Title: Genetics Input/Output Functions
Description: Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between genio versions 1.0.23 dated 2021-06-11 and 1.0.25 dated 2021-07-26
genio-1.0.23/genio/R/real_path.R |only genio-1.0.25/genio/DESCRIPTION | 10 genio-1.0.25/genio/MD5 | 69 +- genio-1.0.25/genio/NEWS.md | 84 ++ genio-1.0.25/genio/R/add_ext.R | 2 genio-1.0.25/genio/R/add_ext_read.R |only genio-1.0.25/genio/R/count_lines.R | 7 genio-1.0.25/genio/R/read_bed.R | 13 genio-1.0.25/genio/R/read_bim.R | 4 genio-1.0.25/genio/R/read_eigenvec.R | 7 genio-1.0.25/genio/R/read_fam.R | 4 genio-1.0.25/genio/R/read_ind.R | 4 genio-1.0.25/genio/R/read_matrix.R | 11 genio-1.0.25/genio/R/read_phen.R | 4 genio-1.0.25/genio/R/read_snp.R | 4 genio-1.0.25/genio/R/read_tab_generic.R | 4 genio-1.0.25/genio/inst/doc/genio.R | 12 genio-1.0.25/genio/inst/doc/genio.Rmd | 12 genio-1.0.25/genio/inst/doc/genio.html | 304 +++++----- genio-1.0.25/genio/man/count_lines.Rd | 4 genio-1.0.25/genio/man/read_bed.Rd | 11 genio-1.0.25/genio/man/read_bim.Rd | 4 genio-1.0.25/genio/man/read_eigenvec.Rd | 5 genio-1.0.25/genio/man/read_fam.Rd | 4 genio-1.0.25/genio/man/read_ind.Rd | 4 genio-1.0.25/genio/man/read_matrix.Rd | 7 genio-1.0.25/genio/man/read_phen.Rd | 4 genio-1.0.25/genio/man/read_snp.Rd | 4 genio-1.0.25/genio/src/RcppExports.cpp | 5 genio-1.0.25/genio/src/read_bed_cpp.cpp | 27 genio-1.0.25/genio/src/write_bed_cpp.cpp | 2 genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.bed |only genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.bim |only genio-1.0.25/genio/tests/testthat/HumanOrigins249_tiny.fam |only genio-1.0.25/genio/tests/testthat/test-genio.R | 367 ++++++++----- genio-1.0.25/genio/tests/testthat/test-grm.R | 50 + genio-1.0.25/genio/tests/testthat/test-write_bed.R | 142 +++-- genio-1.0.25/genio/vignettes/genio.Rmd | 12 38 files changed, 740 insertions(+), 467 deletions(-)
Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format
for describing software metadata, as detailed at
<https://codemeta.github.io>. This package provides utilities to
generate, parse, and modify 'codemeta.json' files automatically for R
packages, as well as tools and examples for working with
'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>),
Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>),
Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>),
rOpenSci [fnd] (https://ropensci.org/),
Katrin Leinweber [ctb] (<https://orcid.org/0000-0001-5135-5758>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Arfon Smith [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>),
Michael Rustler [ctb] (<https://orcid.org/0000-0003-0647-7726>),
Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>),
Sebastian Kreutzer [ctb] (<https://orcid.org/0000-0002-0734-2199>),
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between codemetar versions 0.3.1 dated 2021-06-02 and 0.3.2 dated 2021-07-26
DESCRIPTION | 6 MD5 | 27 +- NEWS.md | 11 - R/codemeta_readme.R | 4 R/guess_other_metadata.R | 3 README.md | 38 +-- build/vignette.rds |binary inst/doc/codemetar.html | 301 +++++------------------------ inst/examples/README_ex.md | 2 man/codemetar-package.Rd | 9 man/rmdhunks/whybother.Rmd | 2 man/write_codemeta.Rd | 2 tests/testthat/_snaps |only tests/testthat/test-add_repository_terms.R | 12 - tests/testthat/test-guess_metadata.R | 1 15 files changed, 119 insertions(+), 299 deletions(-)
Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between param6 versions 0.1.0 dated 2021-03-17 and 0.2.0 dated 2021-07-26
param6-0.1.0/param6/R/Dictionary.R |only param6-0.1.0/param6/R/Dictionary_S3methods.R |only param6-0.1.0/param6/R/Dictionary_methods.R |only param6-0.1.0/param6/man/Dictionary.Rd |only param6-0.1.0/param6/man/as.character.Dictionary.Rd |only param6-0.1.0/param6/man/c.Dictionary.Rd |only param6-0.1.0/param6/man/length.Dictionary.Rd |only param6-0.1.0/param6/man/sub-.Dictionary.Rd |only param6-0.1.0/param6/man/summary.Dictionary.Rd |only param6-0.1.0/param6/tests/testthat/test_Dictionary.R |only param6-0.1.0/param6/tests/testthat/test_helpers.R |only param6-0.1.0/param6/tests/testthat/test_paramset.R |only param6-0.1.0/param6/tests/testthat/test_prm.R |only param6-0.2.0/param6/DESCRIPTION | 10 param6-0.2.0/param6/MD5 | 56 +-- param6-0.2.0/param6/NAMESPACE | 10 param6-0.2.0/param6/NEWS.md | 19 + param6-0.2.0/param6/R/ParameterSet.R | 158 ++++++++- param6-0.2.0/param6/R/ParameterSet_S3methods.R | 122 +++++-- param6-0.2.0/param6/R/ParameterSet_helpers.R | 201 +++++++---- param6-0.2.0/param6/R/ParameterSet_methods.R | 331 +++++++++++++++---- param6-0.2.0/param6/R/cnd.R | 9 param6-0.2.0/param6/R/helpers.R | 61 +-- param6-0.2.0/param6/R/prm.R | 11 param6-0.2.0/param6/R/support_dictionary.R | 29 + param6-0.2.0/param6/R/tools.R |only param6-0.2.0/param6/R/zzz.R | 2 param6-0.2.0/param6/README.md | 8 param6-0.2.0/param6/man/ParameterSet.Rd | 179 +++++++++- param6-0.2.0/param6/man/c.ParameterSet.Rd | 10 param6-0.2.0/param6/man/cpset.Rd |only param6-0.2.0/param6/man/expect_equal_ps.Rd |only param6-0.2.0/param6/man/pset.Rd | 29 + param6-0.2.0/param6/man/sub-.ParameterSet.Rd | 17 param6-0.2.0/param6/man/support_dictionary.Rd | 6 param6-0.2.0/param6/tests/testthat/helpers.R |only param6-0.2.0/param6/tests/testthat/test-helpers.R |only param6-0.2.0/param6/tests/testthat/test-paramset.R |only param6-0.2.0/param6/tests/testthat/test-prm.R |only 39 files changed, 963 insertions(+), 305 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods.
Includes utilities for public key encryption, creating and verifying digital signatures,
and managing your local keyring. Note that some functionality depends on the version of
GnuPG that is installed on the system. On Windows this package can be used together with
'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gpg versions 1.2.2 dated 2019-12-02 and 1.2.3 dated 2021-07-26
DESCRIPTION | 9 MD5 | 19 NEWS | 3 build/vignette.rds |binary cleanup | 2 configure | 35 - inst/doc/intro.Rmd | 2 inst/doc/intro.html | 1605 +++++----------------------------------------------- src/Makevars.ucrt |only src/Makevars.win | 3 vignettes/intro.Rmd | 2 11 files changed, 224 insertions(+), 1456 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between tidybayes versions 2.3.1 dated 2020-11-02 and 3.0.0 dated 2021-07-26
tidybayes-2.3.1/tidybayes/R/fitted_draws.R |only tidybayes-2.3.1/tidybayes/tests/figs |only tidybayes-2.3.1/tidybayes/tests/testthat/test.fitted_draws.R |only tidybayes-3.0.0/tidybayes/DESCRIPTION | 46 tidybayes-3.0.0/tidybayes/MD5 | 227 - tidybayes-3.0.0/tidybayes/NAMESPACE | 905 ++-- tidybayes-3.0.0/tidybayes/NEWS.md | 343 + tidybayes-3.0.0/tidybayes/R/add_draws.R | 207 - tidybayes-3.0.0/tidybayes/R/compare_levels.R | 449 +- tidybayes-3.0.0/tidybayes/R/density_bins.R | 203 - tidybayes-3.0.0/tidybayes/R/deprecated.R | 1978 +++++----- tidybayes-3.0.0/tidybayes/R/emmeans_comparison.R | 166 tidybayes-3.0.0/tidybayes/R/epred_draws.R |only tidybayes-3.0.0/tidybayes/R/epred_rvars.R |only tidybayes-3.0.0/tidybayes/R/gather_draws.R | 60 tidybayes-3.0.0/tidybayes/R/gather_emmeans_draws.R | 283 - tidybayes-3.0.0/tidybayes/R/gather_pairs.R | 292 - tidybayes-3.0.0/tidybayes/R/gather_rvars.R |only tidybayes-3.0.0/tidybayes/R/gather_variables.R | 205 - tidybayes-3.0.0/tidybayes/R/get_variables.R | 107 tidybayes-3.0.0/tidybayes/R/ggdist-curve_interval.R |only tidybayes-3.0.0/tidybayes/R/ggdist-cut_cdf_qi.R |only tidybayes-3.0.0/tidybayes/R/ggdist-stat_pointinterval.R | 10 tidybayes-3.0.0/tidybayes/R/linpred_draws.R |only tidybayes-3.0.0/tidybayes/R/linpred_rvars.R |only tidybayes-3.0.0/tidybayes/R/nest_rvars.R |only tidybayes-3.0.0/tidybayes/R/predict_curve.R | 259 - tidybayes-3.0.0/tidybayes/R/predicted_draws.R | 687 ++- tidybayes-3.0.0/tidybayes/R/predicted_rvars.R |only tidybayes-3.0.0/tidybayes/R/recover_types.R | 314 - tidybayes-3.0.0/tidybayes/R/residual_draws.R | 118 tidybayes-3.0.0/tidybayes/R/sample_draws.R | 133 tidybayes-3.0.0/tidybayes/R/spread_draws.R | 1353 +++--- tidybayes-3.0.0/tidybayes/R/spread_rvars.R |only tidybayes-3.0.0/tidybayes/R/summarise_draws.R |only tidybayes-3.0.0/tidybayes/R/testthat.R |only tidybayes-3.0.0/tidybayes/R/tidy_draws.R | 543 +- tidybayes-3.0.0/tidybayes/R/tidybayes-models.R | 143 tidybayes-3.0.0/tidybayes/R/ungather_draws.R | 146 tidybayes-3.0.0/tidybayes/R/unspread_draws.R | 233 - tidybayes-3.0.0/tidybayes/R/util.R | 291 - tidybayes-3.0.0/tidybayes/build/partial.rdb |binary tidybayes-3.0.0/tidybayes/build/vignette.rds |binary tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.R | 206 - tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.Rmd | 1889 ++++----- tidybayes-3.0.0/tidybayes/inst/doc/tidy-brms.html | 1932 ++++----- tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.R |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.Rmd |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-posterior.html |only tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.R | 172 tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.Rmd | 1340 +++--- tidybayes-3.0.0/tidybayes/inst/doc/tidy-rstanarm.html | 1020 ++--- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.R | 129 tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.Rmd | 1428 +++---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes-residuals.html | 999 +---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.R | 110 tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.Rmd | 1630 ++++---- tidybayes-3.0.0/tidybayes/inst/doc/tidybayes.html | 1470 +++---- tidybayes-3.0.0/tidybayes/man/add_draws.Rd | 155 tidybayes-3.0.0/tidybayes/man/add_predicted_draws.Rd | 714 +-- tidybayes-3.0.0/tidybayes/man/add_predicted_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/compare_levels.Rd | 277 - tidybayes-3.0.0/tidybayes/man/density_bins.Rd | 175 tidybayes-3.0.0/tidybayes/man/emmeans_comparison.Rd | 142 tidybayes-3.0.0/tidybayes/man/gather_emmeans_draws.Rd | 203 - tidybayes-3.0.0/tidybayes/man/gather_pairs.Rd | 232 - tidybayes-3.0.0/tidybayes/man/nest_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/recover_types.Rd | 269 - tidybayes-3.0.0/tidybayes/man/reexports.Rd | 281 - tidybayes-3.0.0/tidybayes/man/sample_draws.Rd | 124 tidybayes-3.0.0/tidybayes/man/spread_draws.Rd | 496 +- tidybayes-3.0.0/tidybayes/man/spread_rvars.Rd |only tidybayes-3.0.0/tidybayes/man/summarise_draws.grouped_df.Rd |only tidybayes-3.0.0/tidybayes/man/tidy_draws.Rd | 197 tidybayes-3.0.0/tidybayes/man/tidybayes-deprecated.Rd | 492 +- tidybayes-3.0.0/tidybayes/man/tidybayes-models.Rd | 137 tidybayes-3.0.0/tidybayes/tests/models/models.rstan.m_gqs.rds |only tidybayes-3.0.0/tidybayes/tests/testthat/_snaps |only tidybayes-3.0.0/tidybayes/tests/testthat/test.add_draws.R | 78 tidybayes-3.0.0/tidybayes/tests/testthat/test.as_constructor.R | 90 tidybayes-3.0.0/tidybayes/tests/testthat/test.combine_chains.R | 76 tidybayes-3.0.0/tidybayes/tests/testthat/test.compare_levels.R | 470 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.compose_data.R | 264 - tidybayes-3.0.0/tidybayes/tests/testthat/test.emmeans_comparison.R | 50 tidybayes-3.0.0/tidybayes/tests/testthat/test.epred_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.epred_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_draws.R | 88 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_emmeans_draws.R | 155 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_pairs.R | 111 tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.gather_variables.R | 86 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_dotsinterval.R | 60 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_interval.R | 73 tidybayes-3.0.0/tidybayes/tests/testthat/test.geom_pointinterval.R | 71 tidybayes-3.0.0/tidybayes/tests/testthat/test.get_variables.R | 70 tidybayes-3.0.0/tidybayes/tests/testthat/test.linpred_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.linpred_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.nest_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.point_interval.R | 58 tidybayes-3.0.0/tidybayes/tests/testthat/test.predicted_draws.R | 476 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.predicted_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.residual_draws.R | 110 tidybayes-3.0.0/tidybayes/tests/testthat/test.spread_draws.R | 1020 ++--- tidybayes-3.0.0/tidybayes/tests/testthat/test.spread_rvars.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.stat_dist_slabinterval.R | 64 tidybayes-3.0.0/tidybayes/tests/testthat/test.stat_eye.R | 112 tidybayes-3.0.0/tidybayes/tests/testthat/test.summarise_draws.R |only tidybayes-3.0.0/tidybayes/tests/testthat/test.tidy_draws.R | 443 +- tidybayes-3.0.0/tidybayes/tests/testthat/test.ungather_draws.R | 184 tidybayes-3.0.0/tidybayes/tests/testthat/test.unspread_draws.R | 146 tidybayes-3.0.0/tidybayes/tests/testthat/test.util.R | 64 tidybayes-3.0.0/tidybayes/tests/testthat/test.x_at_y.R | 131 tidybayes-3.0.0/tidybayes/vignettes/tidy-brms.Rmd | 1889 ++++----- tidybayes-3.0.0/tidybayes/vignettes/tidy-posterior.Rmd |only tidybayes-3.0.0/tidybayes/vignettes/tidy-rstanarm.Rmd | 1340 +++--- tidybayes-3.0.0/tidybayes/vignettes/tidybayes-residuals.Rmd | 1428 +++---- tidybayes-3.0.0/tidybayes/vignettes/tidybayes.Rmd | 1630 ++++---- 117 files changed, 18216 insertions(+), 18541 deletions(-)
Title: Observers Needed to Evaluate Subjective Tests
Description: This ONEST software implements the method of assessing the pathologist agreement in reading PD-L1 assays (Reisenbichler et al. (2020 <doi:10.1038/s41379-020-0544-x>)), to determine the minimum number of evaluators needed to estimate agreement involving a large number of raters. Input to the program should be binary(1/0) pathology data, where “0” may stand for negative and “1” for positive. Additional examples were given using the data from Rimm et al. (2017 <doi:10.1001/jamaoncol.2017.0013>).
Author: Gang Han [aut, cre],
Baihong Guo [aut]
Maintainer: Gang Han <hangang.true@gmail.com>
Diff between ONEST versions 0.0.1 dated 2020-09-07 and 0.1.0 dated 2021-07-26
DESCRIPTION | 8 - MD5 | 21 +-- NAMESPACE | 2 NEWS.md |only R/ONEST.R | 16 ++ R/ONEST_inflation_test.R |only build/vignette.rds |binary data/NCCN_22c3_t.rdata |only inst/doc/ONEST.R | 13 + inst/doc/ONEST.Rmd | 19 ++ inst/doc/ONEST.html | 293 ++++++++++---------------------------------- man/NCCN_22c3_t.Rd |only man/ONEST_inflation_test.Rd |only vignettes/ONEST.Rmd | 19 ++ 14 files changed, 147 insertions(+), 244 deletions(-)
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between dipsaus versions 0.1.6 dated 2021-07-08 and 0.1.7 dated 2021-07-26
dipsaus-0.1.6/dipsaus/R/map-qs.R |only dipsaus-0.1.6/dipsaus/R/map-redis.R |only dipsaus-0.1.6/dipsaus/R/parallels-workers.R |only dipsaus-0.1.6/dipsaus/R/queue-qs.R |only dipsaus-0.1.6/dipsaus/R/queue-redis.R |only dipsaus-0.1.6/dipsaus/man/MasterEvaluator.Rd |only dipsaus-0.1.6/dipsaus/man/make_async_evaluator.Rd |only dipsaus-0.1.7/dipsaus/DESCRIPTION | 11 dipsaus-0.1.7/dipsaus/MD5 | 57 +-- dipsaus-0.1.7/dipsaus/NAMESPACE | 12 dipsaus-0.1.7/dipsaus/NEWS.md | 13 dipsaus-0.1.7/dipsaus/R/RcppExports.R | 4 dipsaus-0.1.7/dipsaus/R/aaa.R | 61 +++ dipsaus-0.1.7/dipsaus/R/cpp-fastquantile.R |only dipsaus-0.1.7/dipsaus/R/language.R | 47 ++ dipsaus-0.1.7/dipsaus/R/map-s3.R | 49 -- dipsaus-0.1.7/dipsaus/R/persist.R | 2 dipsaus-0.1.7/dipsaus/R/shiny-compoundInput2.R | 15 dipsaus-0.1.7/dipsaus/R/shiny-flex-div.R | 33 + dipsaus-0.1.7/dipsaus/R/shiny-setInputs.R | 50 ++ dipsaus-0.1.7/dipsaus/R/shiny-swal-alert.R |only dipsaus-0.1.7/dipsaus/R/shortcuts.R |only dipsaus-0.1.7/dipsaus/R/systems.R | 53 ++ dipsaus-0.1.7/dipsaus/R/zzz.R | 2 dipsaus-0.1.7/dipsaus/inst/doc/r_expr_addons.html | 6 dipsaus-0.1.7/dipsaus/inst/doc/shiny_customized_widgets.html | 178 ++++------ dipsaus-0.1.7/dipsaus/inst/doc/utility_functions.html | 2 dipsaus-0.1.7/dipsaus/inst/rstudio |only dipsaus-0.1.7/dipsaus/inst/shiny-addons/dipsaus/dipsaus-dipterix-lib.js | 149 ++++---- dipsaus-0.1.7/dipsaus/man/dipsaus-rstudio-shortcuts.Rd |only dipsaus-0.1.7/dipsaus/man/fastquantile.Rd |only dipsaus-0.1.7/dipsaus/man/get_ip.Rd |only dipsaus-0.1.7/dipsaus/man/grapes-help-set-grapes.Rd | 4 dipsaus-0.1.7/dipsaus/man/grapes-set-help-grapes.Rd |only dipsaus-0.1.7/dipsaus/man/map.Rd | 45 -- dipsaus-0.1.7/dipsaus/man/shiny_alert2.Rd |only dipsaus-0.1.7/dipsaus/src/RcppExports.cpp | 13 dipsaus-0.1.7/dipsaus/src/rcpp_median.cpp |only 38 files changed, 492 insertions(+), 314 deletions(-)
Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix
Description: Implements a constrained version of hierarchical agglomerative
clustering, in which each observation is associated to a position, and
only adjacent clusters can be merged. Typical application fields in
bioinformatics include Genome-Wide Association Studies or Hi-C data
analysis, where the similarity between items is a decreasing function of
their genomic distance. Taking advantage of this feature, the implemented
algorithm is time and memory efficient. This algorithm is described in
Ambroise et al (2019) <https://almob.biomedcentral.com/articles/10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut],
Shubham Chaturvedi [aut],
Alia Dehman [aut],
Pierre Neuvial [aut, cre],
Guillem Rigaill [aut],
Nathalie Vialaneix [aut],
Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>
Diff between adjclust versions 0.5.99 dated 2020-06-18 and 0.6.3 dated 2021-07-26
adjclust-0.5.99/adjclust/R/res_adjclust_0.3.0.R |only adjclust-0.5.99/adjclust/data |only adjclust-0.5.99/adjclust/man/res_adjclust_0.3.0.Rd |only adjclust-0.5.99/adjclust/src/init.c |only adjclust-0.6.3/adjclust/DESCRIPTION | 27 adjclust-0.6.3/adjclust/MD5 | 76 +- adjclust-0.6.3/adjclust/NAMESPACE | 7 adjclust-0.6.3/adjclust/NEWS.md | 23 adjclust-0.6.3/adjclust/R/RcppExports.R |only adjclust-0.6.3/adjclust/R/adjclust.R | 117 ++- adjclust-0.6.3/adjclust/R/buildHeap.R | 2 adjclust-0.6.3/adjclust/R/chac.R | 20 adjclust-0.6.3/adjclust/R/plotSim.R | 5 adjclust-0.6.3/adjclust/README.md | 15 adjclust-0.6.3/adjclust/build/vignette.rds |binary adjclust-0.6.3/adjclust/inst/CITATION |only adjclust-0.6.3/adjclust/inst/WORDLIST |only adjclust-0.6.3/adjclust/inst/doc/hicClust.R | 22 adjclust-0.6.3/adjclust/inst/doc/hicClust.Rmd | 4 adjclust-0.6.3/adjclust/inst/doc/hicClust.html | 365 ++------- adjclust-0.6.3/adjclust/inst/doc/notesCHAC.R | 8 adjclust-0.6.3/adjclust/inst/doc/notesCHAC.Rmd | 25 adjclust-0.6.3/adjclust/inst/doc/notesCHAC.html | 352 ++------- adjclust-0.6.3/adjclust/inst/doc/snpClust.R | 27 adjclust-0.6.3/adjclust/inst/doc/snpClust.Rmd | 3 adjclust-0.6.3/adjclust/inst/doc/snpClust.html | 367 ++-------- adjclust-0.6.3/adjclust/inst/extdata/res_adjclust_0.3.0.rds |only adjclust-0.6.3/adjclust/man/adjClust.Rd | 16 adjclust-0.6.3/adjclust/man/figures/README-adjClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-2.png |binary adjclust-0.6.3/adjclust/man/figures/README-hicClust-3.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-1.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-2.png |binary adjclust-0.6.3/adjclust/man/figures/README-snpClust-3.png |binary adjclust-0.6.3/adjclust/man/plotSim.Rd | 4 adjclust-0.6.3/adjclust/man/select.Rd | 2 adjclust-0.6.3/adjclust/src/Makevars |only adjclust-0.6.3/adjclust/src/Makevars.win |only adjclust-0.6.3/adjclust/src/RcppExports.cpp |only adjclust-0.6.3/adjclust/src/adjClustFast.cpp |only adjclust-0.6.3/adjclust/tests/testthat/test_ascendingCompatibility.R | 19 adjclust-0.6.3/adjclust/vignettes/hicClust.Rmd | 4 adjclust-0.6.3/adjclust/vignettes/notesCHAC.Rmd | 25 adjclust-0.6.3/adjclust/vignettes/snpClust.Rmd | 3 45 files changed, 509 insertions(+), 1029 deletions(-)
Title: The Ramer-Douglas-Peucker Algorithm
Description: Pretty fast implementation of the Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2D curve.
