Title: Time Zone Database Information
Description: Provides an up-to-date copy of the Internet Assigned Numbers
Authority (IANA) Time Zone Database. It is updated periodically to
reflect changes made by political bodies to time zone boundaries, UTC
offsets, and daylight saving time rules. Additionally, this package
provides a C++ interface for working with the 'date' library. 'date'
provides comprehensive support for working with dates and date-times,
which this package exposes to make it easier for other R packages to
utilize. Headers are provided for calendar specific calculations,
along with a limited interface for time zone manipulations.
Author: Davis Vaughan [aut, cre],
Howard Hinnant [cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between tzdb versions 0.3.0 dated 2022-03-28 and 0.4.0 dated 2023-05-12
DESCRIPTION | 19 - LICENSE | 2 MD5 | 84 ++-- NEWS.md | 10 README.md | 18 - inst/include/date/date.h | 6 inst/include/date/iso_week.h | 18 - inst/include/date/ptz.h | 84 ++++ inst/include/date/tz.h | 2 inst/tzdata/CONTRIBUTING | 2 inst/tzdata/Makefile | 297 +++++++++++------ inst/tzdata/NEWS | 515 +++++++++++++++++++++++++++++- inst/tzdata/africa | 320 +++++------------- inst/tzdata/antarctica | 34 - inst/tzdata/asia | 613 ++++++++++++++++++++++-------------- inst/tzdata/australasia | 185 +++------- inst/tzdata/backward | 295 ++++++++++++++--- inst/tzdata/backzone | 705 +++++++++++++++++++++++++++++++++++++++++ inst/tzdata/calendars | 4 inst/tzdata/checklinks.awk | 24 + inst/tzdata/checktab.awk | 5 inst/tzdata/etcetera | 23 - inst/tzdata/europe | 715 ++++++++++-------------------------------- inst/tzdata/iso3166.tab | 6 inst/tzdata/leap-seconds.list | 8 inst/tzdata/leapseconds | 8 inst/tzdata/leapseconds.awk | 50 +- inst/tzdata/northamerica | 454 +++++++++++--------------- inst/tzdata/southamerica | 91 +++-- inst/tzdata/theory.html | 108 +++--- inst/tzdata/version | 2 inst/tzdata/windowsZones.xml | 10 inst/tzdata/ziguard.awk | 325 ++++++++++++++++--- inst/tzdata/zishrink.awk | 62 ++- inst/tzdata/zone.tab | 62 +-- inst/tzdata/zone1970.tab | 148 ++++---- man/tzdb-package.Rd | 4 src/Makevars | 6 src/Makevars.win | 2 src/tz.cpp | 6 tests/testthat/test-names.R | 2 tests/testthat/test-path.R | 2 tests/testthat/test-version.R | 2 43 files changed, 3362 insertions(+), 1976 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' and 'all.primer.tutorials' packages.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.2.2 dated 2023-05-08 and 0.2.3 dated 2023-05-12
DESCRIPTION | 10 +- MD5 | 44 ++++++---- NAMESPACE | 1 NEWS.md | 12 ++ R/check_tutorial_defaults.R | 4 R/knit_tutorials.R | 14 +-- R/submission_functions.R | 2 R/write_answers.R | 7 + README.md | 50 +++++------- build/vignette.rds |binary inst/doc/addins.R |only inst/doc/addins.Rmd |only inst/doc/addins.html |only inst/doc/books.Rmd |only inst/doc/books.html |only inst/doc/instructions.R | 3 inst/doc/instructions.Rmd | 144 +---------------------------------- inst/doc/instructions.html | 124 +----------------------------- inst/doc/testing.Rmd |only inst/doc/testing.html |only man/knit_tutorials.Rd | 7 - man/submission_functions.Rd | 2 man/write_answers.Rd | 6 + tests/testthat/test-knit_tutorials.R | 4 vignettes/addins.Rmd |only vignettes/books.Rmd |only vignettes/instructions.Rmd | 144 +---------------------------------- vignettes/testing.Rmd |only 28 files changed, 107 insertions(+), 471 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with 'Stan', 'NIMBLE', 'JAGS', and other software.
Author: Casey Youngflesh [aut, cre] ,
Christian Che-Castaldo [aut] ,
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.15.5 dated 2022-02-08 and 0.16.0 dated 2023-05-12
DESCRIPTION | 11 MD5 | 35 - NEWS.md | 94 ++--- R/MCMCchains.R | 13 R/MCMCdiag.R | 65 +++ R/MCMCplot.R | 3 R/MCMCpstr.R | 3 R/MCMCsummary.R | 84 +++- build/vignette.rds |binary inst/doc/MCMCvis.Rmd | 6 inst/doc/MCMCvis.html | 765 ++++++++++++++++++++++++++++++++++-------- man/MCMCchains.Rd | 2 man/MCMCdiag.Rd | 4 man/MCMCplot.Rd | 2 man/MCMCpstr.Rd | 2 man/MCMCsummary.Rd | 6 tests/testdata/cmdstanfit.rda |only tests/testthat/test_master.R | 78 ++-- vignettes/MCMCvis.Rmd | 6 19 files changed, 916 insertions(+), 263 deletions(-)
Title: Colocalisation Tests of Two Genetic Traits
Description: Performs the colocalisation tests described in
Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>,
Wallace (2020) <doi:10.1371/journal.pgen.1008720>,
Wallace (2021) <doi:10.1371/journal.pgen.1009440>.
