Mon, 02 Aug 2021

Package SpatialEpi updated to version 1.2.5 with previous version 1.2.4 dated 2021-07-27

Title: Methods and Data for Spatial Epidemiology
Description: Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb], Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>), Michelle Ross [ctb], Jon Wakefield [aut], Mikael Moise [aut] (<https://orcid.org/0000-0002-3608-1178>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>

Diff between SpatialEpi versions 1.2.4 dated 2021-07-27 and 1.2.5 dated 2021-08-02

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Package tidycat updated to version 0.1.2 with previous version 0.1.1 dated 2020-06-05

Title: Expand Tidy Output for Categorical Parameter Estimates
Description: Create additional rows and columns on broom::tidy() output to allow for easier control on categorical parameter estimates.
Author: Guy J. Abel [aut, cre] (<https://orcid.org/0000-0002-4893-5687>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>

Diff between tidycat versions 0.1.1 dated 2020-06-05 and 0.1.2 dated 2021-08-02

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Package tab updated to version 5.1.1 with previous version 4.1.1 dated 2019-06-17

Title: Create Summary Tables for Statistical Reports
Description: Contains functions for creating various types of summary tables, e.g. comparing characteristics across levels of a categorical variable and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards models. Functions are available to handle data from simple random samples as well as complex surveys.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen <vandomed@gmail.com>

Diff between tab versions 4.1.1 dated 2019-06-17 and 5.1.1 dated 2021-08-02

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Package rRofex updated to version 2.0.6 with previous version 2.0.5 dated 2021-04-28

Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre], Juan Francisco Gomez [ctb], Matba Rofex [cph]
Maintainer: Augusto Hassel <mpi-augusto@primary.com.ar>

Diff between rRofex versions 2.0.5 dated 2021-04-28 and 2.0.6 dated 2021-08-02

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Package RCT updated to version 1.1.1 with previous version 1.1 dated 2021-02-01

Title: Assign Treatments, Power Calculations, Balances, Impact Evaluation of Experiments
Description: Assists in the whole process of designing and evaluating Randomized Control Trials. Robust treatment assignment by strata/blocks, that handles misfits; Power calculations of the minimum detectable treatment effect or minimum populations; Balance tables of T-test of covariates; Balance Regression: (treatment ~ all x variables) with F-test of null model; Impact_evaluation: Impact evaluation regressions. This function gives you the option to include control_vars, fixed effect variables, cluster variables (for robust SE), multiple endogenous variables and multiple heterogeneous variables (to test treatment effect heterogeneity) summary_statistics: Function that creates a summary statistics table with statistics rank observations in n groups: Creates a factor variable with n groups. Each group has a min and max label attach to each category. Athey, Susan, and Guido W. Imbens (2017) <arXiv:1607.00698>.
Author: Isidoro Garcia-Urquieta [aut, cre]
Maintainer: Isidoro Garcia-Urquieta <isidoro.gu@gmail.com>

Diff between RCT versions 1.1 dated 2021-02-01 and 1.1.1 dated 2021-08-02

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Package exampletestr updated to version 1.6.4 with previous version 1.6.3 dated 2021-04-24

Title: Help for Writing Unit Tests Based on Function Examples
Description: Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package. Sort of like python 'doctests' for R.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>), Thomas Quinn [rev] (<https://orcid.org/0000-0003-0286-6329>), Laurent Gatto [rev] (<https://orcid.org/0000-0002-1520-2268>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between exampletestr versions 1.6.3 dated 2021-04-24 and 1.6.4 dated 2021-08-02

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Package dLagM updated to version 1.1.6.2 with previous version 1.1.4 dated 2020-07-13

Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>

Diff between dLagM versions 1.1.4 dated 2020-07-13 and 1.1.6.2 dated 2021-08-02

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Sun, 01 Aug 2021

Package unitizer updated to version 1.4.15 with previous version 1.4.14 dated 2021-04-30

Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test code with earlier versions of those same objects. If objects are unchanged the tests pass, otherwise execution stops with error details. If in interactive mode, tests can be reviewed through the provided interactive environment.
Author: Brodie Gaslam [aut, cre], R Core Team [cph] (Traceback function sources.)
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>

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Package GeoTcgaData updated to version 1.0.1 with previous version 1.0.0.1 dated 2021-07-26

Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>

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Package fwildclusterboot updated to version 0.3.6 with previous version 0.3.5 dated 2021-06-20

Title: Fast Wild Cluster Bootstrap Inference for Linear Regression Models
Description: Implementation of the fast algorithm for wild cluster bootstrap inference developed in Roodman et al (2019, STATA Journal) for linear regression models <https://journals.sagepub.com/doi/full/10.1177/1536867X19830877>, which makes it feasible to quickly calculate bootstrap test statistics based on a large number of bootstrap draws even for large samples - as long as the number of bootstrapping clusters is not too large. Multiway clustering, regression weights, bootstrap weights, fixed effects and subcluster bootstrapping are supported. Further, both restricted (WCR) and unrestricted (WCU) bootstrap are supported. Methods are provided for a variety of fitted models, including 'lm()', 'feols()' (from package 'fixest') and 'felm()' (from package 'lfe').
Author: Alexander Fischer [aut, cre], David Roodman [aut], Achim Zeileis [ctb] (Author of included sandwich fragments), Nathaniel Graham [ctb] (Contributor to included sandwich fragments), Susanne Koell [ctb] (Contributor to included sandwich fragments), Laurent Berge [ctb] (Author of included fixest fragments), Sebastian Krantz [ctb]
Maintainer: Alexander Fischer <alexander-fischer1801@t-online.de>

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Package colourvision updated to version 2.0.4 with previous version 2.0.3 dated 2021-01-31

Title: Colour Vision Models
Description: Colour vision models, colour spaces and colour thresholds. Provides flexibility to build user-defined colour vision models for n number of photoreceptor types. Also includes Vorobyev & Osorio (1998) Receptor Noise Limited models <doi:10.1098/rspb.1998.0302>, Chittka (1992) colour hexagon <doi:10.1007/BF00199331>, and Endler & Mielke (2005) model <doi:10.1111/j.1095-8312.2005.00540.x>. Models have been extended to accept any number of photoreceptor types.
Author: Felipe M. Gawryszewski
Maintainer: Felipe Malheiros Gawrysewski <f.gawry@gmail.com>

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Package jsTreeR updated to version 1.3.0 with previous version 1.2.0 dated 2021-01-16

Title: A Wrapper of the JavaScript Library 'jsTree'
Description: Creates interactive trees that can be included in 'Shiny' apps and R markdown documents. A tree allows to represent hierarchical data (e.g. the contents of a directory). Similar to the 'shinyTree' package but offers more features and options, such as the grid extension, restricting the drag-and-drop behavior, and settings for the search functionality. It is possible to attach some data to the nodes of a tree and then to get these data in 'Shiny' when a node is selected. Also provides a 'Shiny' gadget allowing to manipulate one or more folders.
Author: Stéphane Laurent [aut, cre], jQuery contributors [ctb, cph] (jQuery), Ivan Bozhanov [ctb, cph] (jsTree), Vedran Opacic [ctb, cph] (jsTree bootstrap theme), Avi Deitcher [ctb, cph] (jsTreeGrid), Philip Hutchison [ctb, cph] (PDFObject), Terence Eden [ctb, cph] (SuperTinyIcons)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

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Package tidyUSDA updated to version 0.3.2 with previous version 0.3.1 dated 2021-03-12

Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for Analysis and Visualization
Description: Provides a consistent API to pull United States Department of Agriculture census and survey data from the National Agricultural Statistics Service (NASS) QuickStats service.
Author: Brad Lindblad [aut, cre], Michael Thomas [ctb], Alex Mindeman [ctb]
Maintainer: Brad Lindblad <me@bradlindblad.com>

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Sat, 31 Jul 2021

Package rbibutils updated to version 2.2.2 with previous version 2.2.1 dated 2021-06-17

Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography formats, including 'Bibtex', 'Biblatex', 'Endnote', and 'Bibentry'. Includes a port of the 'bibutils' utilities by Chris Putnam <https://sourceforge.net/projects/bibutils/>. Supports all bibliography formats and character encodings implemented in 'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and modifications to bibutils' C code, conversion to Bibentry (R and C code)), Chris Putman [aut] (src/*, author of the bibutils libraries, https://sourceforge.net/projects/bibutils/), Richard Mathar [ctb] (src/addsout.c), Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>

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Package LHD updated to version 1.3.3 with previous version 1.3.2 dated 2021-04-05

Title: Latin Hypercube Designs (LHDs)
Description: Contains different algorithms and construction methods for optimal Latin hypercube designs (LHDs) with flexible sizes. Our package is comprehensive since it is capable of generating maximin distance LHDs, maximum projection LHDs, and orthogonal and nearly orthogonal LHDs. Detailed comparisons and summary of all the algorithms and construction methods in this package can be found at Hongzhi Wang, Qian Xiao and Abhyuday Mandal (2021) <arXiv:2010.09154>. This package is particularly useful in the area of Design and Analysis of Experiments (DAE). More specifically, design of computer experiments.
Author: Hongzhi Wang [aut, cre], Qian Xiao [aut], Abhyuday Mandal [aut]
Maintainer: Hongzhi Wang <hw34508@uga.edu>

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Package critpath updated to version 0.1.4 with previous version 0.1.3 dated 2021-06-27

Title: Setting the Critical Path
Description: Solving the problem of project management using CPM (Critical Path Method), PERT (Program Evaluation and Review Technique) and LESS (Least Cost Estimating and Scheduling) methods. The package sets the critical path, schedule and Gantt chart. In addition, it allows you to draw a graph with marked critical activities. For more information about project management, see: Taha H. A. (2017, ISBN:978-1-292-16554-7), Konarzewska I., Jewczak M., Kucharski A. (2020, ISBN:978-83-8220-112-3), Rama Murthy P. (2007, ISBN:978-81-224-2944-2).
Author: Adam Kucharski
Maintainer: Adam Kucharski <aqcharski@interia.pl>

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Package tidywikidatar updated to version 0.4.0 with previous version 0.3.0 dated 2021-06-07

Title: Explore 'Wikidata' Through Tidy Data Frames
Description: Query 'Wikidata' API <https://www.wikidata.org/wiki/Wikidata:Main_Page> with ease, get tidy data frames in response, and cache data in a local 'SQLite' database.
Author: Giorgio Comai [aut, cre, cph] (<https://orcid.org/0000-0002-0515-9542>), EDJNet [fnd]
Maintainer: Giorgio Comai <g@giorgiocomai.eu>

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Package pacs updated to version 0.2.8 with previous version 0.2.5 dated 2021-07-29

Title: Supplementary Tools for R Packages Developers
Description: Supplementary utils for CRAN maintainers and R packages developers. Validating the library or packages. Exploring a complexity of a specific package like evaluating sizes in bytes of all its dependencies. Assessing the life duration of a specific package version. Checking a package CRAN check page status for any errors and warnings. Retrieving a DESCRIPTION file for any package version. Getting a list of all releases for a specific package.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>

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Package abess updated to version 0.2.0 with previous version 0.1.0 dated 2021-04-21

