Title: Dynamic Updating Methods for Player Ratings Estimation
Description: Implements schemes for estimating player or
team skill based on dynamic updating. Implemented methods include
Elo, Glicko, Glicko-2 and Stephenson. Contains pdf documentation
of a reproducible analysis using approximately two million chess
matches.
Author: Alec Stephenson and Jeff Sonas.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between PlayerRatings versions 1.0-2 dated 2019-02-13 and 1.0-3 dated 2019-02-19
DESCRIPTION | 12 MD5 | 33 NAMESPACE | 39 - R/ratings.R | 1692 ++++++++++++++++++++++++++--------------------- inst/doc/AFLRatings.R | 72 +- inst/doc/AFLRatings.Rnw | 500 +++++++------ inst/doc/AFLRatings.pdf |binary inst/doc/glicko.pdf |only inst/doc/glicko2.pdf |only man/aflodds.Rd | 3 man/elo.Rd | 215 +++-- man/fide.Rd | 11 man/glicko.Rd | 207 +++-- man/glicko2.Rd |only man/predict.rating.Rd | 130 +-- man/steph.Rd | 17 src/PlayerRatings_init.c | 4 src/ratings.c | 40 + vignettes/AFLRatings.Rnw | 500 +++++++------ 19 files changed, 1949 insertions(+), 1526 deletions(-)
Title: Translate Integers into English
Description: Allow numbers to be presented in an English language
version, one, two, three, ...
Author: John Fox, Bill Venables, Anthony Damico and Anne Pier Salverda
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between english versions 1.1-4 dated 2018-08-07 and 1.2-0 dated 2019-02-19
DESCRIPTION | 10 +- MD5 | 14 ++- NAMESPACE | 2 R/english.R | 5 - R/indefinite.R |only man/as.english.Rd | 176 +++++++++++++++++++++++++------------------------ man/english-package.Rd | 13 ++- man/indefinite.Rd |only man/words.Rd | 2 9 files changed, 119 insertions(+), 103 deletions(-)
Title: Client for the Cancer Imaging Archive REST API
Description: A wrapper for The Cancer Imaging Archive's REST API. The Cancer
Imaging Archive (TCIA) hosts de-identified medical images of cancer
available for public download, as well as rich metadata for each image
series. TCIA provides a REST API for programmatic access to the data.
This package provides simple functions to access each API endpoint.
For more information, see <https://github.com/pamelarussell/TCIApathfinder>
and TCIA's website.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@ucdenver.edu>
Diff between TCIApathfinder versions 1.0.2 dated 2018-01-24 and 1.0.3 dated 2019-02-19
DESCRIPTION | 6 MD5 | 10 - NEWS.md |only build/vignette.rds |binary inst/CITATION |only inst/doc/introduction.html | 391 +++++++++++++++++++++++++++++++++++---------- inst/doc/radiomics.html | 360 +++++++++++++++++++++++++++++++++-------- 7 files changed, 615 insertions(+), 152 deletions(-)
More information about TCIApathfinder at CRAN
Permanent link
Title: Working Examples for Reproducible Research Documents
Description: Templates, guides, and scripts for
writing documents in 'LaTeX' and 'R markdown' to produce
guides, slides, and reports. Special care is taken to
illustrate use of templates and customization opportunities.
Challenges and opportunities of 'HTML' output from 'R markdown'
receive special attention. Includes several vignettes
to assist new users of literate programming.
Author: Paul Johnson [aut, cre],
Brent Kaplan [ctb],
Meghan Sullivan [ctb],
Charles Redmon [ctb],
Zack Roman [ctb],
Chong Xing [ctb],
Longcan 'Emma' Huang [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>
Diff between stationery versions 0.98.5.5 dated 2018-10-08 and 0.98.6 dated 2019-02-19
stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rmd2html-guide/skeleton/theme/R.bib |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rmd2pdf-guide/skeleton/theme/R.bib |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rmd2pdf-report/skeleton/theme/R.bib |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-guide-knit/skeleton/theme/R.bib |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-guide-knit/skeleton/theme/addressFooter.tex |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-guide-sweave/skeleton/theme/R.bib |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-guide-sweave/skeleton/theme/addressFooter.tex |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-report-knit/skeleton/theme/addressFooter.tex |only stationery-0.98.5.5/stationery/inst/rmarkdown/templates/rnw2pdf-report-sweave/skeleton/theme/R.bib |only 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Title: Computing Envelope Estimators
Description: Provides a general routine, envMU, which allows estimation of the M envelope of span(U) given root n consistent estimators of M and U. The routine envMU does not presume a model. This package implements response envelopes, partial response envelopes, envelopes in the predictor space, heteroscedastic envelopes, simultaneous envelopes, scaled response envelopes, scaled envelopes in the predictor space, groupwise envelopes, weighted envelopes, envelopes in logistic regression and envelopes in Poisson regression. For each of these model-based routines the package provides inference tools including bootstrap, cross validation, estimation and prediction, hypothesis testing on coefficients are included except for weighted envelopes. Tools for selection of dimension include AIC, BIC and likelihood ratio testing. Background is available at Cook, R. D., Forzani, L. and Su, Z. (2016) <doi:10.1016/j.jmva.2016.05.006>. Optimization is based on a clockwise coordinate descent algorithm.
Author: Minji Lee, Zhihua Su
Maintainer: Minji Lee <mlee9@ufl.edu>
Diff between Renvlp versions 2.5 dated 2018-01-18 and 2.6 dated 2019-02-19
Renvlp-2.5/Renvlp/build |only Renvlp-2.5/Renvlp/inst |only Renvlp-2.5/Renvlp/vignettes |only Renvlp-2.6/Renvlp/DESCRIPTION | 13 - Renvlp-2.6/Renvlp/MD5 | 48 +-- Renvlp-2.6/Renvlp/R/senv.R | 376 ++++++++++++++--------------- Renvlp-2.6/Renvlp/R/u.senv.R | 4 Renvlp-2.6/Renvlp/R/u.sxenv.R | 4 Renvlp-2.6/Renvlp/R/weighted.env.R | 2 Renvlp-2.6/Renvlp/R/weighted.penv.R | 2 Renvlp-2.6/Renvlp/R/weighted.xenv.R | 2 Renvlp-2.6/Renvlp/man/Renvlp.Rd | 6 Renvlp-2.6/Renvlp/man/boot.genv.Rd | 2 Renvlp-2.6/Renvlp/man/boot.penv.Rd | 4 Renvlp-2.6/Renvlp/man/boot.stenv.Rd | 6 Renvlp-2.6/Renvlp/man/boot.xenv.Rd | 2 Renvlp-2.6/Renvlp/man/cv.genv.Rd | 4 Renvlp-2.6/Renvlp/man/cv.penv.Rd | 4 Renvlp-2.6/Renvlp/man/genv.Rd | 6 Renvlp-2.6/Renvlp/man/pred.henv.Rd | 2 Renvlp-2.6/Renvlp/man/weighted.env.Rd | 5 Renvlp-2.6/Renvlp/man/weighted.penv.Rd | 5 Renvlp-2.6/Renvlp/man/weighted.pred.env.Rd | 2 Renvlp-2.6/Renvlp/man/weighted.xenv.Rd | 5 Renvlp-2.6/Renvlp/man/xenv.Rd | 2 25 files changed, 251 insertions(+), 255 deletions(-)
Title: Project Management Tools
Description: Tools for data importation, recoding, and inspection that
are used at the University of Kansas Center for Research Methods
and Data Analysis. There are functions to create new project
folders, R code templates, create uniquely named output
directories, and to quickly obtain a visual summary for each
variable in a data frame. The main feature here is the systematic
implementation of the "variable key" framework for data
importation and recoding. We are eager to have community feedback
about the variable key and the vignette about it.
Author: Paul Johnson [aut, cre],
Benjamin Kite [aut],
Charles Redmon [aut],
Jared Harpole [ctb],
Kenna Whitley [ctb],
Po-Yi Chen [ctb],
Shadi Pirhosseinloo [ctb]
Maintainer: Paul Johnson <pauljohn@ku.edu>
Diff between kutils versions 1.60 dated 2019-01-23 and 1.64 dated 2019-02-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/modelcomparison.R | 2 ++ R/semTable.R | 24 +++++++++++++++--------- inst/doc/variablekey.pdf |binary 5 files changed, 25 insertions(+), 17 deletions(-)
Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (<https://mc-stan.org/>).
Author: Robert Kubinec [aut, cre],
Jonah Gabry [ctb],
Ben Goodrich [ctb],
Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>
Diff between idealstan versions 0.7.0 dated 2019-02-19 and 0.7.1 dated 2019-02-19
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NEWS.md | 3 +++ 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Download, Manipulate, and Present American Community Survey and
Decennial Data from the US Census
Description: Provides a general toolkit for downloading, managing,
analyzing, and presenting data from the U.S. Census
(<https://www.census.gov/data/developers/data-sets.html>), including
SF1 (Decennial short-form), SF3 (Decennial long-form), and the
American Community Survey (ACS). Confidence intervals provided with
ACS data are converted to standard errors to be bundled with
estimates in complex acs objects. Package provides new methods to
conduct standard operations on acs objects and present/plot data in
statistically appropriate ways.
