Fri, 15 Oct 2021

Package retriever updated to version 0.2.0 with previous version 0.1.0 dated 2021-10-08

Title: Generate Disease-Specific Response Signatures from the LINCS-L1000 Data
Description: Generates disease-specific drug-response profiles that are independent of time, concentration, and cell-line. Based on the cell lines used as surrogates, the returned profiles represent the unique transcriptional changes induced by a compound in a given disease.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>), Marieke Kuijjer [aut] (<https://orcid.org/0000-0001-6280-3130>)
Maintainer: Daniel Osorio <daniecos@uio.no>

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Package Rage updated to version 1.2.0 with previous version 1.1.0 dated 2021-07-09

Title: Life History Metrics from Matrix Population Models
Description: Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>), Danny Buss [ctb], Pol Capdevila [aut] (<https://orcid.org/0000-0002-2842-4302>), Hal Caswell [aut] (<https://orcid.org/0000-0003-4394-6894>), Judy P. Che-Castaldo [aut] (<https://orcid.org/0000-0002-9118-9202>), John Jackson [aut] (<https://orcid.org/0000-0002-4563-2840>), Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>), Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>), Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>), William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>), Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>), Caroline Schuette [ctb] (<https://orcid.org/0000-0002-2063-8736>), Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>), Chelsea C. Thomas [aut] (<https://orcid.org/0000-0002-8155-9353>)
Maintainer: Owen Jones <jones@biology.sdu.dk>

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More information about Rage at CRAN
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Package pchc updated to version 0.6 with previous version 0.5 dated 2021-03-21

Title: Bayesian Network Learning with the PCHC and Related Algorithms
Description: Bayesian network learning using the PCHC algorithm. PCHC stands for PC Hill-Climbing, a new hybrid algorithm that uses PC to construct the skeleton of the BN and then applies the Hill-Climbing greedy search. More algorithms and variants have been added, such as MMHC, FEDHC, and the Tabu search variants, PCTABU, MMTABU and FEDTABU. The relevant papers are a) Tsagris M. (2021). A new scalable Bayesian network learning algorithm with applications to economics. Computational Economics, 57(1): 341-367. <doi:10.1007/s10614-020-10065-7>. b) Tsagris M. (2021). The FEDHC Bayesian network learning algorithm. <arXiv:2012.00113>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

Diff between pchc versions 0.5 dated 2021-03-21 and 0.6 dated 2021-10-15

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Package POFIBGE updated to version 0.1.4 with previous version 0.1.3 dated 2021-06-24

Title: Downloading, Reading and Analysing POF Microdata
Description: Provides tools for downloading, reading and analysing the POF, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package PNSIBGE updated to version 0.1.5 with previous version 0.1.4 dated 2021-06-24

Title: Downloading, Reading and Analysing PNS Microdata
Description: Provides tools for downloading, reading and analysing the PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package isoreader updated to version 1.3.1 with previous version 1.3.0 dated 2021-02-16

Title: Read Stable Isotope Data Files
Description: Interface to the raw data file formats commonly encountered in scientific disciplines that make use of stable isotopes.
Author: Sebastian Kopf [aut, cre] (<https://orcid.org/0000-0002-2044-0201>), Brett Davidheiser-Kroll [aut] (<https://orcid.org/0000-0002-6153-7851>), Ilja Kocken [aut] (<https://orcid.org/0000-0003-2196-8718>)
Maintainer: Sebastian Kopf <sebastian.kopf@colorado.edu>

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Package dm updated to version 0.2.5 with previous version 0.2.4 dated 2021-09-30

Title: Relational Data Models
Description: Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut], Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), Darko Bergant [aut], Katharina Brunner [ctb], James Wondrasek [ctb], energie360° AG [fnd], cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package arkdb updated to version 0.0.13 with previous version 0.0.12 dated 2021-04-05

Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Richard FitzJohn [ctb], Brandon Bertelsen [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package Rcompadre updated to version 1.1.0 with previous version 1.0.0 dated 2021-04-30

Title: Utilities for using the 'COM(P)ADRE' Matrix Model Database
Description: Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.
Author: Patrick Barks [aut] (<https://orcid.org/0000-0002-5947-8151>), Danny Buss [aut], Roberto Salguero-Gomez [aut] (<https://orcid.org/0000-0002-6085-4433>), Iain Stott [aut] (<https://orcid.org/0000-0003-2724-7436>), William K. Petry [aut] (<https://orcid.org/0000-0002-5230-5987>), Tamora James [aut] (<https://orcid.org/0000-0003-1363-4742>), Owen Jones [aut, cre] (<https://orcid.org/0000-0001-5720-4686>), Julia Jones [aut] (<https://orcid.org/0000-0001-9223-1778>), Gesa Römer [aut] (<https://orcid.org/0000-0002-4859-5870>), Sam Levin [aut] (<https://orcid.org/0000-0002-3289-9925>)
Maintainer: Owen Jones <jones@biology.sdu.dk>

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Package DTAplots updated to version 1.0.2.5 with previous version 1.0.2.4 dated 2021-03-17

Title: Creates Plots Accompanying Bayesian Diagnostic Test Accuracy Meta-Analyses
Description: Function to create forest plots. Functions to use posterior samples from Bayesian bivariate meta-analysis model, Bayesian hierarchical summary receiver operating characteristic (HSROC) meta-analysis model or Bayesian latent class (LC) meta-analysis model to create Summary Receiver Operating Characteristic (SROC) plots using methods described by Harbord et al (2007)<doi:10.1093/biostatistics/kxl004>.
Author: Ian Schiller [aut, cre], Nandini Dendukuri [ctb]
Maintainer: Ian Schiller <ian.schiller@rimuhc.ca>

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Package COVIDIBGE updated to version 0.1.6 with previous version 0.1.5 dated 2021-06-24

Title: Downloading, Reading and Analysing PNAD COVID19 Microdata
Description: Provides tools for downloading, reading and analysing the PNAD COVID19, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Gabriel Assuncao [aut, cre], Luna Hidalgo [aut], Douglas Braga [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package migrate updated to version 0.4.0 with previous version 0.3.0 dated 2020-12-07

Title: Create Credit State Migration (Transition) Matrices
Description: Tools to help convert credit risk data at two time points into traditional credit state migration (aka, "transition") matrices. At a higher level, 'migrate' is intended to help an analyst understand how risk moved in their credit portfolio over a time interval. References to this methodology include: 1. Schuermann, T. (2008) <doi:10.1002/9780470061596.risk0409>. 2. Perederiy, V. (2017) <arXiv:1708.00062>.
Author: Michael Thomas [aut, cre], Brad Lindblad [ctb]
Maintainer: Michael Thomas <mthomas@ketchbrookanalytics.com>

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Package islasso updated to version 1.4.0 with previous version 1.3.1 dated 2021-06-16

Title: The Induced Smoothed Lasso
Description: An implementation of the induced smoothing (IS) idea to lasso regularization models to allow estimation and inference on the model coefficients (currently hypothesis testing only). Linear, logistic, Poisson and gamma regressions with several link functions are implemented. The algorithm is described in the original paper: Cilluffo, G., Sottile, G., La Grutta, S. and Muggeo, V. (2019) The Induced Smoothed lasso: A practical framework for hypothesis testing in high dimensional regression. <doi:10.1177/0962280219842890>, and discussed in a tutorial: Sottile, G., Cilluffo, G., and Muggeo, V. (2019) The R package islasso: estimation and hypothesis testing in lasso regression. <doi:10.13140/RG.2.2.16360.11521>.
Author: Gianluca Sottile [aut, cre], Giovanna Cilluffo [aut, ctb], Vito MR Muggeo [aut, cre]
Maintainer: Gianluca Sottile <gianluca.sottile@unipa.it>

