Title: An R Interface to the JBrowse 2 Genome Browser
Description: Provides an R interface to the JBrowse 2 genome browser.
Enables embedding a JB2 genome browser in a Shiny app or R Markdown
document. The browser can also be launched from an interactive R console.
The browser can be loaded with a variety of common genomics data types,
and can be used with a custom theme.
Author: Elliot Hershberg [aut, cre] (<https://orcid.org/0000-0003-2068-3366>),
the JBrowse 2 Team [aut]
Maintainer: Elliot Hershberg <eahershberg@gmail.com>
Diff between JBrowseR versions 0.8.1 dated 2021-07-07 and 0.9.0 dated 2021-10-17
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++-------- NEWS.md | 10 ++++++-- R/wiggle.R | 4 +-- build/vignette.rds |binary inst/doc/JBrowseR.html | 1 inst/doc/creating-urls.html | 1 inst/doc/custom-browser-tutorial.html | 1 inst/doc/json-tutorial.html | 1 inst/htmlwidgets/JBrowseR.js | 41 +++++++++++++++++----------------- man/track_wiggle.Rd | 4 +-- 11 files changed, 51 insertions(+), 40 deletions(-)
Title: Geocoding Made Easy
Description: An intuitive interface for getting data from geocoding services.
Author: Jesse Cambon [aut, cre] (<https://orcid.org/0000-0001-6854-1514>),
Diego Hernangómez [aut] (<https://orcid.org/0000-0001-8457-4658>),
Christopher Belanger [aut] (<https://orcid.org/0000-0003-2070-5721>),
Daniel Possenriede [aut] (<https://orcid.org/0000-0002-6738-9845>)
Maintainer: Jesse Cambon <jesse.cambon@gmail.com>
Diff between tidygeocoder versions 1.0.3 dated 2021-04-19 and 1.0.4 dated 2021-10-17
DESCRIPTION | 17 MD5 | 97 ++--- NAMESPACE | 2 NEWS.md | 57 ++- R/api_url.R | 19 - R/batch_geocoding.R | 43 +- R/data.R | 38 +- R/documentation.R | 23 + R/geo.R | 353 +++++++++++++------- R/geo_methods.R | 4 R/geocode.R | 12 R/geocode_combine.R |only R/global_variables.R | 12 R/input_handling.R | 7 R/query_factory.R | 2 R/results_processing.R | 41 +- R/reverse_batch_geocoding.R | 27 - R/reverse_geo.R | 205 +++++++---- R/reverse_geocode.R | 4 R/utils.R | 226 ++++++++++++- R/zzz.R |only README.md | 81 ++-- build/vignette.rds |binary data/api_info_reference.rda |binary data/api_key_reference.rda |binary data/api_parameter_reference.rda |binary data/min_time_reference.rda |binary inst/CITATION | 60 +-- inst/doc/tidygeocoder.R | 52 +-- inst/doc/tidygeocoder.Rmd | 103 +++-- inst/doc/tidygeocoder.html | 588 +++++++++++++++++++--------------- man/api_info_reference.Rd | 8 man/api_key_reference.Rd | 4 man/api_parameter_reference.Rd | 17 man/batch_limit_reference.Rd | 2 man/extract_results.Rd | 4 man/extract_reverse_results.Rd | 6 man/figures/README-usamap-1.png |binary man/figures/tidygeocoder_hex.png |binary man/geo.Rd | 155 +++++--- man/geo_census.Rd | 2 man/geo_combine.Rd |only man/geocode.Rd | 16 man/geocode_combine.Rd |only man/min_time_reference.Rd | 9 man/reverse_geo.Rd | 127 ++++--- man/reverse_geocode.Rd | 8 man/tidygeocoder-package.Rd | 2 tests/testthat/test-geocode-combine.R |only tests/testthat/test-geocode.R | 55 +-- tests/testthat/test-utils.R | 3 vignettes/tidygeocoder.Rmd | 103 +++-- 52 files changed, 1637 insertions(+), 957 deletions(-)
Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
Author: Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>),
Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>),
Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>),
Jeff Farrell [ctb],
Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>),
Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>),
Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>),
Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>),
Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>),
Patrick Roelli [ctb],
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>),
Karthik Shekhar [ctb],
Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>),
Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>),
Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>),
Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>),
Satija Lab and Collaborators [fnd]
Maintainer: Paul Hoffman <seurat@nygenome.org>
Diff between Seurat versions 4.0.4 dated 2021-08-20 and 4.0.5 dated 2021-10-17
DESCRIPTION | 8 ++-- MD5 | 44 +++++++++++++------------- NEWS.md | 7 ++++ R/data.R | 4 +- R/dimensional_reduction.R | 11 +----- R/generics.R | 8 +++- R/integration.R | 20 ++++++++++-- R/preprocessing.R | 6 ++- R/tree.R | 10 +++--- R/visualization.R | 20 ++++++------ README.md | 2 - build/partial.rdb |binary man/BuildClusterTree.Rd | 10 +++--- man/ColorDimSplit.Rd | 11 +++--- man/FindMarkers.Rd | 8 +++- man/IntegrateData.Rd | 68 ++++++++++++++++++++++++----------------- man/IntegrateEmbeddings.Rd | 16 ++++++++- man/Load10X_Spatial.Rd | 6 ++- man/PlotClusterTree.Rd | 9 +++-- man/RunSPCA.Rd | 1 man/cc.genes.Rd | 2 - man/cc.genes.updated.2019.Rd | 2 - tests/testthat/test_load_10X.R | 38 ++++++++++------------ 23 files changed, 184 insertions(+), 127 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.5.0 dated 2020-03-11 and 3.6.0 dated 2021-10-17
rcdk-3.5.0/rcdk/man/do.typing.Rd |only rcdk-3.6.0/rcdk/CHANGELOG | 28 rcdk-3.6.0/rcdk/DESCRIPTION | 12 rcdk-3.6.0/rcdk/MD5 | 88 - rcdk-3.6.0/rcdk/NAMESPACE | 4 rcdk-3.6.0/rcdk/NEWS | 3 rcdk-3.6.0/rcdk/R/atoms.R | 23 rcdk-3.6.0/rcdk/R/bonds.R | 29 rcdk-3.6.0/rcdk/R/deprecated_functions.R |only rcdk-3.6.0/rcdk/R/desc.R | 75 - rcdk-3.6.0/rcdk/R/fingerprint.R | 9 rcdk-3.6.0/rcdk/R/frags.R | 3 rcdk-3.6.0/rcdk/R/io.R | 2 rcdk-3.6.0/rcdk/R/molecule.R | 2 rcdk-3.6.0/rcdk/R/props.R | 11 rcdk-3.6.0/rcdk/R/rcdk.R | 47 rcdk-3.6.0/rcdk/R/smiles.R | 2 rcdk-3.6.0/rcdk/R/smsd.R | 2 rcdk-3.6.0/rcdk/R/visual.R | 10 rcdk-3.6.0/rcdk/build/vignette.rds |binary rcdk-3.6.0/rcdk/inst/cont/rcdk.jar |binary rcdk-3.6.0/rcdk/inst/doc/molform.Rmd | 2 rcdk-3.6.0/rcdk/inst/doc/molform.html | 545 +++------- rcdk-3.6.0/rcdk/inst/doc/using-rcdk.R | 4 rcdk-3.6.0/rcdk/inst/doc/using-rcdk.Rmd | 14 rcdk-3.6.0/rcdk/inst/doc/using-rcdk.html | 1068 +++++++------------- rcdk-3.6.0/rcdk/inst/molfiles/alanine.sdf |only rcdk-3.6.0/rcdk/inst/molfiles/glutamine.sdf |only rcdk-3.6.0/rcdk/inst/unitTests/runit.atoms.R | 2 rcdk-3.6.0/rcdk/inst/unitTests/runit.bonds.R |only rcdk-3.6.0/rcdk/inst/unitTests/runit.descs.R |only rcdk-3.6.0/rcdk/inst/unitTests/runit.fingerprints.R | 4 rcdk-3.6.0/rcdk/inst/unitTests/runit.frags.R | 6 rcdk-3.6.0/rcdk/inst/unitTests/runit.match.R | 6 rcdk-3.6.0/rcdk/inst/unitTests/runit.rcdk.R | 14 rcdk-3.6.0/rcdk/man/Atoms.Rd | 3 rcdk-3.6.0/rcdk/man/Molecule.Rd | 2 rcdk-3.6.0/rcdk/man/bpdata.Rd | 6 rcdk-3.6.0/rcdk/man/convert.implicit.to.explicit.Rd | 2 rcdk-3.6.0/rcdk/man/get.bond.order.Rd |only rcdk-3.6.0/rcdk/man/get.chem.object.builder.Rd | 4 rcdk-3.6.0/rcdk/man/get.desc.categories.Rd | 2 rcdk-3.6.0/rcdk/man/get.exhaustive.fragments.Rd | 2 rcdk-3.6.0/rcdk/man/get.volume.Rd | 2 rcdk-3.6.0/rcdk/man/rcdk-deprecated.Rd |only rcdk-3.6.0/rcdk/man/set.atom.types.Rd |only rcdk-3.6.0/rcdk/man/smiles.flavors.Rd | 2 rcdk-3.6.0/rcdk/man/view.table.Rd |only rcdk-3.6.0/rcdk/vignettes/molform.Rmd | 2 rcdk-3.6.0/rcdk/vignettes/using-rcdk.Rmd | 14 50 files changed, 878 insertions(+), 1178 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.24 dated 2020-12-18 and 0.28 dated 2021-10-17
