Sat, 24 Oct 2020

Package modelsummary updated to version 0.6.3 with previous version 0.6.2 dated 2020-09-29

Title: Summary Tables and Plots for Statistical Models and Data: Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several statistical models side-by-side. Draw coefficient plots, multi-level cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and correlation matrices. This package supports dozens of statistical models, and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint, Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or 'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre] (<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>

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Package florestal updated to version 0.1.3 with previous version 0.1.1 dated 2020-07-07

Title: Results for Forest Inventories
Description: The functions return sampling parameters for forest inventories with tables and graphics. Methods used in the package refers to Pellico e Brena (1997) <https://bit.ly/2BDbHJI>.
Author: Igor Cobelo Ferreira
Maintainer: Igor Cobelo Ferreira <cobelo.igor@gmail.com>

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Package digest updated to version 0.6.27 with previous version 0.6.26 dated 2020-10-17

Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash' and 'blake3' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell, Matthew de Queljoe, Ion Suruceanu, Bill Denney, Dirk Schumacher, and Winston Chang.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between digest versions 0.6.26 dated 2020-10-17 and 0.6.27 dated 2020-10-24

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Package V8 updated to version 3.3.0 with previous version 3.2.0 dated 2020-06-19

Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8: Google's open source JavaScript and WebAssembly engine. This package can be compiled either with V8 version 6 and up, a NodeJS shared library, or the legacy 3.14/3.15 branch of V8.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package vasicek updated to version 0.0.2 with previous version 0.0.1 dated 2020-10-10

Title: Miscellaneous Functions for Vasicek Distribution
Description: Provide a collection of miscellaneous R functions related to the Vasicek distribution with the intent to make the lives of risk modelers easier.
Author: WenSui Liu
Maintainer: WenSui Liu <liuwensui@gmail.com>

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Package gemma2 updated to version 0.1.3 with previous version 0.1.1 dated 2019-10-01

Title: GEMMA Multivariate Linear Mixed Model
Description: Fits a multivariate linear mixed effects model that uses a polygenic term, after Zhou & Stephens (2014) (<https://www.nature.com/articles/nmeth.2848>). Of particular interest is the estimation of variance components with restricted maximum likelihood (REML) methods. Genome-wide efficient mixed-model association (GEMMA), as implemented in the package 'gemma2', uses an expectation-maximization algorithm for variance components inference for use in quantitative trait locus studies.
Author: Frederick Boehm [aut, cre] (<https://orcid.org/0000-0002-1644-5931>)
Maintainer: Frederick Boehm <frederick.boehm@gmail.com>

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Package syllabifyr updated to version 0.1.1 with previous version 0.1.0 dated 2018-07-10

Title: Syllabifier for CMU Dictionary Transcriptions
Description: Implements tidy syllabification of transcription. Based on @kylebgorman's 'python' implementation <https://github.com/kylebgorman/syllabify>.
Author: Josef Fruehwald
Maintainer: Josef Fruehwald <jofrhwld@gmail.com>

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Package mvSLOUCH updated to version 2.6 with previous version 2.5 dated 2020-06-03

Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F.Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Author: Krzysztof Bartoszek <krzbar@protonmail.ch>
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>

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Package GET updated to version 0.2 with previous version 0.1-8 dated 2020-08-29

Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T in various applications. A 100(1-alpha)% global envelope is a band bounded by two vectors such that the probability that T falls outside this envelope in any of the d points is equal to alpha. Global means that the probability is controlled simultaneously for all the d elements of the vectors. The global envelopes can be used for graphical Monte Carlo and permutation tests where the test statistic is a multivariate vector or function (e.g. goodness-of-fit testing for point patterns and random sets, functional analysis of variance, functional general linear model, n-sample test of correspondence of distribution functions), for central regions of functional or multivariate data (e.g. outlier detection, functional boxplot) and for global confidence and prediction bands (e.g. confidence band in polynomial regression, Bayesian posterior prediction). See Myllymäki and Mrkvička (2020) <arXiv:1911.06583>, Myllymäki et al. (2017) <doi: 10.1111/rssb.12172>, Mrkvička et al. (2017) <doi: 10.1007/s11222-016-9683-9>, Mrkvička et al. (2020) <doi: 10.14736/kyb-2020-3-0432>, Mrkvička et al. (2019) <doi: 10.1007/s11009-019-09756-y>, Mrkvička et al. (2019) <arXiv:1902.04926>, Mrkvička et al. (2016) <doi: 10.1016/j.spasta.2016.04.005>, and Myllymäki et al. (2020) <doi: 10.1016/j.spasta.2020.100436>.
Author: Mari Myllymäki [aut, cre], Tomáš Mrkvička [aut], Pavel Grabarnik [ctb], Ute Hahn [ctb], Mikko Kuronen [ctb], Michael Rost [ctb], Henri Seijo [ctb]
Maintainer: Mari Myllymäki <mari.myllymaki@luke.fi>

