Title: Simple Scraping and Tidy Webpage Summaries
Description: Simple tools for scraping webpages, extracting common html tags and parsing contents to a tidy, tabular format. Tools help with extraction of page titles, links, images, rss feeds, social media handles and page metadata.
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Diff between htmldf versions 0.2.0 dated 2021-02-21 and 0.3.0 dated 2021-07-12
htmldf-0.2.0/htmldf/inst |only htmldf-0.3.0/htmldf/DESCRIPTION | 7 +++---- htmldf-0.3.0/htmldf/MD5 | 7 +++---- htmldf-0.3.0/htmldf/R/get_time.R | 12 ++++++++---- htmldf-0.3.0/htmldf/R/html_df.R | 16 +++++++++++++--- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Access the 'Geographic Name Resolution Service'
Description: Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.
Author: Brad Boyle [aut],
Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between GNRS versions 0.2.0 dated 2021-03-28 and 0.3.0 dated 2021-07-12
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++++++------------ NAMESPACE | 4 ++++ NEWS | 14 ++++++++++++++ R/data.R | 2 +- R/gnrs.R | 18 ++++++++++++++++-- R/gnrs_acknowledgements.R |only R/gnrs_citations.R |only R/gnrs_get_counties.R | 20 +++++++++++++++++++- R/gnrs_get_countries.R | 17 +++++++++++++++-- R/gnrs_get_states.R | 21 +++++++++++++++++++-- R/gnrs_metadata.R |only R/gnrs_sources.R |only R/gnrs_version.R | 17 +++++++++++++++-- build/vignette.rds |binary inst/doc/GNRS.html | 33 +++++++++++++++++++++++++-------- man/GNRS_acknowledgments.Rd |only man/GNRS_citations.Rd |only man/GNRS_metadata.Rd |only man/GNRS_sources.Rd |only man/gnrs_testfile.Rd | 2 +- 21 files changed, 152 insertions(+), 34 deletions(-)
Title: Post-Processing MCMC Outputs of Bayesian Factor Analytic Models
Description: A well known identifiability issue in factor analytic models is the invariance with respect to orthogonal transformations. This problem burdens the inference under a Bayesian setup, where Markov chain Monte Carlo (MCMC) methods are used to generate samples from the posterior distribution. The package applies a series of rotation, sign and permutation transformations (Papastamoulis and Ntzoufras (2020) <arXiv:2004.05105>) into raw MCMC samples of factor loadings, which are provided by the user. The post-processed output is identifiable and can be used for MCMC inference on any parametric function of factor loadings. Comparison of multiple MCMC chains is also possible.
Author: Panagiotis Papastamoulis [aut, cre]
(<https://orcid.org/0000-0001-9468-7613>)
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between factor.switching versions 1.1 dated 2020-04-15 and 1.2 dated 2021-07-12
DESCRIPTION | 10 - MD5 | 10 - NAMESPACE | 1 R/factorRotations.R | 253 +++++++++++++++++++++++++++++++++++ build/partial.rdb |binary man/procrustes_switching.Rd |only man/weighted_procrustes_switching.Rd |only 7 files changed, 265 insertions(+), 9 deletions(-)
More information about factor.switching at CRAN
Permanent link
Title: Combine Parameter Estimates via Parametric Bootstrap
Description: Propagate uncertainty from several estimates when combining these estimates via a function.
This is done by using the parametric bootstrap to simulate values from the distribution of each estimate to build up an empirical distribution of the combined parameter.
Finally either the percentile method is used or the highest density interval is chosen to derive a confidence interval for the combined parameter with the desired coverage.
References: Davison and Hinkley (1997,ISBN:0-521-57471-4) for the parametric bootstrap and percentile method, Gelman et al. (2014,ISBN:978-1-4398-4095-5) for the highest density interval, Stockdale et al. (2020)<doi:10.1016/j.jhep.2020.04.008> for an example of combining conditional prevalences.
Author: Marc Henrion [aut, cre] (<https://orcid.org/0000-0003-1242-839X>)
Maintainer: Marc Henrion <mhenrion@mlw.mw>
Diff between bootComb versions 1.0.1 dated 2020-11-18 and 1.0.2 dated 2021-07-12
DESCRIPTION | 7 +++---- MD5 | 11 ++++++----- NEWS.md | 5 +++++ R/adjustPrevalence.R | 5 ++++- R/simulations.R | 2 +- README.md | 10 ++++++++++ inst |only 7 files changed, 29 insertions(+), 11 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models with and without asymmetry (leverage) via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002> and Hosszejni and Kastner (2019) <doi:10.1007/978-3-030-30611-3_8>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05> and the package vignette.
Author: Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>),
Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 3.0.6 dated 2021-05-20 and 3.1.0 dated 2021-07-12
.Rinstignore | 1 DESCRIPTION | 9 MD5 | 93 ++++++---- NAMESPACE | 6 NEWS.md | 18 + R/exports.R | 4 R/plotting.R | 4 R/stochvol-package.R | 2 R/utilities_svdraws.R | 20 +- R/wrappers.R | 268 ++++++++++++++++++++++++++--- build/partial.rdb |binary build/vignette.rds |binary data/exrates.RData |binary inst/doc/article.pdf |binary inst/doc/article2.R | 174 +++++++++---------- inst/doc/article2.Rnw | 50 ++--- inst/doc/article2.pdf |binary inst/doc/jss3813-comtimeplot-1.pdf |only inst/doc/jss3813-corimageplot-1.pdf |only inst/doc/jss3813-cortimeplot-1.pdf |only inst/doc/jss3813-evdiag-1.pdf |only inst/doc/jss3813-fsvprepdata-1.pdf |only inst/doc/jss3813-loadplot2-1.png |only inst/doc/jss3813-loadplot2-2.pdf |only inst/doc/jss3813-logdetcovn-1.pdf |only inst/doc/jss3813-preddist-1.png |only inst/doc/jss3813-varplot-1.pdf |only inst/doc/jss3813-varplot2-1.pdf |only inst/doc/jss3813-voltimeplot-1.pdf |only inst/examples/predict.R | 8 inst/examples/svlm.R |only inst/examples/svsample.R | 4 inst/include/adaptation.hpp | 12 - inst/include/type_definitions.hpp | 4 man/predict.svdraws.Rd | 8 man/svlm.Rd |only man/svsample.Rd | 27 +- man/svsample_roll.Rd | 2 src/exports.cc | 38 +++- src/sampling_latent_states.cc | 74 ++++---- src/sampling_main.cc | 253 +++++++++++++++++++++++++++- src/sampling_main.h | 41 +++- src/single_update.cc | 18 - src/utils_latent_states.cc | 49 +++-- src/utils_latent_states.h | 16 - src/utils_main.h | 1 tests/testthat/test-cpp.R | 1 tests/testthat/test-formula.R |only tests/testthat/test-samplers.R | 316 ++++++++++++++--------------------- vignettes/.install_extras | 1 vignettes/article2.Rnw | 50 ++--- vignettes/jss3813-comtimeplot-1.pdf |only vignettes/jss3813-corimageplot-1.pdf |only vignettes/jss3813-cortimeplot-1.pdf |only vignettes/jss3813-evdiag-1.pdf |only vignettes/jss3813-fsvprepdata-1.pdf |only vignettes/jss3813-loadplot2-1.png |only vignettes/jss3813-loadplot2-2.pdf |only vignettes/jss3813-logdetcovn-1.pdf |only vignettes/jss3813-preddist-1.png |only vignettes/jss3813-varplot-1.pdf |only vignettes/jss3813-varplot2-1.pdf |only vignettes/jss3813-voltimeplot-1.pdf |only 63 files changed, 1041 insertions(+), 531 deletions(-)
Title: Simulated Predicted Probabilities for Multinomial Logit Models
Description: Functions to easily return simulated predicted probabilities and
first differences for multinomial logit models. It takes a specified
scenario and a multinomial model to predict probabilities with a set of
coefficients, drawn from a simulated sampling distribution. The simulated
predictions allow for meaningful plots with means and confidence intervals.
