG-2.0.3/BiDAG/src/cppfns.cpp | 20 +- 45 files changed, 480 insertions(+), 354 deletions(-)
Title: Inference for Spatiotemporal Partially Observed Markov Processes
Description: Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. To do so, it relies on and extends a number of facilities that the 'pomp' package provides for inference on time series data using partially-observed Markov process (POMP) models. Implemented methods include filtering and inference methods in Park and Ionides (2020) <doi:10.1007/s11222-020-09957-3>, Rebeschini and van Handel (2015) <doi:10.1214/14-AAP1061>, Evensen and van Leeuwen (1996) <doi:10.1029/94JC00572> and Ionides et al. (2021) <arXiv:2002.05211v2>. Pre-print statistical software article: Asfaw et al. (2021) <arXiv:2101.01157>.
Author: Kidus Asfaw [aut, cre],
Aaron A. King [aut],
Edward Ionides [aut],
Joonha Park [ctb],
Allister Ho [ctb]
Maintainer: Kidus Asfaw <kasfaw@umich.edu>
Diff between spatPomp versions 0.23.0.0 dated 2021-07-09 and 0.25.0.0 dated 2021-07-27
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/plot.R | 51 +++++++++++++++++++++++++++++++++++---------------- man/plot.Rd | 10 +++++++++- man/reexports.Rd | 2 +- 5 files changed, 54 insertions(+), 27 deletions(-)
Title: Create Representative Records After Entity Resolution
Description: An implementation of Kaplan, Betancourt, Steorts (2020) <arXiv:1810.01538> that creates representative records for use in downstream tasks after entity resolution is performed. Multiple methods for creating the representative records (data sets) are provided.
Author: Andee Kaplan [aut, cre],
Brenda Betancourt [aut],
Rebecca C. Steorts [aut]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>
Diff between representr versions 0.1.1 dated 2020-10-20 and 0.1.2 dated 2021-07-27
DESCRIPTION | 8 MD5 | 22 +- NEWS.md | 6 R/pp_weights.R | 3 R/rl_reg.R | 2 build/vignette.rds |binary inst/doc/representr.R | 42 ---- inst/doc/representr.Rmd | 87 ++++----- inst/doc/representr.html | 450 +++++++++++++++-------------------------------- man/pp_weights.Rd | 3 man/rl_reg1.Rd | 2 vignettes/representr.Rmd | 87 ++++----- 12 files changed, 266 insertions(+), 446 deletions(-)
Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>),
John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between popkin versions 1.3.8 dated 2021-02-11 and 1.3.13 dated 2021-07-27
DESCRIPTION | 9 MD5 | 89 + NAMESPACE | 2 NEWS.md | 116 +- R/fst.R | 2 R/inbr.R | 3 R/inbr_diag.R | 8 R/n_eff.R | 2 R/phylo_max_edge.R |only R/plot_admix.R |only R/plot_phylo.R |only R/plot_popkin.R | 284 ++++-- R/popkin-package.R | 18 R/popkin.R | 13 R/popkin_A.R | 6 R/popkin_A_min_subpops.R | 3 R/popkin_af.R |only R/pwfst.R | 2 R/rescale_popkin.R | 2 R/validate_kinship.R | 30 R/weights_subpops.R | 83 + README.md | 5 build/vignette.rds |binary inst/CITATION | 18 inst/doc/popkin.R | 33 inst/doc/popkin.Rmd | 45 inst/doc/popkin.html | 70 + man/fst.Rd | 2 man/inbr.Rd | 3 man/inbr_diag.Rd | 8 man/n_eff.Rd | 2 man/plot_phylo.Rd |only man/plot_popkin.Rd | 115 +- man/popkin-package.Rd | 18 man/popkin.Rd | 13 man/popkin_A.Rd | 4 man/popkin_A_min_subpops.Rd | 3 man/popkin_af.Rd |only man/pwfst.Rd | 2 man/rescale_popkin.Rd | 2 man/validate_kinship.Rd | 16 man/weights_subpops.Rd | 24 tests/testthat/Xs.RData |binary tests/testthat/Xs.bim | 2000 +++++++++++++++++++++---------------------- tests/testthat/Xs.grm.N.bin |only tests/testthat/Xs.grm.bin |only tests/testthat/Xs.grm.id |only tests/testthat/make_data.R | 3 tests/testthat/test_popkin.R | 371 +++++++ vignettes/popkin.Rmd | 45 50 files changed, 2153 insertions(+), 1321 deletions(-)
Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre],
Pierre Roudier [aut, ctb],
Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between aqp versions 1.29 dated 2021-04-07 and 1.30 dated 2021-07-27
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aqp-1.30/aqp/R/dice.R | 2 aqp-1.30/aqp/R/estimateAWC.R | 32 - aqp-1.30/aqp/R/factor-level-setters.R | 150 ++--- aqp-1.30/aqp/R/findOverlap-fixOverlap.R | 2 aqp-1.30/aqp/R/genSlabLabels.R | 108 +-- aqp-1.30/aqp/R/getSurfaceHorizonDepth.R | 278 ++++++--- aqp-1.30/aqp/R/glom.R | 300 +++++++--- aqp-1.30/aqp/R/harmonize.R | 2 aqp-1.30/aqp/R/invertLabelColor.R | 58 - aqp-1.30/aqp/R/missingDataGrid.R | 2 aqp-1.30/aqp/R/mixMunsell.R | 238 +++++-- aqp-1.30/aqp/R/mollicEpipedon.R | 8 aqp-1.30/aqp/R/munsell2rgb.R | 172 ++++- aqp-1.30/aqp/R/mutate_profile.R | 2 aqp-1.30/aqp/R/perturb.R | 13 aqp-1.30/aqp/R/plotColorMixture.R | 118 +++ aqp-1.30/aqp/R/prepanel.depth_function.R | 170 ++--- aqp-1.30/aqp/R/previewColors.R | 47 + aqp-1.30/aqp/R/profile_compare.R | 2 aqp-1.30/aqp/R/slab.R | 2 aqp-1.30/aqp/R/soilColorIndices.R | 12 aqp-1.30/aqp/R/soilPalette.R | 150 ++--- aqp-1.30/aqp/R/spc2mpspline.R | 4 aqp-1.30/aqp/R/spec2Munsell.R |only aqp-1.30/aqp/R/transform.R | 2 aqp-1.30/aqp/R/zzz.R | 14 aqp-1.30/aqp/build/partial.rdb |binary aqp-1.30/aqp/data/datalist | 2 aqp-1.30/aqp/data/sp5.rda |binary aqp-1.30/aqp/data/spectral.reference.rda |only aqp-1.30/aqp/data/traditionalColorNames.rda |only aqp-1.30/aqp/demo/slope_effect_hz_thickness.R | 222 +++---- aqp-1.30/aqp/inst/WORDLIST |only aqp-1.30/aqp/inst/_pkgdown.yml | 16 aqp-1.30/aqp/inst/example-data/jacobs2000-hz-data.csv | 94 +-- aqp-1.30/aqp/inst/example-data/jacobs2000-site-data.csv | 16 aqp-1.30/aqp/man/PMS2Munsell.Rd |only aqp-1.30/aqp/man/aggregateColor.Rd | 5 aqp-1.30/aqp/man/aggregateSoilDepth.Rd | 2 aqp-1.30/aqp/man/alignTransect.Rd | 3 aqp-1.30/aqp/man/aqp_df_class.Rd | 6 aqp-1.30/aqp/man/bootstrapSoilTexture.Rd | 4 aqp-1.30/aqp/man/brierScore.Rd | 4 aqp-1.30/aqp/man/coercion-methods.Rd | 98 +-- aqp-1.30/aqp/man/compositeSPC.Rd | 42 - 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aqp-1.30/aqp/tests/testthat/test-mixMunsell.R | 35 - aqp-1.30/aqp/tests/testthat/test-mollic.R | 48 + aqp-1.30/aqp/tests/testthat/test-overlap.R | 92 +-- aqp-1.30/aqp/tests/testthat/test-slab.R | 234 +++---- aqp-1.30/aqp/tests/testthat/test-slabPlot.R | 2 aqp-1.30/aqp/tests/testthat/test-slice.R | 90 +-- aqp-1.30/aqp/tests/testthat/test-soil-depth.R | 6 aqp-1.30/aqp/tests/testthat/test-spec2Munsell.R |only aqp-1.30/aqp/tests/testthat/test-subsetHz.R |only aqp-1.30/aqp/tests/testthat/test-surface-thickness.R | 96 +-- 152 files changed, 4203 insertions(+), 3026 deletions(-)
Title: Pixar Films and Achievements
Description: Data about Disney Pixar films provided by Wikipedia. This
package contains data about the films, the people involved, and their
awards.
Author: Eric Leung [aut, cre] (<https://orcid.org/0000-0002-8724-1872>)
Maintainer: Eric Leung <erictleung@outlook.com>
Diff between pixarfilms versions 0.2.0 dated 2021-05-03 and 0.2.1 dated 2021-07-27
pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_academy.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_box_office_budget.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_box_office_numbers.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_box_office_worldwide.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_genres.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_pixar_films.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_pixar_people.txt |only pixarfilms-0.2.0/pixarfilms/tests/testthat/test-data_public_response.txt |only pixarfilms-0.2.1/pixarfilms/DESCRIPTION | 19 pixarfilms-0.2.1/pixarfilms/MD5 | 33 - pixarfilms-0.2.1/pixarfilms/NEWS.md | 6 pixarfilms-0.2.1/pixarfilms/R/data.R | 7 pixarfilms-0.2.1/pixarfilms/README.md | 61 ++- pixarfilms-0.2.1/pixarfilms/inst/WORDLIST | 4 pixarfilms-0.2.1/pixarfilms/inst/doc/pixar_film_ratings.R | 39 + pixarfilms-0.2.1/pixarfilms/inst/doc/pixar_film_ratings.Rmd | 74 ++- pixarfilms-0.2.1/pixarfilms/inst/doc/pixar_film_ratings.html | 203 +++++----- pixarfilms-0.2.1/pixarfilms/man/academy.Rd | 5 pixarfilms-0.2.1/pixarfilms/man/box_office.Rd | 2 pixarfilms-0.2.1/pixarfilms/tests/testthat/_snaps |only pixarfilms-0.2.1/pixarfilms/tests/testthat/test-data.R | 101 +--- pixarfilms-0.2.1/pixarfilms/vignettes/pixar_film_ratings.Rmd | 74 ++- 22 files changed, 369 insertions(+), 259 deletions(-)
Title: Estimating the Optimal Number of Migration Edges from 'Treemix'
Description: The popular population genetic software 'Treemix' by
'Pickrell and Pritchard' (2012) <DOI:10.1371/journal.pgen.1002967>
estimates the number of migration edges on a population tree.
However, it can be difficult to determine the number of migration
edges to include. Previously, it was customary to stop adding migration
edges when 99.8% of variation in the data was explained, but 'OptM'
automates this process using an ad hoc statistic based on the
second-order rate of change in the log likelihood. 'OptM' also
has added functionality for various threshold modeling
to compare with the ad hoc statistic.
Author: Robert Fitak [aut, cre]
Maintainer: Robert Fitak <rfitak9@gmail.com>
Diff between OptM versions 0.1.3 dated 2019-04-28 and 0.1.5 dated 2021-07-27
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ R/optM.R | 41 ++++++++++++++++++++++++++++++++--------- R/plot_optM.R | 6 +++--- README.md | 16 +++++++++++----- inst/CITATION | 7 +++---- man/optM.Rd | 14 +++++++++++++- 7 files changed, 73 insertions(+), 34 deletions(-)
Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share
'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or
'AFNI/SUMA' surfaces. The viewer widget can be either standalone or
embedded into 'R-shiny' applications. The standalone version only require
a web browser with 'WebGL2' support (for example, 'Chrome'). It can be
inserted into any websites; see <https://dipterix.org/project/threebrain/>).
as an example. The 'R-shiny' support allows the 3D viewer to be dynamically
generated from reactive user inputs. This feature has been fully adopted by
'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to
analyze 'iEEG/eCoG' data. Documentation about 'threeBrain' is provided
by <https://dipterix.org/threeBrain/> and several vignettes included
in this package. To cite the package, please check our 'NeuroImage' paper
by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>),
or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut],
Brian Metzger [aut],
Elizabeth Nesbitt [res],
Meng Li [ths],
Michael Beauchamp [aut, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between threeBrain versions 0.1.9 dated 2021-01-10 and 0.2.0 dated 2021-07-27
threeBrain-0.1.9/threeBrain/inst/FreeSurferColorLUT.json |only threeBrain-0.2.0/threeBrain/DESCRIPTION | 53 threeBrain-0.2.0/threeBrain/MD5 | 83 threeBrain-0.2.0/threeBrain/NAMESPACE | 12 threeBrain-0.2.0/threeBrain/NEWS.md | 19 threeBrain-0.2.0/threeBrain/R/aaa.R | 6 threeBrain-0.2.0/threeBrain/R/cache_fs.R | 2 threeBrain-0.2.0/threeBrain/R/class_brain.R | 9 threeBrain-0.2.0/threeBrain/R/class_brainatlas.R | 120 threeBrain-0.2.0/threeBrain/R/class_multibrain.R | 15 threeBrain-0.2.0/threeBrain/R/fs_brain.R | 9 threeBrain-0.2.0/threeBrain/R/fs_brain2.R | 4 threeBrain-0.2.0/threeBrain/R/fs_import-atlas.R | 2 threeBrain-0.2.0/threeBrain/R/fs_import-t1.R | 2 threeBrain-0.2.0/threeBrain/R/geom_free.R | 19 threeBrain-0.2.0/threeBrain/R/loaders.R | 41 threeBrain-0.2.0/threeBrain/R/s3_geom.R | 16 threeBrain-0.2.0/threeBrain/R/suma_import-atlas.R | 2 threeBrain-0.2.0/threeBrain/R/suma_import-t1.R | 2 threeBrain-0.2.0/threeBrain/R/threejs_brain.R | 177 threeBrain-0.2.0/threeBrain/R/utils.R | 143 threeBrain-0.2.0/threeBrain/R/utils_orient.R | 8 threeBrain-0.2.0/threeBrain/R/utils_palette_voxel.R |only threeBrain-0.2.0/threeBrain/R/zzz.R | 52 threeBrain-0.2.0/threeBrain/inst/CITATION |only threeBrain-0.2.0/threeBrain/inst/WORDLIST | 61 threeBrain-0.2.0/threeBrain/inst/commands/launch.zip |binary threeBrain-0.2.0/threeBrain/inst/commands/linux.sh | 20 threeBrain-0.2.0/threeBrain/inst/commands/mac.command | 18 threeBrain-0.2.0/threeBrain/inst/doi.svg |only threeBrain-0.2.0/threeBrain/inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/dipterix.css | 36 threeBrain-0.2.0/threeBrain/inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js |48105 +++++----- threeBrain-0.2.0/threeBrain/inst/htmlwidgets/threejs_brain.js | 156 threeBrain-0.2.0/threeBrain/inst/palettes |only threeBrain-0.2.0/threeBrain/inst/sample_data |only threeBrain-0.2.0/threeBrain/man/create_group.Rd | 12 threeBrain-0.2.0/threeBrain/man/default_template_directory.Rd |only threeBrain-0.2.0/threeBrain/man/freesurfer_brain.Rd | 5 threeBrain-0.2.0/threeBrain/man/geom_freemesh.Rd | 4 threeBrain-0.2.0/threeBrain/man/merge_brain.Rd | 3 threeBrain-0.2.0/threeBrain/man/reorient_volume.Rd | 4 threeBrain-0.2.0/threeBrain/man/template_subject.Rd | 11 threeBrain-0.2.0/threeBrain/man/threejs_brain.Rd | 59 threeBrain-0.2.0/threeBrain/man/voxel_colormap.Rd |only threeBrain-0.2.0/threeBrain/man/voxel_cube.Rd |only 45 files changed, 25713 insertions(+), 23577 deletions(-)
Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching.
The contents include themes for plots, functions for simulating
quantities of interest from regression models, functions for simulating various
forms of fake data for instructional/research purposes, and many more. All told, the functions
provided here are broadly useful for data organization, data presentation, data recoding,
and data simulation.
Author: Steve Miller [aut, cre],
Ben Bolker [ctb],
Dave Armstrong [ctb],
John Fox [ctb],
Winston Chang [ctb],
Brian Ripley [ctb],
Bill Venables [ctb],
Pascal van Kooten [ctb],
Gerko Vink [ctb],
Paul Williamson [ctb]
Maintainer: Steve Miller <steven.v.miller@gmail.com>
Diff between stevemisc versions 1.1.0 dated 2021-06-14 and 1.2.0 dated 2021-07-27
DESCRIPTION | 11 - MD5 | 42 +++-- NAMESPACE | 8 NEWS.md | 9 + R/data.R | 26 +++ R/ggplot-themes.R | 169 ++++++++++++++++++++ R/prepare_refs.R |only R/print_refs.R |only R/r2sd.R | 26 ++- R/revcode.R |only README.md | 242 +++++++++++++++++++++++++----- data/stevepubs.rda |only man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-15-2.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-16-2.png |only man/figures/README-unnamed-chunk-17-1.png |only man/figures/README-unnamed-chunk-17-2.png |only man/figures/README-unnamed-chunk-17-3.png |only man/figures/README-unnamed-chunk-17-4.png |only man/figures/README-unnamed-chunk-18-1.png |only man/figures/README-unnamed-chunk-18-2.png |only man/figures/README-unnamed-chunk-18-3.png |only man/figures/README-unnamed-chunk-18-4.png |only man/figures/README-unnamed-chunk-19-1.png |only man/ggplot-themes.Rd | 32 +++ man/prepare_refs.Rd |only man/print_refs.Rd |only man/r2sd.Rd | 15 + man/revcode.Rd |only man/stevepubs.Rd |only 31 files changed, 517 insertions(+), 63 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.3.0 dated 2021-04-16 and 2.4.0 dated 2021-07-27
DESCRIPTION | 8 MD5 | 24 - NAMESPACE | 4 NEWS.md | 44 +++ R/fbGetAdAccountCustomAudiences.R |only R/fbGetAdCreative.R | 5 R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-authorization.html | 229 +--------------- inst/doc/rfacebookstat-cost-data.html | 245 +---------------- inst/doc/rfacebookstat-get-statistics.html | 407 +++++++---------------------- man/fbGetAdAccountCustomAudiences.Rd |only man/fbGetAdCreative.Rd | 4 14 files changed, 226 insertions(+), 746 deletions(-)
Title: Methods for Working with Uncertainty in Rankings
Description: Provides methods for measuring and describing uncertainty in
rankings. See Rising (2021) <arXiv:2107.03459> for background.
Author: Justin Rising [aut, cre]
Maintainer: Justin Rising <justin.rising@us.af.mil>
Diff between rankUncertainty versions 1.0.0.0 dated 2021-07-12 and 1.0.1.0 dated 2021-07-27
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- src/RcppExports.cpp | 5 +++++ src/makeCanonicalRep.cpp | 2 +- tests/testthat/test-generateIntervals.R | 6 +----- 5 files changed, 14 insertions(+), 14 deletions(-)
More information about rankUncertainty at CRAN
Permanent link
Title: Download and Import Open Stree tMap Data Extracts
Description: Match, download, convert and import Open Street Map data extracts
obtained from several providers.
