Title: A Soil Survey Toolkit
Description: Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.
Author: Dylan Beaudette [cre],
Jay Skovlin [aut],
Stephen Roecker [aut],
USDA-NRCS Soil Survey Staff [ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>
Diff between sharpshootR versions 1.6.5 dated 2020-10-20 and 1.7 dated 2021-01-27
sharpshootR-1.6.5/sharpshootR/data/plss.centroids.sample.rda |only sharpshootR-1.7/sharpshootR/DESCRIPTION | 11 sharpshootR-1.7/sharpshootR/MD5 | 36 sharpshootR-1.7/sharpshootR/NAMESPACE | 13 sharpshootR-1.7/sharpshootR/R/HenryTimeLine.R |only sharpshootR-1.7/sharpshootR/R/PLSS2LL.R | 578 ++++++--- sharpshootR-1.7/sharpshootR/R/huePositionPlot.R |only sharpshootR-1.7/sharpshootR/R/multinominal2logical.R | 65 + sharpshootR-1.7/sharpshootR/R/water-balance.R | 596 +++++----- sharpshootR-1.7/sharpshootR/man/CDECquery.Rd | 4 sharpshootR-1.7/sharpshootR/man/HenryTimeLine.Rd |only sharpshootR-1.7/sharpshootR/man/LL2PLSS.Rd | 69 - sharpshootR-1.7/sharpshootR/man/PLSS2LL.Rd | 104 - sharpshootR-1.7/sharpshootR/man/aggregateColorPlot.Rd | 134 +- sharpshootR-1.7/sharpshootR/man/formatPLSS.Rd | 90 - sharpshootR-1.7/sharpshootR/man/huePositionPlot.Rd |only sharpshootR-1.7/sharpshootR/man/monthlyWB.Rd | 4 sharpshootR-1.7/sharpshootR/man/multinominal2logical.Rd | 112 - sharpshootR-1.7/sharpshootR/man/plotWB.Rd | 64 - sharpshootR-1.7/sharpshootR/man/table5.2.Rd | 2 sharpshootR-1.7/sharpshootR/tests/testthat/test-PLSS2LL.R |only sharpshootR-1.7/sharpshootR/tests/testthat/test-multinominal2logical.R | 79 - 22 files changed, 1218 insertions(+), 743 deletions(-)
Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent,
plant, ant, and weather data from the Portal Project. Portal is a
long-term (and ongoing) experimental monitoring site in the Chihuahua
desert. The raw data files can be found at
<https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>),
Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>),
Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>),
Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>),
Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>),
Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>),
Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>),
Ethan P, White [aut] (<https://orcid.org/0000-0001-6728-7745>),
S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>),
Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.3.6 dated 2020-11-23 and 0.3.7 dated 2021-01-27
DESCRIPTION | 8 - MD5 | 22 +-- R/Weather.R | 148 ++++++++++++++++++------- R/summarize_rodents.R | 5 build/vignette.rds |binary inst/doc/portal_researcher_examples.html | 16 ++ inst/doc/rodent-abundance-demo.html | 178 +++++++++++++++---------------- man/summarize_plant_data.Rd | 7 + man/summarize_rodent_data.Rd | 7 + man/weather.Rd | 2 tests/testthat/test-04-weather.R | 5 tests/testthat/test-99-regression.R | 8 - 12 files changed, 252 insertions(+), 154 deletions(-)
Title: The Pareto, Piecewise Pareto and Generalized Pareto Distribution
Description: Utilities for the Pareto, piecewise Pareto and generalized Pareto distribution
that are useful for reinsurance pricing. In particular, the package provides
a non-trivial algorithm that can be used to match the expected losses of a
tower of reinsurance layers with a layer-independent collective risk model.
The theoretical background of the matching algorithm and most other methods
are described in Ulrich Riegel (2018) <doi:10.1007/s13385-018-0177-3>.
Author: Ulrich Riegel [aut, cre]
Maintainer: Ulrich Riegel <ulrich.riegel@gmx.de>
Diff between Pareto versions 2.2.1 dated 2020-09-11 and 2.2.2 dated 2021-01-27
DESCRIPTION | 6 MD5 | 21 +- NAMESPACE | 1 NEWS.md | 4 R/Functions.R | 157 +++++++++++++++++++++- inst/doc/Pareto.R | 6 inst/doc/Pareto.Rmd | 23 +++ inst/doc/Pareto.html | 213 ++++++++++++++++++++---------- man/Fit_PML_Curve.Rd |only man/Fit_References.Rd | 3 tests/testthat/test_functions_PPP_Model.R | 16 ++ vignettes/Pareto.Rmd | 23 +++ 12 files changed, 389 insertions(+), 84 deletions(-)
Title: Optimal Capital Allocations
Description: Computes optimal capital allocations based on some standard principles such as Haircut, Overbeck type II and the Covariance Allocation Principle. It also provides some shortcuts for obtaining the Value at Risk and the Expectation Shortfall, using both the normal and the t-student distribution, see Urbina and Guillén (2014)<doi:10.1016/j.eswa.2014.05.017> and Urbina (2013)<http://hdl.handle.net/2099.1/19443>.
Author: Jilber Urbina
Maintainer: Jilber Urbina <jurbina@cipadla.com>
Diff between OCA versions 0.2 dated 2020-05-30 and 0.3 dated 2021-01-27
DESCRIPTION | 10 +++---- MD5 | 20 +++++++-------- R/ES.R | 20 ++++++++++++--- R/Overbeck2.R | 2 - R/Risk.R | 9 +++---- R/VaR.R | 67 +++++++++++++++-------------------------------------- R/hap.R | 2 - man/ES.Rd | 27 +++++++++++---------- man/OCA-package.Rd | 6 ++-- man/Risk.Rd | 27 ++++++++++++--------- man/VaR.Rd | 22 +++++++++++------ 11 files changed, 105 insertions(+), 107 deletions(-)
Title: Interface to 'MLeap'
Description: A 'sparklyr' <https://spark.rstudio.com> extension that provides
an interface to 'MLeap' <https://github.com/combust/mleap>, an open source library
that enables exporting and serving of 'Apache Spark' pipelines.
Author: Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>)
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between mleap versions 1.0.0 dated 2020-01-10 and 1.1.0 dated 2021-01-27
DESCRIPTION | 29 +++++++++++++++++++---------- MD5 | 12 +++++++----- R/dependencies.R | 2 +- inst/java/mleap-2.0-2.11.jar |binary inst/java/mleap-2.3-2.11.jar |binary inst/java/mleap-2.4-2.11.jar |binary inst/java/mleap-2.4-2.12.jar |only inst/java/mleap-3.0-2.12.jar |only 8 files changed, 27 insertions(+), 16 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker <DOI:10.1007/978-3-319-21416-0>, "Meta-Analysis with R" (2015):
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from 'RevMan 5';
- prediction interval, Hartung-Knapp method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression;
- generalised linear mixed models;
- produce forest plot summarising several (subgroup) meta-analyses.
Author: Guido Schwarzer [cre, aut] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.16-1 dated 2021-01-19 and 4.16-2 dated 2021-01-27
DESCRIPTION | 8 +- MD5 | 34 ++++----- NEWS.md | 30 ++++++++ R/drapery.R | 55 +++++++++------ R/forest.R | 58 +++++++++++++--- R/funnel.R | 101 +++++++++++++++++------------ R/metabin.R | 20 ++--- R/metabind.R | 183 ++++++++++++++++++++++++++++++++--------------------- R/metacont.R | 12 +-- R/metacor.R | 12 +-- R/metagen.R | 20 +++-- R/metainc.R | 12 +-- R/metamean.R | 12 +-- R/metamerge.R | 26 ------- R/metaprop.R | 12 +-- R/metarate.R | 12 +-- man/forest.meta.Rd | 8 +- man/funnel.meta.Rd | 26 ++++--- 18 files changed, 382 insertions(+), 259 deletions(-)
Title: Exploratory Data Analysis System
Description: Performs an exploratory data analysis through a 'shiny' interface. It includes basic methods such as the mean, median, mode, normality test, among others. It also includes clustering techniques such as Principal Components Analysis, Hierarchical Clustering and the K-Means Method.
Author: Oldemar Rodriguez [aut, cre],
Diego Jiménez [ctb]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between discoveR versions 2.1.6 dated 2021-01-22 and 2.1.7 dated 2021-01-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/app_ui.R | 1 + R/discoveR.R | 2 +- R/mod_acercade.R | 2 +- man/discoveR.Rd | 2 +- 7 files changed, 15 insertions(+), 13 deletions(-)
Title: Interface to the Global 'Biodiversity' Information Facility API
Description: A programmatic interface to the Web Service methods
provided by the Global Biodiversity Information Facility ('GBIF';
<https://www.gbif.org/developer/summary>). 'GBIF' is a database
of species occurrence records from sources all over the globe.
'rgbif' includes functions for searching for taxonomic names,
retrieving information on data providers, getting species occurrence
records, getting counts of occurrence records, and using the 'GBIF'
tile map service to make 'rasters' summarizing huge amounts of data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Damiano Oldoni [aut] (<https://orcid.org/0000-0003-3445-7562>),
Vijay Barve [ctb] (<https://orcid.org/0000-0002-4852-2567>),
Peter Desmet [ctb] (<https://orcid.org/0000-0002-8442-8025>),
Laurens Geffert [ctb],
Dan Mcglinn [ctb] (<https://orcid.org/0000-0003-2359-3526>),
Karthik Ram [ctb] (<https://orcid.org/0000-0002-0233-1757>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rgbif versions 3.5.0 dated 2021-01-13 and 3.5.2 dated 2021-01-27
DESCRIPTION | 9 ++---- MD5 | 32 ++++++++++----------- NEWS.md | 19 ++++++++++++ R/download_predicate_dsl.R | 46 +++++++++++++++++++++---------- R/gbif_issues.R | 16 ++++++---- R/occ_download_meta.R | 41 ++++++++++++++++++++------- R/wkt_parse.R | 2 + man/download_predicate_dsl.Rd | 5 ++- man/occ_data.Rd | 9 ++---- man/occ_search.Rd | 9 ++---- man/wkt_parse.Rd | 2 + tests/testthat/test-gbif_issues.R | 4 ++ tests/testthat/test-occ_data.R | 2 + tests/testthat/test-occ_issues.R | 2 - tests/testthat/test-occ_search.r | 1 tests/testthat/test-predicate_builders.R | 9 +++--- tests/testthat/test-wkt_parse.R | 2 + 17 files changed, 142 insertions(+), 68 deletions(-)
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Description: Functions for fitting and doing predictions with
Gaussian process models using Vecchia's (1988) approximation.
Package also includes functions for reordering input locations,
finding ordered nearest neighbors (with help from 'FNN' package),
grouping operations, and conditional simulations.
Covariance functions for spatial and spatial-temporal data
on Euclidean domains and spheres are provided. The original
approximation is due to Vecchia (1988)
<http://www.jstor.org/stable/2345768>, and the reordering and
grouping methods are from Guinness (2018)
<doi:10.1080/00401706.2018.1437476>.
Model fitting employs a Fisher scoring algorithm described
in Guinness (2019) <arXiv:1905.08374>.
Author: Joseph Guinness [aut, cre],
Matthias Katzfuss [aut],
Youssef Fahmy [aut]
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Diff between GpGp versions 0.3.1 dated 2020-10-17 and 0.3.2 dated 2021-01-27
DESCRIPTION | 8 +- MD5 | 18 +++--- NEWS.md | 11 ++++ R/fit_model.R | 44 ++++++++++++++-- R/jason3.R | 4 - man/jason3.Rd | 2 src/covmatrix_funs.h | 129 ++++++++++++++++++++++-------------------------- src/covmatrix_funs_01.h | 8 ++ src/covmatrix_funs_02.h | 6 ++ src/onepass.h | 127 ++++++++++++++++++++++++----------------------- 10 files changed, 205 insertions(+), 152 deletions(-)
Title: Spatial Influence of Landscape
Description: Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.
Author: Carpentier F. and Martin O.