qtl2-0.24/qtl2/tests/figs |only qtl2-0.28/qtl2/DESCRIPTION | 10 qtl2-0.28/qtl2/MD5 | 214 ++++++++-------- qtl2-0.28/qtl2/NAMESPACE | 3 qtl2-0.28/qtl2/NEWS.md | 66 ++++ qtl2-0.28/qtl2/R/CCcolors-data.R | 16 + qtl2-0.28/qtl2/R/calc_genoprob.R | 2 qtl2-0.28/qtl2/R/calc_genoprob2.R | 2 qtl2-0.28/qtl2/R/calc_het.R | 5 qtl2-0.28/qtl2/R/calc_kinship.R | 6 qtl2-0.28/qtl2/R/calc_raw_summaries.R | 8 qtl2-0.28/qtl2/R/create_gene_query_func.R | 2 qtl2-0.28/qtl2/R/create_snpinfo.R | 6 qtl2-0.28/qtl2/R/create_variant_query_func.R | 2 qtl2-0.28/qtl2/R/est_herit.R | 9 qtl2-0.28/qtl2/R/est_map.R | 1 qtl2-0.28/qtl2/R/find_ibd_segments.R | 2 qtl2-0.28/qtl2/R/find_index_snp.R | 2 qtl2-0.28/qtl2/R/fit1.R | 4 qtl2-0.28/qtl2/R/fit1_pg.R | 2 qtl2-0.28/qtl2/R/genoprob_to_snpprob.R | 2 qtl2-0.28/qtl2/R/index_snps.R | 2 qtl2-0.28/qtl2/R/plot_coef.R | 6 qtl2-0.28/qtl2/R/plot_genoprob.R | 2 qtl2-0.28/qtl2/R/plot_onegeno.R | 2 qtl2-0.28/qtl2/R/plot_sdp.R |only qtl2-0.28/qtl2/R/plot_snpasso.R | 28 +- qtl2-0.28/qtl2/R/plot_snpasso_and_genes.R | 7 qtl2-0.28/qtl2/R/plot_snpasso_and_sdp.R |only qtl2-0.28/qtl2/R/plot_snpasso_sdp_and_genes.R |only qtl2-0.28/qtl2/R/predict_snpgeno.R | 2 qtl2-0.28/qtl2/R/qtl2-package.R | 15 + qtl2-0.28/qtl2/R/qtl2version.R | 2 qtl2-0.28/qtl2/R/read_pheno.R | 4 qtl2-0.28/qtl2/R/recode_snps.R | 2 qtl2-0.28/qtl2/R/replace_ids.R | 20 + qtl2-0.28/qtl2/R/scan1_pg.R | 5 qtl2-0.28/qtl2/R/scan1coef.R | 2 qtl2-0.28/qtl2/R/scan1coef_pg.R | 2 qtl2-0.28/qtl2/R/scan1snps.R | 2 qtl2-0.28/qtl2/R/sim_geno.R | 6 qtl2-0.28/qtl2/R/sim_geno2.R | 6 qtl2-0.28/qtl2/R/summary_cross2.R | 6 qtl2-0.28/qtl2/R/top_snps.R | 2 qtl2-0.28/qtl2/R/viterbi.R | 6 qtl2-0.28/qtl2/R/viterbi2.R | 6 qtl2-0.28/qtl2/README.md | 23 + qtl2-0.28/qtl2/build |only qtl2-0.28/qtl2/data/CCaltcolors.RData |only qtl2-0.28/qtl2/data/CCcolors.RData |binary qtl2-0.28/qtl2/data/CCorigcolors.RData |binary qtl2-0.28/qtl2/inst/CITATION | 2 qtl2-0.28/qtl2/inst/extdata/ReadMe.md | 4 qtl2-0.28/qtl2/man/CCcolors.Rd | 6 qtl2-0.28/qtl2/man/calc_raw_founder_maf.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_geno_freq.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_het.Rd | 2 qtl2-0.28/qtl2/man/calc_raw_maf.Rd | 2 qtl2-0.28/qtl2/man/create_gene_query_func.Rd | 2 qtl2-0.28/qtl2/man/create_snpinfo.Rd | 2 qtl2-0.28/qtl2/man/create_variant_query_func.Rd | 2 qtl2-0.28/qtl2/man/est_herit.Rd | 3 qtl2-0.28/qtl2/man/find_ibd_segments.Rd | 2 qtl2-0.28/qtl2/man/find_index_snp.Rd | 2 qtl2-0.28/qtl2/man/genoprob_to_snpprob.Rd | 2 qtl2-0.28/qtl2/man/index_snps.Rd | 2 qtl2-0.28/qtl2/man/plot_coef.Rd | 1 qtl2-0.28/qtl2/man/plot_genoprob.Rd | 2 qtl2-0.28/qtl2/man/plot_onegeno.Rd | 2 qtl2-0.28/qtl2/man/plot_sdp.Rd |only qtl2-0.28/qtl2/man/plot_snpasso.Rd | 14 - qtl2-0.28/qtl2/man/predict_snpgeno.Rd | 2 qtl2-0.28/qtl2/man/qtl2-package.Rd | 24 + qtl2-0.28/qtl2/man/read_pheno.Rd | 4 qtl2-0.28/qtl2/man/recode_snps.Rd | 2 qtl2-0.28/qtl2/man/replace_ids.Rd | 10 qtl2-0.28/qtl2/man/scan1snps.Rd | 2 qtl2-0.28/qtl2/man/top_snps.Rd | 2 qtl2-0.28/qtl2/src/RcppExports.cpp | 5 