Author: Andrea Gilardi [aut, cre] (<https://orcid.org/0000-0002-9424-7439>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Barry Rowlingson [ctb] (<https://orcid.org/0000-0002-8586-6625>),
Salva Fernández [rev] (Salva reviewed the package (v. 0.1) for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/395>),
Nicholas Potter [rev] (Nicholas reviewed the package (v. 0.1) for
rOpenSci, see
<https://github.com/ropensci/software-review/issues/395>)
Maintainer: Andrea Gilardi <andrea.gilardi@unimib.it>
Diff between osmextract versions 0.3.0 dated 2021-06-10 and 0.3.1 dated 2021-07-27
osmextract-0.3.0/osmextract/data/datalist |only osmextract-0.3.1/osmextract/DESCRIPTION | 12 osmextract-0.3.1/osmextract/MD5 | 126 osmextract-0.3.1/osmextract/NAMESPACE | 47 osmextract-0.3.1/osmextract/NEWS.md | 157 osmextract-0.3.1/osmextract/R/data.R | 248 - osmextract-0.3.1/osmextract/R/download.R | 326 - osmextract-0.3.1/osmextract/R/find.R | 244 - osmextract-0.3.1/osmextract/R/get-key-values.R | 696 +-- osmextract-0.3.1/osmextract/R/get-network.R |only osmextract-0.3.1/osmextract/R/get.R | 522 +- osmextract-0.3.1/osmextract/R/globals.R | 16 osmextract-0.3.1/osmextract/R/match.R | 989 ++-- osmextract-0.3.1/osmextract/R/osmextract-package.R |only osmextract-0.3.1/osmextract/R/providers.R | 174 osmextract-0.3.1/osmextract/R/read.R | 618 +- osmextract-0.3.1/osmextract/R/search.R | 58 osmextract-0.3.1/osmextract/R/update.R | 414 - osmextract-0.3.1/osmextract/R/utils.R | 90 osmextract-0.3.1/osmextract/R/vectortranslate.R | 1102 ++--- osmextract-0.3.1/osmextract/R/zzz.R | 54 osmextract-0.3.1/osmextract/build/vignette.rds |binary osmextract-0.3.1/osmextract/inst/doc/osmextract.R | 808 +-- osmextract-0.3.1/osmextract/inst/doc/osmextract.Rmd | 1702 +++---- osmextract-0.3.1/osmextract/inst/doc/osmextract.html | 2194 +++++----- osmextract-0.3.1/osmextract/inst/doc/providers.R | 48 osmextract-0.3.1/osmextract/inst/doc/providers.Rmd | 190 osmextract-0.3.1/osmextract/inst/doc/providers.html | 640 +- osmextract-0.3.1/osmextract/inst/doc/providers_comparisons.R | 148 osmextract-0.3.1/osmextract/inst/doc/providers_comparisons.Rmd | 308 - osmextract-0.3.1/osmextract/inst/doc/providers_comparisons.html | 665 +-- osmextract-0.3.1/osmextract/inst/osmconf.ini | 254 - osmextract-0.3.1/osmextract/man/bbbike_zones.Rd | 88 osmextract-0.3.1/osmextract/man/figures/README-points-lines-iow-2.png |binary osmextract-0.3.1/osmextract/man/figures/logo.svg | 272 - osmextract-0.3.1/osmextract/man/geofabrik_zones.Rd | 152 osmextract-0.3.1/osmextract/man/oe_download.Rd | 204 osmextract-0.3.1/osmextract/man/oe_download_directory.Rd | 42 osmextract-0.3.1/osmextract/man/oe_find.Rd | 170 osmextract-0.3.1/osmextract/man/oe_get.Rd | 486 +- osmextract-0.3.1/osmextract/man/oe_get_keys.Rd | 266 - osmextract-0.3.1/osmextract/man/oe_get_network.Rd |only osmextract-0.3.1/osmextract/man/oe_match.Rd | 366 - osmextract-0.3.1/osmextract/man/oe_match_pattern.Rd | 74 osmextract-0.3.1/osmextract/man/oe_providers.Rd | 54 osmextract-0.3.1/osmextract/man/oe_read.Rd | 370 - osmextract-0.3.1/osmextract/man/oe_search.Rd | 70 osmextract-0.3.1/osmextract/man/oe_update.Rd | 164 osmextract-0.3.1/osmextract/man/oe_vectortranslate.Rd | 464 +- osmextract-0.3.1/osmextract/man/openstreetmap_fr_zones.Rd | 80 osmextract-0.3.1/osmextract/man/osmextract-package.Rd |only osmextract-0.3.1/osmextract/man/test_zones.Rd | 34 osmextract-0.3.1/osmextract/tests/testthat.R | 8 osmextract-0.3.1/osmextract/tests/testthat/_snaps/get-keys.md | 60 osmextract-0.3.1/osmextract/tests/testthat/test-download.R | 98 osmextract-0.3.1/osmextract/tests/testthat/test-find.R | 90 osmextract-0.3.1/osmextract/tests/testthat/test-get-keys.R | 314 - osmextract-0.3.1/osmextract/tests/testthat/test-get-network.R |only osmextract-0.3.1/osmextract/tests/testthat/test-get.R | 60 osmextract-0.3.1/osmextract/tests/testthat/test-match.R | 326 - osmextract-0.3.1/osmextract/tests/testthat/test-providers.R | 8 osmextract-0.3.1/osmextract/tests/testthat/test-read.R | 421 - osmextract-0.3.1/osmextract/tests/testthat/test-update.R | 39 osmextract-0.3.1/osmextract/tests/testthat/test-vectortranslate.R | 180 osmextract-0.3.1/osmextract/vignettes/osmextract.Rmd | 1702 +++---- osmextract-0.3.1/osmextract/vignettes/providers.Rmd | 190 osmextract-0.3.1/osmextract/vignettes/providers_comparisons.Rmd | 308 - 67 files changed, 10268 insertions(+), 9742 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb],
Michał Bojanowski [ctb],
Ben Bolker [ctb],
Christian Schmid [ctb]
Maintainer: Pavel N. Krivitsky <pavel+ergm@unsw.edu.au>
Diff between ergm versions 4.0.1 dated 2021-06-21 and 4.1.2 dated 2021-07-27
ergm-4.0.1/ergm/tests/testthat/test-proposal-bdtnt.R |only ergm-4.0.1/ergm/tests/testthat/test-proposal-strattnt.R |only ergm-4.1.2/ergm/DESCRIPTION | 16 - ergm-4.1.2/ergm/MD5 | 96 +++--- ergm-4.1.2/ergm/NAMESPACE | 1 ergm-4.1.2/ergm/R/InitErgmConstraint.R | 6 ergm-4.1.2/ergm/R/InitErgmConstraint.hints.R | 51 +-- ergm-4.1.2/ergm/R/InitErgmProposal.R | 32 +- ergm-4.1.2/ergm/R/InitErgmTerm.operator.R | 23 + ergm-4.1.2/ergm/R/check.ErgmTerm.R | 14 ergm-4.1.2/ergm/R/ergm-package.R | 1 ergm-4.1.2/ergm/R/ergm.R | 2 ergm-4.1.2/ergm/R/ergm.bounddeg.R | 1 ergm-4.1.2/ergm/R/ergm.etamap.R | 10 ergm-4.1.2/ergm/R/ergm.getMCMCsample.R | 12 ergm-4.1.2/ergm/R/ergm_model.R | 14 ergm-4.1.2/ergm/R/ergm_proposal.R | 1 ergm-4.1.2/ergm/R/get.node.attr.R | 4 ergm-4.1.2/ergm/R/gof.ergm.R | 2 ergm-4.1.2/ergm/R/param_names.R | 2 ergm-4.1.2/ergm/R/summary.ergm.R | 2 ergm-4.1.2/ergm/build/ergm.pdf |binary ergm-4.1.2/ergm/build/partial.rdb |binary ergm-4.1.2/ergm/inst/CITATION | 6 ergm-4.1.2/ergm/inst/NEWS.Rd | 50 +++ ergm-4.1.2/ergm/inst/doc/ergm-term-crossRef.html | 33 +- ergm-4.1.2/ergm/inst/doc/ergm.pdf |binary ergm-4.1.2/ergm/inst/doc/nodal_attributes.html | 6 ergm-4.1.2/ergm/inst/include/ergm_BDStratBlocks.h | 183 +++++++----- ergm-4.1.2/ergm/inst/include/ergm_changestats_auxnet.h | 22 + ergm-4.1.2/ergm/inst/include/ergm_stubs.c | 80 ----- ergm-4.1.2/ergm/inst/include/ergm_weighted_population.h | 199 +++++++++++--- ergm-4.1.2/ergm/man/check.ErgmTerm.Rd | 6 ergm-4.1.2/ergm/man/ergm-constraints.Rd | 11 ergm-4.1.2/ergm/man/ergm-package.Rd | 1 ergm-4.1.2/ergm/man/ergm-terms.Rd | 2 ergm-4.1.2/ergm/man/ergm_bd_init.Rd | 1 ergm-4.1.2/ergm/man/ergm_dyadgen_select.Rd | 1 ergm-4.1.2/ergm/man/ergm_model.Rd | 1 ergm-4.1.2/ergm/man/nodal_attributes-API.Rd | 5 ergm-4.1.2/ergm/src/MHproposals.c | 78 ++--- ergm-4.1.2/ergm/src/changestats_auxnet.c | 16 - ergm-4.1.2/ergm/src/changestats_interaction.c | 2 ergm-4.1.2/ergm/src/ergm_dyadgen.c | 5 ergm-4.1.2/ergm/src/init.c | 2 ergm-4.1.2/ergm/src/test_weighted_population.c |only ergm-4.1.2/ergm/tests/testthat/test-offsets.R | 2 ergm-4.1.2/ergm/tests/testthat/test-operators.R | 30 +- ergm-4.1.2/ergm/tests/testthat/test-proposal-bdstrattnt.R | 179 ++++++++++++ ergm-4.1.2/ergm/tests/testthat/test-weighted-population.R |only ergm-4.1.2/ergm/tests/u_function.R | 3 51 files changed, 801 insertions(+), 413 deletions(-)
Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index
Scores
Description: EQ-5D is a popular health related quality of life instrument used
in the clinical and economic evaluation of health care. Developed by the
EuroQol group <https://euroqol.org/>, the instrument consists of two
components: health state description and evaluation. For the description
component a subject self-rates their health in terms of five dimensions;
mobility, self-care, usual activities, pain/discomfort, and
anxiety/depression using either a three-level (EQ-5D-3L,
<https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/>) or a five-level
(EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>)
scale. Frequently the scores on these five dimensions are converted to a
single utility index using country specific value sets, which can be used
in the clinical and economic evaluation of health care as well as in
population health surveys. The eq5d package provides methods to calculate
index scores from a subject's dimension scores. 29 TTO and 11 VAS EQ-5D-3L
value sets including those for countries in Szende et al (2007)
<doi:10.1007/1-4020-5511-0> and Szende et al (2014)
<doi:10.1007/978-94-007-7596-1>, 28 EQ-5D-5L EQ-VT value sets from the
EuroQol website, the EQ-5D-5L crosswalk value sets developed by
van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008>, the
crosswalk value set for Russia and reverse crosswalk value sets. Two
EQ-5D-Y value sets are also included. Methods are also included for the
analysis of EQ-5D profiles along with a shiny web tool to enable the
calculation, visualisation and automated statistical analysis of EQ-5D
data via a web browser using EQ-5D dimension scores stored in CSV or
Excel files.
Author: Fraser Morton [aut, cre],
Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>
Diff between eq5d versions 0.9.0 dated 2021-04-12 and 0.10.0 dated 2021-07-27
DESCRIPTION | 23 ++++++----- MD5 | 43 ++++++++++++--------- NAMESPACE | 1 NEWS.md | 14 +++++++ R/data.R | 17 +++++++- R/eq5d.R | 13 +++++- R/eq5drcw.R |only README.md | 56 +++++++++++++++++----------- data/rcw.RData |only data/tto.RData |binary data/vt.RData |binary inst/doc/eq5d.R | 6 +++ inst/doc/eq5d.Rmd | 14 +++++-- inst/doc/eq5d.html | 84 +++++++++++++++++++++++------------------- inst/shiny/server.R | 3 + man/RCW.Rd |only man/TTO.Rd | 4 +- man/VT.Rd | 4 +- man/eq5d-package.Rd | 17 ++++---- man/eq5drcw.Rd |only tests/testthat/test-eq5d.R | 1 tests/testthat/test-eq5d3l.R | 8 ++++ tests/testthat/test-eq5d5l.R | 24 ++++++++---- tests/testthat/test-eq5drcw.R |only vignettes/eq5d.Rmd | 14 +++++-- 25 files changed, 225 insertions(+), 121 deletions(-)
Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the
pair correlation function from point patterns to patterns of objects of
finite size and irregular shape (e.g. lakes within a country). This is a
reimplementation of the method suggested by Nuske et al. (2009)
<doi:10.1016/j.foreco.2009.09.050> using the libraries 'GEOS' and 'GDAL'
directly instead of through 'PostGIS'.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Maintainer: Robert Nuske <robert.nuske@nw-fva.de>
Diff between apcf versions 0.1.5 dated 2020-07-05 and 0.1.6 dated 2021-07-27
DESCRIPTION | 9 +-- MD5 | 31 +++++------ NEWS.md | 4 + R/pat2dists.R | 2 README.md | 8 +- build/partial.rdb |binary build/vignette.rds |binary configure | 2 configure.ac | 2 inst/doc/intro.Rmd | 2 inst/doc/intro.html | 137 ++++++++++++++++++++++++-------------------------- man/pat2dists.Rd | 2 src/Makevars.ucrt |only src/Makevars.win | 22 ++++---- src/import_export.cpp | 9 +-- tools/winlibs.R | 7 +- vignettes/intro.Rmd | 2 17 files changed, 121 insertions(+), 118 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 2.0.1 dated 2021-02-24 and 2.1.0 dated 2021-07-27
DESCRIPTION | 11 - MD5 | 36 ++-- NEWS.md | 10 + R/Connection.R | 88 +++++---- R/Driver.R | 24 ++ R/File_Parser.R | 234 +++++++++++++++----------- R/Result.R | 4 R/sql_translate_env.R | 243 +++++++++++++++++++++++---- R/table.R | 4 R/util.R | 1 build/vignette.rds |binary man/dbConnect-AthenaDriver-method.Rd | 5 man/install_boto.Rd | 5 tests/testthat/test-datatransfer-datatable.R | 8 tests/testthat/test-datatransfer-vroom.R | 6 tests/testthat/test-dbDisconnect.R | 7 tests/testthat/test-dplyr-sql-trans-env.R | 98 ++++++++++ tests/testthat/test-file-parser.R | 41 +++- tests/testthat/test-metadata.R | 2 19 files changed, 606 insertions(+), 221 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 2.0.1 dated 2021-02-24 and 2.1.0 dated 2021-07-27
DESCRIPTION | 12 - MD5 | 34 +-- NEWS.md | 10 R/Connection.R | 116 +++++----- R/Driver.R | 24 ++ R/File_Parser.R | 230 +++++++++++++-------- R/Result.R | 4 R/Table.R | 4 R/sql_translate_env.R | 285 +++++++++++++++++++++------ R/utils.R | 45 +++- build/vignette.rds |binary man/dbConnect-AthenaDriver-method.Rd | 5 tests/testthat/test-datatransfer-datatable.R | 6 tests/testthat/test-datatransfer-vroom.R | 6 tests/testthat/test-dbDisconnect.R | 7 tests/testthat/test-dplyr-sql-trans-env.R | 98 +++++++++ tests/testthat/test-file-parser.R | 42 ++- tests/testthat/test-metadata.R | 2 18 files changed, 667 insertions(+), 263 deletions(-)
Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in `mrgsolve`, typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format.
