Fri, 15 Jul 2022

Package BNPmix updated to version 1.0.2 with previous version 1.0.1 dated 2022-07-08

Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data. See Corradin et al. (2021) <doi:10.18637/jss.v100.i15> for more details.
Author: Riccardo Corradin [aut, cre], Antonio Canale [ctb], Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>

Diff between BNPmix versions 1.0.1 dated 2022-07-08 and 1.0.2 dated 2022-07-15

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Package mada updated to version 0.5.11 with previous version 0.5.10 dated 2020-05-25

Title: Meta-Analysis of Diagnostic Accuracy
Description: Provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutter & Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Holling et al. (2012) is also available. Standard methods like summary, plot and so on are provided.
Author: Philipp Doebler with contributions from Bernardo Sousa-Pinto
Maintainer: Philipp Doebler <philipp.doebler@googlemail.com>

Diff between mada versions 0.5.10 dated 2020-05-25 and 0.5.11 dated 2022-07-15

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Package BAMMtools updated to version 2.1.10 with previous version 2.1.9 dated 2022-04-23

Title: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>

Diff between BAMMtools versions 2.1.9 dated 2022-04-23 and 2.1.10 dated 2022-07-15

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New package text2sdg with initial version 0.1.4
Package: text2sdg
Version: 0.1.4
Date: 2022-07-13
Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications.
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>
URL: https://github.com/dwulff/text2sdg
BugReports: https://github.com/dwulff/text2sdg/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: magrittr, dplyr, corpustools (>= 0.4.2), tidyr, tibble, stringr, ggplot2
Suggests: testthat, knitr, rmarkdown
LazyData: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-13 11:50:09 UTC; dominik
Author: Dirk U. Wulff [aut] , Dominik S. Meier [aut, cre] , Rui Mata [ctb]
Repository: CRAN
Date/Publication: 2022-07-15 15:20:02 UTC

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New package multiocc with initial version 0.1.0
Package: multiocc
Title: Fits Multivariate Spatio-Temporal Occupancy Model
Version: 0.1.0
Depends: R (>= 4.1.0)
Description: Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.
License: GPL-2
Imports: MASS, truncnorm, tmvtnorm, fields, interp, MCMCpack, stats
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-14 15:05:11 UTC; erhardrj
Author: Staci Hepler [aut, cre], Rob Erhardt [aut]
Maintainer: Staci Hepler <heplersa@wfu.edu>
Repository: CRAN
Date/Publication: 2022-07-15 16:10:02 UTC

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Package isocalcR updated to version 0.1.0 with previous version 0.0.2 dated 2021-07-31

Title: Isotope Calculations in R
Description: Perform common calculations based on published stable isotope theory, such as calculating carbon isotope discrimination and intrinsic water use efficiency from wood or leaf carbon isotope composition. See Farquhar, O'Leary, and Berry (1982) <doi:10.1071/PP9820121>.
Author: Justin Mathias
Maintainer: Justin Mathias <justin.m.mathias@gmail.com>

Diff between isocalcR versions 0.0.2 dated 2021-07-31 and 0.1.0 dated 2022-07-15

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New package InteRD with initial version 0.1.0
Package: InteRD
Title: The Integrated and Robust Deconvolution
Version: 0.1.0
Description: We developed the Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors. Moreover, the proposed algorithm is robust to inaccurate external information imposed in the deconvolution system.
License: Artistic-2.0
Encoding: UTF-8
URL: https://github.com/chencxxy28/InteRD
BugReports: https://github.com/chencxxy28/InteRD/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: Rcpp (>= 0.11.0), L1pack, limSolve, cowplot, ggplot2, pheatmap, stats,DescTools, mgcv, reshape2, Biobase
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-07-13 23:46:21 UTC; chixiang.chen
Author: Chixiang Chen [cre, aut], Yuk Yee Leung [aut], Matei Lonita [aut], Li-San Wang [aut], Mingyao Li [aut]
Maintainer: Chixiang Chen <chencxxy@hotmail.com>
Repository: CRAN
Date/Publication: 2022-07-15 16:00:05 UTC