Title: Adaptive Best Subset Selection in Polynomial Time
Description: Extremely efficient toolkit for solving the best subset selection problem in linear regression, logistic regression, Poisson regression, Cox proportional hazard model, multiple-response regression, multinomial logistic regression, and (sequential) principal component analysis. It implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times.
Author: Jin Zhu [aut, cre] (<https://orcid.org/0000-0001-8550-5822>), Kangkang Jiang [aut], Yanhang Zhang [aut], Liyuan Hu [aut], Junhao Huang [aut], Junxian Zhu [aut], Canhong Wen [aut], Heping Zhang [aut] (<https://orcid.org/0000-0002-0688-4076>), Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>), spectra contributors [cph] (Spectra implementation)
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>

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Package fritools updated to version 2.2.1 with previous version 2.2.0 dated 2021-07-26

Title: Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. These are utilities for packages <https://CRAN.R-project.org/package=cleanr>, <https://CRAN.R-project.org/package=document>, <https://CRAN.R-project.org/package=fakemake>, <https://CRAN.R-project.org/package=packager> and <https://CRAN.R-project.org/package=rasciidoc>. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package ProjectTemplate updated to version 0.10.2 with previous version 0.10.1 dated 2021-02-08

Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to automatically build a directory structure for a new R project. Using this structure, 'ProjectTemplate' automates data loading, preprocessing, library importing and unit testing.
Author: Aleksandar Blagotic [ctb], Diego Valle-Jones [ctb], Jeffrey Breen [ctb], Joakim Lundborg [ctb], John Myles White [aut, cph], Josh Bode [ctb], Kenton White [ctb, cre], Kirill Mueller [ctb], Matteo Redaelli [ctb], Noah Lorang [ctb], Patrick Schalk [ctb], Dominik Schneider [ctb], Gerold Hepp [ctb], Zunaira Jamile [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>

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Package postcards updated to version 0.2.2 with previous version 0.2.1 dated 2021-07-30

Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>

Diff between postcards versions 0.2.1 dated 2021-07-30 and 0.2.2 dated 2021-07-31

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Package lfe updated to version 2.8-7 with previous version 2.8-6 dated 2021-01-11

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024> Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>). WARNING: This package is NOT under active development anymore, no further improvements are to be expected, and the package is at risk of being removed from CRAN.
Author: Simen Gaure [aut] (<https://orcid.org/0000-0001-7251-8747>), Grant McDermott [ctb], Karl Dunkle Werner [ctb], Matthieu Stigler [ctb, cre] (<https://orcid.org/0000-0002-6802-4290>), Daniel Lüdecke [ctb]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>

Diff between lfe versions 2.8-6 dated 2021-01-11 and 2.8-7 dated 2021-07-31

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Package isocalcR updated to version 0.0.2 with previous version 0.0.1 dated 2021-07-08

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

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Package ecocomDP updated to version 1.1.0 with previous version 1.0.0 dated 2021-06-10

Title: Work with Datasets in the Ecological Community Design Pattern
Description: Tools to create, use, and convert 'ecocomDP' datasets. 'ecocomDP' is a dataset design pattern for harmonizing ecological community surveys in a research question agnostic format, from source datasets published across multiple repositories, and with methods that keep the derived datasets up-to-date as the underlying sources change. Described in O'Brien et al. (2021), <doi:10.1016/j.ecoinf.2021.101374>.
Author: Colin Smith [aut, cre, cph] (<https://orcid.org/0000-0003-2261-9931>), Eric Sokol [aut] (<https://orcid.org/0000-0001-5923-0917>), Margaret O'Brien [aut] (<https://orcid.org/0000-0002-1693-8322>), Matt Bitters [ctb], Melissa Chen [ctb], Savannah Gonzales [ctb], Matt Helmus [ctb], Brendan Hobart [ctb], Ruvi Jaimes [ctb], Lara Janson [ctb], Marta Jarzyna [ctb], Michael Just [ctb], Daijiang Li [ctb], Wynne Moss [ctb], Kari Norman [ctb], Stephanie Parker [ctb], Natalie Robinson [ctb], Thilina Surasinghe [ctb]
Maintainer: Colin Smith <colin.smith@wisc.edu>

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Package DBItest updated to version 1.7.1 with previous version 1.7.0 dated 2019-12-16

Title: Testing 'DBI' 'Backends'
Description: A helper that tests 'DBI' back ends for conformity to the interface.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>), RStudio [cph], R Consortium [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package apollo updated to version 0.2.5 with previous version 0.2.4 dated 2021-02-25

Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds has developed flexible code for the estimation and application of choice models in R. Users are able to write their own model functions or use a mix of already available ones. Random heterogeneity, both continuous and discrete and at the level of individuals and choices, can be incorporated for all models. There is support for both standalone models and hybrid model structures. Both classical and Bayesian estimation is available, and multiple discrete continuous models are covered in addition to discrete choice. Multi-threading processing is supported for estimation and a large number of pre and post-estimation routines, including for computing posterior (individual-level) distributions are available. For examples, a manual, and a support forum, visit <http://www.ApolloChoiceModelling.com>. For more information on choice models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess, S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview of the field.
Author: Stephane Hess [aut], David Palma [aut, cre], Thomas Hancock [ctb]
Maintainer: David Palma <D.Palma@leeds.ac.uk>

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Package shinyToastify updated to version 2.0.0 with previous version 1.0.0 dated 2021-07-15

Title: Pretty Notifications for 'Shiny'
Description: This is a wrapper of the 'React' library 'React-Toastify'. It allows to show some notifications (toasts) in 'Shiny' applications. There are options for the style, the position, the transition effect, and more.
Author: Stéphane Laurent [aut, cre], Fadi Khadra [cph] ('React-Toastify' library (https://fkhadra.github.io/react-toastify/introduction))
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

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Package tidytable updated to version 0.6.4 with previous version 0.6.3 dated 2021-06-22

Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible, giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre], Abdessabour Moutik [ctb], Matt Carlson [ctb], Ivan Leung [ctb], Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>

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Package mob updated to version 0.4.2 with previous version 0.4.1 dated 2021-04-05

Title: Monotonic Optimal Binning
Description: Generate the monotonic binning and perform the woe (weight of evidence) transformation for the logistic regression used in the consumer credit scorecard development. The woe transformation is a piecewise transformation that is linear to the log odds. For a numeric variable, all of its monotonic functional transformations will converge to the same woe transformation.
Author: WenSui Liu
Maintainer: WenSui Liu <liuwensui@gmail.com>

Diff between mob versions 0.4.1 dated 2021-04-05 and 0.4.2 dated 2021-07-31

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Package ggpp updated to version 0.4.2 with previous version 0.4.1 dated 2021-07-14

Title: Grammar Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Geomas: geom_table(), geom_plot() and geom_grob() add insets to plots using native data coordinates, while geom_table_npc(), geom_plot_npc() and geom_grob_npc() do the same using "npc" coordinates through new aesthetics "npcx" and "npcy". Statistics: select observations based on 2D density. Positions: radial nudging away from a center point and nudging away from a line or curve.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Kamil Slowikowski [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Fri, 30 Jul 2021

Package RcppAnnoy updated to version 0.0.19 with previous version 0.0.18 dated 2020-12-15

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

Diff between RcppAnnoy versions 0.0.18 dated 2020-12-15 and 0.0.19 dated 2021-07-30

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Package bndovb updated to version 1.1 with previous version 1.0 dated 2021-06-21

Title: Bounding Omitted Variable Bias Using Auxiliary Data
Description: Functions to implement a Hwang(2021) <doi:10.2139/ssrn.3866876> estimator, which bounds an omitted variable bias using auxiliary data.
Author: Yujung Hwang [aut, cre] (<https://orcid.org/0000-0002-8136-8987>)
Maintainer: Yujung Hwang <yujungghwang@gmail.com>

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Package postcards updated to version 0.2.1 with previous version 0.2.0 dated 2021-01-06

Title: Create Beautiful, Simple Personal Websites
Description: A collection of R Markdown templates for creating simple and easy to personalize single page websites.
Author: Sean Kross [aut, cre] (<https://orcid.org/0000-0001-5215-0316>)
Maintainer: Sean Kross <sean@seankross.com>

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Package micemd updated to version 1.7.0 with previous version 1.6.0 dated 2019-07-09

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>

Diff between micemd versions 1.6.0 dated 2019-07-09 and 1.7.0 dated 2021-07-30

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Package AtmChile updated to version 0.1.2 with previous version 0.1.1 dated 2021-07-13

Title: Download Air Quality and Meteorological Information of Chile
Description: Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<http://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.
Author: Francisco Catalan Meyer [aut, cre] (<https://orcid.org/0000-0003-3506-5376>), Manuel Leiva [aut] (<https://orcid.org/0000-0001-8891-0399>), Richard Toro [aut]
Maintainer: Francisco Catalan Meyer <francisco.catalan@ug.uchile.cl>

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Package dssd updated to version 0.3.0 with previous version 0.2.2 dated 2021-02-25

Title: Distance Sampling Survey Design
Description: Creates survey designs for distance sampling surveys. These designs can be assessed for various effort and coverage statistics. Once the user is satisfied with the design characteristics they can generate a set of transects to use in their distance sampling survey. Many of the designs implemented in this R package were first made available in our 'Distance' for Windows software and are detailed in Chapter 7 of Advanced Distance Sampling, Buckland et. al. (2008, ISBN-13: 978-0199225873). Find out more about estimating animal/plant abundance with distance sampling at <http://distancesampling.org/>.
Author: Laura Marshall [aut, cre], Rexstad Eric [ctb]
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>

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Package dataRetrieval updated to version 2.7.9 with previous version 2.7.8 dated 2021-06-26

Title: Retrieval Functions for USGS and EPA Hydrologic and Water Quality Data
Description: Collection of functions to help retrieve U.S. Geological Survey (USGS) and U.S. Environmental Protection Agency (EPA) water quality and hydrology data from web services. USGS web services are discovered from National Water Information System (NWIS) <https://waterservices.usgs.gov/> and <https://waterdata.usgs.gov/nwis>. Both EPA and USGS water quality data are obtained from the Water Quality Portal <https://www.waterqualitydata.us/>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>), Robert Hirsch [aut] (<https://orcid.org/0000-0002-4534-075X>), David Lorenz [aut], Jordan Read [ctb], Jordan Walker [ctb], Lindsay Carr [ctb], David Watkins [aut] (<https://orcid.org/0000-0002-7544-0700>), David Blodgett [ctb], Mike Johnson [aut] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>

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Package lidaRtRee updated to version 3.1.0 with previous version 3.0.2 dated 2021-04-10

Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
Description: Provides functions for forest analysis using airborne laser scanning (LiDAR remote sensing) data: tree detection (method 1 in Eysn et al. (2015) <doi:10.3390/f6051721>) and segmentation; forest parameters estimation and mapping with the area-based approach. It includes complementary steps for forest mapping: co-registration of field plots with LiDAR data (Monnet and Mermin (2014) <doi:10.3390/f5092307>); extraction of both physical (gaps, edges, trees) and statistical features from LiDAR data useful for e.g. habitat suitability modeling (Glad et al. (2020) <doi:10.1002/rse2.117>); model calibration with ground reference, and maps export.
Author: Jean-Matthieu Monnet [aut, cre], Pascal Obstétar [ctb]
Maintainer: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>

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Package ThresholdROC updated to version 2.9.0 with previous version 2.8.3 dated 2020-09-28

Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. We also provide functions for sample size determination and estimation of diagnostic accuracy measures. We also include graphical tools. The statistical methodology used here can be found in Perez-Jaume et al (2017) <doi:10.18637/jss.v082.i04>.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>

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Package gimms updated to version 1.2.1 with previous version 1.2.0 dated 2021-04-16

Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS NDVI3g files currently available online; download (and re-arrange, in the case of NDVI3g.v0) the half-monthly data sets; import downloaded files from ENVI binary (NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based on the widespread 'raster' package; conduct quality control; and generate monthly composites (e.g., maximum values) from the half-monthly input data. As a special gimmick, a method is included to conveniently apply the Mann-Kendall trend test upon 'Raster*' images, optionally featuring trend-free pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>

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Package gginnards updated to version 0.1.0-1 with previous version 0.1.0 dated 2021-05-27

Title: Explore the Innards of 'ggplot2' Objects
Description: Extensions to 'ggplot2' providing low-level debug tools: statistics and geometries echoing their data argument. Layer manipulation: deletion, insertion, extraction and reordering of layers. Deletion of unused variables from the data object embedded in "ggplot" objects.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package ADP updated to version 0.1.5 with previous version 0.1.3 dated 2021-07-28

Title: Adoption Probability, Triers and Users Rate of a New Product
Description: Calculate users prevalence of a product based on the prevalence of triers in the population. The measurement of triers is relatively easy. It is just a question of whether a person tried a product even once in his life or not. On the other hand, The measurement of people who also adopt it as part of their life is more complicated since adopting an innovative product is a subjective view of the individual. Mickey Kislev and Shira Kislev developed a formula to calculate the prevalence of a product's users to overcome this difficulty. The current package assists in calculating the users prevalence of a product based on the prevalence of triers in the population. See for: Kislev, M. M., and S. Kislev (2020) <doi:10.5539/ijms.v12n4p63>.
Author: Mickey Kislev [cre], Shira Kislev [aut]
Maintainer: Mickey Kislev <mickeykislev@researchgap.ac>

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Package openSkies updated to version 1.1.2 with previous version 1.1.1 dated 2021-04-17

Title: An R Package to Retrieve, Analyze and Visualize Air Traffic Data
Description: Provides functionalities and data structures to retrieve, analyze and visualize aviation data. It includes a client interface to the 'OpenSky' API <https://opensky-network.org>. It allows retrieval of flight information, as well as aircraft state vectors.
Author: Rafael Ayala, Daniel Ayala, David Ruiz, Aleix Sellés, Lara Sellés Vidal
Maintainer: Rafael Ayala <rafael.ayala@oist.jp>

Diff between openSkies versions 1.1.1 dated 2021-04-17 and 1.1.2 dated 2021-07-30

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Package graphsim updated to version 1.0.2 with previous version 1.0.1 dated 2020-07-17

Title: Simulate Expression Data from 'igraph' Networks
Description: Functions to develop simulated continuous data (e.g., gene expression) from a sigma covariance matrix derived from a graph structure in 'igraph' objects. Intended to extend 'mvtnorm' to take 'igraph' structures rather than sigma matrices as input. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. This allows the use of simulated data that correctly accounts for pathway relationships and correlations. Here we present a versatile statistical framework to simulate correlated gene expression data from biological pathways, by sampling from a multivariate normal distribution derived from a graph structure. This package allows the simulation of biological pathways from a graph structure based on a statistical model of gene expression. For example methods to infer biological pathways and gene regulatory networks from gene expression data can be tested on simulated datasets using this framework. This also allows for pathway structures to be considered as a confounding variable when simulating gene expression data to test the performance of genomic analyses.
Author: S. Thomas Kelly [aut, cre], Michael A. Black [aut, ths], Robrecht Cannoodt [ctb], Jason Cory Brunson [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>

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Package cmfrec updated to version 3.2.2 with previous version 3.2.1 dated 2021-07-29

Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization, Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the product of two low-dimensional matrices aided with secondary information matrices about rows and/or columns of 'X' which are also factorized using the same latent components. The intended usage is for recommender systems, dimensionality reduction, and missing value imputation. Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky, (2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model, (Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>), or the enhanced model with 'implicit features' (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009) <doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver (Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>), providing efficient methods for sparse and dense data, and mixtures thereof. Supports L1 and L2 regularization in the main models, offers alternative most-popular and content-based models, and implements functionality for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph], Jorge Nocedal [cph] (Copyright holder of included LBFGS library), Naoaki Okazaki [cph] (Copyright holder of included LBFGS library), David Blackman [cph] (Copyright holder of original Xoshiro code), Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package iForecast updated to version 1.0.3 with previous version 1.0.2 dated 2021-02-21

Title: Machine Learning Time Series Forecasting
Description: Compute both static and recursive time series forecasts of machine learning models.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>

Diff between iForecast versions 1.0.2 dated 2021-02-21 and 1.0.3 dated 2021-07-30

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Package emayili updated to version 0.4.15 with previous version 0.4.12 dated 2021-07-13

Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre], Matt Dennis [ctb], Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>), Daniel Fahey [ctb], Johann R. Kleinbub [ctb], Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>

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Package UCSCXenaShiny updated to version 1.1.1 with previous version 1.1.0 dated 2021-07-16

Title: Interactive Analysis of UCSC Xena Data
Description: Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>), Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>), Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>), Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>), Yin Li [aut], Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>

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Package RawHummus updated to version 0.1.5 with previous version 0.1.0 dated 2021-07-19

Title: Raw Data Quality Control Tool for LC-MS System
Description: Assess LC–MS system performance by visualizing instrument log files and monitoring raw quality control samples within a project.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>

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Package logr updated to version 1.2.5 with previous version 1.2.4 dated 2021-06-16

Title: Creates Log Files
Description: Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>

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Package epiR updated to version 2.0.33 with previous version 2.0.31 dated 2021-07-19

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay, Charles Reynard, Allison Cheung and Nagendra Singanallur.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

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Package echarty updated to version 0.3.1 with previous version 0.2.0 dated 2021-06-13

Title: Minimal R/Shiny Interface to JavaScript Library 'ECharts'
Description: The goal is to deliver the full functionality of 'ECharts' with minimal overhead. 'ECharts' is based on data structures and 'echarty' users build R lists for these same data structures. One to three 'echarty' commands are usually sufficient to produce any chart.
Author: Larry Helgason [aut, cre, cph], John Coene [aut, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>

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Package dlookr updated to version 0.5.0 with previous version 0.4.5 dated 2021-05-29

Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation. Data diagnostics provides information and visualization of missing values and outliers and unique and negative values to help you understand the distribution and quality of your data. Data exploration provides information and visualization of the descriptive statistics of univariate variables, normality tests and outliers, correlation of two variables, and relationship between target variable and predictor. Data transformation supports binning for categorizing continuous variables, imputates missing values and outliers, resolving skewness. And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>

Diff between dlookr versions 0.4.5 dated 2021-05-29 and 0.5.0 dated 2021-07-30

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Thu, 29 Jul 2021

Package riskmetric updated to version 0.1.1 with previous version 0.1.0 dated 2021-05-13

Title: Risk Metrics to Evaluating R Packages
Description: Facilities for assessing R packages against a number of metrics to help quantify their robustness.
Author: R Validation Hub [aut], Doug Kelkhoff [aut, cre], Marly Gotti [aut], Eli Miller [aut], Kevin K [aut], Yilong Zhang [aut], Eric Milliman [aut], Juliane Manitz [aut], Mark Padgham [ctb], PSI special interest group Application and Implementation of Methodologies in Statistics [cph]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>

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Package solitude updated to version 1.1.3 with previous version 1.1.1 dated 2020-09-17

Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre], David Zimmermann [ctb]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>

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Package RblDataLicense updated to version 0.2.4 with previous version 0.2.3 dated 2020-09-20

Title: R Interface to 'Bloomberg Data License'
Description: R interface to access prices and market data with the 'Bloomberg Data License' service from <https://www.bloomberg.com/professional/product/data-license/>. As a prerequisite, a valid Data License from 'Bloomberg' is needed together with the corresponding SFTP credentials and whitelisting of the IP from which accessing the service. This software and its author are in no way affiliated, endorsed, or approved by 'Bloomberg' or any of its affiliates. 'Bloomberg' is a registered trademark.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>

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Package cmfrec updated to version 3.2.1 with previous version 3.1.2 dated 2021-06-28

Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization, Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the product of two low-dimensional matrices aided with secondary information matrices about rows and/or columns of 'X' which are also factorized using the same latent components. The intended usage is for recommender systems, dimensionality reduction, and missing value imputation. Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky, (2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model, (Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>), or the enhanced model with 'implicit features' (Rendle, Zhang, Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009) <doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver (Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>), providing efficient methods for sparse and dense data, and mixtures thereof. Supports L1 and L2 regularization in the main models, offers alternative most-popular and content-based models, and implements functionality for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph], Jorge Nocedal [cph] (Copyright holder of included LBFGS library), Naoaki Okazaki [cph] (Copyright holder of included LBFGS library), David Blackman [cph] (Copyright holder of original Xoshiro code), Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package sommer updated to version 4.1.4 with previous version 4.1.3 dated 2021-04-05

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

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Package MALDIquant updated to version 1.20 with previous version 1.19.3 dated 2019-05-12

Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre] (<https://orcid.org/0000-0001-7406-4443>), Korbinian Strimmer [ths] (<https://orcid.org/0000-0001-7917-2056>)
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>

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Package Guerry updated to version 1.7.1 with previous version 1.7.0 dated 2020-01-29

Title: Maps, Data and Methods Related to Guerry (1833) "Moral Statistics of France"
Description: Maps of France in 1830, multivariate datasets from A.-M. Guerry and others, and statistical and graphic methods related to Guerry's "Moral Statistics of France". The goal is to facilitate the exploration and development of statistical and graphic methods for multivariate data in a geo-spatial context of historical interest.
Author: Michael Friendly [aut, cre], Stephane Dray [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package opitools updated to version 1.8.0 with previous version 1.0.2 dated 2021-03-05

Title: Analyzing the Opinions in a Big Text Document
Description: Designed for performing impact analysis of opinions in a digital text document (DTD). The package allows a user to assess the extent to which a theme or subject within a document impacts the overall opinion expressed in the document. The package can be applied to a wide range of opinion-based DTD, including commentaries on social media platforms (such as 'Facebook', 'Twitter' and 'Youtube'), online products reviews, and so on. The utility of 'opitools' was originally demonstrated in Adepeju and Jimoh (2021) <doi:10.31235/osf.io/c32qh> in the assessment of COVID-19 impacts on neighbourhood policing using Twitter data. Further examples can be found in the vignette of the package.
Author: Monsuru Adepeju [cre, aut],
Maintainer: Monsuru Adepeju <monsuur2010@yahoo.com>

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Package LSTS updated to version 2.1 with previous version 2.0 dated 2021-04-18

Title: Locally Stationary Time Series
Description: A set of functions that allow stationary analysis and locally stationary time series analysis.
Author: Ricardo Olea [aut, cph], Wilfredo Palma [aut, cph], Pilar Rubio [aut], Mauricio Vargas [aut, cre] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Mauricio Vargas <mavargas11@uc.cl>

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Package JuliaConnectoR updated to version 1.0.0 with previous version 0.6.3 dated 2021-03-27

Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R. Imported 'Julia' functions can directly be called as R functions. Data structures can be translated between 'Julia' and R.
Author: Stefan Lenz [aut, cre] (<https://orcid.org/0000-0001-9135-1743>), Harald Binder [aut] (<https://orcid.org/0000-0002-5666-8662>)
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>

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Package XLConnect updated to version 1.0.4 with previous version 1.0.3 dated 2021-04-11