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Package survivalMPLdc updated to version 0.1.1 with previous version 0.1.0 dated 2020-10-13

Title: Penalised Likelihood for Survival Analysis with Dependent Censoring
Description: Fitting Cox proportional hazard model under dependent right censoring using copula and maximum penalised likelihood methods.
Author: Jing Xu [aut, cre], Jun Ma [aut], Thomas Fung [aut] (<https://orcid.org/0000-0003-2601-0728>)
Maintainer: Jing Xu <kenny.xu@duke-nus.edu.sg>

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Package rerddapXtracto updated to version 1.0.1 with previous version 1.0.0 dated 2020-07-29

Title: Extracts Environmental Data from 'ERDDAP' Web Services
Description: Contains three functions that access environmental data from any 'ERDDAP' data web service. The rxtracto() function extracts data along a trajectory for a given "radius" around the point. The rxtracto_3D() function extracts data in a box. The rxtractogon() function extracts data in a polygon. All of those three function use the 'rerddap' package to extract the data, and should work with any 'ERDDAP' server. There are also two functions, plotBBox() and plotTrack() that use the 'plotdap' package to simplify the creation of maps of the data.
Author: Roy Mendelssohn [aut, cre]
Maintainer: Roy Mendelssohn <roy.mendelssohn@noaa.gov>

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Package koRpus.lang.en updated to version 0.1-4 with previous version 0.1-3 dated 2019-05-13

Title: Language Support for 'koRpus' Package: English
Description: Adds support for the English language to the 'koRpus' package. To ask for help, report bugs, suggest feature improvements, or discuss the global development of the package, please consider subscribing to the koRpus-dev mailing list (<https://korpusml.reaktanz.de>).
Author: Meik Michalke [aut, cre], Elen Le Foll [ctb] (BNC tagset)
Maintainer: Meik Michalke <meik.michalke@hhu.de>

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New package visualpred with initial version 0.1.0
Package: visualpred
Title: Visualization 2D of Binary Classification Models
Version: 0.1.0
Authors@R: person(given = "Javier", family = "Portela", role = c("aut", "cre"), email = "javipgm@gmail.com")
Description: Visual 2D point and contour plots for binary classification modeling under algorithms such as glm(), randomForest(), gbm(), nnet() and svm(), presented over two dimensions generated by FAMD and MCA methods. Package 'FactoMineR' for multivariate reduction functions and package 'MBA' for interpolation functions are used. The package can be used to visualize the discriminant power of input variables and algorithmic modeling, explore outliers, compare algorithm behaviour, etc. It has been created initially for teaching purposes, but it has also many practical uses.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: gbm, randomForest, nnet (>= 7.3.12), e1071, MASS (>= 7.3.51.4), magrittr, FactoMineR (>= 2.3), ggplot2 (>= 3.3.0), mltools, dplyr, data.table, MBA, pROC, ggrepel
Suggests: knitr, markdown,egg
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2020-10-17 05:51:45 UTC; Usuario
Author: Javier Portela [aut, cre]
Maintainer: Javier Portela <javipgm@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:40:02 UTC

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New package Snake with initial version 1.0
Package: Snake
Title: Game of Snake
Version: 1.0
Date: 2020-10-08
Authors@R: person("Carsten", "Croonenbroeck", email = "carsten.croonenbroeck@uni-rostock.de", role = c("aut", "cre"))
Description: Implements snake in R as a programming example, see <https://en.wikipedia.org/wiki/Snake_(video_game_genre)>.
Depends: R (>= 3.5.0)
Imports: tcltk, grid
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2020-10-17 11:59:56 UTC; ccroo
Author: Carsten Croonenbroeck [aut, cre]
Maintainer: Carsten Croonenbroeck <carsten.croonenbroeck@uni-rostock.de>
Repository: CRAN
Date/Publication: 2020-10-24 09:50:08 UTC