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Package shinybrms updated to version 1.5.2 with previous version 1.5.1 dated 2021-03-06

Title: Graphical User Interface ('shiny' App) for 'brms'
Description: A graphical user interface (GUI) for fitting Bayesian regression models using the package 'brms' which in turn relies on 'Stan' (<https://mc-stan.org/>). The 'shinybrms' GUI is a 'shiny' app.
Author: Frank Weber [aut, cre] (<https://orcid.org/0000-0002-4842-7922>), Thomas Park [ctb, cph] ('Bootswatch' theme "United"), Twitter, Inc. [ctb, cph] ('Bootstrap' (basis for the 'Bootswatch' theme "United")), Google, LLC [ctb, cph] ("Open Sans" font)
Maintainer: Frank Weber <fweber144@protonmail.com>

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Package MortCast updated to version 2.6-1 with previous version 2.6-0 dated 2021-10-08

Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using the Kannisto, Lee-Carter and related methods as described in Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova, Nan Li and Patrick Gerland
Maintainer: Hana Sevcikova <hanas@uw.edu>

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Package arm updated to version 1.12-2 with previous version 1.11-2 dated 2020-07-27

Title: Data Analysis Using Regression and Multilevel/Hierarchical Models
Description: Functions to accompany A. Gelman and J. Hill, Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge University Press, 2007.
Author: Andrew Gelman [aut], Yu-Sung Su [aut, cre], Masanao Yajima [ctb], Jennifer Hill [ctb], Maria Grazia Pittau [ctb], Jouni Kerman [ctb], Tian Zheng [ctb], Vincent Dorie [ctb]
Maintainer: Yu-Sung Su <suyusung@tsinghua.edu.cn>

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Package wpa updated to version 1.6.2 with previous version 1.6.1 dated 2021-09-01

Title: Tools for Analysing and Visualising Workplace Analytics Data
Description: Opinionated functions that enable easier and faster analysis of Workplace Analytics data. There are three main types of functions in 'wpa': (i) Standard functions create a 'ggplot' visual or a summary table based on a specific Workplace Analytics metric; (2) Report Generation functions generate HTML reports on a specific analysis area, e.g. Collaboration; (3) Other miscellaneous functions cover more specific applications (e.g. Subject Line text mining) of Workplace Analytics data. This package adheres to 'tidyverse' principles and works well with the pipe syntax. 'wpa' is built with the beginner-to-intermediate R users in mind, and is optimised for simplicity.
Author: Martin Chan [aut, cre], Carlos Morales [aut], Mark Powers [ctb], Ainize Cidoncha [ctb], Rosamary Ochoa Vargas [ctb], Tannaz Sattari [ctb], Lucas Hogner [ctb], Jasminder Thind [ctb], Simone Liebal [ctb], Aleksey Ashikhmin [ctb], Ellen Trinklein [ctb], Microsoft Corporation [cph]
Maintainer: Martin Chan <martin.chan@microsoft.com>

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Package randomForestSRC updated to version 2.13.0 with previous version 2.12.1 dated 2021-09-05

Title: Fast Unified Random Forests for Survival, Regression, and Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>

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Package Tplyr updated to version 0.4.2 with previous version 0.4.1 dated 2021-07-13

Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>), Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>), Ashley Tarasiewicz [aut], Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>), Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>

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Package postGGIR updated to version 2.4.0.1 with previous version 2.4.0 dated 2021-07-14

Title: Data Processing after Running 'GGIR' for Accelerometer Data
Description: Generate all necessary R/Rmd/shell files for data processing after running 'GGIR' (v2.4.0) for accelerometer data. In part 1, all csv files in the GGIR output directory were read, transformed and then merged. In part 2, the GGIR output files were checked and summarized in one excel sheet. In part 3, the merged data was cleaned according to the number of valid hours on each night and the number of valid days for each subject. In part 4, the cleaned activity data was imputed by the average Euclidean norm minus one (ENMO) over all the valid days for each subject. Finally, a comprehensive report of data processing was created using Rmarkdown, and the report includes few exploratory plots and multiple commonly used features extracted from minute level actigraphy data.
Author: Wei Guo [aut, cre], Vadim Zipunnikov [aut], Kathleen Merikangas [aut]
Maintainer: Wei Guo <wei.guo3@nih.gov>

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Package micemd updated to version 1.8.0 with previous version 1.7.0 dated 2021-07-30

Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team), Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>

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Package ghypernet updated to version 1.1.0 with previous version 1.0.1 dated 2020-10-21

Title: Fit and Simulate Generalised Hypergeometric Ensembles of Graphs
Description: Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arXiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.
Author: Giona Casiraghi [aut, cre] (<https://orcid.org/0000-0003-0233-5747>), Vahan Nanumyan [aut] (<https://orcid.org/0000-0001-9054-3217>), Laurence Brandenberger [ctb], Giacomo Vaccario [ctb]
Maintainer: Giona Casiraghi <giona@ethz.ch>

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Package ebdbNet updated to version 1.2.6 with previous version 1.2.5 dated 2016-11-21

Title: Empirical Bayes Estimation of Dynamic Bayesian Networks
Description: Infer the adjacency matrix of a network from time course data using an empirical Bayes estimation procedure based on Dynamic Bayesian Networks.
Author: Andrea Rau <andrea.rau@inra.fr>
Maintainer: Andrea Rau <andrea.rau@inra.fr>

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Package TPmsm updated to version 1.2.5 with previous version 1.2.4 dated 2021-10-09

Title: Estimation of Transition Probabilities in Multistate Models
Description: Estimation of transition probabilities for the illness-death model and or the three-state progressive model.
Author: Artur Araujo [aut, cre] (<https://orcid.org/0000-0003-1419-4208>), Javier Roca-Pardinas [aut] (<https://orcid.org/0000-0003-3107-4515>), Luis Meira-Machado [aut] (<https://orcid.org/0000-0002-8577-7665>)
Maintainer: Artur Araujo <artur.stat@gmail.com>

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Package stringfish updated to version 0.15.4 with previous version 0.15.3 dated 2021-10-10

Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph], Phillip Hazel [ctb] (Bundled PCRE2 code), Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code), University of Cambridge [cph] (Bundled PCRE2 code), Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with PCRE2), Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash code)
Maintainer: Travers Ching <traversc@gmail.com>

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Package phenofit updated to version 0.3.2 with previous version 0.2.7 dated 2020-04-02

Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>; Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636. <doi:10.1029/2020JG005636>; Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24; Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Author: Dongdong Kong [aut, cre], Mingzhong Xiao [aut], Yongqiang Zhang [aut], Xihui Gu [aut], Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>

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Package ncdf4.helpers updated to version 0.3-6 with previous version 0.3-5 dated 2020-06-08

Title: Helper Functions for Use with the 'ncdf4' Package
Description: Contains a collection of helper functions for dealing with 'NetCDF' files <https://www.unidata.ucar.edu/software/netcdf/> opened using 'ncdf4', particularly 'NetCDF' files that conform to the Climate and Forecast (CF) Metadata Conventions <http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html>.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts Consortium (PCIC)
Maintainer: Lee Zeman <lzeman@uvic.ca>