Author: Ezra Haber Glenn [aut, cre]
Maintainer: Ezra Haber Glenn <eglenn@mit.edu>
Diff between acs versions 2.1.3 dated 2018-03-02 and 2.1.4 dated 2019-02-19
DESCRIPTION | 8 +++--- MD5 | 28 ++++++++++----------- R/acs.R | 43 +++++++++++++++++++++----------- README.md | 49 ++++++++++++++++++------------------- data/cpi.rda |binary data/fips.american.indian.area.rda |binary data/fips.county.rda |binary data/fips.county.subdivision.rda |binary data/fips.place.rda |binary data/fips.school.rda |binary data/fips.state.rda |binary data/kansas07.rda |binary data/kansas09.rda |binary data/lawrence10.rda |binary man/acs-package.Rd | 2 - 15 files changed, 73 insertions(+), 57 deletions(-)
Title: HTML Output Formats and Templates for 'rmarkdown' Documents
Description: HTML formats and templates for 'rmarkdown' documents, with some extra
features such as automatic table of contents, lightboxed figures, dynamic
crosstab helper.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between rmdformats versions 0.3.4 dated 2019-01-10 and 0.3.5 dated 2019-02-19
DESCRIPTION | 8 ++--- MD5 | 28 +++++++++--------- NEWS | 8 +++++ README.md | 4 +- inst/doc/introduction.html | 28 ++++++++++++++++-- inst/rmarkdown/templates/html_clean/template.yaml | 2 - inst/rmarkdown/templates/html_docco/template.yaml | 2 - inst/rmarkdown/templates/material/template.yaml | 2 - inst/rmarkdown/templates/readthedown/template.yaml | 2 - inst/templates/html_clean/Makefile | 2 - inst/templates/html_docco/Makefile | 2 - inst/templates/material/Makefile | 2 - inst/templates/material/material.css | 32 +++++++++++++++------ inst/templates/material/material.html | 9 +++-- inst/templates/readthedown/Makefile | 2 - 15 files changed, 91 insertions(+), 42 deletions(-)
Title: Tools for working with the National Hydrography Dataset
Description: Tools for working with the National Hydrography Dataset, with
functions for querying, downloading, and networking both the NHD
<https://www.usgs.gov/core-science-systems/ngp/national-hydrography>
and NHDPlus <http://www.horizon-systems.com/nhdplus> datasets.
Author: Joseph Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between nhdR versions 0.5.0 dated 2019-01-30 and 0.5.1 dated 2019-02-19
nhdR-0.5.0/nhdR/tests/testthat/test-extract.R |only nhdR-0.5.0/nhdR/tests/testthat/test-nhd_get.R |only nhdR-0.5.1/nhdR/DESCRIPTION | 6 +- nhdR-0.5.1/nhdR/MD5 | 44 ++++++++-------- nhdR-0.5.1/nhdR/NAMESPACE | 1 nhdR-0.5.1/nhdR/NEWS.md | 8 ++ nhdR-0.5.1/nhdR/R/load.R | 21 +++++-- nhdR-0.5.1/nhdR/R/network.R | 61 +++++++++++++++------- nhdR-0.5.1/nhdR/R/query.R | 8 ++ nhdR-0.5.1/nhdR/R/utils.R | 20 ++++--- nhdR-0.5.1/nhdR/R/zzz.R | 2 nhdR-0.5.1/nhdR/README.md | 1 nhdR-0.5.1/nhdR/inst/doc/demo.html | 24 ++++---- nhdR-0.5.1/nhdR/inst/doc/flow.html | 70 +++++++++++++------------- nhdR-0.5.1/nhdR/inst/doc/network.html | 40 +++++++------- nhdR-0.5.1/nhdR/man/extract_network.Rd | 11 +++- nhdR-0.5.1/nhdR/man/leaf_reaches.Rd | 2 nhdR-0.5.1/nhdR/man/nhd_load.Rd | 2 nhdR-0.5.1/nhdR/man/nhd_plus_load.Rd | 7 +- nhdR-0.5.1/nhdR/man/nhd_plus_query.Rd | 2 nhdR-0.5.1/nhdR/man/terminal_reaches.Rd | 19 +++---- nhdR-0.5.1/nhdR/tests/testthat/test-get.R |only nhdR-0.5.1/nhdR/tests/testthat/test-info.R |only nhdR-0.5.1/nhdR/tests/testthat/test-list.R |only nhdR-0.5.1/nhdR/tests/testthat/test-network.R |only nhdR-0.5.1/nhdR/tests/testthat/test-query.R | 1 26 files changed, 204 insertions(+), 146 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@umich.edu>
Diff between tidybayes versions 1.0.3 dated 2018-10-22 and 1.0.4 dated 2019-02-19
tidybayes-1.0.3/tidybayes/man/figures/preview.png |only tidybayes-1.0.4/tidybayes/DESCRIPTION | 28 tidybayes-1.0.4/tidybayes/MD5 | 207 +- tidybayes-1.0.4/tidybayes/NAMESPACE | 25 tidybayes-1.0.4/tidybayes/NEWS.md | 20 tidybayes-1.0.4/tidybayes/R/add_draws.R |only tidybayes-1.0.4/tidybayes/R/compare_levels.R | 422 ++-- tidybayes-1.0.4/tidybayes/R/gather_emmeans_draws.R | 36 tidybayes-1.0.4/tidybayes/R/gather_pairs.R | 286 +- tidybayes-1.0.4/tidybayes/R/geom_halfeyeh.R | 3 tidybayes-1.0.4/tidybayes/R/geom_lineribbon.R | 338 +-- tidybayes-1.0.4/tidybayes/R/geom_pointinterval.R | 7 tidybayes-1.0.4/tidybayes/R/geom_pointintervalh.R | 2 tidybayes-1.0.4/tidybayes/R/point_interval.R | 878 ++++---- tidybayes-1.0.4/tidybayes/R/predict_curve.R | 456 ++-- tidybayes-1.0.4/tidybayes/R/predicted_draws.R | 546 ++--- tidybayes-1.0.4/tidybayes/R/recover_types.R | 314 +-- tidybayes-1.0.4/tidybayes/R/residual_draws.R |only tidybayes-1.0.4/tidybayes/R/sample_draws.R |only tidybayes-1.0.4/tidybayes/R/spread_draws.R | 7 tidybayes-1.0.4/tidybayes/R/stat_lineribbon.R | 240 +- tidybayes-1.0.4/tidybayes/R/stat_pointinterval.R | 7 tidybayes-1.0.4/tidybayes/R/stat_pointintervalh.R | 2 tidybayes-1.0.4/tidybayes/R/tidy_draws.R | 6 tidybayes-1.0.4/tidybayes/R/ungather_draws.R | 2 tidybayes-1.0.4/tidybayes/R/util.R | 4 tidybayes-1.0.4/tidybayes/R/x_at_y.R | 7 tidybayes-1.0.4/tidybayes/build/vignette.rds |binary tidybayes-1.0.4/tidybayes/inst/doc/tidy-brms.R | 75 tidybayes-1.0.4/tidybayes/inst/doc/tidy-brms.Rmd | 87 tidybayes-1.0.4/tidybayes/inst/doc/tidy-brms.html | 985 +++++----- tidybayes-1.0.4/tidybayes/inst/doc/tidy-rstanarm.R | 33 tidybayes-1.0.4/tidybayes/inst/doc/tidy-rstanarm.Rmd | 36 tidybayes-1.0.4/tidybayes/inst/doc/tidy-rstanarm.html | 235 +- tidybayes-1.0.4/tidybayes/inst/doc/tidybayes-residuals.R |only tidybayes-1.0.4/tidybayes/inst/doc/tidybayes-residuals.Rmd |only tidybayes-1.0.4/tidybayes/inst/doc/tidybayes-residuals.html |only tidybayes-1.0.4/tidybayes/inst/doc/tidybayes.R | 38 tidybayes-1.0.4/tidybayes/inst/doc/tidybayes.Rmd | 42 tidybayes-1.0.4/tidybayes/inst/doc/tidybayes.html | 707 ++++--- tidybayes-1.0.4/tidybayes/man/add_draws.Rd |only tidybayes-1.0.4/tidybayes/man/add_predicted_draws.Rd | 54 tidybayes-1.0.4/tidybayes/man/figures/preview.gif |only tidybayes-1.0.4/tidybayes/man/gather_emmeans_draws.Rd | 20 tidybayes-1.0.4/tidybayes/man/geom_halfeyeh.Rd | 2 tidybayes-1.0.4/tidybayes/man/geom_lineribbon.Rd | 4 tidybayes-1.0.4/tidybayes/man/geom_pointinterval.Rd | 9 tidybayes-1.0.4/tidybayes/man/recover_types.Rd | 2 tidybayes-1.0.4/tidybayes/man/sample_draws.Rd |only tidybayes-1.0.4/tidybayes/man/stat_lineribbon.Rd | 4 tidybayes-1.0.4/tidybayes/man/stat_pointinterval.Rd | 9 tidybayes-1.0.4/tidybayes/tests/figs/deps.txt | 9 tidybayes-1.0.4/tidybayes/tests/figs/geom-eye/one-parameter-horizontal-eye-mode-hdi.svg | 96 tidybayes-1.0.4/tidybayes/tests/figs/geom-eye/one-parameter-horizontal-eye.svg | 96 tidybayes-1.0.4/tidybayes/tests/figs/geom-eye/one-parameter-horizontal-half-eye-mode-hdi.svg | 100 - 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tidybayes-1.0.4/tidybayes/tests/testthat/test.geom_pointinterval.R | 180 - tidybayes-1.0.4/tidybayes/tests/testthat/test.get_variables.R | 70 tidybayes-1.0.4/tidybayes/tests/testthat/test.point_interval.R | 4 tidybayes-1.0.4/tidybayes/tests/testthat/test.predicted_draws.R | 315 +-- tidybayes-1.0.4/tidybayes/tests/testthat/test.spread_draws.R | 635 +++--- tidybayes-1.0.4/tidybayes/tests/testthat/test.ungather_draws.R | 4 tidybayes-1.0.4/tidybayes/tests/testthat/test.unspread_draws.R | 4 tidybayes-1.0.4/tidybayes/vignettes/tidy-brms.Rmd | 87 tidybayes-1.0.4/tidybayes/vignettes/tidy-rstanarm.Rmd | 36 tidybayes-1.0.4/tidybayes/vignettes/tidybayes-residuals.Rmd |only tidybayes-1.0.4/tidybayes/vignettes/tidybayes.Rmd | 42 110 files changed, 7421 insertions(+), 6638 deletions(-)
Title: Functional Summary and Meta-Analysis of Gene Expression Data
Description: Rank-based tests for enrichment of KOG (euKaryotic Orthologous Groups) classes with up- or down-regulated genes based on a continuous measure. The meta-analysis is based on correlation of KOG delta-ranks across datasets (delta-rank is the difference between mean rank of genes belonging to a KOG class and mean rank of all other genes). With binary measure (1 or 0 to indicate significant and non-significant genes), one-tailed Fisher's exact test for over-representation of each KOG class among significant genes will be performed.