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New package MGDrivE2 with initial version 1.0.1
Package: MGDrivE2
Type: Package
Title: Mosquito Gene Drive Explorer 2
Version: 1.0.1
Authors@R: c( person("Sean L.", "Wu", email = "slwood89@gmail.com", role = c("aut","cre")), person("Jared B.", "Bennett", email = "jared_bennett@berkeley.edu ", role = "aut"), person("Héctor Manuel", "Sánchez Castellanos", email = "sanchez.hmsc@berkeley.edu", role = "ctb"), person("Tomás M.", "León", email = "tomas.leon@berkeley.edu", role = "ctb"), person("Andrew J.", "Dolgert", email = "adolgert@uw.edu", role = "ctb"), person("John M.", "Marshall", email = "john.marshall@berkeley.edu", role = "aut") )
Maintainer: Sean L. Wu <slwood89@gmail.com>
URL: https://marshalllab.github.io/MGDrivE/, https://www.marshalllab.com/
BugReports: https://github.com/MarshallLab/MGDrivE/issues
Description: A simulation modeling framework which significantly extends capabilities from the 'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets. For more information about 'MGDrivE', see our publication: <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13318>. Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations, epidemiological dynamics, time-varying parameters, and a continuous-time simulation framework with various sampling algorithms for both deterministic and stochastic interpretations. 'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we suggest installing that package initially.
License: GPL-3
Encoding: UTF-8
ByteCompile: true
LazyData: true
Depends: R (>= 3.1.0)
Imports: Matrix, deSolve
Suggests: MGDrivE, knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 21:06:45 UTC; slwu89
Author: Sean L. Wu [aut, cre], Jared B. Bennett [aut], Héctor Manuel Sánchez Castellanos [ctb], Tomás M. León [ctb], Andrew J. Dolgert [ctb], John M. Marshall [aut]
Repository: CRAN
Date/Publication: 2020-10-24 09:30:03 UTC

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New package hetu with initial version 1.0.1
Package: hetu
Type: Package
Title: Structural Handling of Finnish Personal Identity Numbers
Version: 1.0.1
Encoding: UTF-8
Date: 2020-10-15
Authors@R: c( person("Pyry", "Kantanen", email = "pyry.kantanen@gmail.com", role = c("aut", "cre")), person("Mans", "Magnusson", role = "aut"), person("Jussi", "Paananen", role = "aut"), person("Leo", "Lahti", role = "aut") )
MailingList: rOpenGov <ropengov-forum@googlegroups.com>
Description: Structural handling of Finnish identity numbers (persons and companies); extract information, check ID validity and diagnostics.
License: BSD_2_clause + file LICENSE
VignetteBuilder: knitr
BugReports: https://github.com/ropengov/hetu/issues
URL: https://github.com/ropengov/hetu
Depends: R (>= 4.0.0)
Suggests: Cairo, checkmate, lubridate, dplyr, knitr, testthat, rmarkdown, covr
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-16 07:51:07 UTC; pyrykantanen
Author: Pyry Kantanen [aut, cre], Mans Magnusson [aut], Jussi Paananen [aut], Leo Lahti [aut]
Maintainer: Pyry Kantanen <pyry.kantanen@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:10:02 UTC

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New package flipdownr with initial version 0.1.0
Package: flipdownr
Type: Package
Title: Implement a Countdown in 'RMarkdown' Documents and 'shiny' Applications
Version: 0.1.0
Authors@R: c( person("Mohamed El Fodil", "Ihaddaden", email = "ihaddaden.fodeil@gmail.com", role = c("aut", "cre")), person("Butcher", "Peter", role = c("ctb", "cph"), comment = "flipdown.js library developer"))
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Description: Allows the user to create a countdown in 'RMarkdown' documents and 'shiny' applications. The package is a wrapper of the 'JavaScript' library 'flipdown.js'. See <https://pbutcher.uk/flipdown/> for more info.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Imports: htmltools, glue, jsonlite
URL: https://github.com/feddelegrand7/flipdownr
BugReports: https://github.com/feddelegrand7/flipdownr/issues
NeedsCompilation: no
Packaged: 2020-10-16 15:01:25 UTC; Administrateur
Author: Mohamed El Fodil Ihaddaden [aut, cre], Butcher Peter [ctb, cph] (flipdown.js library developer)
Repository: CRAN
Date/Publication: 2020-10-24 09:20:02 UTC