Author: Chris Wallace [aut, cre],
Claudia Giambartolomei [aut],
Vincent Plagnol [ctb]
Maintainer: Chris Wallace <cew54@cam.ac.uk>
Diff between coloc versions 5.1.0.1 dated 2022-07-05 and 5.2.2 dated 2023-05-12
coloc-5.1.0.1/coloc/man/alpha_to_logbf.Rd |only coloc-5.2.2/coloc/DESCRIPTION | 23 - coloc-5.2.2/coloc/MD5 | 92 +++--- coloc-5.2.2/coloc/NAMESPACE | 4 coloc-5.2.2/coloc/NEWS.md | 23 + coloc-5.2.2/coloc/R/boundaries.R |only coloc-5.2.2/coloc/R/check.R | 225 ++++++++------- coloc-5.2.2/coloc/R/claudia.R | 285 ++++++++++--------- coloc-5.2.2/coloc/R/plot.R | 76 ++++- coloc-5.2.2/coloc/R/sensitivity.R | 6 coloc-5.2.2/coloc/R/split.R | 65 +++- coloc-5.2.2/coloc/R/susie.R | 337 ++++++++++------------- coloc-5.2.2/coloc/R/testdata.R | 115 ++++--- coloc-5.2.2/coloc/R/zzz.R | 3 coloc-5.2.2/coloc/README.md | 16 - coloc-5.2.2/coloc/build/vignette.rds |binary coloc-5.2.2/coloc/data/coloc_test_data.rda |binary coloc-5.2.2/coloc/data/datalist |only coloc-5.2.2/coloc/inst/CITATION | 4 coloc-5.2.2/coloc/inst/doc/a01_intro.Rmd | 2 coloc-5.2.2/coloc/inst/doc/a01_intro.html | 6 coloc-5.2.2/coloc/inst/doc/a02_data.Rmd | 21 + coloc-5.2.2/coloc/inst/doc/a02_data.html | 197 +++++++------ coloc-5.2.2/coloc/inst/doc/a03_enumeration.html | 67 ++-- coloc-5.2.2/coloc/inst/doc/a04_sensitivity.html | 60 ++-- coloc-5.2.2/coloc/inst/doc/a05_conditioning.R | 8 coloc-5.2.2/coloc/inst/doc/a05_conditioning.Rmd | 18 - coloc-5.2.2/coloc/inst/doc/a05_conditioning.html | 136 +++------ coloc-5.2.2/coloc/inst/doc/a06_SuSiE.Rmd | 20 - coloc-5.2.2/coloc/inst/doc/a06_SuSiE.html | 207 ++++++-------- coloc-5.2.2/coloc/man/check_dataset.Rd | 54 +-- coloc-5.2.2/coloc/man/coloc.bf_bf.Rd | 4 coloc-5.2.2/coloc/man/coloc.signals.Rd | 6 coloc-5.2.2/coloc/man/coloc.susie_bf.Rd | 14 coloc-5.2.2/coloc/man/combine.abf.Rd | 4 coloc-5.2.2/coloc/man/findends.Rd |only coloc-5.2.2/coloc/man/findpeaks.Rd |only coloc-5.2.2/coloc/man/finemap.bf.Rd |only coloc-5.2.2/coloc/man/finemap.signals.Rd | 5 coloc-5.2.2/coloc/man/logbf_to_pp.Rd | 4 coloc-5.2.2/coloc/man/plot_dataset.Rd | 19 + coloc-5.2.2/coloc/man/runsusie.Rd | 20 - coloc-5.2.2/coloc/man/sensitivity.Rd | 2 coloc-5.2.2/coloc/man/subset_dataset.Rd |only coloc-5.2.2/coloc/tests/testthat/test-abf.R | 60 +--- coloc-5.2.2/coloc/tests/testthat/test-check.R |only coloc-5.2.2/coloc/tests/testthat/test-susie.R | 10 coloc-5.2.2/coloc/vignettes/a01_intro.Rmd | 2 coloc-5.2.2/coloc/vignettes/a02_data.Rmd | 21 + coloc-5.2.2/coloc/vignettes/a05_conditioning.Rmd | 18 - coloc-5.2.2/coloc/vignettes/a06_SuSiE.Rmd | 20 - 51 files changed, 1216 insertions(+), 1063 deletions(-)
Title: Software Bibliographies for R Projects
Description: Detect libraries used in a project and automatically create software bibliographies in 'PDF', 'Word', 'Rmarkdown', and 'BibTeX' formats.