The methodological approach is based on the principles laid out by King,
Tomz, and Wittenberg (2000) <doi:10.2307/2669316> and Hanmer and Ozan Kalkan
(2016) <doi:10.1111/j.1540-5907.2012.00602.x>.
Author: Manuel Neumann [aut, cre] (<https://orcid.org/0000-0002-7953-3939>)
Maintainer: Manuel Neumann <manuel.neumann@mzes.uni-mannheim.de>
Diff between MNLpred versions 0.0.6 dated 2021-03-04 and 0.0.7 dated 2021-07-12
DESCRIPTION | 6 +-- MD5 | 20 +++++------ NEWS.md | 5 ++ R/mnl_fd2_ova.R | 55 +++++++++++++++++-------------- R/mnl_fd_ova.R | 6 +-- R/mnl_pred_ova.R | 59 +++++++++++++++++----------------- README.md | 8 +++- build/vignette.rds |binary inst/CITATION | 4 +- inst/doc/OVA_Predictions_For_MNL.html | 35 ++++++++++---------- tests/testthat/test_inputvariants.R | 30 +++++++++++++++++ 11 files changed, 139 insertions(+), 89 deletions(-)
Title: Filter Based Feature Selection for 'mlr3'
Description: Extends 'mlr3' with filter methods for feature selection.
Besides standalone filter methods built-in methods of any
machine-learning algorithm are supported. Partial scoring of
multivariate filter methods is supported.
Author: Patrick Schratz [aut, cre] (<https://orcid.org/0000-0003-0748-6624>),
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Martin Binder [aut]
Maintainer: Patrick Schratz <patrick.schratz@gmail.com>
Diff between mlr3filters versions 0.4.1 dated 2021-03-08 and 0.4.2 dated 2021-07-12
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 7 +++++++ R/Filter.R | 2 ++ R/FilterCMIM.R | 2 +- R/FilterDISR.R | 4 ++-- R/FilterJMI.R | 2 +- R/FilterJMIM.R | 2 +- R/FilterMIM.R | 2 +- R/FilterMRMR.R | 2 +- R/FilterNJMIM.R | 2 +- R/FilterPermutation.R | 2 +- R/helper.R | 3 ++- man/mlr_filters_disr.Rd | 2 +- man/mlr_filters_permutation.Rd | 2 +- tests/testthat/test_filter.R | 14 ++++++++++++++ 16 files changed, 54 insertions(+), 30 deletions(-)
Title: GUI Tools for Interactive Image Processing with 'magick'
Description: Enables us to use the functions of the package 'magick' interactively.
Author: Shota Ochi [aut, cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between magickGUI versions 1.2.2 dated 2021-01-08 and 1.3.0 dated 2021-07-12
DESCRIPTION | 8 ++--- MD5 | 36 +++++++++++++++----------- NAMESPACE | 4 ++ NEWS.md | 7 +++++ R/interactive_blur.R | 2 - R/interactive_composite.R | 2 - R/interactive_crop.R | 2 - R/interactive_modulate.R | 2 - R/interactive_motion_blur.R |only R/interactive_quantize.R | 2 - R/interactive_shade.R |only R/interactive_threshold.R | 2 - R/misc.R | 2 + man/interactive_composite.Rd | 2 - man/interactive_crop.Rd | 2 - man/interactive_modulate.Rd | 2 - man/interactive_motion_blur.Rd |only man/interactive_quantize.Rd | 2 - man/interactive_shade.Rd |only man/interactive_threshold.Rd | 2 - tests/testthat/test_interactive_motion_blur.R |only tests/testthat/test_interactive_shade.R |only 22 files changed, 49 insertions(+), 30 deletions(-)
Title: Predict Epidemic Curves with Generalized SEIR Modeling
Description: Performs generalized Susceptible-Exposed-Infected-Recovered (SEIR) modeling to predict epidemic curves. The method is described in Peng et al. (2020) <doi:10.1101/2020.02.16.20023465>.