Diff between ncdf4.helpers versions 0.3-5 dated 2020-06-08 and 0.3-6 dated 2021-10-15

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Package igraph updated to version 1.2.7 with previous version 1.2.6 dated 2020-10-06

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamás Nepusz <ntamas@gmail.com>

Diff between igraph versions 1.2.6 dated 2020-10-06 and 1.2.7 dated 2021-10-15

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 igraph-1.2.7/igraph/src/drl_layout_3d.h                           |   62 
 igraph-1.2.7/igraph/src/drl_parse.cpp                             |  240 
 igraph-1.2.7/igraph/src/drl_parse.h                               |   74 
 igraph-1.2.7/igraph/src/eigen.c                                   | 2669 +-
 igraph-1.2.7/igraph/src/embedding.c                               | 1703 -
 igraph-1.2.7/igraph/src/fast_community.c                          | 1666 -
 igraph-1.2.7/igraph/src/feedback_arc_set.c                        | 1046 -
 igraph-1.2.7/igraph/src/flow.c                                    | 3469 +--
 igraph-1.2.7/igraph/src/foreign-dl-header.h                       |   37 
 igraph-1.2.7/igraph/src/foreign-dl-lexer.c                        |   95 
 igraph-1.2.7/igraph/src/foreign-dl-lexer.l                        |    7 
 igraph-1.2.7/igraph/src/foreign-gml-header.h                      |   18 
 igraph-1.2.7/igraph/src/foreign-gml-lexer.c                       |   48 
 igraph-1.2.7/igraph/src/foreign-gml-lexer.l                       |    8 
 igraph-1.2.7/igraph/src/foreign-graphml.c                         | 3179 +--
 igraph-1.2.7/igraph/src/foreign-lgl-header.h                      |   26 
 igraph-1.2.7/igraph/src/foreign-lgl-lexer.c                       |   48 
 igraph-1.2.7/igraph/src/foreign-lgl-lexer.l                       |    8 
 igraph-1.2.7/igraph/src/foreign-ncol-header.h                     |   24 
 igraph-1.2.7/igraph/src/foreign-ncol-lexer.c                      |   48 
 igraph-1.2.7/igraph/src/foreign-ncol-lexer.l                      |    8 
 igraph-1.2.7/igraph/src/foreign-pajek-header.h                    |   42 
 igraph-1.2.7/igraph/src/foreign-pajek-lexer.c                     |   48 
 igraph-1.2.7/igraph/src/foreign-pajek-lexer.l                     |    8 
 igraph-1.2.7/igraph/src/foreign-pajek-parser.c                    |    4 
 igraph-1.2.7/igraph/src/foreign-pajek-parser.y                    |    4 
 igraph-1.2.7/igraph/src/foreign.c                                 | 5304 ++---
 igraph-1.2.7/igraph/src/forestfire.c                              |  343 
 igraph-1.2.7/igraph/src/fortran_intrinsics.c                      |   38 
 igraph-1.2.7/igraph/src/games.c                                   | 6785 +++---
 igraph-1.2.7/igraph/src/gengraph_box_list.cpp                     |  119 
 igraph-1.2.7/igraph/src/gengraph_box_list.h                       |   82 
 igraph-1.2.7/igraph/src/gengraph_definitions.h                    |  119 
 igraph-1.2.7/igraph/src/gengraph_degree_sequence.cpp              |  451 
 igraph-1.2.7/igraph/src/gengraph_degree_sequence.h                |  111 
 igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.cpp            | 1080 -
 igraph-1.2.7/igraph/src/gengraph_graph_molloy_hash.h              |  311 
 igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.cpp       | 2775 +-
 igraph-1.2.7/igraph/src/gengraph_graph_molloy_optimized.h         |  447 
 igraph-1.2.7/igraph/src/gengraph_hash.h                           |  342 
 igraph-1.2.7/igraph/src/gengraph_header.h                         |   85 
 igraph-1.2.7/igraph/src/gengraph_mr-connected.cpp                 |  196 
 igraph-1.2.7/igraph/src/gengraph_powerlaw.cpp                     |  356 
 igraph-1.2.7/igraph/src/gengraph_powerlaw.h                       |   86 
 igraph-1.2.7/igraph/src/gengraph_qsort.h                          |  718 
 igraph-1.2.7/igraph/src/gengraph_random.cpp                       |   60 
 igraph-1.2.7/igraph/src/gengraph_random.h                         |   54 
 igraph-1.2.7/igraph/src/gengraph_vertex_cover.h                   |   68 
 igraph-1.2.7/igraph/src/glet.c                                    | 1404 -
 igraph-1.2.7/igraph/src/glpk_support.c                            |   87 
 igraph-1.2.7/igraph/src/gml_tree.c                                |  370 
 igraph-1.2.7/igraph/src/hacks.c                                   |   13 
 igraph-1.2.7/igraph/src/heap.c                                    | 1273 -
 igraph-1.2.7/igraph/src/heap.pmt                                  |  326 
 igraph-1.2.7/igraph/src/hrg_dendro.h                              |  351 
 igraph-1.2.7/igraph/src/hrg_graph.h                               |  158 
 igraph-1.2.7/igraph/src/hrg_graph_simp.h                          |  134 
 igraph-1.2.7/igraph/src/hrg_rbtree.h                              |  148 
 igraph-1.2.7/igraph/src/hrg_splittree_eq.h                        |  180 
 igraph-1.2.7/igraph/src/igraph_arpack_internal.h                  |  310 
 igraph-1.2.7/igraph/src/igraph_blas_internal.h                    |   69 
 igraph-1.2.7/igraph/src/igraph_buckets.c                          |  210 
 igraph-1.2.7/igraph/src/igraph_cliquer.c                          |  124 
 igraph-1.2.7/igraph/src/igraph_cliquer.h                          |   16 
 igraph-1.2.7/igraph/src/igraph_error.c                            |  219 
 igraph-1.2.7/igraph/src/igraph_estack.c                           |   54 
 igraph-1.2.7/igraph/src/igraph_estack.h                           |   22 
 igraph-1.2.7/igraph/src/igraph_f2c.h                              |  286 
 igraph-1.2.7/igraph/src/igraph_fixed_vectorlist.c                 |   98 
 igraph-1.2.7/igraph/src/igraph_flow_internal.h                    |   25 
 igraph-1.2.7/igraph/src/igraph_glpk_support.h                     |   20 
 igraph-1.2.7/igraph/src/igraph_gml_tree.h                         |   74 
 igraph-1.2.7/igraph/src/igraph_grid.c                             |  832 
 igraph-1.2.7/igraph/src/igraph_hacks_internal.h                   |   32 
 igraph-1.2.7/igraph/src/igraph_handle_exceptions.h                |only
 igraph-1.2.7/igraph/src/igraph_hashtable.c                        |  148 
 igraph-1.2.7/igraph/src/igraph_heap.c                             |   10 
 igraph-1.2.7/igraph/src/igraph_hrg.cc                             | 1549 -
 igraph-1.2.7/igraph/src/igraph_hrg_types.cc                       | 5912 ++---
 igraph-1.2.7/igraph/src/igraph_interrupt_internal.h               |   38 
 igraph-1.2.7/igraph/src/igraph_isoclasses.h                       |only
 igraph-1.2.7/igraph/src/igraph_lapack_internal.h                  |  280 
 igraph-1.2.7/igraph/src/igraph_marked_queue.c                     |  112 
 igraph-1.2.7/igraph/src/igraph_marked_queue.h                     |   28 
 igraph-1.2.7/igraph/src/igraph_math.h                             |   40 
 igraph-1.2.7/igraph/src/igraph_psumtree.c                         |  102 
 igraph-1.2.7/igraph/src/igraph_set.c                              |  250 
 igraph-1.2.7/igraph/src/igraph_stack.c                            |   32 
 igraph-1.2.7/igraph/src/igraph_strvector.c                        |  651 
 igraph-1.2.7/igraph/src/igraph_threading.h                        |   16 
 igraph-1.2.7/igraph/src/igraph_trie.c                             |  504 
 igraph-1.2.7/igraph/src/igraph_types_internal.h                   |  246 
 igraph-1.2.7/igraph/src/igraph_version.h                          |   20 
 igraph-1.2.7/igraph/src/include/igraph.h                          |   12 
 igraph-1.2.7/igraph/src/include/igraph_adjlist.h                  |  145 
 igraph-1.2.7/igraph/src/include/igraph_arpack.h                   |  114 
 igraph-1.2.7/igraph/src/include/igraph_array.h                    |   10 
 igraph-1.2.7/igraph/src/include/igraph_array_pmt.h                |   46 