Author: Mikhail V. Matz
Maintainer: Mikhail V. Matz <matz@utexas.edu>
Diff between KOGMWU versions 1.1 dated 2016-11-17 and 1.2 dated 2019-02-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ data/adults.3dHeat.logFoldChange.rda |binary data/gene2kog.rda |binary data/larvae.longTerm.rda |binary data/larvae.shortTerm.rda |binary man/KOGMWU-package.Rd | 11 ++++++----- 7 files changed, 16 insertions(+), 15 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] (<https://orcid.org/0000-0002-7624-244X>),
Francois Guilhaumon [aut] (<https://orcid.org/0000-0003-4707-8932>)
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.1.0 dated 2019-01-28 and 1.1.1 dated 2019-02-19
sars-1.1.0/sars/R/mmSAR2.R |only sars-1.1.1/sars/DESCRIPTION | 17 - sars-1.1.1/sars/MD5 | 125 +++++----- sars-1.1.1/sars/NAMESPACE | 45 +++ sars-1.1.1/sars/NEWS.md | 6 sars-1.1.1/sars/R/class_plot.R | 80 +++--- sars-1.1.1/sars/R/class_print.R | 65 ++--- sars-1.1.1/sars/R/class_summary.R | 39 +-- sars-1.1.1/sars/R/coleman.R | 17 - sars-1.1.1/sars/R/coleman_plot.R | 14 - sars-1.1.1/sars/R/compmod.R | 46 +-- sars-1.1.1/sars/R/data_coleman.R | 2 sars-1.1.1/sars/R/gdm.R | 2 sars-1.1.1/sars/R/link_functions.R | 8 sars-1.1.1/sars/R/mod_linear_power.R | 35 +- sars-1.1.1/sars/R/obs_shape.R | 63 ++--- sars-1.1.1/sars/R/optim.R | 189 +++++++-------- sars-1.1.1/sars/R/sar_asymp.R | 1 sars-1.1.1/sars/R/sar_average.R | 229 ++++++++----------- sars-1.1.1/sars/R/sar_betap.R | 1 sars-1.1.1/sars/R/sar_chapman.R | 1 sars-1.1.1/sars/R/sar_conf_int.R | 6 sars-1.1.1/sars/R/sar_epm1.R | 1 sars-1.1.1/sars/R/sar_epm2.R | 1 sars-1.1.1/sars/R/sar_gompertz.R | 1 sars-1.1.1/sars/R/sar_heleg.R | 1 sars-1.1.1/sars/R/sar_koba.R | 1 sars-1.1.1/sars/R/sar_linear.R | 2 sars-1.1.1/sars/R/sar_loga.R | 1 sars-1.1.1/sars/R/sar_mmf.R | 1 sars-1.1.1/sars/R/sar_monod.R | 1 sars-1.1.1/sars/R/sar_negexpo.R | 1 sars-1.1.1/sars/R/sar_p1.R | 1 sars-1.1.1/sars/R/sar_p2.R | 1 sars-1.1.1/sars/R/sar_power.R | 1 sars-1.1.1/sars/R/sar_powerR.R | 1 sars-1.1.1/sars/R/sar_ratio.R | 1 sars-1.1.1/sars/R/sar_weibull3.R | 1 sars-1.1.1/sars/R/sar_weibull4.R | 1 sars-1.1.1/sars/R/sars.R |only sars-1.1.1/sars/R/style.R | 2 sars-1.1.1/sars/README.md | 178 ++++++-------- sars-1.1.1/sars/build |only sars-1.1.1/sars/inst/CITATION | 10 sars-1.1.1/sars/inst/REFERENCES.bib | 182 ++++++++++++++- sars-1.1.1/sars/inst/_pkgdown.yml |only sars-1.1.1/sars/inst/doc |only sars-1.1.1/sars/inst/model_factory.R | 33 ++ sars-1.1.1/sars/man/cole_sim.Rd | 2 sars-1.1.1/sars/man/lin_pow.Rd | 2 sars-1.1.1/sars/man/sar_average.Rd | 2 sars-1.1.1/sars/man/sars-package.Rd | 2 sars-1.1.1/sars/tests/testthat.R | 2 sars-1.1.1/sars/tests/testthat/test_coleman.R | 7 sars-1.1.1/sars/tests/testthat/test_fit_collection.R | 7 sars-1.1.1/sars/tests/testthat/test_gdm.R | 8 sars-1.1.1/sars/tests/testthat/test_lin_pow.R | 2 sars-1.1.1/sars/tests/testthat/test_loga.R | 2 sars-1.1.1/sars/tests/testthat/test_monod.R | 1 sars-1.1.1/sars/tests/testthat/test_multi.R | 18 - sars-1.1.1/sars/tests/testthat/test_p2.R | 3 sars-1.1.1/sars/tests/testthat/test_power.R | 6 sars-1.1.1/sars/tests/testthat/test_sar_linear.R | 8 sars-1.1.1/sars/tests/testthat/test_weibull3.R | 3 sars-1.1.1/sars/vignettes |only 65 files changed, 819 insertions(+), 670 deletions(-)
Title: Extra Themes, Scales and Geoms for 'ggplot2'
Description: Some extra themes, geoms, and scales for 'ggplot2'.
Provides 'ggplot2' themes and scales that replicate the look of plots
by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata',
'Excel', and 'The Wall Street Journal', among others.
Provides 'geoms' for Tufte's box plot and range frame.
Author: Jeffrey B. Arnold [aut, cre] (<https://orcid.org/0000-0001-9953-3904>),
Gergely Daroczi [ctb],
Bo Werth [ctb],
Brian Weitzner [ctb],
Joshua Kunst [ctb],
Baptise Auguie [ctb],
Bob Rudis [ctb],
Hadley Wickham [ctb] (Code from the ggplot2 package.),
Justin Talbot [ctb] (Code from the labeling package),
Joshua London [ctb]
Maintainer: Jeffrey B. Arnold <jeffrey.arnold@gmail.com>
Diff between ggthemes versions 4.0.1 dated 2018-08-24 and 4.1.0 dated 2019-02-19
DESCRIPTION | 13 +-- MD5 | 65 ++++++++------- NAMESPACE | 22 +++++ NEWS.md | 7 + R/excel.R | 3 R/fivethirtyeight.R | 1 R/geom-rangeframe.R | 10 +- R/geom-tufteboxplot.R | 9 +- R/ggthemes-package.R | 4 R/igray.R | 1 R/stat-fivenumber.R | 3 R/stata.R | 2 R/tableau.R | 43 ++++++++-- R/theme-foundation.R | 1 R/theme-map.R | 1 R/tufte.R | 1 R/wsj.R | 1 build/ggthemes.pdf |binary data/ggthemes_data.rda |binary inst/WORDLIST | 40 +++++---- inst/examples/ex-scale_colour_gradient2_tableau.R | 3 man/macros |only man/scale_color_tableau.Rd | 19 +++- man/scale_colour_gradient2_tableau.Rd | 7 + man/scale_colour_gradient_tableau.Rd | 7 + man/tableau_color_pal.Rd | 4 man/tableau_gradient_pal.Rd | 4 man/theme_excel.Rd | 3 tests/figs/deps.txt | 9 -- tests/figs/few/theme-few.svg | 90 +++++++++++----------- tests/spelling.R | 4 tests/testthat/test-excel.R | 3 tests/testthat/test-few.R | 1 tests/testthat/test-tableau.R | 24 +++++ 34 files changed, 261 insertions(+), 144 deletions(-)
Title: Computing Essential Biodiversity Variables from Global Forest
Change Data
Description: Metrics of two Essential Biodiversity Variables: forest extents and forest fragmentation indices (O'connor et al., 2015) <doi:10.1002/rse2.4> are computed by processing Global Forest Change data (Hansen et al., 2013) <doi:10.1126/science.1244693>. The Forest Change Data are extracted using either Geographic Administrative Units, see <https://gadm.org/>, or user-defined polygons. Most of the procedures can be understood implementing two functions: FCPolygon() and EBVmetric().
Author: Wilson Lara <wilarhen@temple.edu>, Victor Gutierrez-Velez <victorhugo@temple.edu>
Maintainer: Wilson Lara <wilarhen@temple.edu>
Diff between forestChange versions 0.3 dated 2018-12-22 and 0.4 dated 2019-02-19
DESCRIPTION | 12 ++++----- MD5 | 29 ++++++++++++----------- NAMESPACE | 9 ++++--- NEWS |only R/EBVmetric.R | 8 +++--- R/FCPolygon.R | 10 ++++---- R/GFCurls.R | 55 ++++++++++++++++++++++---------------------- R/HansenUrltoExtent.R | 11 ++++---- R/getGADM.R | 7 ++++- build/partial.rdb |binary man/EBVmetric.Rd | 12 ++++----- man/FCPolygon.Rd | 22 ++++++++--------- man/GFCurls.Rd | 27 ++++++++------------- man/HansenUrltoExtent.Rd | 11 ++++---- man/forestChange-package.Rd | 2 + man/getGADM.Rd | 7 ++++- 16 files changed, 115 insertions(+), 107 deletions(-)
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides:
'let()'
(converts non-standard evaluation interfaces to parametric standard
evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'),
'%.>%' dot-pipe (an 'S3' configurable pipe),
'build_frame()'/'draw_frame()' ('data.frame' example tools),
'qc()' (quoting concatenate),
':=' (named map builder),
and more.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.8.3 dated 2019-01-29 and 1.8.4 dated 2019-02-19
wrapr-1.8.3/wrapr/tests/testthat |only wrapr-1.8.3/wrapr/tests/testthat.R |only wrapr-1.8.4/wrapr/DESCRIPTION | 10 +- wrapr-1.8.4/wrapr/MD5 | 82 +++++++++++---------- wrapr-1.8.4/wrapr/NAMESPACE | 2 wrapr-1.8.4/wrapr/NEWS.md | 6 + wrapr-1.8.4/wrapr/R/clean_fit.R | 18 ++++ wrapr-1.8.4/wrapr/R/run_package_tests.R |only wrapr-1.8.4/wrapr/R/run_wrapr_tests.R |only wrapr-1.8.4/wrapr/inst/doc/CornerCases.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/DebugFnW.html | 30 ++++++- wrapr-1.8.4/wrapr/inst/doc/FrameTools.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/Function_Objects.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/Named_Arguments.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/QuotingConcatinate.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/SubstitutionModes.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/bquote.html | 30 ++++++- wrapr-1.8.4/wrapr/inst/doc/dot_pipe.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/lambda.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/let.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/named_map_builder.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/doc/wrapr_applicable.html | 28 ++++++- wrapr-1.8.4/wrapr/inst/unit_tests |only wrapr-1.8.4/wrapr/man/clean_fit_glm.Rd | 9 ++ wrapr-1.8.4/wrapr/man/clean_fit_lm.Rd | 6 + wrapr-1.8.4/wrapr/man/run_package_tests.Rd |only wrapr-1.8.4/wrapr/man/run_wrapr_tests.Rd |only wrapr-1.8.4/wrapr/tests/package_test_runner.R |only 28 files changed, 411 insertions(+), 90 deletions(-)
Title: Tukey Curve Depth and Distance in the Space of Curves
Description: Data recorded as paths or trajectories may be suitably described
by curves, which are independent of their parametrization. For the space of
such curves, the package provides functionalities for reading curves, sampling
points on curves, calculating distance between curves and for computing Tukey
curve depth of a curve w.r.t. to a bundle of curves. For details see
Lafaye De Micheaux, Mozharovskyi, and Vimond (2019) <arXiv:1901.00180>.