Author: Selcuk Korkmaz [aut, cre] (<https://orcid.org/0000-0003-4632-6850>)
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between genSEIR versions 0.1.0 dated 2021-06-23 and 0.1.1 dated 2021-07-12
genSEIR-0.1.0/genSEIR/R/plotSEIQRDP.R |only genSEIR-0.1.0/genSEIR/man/plotSEIQRDP.Rd |only genSEIR-0.1.1/genSEIR/DESCRIPTION | 12 ++-- genSEIR-0.1.1/genSEIR/MD5 | 42 +++++++------- genSEIR-0.1.1/genSEIR/NAMESPACE | 7 ++ genSEIR-0.1.1/genSEIR/R/RK4.R | 4 - genSEIR-0.1.1/genSEIR/R/SEIQRDP.R | 15 +++-- genSEIR-0.1.1/genSEIR/R/SEIQRDP_for_fitting.R | 41 ++++++++----- genSEIR-0.1.1/genSEIR/R/checkRates.R | 4 - genSEIR-0.1.1/genSEIR/R/fit_SEIQRDP.R | 69 ++++++++++++++--------- genSEIR-0.1.1/genSEIR/R/getKappaFun.R | 18 +++--- genSEIR-0.1.1/genSEIR/R/getLambdaFun.R | 14 ++-- genSEIR-0.1.1/genSEIR/R/globals.R | 7 ++ genSEIR-0.1.1/genSEIR/R/plot_SEIQRDP.R |only genSEIR-0.1.1/genSEIR/R/predict_SEIQRDP.R |only genSEIR-0.1.1/genSEIR/README.md | 12 ++++ genSEIR-0.1.1/genSEIR/man/RK4.Rd | 4 - genSEIR-0.1.1/genSEIR/man/SEIQRDP.Rd | 15 +++-- genSEIR-0.1.1/genSEIR/man/SEIQRDP_for_fitting.Rd | 16 +++++ genSEIR-0.1.1/genSEIR/man/checkRates.Rd | 4 - genSEIR-0.1.1/genSEIR/man/fit_SEIQRDP.Rd | 37 ++++++++---- genSEIR-0.1.1/genSEIR/man/getKappaFun.Rd | 2 genSEIR-0.1.1/genSEIR/man/getLambdaFun.Rd | 6 +- genSEIR-0.1.1/genSEIR/man/plot_SEIQRDP.Rd |only genSEIR-0.1.1/genSEIR/man/predict_SEIQRDP.Rd |only 25 files changed, 210 insertions(+), 119 deletions(-)
Title: General Engine for Eco-Evolutionary Simulations
Description: Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term.
Author: ETH Zürich [cph],
Oskar Hagen [aut, cre] (Landscape Ecology, WSL and ETH Zürich,
Switzerland),
Benjamin Flueck [aut] (Landscape Ecology, WSL and ETH Zürich,
Switzerland),
Fabian Fopp [aut] (Landscape Ecology, WSL and ETH Zürich, Switzerland),
Juliano S. Cabral [aut] (Ecosystem Modeling, Center for Computational
and Theoretical Biology, University of Würzburg, Würzburg, Germany),
Florian Hartig [aut] (Theoretical Ecology, University of Regensburg,
Regensburg, Germany),
Mikael Pontarp [aut] (Department of Biology, Lund University, Lund,
Sweden),
Charles Novaes de Santana [ctb] (Landscape Ecology, WSL and ETH Zürich,
Switzerland),
Thiago F. Rangel [aut] (Department of Ecology, Universidade Federal de
Goiás, Goiás, Brazil),
Theo Gaboriau [ctb] (Depatment of Computational Biology, Lausanne
University, Switzerland),
Loïc Pellissier [aut, ths] (Landscape Ecology, WSL and ETH Zürich,
Switzerland)
Maintainer: Oskar Hagen <oskar@hagen.bio>
Diff between gen3sis versions 1.2 dated 2020-12-15 and 1.3 dated 2021-07-12
DESCRIPTION | 10 MD5 | 31 - R/gen3sis_main.R | 5 R/input_creation.R | 4 README.md | 13 build/vignette.rds |binary inst/doc/create_config.html | 672 ++++++++++++----------------------- inst/doc/create_input_landscape.R | 1 inst/doc/create_input_landscape.Rmd | 1 inst/doc/create_input_landscape.html | 283 ++------------ inst/doc/design_landscape.html | 388 +++++--------------- inst/doc/introduction.R | 19 inst/doc/introduction.Rmd | 22 - inst/doc/introduction.html | 322 +++------------- inst/logo/richness_plot.png |only vignettes/create_input_landscape.Rmd | 1 vignettes/introduction.Rmd | 22 - 17 files changed, 577 insertions(+), 1217 deletions(-)
Title: Testing for Equivalence and Noninferiority
Description: Making available in R the complete set of programs accompanying S. Wellek's (2010) monograph
''Testing Statistical Hypotheses of Equivalence and Noninferiority. Second Edition''
(Chapman&Hall/CRC).
Author: Stefan Wellek,
Peter Ziegler
Maintainer: Stefan Wellek <stefan.wellek@zi-mannheim.de>
Diff between EQUIVNONINF versions 1.0 dated 2017-09-19 and 1.0.2 dated 2021-07-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/bi1st.R | 2 +- R/bi2aeq3.R | 12 +++++++----- R/bi2ste3.R | 13 +++++++------ man/bi2aeq3.Rd | 2 +- man/bi2rlv2.Rd | 2 +- man/bi2ste3.Rd | 2 +- 8 files changed, 29 insertions(+), 26 deletions(-)
Title: Analysis of Single-Cell Chromatin Data
Description: A framework for the analysis and exploration of single-cell chromatin data.
The 'Signac' package contains functions for quantifying single-cell chromatin data,
computing per-cell quality control metrics, dimension reduction
and normalization, visualization, and DNA sequence motif analysis.
Reference: Stuart et al. (2020) <doi:10.1101/2020.11.09.373613>.
Author: Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>),
Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>),
Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>),
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Tim Stuart <tstuart@nygenome.org>
Diff between Signac versions 1.2.1 dated 2021-05-11 and 1.3.0 dated 2021-07-12
Signac-1.2.1/Signac/man/FoldChange.Rd |only Signac-1.3.0/Signac/DESCRIPTION | 19 ++-- Signac-1.3.0/Signac/LICENSE | 2 Signac-1.3.0/Signac/MD5 | 32 +++---- Signac-1.3.0/Signac/NAMESPACE | 3 Signac-1.3.0/Signac/NEWS.md | 18 ++++ Signac-1.3.0/Signac/R/differential_accessibility.R |only Signac-1.3.0/Signac/R/fragments.R | 12 ++ Signac-1.3.0/Signac/R/links.R | 8 - Signac-1.3.0/Signac/R/objects.R | 14 ++- Signac-1.3.0/Signac/R/peaks.R | 24 ++++- Signac-1.3.0/Signac/R/quantification.R | 2 Signac-1.3.0/Signac/R/utilities.R | 84 -------------------- Signac-1.3.0/Signac/R/visualization.R | 2 Signac-1.3.0/Signac/build/partial.rdb |binary Signac-1.3.0/Signac/data/blacklist_hg38_unified.rda |binary Signac-1.3.0/Signac/man/CallPeaks.Rd | 10 +- Signac-1.3.0/Signac/man/reexports.Rd | 5 - 18 files changed, 109 insertions(+), 126 deletions(-)
Title: Install, Update, Load Packages from CRAN, 'GitHub', and
'Bioconductor' in One Step
Description: Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor'
packages in a single function call. By accepting bare unquoted names for packages,
it's easy to add or remove packages from the list.