 igraph-1.2.7/igraph/src/include/igraph_attributes.h               |  545 
 igraph-1.2.7/igraph/src/include/igraph_bipartite.h                |   88 
 igraph-1.2.7/igraph/src/include/igraph_blas.h                     |   27 
 igraph-1.2.7/igraph/src/include/igraph_centrality.h               |  242 
 igraph-1.2.7/igraph/src/include/igraph_cliques.h                  |   78 
 igraph-1.2.7/igraph/src/include/igraph_cocitation.h               |   38 
 igraph-1.2.7/igraph/src/include/igraph_cohesive_blocks.h          |   24 
 igraph-1.2.7/igraph/src/include/igraph_coloring.h                 |   24 
 igraph-1.2.7/igraph/src/include/igraph_community.h                |  271 
 igraph-1.2.7/igraph/src/include/igraph_complex.h                  |   78 
 igraph-1.2.7/igraph/src/include/igraph_components.h               |   39 
 igraph-1.2.7/igraph/src/include/igraph_constants.h                |  211 
 igraph-1.2.7/igraph/src/include/igraph_constructors.h             |   58 
 igraph-1.2.7/igraph/src/include/igraph_conversion.h               |   37 
 igraph-1.2.7/igraph/src/include/igraph_datatype.h                 |   49 
 igraph-1.2.7/igraph/src/include/igraph_decls.h                    |   29 
 igraph-1.2.7/igraph/src/include/igraph_dqueue.h                   |   14 
 igraph-1.2.7/igraph/src/include/igraph_dqueue_pmt.h               |   46 
 igraph-1.2.7/igraph/src/include/igraph_eigen.h                    |  132 
 igraph-1.2.7/igraph/src/include/igraph_embedding.h                |   57 
 igraph-1.2.7/igraph/src/include/igraph_epidemics.h                |   24 
 igraph-1.2.7/igraph/src/include/igraph_error.h                    |  373 
 igraph-1.2.7/igraph/src/include/igraph_flow.h                     |  156 
 igraph-1.2.7/igraph/src/include/igraph_foreign.h                  |   64 
 igraph-1.2.7/igraph/src/include/igraph_games.h                    |  287 
 igraph-1.2.7/igraph/src/include/igraph_graphlets.h                |   30 
 igraph-1.2.7/igraph/src/include/igraph_heap.h                     |   10 
 igraph-1.2.7/igraph/src/include/igraph_heap_pmt.h                 |   42 
 igraph-1.2.7/igraph/src/include/igraph_hrg.h                      |   67 
 igraph-1.2.7/igraph/src/include/igraph_interface.h                |  109 
 igraph-1.2.7/igraph/src/include/igraph_interrupt.h                |   16 
 igraph-1.2.7/igraph/src/include/igraph_iterators.h                |  208 
 igraph-1.2.7/igraph/src/include/igraph_lapack.h                   |  100 
 igraph-1.2.7/igraph/src/include/igraph_layout.h                   |  263 
 igraph-1.2.7/igraph/src/include/igraph_lsap.h                     |   10 
 igraph-1.2.7/igraph/src/include/igraph_matching.h                 |   28 
 igraph-1.2.7/igraph/src/include/igraph_matrix.h                   |   12 
 igraph-1.2.7/igraph/src/include/igraph_matrix_pmt.h               |  286 
 igraph-1.2.7/igraph/src/include/igraph_memory.h                   |   14 
 igraph-1.2.7/igraph/src/include/igraph_microscopic_update.h       |   38 
 igraph-1.2.7/igraph/src/include/igraph_mixing.h                   |   30 
 igraph-1.2.7/igraph/src/include/igraph_motifs.h                   |   48 
 igraph-1.2.7/igraph/src/include/igraph_neighborhood.h             |   27 
 igraph-1.2.7/igraph/src/include/igraph_nongraph.h                 |   49 
 igraph-1.2.7/igraph/src/include/igraph_operators.h                |   44 
 igraph-1.2.7/igraph/src/include/igraph_paths.h                    |  181 
 igraph-1.2.7/igraph/src/include/igraph_pmt.h                      |  186 
 igraph-1.2.7/igraph/src/include/igraph_pmt_off.h                  |   78 
 igraph-1.2.7/igraph/src/include/igraph_progress.h                 |  114 
 igraph-1.2.7/igraph/src/include/igraph_psumtree.h                 |   30 
 igraph-1.2.7/igraph/src/include/igraph_qsort.h                    |   16 
 igraph-1.2.7/igraph/src/include/igraph_random.h                   |   77 
 igraph-1.2.7/igraph/src/include/igraph_scan.h                     |   50 
 igraph-1.2.7/igraph/src/include/igraph_scg.h                      |  219 
 igraph-1.2.7/igraph/src/include/igraph_separators.h               |   26 
 igraph-1.2.7/igraph/src/include/igraph_sparsemat.h                |  464 
 igraph-1.2.7/igraph/src/include/igraph_spmatrix.h                 |   42 
 igraph-1.2.7/igraph/src/include/igraph_stack.h                    |   10 
 igraph-1.2.7/igraph/src/include/igraph_stack_pmt.h                |   38 
 igraph-1.2.7/igraph/src/include/igraph_statusbar.h                |   86 
 igraph-1.2.7/igraph/src/include/igraph_structural.h               |  128 
 igraph-1.2.7/igraph/src/include/igraph_strvector.h                |   68 
 igraph-1.2.7/igraph/src/include/igraph_threading.h.in             |   16 
 igraph-1.2.7/igraph/src/include/igraph_topology.h                 |  293 
 igraph-1.2.7/igraph/src/include/igraph_transitivity.h             |   60 
 igraph-1.2.7/igraph/src/include/igraph_types.h                    |   34 
 igraph-1.2.7/igraph/src/include/igraph_vector.h                   |   55 
 igraph-1.2.7/igraph/src/include/igraph_vector_pmt.h               |  302 
 igraph-1.2.7/igraph/src/include/igraph_vector_ptr.h               |   38 
 igraph-1.2.7/igraph/src/include/igraph_vector_type.h              |   18 
 igraph-1.2.7/igraph/src/include/igraph_version.h.in               |   18 
 igraph-1.2.7/igraph/src/include/igraph_visitor.h                  |   80 
 igraph-1.2.7/igraph/src/infomap.cc                                |  462 
 igraph-1.2.7/igraph/src/infomap_FlowGraph.cc                      |  637 
 igraph-1.2.7/igraph/src/infomap_FlowGraph.h                       |   68 
 igraph-1.2.7/igraph/src/infomap_Greedy.cc                         | 1077 -
 igraph-1.2.7/igraph/src/infomap_Greedy.h                          |   98 
 igraph-1.2.7/igraph/src/infomap_Node.cc                           |   87 
 igraph-1.2.7/igraph/src/infomap_Node.h                            |   43 
 igraph-1.2.7/igraph/src/init.c                                    |   22 
 igraph-1.2.7/igraph/src/interrupt.c                               |   35 
 igraph-1.2.7/igraph/src/iterators.c                               | 2119 +-
 igraph-1.2.7/igraph/src/lad.c                                     | 2940 +-
 igraph-1.2.7/igraph/src/lapack.c                                  | 1311 -
 igraph-1.2.7/igraph/src/layout.c                                  | 3804 +--
 igraph-1.2.7/igraph/src/layout_dh.c                               |  673 
 igraph-1.2.7/igraph/src/layout_fr.c                               | 1143 -
 igraph-1.2.7/igraph/src/layout_gem.c                              |  375 
 igraph-1.2.7/igraph/src/layout_kk.c                               | 1098 -
 igraph-1.2.7/igraph/src/lsap.c                                    |  753 
 igraph-1.2.7/igraph/src/matching.c                                | 1534 -
 igraph-1.2.7/igraph/src/math.c                                    |  320 
 igraph-1.2.7/igraph/src/matrix.c                                  |  120 
 igraph-1.2.7/igraph/src/matrix.pmt                                | 1366 -
 igraph-1.2.7/igraph/src/maximal_cliques.c                         |  607 
 igraph-1.2.7/igraph/src/maximal_cliques_template.h                |  551 
 igraph-1.2.7/igraph/src/memory.c                                  |   30 
 igraph-1.2.7/igraph/src/microscopic_update.c                      | 1100 -
 igraph-1.2.7/igraph/src/mixing.c                                  |  372 
 igraph-1.2.7/igraph/src/motifs.c                                  | 1651 -
 igraph-1.2.7/igraph/src/operators.c                               | 1891 -
 igraph-1.2.7/igraph/src/optimal_modularity.c                      |  345 
 igraph-1.2.7/igraph/src/other.c                                   |  480 
 igraph-1.2.7/igraph/src/paths.c                                   |  210 
 igraph-1.2.7/igraph/src/plfit/error.c                             |   11 