Urs Ramer (1972), "An iterative procedure for the polygonal approximation of plane curves" <doi:10.1016/S0146-664X(72)80017-0>.
David H. Douglas and Thomas K. Peucker (1973), "Algorithms for the Reduction of the Number of Points Required to Represent a Digitized Line or its Caricature" <doi:10.3138/FM57-6770-U75U-7727>.
Author: Robert Dahl Jacobsen [aut, cre]
Maintainer: Robert Dahl Jacobsen <cran@dahl-jacobsen.dk>
Diff between RDP versions 0.1.5 dated 2021-07-02 and 0.1.6 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- man/RDP-package.Rd | 2 +- src/RamerDouglasPeucker.cpp | 39 +++++++++++++++------------------------ 4 files changed, 22 insertions(+), 31 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian Montgomery [ctb],
Angelina Panagopoulou [ctb],
Hugh Parsonage [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.59.0 dated 2021-06-01 and 0.60.0 dated 2021-07-26
DESCRIPTION | 8 MD5 | 208 ++++++++++++------------ NEWS | 11 + R/anyMissing.R | 16 - R/rowAlls.R | 147 ++++++++++++++--- R/rowCollapse.R | 34 +++ R/rowCounts.R | 61 ++++++- R/rowCumsums.R | 182 ++++++++++++++++++--- R/rowDiffs.R | 64 +++++++ R/rowIQRs.R | 20 +- R/rowLogSumExps.R | 54 ++++-- R/rowMads.R | 56 ++++++ R/rowMeans2.R | 46 ++++- R/rowMedians.R | 61 ++++++- R/rowOrderStats.R | 46 ++++- R/rowProds.R | 26 ++- R/rowQuantiles.R | 20 +- R/rowRanges.R | 134 ++++++++++++++- R/rowRanks.R | 39 ++++ R/rowSds.R | 8 R/rowSums2.R | 46 ++++- R/rowTabulates.R | 25 ++ R/rowVars.R | 154 ++++++++++++++++- R/rowWeightedMeans.R | 66 +++++++ R/rowWeightedMedians.R | 18 +- R/varDiff.R | 56 +++++- R/weightedMad.R | 18 +- R/weightedVar.R | 22 +- inst/WORDLIST | 1 inst/doc/matrixStats-methods.html | 2 man/anyMissing.Rd | 13 + man/rowAlls.Rd | 13 + man/rowCollapse.Rd | 9 - man/rowCounts.Rd | 9 - man/rowCumsums.Rd | 21 +- man/rowDiffs.Rd | 9 - man/rowIQRs.Rd | 9 - man/rowLogSumExps.Rd | 27 +-- man/rowMeans2.Rd | 11 + man/rowMedians.Rd | 27 +-- man/rowOrderStats.Rd | 11 + man/rowProds.Rd | 9 - man/rowQuantiles.Rd | 11 + man/rowRanges.Rd | 23 +- man/rowRanks.Rd | 10 - man/rowSds.Rd | 13 + man/rowSums2.Rd | 11 + man/rowTabulates.Rd | 9 - man/rowVars.Rd | 9 - man/rowWeightedMeans.Rd | 11 + man/rowWeightedMedians.Rd | 11 + man/varDiff.Rd | 21 +- man/weightedMad.Rd | 9 - man/weightedVar.Rd | 17 + tests/rowAllAnys.R | 297 ++++++++++++++++++++++++---------- tests/rowAllAnys_subset.R | 249 ++++++++++++++++------------- tests/rowCollapse.R | 101 +++++++++-- tests/rowCollapse_subset.R | 65 +++++-- tests/rowCounts.R | 176 ++++++++++++-------- tests/rowCounts_subset.R | 88 ++++++---- tests/rowCumMinMaxs.R | 186 +++++++++++++++------ tests/rowCumMinMaxs_subset.R | 56 ++++-- tests/rowCumprods.R | 147 ++++++++++++----- tests/rowCumprods_subset.R | 35 +++- tests/rowCumsums.R | 113 +++++++++---- tests/rowCumsums_subset.R | 37 +++- tests/rowDiffs.R | 100 ++++++++--- tests/rowDiffs_subset.R | 55 ++++-- tests/rowIQRs.R | 61 +++++-- tests/rowIQRs_subset.R | 37 +++- tests/rowLogSumExps.R | 45 ++++- tests/rowLogSumExps_subset.R | 44 +++-- tests/rowMads.R | 317 ++++++++++++++++++++++--------------- tests/rowMads_subset.R | 67 ++++--- tests/rowMeans2.R | 242 +++++++++++++++++++--------- tests/rowMeans2_subset.R | 35 +++- tests/rowMedians.R | 234 ++++++++++++++++++--------- tests/rowMedians_subset.R | 41 +++- tests/rowOrderStats.R | 32 +++ tests/rowOrderStats_subset.R | 52 +++--- tests/rowProds.R | 119 ++++++++----- tests/rowProds_subset.R | 39 +++- tests/rowQuantiles.R | 137 ++++++++++----- tests/rowQuantiles_subset.R | 35 ++-- tests/rowRanges.R | 218 +++++++++++++++---------- tests/rowRanges_subset.R | 79 +++++---- tests/rowRanks.R | 67 +++++++ tests/rowRanks_subset.R | 59 +++++- tests/rowSds.R | 191 +++++++++++++--------- tests/rowSds_subset.R | 76 ++++++-- tests/rowSums2.R | 208 ++++++++++++++++-------- tests/rowSums2_subset.R | 41 +++- tests/rowTabulates.R | 61 +++++++ tests/rowTabulates_subset.R | 36 ++-- tests/rowVarDiffs.R | 64 +++++-- tests/rowVarDiffs_mad,iqr_subset.R | 30 ++- tests/rowVarDiffs_var,sd_subset.R | 32 ++- tests/rowVars.R | 242 ++++++++++++++++------------ tests/rowVars_subset.R | 76 ++++++-- tests/rowWeightedMeans.R | 188 +++++++++++++++++++++ tests/rowWeightedMeans_subset.R | 61 +++++-- tests/rowWeightedMedians.R | 161 ++++++++++++++++++ tests/rowWeightedMedians_subset.R | 48 ++++- tests/rowWeightedVars.R | 176 +++++++++++++++++++- tests/rowWeightedVars_subset.R | 27 ++- 105 files changed, 5422 insertions(+), 1933 deletions(-)
Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing:
(a) Methods and operators that work natively on CSR formats (compressed sparse row,
a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(),
mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag();
(b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types,
including the 'float32' type from 'float';
(c) Coercion methods between pairs of classes which are not present in 'Matrix',
such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions;
(d) Utility functions for sparse matrices such as sorting the indices or removing
zero-valued entries;
(e) Fast transposes that work by outputting in the opposite storage format;
(f) Faster replacements for many 'Matrix' methods for all sparse types, such as
slicing and elementwise multiplication.