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Package fixest updated to version 0.7.0 with previous version 0.6.0 dated 2020-07-13

Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@uni.lu>

Diff between fixest versions 0.6.0 dated 2020-07-13 and 0.7.0 dated 2020-10-24

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 fixest-0.7.0/fixest/vignettes/exporting_tables.Rmd   |   31 
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 fixest-0.7.0/fixest/vignettes/standard_errors.Rmd    |  122 
 59 files changed, 5689 insertions(+), 3338 deletions(-)

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New package APML with initial version 0.0.1
Package: APML
Type: Package
Title: An Approach for Machine-Learning Modelling
Version: 0.0.1
Authors@R: c(person("Xinlei","Deng",role=c("aut","cre","cph"),email="xdeng3@albany.edu"), person("Wangjian","Zhang",role="aut"), person("Shao","Lin",role="aut"))
Description: We include 1) data cleaning including variable scaling, missing values and unbalanced variables identification and removing, and strategies for variable balance improving; 2) modeling based on random forest and gradient boosted model including feature selection, model training, cross-validation and external testing. For more information, please see H2O.ai (Oct. 2016). R Interface for H2O, R package version 3.10.0.8. <https://github.com/h2oai/h2o-3>; Zhang W (2016). <doi:10.1016/j.scitotenv.2016.02.023>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: tidyverse,h2o,DMwR,dummies,dplyr,ggplot2,pROC,survival
NeedsCompilation: no
Packaged: 2020-10-08 15:51:07 UTC; xd129664
Author: Xinlei Deng [aut, cre, cph], Wangjian Zhang [aut], Shao Lin [aut]
Maintainer: Xinlei Deng <xdeng3@albany.edu>
Repository: CRAN
Date/Publication: 2020-10-24 09:20:05 UTC

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Package RPESE updated to version 1.1.0 with previous version 1.0.5 dated 2020-06-19

Title: Estimates of Standard Errors for Risk and Performance Measures
Description: Estimates of standard errors of popular risk and performance measures for asset or portfolio returns using methods as described in Chen and Martin (2018) <https://www.ssrn.com/abstract=3085672>.
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>, Xin Chen <chenx26@uw.edu>
Maintainer: Anthony Christidis <anthony.christidis@stat.ubc.ca>

Diff between RPESE versions 1.0.5 dated 2020-06-19 and 1.1.0 dated 2020-10-24

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Package nlme updated to version 3.1-150 with previous version 3.1-149 dated 2020-08-23

Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version), Douglas Bates [aut] (up to 2007), Saikat DebRoy [ctb] (up to 2002), Deepayan Sarkar [ctb] (up to 2005), EISPACK authors [ctb] (src/rs.f), Siem Heisterkamp [ctb] (Author fixed sigma), Bert Van Willigen [ctb] (Programmer fixed sigma), R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>

Diff between nlme versions 3.1-149 dated 2020-08-23 and 3.1-150 dated 2020-10-24

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 nlme-3.1-150/nlme/R/VarCov.R        |   38 ++++++++++++++++++++----------------
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 7 files changed, 42 insertions(+), 24 deletions(-)

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Package HypergeoMat updated to version 3.1.0 with previous version 3.0.0 dated 2019-10-26

Title: Hypergeometric Function of a Matrix Argument
Description: Evaluates the hypergeometric functions of a matrix argument, which appear in random matrix theory. This is an implementation of Koev & Edelman's algorithm (2006) <doi:10.1090/S0025-5718-06-01824-2>.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between HypergeoMat versions 3.0.0 dated 2019-10-26 and 3.1.0 dated 2020-10-24

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 7 files changed, 427 insertions(+), 95 deletions(-)