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New package ExposR with initial version 1.0
Package: ExposR
Title: Models Topographic Exposure to Hurricane Winds
Version: 1.0
Date: 2022-07-14
Description: The EXPOS model uses a digital elevation model (DEM) to estimate exposed and protected areas for a given hurricane wind direction and inflection angle. The resulting topographic exposure maps can be combined with output from the HURRECON model to estimate hurricane wind damage across a region. For details on the original version of the EXPOS model written in 'Borland Pascal', see: Boose, Foster, and Fluet (1994) <doi:10.2307/2937142>, Boose, Chamberlin, and Foster (2001) <doi:10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2>, and Boose, Serrano, and Foster (2004) <doi:10.1890/02-4057>.
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
Imports: graphics, grDevices, raster, rgdal, utils
Suggests: knitr, qpdf, testthat (>= 3.0.0), rmarkdown
URL: https://github.com/expos-model/ExposR
BugReports: https://github.com/expos-model/ExposR/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-14 12:23:51 UTC; erb709
Author: Emery Boose [aut, cre], President and Fellows of Harvard College [cph]
Maintainer: Emery Boose <boose@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-07-15 16:10:04 UTC

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New package cgaim with initial version 1.0.0
Package: cgaim
Title: Constrained Groupwise Additive Index Models
Version: 1.0.0
Description: Fits constrained groupwise additive index models and provides functions for inference and interpretation of these models. The method is described in Masselot, Chebana, Campagna, Lavigne, Ouarda, Gosselin (2022) "Constrained groupwise additive index models" <doi:10.1093/biostatistics/kxac023>.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 2.1.0)
Imports: graphics, stats, scam, scar, quadprog, osqp, limSolve, Matrix, grDevices, methods, MASS, cgam, mgcv, gratia, doParallel, coneproj, TruncatedNormal, foreach
NeedsCompilation: no
Packaged: 2022-07-13 20:59:06 UTC; PierreMasselot
Author: Pierre Masselot [aut, cre]
Maintainer: Pierre Masselot <pierre.masselot@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2022-07-15 15:50:02 UTC

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Package individual updated to version 0.1.9 with previous version 0.1.7 dated 2021-10-25

Title: Framework for Specifying and Simulating Individual Based Models
Description: A framework which provides users a set of useful primitive elements for specifying individual based simulation models, with special attention models for infectious disease epidemiology. Users build models by specifying variables for each characteristic of individuals in the simulated population by using data structures exposed by the package. The package provides efficient methods for finding subsets of individuals based on these variables, or cohorts. Cohorts can then be targeted for variable updates or scheduled for events. Variable updates queued during a time step are executed at the end of a discrete time step, and the code places no restrictions on how individuals are allowed to interact. These data structures are designed to provide an intuitive way for users to turn their conceptual model of a system into executable code, which is fast and memory efficient.
Author: Giovanni Charles [aut, cre] , Sean L. Wu [aut] , Peter Winskill [aut] , Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <giovanni.charles@gmail.com>

Diff between individual versions 0.1.7 dated 2021-10-25 and 0.1.9 dated 2022-07-15

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Package cvms updated to version 1.3.4 with previous version 1.3.3 dated 2021-11-14

Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models and get relevant evaluation metrics in a tidy format. Validate the best model on a test set and compare it to a baseline evaluation. Alternatively, evaluate predictions from an external model. Currently supports regression and classification (binary and multiclass). Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R., & Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre], Hugh Benjamin Zachariae [aut], Indrajeet Patil [ctb]
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>

Diff between cvms versions 1.3.3 dated 2021-11-14 and 1.3.4 dated 2022-07-15

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New package subniche with initial version 1.5
Package: subniche
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Version: 1.5
Date: 2022-07-14
BugReports: https://github.com/KarasiewiczStephane/WitOMI/issues
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays. For details see Karasiewicz et al. (2017) <doi:10.7717/Peerj.3364>.
Suggests: adegraphics, ape, CircStats, deldir, lattice, maptools, MASS, pixmap, spdep, splancs, waveslim
Depends: ade4, SIBER, polyclip, wordcloud
License: GPL (>= 2)
NeedsCompilation: no
LazyData: true
Packaged: 2022-07-15 09:49:56 UTC; frenc
Author: Stephane Karasiewicz [aut, cre]
Maintainer: Stephane Karasiewicz <skaraz.science@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-15 12:50:02 UTC