Author: Pavlo Mozharovskyi [aut, cre],
Pierre Lafaye De Micheaux [aut],
Myriam Vimond [aut]
Maintainer: Pavlo Mozharovskyi <pavlo.mozharovskyi@telecom-paristech.fr>
Diff between curveDepth versions 0.1.0.8 dated 2019-01-21 and 0.1.0.9 dated 2019-02-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/RcppExports.R | 9 ++++++--- man/dist.images.Rd | 9 ++++++--- src/depthsCurveHfsp.cpp | 15 ++++++++++++--- 5 files changed, 32 insertions(+), 17 deletions(-)
Title: Statistical Reporting in Clinical Trials
Description: It enables to create easily formatted statistical tables in 'Microsoft Word' documents in pretty formats according to 'clinical standards'. It can be used also outside the scope of clinical trials, for any statistical reporting in 'Word'. Descriptive tables for quantitative statistics (mean, median, max etc..) and/or qualitative statistics (frequencies and percentages) are available and formatted tables of Least Square Means of Linear Models, Linear Mixed Models and Generalized Linear Mixed Models coming from emmeans() function are also available. The package works with 'officer' and 'flextable' packages to export the outputs into 'Microsoft Word' documents.
Author: JF COLLIN
Maintainer: JF COLLIN <jfcollin@live.fr>
Diff between ClinReport versions 0.9.1.1 dated 2019-02-08 and 0.9.1.6 dated 2019-02-19
DESCRIPTION | 10 - MD5 | 63 ++++-- NAMESPACE | 8 NEWS.md |only R/data-data.R | 2 R/desc.R | 25 +- R/gg_desc_lsmeans.R |only R/gg_desc_quali.R |only R/gg_desc_quanti.R |only R/pkgname.R | 8 R/plot.desc.R |only R/prettyround.R | 5 R/regroup.desc.R | 5 R/report.doc.R | 463 ++++++++++++++++++++++++++++++++++++++++--------- R/report.lsmeans.R | 179 +++++++++++++----- R/report.quali.R | 36 ++- R/report.quanti.R | 134 ++++++++++---- R/spacetable.R | 4 R/split.desc.R |only data/data.RData |binary inst/clean.character.R |only inst/data.creation.R | 38 ++-- inst/dev_check_build.R |only inst/test.R | 283 ++++++++++++++++++++++++----- man/ClinReport.Rd | 10 - man/data.Rd | 2 man/desc.Rd | 23 +- man/gg_desc_lsmeans.Rd |only man/gg_desc_quali.Rd |only man/gg_desc_quanti.Rd |only man/plot.desc.Rd |only man/prettyround.Rd | 4 man/regroup.Rd | 5 man/report.doc.Rd | 286 +++++++++++++++++++++++++----- man/report.lsmeans.Rd | 77 +++++--- man/report.quali.Rd | 30 ++- man/report.quanti.Rd | 27 +- man/spacetable.Rd | 4 man/split.desc.Rd |only 39 files changed, 1330 insertions(+), 401 deletions(-)
Title: R's Shortest Path Problem with Forbidden Subpaths
Description: An implementation of functionalities to transform directed graphs that are bound to a set of
known forbidden paths. There are several transformations, following the rules provided by Villeneuve
and Desaulniers (2005) <doi: 10.1016/j.ejor.2004.01.032>, and Hsu et al. (2009) <doi: 10.1007/978-3-642-03095-6_60>.
The resulting graph is generated in a data-frame format. See rsppfp website for more information,
documentation an examples.
Author: Melina Vidoni [aut, cre] (<https://orcid.org/0000-0002-4099-1430>),
Aldo Vecchietti [aut]
Maintainer: Melina Vidoni <melinavidoni@santafe-conicet.gov.ar>
Diff between rsppfp versions 1.0.3 dated 2018-11-20 and 1.0.4 dated 2019-02-19
DESCRIPTION | 8 +- MD5 | 36 ++++++------- NAMESPACE | 1 NEWS.md | 9 +++ R/hsu.R | 4 - R/igraph.R | 38 ++++++++++---- R/privates.R | 9 ++- R/villeneuve.R | 4 - README.md | 11 +++- build/vignette.rds |binary inst/doc/benchmark.html | 24 ++++++++ inst/doc/igraph.R | 37 +++++++++---- inst/doc/igraph.Rmd | 39 ++++++++++---- inst/doc/igraph.html | 105 ++++++++++++++++++++++++++------------- inst/doc/rsppfp.html | 102 +++++++++++++++++++++++-------------- man/get_shortest_path.Rd | 2 tests/testthat/test-hsu.R | 41 ++++++++------- tests/testthat/test-villeneuve.R | 15 ++--- vignettes/igraph.Rmd | 39 ++++++++++---- 19 files changed, 345 insertions(+), 179 deletions(-)
Title: Rolling Entry Matching
Description: Functions to perform propensity score matching on rolling entry interventions for which a suitable "entry" date is not observed for nonparticipants. For more details, please reference Witman, Beadles, Liu, Larsen, Kafali, Gandhi, Amico, and Hoerger (2018) <https://onlinelibrary.wiley.com/doi/abs/10.1111/1475-6773.13086>.
Author: Rob Chew [aut, cre], Kasey Jones [aut, cre], Mahin Manley [aut], Allison Witman [res], Chris Beadles [res], Yiyan Liu [res], Ann Larson [res]
Maintainer: Rob Chew <rchew@rti.org>
Diff between rollmatch versions 1.0.1 dated 2018-05-30 and 2.0.1 dated 2019-02-19
rollmatch-1.0.1/rollmatch/R/print.rollmatch.R |only rollmatch-1.0.1/rollmatch/R/summary.rollmatch.R |only rollmatch-1.0.1/rollmatch/man/addBalanceTable.Rd |only rollmatch-1.0.1/rollmatch/man/addMatchesColumns.Rd |only rollmatch-1.0.1/rollmatch/man/chr_2_factor.Rd |only rollmatch-1.0.1/rollmatch/man/createComparison.Rd |only rollmatch-1.0.1/rollmatch/man/createMatches.Rd |only rollmatch-1.0.1/rollmatch/man/createWeights.Rd |only rollmatch-1.0.1/rollmatch/man/makeOutput.Rd |only rollmatch-1.0.1/rollmatch/man/runModel.Rd |only rollmatch-1.0.1/rollmatch/man/trimPool.Rd |only rollmatch-2.0.1/rollmatch/DESCRIPTION | 14 rollmatch-2.0.1/rollmatch/MD5 | 37 - rollmatch-2.0.1/rollmatch/NAMESPACE | 10 rollmatch-2.0.1/rollmatch/R/print_rollmatch.R |only rollmatch-2.0.1/rollmatch/R/reduce_data.R |only rollmatch-2.0.1/rollmatch/R/rollmatch.R | 279 +++------- rollmatch-2.0.1/rollmatch/R/run_checks.R |only rollmatch-2.0.1/rollmatch/R/score_data.R |only rollmatch-2.0.1/rollmatch/R/summarize_rollmatch.R |only rollmatch-2.0.1/rollmatch/R/utility_functions.R | 524 ++++++------------- rollmatch-2.0.1/rollmatch/man/add_balance_table.Rd |only rollmatch-2.0.1/rollmatch/man/add_matches_columns.Rd |only rollmatch-2.0.1/rollmatch/man/check_lookback.Rd |only rollmatch-2.0.1/rollmatch/man/compare_pool.Rd |only rollmatch-2.0.1/rollmatch/man/create_matches.Rd |only rollmatch-2.0.1/rollmatch/man/make_output.Rd |only rollmatch-2.0.1/rollmatch/man/reduce_data.Rd |only rollmatch-2.0.1/rollmatch/man/rollmatch.Rd | 118 ++-- rollmatch-2.0.1/rollmatch/man/run_checks_one.Rd |only rollmatch-2.0.1/rollmatch/man/run_checks_two.Rd |only rollmatch-2.0.1/rollmatch/man/score_data.Rd |only rollmatch-2.0.1/rollmatch/man/trim_pool.Rd |only 33 files changed, 384 insertions(+), 598 deletions(-)
Title: Robust Estimation for Compositional Data
Description: Methods for analysis of compositional data including robust
methods, imputation, methods to replace rounded zeros, (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors and (robust) Anderson-Darling normality tests for
compositional data as well as popular log-ratio transformations (addLR, cenLR,
isomLR, and their inverse transformations). In addition, visualisation and
diagnostic tools are implemented as well as high and low-level plot functions
for the ternary diagram.