Author: Felicien Le Louedec [aut, cre]
(<https://orcid.org/0000-0003-3699-2729>)
Maintainer: Felicien Le Louedec <lelouedec.felicien@iuct-oncopole.fr>
Diff between mapbayr versions 0.4.1 dated 2021-04-30 and 0.5.0 dated 2021-07-27
mapbayr-0.4.1/mapbayr/tests/testthat/test-LBFGSB_donotmove.R |only mapbayr-0.5.0/mapbayr/DESCRIPTION | 6 mapbayr-0.5.0/mapbayr/MD5 | 62 - mapbayr-0.5.0/mapbayr/NAMESPACE | 1 mapbayr-0.5.0/mapbayr/NEWS.md | 18 mapbayr-0.5.0/mapbayr/R/get.R | 355 ++--- mapbayr-0.5.0/mapbayr/R/mapbayest.R | 177 +- mapbayr-0.5.0/mapbayr/R/mapbayest_check_and_preprocess.R | 474 ++++--- mapbayr-0.5.0/mapbayr/R/mapbayest_ofv_computation.R | 150 +- mapbayr-0.5.0/mapbayr/R/mapbayest_optimization.R | 132 +- mapbayr-0.5.0/mapbayr/R/mapbayest_postprocess.R | 197 +-- mapbayr-0.5.0/mapbayr/R/mapbayests.R | 595 +++++----- mapbayr-0.5.0/mapbayr/R/mrgmod.R | 448 +++---- mapbayr-0.5.0/mapbayr/R/read_mrgsolve_model.R | 60 - mapbayr-0.5.0/mapbayr/R/zzz_utils.R | 98 - mapbayr-0.5.0/mapbayr/README.md | 39 mapbayr-0.5.0/mapbayr/inst/WORDLIST | 1 mapbayr-0.5.0/mapbayr/man/compute_ofv.Rd | 4 mapbayr-0.5.0/mapbayr/man/data_helpers.Rd | 68 - mapbayr-0.5.0/mapbayr/man/mapbayest.Rd | 2 mapbayr-0.5.0/mapbayr/man/mbrlib.Rd | 28 mapbayr-0.5.0/mapbayr/man/obs_lines.mrgmod.Rd | 56 mapbayr-0.5.0/mapbayr/man/postprocess.Rd | 5 mapbayr-0.5.0/mapbayr/tests/testthat/test-annotated.R |only mapbayr-0.5.0/mapbayr/tests/testthat/test-compute_ofv.R | 2 mapbayr-0.5.0/mapbayr/tests/testthat/test-get_param.R | 61 - mapbayr-0.5.0/mapbayr/tests/testthat/test-mbrest.R | 4 mapbayr-0.5.0/mapbayr/tests/testthat/test-methods.R | 58 mapbayr-0.5.0/mapbayr/tests/testthat/test-multi-ID.R | 10 mapbayr-0.5.0/mapbayr/tests/testthat/test-no_data.R | 19 mapbayr-0.5.0/mapbayr/tests/testthat/test-output.R | 4 mapbayr-0.5.0/mapbayr/tests/testthat/test-plot.R |only mapbayr-0.5.0/mapbayr/tests/testthat/test-read_mrgsolve_model.R | 59 mapbayr-0.5.0/mapbayr/tests/testthat/test-reset-conditions.R |only 34 files changed, 1739 insertions(+), 1454 deletions(-)
Title: Violin Plot
Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Author: Daniel Adler [aut, cph],
S. Thomas Kelly [aut, cre],
Tom M. Elliott [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between vioplot versions 0.3.6 dated 2021-03-29 and 0.3.7 dated 2021-07-27
DESCRIPTION | 13 +-- MD5 | 18 ++--- NEWS.md | 4 + build/vignette.rds |binary inst/CITATION | 4 - inst/doc/violin_area.html | 57 +++-------------- inst/doc/violin_customisation.html | 53 +++------------- inst/doc/violin_formulae.html | 53 +++------------- inst/doc/violin_split.html | 121 +++++++++++-------------------------- inst/doc/violin_ylog.html | 53 +++------------- 10 files changed, 103 insertions(+), 273 deletions(-)
Title: Methods and Data for Spatial Epidemiology
Description: Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb],
Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>),
Michelle Ross [ctb],
Jon Wakefield [aut],
Mikael Moise [aut] (<https://orcid.org/0000-0002-3608-1178>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between SpatialEpi versions 1.2.3 dated 2018-06-02 and 1.2.4 dated 2021-07-27
SpatialEpi-1.2.3/SpatialEpi/build/partial.rdb |only SpatialEpi-1.2.3/SpatialEpi/inst/extdata |only SpatialEpi-1.2.3/SpatialEpi/man/MCMC_simulation.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/NumericVectorEquality.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/ProbSampleReplace.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/SpatialEpi-package.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/besag_newell_internal.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/binomialLogLkhd.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/check_overlap.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/clean_moves_matrix.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/coeff.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/computeAllLogLkhd.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/kulldorffMC.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/ldmultinom.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/ldnbinom.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/normalize.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/poissonLogLkhd.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/return_birth_moves.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/return_death_moves.Rd |only SpatialEpi-1.2.3/SpatialEpi/man/return_local_moves.Rd |only SpatialEpi-1.2.4/SpatialEpi/DESCRIPTION | 26 SpatialEpi-1.2.4/SpatialEpi/MD5 | 154 +- SpatialEpi-1.2.4/SpatialEpi/NAMESPACE | 38 SpatialEpi-1.2.4/SpatialEpi/NEWS.md | 13 SpatialEpi-1.2.4/SpatialEpi/R/EBpostdens.R | 34 SpatialEpi-1.2.4/SpatialEpi/R/EBpostthresh.R | 33 SpatialEpi-1.2.4/SpatialEpi/R/GammaPriorCh.R | 31 SpatialEpi-1.2.4/SpatialEpi/R/LogNormalPriorCh.R | 27 SpatialEpi-1.2.4/SpatialEpi/R/NYleukemia.R |only SpatialEpi-1.2.4/SpatialEpi/R/NYleukemia_sf.R |only SpatialEpi-1.2.4/SpatialEpi/R/SpatialEpi-package.R |only SpatialEpi-1.2.4/SpatialEpi/R/bayes_cluster.R | 290 ++- SpatialEpi-1.2.4/SpatialEpi/R/besag_newell.R | 79 + SpatialEpi-1.2.4/SpatialEpi/R/circle.R | 26 SpatialEpi-1.2.4/SpatialEpi/R/create_geo_objects.R | 41 SpatialEpi-1.2.4/SpatialEpi/R/eBayes.R | 35 SpatialEpi-1.2.4/SpatialEpi/R/estimate_lambda.R | 23 SpatialEpi-1.2.4/SpatialEpi/R/expected.R | 37 SpatialEpi-1.2.4/SpatialEpi/R/grid2latlong.R | 34 SpatialEpi-1.2.4/SpatialEpi/R/kulldorff.R | 90 + SpatialEpi-1.2.4/SpatialEpi/R/latlong2grid.R | 42 SpatialEpi-1.2.4/SpatialEpi/R/mapvariable.R | 35 SpatialEpi-1.2.4/SpatialEpi/R/pennLC.R |only SpatialEpi-1.2.4/SpatialEpi/R/plotmap.R | 34 SpatialEpi-1.2.4/SpatialEpi/R/polygon2spatial_polygon.R | 50 SpatialEpi-1.2.4/SpatialEpi/R/process_MCMC_sample.R | 24 SpatialEpi-1.2.4/SpatialEpi/R/scotland.R |only SpatialEpi-1.2.4/SpatialEpi/R/scotland_sf.R |only SpatialEpi-1.2.4/SpatialEpi/R/sf_objects.R |only SpatialEpi-1.2.4/SpatialEpi/R/zones.R | 29 SpatialEpi-1.2.4/SpatialEpi/build/vignette.rds |only SpatialEpi-1.2.4/SpatialEpi/data/NYleukemia_sf.rda |only SpatialEpi-1.2.4/SpatialEpi/data/pennLC_sf.rda |only SpatialEpi-1.2.4/SpatialEpi/data/scotland_sf.rda |only SpatialEpi-1.2.4/SpatialEpi/inst/doc |only SpatialEpi-1.2.4/SpatialEpi/man/EBpostdens.Rd | 75 - SpatialEpi-1.2.4/SpatialEpi/man/EBpostthresh.Rd | 53 SpatialEpi-1.2.4/SpatialEpi/man/GammaPriorCh.Rd | 36 SpatialEpi-1.2.4/SpatialEpi/man/LogNormalPriorCh.Rd | 38 SpatialEpi-1.2.4/SpatialEpi/man/NYleukemia.Rd | 40 SpatialEpi-1.2.4/SpatialEpi/man/NYleukemia_sf.Rd |only SpatialEpi-1.2.4/SpatialEpi/man/bayes_cluster.Rd | 95 - SpatialEpi-1.2.4/SpatialEpi/man/besag_newell.Rd | 73 - SpatialEpi-1.2.4/SpatialEpi/man/circle.Rd | 31 SpatialEpi-1.2.4/SpatialEpi/man/create_geo_objects.Rd | 37 SpatialEpi-1.2.4/SpatialEpi/man/eBayes.Rd | 36 SpatialEpi-1.2.4/SpatialEpi/man/estimate_lambda.Rd | 34 SpatialEpi-1.2.4/SpatialEpi/man/expected.Rd | 37 SpatialEpi-1.2.4/SpatialEpi/man/grid2latlong.Rd | 31 SpatialEpi-1.2.4/SpatialEpi/man/kulldorff.Rd | 101 - SpatialEpi-1.2.4/SpatialEpi/man/latlong2grid.Rd | 34 SpatialEpi-1.2.4/SpatialEpi/man/mapvariable.Rd | 67 SpatialEpi-1.2.4/SpatialEpi/man/pennLC.Rd | 40 SpatialEpi-1.2.4/SpatialEpi/man/pennLC_sf.Rd |only SpatialEpi-1.2.4/SpatialEpi/man/plotmap.Rd | 66 SpatialEpi-1.2.4/SpatialEpi/man/polygon2spatial_polygon.Rd | 53 SpatialEpi-1.2.4/SpatialEpi/man/process_MCMC_sample.Rd | 31 SpatialEpi-1.2.4/SpatialEpi/man/scotland.Rd | 40 SpatialEpi-1.2.4/SpatialEpi/man/scotland_sf.Rd |only SpatialEpi-1.2.4/SpatialEpi/man/zones.Rd | 38 SpatialEpi-1.2.4/SpatialEpi/src/RcppExports.cpp | 5 SpatialEpi-1.2.4/SpatialEpi/src/bayes_cluster.cpp | 943 ++++++------- SpatialEpi-1.2.4/SpatialEpi/src/cluster_detection.cpp | 106 - SpatialEpi-1.2.4/SpatialEpi/tests |only SpatialEpi-1.2.4/SpatialEpi/vignettes |only 85 files changed, 2159 insertions(+), 1206 deletions(-)
Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'.
This package provides a Database Interface 'DBI' compliant
driver for 'R' to access 'PostgreSQL' database systems.
In order to build and install this package from source, 'PostgreSQL'
itself must be present your system to provide 'PostgreSQL' functionality
via its libraries and header files. These files are provided as
'postgresql-devel' package under some Linux distributions.
On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Diff between RPostgreSQL versions 0.6-2 dated 2017-06-24 and 0.7 dated 2021-07-27
RPostgreSQL-0.6-2/RPostgreSQL/configure.in |only RPostgreSQL-0.7/RPostgreSQL/ChangeLog | 10 RPostgreSQL-0.7/RPostgreSQL/DESCRIPTION | 12 RPostgreSQL-0.7/RPostgreSQL/LICENSE | 10 RPostgreSQL-0.7/RPostgreSQL/MD5 | 52 RPostgreSQL-0.7/RPostgreSQL/R/PostgreSQLSupport.R | 32 RPostgreSQL-0.7/RPostgreSQL/configure | 722 +- RPostgreSQL-0.7/RPostgreSQL/configure.ac |only RPostgreSQL-0.7/RPostgreSQL/man/PostgreSQL.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/man/PostgreSQLConnection-class.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/man/PostgreSQLDriver-class.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/man/PostgreSQLObject-class.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/man/PostgreSQLResult-class.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/man/dbReadTable-methods.Rd | 2 RPostgreSQL-0.7/RPostgreSQL/src/Makevars.win | 2 RPostgreSQL-0.7/RPostgreSQL/src/RS-PostgreSQL.c | 24 RPostgreSQL-0.7/RPostgreSQL/src/S4R.h | 61 RPostgreSQL-0.7/RPostgreSQL/src/config.guess | 1165 ++-- RPostgreSQL-0.7/RPostgreSQL/src/config.sub | 2633 +++++----- RPostgreSQL-0.7/RPostgreSQL/src/libpq/Makefile.global.win32 | 10 RPostgreSQL-0.7/RPostgreSQL/src/libpq/Makefile.global.win64 | 10 RPostgreSQL-0.7/RPostgreSQL/src/libpq/Makefile.win | 1 RPostgreSQL-0.7/RPostgreSQL/tests/dbColumnInfo.R | 2 RPostgreSQL-0.7/RPostgreSQL/tests/dbColumnInfo.Rout.save | 9 RPostgreSQL-0.7/RPostgreSQL/tests/dbWriteTableFailTest.Rout.save | 5 RPostgreSQL-0.7/RPostgreSQL/tests/openSendQuery.Rout.save | 8 RPostgreSQL-0.7/RPostgreSQL/tests/unknowntype.Rout.save | 5 RPostgreSQL-0.7/RPostgreSQL/tests/utf.R |only RPostgreSQL-0.7/RPostgreSQL/tests/utf.Rout.save |only 29 files changed, 2557 insertions(+), 2228 deletions(-)
Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R.
Enables clustering using the leiden algorithm for partition a graph into communities.
See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg>
Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl],
Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between leiden versions 0.3.8 dated 2021-05-24 and 0.3.9 dated 2021-07-27
DESCRIPTION | 13 ++-- MD5 | 16 ++--- NEWS.md | 6 +- inst/CITATION | 4 - inst/doc/benchmarking.html | 118 ++++++++++++++++++++++---------------------- inst/doc/run_bipartite.html | 4 - inst/doc/run_igraph.html | 30 +++++------ inst/doc/run_leiden.html | 32 +++++------ inst/doc/run_multiplex.html | 20 +++---- 9 files changed, 124 insertions(+), 119 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Simon Couch [aut, cre] (<https://orcid.org/0000-0001-5676-5107>),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>),
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb],
Matthew Lincoln [ctb],
Alessandro Gasparini [ctb],
Lukasz Komsta [ctb],
Frederick Novometsky [ctb],
Wilson Freitas [ctb],
Michelle Evans [ctb],
Jason Cory Brunson [ctb],
Simon Jackson [ctb],
Ben Whalley [ctb],
Karissa Whiting [ctb],
Yves Rosseel [ctb],
Michael Kuehn [ctb],
Jorge Cimentada [ctb],
Erle Holgersen [ctb],
Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>),
Ethan Christensen [ctb],
Steven Pav [ctb],
Paul PJ [ctb],
Ben Schneider [ctb],
Patrick Kennedy [ctb],
Lily Medina [ctb],
Brian Fannin [ctb],
Jason Muhlenkamp [ctb],
Matt Lehman [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Nic Crane [ctb],
Andrew Bates [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>),
Hideaki Hayashi [ctb],
Luis Tobalina [ctb],
Annie Wang [ctb],
Wei Yang Tham [ctb],
Clara Wang [ctb],
Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>),
Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>),
E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>),
Alex Wang [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>),
Jared Wilber [ctb],
Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>),
Eduard Szoecs [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Angus Moore [ctb],
Nick Williams [ctb],
Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>),
Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>),
Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>),
Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>),
Kevin Zarca [ctb],
Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>),
Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>),
James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>),
Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>),
Joseph Larmarange [ctb],
Max Kuhn [ctb],
Michal Bojanowski [ctb],
Hakon Malmedal [ctb],
Clara Wang [ctb],
Sergio Oller [ctb],
Luke Sonnet [ctb],
Jim Hester [ctb],
Cory Brunson [ctb],
Ben Schneider [ctb],
Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>),
Mara Averick [ctb],
Aaron Jacobs [ctb],
Andreas Bender [ctb],
Sven Templer [ctb],
Paul-Christian Buerkner [ctb],
Matthew Kay [ctb],
Erwan Le Pennec [ctb],
Johan Junkka [ctb],
Hao Zhu [ctb],
Benjamin Soltoff [ctb],
Zoe Wilkinson Saldana [ctb],
Tyler Littlefield [ctb],
Charles T. Gray [ctb],
Shabbh E. Banks [ctb],
Serina Robinson [ctb],
Roger Bivand [ctb],
Riinu Ots [ctb],
Nicholas Williams [ctb],
Nina Jakobsen [ctb],
Michael Weylandt [ctb],
Lisa Lendway [ctb],
Karl Hailperin [ctb],
Josue Rodriguez [ctb],
Jenny Bryan [ctb],
Chris Jarvis [ctb],
Greg Macfarlane [ctb],
Brian Mannakee [ctb],
Drew Tyre [ctb],
Shreyas Singh [ctb],
Laurens Geffert [ctb],
Hong Ooi [ctb],
Henrik Bengtsson [ctb],
Eduard Szocs [ctb],
David Hugh-Jones [ctb],
Matthieu Stigler [ctb],
Hugo Tavares [ctb] (<https://orcid.org/0000-0001-9373-2726>),
R. Willem Vervoort [ctb],
Brenton M. Wiernik [ctb],
Josh Yamamoto [ctb],
Jasme Lee [ctb]
Maintainer: Simon Couch <scouch2@jhu.edu>
Diff between broom versions 0.7.8 dated 2021-06-24 and 0.7.9 dated 2021-07-27
broom-0.7.8/broom/R/rchoice-tidiers.R |only broom-0.7.8/broom/man/glance.Rchoice.Rd |only broom-0.7.8/broom/man/tidy.Rchoice.Rd |only broom-0.7.8/broom/tests/testthat/test-rchoice.R |only broom-0.7.9/broom/DESCRIPTION | 24 +- broom-0.7.9/broom/MD5 | 40 +-- broom-0.7.9/broom/NAMESPACE | 2 broom-0.7.9/broom/NEWS.md | 6 broom-0.7.9/broom/R/cmprsk-tidiers.R | 2 broom-0.7.9/broom/R/ergm-tidiers.R | 29 ++ broom-0.7.9/broom/R/fixest-tidiers.R | 2 broom-0.7.9/broom/R/lfe-tidiers.R | 5 broom-0.7.9/broom/inst/WORDLIST | 2 broom-0.7.9/broom/inst/doc/adding-tidiers.html | 4 broom-0.7.9/broom/inst/doc/available-methods.html | 262 ++++++++++------------ broom-0.7.9/broom/inst/doc/bootstrapping.html | 4 broom-0.7.9/broom/inst/doc/broom.html | 34 +- broom-0.7.9/broom/inst/doc/broom_and_dplyr.html | 30 +- broom-0.7.9/broom/man/augment.felm.Rd | 5 broom-0.7.9/broom/man/broom.Rd | 1 broom-0.7.9/broom/man/glance.felm.Rd | 5 broom-0.7.9/broom/man/tidy.ergm.Rd | 24 ++ broom-0.7.9/broom/man/tidy.felm.Rd | 5 23 files changed, 275 insertions(+), 211 deletions(-)
Title: Shapley Value Regression for Relative Importance of Attributes
Description: Shapley Value Regression for calculating the relative importance of independent variables in linear regression with avoiding the collinearity.
Author: Jingyi Liang
Maintainer: Jingyi Liang <jingyiliang19@163.com>
Diff between ShapleyValue versions 0.1.0 dated 2021-05-25 and 0.2.0 dated 2021-07-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ShapleyValue.R | 24 ++++++++++++++---------- 3 files changed, 19 insertions(+), 15 deletions(-)
Title: Efficient Computation of Ordinary and Generalized Poisson
Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between PoissonBinomial versions 1.2.3 dated 2021-03-28 and 1.2.4 dated 2021-07-27
DESCRIPTION | 8 MD5 | 28 NAMESPACE | 1 NEWS.md | 5 R/RcppExports.R | 240 +++---- R/gpbinom.R | 692 ++++++++++----------- R/pbinom.R | 913 ++++++++++++++--------------- R/utility.R | 18 build/partial.rdb |binary build/vignette.rds |binary inst/doc/proc_approx.html | 24 inst/doc/proc_exact.html | 18 inst/include/PoissonBinomial_RcppExports.h | 21 src/PoissonBinomial.cpp | 12 src/RcppExports.cpp | 41 - 15 files changed, 974 insertions(+), 1047 deletions(-)
More information about PoissonBinomial at CRAN
Permanent link
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org>
or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb],
Christine Laney [aut, ctb],
Nathan Mietkiewicz [aut, ctb],
Eric Sokol [aut, ctb],
Kaelin Cawley [aut, ctb],
NEON (National Ecological Observatory Network) [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 2.1.0 dated 2021-06-05 and 2.1.1 dated 2021-07-27
DESCRIPTION | 13 +++----- MD5 | 28 ++++++++--------- R/byFileAOP.R | 3 + R/byTileAOP.R | 3 + R/footRaster.R | 2 - R/getReadmePublicationDate.R | 67 ++++++++++++++----------------------------- R/getVarsEddy.R | 3 + R/readTableNEON.R | 3 + R/stackByTable.R | 8 +++-- R/stackEddy.R | 65 ++++++++++++++++++++++++++++++++--------- R/sysdata.rda |binary R/zipsByProduct.R | 3 + README.md | 11 +++++++ data/table_types.rda |binary man/stackEddy.Rd | 2 - 15 files changed, 121 insertions(+), 90 deletions(-)
Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 0.5.2 dated 2021-06-17 and 0.5.3 dated 2021-07-27
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ inst/doc/ipaddress-examples.R | 2 +- inst/doc/ipaddress-examples.Rmd | 2 +- inst/doc/ipaddress-examples.html | 20 ++++++++++---------- tests/testthat/test-ip_to_integer.R | 2 ++ vignettes/ipaddress-examples.Rmd | 2 +- 8 files changed, 31 insertions(+), 23 deletions(-)
Title: Genetics Input/Output Functions
Description: Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between genio versions 1.0.23 dated 2021-06-11 and 1.0.25 dated 2021-07-26
genio-1.0.23/genio/R/real_path.R |only genio-1.0.25/genio/DESCRIPTION | 10 genio-1.0.25/genio/MD5 | 69 +- genio-1.0.25/genio/NEWS.md | 84 ++ genio-1.0.25/genio/R/add_ext.R | 2 genio-1.0.25/genio/R/add_ext_read.R |only genio-1.0.25/genio/R/count_lines.R | 7 genio-1.0.25/genio/R/read_bed.R | 13 genio-1.0.25/genio/R/read_bim.R | 4 genio-1.0.25/genio/R/read_eigenvec.R | 7 genio-1.0.25/genio/R/read_fam.R | 4 genio-1.0.25/genio/R/read_ind.R | 4 genio-1.0.25/genio/R/read_matrix.R | 11 genio-1.0.25/genio/R/read_phen.R | 4 genio-1.0.25/genio/R/read_snp.R | 4 genio-1.0.25/genio/R/read_tab_generic.R | 4 genio-1.0.25/genio/inst/doc/genio.R | 12 genio-1.0.25/genio/inst/doc/genio.Rmd | 12 genio-1.0.25/genio/inst/doc/genio.html | 304 +++++----- genio-1.0.25/genio/man/count_lines.Rd | 4 genio-1.0.25/genio/man/read_bed.Rd | 11 genio-1.0.25/genio/man/read_bim.Rd | 4 genio-1.0.25/genio/man/read_eigenvec.Rd | 5 genio-1.0.25/genio/man/read_fam.Rd | 4 genio-1.0.25/genio/man/read_ind.Rd | 4 genio-1.0.25/genio/man/read_matrix.Rd | 7 genio-1.0.25/genio/man/read_phen.Rd | 4 genio-1.0.25/genio/man/read_snp.Rd | 4 genio-1.0.25/genio/src/RcppExports.cpp | 5 genio-1.0.25/genio/src/read_bed_cpp.cpp | 27 genio-1.0.25/genio/src/write_bed_cpp.cpp | 2 genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.bed |only genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.bim |only genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.fam |only genio-1.0.25/genio/tests/testthat/test-genio.R | 367 ++++++++----- genio-1.0.25/genio/tests/testthat/test-grm.R | 50 + genio-1.0.25/genio/tests/testthat/test-write_bed.R | 142 +++-- genio-1.0.25/genio/vignettes/genio.Rmd | 12 38 files changed, 740 insertions(+), 467 deletions(-)
Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format
for describing software metadata, as detailed at
<https://codemeta.github.io>. This package provides utilities to
generate, parse, and modify 'codemeta.json' files automatically for R
packages, as well as tools and examples for working with
'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>),
Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>),
Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>),
rOpenSci [fnd] (https://ropensci.org/),
Katrin Leinweber [ctb] (<https://orcid.org/0000-0001-5135-5758>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Arfon Smith [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>),
Michael Rustler [ctb] (<https://orcid.org/0000-0003-0647-7726>),
Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>),
Sebastian Kreutzer [ctb] (<https://orcid.org/0000-0002-0734-2199>),
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between codemetar versions 0.3.1 dated 2021-06-02 and 0.3.2 dated 2021-07-26
DESCRIPTION | 6 MD5 | 27 +- NEWS.md | 11 - R/codemeta_readme.R | 4 R/guess_other_metadata.R | 3 README.md | 38 +-- build/vignette.rds |binary inst/doc/codemetar.html | 301 +++++------------------------ inst/examples/README_ex.md | 2 man/codemetar-package.Rd | 9 man/rmdhunks/whybother.Rmd | 2 man/write_codemeta.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-add_repository_terms.R | 12 - tests/testthat/test-guess_metadata.R | 1 15 files changed, 119 insertions(+), 299 deletions(-)
Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between param6 versions 0.1.0 dated 2021-03-17 and 0.2.0 dated 2021-07-26
param6-0.1.0/param6/R/Dictionary.R |only param6-0.1.0/param6/R/Dictionary_S3methods.R |only param6-0.1.0/param6/R/Dictionary_methods.R |only param6-0.1.0/param6/man/Dictionary.Rd |only param6-0.1.0/param6/man/as.character.Dictionary.Rd |only param6-0.1.0/param6/man/c.Dictionary.Rd |only param6-0.1.0/param6/man/length.Dictionary.Rd |only param6-0.1.0/param6/man/sub-.Dictionary.Rd |only param6-0.1.0/param6/man/summary.Dictionary.Rd |only param6-0.1.0/param6/tests/testthat/test_Dictionary.R |only param6-0.1.0/param6/tests/testthat/test_helpers.R |only param6-0.1.0/param6/tests/testthat/test_paramset.R |only param6-0.1.0/param6/tests/testthat/test_prm.R |only param6-0.2.0/param6/DESCRIPTION | 10 param6-0.2.0/param6/MD5 | 56 +-- param6-0.2.0/param6/NAMESPACE | 10 param6-0.2.0/param6/NEWS.md | 19 + param6-0.2.0/param6/R/ParameterSet.R | 158 ++++++++- param6-0.2.0/param6/R/ParameterSet_S3methods.R | 122 +++++-- param6-0.2.0/param6/R/ParameterSet_helpers.R | 201 +++++++---- param6-0.2.0/param6/R/ParameterSet_methods.R | 331 +++++++++++++++---- param6-0.2.0/param6/R/cnd.R | 9 param6-0.2.0/param6/R/helpers.R | 61 +-- param6-0.2.0/param6/R/prm.R | 11 param6-0.2.0/param6/R/support_dictionary.R | 29 + param6-0.2.0/param6/R/tools.R |only param6-0.2.0/param6/R/zzz.R | 2 param6-0.2.0/param6/README.md | 8 param6-0.2.0/param6/man/ParameterSet.Rd | 179 +++++++++- param6-0.2.0/param6/man/c.ParameterSet.Rd | 10 param6-0.2.0/param6/man/cpset.Rd |only param6-0.2.0/param6/man/expect_equal_ps.Rd |only param6-0.2.0/param6/man/pset.Rd | 29 + param6-0.2.0/param6/man/sub-.ParameterSet.Rd | 17 param6-0.2.0/param6/man/support_dictionary.Rd | 6 param6-0.2.0/param6/tests/testthat/helpers.R |only param6-0.2.0/param6/tests/testthat/test-helpers.R |only param6-0.2.0/param6/tests/testthat/test-paramset.R |only param6-0.2.0/param6/tests/testthat/test-prm.R |only 39 files changed, 963 insertions(+), 305 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods.