Title: Excel Connector for R
Description: Provides comprehensive functionality to read, write and format Excel data.
Author: Mirai Solutions GmbH [aut], Martin Studer [cre], The Apache Software Foundation [ctb, cph] (Apache POI), Graph Builder [ctb, cph] (Curvesapi Java library), Brett Woolridge [ctb, cph] (SparseBitSet Java library)
Maintainer: Martin Studer <martin.studer@mirai-solutions.com>

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Package ggeffects updated to version 1.1.1 with previous version 1.1.0 dated 2021-04-30

Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs
Description: Compute marginal effects and adjusted predictions from statistical models and returns the result as tidy data frames. These data frames are ready to use with the 'ggplot2'-package. Effects and predictions can be calculated for many different models. Interaction terms, splines and polynomial terms are also supported. The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>), Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package AlphaSimR updated to version 1.0.3 with previous version 1.0.2 dated 2021-07-28

Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>), John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>), Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>), David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>

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Package RVIpkg updated to version 0.2.6 with previous version 0.2.5 dated 2021-07-20

Title: Regional Vulnerability Index
Description: The Regional Vulnerability Index (RVI), a statistical measure of brain structural abnormality, quantifies an individual's similarity to the expected pattern of deficits in schizophrenia (Kochunov P, Fan F, Ryan MC, et al. (2020) <doi:10.1002/hbm.25045>).
Author: Peter Kochunov [aut], Si Gao [aut, cre], Fatima Talib [aut]
Maintainer: Si Gao <sgao@som.umaryland.edu>

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Package roadoi updated to version 0.7.1 with previous version 0.7 dated 2021-01-20

Title: Find Free Versions of Scholarly Publications via Unpaywall
Description: This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.
Author: Najko Jahn [aut, cre], Tuija Sonkkila [rev] (Tuija Sonkkila reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/115, <https://orcid.org/0000-0002-6892-9305>), Ross Mounce [rev] (Ross Mounce reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/115, <https://orcid.org/0000-0002-3520-2046>), Anne Hobert [ctb] (<https://orcid.org/0000-0003-2429-2995>), Delwen Franzen [ctb]
Maintainer: Najko Jahn <najko.jahn@gmail.com>

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More information about roadoi at CRAN
Permanent link

Package gdalcubes updated to version 0.4.1 with previous version 0.4.0 dated 2021-07-13

Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time, applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values, exporting data cubes as 'netCDF' or 'GeoTIFF' files, and plotting. The package implements lazy evaluation and multithreading. All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries. See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] (<https://orcid.org/0000-0001-5281-3896>), Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Lewis Van Winkle [cph], Ole Christian Eidheim [cph], Howard Hinnant [cph], Adrian Colomitchi [cph], Florian Dang [cph], Paul Thompson [cph], Tomasz Kamiński [cph], Dropbox, Inc. [cph]
Maintainer: Marius Appel <marius.appel@uni-muenster.de>

Diff between gdalcubes versions 0.4.0 dated 2021-07-13 and 0.4.1 dated 2021-07-29

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More information about gdalcubes at CRAN
Permanent link

Package arrow updated to version 5.0.0 with previous version 4.0.1 dated 2021-05-28

Title: Integration to 'Apache' 'Arrow'
Description: 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.
Author: Neal Richardson [aut, cre], Ian Cook [aut], Nic Crane [aut], Jonathan Keane [aut], Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>), Jeroen Ooms [aut], Javier Luraschi [ctb], Jeffrey Wong [ctb], Apache Arrow [aut, cph]
Maintainer: Neal Richardson <neal@ursalabs.org>

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More information about arrow at CRAN
Permanent link

Package tsbox updated to version 0.3.0 with previous version 0.2.1 dated 2020-04-29

Title: Class-Agnostic Time Series
Description: Time series toolkit with identical behavior for all time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo', 'timeSeries', 'tsibble', 'tis' or 'irts'. Also converts reliably between these classes.
Author: Christoph Sax [aut, cre] (<https://orcid.org/0000-0002-7192-7044>)
Maintainer: Christoph Sax <christoph.sax@gmail.com>

Diff between tsbox versions 0.2.1 dated 2020-04-29 and 0.3.0 dated 2021-07-29

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Package statgenGWAS updated to version 1.0.7 with previous version 1.0.6 dated 2021-07-26

Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre] (<https://orcid.org/0000-0002-8673-2514>), Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>), Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>), Martin Boer [ctb], Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>), Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>), Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>), Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>), Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>), Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>), Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Package pillar updated to version 1.6.2 with previous version 1.6.1 dated 2021-05-16

Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

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Package param6 updated to version 0.2.1 with previous version 0.2.0 dated 2021-07-26

Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

Diff between param6 versions 0.2.0 dated 2021-07-26 and 0.2.1 dated 2021-07-29

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More information about param6 at CRAN
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Package fRLR updated to version 1.2.1 with previous version 1.2 dated 2021-07-28

Title: Fit Repeated Linear Regressions
Description: When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz/regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Author: Lijun Wang [aut, cre, cph]
Maintainer: Lijun Wang <szcfweiya@gmail.com>

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Package dPCP updated to version 1.0.4 with previous version 1.0.3 dated 2020-09-25

Title: Automated Analysis of Multiplex Digital PCR Data
Description: The automated clustering and quantification of the digital PCR data is based on the combination of 'DBSCAN' (Hahsler et al. (2019) <doi:10.18637/jss.v091.i01>) and 'c-means' (Bezdek et al. (1981) <doi:10.1007/978-1-4757-0450-1>) algorithms. The analysis is independent of multiplexing geometry, dPCR system, and input amount. The details about input data and parameters are available in the vignette.
Author: Alfonso De Falco [aut, cre] (<https://orcid.org/0000-0001-9985-9920>), Michel Mittelbronn [ctb], Christophe Olinger [ctb], Daniel Stieber [ctb], Laboratoire national de santé [cph]
Maintainer: Alfonso De Falco <alfonsodefalco90@gmail.com>

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Package convey updated to version 0.2.4 with previous version 0.2.3 dated 2021-03-18

Title: Income Concentration Analysis with Complex Survey Samples
Description: Variance estimation on indicators of income concentration and poverty using complex sample survey designs. Wrapper around the 'survey' package.
Author: Djalma Pessoa [aut], Anthony Damico [aut, cre], Guilherme Jacob [aut]
Maintainer: Anthony Damico <ajdamico@gmail.com>

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Package biClassify updated to version 1.2 with previous version 1.1 dated 2021-07-27

Title: Binary Classification Using Extensions of Discriminant Analysis
Description: Implements methods for sample size reduction within Linear and Quadratic Discriminant Analysis in Lapanowski and Gaynanova (2020) <arXiv:2005.03858>. Also includes methods for non-linear discriminant analysis with simultaneous sparse feature selection in Lapanowski and Gaynanova (2019) PMLR 89:1704-1713.
Author: Alexander F. Lapanowski [aut, cre], Irina Gaynanova [aut]
Maintainer: Alexander F. Lapanowski <aflapan@gmail.com>

Diff between biClassify versions 1.1 dated 2021-07-27 and 1.2 dated 2021-07-29

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Package Rilostat updated to version 1.1.8 with previous version 1.1.7 dated 2021-03-16

Title: ILO Open Data via Ilostat Bulk Download Facility or SDMX Web Service
Description: Tools to download data from the ilostat database <https://ilostat.ilo.org> together with search and manipulation utilities.
Author: ILO Department of Statistics [cph, fnd], David Bescond [aut, cre] (<https://orcid.org/0000-0002-1642-0304>), Mabelin Villarreal-Fuentes [ctb] (<https://orcid.org/0000-0001-5644-5760>)
Maintainer: David Bescond <bescond@ilo.org>

Diff between Rilostat versions 1.1.7 dated 2021-03-16 and 1.1.8 dated 2021-07-29

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Package DDPNA updated to version 0.3.0 with previous version 0.2.7 dated 2021-04-28

Title: Disease-Drived Differential Proteins Co-Expression Network Analysis
Description: Functions designed to connect disease-related differential proteins and co-expression network. It provides the basic statics analysis included t test, ANOVA analysis. The network construction is not offered by the package, you can used 'WGCNA' package which you can learn in Peter et al. (2008) <doi:10.1186/1471-2105-9-559>. It also provides module analysis included PCA analysis, two enrichment analysis, Planner maximally filtered graph extraction and hub analysis.
Author: Kefu Liu [aut, cre]
Maintainer: Kefu Liu <liukefu19@163.com>

Diff between DDPNA versions 0.2.7 dated 2021-04-28 and 0.3.0 dated 2021-07-29

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Wed, 28 Jul 2021

Package DSAIRM updated to version 0.9.3 with previous version 0.8.7 dated 2021-03-20

Title: Dynamical Systems Approach to Immune Response Modeling
Description: Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Author: Andreas Handel [aut, cre] (<https://orcid.org/0000-0002-4622-1146>), Cody Dailey [ctb], Yang Ge [ctb], Spencer Hall [ctb], Brian McKay [ctb], Sina Solaimanpour [ctb], Alexis Vittengl [ctb], Henok Woldu [ctb]
Maintainer: Andreas Handel <ahandel@uga.edu>

Diff between DSAIRM versions 0.8.7 dated 2021-03-20 and 0.9.3 dated 2021-07-28

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Permanent link

Package mgsub updated to version 1.7.3 with previous version 1.7.2 dated 2020-07-22

Title: Safe, Multiple, Simultaneous String Substitution
Description: Designed to enable simultaneous substitution in strings in a safe fashion. Safe means it does not rely on placeholders (which can cause errors in same length matches).
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>

Diff between mgsub versions 1.7.2 dated 2020-07-22 and 1.7.3 dated 2021-07-28

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Package rscorecard updated to version 0.20.0 with previous version 0.19.1 dated 2021-07-20

Title: A Method to Download Department of Education College Scorecard Data
Description: A method to download Department of Education College Scorecard data using the public API <https://collegescorecard.ed.gov/data/documentation/>. It is based on the 'dplyr' model of piped commands to select and filter data in a single chained function call. An API key from the U.S. Department of Education is required.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>

Diff between rscorecard versions 0.19.1 dated 2021-07-20 and 0.20.0 dated 2021-07-28

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Permanent link

Package gllvm updated to version 1.3.1 with previous version 1.3.0 dated 2021-04-30

Title: Generalized Linear Latent Variable Models
Description: Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either Laplace approximation method or variational approximation method implemented via TMB (Kristensen et al., (2016), <doi:10.18637/jss.v070.i05>). For details see Niku et al. (2019a) <doi:10.1371/journal.pone.0216129> and Niku et al. (2019b) <doi:10.1111/2041-210X.13303>.
Author: Jenni Niku [aut, cre], Wesley Brooks [aut], Riki Herliansyah [aut], Francis K.C. Hui [aut], Sara Taskinen [aut], David I. Warton [aut], Bert van der Veen [aut]
Maintainer: Jenni Niku <jenni.m.e.niku@jyu.fi>

Diff between gllvm versions 1.3.0 dated 2021-04-30 and 1.3.1 dated 2021-07-28

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Package Qtools updated to version 1.5.5 with previous version 1.5.4 dated 2021-02-07

Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These include methods for transformation-based quantile regression, quantile-based measures of location, scale and shape, methods for quantiles of discrete variables, quantile-based multiple imputation, restricted quantile regression, and directional quantile classification. A vignette is given in Geraci (2016, The R Journal) <doi:10.32614/RJ-2016-037> and included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>), Alessio Farcomeni [ctb] (Contributions to midrq code, <https://orcid.org/0000-0002-7104-5826>), Cinzia Viroli [ctb] (Contributions to dqc code, <https://orcid.org/0000-0002-3278-5266>)
Maintainer: Marco Geraci <marco.geraci@uniroma1.it>