qtl2-0.28/qtl2/src/brent_fmin.cpp | 9 qtl2-0.28/qtl2/src/brent_fmin.h | 5 qtl2-0.28/qtl2/src/cross.cpp | 2 qtl2-0.28/qtl2/src/cross_genril.cpp | 2 qtl2-0.28/qtl2/src/cross_hsf1.cpp |only qtl2-0.28/qtl2/src/cross_hsf1.h |only qtl2-0.28/qtl2/src/hmm_util.cpp | 4 qtl2-0.28/qtl2/src/lmm.cpp | 7 qtl2-0.28/qtl2/tests/testthat/_snaps |only qtl2-0.28/qtl2/tests/testthat/test-basic_summaries.R | 2 qtl2-0.28/qtl2/tests/testthat/test-calc_raw_summaries.R | 2 qtl2-0.28/qtl2/tests/testthat/test-calcerrorlod.R | 2 qtl2-0.28/qtl2/tests/testthat/test-check_cross.R | 2 qtl2-0.28/qtl2/tests/testthat/test-create_snpinfo.R | 22 + qtl2-0.28/qtl2/tests/testthat/test-find_ibd_segments.R | 2 qtl2-0.28/qtl2/tests/testthat/test-find_peaks.R | 2 qtl2-0.28/qtl2/tests/testthat/test-fit1_binary.R | 2 qtl2-0.28/qtl2/tests/testthat/test-hmmbasic-hsf1.R |only qtl2-0.28/qtl2/tests/testthat/test-index_snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-plot_sdp.R |only qtl2-0.28/qtl2/tests/testthat/test-predict_snpgeno.R | 4 qtl2-0.28/qtl2/tests/testthat/test-recode_snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-replace_ids.R | 73 +++++ qtl2-0.28/qtl2/tests/testthat/test-scan1snps.R | 2 qtl2-0.28/qtl2/tests/testthat/test-snpprobs.R | 2 qtl2-0.28/qtl2/tests/testthat/test-top_snps.R | 4 105 files changed, 564 insertions(+), 219 deletions(-)
Title: Fast Kalman Filter
Description: This is a fast and flexible implementation of the Kalman
filter and smoother, which can deal with NAs. It is entirely written in C and relies fully on linear algebra subroutines contained in
BLAS and LAPACK. Due to the speed of the filter, the fitting of
high-dimensional linear state space models to large datasets
becomes possible. This package also contains a plot function
for the visualization of the state vector and graphical
diagnostics of the residuals.
Author: David Luethi [aut],
Philipp Erb [aut],
Simon Otziger [aut],
Daniel McDonald [aut],
Paul Smith [aut, cre] (<https://orcid.org/0000-0002-0034-3412>)
Maintainer: Paul Smith <paul@waternumbers.co.uk>
Diff between FKF versions 0.2.1 dated 2021-09-28 and 0.2.2 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ README.md | 2 +- inst/doc/FKF.html | 20 ++++++++++---------- src/fkflib.c | 7 ++++--- 6 files changed, 28 insertions(+), 22 deletions(-)
Title: Automated Backtesting of Portfolios over Multiple Datasets
Description: Automated backtesting of multiple portfolios over multiple
datasets of stock prices in a rolling-window fashion. Intended for
researchers and practitioners to backtest a set of different portfolios,
as well as by a course instructor to assess the students in their portfolio
design in a fully automated and convenient manner, with results conveniently
formatted in tables and plots. Each portfolio design is easily defined as a
function that takes as input a window of the stock prices and outputs the
portfolio weights. Multiple portfolios can be easily specified as a list
of functions or as files in a folder. Multiple datasets can be conveniently
extracted randomly from different markets, different time periods, and
different subsets of the stock universe. The results can be later assessed
and ranked with tables based on a number of performance criteria (e.g.,
expected return, volatility, Sharpe ratio, drawdown, turnover rate, return
on investment, computational time, etc.), as well as plotted in a number of
ways with nice barplots and boxplots.