Maintainer: Martin Olivier <olivier.martin@inra.fr>
Diff between siland versions 2.0.4 dated 2020-12-07 and 2.0.5 dated 2021-01-27
DESCRIPTION | 8 MD5 | 56 +-- NAMESPACE | 120 ++++--- R/Fsiland.quantile.R | 63 ++-- R/bufferforsiland.R | 4 R/miscsiland.R | 748 ++++++++++++++++++++++++------------------------ R/plot.Bsiland.R |only R/plot.Fsiland.R |only R/plotBsiland.land.R | 2 R/summary.Bsiland.R | 32 +- build/partial.rdb |binary build/vignette.rds |binary data/dataCmoth.RData |binary data/dataSiland.RData |binary data/landCmoth.RData |binary data/landSiland.RData |binary data/likresB1.RData |binary data/resB1.RData |binary data/resB2.RData |binary data/resB3.RData |binary data/resF1.RData |binary data/resF3.RData |binary data/resF4.RData |binary data/resF5.1.RData |binary data/resF5.2.RData |binary data/resY.RData |binary inst/doc/siland.html | 25 - man/landSiland.Rd | 12 man/plot.Bsiland.Rd |only man/plot.Fsiland.Rd |only man/plotBsiland.land.Rd | 8 31 files changed, 544 insertions(+), 534 deletions(-)
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez [aut, cre],
Jose Emmanuel Chacon [cph],
Carlos Aguero [cph],
Jorge Arce [cph]
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 3.0.4 dated 2020-06-07 and 3.0.9 dated 2021-01-27
DESCRIPTION | 22 MD5 | 84 + NAMESPACE | 27 R/RSDA.R | 4 R/data.R | 24 R/mcfa_scatterplot.R | 4 R/sym.predict.R | 2 R/sym_interval_pca.R | 6 R/sym_regression.R |only build/vignette.rds |binary data/Cardiological.rda |binary data/USCrime.rda |binary data/VeterinaryData.rda |binary data/abalone.rda |binary data/cardiologicalv2.rda |only data/ex1_db2so.rda |binary data/ex_cfa1.rda |binary data/ex_cfa2.rda |binary data/ex_mcfa1.rda |binary data/ex_mcfa2.rda |binary data/example1.rda |binary data/example2.rda |binary data/example3.rda |binary data/example4.rda |binary data/example5.rda |binary data/example6.rda |binary data/example7.rda |binary data/int_prost_test.rda |binary data/int_prost_train.rda |binary data/uscrime_int.rda |binary data/uscrime_intv2.rda |only inst/doc/introduction.html | 1690 +++++++++++++++-------------------- man/RSDA.Rd | 4 man/cardiologicalv2.Rd |only man/method_summary.Rd |only man/sym.gbm.Rd |only man/sym.knn.Rd |only man/sym.nnet.Rd |only man/sym.predict.Rd | 2 man/sym.predict.symbolic_gbm_cm.Rd |only man/sym.predict.symbolic_gbm_crm.Rd |only man/sym.predict.symbolic_knn_cm.Rd |only man/sym.predict.symbolic_knn_crm.Rd |only man/sym.predict.symbolic_nnet_cm.Rd |only man/sym.predict.symbolic_nnet_crm.Rd |only man/sym.predict.symbolic_rf_cm.Rd |only man/sym.predict.symbolic_rf_crm.Rd |only man/sym.predict.symbolic_rt_cm.Rd |only man/sym.predict.symbolic_rt_crm.Rd |only man/sym.predict.symbolic_svm_cm.Rd |only man/sym.predict.symbolic_svm_crm.Rd |only man/sym.rf.Rd |only man/sym.rt.Rd |only man/sym.svm.Rd |only man/uscrime_intv2.Rd |only 55 files changed, 884 insertions(+), 985 deletions(-)
Title: Download Data from the Philadelphia District Attorney's Office
Description: Provides a series of helper functions to download and
clean the data that is publicly available on the Philadelphia District
Attorney's Office Public Data Dashboard
(<https://data.philadao.com/download.html>). This package is not an
official product of the Philadelphia District Attorney's Office - it is
merely a way to handle their already public and freely available data.
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>)
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between phillydaodata versions 1.0.0 dated 2020-11-14 and 1.0.1 dated 2021-01-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/setup.R | 1 + 4 files changed, 11 insertions(+), 6 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party party package, but on core R
only.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 1.1.0 dated 2021-01-20 and 1.2.0 dated 2021-01-27
DESCRIPTION | 10 +- MD5 | 22 ++++-- NAMESPACE | 2 NEWS.md | 11 +++ R/compare_vectors.R |only R/r.R |only R/test_helpers.R | 14 +++- README.md | 1 inst/NEWS.rd | 13 +++ inst/doc/An_Introduction_to_fritools.html | 2 inst/runit_tests/runit-compare_vectors.R |only inst/runit_tests/runit-r.R |only inst/runit_tests/runit-search_files.R | 101 +++++++++++++++--------------- man/compare_vectors.Rd |only man/r_cmd_install.Rd |only 15 files changed, 111 insertions(+), 65 deletions(-)
Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including
moving specified levels to front, ordering by first appearance,
reversing, and randomly shuffling), and tools for modifying factor
levels (including collapsing rare levels into other, 'anonymising',
and manually 'recoding').
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between forcats versions 0.5.0 dated 2020-03-01 and 0.5.1 dated 2021-01-27
DESCRIPTION | 17 - LICENSE |only MD5 | 25 +- NEWS.md | 6 R/lump.R | 4 R/recode.R | 11 - README.md | 23 +- build/vignette.rds |binary inst/doc/forcats.Rmd | 2 inst/doc/forcats.html | 466 +++++++++++++++---------------------------------- man/fct_recode.Rd | 11 - man/forcats-package.Rd | 2 man/gss_cat.Rd | 6 vignettes/forcats.Rmd | 2 14 files changed, 212 insertions(+), 363 deletions(-)
Title: Panel Vector Autoregression
Description: We extend two general methods of moment estimators to panel vector
autoregression models (PVAR) with p lags of endogenous variables, predetermined
and strictly exogenous variables. This general PVAR model contains the first
difference GMM estimator by Holtz-Eakin et al. (1988) <doi:10.2307/1913103>,
Arellano and Bond (1991) <doi:10.2307/2297968> and the system GMM estimator
by Blundell and Bond (1998) <doi:10.1016/S0304-4076(98)00009-8>. We also
provide specification tests (Hansen overidentification test, lag selection
criterion and stability test of the PVAR polynomial) and classical structural
analysis for PVAR models such as orthogonal and generalized impulse response
functions, bootstrapped confidence intervals for impulse response analysis and
forecast error variance decompositions.
Author: Michael Sigmund [aut],
Robert Ferstl [aut, cre]
Maintainer: Robert Ferstl <robert.ferstl@ur.de>
Diff between panelvar versions 0.5.2 dated 2019-01-22 and 0.5.3 dated 2021-01-27
panelvar-0.5.2/panelvar/data/datalist |only panelvar-0.5.3/panelvar/DESCRIPTION | 8 panelvar-0.5.3/panelvar/MD5 | 99 +-- panelvar-0.5.3/panelvar/NAMESPACE | 153 +++--- panelvar-0.5.3/panelvar/R/datafiles.R | 13 panelvar-0.5.3/panelvar/R/helper_functions.R | 106 ++++ panelvar-0.5.3/panelvar/R/pvar.R | 10 panelvar-0.5.3/panelvar/build/partial.rdb |binary panelvar-0.5.3/panelvar/inst/CITATION | 14 panelvar-0.5.3/panelvar/man/Andrews_Lu_MMSC.Rd | 64 +- panelvar-0.5.3/panelvar/man/Cigar.Rd | 80 +-- panelvar-0.5.3/panelvar/man/Dahlberg.Rd | 80 +-- panelvar-0.5.3/panelvar/man/abdata.Rd | 72 +- panelvar-0.5.3/panelvar/man/bootstrap_irf.Rd | 77 +-- panelvar-0.5.3/panelvar/man/coef.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/coef.pvargmm.Rd | 40 - panelvar-0.5.3/panelvar/man/coef.pvarhk.Rd | 32 - panelvar-0.5.3/panelvar/man/ex1_dahlberg_data.Rd | 30 - panelvar-0.5.3/panelvar/man/ex1_dahlberg_data_bs.Rd | 30 - panelvar-0.5.3/panelvar/man/ex2_nlswork2_data_bs.Rd | 30 - panelvar-0.5.3/panelvar/man/ex3_abdata.Rd | 30 - panelvar-0.5.3/panelvar/man/extract.Rd | 60 +- panelvar-0.5.3/panelvar/man/fevd_orthogonal.Rd | 85 +-- panelvar-0.5.3/panelvar/man/fixedeffects.Rd | 50 - panelvar-0.5.3/panelvar/man/girf.Rd | 50 - panelvar-0.5.3/panelvar/man/hansen_j_test.Rd | 46 - panelvar-0.5.3/panelvar/man/knit_print.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/knit_print.pvargmm.Rd | 32 - panelvar-0.5.3/panelvar/man/knit_print.pvarhk.Rd | 32 - panelvar-0.5.3/panelvar/man/knit_print.summary.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/knit_print.summary.pvargmm.Rd | 32 - panelvar-0.5.3/panelvar/man/knit_print.summary.pvarhk.Rd | 32 - panelvar-0.5.3/panelvar/man/nlswork2.Rd | 30 - panelvar-0.5.3/panelvar/man/oirf.Rd | 32 - panelvar-0.5.3/panelvar/man/plot.pvarstability.Rd | 32 - panelvar-0.5.3/panelvar/man/print.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/print.pvargmm.Rd | 32 - panelvar-0.5.3/panelvar/man/print.pvarhk.Rd | 32 - panelvar-0.5.3/panelvar/man/print.pvarstability.Rd | 32 - panelvar-0.5.3/panelvar/man/print.summary.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/print.summary.pvargmm.Rd | 32 - panelvar-0.5.3/panelvar/man/print.summary.pvarhk.Rd | 32 - panelvar-0.5.3/panelvar/man/pvalue.Rd | 60 +- panelvar-0.5.3/panelvar/man/pvarfeols.Rd | 80 +-- panelvar-0.5.3/panelvar/man/pvargmm.Rd | 302 ++++++------ panelvar-0.5.3/panelvar/man/pvarhk.Rd | 79 +-- panelvar-0.5.3/panelvar/man/se.Rd | 60 +- panelvar-0.5.3/panelvar/man/stability.Rd | 62 +- panelvar-0.5.3/panelvar/man/summary.pvarfeols.Rd | 32 - panelvar-0.5.3/panelvar/man/summary.pvargmm.Rd | 32 - panelvar-0.5.3/panelvar/man/summary.pvarhk.Rd | 32 - 51 files changed, 1344 insertions(+), 1196 deletions(-)
Title: Interpreting Glucose Data from Continuous Glucose Monitors
Description: Implements a wide range of metrics for measuring glucose control and glucose variability based on continuous glucose monitoring data. The list of implemented metrics is summarized in Rodbard (2009) <doi:10.1089/dia.2009.0015>. Additional visualization tools include time-series and lasagna plots.
Author: Steve Broll [aut],
Jacek Urbanek [aut],
David Buchanan [aut],
Elizabeth Chun [aut],
John Muschelli [aut] (<https://orcid.org/0000-0001-6469-1750>),
John Schwenck [ctb],
Mary Martin [ctb],
Pratik Patel [ctb],
Marielle Hicban [ctb],
Nhan Nguyen [ctb],
Irina Gaynanova [aut, cre] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Diff between iglu versions 2.0.1 dated 2020-09-15 and 2.1.0 dated 2021-01-27
DESCRIPTION | 40 MD5 | 118 +- NAMESPACE | 10 NEWS.md | 10 R/AUC.R | 25 R/above_percent.R | 6 R/active_percent.R | 76 + R/agp_metrics.R |only R/agp_profile.R |only R/all_metrics.R |only R/below_percent.R | 8 R/cogi.r |only R/import_packages.R | 2 R/in_range_percent.R | 8 R/lasagna_plots.R | 84 + R/mag.R |only R/optimized_iglu_functions.R |only R/plot_agp.R |only R/plot_daily.R |only R/plot_glu.R | 80 + R/plot_ranges.R |only R/roc.R | 1 R/sd_measures.R | 47 - README.md | 27 build/partial.rdb |binary inst/doc/iglu.Rmd | 2 inst/doc/iglu.html | 114 +- inst/doc/metrics_list.Rmd | 2 inst/doc/metrics_list.html | 98 +- inst/shiny_iglu/rsconnect/shinyapps.io/irinagain/shiny_iglu.dcf | 4 inst/shiny_iglu/server.R | 431 ++++++++-- inst/shiny_iglu/ui.R | 47 - man/above_percent.Rd | 4 man/active_percent.Rd | 30 man/agp.Rd |only man/agp_metrics.Rd |only man/all_metrics.Rd |only man/below_percent.Rd | 5 man/cogi.Rd |only man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-3-2.png |binary man/in_range_percent.Rd | 6 man/mag.Rd |only man/optimized_iglu_functions.Rd |only man/plot_agp.Rd |only man/plot_daily.Rd |only man/plot_glu.Rd | 26 man/plot_lasagna.Rd | 25 man/plot_lasagna_1subject.Rd | 25 man/plot_ranges.Rd |only man/roc.Rd | 1 man/sd_measures.Rd | 23 vignettes/iglu.Rmd | 2 vignettes/iglu_files/figure-html/unnamed-chunk-15-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-15-2.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-16-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-17-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-18-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-19-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-20-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-21-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-22-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-23-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-24-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-25-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-26-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-27-1.png |binary vignettes/iglu_files/figure-html/unnamed-chunk-28-1.png |binary vignettes/metrics_list.Rmd | 2 69 files changed, 1025 insertions(+), 364 deletions(-)
Title: Fast, Dependency-Free Geodesic Distance Calculations
Description: Dependency-free, ultra fast calculation of geodesic
distances. Includes the reference nanometre-accuracy geodesic
distances of Karney (2013) <doi:10.1007/s00190-012-0578-z>, as used by
the 'sf' package, as well as Haversine and Vincenty distances. Default
distance measure is the "Mapbox cheap ruler" which is generally more
accurate than Haversine or Vincenty for distances out to a few hundred
kilometres, and is considerably faster. The main function accepts one
or two inputs in almost any generic rectangular form, and returns
either matrices of pairwise distances, or vectors of sequential
distances.
Author: Mark Padgham [aut, cre],
Michael D. Sumner [aut],
Charles F.F Karney [cph] (Original author of included code for geodesic
distances)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between geodist versions 0.0.6 dated 2020-10-15 and 0.0.7 dated 2021-01-27
DESCRIPTION | 6 MD5 | 10 NEWS.md | 48 + R/utils.R | 55 +- build/vignette.rds |binary inst/doc/geodist.html | 1317 -------------------------------------------------- 6 files changed, 86 insertions(+), 1350 deletions(-)
Title: Modelling of Population Growth
Description: Modelling of population growth under static and dynamic environmental conditions.
Includes functions for model fitting and making prediction under isothermal and
dynamic conditions. The methods (algorithms & models) are based on
predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).