Author: Matthias Templ [aut, cre],
Karel Hron [aut],
Peter Filzmoser [aut],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb],
Dominika Miksova [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.0.9 dated 2018-11-08 and 2.0.10 dated 2019-02-19
robCompositions-2.0.10/robCompositions/DESCRIPTION | 12 robCompositions-2.0.10/robCompositions/MD5 | 179 ++++------ robCompositions-2.0.10/robCompositions/NEWS | 10 robCompositions-2.0.10/robCompositions/R/aDist.R | 6 robCompositions-2.0.10/robCompositions/R/addLR.R | 8 robCompositions-2.0.10/robCompositions/R/addLRinv.R | 6 robCompositions-2.0.10/robCompositions/R/balZav.R | 11 robCompositions-2.0.10/robCompositions/R/balances.R | 6 robCompositions-2.0.10/robCompositions/R/biplot.factanal.R | 4 robCompositions-2.0.10/robCompositions/R/biplot.pcaCoDa.R | 4 robCompositions-2.0.10/robCompositions/R/ced.R | 12 robCompositions-2.0.10/robCompositions/R/cenLR.R | 12 robCompositions-2.0.10/robCompositions/R/cenLRinv.R | 6 robCompositions-2.0.10/robCompositions/R/clustCoDa.R | 8 robCompositions-2.0.10/robCompositions/R/clustCoDa_qmode.R | 8 robCompositions-2.0.10/robCompositions/R/compareMahal.R | 6 robCompositions-2.0.10/robCompositions/R/coord.R | 14 robCompositions-2.0.10/robCompositions/R/corCoDa.R | 10 robCompositions-2.0.10/robCompositions/R/daCoDa.R | 10 robCompositions-2.0.10/robCompositions/R/daFisher.R | 12 robCompositions-2.0.10/robCompositions/R/dataSets.R | 2 robCompositions-2.0.10/robCompositions/R/gmean.R | 2 robCompositions-2.0.10/robCompositions/R/ilr.2x2.R | 11 robCompositions-2.0.10/robCompositions/R/impAll.R | 10 robCompositions-2.0.10/robCompositions/R/impCoda.R | 4 robCompositions-2.0.10/robCompositions/R/impKNNa.R | 10 robCompositions-2.0.10/robCompositions/R/impRZalr.R | 11 robCompositions-2.0.10/robCompositions/R/impRZilr.R | 20 - robCompositions-2.0.10/robCompositions/R/imputeBDLs.R | 82 ++-- robCompositions-2.0.10/robCompositions/R/imputeUDLs.R | 10 robCompositions-2.0.10/robCompositions/R/ind2x2.R | 9 robCompositions-2.0.10/robCompositions/R/indTab.R | 9 robCompositions-2.0.10/robCompositions/R/int2x2.R | 7 robCompositions-2.0.10/robCompositions/R/intArray.R | 12 robCompositions-2.0.10/robCompositions/R/intTab.R | 13 robCompositions-2.0.10/robCompositions/R/isomLR.R | 34 - robCompositions-2.0.10/robCompositions/R/lmCoDaX.R | 6 robCompositions-2.0.10/robCompositions/R/outCoDa.R | 18 - robCompositions-2.0.10/robCompositions/R/pTab.R | 9 robCompositions-2.0.10/robCompositions/R/pcaCoDa.R | 10 robCompositions-2.0.10/robCompositions/R/rSDev.R | 9 robCompositions-2.0.10/robCompositions/R/rSDev.test.R | 9 robCompositions-2.0.10/robCompositions/R/rdcm.R | 7 robCompositions-2.0.10/robCompositions/R/stats.R | 9 robCompositions-2.0.10/robCompositions/R/ternaryDiag.R | 8 robCompositions-2.0.10/robCompositions/R/variation.R | 7 robCompositions-2.0.10/robCompositions/inst/doc/imputation.pdf |binary robCompositions-2.0.10/robCompositions/inst/doc/robCompositions-overview.pdf |binary robCompositions-2.0.10/robCompositions/man/aDist.Rd | 6 robCompositions-2.0.10/robCompositions/man/addLR.Rd | 8 robCompositions-2.0.10/robCompositions/man/addLRinv.Rd | 6 robCompositions-2.0.10/robCompositions/man/balances.Rd | 4 robCompositions-2.0.10/robCompositions/man/biplot.factanal.Rd | 4 robCompositions-2.0.10/robCompositions/man/biplot.pcaCoDa.Rd | 4 robCompositions-2.0.10/robCompositions/man/ced.Rd | 10 robCompositions-2.0.10/robCompositions/man/cenLR.Rd | 12 robCompositions-2.0.10/robCompositions/man/cenLRinv.Rd | 6 robCompositions-2.0.10/robCompositions/man/clustCoDa.Rd | 8 robCompositions-2.0.10/robCompositions/man/clustCoDa_qmode.Rd | 6 robCompositions-2.0.10/robCompositions/man/compareMahal.Rd | 6 robCompositions-2.0.10/robCompositions/man/coord.Rd | 14 robCompositions-2.0.10/robCompositions/man/corCoDa.Rd | 7 robCompositions-2.0.10/robCompositions/man/daCoDa.Rd | 10 robCompositions-2.0.10/robCompositions/man/daFisher.Rd | 12 robCompositions-2.0.10/robCompositions/man/gjovik.Rd | 66 --- robCompositions-2.0.10/robCompositions/man/gmean.Rd | 2 robCompositions-2.0.10/robCompositions/man/ilr.2x2.Rd | 11 robCompositions-2.0.10/robCompositions/man/impAll.Rd | 10 robCompositions-2.0.10/robCompositions/man/impCoda.Rd | 4 robCompositions-2.0.10/robCompositions/man/impKNNa.Rd | 10 robCompositions-2.0.10/robCompositions/man/impRZalr.Rd | 13 robCompositions-2.0.10/robCompositions/man/impRZilr.Rd | 21 - robCompositions-2.0.10/robCompositions/man/imputeBDLs.Rd | 14 robCompositions-2.0.10/robCompositions/man/imputeUDLs.Rd | 10 robCompositions-2.0.10/robCompositions/man/ind2x2.Rd | 7 robCompositions-2.0.10/robCompositions/man/indTab.Rd | 9 robCompositions-2.0.10/robCompositions/man/int2x2.Rd | 5 robCompositions-2.0.10/robCompositions/man/intArray.Rd | 12 robCompositions-2.0.10/robCompositions/man/intTab.Rd | 11 robCompositions-2.0.10/robCompositions/man/lmCoDaX.Rd | 6 robCompositions-2.0.10/robCompositions/man/outCoDa.Rd | 18 - robCompositions-2.0.10/robCompositions/man/pTab.Rd | 7 robCompositions-2.0.10/robCompositions/man/pcaCoDa.Rd | 10 robCompositions-2.0.10/robCompositions/man/pivotCoord.Rd | 34 - robCompositions-2.0.10/robCompositions/man/rSDev.Rd | 7 robCompositions-2.0.10/robCompositions/man/rSDev.test.Rd | 7 robCompositions-2.0.10/robCompositions/man/rdcm.Rd | 7 robCompositions-2.0.10/robCompositions/man/stats.Rd | 7 robCompositions-2.0.10/robCompositions/man/ternaryDiag.Rd | 8 robCompositions-2.0.10/robCompositions/man/variation.Rd | 2 robCompositions-2.0.9/robCompositions/man/balZav.Rd |only 91 files changed, 519 insertions(+), 604 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: Sample Size Calculation for RNA-Seq Experimental Design
Description: We propose a procedure for sample size calculation while
controlling false discovery rate for RNA-seq experimental design. Our
procedure depends on the Voom method proposed for RNA-seq data analysis
by Law et al. (2014) <DOI:10.1186/gb-2014-15-2-r29> and the sample size
calculation method proposed for microarray experiments by Liu and Hwang
(2007) <DOI:10.1093/bioinformatics/btl664>. We develop a set of functions
that calculates appropriate sample sizes for two-sample t-test for RNA-seq
experiments with fixed or varied set of parameters. The outputs also contain a
plot of power versus sample size, a table of power at different sample sizes,
and a table of critical test values at different sample sizes.
To install this package, please use
'source("http://bioconductor.org/biocLite.R"); biocLite("ssizeRNA")'.
Author: Ran Bi [aut, cre],
Peng Liu [aut],
Tim Triche [ctb]
Maintainer: Ran Bi <biranpier@gmail.com>
Diff between ssizeRNA versions 1.2.9 dated 2017-01-09 and 1.3.1 dated 2019-02-19
DESCRIPTION | 12 ++++++------ MD5 | 28 ++++++++++++++-------------- R/check.power.R | 2 +- R/sim.counts.R | 2 +- R/ssize.twoSampVaryDelta.R | 2 +- R/ssizeRNA_single.R | 2 +- R/ssizeRNA_vary.R | 2 +- inst/NEWS.txt | 6 ++++++ inst/doc/ssizeRNA.pdf |binary man/check.power.Rd | 2 +- man/hammer.eset.Rd | 2 +- man/sim.counts.Rd | 2 +- man/ssize.twoSampVaryDelta.Rd | 2 +- man/ssizeRNA_single.Rd | 2 +- man/ssizeRNA_vary.Rd | 2 +- 15 files changed, 37 insertions(+), 31 deletions(-)
Title: Sample Selection Models
Description: Two-step
and maximum likelihood estimation
of Heckman-type sample selection models:
standard sample selection models (Tobit-2),
endogenous switching regression models (Tobit-5),
sample selection models with binary dependent outcome variable,
interval regression with sample selection (only ML estimation),
and endogenous treatment effects models.
Author: Arne Henningsen [aut, cre],
Ott Toomet [aut],
Sebastian Petersen [ctb]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between sampleSelection versions 1.2-0 dated 2017-12-07 and 1.2-2 dated 2019-02-19
DESCRIPTION | 8 +-- MD5 | 20 ++++---- NAMESPACE | 1 NEWS | 6 ++ R/invMillsRatio.R | 78 ++++++++++++++++----------------- build/vignette.rds |binary inst/doc/intReg.pdf |binary inst/doc/selection.pdf |binary inst/doc/treatReg.pdf |binary tests/binarySelectionOutcome.Rout.save | 8 +-- tests/invMillsRatioTest.Rout.save | 42 ++++++++--------- 11 files changed, 85 insertions(+), 78 deletions(-)
More information about sampleSelection at CRAN
Permanent link
Title: Interface to the "Geonames" Spatial Query Web Service
Description: The web service at <https://www.geonames.org/> provides a number of spatial data queries, including
administrative area hierarchies, city locations and some country postal code queries. A (free) username
is required and rate limits exist.