Author: Daniel P. Palomar [cre, aut],
Rui Zhou [aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between portfolioBacktest versions 0.3.0 dated 2021-09-21 and 0.3.1 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ inst/CITATION | 4 ++-- tests/testthat/test-stockDataDownload.R | 2 +- 5 files changed, 17 insertions(+), 11 deletions(-)
More information about portfolioBacktest at CRAN
Permanent link
Title: Repeated Measurement Models for Discrete Times
Description: Companion R package for the course "Statistical analysis
of correlated and repeated measurements for health science
researchers" taught by the section of Biostatistics of the University
of Copenhagen. It provides functions for computing summary statistics
and obtaining graphical displays of longitudinal data, as well as for
statistical modeling and statistical inference using linear mixed model.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julie Forman [aut] (<https://orcid.org/0000-0001-7368-0869>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between LMMstar versions 0.3.2 dated 2021-10-05 and 0.3.3 dated 2021-10-17
DESCRIPTION | 8 - MD5 | 46 ++++----- R/estimate.R | 6 - R/fitted.R | 8 + R/model.matrix.R | 121 ++++++++++++++++++------- R/residuals.R | 70 ++++++++------ R/structure-skeleton.R | 13 +- inst/doc-software/figures/diag-correlation.pdf |binary inst/doc-software/figures/diag-scatterplot.pdf |binary inst/doc-software/figures/fit-autoplot.pdf |binary inst/doc-software/figures/fit-emmip.pdf |binary inst/doc-software/figures/gg-baseAdj.pdf |binary inst/doc-software/overview.aux | 92 +++++++++---------- inst/doc-software/overview.log | 102 ++++++++++----------- inst/doc-software/overview.org | 41 ++++++++ inst/doc-software/overview.pdf |binary inst/doc-software/overview.tex | 87 +++++++++++++---- inst/doc/overview.pdf |binary man/residuals.Rd | 3 tests/testthat.R | 1 tests/testthat/test-linear-regression.R | 29 +++-- tests/testthat/test-mixed-model.R | 14 +- tests/testthat/test-previous-bug.R | 50 +++++----- tests/testthat/test-ttest.R | 12 -- 24 files changed, 427 insertions(+), 276 deletions(-)
Title: Script Based 'NONMEM' Model Development
Description: Industrialisation of 'NONMEM'
<https://www.iconplc.com/innovation/nonmem/> via fully and rapidly reusable
model development 'workflows' entirely within 'RStudio'. Quickly get started
with new models by importing 'NONMEM' templates from the built-in code
library. Manipulate 'NONMEM' code from within R either via the tracked
'manual edit' interface or 'programmatically' via convenience functions.
Script 'workflows' by piping sequences of model building steps from control
file creation, to execution, to post-processing and evaluation. Run caching
makes 'workflows' R markdown friendly for easy documentation of thoughts and
modelling decisions alongside executable code. Share, reuse and recycle
'workflows' for new problems.
Author: Tarj Sahota [aut, cre, cph],
AstraZeneca [cph],
Nuria Buil Bruna [ctb],
Stein Schalkwijk [ctb]
Maintainer: Tarj Sahota <t.sahota0@gmail.com>
Diff between NMproject versions 0.6.5 dated 2021-09-02 and 0.6.7 dated 2021-10-17
DESCRIPTION | 11 MD5 | 83 +++-- NAMESPACE | 7 NEWS.md | 17 + R/NMproject-options.R | 15 + R/addin-apps.R | 5 R/apply_manual_edit.R | 17 - R/find-nonmem.R | 141 ++++++++-- R/make_project.R | 55 +-- R/manual-edit.R | 93 +++--- R/nm_render.R | 14 R/output_table.R | 10 R/run_nm.R | 49 ++- R/snippet_setup.R |only R/subroutine.R | 86 ++++-- R/with_temp_git_config.R |only R/zzz.R | 1 README.md | 2 inst/extdata/CodeLibrary/DerivedData |only inst/extdata/examples/theopp/Scripts/s02_model_log.Rmd | 12 inst/extdata/examples/theopp/Scripts/s04_covariate_modelling.Rmd | 4 inst/extdata/examples/theopp/Scripts/s05_advanced_usage.Rmd | 4 inst/extdata/r.snippets |only inst/rmarkdown/templates/basic_boot/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_boot/template.yaml | 1 inst/rmarkdown/templates/basic_gof/skeleton/skeleton.Rmd | 19 - inst/rmarkdown/templates/basic_gof/template.yaml | 1 inst/rmarkdown/templates/basic_ppc/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_ppc/template.yaml | 1 inst/rmarkdown/templates/basic_vpc/skeleton/skeleton.Rmd | 12 inst/rmarkdown/templates/basic_vpc/template.yaml | 1 inst/rmarkdown/templates/nm_general/skeleton/skeleton.Rmd | 10 inst/rmarkdown/templates/nm_general/template.yaml | 1 inst/rmarkdown/templates/nm_log/skeleton/skeleton.Rmd | 37 +- inst/rmarkdown/templates/nm_log/template.yaml | 1 inst/templates/README.Rmd | 2 man/find_nonmem.Rd | 7 man/psn_available.Rd |only man/psn_check.Rd |only man/setup_code_completion.Rd |only man/subroutine.Rd | 2 man/system_nm_available.Rd |only man/system_nm_intern.Rd |only man/temp_files.Rd | 13 tests/testthat/test-basic.R | 12 tests/testthat/test-manual_edit.R | 38 +- tests/testthat/test-theopp.R | 12 47 files changed, 550 insertions(+), 270 deletions(-)
Title: Brazilian COVID-19 Pandemic Data
Description: Set of functions to import COVID-19 pandemic data into R. The Brazilian COVID-19 data, obtained from the official Brazilian repository at <https://covid.saude.gov.br/>, is available at country, region, state, and city-levels. The package also downloads the world-level COVID-19 data from the John Hopkins University's repository.