Author: Alberto Garre [aut, cre] (<https://orcid.org/0000-0002-4404-3550>),
Jeroen Koomen [aut],
Heidy den Besten [aut],
Marcel Zwietering [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between biogrowth versions 0.1.2 dated 2020-11-26 and 0.2.0 dated 2021-01-27
DESCRIPTION | 14 MD5 | 115 - NAMESPACE | 5 NEWS.md | 17 R/MCMCgrowth_class.R | 95 + R/TimeDistribution_class.R | 4 R/baranyi_model.R | 6 R/data.R | 40 R/fit_dynamic_growth.R | 87 - R/fit_iso_growth.R | 36 R/fit_multi_dynamic.R | 81 R/fit_secondary_models.R | 27 R/functions_counts.R | 22 R/helpers.R | 50 R/meatinfo_primary.R | 18 R/metainfo_secondary.R | 105 - R/predict_MCMC_growth.R | 52 R/predict_dynamic_growth.R | 55 R/predict_isothermal_growth.R | 55 R/predict_stochastic_growth.R | 163 + README.md | 111 - build/vignette.rds |binary data/arabian_tractors.rda |only data/growth_salmonella.rda |only inst/doc/Publication-ready-figures-with-biogrowth.R | 37 inst/doc/Publication-ready-figures-with-biogrowth.Rmd | 39 inst/doc/Publication-ready-figures-with-biogrowth.html | 91 - inst/doc/biogrowth_basics.R | 146 + inst/doc/biogrowth_basics.Rmd | 652 +++++-- inst/doc/biogrowth_basics.html | 1426 +++++++++-------- inst/doc/dynamic_for_static.R |only inst/doc/dynamic_for_static.Rmd |only inst/doc/dynamic_for_static.html |only man/MCMCgrowth.Rd | 53 man/Q0_to_lambda.Rd |only man/TimeDistribution.Rd | 4 man/arabian_tractors.Rd |only man/check_secondary_pars.Rd | 25 man/check_stochastic_pars.Rd |only man/distribution_to_logcount.Rd | 16 man/example_cardinal.Rd | 4 man/example_dynamic_growth.Rd | 4 man/example_env_conditions.Rd | 4 man/figures/README-example-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/fit_MCMC_growth.Rd | 22 man/fit_dynamic_growth.Rd | 22 man/fit_isothermal_growth.Rd | 19 man/fit_multiple_growth.Rd | 18 man/fit_multiple_growth_MCMC.Rd | 19 man/fit_secondary_growth.Rd | 13 man/growth_salmonella.Rd |only man/iso_Baranyi.Rd | 2 man/iso_repGompertz.Rd | 2 man/lambda_to_Q0.Rd |only man/logistic_model.Rd |only man/predict_MCMC_growth.Rd | 27 man/predict_dynamic_growth.Rd | 20 man/predict_isothermal_growth.Rd | 5 man/predict_stochastic_growth.Rd | 80 man/richards_model.Rd |only man/trilinear_model.Rd | 2 vignettes/Publication-ready-figures-with-biogrowth.Rmd | 39 vignettes/biogrowth_basics.Rmd | 652 +++++-- vignettes/dynamic_for_static.Rmd |only 65 files changed, 2990 insertions(+), 1611 deletions(-)
Title: Count and Continuous Generalized Variability Indexes
Description: Univariate Poisson dispersion index for count data, univariate exponential variation index for positive continuous data functions are performed. Also, the generalized dispersion index and the marginal dispersion index functions are carried out. Finally, the generalized variation index and the marginal variation index functions are computed.
Author: Aboubacar Y. Touré and Célestin C. Kokonendji
Maintainer: Aboubacar Y. Touré <aboubacaryacoubatoure.ussgb@gmail.com>
Diff between GWI versions 1.0.0 dated 2021-01-26 and 1.0.1 dated 2021-01-27
DESCRIPTION | 19 ++++++++----------- MD5 | 19 ++++++++++--------- R/di.R | 9 +++++---- R/gmdi.R | 17 ++++++++--------- R/gmvi.R | 15 +++++++-------- R/vi.R | 9 +++++---- man/GWI-package.Rd |only man/di.fun.Rd | 5 +++-- man/gmdi.fun.Rd | 13 ++++++------- man/gmvi.fun.Rd | 10 ++++------ man/vi.fun.Rd | 5 +++-- 11 files changed, 59 insertions(+), 62 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Specialization of method ggplot(): accept and convert on the fly
time series data. Geom: "table", "plot" and "grob" add insets to plots
using native data coordinates, while "table_npc", "plot_npc" and "grob_npc"
do the same using "npc" coordinates through new aesthetics "npcx" and "npcy".
Statistics: locate and tag peaks and valleys; count observations in different
quadrants of a plot; select observations based on 2D density; label with the
equation of a polynomial fitted with lm() or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' are supported. Scales and stats to build volcano and quadrant plots
based on outcomes, fold changes, p-values and false discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.3.8 dated 2021-01-25 and 0.3.8-1 dated 2021-01-27
DESCRIPTION | 14 MD5 | 14 NEWS.md | 6 inst/doc/grammar-extensions.html | 6 inst/doc/model-based-annotations.R | 93 ++++- inst/doc/model-based-annotations.Rmd | 101 +++++ inst/doc/model-based-annotations.html | 581 ++++++++++++++++++---------------- vignettes/model-based-annotations.Rmd | 101 +++++ 8 files changed, 611 insertions(+), 305 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database
(<https://ebird.org/home>), including functions for searching for bird
observations by geographic location (latitude, longitude), eBird
hotspots, location identifiers, by notable sightings, by region, and by
taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Andy Teucher [aut],
Guy Babineau [ctb],
Marianna Foos [ctb],
David Bradnum [ctb],
Sebastian Pardo [aut, cre] (<https://orcid.org/0000-0002-4147-5796>)
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 1.1.0 dated 2019-10-24 and 1.2.0 dated 2021-01-27
DESCRIPTION | 28 MD5 | 82 +- NAMESPACE | 6 NEWS.md | 9 R/ebirdchecklistfeed.R |only R/ebirdfreq.R | 28 R/ebirdgeo.R | 8 R/ebirdhistorical.R | 7 R/ebirdhotspot.R | 2 R/ebirdhotspotlist.R |only R/ebirdnotable.R | 6 R/ebirdregion.R | 16 R/ebirdregioninfo.R | 4 R/ebirdregionspecies.R |only R/ebirdsubregionlist.R |only R/ebirdtaxonomy.R | 37 - R/nearestobs.R | 25 R/zzz.R | 17 README.md | 473 +++++++++----- build/vignette.rds |binary inst/doc/rebird_vignette.Rmd | 707 +++++++++------------ inst/doc/rebird_vignette.html | 1013 +++++++++++++------------------ inst/vign/rebird_vignette.Rmd | 171 ++--- inst/vign/rebird_vignette.md | 707 +++++++++------------ man/ebirdchecklistfeed.Rd |only man/ebirdfreq.Rd | 66 +- man/ebirdgeo.Rd | 25 man/ebirdhistorical.Rd | 26 man/ebirdhotspot.Rd | 15 man/ebirdhotspotlist.Rd |only man/ebirdloc.Rd | 15 man/ebirdnotable.Rd | 26 man/ebirdregion.Rd | 46 - man/ebirdregionspecies.Rd |only man/ebirdsubregionlist.Rd |only man/ebirdtaxonomy.Rd | 48 + man/nearestobs.Rd | 47 - man/rebird-package.Rd | 20 tests/testthat/test-ebirdchecklistfeed.R |only tests/testthat/test-ebirdfreq.R | 30 tests/testthat/test-ebirdhistorical.R | 13 tests/testthat/test-ebirdhotspotlist.R |only tests/testthat/test-ebirdnotable.R | 6 tests/testthat/test-ebirdregion.R | 8 tests/testthat/test-ebirdregionspecies.R |only tests/testthat/test-ebirdsubregionlist.R |only tests/testthat/test-nearestobs.R | 4 vignettes/rebird_vignette.Rmd | 707 +++++++++------------ 48 files changed, 2274 insertions(+), 2174 deletions(-)
Title: Semiparametric Proportional Odds Rate Model
Description: R implementation of the methods described in "A rank-based empirical likelihood approach to two-sample proportional odds model and its goodness-of-fit" by Zhong Guan and Cheng Peng, Journal of Nonparametric Statistics, 23, no. 3, 763--780.
Author: Zhong Guan <zguan@iusb.edu>; Cheng Peng <cpeng@usm.maine.edu>
Maintainer: Zhong Guan <zguan@iusb.edu>
Diff between sporm versions 1.1 dated 2011-01-19 and 1.1.1 dated 2021-01-27
DESCRIPTION | 17 ++++++++--------- MD5 |only NAMESPACE |only R/ell.theta.R | 2 +- man/H.Binv.Rd | 5 +---- man/V.theta.Rd | 13 ++----------- man/confid.int.theta.Rd | 4 +--- man/dd.est.Rd | 7 +------ man/ell.theta.Rd | 13 +++++-------- man/elltheta.rd | 2 +- man/grad.hessinv.Rd | 4 +--- man/ks.sporm.Rd | 3 --- man/ks.stat.Rd | 3 --- man/mrle.sporm.Rd | 7 +------ man/newton.theta.Rd | 4 +--- man/phi.Rd | 12 ++---------- man/plotor.Rd | 14 +------------- man/sporm-package.Rd | 5 +---- man/test.theta.Rd | 3 --- 19 files changed, 27 insertions(+), 91 deletions(-)
Title: Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment. See also
Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>. and Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464>.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Nils Kehrein [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [aut],
Alexander Singer [ctb],
Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>
Diff between morse versions 3.2.7 dated 2020-11-09 and 3.3.0 dated 2021-01-27
morse-3.2.7/morse/man/LCx.Rd |only morse-3.2.7/morse/man/LCx.survFit.Rd |only morse-3.2.7/morse/man/MFx.survFit.Rd |only morse-3.2.7/morse/man/MFx_ode.Rd |only morse-3.2.7/morse/man/MFx_ode.survFit.Rd |only morse-3.2.7/morse/man/ppc.Rd |only morse-3.2.7/morse/man/ppc.reproFitTT.Rd |only morse-3.2.7/morse/man/ppc.survFitCstExp.Rd |only morse-3.2.7/morse/man/ppc.survFitPredict_Nsurv.Rd |only morse-3.2.7/morse/man/ppc.survFitTKTD.Rd |only morse-3.2.7/morse/man/ppc.survFitTT.Rd |only morse-3.2.7/morse/man/ppc.survFitVarExp.Rd |only morse-3.2.7/morse/man/predict.survFit.Rd |only morse-3.2.7/morse/man/predict_Nsurv.Rd |only morse-3.2.7/morse/man/predict_Nsurv.survFit.Rd |only morse-3.2.7/morse/man/predict_Nsurv_check.Rd |only morse-3.2.7/morse/man/predict_Nsurv_check.survFitPredict_Nsurv.Rd |only morse-3.2.7/morse/man/predict_Nsurv_ode.Rd |only morse-3.2.7/morse/man/survFit.survDataCstExp.Rd |only morse-3.2.7/morse/man/survFit.survDataVarExp.Rd |only morse-3.3.0/morse/DESCRIPTION | 9 morse-3.3.0/morse/MD5 | 106 +- morse-3.3.0/morse/NAMESPACE | 2 morse-3.3.0/morse/NEWS | 25 morse-3.3.0/morse/R/LCx.R | 2 morse-3.3.0/morse/R/LCx.survFit.R | 45 - morse-3.3.0/morse/R/MFx.survFit.R | 10 morse-3.3.0/morse/R/MFx_ode.survFit.R | 32 morse-3.3.0/morse/R/modelData.survDataCstExp.R | 3 morse-3.3.0/morse/R/modelData.survDataVarExp.R | 8 morse-3.3.0/morse/R/morse.R | 27 morse-3.3.0/morse/R/ppc.R | 2 morse-3.3.0/morse/R/ppc.reproFitTT.R | 202 ++--- morse-3.3.0/morse/R/ppc.survFitCstExp.R | 2 morse-3.3.0/morse/R/ppc.survFitPredict_Nsurv.R | 2 morse-3.3.0/morse/R/ppc.survFitTKTD.R | 202 ++--- morse-3.3.0/morse/R/ppc.survFitTT.R | 368 +++++----- morse-3.3.0/morse/R/ppc.survFitVarExp.R | 2 morse-3.3.0/morse/R/predict.survFit.R | 14 morse-3.3.0/morse/R/predict_Nsurv.R | 68 + morse-3.3.0/morse/R/predict_Nsurv_check.R | 4 morse-3.3.0/morse/R/predict_Nsurv_ode.R | 75 +- morse-3.3.0/morse/R/predict_ode.survFit.R | 155 +--- morse-3.3.0/morse/R/survFit.R | 2 morse-3.3.0/morse/R/survFit.survDataCstExp.R | 1 morse-3.3.0/morse/R/survFit.survDataVarExp.R | 2 morse-3.3.0/morse/R/survFitTKTD.R | 7 morse-3.3.0/morse/R/survFitTT.R | 18 morse-3.3.0/morse/build/vignette.rds |binary morse-3.3.0/morse/data/FOCUSprofile.rda |only morse-3.3.0/morse/inst/doc/MinimalWorkingExample.R |only morse-3.3.0/morse/inst/doc/MinimalWorkingExample.Rmd |only morse-3.3.0/morse/inst/doc/MinimalWorkingExample.html |only morse-3.3.0/morse/inst/doc/modelling.pdf |binary morse-3.3.0/morse/inst/doc/tutorial.html | 68 - morse-3.3.0/morse/man/FOCUSprofile.Rd |only morse-3.3.0/morse/man/LCX.Rd |only morse-3.3.0/morse/man/MFx.Rd | 209 +++++ morse-3.3.0/morse/man/PPC.Rd |only morse-3.3.0/morse/man/morse-package.Rd | 5 morse-3.3.0/morse/man/predict.Rd |only morse-3.3.0/morse/man/predict_check.Rd |only morse-3.3.0/morse/man/survFit.Rd | 172 ++++ morse-3.3.0/morse/man/survFitTKTD.Rd | 3 morse-3.3.0/morse/src |only morse-3.3.0/morse/tests/testthat/test-LCx.R |only morse-3.3.0/morse/tests/testthat/test-MFx.R | 48 - morse-3.3.0/morse/tests/testthat/test-modelData.R | 79 -- morse-3.3.0/morse/tests/testthat/test-predict.R |only morse-3.3.0/morse/vignettes/MinimalWorkingExample.Rmd |only 70 files changed, 1187 insertions(+), 792 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>),
Ben Baumer [ctb],
Brian Diggs [ctb],
Brian Zhang [ctb],
Cassio Pereira [ctb],
Christophe Dervieux [ctb],
David Hall [ctb],
David Hugh-Jones [ctb],
David Robinson [ctb],
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Elio Campitelli [ctb],
Ellis Hughes [ctb],
Emily Riederer [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Forest Fang [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Garrick Aden-Buie [ctb],
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Hao Zhu [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Ian Lyttle [ctb],
Hodges Daniel [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Javier Luraschi [ctb],
Jeff Arnold [ctb],
Jenny Bryan [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Jonathan Sidi [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kamil Slowikowski [ctb],
Karl Forner [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Lorenz Walthert [ctb],
Lucas Gallindo [ctb],
Marius Hofert [ctb],
Martin Modrák [ctb],
Michael Chirico [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Miller Patrick [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Niels Richard Hansen [ctb],
Noam Ross [ctb],
Obada Mahdi [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Ruaridh Williamson [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Sylvain Rousseau [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tim Mastny [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.30 dated 2020-09-22 and 1.31 dated 2021-01-27
DESCRIPTION | 12 - MD5 | 76 +++--- NAMESPACE | 5 R/block.R | 25 ++ R/defaults.R | 7 R/engine.R | 33 +- R/highlight.R | 2 R/hooks-html.R | 2 R/hooks-md.R | 6 R/hooks-rst.R | 2 R/output.R | 23 +- R/package.R | 3 R/parser.R | 4 R/plot.R | 154 +++++++------ R/table.R | 28 +- R/utils-conversion.R | 26 +- R/utils-vignettes.R | 7 R/utils.R | 124 +++++----- README.md | 23 +- build/vignette.rds |binary inst/doc/docco-classic.html | 2 inst/doc/docco-linear.html | 2 inst/doc/knit_expand.html | 4 inst/doc/knit_print.html | 489 +++++++++++-------------------------------- inst/doc/knitr-html.html | 2 inst/doc/knitr-intro.html | 322 +++++----------------------- inst/doc/knitr-markdown.html | 4 inst/doc/knitr-refcard.pdf |binary man/combine_words.Rd | 13 + man/include_url.Rd | 6 man/kable.Rd | 16 - man/knit2wp.Rd | 13 - man/knit_exit.Rd | 6 man/output_type.Rd | 42 ++- man/read_chunk.Rd | 4 man/vignette_engines.Rd | 2 tests/testit/test-hooks-md.R | 11 tests/testit/test-plot.R | 4 tests/testit/test-utils.R | 250 +++++++++++---------- 39 files changed, 741 insertions(+), 1013 deletions(-)
Title: Tools Graph Matching
Description: Graph matching methods and analysis. The package
works for both 'igraph' objects and matrix objects. You provide the adjacency
matrices of two graphs and some other information you might know, choose the
graph matching method, and it returns the graph matching results. 'iGraphMatch'
also provides a bunch of useful functions you might need related to graph
matching.