Author: Desi Quintans [aut, cre]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between librarian versions 1.7.0 dated 2019-03-13 and 1.8.1 dated 2021-07-12
DESCRIPTION | 11 -- MD5 | 33 +++--- NAMESPACE | 1 NEWS.md | 31 +++++ R/check_pkg_status.R | 2 R/console_output.R | 20 ++- R/exported_functions.R | 189 ++++++++++++++++++++++++++-------- R/internal_functions.R | 6 - README.md | 8 + build/vignette.rds |binary inst/doc/intro-to-librarian.R | 2 inst/doc/intro-to-librarian.html | 213 ++++----------------------------------- man/browse_cran.Rd | 2 man/lib_startup.Rd | 2 man/shelf.Rd | 26 ++-- man/stock.Rd |only man/unshelf.Rd | 19 ++- man/wrap_text.Rd | 2 18 files changed, 279 insertions(+), 288 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines types of spatial data such as point patterns,
mainly in two dimensions, but also in higher dimensions.
Provides class support, and functions for geometrical operations
on spatial data, used in the 'spatstat' family of packages.
Excludes spatial data on a linear network, which are covered by
the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Sebastian Meyer [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Waagepetersen [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 2.2-0 dated 2021-06-15 and 2.2-2 dated 2021-07-12
DESCRIPTION | 8 ++--- MD5 | 20 +++++++------ NAMESPACE | 2 + NEWS | 28 ++++++++++++++++++ R/as.im.R | 63 +++++++++++++++++++++++++++++++++++++++++- R/images.R | 6 ++-- R/options.R | 8 ++++- R/owin2mask.R |only inst/doc/packagesizes.txt | 1 man/owin2mask.Rd |only man/spatstat.geom-internal.Rd | 4 ++ man/where.max.Rd | 3 +- 12 files changed, 123 insertions(+), 20 deletions(-)
Title: Hierarchical Cluster Analysis of Nominal Data
Description: Similarity measures for hierarchical clustering of objects characterized by
nominal (categorical) variables. Evaluation criteria for nominal data clustering.
Author: Zdenek Sulc [aut, cre],
Jana Cibulkova [aut],
Hana Rezankova [aut]
Maintainer: Zdenek Sulc <zdenek.sulc@vse.cz>
Diff between nomclust versions 2.2.1 dated 2020-11-09 and 2.5.0 dated 2021-07-12
nomclust-2.2.1/nomclust/R/eskin_fx.R |only nomclust-2.2.1/nomclust/R/good1_fx.R |only nomclust-2.2.1/nomclust/R/good2_fx.R |only nomclust-2.2.1/nomclust/R/good3_fx.R |only nomclust-2.2.1/nomclust/R/good4_fx.R |only nomclust-2.2.1/nomclust/R/iof_fx.R |only nomclust-2.2.1/nomclust/R/lin1_fx.R |only nomclust-2.2.1/nomclust/R/lin_fx.R |only nomclust-2.2.1/nomclust/R/of_fx.R |only nomclust-2.2.1/nomclust/R/sm_fx.R |only nomclust-2.2.1/nomclust/R/ve_fx.R |only nomclust-2.2.1/nomclust/R/vm_fx.R |only nomclust-2.5.0/nomclust/DESCRIPTION | 14 - nomclust-2.5.0/nomclust/MD5 | 111 ++++++----- nomclust-2.5.0/nomclust/NAMESPACE | 11 - nomclust-2.5.0/nomclust/R/EVAL.R | 51 +++-- nomclust-2.5.0/nomclust/R/RcppExports.R |only nomclust-2.5.0/nomclust/R/SIMILARITY.R |only nomclust-2.5.0/nomclust/R/as.agnes.R |only nomclust-2.5.0/nomclust/R/as.hclust.nomclust.R |only nomclust-2.5.0/nomclust/R/dend.plot.R | 51 +++-- nomclust-2.5.0/nomclust/R/eskin.R | 51 ++--- nomclust-2.5.0/nomclust/R/eval.plot.R | 25 +- nomclust-2.5.0/nomclust/R/evalclust.R | 46 +++- nomclust-2.5.0/nomclust/R/good1.R | 65 ++---- nomclust-2.5.0/nomclust/R/good2.R | 62 ++---- nomclust-2.5.0/nomclust/R/good3.R | 60 ++---- nomclust-2.5.0/nomclust/R/good4.R | 60 ++---- nomclust-2.5.0/nomclust/R/iof.R | 58 ++--- nomclust-2.5.0/nomclust/R/lin.R | 63 ++---- nomclust-2.5.0/nomclust/R/lin1.R | 67 ++---- nomclust-2.5.0/nomclust/R/nomclust.R | 242 ++++++++----------------- nomclust-2.5.0/nomclust/R/nomprox.R | 101 ++++++++-- nomclust-2.5.0/nomclust/R/of.R | 55 ++--- nomclust-2.5.0/nomclust/R/plot.nomclust.R |only nomclust-2.5.0/nomclust/R/print.nomclust.R |only nomclust-2.5.0/nomclust/R/sm.R | 50 ++--- nomclust-2.5.0/nomclust/R/summary.nomclust.R |only nomclust-2.5.0/nomclust/R/ve.R | 68 ++----- nomclust-2.5.0/nomclust/R/vm.R | 71 ++----- nomclust-2.5.0/nomclust/data/CA.methods.RData |binary nomclust-2.5.0/nomclust/data/data20.RData |binary nomclust-2.5.0/nomclust/man/as.agnes.Rd |only nomclust-2.5.0/nomclust/man/dend.plot.Rd | 20 +- nomclust-2.5.0/nomclust/man/eskin.Rd | 6 nomclust-2.5.0/nomclust/man/eval.plot.Rd | 22 +- nomclust-2.5.0/nomclust/man/evalclust.Rd | 32 ++- nomclust-2.5.0/nomclust/man/good1.Rd | 6 nomclust-2.5.0/nomclust/man/good2.Rd | 6 nomclust-2.5.0/nomclust/man/good3.Rd | 6 nomclust-2.5.0/nomclust/man/good4.Rd | 6 nomclust-2.5.0/nomclust/man/iof.Rd | 6 nomclust-2.5.0/nomclust/man/lin.Rd | 6 nomclust-2.5.0/nomclust/man/lin1.Rd | 6 nomclust-2.5.0/nomclust/man/nomclust.Rd | 95 ++++----- nomclust-2.5.0/nomclust/man/nomprox.Rd | 66 +++++- nomclust-2.5.0/nomclust/man/of.Rd | 6 nomclust-2.5.0/nomclust/man/sm.Rd | 6 nomclust-2.5.0/nomclust/man/ve.Rd | 6 nomclust-2.5.0/nomclust/man/vm.Rd | 6 nomclust-2.5.0/nomclust/src |only 61 files changed, 828 insertions(+), 861 deletions(-)
Title: Read-Write API Client Library for 'Wikidata'
Description: An API client for the Wikidata <https://www.wikidata.org/wiki/Wikidata:Main_Page> store of
semantic data.