Author: Fabio Demarqui [aut, cre],
Cristiano Santos [aut],
Matheus Costa [ctb]
Maintainer: Fabio Demarqui <fndemarqui@est.ufmg.br>
Diff between covid19br versions 0.1.2 dated 2021-10-08 and 0.1.3 dated 2021-10-17
covid19br-0.1.2/covid19br/data/ibgeCities.rda |only covid19br-0.1.2/covid19br/data/ibgeRegions.rda |only covid19br-0.1.2/covid19br/data/ibgeStates.rda |only covid19br-0.1.2/covid19br/data/mundi.rda |only covid19br-0.1.2/covid19br/man/ibgeCities.Rd |only covid19br-0.1.2/covid19br/man/ibgeRegions.Rd |only covid19br-0.1.2/covid19br/man/ibgeStates.Rd |only covid19br-0.1.2/covid19br/man/mundi.Rd |only covid19br-0.1.3/covid19br/DESCRIPTION | 8 covid19br-0.1.3/covid19br/MD5 | 56 +- covid19br-0.1.3/covid19br/NAMESPACE | 3 covid19br-0.1.3/covid19br/NEWS.md | 11 covid19br-0.1.3/covid19br/R/covid19br.R | 3 covid19br-0.1.3/covid19br/R/data_doc.R | 86 +-- covid19br-0.1.3/covid19br/R/downloadData.R | 37 + covid19br-0.1.3/covid19br/R/utils.R | 65 ++ covid19br-0.1.3/covid19br/build/vignette.rds |binary covid19br-0.1.3/covid19br/data/election2018Cities.rda |only covid19br-0.1.3/covid19br/data/election2018Regions.rda |only covid19br-0.1.3/covid19br/data/election2018States.rda |only covid19br-0.1.3/covid19br/inst/doc/covid19br.R | 3 covid19br-0.1.3/covid19br/inst/doc/covid19br.Rmd | 17 covid19br-0.1.3/covid19br/inst/doc/covid19br.html | 421 ++++++++--------- covid19br-0.1.3/covid19br/inst/doc/election2018.R |only covid19br-0.1.3/covid19br/inst/doc/election2018.Rmd |only covid19br-0.1.3/covid19br/inst/doc/election2018.html |only covid19br-0.1.3/covid19br/inst/doc/maps.R | 23 covid19br-0.1.3/covid19br/inst/doc/maps.Rmd | 32 + covid19br-0.1.3/covid19br/inst/doc/maps.html | 234 +++++---- covid19br-0.1.3/covid19br/man/add_epi_rates.Rd | 2 covid19br-0.1.3/covid19br/man/add_geo.Rd | 48 + covid19br-0.1.3/covid19br/man/downloadCovid19.Rd | 34 + covid19br-0.1.3/covid19br/man/election2018Cities.Rd |only covid19br-0.1.3/covid19br/man/election2018Regions.Rd |only covid19br-0.1.3/covid19br/man/election2018States.Rd |only covid19br-0.1.3/covid19br/vignettes/covid19br.Rmd | 17 covid19br-0.1.3/covid19br/vignettes/election2018.Rmd |only covid19br-0.1.3/covid19br/vignettes/maps.Rmd | 32 + 38 files changed, 673 insertions(+), 459 deletions(-)
Title: Multivariate Functional Principal Component Analysis for Data
Observed on Different Dimensional Domains
Description: Calculate a multivariate functional principal component analysis
for data observed on different dimensional domains. The estimation algorithm
relies on univariate basis expansions for each element of the multivariate
functional data (Happ & Greven, 2018) <doi:10.1080/01621459.2016.1273115>.
Multivariate and univariate functional data objects are
represented by S4 classes for this type of data implemented in the package
'funData'. For more details on the general concepts of both packages and a case
study, see Happ-Kurz (2020) <doi:10.18637/jss.v093.i05>.
Author: Clara Happ-Kurz [aut, cre] (<https://orcid.org/0000-0003-4737-3835>)
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between MFPCA versions 1.3-8 dated 2021-08-09 and 1.3-9 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/UMPCA.R | 2 +- build/partial.rdb |binary configure | 18 +++++++++--------- configure.ac | 5 +++-- man/ttv.Rd | 2 +- 8 files changed, 31 insertions(+), 24 deletions(-)
Title: An S4 Class for Functional Data
Description: S4 classes for univariate and multivariate functional data with
utility functions. See <doi:10.18637/jss.v093.i05> for a detailed description
of the package functionalities and its interplay with the MFPCA package for
multivariate functional principal component analysis
<https://CRAN.R-project.org/package=MFPCA>.