 igraph-1.2.7/igraph/src/plfit/error.h                             |    6 
 igraph-1.2.7/igraph/src/plfit/gss.c                               |    7 
 igraph-1.2.7/igraph/src/plfit/gss.h                               |    8 
 igraph-1.2.7/igraph/src/plfit/hzeta.c                             |only
 igraph-1.2.7/igraph/src/plfit/hzeta.h                             |only
 igraph-1.2.7/igraph/src/plfit/kolmogorov.c                        |    6 
 igraph-1.2.7/igraph/src/plfit/kolmogorov.h                        |   10 
 igraph-1.2.7/igraph/src/plfit/mt.c                                |only
 igraph-1.2.7/igraph/src/plfit/mt.h                                |only
 igraph-1.2.7/igraph/src/plfit/options.c                           |   31 
 igraph-1.2.7/igraph/src/plfit/platform.c                          |only
 igraph-1.2.7/igraph/src/plfit/platform.h                          |   25 
 igraph-1.2.7/igraph/src/plfit/plfit.c                             | 1037 
 igraph-1.2.7/igraph/src/plfit/plfit.h                             |  104 
 igraph-1.2.7/igraph/src/plfit/plfit.inc                           |    5 
 igraph-1.2.7/igraph/src/plfit/rbinom.c                            |only
 igraph-1.2.7/igraph/src/plfit/sampling.c                          |only
 igraph-1.2.7/igraph/src/plfit/sampling.h                          |only
 igraph-1.2.7/igraph/src/pottsmodel_2.cpp                          | 3914 +--
 igraph-1.2.7/igraph/src/pottsmodel_2.h                            |  130 
 igraph-1.2.7/igraph/src/progress.c                                |  131 
 igraph-1.2.7/igraph/src/prpack.cpp                                |   24 
 igraph-1.2.7/igraph/src/prpack.h                                  |   26 
 igraph-1.2.7/igraph/src/prpack/prpack_base_graph.h                |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_csc.h                       |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_csr.h                       |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_edge_list.h                 |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_igraph_graph.h              |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_ge_graph.h     |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_graph.h        |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_gs_graph.h     |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_scc_graph.h    |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_preprocessed_schur_graph.h  |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_result.h                    |    6 
 igraph-1.2.7/igraph/src/prpack/prpack_solver.cpp                  |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_solver.h                    |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_utils.cpp                   |    2 
 igraph-1.2.7/igraph/src/prpack/prpack_utils.h                     |    2 
 igraph-1.2.7/igraph/src/pstdint.h                                 | 1170 -
 igraph-1.2.7/igraph/src/qsort.c                                   |  262 
 igraph-1.2.7/igraph/src/random.c                                  | 2529 +-
 igraph-1.2.7/igraph/src/random_walk.c                             |  163 
 igraph-1.2.7/igraph/src/rinterface.c                              |  173 
 igraph-1.2.7/igraph/src/sbm.c                                     |  974 
 igraph-1.2.7/igraph/src/scan.c                                    | 1351 -
 igraph-1.2.7/igraph/src/scg.c                                     | 3176 +--
 igraph-1.2.7/igraph/src/scg_approximate_methods.c                 |  239 
 igraph-1.2.7/igraph/src/scg_exact_scg.c                           |   78 
 igraph-1.2.7/igraph/src/scg_headers.h                             |   86 
 igraph-1.2.7/igraph/src/scg_kmeans.c                              |  134 
 igraph-1.2.7/igraph/src/scg_optimal_method.c                      |  391 
 igraph-1.2.7/igraph/src/scg_utils.c                               |  115 
 igraph-1.2.7/igraph/src/separators.c                              | 1365 -
 igraph-1.2.7/igraph/src/sir.c                                     |  362 
 igraph-1.2.7/igraph/src/spanning_trees.c                          |  566 
 igraph-1.2.7/igraph/src/sparsemat.c                               | 3936 +--
 igraph-1.2.7/igraph/src/spectral_properties.c                     |  727 
 igraph-1.2.7/igraph/src/spmatrix.c                                |  996 
 igraph-1.2.7/igraph/src/st-cuts.c                                 | 2575 +-
 igraph-1.2.7/igraph/src/stack.pmt                                 |  276 
 igraph-1.2.7/igraph/src/statusbar.c                               |   88 
 igraph-1.2.7/igraph/src/structural_properties.c                   |10394 +++++-----
 igraph-1.2.7/igraph/src/structural_properties_internal.h          |   31 
 igraph-1.2.7/igraph/src/structure_generators.c                    | 3288 +--
 igraph-1.2.7/igraph/src/sugiyama.c                                | 1898 -
 igraph-1.2.7/igraph/src/topology.c                                | 4767 ++--
 igraph-1.2.7/igraph/src/triangles.c                               | 1352 -
 igraph-1.2.7/igraph/src/triangles_template.h                      |  161 
 igraph-1.2.7/igraph/src/triangles_template1.h                     |  111 
 igraph-1.2.7/igraph/src/type_indexededgelist.c                    | 2204 +-
 igraph-1.2.7/igraph/src/types.c                                   |  192 
 igraph-1.2.7/igraph/src/uuid/gen_uuid.c                           |    2 
 igraph-1.2.7/igraph/src/vector.c                                  |  598 
 igraph-1.2.7/igraph/src/vector.pmt                                | 2575 +-
 igraph-1.2.7/igraph/src/vector_ptr.c                              |  453 
 igraph-1.2.7/igraph/src/version.c                                 |   54 
 igraph-1.2.7/igraph/src/visitors.c                                |  811 
 igraph-1.2.7/igraph/src/walktrap.cpp                              |  155 
 igraph-1.2.7/igraph/src/walktrap_communities.cpp                  | 1479 -
 igraph-1.2.7/igraph/src/walktrap_communities.h                    |  202 
 igraph-1.2.7/igraph/src/walktrap_graph.cpp                        |  304 
 igraph-1.2.7/igraph/src/walktrap_graph.h                          |   66 
 igraph-1.2.7/igraph/src/walktrap_heap.cpp                         |  238 
 igraph-1.2.7/igraph/src/walktrap_heap.h                           |  117 
 igraph-1.2.7/igraph/src/zeroin.c                                  |  277 
 igraph-1.2.7/igraph/tests/testthat.R                              |    2 
 igraph-1.2.7/igraph/tests/testthat/test-make_graph.R              |   22 
 igraph-1.2.7/igraph/tests/testthat/test-make_lattice.R            |only
 igraph-1.2.7/igraph/tests/testthat/test_add.edges.R               |    2 
 igraph-1.2.7/igraph/tests/testthat/test_all.st.cuts.R             |    6 
 igraph-1.2.7/igraph/tests/testthat/test_are.connected.R           |   18 
 igraph-1.2.7/igraph/tests/testthat/test_arpack.R                  |    4 
 igraph-1.2.7/igraph/tests/testthat/test_as.directed.R             |    4 
 igraph-1.2.7/igraph/tests/testthat/test_ba.game.R                 |   18 
 igraph-1.2.7/igraph/tests/testthat/test_bipartite.projection.R    |   36 
 igraph-1.2.7/igraph/tests/testthat/test_bipartite.random.game.R   |   20 
 igraph-1.2.7/igraph/tests/testthat/test_bug-1073705-indexing.R    |    4 
 igraph-1.2.7/igraph/tests/testthat/test_cliques.R                 |    3 
 igraph-1.2.7/igraph/tests/testthat/test_communities.R             |    5 
 igraph-1.2.7/igraph/tests/testthat/test_correlated.R              |    8 
 igraph-1.2.7/igraph/tests/testthat/test_count.multiple.R          |    2 
 igraph-1.2.7/igraph/tests/testthat/test_degree.sequence.game.R    |    4 
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Package GA updated to version 3.2.2 with previous version 3.2.1 dated 2021-04-21