Author: Barry Rowlingson
Maintainer: Barry Rowlingson <b.rowlingson@gmail.com>
Diff between geonames versions 0.998 dated 2014-12-19 and 0.999 dated 2019-02-19
DESCRIPTION | 16 +++++---- MD5 | 66 +++++++++++++++++++-------------------- NAMESPACE | 2 - R/general.R | 4 +- R/geonames.R | 12 +++---- R/search.R | 6 +++ README.md | 2 - man/GNcities.Rd | 4 +- man/GNcountryCode.Rd | 4 +- man/GNcountryInfo.Rd | 4 +- man/GNcountrySubdivision.Rd | 7 ++-- man/GNearthquakes.Rd | 4 +- man/GNfindNearByWeather.Rd | 4 +- man/GNfindNearby.Rd | 4 +- man/GNfindNearbyPlaceName.Rd | 4 +- man/GNfindNearbyPostalCodes.Rd | 4 +- man/GNfindNearbyStreets.Rd | 4 +- man/GNfindNearbyWikipedia.Rd | 4 +- man/GNfindNearestAddress.Rd | 4 +- man/GNfindNearestIntersection.Rd | 4 +- man/GNgtopo30.Rd | 4 +- man/GNneighbourhood.Rd | 4 +- man/GNpostalCodeCountryInfo.Rd | 4 +- man/GNpostalCodeLookup.Rd | 4 +- man/GNpostalCodeSearch.Rd | 4 +- man/GNsearch.Rd | 11 +++++- man/GNsrtm3.Rd | 4 +- man/GNtimezone.Rd | 4 +- man/GNweather.Rd | 4 +- man/GNweatherIcao.Rd | 4 +- man/GNwikipediaBoundingBox.Rd | 4 +- man/GNwikipediaSearch.Rd | 4 +- man/geonames.Rd | 4 +- man/hierarchy.Rd | 8 ++-- 34 files changed, 124 insertions(+), 106 deletions(-)
Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP,
setup a secure tunnel, or run a command or script on the host while
streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between ssh versions 0.3 dated 2018-10-07 and 0.4 dated 2019-02-19
DESCRIPTION | 12 +++---- MD5 | 41 +++++++++++++------------ NAMESPACE | 4 ++ NEWS | 8 ++++ R/connect.R | 27 +++++++++------- R/init.R |only R/scp.R | 7 ++-- R/writer.R |only build/vignette.rds |binary configure | 6 +-- inst/WORDLIST | 10 +----- inst/doc/intro.Rmd | 19 ++++------- inst/doc/intro.html | 84 +++++++++++++++++++++++++++++++++++++++++++++------- man/scp.Rd | 1 man/ssh.Rd | 4 +- man/ssh_exec.Rd | 3 + man/ssh_tunnel.Rd | 4 +- src/Makevars.win | 15 +++++---- src/scp.c | 18 +++++++---- src/session.c | 58 ++++++++++++++++++++++++++--------- src/writer.c |only tools/winlibs.R | 11 ++++-- vignettes/intro.Rmd | 19 ++++------- 23 files changed, 234 insertions(+), 117 deletions(-)
Title: Business Process Analysis in R
Description: Comprehensive Business Process Analysis toolkit. Creates S3-class for event log objects, and related handler functions. Imports related packages for filtering event data, computation of descriptive statistics, handling of 'Petri Net' objects and visualization of process maps. See also packages 'edeaR','processmapR', 'eventdataR' and 'processmonitR'.
Author: Gert Janssenswillen [aut, cre]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between bupaR versions 0.4.1 dated 2018-07-01 and 0.4.2 dated 2019-02-19
DESCRIPTION | 8 ++-- MD5 | 32 +++++++++-------- NAMESPACE | 4 ++ R/act_collapse.R | 91 ++++++++++++++++++++++++++++++++++++++++++++++--- R/eventlog.R | 84 +++++++++++++++++++++++++-------------------- R/group_by.eventlog.R | 15 +++----- R/n_cases.R | 4 -- R/print.eventlog.R | 35 ++++++++++++++---- R/re_map.R | 5 +- R/sample_n.eventlog.R | 4 +- R/summarize.eventlog.R |only R/summary.eventlog.R | 2 - R/utils.R | 8 ++++ man/act_collapse.Rd | 10 ++++- man/eventlog.Rd | 8 +++- man/re_map.Rd | 2 - man/sample_n.Rd | 5 +- man/summarize.Rd |only 18 files changed, 225 insertions(+), 92 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-09-11 1.0-16.1
2016-07-25 1.0-16
2016-05-17 1.0-15
2015-01-16 1.0-11
2013-09-14 1.0-10
2013-06-17 1.0-9
2013-05-28 1.0-8
2013-05-22 1.0-7
2013-01-23 1.0-4
2013-01-11 1.0-3
2012-05-31 1.0-2
2010-09-01 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-15 0.8.2
2018-10-04 0.8.1
2018-07-20 0.8.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-16 0.1.4
2016-10-22 0.1.3
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
<http://pj.freefaculty.org/guides>. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette 'rockchalk' offers a
fairly comprehensive overview. The vignette 'Rstyle' has advice
about coding in R. The package title 'rockchalk' refers to our
school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre],
Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.129 dated 2018-11-09 and 1.8.140 dated 2019-02-19
rockchalk-1.8.129/rockchalk/man/outreg0.Rd |only rockchalk-1.8.140/rockchalk/DESCRIPTION | 11 rockchalk-1.8.140/rockchalk/MD5 | 102 - rockchalk-1.8.140/rockchalk/NAMESPACE | 9 rockchalk-1.8.140/rockchalk/R/drawnorm.R |only rockchalk-1.8.140/rockchalk/R/mcDiagnose.R | 10 rockchalk-1.8.140/rockchalk/R/outreg.R | 896 ++-------- rockchalk-1.8.140/rockchalk/R/plotCurves.R | 26 rockchalk-1.8.140/rockchalk/R/plotSlopes.R | 776 ++++++-- rockchalk-1.8.140/rockchalk/R/plyr.replace.R | 2 rockchalk-1.8.140/rockchalk/R/predictOMatic.R | 23 rockchalk-1.8.140/rockchalk/R/utils.R | 13 rockchalk-1.8.140/rockchalk/build/vignette.rds |binary rockchalk-1.8.140/rockchalk/data/cheating.RData |binary rockchalk-1.8.140/rockchalk/data/religioncrime.RData |binary rockchalk-1.8.140/rockchalk/inst/ChangeLog | 8 rockchalk-1.8.140/rockchalk/inst/NEWS | 10 rockchalk-1.8.140/rockchalk/inst/doc/Rchaeology.pdf |binary rockchalk-1.8.140/rockchalk/inst/doc/Rstyle.pdf |binary rockchalk-1.8.140/rockchalk/inst/doc/outreg.R |only rockchalk-1.8.140/rockchalk/inst/doc/outreg.Rnw |only rockchalk-1.8.140/rockchalk/inst/doc/outreg.pdf |only rockchalk-1.8.140/rockchalk/inst/doc/rockchalk.R | 126 - rockchalk-1.8.140/rockchalk/inst/doc/rockchalk.Rnw | 112 - rockchalk-1.8.140/rockchalk/inst/doc/rockchalk.pdf |binary rockchalk-1.8.140/rockchalk/inst/examples/centeredRegression.R | 6 rockchalk-1.8.140/rockchalk/inst/examples/mcDiagnose-ex.R | 3 rockchalk-1.8.140/rockchalk/inst/examples/plotSlopes-ex.R | 62 rockchalk-1.8.140/rockchalk/inst/examples/testSlopes-ex.R | 2 rockchalk-1.8.140/rockchalk/man/descriptiveTable.Rd | 4 rockchalk-1.8.140/rockchalk/man/drawnorm.Rd |only rockchalk-1.8.140/rockchalk/man/genCorrelatedData.Rd | 4 rockchalk-1.8.140/rockchalk/man/genCorrelatedData2.Rd | 4 rockchalk-1.8.140/rockchalk/man/genCorrelatedData3.Rd | 7 rockchalk-1.8.140/rockchalk/man/genX.Rd | 4 rockchalk-1.8.140/rockchalk/man/mcDiagnose.Rd | 3 rockchalk-1.8.140/rockchalk/man/mcGraph.Rd | 20 rockchalk-1.8.140/rockchalk/man/newdata.Rd | 2 rockchalk-1.8.140/rockchalk/man/outreg.Rd | 20 rockchalk-1.8.140/rockchalk/man/pctable.Rd | 10 rockchalk-1.8.140/rockchalk/man/plot.testSlopes.Rd | 3 rockchalk-1.8.140/rockchalk/man/plotCurves.Rd | 12 rockchalk-1.8.140/rockchalk/man/plotFancy.Rd | 25 rockchalk-1.8.140/rockchalk/man/plotFancyCategories.Rd |only rockchalk-1.8.140/rockchalk/man/plotPlane.Rd | 23 rockchalk-1.8.140/rockchalk/man/plotSlopes.Rd | 231 +- rockchalk-1.8.140/rockchalk/man/predictOMatic.Rd | 4 rockchalk-1.8.140/rockchalk/man/se.bars.Rd |only rockchalk-1.8.140/rockchalk/man/summarize.Rd | 4 rockchalk-1.8.140/rockchalk/man/summary.factor.Rd | 2 rockchalk-1.8.140/rockchalk/man/testSlopes.Rd | 2 rockchalk-1.8.140/rockchalk/man/waldt.Rd | 3 rockchalk-1.8.140/rockchalk/vignettes/outreg.Rnw |only rockchalk-1.8.140/rockchalk/vignettes/outreg.lyx |only rockchalk-1.8.140/rockchalk/vignettes/rockchalk.Rnw | 112 - rockchalk-1.8.140/rockchalk/vignettes/rockchalk.lyx | 264 ++ rockchalk-1.8.140/rockchalk/vignettes/theme |only 57 files changed, 1666 insertions(+), 1294 deletions(-)
Title: Random Perturbation of Count Matrices
Description: The perturbR() function incrementally perturbs network edges (using the rewireR function)and compares the resulting community detection solutions
from the rewired networks with the solution found for the original network.