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between softbib versions 0.0.1 dated 2023-04-03 and 0.0.2 dated 2023-05-12
DESCRIPTION | 8 +++++--- MD5 | 6 ++++-- NEWS.md |only README.md | 12 +++++++++++- inst/CITATION |only 5 files changed, 20 insertions(+), 6 deletions(-)
Title: Calculate Crosstab and Topline Tables of Weighted Survey Data
Description: Calculate common types of tables for weighted survey data.
Options include topline and (2-way and 3-way) crosstab tables of
categorical or ordinal data as well as summary tables of weighted
numeric variables. Optionally, include the margin of error at
selected confidence intervals including the design effect. The
design effect is calculated as described by
Kish (1965) <doi:10.1002/bimj.19680100122> beginning
on page 257. Output takes the form of tibbles (simple data frames).
This package conveniently handles labelled data, such as that
commonly used by 'Stata' and 'SPSS.' Complex survey design is
not supported at this time.
Author: John D. Johnson [aut, cre]
Maintainer: John D. Johnson <john.d.johnson@marquette.edu>
Diff between pollster versions 0.1.5 dated 2023-04-25 and 0.1.6 dated 2023-05-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 3 +++ R/Topline.R | 3 ++- inst/doc/toplines.html | 28 +++++++++++----------------- 5 files changed, 23 insertions(+), 25 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 (effect size) of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Si Gao [aut, cre, dtc] ,
Peter Kochunov [aut, dtc, cph, fnd] ,
Kathryn Hatch [ctb, dtc] ,
Yizhou Ma [ctb, dtc] ,
Fatima Talib [ctb]
Maintainer: Si Gao <sgao@som.umaryland.edu>
Diff between RVIpkg versions 0.3.1 dated 2022-09-23 and 0.3.2 dated 2023-05-12
DESCRIPTION | 8 - MD5 | 16 +-- R/RVI_func.R | 224 +++++++++++++++++++++++++----------------------- R/sysdata.rda |binary build/partial.rdb |binary data/EP.GM.rda |binary data/EP.Subcortical.rda |binary data/EP.WM.rda |binary man/RVI_func.Rd | 18 +++ 9 files changed, 147 insertions(+), 119 deletions(-)
Title: Creates Statistical Reports
Description: Contains functions to create regulatory-style statistical reports.
Originally designed to create tables, listings, and figures for the
pharmaceutical, biotechnology, and medical device industries, these
reports are generalized enough that they could be used in any industry.
Generates text, rich-text, PDF, HTML, and Microsoft Word file formats.
The package specializes
in printing wide and long tables with automatic page wrapping and splitting.
Reports can be produced with a minimum of function calls, and without
relying on other table packages. The package supports titles, footnotes,
page header, page footers, spanning headers, page by variables,
and automatic page numbering.
Author: David Bosak [aut, cre],
Kevin Kramer [ctb],
Duong Tran [ctb],
Raphael Huang [ctb],
Archytas Clinical Solutions [cph]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between reporter versions 1.3.9 dated 2023-03-17 and 1.4.1 dated 2023-05-12
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Title: Plant Photobiology Related Functions and Data
Description: Provides functions for quantifying visible (VIS) and ultraviolet
(UV) radiation in relation to the photoreceptors Phytochromes,
Cryptochromes, and UVR8 which are present in plants. It also includes data
sets on the optical properties of plants. Part of the 'r4photobiology'
suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyPlants versions 0.4.2 dated 2019-06-14 and 0.4.3 dated 2023-05-12
photobiologyPlants-0.4.2/photobiologyPlants/NEWS |only photobiologyPlants-0.4.2/photobiologyPlants/R/McCree-photosynthesis-mspct.r |only photobiologyPlants-0.4.2/photobiologyPlants/R/uvr8-Glasgow-spct.r |only photobiologyPlants-0.4.3/photobiologyPlants/DESCRIPTION | 24 photobiologyPlants-0.4.3/photobiologyPlants/MD5 | 132 +- photobiologyPlants-0.4.3/photobiologyPlants/NAMESPACE | 4 photobiologyPlants-0.4.3/photobiologyPlants/NEWS.md |only photobiologyPlants-0.4.3/photobiologyPlants/R/McCree-photosynthesis-mspct.R |only photobiologyPlants-0.4.3/photobiologyPlants/R/Pfr-P-ratio-mono.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/Pfr-P-ratio.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/Pfr-Ptot.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/PfrPtot-RFR.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/Phy-Sigma-FR.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/Phy-Sigma-R.