Title: Genetic Algorithms
Description: Flexible general-purpose toolbox implementing genetic algorithms (GAs) for stochastic optimisation. Binary, real-valued, and permutation representations are available to optimize a fitness function, i.e. a function provided by users depending on their objective function. Several genetic operators are available and can be combined to explore the best settings for the current task. Furthermore, users can define new genetic operators and easily evaluate their performances. Local search using general-purpose optimisation algorithms can be applied stochastically to exploit interesting regions. GAs can be run sequentially or in parallel, using an explicit master-slave parallelisation or a coarse-grain islands approach.
Author: Luca Scrucca [aut, cre] (<https://orcid.org/0000-0003-3826-0484>)
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>

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Package cmsafvis updated to version 1.1.7 with previous version 1.1.5 dated 2021-09-06

Title: Tools to Visualize CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF) is a ground segment of the European Organization for the Exploitation of Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application Facilities. The CM SAF contributes to the sustainable monitoring of the climate system by providing essential climate variables related to the energy and water cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of eight National Meteorological and Hydrological Services. The 'cmsafvis' R-package provides a collection of R-operators for the analysis and visualization of CM SAF NetCDF data. CM SAF climate data records are provided for free via (<https://wui.cmsaf.eu/safira>). Detailed information and test data are provided on the CM SAF webpage (<http://www.cmsaf.eu/R_toolbox>).
Author: Steffen Kothe [aut, cre], Danny Parsons [ctb]
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>

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Package tidyndr updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-23

Title: Analysis of the Nigeria National Data Repository (NDR)
Description: The goal is to simplify routine analysis of the Nigeria National Data Repository (NDR) <https://ndr.shieldnigeriaproject.com> using the PEPFAR Monitoring, Evaluation, and Reporting (MER) indicators (see <https://datim.zendesk.com/hc/en-us/articles/360000084446-MER-Indicator-Reference-Guides>). It is designed to import in to R patient-level line-list downloaded as 'csv' file from the front-end of the NDR.
Author: Stephen Balogun [aut, cre] (<https://orcid.org/0000-0002-9928-3703>), Scholastica Olanrewaju [ctb], Oluwaseun Okunuga [ctb], Temitope Kolade [ctb], Geraldine Abone [ctb]
Maintainer: Stephen Balogun <stephentaiyebalogun@gmail.com>

Diff between tidyndr versions 0.1.0 dated 2021-03-23 and 0.1.1 dated 2021-10-15

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Package natstrat updated to version 2.0.0 with previous version 1.0.0 dated 2021-05-26

Title: Obtain Unweighted Natural Strata that Balance Many Covariates
Description: Natural strata can be used in observational studies to balance the distributions of many covariates across any number of treatment groups and any number of comparisons. These strata have proportional amounts of units within each stratum across the treatments, allowing for simple interpretation and aggregation across strata. Within each stratum, the units are chosen using randomized rounding of a linear program that balances many covariates. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
Author: Katherine Brumberg [aut, cre]
Maintainer: Katherine Brumberg <kbrum@wharton.upenn.edu>

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New package MALDIrppa with initial version 1.0.5-1
Package: MALDIrppa
Title: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Version: 1.0.5-1
Date: 2021-10-09
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>
Depends: R (>= 3.2.5), MALDIquant, signal, robustbase, lattice
ByteCompile: yes
Description: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data (Palarea-Albaladejo et al. (2018) <doi:10.1093/bioinformatics/btx628>).
License: GPL (>= 2)
Repository: CRAN
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2021-10-11 14:43:03 UTC; Japal
Author: Javier Palarea-Albaladejo [cre, aut] (<https://orcid.org/0000-0003-0162-669X>), Paolo Ribeca [ctb] (<https://orcid.org/0000-0001-5599-3933>), William Constantine [ctb] (Author of original C code used in archived wtmsa and ifultools R packages.), Keith L. Davidson [ctb] (Author of original C code used in archived wtmsa and ifultools R packages.), Insightful Corp. [cph] (Copyright holder named in some original C code used in archived wtmsa and ifultools R packages.)
Date/Publication: 2021-10-15 09:30:05 UTC