Includes utilities for public key encryption, creating and verifying digital signatures,
and managing your local keyring. Note that some functionality depends on the version of
GnuPG that is installed on the system. On Windows this package can be used together with
'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gpg versions 1.2.2 dated 2019-12-02 and 1.2.3 dated 2021-07-26
DESCRIPTION | 9 MD5 | 19 NEWS | 3 build/vignette.rds |binary cleanup | 2 configure | 35 - inst/doc/intro.Rmd | 2 inst/doc/intro.html | 1605 +++++----------------------------------------------- src/Makevars.ucrt |only src/Makevars.win | 3 vignettes/intro.Rmd | 2 11 files changed, 224 insertions(+), 1456 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between tidybayes versions 2.3.1 dated 2020-11-02 and 3.0.0 dated 2021-07-26
tidybayes-2.3.1/tidybayes/R/fitted_draws.R |only tidybayes-2.3.1/tidybayes/tests/figs |only tidybayes-2.3.1/tidybayes/tests/testthat/test.fitted_draws.R |only tidybayes-3.0.0/tidybayes/DESCRIPTION | 46 tidybayes-3.0.0/tidybayes/MD5 | 227 - tidybayes-3.0.0/tidybayes/NAMESPACE | 905 ++-- tidybayes-3.0.0/tidybayes/NEWS.md | 343 + tidybayes-3.0.0/tidybayes/R/add_draws.R | 207 - tidybayes-3.0.0/tidybayes/R/compare_levels.R | 449 +- tidybayes-3.0.0/tidybayes/R/density_bins.R | 203 - tidybayes-3.0.0/tidybayes/R/deprecated.R | 1978 +++++----- tidybayes-3.0.0/tidybayes/R/emmeans_comparison.R | 166 tidybayes-3.0.0/tidybayes/R/epred_draws.R |only tidybayes-3.0.0/tidybayes/R/epred_rvars.R |only tidybayes-3.0.0/tidybayes/R/gather_draws.R | 60 tidybayes-3.0.0/tidybayes/R/gather_emmeans_draws.R | 283 - tidybayes-3.0.0/tidybayes/R/gather_pairs.R | 292 - tidybayes-3.0.0/tidybayes/R/gather_rvars.R |only tidybayes-3.0.0/tidybayes/R/gather_variables.R | 205 - tidybayes-3.0.0/tidybayes/R/get_variables.R | 107 tidybayes-3.0.0/tidybayes/R/ggdist-curve_interval.R |only tidybayes-3.0.0/tidybayes/R/ggdist-cut_cdf_qi.R |only tidybayes-3.0.0/tidybayes/R/ggdist-stat_pointinterval.R | 10 tidybayes-3.0.0/tidybayes/R/linpred_draws.R |only tidybayes-3.0.0/tidybayes/R/linpred_rvars.R |only tidybayes-3.0.0/tidybayes/R/nest_rvars.R |only tidybayes-3.0.0/tidybayes/R/predict_curve.R | 259 - tidybayes-3.0.0/tidybayes/R/predicted_draws.R | 687 ++- tidybayes-3.0.0/tidybayes/R/predicted_rvars.R |only tidybayes-3.0.0/tidybayes/R/recover_types.R | 314 - tidybayes-3.0.0/tidybayes/R/residual_draws.R | 118 tidybayes-3.0.0/tidybayes/R/sample_draws.R | 133 tidybayes-3.0.0/tidybayes/R/spread_draws.R | 1353 +++--- tidybayes-3.0.0/tidybayes/R/spread_rvars.R |only tidybayes-3.0.0/tidybayes/R/summarise_draws.R |only tidybayes-3.0.0/tidybayes/R/testthat.R |only tidybayes-3.0.0/tidybayes/R/tidy_draws.R | 543 +- tidybayes-3.0.0/tidybayes/R/tidybayes-models.R | 143 tidybayes-3.0.0/tidybayes/R/ungather_draws.R | 146 tidybayes-3.0.0/tidybayes/R/unspread_draws.R | 233 - tidybayes-3.0.0/tidybayes/R/util.R | 291 - tidybayes-3.0.0/tidybayes/build/partial.rdb |binary tidybayes-3.0.0/tidybayes/build/vignette.rds |binary tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.R | 206 - tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.Rmd | 1889 ++++----- tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.html | 1932 ++++----- tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.R |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.Rmd |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.html |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.R | 172 tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.Rmd | 1340 +++--- tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.html | 1020 ++--- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.R | 129 tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.Rmd | 1428 +++---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.html | 999 +---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.R | 110 tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.Rmd | 1630 ++++---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.html | 1470 +++---- tidybayes-3.0.0/tidybayes/man/add_draws.Rd | 155 tidybayes-3.0.0/tidybayes/man/add_predicted_draws.Rd | 714 +-- tidybayes-3.0.0/tidybayes/man/add_predicted_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/compare_levels.Rd | 277 - tidybayes-3.0.0/tidybayes/man/density_bins.Rd | 175 tidybayes-3.0.0/tidybayes/man/emmeans_comparison.Rd | 142 tidybayes-3.0.0/tidybayes/man/gather_emmeans_draws.Rd | 203 - tidybayes-3.0.0/tidybayes/man/gather_pairs.Rd | 232 - tidybayes-3.0.0/tidybayes/man/nest_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/recover_types.Rd | 269 - tidybayes-3.0.0/tidybayes/man/reexports.Rd | 281 - tidybayes-3.0.0/tidybayes/man/sample_draws.Rd | 124 tidybayes-3.0.0/tidybayes/man/spread_draws.Rd | 496 +- tidybayes-3.0.0/tidybayes/man/spread_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/summarise_draws.grouped_df.Rd |only tidybayes-3.0.0/tidybayes/man/tidy_draws.Rd | 197 tidybayes-3.0.0/tidybayes/man/tidybayes-deprecated.Rd | 492 +- tidybayes-3.0.0/tidybayes/man/tidybayes-models.Rd | 137 tidybayes-3.0.0/tidybayes/tests/models/models.rstan.m_gqs.rds |only tidybayes-3.0.0/tidybayes/tests/testthat/_snaps |only tidybayes-3.0.0/tidybayes/tests/testthat/test.add_draws.R | 78 tidybayes-3.0.0/tidybayes/tests/testthat/test.as_constructor.R | 90 tidybayes-3.0.0/tidybayes/tests/testthat/test.combine_chains.R | 76 tidybayes-3.0.0/tidybayes/tests/testthat/test.compare_levels.R | 470 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.compose_data.R | 264 - tidybayes-3.0.0/tidybayes/tests/testthat/test.emmeans_comparison.R | 50 tidybayes-3.0.0/tidybayes/tests/testthat/test.epred_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.epred_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_draws.R | 88 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_emmeans_draws.R | 155 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_pairs.R | 111 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_variables.R | 86 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_dotsinterval.R | 60 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_interval.R | 73 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_pointinterval.R | 71 tidybayes-3.0.0/tidybayes/tests/testthat/test.get_variables.R | 70 tidybayes-3.0.0/tidybayes/tests/testthat/test.linpred_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.linpred_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.nest_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.point_interval.R | 58 tidybayes-3.0.0/tidybayes/tests/testthat/test.predicted_draws.R | 476 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.predicted_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.residual_draws.R | 110 tidybayes-3.0.0/tidybayes/tests/testthat/test.spread_draws.R | 1020 ++--- tidybayes-3.0.0/tidybayes/tests/testthat/test.spread_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.stat_dist_slabinterval.R | 64 tidybayes-3.0.0/tidybayes/tests/testthat/test.stat_eye.R | 112 tidybayes-3.0.0/tidybayes/tests/testthat/test.summarise_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.tidy_draws.R | 443 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.ungather_draws.R | 184 tidybayes-3.0.0/tidybayes/tests/testthat/test.unspread_draws.R | 146 tidybayes-3.0.0/tidybayes/tests/testthat/test.util.R | 64 tidybayes-3.0.0/tidybayes/tests/testthat/test.x_at_y.R | 131 tidybayes-3.0.0/tidybayes/vignettes/tidy-brms.Rmd | 1889 ++++----- tidybayes-3.0.0/tidybayes/vignettes/tidy-posterior.Rmd |only tidybayes-3.0.0/tidybayes/vignettes/tidy-rstanarm.Rmd | 1340 +++--- tidybayes-3.0.0/tidybayes/vignettes/tidybayes-residuals.Rmd | 1428 +++---- tidybayes-3.0.0/tidybayes/vignettes/tidybayes.Rmd | 1630 ++++---- 117 files changed, 18216 insertions(+), 18541 deletions(-)
Title: Observers Needed to Evaluate Subjective Tests
Description: This ONEST software implements the method of assessing the pathologist agreement in reading PD-L1 assays (Reisenbichler et al. (2020 <doi:10.1038/s41379-020-0544-x>)), to determine the minimum number of evaluators needed to estimate agreement involving a large number of raters. Input to the program should be binary(1/0) pathology data, where “0” may stand for negative and “1” for positive. Additional examples were given using the data from Rimm et al. (2017 <doi:10.1001/jamaoncol.2017.0013>).
Author: Gang Han [aut, cre],
Baihong Guo [aut]
Maintainer: Gang Han <hangang.true@gmail.com>
Diff between ONEST versions 0.0.1 dated 2020-09-07 and 0.1.0 dated 2021-07-26
DESCRIPTION | 8 - MD5 | 21 +-- NAMESPACE | 2 NEWS.md |only R/ONEST.R | 16 ++ R/ONEST_inflation_test.R |only build/vignette.rds |binary data/NCCN_22c3_t.rdata |only inst/doc/ONEST.R | 13 + inst/doc/ONEST.Rmd | 19 ++ inst/doc/ONEST.html | 293 ++++++++++---------------------------------- man/NCCN_22c3_t.Rd |only man/ONEST_inflation_test.Rd |only vignettes/ONEST.Rmd | 19 ++ 14 files changed, 147 insertions(+), 244 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.1.6 dated 2021-07-08 and 0.1.7 dated 2021-07-26
dipsaus-0.1.6/dipsaus/R/map-qs.R |only dipsaus-0.1.6/dipsaus/R/map-redis.R |only dipsaus-0.1.6/dipsaus/R/parallels-workers.R |only dipsaus-0.1.6/dipsaus/R/queue-qs.R |only dipsaus-0.1.6/dipsaus/R/queue-redis.R |only dipsaus-0.1.6/dipsaus/man/MasterEvaluator.Rd |only dipsaus-0.1.6/dipsaus/man/make_async_evaluator.Rd |only dipsaus-0.1.7/dipsaus/DESCRIPTION | 11 dipsaus-0.1.7/dipsaus/MD5 | 57 +-- dipsaus-0.1.7/dipsaus/NAMESPACE | 12 dipsaus-0.1.7/dipsaus/NEWS.md | 13 dipsaus-0.1.7/dipsaus/R/RcppExports.R | 4 dipsaus-0.1.7/dipsaus/R/aaa.R | 61 +++ dipsaus-0.1.7/dipsaus/R/cpp-fastquantile.R |only dipsaus-0.1.7/dipsaus/R/language.R | 47 ++ dipsaus-0.1.7/dipsaus/R/map-s3.R | 49 -- dipsaus-0.1.7/dipsaus/R/persist.R | 2 dipsaus-0.1.7/dipsaus/R/shiny-compoundInput2.R | 15 dipsaus-0.1.7/dipsaus/R/shiny-flex-div.R | 33 + dipsaus-0.1.7/dipsaus/R/shiny-setInputs.R | 50 ++ dipsaus-0.1.7/dipsaus/R/shiny-swal-alert.R |only dipsaus-0.1.7/dipsaus/R/shortcuts.R |only dipsaus-0.1.7/dipsaus/R/systems.R | 53 ++ dipsaus-0.1.7/dipsaus/R/zzz.R | 2 dipsaus-0.1.7/dipsaus/inst/doc/r_expr_addons.html | 6 dipsaus-0.1.7/dipsaus/inst/doc/shiny_customized_widgets.html | 178 ++++------ dipsaus-0.1.7/dipsaus/inst/doc/utility_functions.html | 2 dipsaus-0.1.7/dipsaus/inst/rstudio |only dipsaus-0.1.7/dipsaus/inst/shiny-addons/dipsaus/dipsaus-dipterix-lib.js | 149 ++++---- dipsaus-0.1.7/dipsaus/man/dipsaus-rstudio-shortcuts.Rd |only dipsaus-0.1.7/dipsaus/man/fastquantile.Rd |only dipsaus-0.1.7/dipsaus/man/get_ip.Rd |only dipsaus-0.1.7/dipsaus/man/grapes-help-set-grapes.Rd | 4 dipsaus-0.1.7/dipsaus/man/grapes-set-help-grapes.Rd |only dipsaus-0.1.7/dipsaus/man/map.Rd | 45 -- dipsaus-0.1.7/dipsaus/man/shiny_alert2.Rd |only dipsaus-0.1.7/dipsaus/src/RcppExports.cpp | 13 dipsaus-0.1.7/dipsaus/src/rcpp_median.cpp |only 38 files changed, 492 insertions(+), 314 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and
only adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019) <https://almob.biomedcentral.com/articles/10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre],
Guillem Rigaill [aut],
Nathalie Vialaneix [aut],
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.5.99 dated 2020-06-18 and 0.6.3 dated 2021-07-26
adjclust-0.5.99/adjclust/R/res_adjclust_0.3.0.R |only adjclust-0.5.99/adjclust/data |only adjclust-0.5.99/adjclust/man/res_adjclust_0.3.0.Rd |only adjclust-0.5.99/adjclust/src/init.c |only adjclust-0.6.3/adjclust/DESCRIPTION | 27 adjclust-0.6.3/adjclust/MD5 | 76 +- adjclust-0.6.3/adjclust/NAMESPACE | 7 adjclust-0.6.3/adjclust/NEWS.md | 23 adjclust-0.6.3/adjclust/R/RcppExports.R |only adjclust-0.6.3/adjclust/R/adjclust.R | 117 ++- adjclust-0.6.3/adjclust/R/buildHeap.R | 2 adjclust-0.6.3/adjclust/R/chac.R | 20 adjclust-0.6.3/adjclust/R/plotSim.R | 5 adjclust-0.6.3/adjclust/README.md | 15 adjclust-0.6.3/adjclust/build/vignette.rds |binary adjclust-0.6.3/adjclust/inst/CITATION |only adjclust-0.6.3/adjclust/inst/WORDLIST |only adjclust-0.6.3/adjclust/inst/doc/hicClust.R | 22 adjclust-0.6.3/adjclust/inst/doc/hicClust.Rmd | 4 adjclust-0.6.3/adjclust/inst/doc/hicClust.html | 365 ++------- adjclust-0.6.3/adjclust/inst/doc/notesCHAC.R | 8 adjclust-0.6.3/adjclust/inst/doc/notesCHAC.Rmd | 25 adjclust-0.6.3/adjclust/inst/doc/notesCHAC.html | 352 ++------- adjclust-0.6.3/adjclust/inst/doc/snpClust.R | 27 adjclust-0.6.3/adjclust/inst/doc/snpClust.Rmd | 3 adjclust-0.6.3/adjclust/inst/doc/snpClust.html | 367 ++-------- adjclust-0.6.3/adjclust/inst/extdata/res_adjclust_0.3.0.rds |only adjclust-0.6.3/adjclust/man/adjClust.Rd | 16 adjclust-0.6.3/adjclust/man/figures/README-adjClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-2.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-3.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-2.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-3.png |binary adjclust-0.6.3/adjclust/man/plotSim.Rd | 4 adjclust-0.6.3/adjclust/man/select.Rd | 2 adjclust-0.6.3/adjclust/src/Makevars |only adjclust-0.6.3/adjclust/src/Makevars.win |only adjclust-0.6.3/adjclust/src/RcppExports.cpp |only adjclust-0.6.3/adjclust/src/adjClustFast.cpp |only adjclust-0.6.3/adjclust/tests/testthat/test_ascendingCompatibility.R | 19 adjclust-0.6.3/adjclust/vignettes/hicClust.Rmd | 4 adjclust-0.6.3/adjclust/vignettes/notesCHAC.Rmd | 25 adjclust-0.6.3/adjclust/vignettes/snpClust.Rmd | 3 45 files changed, 509 insertions(+), 1029 deletions(-)
Title: The Ramer-Douglas-Peucker Algorithm
Description: Pretty fast implementation of the Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2D curve.
Urs Ramer (1972), "An iterative procedure for the polygonal approximation of plane curves" <doi:10.1016/S0146-664X(72)80017-0>.
David H. Douglas and Thomas K. Peucker (1973), "Algorithms for the Reduction of the Number of Points Required to Represent a Digitized Line or its Caricature" <doi:10.3138/FM57-6770-U75U-7727>.