Author: Clara Happ-Kurz [aut, cre]
Maintainer: Clara Happ-Kurz <chk_R@gmx.de>
Diff between funData versions 1.3-7 dated 2021-08-03 and 1.3-8 dated 2021-10-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ README.md | 4 ++-- 4 files changed, 15 insertions(+), 9 deletions(-)
Title: Computation of Tree (Im)Balance Indices
Description: The aim of the 'R' package 'treebalance' is to provide functions for the computation of
a large variety of (im)balance indices for rooted trees. The package accompanies the manuscript
''Tree balance indices: a comprehensive survey'' by M. Fischer, L. Herbst, S. Kersting,
L. Kuehn and K. Wicke (2021) <arXiv:2109.12281>, which gives a precise definition for the terms
'balance index' and 'imbalance index' (Section 3) and provides an overview of the terminology in
this manual (Section 2). For further information on (im)balance indices, see also
Fischer et al. (2021) <https://treebalance.wordpress.com>.
Considering both established and new (im)balance indices, 'treebalance' provides (among
others) functions for calculating the following 18 established indices: the average leaf depth,
the B1 and B2 index, the Colijn-Plazzotta rank, the normal, corrected, quadratic and equal
weights Colless index, the family of Colless-like indices, the family of I-based indices, the
Rogers J index, the Furnas rank, the rooted quartet index, the s-shape statistic, the Sackin
index, the symmetry nodes index, the total cophenetic index and the variance of leaf depths.
Additionally, we include 5 tree shape statistics that satisfy the definition of an (im)balance
index but have not been thoroughly analyzed in terms of tree balance in the literature yet.
These are: the maximum width, the maximum difference in widths, the maximal depth, the
stairs1 and the stairs2 index.
As input, most functions of 'treebalance' require a rooted (phylogenetic) tree in 'phylo' format
(as introduced in 'ape' 1.9 in November 2006). 'phylo' is used to store (phylogenetic) trees
with no vertices of out-degree one. For further information on the format we kindly refer the
reader to E. Paradis (2012) <http://ape-package.ird.fr/misc/FormatTreeR_24Oct2012.pdf>.
Author: Mareike Fischer [aut],
Lina Herbst [aut],
Sophie Kersting [aut],
Luise Kuehn [aut, cre],
Kristina Wicke [aut]
Maintainer: Luise Kuehn <treebalanceindices@gmail.com>
Diff between treebalance versions 1.0.0 dated 2021-09-22 and 1.1.0 dated 2021-10-17
DESCRIPTION | 18 ++++----- MD5 | 15 ++++--- NEWS.md |only R/colPlaLab.R | 97 +++++++++++++++++++++++++++++++++++---------------- R/colPlaLab_inv.R | 2 - R/furnasI_inv.R | 71 +++++++++++++++++-------------------- man/colPlaLab.Rd | 44 +++++++++++++++-------- man/colPlaLab_inv.Rd | 2 - man/furnasI_inv.Rd | 2 - 9 files changed, 151 insertions(+), 100 deletions(-)
Title: 'Dang' Associated New Goodies
Description: A collection of utility functions.
Author: Dirk Eddelbuettel with contributions by Brodie Gaslam, Kevin Denny,
Kabira Namit, Colin Gillespie, R Core, Josh Ulrich, Jordan Mark Barbone,
and others.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dang versions 0.0.13 dated 2021-02-17 and 0.0.14 dated 2021-10-17
ChangeLog | 86 ++++++++++++++++++++++++++++++++++++++++++++-- DESCRIPTION | 13 ++++-- MD5 | 26 +++++++++---- R/checkCRANStatus.R | 2 - R/datatable.R | 2 - R/intradayMarketMonitor.R | 11 ++++- R/readAndConvert.R |only R/rollMinMax.R |only R/wday.R |only README.md | 17 ++++----- inst/NEWS.Rd | 22 +++++++++++ man/readAndConvert.Rd |only man/rollMinMax.Rd |only man/wday.Rd |only src/checkNonAscii.cpp | 38 ++++++++++---------- src/init.c | 6 ++- src/readAndConvert.cpp |only src/rollMinMax.cpp |only 18 files changed, 174 insertions(+), 49 deletions(-)
Title: Import 'OpenStreetMap' Data as Simple Features or Spatial
Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf'
or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web
server (<https://overpass-api.de/>) and processed with very fast 'C++'
routines for return to 'R'.