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New package L1mstate with initial version 1.0.1
Package: L1mstate
Title: L1-Regularized Multi-State Models
Version: 1.0.1
Date: 2021-10-7
Author: Xuan Dang
Maintainer: Xuan Dang <xuandang11289@gmail.com>
Description: Fitting the regularization path of the L1-regularized multi-state models since they can exploit sparsity structure of input. Different tuning regularization parameter methods are provided. The cumulative hazard rate estimation and the transition probability predictions can be made from the fitted models.
License: GPL (>= 2)
Encoding: UTF-8
Imports: Rcpp (>= 1.0.1)
LinkingTo: Rcpp, RcppEigen
Depends: Matrix (>= 1.2-10), MASS, mstate, colorspace
NeedsCompilation: yes
Packaged: 2021-10-11 13:43:10 UTC; xuand
Repository: CRAN
Date/Publication: 2021-10-15 09:10:12 UTC

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Package ivreg updated to version 0.6-1 with previous version 0.6-0 dated 2021-05-28

Title: Instrumental-Variables Regression by '2SLS', '2SM', or '2SMM', with Diagnostics
Description: Instrumental variable estimation for linear models by two-stage least-squares (2SLS) regression or by robust-regression via M-estimation (2SM) or MM-estimation (2SMM). The main ivreg() model-fitting function is designed to provide a workflow as similar as possible to standard lm() regression. A wide range of methods is provided for fitted ivreg model objects, including extensive functionality for computing and graphing regression diagnostics in addition to other standard model tools.
Author: John Fox [aut, cre] (<https://orcid.org/0000-0002-1196-8012>), Christian Kleiber [aut] (<https://orcid.org/0000-0002-6781-4733>), Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>), Nikolas Kuschnig [ctb] (<https://orcid.org/0000-0002-6642-2543>)
Maintainer: John Fox <jfox@mcmaster.ca>

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Package hockeyR updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-20

Title: Collect and Clean Hockey Stats
Description: Various functions to scrape hockey play-by-play data from the <https://www.nhl.com/>. It also contains functions to scrape data from <https://www.hockey-reference.com/>, including standings, player stats, and jersey number history.
Author: Daniel Morse [aut, cre]
Maintainer: Daniel Morse <danmorse8642@gmail.com>

Diff between hockeyR versions 0.1.0 dated 2021-09-20 and 0.1.1 dated 2021-10-15

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Package glmtlp updated to version 2.0.0 with previous version 1.1 dated 2018-02-07

Title: Generalized Linear Models with Truncated Lasso Penalty
Description: Extremely efficient procedures for fitting regularization path with l0, l1, and truncated lasso penalty for linear regression and logistic regression models. This version is a completely new version compared with our previous version, which was mainly based on R. New core algorithms are developed and are now written in C++ and highly optimized.
Author: Chunlin Li [aut], Yu Yang [aut, cre], Chong Wu [aut]
Maintainer: Yu Yang <yang6367@umn.edu>

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Package dfvad updated to version 0.3.6 with previous version 0.3.0 dated 2020-03-05

Title: Diewert and Fox's Method of Value Added Growth Decomposition
Description: Decomposing value added growth into explanatory factors. A cost constrained value added function is defined to specify the production frontier. Industry estimates can also be aggregated using a weighted average approach. Details about the methodology and data can be found in Diewert and Fox (2018) <doi:10.1093/oxfordhb/9780190226718.013.19> and Zeng, Parsons, Diewert and Fox (2018) <https://www.business.unsw.edu.au/research-site/centreforappliedeconomicresearch-site/Documents/emg2018-6_SZeng_EMG-Slides.pdf>.
Author: Shipei Zeng
Maintainer: Shipei Zeng <shipei.zeng@unswalumni.com>

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New package uniset with initial version 0.2.1
Package: uniset
Title: Dynamic Settings File
Version: 0.2.1
Maintainer: Bernhard Pollner <bernhard.pollner@mac.com>
Description: Any package (subsequently called 'target package') is enabled to provide its users an easily accessible, user-friendly and human readable text file where key=value pairs (used by functions defined in the target package) can be saved. This settings file lives in a location defined by the user of the target package, and its user-defined values remain unchanged even when the author of the target package is introducing or deleting keys, or when the target package is updated or re-installed.
URL: https://bpollner.github.io/uniset/
BugReports: https://github.com/bpollner/uniset/issues
Language: en-US
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.3.2)
Imports: easycsv
Suggests: covr, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2021-10-14 12:36:42 UTC; bernhard
Author: Bernhard Pollner [cre, aut], Zoltan Kovacs [aut]
Repository: CRAN
Date/Publication: 2021-10-15 07:50:01 UTC

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New package slasso with initial version 1.0.0
Package: slasso
Title: S-LASSO Estimator for the Function-on-Function Linear Regression
Version: 1.0.0
Description: Implements the smooth LASSO estimator for the function-on-function linear regression model described in Centofanti et al. (2020) <arXiv:2007.00529>.
License: GPL (>= 3)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Depends: inline
Imports: Rcpp, RcppArmadillo, fda, fda.usc, matrixcalc, parallel, matrixStats, MASS, plot3D, methods, cxxfunplus
URL: https://github.com/unina-sfere/slasso
BugReports: https://github.com/unina-sfere/slasso
SystemRequirements: GNU make
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: yes
Packaged: 2021-10-14 12:23:55 UTC; fabio
Author: Fabio Centofanti [cre, aut], Antonio Lepore [aut], Simone Vantini [aut], Matteo Fontana [aut]
Maintainer: Fabio Centofanti <fabio.centofanti@unina.it>
Repository: CRAN
Date/Publication: 2021-10-15 07:40:02 UTC

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New package pharmr with initial version 0.33.1
Package: pharmr
Encoding: UTF-8
Version: 0.33.1
Date: 2021-10-13
Title: Interface to the 'Pharmpy' 'Pharmacometrics' Library
Maintainer: Rikard Nordgren <rikard.nordgren@farmaci.uu.se>
Depends: R (>= 3.3.0), altair (>= 4.0.0)
SystemRequirements: Python (>= 3.6.0)
Imports: reticulate (>= 1.19), utils
Suggests: testthat, magrittr, here
NeedsCompilation: no
Description: Interface to the 'Pharmpy' 'pharmacometrics' library. The 'Reticulate' package is used to interface Python from R.
Config/reticulate: list( packages = list( list(package = "altair"), list(package = "pharmpy-core") ) )
URL: https://github.com/pharmpy/pharmr
BugReports: https://github.com/pharmpy/pharmr/issues
License: BSD_2_clause + file LICENSE
Packaged: 2021-10-14 11:49:57 UTC; rikard
Author: Rikard Nordgren [aut, cre, cph], Stella Belin [aut, cph], Mats O. Karlsson [sad], Andrew C. Hooker [sad], Sebastian Ueckert [sad] (<https://orcid.org/0000-0002-3712-0255>), Simon Carter [rev], Simon Buatois [rev], João A. Abrantes [rev], F. Hoffmann-La Roche Ltd. [fnd]
Repository: CRAN
Date/Publication: 2021-10-15 07:30:02 UTC