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/Phy-Sigma.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/carotenoids-mspct.r | 2 photobiologyPlants-0.4.3/photobiologyPlants/R/chlorophylls-mspct.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/photobiologyPlants.r | 9 photobiologyPlants-0.4.3/photobiologyPlants/R/phy-reaction-rates.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/phytochrome-data.r | 3 photobiologyPlants-0.4.3/photobiologyPlants/R/plant-qq-ratios.r | 178 +++ photobiologyPlants-0.4.3/photobiologyPlants/R/uvr8-mspct.r |only photobiologyPlants-0.4.3/photobiologyPlants/README.md | 37 photobiologyPlants-0.4.3/photobiologyPlants/build/partial.rdb |only photobiologyPlants-0.4.3/photobiologyPlants/build/vignette.rds |binary photobiologyPlants-0.4.3/photobiologyPlants/data/CRYs.mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/McCree.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/PHOTs.mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/UVR8s.mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/ZTLs.mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/carotenoids-mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/chlorophylls-fluorescence-mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/chlorophylls-mspct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/leaves.spct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/data/phytochrome.spct.rda |binary photobiologyPlants-0.4.3/photobiologyPlants/inst/CITATION | 13 photobiologyPlants-0.4.3/photobiologyPlants/inst/doc/user-guide.R | 94 - photobiologyPlants-0.4.3/photobiologyPlants/inst/doc/user-guide.Rmd | 2 photobiologyPlants-0.4.3/photobiologyPlants/inst/doc/user-guide.html | 546 +++++----- photobiologyPlants-0.4.3/photobiologyPlants/man/B_G.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/Betula_ermanii.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/CRYs.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/McCree_photosynthesis.mspct.Rd | 15 photobiologyPlants-0.4.3/photobiologyPlants/man/PHOTs.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/PHYs.mspct.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/Pfr_P_ratio.Rd | 12 photobiologyPlants-0.4.3/photobiologyPlants/man/Pfr_P_ratio_mono.Rd | 3 photobiologyPlants-0.4.3/photobiologyPlants/man/Pfr_Ptot.Rd | 11 photobiologyPlants-0.4.3/photobiologyPlants/man/Pfr_Ptot_R_FR.Rd | 3 photobiologyPlants-0.4.3/photobiologyPlants/man/Phy_Sigma.Rd | 3 photobiologyPlants-0.4.3/photobiologyPlants/man/Phy_Sigma_FR.Rd | 3 photobiologyPlants-0.4.3/photobiologyPlants/man/Phy_Sigma_R.Rd | 3 photobiologyPlants-0.4.3/photobiologyPlants/man/Phy_reaction_rates.Rd | 12 photobiologyPlants-0.4.3/photobiologyPlants/man/R_FR.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/Solidago_altissima.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/UVA1_UV.Rd |only photobiologyPlants-0.4.3/photobiologyPlants/man/UVA2_UV.Rd |only photobiologyPlants-0.4.3/photobiologyPlants/man/UVA_PAR.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/UVA_UV.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/UVAlw_UV.Rd |only photobiologyPlants-0.4.3/photobiologyPlants/man/UVAsw_UV.Rd |only photobiologyPlants-0.4.3/photobiologyPlants/man/UVB_PAR.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/UVB_UV.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/UVR8s.mspct.Rd | 78 - photobiologyPlants-0.4.3/photobiologyPlants/man/UV_PAR.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/ZTLs.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/carotenoids.mspct.Rd | 8 photobiologyPlants-0.4.3/photobiologyPlants/man/chlorophylls.mspct.Rd | 9 photobiologyPlants-0.4.3/photobiologyPlants/man/chlorophylls_fluorescence.mspct.Rd | 6 photobiologyPlants-0.4.3/photobiologyPlants/man/figures/README-example1a-1.png |binary photobiologyPlants-0.4.3/photobiologyPlants/man/figures/logo.png |only photobiologyPlants-0.4.3/photobiologyPlants/man/photobiologyPlants-package.Rd | 19 photobiologyPlants-0.4.3/photobiologyPlants/vignettes/user-guide.Rmd | 2 73 files changed, 827 insertions(+), 524 deletions(-)
More information about photobiologyPlants at CRAN
Permanent link
Title: State-Space Models Inference by Kalman or Viking
Description: Inference methods for state-space models, relying on the Kalman Filter or on Viking (Variational Bayesian VarIance tracKING). See J. de Vilmarest (2022) <https://theses.hal.science/tel-03716104/>.
