Mon, 16 Nov 2020

Package tipr updated to version 0.2.0 with previous version 0.1.1 dated 2017-11-28

Title: Tipping Point Analyses
Description: The strength of evidence provided by epidemiological and observational studies is inherently limited by the potential for unmeasured confounding. We focus on three key quantities: the observed bound of the confidence interval closest to the null, a plausible residual effect size for an unmeasured continuous or binary confounder, and a realistic mean difference or prevalence difference for this hypothetical confounder. Building on the methods put forth by Lin, Psaty, & Kronmal (1998) DOI:10.2307/2533848, we can use these quantities to assess how an unmeasured confounder may tip our result to insignificance, rendering the study inconclusive.
Author: Lucy D'Agostino McGowan
Maintainer: Lucy D'Agostino McGowan <lucydagostino@gmail.com>

Diff between tipr versions 0.1.1 dated 2017-11-28 and 0.2.0 dated 2020-11-16

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 tipr-0.2.0/tipr/MD5                               |   24 +-
 tipr-0.2.0/tipr/NAMESPACE                         |    1 
 tipr-0.2.0/tipr/NEWS.md                           |    6 
 tipr-0.2.0/tipr/R/tip-helpers.R                   |  168 ++++++++++----
 tipr-0.2.0/tipr/R/tip.R                           |  254 +++++++++++++++++-----
 tipr-0.2.0/tipr/R/tipr-package.R                  |   20 +
 tipr-0.2.0/tipr/R/utils.R                         |   25 ++
 tipr-0.2.0/tipr/README.md                         |  166 +++++++++++---
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 tipr-0.2.0/tipr/man/tipr.Rd                       |   16 +
 tipr-0.2.0/tipr/tests/testthat/test-tip-helpers.R |   61 +++--
 14 files changed, 631 insertions(+), 200 deletions(-)

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Package sysfonts updated to version 0.8.2 with previous version 0.8.1 dated 2020-05-08

Title: Loading Fonts into R
Description: Loading system fonts and Google Fonts <https://fonts.google.com/> into R, in order to support other packages such as 'R2SWF' and 'showtext'.
Author: Yixuan Qiu and authors/contributors of the included fonts. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

Diff between sysfonts versions 0.8.1 dated 2020-05-08 and 0.8.2 dated 2020-11-16

 DESCRIPTION             |   10 +++++-----
 MD5                     |    8 ++++----
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 5 files changed, 22 insertions(+), 15 deletions(-)

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Package RcppArmadillo updated to version 0.10.1.2.0 with previous version 0.10.1.0.0 dated 2020-10-20

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed under Apache License 2; previous releases were under licensed as MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that; 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that Armadillo requires a fairly recent compiler; for the g++ family at least version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.10.1.0.0 dated 2020-10-20 and 0.10.1.2.0 dated 2020-11-16

 ChangeLog                                       |   35 ++
 DESCRIPTION                                     |   10 
 MD5                                             |   54 +--
 R/RcppExports.R                                 |    9 
 build/vignette.rds                              |binary
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 inst/doc/RcppArmadillo-intro.pdf                |binary
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 inst/include/armadillo_bits/field_meat.hpp      |   57 ++-
 inst/include/armadillo_bits/fn_eigs_gen.hpp     |  263 ---------------
 inst/include/armadillo_bits/fn_eigs_sym.hpp     |  114 ------
 inst/include/armadillo_bits/sp_auxlib_bones.hpp |   80 ----
 inst/include/armadillo_bits/sp_auxlib_meat.hpp  |  404 ++----------------------
 inst/tinytest/test_sparseConversion.R           |    5 
 src/RcppArmadillo.cpp                           |   62 +--
 src/RcppExports.cpp                             |    2 
 28 files changed, 377 insertions(+), 1060 deletions(-)

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Package powdR updated to version 1.2.4 with previous version 1.2.3 dated 2020-10-15

Title: Full Pattern Summation of X-Ray Powder Diffraction Data
Description: Full pattern summation of X-ray powder diffraction data as described in Chipera and Bish (2002) <doi:10.1107/S0021889802017405>. Derives quantitative estimates of crystalline and amorphous phase concentrations in complex mixtures.
Author: Benjamin Butler [aut, cre], Stephen Hillier [aut], Dylan Beaudette [ctb], Dennis Eberl [ctb]
Maintainer: Benjamin Butler <benjamin.butler@hutton.ac.uk>

Diff between powdR versions 1.2.3 dated 2020-10-15 and 1.2.4 dated 2020-11-16

 DESCRIPTION                  |    8 ++--
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 13 files changed, 224 insertions(+), 66 deletions(-)

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Package PivotalR updated to version 0.1.18.4 with previous version 0.1.18.3.1 dated 2019-01-05

Title: A Fast, Easy-to-Use Tool for Manipulating Tables in Databases and a Wrapper of MADlib
Description: Provides an R interface for the 'VMware Data Stack' running on 'PostgreSQL' or 'Greenplum' databases with parallel and distributed computation ability for big data processing. 'PivotalR' provides an R interface to various database operations on tables or views. These operations are almost the same as the corresponding native R operations. Thus users of R do not need to learn 'SQL' when they operate on objects in the database. It also provides a wrapper for 'Apache MADlib', which is an open-source library for parallel and scalable in-database analytics.
Author: Predictive Analytics Team at VMware. <user@madlb.apache.org>
Maintainer: Orhan Kislal <okislal@vmware.com>

Diff between PivotalR versions 0.1.18.3.1 dated 2019-01-05 and 0.1.18.4 dated 2020-11-16

 DESCRIPTION                      |   36 +++++++----------
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 NAMESPACE                        |    7 +--
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 41 files changed, 180 insertions(+), 243 deletions(-)

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Package rBiasCorrection updated to version 0.2.4 with previous version 0.2.3 dated 2020-09-23

Title: Correct Bias in DNA Methylation Analyses
Description: Implementation of the algorithms (with minor modifications) to correct bias in quantitative DNA methylation analyses as described by Moskalev et al. (2011) <doi:10.1093/nar/gkr213>.
Author: Lorenz A. Kapsner [cre, aut, cph] (<https://orcid.org/0000-0003-1866-860X>), Evgeny A. Moskalev [aut]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>

Diff between rBiasCorrection versions 0.2.3 dated 2020-09-23 and 0.2.4 dated 2020-11-16

 DESCRIPTION                                |    6 
 MD5                                        |   14 -
 R/createbarerrorplots.R                    |  261 ++++++++++++++---------------
 R/plotting_utility.R                       |  126 +++++++-------
 R/regression_utility.R                     |   53 +++--
 R/utils.R                                  |   24 +-
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 8 files changed, 269 insertions(+), 245 deletions(-)

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Package Peptides updated to version 2.4.3 with previous version 2.4.2 dated 2020-05-10

Title: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
Description: Includes functions to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), Paola Rondon-Villarreal [aut, ths] (<https://orcid.org/0000-0001-8209-3885>), Rodrigo Torres [aut, ths] (<https://orcid.org/0000-0003-1113-3020>), J. Sebastian Paez [ctb] (<https://orcid.org/0000-0002-0065-1474>), Luis Pedro Coelho [ctb] (<https://orcid.org/0000-0002-9280-7885>), Richèl J.C. Bilderbeek [ctb] (<https://orcid.org/0000-0003-1107-7049>), Florian C. Sigloch [ctb] (<https://orcid.org/0000-0001-8130-6885>)
Maintainer: Daniel Osorio <dcosorioh@tamu.edu>

Diff between Peptides versions 2.4.2 dated 2020-05-10 and 2.4.3 dated 2020-11-16

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 33 files changed, 129 insertions(+), 94 deletions(-)