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New package healthfinance with initial version 0.1.0
Package: healthfinance
Title: Financial Projections and Planning for Health Care Practices
Version: 0.1.0
Authors@R: c( person(given = "Raoul", family = "Wadhwa", role = c("aut", "cre"), email = "raoulwadhwa@gmail.com"), person(given = "Vigneshwar", family = "Subramanian", role = "aut", email = "vs347@cornell.edu"), person(given = "Milind", family = "Desai", role = "aut"))
Description: Provides a shiny interface for a free, open-source managerial accounting-like system for health care practices. This package allows health care administrators to project revenue with monthly adjustments and procedure-specific boosts up to a 3-year period. Granular data (patient-level) to aggregated data (department- or hospital-level) can all be used as valid inputs provided historical volume and revenue data is available. For more details on managerial accounting techniques, see Brewer et al. (2015, ISBN:9780078025792).
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: ggplot2 (>= 3.3), lubridate (>= 1.7), readr (>= 1.3), scales (>= 1.1), shiny (>= 1.4), tibble (>= 3.0)
RoxygenNote: 7.1.1
URL: https://rrrlw.github.io/healthfinance/
BugReports: https://github.com/rrrlw/healthfinance/issues
Suggests: testthat (>= 2.3)
NeedsCompilation: no
Packaged: 2020-10-15 20:13:27 UTC; appveyor
Author: Raoul Wadhwa [aut, cre], Vigneshwar Subramanian [aut], Milind Desai [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 09:00:02 UTC

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New package drought with initial version 1.0
Package: drought
Type: Package
Title: Statistical Modeling and Assessment of Drought
Version: 1.0
Date: 2020-10-10
Author: Zengchao Hao
Maintainer: Zengchao Hao <z.hao4univ@gmail.com>
Description: Provide tools for drought monitoring based on univariate and multivariate drought indicators.Statistical drought prediction based on Ensemble Streamflow Prediction (ESP) and drought risk assessments are also provided. Please see Hao Zengchao et al. (2017) <doi:10.1016/j.envsoft.2017.02.008>.
Depends: R (>= 3.5.0)
Imports: stats,copula
Suggests: MASS
License: GPL-3
LazyData: true
Repository: CRAN
RoxygenNote: 7.1.0
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2020-10-15 00:44:34 UTC; HAO
Date/Publication: 2020-10-24 08:30:02 UTC

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New package assert with initial version 1.0.0
Package: assert
Title: Validate Function Arguments
Version: 1.0.0
Authors@R: person(given = "Olivier", family = "Binette", role = c("aut", "cre", "cph"), email = "olivier.binette@gmail.com")
Description: Lightweight validation tool for checking function arguments and validating data analysis scripts. This is an alternative to stopifnot() from the 'base' package and to assert_that() from the 'assertthat' package. It provides more informative error messages and facilitates debugging.
Imports: rlang
URL: https://github.com/OlivierBinette/assert
BugReports: https://github.com/OlivierBinette/assert/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
NeedsCompilation: no
Packaged: 2020-10-15 14:09:04 UTC; olivierbinette
Author: Olivier Binette [aut, cre, cph]
Maintainer: Olivier Binette <olivier.binette@gmail.com>
Repository: CRAN
Date/Publication: 2020-10-24 08:50:02 UTC

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New package anovir with initial version 0.1.0
Package: anovir
Type: Package
Title: Analysis of Virulence
Version: 0.1.0
Authors@R: c(person("Philip", "Agnew", email = "philip.agnew@ird.fr", role = c("aut", "cre")), person("Jimmy","Lopez", email = "jimmy.lopez@ird.fr", role = c("aut")))
Maintainer: Philip Agnew <philip.agnew@ird.fr>
Description: Epidemiological population dynamics models traditionally define a pathogen's virulence as the increase in the per capita rate of mortality of infected hosts due to infection. This package provides functions allowing virulence to be estimated by maximum likelihood techniques. The approach is based on the analysis of relative survival comparing survival in matching cohorts of infected vs. uninfected hosts (Agnew 2019) <doi:10.1101/530709>.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: bbmle, R (>= 2.10), stats4
Suggests: knitr, rmarkdown, stats, testthat
Collate: 'anovir-package.R' 'private_functions.R' 'nll_recovery.R' 'nll_recovery_II.R' 'data_descriptions.R' 'main.R' 'play_file.R' 'nll_functions.R' 'nll_frailty_correlated.R'
VignetteBuilder: knitr
URL: https://www.biorxiv.org/content/10.1101/530709v1
NeedsCompilation: no
Packaged: 2020-10-15 16:10:52 UTC; philipagnew
Author: Philip Agnew [aut, cre], Jimmy Lopez [aut]
Repository: CRAN
Date/Publication: 2020-10-24 08:50:05 UTC