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included
robinmap library)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.5 dated 2021-06-22 and 0.1.6 dated 2021-07-26
DESCRIPTION | 17 +- MD5 | 65 +++++---- NAMESPACE | 3 R/MatrixExtra.R | 4 R/RcppExports.R | 4 R/assignment.R | 6 R/conversions.R | 4 R/matmul.R | 75 ++++++----- R/rbind.R | 6 R/slice.R | 10 - R/utils.R | 249 +++++++++++++++++++++++++++++++++++-- R/zzz.R | 9 + configure | 21 +-- configure.ac | 4 inst/COPYRIGHTS |only man/MatrixExtra-options.Rd | 9 + man/MatrixExtra.Rd | 4 man/emptySparse.Rd |only man/filterSparse.Rd |only man/mapSparse.Rd |only man/matmult.Rd | 19 ++ src/Makevars.in | 4 src/Makevars.win.in | 5 src/MatrixExtra.h | 16 ++ src/RcppExports.cpp | 12 + src/assignment.cpp | 4 src/matmul.cpp | 255 +++++++++++++++----------------------- src/misc.cpp | 19 ++ src/operators.cpp | 2 src/robinmap |only src/slice.cpp | 10 - src/slice_coo.cpp | 16 +- tests/testthat/test-conversions.R | 16 ++ tests/testthat/test-utilities.R | 57 ++++++++ 34 files changed, 655 insertions(+), 270 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of linear
regression, GLM, and Cox regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge. For more
information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>,
Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang
(2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015)
<doi:10.1111/biom.12300>, or visit the package homepage
<https://pbreheny.github.io/grpreg/>.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>),
Yaohui Zeng [ctb],
Ryan Kurth [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.3.1 dated 2021-03-30 and 3.4.0 dated 2021-07-26
grpreg-3.3.1/grpreg/man/predict-grpsurv.Rd |only grpreg-3.3.1/grpreg/src/lcdfit_binomial.c |only grpreg-3.3.1/grpreg/src/lcdfit_poisson.c |only grpreg-3.4.0/grpreg/DESCRIPTION | 16 grpreg-3.4.0/grpreg/MD5 | 78 ++-- grpreg-3.4.0/grpreg/NAMESPACE | 28 - grpreg-3.4.0/grpreg/NEWS.md | 15 grpreg-3.4.0/grpreg/R/G.R | 1 grpreg-3.4.0/grpreg/R/cv-grpreg.R | 17 grpreg-3.4.0/grpreg/R/cv-grpsurv.R | 2 grpreg-3.4.0/grpreg/R/expand_spline.R |only grpreg-3.4.0/grpreg/R/gBridge.R | 25 - grpreg-3.4.0/grpreg/R/gen_nonlinear_data.R |only grpreg-3.4.0/grpreg/R/grpreg.R | 52 ++ grpreg-3.4.0/grpreg/R/grpsurv.R | 36 + grpreg-3.4.0/grpreg/R/logLik.R | 2 grpreg-3.4.0/grpreg/R/plot_spline.R |only grpreg-3.4.0/grpreg/R/predict-cv.R | 6 grpreg-3.4.0/grpreg/R/predict-surv.R | 89 ++++ grpreg-3.4.0/grpreg/R/predict.R | 9 grpreg-3.4.0/grpreg/R/predict_spline.R |only grpreg-3.4.0/grpreg/R/residuals.R |only grpreg-3.4.0/grpreg/R/setupLambda.R | 7 grpreg-3.4.0/grpreg/build/partial.rdb |binary grpreg-3.4.0/grpreg/build/vignette.rds |binary grpreg-3.4.0/grpreg/inst/doc/getting-started.html | 287 +++------------ grpreg-3.4.0/grpreg/inst/tinytest/additive-models.R |only grpreg-3.4.0/grpreg/inst/tinytest/basic-functionality.R | 56 +- grpreg-3.4.0/grpreg/inst/tinytest/cv.R | 21 - grpreg-3.4.0/grpreg/inst/tinytest/extra-features.R | 64 ++- grpreg-3.4.0/grpreg/inst/tinytest/gBridge.R | 18 grpreg-3.4.0/grpreg/inst/tinytest/grpsurv.R | 51 ++ grpreg-3.4.0/grpreg/inst/tinytest/surv-torture.R | 10 grpreg-3.4.0/grpreg/inst/tinytest/torture.R | 10 grpreg-3.4.0/grpreg/man/expand_spline.Rd |only grpreg-3.4.0/grpreg/man/gBridge.Rd | 13 grpreg-3.4.0/grpreg/man/gen_nonlinear_data.Rd |only grpreg-3.4.0/grpreg/man/grpreg.Rd | 11 grpreg-3.4.0/grpreg/man/plot_spline.Rd |only grpreg-3.4.0/grpreg/man/predict.grpsurv.Rd |only grpreg-3.4.0/grpreg/man/residuals.grpreg.Rd |only grpreg-3.4.0/grpreg/src/gdfit_gaussian.c | 30 - grpreg-3.4.0/grpreg/src/gdfit_glm.c | 42 +- grpreg-3.4.0/grpreg/src/lcdfit_gaussian.c | 28 - grpreg-3.4.0/grpreg/src/lcdfit_glm.c | 48 +- grpreg-3.4.0/grpreg/vignettes/web/adaptive-rescaling.rmd |only grpreg-3.4.0/grpreg/vignettes/web/additive-models.rmd |only grpreg-3.4.0/grpreg/vignettes/web/models.rmd | 2 48 files changed, 626 insertions(+), 448 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 1.0.0 dated 2021-07-16 and 1.0.0.1 dated 2021-07-26
GeoTcgaData-1.0.0.1/GeoTcgaData/DESCRIPTION | 12 GeoTcgaData-1.0.0.1/GeoTcgaData/MD5 | 37 - GeoTcgaData-1.0.0.1/GeoTcgaData/NAMESPACE | 5 GeoTcgaData-1.0.0.1/GeoTcgaData/R/RNA_seq.R |only GeoTcgaData-1.0.0.1/GeoTcgaData/R/SNP.R | 10 GeoTcgaData-1.0.0.1/GeoTcgaData/R/TCGA_id_conversion.R | 6 GeoTcgaData-1.0.0.1/GeoTcgaData/R/ann_merge.r | 188 ++--- GeoTcgaData-1.0.0.1/GeoTcgaData/R/data.R | 11 GeoTcgaData-1.0.0.1/GeoTcgaData/R/fpkm_count_conversion.r | 34 - GeoTcgaData-1.0.0.1/GeoTcgaData/R/sysdata.rda |binary GeoTcgaData-1.0.0.1/GeoTcgaData/README.md | 88 ++ GeoTcgaData-1.0.0.1/GeoTcgaData/data/gene_cov.rda |only GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.R | 51 + GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.Rmd | 67 + GeoTcgaData-1.0.0.1/GeoTcgaData/inst/doc/GeoTcgaData.html | 372 ++++++----- GeoTcgaData-1.0.0.1/GeoTcgaData/inst/extdata/build_data.R |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/diff_RNA.Rd |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/diff_SNP.Rd | 8 GeoTcgaData-1.0.0.1/GeoTcgaData/man/gene_cov.Rd |only GeoTcgaData-1.0.0.1/GeoTcgaData/man/id_conversion.Rd | 4 GeoTcgaData-1.0.0.1/GeoTcgaData/vignettes/GeoTcgaData.Rmd | 67 + GeoTcgaData-1.0.0/GeoTcgaData/inst/extdata/build_hgnc_file.R |only GeoTcgaData-1.0.0/GeoTcgaData/man/ann_merge.Rd |only 23 files changed, 637 insertions(+), 323 deletions(-)
Title: Rhythmic Patterns Modeling by FMM Models
Description: Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Author: Itziar Fernandez, Alejandro Rodriguez-Collado, Yolanda Larriba, Adrian Lamela, Christian Canedo, Cristina Rueda
Maintainer: Itziar Fernandez <itziar.fernandez@uva.es>
Diff between FMM versions 0.1.2 dated 2021-03-01 and 0.3.0 dated 2021-07-26
DESCRIPTION | 12 MD5 | 66 +- NAMESPACE | 28 - NEWS.md | 37 + R/Class.R | 71 +- R/FMM-methods.R | 355 ++++++------- R/FMM_internal.R | 546 +++++++++----------- R/FMM_internal_restr.R |only R/ecgData-data.R |only R/extractWaves.R | 59 +- R/fitFMM.R | 333 ++++++++---- R/fitFMM_back.R | 364 ++++--------- R/fitFMM_restr.R | 1250 +++++++++-------------------------------------- R/fitFMM_unit.R | 222 ++++---- R/generateFMM.R | 171 +++--- R/getFMMPeaks.R | 119 ++-- R/mouseGeneExp-data.R |only R/neuronalAPTrain-data.R | 52 - R/neuronalSpike-data.R | 52 - R/plotFMM.R | 295 ++++++----- R/stopFunctions.R | 86 +-- README.md |only man/Class.Rd | 136 ++--- man/FMM-getS4.Rd | 116 ++-- man/FMM-internal.Rd | 129 ++-- man/FMM-methods.Rd | 216 ++++---- man/FMM-package.Rd | 78 +- man/ecgData.Rd | 81 +-- man/extractWaves.Rd | 65 +- man/fitFMM.Rd | 272 ++++------ man/generateFMM.Rd | 171 ++---- man/getFMMPeaks.Rd | 85 +-- man/mouseGeneExp.Rd | 62 +- man/neuronalAPTrain.Rd | 64 +- man/neuronalSpike.Rd | 64 +- man/plotFMM.Rd | 144 +++-- 36 files changed, 2566 insertions(+), 3235 deletions(-)
Title: A Comprehensive R Interface for the DSSAT Cropping Systems Model
Description: The purpose of this package is to provide a comprehensive
R interface to the Decision Support System for Agrotechnology
Transfer Cropping Systems Model (DSSAT-CSM) documented by
Jones et al (2003) <doi:10.1016/S1161-0301(02)00107-7>. The package
provides cross-platform functions to read and write input files,
run DSSAT-CSM, and read output files.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>
Diff between DSSAT versions 0.0.2 dated 2020-05-18 and 0.0.3 dated 2021-07-26
DESCRIPTION | 15 +++++++-------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/read_pest.R | 2 +- R/read_tier_data.R | 2 +- R/v_fmt_filex.R | 2 +- README.md | 3 +++ 7 files changed, 23 insertions(+), 17 deletions(-)
Title: Transformation-Free Linear Regression for Compositional Outcomes
and Predictors
Description: Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2021) <doi:10.1111/biom.13465>
for transformation-free linear regression for compositional outcomes and predictors.
Author: Jacob Fiksel [aut, cre] (<https://orcid.org/0000-0001-7067-1334>),
Abhirup Datta [aut]
Maintainer: Jacob Fiksel <jfiksel@gmail.com>
Diff between codalm versions 0.1.1 dated 2021-06-21 and 0.1.2 dated 2021-07-26
DESCRIPTION | 12 - MD5 | 27 +-- R/codalm_em.R | 6 R/data.R |only R/independence_test.R | 2 build/vignette.rds |binary data |only inst/doc/codalm_quickstart.R | 3 inst/doc/codalm_quickstart.Rmd | 7 inst/doc/codalm_quickstart.html | 331 ++++++++++------------------------------ man/codalm.Rd | 2 man/codalm_ci.Rd | 2 man/codalm_indep_test.Rd | 2 man/educFM.Rd |only man/predict_codalm.Rd | 2 vignettes/codalm_quickstart.Rmd | 7 16 files changed, 120 insertions(+), 283 deletions(-)
Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model.