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Package LNIRT updated to version 0.5.0 with previous version 0.4.0 dated 2019-03-31

Title: LogNormal Response Time Item Response Theory Models
Description: Allows the simultaneous analysis of responses and response times in an Item Response Theory (IRT) modelling framework. Supports variable person speed functions (intercept, trend, quadratic), and covariates for item and person (random) parameters. Data missing-by-design can be specified. Parameter estimation is done with a MCMC algorithm. LNIRT replaces the package CIRT, which was written by Rinke Klein Entink. For reference, see the paper by Fox, Klein Entink and Van der Linden (2007), "Modeling of Responses and Response Times with the Package cirt", Journal of Statistical Software, <doi:10.18637/jss.v020.i07>.
Author: Jean-Paul Fox, Konrad Klotzke, Rinke Klein Entink
Maintainer: Konrad Klotzke <omd.bms.utwente.stats@gmail.com>

Diff between LNIRT versions 0.4.0 dated 2019-03-31 and 0.5.0 dated 2020-11-16

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 31 files changed, 8198 insertions(+), 5260 deletions(-)

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New package PubMedMining with initial version 1.0.0
Package: PubMedMining
Title: Text-Mining of the 'PubMed' Repository
Version: 1.0.0
Authors@R: person(given = "Jeff", family = "DIDIER", role = c("aut", "cre"), email = "jeff.didier.001@student.uni.lu")
Description: Easy function for text-mining the 'PubMed' repository based on defined sets of terms. The relationship between fix-terms (related to your research topic) and pub-terms (terms which pivot around your research focus) is calculated using the pointwise mutual information algorithm ('PMI'). Church, Kenneth Ward and Hanks, Patrick (1990) <https://www.aclweb.org/anthology/J90-1003/> A text file is generated with the 'PMI'-scores for each fix-term. Then for each collocation pairs (a fix-term + a pub-term), a text file is generated with related article titles and publishing years. Additional Author section will follow in the next version updates.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: easyPubMed, stringr, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-11-11 18:23:57 UTC; Master Jeff
Author: Jeff DIDIER [aut, cre]
Maintainer: Jeff DIDIER <jeff.didier.001@student.uni.lu>
Repository: CRAN
Date/Publication: 2020-11-16 16:20:02 UTC

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New package POV with initial version 0.1.4
Package: POV
Type: Package
Title: Partition of Variation Variance Component Analysis Method
Version: 0.1.4
Author: Paul Deen [aut, cre]
Maintainer: Paul Deen <paulext@gmail.com>
Description: An implementation of the Partition Of variation (POV) method as developed by Dr. Thomas A Little <https://thomasalittleconsulting.com> in 1993 for the analysis of semiconductor data for hard drive manufacturing. POV is based on sequential sum of squares and is an exact method that explains all observed variation. It quantitates both the between and within factor variation effects and can quantitate the influence of both continuous and categorical factors.
Authors@R: person("Paul", "Deen", email = "paulext@gmail.com", role = c("aut", "cre"))
URL: https://github.com/PaulAntonDeen/POV-R-Package, https://thomasalittleconsulting.com
BugReports: https://github.com/PaulAntonDeen/POV-R-Package/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, knitr, rmarkdown
Imports: broom, formula.tools, stats
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-11-11 18:03:20 UTC; pauldeen
Repository: CRAN
Date/Publication: 2020-11-16 16:20:05 UTC

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Package pec updated to version 2020.11.17 with previous version 2019.11.03 dated 2019-11-03

Title: Prediction Error Curves for Risk Prediction Models in Survival Analysis
Description: Validation of risk predictions obtained from survival models and competing risk models based on censored data using inverse weighting and cross-validation. Most of the 'pec' functionality has been moved to 'riskRegression'.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds <tag@biostat.ku.dk>

Diff between pec versions 2019.11.03 dated 2019-11-03 and 2020.11.17 dated 2020-11-16

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 37 files changed, 350 insertions(+), 146 deletions(-)

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New package mcbette with initial version 1.12
Package: mcbette
Title: Model Comparison Using 'babette'
Version: 1.12
Authors@R: c( person( "Richèl J.C.", "Bilderbeek", email = "richel@richelbilderbeek.nl", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1107-7049") ), person( "Joëlle", "Barido-Sottani", role = "rev", comment = c("Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/360") ), person( "Vikram", "Baliga", role = "rev", comment = c( "Vikram reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/360", ORCID = "0000-0002-9367-8974" ) ) )
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).
License: GPL-3
LazyData: true
RoxygenNote: 7.1.1
VignetteBuilder: knitr
URL: https://github.com/ropensci/mcbette/
BugReports: https://github.com/ropensci/mcbette/issues
Imports: babette (>= 2.1.5), beautier (>= 2.4), beastier (>= 2.2.1), curl, devtools, mauricer (>= 2.3), Rmpfr, testit, txtplot
Suggests: ape, ggplot2, hunspell, knitr, lintr, nLTT, phangorn, rappdirs, rmarkdown, spelling, stringr, testthat (>= 2.1.0), tracerer
Language: en-US
Encoding: UTF-8
SystemRequirements: BEAST2 (https://www.beast2.org/)
NeedsCompilation: no
Packaged: 2020-11-11 16:28:15 UTC; richel
Author: Richèl J.C. Bilderbeek [aut, cre] (<https://orcid.org/0000-0003-1107-7049>), Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/360), Vikram Baliga [rev] (Vikram reviewed the package for rOpenSci, see https://github.com/ropensci/software-review/issues/360, <https://orcid.org/0000-0002-9367-8974>)
Repository: CRAN
Date/Publication: 2020-11-16 16:10:02 UTC

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New package fredr with initial version 2.0.0
Package: fredr
Title: An R Client for the 'FRED' API
Version: 2.0.0
Authors@R: c(person(given = "Sam", family = "Boysel", role = c("aut", "cre"), email = "sboysel@gmail.com"), person(given = "Davis", family = "Vaughan", role = "aut", email = "davis@rstudio.com"))
Maintainer: Sam Boysel <sboysel@gmail.com>
Description: An R client for the 'Federal Reserve Economic Data' ('FRED') API <https://research.stlouisfed.org/docs/api/>. Functions to retrieve economic time series and other data from 'FRED'.
License: MIT + file LICENSE
URL: https://github.com/sboysel/fredr
BugReports: https://github.com/sboysel/fredr/issues
Depends: R (>= 3.2.2)
Imports: httr, jsonlite, rlang, tibble
Suggests: covr, dplyr, ggplot2, knitr, purrr, rmarkdown, testthat, xts, zoo
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-11-11 20:57:56 UTC; davis
Author: Sam Boysel [aut, cre], Davis Vaughan [aut]
Repository: CRAN
Date/Publication: 2020-11-16 16:30:06 UTC

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New package USP with initial version 0.1.1
Package: USP
Title: U-Statistic Permutation Tests of Independence for all Data Types
Version: 0.1.1
Author: Thomas B. Berrett <tom.berrett@warwick.ac.uk> [aut,cre], Ioannis Kontoyiannis <yiannis@maths.cam.ac.uk> [aut], Richard J. Samworth <r.samworth@statslab.cam.ac.uk> [aut]
Maintainer: Thomas B. Berrett <tom.berrett@warwick.ac.uk>
Description: Implements various independence tests for discrete, continuous, and infinite-dimensional data. The tests are based on a U-statistic permutation test, the USP of Berrett, Kontoyiannis and Samworth (2020) <arXiv:2001.05513>, and shown to be minimax rate optimal in a wide range of settings. As the permutation principle is used, all tests have exact, non-asymptotic Type I error control at the nominal level.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: stats, Rdpack
RdMacros: Rdpack
NeedsCompilation: no
Packaged: 2020-11-11 14:40:27 UTC; thomas
Repository: CRAN
Date/Publication: 2020-11-16 16:00:02 UTC