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Package phenology updated to version 7.8 with previous version 7.6 dated 2020-10-22

Title: Tools to Manage a Parametric Function that Describes Phenology and More
Description: Functions used to fit and test the phenology of species based on counts. Based on Girondot, M. (2010) <doi:10.3354/esr00292> for the phenology function, Girondot, M. (2017) <doi:10.1016/j.ecolind.2017.05.063> for the convolution of negative binomial, Girondot, M. and Rizzo, A. (2015) <doi:10.2993/etbi-35-02-337-353.1> for Bayesian estimate, Pfaller JB, ..., Girondot M (2019) <doi:10.1007/s00227-019-3545-x> for tag-loss estimate, Hancock J, ..., Girondot M (2019) <doi:10.1016/j.ecolmodel.2019.04.013> for nesting history, Laloe J-O, ..., Girondot M, Hays GC (2020) <doi:10.1007/s00227-020-03686-x> for aggregating several seasons.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@gmail.com>

Diff between phenology versions 7.6 dated 2020-10-22 and 7.8 dated 2022-07-15

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 R/plot.ECFOCF.R              |  344 +++++++++++++++++++++-------------
 R/plot.IP.R                  |   32 ++-
 R/plot.TableECFOCF.R         |    8 
 R/plot.Tagloss.R             |  230 +++++++++++++---------
 R/plot.TaglossData.R         |    7 
 R/plot.fitRMU.R              |   60 ++++-
 R/plot.phenology.R           |   26 +-
 R/print.phenology.R          |    9 
 R/summary.phenology.R        |  182 ++++++++++++++---
 R/toggle_Min_PMin.R          |    2 
 inst/shiny/server.R          |    2 
 man/Bayesian.remigration.Rd  |    6 
 man/CI.RMU.Rd                |   15 +
 man/ECFOCF_f.Rd              |   13 -
 man/ECFOCF_full.Rd           |only
 man/ExponentialRegression.Rd |only
 man/IPFit.Rd                 |    6 
 man/IPModel.Rd               |    2 
 man/Parameter_Global_Year.Rd |    5 
 man/TableECFOCF.Rd           |    4 
 man/Tagloss_L.Rd             |   22 +-
 man/Tagloss_LengthObs.Rd     |    3 
 man/Tagloss_cumul.Rd         |   13 -
 man/Tagloss_daymax.Rd        |    3 
 man/Tagloss_fit.Rd           |   30 +-
 man/Tagloss_format.Rd        |   24 ++
 man/Tagloss_mcmc.Rd          |   18 +
 man/Tagloss_mcmc_p.Rd        |only
 man/Tagloss_model.Rd         |   45 +++-
 man/Tagloss_simulate.Rd      |    3 
 man/adapt_parameters.Rd      |    2 
 man/add_phenology.Rd         |   11 -
 man/figures                  |only
 man/fitCF.Rd                 |   51 +++--
 man/fitCF_MHmcmc.Rd          |only
 man/fitCF_MHmcmc_p.Rd        |only
 man/fitRMU.Rd                |   32 ++-
 man/fitRMU_MHmcmc.Rd         |    4 
 man/fitRMU_MHmcmc_p.Rd       |    9 
 man/fit_phenology.Rd         |   44 +++-
 man/generateCF.Rd            |only
 man/likelihood_phenology.Rd  |   11 -
 man/lnLCF.Rd                 |    6 
 man/logLik.ECFOCF.Rd         |    6 
 man/logLik.Tagloss.Rd        |    1 
 man/map_phenology.Rd         |    2 
 man/o_4p_p1p2.Rd             |    1 
 man/phenology-package.Rd     |   26 +-
 man/phenology_MHmcmc.Rd      |   10 
 man/phenology_MHmcmc_p.Rd    |    2 
 man/plot.ECFOCF.Rd           |   26 ++
 man/plot.IP.Rd               |    5 
 man/plot.TableECFOCF.Rd      |    4 
 man/plot.Tagloss.Rd          |   38 +++
 man/plot.TaglossData.Rd      |    3 
 man/plot.fitRMU.Rd           |   29 ++
 man/plot.phenology.Rd        |   19 -
 man/print.phenology.Rd       |    9 
 man/summary.phenology.Rd     |   15 -
 man/toggle_Min_PMin.Rd       |    2 
 109 files changed, 2764 insertions(+), 1650 deletions(-)