Diff between Qtools versions 1.5.4 dated 2021-02-07 and 1.5.5 dated 2021-07-28

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Package AlphaSimR updated to version 1.0.2 with previous version 1.0.1 dated 2021-05-14

Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] (<https://orcid.org/0000-0003-0558-6656>), Gregor Gorjanc [ctb] (<https://orcid.org/0000-0001-8008-2787>), John Hickey [ctb] (<https://orcid.org/0000-0001-5675-3974>), Daniel Money [ctb] (<https://orcid.org/0000-0001-5151-3648>), David Wilson [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>

Diff between AlphaSimR versions 1.0.1 dated 2021-05-14 and 1.0.2 dated 2021-07-28

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Package pomp updated to version 3.5 with previous version 3.4 dated 2021-05-13

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Eamon B. O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

Diff between pomp versions 3.4 dated 2021-05-13 and 3.5 dated 2021-07-28

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Package insurancerating updated to version 0.6.7 with previous version 0.6.6 dated 2021-05-19

Title: Analytic Insurance Rating Techniques
Description: Methods for insurance rating. It helps actuaries to implement GLMs within all relevant steps needed to construct a risk premium from raw data. It provides a data driven strategy for the construction of insurance tariff classes. This strategy is based on the work by Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>. It also provides recipes on how to easily perform one-way, or univariate, analyses on an insurance portfolio. In addition it adds functionality to include reference categories in the levels of the coefficients in the output of a generalized linear regression analysis.
Author: Martin Haringa [aut, cre]
Maintainer: Martin Haringa <mtharinga@gmail.com>

Diff between insurancerating versions 0.6.6 dated 2021-05-19 and 0.6.7 dated 2021-07-28

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Package fastai updated to version 2.0.9 with previous version 2.0.8 dated 2021-05-16

Title: Interface to 'fastai'
Description: The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.
Author: Turgut Abdullayev [ctb, cre, cph, aut]
Maintainer: Turgut Abdullayev <turqut.a.314@gmail.com>

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Package deepNN updated to version 1.1 with previous version 1.0 dated 2020-03-05

Title: Deep Learning
Description: Implementation of some Deep Learning methods. Includes multilayer perceptron, different activation functions, regularisation strategies, stochastic gradient descent and dropout. Thanks go to the following references for helping to inspire and develop the package: Ian Goodfellow, Yoshua Bengio, Aaron Courville, Francis Bach (2016, ISBN:978-0262035613) Deep Learning. Terrence J. Sejnowski (2018, ISBN:978-0262038034) The Deep Learning Revolution. Grant Sanderson (3brown1blue) <https://www.youtube.com/playlist?list=PLZHQObOWTQDNU6R1_67000Dx_ZCJB-3pi> Neural Networks YouTube playlist. Michael A. Nielsen <http://neuralnetworksanddeeplearning.com/> Neural Networks and Deep Learning.
Author: Benjamin Taylor [aut, cre]
Maintainer: Benjamin Taylor <benjamin.taylor.software@gmail.com>

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Package protolite updated to version 2.1.1 with previous version 2.1 dated 2020-01-13

Title: Highly Optimized Protocol Buffer Serializers
Description: Pure C++ implementations for reading and writing several common data formats based on Google protocol-buffers. Currently supports 'rexp.proto' for serialized R objects, 'geobuf.proto' for binary geojson, and 'mvt.proto' for vector tiles. This package uses the auto-generated C++ code by protobuf-compiler, hence the entire serialization is optimized at compile time. The 'RProtoBuf' package on the other hand uses the protobuf runtime library to provide a general- purpose toolkit for reading and writing arbitrary protocol-buffer data in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package lwgeom updated to version 0.2-7 with previous version 0.2-6 dated 2021-04-02

Title: Bindings to Selected 'liblwgeom' Functions for Simple Features
Description: Access to selected functions found in 'liblwgeom' <https://github.com/postgis/postgis/tree/master/liblwgeom>, the light-weight geometry library used by 'PostGIS' <http://postgis.net/>.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Colin Rundel [ctb], Andy Teucher [ctb], liblwgeom developers [cph]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package cld3 updated to version 1.4.2 with previous version 1.4.1 dated 2021-01-11

Title: Google's Compact Language Detector 3
Description: Google's Compact Language Detector 3 is a neural network model for language identification and the successor of 'cld2' (available from CRAN). The algorithm is still experimental and takes a novel approach to language detection with different properties and outcomes. It can be useful to combine this with the Bayesian classifier results from 'cld2'. See <https://github.com/google/cld3#readme> for more information.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>), Google Inc [cph] (CLD3 C++ library)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package rebmix updated to version 2.13.1 with previous version 2.13.0 dated 2021-07-14

Title: Finite Mixture Modeling, Clustering & Classification
Description: Random univariate and multivariate finite mixture model generation, estimation, clustering, latent class analysis and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, Gumbel, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre] (<https://orcid.org/0000-0003-0637-3812>), Branislav Panic [ctb] (<https://orcid.org/0000-0001-8349-8550>), Jernej Klemenc [ctb] (<https://orcid.org/0000-0002-6778-6728>), Simon Oman [ctb] (<https://orcid.org/0000-0001-8213-0818>)
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>

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Package fairadapt updated to version 0.2.0 with previous version 0.1.0 dated 2019-11-28

Title: Fair Data Adaptation with Quantile Preservation
Description: An implementation of the fair data adaptation with quantile preservation described in Plecko & Meinshausen (2019) <arXiv:1911.06685>. The adaptation procedure uses the specified causal graph to pre-process the given training and testing data in such a way to remove the bias caused by the protected attribute. The procedure uses tree ensembles for quantile regression.
Author: Drago Plecko [aut, cre]
Maintainer: Drago Plecko <drago.plecko@stat.math.ethz.ch>

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Package blockcluster updated to version 4.5.1 with previous version 4.5.0 dated 2021-07-13

Title: Co-Clustering Package for Binary, Categorical, Contingency and Continuous Data-Sets
Description: Simultaneous clustering of rows and columns, usually designated by biclustering, co-clustering or block clustering, is an important technique in two way data analysis. It consists of estimating a mixture model which takes into account the block clustering problem on both the individual and variables sets. The 'blockcluster' package provides a bridge between the C++ core library build on top of the 'STK++' library, and the R statistical computing environment. This package allows to co-cluster binary <doi:10.1016/j.csda.2007.09.007>, contingency <doi:10.1080/03610920903140197>, continuous <doi:10.1007/s11634-013-0161-3> and categorical data-sets <doi:10.1007/s11222-014-9472-2>. It also provides utility functions to visualize the results. This package may be useful for various applications in fields of Data mining, Information retrieval, Biology, computer vision and many more. More information about the project and comprehensive tutorial can be found on the link mentioned in URL.
Author: Serge Iovleff [aut, cre], Parmeet Singh Bhatia [aut], Josselin Demont [ctb], Vincent Brault [ctb], Vincent Kubicki [ctb], Gerard Goavert [ctb], Christophe Biernacki [ctb], Gilles Celeux [ctb]
Maintainer: Serge Iovleff <Serge.Iovleff@stkpp.org>

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Package tergm updated to version 4.0.2 with previous version 4.0.1 dated 2021-06-24

Title: Fit, Simulate and Diagnose Models for Network Evolution Based on Exponential-Family Random Graph Models
Description: An integrated set of extensions to the 'ergm' package to analyze and simulate network evolution based on exponential-family random graph models (ERGM). 'tergm' is a part of the 'statnet' suite of packages for network analysis. See Krivitsky and Handcock (2014) <doi:10.1111/rssb.12014> and Carnegie, Krivitsky, Hunter, and Goodreau (2015) <doi:10.1080/10618600.2014.903087>.
Author: Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>), Mark S. Handcock [aut, ths], David R. Hunter [ctb], Steven M. Goodreau [ctb, ths], Martina Morris [ctb, ths], Nicole Bohme Carnegie [ctb], Carter T. Butts [ctb], Ayn Leslie-Cook [ctb], Skye Bender-deMoll [ctb], Li Wang [ctb], Kirk Li [ctb], Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel+tergm@unsw.edu.au>

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Package osmdata updated to version 0.1.6 with previous version 0.1.5 dated 2021-03-22

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (<https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Andrea Gilardi [ctb], Enrico Spinielli [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package IntCal updated to version 0.2.2 with previous version 0.2.1 dated 2021-07-19

Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided here in a single data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, and to plot the curves and their underlying data, as well as functions to calibrate radiocarbon dates.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package fRLR updated to version 1.2 with previous version 1.1 dated 2019-01-08

Title: Fit Repeated Linear Regressions
Description: When fitting a set of linear regressions which have some same variables, we can separate the matrix and reduce the computation cost. This package aims to fit a set of repeated linear regressions faster. More details can be found in this blog Lijun Wang (2017) <https://stats.hohoweiya.xyz//regression/2017/09/26/An-R-Package-Fit-Repeated-Linear-Regressions/>.
Author: Lijun Wang [aut, cre, cph]
Maintainer: Lijun Wang <szcfweiya@gmail.com>

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Package findInGit updated to version 0.1.1 with previous version 0.1.0 dated 2021-07-27

Title: Find Pattern in Files of All Branches of a 'git' Repository
Description: Creates a HTML widget which displays the results of searching for a pattern in files in a given 'git' repository, including all its branches. The results can also be returned in a dataframe.
Author: Stéphane Laurent [aut, cre], Rob Burns [cph] ('ansi-to-html' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

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Package fdaPOIFD updated to version 1.0.1 with previous version 1.0.0 dated 2021-01-13

Title: Partially Observed Integrated Functional Depth
Description: Integrated Depths for Partially Observed Functional Data (PoFD). Applications to visualization, outlier detection and classification. Software companion for Elías, Antonio, Jiménez, Raúl, Paganoni, Anna M. and Sangalli, Laura M., (2020), "Integrated Depth for Partially Observed Functional Data".
Author: Antonio Elías [aut, cre], Raúl Jiménez [ctb], Anna M. Paganoni [ctb], Laura M. Sangalli [ctb]
Maintainer: Antonio Elías <antonioefz91@gmail.com>

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Package e1071 updated to version 1.7-8 with previous version 1.7-7 dated 2021-05-23

Title: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre], Evgenia Dimitriadou [aut, cph], Kurt Hornik [aut], Andreas Weingessel [aut], Friedrich Leisch [aut], Chih-Chung Chang [ctb, cph] (libsvm C++-code), Chih-Chen Lin [ctb, cph] (libsvm C++-code)
Maintainer: David Meyer <David.Meyer@R-project.org>

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Package DALEX updated to version 2.3.0 with previous version 2.2.1 dated 2021-06-01

Title: moDel Agnostic Language for Exploration and eXplanation
Description: Unverified black box model is the path to the failure. Opaqueness leads to distrust. Distrust leads to ignoration. Ignoration leads to rejection. DALEX package xrays any model and helps to explore and explain its behaviour. Machine Learning (ML) models are widely used and have various applications in classification or regression. Models created with boosting, bagging, stacking or similar techniques are often used due to their high performance. But such black-box models usually lack of direct interpretability. DALEX package contains various methods that help to understand the link between input variables and model output. Implemented methods help to explore model on the level of a single instance as well as a level of the whole dataset. All model explainers are model agnostic and can be compared across different models. DALEX package is the cornerstone for 'DrWhy.AI' universe of packages for visual model exploration. Find more details in (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>), Szymon Maksymiuk [aut] (<https://orcid.org/0000-0002-3120-1601>), Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>