Author: Joseph de Vilmarest [aut, cre]
Maintainer: Joseph de Vilmarest <joseph.de-vilmarest@vikingconseil.fr>
Diff between viking versions 1.0.0 dated 2022-10-07 and 1.0.1 dated 2023-05-12
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/kalman_smoothing.R | 1 - R/plot-statespace.R | 4 ++-- R/statespace.R | 2 +- 5 files changed, 11 insertions(+), 12 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.3.0 dated 2022-12-22 and 1.3.1 dated 2023-05-12
DESCRIPTION | 6 +-- MD5 | 16 +++++----- NEWS.md | 8 ++++- R/app.R | 29 +++++++++---------- R/tools.R | 1 inst/WORDLIST | 5 ++- inst/templates/app_structure/app/main.R | 15 ++++++--- inst/templates/unit_tests/tests/testthat/test-main.R | 2 - tests/testthat/test-app.R | 18 +++++++++++ 9 files changed, 67 insertions(+), 33 deletions(-)
Title: Work with Custom Distribution Functions
Description: Create, transform, and summarize custom random
variables with distribution functions (analogues of 'p*()', 'd*()',
'q*()', and 'r*()' functions from base R). Two types of distributions
are supported: "discrete" (random variable has finite number of output
values) and "continuous" (infinite number of values in the form of
continuous random variable). Functions for distribution
transformations and summaries are available. Implemented approaches
often emphasize approximate and numerical solutions: all distributions
assume finite support and finite values of density function; some
methods implemented with simulation techniques.
Author: Evgeni Chasnovski [aut, cre]
Maintainer: Evgeni Chasnovski <evgeni.chasnovski@gmail.com>
Diff between pdqr versions 0.3.0 dated 2021-01-21 and 0.3.1 dated 2023-05-12
pdqr-0.3.0/pdqr/tests/figs |only pdqr-0.3.1/pdqr/DESCRIPTION | 9 pdqr-0.3.1/pdqr/MD5 | 141 - pdqr-0.3.1/pdqr/NEWS.md | 4 pdqr-0.3.1/pdqr/R/utils-new.R | 10 pdqr-0.3.1/pdqr/README.md | 202 - pdqr-0.3.1/pdqr/build/vignette.rds |binary pdqr-0.3.1/pdqr/inst/doc/pdqr-01-create.html | 1175 +++++---- pdqr-0.3.1/pdqr/inst/doc/pdqr-02-convert.html | 1014 ++++---- pdqr-0.3.1/pdqr/inst/doc/pdqr-03-transform.html | 1017 ++++---- pdqr-0.3.1/pdqr/inst/doc/pdqr-04-summarize.html | 1254 +++++----- pdqr-0.3.1/pdqr/man/figures/README-pdqr-quick_diff-means-1.png |binary pdqr-0.3.1/pdqr/man/figures/README-pdqr-quick_mixture-hdr-1.png |binary pdqr-0.3.1/pdqr/man/figures/README-pdqr-summarize_roc-1.png |binary pdqr-0.3.1/pdqr/man/figures/README-pdqr-transform_form-1.png |binary pdqr-0.3.1/pdqr/man/figures/README-pdqr-transform_form-2.png |binary pdqr-0.3.1/pdqr/man/form_estimate.Rd | 3 pdqr-0.3.1/pdqr/man/pdqr-package.Rd | 11 pdqr-0.3.1/pdqr/man/summ_moment.Rd | 3 pdqr-0.3.1/pdqr/tests/testthat/_snaps |only pdqr-0.3.1/pdqr/tests/testthat/helper-expectations.R | 4 21 files changed, 2780 insertions(+), 2067 deletions(-)
Title: Create Contour Polygons from Regular Grids
Description: Regularly spaced grids containing continuous data are transformed
to contour polygons. A grid can be defined by a data.frame (x, y, value),
an 'sf' object or a raster from 'terra'.
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between mapiso versions 0.2.0 dated 2022-09-08 and 0.3.0 dated 2023-05-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/mapiso.R | 8 ++++---- README.md | 4 ++-- man/figures/README-data.frame-1.png |binary man/figures/README-raster-1.png |binary 7 files changed, 22 insertions(+), 16 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in
'mlr3' and its companion packages. Comes with helper functions for
functional programming, for printing, to work with 'data.table', as
well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] ,
Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.11.0 dated 2022-09-22 and 0.12.0 dated 2023-05-12
DESCRIPTION | 8 ++-- MD5 | 33 ++++++++++--------- NAMESPACE | 3 + NEWS.md | 7 ++++ R/Callback.R | 3 + R/Context.R | 3 + R/Dictionary.R | 3 + R/dictionary_sugar.R | 64 ++++++++++++++++++++++++++++++++++++++ R/encapsulate.R | 15 +++++++- R/zzz.R | 2 - README.md | 2 - man/Callback.Rd | 9 ++++- man/Context.Rd | 9 ++++- man/Dictionary.Rd | 9 ++++- man/dictionary_sugar_inc_get.Rd |only man/encapsulate.Rd | 2 + tests/testthat/test_Dictionary.R | 25 ++++++++++++++ tests/testthat/test_encapsulate.R | 14 ++++++++ 18 files changed, 180 insertions(+), 31 deletions(-)
Title: Local Partial Autocorrelation Function Estimation for Locally
Stationary Wavelet Processes
Description: Provides the method for computing the local partial autocorrelation function for locally stationary wavelet time series from Killick, Knight, Nason, Eckley (2020) <doi:10.1214/20-EJS1748>.