Author: Daniel Sussman [aut, cre],
Zihuan Qiao [aut],
Joshua Agterberg [ctb],
Lujia Wang [ctb],
Vince Lyzinski [ctb]
Maintainer: Daniel Sussman <sussman@bu.edu>
Diff between iGraphMatch versions 1.0.0 dated 2021-01-25 and 1.0.1 dated 2021-01-27
DESCRIPTION | 7 +- MD5 | 39 +++++++------ NEWS.md |only R/data.R | 4 - R/gm_indefinite.R | 2 R/gm_isorank.R | 2 R/gm_percolation.R | 2 R/gm_umeyama.R | 2 R/largest_common_cc.R | 6 +- R/match_report.R | 2 man/C.Elegans.Rd | 2 man/Enron.Rd | 2 man/gm_Umeyama.Rd | 2 man/gm_fw.Rd | 2 man/gm_isorank.Rd | 2 man/gm_perco.Rd | 2 man/largest_common_cc.Rd | 6 +- src/lapjv.cpp | 58 ++++++++++---------- src/lapjv.h | 9 +-- src/lapmod.cpp | 132 +++++++++++++++++++++++------------------------ src/rlapjv.cpp | 6 +- 21 files changed, 145 insertions(+), 144 deletions(-)
Title: Estimate Gaussian Mixture Vector Autoregressive Model
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive (GMVAR) model, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (2020) <arXiv:2007.04713>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 1.4.0 dated 2021-01-11 and 1.4.1 dated 2021-01-27
DESCRIPTION | 12 - MD5 | 81 +++++------ NAMESPACE | 1 NEWS.md | 9 + R/GIRF.R | 33 ++-- R/GMVARconstruction.R | 32 +--- R/MAINest.R | 78 ++-------- R/WaldAndLR.R | 42 ++--- R/argumentChecks.R | 5 R/diagnosticPlot.R | 37 +---- R/generateParams.R | 24 +-- R/geneticAlgorithm.R | 8 - R/matcal.R | 73 ++++++++++ R/numericalDifferentiation.R | 2 R/parameterReforms.R | 60 +++++--- R/predictMethod.R | 27 +-- R/quantileResidualTests.R | 31 +--- R/simulateGMVAR.R | 11 - R/standardErrors.R | 27 --- README.md | 24 +-- inst/doc/intro-to-gmvarkit.html | 4 man/GIRF.Rd | 33 ++-- man/LR_test.Rd | 16 +- man/Wald_test.Rd | 26 +-- man/alt_gmvar.Rd | 13 - man/calc_gradient.Rd | 2 man/check_parameters.Rd | 5 man/fitGMVAR.Rd | 41 +---- man/gmvar_to_sgmvar.Rd | 8 - man/iterate_more.Rd | 35 ---- man/predict.gmvar.Rd | 27 +-- man/print_std_errors.Rd | 27 --- man/profile_logliks.Rd | 37 +---- man/quantile_residual_tests.Rd | 31 +--- man/redecompose_Omegas.Rd |only man/simulateGMVAR.Rd | 11 - man/sort_and_standardize_alphas.Rd |only man/sort_components.Rd | 10 - man/swap_parametrization.Rd | 11 - tests/testthat/Rplots.pdf |only tests/testthat/test_matcal.R | 238 ++++++++++++++++++++++----------- tests/testthat/test_parameterReforms.R | 125 ++++++++++++++--- tests/testthat/test_standardErrors.R | 26 +-- 43 files changed, 694 insertions(+), 649 deletions(-)
Title: Generalized Linear Mixed Models using Adaptive Gaussian
Quadrature
Description: Fits generalized linear mixed models for a single grouping factor under
maximum likelihood approximating the integrals over the random effects with an
adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995)
<doi:10.1080/10618600.1995.10474663>.
Author: Dimitris Rizopoulos [aut, cre]
(<https://orcid.org/0000-0001-9397-0900>)
Maintainer: Dimitris Rizopoulos <d.rizopoulos@erasmusmc.nl>
Diff between GLMMadaptive versions 0.7-15 dated 2020-10-13 and 0.8-0 dated 2021-01-27
GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/GLMMadaptive_basics.R |only GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/GLMMadaptive_basics.Rmd |only GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/GLMMadaptive_basics.html |only GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/Methods_MixMod.R |only GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/Methods_MixMod.Rmd |only GLMMadaptive-0.7-15/GLMMadaptive/inst/doc/Methods_MixMod.html |only GLMMadaptive-0.7-15/GLMMadaptive/vignettes/GLMMadaptive_basics.Rmd |only GLMMadaptive-0.7-15/GLMMadaptive/vignettes/Methods_MixMod.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/DESCRIPTION | 8 GLMMadaptive-0.8-0/GLMMadaptive/MD5 | 70 GLMMadaptive-0.8-0/GLMMadaptive/NAMESPACE | 4 GLMMadaptive-0.8-0/GLMMadaptive/NEWS.md | 13 GLMMadaptive-0.8-0/GLMMadaptive/R/Fit_Funs.R | 75 GLMMadaptive-0.8-0/GLMMadaptive/R/methods.R | 4 GLMMadaptive-0.8-0/GLMMadaptive/R/mixed_model.R | 9 GLMMadaptive-0.8-0/GLMMadaptive/README.md | 8 GLMMadaptive-0.8-0/GLMMadaptive/build/vignette.rds |binary GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Custom_Models.R | 8 GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Custom_Models.Rmd | 10 GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Custom_Models.html | 859 +++------- GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Dynamic_Predictions.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Dynamic_Predictions.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Dynamic_Predictions.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/GLMMadaptive.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/GLMMadaptive.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/GLMMadaptive.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Goodness_of_Fit.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Goodness_of_Fit.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Goodness_of_Fit.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Methods.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Methods.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Methods.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Multiple_Comparisons.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Multiple_Comparisons.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Multiple_Comparisons.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Optimization.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Optimization.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Optimization.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Ordinal_Mixed_Models.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Ordinal_Mixed_Models.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/Ordinal_Mixed_Models.html |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/ZeroInflated_and_TwoPart_Models.R |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/ZeroInflated_and_TwoPart_Models.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/inst/doc/ZeroInflated_and_TwoPart_Models.html |only GLMMadaptive-0.8-0/GLMMadaptive/man/GLMMadaptive.Rd | 4 GLMMadaptive-0.8-0/GLMMadaptive/man/extra_fams.Rd | 4 GLMMadaptive-0.8-0/GLMMadaptive/man/mixed_model.Rd | 2 GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Custom_Models.Rmd | 10 GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Dynamic_Predictions.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/GLMMadaptive.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Goodness_of_Fit.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Methods.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Multiple_Comparisons.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Optimization.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/Ordinal_Mixed_Models.Rmd |only GLMMadaptive-0.8-0/GLMMadaptive/vignettes/ZeroInflated_and_TwoPart_Models.Rmd |only 56 files changed, 476 insertions(+), 612 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.11 dated 2021-01-13 and 0.0.12 dated 2021-01-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/fselect.R | 32 +++++++++++++++++++++++--------- man/f1st.Rd | 2 +- 4 files changed, 31 insertions(+), 17 deletions(-)
Title: Semiparametric Analysis of Change-Point
Description: Semiparametric empirical likelihood ratio
based tests of change-point with one-change or epidemic alternatives
with data-based model diagnostic are contained.
Author: Zhong Guan <zguan@iusb.edu>
Maintainer: Zhong Guan <zguan@iusb.edu>
Diff between sac versions 1.0.1 dated 2009-02-25 and 1.0.2 dated 2021-01-27
DESCRIPTION | 29 ++++++++++++++++------------- MD5 |only NAMESPACE | 9 ++++----- R/SemiparChangePoint.R | 39 +++++++++++++++++++++------------------ R/cumsum.test.R | 12 +++++++----- R/plots.R | 2 +- R/schapt.R | 6 +++--- man/BootsModelTest.Rd | 4 +--- man/CriticalValues.Rd | 3 +-- man/Pvalues.Rd | 5 ++--- man/SemiparChangePoint.Rd | 2 +- man/cumsum.test.Rd | 6 ++---- man/schapt.Rd | 19 +++++++++---------- 13 files changed, 68 insertions(+), 68 deletions(-)
Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing the landscape of a tree space, and for
calculating the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.0.0 dated 2021-01-20 and 2.0.2 dated 2021-01-27
DESCRIPTION | 6 +-- MD5 | 30 ++++++++--------- NAMESPACE | 2 + NEWS.md | 7 ++++ R/shiny.R | 6 ++- R/zzz.R | 4 +- build/partial.rdb |binary inst/WORDLIST | 2 + inst/doc/Using-TreeDist.html | 6 +-- inst/doc/using-distances.html | 2 - src/day_1985.cpp | 2 - src/tree_distances.cpp | 47 ++++++++++++++++++++------- tests/figs/deps.txt | 4 +- tests/figs/plot-r/visualize-mci-matching.svg | 20 +++++------ tests/testthat/test-plot.R | 4 ++ tests/testthat/test-tree_distance.R | 34 +++++++++++++++++++ 16 files changed, 126 insertions(+), 50 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following
mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package
is not available from CRAN; see <https://www.gurobi.com/downloads/>. See vignette for installing 'Rsymphony' package
on Mac systems.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.2.0 dated 2021-01-22 and 1.2.2 dated 2021-01-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/plot_functions.R | 4 ++-- man/plot-methods.Rd | 4 ++-- tests/testthat/test-gfi.R | 3 +-- tests/testthat/test_excluding.R | 1 + 6 files changed, 15 insertions(+), 15 deletions(-)
Title: Application Directories: Determine Where to Save Data, Caches,
and Logs
Description: An easy way to determine which directories on the
users computer you should use to save data, caches and logs. A port of
Python's 'Appdirs' (<https://github.com/ActiveState/appdirs>) to
R.