Author: Thomas Shafee [aut, cre], Oliver Keyes [aut, cre], Serena Signorelli [aut, cre],
Alex Lum [ctb], Christian Graul [ctb], Mikhail Popov [ctb]
Maintainer: Thomas Shafee <T.Shafee@latrobe.edu.au>
Diff between WikidataR versions 2.2.0 dated 2021-07-05 and 2.3.1 dated 2021-07-12
WikidataR-2.2.0/WikidataR/build |only WikidataR-2.2.0/WikidataR/inst/doc |only WikidataR-2.2.0/WikidataR/vignettes |only WikidataR-2.3.1/WikidataR/DESCRIPTION | 12 WikidataR-2.3.1/WikidataR/MD5 | 56 +-- WikidataR-2.3.1/WikidataR/NAMESPACE | 114 +++--- WikidataR-2.3.1/WikidataR/NEWS | 8 WikidataR-2.3.1/WikidataR/R/WikidataR.R | 14 WikidataR-2.3.1/WikidataR/R/disambiguators.R |only WikidataR-2.3.1/WikidataR/R/gets.R | 82 ++++ WikidataR-2.3.1/WikidataR/R/queries.R | 84 +++- WikidataR-2.3.1/WikidataR/R/schol.R | 28 - WikidataR-2.3.1/WikidataR/R/utils.R | 221 ++++-------- WikidataR-2.3.1/WikidataR/R/writes.R | 4 WikidataR-2.3.1/WikidataR/man/WikidataR.Rd | 3 WikidataR-2.3.1/WikidataR/man/disambiguate_QIDs.Rd |only WikidataR-2.3.1/WikidataR/man/filter_qids.Rd |only WikidataR-2.3.1/WikidataR/man/get_example.Rd | 2 WikidataR-2.3.1/WikidataR/man/get_names_from_properties.Rd | 2 WikidataR-2.3.1/WikidataR/man/get_random.Rd | 4 WikidataR-2.3.1/WikidataR/man/identifier_from_identifier.Rd | 2 WikidataR-2.3.1/WikidataR/man/qid_from_DOI.Rd | 2 WikidataR-2.3.1/WikidataR/man/qid_from_ORCID.Rd | 2 WikidataR-2.3.1/WikidataR/man/qid_from_identifier.Rd | 2 WikidataR-2.3.1/WikidataR/man/qid_from_name.Rd | 2 WikidataR-2.3.1/WikidataR/man/query_wikidata.Rd | 9 WikidataR-2.3.1/WikidataR/man/searcher.Rd | 2 WikidataR-2.3.1/WikidataR/man/sparql_query.Rd | 2 WikidataR-2.3.1/WikidataR/man/wd_query.Rd | 2 WikidataR-2.3.1/WikidataR/man/wd_rand_query.Rd | 2 WikidataR-2.3.1/WikidataR/man/write_wikidata.Rd | 2 31 files changed, 379 insertions(+), 284 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space, for
calculating the median of sets of trees, and for computing the information
content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.0.3 dated 2021-01-31 and 2.1.0 dated 2021-07-12
TreeDist-2.0.3/TreeDist/man/ClusteringEntropy.Rd |only TreeDist-2.0.3/TreeDist/man/Project.Rd |only TreeDist-2.0.3/TreeDist/man/ProjectionQuality.Rd |only TreeDist-2.0.3/TreeDist/man/SpectralClustering.Rd |only TreeDist-2.0.3/TreeDist/man/SplitwiseInfo.Rd |only TreeDist-2.0.3/TreeDist/tests/figs/deps.txt |only TreeDist-2.1.0/TreeDist/DESCRIPTION | 28 TreeDist-2.1.0/TreeDist/MD5 | 128 +-- TreeDist-2.1.0/TreeDist/NAMESPACE | 26 TreeDist-2.1.0/TreeDist/NEWS.md | 26 TreeDist-2.1.0/TreeDist/R/ClusterTable.R | 21 TreeDist-2.1.0/TreeDist/R/Information.R | 73 +- TreeDist-2.1.0/TreeDist/R/Plot3.R |only TreeDist-2.1.0/TreeDist/R/RcppExports.R | 4 TreeDist-2.1.0/TreeDist/R/TreeDist-package.R | 9 TreeDist-2.1.0/TreeDist/R/shiny.R | 27 TreeDist-2.1.0/TreeDist/R/spectral_clustering.R | 55 + TreeDist-2.1.0/TreeDist/R/tree_distance_kendall-colijn.R | 172 ++++ TreeDist-2.1.0/TreeDist/R/tree_distance_mast.R | 10 TreeDist-2.1.0/TreeDist/R/tree_distance_msd.R | 1 TreeDist-2.1.0/TreeDist/R/tree_distance_path.R | 17 TreeDist-2.1.0/TreeDist/R/tree_distance_utilities.R | 17 TreeDist-2.1.0/TreeDist/R/tree_information.R | 314 ++++++--- TreeDist-2.1.0/TreeDist/R/trustworthiness.R | 34 TreeDist-2.1.0/TreeDist/R/zzz.R | 5 TreeDist-2.1.0/TreeDist/build/partial.rdb |binary TreeDist-2.1.0/TreeDist/build/vignette.rds |binary TreeDist-2.1.0/TreeDist/inst/REFERENCES.bib | 100 ++ TreeDist-2.1.0/TreeDist/inst/WORDLIST | 2 TreeDist-2.1.0/TreeDist/inst/doc/Generalized-RF.html | 206 ----- TreeDist-2.1.0/TreeDist/inst/doc/Robinson-Foulds.R | 2 TreeDist-2.1.0/TreeDist/inst/doc/Robinson-Foulds.Rmd | 2 TreeDist-2.1.0/TreeDist/inst/doc/Robinson-Foulds.html | 206 ----- TreeDist-2.1.0/TreeDist/inst/doc/Using-TreeDist.html | 212 ------ TreeDist-2.1.0/TreeDist/inst/doc/information.Rmd | 4 TreeDist-2.1.0/TreeDist/inst/doc/information.html | 210 ------ TreeDist-2.1.0/TreeDist/inst/doc/treespace.R | 58 + TreeDist-2.1.0/TreeDist/inst/doc/treespace.Rmd | 98 +- TreeDist-2.1.0/TreeDist/inst/doc/treespace.html | 302 ++------ TreeDist-2.1.0/TreeDist/inst/doc/using-distances.html | 208 ------ TreeDist-2.1.0/TreeDist/inst/treespace/app.R | 157 ++-- TreeDist-2.1.0/TreeDist/man/AllSplitPairings.Rd | 82 +- TreeDist-2.1.0/TreeDist/man/ClusterTable-methods.Rd | 12 TreeDist-2.1.0/TreeDist/man/KendallColijn.Rd | 58 + TreeDist-2.1.0/TreeDist/man/MapTrees.Rd |only TreeDist-2.1.0/TreeDist/man/MappingQuality.Rd |only TreeDist-2.1.0/TreeDist/man/MeilaVariationOfInformation.Rd | 120 +-- TreeDist-2.1.0/TreeDist/man/PathDist.Rd | 17 TreeDist-2.1.0/TreeDist/man/Plot3.Rd |only TreeDist-2.1.0/TreeDist/man/SpectralEigens.Rd |only