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Package rsyntax updated to version 0.1.1 with previous version 0.1.0 dated 2020-06-02

Title: Extract Semantic Relations from Text by Querying and Reshaping Syntax
Description: Various functions for querying and reshaping dependency trees, as for instance created with the 'spacyr' or 'udpipe' packages. This enables the automatic extraction of useful semantic relations from texts, such as quotes (who said what) and clauses (who did what). Method proposed in Van Atteveldt et al. (2017) <doi:10.1017/pan.2016.12>.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>

Diff between rsyntax versions 0.1.0 dated 2020-06-02 and 0.1.1 dated 2020-11-16

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New package NeuralSens with initial version 0.2.2
Package: NeuralSens
Version: 0.2.2
Title: Sensitivity Analysis of Neural Networks
Date: 2020-11-11
Description: Analysis functions to quantify inputs importance in neural network models. Functions are available for calculating and plotting the inputs importance and obtaining the activation function of each neuron layer and its derivatives. The importance of a given input is defined as the distribution of the derivatives of the output with respect to that input in each training data point.
Author: José Portela González [aut], Antonio Muñoz San Roque [aut], Jaime Pizarroso Gonzalo [aut, ctb, cre]
Maintainer: Jaime Pizarroso Gonzalo <jpizarroso@comillas.edu>
Imports: ggplot2, gridExtra, NeuralNetTools, reshape2, caret, fastDummies, stringr, Hmisc, ggforce, scales, ggnewscale
Suggests: h2o, neural, RSNNS, nnet, neuralnet, e1071
RoxygenNote: 7.1.1
NeedsCompilation: no
URL: https://github.com/JaiPizGon/NeuralSens
BugReports: https://github.com/JaiPizGon/NeuralSens/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Authors@R: c( person(given = "José", family = "Portela González", email = "Jose.Portela@iit.comillas.edu", role = "aut"), person(given = "Antonio", family = "Muñoz San Roque", email = "antonio.munoz@iit.comillas.edu", role = "aut"), person(given = "Jaime", family = "Pizarroso Gonzalo", email = "jpizarroso@comillas.edu", role = c("aut","ctb", "cre")) )
Packaged: 2020-11-11 14:49:17 UTC; Jaime
Repository: CRAN
Date/Publication: 2020-11-16 16:00:05 UTC

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Package jtools updated to version 2.1.1 with previous version 2.1.0 dated 2020-06-23

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written for the purpose of more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Just about everything supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <jacob.long@sc.edu>

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Package cNORM updated to version 1.2.4 with previous version 1.2.3 dated 2020-06-18

Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low confidence for assessing extreme scores. The continuous norming method introduced by A. Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>) and generates continuous test norm scores on the basis of the raw data from standardization samples, without requiring assumptions about the distribution of the raw data: Norm scores are directly established from raw data by modeling the latter ones as a function of both percentile scores and an explanatory variable (e.g., age). The method minimizes bias arising from sampling and measurement error, while handling marked deviations from normality, addressing bottom or ceiling effects and capturing almost all of the variance in the original norm data sample. An online demonstration is available via <https://cnorm.shinyapps.io/cNORM/>.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>), Alexandra Lenhard [aut], Sebastian Gary [aut]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>

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Package soundcorrs updated to version 0.4.0 with previous version 0.3.0 dated 2020-09-18

Title: Semi-Automatic Analysis of Sound Correspondences
Description: A set of tools that can be used in computer-aided analysis of sound correspondences between languages, plus several helper functions. Analytic functions range from purely qualitative analysis, through statistic methods yielding qualitative results, to an entirely quantitative approach.
Author: Kamil Stachowski [aut, cre]
Maintainer: Kamil Stachowski <kamil.stachowski@gmail.com>

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Package s2dv updated to version 0.1.1 with previous version 0.1.0 dated 2020-11-12

Title: A Set of Common Tools for Seasonal to Decadal Verification
Description: The advanced version of package 's2dverification'. It is intended for 'seasonal to decadal' (s2d) climate forecast verification, but it can also be used in other kinds of forecasts or general climate analysis. This package is specially designed for the comparison between the experimental and observational datasets. The functionality of the included functions covers from data retrieval, data post-processing, skill scores against observation, to visualization. Compared to 's2dverification', 's2dv' is more compatible with the package 'startR', able to use multiple cores for computation and handle multi-dimensional arrays with a higher flexibility.
Author: BSC-CNS [aut, cph], An-Chi Ho [aut, cre], Nuria Perez-Zanon [aut], Roberto Bilbao [ctb], Carlos Delgado [ctb], Andrea Manrique [ctb], Deborah Verfaillie [ctb]
Maintainer: An-Chi Ho <an.ho@bsc.es>

Diff between s2dv versions 0.1.0 dated 2020-11-12 and 0.1.1 dated 2020-11-16

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Package regmedint updated to version 0.2.0 with previous version 0.1.0 dated 2020-05-11

Title: Regression-Based Causal Mediation Analysis with an Interaction Term
Description: 'R' re-implementation of the regression-based causal mediation analysis with a treatment-mediator interaction term, as originally implemented in the 'SAS' macro by Valeri and VanderWeele (2013) <doi:10.1037/a0031034> and Valeri and VanderWeele (2015) <doi:10.1097/EDE.0000000000000253>. Linear and logistic models are supported for the mediator model. Linear, logistic, loglinear, Poisson, negative binomial, Cox, and accelerated failure time (exponential and Weibull) models are supported for the outcome model.
Author: Kazuki Yoshida [cre, aut] (<https://orcid.org/0000-0002-2030-3549>), Yi Li [ctb, aut] (<https://orcid.org/0000-0002-9359-210X>), Maya Mathur [ctb] (<https://orcid.org/0000-0001-6698-2607>)
Maintainer: Kazuki Yoshida <kazukiyoshida@mail.harvard.edu>

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 NEWS.md                                                                            |    7 
 R/00_package_information.R                                                         |    2 
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 man/fit_mreg.Rd                                                                    |    2 
 man/fit_yreg.Rd                                                                    |    2 
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 man/new_regmedint.Rd                                                               |    2 
 man/regmedint.Rd                                                                   |    7 
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 man/theta_hat.Rd                                                                   |    2 
 man/validate_args.Rd                                                               |    2 
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Package politeness updated to version 0.7.5 with previous version 0.7.0 dated 2020-10-18

Title: Detecting Politeness Features in Text
Description: Detecting markers of politeness in English natural language. This package allows researchers to easily visualize and quantify politeness between groups of documents. This package combines prior research on the linguistic markers of politeness. We thank the Spencer Foundation, the Hewlett Foundation, and Harvard's Institute for Quantitative Social Science for support.
Author: Mike Yeomans, Alejandro Kantor, Dustin Tingley
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>

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Package multiclassPairs updated to version 0.3.1 with previous version 0.3.0 dated 2020-11-10

Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>

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Package Luminescence updated to version 0.9.8 with previous version 0.9.7 dated 2020-01-08

Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence dating data analysis. This includes, amongst others, data import, export, application of age models, curve deconvolution, sequence analysis and plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc] (<https://orcid.org/0000-0002-0734-2199>), Christoph Burow [aut, trl, dtc] (<https://orcid.org/0000-0002-5023-4046>), Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>), Margret C. Fuchs [aut], Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>), Manfred Fischer [aut, trl], Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>), Norbert Mercier [ctb] (<https://orcid.org/0000-0002-6375-9108>), Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>), Claire Christophe [ctb], Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>), Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>), Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>), Anne Philippe [ctb], Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>), Svenja Riedesel [aut] (<https://orcid.org/0000-0003-2936-8776>), Martin Autzen [aut] (<https://orcid.org/0000-0001-6249-426X>), Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>), Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@aber.ac.uk>