Author: Hadley Wickham [trl, cre, cph],
RStudio [cph],
Sridhar Ratnakumar [aut],
Trent Mick [aut],
ActiveState [cph] (R/appdir.r, R/cache.r, R/data.r, R/log.r translated
from appdirs),
Eddy Petrisor [ctb],
Trevor Davis [trl, aut],
Gabor Csardi [ctb],
Gregory Jefferis [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rappdirs versions 0.3.1 dated 2016-03-28 and 0.3.2 dated 2021-01-27
rappdirs-0.3.1/rappdirs/tests/test-all.R |only rappdirs-0.3.1/rappdirs/tests/testthat/test-site_config_dir.r |only rappdirs-0.3.1/rappdirs/tests/testthat/test-site_data_dir.r |only rappdirs-0.3.1/rappdirs/tests/testthat/test-user_cache_dir.r |only rappdirs-0.3.1/rappdirs/tests/testthat/test-user_config_dir.r |only rappdirs-0.3.1/rappdirs/tests/testthat/test-user_log_dir.r |only rappdirs-0.3.2/rappdirs/DESCRIPTION | 69 +-- rappdirs-0.3.2/rappdirs/MD5 | 51 +- rappdirs-0.3.2/rappdirs/NAMESPACE | 3 rappdirs-0.3.2/rappdirs/NEWS.md | 12 rappdirs-0.3.2/rappdirs/R/appdir.r | 48 -- rappdirs-0.3.2/rappdirs/R/cache.r | 76 +-- rappdirs-0.3.2/rappdirs/R/data.r | 228 ++++------ rappdirs-0.3.2/rappdirs/R/log.r | 46 +- rappdirs-0.3.2/rappdirs/R/rappdirs-package.r | 64 -- rappdirs-0.3.2/rappdirs/R/utils.r | 175 ++++--- rappdirs-0.3.2/rappdirs/README.md | 168 ++----- rappdirs-0.3.2/rappdirs/man/app_dir.Rd | 38 - rappdirs-0.3.2/rappdirs/man/rappdirs-package.Rd | 95 +--- rappdirs-0.3.2/rappdirs/man/site_data_dir.Rd | 58 +- rappdirs-0.3.2/rappdirs/man/user_cache_dir.Rd | 70 +-- rappdirs-0.3.2/rappdirs/man/user_data_dir.Rd | 104 ++-- rappdirs-0.3.2/rappdirs/man/user_log_dir.Rd | 44 + rappdirs-0.3.2/rappdirs/src/init.c |only rappdirs-0.3.2/rappdirs/src/win-path.c | 4 rappdirs-0.3.2/rappdirs/tests/testthat.R |only rappdirs-0.3.2/rappdirs/tests/testthat/_snaps |only rappdirs-0.3.2/rappdirs/tests/testthat/test-appdir.r | 16 rappdirs-0.3.2/rappdirs/tests/testthat/test-cache.r |only rappdirs-0.3.2/rappdirs/tests/testthat/test-data.r |only rappdirs-0.3.2/rappdirs/tests/testthat/test-log.r |only rappdirs-0.3.2/rappdirs/tests/testthat/test-utils.r | 35 + 32 files changed, 649 insertions(+), 755 deletions(-)
Title: Extensions for 'Flextable'
Description: Build display tables easily by extending the functionality of the
'flextable' package. Features include spanning header, grouping rows,
parsing markdown and so on.
Author: Atsushi Yasumoto [aut, cph, cre]
(<https://orcid.org/0000-0002-8335-495X>),
Romain François [ctb] (<https://orcid.org/0000-0002-2444-4226>)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>
Diff between ftExtra versions 0.1.0 dated 2020-10-28 and 0.1.1 dated 2021-01-27
ftExtra-0.1.0/ftExtra/vignettes/example.bib |only ftExtra-0.1.1/ftExtra/DESCRIPTION | 8 ftExtra-0.1.1/ftExtra/MD5 | 27 ftExtra-0.1.1/ftExtra/NEWS.md | 7 ftExtra-0.1.1/ftExtra/R/as-paragraph-md.R | 14 ftExtra-0.1.1/ftExtra/build/vignette.rds |binary ftExtra-0.1.1/ftExtra/inst/doc/format_columns.R | 51 + ftExtra-0.1.1/ftExtra/inst/doc/format_columns.Rmd | 97 ++ ftExtra-0.1.1/ftExtra/inst/doc/format_columns.html | 591 +++++------------- ftExtra-0.1.1/ftExtra/inst/doc/group-rows.html | 403 +----------- ftExtra-0.1.1/ftExtra/inst/doc/transform-headers.html | 367 ----------- ftExtra-0.1.1/ftExtra/inst/lua/math.lua | 2 ftExtra-0.1.1/ftExtra/man/separate_header.Rd | 3 ftExtra-0.1.1/ftExtra/man/span_header.Rd | 3 ftExtra-0.1.1/ftExtra/vignettes/format_columns.Rmd | 97 ++ 15 files changed, 533 insertions(+), 1137 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.42 dated 2020-11-07 and 2.43 dated 2021-01-27
Epi-2.42/Epi/R/factorize.R |only Epi-2.43/Epi/CHANGES | 36 ++ Epi-2.43/Epi/DESCRIPTION | 12 Epi-2.43/Epi/MD5 | 79 +++-- Epi-2.43/Epi/NAMESPACE | 112 ++++---- Epi-2.43/Epi/R/Relevel.Lexis.R |only Epi-2.43/Epi/R/Relevel.R | 15 - Epi-2.43/Epi/R/addCov.Lexis.R | 190 ++++++------- Epi-2.43/Epi/R/boxes.MS.R | 16 - Epi-2.43/Epi/R/ci.Crisk.R |only Epi-2.43/Epi/R/cutLexis.R | 27 + Epi-2.43/Epi/R/foreign.R | 20 - Epi-2.43/Epi/R/lexis.R | 13 Epi-2.43/Epi/R/mcutLexis.R | 20 - Epi-2.43/Epi/R/rcutLexis.R | 23 + Epi-2.43/Epi/R/stack.Lexis.R | 5 Epi-2.43/Epi/data/st2alb.rda |only Epi-2.43/Epi/data/st2clin.rda |only Epi-2.43/Epi/data/steno2.rda |only Epi-2.43/Epi/inst/doc/crisk.R |only Epi-2.43/Epi/inst/doc/crisk.pdf |only Epi-2.43/Epi/inst/doc/flup.pdf |binary Epi-2.43/Epi/inst/doc/index.html | 7 Epi-2.43/Epi/inst/doc/simLexis.pdf |binary Epi-2.43/Epi/inst/doc/yll.pdf |binary Epi-2.43/Epi/man/Relevel.Rd | 38 +- Epi-2.43/Epi/man/addCov.Lexis.Rd | 63 +--- Epi-2.43/Epi/man/boxes.MS.Rd | 6 Epi-2.43/Epi/man/ci.Crisk.Rd |only Epi-2.43/Epi/man/crr.Lexis.Rd | 2 Epi-2.43/Epi/man/cutLexis.Rd | 2 Epi-2.43/Epi/man/effx.Rd | 5 Epi-2.43/Epi/man/mcutLexis.Rd | 2 Epi-2.43/Epi/man/rcutLexis.Rd | 12 Epi-2.43/Epi/man/steno2.Rd |only Epi-2.43/Epi/man/subset.Lexis.Rd | 4 Epi-2.43/Epi/man/transform.Lexis.Rd | 122 ++++---- Epi-2.43/Epi/vignettes/crisk.R |only Epi-2.43/Epi/vignettes/crisk.rnw |only Epi-2.43/Epi/vignettes/crisk.tex |only Epi-2.43/Epi/vignettes/fixall | 6 Epi-2.43/Epi/vignettes/flup.tex | 83 ++--- Epi-2.43/Epi/vignettes/sL.tex | 501 ++++++++++++++---------------------- Epi-2.43/Epi/vignettes/simLexis.rnw | 2 Epi-2.43/Epi/vignettes/simLexis.tex | 52 +-- Epi-2.43/Epi/vignettes/yl.tex | 324 +++++++++-------------- Epi-2.43/Epi/vignettes/yll.tex | 12 47 files changed, 861 insertions(+), 950 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE)
biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>,
geometric adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method <doi:10.12702/1984-7033.v04n01a02>, power law residuals
(POLAR) statistics by Doring et al. (2015)
<doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for
computing biometrical analysis such as path analysis, canonical
correlation, partial correlation, clustering analysis, and tools for
inspecting, manipulating, summarizing and plotting typical
multi-environment trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.11.0 dated 2020-12-12 and 1.12.0 dated 2021-01-27
metan-1.11.0/metan/R/ge_simula.R |only metan-1.11.0/metan/man/ge_simula.Rd |only metan-1.12.0/metan/DESCRIPTION | 6 metan-1.12.0/metan/MD5 | 84 metan-1.12.0/metan/NAMESPACE | 10 metan-1.12.0/metan/NEWS.md | 40 metan-1.12.0/metan/R/WAASB.R | 2 metan-1.12.0/metan/R/anova_joint.R | 7 metan-1.12.0/metan/R/arrange_ggplot.R | 35 metan-1.12.0/metan/R/corr_ci.R | 14 metan-1.12.0/metan/R/covcor_design.R | 12 metan-1.12.0/metan/R/cv_ammi.R | 20 metan-1.12.0/metan/R/cv_ammif.R | 24 metan-1.12.0/metan/R/cv_blup.R | 17 metan-1.12.0/metan/R/data_simula.R |only metan-1.12.0/metan/R/gafem.R | 83 metan-1.12.0/metan/R/gamem.R | 2 metan-1.12.0/metan/R/get_model_data.R | 15 metan-1.12.0/metan/R/gge.R | 279 metan-1.12.0/metan/R/mgidi.R | 9 metan-1.12.0/metan/R/path_coeff.R | 208 metan-1.12.0/metan/R/plot_ci.R | 112 metan-1.12.0/metan/R/residual_plots.R | 2 metan-1.12.0/metan/R/select_helpers.R | 6 metan-1.12.0/metan/R/utilities.R | 241 metan-1.12.0/metan/R/utils_sets.R | 35 metan-1.12.0/metan/R/wsmp.R | 6 metan-1.12.0/metan/R/zzz.R | 6 metan-1.12.0/metan/build/metan.pdf |32575 +++++++++++------------ metan-1.12.0/metan/build/partial.rdb |binary metan-1.12.0/metan/inst/doc/metan_start.html | 77 metan-1.12.0/metan/man/arrange_ggplot.Rd | 36 metan-1.12.0/metan/man/corr_ci.Rd | 13 metan-1.12.0/metan/man/covcor_design.Rd | 6 metan-1.12.0/metan/man/data_simula.Rd |only metan-1.12.0/metan/man/figures/README-AMMI-1.png |binary metan-1.12.0/metan/man/figures/README-GGE-1.png |binary metan-1.12.0/metan/man/gafem.Rd | 22 metan-1.12.0/metan/man/path_coeff.Rd | 55 metan-1.12.0/metan/man/plot.gge.Rd | 4 metan-1.12.0/metan/man/plot_ci.Rd | 35 metan-1.12.0/metan/man/reexports.Rd | 4 metan-1.12.0/metan/man/utils_num_str.Rd | 15 metan-1.12.0/metan/man/utils_rows_cols.Rd | 37 metan-1.12.0/metan/man/utils_sets.Rd | 14 45 files changed, 17416 insertions(+), 16752 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented wing2015() for
segment_snags()),
Bourdon Jean-François [ctb] (Contributed to Roussel2020() for
track_sensor()),
Gatziolis Demetrios [ctb] (Implemented Gatziolis2019() for
track_sensor())
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 3.1.0 dated 2021-01-18 and 3.1.1 dated 2021-01-27
lidR-3.1.0/lidR/inst/extdata/Megaplot.lax |only lidR-3.1.0/lidR/inst/extdata/MixedConifer.lax |only lidR-3.1.1/lidR/DESCRIPTION | 8 +-- lidR-3.1.1/lidR/MD5 | 28 +++++----- lidR-3.1.1/lidR/NEWS.md | 6 ++ lidR-3.1.1/lidR/R/las_tools.R | 7 ++ lidR-3.1.1/lidR/inst/include/lidR/GridPartition.h | 4 - lidR-3.1.1/lidR/inst/include/lidR/Octree.h | 3 - lidR-3.1.1/lidR/inst/include/lidR/QuadTree.h | 3 - lidR-3.1.1/lidR/src/LAS.cpp | 10 +-- lidR-3.1.1/lidR/src/RcppFunction.cpp | 36 +++++++++++--- lidR-3.1.1/lidR/tests/testthat/Rplots.pdf |binary lidR-3.1.1/lidR/tests/testthat/test-catalog_laxindex.R | 1 lidR-3.1.1/lidR/tests/testthat/test-normalize_intensity.R | 7 ++ lidR-3.1.1/lidR/tests/testthat/test-quantization.R | 6 ++ lidR-3.1.1/lidR/tests/testthat/test-spTransform.R | 2 16 files changed, 85 insertions(+), 36 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: LUOMUS - Finnish Museum of Natural History [cph],
William Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William Morris <willi@mmorris.email>
Diff between finbif versions 0.4.0 dated 2020-12-17 and 0.4.1 dated 2021-01-27
finbif-0.4.0/finbif/tests/figs |only finbif-0.4.1/finbif/DESCRIPTION | 9 finbif-0.4.1/finbif/MD5 | 95 finbif-0.4.1/finbif/NAMESPACE | 3 finbif-0.4.1/finbif/NEWS.md | 99 finbif-0.4.1/finbif/R/finbif-package.R | 2 finbif-0.4.1/finbif/R/finbif_occurrence.R | 25 finbif-0.4.1/finbif/R/finbif_request_token.R | 15 finbif-0.4.1/finbif/R/finbif_taxa.R | 50 finbif-0.4.1/finbif/R/methods.R | 3 finbif-0.4.1/finbif/R/sysdata.rda |binary finbif-0.4.1/finbif/R/utils.R | 19 finbif-0.4.1/finbif/R/variables.R | 13 finbif-0.4.1/finbif/README.md | 2 finbif-0.4.1/finbif/inst/NEWS.Rd | 25 finbif-0.4.1/finbif/inst/doc/finbif.html | 751 finbif-0.4.1/finbif/inst/doc/v02_occurrence_data.html | 701 finbif-0.4.1/finbif/inst/doc/v03_selecting_variables.html | 510 finbif-0.4.1/finbif/inst/doc/v04_metadata.html | 741 finbif-0.4.1/finbif/inst/doc/v05_filtering.html | 832 finbif-0.4.1/finbif/inst/doc/v06_plotting.html | 345 finbif-0.4.1/finbif/man/finbif-package.Rd | 2 finbif-0.4.1/finbif/man/finbif_occurrence.Rd | 2 finbif-0.4.1/finbif/man/finbif_taxa.Rd | 27 finbif-0.4.1/finbif/man/variables.Rd | 13 finbif-0.4.1/finbif/tests/api-dev-cassettes/finbif_occurrence.yml |12910 +++++++++- finbif-0.4.1/finbif/tests/api-dev-cassettes/finbif_occurrence_collection.yml |only finbif-0.4.1/finbif/tests/api-dev-cassettes/finbif_occurrence_has_media.yml |only finbif-0.4.1/finbif/tests/api-dev-cassettes/taxon_name.yml |only finbif-0.4.1/finbif/tests/cassettes/finbif_occurrence.yml |12348 +++++++++ finbif-0.4.1/finbif/tests/cassettes/finbif_occurrence_collection.yml |only finbif-0.4.1/finbif/tests/cassettes/finbif_occurrence_has_media.yml |only finbif-0.4.1/finbif/tests/cassettes/taxon_name.yml |only finbif-0.4.1/finbif/tests/testthat/_snaps |only finbif-0.4.1/finbif/tests/testthat/helper-finbif.R | 25 finbif-0.4.1/finbif/tests/testthat/test-finbif_api_get.R | 61 finbif-0.4.1/finbif/tests/testthat/test-finbif_check_taxa.R | 39 finbif-0.4.1/finbif/tests/testthat/test-finbif_clear_cache.R | 2 finbif-0.4.1/finbif/tests/testthat/test-finbif_collections.R | 49 finbif-0.4.1/finbif/tests/testthat/test-finbif_coords.R | 2 finbif-0.4.1/finbif/tests/testthat/test-finbif_dates.R | 24 finbif-0.4.1/finbif/tests/testthat/test-finbif_occurrence.R | 265 finbif-0.4.1/finbif/tests/testthat/test-finbif_records.R | 85 finbif-0.4.1/finbif/tests/testthat/test-finbif_request_token.R | 2 finbif-0.4.1/finbif/tests/testthat/test-finbif_taxa.R | 34 finbif-0.4.1/finbif/tests/testthat/test-finbif_token.R | 2 finbif-0.4.1/finbif/tests/testthat/test-map-utils.R | 2 finbif-0.4.1/finbif/tests/testthat/test-metadata.R | 17 finbif-0.4.1/finbif/tests/testthat/test-onload.R | 2 finbif-0.4.1/finbif/tests/testthat/test-utils.R | 2 finbif-0.4.1/finbif/tests/testthat/test-zzz-finbif.R | 2 51 files changed, 26862 insertions(+), 3295 deletions(-)
Title: Ancient Demographic Modelling Using Radiocarbon
Description: Provides tools to directly model underlying population dynamics using date datasets (radiocarbon and other) with a Continuous Piecewise Linear (CPL) model framework. Various other model types included. Taphonomic loss included optionally as a power function. Model comparison framework using BIC. Package also calibrates 14C samples, generates Summed Probability Distributions (SPD), and performs SPD simulation analysis to generate a Goodness-of-fit test for the best selected model.