TreeDist-2.1.0/TreeDist/man/SplitEntropy.Rd | 105 +-- TreeDist-2.1.0/TreeDist/man/SplitSharedInformation.Rd | 188 ++--- TreeDist-2.1.0/TreeDist/man/TreeDist-package.Rd | 9 TreeDist-2.1.0/TreeDist/man/TreeInfo.Rd |only TreeDist-2.1.0/TreeDist/man/median.multiPhylo.Rd | 6 TreeDist-2.1.0/TreeDist/src/RcppExports.cpp | 13 TreeDist-2.1.0/TreeDist/src/SplitList.h | 5 TreeDist-2.1.0/TreeDist/src/day_1985.cpp | 345 ++++++---- TreeDist-2.1.0/TreeDist/src/information.h |only TreeDist-2.1.0/TreeDist/src/ints.h | 4 TreeDist-2.1.0/TreeDist/src/tree_distance_functions.cpp | 10 TreeDist-2.1.0/TreeDist/src/tree_distances.h | 4 TreeDist-2.1.0/TreeDist/tests/testthat.R | 2 TreeDist-2.1.0/TreeDist/tests/testthat/_snaps |only TreeDist-2.1.0/TreeDist/tests/testthat/test-Plot3.R |only TreeDist-2.1.0/TreeDist/tests/testthat/test-plot.R | 6 TreeDist-2.1.0/TreeDist/tests/testthat/test-split_info.R |only TreeDist-2.1.0/TreeDist/tests/testthat/test-tree_distance.R | 6 TreeDist-2.1.0/TreeDist/tests/testthat/test-tree_distance_kc.R |only TreeDist-2.1.0/TreeDist/tests/testthat/test-tree_information.R | 143 ++++ TreeDist-2.1.0/TreeDist/vignettes/Robinson-Foulds.Rmd | 2 TreeDist-2.1.0/TreeDist/vignettes/information.Rmd | 4 TreeDist-2.1.0/TreeDist/vignettes/treespace.Rmd | 98 +- 73 files changed, 1936 insertions(+), 2037 deletions(-)
Title: Optimal Test Design Approach to Fixed and Adaptive Test
Construction
Description: Use the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and
van der Linden (2018) <doi:10.1201/9781315117430> in constructing fixed and adaptive tests. Supports the following
mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package
is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>)
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between TestDesign versions 1.2.4 dated 2021-06-05 and 1.2.5 dated 2021-07-12
TestDesign-1.2.4/TestDesign/man/plotExposure-methods.Rd |only TestDesign-1.2.4/TestDesign/man/plotInfo-methods.Rd |only TestDesign-1.2.4/TestDesign/man/saveOutput.Rd |only TestDesign-1.2.5/TestDesign/DESCRIPTION | 11 TestDesign-1.2.5/TestDesign/MD5 | 17 TestDesign-1.2.5/TestDesign/NAMESPACE | 4 TestDesign-1.2.5/TestDesign/NEWS.md | 10 TestDesign-1.2.5/TestDesign/R/shadow_functions.R | 283 ++++------------ TestDesign-1.2.5/TestDesign/R/static_functions.R | 95 ----- TestDesign-1.2.5/TestDesign/R/theta_functions.R | 5 TestDesign-1.2.5/TestDesign/man/Shadow-methods.Rd | 4 11 files changed, 109 insertions(+), 320 deletions(-)
More information about rankUncertainty at CRAN
Permanent link
Title: Inbreeding-Purging Estimation in Pedigreed Populations
Description: Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load.
In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included.
Caballero A. and Toro M.A. (2000) <doi:10.1017/s0016672399004449>.
García-Dorado A., Wang J. and López-Cortegano E. (2016) <doi:10.1534/g3.116.032425>.
Gulisija D. and Crow J.F. (2007) <doi:10.1111/j.1558-5646.2007.00088.x>.
Gutiérrez J.P., Cervantes I., Goyache F. (2009) <doi:10.1111/j.1439-0388.2009.00810.x>.
López-Cortegano E., Bersabé D., Wang J., García-Dorado A. (2018) <doi:10.1038/s41437-017-0045-y>.
Author: Eugenio López-Cortegano [aut, cre]
(<https://orcid.org/0000-0001-6914-6305>)
Maintainer: Eugenio López-Cortegano <elcortegano@gmail.com>
Diff between purgeR versions 1.1 dated 2021-05-10 and 1.2 dated 2021-07-12
DESCRIPTION | 11 +++-- MD5 | 71 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 6 +++ R/Nancestors.R | 4 +- R/RcppExports.R | 5 +- R/check.R | 12 +++--- R/opurging.R | 21 +++++----- R/purgeR.R | 3 + R/rename.R | 8 ++-- R/sort.R |only build/vignette.rds |binary data/arrui.rda |binary data/atlas.rda |binary data/dama.rda |binary data/darwin.rda |binary data/dorcas.rda |binary inst/doc/ip.Rmd | 8 ++-- inst/doc/ip.html | 14 +++---- inst/doc/purgeR-tutorial.R | 7 ++- inst/doc/purgeR-tutorial.Rmd | 50 +++++++++++++------------ inst/doc/purgeR-tutorial.html | 55 ++++++++++++++------------- inst/extdata/arrui_op.rda |binary man/check_basic.Rd | 7 ++- man/check_order.Rd | 4 +- man/ip_op.Rd | 23 ++++++----- man/op.Rd | 4 +- man/ped_sort.Rd |only man/ped_sort_i.Rd |only man/pop_Nancestors.Rd | 4 +- man/purgeR.Rd | 3 + src/RcppExports.cpp | 9 ++-- src/opurging.cpp | 59 +++++++++++++++++++++-------- src/populationSize.cpp | 1 tests/testthat/test_inbreeding.R | 19 +++++---- tests/testthat/test_preprocessing.R | 15 +++++++ vignettes/ip.Rmd | 8 ++-- vignettes/purgeR-tutorial.Rmd | 50 +++++++++++++------------ 38 files changed, 281 insertions(+), 201 deletions(-)
Title: Plot Heatmap
Description: The flexibility and excellence of 'ggplot2' is unquestionable,
so many drawing tools basically need 'ggplot2' as the operating object.