Diff between Luminescence versions 0.9.7 dated 2020-01-08 and 0.9.8 dated 2020-11-16

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 Luminescence-0.9.8/Luminescence/R/read_SPE2R.R                                       |   14 
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 Luminescence-0.9.8/Luminescence/man/names_RLum.Rd                                    |    4 
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 Luminescence-0.9.8/Luminescence/man/plot_DRCSummary.Rd                               |    4 
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 Luminescence-0.9.8/Luminescence/man/plot_FilterCombinations.Rd                       |   10 
 Luminescence-0.9.8/Luminescence/man/plot_GrowthCurve.Rd                              |    4 
 Luminescence-0.9.8/Luminescence/man/plot_Histogram.Rd                                |    4 
 Luminescence-0.9.8/Luminescence/man/plot_KDE.Rd                                      |    2 
 Luminescence-0.9.8/Luminescence/man/plot_NRt.Rd                                      |    4 
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 Luminescence-0.9.8/Luminescence/man/plot_RLum.Rd                                     |    4 
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 Luminescence-0.9.8/Luminescence/man/plot_Risoe.BINfileData.Rd                        |    4 
 Luminescence-0.9.8/Luminescence/man/plot_ViolinPlot.Rd                               |   15 
 Luminescence-0.9.8/Luminescence/man/read_BIN2R.Rd                                    |   27 
 Luminescence-0.9.8/Luminescence/man/read_Daybreak2R.Rd                               |    4 
 Luminescence-0.9.8/Luminescence/man/read_PSL2R.Rd                                    |    2 
 Luminescence-0.9.8/Luminescence/man/read_RF2R.Rd                                     |only
 Luminescence-0.9.8/Luminescence/man/read_SPE2R.Rd                                    |   14 
 Luminescence-0.9.8/Luminescence/man/read_XSYG2R.Rd                                   |   14 
 Luminescence-0.9.8/Luminescence/man/replicate_RLum.Rd                                |    4 
 Luminescence-0.9.8/Luminescence/man/report_RLum.Rd                                   |   25 
 Luminescence-0.9.8/Luminescence/man/sTeve.Rd                                         |    2 
 Luminescence-0.9.8/Luminescence/man/scale_GammaDose.Rd                               |   24 
 Luminescence-0.9.8/Luminescence/man/set_RLum.Rd                                      |    4 
 Luminescence-0.9.8/Luminescence/man/set_Risoe.BINfileData.Rd                         |    4 
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 Luminescence-0.9.8/Luminescence/man/structure_RLum.Rd                                |    4 
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 Luminescence-0.9.8/Luminescence/man/tune_Data.Rd                                     |    2 
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Package JointAI updated to version 1.0.1 with previous version 1.0.0 dated 2020-08-31

Title: Joint Analysis and Imputation of Incomplete Data
Description: Joint analysis and imputation of incomplete data in the Bayesian framework, using (generalized) linear (mixed) models and extensions there of, survival models, or joint models for longitudinal and survival data. Incomplete covariates, if present, are automatically imputed. The package performs some preprocessing of the data and creates a 'JAGS' model, which will then automatically be passed to 'JAGS' <http://mcmc-jags.sourceforge.net/> with the help of the package 'rjags'.
Author: Nicole S. Erler [aut, cre] (<https://orcid.org/0000-0002-9370-6832>)
Maintainer: Nicole S. Erler <n.erler@erasmusmc.nl>

Diff between JointAI versions 1.0.0 dated 2020-08-31 and 1.0.1 dated 2020-11-16

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New package fsn with initial version 0.1
Package: fsn
Type: Package
Title: Rosenthal's Fail Safe Number and Related Functions
Version: 0.1
URL:
Date: 2020-11-11
Authors@R: c(person("Michail", "Tsagris", role = c("aut", "cre"), email = "mtsagris@uoc.gr"), person("Constantinos", "Frangos", role = "aut", email = "kfragkos@outlook.com"), person("Christos", "Frangos", role = "ctb", email = "cfragos@teiath.gr"))
Author: Michail Tsagris [aut, cre], Constantinos Frangos [aut], Christos Frangos [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 3.6.0)
Imports: graphics, grDevices, Rfast, stats
Description: Estimation of Rosenthal's fail safe number including confidence intervals. The relevant papers are the following. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2014). "Publication Bias in Meta-Analysis: Confidence Intervals for Rosenthal's Fail-Safe Number". International Scholarly Research Notices, Volume 2014. <doi:10.1155/2014/825383>. Konstantinos C. Fragkos, Michail Tsagris and Christos C. Frangos (2017). "Exploring the distribution for the estimator of Rosenthal's fail-safe number of unpublished studies in meta-analysis". Communications in Statistics-Theory and Methods, 46(11):5672--5684. <doi:10.1080/03610926.2015.1109664>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2020-11-11 12:10:06 UTC; user
Repository: CRAN
Date/Publication: 2020-11-16 12:10:03 UTC

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Package doc2concrete updated to version 0.5.0 with previous version 0.4.6 dated 2020-06-19

Title: Measuring Concreteness in Natural Language
Description: Models for detecting concreteness in natural language. This package is built in support of Yeomans (2020) <doi:10.17605/OSF.IO/DYZN6>, which reviews linguistic models of concreteness in several domains. Here, we provide an implementation of the best-performing domain-general model (from Brysbaert et al., (2014) <doi:10.3758/s13428-013-0403-5>) as well as two pre-trained models for the feedback and plan-making domains.
Author: Mike Yeomans
Maintainer: Mike Yeomans <mk.yeomans@gmail.com>

Diff between doc2concrete versions 0.4.6 dated 2020-06-19 and 0.5.0 dated 2020-11-16

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New package ShinyQuickStarter with initial version 1.0.0
Package: ShinyQuickStarter
Type: Package
Title: Quick Setup for ShinyDashboard Apps
Version: 1.0.0
Authors@R: c(person("Leon", "Binder", email = "leon.binder@th-deg.de", role = c("cre", "aut")), person("Bernhard", "Bauer", email = "bernhard.bauer@th-deg.de", role = c("aut")), person("Michael", "Scholz", email = "michael.scholz@th-deg.de", role = c("aut")), person("Bernhard", "Daffner", email = "bernhard.daffner@th-deg.de", role = c("aut")), person("Jörg", "Bauer", email = "joerg.bauer@th-deg.de", role = c("aut")))
Maintainer: Leon Binder <leon.binder@th-deg.de>
Description: This RStudio addin enables faster creation of the project structure and design of ShinyDashboard apps. The graphical interface allows you to add certain code templates interactively. In addition to generating the basic project structure, the navigation in the app itself can also be defined or the app can be structured with modules.
License: GPL-3
Depends: R (>= 3.2.0)
Imports: shiny, shinyFiles, shinyWidgets, shinyalert, miniUI, colourpicker, grDevices, data.table, DT, dplyr, fs, readr, rlist, shinycssloaders, shinyjs, stringi, stringr, styler, utils, visNetwork
Encoding: UTF-8
StagedInstall: yes
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-11-11 10:36:26 UTC; Leon
Author: Leon Binder [cre, aut], Bernhard Bauer [aut], Michael Scholz [aut], Bernhard Daffner [aut], Jörg Bauer [aut]
Repository: CRAN
Date/Publication: 2020-11-16 10:10:02 UTC