Author: Rebecca Killick [aut, cre],
Guy Nason [aut],
Marina Knight [aut],
Matt Nunes [aut],
Idris Eckley [ctb]
Maintainer: Rebecca Killick <r.killick@lancs.ac.uk>
Diff between lpacf versions 1.0 dated 2023-04-14 and 1.0.1 dated 2023-05-12
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 4 ++++ man/lpacf-package.Rd | 4 ++-- man/lpacf.Epan.Rd | 6 +++--- man/lpacf.Rd | 6 +++--- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Stochastic Search Inconsistency Factor Selection
Description: Evaluating the consistency assumption of Network Meta-Analysis both globally and locally in the Bayesian framework. Inconsistencies are located by applying Bayesian variable selection to the inconsistency factors. The implementation of the method is described by Seitidis et al. (2022) <arXiv:2211.07258>.
Author: Georgios Seitidis [aut, cre] ,
Stavros Nikolakopoulos [aut] ,
Ioannis Ntzoufras [aut] ,
Dimitris Mavridis [aut]
Maintainer: Georgios Seitidis <g.seitidis@uoi.gr>
Diff between ssifs versions 1.0.1 dated 2023-05-08 and 1.0.2 dated 2023-05-12
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 2 ++ R/ssifs.R | 19 +++++++++++++------ README.md | 4 ++-- 5 files changed, 24 insertions(+), 15 deletions(-)
Title: Econometric Production Analysis with Ray-Based Distance
Functions
Description: Econometric analysis of multiple-input-multiple-output
production technologies with ray-based input distance functions as suggested
by Price and Henningsen (2022): "A Ray-Based Input Distance Function to Model
Zero-Valued Output Quantities: Derivation and an Empirical Application",
<https://ideas.repec.org/p/foi/wpaper/2022_03.html>.
Author: Arne Henningsen [aut, cre],
Juan Jose Price [aut]
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between micEconDistRay versions 0.1-0 dated 2023-05-08 and 0.1-2 dated 2023-05-12
DESCRIPTION | 8 - MD5 | 12 - R/zzz.R | 8 - inst |only tests/MuseumsDk_test.Rout.save | 6 tests/appleProdFr86_test.R | 69 ++++---- tests/appleProdFr86_test.Rout.save | 287 ++++++++++++++++++------------------- 7 files changed, 196 insertions(+), 194 deletions(-)
More information about micEconDistRay at CRAN
Permanent link
Title: Poisson Network Autoregressive Models
Description: Quasi likelihood-based methods for estimating Poisson Network Autoregression with p lags, PNAR, following generalized linear models are provided. PNAR models with the identity and with the logarithmic link function are allowed. The inclusion of exogenous covariates is also possible. Moreover, it provides tools for testing the linearity of linear PNAR model versus several nonlinear alternatives. Finally, it allows generating multivariate count distributions, from linear and nonlinear PNAR models, where the dependence between Poisson random variables is generated by suitable copulas. References include: Armillotta, M. and K. Fokianos (2022a). Poisson network autoregression. <arXiv:2104.06296>. Armillotta, M. and K. Fokianos (2022b). Testing linearity for network autoregressive models. <arXiv:2202.03852>. Armillotta, M., Tsagris, M. and Fokianos, K. (2022c). The R-package PNAR for modelling count network time series. <arXiv:2211.02582>.