In order to develop a heatmap drawing system based on ggplot2, we developed
this tool, mainly to solve the heatmap puzzle problem and the flexible
connection between the heatmap and the 'ggplot2' object.
The advantages of this tool are as follows:
1. More flexible label settings;
2. Realize the linkage of heatmap and 'ggplot2' drawing system,
which is helpful for operations such as puzzles;
3. Simple and easy to operate;
4. Optimization of clustering tree visualization.
Author: Baiwei Luo [aut, cre]
Maintainer: Baiwei Luo <2734782653@qq.com>
Diff between ggheatmap versions 1.1 dated 2021-07-11 and 2.0 dated 2021-07-12
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ggheatmap.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Annotate the Gene Symbols for Probes in Expression Array
Description: We curated 147 of expression array, from 3 species(human,mouse,rat),
3 companies('Affymetrix','Illumina','Agilent'),
by aligning the 'Fasta' sequences of all probes of each platform to their corresponding reference genome,
and then annotate them to genes.
Author: Jianming Zeng [aut],
Yujia Xiang [aut],
Yonghe Xia [ctb, cre]
Maintainer: Yonghe Xia <xiayh17@gmail.com>
Diff between AnnoProbe versions 0.1.5 dated 2021-07-07 and 0.1.6 dated 2021-07-12
AnnoProbe-0.1.5/AnnoProbe/README.md |only AnnoProbe-0.1.6/AnnoProbe/DESCRIPTION | 12 ++++++------ AnnoProbe-0.1.6/AnnoProbe/MD5 | 15 +++++++-------- AnnoProbe-0.1.6/AnnoProbe/NAMESPACE | 1 + AnnoProbe-0.1.6/AnnoProbe/R/check_diff_genes.R | 2 +- AnnoProbe-0.1.6/AnnoProbe/R/geoChina.R | 13 +++++++------ AnnoProbe-0.1.6/AnnoProbe/R/idmap.R | 19 ++++++++++--------- AnnoProbe-0.1.6/AnnoProbe/man/geoChina.Rd | 6 +++--- AnnoProbe-0.1.6/AnnoProbe/man/idmap.Rd | 8 ++++---- 9 files changed, 39 insertions(+), 37 deletions(-)
Title: Atlas of Living Australia (ALA) Data and Resources in R
Description: The Atlas of Living Australia (ALA) provides tools to enable users
of biodiversity information to find, access, combine and visualise data on
Australian plants and animals; these have been made available from
<https://ala.org.au/>. ALA4R provides a subset of the tools to be
directly used within R. It enables the R community to directly access data
and resources hosted by the ALA.
ALA4R is deprecated and will be removed from CRAN at the end of 2021.
The package to replace ALA4R, 'galah', is now available on CRAN <https://CRAN.R-project.org/package=galah>.
For an introduction to 'galah', visit the GitHub page <https://github.com/AtlasOfLivingAustralia/galah>.
Author: Martin Westgate [aut, cre],
Matilda Stevenson [aut],
Peggy Newman [aut],
Ben Raymond [aut],
Jeremy VanDerWal [aut],
Lee Belbin [aut],
Michael Sumner [ctb],
Tom August [ctb],
John Baumgartner [ctb]
Maintainer: Martin Westgate <martin.westgate@csiro.au>
Diff between ALA4R versions 1.9.0 dated 2020-11-01 and 1.9.1 dated 2021-07-12
DESCRIPTION | 22 ++- MD5 | 54 ++++--- NEWS.md | 7 + R/ALA4R.R | 13 + R/ala_cache_filename.R | 9 - R/occurrences.R | 2 R/occurrences_s3.R | 16 +- R/onload.R | 2 R/zzz.R | 5 README.md | 19 +- build/vignette.rds |binary inst/CITATION | 7 - inst/doc/ALA4R.Rmd | 9 + inst/doc/ALA4R.html | 167 +++++++++++------------- man/ALA4R.Rd | 15 +- man/ala_cache_filename.Rd | 4 man/occurrences.Rd | 2 man/occurrences_s3.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/fbb4c6da784e33856e8ded356d3f871a |only tests/testthat/test-fields.R | 2 tests/testthat/test-images.R | 20 -- tests/testthat/test-intersect.R | 11 - tests/testthat/test-occurrences.R | 15 +- tests/testthat/test-sites_by_species.R | 4 tests/testthat/test-specieslist.R | 6 tests/testthat/test-taxinfo.R | 3 tests/testthat/test-utilities.R | 22 +-- vignettes/ALA4R.Rmd | 9 + 29 files changed, 232 insertions(+), 215 deletions(-)
Title: Tools for Internationalization and Portability in R Packages
Description: Translating messages in R packages is managed using the po top-level directory and the 'gettext' program. This package provides some helper functions for building this support in R packages, e.g. common validation & I/O tasks.