These comparisons aid in understanding the stability of the
original solution. The package requires symmetric, weighted (specifically, count) matrices/networks.
Author: KM Gates [aut, cre],
Zachary Fisher [aut],
Cara Arizmendi [aut]
Maintainer: KM Gates <gateskm@email.unc.edu>
Diff between perturbR versions 0.1.2 dated 2018-07-27 and 0.1.3 dated 2019-02-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/perturbR.R | 10 +++++----- build/vignette.rds |binary inst/doc/perturbR-vignette.html | 28 +++++++++++++++++++++++++--- 5 files changed, 38 insertions(+), 16 deletions(-)
Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (www.mc-stan.org).
Author: Robert Kubinec [aut, cre],
Jonah Gabry [ctb],
Ben Goodrich [ctb],
Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>
Diff between idealstan versions 0.5.1 dated 2018-12-06 and 0.7.0 dated 2019-02-19
idealstan-0.5.1/idealstan/inst/doc/Time_Series.html |only idealstan-0.5.1/idealstan/inst/doc/Time_Series.html.asis |only idealstan-0.5.1/idealstan/src/stan_files/chunks/l_nonhier_prior.stan |only idealstan-0.5.1/idealstan/vignettes/Time_Series.html.asis |only idealstan-0.7.0/idealstan/DESCRIPTION | 12 idealstan-0.7.0/idealstan/MD5 | 58 - idealstan-0.7.0/idealstan/NAMESPACE | 2 idealstan-0.7.0/idealstan/NEWS.md | 9 idealstan-0.7.0/idealstan/R/Estimate.R | 148 +++ idealstan-0.7.0/idealstan/R/Generics.R | 31 idealstan-0.7.0/idealstan/R/Helpers.R | 385 +++------- idealstan-0.7.0/idealstan/R/Plot.R | 170 +++- idealstan-0.7.0/idealstan/R/Simulate.R | 39 - idealstan-0.7.0/idealstan/R/data_info.R | 14 idealstan-0.7.0/idealstan/R/idealstan-internal.R | 1 idealstan-0.7.0/idealstan/R/stanmodels.R | 2 idealstan-0.7.0/idealstan/build/vignette.rds |binary idealstan-0.7.0/idealstan/data/delaware.rda |only idealstan-0.7.0/idealstan/inst/include/meta_header.hpp | 2 idealstan-0.7.0/idealstan/man/delaware.Rd |only idealstan-0.7.0/idealstan/man/id_estimate.Rd | 105 -- idealstan-0.7.0/idealstan/man/id_plot_cov.Rd | 6 idealstan-0.7.0/idealstan/man/id_plot_legis.Rd | 9 idealstan-0.7.0/idealstan/man/id_plot_legis_dyn.Rd | 4 idealstan-0.7.0/idealstan/man/id_plot_legis_var.Rd | 2 idealstan-0.7.0/idealstan/man/id_sim_gen.Rd | 5 idealstan-0.7.0/idealstan/src/stan_files/chunks/build_params_v2.stan | 8 idealstan-0.7.0/idealstan/src/stan_files/chunks/calc_rlnorm_gp.stan |only idealstan-0.7.0/idealstan/src/stan_files/chunks/create_constrained.stan | 2 idealstan-0.7.0/idealstan/src/stan_files/chunks/l_gp_prior.stan |only idealstan-0.7.0/idealstan/src/stan_files/irt_standard.stan | 125 ++- idealstan-0.7.0/idealstan/src/stan_files/irt_standard_noid.stan | 92 ++ idealstan-0.7.0/idealstan/src/stan_files/sim_gp.stan |only idealstan-0.7.0/idealstan/vignettes/Time_Series.Rmd | 252 ++++-- idealstan-0.7.0/idealstan/vignettes/Time_Series.html |only 35 files changed, 934 insertions(+), 549 deletions(-)
Title: Relationship Inference for DNA Mixtures
Description: Makes relationship inference involving DNA mixtures with unknown profiles.
Author: Guro Dorum, Elias Hernandis, Navreet Kaur, Thore Egeland
Maintainer: Guro Dorum <guro.dorum@gmail.com>
Diff between relMix versions 1.2.3 dated 2017-04-03 and 1.3 dated 2019-02-19
relMix-1.2.3/relMix/R/allGenosRel.R |only relMix-1.2.3/relMix/man/allGenosRel.Rd |only relMix-1.3/relMix/DESCRIPTION | 16 relMix-1.3/relMix/MD5 | 117 relMix-1.3/relMix/NAMESPACE | 24 relMix-1.3/relMix/NEWS.md |only relMix-1.3/relMix/R/allGenos.R | 27 relMix-1.3/relMix/R/checkFrequenciesFile.R |only relMix-1.3/relMix/R/checkMixtureFile.R |only relMix-1.3/relMix/R/checkPedigreeFile.R |only relMix-1.3/relMix/R/checkReferenceFile.R |only relMix-1.3/relMix/R/createDatamatrix.R | 50 relMix-1.3/relMix/R/db.R |only relMix-1.3/relMix/R/db2.R |only relMix-1.3/relMix/R/generateMix.R | 43 relMix-1.3/relMix/R/globals.R | 14 relMix-1.3/relMix/R/mixLikDrop.R | 132 relMix-1.3/relMix/R/relMix.R | 134 relMix-1.3/relMix/R/relMixGUI.R | 1763 +++++----- relMix-1.3/relMix/R/util.R |only relMix-1.3/relMix/README.md |only relMix-1.3/relMix/build/vignette.rds |binary relMix-1.3/relMix/inst/doc/relMixVignette.R | 174 relMix-1.3/relMix/inst/doc/relMixVignette.Rmd | 30 relMix-1.3/relMix/inst/doc/relMixVignette.html | 1154 +++--- relMix-1.3/relMix/inst/extdata/custom_pedigree_maternity_duo.R | 3 relMix-1.3/relMix/inst/extdata/custom_pedigree_unrelated_duo.R | 3 relMix-1.3/relMix/inst/extdata/mixture_ex1_vignette.txt |only relMix-1.3/relMix/inst/extdata/references_ex1_vignette.txt |only relMix-1.3/relMix/inst/extdata/testdata |only relMix-1.3/relMix/man/allGenos.Rd | 46 relMix-1.3/relMix/man/checkFrequenciesFile.Rd |only relMix-1.3/relMix/man/checkMixtureFile.Rd |only relMix-1.3/relMix/man/checkPedigreeFile.Rd |only relMix-1.3/relMix/man/checkReferenceFile.Rd |only relMix-1.3/relMix/man/createDatamatrix.Rd | 84 relMix-1.3/relMix/man/db.Rd | 33 relMix-1.3/relMix/man/db2.Rd | 58 relMix-1.3/relMix/man/generateMix.Rd | 94 relMix-1.3/relMix/man/mixLikDrop.Rd | 113 relMix-1.3/relMix/man/relMix.Rd | 134 relMix-1.3/relMix/man/relMixGUI.Rd | 27 relMix-1.3/relMix/vignettes/contributors_ex1.png |binary relMix-1.3/relMix/vignettes/contributors_ex2.png |binary relMix-1.3/relMix/vignettes/database_crop.png |binary relMix-1.3/relMix/vignettes/database_options.png |binary relMix-1.3/relMix/vignettes/database_options_ex2.png |binary relMix-1.3/relMix/vignettes/dropout_ex1.png |binary relMix-1.3/relMix/vignettes/dropout_ex2.png |binary relMix-1.3/relMix/vignettes/mutations_ex2.png |binary relMix-1.3/relMix/vignettes/pedigrees_ex1.png |binary relMix-1.3/relMix/vignettes/relMixVignette.Rmd | 30 relMix-1.3/relMix/vignettes/relMix_screenshot.png |binary relMix-1.3/relMix/vignettes/results_ex1.png |binary relMix-1.3/relMix/vignettes/results_ex2.png |binary relMix-1.3/relMix/vignettes/scaling_ex2.png |binary 56 files changed, 2282 insertions(+), 2021 deletions(-)
Title: Import and Export 'SPSS', 'Stata' and 'SAS' Files
Description: Import foreign statistical formats into R via the
embedded 'ReadStat' C library,
<https://github.com/WizardMac/ReadStat>.