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New package RCBR with initial version 0.5.9
Package: RCBR
Title: Random Coefficient Binary Response Estimation
Description: Nonparametric maximum likelihood estimation methods for random coefficient binary response models and some related functionality for sequential processing of hyperplane arrangements. See J. Gu and R. Koenker (2020) <DOI:10.1080/01621459.2020.1802284>.
Version: 0.5.9
Authors@R: c( person( "Roger", "Koenker", email= "rkoenker@uiuc.edu", role = c("aut", "cre")), person("Jiaying", "Gu", email = "jiaying.gu@utoronto.ca", role = "aut") )
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Depends: R (>= 2.10), Matrix
Suggests: knitr, digest
Imports: methods, Rmosek, REBayes, orthopolynom, Formula, mvtnorm
LazyData: TRUE
SystemRequirements: MOSEK (http://www.mosek.com) and MOSEK License for use of Rmosek,
License: GPL (>= 2)
URL: https://www.r-project.org
NeedsCompilation: no
Encoding: UTF-8
Author: Roger Koenker [aut, cre], Jiaying Gu [aut]
RoxygenNote: 7.1.1
Packaged: 2020-11-11 11:25:06 UTC; roger
Repository: CRAN
Date/Publication: 2020-11-16 10:10:05 UTC

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New package TreeDiagram with initial version 0.1.0
Package: TreeDiagram
Type: Package
Title: Tree Diagram
Version: 0.1.0
Author: Wen Tian (Wendy) Wang,Lloyd Elliott
Maintainer: Wen Tian (Wendy) Wang <wtwang@sfu.ca>
Date: 2020-11-09
Description: Visualizing cuts for either axis-align or non axis-align tree methods (e.g. decision tree, random tessellation process).
License: BSD_2_clause + file LICENCE
Encoding: UTF-8
Imports: ggplot2,ape,cowplot,tree,stringr,spatstat,utils,stats
Suggests: testthat
Packaged: 2020-11-10 01:57:21 UTC; wendywang
RoxygenNote: 7.1.1
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2020-11-16 09:10:10 UTC

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Package tidyxl updated to version 1.0.7 with previous version 1.0.6 dated 2020-05-09

Title: Read Untidy Excel Files
Description: Imports non-tabular from Excel files into R. Exposes cell content, position and formatting in a tidy structure for further manipulation. Tokenizes Excel formulas. Supports '.xlsx' and '.xlsm' via the embedded 'RapidXML' C++ library <http://rapidxml.sourceforge.net>. Does not support '.xlsb' or '.xls'.
Author: Duncan Garmonsway [aut, cre], Hadley Wickham [ctb] (Author of included readxl fragments), Jenny Bryan [ctb] (Author of included readxl fragments), RStudio [cph] (Copyright holder of included readxl fragments), Marcin Kalicinski [ctb, cph] (Author of included RapidXML code)
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>

Diff between tidyxl versions 1.0.6 dated 2020-05-09 and 1.0.7 dated 2020-11-16

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New package ML2Pvae with initial version 1.0.0
Package: ML2Pvae
Type: Package
Title: Variational Autoencoder Models for IRT Parameter Estimation
Version: 1.0.0
Authors@R: c( person("Geoffrey", "Converse", email = "converseg@gmail.com", role = c("aut", "cre", "cph")), person("Suely", "Oliveira", email = "suely-oliveira@uiowa.edu", role = c("ctb", "ths")), person("Mariana", "Curi", email = "mcuri@icmc.usp.br", role = c("ctb")) )
Maintainer: Geoffrey Converse <converseg@gmail.com>
Description: Based on the work of Curi, Converse, Hajewski, and Oliveira (2019) <doi:10.1109/IJCNN.2019.8852333>. This package provides easy-to-use functions which create a variational autoencoder (VAE) to be used for parameter estimation in Item Response Theory (IRT) - namely the Multidimensional Logistic 2-Parameter (ML2P) model. To use a neural network as such, nontrivial modifications to the architecture must be made, such as restricting the nonzero weights in the decoder according to some binary matrix Q. The functions in this package allow for straight-forward construction, training, and evaluation so that minimal knowledge of 'tensorflow' or 'keras' is required.
Note: The developer version of 'keras' should be used, rather than the CRAN version. The latter will cause tests to fail on an initial run, but work on subsequent tries. To avoid this, use devtools::install_github("rstudio/keras"). The user also must have an installation of 'Python 3'.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: keras (>= 2.3.0), reticulate (>= 1.0), tensorflow (>= 2.2.0), tfprobability (>= 0.11.0)
RoxygenNote: 7.1.1
Suggests: knitr, rmarkdown, testthat, R.rsp
VignetteBuilder: R.rsp
Depends: R (>= 3.6)
URL: https://converseg.github.io
SystemRequirements: TensorFlow (https://www.tensorflow.org), Keras (https://keras.io), TensorFlow Probability (https://www.tensorflow.org/probability)
Config/reticulate: list( packages = list( list(package = "keras", pip = TRUE), list(package = "tensorflow", pip = TRUE), list(package = "tensorflow-probability", pip = TRUE) ) )
NeedsCompilation: no
Packaged: 2020-11-10 16:37:02 UTC; gconverse
Author: Geoffrey Converse [aut, cre, cph], Suely Oliveira [ctb, ths], Mariana Curi [ctb]
Repository: CRAN
Date/Publication: 2020-11-16 09:10:12 UTC

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Package KMunicate updated to version 0.2.0 with previous version 0.1.0 dated 2020-09-03

Title: KMunicate-Style Kaplan–Meier Plots
Description: Produce Kaplan–Meier plots in the style recommended following the KMunicate study by Morris et al. (2019) <doi:10.1136/bmjopen-2019-030215>. The KMunicate style consists of Kaplan-Meier curves with confidence intervals to quantify uncertainty and an extended risk table (per treatment arm) depicting the number of study subjects at risk, events, and censored observations over time. The resulting plots are built using 'ggplot2' and can be further customised to a certain extent, including themes, fonts, and colour scales.
Author: Alessandro Gasparini [aut, cre, cph] (<https://orcid.org/0000-0002-8319-7624>), Ary Serpa Neto [ctb]
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>

Diff between KMunicate versions 0.1.0 dated 2020-09-03 and 0.2.0 dated 2020-11-16

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Package hutils updated to version 1.6.0 with previous version 1.5.1 dated 2019-10-05

Title: Miscellaneous R Functions and Aliases
Description: Provides utility functions for, and drawing on, the 'data.table' package. The package also collates useful miscellaneous functions extending base R not available elsewhere. The name is a portmanteau of 'utils' and the author.
Author: Hugh Parsonage [aut, cre], Michael Frasco [ctb], Ben Hamner [ctb]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>

Diff between hutils versions 1.5.1 dated 2019-10-05 and 1.6.0 dated 2020-11-16

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Package ggraph updated to version 2.0.4 with previous version 2.0.3 dated 2020-05-20

Title: An Implementation of Grammar of Graphics for Graphs and Networks
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.
Author: Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

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Package genpathmox updated to version 0.5 with previous version 0.4 dated 2020-05-11

Title: Generalized Pathmox Approach Segmentation Tree Analysis
Description: Provides a very interesting solution for handling segmentation variables in complex statistical methodology. It contains en extended version of the "Pathmox" algorithm (Lamberti, Sanchez and Aluja,(2016)<doi:10.1002/asmb.2168>) in the context of Partial Least Squares Path Modeling including the F-block test (to detect the responsible latent endogenous equations of the difference), the F-coefficient (to detect the path coefficients responsible of the difference) and the "invariance" test (to realize a comparison between the sub-models' latent variables). Furthermore, the package contains a generalized version of the "Pathmox" algorithm to approach different methodologies: linear regression and least absolute regression models.
Author: Giuseppe Lamberti [aut, cre]
Maintainer: Giuseppe Lamberti <giuseppelamb@hotmail.com>