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Package ctmm updated to version 0.6.1 with previous version 0.6.0 dated 2021-01-10

Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data. The package is described in Calabrese et al (2016) <doi:10.1111/2041-210X.12559>, with models and methods based on those introduced in Fleming & Calabrese et al (2014) <doi:10.1086/675504>, Fleming et al (2014) <doi:10.1111/2041-210X.12176>, Fleming et al (2015) <doi:10.1103/PhysRevE.91.032107>, Fleming et al (2015) <doi:10.1890/14-2010.1>, Fleming et al (2016) <doi:10.1890/15-1607>, Péron & Fleming et al (2016) <doi:10.1186/s40462-016-0084-7>, Fleming & Calabrese (2017) <doi:10.1111/2041-210X.12673>, Péron et al (2017) <doi:10.1002/ecm.1260>, Fleming et al (2017) <doi:10.1016/j.ecoinf.2017.04.008>, Fleming et al (2018) <doi:10.1002/eap.1704>, Winner & Noonan et al (2018) <doi:10.1111/2041-210X.13027>, Fleming et al (2019) <doi:10.1111/2041-210X.13270>, Noonan & Fleming et al (2019) <doi:10.1186/s40462-019-0177-1>, Fleming et al (2020) <doi:10.1101/2020.06.12.130195>, and Noonan et al (2021) <doi:10.1111/2041-210X.13597>.
Author: Christen H. Fleming [aut, cre], Justin M. Calabrese [aut], Xianghui Dong [ctb], Kevin Winner [ctb], Guillaume Péron [ctb], Michael J. Noonan [ctb], Bart Kranstauber [ctb], Eliezer Gurarie [ctb], Kamran Safi [ctb], Paul C. Cross [dtc], Thomas Mueller [dtc], Rogério C. de Paula [dtc], Thomas Akre [dtc], Jonathan Drescher-Lehman [dtc], Autumn-Lynn Harrison [dtc], Ronaldo G. Morato [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>

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Package kindisperse updated to version 0.10.2 with previous version 0.10.1 dated 2021-07-17

Title: Simulate and Estimate Close-Kin Dispersal Kernels
Description: Functions for simulating and estimating kinship-related dispersal. Based on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A. Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito". Assumes an additive variance model of dispersal in two dimensions, compatible with Wright's neighbourhood area. Simple and composite dispersal simulations are supplied, as well as the functions needed to estimate parent-offspring dispersal for simulated or empirical data, and to undertake sampling design for future field studies of dispersal. For ease of use an integrated Shiny app is also included.
Author: Moshe-Elijah Jasper [aut, cre] (<https://orcid.org/0000-0003-4541-3223>)
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>

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Package stringdist updated to version 0.9.7 with previous version 0.9.6.3 dated 2020-10-09

Title: Approximate String Matching, Fuzzy Text Search, and String Distance Functions
Description: Implements an approximate string matching version of R's native 'match' function. Also offers fuzzy text search based on various string distance measures. Can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences. This package is built for speed and runs in parallel by using 'openMP'. An API for C or C++ is exposed as well. Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
Author: Mark van der Loo [aut, cre] (<https://orcid.org/0000-0002-9807-4686>), Jan van der Laan [ctb], R Core Team [ctb], Nick Logan [ctb], Chris Muir [ctb], Johannes Gruber [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

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Package OptCirClust updated to version 0.0.4 with previous version 0.0.3 dated 2020-12-18

Title: Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible
Description: Fast, optimal, and reproducible clustering algorithms for circular, periodic, or framed data. The algorithms introduced here are based on a core algorithm for optimal framed clustering the authors have developed (Debnath & Song 2021) <doi:10.1109/TCBB.2021.3077573>. The runtime of these algorithms is O(K N log^2 N), where K is the number of clusters and N is the number of circular data points. On a desktop computer using a single processor core, millions of data points can be grouped into a few clusters within seconds. One can apply the algorithms to characterize events along circular DNA molecules, circular RNA molecules, and circular genomes of bacteria, chloroplast, and mitochondria. One can also cluster climate data along any given longitude or latitude. Periodic data clustering can be formulated as circular clustering. The algorithms offer a general high-performance solution to circular, periodic, or framed data clustering.
Author: Tathagata Debnath [aut] (<https://orcid.org/0000-0001-6445-275X>), Joe Song [aut, cre] (<https://orcid.org/0000-0002-6883-6547>)
Maintainer: Joe Song <joemsong@cs.nmsu.edu>

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Package matrixcalc updated to version 1.0-5 with previous version 1.0-4 dated 2021-06-03

Title: Collection of Functions for Matrix Calculations
Description: A collection of functions to support matrix calculations for probability, econometric and numerical analysis. There are additional functions that are comparable to APL functions which are useful for actuarial models such as pension mathematics. This package is used for teaching and research purposes at the Department of Finance and Risk Engineering, New York University, Polytechnic Institute, Brooklyn, NY 11201. Horn, R.A. (1990) Matrix Analysis. ISBN 978-0521386326. Lancaster, P. (1969) Theory of Matrices. ISBN 978-0124355507. Lay, D.C. (1995) Linear Algebra: And Its Applications. ISBN 978-0201845563.
Author: Frederick Novomestky <fnovomes@poly.edu>
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>

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Package covid19india updated to version 0.1.3 with previous version 0.1.2 dated 2021-07-21

Title: Pulling Clean Data from Covid19india.org
Description: Pull raw and pre-cleaned versions of national and state-level COVID-19 time-series data from covid19india.org <https://www.covid19india.org>. Easily obtain and merge case count data, testing data, and vaccine data. Also assists in calculating the time-varying effective reproduction number with sensible parameters for COVID-19.
Author: Max Salvatore [aut, cre], Michael Kleinsasser [aut]
Maintainer: Max Salvatore <mmsalva@umich.edu>

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Package wcde updated to version 0.0.2 with previous version 0.0.1 dated 2021-06-23

Title: Download Data from the Wittgenstein Human Capital Data Explorer
Description: Download and plot education specific demographic data from the Wittgenstein Human Capital Data Explorer <http://dataexplorer.wittgensteincentre.org/>.
Author: Guy J. Abel [aut, cre, ctb] (<https://orcid.org/0000-0002-4893-5687>), Samir K.C. [ctb] (<https://orcid.org/0000-0002-5213-9181>), Michaela Potancokova [ctb], Claudia Reiter [ctb] (<https://orcid.org/0000-0002-1485-3851>), Andrea Tamburini [ctb], Dilek Yildiz [ctb] (<https://orcid.org/0000-0001-6192-0634>)
Maintainer: Guy J. Abel <g.j.abel@gmail.com>

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Package covid19italy updated to version 0.3.1 with previous version 0.3.0 dated 2020-07-21

Title: The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset
Description: Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.
Author: Rami Krispin [aut, cre]
Maintainer: Rami Krispin <rami.krispin@gmail.com>

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Package TestDataImputation updated to version 2.1 with previous version 1.2 dated 2020-11-16

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

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Package summarytools updated to version 1.0.0 with previous version 0.9.9 dated 2021-03-19

Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>

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Package BiDAG updated to version 2.0.3 with previous version 2.0.2 dated 2021-04-30

Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data or categorical data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks. References: J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>, N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>, D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>, J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>, M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.suter@bsse.ethz.ch>

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Tue, 27 Jul 2021

Package spatPomp updated to version 0.25.0.0 with previous version 0.23.0.0 dated 2021-07-09

Title: Inference for Spatiotemporal Partially Observed Markov Processes
Description: Inference on panel data using spatiotemporal partially-observed Markov process (SpatPOMP) models. To do so, it relies on and extends a number of facilities that the 'pomp' package provides for inference on time series data using partially-observed Markov process (POMP) models. Implemented methods include filtering and inference methods in Park and Ionides (2020) <doi:10.1007/s11222-020-09957-3>, Rebeschini and van Handel (2015) <doi:10.1214/14-AAP1061>, Evensen and van Leeuwen (1996) <doi:10.1029/94JC00572> and Ionides et al. (2021) <arXiv:2002.05211v2>. Pre-print statistical software article: Asfaw et al. (2021) <arXiv:2101.01157>.
Author: Kidus Asfaw [aut, cre], Aaron A. King [aut], Edward Ionides [aut], Joonha Park [ctb], Allister Ho [ctb]
Maintainer: Kidus Asfaw <kasfaw@umich.edu>

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Package representr updated to version 0.1.2 with previous version 0.1.1 dated 2020-10-20

Title: Create Representative Records After Entity Resolution
Description: An implementation of Kaplan, Betancourt, Steorts (2020) <arXiv:1810.01538> that creates representative records for use in downstream tasks after entity resolution is performed. Multiple methods for creating the representative records (data sets) are provided.
Author: Andee Kaplan [aut, cre], Brenda Betancourt [aut], Rebecca C. Steorts [aut]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>

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Package popkin updated to version 1.3.13 with previous version 1.3.8 dated 2021-02-11

Title: Estimate Kinship and FST under Arbitrary Population Structure
Description: Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>), John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>

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Package aqp updated to version 1.30 with previous version 1.29 dated 2021-04-07

Title: Algorithms for Quantitative Pedology
Description: The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps/>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Author: Dylan Beaudette [aut, cre], Pierre Roudier [aut, ctb], Andrew Brown [aut, ctb]
Maintainer: Dylan Beaudette <dylan.beaudette@usda.gov>

Diff between aqp versions 1.29 dated 2021-04-07 and 1.30 dated 2021-07-27

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Permanent link

Package pixarfilms updated to version 0.2.1 with previous version 0.2.0 dated 2021-05-03

Title: Pixar Films and Achievements
Description: Data about Disney Pixar films provided by Wikipedia. This package contains data about the films, the people involved, and their awards.
Author: Eric Leung [aut, cre] (<https://orcid.org/0000-0002-8724-1872>)
Maintainer: Eric Leung <erictleung@outlook.com>

Diff between pixarfilms versions 0.2.0 dated 2021-05-03 and 0.2.1 dated 2021-07-27

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Permanent link

Package OptM updated to version 0.1.5 with previous version 0.1.3 dated 2019-04-28

Title: Estimating the Optimal Number of Migration Edges from 'Treemix'
Description: The popular population genetic software 'Treemix' by 'Pickrell and Pritchard' (2012) <DOI:10.1371/journal.pgen.1002967> estimates the number of migration edges on a population tree. However, it can be difficult to determine the number of migration edges to include. Previously, it was customary to stop adding migration edges when 99.8% of variation in the data was explained, but 'OptM' automates this process using an ad hoc statistic based on the second-order rate of change in the log likelihood. 'OptM' also has added functionality for various threshold modeling to compare with the ad hoc statistic.
Author: Robert Fitak [aut, cre]
Maintainer: Robert Fitak <rfitak9@gmail.com>

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Package threeBrain updated to version 0.2.0 with previous version 0.1.9 dated 2021-01-10

Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome'). It can be inserted into any websites; see <https://dipterix.org/project/threebrain/>). as an example. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. This feature has been fully adopted by 'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to analyze 'iEEG/eCoG' data. Documentation about 'threeBrain' is provided by <https://dipterix.org/threeBrain/> and several vignettes included in this package. To cite the package, please check our 'NeuroImage' paper by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>), or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph], John Magnotti [aut], Brian Metzger [aut], Elizabeth Nesbitt [res], Meng Li [ths], Michael Beauchamp [aut, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