Author: Adrian Timpson [aut, cre] (<https://orcid.org/0000-0003-0292-8729>)
Maintainer: Adrian Timpson <a.timpson@ucl.ac.uk>
Diff between ADMUR versions 1.0.1 dated 2020-11-29 and 1.0.2 dated 2021-01-27
DESCRIPTION | 12 MD5 | 61 +- NAMESPACE | 7 NEWS.md | 34 + R/functions.R | 237 ++++++---- README.md | 9 build/ADMUR.pdf |binary data/bluhm2421.RData |only data/bryson1848.RData |only data/data1.RData |binary data/data2.RData |binary data/data3.RData |binary inst/CITATION | 4 inst/doc/guide.R | 180 ++++++- inst/doc/guide.Rmd | 245 +++++++++- inst/doc/guide.html | 282 +++++++++--- inst/doc/replicating-timpson-rstb.2020.R | 9 inst/doc/replicating-timpson-rstb.2020.Rmd | 9 inst/doc/replicating-timpson-rstb.2020.html | 21 man/CPLparsToHinges.Rd |only man/bluhm2421.Rd |only man/bryson1848.Rd |only man/convertPars.Rd | 119 ++++- man/mcmc.Rd | 36 + man/objectiveFunction.Rd | 9 man/phaseCalibrator.Rd | 2 man/plotCalArray.Rd | 1 vignettes/four_logos.png |binary vignettes/further_models.png |binary vignettes/guide.Rmd | 245 +++++++++- vignettes/mcmc_pop_without_taph.png |only vignettes/mcmc_taph.png |only vignettes/model_plot.svg | 524 +++++++++++------------ vignettes/replicating-timpson-rstb.2020.Rmd | 9 vignettes/taphonomy_bryson_bluhm.png |only vignettes/vignette.3CPL.JDEoptim.best.taph.RData |only 36 files changed, 1459 insertions(+), 596 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package (see also Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>) can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymisation methods are included. Note that the package
includes a graphical user interface (Meindl and Templ, 2019 <doi:10.3390/a12090191>) that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>),
Bernhard Meindl [aut],
Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.5.1 dated 2020-02-11 and 5.6.0 dated 2021-01-27
sdcMicro-5.5.1/sdcMicro/R/LLmodGlobalRisk.R |only sdcMicro-5.5.1/sdcMicro/man/LLmodGlobalRisk.Rd |only sdcMicro-5.6.0/sdcMicro/DESCRIPTION | 14 sdcMicro-5.6.0/sdcMicro/MD5 | 116 ++--- sdcMicro-5.6.0/sdcMicro/NAMESPACE | 2 sdcMicro-5.6.0/sdcMicro/NEWS | 10 sdcMicro-5.6.0/sdcMicro/R/0classes.r | 25 - sdcMicro-5.6.0/sdcMicro/R/GUIfunctions.R | 5 sdcMicro-5.6.0/sdcMicro/R/addNoise.r | 6 sdcMicro-5.6.0/sdcMicro/R/aux_functions.r | 37 - sdcMicro-5.6.0/sdcMicro/R/dRisk.R | 10 sdcMicro-5.6.0/sdcMicro/R/dUtility.R | 2 sdcMicro-5.6.0/sdcMicro/R/dataGen.r | 3 sdcMicro-5.6.0/sdcMicro/R/dataSets.R | 8 sdcMicro-5.6.0/sdcMicro/R/freqCalc.r | 4 sdcMicro-5.6.0/sdcMicro/R/localSuppression.R | 4 sdcMicro-5.6.0/sdcMicro/R/microaggregation.R | 2 sdcMicro-5.6.0/sdcMicro/R/modRisk.R | 200 +++++----- sdcMicro-5.6.0/sdcMicro/R/muargus_compatibility_functions.R | 4 sdcMicro-5.6.0/sdcMicro/R/pram.R | 14 sdcMicro-5.6.0/sdcMicro/R/report.R | 55 +- sdcMicro-5.6.0/sdcMicro/R/riskyCells.R | 2 sdcMicro-5.6.0/sdcMicro/R/sdcMicro-package.R | 34 + sdcMicro-5.6.0/sdcMicro/R/suda2.R | 118 +++-- sdcMicro-5.6.0/sdcMicro/README.md | 4 sdcMicro-5.6.0/sdcMicro/build/partial.rdb |binary sdcMicro-5.6.0/sdcMicro/build/vignette.rds |binary sdcMicro-5.6.0/sdcMicro/data/CASCrefmicrodata.rda |binary sdcMicro-5.6.0/sdcMicro/data/EIA.rda |binary sdcMicro-5.6.0/sdcMicro/data/Tarragona.rda |binary sdcMicro-5.6.0/sdcMicro/data/casc1.rda |binary sdcMicro-5.6.0/sdcMicro/data/francdat.rda |binary sdcMicro-5.6.0/sdcMicro/data/free1.rda |binary sdcMicro-5.6.0/sdcMicro/data/microData.rda |binary sdcMicro-5.6.0/sdcMicro/data/testdata.RData |binary sdcMicro-5.6.0/sdcMicro/data/testdata2.RData |binary sdcMicro-5.6.0/sdcMicro/inst/doc/sdc_guidelines.pdf |binary sdcMicro-5.6.0/sdcMicro/inst/templates/report-template-simple.rmd | 2 sdcMicro-5.6.0/sdcMicro/man/CASCrefmicrodata.Rd | 8 sdcMicro-5.6.0/sdcMicro/man/EIA.Rd | 8 sdcMicro-5.6.0/sdcMicro/man/Tarragona.Rd | 8 sdcMicro-5.6.0/sdcMicro/man/addNoise.Rd | 4 sdcMicro-5.6.0/sdcMicro/man/argus_microaggregation.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/argus_rankswap.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/casc1.Rd | 6 sdcMicro-5.6.0/sdcMicro/man/dRisk.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/dUtility.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/dataGen.Rd | 3 sdcMicro-5.6.0/sdcMicro/man/francdat.Rd | 8 sdcMicro-5.6.0/sdcMicro/man/free1.Rd | 6 sdcMicro-5.6.0/sdcMicro/man/freqCalc.Rd | 4 sdcMicro-5.6.0/sdcMicro/man/microData.Rd | 6 sdcMicro-5.6.0/sdcMicro/man/microaggregation.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/modRisk.Rd | 32 + sdcMicro-5.6.0/sdcMicro/man/pram.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/riskyCells.Rd | 2 sdcMicro-5.6.0/sdcMicro/man/sdcMicro-package.Rd | 28 + sdcMicro-5.6.0/sdcMicro/man/sdcMicroObj-class.Rd | 24 - sdcMicro-5.6.0/sdcMicro/man/suda2.Rd | 55 +- sdcMicro-5.6.0/sdcMicro/man/testdata.Rd | 6 60 files changed, 528 insertions(+), 373 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and their dependencies) are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.5-19 dated 2021-01-05 and 1.5-21 dated 2021-01-27
ChangeLog | 2183 ++++++++++++-------------- DESCRIPTION | 11 MD5 | 50 NEWS.md | 10 R/gdal.R | 8 R/ogr.R | 4 R/ogr_sp.R | 6 R/ogr_write.R | 10 R/sgdf_gdal.R | 2 R/sp_gdal.R | 8 R/subs.R | 2 configure | 18 inst/ChangeLog | 2183 ++++++++++++-------------- inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.html | 18 inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 49 man/spTransform-methods.Rd | 2 src/OGR_write.cpp | 77 src/gdal-bindings.cpp | 148 + src/ogr_proj.cpp | 34 src/proj6.cpp | 157 + tests/srs_rendering.Rout.save | 38 tests/test_proj.Rout.save | 4 tests/tripup.R | 10 tests/tripup.Rout.save | 42 26 files changed, 2573 insertions(+), 2503 deletions(-)
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Gerko Vink [ctb],
Rianne Schouten [ctb],
Alexander Robitzsch [ctb],
Patrick Rockenschaub [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Margarita Moreno-Betancur [ctb],
Ian White [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb],
Vincent Arel-Bundock [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.12.0 dated 2020-11-14 and 3.13.0 dated 2021-01-27
DESCRIPTION | 13 ++-- MD5 | 30 +++++---- NAMESPACE | 2 NEWS.md | 12 +++ R/imports.R | 2 R/mice.impute.mnar.norm.R | 2 R/mice.impute.rf.R | 2 R/mids2spss.R | 129 ++++++++++-------------------------------- R/with.R | 6 + build |only man/D2.Rd | 2 man/mice.impute.jomoImpute.Rd | 4 - man/mice.impute.mnar.Rd | 2 man/mids2spss.Rd | 40 ++++--------- man/with.mids.Rd | 2 tests/testthat/test-D1.R | 4 - tests/testthat/test-with.R |only 17 files changed, 97 insertions(+), 155 deletions(-)
Title: Download Data from the European Social Survey on the Fly
Description: Download data from the European Social Survey directly from their website <http://www.europeansocialsurvey.org/>. There are two families of functions that allow you to download and interactively check all countries and rounds available.
Author: Jorge Cimentada [aut, cre],
Thomas Leeper [rev] (Thomas reviewed the package for rOpensci,see
https://github.com/ropensci/software-review/issues/201),
Nujcharee Haswell [rev] (Nujcharee reviewed the package for rOpensci,
see https://github.com/ropensci/software-review/issues/201),
Jorge Lopez [ctb],
François Briatte [ctb]
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>
Diff between essurvey versions 1.0.5 dated 2019-12-11 and 1.0.6 dated 2021-01-27
essurvey-1.0.5/essurvey/R/utils.R |only essurvey-1.0.6/essurvey/DESCRIPTION | 18 +- essurvey-1.0.6/essurvey/MD5 | 29 ++-- essurvey-1.0.6/essurvey/NEWS.md | 8 + essurvey-1.0.6/essurvey/R/check_args.R | 48 +++---- essurvey-1.0.6/essurvey/R/essurvey-package.R | 2 essurvey-1.0.6/essurvey/R/import_rounds.R | 56 ++++---- essurvey-1.0.6/essurvey/R/import_sddf_country.R | 54 ++++---- essurvey-1.0.6/essurvey/R/read_format_data.R | 6 essurvey-1.0.6/essurvey/README.md | 27 ---- essurvey-1.0.6/essurvey/build/vignette.rds |binary essurvey-1.0.6/essurvey/inst/doc/intro_ess.html | 64 +++++++--- essurvey-1.0.6/essurvey/man/essurvey-package.Rd | 6 essurvey-1.0.6/essurvey/man/import_rounds.Rd | 8 - essurvey-1.0.6/essurvey/man/import_sddf_country.Rd | 4 essurvey-1.0.6/essurvey/tests/testthat/test-4-recode_missings.R | 59 ++++----- 16 files changed, 204 insertions(+), 185 deletions(-)
Title: U-Statistic Permutation Tests of Independence for all Data Types
Description: Implements various independence tests for discrete, continuous, and infinite-dimensional data. The tests are based on a U-statistic permutation test, the USP of Berrett, Kontoyiannis and Samworth (2020) <arXiv:2001.05513>, and shown to be minimax rate optimal in a wide range of settings. As the permutation principle is used, all tests have exact, non-asymptotic Type I error control at the nominal level.