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 R/30_fun_invariance_test.R    |   12 --
 R/43_fun_reg.pathmox.R        |    6 -
 R/print_print.xtree.pls.R     |    8 -
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 man/invariance_test.Rd        |   12 --
 man/pls.pathmox.Rd            |   86 ++++++++++-----
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 15 files changed, 277 insertions(+), 268 deletions(-)

More information about genpathmox at CRAN
Permanent link

New package geneExpressionFromGEO with initial version 0.2
Encoding: UTF-8
Package: geneExpressionFromGEO
Title: Retrieves Gene Expression Dataset from GEO Code and Platform ID
Version: 0.2
Authors@R: person("Davide", "Chicco", email = "davidechicco@davidechicco.it", role = c("aut", "cre"))
Description: A function that reads in the GEO code and the platform ID of a gene expression dataset, retrieves its data from GEO, (optional) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.
BugReports: https://stackoverflow.com/questions/tagged/geneExpressionFromGEO
Depends: R (>= 3.1.0)
License: GPL-3
LazyData: true
Imports: Biobase, annotate, GEOquery
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-11-10 20:31:47 UTC; davidechicco
Author: Davide Chicco [aut, cre]
Maintainer: Davide Chicco <davidechicco@davidechicco.it>
Repository: CRAN
Date/Publication: 2020-11-16 09:20:06 UTC

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New package dotgen with initial version 0.1.0
Package: dotgen
Title: Gene-Set Analysis via Decorrelation by Orthogonal Transformation
Version: 0.1.0
Date: 2020-11-03
Description: Decorrelates a set of summary statistics (i.e., Z-scores or P-values per SNP) via Decorrelation by Orthogonal Transformation (DOT) approach and performs gene-set analyses by combining transformed statistic values; operations are performed with algorithms that rely only on the association summary results and the linkage disequilibrium (LD). For more details on DOT and its power, see Olga (2020) <doi:10.1371/journal.pcbi.1007819>.
Authors@R: c( person("Olga", "Vsevolozhskaya", email = "ovs222@@g.uky.edu", role = "aut", comment = c(ORCID = "0000-0001-9376-3645")), person("Dmitri", "Zaykin", email = "zaykin@@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-9444-2859")), person("Xiaoran", "Tong", email = "tongxia1@msu.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4648-3330")))
Depends: R (>= 3.5.0), mvtnorm
License: GPL (>= 2)
URL: https://github.com/xiaoran831213/dotgen
Encoding: UTF-8
Author: Olga Vsevolozhskaya [aut] (<https://orcid.org/0000-0001-9376-3645>), Dmitri Zaykin [aut] (<https://orcid.org/0000-0002-9444-2859>), Xiaoran Tong [aut, cre] (<https://orcid.org/0000-0002-4648-3330>)
Maintainer: Xiaoran Tong <tongxia1@msu.edu>
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-11-11 05:21:17 UTC; xt
Repository: CRAN
Date/Publication: 2020-11-16 09:40:02 UTC

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Package ClustBlock updated to version 2.3.0 with previous version 2.2.1 dated 2020-10-02

Title: Clustering of Datasets
Description: Hierarchical and partitioning algorithms of blocks of variables. The partitioning algorithm includes an option called noise cluster to set aside atypical blocks of variables. The CLUSTATIS method (for quantitative blocks) (Llobell, Cariou, Vigneau, Labenne & Qannari (2020) <doi:10.1016/j.foodqual.2018.05.013>, Llobell, Vigneau & Qannari (2019) <doi:10.1016/j.foodqual.2019.02.017>) and the CLUSCATA method (for Check-All-That-Apply data) (Llobell, Cariou, Vigneau, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2018.09.006>, Llobell, Giacalone, Labenne & Qannari (2019) <doi:10.1016/j.foodqual.2019.05.017>) are the core of this package.
Author: Fabien Llobell [aut, cre] (Oniris/XLSTAT), Evelyne Vigneau [ctb] (Oniris), Veronique Cariou [ctb] (Oniris), El Mostafa Qannari [ctb] (Oniris)
Maintainer: Fabien Llobell <fllobell@hotmail.fr>

Diff between ClustBlock versions 2.2.1 dated 2020-10-02 and 2.3.0 dated 2020-11-16

 DESCRIPTION                      |    8 +++---
 MD5                              |   44 +++++++++++++++++-----------------
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 man/clustatis_FreeSort_kmeans.Rd |    4 +--
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 24 files changed, 158 insertions(+), 190 deletions(-)

More information about ClustBlock at CRAN
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Package trekcolors updated to version 0.1.2 with previous version 0.1.1 dated 2019-10-16

Title: Star Trek Color Palettes
Description: Provides a dataset of predefined color palettes based on the Star Trek science fiction series, associated color palette functions, and additional functions for generating customized palettes that are on theme. The package also offers functions for applying the palettes to plots made using the 'ggplot2' package.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

Diff between trekcolors versions 0.1.1 dated 2019-10-16 and 0.1.2 dated 2020-11-16

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More information about trekcolors at CRAN
Permanent link

Package TestDataImputation updated to version 1.2 with previous version 1.1 dated 2019-03-08

Title: Missing Item Responses Imputation for Test and Assessment Data
Description: Functions for imputing missing item responses for dichotomous and polytomous test and assessment data. This package enables missing imputation methods that are suitable for test and assessment data, including: listwise (LW) deletion (see De Ayala et al. 2001 <doi:10.1111/j.1745-3984.2001.tb01124.x>), treating as incorrect (IN, see Lord, 1974 <doi: 10.1111/j.1745-3984.1974.tb00996.x>; Mislevy & Wu, 1996 <doi: 10.1002/j.2333-8504.1996.tb01708.x>; Pohl et al., 2014 <doi: 10.1177/0013164413504926>), person mean imputation (PM), item mean imputation (IM), two-way imputation (TW, see Sijtsma & van der Ark, 2003 <doi: 10.1207/s15327906mbr3804_4>), logistic regression imputation (LR), and expectation–maximization (EM) imputation (see Finch, 2008 <doi: 10.1111/j.1745-3984.2008.00062.x>).
Author: Shenghai Dai [aut, cre], Xiaolin Wang [aut], Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>

Diff between TestDataImputation versions 1.1 dated 2019-03-08 and 1.2 dated 2020-11-16

 DESCRIPTION           |   22 +++++++-----
 MD5                   |   34 +++++++++---------
 NAMESPACE             |    7 ++-
 R/EMimpute.r          |   24 ++++++++-----
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 18 files changed, 290 insertions(+), 119 deletions(-)

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Permanent link

Package rtrek updated to version 0.3.2 with previous version 0.3.0 dated 2019-12-15

Title: Datasets and Functions Relating to Star Trek
Description: Provides datasets related to the Star Trek fictional universe and functions for working with the data. The package also provides access to real world datasets based on the televised series and other related licensed media productions. It interfaces with the Star Trek API (STAPI) (<http://stapi.co/>), Memory Alpha (<https://memory-alpha.fandom.com/wiki/Portal:Main>), and Memory Beta (<https://memory-beta.fandom.com/wiki/Main_Page>) to retrieve data, metadata and other information relating to Star Trek. It also contains several local datasets covering a variety of topics. The package also provides functions for working with data from other Star Trek-related R data packages containing larger datasets not stored in 'rtrek'.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