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Package PerFit updated to version 1.4.6 with previous version 1.4.5 dated 2021-02-21

Title: Person Fit
Description: Several person-fit statistics (PFSs; Meijer and Sijtsma, 2001, <doi:10.1177/01466210122031957>) are offered. These statistics allow assessing whether individual response patterns to tests or questionnaires are (im)plausible given the other respondents in the sample or given a specified item response theory model. Some PFSs apply to dichotomous data, such as the likelihood-based PFSs (lz, lz*) and the group-based PFSs (personal biserial correlation, caution index, (normed) number of Guttman errors, agreement/disagreement/dependability statistics, U3, ZU3, NCI, Ht). PFSs suitable to polytomous data include extensions of lz, U3, and (normed) number of Guttman errors.
Author: Jorge N. Tendeiro
Maintainer: Jorge N. Tendeiro <tendeiro@hiroshima-u.ac.jp>

Diff between PerFit versions 1.4.5 dated 2021-02-21 and 1.4.6 dated 2021-10-15

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New package palmid with initial version 0.0.3
Package: palmid
Title: RdRP Analysis Suite
Description: R Analysis suite for viral RNA dependent RNA polymerase (RdRP). Statistical and meta-data analysis of 'palmscan' output and 'palmDB'/ 'DIAMOND' alignment files. Cross reference an input RNA virus against 145,000 RdRP identified in the Serratus project.
Version: 0.0.3
URL: https://serratus.io/palmid
BugReports: https://github.com/ababaian/palmid/issues
License: AGPL-3
Encoding: UTF-8
LazyData: true
Suggests: sf, rnaturalearth, rnaturalearthdata
Imports: dbplyr, downloadthis, DBI, DT, ggplotify, ggwordcloud, ggExtra, grDevices, gridExtra (>= 2.3), htmltools, htmlwidgets, leaflet, methods, plotly, rmarkdown, RPostgreSQL, scales, stats, utils, viridisLite
Depends: R (>= 3.5.0), dplyr, ggplot2 (>= 3.3.3)
NeedsCompilation: no
Packaged: 2021-10-14 13:45:13 UTC; ab
Author: Artem Babaian [aut, cre]
Maintainer: Artem Babaian <artem@rRNA.ca>
Repository: CRAN
Date/Publication: 2021-10-15 07:50:04 UTC

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New package paletteknife with initial version 0.4.1
Package: paletteknife
Title: Create Colour Scales and Legend from Continuous or Categorical Vectors
Version: 0.4.1
Description: Streamlines the steps for adding colour scales and associated legends when working with base R graphics, especially for interactive use. Popular palettes are included and pretty legends produced when mapping a large variety of vector classes to a colour scale. An additional helper for adding axes and grid lines complements the base::plot() work flow.
License: MIT + file LICENSE
URL: https://github.com/johnxhobbs/paletteknife
BugReports: https://github.com/johnxhobbs/paletteknife/issues
Encoding: UTF-8
Depends: graphics, grDevices
NeedsCompilation: no
Packaged: 2021-10-14 12:30:26 UTC; john
Author: John Hobbs [aut, cre]
Maintainer: John Hobbs <johnxhobbs@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-15 07:40:05 UTC

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New package owidR with initial version 1.0.0
Package: owidR
Title: A Package for Importing Data from Our World in Data
Version: 1.0.0
Author: Piers York
Maintainer: Piers York <piersyork@gmail.com>
Description: Scrapes data from the Our World in Data website to offer easy to use functions for searching for datasets and downloading them into R.
URL: <https://github.com/piersyork/owidR>, https://github.com/owid/covid-19-data/, <https://ourworldindata.org/>
Imports: dplyr, rvest, readr, leaflet, stringr, ggplot2, sf, magrittr, forcats, jsonlite, htmltools, purrr, xml2, curl, ggrepel, scales, rlang, grDevices
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
Suggests: testthat (>= 3.0.0), utils, showtext, sysfonts
NeedsCompilation: no
Packaged: 2021-10-14 14:28:54 UTC; piers
Repository: CRAN
Date/Publication: 2021-10-15 07:50:07 UTC

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Package LDLcalc updated to version 1.1 with previous version 1.0 dated 2021-09-30

Title: Calculate and Predict the Low Density Lipoprotein Values
Description: A wide variety of ways to calculate (through equations) or predict (using 9 Machine learning methods as well as a stack algorithm combination of them all) the Low Density Lipoprotein values of patients based on the values of three other metrics as Total Cholesterol , Triglyceride and High Density Lipoprotein.
Author: Petros Paplomatas [aut, cre], Kostas Anagnostopoulos [aut]
Maintainer: Petros Paplomatas <P.paplomatas@hotmail.com>

Diff between LDLcalc versions 1.0 dated 2021-09-30 and 1.1 dated 2021-10-15

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Package parcats updated to version 0.0.3 with previous version 0.0.2 dated 2020-09-09

Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
Description: Complex graphical representations of data are best explored using interactive elements. 'parcats' adds interactive graphing capabilities to the 'easyalluvial' package. The 'plotly.js' parallel categories diagrams offer a good framework for creating interactive flow graphs that allow manual drag and drop sorting of dimensions and categories, highlighting single flows and displaying mouse over information. The 'plotly.js' dependency is quite heavy and therefore is outsourced into a separate package.
Author: Bjoern Koneswarakantha [aut, cre] (<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>

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Package rminizinc updated to version 0.0.8 with previous version 0.0.7 dated 2021-08-04

Title: R Interface to 'MiniZinc'
Description: Constraint optimization, or constraint programming, is the name given to identifying feasible solutions out of a very large set of candidates, where the problem can be modeled in terms of arbitrary constraints. 'MiniZinc' is a free and open-source constraint modeling language. Constraint satisfaction and discrete optimization problems can be formulated in a high-level modeling language. Models are compiled into an intermediate representation that is understood by a wide range of solvers. 'MiniZinc' itself provides several solvers, for instance 'GeCode'. R users can use the package to solve constraint programming problems without using 'MiniZinc' directly, modify existing 'MiniZinc' models and also create their own models.
Author: Akshit Achara, Lars Kotthoff, Hans W. Borchers, Guido Tack
Maintainer: Akshit Achara <acharaakshit@gmail.com>

Diff between rminizinc versions 0.0.7 dated 2021-08-04 and 0.0.8 dated 2021-10-15

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Package coronavirus updated to version 0.3.31 with previous version 0.3.30 dated 2021-09-19

Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.
Author: Rami Krispin [aut, cre], Jarrett Byrnes [aut] (<https://orcid.org/0000-0002-9791-9472>)
Maintainer: Rami Krispin <rami.krispin@gmail.com>

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Package bignum updated to version 0.3.0 with previous version 0.2.2 dated 2021-09-21

Title: Arbitrary-Precision Integer and Floating-Point Mathematics
Description: Classes for storing and manipulating arbitrary-precision integer vectors and high-precision floating-point vectors. These extend the range and precision of the 'integer' and 'double' data types found in R. This package utilizes the 'Boost.Multiprecision' C++ library. It is specifically designed to work well with the 'tidyverse' collection of R packages.
Author: David Hall [aut, cre, cph] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>

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