Author: Thomas B. Berrett <tom.berrett@warwick.ac.uk> [aut,cre], Ioannis Kontoyiannis <yiannis@maths.cam.ac.uk> [aut], Richard J. Samworth <r.samworth@statslab.cam.ac.uk> [aut]
Maintainer: Thomas B. Berrett <tom.berrett@warwick.ac.uk>
Diff between USP versions 0.1.1 dated 2020-11-16 and 0.1.2 dated 2021-01-27
USP-0.1.1/USP/R/USPDiscrete.R |only USP-0.1.1/USP/man/USPDiscrete.Rd |only USP-0.1.2/USP/DESCRIPTION | 6 +++--- USP-0.1.2/USP/MD5 | 32 ++++++++++++++++---------------- USP-0.1.2/USP/NAMESPACE | 2 +- USP-0.1.2/USP/R/DiscStat.R | 8 +++++--- USP-0.1.2/USP/R/USP.R | 20 ++++++++++++++------ USP-0.1.2/USP/R/USP.test.R |only USP-0.1.2/USP/R/USPFourier.R | 13 ++++++++----- USP-0.1.2/USP/R/USPFourierAdapt.R | 11 +++++++---- USP-0.1.2/USP/R/USPFunctional.R | 9 ++++++--- USP-0.1.2/USP/build/partial.rdb |binary USP-0.1.2/USP/inst/REFERENCES.bib | 13 ++++++++++--- USP-0.1.2/USP/man/DiscStat.Rd | 5 +++-- USP-0.1.2/USP/man/USP.Rd | 10 +++++++--- USP-0.1.2/USP/man/USP.test.Rd |only USP-0.1.2/USP/man/USPFourier.Rd | 12 ++++++++---- USP-0.1.2/USP/man/USPFourierAdapt.Rd | 8 ++++++-- USP-0.1.2/USP/man/USPFunctional.Rd | 8 ++++++-- 19 files changed, 100 insertions(+), 57 deletions(-)
Title: R Interface to Use 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying
feasible solutions out of a very large set of candidates, where the problem can be modeled in terms
of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language.
Constraint satisfaction and discrete optimization problems can be formulated in a high-level
modeling language. Models are compiled into an intermediate representation that is understood by a
wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users
can use the package to solve constraint programming problems without using 'MiniZinc' directly,
modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>
Diff between rminizinc versions 0.0.4 dated 2021-01-22 and 0.0.5 dated 2021-01-27
DESCRIPTION | 6 - MD5 | 79 ++++++++++++------------ NAMESPACE | 2 NEWS.md | 14 ++++ R/AssignItem.R | 6 - R/CommonMZNProblems.R |only R/DeclFunctions.R | 22 ++++-- R/Expression.R | 14 ++-- configure | 18 ++--- configure.ac | 2 configure.win | 18 ++--- data/proot.RData |binary inst/doc/R_MiniZinc.R | 8 ++ inst/doc/R_MiniZinc.Rmd | 65 +++++++++++++++---- inst/doc/R_MiniZinc.html | 61 ++++++++++++++---- inst/minizinc/std/cumulative.mzn | 4 - inst/minizinc/std/cumulative_opt.mzn | 2 inst/minizinc/std/decreasing.mzn | 16 ++-- inst/minizinc/std/fzn_bin_packing_capa_reif.mzn | 2 inst/minizinc/std/fzn_bin_packing_load_reif.mzn | 2 inst/minizinc/std/fzn_count_eq_par.mzn | 4 - inst/minizinc/std/fzn_count_eq_par_reif.mzn | 4 - inst/minizinc/std/fzn_count_geq_par.mzn | 6 - inst/minizinc/std/fzn_count_geq_par_reif.mzn | 6 - inst/minizinc/std/fzn_count_gt_par.mzn | 6 - inst/minizinc/std/fzn_count_gt_par_reif.mzn | 6 - inst/minizinc/std/fzn_count_leq_par.mzn | 6 - inst/minizinc/std/fzn_count_leq_par_reif.mzn | 6 - inst/minizinc/std/fzn_count_lt_par.mzn | 6 - inst/minizinc/std/fzn_count_lt_par_reif.mzn | 6 - inst/minizinc/std/fzn_count_neq_par.mzn | 6 - inst/minizinc/std/fzn_count_neq_par_reif.mzn | 6 - inst/minizinc/std/increasing.mzn | 16 ++-- inst/minizinc/std/stdlib/stdlib_internal.mzn | 7 ++ inst/minizinc/std/stdlib/stdlib_language.mzn | 28 ++++++++ inst/minizinc/std/strictly_decreasing.mzn | 20 +++--- inst/minizinc/std/strictly_increasing.mzn | 26 +++---- man/FloatDecl.Rd | 4 - man/IntDecl.Rd | 4 - man/assignment.Rd |only man/knapsack.Rd |only vignettes/R_MiniZinc.Rmd | 65 +++++++++++++++---- 42 files changed, 381 insertions(+), 198 deletions(-)
Title: Poisson-Tweedie Exponential Family Models
Description: Simulation of models Poisson-Tweedie.
Author: David Pechel Cactcha, Laure Pauline Fotso and Celestin C
Kokonendji
Maintainer: David Pechel Cactcha <davidpechel@uy1.uninet.cm>
Diff between poistweedie versions 1.0 dated 2010-03-11 and 1.0.1 dated 2021-01-27
DESCRIPTION | 12 +++++++----- MD5 | 14 +++++++------- NAMESPACE | 7 ++++--- man/poistweedie.Rd | 7 +------ man/ppoistweedie.Rd | 2 -- man/qpoistweedie.Rd | 2 -- man/rpoistweedie.Rd | 1 - man/varpt.Rd | 7 +------ 8 files changed, 20 insertions(+), 32 deletions(-)
Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as
tasks, predictions, resample results or benchmark results via the
autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are
intended to provide sensible defaults, yet can easily be customized to
create camera-ready figures. Visualizations include barplots,
boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Raphael Sonabend [aut] (<https://orcid.org/0000-0001-9225-4654>),
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.5.0 dated 2020-11-02 and 0.5.1 dated 2021-01-27
DESCRIPTION | 13 ++-- MD5 | 72 ++++++++++++------------- NEWS.md | 9 +++ R/BenchmarkResult.R | 2 R/LearnerClassifGlmnet.R | 2 R/PredictionClassif.R | 2 R/PredictionClust.R | 2 R/ResampleResult.R | 2 R/as_precrec.R | 2 R/plot_learner_prediction.R | 2 README.md | 2 build/partial.rdb |binary man/figures/README-demo-1.png |binary man/figures/README-demo-2.png |binary man/figures/README-demo-3.png |binary man/plot_learner_prediction.Rd | 2 tests/testthat/setup.R | 2 tests/testthat/test_BenchmarkResult.R | 11 +-- tests/testthat/test_Filter.R | 4 - tests/testthat/test_LearnerClassifCVGlmnet.R | 3 - tests/testthat/test_LearnerClassifRpart.R | 4 - tests/testthat/test_LearnerClasssifGlmnet.R | 3 - tests/testthat/test_LearnerClustHierarchical.R | 4 - tests/testthat/test_LearnerRegrCVGlmnet.R | 3 - tests/testthat/test_LearnerRegrGlmnet.R | 3 - tests/testthat/test_LearnerRegrRpart.R | 4 - tests/testthat/test_PredictionClassif.R | 6 -- tests/testthat/test_PredictionClust.R | 6 -- tests/testthat/test_PredictionRegr.R | 6 -- tests/testthat/test_ResampleResult.R | 32 +++++------ tests/testthat/test_Task.R | 6 -- tests/testthat/test_TaskClassif.R | 8 +- tests/testthat/test_TaskClust.R | 9 +-- tests/testthat/test_TaskDens.R | 6 -- tests/testthat/test_TaskRegr.R | 7 -- tests/testthat/test_TaskSurv.R | 9 +-- tests/testthat/test_plot_learner_prediction.R | 24 +++----- 37 files changed, 121 insertions(+), 151 deletions(-)
Title: Easily Install and Load the 'mlr3' Package Family
Description: The 'mlr3' package family is a set of packages for
machine-learning purposes built in a modular fashion. This wrapper
package is aimed to simplify the installation and loading of the core
'mlr3' packages. Get more information about the 'mlr3' project at
<https://mlr3book.mlr-org.com/>.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3verse versions 0.1.3 dated 2020-07-06 and 0.2.0 dated 2021-01-27
DESCRIPTION | 35 ++++---- MD5 | 30 +++++-- NAMESPACE | 157 ++++++++++++++++++++++++++++++++++++--- NEWS.md | 16 +++ R/mlr3verse_info.R | 17 ++-- R/reexports_bbotk.R |only R/reexports_data.table.R |only R/reexports_mlr3.R |only R/reexports_mlr3cluster.R |only R/reexports_mlr3filters.R |only R/reexports_mlr3fselect.R |only R/reexports_mlr3pipelines.R |only R/reexports_mlr3proba.R |only R/reexports_mlr3tuning.R |only R/reexports_mlr3viz.R |only R/reexports_paradox.R |only R/zzz.R | 51 ++++++++---- README.md | 177 ++++++++++++++++++++++---------------------- inst/WORDLIST | 30 +++---- man/mlr3verse-package.Rd | 29 ++++++- man/mlr3verse_info.Rd | 2 man/reexports.Rd |only 22 files changed, 379 insertions(+), 165 deletions(-)
Title: Connector Between 'mlr3' and 'OpenML'
Description: Provides an interface to 'OpenML.org' to list and
download machine learning data and tasks. Data and tasks can be
automatically converted to 'mlr3' tasks. For a more sophisticated
interface which also allows uploading experiments, see the 'OpenML'
package.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3oml versions 0.4.0 dated 2020-10-20 and 0.4.1 dated 2021-01-27
DESCRIPTION | 11 ++-- MD5 | 43 ++++++++-------- NAMESPACE | 1 NEWS.md | 4 + R/OMLData.R | 2 R/OMLTask.R | 2 R/list_oml_data_sets.R | 2 R/list_oml_tasks.R | 2 R/read_arff.R | 48 ++++++++++++------ README.md | 72 +++++++++++++-------------- build/partial.rdb |binary man/list_oml_data_sets.Rd | 1 man/list_oml_tasks.Rd | 1 man/read_arff.Rd |only tests/testthat/helper.R | 10 +-- tests/testthat/test_OMLData.R | 7 -- tests/testthat/test_OMLResamplingConnector.R | 2 tests/testthat/test_OMLTask.R | 4 - tests/testthat/test_OMLTaskConnector.R | 2 tests/testthat/test_list_oml_data.R | 2 tests/testthat/test_list_oml_task.R | 2 tests/testthat/test_manual.R | 4 - tests/testthat/test_read_arff.R | 7 +- 23 files changed, 122 insertions(+), 107 deletions(-)
Title: Fast Implementation of (Local) Population Stratification Methods
Description: Fast implementations to compute the genetic covariance matrix, the Jaccard similarity matrix, the s-matrix (the weighted Jaccard similarity matrix), and the (classic or robust) genomic relationship matrix of a (dense or sparse) input matrix (see Hahn, Lutz, Hecker, Prokopenko, Cho, Silverman, Weiss, and Lange (2020) <doi:10.1002/gepi.22356>). Full support for sparse matrices from the R-package 'Matrix'. Additionally, an implementation of the power method (von Mises iteration) to compute the largest eigenvector of a matrix is included, a function to perform an automated full run of global and local correlations in population stratification data, a function to compute sliding windows, and a function to invert minor alleles and to select those variants/loci exceeding a minimal cutoff value. New functionality in locStra allows one to extract the k leading eigenvectors of the genetic covariance matrix, Jaccard similarity matrix, s-matrix, and genomic relationship matrix without actually computing the similarity matrices.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between locStra versions 1.6 dated 2020-12-15 and 1.7 dated 2021-01-27
DESCRIPTION | 10 +-- MD5 | 17 ++--- NAMESPACE | 1 R/RcppExports.R | 16 ++--- R/locStra.r | 61 ++++++++++++++----- man/fastSMatrixEVs.Rd | 12 --- man/sMatrix.Rd | 11 --- man/selectVariants.Rd |only src/RcppExports.cpp | 40 +++++------- src/auxcode.cpp | 155 +++++++++++++++----------------------------------- 10 files changed, 137 insertions(+), 186 deletions(-)
Title: Access, Retrieve, and Work with Canadian Census Data and
Geography
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer),
Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for
correspondence),
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.4.0 dated 2021-01-16 and 0.4.1 dated 2021-01-27
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 6 + R/cancensus.R | 134 +++++++++++++++++-------------- R/helpers.R | 8 + R/intersect_geometry.R | 5 - README.md | 4 inst/doc/Making_maps_with_cancensus.html | 8 - 8 files changed, 104 insertions(+), 81 deletions(-)
Title: Compute Scagnostics
Description: Calculates graph theoretic scagnostics. Scagnostics describe various measures of interest for pairs of variables, based on their appearance on a scatterplot. They are useful tool for discovering interesting or unusual scatterplots from a scatterplot matrix, without having to look at every individual plot.