The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots.
This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>),
Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Tomasz Mikołajczyk [aut],
Michal Burdukiewicz [ctb],
Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Diff between auditor versions 1.3.0 dated 2020-05-28 and 1.3.3 dated 2021-07-26
DESCRIPTION | 13 + MD5 | 207 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 10 + R/auditorData.R | 8 - R/check_residuals.R | 16 +- R/model_evaluation.R | 2 R/model_performance.R | 4 R/model_residual.R | 2 R/plot.R | 5 R/plotD3.R | 4 R/plotD3_autocorrelation.R | 4 R/plotD3_cooksdistance.R | 2 R/plotD3_prediction.R | 4 R/plotD3_residual.R | 6 R/plotD3_roc.R | 2 R/plotD3_rroc.R | 2 R/plotD3_scalelocation.R | 4 R/plot_correlation.R | 4 R/plot_residual_density.R | 8 - R/plot_roc.R | 2 R/plot_rroc.R | 2 R/print.R | 12 - R/score.R | 2 R/score_F1.R | 8 - R/score_acc.R | 8 - R/score_auc.R | 11 - R/score_auprc.R | 9 + R/score_dw.R | 2 R/score_gini.R | 6 R/score_mae.R | 2 R/score_mse.R | 2 R/score_peak.R | 2 R/score_precision.R | 8 - R/score_r2.R | 4 R/score_rec.R | 2 R/score_recall.R | 8 - R/score_rmse.R | 2 R/score_rroc.R | 4 R/score_runs.R | 2 R/score_specificity.R | 8 - build/vignette.rds |binary inst/CITATION | 2 inst/WORDLIST |only inst/doc/model_evaluation_audit.Rmd | 2 inst/doc/model_evaluation_audit.html | 6 inst/doc/model_fit_audit.Rmd | 6 inst/doc/model_fit_audit.html | 6 inst/doc/model_performance_audit.Rmd | 4 inst/doc/model_performance_audit.html | 4 inst/doc/model_residuals_audit.Rmd | 16 +- inst/doc/model_residuals_audit.html | 20 +- inst/doc/observation_influence_audit.Rmd | 2 inst/doc/observation_influence_audit.html | 4 man/auditorData.Rd | 8 + man/check_residuals.Rd | 2 man/check_residuals_outliers.Rd | 2 man/check_residuals_trend.Rd | 8 - man/model_evaluation.Rd | 2 man/model_performance.Rd | 4 man/model_residual.Rd | 2 man/plot.Rd | 4 man/plotD3.Rd | 4 man/plotD3_autocorrelation.Rd | 4 man/plotD3_cooksdistance.Rd | 2 man/plotD3_prediction.Rd | 4 man/plotD3_residual.Rd | 6 man/plotD3_roc.Rd | 2 man/plotD3_rroc.Rd | 2 man/plotD3_scalelocation.Rd | 4 man/plot_correlation.Rd | 4 man/plot_residual_density.Rd | 8 - man/plot_roc.Rd | 2 man/plot_rroc.Rd | 2 man/score.Rd | 2 man/score_acc.Rd | 4 man/score_auc.Rd | 2 man/score_auprc.Rd | 82 +++++------ man/score_dw.Rd | 2 man/score_f1.Rd | 4 man/score_gini.Rd | 2 man/score_mae.Rd | 2 man/score_mse.Rd | 2 man/score_one_minus_acc.Rd | 4 man/score_one_minus_auc.Rd | 2 man/score_one_minus_auprc.Rd | 82 +++++------ man/score_one_minus_f1.Rd | 4 man/score_one_minus_gini.Rd | 4 man/score_one_minus_precision.Rd | 4 man/score_one_minus_recall.Rd | 4 man/score_one_minus_specificity.Rd | 4 man/score_peak.Rd | 2 man/score_precision.Rd | 4 man/score_r2.Rd | 4 man/score_rec.Rd | 2 man/score_recall.Rd | 4 man/score_rmse.Rd | 2 man/score_rroc.Rd | 4 man/score_runs.Rd | 2 man/score_specificity.Rd | 4 vignettes/model_evaluation_audit.Rmd | 2 vignettes/model_fit_audit.Rmd | 6 vignettes/model_performance_audit.Rmd | 4 vignettes/model_residuals_audit.Rmd | 16 +- vignettes/observation_influence_audit.Rmd | 2 105 files changed, 430 insertions(+), 400 deletions(-)
Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear
optimization, and related tools. It includes a unified way to call
different optimizers, and classes and methods to handle the results from
the Maximum Likelihood viewpoint. It also includes a number of convenience
tools for testing and developing your own models.
Author: Ott Toomet [aut, cre],
Arne Henningsen [aut],
Spencer Graves [ctb],
Yves Croissant [ctb],
David Hugh-Jones [ctb],
Luca Scrucca [ctb]
Maintainer: Ott Toomet <otoomet@gmail.com>
Diff between maxLik versions 1.4-8 dated 2021-03-22 and 1.5-2 dated 2021-07-26
maxLik-1.4-8/maxLik/tests/basicTest.R |only maxLik-1.4-8/maxLik/tests/basicTest.Rout.save |only maxLik-1.4-8/maxLik/tests/fitNormalDist_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/maxControl_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/maxSG_privateTest.Rout.save |only maxLik-1.4-8/maxLik/tests/methods.R |only maxLik-1.4-8/maxLik/tests/methods.Rout.save |only maxLik-1.4-8/maxLik/tests/parameters_privateTest.Rout.save |only maxLik-1.4-8/maxLik/vignettes/auto |only maxLik-1.5-2/maxLik/DESCRIPTION | 34 +++-- maxLik-1.5-2/maxLik/MD5 | 59 +++++----- maxLik-1.5-2/maxLik/NAMESPACE | 33 +++-- maxLik-1.5-2/maxLik/NEWS | 30 ++++- maxLik-1.5-2/maxLik/R/confint.maxLik.R |only maxLik-1.5-2/maxLik/R/maxBFGSRCompute.R | 4 maxLik-1.5-2/maxLik/R/maxNRCompute.R | 17 +- maxLik-1.5-2/maxLik/R/maxSGACompute.R | 8 - maxLik-1.5-2/maxLik/R/tidyMethods.R |only maxLik-1.5-2/maxLik/build/partial.rdb |binary maxLik-1.5-2/maxLik/build/vignette.rds |binary maxLik-1.5-2/maxLik/inst/doc/intro-to-maximum-likelihood.Rnw | 59 +++++----- maxLik-1.5-2/maxLik/inst/doc/intro-to-maximum-likelihood.pdf |binary maxLik-1.5-2/maxLik/inst/doc/stochastic-gradient-maxLik.pdf |binary maxLik-1.5-2/maxLik/inst/doc/using-maxlik.pdf |binary maxLik-1.5-2/maxLik/inst/tinytest |only maxLik-1.5-2/maxLik/man/bread.maxLik.Rd | 1 maxLik-1.5-2/maxLik/man/confint.maxLik.Rd |only maxLik-1.5-2/maxLik/man/gradient.Rd | 1 maxLik-1.5-2/maxLik/man/maxLik-package.Rd | 19 +-- maxLik-1.5-2/maxLik/man/reexports.Rd |only maxLik-1.5-2/maxLik/man/summary.maxLik.Rd | 7 + maxLik-1.5-2/maxLik/man/summary.maxim.Rd | 41 +----- maxLik-1.5-2/maxLik/man/tidy.maxLik.Rd |only maxLik-1.5-2/maxLik/tests/tinytest.R |only maxLik-1.5-2/maxLik/vignettes/intro-to-maximum-likelihood.Rnw | 59 +++++----- maxLik-1.5-2/maxLik/vignettes/probability-density.pdf |binary 36 files changed, 205 insertions(+), 167 deletions(-)
Title: Wilcoxon Rank Tests for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test)
for clustered data documented in
Jiang et. al (2020) <doi:10.18637/jss.v096.i06>.
Author: Wenjie Wang [cre, ctb] (<https://orcid.org/0000-0003-0363-3180>),
Yujing Jiang [aut],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between clusrank versions 1.0-0 dated 2020-12-10 and 1.0-1 dated 2021-07-26
DESCRIPTION | 33 ++++++++++++++++++++------------- MD5 | 36 +++++++++++++++++++----------------- NAMESPACE | 4 ++++ R/amd.R | 2 +- R/clusWilcox.R | 4 ++-- R/clusranksum.R | 9 +++++---- R/clussignrank.R | 2 +- R/crd.R | 2 +- R/crdstr.R | 2 +- R/crsd.R | 2 +- R/crsdunb.R | 2 +- R/pairwise.clusWilcox.test.R |only R/print.R | 2 +- R/recodeFun.R | 21 ++++++++++----------- R/special.R | 17 ++++++++--------- man/clusWilcox.test.Rd | 2 +- man/pairwise.clusWilcox.test.Rd |only src/Fprop.cpp | 18 ++++++++++++++++++ src/RcppExports.cpp | 5 +++++ src/exact.cpp | 18 ++++++++++++++++++ 20 files changed, 117 insertions(+), 64 deletions(-)
Title: Profile R Code and Visualize with 'Pprof'
Description: Like similar profiling tools,
the 'proffer' package automatically detects
sources of slowness in R code.
The distinguishing feature of 'proffer' is its utilization of
'pprof', which supplies interactive visualizations
that are efficient and easy to interpret.
Behind the scenes, the 'profile' package converts
native Rprof() data to a protocol buffer
that 'pprof' understands.
For the documentation of 'proffer',
visit <https://r-prof.github.io/proffer/>.
To learn about the implementations and methodologies of
'pprof', 'profile', and protocol buffers,
visit <https://github.com/google/pprof>.
<https://developers.google.com/protocol-buffers>,
and <https://github.com/r-prof/profile>, respectively.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between proffer versions 0.1.3 dated 2021-06-28 and 0.1.5 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/pprof.R | 4 ++-- tests/testthat.R | 4 +++- 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution
of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies.
It is based on a spatial geometry for describing the landscape and allocation of different cultivars,
a dispersal kernel for the dissemination of the pathogen, and a SEIR
('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step.
It provides a useful tool to assess the performance of a wide range of deployment options with
respect to their epidemiological, evolutionary and economic outcomes.
Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett,
Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut],
Julien Papaix [aut],
Jean-François Rey [aut, cre] (<https://orcid.org/0000-0003-3281-6701>),
Jean-Loup Gaussen [ctb]
Maintainer: Jean-François Rey <jean-francois.rey@inrae.fr>
Diff between landsepi versions 1.0.2 dated 2020-11-30 and 1.1.0 dated 2021-07-26
landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.R |only landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.Rmd |only landsepi-1.0.2/landsepi/inst/doc/landscape_dispersal.html |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.R |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.Rmd |only landsepi-1.0.2/landsepi/inst/doc/run_exp_design.html |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.R |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.Rmd |only landsepi-1.0.2/landsepi/inst/doc/run_simple_simul.html |only landsepi-1.0.2/landsepi/vignettes/landscape_dispersal.Rmd |only landsepi-1.0.2/landsepi/vignettes/run_exp_design.Rmd |only landsepi-1.0.2/landsepi/vignettes/run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/DESCRIPTION | 43 landsepi-1.1.0/landsepi/MD5 | 117 landsepi-1.1.0/landsepi/R/AgriLand.R | 3 landsepi-1.1.0/landsepi/R/GPKGTools.R | 2 landsepi-1.1.0/landsepi/R/Methods-LandsepiParams.R | 121 landsepi-1.1.0/landsepi/R/RcppExports.R | 2 landsepi-1.1.0/landsepi/R/demo_landsepi.R | 2 landsepi-1.1.0/landsepi/R/graphics.R | 15 landsepi-1.1.0/landsepi/R/landsepi.R | 46 landsepi-1.1.0/landsepi/R/output.R | 317 +- landsepi-1.1.0/landsepi/R/runShiny.R | 4 landsepi-1.1.0/landsepi/R/simul_landsepi.R | 72 landsepi-1.1.0/landsepi/build/vignette.rds |binary landsepi-1.1.0/landsepi/configure | 18 landsepi-1.1.0/landsepi/configure.ac | 2 landsepi-1.1.0/landsepi/data/dispP_a40_b7.rda |binary landsepi-1.1.0/landsepi/data/landscapesTEST.rda |binary landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.R |only landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O1-run_simple_simul.html |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.R |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O2-run_exp_design.html |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.R |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.Rmd |only landsepi-1.1.0/landsepi/inst/doc/O3-landscape_dispersal.html |only landsepi-1.1.0/landsepi/inst/doc/landsepi_poster.Rnw |only landsepi-1.1.0/landsepi/inst/doc/landsepi_poster.pdf |only landsepi-1.1.0/landsepi/inst/doc/list_of_parameters.Rnw | 2 landsepi-1.1.0/landsepi/inst/doc/list_of_parameters.pdf |binary landsepi-1.1.0/landsepi/inst/logos |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/Dockerfile | 4 landsepi-1.1.0/landsepi/inst/shiny-landsepi/global.R | 340 ++ landsepi-1.1.0/landsepi/inst/shiny-landsepi/modules |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/server.R | 1285 +++++++--- landsepi-1.1.0/landsepi/inst/shiny-landsepi/ui.R | 251 + landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/CSIRO_Logo.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/LogoINRAE_Fr_rvb_web.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/PATHO_inra_logo.png |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/Republique_Francaise_RVB.jpg |only landsepi-1.1.0/landsepi/inst/shiny-landsepi/www/landsepi-logo.png |only landsepi-1.1.0/landsepi/man/AgriLand.Rd | 3 landsepi-1.1.0/landsepi/man/allocateLandscapeCroptypes.Rd | 3 landsepi-1.1.0/landsepi/man/epid_output.Rd | 59 landsepi-1.1.0/landsepi/man/evol_output.Rd | 2 landsepi-1.1.0/landsepi/man/landsepi-package.Rd | 47 landsepi-1.1.0/landsepi/man/loadOutputs.Rd | 18 landsepi-1.1.0/landsepi/man/model_landsepi.Rd | 2 landsepi-1.1.0/landsepi/man/runSimul.Rd | 2 landsepi-1.1.0/landsepi/man/setCultivars.Rd | 29 landsepi-1.1.0/landsepi/man/setOutputs.Rd | 20 landsepi-1.1.0/landsepi/man/setPathogen.Rd | 2 landsepi-1.1.0/landsepi/man/simul_landsepi.Rd | 53 landsepi-1.1.0/landsepi/man/video.Rd | 10 landsepi-1.1.0/landsepi/src/Model.cpp | 2 landsepi-1.1.0/landsepi/src/Model.hpp | 2 landsepi-1.1.0/landsepi/src/RcppExports.cpp | 5 landsepi-1.1.0/landsepi/src/initialisation.cpp | 11 landsepi-1.1.0/landsepi/vignettes/O1-run_simple_simul.Rmd |only landsepi-1.1.0/landsepi/vignettes/O2-run_exp_design.Rmd |only landsepi-1.1.0/landsepi/vignettes/O3-landscape_dispersal.Rmd |only landsepi-1.1.0/landsepi/vignettes/landsepi_poster.Rnw |only landsepi-1.1.0/landsepi/vignettes/landsepiposter.pdf |only landsepi-1.1.0/landsepi/vignettes/list_of_parameters.Rnw | 2 landsepi-1.1.0/landsepi/vignettes/listofparameters.pdf |binary 77 files changed, 2085 insertions(+), 833 deletions(-)
Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score
estimating and weighting, nonresponse weighting, and diagnosis
of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>
Diff between twang versions 2.3 dated 2021-06-10 and 2.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/boxplot.mnps.R | 2 +- inst/doc/iptw.pdf |binary inst/doc/mnps.pdf |binary inst/doc/twang.pdf |binary 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following
the method described in Kang et al. (2010), <doi:10.1038/ng.548>.
One of a series of statistical genetic packages for streamlining the
analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre]
(<https://orcid.org/0000-0002-8673-2514>),
Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>),
Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>),
Martin Boer [ctb],
Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>),
Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>),
Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>),
Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>),
Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>),
Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>),
Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenGWAS versions 1.0.5 dated 2020-09-29 and 1.0.6 dated 2021-07-26
DESCRIPTION | 16 MD5 | 87 +-- NEWS.md | 14 R/GWASHelp.R | 54 +- R/codeMarkers.R | 48 + R/createGData.R | 2 R/createGWAS.R | 132 ++++ R/data.R | 68 +- R/kinship.R | 19 R/manhattanPlot.R | 20 R/qqPlot.R | 9 R/qtlPlot.R | 10 R/runSingleTraitGwas.R | 38 - R/utils.R | 9 README.md | 8 build/partial.rdb |only build/vignette.rds |binary data/dropsMap.rda |binary data/dropsMarkers.rda |binary data/dropsPheno.rda |binary inst/doc/GWAS.R | 12 inst/doc/GWAS.Rmd | 36 + inst/doc/GWAS.html | 917 ++++++++++++++-------------------- inst/java/beagle.jar |binary inst/tinytest/test_GWAS.R | 2 inst/tinytest/test_STG.R | 32 - inst/tinytest/test_STGHelper.R | 8 inst/tinytest/test_STGoptions.R | 20 inst/tinytest/test_codeMarkers.R | 12 inst/tinytest/test_kinship.R | 56 +- inst/tinytest/test_plots.R | 24 man/codeMarkers.Rd | 261 ++++----- man/dropsData.Rd | 108 ++-- man/figures/README-manhattanStg-1.png |binary man/figures/README-qqStg-1.png |binary man/figures/README-qtlStgNorm-1.png |binary man/gData.Rd | 2 man/kinship.Rd | 126 ++-- man/plot.GWAS.Rd | 89 +++ man/runSingleTraitGwas.Rd | 97 +-- man/statgenGWAS-package.Rd | 2 man/summary.gData.Rd | 70 +- src/RcppExports.cpp | 5 vignettes/GWAS.Rmd | 36 + vignettes/bibliography.bib | 20 45 files changed, 1374 insertions(+), 1095 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 2.1.0 dated 2021-07-14 and 2.2.0 dated 2021-07-26
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++++++--------- NAMESPACE | 7 +++++++ NEWS.md | 5 +++++ R/batch.R | 1 - R/convert_umlauts_to_ascii.R | 9 ++------- R/csv.R |only R/load_internal_functions.R | 2 +- R/options.R | 9 ++++++--- inst/NEWS.rd | 7 +++++++ inst/runit_tests/runit-csv.R |only man/bulk_read_csv.Rd |only man/bulk_write_csv.Rd |only man/csv.Rd |only man/csv2csv.Rd |only man/load_internal_functions.Rd | 2 +- man/set_hash.Rd |only man/un_hash.Rd |only 18 files changed, 52 insertions(+), 28 deletions(-)
Title: Build a Package from Rmarkdown File
Description: Use Rmarkdown First method to build your package. Start your
package with documentation, functions, examples and tests in the same
unique file. Everything can be set from the Rmarkdown template file
provided in your project, then inflated as a package. Inflating the
template copies the relevant chunks and sections in the appropriate
files required for package development.
Author: Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>),
ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between fusen versions 0.2.2 dated 2021-07-09 and 0.2.3 dated 2021-07-26
fusen-0.2.2/fusen/vignettes/images |only fusen-0.2.3/fusen/DESCRIPTION | 7 fusen-0.2.3/fusen/MD5 | 43 +-- fusen-0.2.3/fusen/NAMESPACE | 1 fusen-0.2.3/fusen/NEWS.md | 8 fusen-0.2.3/fusen/R/fill_description.R | 23 +- fusen-0.2.3/fusen/R/inflate.R | 48 +++- fusen-0.2.3/fusen/inst/dev-template-additional.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-full.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-minimal.Rmd | 2 fusen-0.2.3/fusen/inst/dev-template-teaching.Rmd | 2 fusen-0.2.3/fusen/inst/doc/How-to-use-fusen.html | 13 - fusen-0.2.3/fusen/inst/tests-templates/dev-template-stop-duplicate-fun.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-stop-duplicate-label.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-test-parse-nothing.Rmd | 2 fusen-0.2.3/fusen/inst/tests-templates/dev-template-tests-special-char.Rmd |only fusen-0.2.3/fusen/inst/tests-templates/dev-template-tests.Rmd | 32 ++ fusen-0.2.3/fusen/man/fill_description.Rd | 2 fusen-0.2.3/fusen/man/inflate.Rd | 5 fusen-0.2.3/fusen/tests/testthat/test-fill_description.R | 31 ++ fusen-0.2.3/fusen/tests/testthat/test-inflate.R | 112 +++++++++- 21 files changed, 279 insertions(+), 60 deletions(-)
Title: SOM Algorithm for the Analysis of Multivariate Environmental
Data
Description: Analysis of multivariate environmental high frequency data by Self-Organizing Map and k-means clustering algorithms. By means of the graphical user interface it provides a comfortable way to elaborate by self-organizing map algorithm rather big datasets (txt files up to 100 MB ) obtained by environmental high-frequency monitoring by sensors/instruments. The functions present in the package are based on 'kohonen' and 'openair' packages implemented by functions embedding Vesanto et al. (2001) <http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf> heuristic rules for map initialization parameters, k-means clustering algorithm and map features visualization. Cluster profiles visualization as well as graphs dedicated to the visualization of time-dependent variables Licen et al. (2020) <doi:10.4209/aaqr.2019.08.0414> are provided.