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Package stevemisc updated to version 1.2.0 with previous version 1.1.0 dated 2021-06-14

Title: Steve's Miscellaneous Functions
Description: These are miscellaneous functions that I find useful for my research and teaching. The contents include themes for plots, functions for simulating quantities of interest from regression models, functions for simulating various forms of fake data for instructional/research purposes, and many more. All told, the functions provided here are broadly useful for data organization, data presentation, data recoding, and data simulation.
Author: Steve Miller [aut, cre], Ben Bolker [ctb], Dave Armstrong [ctb], John Fox [ctb], Winston Chang [ctb], Brian Ripley [ctb], Bill Venables [ctb], Pascal van Kooten [ctb], Gerko Vink [ctb], Paul Williamson [ctb]
Maintainer: Steve Miller <steven.v.miller@gmail.com>

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Package rfacebookstat updated to version 2.4.0 with previous version 2.3.0 dated 2021-04-16

Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager from Facebook Marketing API into R. For more details see official documents by Facebook Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>

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Package rankUncertainty updated to version 1.0.1.0 with previous version 1.0.0.0 dated 2021-07-12

Title: Methods for Working with Uncertainty in Rankings
Description: Provides methods for measuring and describing uncertainty in rankings. See Rising (2021) <arXiv:2107.03459> for background.
Author: Justin Rising [aut, cre]
Maintainer: Justin Rising <justin.rising@us.af.mil>

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Package osmextract updated to version 0.3.1 with previous version 0.3.0 dated 2021-06-10

Title: Download and Import Open Stree tMap Data Extracts
Description: Match, download, convert and import Open Street Map data extracts obtained from several providers.
Author: Andrea Gilardi [aut, cre] (<https://orcid.org/0000-0002-9424-7439>), Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>), Barry Rowlingson [ctb] (<https://orcid.org/0000-0002-8586-6625>), Salva Fernández [rev] (Salva reviewed the package (v. 0.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/395>), Nicholas Potter [rev] (Nicholas reviewed the package (v. 0.1) for rOpenSci, see <https://github.com/ropensci/software-review/issues/395>)
Maintainer: Andrea Gilardi <andrea.gilardi@unimib.it>

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Package ergm updated to version 4.1.2 with previous version 4.0.1 dated 2021-06-21

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) <doi:10.18637/jss.v024.i03> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Mark S. Handcock [aut], David R. Hunter [aut], Carter T. Butts [aut], Steven M. Goodreau [aut], Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>), Martina Morris [aut], Li Wang [ctb], Kirk Li [ctb], Skye Bender-deMoll [ctb], Chad Klumb [ctb], Michał Bojanowski [ctb], Ben Bolker [ctb], Christian Schmid [ctb]
Maintainer: Pavel N. Krivitsky <pavel+ergm@unsw.edu.au>

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Package eq5d updated to version 0.10.0 with previous version 0.9.0 dated 2021-04-12

Title: Methods for Analysing 'EQ-5D' Data and Calculating 'EQ-5D' Index Scores
Description: EQ-5D is a popular health related quality of life instrument used in the clinical and economic evaluation of health care. Developed by the EuroQol group <https://euroqol.org/>, the instrument consists of two components: health state description and evaluation. For the description component a subject self-rates their health in terms of five dimensions; mobility, self-care, usual activities, pain/discomfort, and anxiety/depression using either a three-level (EQ-5D-3L, <https://euroqol.org/eq-5d-instruments/eq-5d-3l-about/>) or a five-level (EQ-5D-5L, <https://euroqol.org/eq-5d-instruments/eq-5d-5l-about/>) scale. Frequently the scores on these five dimensions are converted to a single utility index using country specific value sets, which can be used in the clinical and economic evaluation of health care as well as in population health surveys. The eq5d package provides methods to calculate index scores from a subject's dimension scores. 29 TTO and 11 VAS EQ-5D-3L value sets including those for countries in Szende et al (2007) <doi:10.1007/1-4020-5511-0> and Szende et al (2014) <doi:10.1007/978-94-007-7596-1>, 28 EQ-5D-5L EQ-VT value sets from the EuroQol website, the EQ-5D-5L crosswalk value sets developed by van Hout et al. (2012) <doi:10.1016/j.jval.2012.02.008>, the crosswalk value set for Russia and reverse crosswalk value sets. Two EQ-5D-Y value sets are also included. Methods are also included for the analysis of EQ-5D profiles along with a shiny web tool to enable the calculation, visualisation and automated statistical analysis of EQ-5D data via a web browser using EQ-5D dimension scores stored in CSV or Excel files.
Author: Fraser Morton [aut, cre], Jagtar Singh Nijjar [aut]
Maintainer: Fraser Morton <fraser.morton@glasgow.ac.uk>

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Package apcf updated to version 0.1.6 with previous version 0.1.5 dated 2020-07-05

Title: Adapted Pair Correlation Function
Description: The adapted pair correlation function transfers the concept of the pair correlation function from point patterns to patterns of objects of finite size and irregular shape (e.g. lakes within a country). This is a reimplementation of the method suggested by Nuske et al. (2009) <doi:10.1016/j.foreco.2009.09.050> using the libraries 'GEOS' and 'GDAL' directly instead of through 'PostGIS'.
Author: Robert Nuske [aut, cre] (<https://orcid.org/0000-0001-9773-2061>)
Maintainer: Robert Nuske <robert.nuske@nw-fva.de>

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Package RAthena updated to version 2.1.0 with previous version 2.0.1 dated 2021-02-24

Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package noctua updated to version 2.1.0 with previous version 2.0.1 dated 2021-02-24

Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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Package mapbayr updated to version 0.5.0 with previous version 0.4.1 dated 2021-04-30

Title: MAP-Bayesian Estimation of PK Parameters
Description: Performs maximum a posteriori Bayesian estimation of individual pharmacokinetic parameters from a model defined in `mrgsolve`, typically for model-based therapeutic drug monitoring. Internally computes an objective function value from model and data, performs optimization and returns predictions in a convenient format.
Author: Felicien Le Louedec [aut, cre] (<https://orcid.org/0000-0003-3699-2729>)
Maintainer: Felicien Le Louedec <lelouedec.felicien@iuct-oncopole.fr>

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Package vioplot updated to version 0.3.7 with previous version 0.3.6 dated 2021-03-29

Title: Violin Plot
Description: A violin plot is a combination of a box plot and a kernel density plot. This package allows extensive customisation of violin plots.
Author: Daniel Adler [aut, cph], S. Thomas Kelly [aut, cre], Tom M. Elliott [ctb]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>

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Package SpatialEpi updated to version 1.2.4 with previous version 1.2.3 dated 2018-06-02

Title: Methods and Data for Spatial Epidemiology
Description: Methods and data for cluster detection and disease mapping.
Author: Cici Chen [ctb], Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>), Michelle Ross [ctb], Jon Wakefield [aut], Mikael Moise [aut] (<https://orcid.org/0000-0002-3608-1178>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>

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Package RPostgreSQL updated to version 0.7 with previous version 0.6-2 dated 2017-06-24

Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>

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Package leiden updated to version 0.3.9 with previous version 0.3.8 dated 2021-05-24

Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl], Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>

Diff between leiden versions 0.3.8 dated 2021-05-24 and 0.3.9 dated 2021-07-27

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Package broom updated to version 0.7.9 with previous version 0.7.8 dated 2021-06-24

Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical objects in tidy tibbles. This makes it easy to report results, create plots and consistently work with large numbers of models at once. Broom provides three verbs that each provide different types of information about a model. tidy() summarizes information about model components such as coefficients of a regression. glance() reports information about an entire model, such as goodness of fit measures like AIC and BIC. augment() adds information about individual observations to a dataset, such as fitted values or influence measures.
Author: David Robinson [aut], Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>), Simon Couch [aut, cre] (<https://orcid.org/0000-0001-5676-5107>), Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>), Derek Chiu [ctb], Matthieu Gomez [ctb], Boris Demeshev [ctb], Dieter Menne [ctb], Benjamin Nutter [ctb], Luke Johnston [ctb], Ben Bolker [ctb], Francois Briatte [ctb], Jeffrey Arnold [ctb], Jonah Gabry [ctb], Luciano Selzer [ctb], Gavin Simpson [ctb], Jens Preussner [ctb], Jay Hesselberth [ctb], Hadley Wickham [ctb], Matthew Lincoln [ctb], Alessandro Gasparini [ctb], Lukasz Komsta [ctb], Frederick Novometsky [ctb], Wilson Freitas [ctb], Michelle Evans [ctb], Jason Cory Brunson [ctb], Simon Jackson [ctb], Ben Whalley [ctb], Karissa Whiting [ctb], Yves Rosseel [ctb], Michael Kuehn [ctb], Jorge Cimentada [ctb], Erle Holgersen [ctb], Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>), Ethan Christensen [ctb], Steven Pav [ctb], Paul PJ [ctb], Ben Schneider [ctb], Patrick Kennedy [ctb], Lily Medina [ctb], Brian Fannin [ctb], Jason Muhlenkamp [ctb], Matt Lehman [ctb], Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>), Nic Crane [ctb], Andrew Bates [ctb], Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>), Hideaki Hayashi [ctb], Luis Tobalina [ctb], Annie Wang [ctb], Wei Yang Tham [ctb], Clara Wang [ctb], Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>), Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>), E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>), Alex Wang [ctb], Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>), Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>), Jared Wilber [ctb], Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>), Eduard Szoecs [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Angus Moore [ctb], Nick Williams [ctb], Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>), Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>), Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>), Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>), Kevin Zarca [ctb], Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>), Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>), James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>), Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>), Joseph Larmarange [ctb], Max Kuhn [ctb], Michal Bojanowski [ctb], Hakon Malmedal [ctb], Clara Wang [ctb], Sergio Oller [ctb], Luke Sonnet [ctb], Jim Hester [ctb], Cory Brunson [ctb], Ben Schneider [ctb], Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>), Mara Averick [ctb], Aaron Jacobs [ctb], Andreas Bender [ctb], Sven Templer [ctb], Paul-Christian Buerkner [ctb], Matthew Kay [ctb], Erwan Le Pennec [ctb], Johan Junkka [ctb], Hao Zhu [ctb], Benjamin Soltoff [ctb], Zoe Wilkinson Saldana [ctb], Tyler Littlefield [ctb], Charles T. Gray [ctb], Shabbh E. Banks [ctb], Serina Robinson [ctb], Roger Bivand [ctb], Riinu Ots [ctb], Nicholas Williams [ctb], Nina Jakobsen [ctb], Michael Weylandt [ctb], Lisa Lendway [ctb], Karl Hailperin [ctb], Josue Rodriguez [ctb], Jenny Bryan [ctb], Chris Jarvis [ctb], Greg Macfarlane [ctb], Brian Mannakee [ctb], Drew Tyre [ctb], Shreyas Singh [ctb], Laurens Geffert [ctb], Hong Ooi [ctb], Henrik Bengtsson [ctb], Eduard Szocs [ctb], David Hugh-Jones [ctb], Matthieu Stigler [ctb], Hugo Tavares [ctb] (<https://orcid.org/0000-0001-9373-2726>), R. Willem Vervoort [ctb], Brenton M. Wiernik [ctb], Josh Yamamoto [ctb], Jasme Lee [ctb]
Maintainer: Simon Couch <scouch2@jhu.edu>

Diff between broom versions 0.7.8 dated 2021-06-24 and 0.7.9 dated 2021-07-27

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Package ShapleyValue updated to version 0.2.0 with previous version 0.1.0 dated 2021-05-25