Author: Hadley Wickham [aut, cre],
Evan Miller [aut, cph] (Author of included ReadStat code),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between haven versions 2.0.0 dated 2018-11-21 and 2.1.0 dated 2019-02-19
DESCRIPTION | 35 ++-- MD5 | 129 ++++++++------ NAMESPACE | 3 NEWS.md | 34 +++ R/as_factor.R | 22 +- R/haven.R | 26 ++- R/labelled.R | 220 ++++++++++++++++++++++++- R/update.R | 4 R/zap_label.R | 2 R/zap_labels.R | 2 R/zap_missing.R | 2 R/zzz.R | 33 +++ README.md | 69 ++++---- build/vignette.rds |binary inst/doc/semantics.html | 88 ++++++---- man/as_factor.Rd | 10 + man/figures/logo.png |binary man/labelled.Rd | 4 man/labelled_spss.Rd | 4 man/print_labels.Rd | 2 man/read_sas.Rd | 6 man/zap_label.Rd | 2 man/zap_labels.Rd | 2 man/zap_missing.Rd | 2 src/readstat/readstat.h | 41 ++++ src/readstat/readstat_convert.c | 8 src/readstat/readstat_malloc.c | 5 src/readstat/readstat_value.c | 2 src/readstat/readstat_variable.c | 32 ++- src/readstat/readstat_writer.c | 15 + src/readstat/readstat_writer.h | 1 src/readstat/sas/readstat_sas.c | 28 +++ src/readstat/sas/readstat_sas.h | 2 src/readstat/sas/readstat_sas7bcat_read.c | 121 +++++++++----- src/readstat/sas/readstat_sas7bdat_read.c | 172 +++++++++++-------- src/readstat/sas/readstat_sas7bdat_write.c | 7 src/readstat/sas/readstat_xport_read.c | 12 - src/readstat/sas/readstat_xport_write.c | 6 src/readstat/spss/readstat_por_parse.c | 2 src/readstat/spss/readstat_por_parse.rl | 2 src/readstat/spss/readstat_por_read.c | 81 ++++----- src/readstat/spss/readstat_por_write.c | 118 ++++++++++--- src/readstat/spss/readstat_sav.c | 7 src/readstat/spss/readstat_sav_read.c | 250 ++++++++++++++++------------- src/readstat/spss/readstat_sav_write.c | 231 +++++++++++++++++++++----- src/readstat/spss/readstat_spss.c | 47 ++++- src/readstat/spss/readstat_spss.h | 5 src/readstat/stata/readstat_dta_read.c | 11 - src/readstat/txt |only tests/testthat/pillar_double.txt |only tests/testthat/pillar_integer.txt |only tests/testthat/pillar_spss_integer.txt |only tests/testthat/pillar_string.txt |only tests/testthat/pillar_tagged_na.txt |only tests/testthat/test-as-factor.R | 9 + tests/testthat/test-labelled.R | 9 + tests/testthat/test-labelled_spss.R | 5 tests/testthat/test-pillar.R |only tests/testthat/test-read-sav.R | 4 tests/testthat/test-write-dta.R | 8 tests/testthat/test-zap_label.R | 2 tests/testthat/test-zap_labels.R | 2 tests/testthat/test-zap_missing.R | 2 63 files changed, 1393 insertions(+), 555 deletions(-)
Title: Diversity Dynamics using Fossil Sampling Data
Description: Functions to describe sampling and diversity dynamics of fossil occurrence datasets (e.g. from the Paleobiology Database). The package includes methods to calculate range- and occurrence-based metrics of taxonomic richness, extinction and origination rates, along with traditional sampling measures. A powerful subsampling tool is also included that implements frequently used sampling standardization methods in a multiple bin-framework. The plotting of time series and the occurrence data can be simplified by the functions incorporated in the package, as well other calculations, such as environmental affinities and extinction selectivity testing. Details can be found in: Kocsis, A.T.; Reddin, C.J.; Alroy, J. and Kiessling, W. (2019) <doi:10.1101/423780>.
Author: Adam T. Kocsis, John Alroy, Carl J. Reddin, Wolfgang Kiessling
Maintainer: Adam T. Kocsis <adam.t.kocsis@gmail.com>
Diff between divDyn versions 0.7.0 dated 2019-01-08 and 0.7.1 dated 2019-02-19
DESCRIPTION | 15 +- MD5 | 83 ++++++------- R/RcppExports.R | 54 ++++---- R/affinity.R | 302 +++++++++++++++++++++++++------------------------- R/diversityDynamics.r | 13 -- R/plotting.R | 49 +++++++- R/zzz.R |only build/vignette.rds |binary inst/CITATION | 10 - inst/NEWS | 17 ++ inst/doc/handout.R | 72 +++++------ inst/doc/handout.Rmd | 95 +++++++-------- inst/doc/handout.pdf |binary man/affinity.Rd | 116 +++++++++---------- man/bins.Rd | 62 +++++----- man/binstat.Rd | 160 +++++++++++++------------- man/categorize.Rd | 108 ++++++++--------- man/cleansp.Rd | 74 ++++++------ man/collapse.Rd | 108 ++++++++--------- man/corals.Rd | 120 +++++++++---------- man/divDyn.Rd | 284 +++++++++++++++++++++++------------------------ man/fadlad.Rd | 106 ++++++++--------- man/fill.Rd | 66 +++++----- man/georange.Rd | 64 +++++----- man/indices.Rd | 120 +++++++++---------- man/keys.Rd | 60 ++++----- man/modeltab.Rd | 71 +++++------ man/omit.Rd | 110 +++++++++--------- man/parts.Rd | 192 +++++++++++++++---------------- man/ranges.Rd | 230 +++++++++++++++++++------------------- man/ratesplit.Rd | 166 +++++++++++++-------------- man/shades.Rd | 82 ++++++------- man/singletons.Rd | 110 +++++++++--------- man/stages.Rd | 80 ++++++------- man/stratkeys.Rd | 66 +++++----- man/streaklog.Rd | 78 ++++++------ man/subsample.Rd | 259 +++++++++++++++++++++--------------------- man/subtrial.Rd | 198 ++++++++++++++++---------------- man/sumstat.Rd | 88 +++++++------- man/survivors.Rd | 92 +++++++-------- man/tabinate.Rd | 84 ++++++------- man/tsplot.Rd | 151 +++++++++++++------------ vignettes/handout.Rmd | 95 +++++++-------- 43 files changed, 2199 insertions(+), 2111 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2018) <doi:10.1101/309302> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>
Diff between CB2 versions 1.0 dated 2019-02-11 and 1.1 dated 2019-02-19
DESCRIPTION | 14 +++---- MD5 | 49 +++++++++++++-------------- NAMESPACE | 3 + R/RcppExports.R | 12 +++--- R/helpers.R | 46 ++++++++++++------------- R/utils.R | 54 ++++++++++++++++++++++------- README.md | 14 +++++-- build/vignette.rds |binary inst/doc/cb2-tutorial.R | 5 ++ inst/doc/cb2-tutorial.Rmd | 56 ++++++++++++++++++------------- inst/doc/cb2-tutorial.html | 74 ++++++++++++++++++++--------------------- man/calc_mappability.Rd | 6 +-- man/fit_ab.Rd | 12 ++++-- man/get_CPM.Rd | 2 - man/join_count_and_design.Rd | 2 - man/measure_gene_stats.Rd | 4 +- man/plot_PCA.Rd | 8 ++-- man/plot_corr_heatmap.Rd |only man/plot_count_distribution.Rd | 2 - man/plot_dotplot.Rd | 8 ++-- man/quant.Rd | 8 ++-- man/run_estimation.Rd | 10 ++--- man/run_sgrna_quant.Rd | 12 +++--- src/CB2.cpp | 12 +++--- tests/testthat/test.toydata.R | 6 +-- vignettes/cb2-tutorial.Rmd | 56 ++++++++++++++++++------------- 26 files changed, 274 insertions(+), 201 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-27 0.1.1
2016-08-14 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-27 0.0.2
2018-05-31 0.0.1
Title: Tools for Working with ...
Description: In S3 generics, it's useful to take ... so that methods can
have additional argument. But this flexibility comes at a cost: misspelled
arguments will be silently ignored. The ellipsis packages is an experiment
that allows a generic to warn if any arguments passed in ... are not
used.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ellipsis versions 0.0.2 dated 2019-01-09 and 0.1.0 dated 2019-02-19
DESCRIPTION | 6 +++--- MD5 | 24 +++++++++++++----------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/check.R | 35 +++++++++++++++++++++++++++++++++-- R/dots.R | 8 ++++++-- README.md | 2 +- man/check_dots_unnamed.Rd |only man/check_dots_used.Rd | 2 +- src/dots.c | 18 ++++++++++++++---- src/init.c | 6 ++++-- tests/testthat/test-check.R |only tests/testthat/test-dots.R | 6 +++++- tests/testthat/test-safe.R | 1 + 14 files changed, 89 insertions(+), 27 deletions(-)
Title: Analysis of Factorial Experiments
Description: Convenience functions for analyzing factorial experiments using ANOVA or
mixed models. aov_ez(), aov_car(), and aov_4() allow specification of
between, within (i.e., repeated-measures), or mixed (i.e., split-plot)
ANOVAs for data in long format (i.e., one observation per row),
automatically aggregating multiple observations per individual and cell
of the design. mixed() fits mixed models using lme4::lmer() and computes
p-values for all fixed effects using either Kenward-Roger or Satterthwaite
approximation for degrees of freedom (LMM only), parametric bootstrap
(LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs).
afex_plot() provides a high-level interface for interaction or one-way
plots using ggplot2, combining raw data and model estimates. afex uses
type 3 sums of squares as default (imitating commercial statistical software).
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Ben Bolker [aut],
Jake Westfall [aut],
Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),
Søren Højsgaard [ctb],
John Fox [ctb],
Michael A. Lawrence [ctb],
Ulf Mertens [ctb],
Jonathon Love [ctb],
Russell Lenth [ctb],
Rune Haubo Bojesen Christensen [ctb]
Maintainer: Henrik Singmann <singmann+afex@gmail.com>
Diff between afex versions 0.22-1 dated 2018-09-24 and 0.23-0 dated 2019-02-19
DESCRIPTION | 10 MD5 | 53 ++-- NAMESPACE | 1 NEWS | 26 ++ R/afex_plot.R | 220 +++++++++++++++-- R/afex_plot_utils.R | 14 - R/allFit.R | 2 R/mixed.R | 3 R/nice.R | 16 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/afex_anova_example.html | 298 ++++++++++++------------ inst/doc/afex_mixed_example.html | 150 ++++++------ inst/doc/afex_plot_introduction.R | 24 + inst/doc/afex_plot_introduction.Rmd | 30 +- inst/doc/afex_plot_introduction.html | 100 +++++--- inst/doc/afex_plot_supported_models.R |only inst/doc/afex_plot_supported_models.Rmd |only inst/doc/afex_plot_supported_models.html |only inst/extdata/plots_brms.rda |only inst/extdata/plots_rstanarm.rda |only inst/extdata/tmb_example_fit.rda |only man/afex_plot.Rd | 149 ++++++++++-- man/all_fit.Rd | 2 man/nice.Rd | 16 - tests/testthat/test-afex_plot-basics.R | 46 +++ tests/testthat/test-afex_plot-default-support.R |only tests/testthat/test-afex_plot-vignette.R |only tests/testthat/test-mixed-bugs.R | 26 ++ tests/testthat/test-mixed-structure.R | 8 vignettes/afex_plot_introduction.Rmd | 30 +- vignettes/afex_plot_supported_models.Rmd |only 32 files changed, 840 insertions(+), 384 deletions(-)