Author: Mark Padgham [aut, cre],
Bob Rudis [aut],
Robin Lovelace [aut],
Maëlle Salmon [aut],
Andrew Smith [ctb],
James Smith [ctb],
Andrea Gilardi [ctb],
Enrico Spinielli [ctb],
Anthony North [ctb],
Marcin Kalicinski [ctb, cph] (Author of included RapidXML code),
Finkelstein Noam [ctb, cph] (Author of included stub.R code),
Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmdata versions 0.1.7 dated 2021-10-07 and 0.1.8 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ inst/doc/osm-sf-translation.html | 4 ++-- inst/doc/osmdata-sc.html | 4 ++-- inst/doc/osmdata.R | 18 ++++++++++++++---- inst/doc/osmdata.Rmd | 12 +++++++++++- inst/doc/osmdata.html | 6 +++--- tests/testthat/test-getbb.R | 2 ++ vignettes/osmdata.Rmd | 12 +++++++++++- vignettes/osmdata.md |only 11 files changed, 66 insertions(+), 25 deletions(-)
Title: A Parametric Method for Generating Synthetic Data
Description: Builds synthetic data applicable across multiple domains. This package also provides flexibility to control data distribution to make it relevant to many industry examples.
Author: Sidharth Macherla [aut, cre] (<https://orcid.org/0000-0002-4825-2026>)
Maintainer: Sidharth Macherla <msidharthrasik@gmail.com>
Diff between conjurer versions 1.2.0 dated 2020-09-08 and 1.3.0 dated 2021-10-17
DESCRIPTION | 9 MD5 | 22 NAMESPACE | 1 NEWS.md | 15 R/buildHierarchy.R |only R/genTree.R |only R/treeDf.R |only inst/doc/introduction_to_conjurer.R | 35 + inst/doc/introduction_to_conjurer.Rmd | 88 ++- inst/doc/introduction_to_conjurer.html | 967 +++++++++++++++++++-------------- man/buildHierarchy.Rd |only man/genTree.Rd |only man/treeDf.Rd |only vignettes/bibliography.bib | 151 +++++ vignettes/introduction_to_conjurer.Rmd | 88 ++- 15 files changed, 908 insertions(+), 468 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-03 2.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-05 8.1.0-1
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.0.1 dated 2021-09-20 and 2.0.2 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 +++++++- R/check_data.R | 8 ++++---- README.md | 2 +- build/vignette.rds |binary tests/testthat/test-expand_classes.R | 4 ++-- tests/testthat/test-nec.R | 4 +++- 8 files changed, 27 insertions(+), 19 deletions(-)
Title: Color Manipulation Tools
Description: Manipulate and visualize colors in a intuitive,
low-dependency and functional way.
Author: Emil Hvitfeldt [aut, cre] (<https://orcid.org/0000-0002-0679-1945>)
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Diff between prismatic versions 1.0.0 dated 2021-01-05 and 1.1.0 dated 2021-10-17
prismatic-1.0.0/prismatic/R/0_imports.R |only prismatic-1.0.0/prismatic/tests/testthat/test-modify.R |only prismatic-1.1.0/prismatic/DESCRIPTION | 19 - prismatic-1.1.0/prismatic/MD5 | 43 +- prismatic-1.1.0/prismatic/NAMESPACE | 11 prismatic-1.1.0/prismatic/NEWS.md | 5 prismatic-1.1.0/prismatic/R/contrast_ratio.R | 10 prismatic-1.1.0/prismatic/R/extract.R |only prismatic-1.1.0/prismatic/R/prismatic-package.R |only prismatic-1.1.0/prismatic/README.md | 9 prismatic-1.1.0/prismatic/man/best_contrast.Rd |only prismatic-1.1.0/prismatic/man/clr_extract.Rd |only prismatic-1.1.0/prismatic/man/extract_hcl.Rd |only prismatic-1.1.0/prismatic/man/extract_hsl.Rd |only prismatic-1.1.0/prismatic/man/extract_rgb.Rd |only prismatic-1.1.0/prismatic/man/prismatic-package.Rd |only prismatic-1.1.0/prismatic/tests/testthat/Rplots.pdf |binary prismatic-1.1.0/prismatic/tests/testthat/helpers.R | 84 ----- prismatic-1.1.0/prismatic/tests/testthat/test-alpha.R | 31 +- prismatic-1.1.0/prismatic/tests/testthat/test-color-blindness.R | 119 ++++++- prismatic-1.1.0/prismatic/tests/testthat/test-color.R | 34 +- prismatic-1.1.0/prismatic/tests/testthat/test-extract.R |only prismatic-1.1.0/prismatic/tests/testthat/test-greyscale.R | 34 +- prismatic-1.1.0/prismatic/tests/testthat/test-lightness.R | 150 ++++++---- prismatic-1.1.0/prismatic/tests/testthat/test-mix.R | 43 ++ prismatic-1.1.0/prismatic/tests/testthat/test-negate.R | 17 - prismatic-1.1.0/prismatic/tests/testthat/test-rotate.R | 43 ++ prismatic-1.1.0/prismatic/tests/testthat/test-saturate.R | 81 ++++- 28 files changed, 457 insertions(+), 276 deletions(-)
Title: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 1.2.0 dated 2021-09-06 and 1.2.1 dated 2021-10-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/hs_mate_finder.R | 2 +- R/simulateGen.R | 1 + 5 files changed, 13 insertions(+), 8 deletions(-)