Author: Sabina Licen [aut, cre],
Marco Franzon [aut],
Tommaso Rodani [aut],
Pierluigi Barbieri [aut]
Maintainer: Sabina Licen <slicen@units.it>
Diff between SOMEnv versions 1.1.1 dated 2021-03-02 and 1.1.2 dated 2021-07-26
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NAMESPACE | 3 - R/SomEnvGUI.R | 3 - inst/CITATION | 84 +++++++--------------------------------- inst/shiny-examples/myapp/app.R | 20 ++++----- 6 files changed, 38 insertions(+), 92 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations. Uses by default the 's2'
package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb],
Dan Baston [ctb],
Dewey Dunnington [ctb] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 1.0-1 dated 2021-06-29 and 1.0-2 dated 2021-07-26
DESCRIPTION | 6 - MD5 | 71 +++++++++++------------ NAMESPACE | 1 NEWS.md | 18 +++++ R/bind.R | 7 +- R/crs.R | 9 ++ R/maps.R | 10 ++- R/read.R | 7 +- R/sample.R | 49 +++++++--------- R/spatstat.R | 134 ++++++++++++++++++++++---------------------- R/tidyverse.R | 11 +++ configure | 4 - configure.ac | 4 - inst/doc/sf1.html | 10 +-- inst/doc/sf2.html | 14 ++-- inst/doc/sf3.Rmd | 19 +++--- inst/doc/sf3.html | 19 +++--- inst/doc/sf4.Rmd | 14 ++-- inst/doc/sf4.html | 16 ++--- inst/doc/sf5.Rmd | 12 +-- inst/doc/sf5.html | 18 ++--- inst/doc/sf6.html | 2 inst/doc/sf7.html | 8 +- inst/docker/gdal/Dockerfile | 23 ++++--- man/st_crs.Rd | 4 - src/Makevars.ucrt |only src/Makevars.win | 2 src/RcppExports.cpp | 5 + src/gdal_read.cpp | 32 ++++++++-- src/gdal_write.cpp | 18 +++++ src/geos.cpp | 11 +++ tests/geos.R | 12 +++ tests/geos.Rout.save | 35 +++++++++++ tests/spatstat.Rout.save | 43 ++++++-------- vignettes/sf3.Rmd | 19 +++--- vignettes/sf4.Rmd | 14 ++-- vignettes/sf5.Rmd | 12 +-- 37 files changed, 428 insertions(+), 265 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package (see also Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>) can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymisation methods are included. Note that the package
includes a graphical user interface (Meindl and Templ, 2019 <doi:10.3390/a12090191>) that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>),
Bernhard Meindl [aut],
Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.6.0 dated 2021-01-27 and 5.6.1 dated 2021-07-26
DESCRIPTION | 7 MD5 | 67 - NAMESPACE | 4 NEWS | 8 R/addGhostVars.R | 15 R/addNoise.r | 1 R/dRisk.R | 6 R/dUtility.R | 281 ++++++- R/dataGen.r | 4 R/globalRecode.R | 2 R/maG.R | 6 R/shuffle.R | 8 build/partial.rdb |binary build/vignette.rds |binary data/CASCrefmicrodata.rda |binary data/EIA.rda |binary data/Tarragona.rda |binary data/casc1.rda |binary data/francdat.rda |binary data/free1.rda |binary data/microData.rda |binary data/testdata.RData |binary data/testdata2.RData |binary inst/doc/sdcMicro.html | 955 ++++++++++--------------- inst/doc/sdc_guidelines.pdf |binary inst/shiny/sdcApp/controllers/ui_categorical.R | 20 inst/shiny/sdcApp/server.R | 19 man/addNoise.Rd | 1 man/dRisk.Rd | 6 man/dUtility.Rd | 41 - man/dataGen.Rd | 4 man/globalRecode.Rd | 2 man/il_additional.Rd |only man/shuffle.Rd | 8 tests/testthat/test_il_correl.R |only tests/testthat/test_il_variables.R |only 36 files changed, 791 insertions(+), 674 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.6.0 dated 2021-07-22 and 0.6.1 dated 2021-07-26
DESCRIPTION | 6 +- MD5 | 14 +++--- NEWS.md | 7 +++ R/finbif_occurrence.R | 9 ++-- README.md | 2 inst/NEWS.Rd | 9 ++++ tests/cassettes/finbif_occurrence_collection.yml | 48 +++++++++++++++++++---- tests/testthat/test-finbif_occurrence.R | 6 ++ 8 files changed, 77 insertions(+), 24 deletions(-)
Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Author: Zankrut Goyani [aut, cre, cph],
Alok Shrivasatva [aut],
Yogesh Garde [aut],
Arvind Chaudhary [aut],
Kaushal Modha [aut]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>
Diff between selection.index versions 1.1.1 dated 2021-06-03 and 1.1.2 dated 2021-07-26
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 5 ++- R/rcomb.indices.R | 2 + README.md | 14 ++++----- build/vignette.rds |binary inst/doc/Examples.html | 18 ++++++------ man/rcomb.indices.Rd | 72 ++++++++++++++++++++++++------------------------- man/sel.index.Rd | 60 ++++++++++++++++++++-------------------- 9 files changed, 101 insertions(+), 96 deletions(-)
More information about selection.index at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-12 0.3.0
2021-03-28 0.2.0
2021-01-22 0.1.1
2020-04-28 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-01-05 0.1.1
2015-12-15 0.1.0
Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to
make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between rvest versions 1.0.0 dated 2021-03-09 and 1.0.1 dated 2021-07-26
DESCRIPTION | 7 +++---- MD5 | 24 ++++++++++++------------ NEWS.md | 9 ++++++++- R/html.R | 2 +- R/table.R | 6 ++++-- R/utils.R | 1 - build/vignette.rds |binary inst/doc/rvest.html | 1 + man/google_form.Rd | 3 --- man/html_attr.Rd | 2 +- tests/testthat/_snaps/session.md | 2 +- tests/testthat/_snaps/table.md | 16 ++++++++++++++++ tests/testthat/test-table.R | 30 ++++++++++++++++++++++++++++++ 13 files changed, 77 insertions(+), 26 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.17 dated 2021-01-07 and 1.0.18 dated 2021-07-26
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++++------ NAMESPACE | 3 ++- R/additional_info.R |only R/new_xmlreadabs.R |only data/GeneToEntrez.rda |binary data/HGNC2UniprotID.rda |binary data/HGNCdata.rda |binary data/common_words_new.rda |binary man/additional_info.Rd |only man/new_xmlreadabs.Rd |only 11 files changed, 17 insertions(+), 12 deletions(-)
Title: Downloading Time Series from ALFRED Database for Various
Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases.
Its functions return tidy data frames for different releases of the specified time series.
Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between alfred versions 0.1.12 dated 2021-05-12 and 0.2.0 dated 2021-07-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 1 + R/get_alfred_series.R | 6 +++--- tests/testthat/test_download.R | 4 ---- 5 files changed, 11 insertions(+), 14 deletions(-)
Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the
language at a deeper level.
Author: Hadley Wickham [aut, cre],
R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pryr versions 0.1.4 dated 2018-02-17 and 0.1.5 dated 2021-07-26
pryr-0.1.4/pryr/src/object_size.cpp |only pryr-0.1.4/pryr/src/size-info.c |only pryr-0.1.5/pryr/DESCRIPTION | 10 ++-- pryr-0.1.5/pryr/MD5 | 38 ++++++++--------- pryr-0.1.5/pryr/NAMESPACE | 2 pryr-0.1.5/pryr/R/RcppExports.R | 12 ----- pryr-0.1.5/pryr/R/bytes.r | 6 +- pryr-0.1.5/pryr/R/mem.R | 4 - pryr-0.1.5/pryr/R/object_size.R | 2 pryr-0.1.5/pryr/R/partial.r | 2 pryr-0.1.5/pryr/README.md | 49 ++-------------------- pryr-0.1.5/pryr/man/bytes.Rd | 8 +-- pryr-0.1.5/pryr/man/ftype.Rd | 6 +- pryr-0.1.5/pryr/man/inspect.Rd | 7 +-- pryr-0.1.5/pryr/man/is_promise.Rd | 4 + pryr-0.1.5/pryr/man/otype.Rd | 6 +- pryr-0.1.5/pryr/man/partial.Rd | 2 pryr-0.1.5/pryr/man/uneval.Rd | 4 + pryr-0.1.5/pryr/src/RcppExports.cpp | 44 ++----------------- pryr-0.1.5/pryr/src/inspect.cpp | 5 +- pryr-0.1.5/pryr/tests/testthat/test-object_size.R | 14 +++--- 21 files changed, 76 insertions(+), 149 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.0-0 dated 2021-06-07 and 1.1-0 dated 2021-07-26
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 8 README.md | 2 inst/doc/memoiR.Rmd | 7 inst/doc/memoiR.html | 5 inst/rmarkdown/templates/memoir/skeleton/latex/template.tex | 157 ++++++------ vignettes/memoiR.Rmd | 7 8 files changed, 118 insertions(+), 88 deletions(-)
Title: Generalized Waring Regression Model for Count Data
Description: Statistical functions to fit, validate and describe a Generalized
Waring Regression Model (GWRM).
Author: Silverio Vilchez-Lopez [aut, cre],
Antonio Jose Saez-Castillo [aut],
Maria Jose Olmo-Jimenez [aut],
Jose Rodriguez-Avi [aut],
Antonio Conde-Sanchez [aut],
Ana Maria Martinez-Rodriguez [aut]
Maintainer: Silverio Vilchez-Lopez <svilchez@ujaen.es>
Diff between GWRM versions 2.1.0.3 dated 2017-07-31 and 2.1.0.4 dated 2021-07-26
DESCRIPTION | 20 +++++++++++--------- MD5 | 24 ++++++++++++------------ NAMESPACE | 3 ++- R/residuals.R | 3 ++- man/GWRM.Rd | 4 +--- man/add1.gw.Rd | 7 +++---- man/drop1.gw.Rd | 7 +++---- man/goals.Rd | 9 +++++---- man/gw.Rd | 29 ++++++++++++++++++++++------- man/partvar.Rd | 5 +++-- man/predict.gw.Rd | 4 ++-- man/residuals.gw.Rd | 18 +++++++++++++----- man/rgw.Rd | 3 +-- 13 files changed, 80 insertions(+), 56 deletions(-)
Title: Prediction and Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular
data on the torus. The package provides angular
adaptations of usual clustering methods such as the k-means
clustering, pairwise angular distances, which can be used as an
input for distance-based clustering algorithms, and implements
clustering based on the conformal prediction framework. Options
for the conformal scores include scores based on a kernel density
estimate, multivariate von Mises mixtures, and naive k-means clusters.