Diff between rtrek versions 0.3.0 dated 2019-12-15 and 0.3.2 dated 2020-11-16

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 tests/testthat/test-memory-alpha.R |    9 ++++
 tests/testthat/test-memory-beta.R  |   16 ++++++-
 31 files changed, 313 insertions(+), 229 deletions(-)

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Package prettifyAddins updated to version 2.0.3 with previous version 2.0.2 dated 2020-11-09

Title: 'RStudio' Addins to Prettify 'JavaScript', 'C++', 'Python', and More
Description: Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS', 'JavaScript', 'JSX', 'Markdown', 'C(++)', 'LaTeX', 'Python', 'Julia', 'XML', 'Java', 'JSON', 'Ruby', and to reindent 'C(++)', 'Fortran', 'Java', 'Julia', 'Python', 'SAS', 'Scala', 'Shell' and 'SQL'. Two kinds of addins are provided: 'Prettify' and 'Indent'. The 'Indent' addins only reindent the code, while the 'Prettify' addins also modify the code, e.g. trailing semi-colons are added to 'JavaScript' code when they are missing.
Author: Stéphane Laurent [aut, cre], James Long and contributors [ctb, cph] ('Prettier' library), Zeb Zhao [ctb, cph] ('indent.js' library), Marijn Haverbeke [ctb, cph] ('CodeMirror' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between prettifyAddins versions 2.0.2 dated 2020-11-09 and 2.0.3 dated 2020-11-16

 DESCRIPTION        |    6 +++---
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 6 files changed, 17 insertions(+), 12 deletions(-)

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Package inspector updated to version 1.0.2 with previous version 1.0.1 dated 2020-09-16

Title: Validation of Arguments and Objects in User-Defined Functions
Description: Utility functions that implement and automate common sets of validation tasks. These functions are particularly useful to validate inputs, intermediate objects and output values in user-defined functions, resulting in tidier and less verbose functions.
Author: Pedro Fonseca [aut, cre] (<https://orcid.org/0000-0002-5708-081X>), FCT [fnd]
Maintainer: Pedro Fonseca <pedro.teles.fonseca@phd.iseg.ulisboa.pt>

Diff between inspector versions 1.0.1 dated 2020-09-16 and 1.0.2 dated 2020-11-16

 DESCRIPTION              |   12 ++++++------
 MD5                      |   12 ++++++------
 NEWS.md                  |    6 +++++-
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 7 files changed, 39 insertions(+), 35 deletions(-)

More information about inspector at CRAN
Permanent link

New package googleway with initial version 2.7.3
Package: googleway
Type: Package
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Version: 2.7.3
Date: 2020-11-16
Authors@R: c( person("David", "Cooley", ,"dcooley@symbolix.com.au", role = c("aut", "cre")), person("Paulo", "Barcelos", role = "ctb", comment = "Author of c++ decode_pl"), person("Rstudio", role = "ctb", comment = "Functions written for the Leaflet pacakge") )
Description: Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 2.10.0)
Imports: jsonlite (>= 0.9.20), curl, htmlwidgets, htmltools, magrittr, shiny, jpeg, utils, jqr, viridisLite, scales, grDevices, googlePolylines (>= 0.7.1)
RoxygenNote: 7.1.1
BugReports: https://github.com/SymbolixAU/googleway/issues
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-11-16 02:39:53 UTC; dave
Author: David Cooley [aut, cre], Paulo Barcelos [ctb] (Author of c++ decode_pl), Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Repository: CRAN
Date/Publication: 2020-11-16 08:10:10 UTC

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New package GGMncv with initial version 2.0.0
Package: GGMncv
Type: Package
Title: Gaussian Graphical Models with Nonconvex Regularization
Version: 2.0.0
Date: 2020-11-15
Authors@R: person("Donald", "Williams", email = "drwwilliams@ucdavis.edu", role = c("aut", "cre"))
Description: Estimate Gaussian graphical models with nonconvex penalties <doi:10.31234/osf.io/ad57p>, including the atan Wang and Zhu (2016) <doi:10.1155/2016/6495417>, seamless L0 Dicker, Huang, and Lin (2013) <doi:10.5705/ss.2011.074>, exponential Wang, Fan, and Zhu <doi:10.1007/s10463-016-0588-3>, smooth integration of counting and absolute deviation Lv and Fan (2009) <doi:10.1214/09-AOS683>, logarithm Mazumder, Friedman, and Hastie (2011) <doi:10.1198/jasa.2011.tm09738>, Lq, smoothly clipped absolute deviation Fan and Li (2001) <doi:10.1198/016214501753382273>, and minimax concave penalty Zhang (2010) <doi:10.1214/09-AOS729>. There are also extensions for computing variable inclusion probabilities, multiple regression coefficients, and statistical inference <doi:10.1214/15-EJS1031>.
License: GPL-2
Depends: R (>= 4.0.0)
Imports: Rcpp (>= 1.0.4.6), Rdpack (>= 0.11-1), reshape, ggplot2 (>= 3.3.0), glassoFast (>= 1.0), numDeriv (>= 2016.8-1.1), mathjaxr (>= 1.0-1), MASS (>= 7.3-51.5), methods, stats, utils
Suggests: qgraph (>= 1.6.5)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
LinkingTo: Rcpp, RcppArmadillo
RdMacros: Rdpack, mathjaxr
BugReports: https://github.com/donaldRwilliams/GGMncv/issues
NeedsCompilation: yes
Packaged: 2020-11-16 00:02:23 UTC; Donny
Author: Donald Williams [aut, cre]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>
Repository: CRAN
Date/Publication: 2020-11-16 08:10:22 UTC

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Package fmtr updated to version 1.3.0 with previous version 1.2.2 dated 2020-10-10

Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply formats to data frames or vectors. The package aims to provide to functionality similar to that of SAS® formats. Formats are assigned to the format attribute on data frame columns. Then when the fdata() function is called, a new data frame is created with the column data formatted as specified. The package also contains a value() function to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>

Diff between fmtr versions 1.2.2 dated 2020-10-10 and 1.3.0 dated 2020-11-16

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Package findInFiles updated to version 0.1.2 with previous version 0.1.1 dated 2020-10-23

Title: Find Pattern in Files
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given folder. The results can be viewed in the 'RStudio' viewer pane, included in a 'R Markdown' document or in a 'Shiny' app.
Author: Stéphane Laurent [aut, cre], Rob Burns [ctb, cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between findInFiles versions 0.1.1 dated 2020-10-23 and 0.1.2 dated 2020-11-16

 DESCRIPTION     |    6 +++---
 MD5             |    8 ++++----
 NEWS.md         |    5 +++++
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 5 files changed, 29 insertions(+), 13 deletions(-)

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New package ezpickr with initial version 2.1.0
Package: ezpickr
Title: Easy Data Import Using GUI File Picker
Version: 2.1.0
Authors@R: c(person("JooYoung", "Seo", role=c("aut", "cre"), email="jooyoung@psu.edu", comment = c(ORCID = "0000-0002-4064-6012")), person("Soyoung", "Choi", role = "aut", email = "sxc940@psu.edu", comment = c(ORCID = "0000-0002-0998-3352")), person("hyun seung", "Lee", role = "ctb", email = "go4arsenal@gmail.com"), person("Jonghoen", "Kim", role = "ctb", email = "cysics@daum.net"))
Description: Choosing any rectangular data file using interactive GUI dialog box, and seamlessly manipulating tidy data between an 'Excel' window and R session.
License: GPL-3
VignetteBuilder: knitr
URL: https://github.com/jooyoungseo/ezpickr
BugReports: https://github.com/jooyoungseo/ezpickr/issues
Encoding: UTF-8
LazyData: true
Imports: haven, jsonlite, readxl, magrittr, textreadr, tibble, stringr, writexl, purrr, mboxr, vroom, rmarkdown, utils, tidyr
RoxygenNote: 7.1.1
Suggests: testthat, knitr, striprtf, xml2, dplyr, rvest, antiword, covr
NeedsCompilation: no
Packaged: 2020-11-15 15:12:09 UTC; sjysk
Author: JooYoung Seo [aut, cre] (<https://orcid.org/0000-0002-4064-6012>), Soyoung Choi [aut] (<https://orcid.org/0000-0002-0998-3352>), hyun seung Lee [ctb], Jonghoen Kim [ctb]
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Repository: CRAN
Date/Publication: 2020-11-16 08:10:18 UTC