Author: Robert Dahl Jacobsen [aut, cre]
Maintainer: Robert Dahl Jacobsen <cran@dahl-jacobsen.dk>
Diff between RDP versions 0.1.5 dated 2021-07-02 and 0.1.6 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/RDP-package.Rd | 2 +- src/RamerDouglasPeucker.cpp | 39 +++++++++++++++------------------------ 4 files changed, 22 insertions(+), 31 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian Montgomery [ctb],
Angelina Panagopoulou [ctb],
Hugh Parsonage [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.59.0 dated 2021-06-01 and 0.60.0 dated 2021-07-26
DESCRIPTION | 8 MD5 | 208 ++++++++++++------------ NEWS | 11 + R/anyMissing.R | 16 - R/rowAlls.R | 147 ++++++++++++++--- R/rowCollapse.R | 34 +++ R/rowCounts.R | 61 ++++++- R/rowCumsums.R | 182 ++++++++++++++++++--- R/rowDiffs.R | 64 +++++++ R/rowIQRs.R | 20 +- R/rowLogSumExps.R | 54 ++++-- R/rowMads.R | 56 ++++++ R/rowMeans2.R | 46 ++++- R/rowMedians.R | 61 ++++++- R/rowOrderStats.R | 46 ++++- R/rowProds.R | 26 ++- R/rowQuantiles.R | 20 +- R/rowRanges.R | 134 ++++++++++++++- R/rowRanks.R | 39 ++++ R/rowSds.R | 8 R/rowSums2.R | 46 ++++- R/rowTabulates.R | 25 ++ R/rowVars.R | 154 ++++++++++++++++- R/rowWeightedMeans.R | 66 +++++++ R/rowWeightedMedians.R | 18 +- R/varDiff.R | 56 +++++- R/weightedMad.R | 18 +- R/weightedVar.R | 22 +- inst/WORDLIST | 1 inst/doc/matrixStats-methods.html | 2 man/anyMissing.Rd | 13 + man/rowAlls.Rd | 13 + man/rowCollapse.Rd | 9 - man/rowCounts.Rd | 9 - man/rowCumsums.Rd | 21 +- man/rowDiffs.Rd | 9 - man/rowIQRs.Rd | 9 - man/rowLogSumExps.Rd | 27 +-- man/rowMeans2.Rd | 11 + man/rowMedians.Rd | 27 +-- man/rowOrderStats.Rd | 11 + man/rowProds.Rd | 9 - man/rowQuantiles.Rd | 11 + man/rowRanges.Rd | 23 +- man/rowRanks.Rd | 10 - man/rowSds.Rd | 13 + man/rowSums2.Rd | 11 + man/rowTabulates.Rd | 9 - man/rowVars.Rd | 9 - man/rowWeightedMeans.Rd | 11 + man/rowWeightedMedians.Rd | 11 + man/varDiff.Rd | 21 +- man/weightedMad.Rd | 9 - man/weightedVar.Rd | 17 + tests/rowAllAnys.R | 297 ++++++++++++++++++++++++---------- tests/rowAllAnys_subset.R | 249 ++++++++++++++++------------- tests/rowCollapse.R | 101 +++++++++-- tests/rowCollapse_subset.R | 65 +++++-- tests/rowCounts.R | 176 ++++++++++++-------- tests/rowCounts_subset.R | 88 ++++++---- tests/rowCumMinMaxs.R | 186 +++++++++++++++------ tests/rowCumMinMaxs_subset.R | 56 ++++-- tests/rowCumprods.R | 147 ++++++++++++----- tests/rowCumprods_subset.R | 35 +++- tests/rowCumsums.R | 113 +++++++++---- tests/rowCumsums_subset.R | 37 +++- tests/rowDiffs.R | 100 ++++++++--- tests/rowDiffs_subset.R | 55 ++++-- tests/rowIQRs.R | 61 +++++-- tests/rowIQRs_subset.R | 37 +++- tests/rowLogSumExps.R | 45 ++++- tests/rowLogSumExps_subset.R | 44 +++-- tests/rowMads.R | 317 ++++++++++++++++++++++--------------- tests/rowMads_subset.R | 67 ++++--- tests/rowMeans2.R | 242 +++++++++++++++++++--------- tests/rowMeans2_subset.R | 35 +++- tests/rowMedians.R | 234 ++++++++++++++++++--------- tests/rowMedians_subset.R | 41 +++- tests/rowOrderStats.R | 32 +++ tests/rowOrderStats_subset.R | 52 +++--- tests/rowProds.R | 119 ++++++++----- tests/rowProds_subset.R | 39 +++- tests/rowQuantiles.R | 137 ++++++++++----- tests/rowQuantiles_subset.R | 35 ++-- tests/rowRanges.R | 218 +++++++++++++++---------- tests/rowRanges_subset.R | 79 +++++---- tests/rowRanks.R | 67 +++++++ tests/rowRanks_subset.R | 59 +++++- tests/rowSds.R | 191 +++++++++++++--------- tests/rowSds_subset.R | 76 ++++++-- tests/rowSums2.R | 208 ++++++++++++++++-------- tests/rowSums2_subset.R | 41 +++- tests/rowTabulates.R | 61 +++++++ tests/rowTabulates_subset.R | 36 ++-- tests/rowVarDiffs.R | 64 +++++-- tests/rowVarDiffs_mad,iqr_subset.R | 30 ++- tests/rowVarDiffs_var,sd_subset.R | 32 ++- tests/rowVars.R | 242 ++++++++++++++++------------ tests/rowVars_subset.R | 76 ++++++-- tests/rowWeightedMeans.R | 188 +++++++++++++++++++++ tests/rowWeightedMeans_subset.R | 61 +++++-- tests/rowWeightedMedians.R | 161 ++++++++++++++++++ tests/rowWeightedMedians_subset.R | 48 ++++- tests/rowWeightedVars.R | 176 +++++++++++++++++++- tests/rowWeightedVars_subset.R | 27 ++- 105 files changed, 5422 insertions(+), 1933 deletions(-)
Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing:
(a) Methods and operators that work natively on CSR formats (compressed sparse row,
a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(),
mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag();
(b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types,
including the 'float32' type from 'float';
(c) Coercion methods between pairs of classes which are not present in 'Matrix',
such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions;
(d) Utility functions for sparse matrices such as sorting the indices or removing
zero-valued entries;
(e) Fast transposes that work by outputting in the opposite storage format;
(f) Faster replacements for many 'Matrix' methods for all sparse types, such as
slicing and elementwise multiplication.
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included
robinmap library)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.5 dated 2021-06-22 and 0.1.6 dated 2021-07-26
DESCRIPTION | 17 +- MD5 | 65 +++++---- NAMESPACE | 3 R/MatrixExtra.R | 4 R/RcppExports.R | 4 R/assignment.R | 6 R/conversions.R | 4 R/matmul.R | 75 ++++++----- R/rbind.R | 6 R/slice.R | 10 - R/utils.R | 249 +++++++++++++++++++++++++++++++++++-- R/zzz.R | 9 + configure | 21 +-- configure.ac | 4 inst/COPYRIGHTS |only man/MatrixExtra-options.Rd | 9 + man/MatrixExtra.Rd | 4 man/emptySparse.Rd |only man/filterSparse.Rd |only man/mapSparse.Rd |only man/matmult.Rd | 19 ++ src/Makevars.in | 4 src/Makevars.win.in | 5 src/MatrixExtra.h | 16 ++ src/RcppExports.cpp | 12 + src/assignment.cpp | 4 src/matmul.cpp | 255 +++++++++++++++----------------------- src/misc.cpp | 19 ++ src/operators.cpp | 2 src/robinmap |only src/slice.cpp | 10 - src/slice_coo.cpp | 16 +- tests/testthat/test-conversions.R | 16 ++ tests/testthat/test-utilities.R | 57 ++++++++ 34 files changed, 655 insertions(+), 270 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of linear
regression, GLM, and Cox regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge. For more
information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>,
Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang
(2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015)
<doi:10.1111/biom.12300>, or visit the package homepage
<https://pbreheny.github.io/grpreg/>.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>),
Yaohui Zeng [ctb],
Ryan Kurth [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.3.1 dated 2021-03-30 and 3.4.0 dated 2021-07-26
grpreg-3.3.1/grpreg/man/predict-grpsurv.Rd |only grpreg-3.3.1/grpreg/src/lcdfit_binomial.c |only grpreg-3.3.1/grpreg/src/lcdfit_poisson.c |only grpreg-3.4.0/grpreg/DESCRIPTION | 16 grpreg-3.4.0/grpreg/MD5 | 78 ++-- grpreg-3.4.0/grpreg/NAMESPACE | 28 - grpreg-3.4.0/grpreg/NEWS.md | 15 grpreg-3.4.0/grpreg/R/G.R | 1 grpreg-3.4.0/grpreg/R/cv-grpreg.R | 17 grpreg-3.4.0/grpreg/R/cv-grpsurv.R | 2 grpreg-3.4.0/grpreg/R/expand_spline.R |only grpreg-3.4.0/grpreg/R/gBridge.R | 25 - grpreg-3.4.0/grpreg/R/gen_nonlinear_data.R |only grpreg-3.4.0/grpreg/R/grpreg.R | 52 ++ grpreg-3.4.0/grpreg/R/grpsurv.R | 36 + grpreg-3.4.0/grpreg/R/logLik.R | 2 grpreg-3.4.0/grpreg/R/plot_spline.R |only grpreg-3.4.0/grpreg/R/predict-cv.R | 6 grpreg-3.4.0/grpreg/R/predict-surv.R | 89 ++++ grpreg-3.4.0/grpreg/R/predict.R | 9 grpreg-3.4.0/grpreg/R/predict_spline.R |only grpreg-3.4.0/grpreg/R/residuals.R |only grpreg-3.4.0/grpreg/R/setupLambda.R | 7 grpreg-3.4.0/grpreg/build/partial.rdb |binary grpreg-3.4.0/grpreg/build/vignette.rds |binary grpreg-3.4.0/grpreg/inst/doc/getting-started.html | 287 +++------------ grpreg-3.4.0/grpreg/inst/tinytest/additive-models.R |only grpreg-3.4.0/grpreg/inst/tinytest/basic-functionality.R | 56 +- grpreg-3.4.0/grpreg/inst/tinytest/cv.R | 21 - grpreg-3.4.0/grpreg/inst/tinytest/extra-features.R | 64 ++- grpreg-3.4.0/grpreg/inst/tinytest/gBridge.R | 18 grpreg-3.4.0/grpreg/inst/tinytest/grpsurv.R | 51 ++ grpreg-3.4.0/grpreg/inst/tinytest/surv-torture.R | 10 grpreg-3.4.0/grpreg/inst/tinytest/torture.R | 10 grpreg-3.4.0/grpreg/man/expand_spline.Rd |only grpreg-3.4.0/grpreg/man/gBridge.Rd | 13 grpreg-3.4.0/grpreg/man/gen_nonlinear_data.Rd |only grpreg-3.4.0/grpreg/man/grpreg.Rd | 11 grpreg-3.4.0/grpreg/man/plot_spline.Rd |only grpreg-3.4.0/grpreg/man/predict.grpsurv.Rd |only grpreg-3.4.0/grpreg/man/residuals.grpreg.Rd |only grpreg-3.4.0/grpreg/src/gdfit_gaussian.c | 30 - grpreg-3.4.0/grpreg/src/gdfit_glm.c | 42 +- grpreg-3.4.0/grpreg/src/lcdfit_gaussian.c | 28 - grpreg-3.4.0/grpreg/src/lcdfit_glm.c | 48 +- grpreg-3.4.0/grpreg/vignettes/web/adaptive-rescaling.rmd |only grpreg-3.4.0/grpreg/vignettes/web/additive-models.rmd |only grpreg-3.4.0/grpreg/vignettes/web/models.rmd | 2 48 files changed, 626 insertions(+), 448 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 1.0.0 dated 2021-07-16 and 1.0.0.1 dated 2021-07-26
GeoTcgaData-1.0.0.1/GeoTcgaData/DESCRIPTION | 12 GeoTcgaData-1.0.0.1/GeoTcgaData/MD5 | 37 - GeoTcgaData-1.0.0.1/GeoTcgaData/NAMESPACE | 5 GeoTcgaData-1.0.0.1/GeoTcgaData/R/RNA_seq.R |only GeoTcgaData-1.0.0.1/GeoTcgaData/R/SNP.R | 10 GeoTcgaData-1.0.0.1/GeoTcgaData/R/TCGA_id_conversion.R | 6 GeoTcgaData-1.0.0.1/GeoTcgaData/R/ann_merge.r | 188 ++--- GeoTcgaData-1.0.0.1/GeoTcgaData/R/data.R | 11 GeoTcgaData-1.0.0.1/GeoTcgaData/R/fpkm_count_conversion.r | 34 - GeoTcgaData-1.0.0.1/GeoTcgaData/R/sysdata.rda |binary GeoTcgaData-1.0.0.1/GeoTcgaData/README.md | 88 ++ GeoTcgaData-1.0.0.1/GeoTcgaData/data/gene_cov.rda |only GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.R | 51 + GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.Rmd | 67 + GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.html | 372 ++++++----- GeoTcgaData-1.0.0.1/GeoTcgaData/inst/extdata/build_data.R |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/diff_RNA.Rd |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/diff_SNP.Rd | 8 GeoTcgaData-1.0.0.1/GeoTcgaData/man/gene_cov.Rd |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/id_conversion.Rd | 4 GeoTcgaData-1.0.0.1/GeoTcgaData/vignettes/GeoTcgaData.Rmd | 67 + GeoTcgaData-1.0.0/GeoTcgaData/inst/extdata/build_hgnc_file.R |only GeoTcgaData-1.0.0/GeoTcgaData/man/ann_merge.Rd |only 23 files changed, 637 insertions(+), 323 deletions(-)
Title: Rhythmic Patterns Modeling by FMM Models
Description: Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Author: Itziar Fernandez, Alejandro Rodriguez-Collado, Yolanda Larriba, Adrian Lamela, Christian Canedo, Cristina Rueda
Maintainer: Itziar Fernandez <itziar.fernandez@uva.es>
Diff between FMM versions 0.1.2 dated 2021-03-01 and 0.3.0 dated 2021-07-26
DESCRIPTION | 12 MD5 | 66 +- NAMESPACE | 28 - NEWS.md | 37 + R/Class.R | 71 +- R/FMM-methods.R | 355 ++++++------- R/FMM_internal.R | 546 +++++++++----------- R/FMM_internal_restr.R |only R/ecgData-data.R |only R/extractWaves.R | 59 +- R/fitFMM.R | 333 ++++++++---- R/fitFMM_back.R | 364 ++++--------- R/fitFMM_restr.R | 1250 +++++++++-------------------------------------- R/fitFMM_unit.R | 222 ++++---- R/generateFMM.R | 171 +++--- R/getFMMPeaks.R | 119 ++-- R/mouseGeneExp-data.R |only R/neuronalAPTrain-data.R | 52 - R/neuronalSpike-data.R | 52 - R/plotFMM.R | 295 ++++++----- R/stopFunctions.R | 86 +-- README.md |only man/Class.Rd | 136 ++--- man/FMM-getS4.Rd | 116 ++-- man/FMM-internal.Rd | 129 ++-- man/FMM-methods.Rd | 216 ++++---- man/FMM-package.Rd | 78 +- man/ecgData.Rd | 81 +-- man/extractWaves.Rd | 65 +- man/fitFMM.Rd | 272 ++++------ man/generateFMM.Rd | 171 ++---- man/getFMMPeaks.Rd | 85 +-- man/mouseGeneExp.Rd | 62 +- man/neuronalAPTrain.Rd | 64 +- man/neuronalSpike.Rd | 64 +- man/plotFMM.Rd | 144 +++-- 36 files changed, 2566 insertions(+), 3235 deletions(-)
Title: A Comprehensive R Interface for the DSSAT Cropping Systems Model
Description: The purpose of this package is to provide a comprehensive
R interface to the Decision Support System for Agrotechnology
Transfer Cropping Systems Model (DSSAT-CSM) documented by
Jones et al (2003) <doi:10.1016/S1161-0301(02)00107-7>. The package
provides cross-platform functions to read and write input files,
run DSSAT-CSM, and read output files.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between DSSAT versions 0.0.2 dated 2020-05-18 and 0.0.3 dated 2021-07-26
DESCRIPTION | 15 +++++++-------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/read_pest.R | 2 +- R/read_tier_data.R | 2 +- R/v_fmt_filex.R | 2 +- README.md | 3 +++ 7 files changed, 23 insertions(+), 17 deletions(-)
Title: Transformation-Free Linear Regression for Compositional Outcomes
and Predictors
Description: Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2021) <doi:10.1111/biom.13465>
for transformation-free linear regression for compositional outcomes and predictors.
Author: Jacob Fiksel [aut, cre] (<https://orcid.org/0000-0001-7067-1334>),
Abhirup Datta [aut]
Maintainer: Jacob Fiksel <jfiksel@gmail.com>
Diff between codalm versions 0.1.1 dated 2021-06-21 and 0.1.2 dated 2021-07-26
DESCRIPTION | 12 - MD5 | 27 +-- R/codalm_em.R | 6 R/data.R |only R/independence_test.R | 2 build/vignette.rds |binary data |only inst/doc/codalm_quickstart.R | 3 inst/doc/codalm_quickstart.Rmd | 7 inst/doc/codalm_quickstart.html | 331 ++++++++++------------------------------ man/codalm.Rd | 2 man/codalm_ci.Rd | 2 man/codalm_indep_test.Rd | 2 man/educFM.Rd |only man/predict_codalm.Rd | 2 vignettes/codalm_quickstart.Rmd | 7 16 files changed, 120 insertions(+), 283 deletions(-)
Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model.
The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots.
This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>),
Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Tomasz Mikołajczyk [aut],
Michal Burdukiewicz [ctb],
Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Diff between auditor versions 1.3.0 dated 2020-05-28 and 1.3.3 dated 2021-07-26
DESCRIPTION | 13 + MD5 | 207 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 10 + R/auditorData.R | 8 - R/check_residuals.R | 16 +- R/model_evaluation.R | 2 R/model_performance.R | 4 R/model_residual.R | 2 R/plot.R | 5 R/plotD3.R | 4 R/plotD3_autocorrelation.R | 4 R/plotD3_cooksdistance.R | 2 R/plotD3_prediction.R | 4 R/plotD3_residual.R | 6 R/plotD3_roc.R | 2 R/plotD3_rroc.R | 2 R/plotD3_scalelocation.R | 4 R/plot_correlation.R | 4 R/plot_residual_density.R | 8 - R/plot_roc.R | 2 R/plot_rroc.R | 2 R/print.R | 12 - R/score.R | 2 R/score_F1.R | 8 - R/score_acc.R | 8 - R/score_auc.R | 11 - R/score_auprc.R | 9 + R/score_dw.R | 2 R/score_gini.R | 6 R/score_mae.R | 2 R/score_mse.R | 2 R/score_peak.R | 2 R/score_precision.R | 8 - R/score_r2.R | 4 R/score_rec.R | 2 R/score_recall.R | 8 - R/score_rmse.R | 2 R/score_rroc.R | 4 R/score_runs.R | 2 R/score_specificity.R | 8 - build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST |only inst/doc/model_evaluation_audit.Rmd | 2 inst/doc/model_evaluation_audit.html | 6 inst/doc/model_fit_audit.Rmd | 6 inst/doc/model_fit_audit.html | 6 inst/doc/model_performance_audit.Rmd | 4 inst/doc/model_performance_audit.html | 4 inst/doc/model_residuals_audit.Rmd | 16 +- inst/doc/model_residuals_audit.html | 20 +- inst/doc/observation_influence_audit.Rmd | 2 inst/doc/observation_influence_audit.html | 4 man/auditorData.Rd | 8 + man/check_residuals.Rd | 2 man/check_residuals_outliers.Rd | 2 man/check_residuals_trend.Rd | 8 - man/model_evaluation.Rd | 2 man/model_performance.Rd | 4 man/model_residual.Rd | 2 man/plot.Rd | 4 man/plotD3.Rd | 4 man/plotD3_autocorrelation.Rd | 4 man/plotD3_cooksdistance.Rd | 2 man/plotD3_prediction.Rd | 4 man/plotD3_residual.Rd | 6 man/plotD3_roc.Rd | 2 man/plotD3_rroc.Rd | 2 man/plotD3_scalelocation.Rd | 4 man/plot_correlation.Rd | 4 man/plot_residual_density.Rd | 8 - man/plot_roc.Rd | 2 man/plot_rroc.Rd | 2 man/score.Rd | 2 man/score_acc.Rd | 4 man/score_auc.Rd | 2 man/score_auprc.Rd | 82 +++++------ man/score_dw.Rd | 2 man/score_f1.Rd | 4 man/score_gini.Rd | 2 man/score_mae.Rd | 2 man/score_mse.Rd | 2 man/score_one_minus_acc.Rd | 4 man/score_one_minus_auc.Rd | 2 man/score_one_minus_auprc.Rd | 82 +++++------ man/score_one_minus_f1.Rd | 4 man/score_one_minus_gini.Rd | 4 man/score_one_minus_precision.Rd | 4 man/score_one_minus_recall.Rd | 4 man/score_one_minus_specificity.Rd | 4 man/score_peak.Rd | 2 man/score_precision.Rd | 4 man/score_r2.Rd | 4 man/score_rec.Rd | 2 man/score_recall.Rd | 4 man/score_rmse.Rd | 2 man/score_rroc.Rd | 4 man/score_runs.Rd | 2 man/score_specificity.Rd | 4 vignettes/model_evaluation_audit.Rmd | 2 vignettes/model_fit_audit.Rmd | 6 vignettes/model_performance_audit.Rmd | 4 vignettes/model_residuals_audit.Rmd | 16 +- vignettes/observation_influence_audit.Rmd | 2 105 files changed, 430 insertions(+), 400 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience
tools for testing and developing your own models.