Moreover, the package provides some basic data handling tools for
angular data.
Author: Sungkyu Jung [aut, cph],
Seungki Hong [aut, cre],
Kiho Park [ctb],
Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>
Diff between ClusTorus versions 0.1.1 dated 2021-06-30 and 0.1.3 dated 2021-07-26
DESCRIPTION | 8 - MD5 | 28 ++-- R/hyperparam.torus.R | 44 +++--- R/icp.torus.R | 39 +++-- R/kde.torus.R | 19 +- build/partial.rdb |binary inst/doc/ClusTorus.R | 83 ++--------- inst/doc/ClusTorus.Rmd | 112 ++++------------ inst/doc/ClusTorus.html | 327 ++++++++++++++++++++--------------------------- man/ClusTorus-package.Rd | 2 man/cp.torus.kde.Rd | 6 man/hyperparam.torus.Rd | 48 +++--- man/icp.torus.score.Rd | 43 +++--- man/kde.torus.Rd | 10 - vignettes/ClusTorus.Rmd | 112 ++++------------ 15 files changed, 354 insertions(+), 527 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior
distributions and Bayesian models. It includes point-estimates such as
Maximum A Posteriori (MAP), measures of dispersion (Highest Density
Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and
indices used for null-hypothesis testing (such as ROPE percentage, pd
and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>,
@mattansb),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>),
Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.10.0 dated 2021-05-31 and 0.10.5 dated 2021-07-26
DESCRIPTION | 10 MD5 | 144 ++--- NAMESPACE | 74 -- NEWS.md | 8 R/area_under_curve.R | 1 R/bayesfactor_models.R | 42 - R/bayesfactor_parameters.R | 10 R/bayesfactor_restricted.R | 3 R/bci.R | 1 R/bic_to_bf.R | 1 R/check_prior.R | 1 R/convert_bayesian_to_frequentist.R | 9 R/describe_posterior.R | 72 ++ R/describe_prior.R | 1 R/diagnostic_draws.R | 22 R/diagnostic_posterior.R | 21 R/distribution.R | 47 + R/effective_sample.R | 14 R/equivalence_test.R | 3 R/estimate_density.R | 17 R/eti.R | 1 R/format.R | 17 R/hdi.R | 1 R/map_estimate.R | 2 R/mcse.R | 3 R/mediation.R | 56 +- R/overlap.R | 8 R/p_direction.R | 2 R/p_map.R | 2 R/plot.R | 52 -- R/point_estimate.R | 3 R/print.R | 13 R/print.bayesfactor_models.R | 3 R/print.equivalence_test.R | 1 R/print.rope.R | 1 R/print_html.R | 1 R/print_md.R | 1 R/reexports.R | 4 R/reshape_iterations.R | 1 R/rope.R | 1 R/rope_range.R | 3 R/sensitivity_to_prior.R | 1 R/sexit.R | 4 R/sexit_thresholds.R | 4 R/si.R | 6 R/simulate_data.R | 17 R/simulate_simpson.R |only R/unupdate.R | 46 - R/utils.R | 2 R/utils_bayesfactor.R | 38 - R/utils_check_collinearity.R | 2 R/weighted_posteriors.R | 2 build/partial.rdb |binary inst/WORDLIST | 4 inst/doc/bayes_factors.R | 542 ++++++++++----------- inst/doc/bayes_factors.html | 648 ++++++++------------------ inst/doc/bayestestR.html | 2 inst/doc/credible_interval.html | 6 inst/doc/example1.html | 10 inst/doc/example2.html | 22 inst/doc/example3.html | 2 inst/doc/guidelines.html | 2 inst/doc/probability_of_direction.html | 6 inst/doc/region_of_practical_equivalence.html | 8 man/bic_to_bf.Rd | 1 man/convert_bayesian_as_frequentist.Rd | 3 man/describe_posterior.Rd | 15 man/diagnostic_draws.Rd | 10 man/equivalence_test.Rd | 1 man/mediation.Rd | 13 man/reexports.Rd | 4 man/simulate_correlation.Rd | 154 +++--- man/simulate_simpson.Rd |only tests/testthat/test-blavaan.R | 39 - 74 files changed, 978 insertions(+), 1313 deletions(-)
Title: Sparse Group Variable Selection for Gene-Environment
Interactions in the Longitudinal Study
Description: Recently, regularized variable selection has emerged as a powerful tool to identify and dissect gene-environment interactions. Nevertheless, in longitudinal studies with high dimensional genetic factors, regularization methods for G×E interactions have not been systematically developed. In this package, we provide the implementation of sparse group variable selection, based on both the quadratic inference function (QIF) and generalized estimating equation (GEE), to accommodate the bi-level selection for longitudinal G×E studies with high dimensional genomic features. Alternative methods conducting only the group or individual level selection have also been included. The core modules of the package have been developed in C++.
Author: Fei Zhou, Xi Lu, Jie Ren, Cen Wu
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between springer versions 0.1.3 dated 2021-07-24 and 0.1.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Tidy Methods for Bayesian Treatment Effect Models
Description: Functions for extracting tidy data from Bayesian treatment effect models, in particular BART, but extensions are possible. Functionality includes extracting tidy posterior summaries as in 'tidybayes' <https://github.com/mjskay/tidybayes>, estimating (average) treatment effects, common support calculations, and plotting useful summaries of these.
Author: Joshua J Bon [aut, cre] (<https://orcid.org/0000-0003-2313-2949>)
Maintainer: Joshua J Bon <joshuajbon@gmail.com>
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Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for
parameterizing, simulating, and analyzing health economic simulation
models. The package supports cohort discrete time state transition models
(Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>,
N-state partitioned survival models (Glasziou et al. 1990)
<doi:10.1002/sim.4780091106>, and individual-level continuous
time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>,
encompassing both Markov (time-homogeneous and time-inhomogeneous) and
semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is
quantified with standard graphical and tabular summaries of a probabilistic
sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>,
<doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table
make individual-patient simulation, probabilistic sensitivity analysis,
and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre],
Jeroen P. Jansen [aut],
R Core Team [ctb] (hesim uses some slightly modified C functions from
base R)
Maintainer: Devin Incerti <devin.incerti@gmail.com>
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Title: Access Victorian Spatial Data Through Web File Services (WFS)
Description: Easily interfaces R to spatial datasets available through
the Victorian Government's WFS (Web Feature Service): <https://services.land.vic.gov.au/catalogue/publicproxy/guest/dv_geoserver/wfs?request=getCapabilities>,
which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Author: Justin Cally [aut, cre] (<https://orcid.org/0000-0003-4584-2220>),
Rachel Swain [ctb],
Andy Teucher [aut] (<https://orcid.org/0000-0002-7840-692X>, bcdata
author),
Sam Albers [aut] (<https://orcid.org/0000-0002-9270-7884>, bcdata
author),
Stephanie Hazlitt [aut] (<https://orcid.org/0000-0002-3161-2304>,
bcdata author),
Province of British Columbia [cph] (bcdata copyright)
Maintainer: Justin Cally <justin.g.cally@gmail.com>
Diff between VicmapR versions 0.1.6 dated 2021-07-06 and 0.1.7 dated 2021-07-26
DESCRIPTION | 9 MD5 | 100 ++--- NAMESPACE | 104 ++--- NEWS.md | 102 ++--- R/build-query.R | 615 ++++++++++++++++---------------- R/check_geoserver.R | 133 ++++--- R/cql-predicates.R | 582 +++++++++++++++---------------- R/cql-translate.R | 396 ++++++++++----------- R/filter.R | 130 +++--- R/globals.R | 26 - R/listFeatures.R | 109 +++-- R/polygonFormat.R | 76 ++-- R/select.R | 114 +++--- R/utils-classes.R | 84 ++-- R/utils-collect.R | 48 +- R/utils-head.R | 46 +- R/utils-metadata.R | 296 ++++++++------- R/utils-options.R | 134 +++---- R/utils-pipe.R | 28 - R/utils-show_query.R | 48 +- README.md | 432 +++++++++++------------ build/vignette.rds |binary inst/doc/query_vicmap.R | 144 +++---- inst/doc/query_vicmap.Rmd | 274 +++++++------- inst/doc/query_vicmap.html | 637 ++++++++++++++-------------------- inst/shapes/melbourne.geojson | 8 man/CQL.Rd | 52 +- man/check_geoserver.Rd | 52 +- man/collect.Rd | 94 ++--- man/cql_geom_predicates.Rd | 172 ++++----- man/feature_hits.Rd | 50 +- man/filter.Rd | 64 +-- man/geom_col_name.Rd | 88 ++-- man/head.Rd | 68 +-- man/listLayers.Rd | 50 +- man/pipe.Rd | 40 +- man/print.vicmap_promise.Rd | 52 +- man/select.Rd | 64 +-- man/show_query.Rd | 88 ++-- man/vicmap_options.Rd | 70 +-- man/vicmap_query.Rd | 66 +-- man/wfsConnection-class.Rd | 34 - tests/testthat.R | 8 tests/testthat/test-build-query.R | 157 ++++---- tests/testthat/test-check_geoserver.R | 31 + tests/testthat/test-cql-predicates.R | 189 ++++------ tests/testthat/test-filter.R | 49 ++ tests/testthat/test-listLayers.R | 27 + tests/testthat/test-polygonFormat.R | 26 + tests/testthat/test-utils-options.R | 32 + vignettes/query_vicmap.Rmd | 274 +++++++------- 51 files changed, 3347 insertions(+), 3225 deletions(-)
Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts
<https://fonts.google.com/> into R, in order to
support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the
included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between sysfonts versions 0.8.3 dated 2021-01-10 and 0.8.4 dated 2021-07-26
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- configure | 2 +- configure.ac | 2 +- inst/NEWS.Rd | 14 ++++++++++++++ inst/fonts/webfonts.bz2 |binary 6 files changed, 25 insertions(+), 11 deletions(-)
Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType',
'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output
formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted
into polygons or raster images, hence after the plot has been created, it no
longer relies on the font files. No external software such as 'Ghostscript' is
needed to use this package.
Author: Yixuan Qiu and authors/contributors of the
included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between showtext versions 0.9-2 dated 2021-01-10 and 0.9-3 dated 2021-07-26
DESCRIPTION | 8 +- MD5 | 14 +-- build/vignette.rds |binary configure | 2 configure.ac | 2 inst/NEWS.Rd | 9 ++ inst/doc/introduction.html | 160 +++++++++++++++++---------------------------- src/devfuns.c | 2 8 files changed, 85 insertions(+), 112 deletions(-)