Author: Michail Tsagris [aut, cre],
Mirko Armillotta [aut, cph],
Konstantinos Fokianos [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between PNAR versions 1.3 dated 2022-11-02 and 1.4 dated 2023-05-12
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 3 ++- R/lin_estimnarpq.R | 37 ++++++++++++++++++++----------------- R/lin_narpq_init.R |only R/log_lin_estimnarpq.R | 34 ++++++++++++++++++---------------- R/log_lin_narpq_init.R |only man/PNAR-package.Rd | 6 +++--- man/global_optimise_LM_stnarpq.Rd | 4 ++++ man/global_optimise_LM_tnarpq.Rd | 4 ++++ man/lin_estimnarpq.Rd | 19 +++++++++++++++++-- man/lin_narpq_init.Rd |only man/log_lin_estimnarpq.Rd | 23 +++++++++++++++++++---- man/log_lin_narpq_init.Rd |only man/score_test_nonlinpq_h0.Rd | 4 ++++ man/score_test_stnarpq_DV.Rd | 4 ++++ man/score_test_stnarpq_j.Rd | 4 ++++ man/score_test_tnarpq_j.Rd | 4 ++++ 18 files changed, 125 insertions(+), 61 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.0.1 dated 2023-05-10 and 2.1.0 dated 2023-05-12
pathfindR-2.0.1/pathfindR/inst/rmd |only pathfindR-2.0.1/pathfindR/man/create_HTML_report.Rd |only pathfindR-2.1.0/pathfindR/DESCRIPTION | 6 - pathfindR-2.1.0/pathfindR/MD5 | 30 +++---- pathfindR-2.1.0/pathfindR/NEWS.md | 4 + pathfindR-2.1.0/pathfindR/R/core.R | 9 -- pathfindR-2.1.0/pathfindR/R/utility.R | 33 -------- pathfindR-2.1.0/pathfindR/inst/doc/comparing_results.html | 4 - pathfindR-2.1.0/pathfindR/inst/doc/intro_vignette.Rmd | 23 ------ pathfindR-2.1.0/pathfindR/inst/doc/intro_vignette.html | 38 +--------- pathfindR-2.1.0/pathfindR/inst/doc/manual_execution.html | 4 - pathfindR-2.1.0/pathfindR/inst/doc/non_hs_analysis.html | 4 - pathfindR-2.1.0/pathfindR/inst/doc/obtain_data.html | 4 - pathfindR-2.1.0/pathfindR/inst/doc/visualization_vignette.html | 4 - pathfindR-2.1.0/pathfindR/tests/testthat/test-utility.R | 19 ----- pathfindR-2.1.0/pathfindR/vignettes/intro_vignette.Rmd | 23 ------ 16 files changed, 36 insertions(+), 169 deletions(-)
Title: Compute Upper Prediction Bounds on the FDP in Competition-Based
Setups
Description: Implements functions that calculate upper prediction
bounds on the false discovery proportion (FDP) in the list of discoveries
returned by competition-based setups, implementing Ebadi et al. (2022)
<arXiv:2302.11837>. Such setups include target-decoy competition (TDC)
in computational mass spectrometry and the knockoff construction in linear
regression (note this package typically uses the terminology of TDC). Included
is the standardized (TDC-SB) and uniform (TDC-UB) bound on TDC's FDP, and the
simultaneous standardized and uniform bands. Requires
pre-computed Monte Carlo statistics available at
<https://github.com/uni-Arya/fdpbandsdata>. This data can be downloaded by
running the command 'devtools::install_github("uni-Arya/fdpbandsdata")' in R
and restarting R after installation. The size of this data is roughly 81Mb.
Author: Arya Ebadi [aut, cre],
Dong Luo [aut],
Jack Freestone [aut],
William Stafford Noble [aut],
Uri Keich [aut]
Maintainer: Arya Ebadi <aeba3842@uni.sydney.edu.au>
Diff between bandsfdp versions 1.0.0 dated 2023-03-15 and 1.1.0 dated 2023-05-12
bandsfdp-1.0.0/bandsfdp/R/simband.R |only bandsfdp-1.0.0/bandsfdp/R/stband.R |only bandsfdp-1.0.0/bandsfdp/R/uniband.R |only bandsfdp-1.0.0/bandsfdp/man/simband.Rd |only bandsfdp-1.0.0/bandsfdp/man/stband.Rd |only bandsfdp-1.0.0/bandsfdp/man/uniband.Rd |only bandsfdp-1.1.0/bandsfdp/DESCRIPTION | 6 +- bandsfdp-1.1.0/bandsfdp/MD5 | 22 ++++---- bandsfdp-1.1.0/bandsfdp/NAMESPACE | 7 +- bandsfdp-1.1.0/bandsfdp/NEWS.md | 12 ++++ bandsfdp-1.1.0/bandsfdp/R/gen_bound.R |only bandsfdp-1.1.0/bandsfdp/R/sim_bound.R |only bandsfdp-1.1.0/bandsfdp/R/tdc_sb.R |only bandsfdp-1.1.0/bandsfdp/R/tdc_ub.R |only bandsfdp-1.1.0/bandsfdp/README.md | 83 ++++++++++++++++++++++--------- bandsfdp-1.1.0/bandsfdp/man/gen_bound.Rd |only bandsfdp-1.1.0/bandsfdp/man/sim_bound.Rd |only bandsfdp-1.1.0/bandsfdp/man/tdc_sb.Rd |only bandsfdp-1.1.0/bandsfdp/man/tdc_ub.Rd |only 19 files changed, 91 insertions(+), 39 deletions(-)
Title: Generalized Score Matching Estimators
Description: Implementation of the Generalized Score Matching estimator in Yu et al. (2019) <https://jmlr.org/papers/v20/18-278.html> for non-negative graphical models (truncated Gaussian, exponential square-root, gamma, a-b models) and univariate truncated Gaussian distributions. Also includes the original estimator for untruncated Gaussian graphical models from Lin et al. (2016) <doi:10.1214/16-EJS1126>, with the addition of a diagonal multiplier.