Author: Ott Toomet [aut, cre],
Arne Henningsen [aut],
Spencer Graves [ctb],
Yves Croissant [ctb],
David Hugh-Jones [ctb],
Luca Scrucca [ctb]
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.4-8 dated 2021-03-22 and 1.5-2 dated 2021-07-26
maxLik-1.4-8/maxLik/tests/basicTest.R |only maxLik-1.4-8/maxLik/tests/basicTest.Rout.save |only maxLik-1.4-8/maxLik/tests/fitNormalDist_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/maxControl_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/maxSG_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/methods.R |only maxLik-1.4-8/maxLik/tests/methods.Rout.save |only maxLik-1.4-8/maxLik/tests/parameters_privateTest.Rout.save |only maxLik-1.4-8/maxLik/vignettes/auto |only maxLik-1.5-2/maxLik/DESCRIPTION | 34 +++-- maxLik-1.5-2/maxLik/MD5 | 59 +++++----- maxLik-1.5-2/maxLik/NAMESPACE | 33 +++-- maxLik-1.5-2/maxLik/NEWS | 30 ++++- maxLik-1.5-2/maxLik/R/confint.maxLik.R |only maxLik-1.5-2/maxLik/R/maxBFGSRCompute.R | 4 maxLik-1.5-2/maxLik/R/maxNRCompute.R | 17 +- maxLik-1.5-2/maxLik/R/maxSGACompute.R | 8 - maxLik-1.5-2/maxLik/R/tidyMethods.R |only maxLik-1.5-2/maxLik/build/partial.rdb |binary maxLik-1.5-2/maxLik/build/vignette.rds |binary maxLik-1.5-2/maxLik/inst/doc/intro-to-maximum-likelihood.Rnw | 59 +++++----- maxLik-1.5-2/maxLik/inst/doc/intro-to-maximum-likelihood.pdf |binary maxLik-1.5-2/maxLik/inst/doc/stochastic-gradient-maxLik.pdf |binary maxLik-1.5-2/maxLik/inst/doc/using-maxlik.pdf |binary maxLik-1.5-2/maxLik/inst/tinytest |only maxLik-1.5-2/maxLik/man/bread.maxLik.Rd | 1 maxLik-1.5-2/maxLik/man/confint.maxLik.Rd |only maxLik-1.5-2/maxLik/man/gradient.Rd | 1 maxLik-1.5-2/maxLik/man/maxLik-package.Rd | 19 +-- maxLik-1.5-2/maxLik/man/reexports.Rd |only maxLik-1.5-2/maxLik/man/summary.maxLik.Rd | 7 + maxLik-1.5-2/maxLik/man/summary.maxim.Rd | 41 +----- maxLik-1.5-2/maxLik/man/tidy.maxLik.Rd |only maxLik-1.5-2/maxLik/tests/tinytest.R |only maxLik-1.5-2/maxLik/vignettes/intro-to-maximum-likelihood.Rnw | 59 +++++----- maxLik-1.5-2/maxLik/vignettes/probability-density.pdf |binary 36 files changed, 205 insertions(+), 167 deletions(-)
Title: Wilcoxon Rank Tests for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test)
for clustered data documented in
Jiang et. al (2020) <doi:10.18637/jss.v096.i06>.
Author: Wenjie Wang [cre, ctb] (<https://orcid.org/0000-0003-0363-3180>),
Yujing Jiang [aut],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between clusrank versions 1.0-0 dated 2020-12-10 and 1.0-1 dated 2021-07-26
DESCRIPTION | 33 ++++++++++++++++++++------------- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 4 ++++ R/amd.R | 2 +- R/clusWilcox.R | 4 ++-- R/clusranksum.R | 9 +++++---- R/clussignrank.R | 2 +- R/crd.R | 2 +- R/crdstr.R | 2 +- R/crsd.R | 2 +- R/crsdunb.R | 2 +- R/pairwise.clusWilcox.test.R |only R/print.R | 2 +- R/recodeFun.R | 21 ++++++++++----------- R/special.R | 17 ++++++++--------- man/clusWilcox.test.Rd | 2 +- man/pairwise.clusWilcox.test.Rd |only src/Fprop.cpp | 18 ++++++++++++++++++ src/RcppExports.cpp | 5 +++++ src/exact.cpp | 18 ++++++++++++++++++ 20 files changed, 117 insertions(+), 64 deletions(-)
Title: Profile R Code and Visualize with 'Pprof'
Description: Like similar profiling tools,
the 'proffer' package automatically detects
sources of slowness in R code.
The distinguishing feature of 'proffer' is its utilization of
'pprof', which supplies interactive visualizations
that are efficient and easy to interpret.
Behind the scenes, the 'profile' package converts
native Rprof() data to a protocol buffer
that 'pprof' understands.
For the documentation of 'proffer',
visit <https://r-prof.github.io/proffer/>.
To learn about the implementations and methodologies of
'pprof', 'profile', and protocol buffers,
visit <https://github.com/google/pprof>.
<https://developers.google.com/protocol-buffers>,
and <https://github.com/r-prof/profile>, respectively.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between proffer versions 0.1.3 dated 2021-06-28 and 0.1.5 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/pprof.R | 4 ++-- tests/testthat.R | 4 +++- 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut],
Julien Papaix [aut],
Jean-François Rey [aut, cre] (<https://orcid.org/0000-0003-3281-6701>),
Jean-Loup Gaussen [ctb]
Maintainer: Jean-François Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.0.2 dated 2020-11-30 and 1.1.0 dated 2021-07-26
landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.R |only landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.Rmd |only landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.html |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.R |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.Rmd |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.html |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.R |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.Rmd |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.html |only landsepi-1.0.2/landsepi/vignettes/landscape_dispersal.Rmd |only landsepi-1.0.2/landsepi/vignettes/run_exp_design.Rmd |only landsepi-1.0.2/landsepi/vignettes/run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/DESCRIPTION | 43 landsepi-1.1.0/landsepi/MD5 | 117 landsepi-1.1.0/landsepi/R/AgriLand.R | 3 landsepi-1.1.0/landsepi/R/GPKGTools.R | 2 landsepi-1.1.0/landsepi/R/Methods-LandsepiParams.R | 121 landsepi-1.1.0/landsepi/R/RcppExports.R | 2 landsepi-1.1.0/landsepi/R/demo_landsepi.R | 2 landsepi-1.1.0/landsepi/R/graphics.R | 15 landsepi-1.1.0/landsepi/R/landsepi.R | 46 landsepi-1.1.0/landsepi/R/output.R | 317 +- landsepi-1.1.0/landsepi/R/runShiny.R | 4 landsepi-1.1.0/landsepi/R/simul_landsepi.R | 72 landsepi-1.1.0/landsepi/build/vignette.rds |binary landsepi-1.1.0/landsepi/configure | 18 landsepi-1.1.0/landsepi/configure.ac | 2 landsepi-1.1.0/landsepi/data/dispP_a40_b7.rda |binary landsepi-1.1.0/landsepi/data/landscapesTEST.rda |binary landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.R |only landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.html |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.R |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.html |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.R |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.html |only landsepi-1.1.0/landsepi/inst/doc/landsepi_poster.Rnw |only landsepi-1.1.0/landsepi/inst/doc/landsepi_poster.pdf |only landsepi-1.1.0/landsepi/inst/doc/list_of_parameters.Rnw | 2 landsepi-1.1.0/landsepi/inst/doc/list_of_parameters.pdf |binary landsepi-1.1.0/landsepi/inst/logos |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/Dockerfile | 4 landsepi-1.1.0/landsepi/inst/shiny-landsepi/global.R | 340 ++ landsepi-1.1.0/landsepi/inst/shiny-landsepi/modules |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/server.R | 1285 +++++++--- landsepi-1.1.0/landsepi/inst/shiny-landsepi/ui.R | 251 + landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/CSIRO_Logo.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/LogoINRAE_Fr_rvb_web.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/PATHO_inra_logo.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/Republique_Francaise_RVB.jpg |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/landsepi-logo.png |only landsepi-1.1.0/landsepi/man/AgriLand.Rd | 3 landsepi-1.1.0/landsepi/man/allocateLandscapeCroptypes.Rd | 3 landsepi-1.1.0/landsepi/man/epid_output.Rd | 59 landsepi-1.1.0/landsepi/man/evol_output.Rd | 2 landsepi-1.1.0/landsepi/man/landsepi-package.Rd | 47 landsepi-1.1.0/landsepi/man/loadOutputs.Rd | 18 landsepi-1.1.0/landsepi/man/model_landsepi.Rd | 2 landsepi-1.1.0/landsepi/man/runSimul.Rd | 2 landsepi-1.1.0/landsepi/man/setCultivars.Rd | 29 landsepi-1.1.0/landsepi/man/setOutputs.Rd | 20 landsepi-1.1.0/landsepi/man/setPathogen.Rd | 2 landsepi-1.1.0/landsepi/man/simul_landsepi.Rd | 53 landsepi-1.1.0/landsepi/man/video.Rd | 10 landsepi-1.1.0/landsepi/src/Model.cpp | 2 landsepi-1.1.0/landsepi/src/Model.hpp | 2 landsepi-1.1.0/landsepi/src/RcppExports.cpp | 5 landsepi-1.1.0/landsepi/src/initialisation.cpp | 11 landsepi-1.1.0/landsepi/vignettes/O1-run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/vignettes/O2-run_exp_design.Rmd |only landsepi-1.1.0/landsepi/vignettes/O3-landscape_dispersal.Rmd |only landsepi-1.1.0/landsepi/vignettes/landsepi_poster.Rnw |only landsepi-1.1.0/landsepi/vignettes/landsepiposter.pdf |only landsepi-1.1.0/landsepi/vignettes/list_of_parameters.Rnw | 2 landsepi-1.1.0/landsepi/vignettes/listofparameters.pdf |binary 77 files changed, 2085 insertions(+), 833 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>
Diff between twang versions 2.3 dated 2021-06-10 and 2.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/boxplot.mnps.R | 2 +- inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.pdf |binary 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
(<https://orcid.org/0000-0002-8673-2514>),
Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>),
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.5 dated 2020-09-29 and 1.0.6 dated 2021-07-26
DESCRIPTION | 16 MD5 | 87 +-- NEWS.md | 14 R/GWASHelp.R | 54 +- R/codeMarkers.R | 48 + R/createGData.R | 2 R/createGWAS.R | 132 ++++ R/data.R | 68 +- R/kinship.R | 19 R/manhattanPlot.R | 20 R/qqPlot.R | 9 R/qtlPlot.R | 10 R/runSingleTraitGwas.R | 38 - R/utils.R | 9 README.md | 8 build/partial.rdb |only build/vignette.rds |binary data/dropsMap.rda |binary data/dropsMarkers.rda |binary data/dropsPheno.rda |binary inst/doc/GWAS.R | 12 inst/doc/GWAS.Rmd | 36 + inst/doc/GWAS.html | 917 ++++++++++++++-------------------- inst/java/beagle.jar |binary inst/tinytest/test_GWAS.R | 2 inst/tinytest/test_STG.R | 32 - inst/tinytest/test_STGHelper.R | 8 inst/tinytest/test_STGoptions.R | 20 inst/tinytest/test_codeMarkers.R | 12 inst/tinytest/test_kinship.R | 56 +- inst/tinytest/test_plots.R | 24 man/codeMarkers.Rd | 261 ++++----- man/dropsData.Rd | 108 ++-- man/figures/README-manhattanStg-1.png |binary man/figures/README-qqStg-1.png |binary man/figures/README-qtlStgNorm-1.png |binary man/gData.Rd | 2 man/kinship.Rd | 126 ++-- man/plot.GWAS.Rd | 89 +++ man/runSingleTraitGwas.Rd | 97 +-- man/statgenGWAS-package.Rd | 2 man/summary.gData.Rd | 70 +- src/RcppExports.cpp | 5 vignettes/GWAS.Rmd | 36 + vignettes/bibliography.bib | 20 45 files changed, 1374 insertions(+), 1095 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 2.1.0 dated 2021-07-14 and 2.2.0 dated 2021-07-26
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++++++--------- NAMESPACE | 7 +++++++ NEWS.md | 5 +++++ R/batch.R | 1 - R/convert_umlauts_to_ascii.R | 9 ++------- R/csv.R |only R/load_internal_functions.R | 2 +- R/options.R | 9 ++++++--- inst/NEWS.rd | 7 +++++++ inst/runit_tests/runit-csv.R |only man/bulk_read_csv.Rd |only man/bulk_write_csv.Rd |only man/csv.Rd |only man/csv2csv.Rd |only man/load_internal_functions.Rd | 2 +- man/set_hash.Rd |only man/un_hash.Rd |only 18 files changed, 52 insertions(+), 28 deletions(-)
Title: Build a Package from Rmarkdown File
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),
ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between fusen versions 0.2.2 dated 2021-07-09 and 0.2.3 dated 2021-07-26
fusen-0.2.2/fusen/vignettes/images |only fusen-0.2.3/fusen/DESCRIPTION | 7 fusen-0.2.3/fusen/MD5 | 43 +-- fusen-0.2.3/fusen/NAMESPACE | 1 fusen-0.2.3/fusen/NEWS.md | 8 fusen-0.2.3/fusen/R/fill_description.R | 23 +- fusen-0.2.3/fusen/R/inflate.R | 48 +++- fusen-0.2.3/fusen/inst/dev-template-additional.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-full.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-minimal.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-teaching.Rmd | 2 fusen-0.2.3/fusen/inst/doc/How-to-use-fusen.html | 13 - fusen-0.2.3/fusen/inst/tests-templates/dev-template-stop-duplicate-fun.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-stop-duplicate-label.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-test-parse-nothing.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-tests-special-char.Rmd |only fusen-0.2.3/fusen/inst/tests-templates/dev-template-tests.Rmd | 32 ++ fusen-0.2.3/fusen/man/fill_description.Rd | 2 fusen-0.2.3/fusen/man/inflate.Rd | 5 fusen-0.2.3/fusen/tests/testthat/test-fill_description.R | 31 ++ fusen-0.2.3/fusen/tests/testthat/test-inflate.R | 112 +++++++++- 21 files changed, 279 insertions(+), 60 deletions(-)
Title: SOM Algorithm for the Analysis of Multivariate Environmental
Data
Description: Analysis of multivariate environmental high frequency data by Self-Organizing Map and k-means clustering algorithms. By means of the graphical user interface it provides a comfortable way to elaborate by self-organizing map algorithm rather big datasets (txt files up to 100 MB ) obtained by environmental high-frequency monitoring by sensors/instruments. The functions present in the package are based on 'kohonen' and 'openair' packages implemented by functions embedding Vesanto et al. (2001) <http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf> heuristic rules for map initialization parameters, k-means clustering algorithm and map features visualization. Cluster profiles visualization as well as graphs dedicated to the visualization of time-dependent variables Licen et al. (2020) <doi:10.4209/aaqr.2019.08.0414> are provided.
Author: Sabina Licen [aut, cre],
Marco Franzon [aut],
Tommaso Rodani [aut],
Pierluigi Barbieri [aut]
Maintainer: Sabina Licen <slicen@units.it>
Diff between SOMEnv versions 1.1.1 dated 2021-03-02 and 1.1.2 dated 2021-07-26
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NAMESPACE | 3 - R/SomEnvGUI.R | 3 - inst/CITATION | 84 +++++++--------------------------------- inst/shiny-examples/myapp/app.R | 20 ++++----- 6 files changed, 38 insertions(+), 92 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Uses by default the 's2'
package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb],
Dewey Dunnington [ctb] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-1 dated 2021-06-29 and 1.0-2 dated 2021-07-26
DESCRIPTION | 6 - MD5 | 71 +++++++++++------------ NAMESPACE | 1 NEWS.md | 18 +++++ R/bind.R | 7 +- R/crs.R | 9 ++ R/maps.R | 10 ++- R/read.R | 7 +- R/sample.R | 49 +++++++--------- R/spatstat.R | 134 ++++++++++++++++++++++---------------------- R/tidyverse.R | 11 +++ configure | 4 - configure.ac | 4 - inst/doc/sf1.html | 10 +-- inst/doc/sf2.html | 14 ++-- inst/doc/sf3.Rmd | 19 +++--- inst/doc/sf3.html | 19 +++--- inst/doc/sf4.Rmd | 14 ++-- inst/doc/sf4.html | 16 ++--- inst/doc/sf5.Rmd | 12 +-- inst/doc/sf5.html | 18 ++--- inst/doc/sf6.html | 2 inst/doc/sf7.html | 8 +- inst/docker/gdal/Dockerfile | 23 ++++--- man/st_crs.Rd | 4 - src/Makevars.ucrt |only src/Makevars.win | 2 src/RcppExports.cpp | 5 + src/gdal_read.cpp | 32 ++++++++-- src/gdal_write.cpp | 18 +++++ src/geos.cpp | 11 +++ tests/geos.R | 12 +++ tests/geos.Rout.save | 35 +++++++++++ tests/spatstat.Rout.save | 43 ++++++-------- vignettes/sf3.Rmd | 19 +++--- vignettes/sf4.Rmd | 14 ++-- vignettes/sf5.Rmd | 12 +-- 37 files changed, 428 insertions(+), 265 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package (see also Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>) can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymisation methods are included. Note that the package
includes a graphical user interface (Meindl and Templ, 2019 <doi:10.3390/a12090191>) that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>),
Bernhard Meindl [aut],
Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.6.0 dated 2021-01-27 and 5.6.1 dated 2021-07-26
DESCRIPTION | 7 MD5 | 67 - NAMESPACE | 4 NEWS | 8 R/addGhostVars.R | 15 R/addNoise.r | 1 R/dRisk.R | 6 R/dUtility.R | 281 ++++++- R/dataGen.r | 4 R/globalRecode.R | 2 R/maG.R | 6 R/shuffle.R | 8 build/partial.rdb |binary build/vignette.rds |binary data/CASCrefmicrodata.rda |binary data/EIA.rda |binary data/Tarragona.rda |binary data/casc1.rda |binary data/francdat.rda |binary data/free1.rda |binary data/microData.rda |binary data/testdata.RData |binary data/testdata2.RData |binary inst/doc/sdcMicro.html | 955 ++++++++++--------------- inst/doc/sdc_guidelines.pdf |binary inst/shiny/sdcApp/controllers/ui_categorical.R | 20 inst/shiny/sdcApp/server.R | 19 man/addNoise.Rd | 1 man/dRisk.Rd | 6 man/dUtility.Rd | 41 - man/dataGen.Rd | 4 man/globalRecode.Rd | 2 man/il_additional.Rd |only man/shuffle.Rd | 8 tests/testthat/test_il_correl.R |only tests/testthat/test_il_variables.R |only 36 files changed, 791 insertions(+), 674 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.6.0 dated 2021-07-22 and 0.6.1 dated 2021-07-26
DESCRIPTION | 6 +- MD5 | 14 +++--- NEWS.md | 7 +++ R/finbif_occurrence.R | 9 ++-- README.md | 2 inst/NEWS.Rd | 9 ++++ tests/cassettes/finbif_occurrence_collection.yml | 48 +++++++++++++++++++---- tests/testthat/test-finbif_occurrence.R | 6 ++ 8 files changed, 77 insertions(+), 24 deletions(-)
Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Author: Zankrut Goyani [aut, cre, cph],
Alok Shrivasatva [aut],
Yogesh Garde [aut],
Arvind Chaudhary [aut],
Kaushal Modha [aut]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>
Diff between selection.index versions 1.1.1 dated 2021-06-03 and 1.1.2 dated 2021-07-26
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 5 ++- R/rcomb.indices.R | 2 + README.md | 14 ++++----- build/vignette.rds |binary inst/doc/Examples.html | 18 ++++++------ man/rcomb.indices.Rd | 72 ++++++++++++++++++++++++------------------------- man/sel.index.Rd | 60 ++++++++++++++++++++-------------------- 9 files changed, 101 insertions(+), 96 deletions(-)
More information about selection.index at CRAN
Permanent link
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 1.0.0 dated 2021-03-09 and 1.0.1 dated 2021-07-26
DESCRIPTION | 7 +++---- MD5 | 24 ++++++++++++------------ NEWS.md | 9 ++++++++- R/html.R | 2 +- R/table.R | 6 ++++-- R/utils.R | 1 - build/vignette.rds |binary inst/doc/rvest.html | 1 + man/google_form.Rd | 3 --- man/html_attr.Rd | 2 +- tests/testthat/_snaps/session.md | 2 +- tests/testthat/_snaps/table.md | 16 ++++++++++++++++ tests/testthat/test-table.R | 30 ++++++++++++++++++++++++++++++ 13 files changed, 77 insertions(+), 26 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.17 dated 2021-01-07 and 1.0.18 dated 2021-07-26
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++------ NAMESPACE | 3 ++- R/additional_info.R |only R/new_xmlreadabs.R |only data/GeneToEntrez.rda |binary data/HGNC2UniprotID.rda |binary data/HGNCdata.rda |binary data/common_words_new.rda |binary man/additional_info.Rd |only man/new_xmlreadabs.Rd |only 11 files changed, 17 insertions(+), 12 deletions(-)
Title: Downloading Time Series from ALFRED Database for Various
Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases.