Author: Ursula Laa [cre, aut],
Heike Hofmann [aut],
Lee Wilkinson [aut],
Hadley Wickham [aut],
Duncan Temple Lang [aut],
Anushka Anand [aut]
Maintainer: Ursula Laa <ursula.laa@boku.ac.at>
Diff between binostics versions 0.1.2 dated 2019-03-06 and 0.1.3 dated 2021-01-27
binostics-0.1.2/binostics/man/print.scagdf.Rd |only binostics-0.1.3/binostics/CHANGELOG | 5 ++++ binostics-0.1.3/binostics/DESCRIPTION | 17 ++++++------- binostics-0.1.3/binostics/MD5 | 22 +++++++++-------- binostics-0.1.3/binostics/NAMESPACE | 12 ++++++++- binostics-0.1.3/binostics/R/indexfunctions.r |only binostics-0.1.3/binostics/R/scagnostics.r | 27 ++++++---------------- binostics-0.1.3/binostics/man/scagnostic.index.Rd |only binostics-0.1.3/binostics/man/scagnostics.Rd | 4 +-- binostics-0.1.3/binostics/src/GraphMeasures.cpp | 2 + binostics-0.1.3/binostics/src/Scagnostics.cpp | 2 - binostics-0.1.3/binostics/src/Scagnostics.h | 4 +-- binostics-0.1.3/binostics/src/binostics_init.c |only binostics-0.1.3/binostics/src/scag.cpp | 2 - 14 files changed, 52 insertions(+), 45 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-07-01 0.1-2
2013-06-07 0.1-1
2012-11-10 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-17 0.05
2009-01-29 0.04
2007-10-22 0.02
2007-10-21 0.01-1
2007-08-25 0.01
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-12-03 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-12-01 0.8
2009-02-15 0.7
2008-10-07 0.6
2008-05-26 0.5
Title: Model-Based Clustering for Multivariate Partial Ranking Data
Description: Implementation of a model-based clustering algorithm for
ranking data (C. Biernacki, J. Jacques (2013) <doi:10.1016/j.csda.2012.08.008>).
Multivariate rankings as well as partial rankings are taken
into account. This algorithm is based on an extension of the Insertion
Sorting Rank (ISR) model for ranking data, which is a meaningful and
effective model parametrized by a position parameter (the modal ranking,
quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity
of the rank population is modelled by a mixture of ISR, whereas conditional
independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez [aut, cre],
Julien Jacques [aut],
Christophe Biernacki [aut]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between Rankcluster versions 0.94.4 dated 2020-10-06 and 0.94.5 dated 2021-01-27
DESCRIPTION | 8 MD5 | 36 R/resultClass.R | 3 build/vignette.rds |binary inst/doc/Rankcluster.pdf |binary inst/doc/dataFormat.html | 320 ---- src/RankCluster.cpp | 3101 +++++++++++++++++++++++------------------------ src/RankCluster.h | 224 +-- src/Rankcluster_init.c | 21 src/functions.cpp | 1037 +++++++-------- src/functions.h | 65 src/run.cpp | 245 +-- src/run.h | 72 - src/runFunctions.cpp | 318 ++-- src/runFunctions.h | 12 src/runTest.cpp | 166 +- src/runTest.h | 7 src/test.cpp | 764 +++++------ src/test.h | 31 19 files changed, 3040 insertions(+), 3390 deletions(-)
Title: Functions to Find an Acceptable Python Binary
Description: Package designed to find an acceptable python binary.
Author: Trevor L Davis [aut, cre],
Paul Gilbert [aut]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between findpython versions 1.0.5 dated 2019-03-08 and 1.0.7 dated 2021-01-27
DESCRIPTION | 10 +- MD5 | 16 +-- NEWS.md | 4 R/find_python_cmd.r | 161 ++++++++++++++++++++------------------- README.md | 2 man/can_find_python_cmd.Rd | 21 +++-- man/find_python_cmd.Rd | 18 ++-- man/is_python_sufficient.Rd | 14 ++- tests/testthat/test-findpython.r | 81 +++++++++---------- 9 files changed, 178 insertions(+), 149 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Herv<e9>
Maintainer: Maxime Herv<e9> <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-78 dated 2020-09-04 and 0.9-79 dated 2021-01-27
DESCRIPTION | 11 ++++++----- MD5 | 14 +++++++------- NEWS | 3 +++ R/least.rect.R | 4 ++-- R/predict.least.rect.R | 7 ++++++- R/zzz.R | 2 +- man/RVAideMemoire-package.Rd | 4 ++-- man/fp.test.Rd | 4 ++-- 8 files changed, 29 insertions(+), 20 deletions(-)
Title: Utilities for Learning Sparse Bayesian Networks
Description: A set of tools for representing and estimating sparse Bayesian networks from continuous and discrete data, as described in Aragam, Gu, and Zhou (2017) <arXiv:1703.04025>.
Author: Bryon Aragam [aut, cre],
Jiaying Gu [aut]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebnUtils versions 0.0.7 dated 2019-05-29 and 0.0.8 dated 2021-01-27
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/s3-sparse.R | 16 +++++++++++++++- R/s3-sparsebnPath.R | 2 +- R/sparsebnUtils-cytoscape.R | 2 +- R/sparsebnUtils-lambdas.R | 2 +- README.md | 21 ++++++++++++++++----- inst/CITATION | 31 ++++++++++++++----------------- man/generate.lambdas.Rd | 10 +++++++--- man/openCytoscape.Rd | 2 +- man/random.graph.Rd | 3 +-- man/sparsebnData.Rd | 3 +-- man/sparsebnPath.Rd | 2 +- man/sparsebnUtils.Rd | 1 - 15 files changed, 82 insertions(+), 55 deletions(-)
Title: Prepare Reproducible Example Code via the Clipboard
Description: Convenience wrapper that uses the 'rmarkdown'
package to render small snippets of code to target formats that
include both code and output. The goal is to encourage the sharing of
small, reproducible, and runnable examples on code-oriented websites,
such as <https://stackoverflow.com> and <https://github.com>, or in
email. The user's clipboard is the default source of input code and
the default target for rendered output. 'reprex' also extracts clean,
runnable R code from various common formats, such as copy/paste from
an R session.
Author: Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
Jim Hester [aut] (<https://orcid.org/0000-0002-2739-7082>),
David Robinson [aut],
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between reprex versions 0.3.0 dated 2019-05-16 and 1.0.0 dated 2021-01-27
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Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.3.14 dated 2020-11-17 and 0.4.0 dated 2021-01-27
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Title: Verbose Assertions for Tabular Data (Data.frames and
Data.tables)
Description: Simple, flexible, assertions on data.frame or data.table objects with verbose output for vetting. While other assertion packages apply towards more general use-cases, assertable is tailored towards tabular data. It includes functions to check variable names and values, whether the dataset contains all combinations of a given set of unique identifiers, and whether it is a certain length. In addition, assertable includes utility functions to check the existence of target files and to efficiently import multiple tabular data files into one data.table.
Author: Grant Nguyen [aut, cre],
Max Czapanskiy [ctb]
Maintainer: Grant Nguyen <grant.nguyen@gmail.com>
Diff between assertable versions 0.2.7 dated 2019-09-21 and 0.2.8 dated 2021-01-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/assert_coltypes.R | 10 ++++++++-- inst/doc/assertion_template.html | 10 +++++----- inst/doc/data_assertion_intro.html | 4 ++-- inst/doc/file_assertion_intro.html | 30 +++++++++++++++--------------- 6 files changed, 38 insertions(+), 32 deletions(-)
Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language
development platform for in-memory data. It specifies a standardized
language-independent columnar memory format for flat and hierarchical data,
organized for efficient analytic operations on modern hardware. This
package provides an interface to the 'Arrow C++' library.
Author: Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Jeroen Ooms [aut],
Neal Richardson [aut, cre],
Javier Luraschi [ctb],
Jeffrey Wong [ctb],
Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>
Diff between arrow versions 2.0.0 dated 2020-10-20 and 3.0.0 dated 2021-01-27
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arrow-3.0.0/arrow/src/expression.cpp | 89 arrow-3.0.0/arrow/src/filesystem.cpp | 33 arrow-3.0.0/arrow/src/imports.cpp | 1 arrow-3.0.0/arrow/src/io.cpp | 6 arrow-3.0.0/arrow/src/json.cpp | 2 arrow-3.0.0/arrow/src/memorypool.cpp | 62 arrow-3.0.0/arrow/src/message.cpp | 8 arrow-3.0.0/arrow/src/nameof.h | 19 arrow-3.0.0/arrow/src/parquet.cpp | 41 arrow-3.0.0/arrow/src/py-to-r.cpp | 12 arrow-3.0.0/arrow/src/recordbatch.cpp | 21 arrow-3.0.0/arrow/src/recordbatchreader.cpp | 36 arrow-3.0.0/arrow/src/scalar.cpp | 21 arrow-3.0.0/arrow/src/schema.cpp | 5 arrow-3.0.0/arrow/src/symbols.cpp | 2 arrow-3.0.0/arrow/src/table.cpp | 33 arrow-3.0.0/arrow/tests/testthat/golden-files |only arrow-3.0.0/arrow/tests/testthat/helper-data.R | 22 arrow-3.0.0/arrow/tests/testthat/helper-parquet.R | 9 arrow-3.0.0/arrow/tests/testthat/helper-roundtrip.R | 4 arrow-3.0.0/arrow/tests/testthat/test-Array.R | 24 arrow-3.0.0/arrow/tests/testthat/test-RecordBatch.R | 12 arrow-3.0.0/arrow/tests/testthat/test-Table.R | 94 arrow-3.0.0/arrow/tests/testthat/test-arrow.R | 12 arrow-3.0.0/arrow/tests/testthat/test-backwards-compatibility.R |only arrow-3.0.0/arrow/tests/testthat/test-chunked-array.R | 14 arrow-3.0.0/arrow/tests/testthat/test-compute-arith.R |only arrow-3.0.0/arrow/tests/testthat/test-csv.R | 2 arrow-3.0.0/arrow/tests/testthat/test-data-type.R | 104 arrow-3.0.0/arrow/tests/testthat/test-dataset.R | 217 + arrow-3.0.0/arrow/tests/testthat/test-dplyr.R | 124 arrow-3.0.0/arrow/tests/testthat/test-expression.R | 22 arrow-3.0.0/arrow/tests/testthat/test-filesystem.R | 12 arrow-3.0.0/arrow/tests/testthat/test-memory-pool.R |only arrow-3.0.0/arrow/tests/testthat/test-metadata.R | 72 arrow-3.0.0/arrow/tests/testthat/test-parquet.R | 8 arrow-3.0.0/arrow/tests/testthat/test-python-flight.R |only arrow-3.0.0/arrow/tests/testthat/test-python.R | 31 arrow-3.0.0/arrow/tests/testthat/test-read-record-batch.R | 2 arrow-3.0.0/arrow/tests/testthat/test-record-batch-reader.R | 47 arrow-3.0.0/arrow/tests/testthat/test-schema.R | 2 arrow-3.0.0/arrow/tools/autobrew | 2 arrow-3.0.0/arrow/tools/linuxlibs.R | 68 arrow-3.0.0/arrow/vignettes/arrow.Rmd | 2 arrow-3.0.0/arrow/vignettes/dataset.Rmd | 113 arrow-3.0.0/arrow/vignettes/flight.Rmd | 2 arrow-3.0.0/arrow/vignettes/install.Rmd | 59 138 files changed, 3780 insertions(+), 2271 deletions(-)
Title: Automatically Print R Objects to Appropriate Formats According
to the 'knitr' Output Format
Description: Extends the S3 generic function knit_print() in 'knitr'
to automatically print some objects using an appropriate format such as
Markdown or LaTeX. For example, data frames are automatically printed as
tables, and the help() pages can also be rendered in 'knitr' documents.
Author: Yihui Xie
Maintainer: Yihui Xie <xie@yihui.name>
Diff between printr versions 0.1 dated 2017-05-19 and 0.1.1 dated 2021-01-27
DESCRIPTION | 12 - MD5 | 16 - R/help.R | 3 README.md | 15 - build/vignette.rds |binary inst/doc/printr.R | 2 inst/doc/printr.Rmd | 6 inst/doc/printr.html | 478 +++++++++++++++++++++++++++++++++------------------ vignettes/printr.Rmd | 6 9 files changed, 343 insertions(+), 195 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations for a wide variety of models (see support list of insight; Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), used in the computation of marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.5.0 dated 2021-01-15 and 0.5.1 dated 2021-01-27
DESCRIPTION | 6 - MD5 | 24 +++--- R/estimate_means.bayesian.R | 3 R/estimate_response.bayesian.R | 5 - R/estimate_response.frequentist.R | 4 - R/visualisation_matrix.models.R | 5 + README.md | 127 ++++++++++++++++++------------------ man/estimate_means.stanreg.Rd | 3 man/figures/unnamed-chunk-13-1.png |binary man/figures/unnamed-chunk-5-1.png |binary man/figures/unnamed-chunk-8-1.png |binary tests/testthat/test-estimate_link.R | 26 +++++-- tests/testthat/test-mgcv.R | 19 ++++- 13 files changed, 130 insertions(+), 92 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-21 0.1-12
2020-03-19 0.1-11
2020-03-10 0.1-9
2019-04-23 0.1-7
2018-09-17 0.1-6
2018-01-17 0.1-4
2015-11-19 0.1-3
2015-11-14 0.1-2
2015-09-19 0.1-1
2015-07-09 0.1-0