Author: Shiqing Yu, Lina Lin, Wally Gilks
Maintainer: Shiqing Yu <syu.phd@gmail.com>
Diff between genscore versions 1.0.2 dated 2020-04-27 and 1.0.2.1 dated 2023-05-12
DESCRIPTION | 9 MD5 | 12 README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/gen_vignette.html | 1914 ++++++++++++++++++++++++++------------------- src/arms.c | 4 7 files changed, 1123 insertions(+), 824 deletions(-)
Title: Confidence Intervals
Description: Calculates classic and/or bootstrap confidence intervals for
many parameters such as the population mean, variance, interquartile
range (IQR), median absolute deviation (MAD), skewness, kurtosis,
Cramer's V, odds ratio, R-squared, quantiles (incl. median),
proportions, different types of correlation measures, difference in
means, quantiles and medians. Many of the classic confidence intervals
are described in Smithson, M. (2003, ISBN: 978-0761924999). Bootstrap
confidence intervals are calculated with the R package 'boot'. Both
one- and two-sided intervals are supported.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between confintr versions 1.0.0 dated 2023-04-15 and 1.0.1 dated 2023-05-12
confintr-1.0.0/confintr/man/ci_boot.Rd |only confintr-1.0.1/confintr/DESCRIPTION | 6 confintr-1.0.1/confintr/MD5 | 81 +++++------ confintr-1.0.1/confintr/NEWS.md | 119 ++++++++-------- confintr-1.0.1/confintr/R/ci_cor.R | 31 +--- confintr-1.0.1/confintr/R/ci_cramersv.R | 118 ++++++---------- confintr-1.0.1/confintr/R/ci_location_shift.R | 143 ++++++-------------- confintr-1.0.1/confintr/R/ci_measures_of_location.R | 142 +++++++------------ confintr-1.0.1/confintr/R/ci_measures_of_scale.R | 115 +++------------- confintr-1.0.1/confintr/R/ci_oddsratio.R | 33 +--- confintr-1.0.1/confintr/R/ci_proportion.R | 40 +---- confintr-1.0.1/confintr/R/ci_rsquared.R | 71 +++------ confintr-1.0.1/confintr/R/ci_skew_and_kurtosis.R | 65 ++------- confintr-1.0.1/confintr/R/standard_errors.R | 11 - confintr-1.0.1/confintr/R/utils_boot.R | 10 - confintr-1.0.1/confintr/R/utils_general.R | 4 confintr-1.0.1/confintr/build/vignette.rds |binary confintr-1.0.1/confintr/man/ci_IQR.Rd | 22 --- confintr-1.0.1/confintr/man/ci_chisq_ncp.Rd | 40 ++--- confintr-1.0.1/confintr/man/ci_cor.Rd | 27 +-- confintr-1.0.1/confintr/man/ci_cramersv.Rd | 45 ++---- confintr-1.0.1/confintr/man/ci_f_ncp.Rd | 34 +--- confintr-1.0.1/confintr/man/ci_kurtosis.Rd | 22 --- confintr-1.0.1/confintr/man/ci_mad.Rd | 22 --- confintr-1.0.1/confintr/man/ci_mean.Rd | 17 -- confintr-1.0.1/confintr/man/ci_mean_diff.Rd | 29 +--- confintr-1.0.1/confintr/man/ci_median.Rd | 22 --- confintr-1.0.1/confintr/man/ci_median_diff.Rd | 25 +-- confintr-1.0.1/confintr/man/ci_oddsratio.Rd | 20 -- confintr-1.0.1/confintr/man/ci_proportion.Rd | 34 +--- confintr-1.0.1/confintr/man/ci_quantile.Rd | 24 --- confintr-1.0.1/confintr/man/ci_quantile_diff.Rd | 27 +-- confintr-1.0.1/confintr/man/ci_rsquared.Rd | 35 +--- confintr-1.0.1/confintr/man/ci_sd.Rd | 25 --- confintr-1.0.1/confintr/man/ci_skewness.Rd | 22 --- confintr-1.0.1/confintr/man/ci_var.Rd | 37 +---- confintr-1.0.1/confintr/man/cramersv.Rd | 25 ++- confintr-1.0.1/confintr/man/kurtosis.Rd | 2 confintr-1.0.1/confintr/man/moment.Rd | 2 confintr-1.0.1/confintr/man/oddsratio.Rd | 8 - confintr-1.0.1/confintr/man/se.Rd | 7 confintr-1.0.1/confintr/man/skewness.Rd | 2 42 files changed, 594 insertions(+), 970 deletions(-)