Author: Michael Chirico
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between potools versions 0.2.0 dated 2021-06-30 and 0.2.2 dated 2021-07-12
potools-0.2.0/potools/R/add_new_metadata.R |only potools-0.2.2/potools/DESCRIPTION | 8 potools-0.2.2/potools/MD5 | 72 + potools-0.2.2/potools/NAMESPACE | 10 potools-0.2.2/potools/NEWS.md |only potools-0.2.2/potools/R/get_r_messages.R | 33 potools-0.2.2/potools/R/get_src_messages.R | 119 ++- potools-0.2.2/potools/R/msgmerge.R | 14 potools-0.2.2/potools/R/onLoad.R | 4 potools-0.2.2/potools/R/read_translation.R | 2 potools-0.2.2/potools/R/translate_package.R | 38 - potools-0.2.2/potools/R/update_metadata.R |only potools-0.2.2/potools/R/utils.R | 62 + potools-0.2.2/potools/R/write_po_file.R | 364 +++++----- potools-0.2.2/potools/README.md | 43 + potools-0.2.2/potools/build/vignette.rds |binary potools-0.2.2/potools/inst/doc/custom-diagnostic.Rmd | 2 potools-0.2.2/potools/inst/doc/custom-diagnostic.html | 13 potools-0.2.2/potools/inst/extdata/language_metadata.csv | 2 potools-0.2.2/potools/man/check_potools_sys_reqs.Rd |only potools-0.2.2/potools/man/get_message_data.Rd | 17 potools-0.2.2/potools/man/translate_package.Rd | 30 potools-0.2.2/potools/man/write_po_file.Rd |only potools-0.2.2/potools/tests/testthat.R | 5 potools-0.2.2/potools/tests/testthat/helpers.R | 6 potools-0.2.2/potools/tests/testthat/mock_translations/test-translate-package-r_msg-2.input | 36 potools-0.2.2/potools/tests/testthat/mock_translations/test-translate-package-r_msg-5.input |only potools-0.2.2/potools/tests/testthat/mock_translations/test-translate-package-unusual_msg-1.input | 1 potools-0.2.2/potools/tests/testthat/test-diagnostics.R | 6 potools-0.2.2/potools/tests/testthat/test-get-message-data.R | 60 + potools-0.2.2/potools/tests/testthat/test-translate-package.R | 87 +- potools-0.2.2/potools/tests/testthat/test-write-po-file.R |only potools-0.2.2/potools/tests/testthat/test_packages/r-devel/src/main/msg.c | 5 potools-0.2.2/potools/tests/testthat/test_packages/r_err_1 |only potools-0.2.2/potools/tests/testthat/test_packages/r_err_2 |only potools-0.2.2/potools/tests/testthat/test_packages/r_msg/R/foo.R | 13 potools-0.2.2/potools/tests/testthat/test_packages/r_src_c/src/bar.c | 9 potools-0.2.2/potools/tests/testthat/test_packages/unusual_msg/src/z.c |only potools-0.2.2/potools/tests/testthat/testthat-problems.rds |binary potools-0.2.2/potools/vignettes/custom-diagnostic.Rmd | 2 40 files changed, 689 insertions(+), 374 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.0.3 dated 2021-06-25 and 1.0.4 dated 2021-07-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 9 +++++++-- R/coxme.R | 2 +- R/forestcox.R | 23 ++++++++++------------- inst/doc/jstable.html | 28 ++++++++++++++-------------- 7 files changed, 43 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-24 1.2.0
2021-05-13 1.1.8
2021-03-05 1.1.1
2021-01-24 1.0.24
2021-01-13 1.0.23
2020-11-23 1.0.17
2020-11-18 1.0.16
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-05 0.1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-28 0.0.2
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] (<https://orcid.org/0000-0001-5231-5184>)
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.4.4 dated 2021-06-01 and 4.4.5 dated 2021-07-12
DESCRIPTION | 13 ++-- MD5 | 40 +++++++------- NAMESPACE | 30 +++++------ NEWS | 16 +++++ R/as.data.frame.R | 4 + R/confint.secr.R | 8 +- R/extractMoves.R |only R/fastsecrloglik.R | 12 ++-- R/generalsecrloglik.R | 50 ++++++++++-------- R/homerange.R | 66 +++++++++++++++++++++++- R/ip.secr.R | 5 - R/par.secr.fit.R | 3 - R/preparedata.R | 20 +++++-- R/reparameterize.R | 12 +++- R/score.test.R | 4 - R/secr.fit.R | 118 ++++++++++++++++++++++++-------------------- R/sim.popn.R | 58 ++++++++++++--------- R/utility.R | 1 inst/doc/secr-datainput.pdf |binary inst/doc/secr-overview.pdf |binary man/extractMoves.Rd |only man/secr-package.Rd | 4 - 22 files changed, 293 insertions(+), 171 deletions(-)
Title: Bindings for Bayesian TidyModels
Description: Fit Bayesian models using 'brms'/'Stan' with 'parsnip'/'tidymodels'
via 'bayesian' <doi:10.5281/zenodo.5091194>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'brms' and 'Stan' are described in Bürkner (2017)
<doi:10.18637/jss.v080.i01>, Bürkner (2018) <doi:10.32614/RJ-2018-017>,
and Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Hamada S. Badr [aut, cre] (<https://orcid.org/0000-0002-9808-2344>),
Paul-Christian Bürkner [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between bayesian versions 0.0.5 dated 2021-05-31 and 0.0.6 dated 2021-07-12
DESCRIPTION | 10 +- MD5 | 28 +++--- NEWS.md | 6 + R/bayesian.R | 11 +- R/bayesian_make.R | 181 +++++++++++++++++++++++++---------------- README.md | 4 inst/CITATION | 6 - inst/WORDLIST | 3 inst/doc/BugReports.html | 4 inst/doc/GetStarted.R | 12 ++ inst/doc/GetStarted.Rmd | 15 +++ inst/doc/GetStarted.html | 45 +++++++--- man/bayesian.Rd | 9 +- tests/testthat/test-bayesian.R | 3 vignettes/GetStarted.Rmd | 15 +++ 15 files changed, 235 insertions(+), 117 deletions(-)
Title: Bindings for Generalized Additive Models (GAM)
Description: Fit Generalized Additive Models (GAM) using 'mgcv' with 'parsnip'/'tidymodels'
via 'additive' <doi:10.5281/zenodo.5091179>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'mgcv' are described in Wood (2017)
<doi:10.1201/9781315370279>.
Author: Hamada S. Badr [aut, cre] (<https://orcid.org/0000-0002-9808-2344>)
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between additive versions 0.0.1 dated 2021-06-01 and 0.0.2 dated 2021-07-12
DESCRIPTION | 10 +- MD5 | 32 ++++----- NAMESPACE | 3 NEWS.md | 7 + R/additive.R | 12 ++- R/additive_init.R | 4 - R/additive_make.R | 145 +++++++++++++++++++++++++++++++++++++++-- README.md | 4 - inst/CITATION | 14 +-- inst/WORDLIST | 3 inst/doc/BugReports.html | 4 - inst/doc/GetStarted.R | 14 +++ inst/doc/GetStarted.Rmd | 19 ++++- inst/doc/GetStarted.html | 41 ++++++++--- man/additive.Rd | 13 ++- tests/testthat/test-additive.R | 6 + vignettes/GetStarted.Rmd | 19 ++++- 17 files changed, 281 insertions(+), 69 deletions(-)