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Package LKT updated to version 1.2.0 with previous version 1.1.0 dated 2022-02-21

Title: Logistic Knowledge Tracing
Description: Computes Logistic Knowledge Tracing ('LKT') which is a general method for tracking human learning in an educational software system. Please see Pavlik, Eglington, and Harrel-Williams (2021) <https://ieeexplore.ieee.org/document/9616435>. 'LKT' is a method to compute features of student data that are used as predictors of subsequent performance. 'LKT' allows great flexibility in the choice of predictive components and features computed for these predictive components. The system is built on top of 'LiblineaR', which enables extremely fast solutions compared to base glm() in R.
Author: Philip I. Pavlik Jr. [aut, ctb, cre] , Luke G. Eglington [aut, ctb]
Maintainer: Philip I. Pavlik Jr. <imrryr@gmail.com>

Diff between LKT versions 1.1.0 dated 2022-02-21 and 1.2.0 dated 2022-07-15

 DESCRIPTION                      |   17 -
 MD5                              |   33 ++-
 NAMESPACE                        |   65 +++---
 NEWS.md                          |   10 -
 R/LKTfunctions.R                 |  377 +++++++++++++++++++++------------------
 R/data.R                         |   10 +
 README.md                        |  295 ------------------------------
 build/vignette.rds               |binary
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 inst/doc/Basic_Operations.html   |   11 -
 inst/doc/Examples.Rmd            |only
 inst/doc/Examples.html           |only
 man/LKT.Rd                       |   34 ++-
 man/LKT_HDI.Rd                   |only
 man/ViewExcel.Rd                 |only
 man/largerawsample.Rd            |only
 vignettes/Basic_Operations.Rmd   |    4 
 vignettes/Examples.Rmd           |only
 vignettes/Examples.Rmd.orig      |only
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 vignettes/unnamed-chunk-14-2.png |only
 vignettes/unnamed-chunk-14-3.png |only
 23 files changed, 335 insertions(+), 525 deletions(-)

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Package accept updated to version 0.9.1 with previous version 0.9.0 dated 2022-03-22

Title: The Acute COPD Exacerbation Prediction Tool (ACCEPT)
Description: Allows clinicians to predict the rate and severity of future acute exacerbation in Chronic Obstructive Pulmonary Disease (COPD) patients, based on the clinical prediction model published in Adibi et al. (2020) <doi:10.1016/S2213-2600(19)30397-2>.
Author: Amin Adibi [aut, cre], Mohsen Sadatsafavi [aut, cph], Abdollah Safari [aut], Ainsleigh Hill [aut]
Maintainer: Amin Adibi <adibi@alumni.ubc.ca>

Diff between accept versions 0.9.0 dated 2022-03-22 and 0.9.1 dated 2022-07-15

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 NEWS.md     |    7 +++++++
 R/predict.R |   16 ++++++++++++++++
 4 files changed, 30 insertions(+), 7 deletions(-)

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Package dataPreparation updated to version 1.0.5 with previous version 1.0.4 dated 2021-12-21

Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of 'data.table' efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>

Diff between dataPreparation versions 1.0.4 dated 2021-12-21 and 1.0.5 dated 2022-07-15