Its functions return tidy data frames for different releases of the specified time series.
Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between alfred versions 0.1.12 dated 2021-05-12 and 0.2.0 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 1 + R/get_alfred_series.R | 6 +++--- tests/testthat/test_download.R | 4 ---- 5 files changed, 11 insertions(+), 14 deletions(-)
Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the
language at a deeper level.
Author: Hadley Wickham [aut, cre],
R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pryr versions 0.1.4 dated 2018-02-17 and 0.1.5 dated 2021-07-26
pryr-0.1.4/pryr/src/object_size.cpp |only pryr-0.1.4/pryr/src/size-info.c |only pryr-0.1.5/pryr/DESCRIPTION | 10 ++-- pryr-0.1.5/pryr/MD5 | 38 ++++++++--------- pryr-0.1.5/pryr/NAMESPACE | 2 pryr-0.1.5/pryr/R/RcppExports.R | 12 ----- pryr-0.1.5/pryr/R/bytes.r | 6 +- pryr-0.1.5/pryr/R/mem.R | 4 - pryr-0.1.5/pryr/R/object_size.R | 2 pryr-0.1.5/pryr/R/partial.r | 2 pryr-0.1.5/pryr/README.md | 49 ++-------------------- pryr-0.1.5/pryr/man/bytes.Rd | 8 +-- pryr-0.1.5/pryr/man/ftype.Rd | 6 +- pryr-0.1.5/pryr/man/inspect.Rd | 7 +-- pryr-0.1.5/pryr/man/is_promise.Rd | 4 + pryr-0.1.5/pryr/man/otype.Rd | 6 +- pryr-0.1.5/pryr/man/partial.Rd | 2 pryr-0.1.5/pryr/man/uneval.Rd | 4 + pryr-0.1.5/pryr/src/RcppExports.cpp | 44 ++----------------- pryr-0.1.5/pryr/src/inspect.cpp | 5 +- pryr-0.1.5/pryr/tests/testthat/test-object_size.R | 14 +++--- 21 files changed, 76 insertions(+), 149 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.0-0 dated 2021-06-07 and 1.1-0 dated 2021-07-26
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 8 README.md | 2 inst/doc/memoiR.Rmd | 7 inst/doc/memoiR.html | 5 inst/rmarkdown/templates/memoir/skeleton/latex/template.tex | 157 ++++++------ vignettes/memoiR.Rmd | 7 8 files changed, 118 insertions(+), 88 deletions(-)
Title: Generalized Waring Regression Model for Count Data
Description: Statistical functions to fit, validate and describe a Generalized
Waring Regression Model (GWRM).
Author: Silverio Vilchez-Lopez [aut, cre],
Antonio Jose Saez-Castillo [aut],
Maria Jose Olmo-Jimenez [aut],
Jose Rodriguez-Avi [aut],
Antonio Conde-Sanchez [aut],
Ana Maria Martinez-Rodriguez [aut]
Maintainer: Silverio Vilchez-Lopez <svilchez@ujaen.es>
Diff between GWRM versions 2.1.0.3 dated 2017-07-31 and 2.1.0.4 dated 2021-07-26
DESCRIPTION | 20 +++++++++++--------- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- R/residuals.R | 3 ++- man/GWRM.Rd | 4 +--- man/add1.gw.Rd | 7 +++---- man/drop1.gw.Rd | 7 +++---- man/goals.Rd | 9 +++++---- man/gw.Rd | 29 ++++++++++++++++++++++------- man/partvar.Rd | 5 +++-- man/predict.gw.Rd | 4 ++-- man/residuals.gw.Rd | 18 +++++++++++++----- man/rgw.Rd | 3 +-- 13 files changed, 80 insertions(+), 56 deletions(-)
Title: Prediction and Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular
data on the torus. The package provides angular
adaptations of usual clustering methods such as the k-means
clustering, pairwise angular distances, which can be used as an
input for distance-based clustering algorithms, and implements
clustering based on the conformal prediction framework. Options
for the conformal scores include scores based on a kernel density
estimate, multivariate von Mises mixtures, and naive k-means clusters.
Moreover, the package provides some basic data handling tools for
angular data.
Author: Sungkyu Jung [aut, cph],
Seungki Hong [aut, cre],
Kiho Park [ctb],
Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>
Diff between ClusTorus versions 0.1.1 dated 2021-06-30 and 0.1.3 dated 2021-07-26
DESCRIPTION | 8 - MD5 | 28 ++-- R/hyperparam.torus.R | 44 +++--- R/icp.torus.R | 39 +++-- R/kde.torus.R | 19 +- build/partial.rdb |binary inst/doc/ClusTorus.R | 83 ++--------- inst/doc/ClusTorus.Rmd | 112 ++++------------ inst/doc/ClusTorus.html | 327 ++++++++++++++++++++--------------------------- man/ClusTorus-package.Rd | 2 man/cp.torus.kde.Rd | 6 man/hyperparam.torus.Rd | 48 +++--- man/icp.torus.score.Rd | 43 +++--- man/kde.torus.Rd | 10 - vignettes/ClusTorus.Rmd | 112 ++++------------ 15 files changed, 354 insertions(+), 527 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>,
@mattansb),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>),
Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.10.0 dated 2021-05-31 and 0.10.5 dated 2021-07-26
DESCRIPTION | 10 MD5 | 144 ++--- NAMESPACE | 74 -- NEWS.md | 8 R/area_under_curve.R | 1 R/bayesfactor_models.R | 42 - R/bayesfactor_parameters.R | 10 R/bayesfactor_restricted.R | 3 R/bci.R | 1 R/bic_to_bf.R | 1 R/check_prior.R | 1 R/convert_bayesian_to_frequentist.R | 9 R/describe_posterior.R | 72 ++ R/describe_prior.R | 1 R/diagnostic_draws.R | 22 R/diagnostic_posterior.R | 21 R/distribution.R | 47 + R/effective_sample.R | 14 R/equivalence_test.R | 3 R/estimate_density.R | 17 R/eti.R | 1 R/format.R | 17 R/hdi.R | 1 R/map_estimate.R | 2 R/mcse.R | 3 R/mediation.R | 56 +- R/overlap.R | 8 R/p_direction.R | 2 R/p_map.R | 2 R/plot.R | 52 -- R/point_estimate.R | 3 R/print.R | 13 R/print.bayesfactor_models.R | 3 R/print.equivalence_test.R | 1 R/print.rope.R | 1 R/print_html.R | 1 R/print_md.R | 1 R/reexports.R | 4 R/reshape_iterations.R | 1 R/rope.R | 1 R/rope_range.R | 3 R/sensitivity_to_prior.R | 1 R/sexit.R | 4 R/sexit_thresholds.R | 4 R/si.R | 6 R/simulate_data.R | 17 R/simulate_simpson.R |only R/unupdate.R | 46 - R/utils.R | 2 R/utils_bayesfactor.R | 38 - R/utils_check_collinearity.R | 2 R/weighted_posteriors.R | 2 build/partial.rdb |binary inst/WORDLIST | 4 inst/doc/bayes_factors.R | 542 ++++++++++----------- inst/doc/bayes_factors.html | 648 ++++++++------------------ inst/doc/bayestestR.html | 2 inst/doc/credible_interval.html | 6 inst/doc/example1.html | 10 inst/doc/example2.html | 22 inst/doc/example3.html | 2 inst/doc/guidelines.html | 2 inst/doc/probability_of_direction.html | 6 inst/doc/region_of_practical_equivalence.html | 8 man/bic_to_bf.Rd | 1 man/convert_bayesian_as_frequentist.Rd | 3 man/describe_posterior.Rd | 15 man/diagnostic_draws.Rd | 10 man/equivalence_test.Rd | 1 man/mediation.Rd | 13 man/reexports.Rd | 4 man/simulate_correlation.Rd | 154 +++--- man/simulate_simpson.Rd |only tests/testthat/test-blavaan.R | 39 - 74 files changed, 978 insertions(+), 1313 deletions(-)
Title: Sparse Group Variable Selection for Gene-Environment
Interactions in the Longitudinal Study
Description: Recently, regularized variable selection has emerged as a powerful tool to identify and dissect gene-environment interactions. Nevertheless, in longitudinal studies with high dimensional genetic factors, regularization methods for G×E interactions have not been systematically developed. In this package, we provide the implementation of sparse group variable selection, based on both the quadratic inference function (QIF) and generalized estimating equation (GEE), to accommodate the bi-level selection for longitudinal G×E studies with high dimensional genomic features. Alternative methods conducting only the group or individual level selection have also been included. The core modules of the package have been developed in C++.
Author: Fei Zhou, Xi Lu, Jie Ren, Cen Wu
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between springer versions 0.1.3 dated 2021-07-24 and 0.1.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Tidy Methods for Bayesian Treatment Effect Models
Description: Functions for extracting tidy data from Bayesian treatment effect models, in particular BART, but extensions are possible. Functionality includes extracting tidy posterior summaries as in 'tidybayes' <https://github.com/mjskay/tidybayes>, estimating (average) treatment effects, common support calculations, and plotting useful summaries of these.
Author: Joshua J Bon [aut, cre] (<https://orcid.org/0000-0003-2313-2949>)
Maintainer: Joshua J Bon <joshuajbon@gmail.com>
Diff between tidytreatment versions 0.2.0 dated 2021-06-23 and 0.2.1 dated 2021-07-26
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Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
R Core Team [ctb] (hesim uses some slightly modified C functions from
base R)
Maintainer: Devin Incerti <devin.incerti@gmail.com>
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Title: Access Victorian Spatial Data Through Web File Services (WFS)
Description: Easily interfaces R to spatial datasets available through
the Victorian Government's WFS (Web Feature Service): <https://services.land.vic.gov.au/catalogue/publicproxy/guest/dv_geoserver/wfs?request=getCapabilities>,
which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Author: Justin Cally [aut, cre] (<https://orcid.org/0000-0003-4584-2220>),
Rachel Swain [ctb],
Andy Teucher [aut] (<https://orcid.org/0000-0002-7840-692X>, bcdata
author),
Sam Albers [aut] (<https://orcid.org/0000-0002-9270-7884>, bcdata
author),
Stephanie Hazlitt [aut] (<https://orcid.org/0000-0002-3161-2304>,
bcdata author),
Province of British Columbia [cph] (bcdata copyright)
Maintainer: Justin Cally <justin.g.cally@gmail.com>
Diff between VicmapR versions 0.1.6 dated 2021-07-06 and 0.1.7 dated 2021-07-26
DESCRIPTION | 9 MD5 | 100 ++--- NAMESPACE | 104 ++--- NEWS.md | 102 ++--- R/build-query.R | 615 ++++++++++++++++---------------- R/check_geoserver.R | 133 ++++--- R/cql-predicates.R | 582 +++++++++++++++---------------- R/cql-translate.R | 396 ++++++++++----------- R/filter.R | 130 +++--- R/globals.R | 26 - R/listFeatures.R | 109 +++-- R/polygonFormat.R | 76 ++-- R/select.R | 114 +++--- R/utils-classes.R | 84 ++-- R/utils-collect.R | 48 +- R/utils-head.R | 46 +- R/utils-metadata.R | 296 ++++++++------- R/utils-options.R | 134 +++---- R/utils-pipe.R | 28 - R/utils-show_query.R | 48 +- README.md | 432 +++++++++++------------ build/vignette.rds |binary inst/doc/query_vicmap.R | 144 +++---- inst/doc/query_vicmap.Rmd | 274 +++++++------- inst/doc/query_vicmap.html | 637 ++++++++++++++-------------------- inst/shapes/melbourne.geojson | 8 man/CQL.Rd | 52 +- man/check_geoserver.Rd | 52 +- man/collect.Rd | 94 ++--- man/cql_geom_predicates.Rd | 172 ++++----- man/feature_hits.Rd | 50 +- man/filter.Rd | 64 +-- man/geom_col_name.Rd | 88 ++-- man/head.Rd | 68 +-- man/listLayers.Rd | 50 +- man/pipe.Rd | 40 +- man/print.vicmap_promise.Rd | 52 +- man/select.Rd | 64 +-- man/show_query.Rd | 88 ++-- man/vicmap_options.Rd | 70 +-- man/vicmap_query.Rd | 66 +-- man/wfsConnection-class.Rd | 34 - tests/testthat.R | 8 tests/testthat/test-build-query.R | 157 ++++---- tests/testthat/test-check_geoserver.R | 31 + tests/testthat/test-cql-predicates.R | 189 ++++------ tests/testthat/test-filter.R | 49 ++ tests/testthat/test-listLayers.R | 27 + tests/testthat/test-polygonFormat.R | 26 + tests/testthat/test-utils-options.R | 32 + vignettes/query_vicmap.Rmd | 274 +++++++------- 51 files changed, 3347 insertions(+), 3225 deletions(-)
Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts
<https://fonts.google.com/> into R, in order to
support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between sysfonts versions 0.8.3 dated 2021-01-10 and 0.8.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- configure | 2 +- configure.ac | 2 +- inst/NEWS.Rd | 14 ++++++++++++++ inst/fonts/webfonts.bz2 |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.9-2 dated 2021-01-10 and 0.9-3 dated 2021-07-26
DESCRIPTION | 8 +- MD5 | 14 +-- build/vignette.rds |binary configure | 2 configure.ac | 2 inst/NEWS.Rd | 9 ++ inst/doc/introduction.html | 160 +++++++++++++++++---------------------------- src/devfuns.c | 2 8 files changed, 85 insertions(+), 112 deletions(-)
Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut],
Xiaoqing Ye [aut, cre],
Wei Ma [aut, ths],
Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>
Diff between carat versions 1.4 dated 2020-09-26 and 1.5 dated 2021-07-25
DESCRIPTION | 14 - MD5 | 28 +-- R/RcppExports.R | 4 R/class_carandom.R | 23 ++- R/class_careval.R | 37 ++++ R/rand_CLI.R | 219 ++++++++++++++++++++++------ R/rand_completeData.R | 181 ++++++++++++++++------- R/rand_evalRand.R | 42 ++++- R/rand_generatingData.R | 28 +-- R/test_Rfunction.R | 368 ++++++++++++++++++++++++------------------------ data/pats.rda |binary inst/NEWS.Rd | 6 man/evalRand.Rd | 2 src/InnerFun.cpp | 111 ++++++-------- src/RcppExports.cpp | 13 + 15 files changed, 677 insertions(+), 399 deletions(-)
Title: Tour in 'Loon'
Description: Implement tour algorithms in interactive graphical system 'loon'.
Author: Zehao Xu [aut, cre],
R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>
Diff between loon.tourr versions 0.1.1 dated 2021-05-17 and 0.1.2 dated 2021-07-25
DESCRIPTION | 9 ++++----- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/l_layer_callback.R | 2 +- R/l_tour.R | 8 ++++++++ R/l_tour_pairs.R | 7 +++++++ R/tour_generation.R | 10 ++++++---- inst/doc/classification.html | 4 ++-- inst/doc/tours.html | 4 ++-- man/l_layer_callback.Rd | 2 +- 10 files changed, 41 insertions(+), 24 deletions(-)
Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data.
Author: Riccardo Corradin [aut, cre], Antonio Canale [ctb], Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>
Diff between BNPmix versions 0.2.8 dated 2021-03-21 and 0.2.9 dated 2021-07-25
DESCRIPTION | 10 ++++++---- MD5 | 19 +++++++++++++++---- build |only inst |only src/CommonUtilities.cpp | 37 ++++++++++++++++++++++++++++++++++++- src/CommonUtilities.h | 9 +++++++++ src/MAR.cpp | 10 ++++++++-- vignettes |only 8 files changed, 74 insertions(+), 11 deletions(-)
Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between set6 versions 0.2.2 dated 2021-07-16 and 0.2.3 dated 2021-07-25
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 9 +++++++-- R/SetWrapper_ExponentSet.R | 14 +++++++------- README.md | 28 ++++++++++++++-------------- inst/doc/set6.html | 4 ++-- tests/testthat/test_operations_setpower.R | 14 ++++++++++---- 7 files changed, 49 insertions(+), 38 deletions(-)
Title: Data Validation and Organization of Metadata for Local and
Remote Tables
Description: Validate data in data frames, 'tibble' objects, 'Spark'
'DataFrames', and database tables. Validation pipelines can be made using
easily-readable, consecutive validation steps. Upon execution of the
validation plan, several reporting options are available. User-defined
thresholds for failure rates allow for the determination of appropriate
reporting actions. Many other workflows are available including an
information management workflow, where the aim is to record, collect, and
generate useful information on data tables.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between pointblank versions 0.7.0 dated 2021-03-09 and 0.8.0 dated 2021-07-25
pointblank-0.7.0/pointblank/R/utils_translations.R |only pointblank-0.7.0/pointblank/man/print.examination_page.Rd |only pointblank-0.8.0/pointblank/DESCRIPTION | 37 pointblank-0.8.0/pointblank/MD5 | 362 +- pointblank-0.8.0/pointblank/NAMESPACE | 13 pointblank-0.8.0/pointblank/NEWS.md | 38 pointblank-0.8.0/pointblank/R/action_levels.R | 34 pointblank-0.8.0/pointblank/R/all_passed.R | 41 pointblank-0.8.0/pointblank/R/col_exists.R | 2 pointblank-0.8.0/pointblank/R/col_is_character.R | 2 pointblank-0.8.0/pointblank/R/col_is_date.R | 2 pointblank-0.8.0/pointblank/R/col_is_factor.R | 2 pointblank-0.8.0/pointblank/R/col_is_integer.R | 2 pointblank-0.8.0/pointblank/R/col_is_logical.R | 2 pointblank-0.8.0/pointblank/R/col_is_numeric.R | 2 pointblank-0.8.0/pointblank/R/col_is_posix.R | 2 pointblank-0.8.0/pointblank/R/col_schema_match.R | 13 pointblank-0.8.0/pointblank/R/col_vals_between.R | 122 pointblank-0.8.0/pointblank/R/col_vals_decreasing.R | 120 pointblank-0.8.0/pointblank/R/col_vals_equal.R | 119 pointblank-0.8.0/pointblank/R/col_vals_expr.R | 126 pointblank-0.8.0/pointblank/R/col_vals_gt.R | 133 pointblank-0.8.0/pointblank/R/col_vals_gte.R | 119 pointblank-0.8.0/pointblank/R/col_vals_in_set.R | 117 pointblank-0.8.0/pointblank/R/col_vals_increasing.R | 120 pointblank-0.8.0/pointblank/R/col_vals_lt.R | 119 pointblank-0.8.0/pointblank/R/col_vals_lte.R | 119 pointblank-0.8.0/pointblank/R/col_vals_make_set.R | 117 pointblank-0.8.0/pointblank/R/col_vals_make_subset.R | 118 pointblank-0.8.0/pointblank/R/col_vals_not_between.R | 122 pointblank-0.8.0/pointblank/R/col_vals_not_equal.R | 121 pointblank-0.8.0/pointblank/R/col_vals_not_in_set.R | 119 pointblank-0.8.0/pointblank/R/col_vals_not_null.R | 119 pointblank-0.8.0/pointblank/R/col_vals_null.R | 115 pointblank-0.8.0/pointblank/R/col_vals_regex.R | 121 pointblank-0.8.0/pointblank/R/col_vals_within_spec.R |only pointblank-0.8.0/pointblank/R/column_roles.R |only 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Title: Missingness Aware Gaussian Mixture Models
Description: Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data. This package complements existing implementations by allowing for both missing elements in the input vectors and full (as opposed to strictly diagonal) covariance matrices. Estimating is performed using an expectation conditional maximization algorithm that accounts for missingness of both the cluster assignments and the vector components. The output includes the marginal cluster membership probabilities; the mean and covariance of each cluster; the posterior probabilities of cluster membership; and a completed version of the input data, with missing values imputed to their posterior expectations. For additional details, please see McCaw ZR, Julienne H, Aschard H. "MGMM: an R package for fitting Gaussian Mixture Models on Incomplete Data." <doi:10.1101/2019.12.20.884551>.