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New package acled.api with initial version 1.0.7
Package: acled.api
Title: Automated Retrieval of ACLED Conflict Event Data
Version: 1.0.7
Date: 2020-10-14
Authors@R: person(given = "Christoph", family = "Dworschak", role = c("aut", "cre"), email = "c.dworschak@essex.ac.uk", comment = c(ORCID = "0000-0003-0196-9545"))
Author: Christoph Dworschak [aut, cre] (<https://orcid.org/0000-0003-0196-9545>)
Maintainer: Christoph Dworschak <c.dworschak@essex.ac.uk>
Description: Access and manage the application programming interface (API) of the Armed Conflict Location & Event Data Project (ACLED) at <https://acleddata.com/>. It makes it easy to retrieve a user-defined sample (or all of the available data) of ACLED, enabling a seamless integration of regular data updates into the research work flow. When using this package, you acknowledge that you have read ACLED's terms and conditions of use, and that you agree with their attribution requirements.
License: CC BY-NC 4.0
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 7.1.1
Imports: httr, jsonlite
Suggests: testthat
NeedsCompilation: no
Packaged: 2020-10-15 12:35:11 UTC; root
Repository: CRAN
Date/Publication: 2020-10-24 08:40:02 UTC

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Package TraMineR updated to version 2.2-1 with previous version 2.2-0.1 dated 2020-04-29

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>), Nicolas M"{u}ller [aut], Reto B"{u}rgin [aut], Pierre-Alexandre Fonta [aut], Gilbert Ritschard [aut, cre, cph] (<https://orcid.org/0000-0001-7776-0903>)
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

Diff between TraMineR versions 2.2-0.1 dated 2020-04-29 and 2.2-1 dated 2020-10-24

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Package tram updated to version 0.5-2 with previous version 0.5-1 dated 2020-09-04

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>). Multivariate conditional transformation models (<arxiv:1906.03151>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>), Luisa Barbanti [aut], Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package nasapower updated to version 3.0.1 with previous version 3.0.0 dated 2020-10-10

Title: NASA POWER API Client
Description: Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>, Scott Chamberlain reviewed nasapower for rOpenSci, see https://github.com/ropensci/software-review/issues/155), Hazel Kavili [rev] (Hazel Kavili reviewed nasapower for rOpenSci, see https://github.com/ropensci/software-review/issues/155), Alison Boyer [rev] (Alison Boyer reviewed nasapower for rOpenSci, see https://github.com/ropensci/software-review/issues/155), Fernando Miguez [ctb] (<https://orcid.org/0000-0002-4627-8329>, Fernando Miguez provided assistance in identifying improper missing value handling in the POWER data, see <https://github.com/femiguez/apsimx/pull/26>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>

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Package emmeans updated to version 1.5.2 with previous version 1.5.1 dated 2020-09-18

Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph], Paul Buerkner [ctb], Maxime Herve [ctb], Jonathon Love [ctb], Hannes Riebl [ctb], Henrik Singmann [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

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Package Numero updated to version 1.7.2 with previous version 1.7.0 dated 2020-09-14

Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2019) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, 48:369-37, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut], Stefan Mutter [aut], Aaron E. Casey [aut], Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>

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Package metan updated to version 1.10.0 with previous version 1.9.0 dated 2020-09-18

Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment trial data using parametric and non-parametric methods. Parametric methods includes Additive Main Effects and Multiplicative Interaction (AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>, Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>, geometric adaptability index by Mohammadi & Amri (2008) <doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart & Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>, genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's (2004) method <doi:10.12702/1984-7033.v04n01a02>, power law residuals (POLAR) statistics by Doring et al. (2015) <doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>, stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>, weighted average of absolute scores by Olivoto et al. (2019a) <doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>. Non-parametric methods includes superiority index by Lin & Binns (1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic stability by Huehn (1990) <https://link.springer.com/article/10.1007/BF00024241>, TOP third statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for computing biometrical analysis such as path analysis, canonical correlation, partial correlation, clustering analysis, and tools for inspecting, manipulating, summarizing and plotting typical multi-environment trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>

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Package oasis (with last version 3.0.4) was removed from CRAN

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

2018-02-21 3.0.4

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Package febr (with last version 1.1.0) was removed from CRAN

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

2020-03-17 1.1.0
2020-01-25 1.0.3
2019-05-06 1.0.2
2018-11-12 1.0.1
2018-03-09 1.0-0

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Package ctDNAtools (with last version 0.4.0) was removed from CRAN

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2020-03-04 0.4.0

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