 DESCRIPTION                                |    8 ++--
 MD5                                        |   23 +++++++------
 NAMESPACE                                  |    3 +
 NEWS                                       |    7 ++++
 NEWS.md                                    |    7 ++++
 R/factor_manipulation.R                    |   23 +++++++++++++
 R/generate_from_factor.R                   |   49 +++++++++++++++++++++++++++--
 R/generic_functions.R                      |    2 -
 man/build_target_encoding.Rd               |    3 +
 man/compute_probability_ratio.Rd           |only
 man/compute_weight_of_evidence.Rd          |only
 man/get_most_frequent_element.Rd           |only
 tests/testthat/test_factor_manipulation.R  |   13 +++++++
 tests/testthat/test_generate_from_factor.R |   22 +++++++++++++
 14 files changed, 141 insertions(+), 19 deletions(-)

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New package tlars with initial version 0.0.1
Package: tlars
Title: The T-LARS Algorithm: Early-Terminated Forward Variable Selection
Version: 0.0.1
Date: 2022-07-11
Description: Computes the solution path of the Terminating-LARS (T-LARS) algorithm. The T-LARS algorithm is a major building block of the T-Rex selector (see R package 'trex'). The package is based on the papers Machkour, Muma, and Palomar (2021) <arXiv:2110.06048>, Efron, Hastie, Johnstone, and Tibshirani (2004) <doi:10.1214/009053604000000067>, and Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>.
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
URL: https://github.com/jasinmachkour/tlars, https://arxiv.org/abs/2110.06048
BugReports: https://github.com/jasinmachkour/tlars/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, ggplot2, patchwork, testthat (>= 3.0.0)
Imports: Rcpp, methods, stats, graphics
Depends: R (>= 2.10)
LinkingTo: RcppArmadillo, Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-07-11 17:53:53 UTC; phd
Author: Jasin Machkour [aut, cre], Simon Tien [aut], Daniel P. Palomar [aut], Michael Muma [aut]
Repository: CRAN
Date/Publication: 2022-07-15 08:40:02 UTC

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New package dots with initial version 0.0.2
Package: dots
Title: Dot Density Maps
Version: 0.0.2
Description: Generate point data for representing people within spatial data. This collects a suite of tools for creating simple dot density maps. Several functions from different spatial packages are standardized to take the same arguments so that they can be easily substituted for each other.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, magrittr, rlang, rmapshaper, sf, terra, purrr, dplyr, sp
URL: https://github.com/christopherkenny/dots, http://christophertkenny.com/dots/
BugReports: https://github.com/christopherkenny/dots/issues
Depends: R (>= 4.1)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), wacolors
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-11 16:33:36 UTC; chris
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-07-15 08:40:07 UTC

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Package rsat (with last version 0.1.18) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-03-02 0.1.18

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Package N2H4 updated to version 0.6.5 with previous version 0.6.3 dated 2022-05-10

Title: Handling Methods for Naver News Text Crawling
Description: Provides some functions to get Korean text sample from news articles in Naver which is popular news portal service <https://news.naver.com/> in Korea.
Author: Chanyub Park [aut, cre]
Maintainer: Chanyub Park <mrchypark@gmail.com>

Diff between N2H4 versions 0.6.3 dated 2022-05-10 and 0.6.5 dated 2022-07-15

 DESCRIPTION                   |   10 
 MD5                           |   24 +-
 NAMESPACE                     |    1 
 R/getComment.R                |   10 
 R/getContent.R                |  484 +++++++++++++++++++++---------------------
 R/getLike.R                   |   72 +++---
 R/getMainCategory.R           |   84 +++----
 R/getMaxPageNum.R             |    3 
 R/getSubCategory.R            |  104 ++++-----
 R/getUrlList.R                |  104 ++++-----
 R/setUrls.R                   |  204 ++++++++---------
 man/getContentEditDatetime.Rd |   62 ++---
 tests/testthat/test-func.R    |  116 +++++-----
 13 files changed, 643 insertions(+), 635 deletions(-)

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Package PRSPGx (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-06-16 0.2.0
2021-12-15 0.1.0

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