Author: Zachary McCaw [aut, cre] (<https://orcid.org/0000-0002-2006-9828>)
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>
Diff between MGMM versions 0.3.1 dated 2020-08-26 and 0.4.0 dated 2021-07-25
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Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.0.5 dated 2021-07-20 and 1.0.6 dated 2021-07-25
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 ++++- R/svyCreateTableOneJS.R | 6 ++++-- build/vignette.rds |binary inst/doc/jstable.html | 28 ++++++++++++++-------------- man/svyCreateTableOne2.Rd | 3 ++- man/svyCreateTableOneJS.Rd | 3 ++- tests/testthat/test-svyCreateTableOne.R | 18 +++++++++--------- 9 files changed, 47 insertions(+), 40 deletions(-)
Title: API Client for Fantasy Football League Platforms
Description: Helps access various Fantasy Football APIs by handling
authentication and rate-limiting, forming appropriate calls, and
returning tidy dataframes which can be easily connected to other data
sources.
Author: Tan Ho [aut, cre],
Tony ElHabr [ctb],
Joe Sydlowski [ctb]
Maintainer: Tan Ho <tan@tanho.ca>
Diff between ffscrapr versions 1.4.4 dated 2021-07-20 and 1.4.5 dated 2021-07-25
DESCRIPTION | 6 MD5 | 248 ++++++++++++++++---------------- NEWS.md | 12 + R/0_generics.R | 2 R/1_import_dp.R | 9 - R/1_import_nflfastr.R | 8 - R/espn__helpers.R | 6 R/espn_draft.R | 6 R/espn_draftpicks.R | 2 R/espn_franchises.R | 8 - R/espn_league.R | 25 ++- R/espn_players.R | 8 - R/espn_playerscores.R | 8 - R/espn_potentialpoints.R | 7 R/espn_rosters.R | 6 R/espn_schedule.R | 6 R/espn_scoring.R | 6 R/espn_scoringhistory.R | 6 R/espn_standings.R | 6 R/espn_starterpositions.R | 2 R/espn_starters.R | 2 R/flea_draft.R | 6 R/flea_draftpicks.R | 2 R/flea_franchises.R | 2 R/flea_league.R | 2 R/flea_players.R | 2 R/flea_playerscores.R | 7 R/flea_rosters.R | 3 R/flea_schedule.R | 4 R/flea_scoring.R | 2 R/flea_scoringhistory.R | 4 R/flea_standings.R | 2 R/flea_starterpositions.R | 2 R/flea_starters.R | 2 R/flea_transactions.R | 2 R/mfl_draft.R | 6 R/mfl_draftpicks.R | 6 R/mfl_franchises.R | 2 R/mfl_league.R | 2 R/mfl_players.R | 2 R/mfl_playerscores.R | 2 R/mfl_rosters.R | 4 R/mfl_schedule.R | 2 R/mfl_scoring.R | 2 R/mfl_scoringhistory.R | 6 R/mfl_standings.R | 2 R/mfl_starterpositions.R | 2 R/mfl_starters.R | 2 R/mfl_transactions.R | 2 R/sleeper_draft.R | 2 R/sleeper_draftpicks.R | 2 R/sleeper_franchises.R | 2 R/sleeper_league.R | 2 R/sleeper_players.R | 5 R/sleeper_rosters.R | 2 R/sleeper_schedule.R | 2 R/sleeper_scoring.R | 2 R/sleeper_scoringhistory.R | 7 R/sleeper_standings.R | 2 R/sleeper_starterpositions.R | 4 R/sleeper_starters.R | 4 R/sleeper_transactions.R | 4 README.md | 4 inst/doc/espn_authentication.html | 4 inst/doc/espn_basics.R | 6 inst/doc/espn_basics.Rmd | 6 inst/doc/espn_basics.html | 4 inst/doc/espn_getendpoint.R | 6 inst/doc/espn_getendpoint.Rmd | 6 inst/doc/espn_getendpoint.html | 4 inst/doc/ffscrapr_caching.html | 4 inst/doc/ffscrapr_scoringhistory.html | 4 inst/doc/fleaflicker_basics.R | 6 inst/doc/fleaflicker_basics.Rmd | 6 inst/doc/fleaflicker_basics.html | 4 inst/doc/fleaflicker_getendpoint.R | 6 inst/doc/fleaflicker_getendpoint.Rmd | 6 inst/doc/fleaflicker_getendpoint.html | 4 inst/doc/mfl_basics.R | 6 inst/doc/mfl_basics.Rmd | 6 inst/doc/mfl_basics.html | 26 +-- inst/doc/mfl_getendpoint.R | 6 inst/doc/mfl_getendpoint.Rmd | 6 inst/doc/mfl_getendpoint.html | 4 inst/doc/sleeper_basics.R | 6 inst/doc/sleeper_basics.Rmd | 6 inst/doc/sleeper_basics.html | 20 +- inst/doc/sleeper_getendpoint.R | 6 inst/doc/sleeper_getendpoint.Rmd | 6 inst/doc/sleeper_getendpoint.html | 8 - man/dp_clean_html.Rd | 48 +++--- man/dp_cleannames.Rd | 1 man/dp_playerids.Rd | 4 man/dp_values.Rd | 4 man/espn_players.Rd | 8 - man/espn_potentialpoints.Rd | 7 man/ff_connect.Rd | 2 man/ff_draft.Rd | 20 +- man/ff_draftpicks.Rd | 12 + man/ff_franchises.Rd | 14 + man/ff_league.Rd | 14 + man/ff_playerscores.Rd | 17 +- man/ff_rosters.Rd | 15 + man/ff_schedule.Rd | 14 + man/ff_scoring.Rd | 12 + man/ff_scoringhistory.Rd | 23 +- man/ff_standings.Rd | 12 + man/ff_starter_positions.Rd | 10 + man/ff_starters.Rd | 10 + man/ff_transactions.Rd | 8 - man/fleaflicker_players.Rd | 2 man/mfl_players.Rd | 2 man/nflfastr_rosters.Rd | 4 man/nflfastr_weekly.Rd | 4 man/sleeper_players.Rd | 5 tests/testthat/setup.R | 6 tests/testthat/test-ff_scoringhistory.R | 4 vignettes/espn_basics.Rmd | 6 vignettes/espn_getendpoint.Rmd | 6 vignettes/fleaflicker_basics.Rmd | 6 vignettes/fleaflicker_getendpoint.Rmd | 6 vignettes/mfl_basics.Rmd | 6 vignettes/mfl_getendpoint.Rmd | 6 vignettes/sleeper_basics.Rmd | 6 vignettes/sleeper_getendpoint.Rmd | 6 125 files changed, 651 insertions(+), 378 deletions(-)
Title: Capture Hi-C Analysis Engine
Description: Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Author: Erle Holgersen [aut, cre],
Olivia Leavy [aut],
Olivia Fletcher [aut],
Frank Dudbridge [aut],
Syed Haider [aut]
Maintainer: Erle Holgersen <erle.holgersen@gmail.com>
Diff between chicane versions 0.1.5 dated 2021-06-10 and 0.1.6 dated 2021-07-25
chicane-0.1.5/chicane/vignettes/Getting_Started_cache |only chicane-0.1.6/chicane/DESCRIPTION | 8 chicane-0.1.6/chicane/MD5 | 68 chicane-0.1.6/chicane/NEWS | 7 chicane-0.1.6/chicane/R/chicane.R | 12 chicane-0.1.6/chicane/R/combine.replicates.R | 24 chicane-0.1.6/chicane/R/prepare.data.R | 10 chicane-0.1.6/chicane/R/read.bed.R | 5 chicane-0.1.6/chicane/R/test.enrichment.R | 10 chicane-0.1.6/chicane/build/vignette.rds |binary chicane-0.1.6/chicane/inst/doc/Getting_Started.R | 2 chicane-0.1.6/chicane/inst/doc/Getting_Started.Rmd | 39 chicane-0.1.6/chicane/inst/doc/Getting_Started.html | 807 ++++------- chicane-0.1.6/chicane/inst/doc/Visualising_Interactions.html | 550 ++----- chicane-0.1.6/chicane/man/chicane.Rd | 12 chicane-0.1.6/chicane/man/combine.replicates.Rd | 24 chicane-0.1.6/chicane/man/prepare.data.Rd | 10 chicane-0.1.6/chicane/man/test.enrichment.Rd | 10 chicane-0.1.6/chicane/vignettes/Getting_Started.Rmd | 39 19 files changed, 662 insertions(+), 975 deletions(-)
Title: Smooth Effects on Response Penalty for 'CLM'
Description: A regularization method for the cumulative link
models. The 'smooth-effect-on-response penalty' ('SERP') provides
flexible modelling of the ordinal model by enabling the smooth
transition from the general cumulative link model to a coarser form of
the same model. In other words, as the tuning parameter goes from zero
to infinity, the subject-specific effects associated with each
variable in the model tend to a unique global effect. The parameter
estimates of the general cumulative model are mostly unidentifiable or
at least only identifiable within a range of the entire parameter
space. Thus, by maximizing a penalized rather than the usual
non-penalized log-likelihood, this and other numerical problems common
with the general model are to a large extent eliminated. Fitting is
via a modified Newton's method. Several standard model performance and
descriptive methods are also available. For more details on the penalty
implemented here, see, 'Ugba et al. (2021)' <doi:10.3390/stats4030037> and
Tutz and Gertheiss (2016) <doi:10.1177/1471082X16642560>.
Author: Ejike R. Ugba [aut, cre, cph]
Maintainer: Ejike R. Ugba <ejike.ugba@outlook.com>
Diff between serp versions 0.1.8 dated 2021-01-29 and 0.2.0 dated 2021-07-25
DESCRIPTION | 14 LICENSE |only MD5 | 37 +- NEWS.md | 76 +++++ R/serp.R | 23 - R/serp.anova.R | 22 + R/serp.control.R | 31 +- R/serp.fit.R | 84 +++-- R/serp.method.R | 114 +++----- R/serp.misc.R | 112 +++---- R/serp.performance.R | 12 R/serp.vcov.R | 9 README.md | 214 ++++++++++++--- man/figures |only man/serp.Rd | 15 - man/summary.serp.Rd | 7 tests/testthat.R | 1 tests/testthat/test-model-weights.R | 153 ++++++---- tests/testthat/test-penalized-model.R | 454 +++++++++++++++++++++----------- tests/testthat/test-unpenalized-model.R | 167 ++++++----- 20 files changed, 973 insertions(+), 572 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd,
lz4 and xxHash code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library),
Bryce Chamberlain [ctb] (qsavem and qload functions)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.24.1 dated 2021-03-07 and 0.25.1 dated 2021-07-25
qs-0.24.1/qs/src/expand_binding_value.cpp |only qs-0.24.1/qs/src/expand_binding_value.h |only qs-0.25.1/qs/ChangeLog | 13 ++++ qs-0.25.1/qs/DESCRIPTION | 20 ++----- qs-0.25.1/qs/MD5 | 44 ++++++++-------- qs-0.25.1/qs/NAMESPACE | 3 - qs-0.25.1/qs/R/RcppExports.R | 8 --- qs-0.25.1/qs/R/qcache.R |only qs-0.25.1/qs/R/zzz.R | 2 qs-0.25.1/qs/README.md | 4 + qs-0.25.1/qs/build/vignette.rds |binary qs-0.25.1/qs/data/starnames.rda |binary qs-0.25.1/qs/inst/doc/vignette.html | 16 ++++-- qs-0.25.1/qs/inst/doc/vignette.rmd | 8 ++- qs-0.25.1/qs/inst/include/qs_RcppExports.h | 39 -------------- qs-0.25.1/qs/man/qcache.Rd |only qs-0.25.1/qs/src/Makevars.in | 11 +--- qs-0.25.1/qs/src/Makevars.win | 9 +-- qs-0.25.1/qs/src/RcppExports.cpp | 76 +---------------------------- qs-0.25.1/qs/src/extra_functions.h | 10 --- qs-0.25.1/qs/src/qs_common.h | 2 qs-0.25.1/qs/src/qs_deserialize_common.h | 15 ++++- qs-0.25.1/qs/src/qs_functions.cpp | 10 +++ qs-0.25.1/qs/src/qs_serialize_common.h | 57 ++++++++++++++++++++- qs-0.25.1/qs/vignettes/vignette.rmd | 8 ++- 25 files changed, 159 insertions(+), 196 deletions(-)
Title: Bayesian Meta-Analysis via 'Stan'
Description: Performs Bayesian meta-analysis and model-based meta-analysis using 'Stan'.
Includes binomial-normal hierarchical models and option to use weakly informative priors for the
heterogeneity parameter and the treatment effect parameter which are described in
Guenhan, Roever, and Friede (2020) <doi:10.1002/jrsm.1370>.
Author: Burak Kuersad Guenhan [aut, cre]
(<https://orcid.org/0000-0002-7454-8680>),
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cpp.R,
R/stanmodels.R)
Maintainer: Burak Kuersad Guenhan <burakgunhan@gmail.com>
Diff between MetaStan versions 0.2.0 dated 2020-04-09 and 0.4.0 dated 2021-07-25
MetaStan-0.2.0/MetaStan/README.md |only MetaStan-0.4.0/MetaStan/DESCRIPTION | 14 MetaStan-0.4.0/MetaStan/MD5 | 7 MetaStan-0.4.0/MetaStan/build/vignette.rds |binary MetaStan-0.4.0/MetaStan/inst/doc/MetaStan_BNHM.html | 686 +++++++++++--------- 5 files changed, 415 insertions(+), 292 deletions(-)
Title: Plot Heatmap
Description: The flexibility and excellence of 'ggplot2' is unquestionable,
so many drawing tools basically need 'ggplot2' as the operating object.
In order to develop a heatmap drawing system based on ggplot2, we developed
this tool, mainly to solve the heatmap puzzle problem and the flexible
connection between the heatmap and the 'ggplot2' object.
The advantages of this tool are as follows:
1. More flexible label settings;
2. Realize the linkage of heatmap and 'ggplot2' drawing system,
which is helpful for operations such as puzzles;
3. Simple and easy to operate;
4. Optimization of clustering tree visualization.
Author: Baiwei Luo [aut, cre]
Maintainer: Baiwei Luo <2734782653@qq.com>
Diff between ggheatmap versions 2.0 dated 2021-07-12 and 2.1 dated 2021-07-25
DESCRIPTION | 6 MD5 | 6 R/ggheatmap.R | 825 ++++++++++++++++++++++++++++--------------------------- man/ggheatmap.Rd | 34 ++ 4 files changed, 472 insertions(+), 399 deletions(-)
Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix
estimation, particularly useful in high-dimensional settings. This
method relies upon the theory of loss-based estimator selection to
identify the optimal estimator of the covariance matrix from among a
prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph]
(<https://orcid.org/0000-0002-4850-2507>),
Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>),
Brian Collica [aut] (<https://orcid.org/0000-0003-1127-2557>),
Jamarcus Liu [ctb],
Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>),
Sandrine Dudoit [ctb, ths] (<https://orcid.org/0000-0002-6069-8629>)
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Diff between cvCovEst versions 0.3.5 dated 2021-04-18 and 1.0.0 dated 2021-07-25
cvCovEst-0.3.5/cvCovEst/R/plotFunctions.R |only cvCovEst-0.3.5/cvCovEst/man/trueFrobeniusLoss.Rd |only cvCovEst-1.0.0/cvCovEst/DESCRIPTION | 12 cvCovEst-1.0.0/cvCovEst/MD5 | 56 - cvCovEst-1.0.0/cvCovEst/NAMESPACE | 1 cvCovEst-1.0.0/cvCovEst/NEWS.md | 34 cvCovEst-1.0.0/cvCovEst/R/checkArgs.R | 28 cvCovEst-1.0.0/cvCovEst/R/cvCovEst.R | 205 +---- cvCovEst-1.0.0/cvCovEst/R/estimator_plots.R | 12 cvCovEst-1.0.0/cvCovEst/R/foldFunctions.R | 149 +--- cvCovEst-1.0.0/cvCovEst/R/plot_functions.R | 16 cvCovEst-1.0.0/cvCovEst/R/summary_functions.R | 42 - cvCovEst-1.0.0/cvCovEst/README.md | 23 cvCovEst-1.0.0/cvCovEst/build/partial.rdb |binary cvCovEst-1.0.0/cvCovEst/build/vignette.rds |binary cvCovEst-1.0.0/cvCovEst/inst/REFERENCES.bib | 6 cvCovEst-1.0.0/cvCovEst/inst/doc/using_cvCovEst.R | 18 cvCovEst-1.0.0/cvCovEst/inst/doc/using_cvCovEst.Rmd | 31 cvCovEst-1.0.0/cvCovEst/inst/doc/using_cvCovEst.html | 377 ++--------- cvCovEst-1.0.0/cvCovEst/man/checkArgs.Rd | 11 cvCovEst-1.0.0/cvCovEst/man/cvCovEst.Rd | 25 cvCovEst-1.0.0/cvCovEst/man/cvFrobeniusLoss.Rd | 15 cvCovEst-1.0.0/cvCovEst/man/cvMatrixFrobeniusLoss.Rd | 10 cvCovEst-1.0.0/cvCovEst/man/cvScaledMatrixFrobeniusLoss.Rd | 10 cvCovEst-1.0.0/cvCovEst/man/plot.cvCovEst.Rd | 2 cvCovEst-1.0.0/cvCovEst/tests/testthat/test-checkArgs.R | 42 - cvCovEst-1.0.0/cvCovEst/tests/testthat/test-cvCovEst.R | 156 ---- cvCovEst-1.0.0/cvCovEst/tests/testthat/test-foldFunctions.R | 90 ++ cvCovEst-1.0.0/cvCovEst/tests/testthat/test-plot-functions.R | 9 cvCovEst-1.0.0/cvCovEst/vignettes/using_cvCovEst.Rmd | 31 30 files changed, 420 insertions(+), 991 deletions(-)