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Package damr updated to version 0.3.7 with previous version 0.3.4 dated 2019-07-15

Title: Interface to Drosophila Activity Monitor System Result Files
Description: Loads behavioural data from the widely used Drosophila Activity Monitor System (DAMS, TriKinetics <https://trikinetics.com/>) into the rethomics framework.
Author: Quentin Geissmann [aut, cre], Hadley Wickham [aut]
Maintainer: Quentin Geissmann <qgeissmann@gmail.com>

Diff between damr versions 0.3.4 dated 2019-07-15 and 0.3.7 dated 2020-11-16

 DESCRIPTION                    |   10 ++++----
 MD5                            |   22 +++++++++----------
 R/link-dam-metadata.R          |    3 +-
 R/load-dam.R                   |    6 +++--
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 man/single_file_metadata.Rd    |    4 ++-
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 tests/testthat/test-load_dam.R |   46 +++++++++++++++++++++++++++++++++++++++++
 12 files changed, 130 insertions(+), 45 deletions(-)

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Package winch updated to version 0.0.6 with previous version 0.0.5 dated 2020-11-09

Title: Portable Native and Joint Stack Traces
Description: Obtain the native stack trace and fuse it with R's stack trace for easier debugging of R packages with native code.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), R Consortium [fnd], Ian Lance Taylor [aut] (Bundled libbacktrace library), Free Software Foundation [cph] (Bundled libbacktrace library)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package trekfont updated to version 0.9.4 with previous version 0.9.3 dated 2018-11-12

Title: Star Trek Fonts Collection
Description: Provides a collection of true type and open type Star Trek-themed fonts.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

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Package RcppAnnoy updated to version 0.0.17 with previous version 0.0.16 dated 2020-03-08

Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package mlr3pipelines updated to version 0.3.1 with previous version 0.3.0 dated 2020-09-13

Title: Preprocessing Operators and Pipelines for 'mlr3'
Description: Dataflow programming toolkit that enriches 'mlr3' with a diverse set of pipelining operators ('PipeOps') that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can therefore be resampled, benchmarked, and tuned.
Author: Martin Binder [aut, cre], Florian Pfisterer [aut] (<https://orcid.org/0000-0001-8867-762X>), Lennart Schneider [aut] (<https://orcid.org/0000-0003-4152-5308>), Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>), Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>), Susanne Dandl [aut]
Maintainer: Martin Binder <mlr.developer@mb706.com>

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Package lefko3 updated to version 3.1.2 with previous version 3.1.1 dated 2020-11-13

Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological analyses. Specializes on the construction of historical matrices, which are 2d matrices comprising 3 time intervals of demographic information. Estimates both raw and function-based forms of historical and standard ahistorical matrices. Methodology based on Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre] (<https://orcid.org/0000-0002-5234-3131>), Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>

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Package lcars updated to version 0.3.6 with previous version 0.3.1 dated 2020-02-06

Title: LCARS Aesthetic for Shiny
Description: Provides Shiny widgets and theme that support a 'Library Computer Access/Retrieval System' (LCARS) aesthetic for Shiny apps. The package also includes functions for adding a minimal LCARS theme to static 'ggplot2' graphs. More details about LCARS can be found at <https://en.wikipedia.org/wiki/LCARS>.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>

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Package contact updated to version 1.2.5 with previous version 1.2.4 dated 2020-07-21

Title: Creating Contact and Social Networks
Description: Process spatially- and temporally-discrete data into contact and social networks, and facilitate network analysis by randomizing individuals' movement paths and/or related categorical variables. To use this package, users need only have a dataset containing spatial data (i.e., latitude/longitude, or planar x & y coordinates), individual IDs relating spatial data to specific individuals, and date/time information relating spatial locations to temporal locations. The functionality of this package ranges from data "cleaning" via multiple filtration functions, to spatial and temporal data interpolation, and network creation and analysis. Functions within this package are not limited to describing interpersonal contacts. Package functions can also identify and quantify "contacts" between individuals and fixed areas (e.g., home ranges, water bodies, buildings, etc.). As such, this package is an incredibly useful resource for facilitating epidemiological, ecological, ethological and sociological research.
Author: Trevor Farthing [aut, cre], Daniel Dawson [aut], Cristina Lanzas [ctb]
Maintainer: Trevor Farthing <tsfarthi@ncsu.edu>

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Package shinyEventLogger (with last version 0.1.1) was removed from CRAN

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2019-02-22 0.1.1

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2019-05-31 0.5
2018-08-17 0.4.0
2016-03-27 0.3.0

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2020-02-04 1.1.4
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Package LPsmooth (with last version 0.1.1) was removed from CRAN

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2020-08-10 0.1.1

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

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2020-10-10 0.2.0

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Package migest (with last version 1.8.2) was removed from CRAN

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2020-08-05 1.8.2
2019-10-05 1.8.1
2019-02-24 1.8.0
2018-02-05 1.7.4
2016-10-26 1.7.3
2016-05-15 1.7.2
2015-10-06 1.7.1
2015-06-18 1.7
2014-07-27 1.6
2014-03-27 1.5
2013-10-02 1.4
2013-05-24 1.3
2013-04-23 1.2
2013-04-09 1.1
2012-11-06 1.0

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Package FSinR (with last version 2.0.3) was removed from CRAN

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2020-08-12 2.0.3
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Package pak (with last version 0.1.2) was removed from CRAN

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2019-02-19 0.1.2

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Package USgrid updated to version 0.1.1 with previous version 0.1.0 dated 2020-01-24

Title: The Demand and Supply for Electricity in the US
Description: Provides a set of regular time-series datasets, describing the US electricity grid. That includes the total demand and supply, and as well as the demand by energy source (coal, solar, wind, etc.). Source: US Energy Information Administration (Dec 2019) <https://www.eia.gov/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>

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Package ffscrapr updated to version 1.1.0 with previous version 1.0.0 dated 2020-08-17

Title: API Client for Fantasy Football League Platforms
Description: Helps access various Fantasy Football APIs by handling authentication and rate-limiting, forming appropriate calls, and returning tidy dataframes which can be easily connected to other data sources.
Author: Tan Ho [aut, cre]
Maintainer: Tan Ho <tan@tanho.ca>

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More information about ffscrapr at CRAN
Permanent link

Package directPA updated to version 1.5 with previous version 1.4 dated 2019-11-07

Title: Direction Analysis for Pathways and Kinases
Description: Direction analysis is a set of tools designed to identify combinatorial effects of multiple treatments/conditions on pathways and kinases profiled by microarray, RNA-seq, proteomics, or phosphoproteomics data. See Yang P et al (2014) <doi:10.1093/bioinformatics/btt616>; and Yang P et al. (2016) <doi:10.1002/pmic.201600068>.
Author: Pengyi Yang & Ellis Patrick
Maintainer: Pengyi Yang <yangpy7@gmail.com>

Diff between directPA versions 1.4 dated 2019-11-07 and 1.5 dated 2020-11-16

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 6 files changed, 49 insertions(+), 29 deletions(-)

More information about directPA at CRAN
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