Title: Shapley Value Regression for Relative Importance of Attributes
Description: Shapley Value Regression for calculating the relative importance of independent variables in linear regression with avoiding the collinearity.
Author: Jingyi Liang
Maintainer: Jingyi Liang <jingyiliang19@163.com>

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Package PoissonBinomial updated to version 1.2.4 with previous version 1.2.3 dated 2021-03-28

Title: Efficient Computation of Ordinary and Generalized Poisson Binomial Distributions
Description: Efficient implementations of multiple exact and approximate methods as described in Hong (2013) <doi:10.1016/j.csda.2012.10.006>, Biscarri, Zhao & Brunner (2018) <doi:10.1016/j.csda.2018.01.007> and Zhang, Hong & Balakrishnan (2018) <doi:10.1080/00949655.2018.1440294> for computing the probability mass, cumulative distribution and quantile functions, as well as generating random numbers for both the ordinary and generalized Poisson binomial distribution.
Author: Florian Junge [aut, cre]
Maintainer: Florian Junge <florian.junge@h-da.de>

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Package neonUtilities updated to version 2.1.1 with previous version 2.1.0 dated 2021-06-05

Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Claire Lunch [aut, cre, ctb], Christine Laney [aut, ctb], Nathan Mietkiewicz [aut, ctb], Eric Sokol [aut, ctb], Kaelin Cawley [aut, ctb], NEON (National Ecological Observatory Network) [aut]
Maintainer: Claire Lunch <clunch@battelleecology.org>

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Package ipaddress updated to version 0.5.3 with previous version 0.5.2 dated 2021-06-17

Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet Protocol) addresses and networks, inspired by the Python 'ipaddress' module. Offers full support for both IPv4 and IPv6 (Internet Protocol versions 4 and 6) address spaces. It is specifically designed to work well with the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>

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Mon, 26 Jul 2021

Package genio updated to version 1.0.25 with previous version 1.0.23 dated 2021-06-11

Title: Genetics Input/Output Functions
Description: Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>

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Package codemetar updated to version 0.3.2 with previous version 0.3.1 dated 2021-06-02

Title: Generate 'CodeMeta' Metadata for R Packages
Description: The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Anna Krystalli [rev, ctb] (<https://orcid.org/0000-0002-2378-4915>), Toph Allen [rev] (<https://orcid.org/0000-0003-4580-091X>), Maëlle Salmon [ctb, aut] (<https://orcid.org/0000-0002-2815-0399>), rOpenSci [fnd] (https://ropensci.org/), Katrin Leinweber [ctb] (<https://orcid.org/0000-0001-5135-5758>), Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>), Arfon Smith [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Sebastian Meyer [ctb] (<https://orcid.org/0000-0002-1791-9449>), Michael Rustler [ctb] (<https://orcid.org/0000-0003-0647-7726>), Hauke Sonnenberg [ctb] (<https://orcid.org/0000-0001-9134-2871>), Sebastian Kreutzer [ctb] (<https://orcid.org/0000-0002-0734-2199>), Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>)
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package param6 updated to version 0.2.0 with previous version 0.1.0 dated 2021-03-17

Title: A Fast and Lightweight R6 Parameter Interface
Description: By making use of 'set6', alongside the S3 and R6 paradigms, this package provides a fast and lightweight R6 interface for parameters and parameter sets.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>)
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

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Package gpg updated to version 1.2.3 with previous version 1.2.2 dated 2019-12-02

Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic methods. Includes utilities for public key encryption, creating and verifying digital signatures, and managing your local keyring. Note that some functionality depends on the version of GnuPG that is installed on the system. On Windows this package can be used together with 'GPG4Win' which provides a GUI for managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package tidybayes updated to version 3.0.0 with previous version 2.3.1 dated 2020-11-02

Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided to help extract tidy data frames of draws from Bayesian models and that generate point summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre], Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>

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Package ONEST updated to version 0.1.0 with previous version 0.0.1 dated 2020-09-07

Title: Observers Needed to Evaluate Subjective Tests
Description: This ONEST software implements the method of assessing the pathologist agreement in reading PD-L1 assays (Reisenbichler et al. (2020 <doi:10.1038/s41379-020-0544-x>)), to determine the minimum number of evaluators needed to estimate agreement involving a large number of raters. Input to the program should be binary(1/0) pathology data, where “0” may stand for negative and “1” for positive. Additional examples were given using the data from Rimm et al. (2017 <doi:10.1001/jamaoncol.2017.0013>).
Author: Gang Han [aut, cre], Baihong Guo [aut]
Maintainer: Gang Han <hangang.true@gmail.com>

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Package dipsaus updated to version 0.1.7 with previous version 0.1.6 dated 2021-07-08

Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using 'RcppParallel' and 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>

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Package adjclust updated to version 0.6.3 with previous version 0.5.99 dated 2020-06-18

Title: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix
Description: Implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient. This algorithm is described in Ambroise et al (2019) <https://almob.biomedcentral.com/articles/10.1186/s13015-019-0157-4>.
Author: Christophe Ambroise [aut], Shubham Chaturvedi [aut], Alia Dehman [aut], Pierre Neuvial [aut, cre], Guillem Rigaill [aut], Nathalie Vialaneix [aut], Gabriel Hoffman [aut]
Maintainer: Pierre Neuvial <pierre.neuvial@math.univ-toulouse.fr>

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Package RDP updated to version 0.1.6 with previous version 0.1.5 dated 2021-07-02

Title: The Ramer-Douglas-Peucker Algorithm
Description: Pretty fast implementation of the Ramer-Douglas-Peucker algorithm for reducing the number of points on a 2D curve. Urs Ramer (1972), "An iterative procedure for the polygonal approximation of plane curves" <doi:10.1016/S0146-664X(72)80017-0>. David H. Douglas and Thomas K. Peucker (1973), "Algorithms for the Reduction of the Number of Points Required to Represent a Digitized Line or its Caricature" <doi:10.3138/FM57-6770-U75U-7727>.
Author: Robert Dahl Jacobsen [aut, cre]
Maintainer: Robert Dahl Jacobsen <cran@dahl-jacobsen.dk>

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Package matrixStats updated to version 0.60.0 with previous version 0.59.0 dated 2021-06-01

Title: Functions that Apply to Rows and Columns of Matrices (and to Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph], Constantin Ahlmann-Eltze [ctb], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Jan Gleixner [ctb], Peter Hickey [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb], Brian Montgomery [ctb], Angelina Panagopoulou [ctb], Hugh Parsonage [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package MatrixExtra updated to version 0.1.6 with previous version 0.1.5 dated 2021-06-22

Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing: (a) Methods and operators that work natively on CSR formats (compressed sparse row, a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(), mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag(); (b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types, including the 'float32' type from 'float'; (c) Coercion methods between pairs of classes which are not present in 'Matrix', such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions; (d) Utility functions for sparse matrices such as sorting the indices or removing zero-valued entries; (e) Fast transposes that work by outputting in the opposite storage format; (f) Faster replacements for many 'Matrix' methods for all sparse types, such as slicing and elementwise multiplication.
Author: David Cortes [aut, cre, cph], Dmitry Selivanov [cph], Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included robinmap library)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>

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Package grpreg updated to version 3.4.0 with previous version 3.3.1 dated 2021-03-30

Title: Regularization Paths for Regression Models with Grouped Covariates
Description: Efficient algorithms for fitting the regularization path of linear regression, GLM, and Cox regression models with grouped penalties. This includes group selection methods such as group lasso, group MCP, and group SCAD as well as bi-level selection methods such as the group exponential lasso, the composite MCP, and the group bridge. For more information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>, Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015) <doi:10.1111/biom.12300>, or visit the package homepage <https://pbreheny.github.io/grpreg/>.
Author: Patrick Breheny [aut, cre] (<https://orcid.org/0000-0002-0650-1119>), Yaohui Zeng [ctb], Ryan Kurth [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>

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Package GeoTcgaData updated to version 1.0.0.1 with previous version 1.0.0 dated 2021-07-16

Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>

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Package FMM updated to version 0.3.0 with previous version 0.1.2 dated 2021-03-01

Title: Rhythmic Patterns Modeling by FMM Models
Description: Provides a collection of functions to fit and explore single, multi-component and restricted Frequency Modulated Moebius (FMM) models. 'FMM' is a nonlinear parametric regression model capable of fitting non-sinusoidal shapes in rhythmic patterns. Details about the mathematical formulation of 'FMM' models can be found in Rueda et al. (2019) <doi:10.1038/s41598-019-54569-1>.
Author: Itziar Fernandez, Alejandro Rodriguez-Collado, Yolanda Larriba, Adrian Lamela, Christian Canedo, Cristina Rueda
Maintainer: Itziar Fernandez <itziar.fernandez@uva.es>

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Package DSSAT updated to version 0.0.3 with previous version 0.0.2 dated 2020-05-18

Title: A Comprehensive R Interface for the DSSAT Cropping Systems Model
Description: The purpose of this package is to provide a comprehensive R interface to the Decision Support System for Agrotechnology Transfer Cropping Systems Model (DSSAT-CSM) documented by Jones et al (2003) <doi:10.1016/S1161-0301(02)00107-7>. The package provides cross-platform functions to read and write input files, run DSSAT-CSM, and read output files.
Author: Phillip D. Alderman [aut, cre]
Maintainer: Phillip D. Alderman <phillip.alderman@okstate.edu>

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Package codalm updated to version 0.1.2 with previous version 0.1.1 dated 2021-06-21

Title: Transformation-Free Linear Regression for Compositional Outcomes and Predictors
Description: Implements the expectation-maximization (EM) algorithm as described in Fiksel et al. (2021) <doi:10.1111/biom.13465> for transformation-free linear regression for compositional outcomes and predictors.
Author: Jacob Fiksel [aut, cre] (<https://orcid.org/0000-0001-7067-1334>), Abhirup Datta [aut]
Maintainer: Jacob Fiksel <jfiksel@gmail.com>

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Package auditor updated to version 1.3.3 with previous version 1.3.0 dated 2020-05-28

Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model. The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots. This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre] (<https://orcid.org/0000-0001-6563-5742>), Przemyslaw Biecek [aut, ths] (<https://orcid.org/0000-0001-8423-1823>), Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>), Tomasz Mikołajczyk [aut], Michal Burdukiewicz [ctb], Szymon Maksymiuk [ctb]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>

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Package maxLik updated to version 1.5-2 with previous version 1.4-8 dated 2021-03-22

Title: Maximum Likelihood Estimation and Related Tools
Description: Functions for Maximum Likelihood (ML) estimation, non-linear optimization, and related tools. It includes a unified way to call different optimizers, and classes and methods to handle the results from the Maximum Likelihood viewpoint. It also includes a number of convenience tools for testing and developing your own models.
Author: Ott Toomet [aut, cre], Arne Henningsen [aut], Spencer Graves [ctb], Yves Croissant [ctb], David Hugh-Jones [ctb], Luca Scrucca [ctb]
Maintainer: Ott Toomet <otoomet@gmail.com>

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Package clusrank updated to version 1.0-1 with previous version 1.0-0 dated 2020-12-10

Title: Wilcoxon Rank Tests for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data documented in Jiang et. al (2020) <doi:10.18637/jss.v096.i06>.
Author: Wenjie Wang [cre, ctb] (<https://orcid.org/0000-0003-0363-3180>), Yujing Jiang [aut], Mei-Ling Ting Lee [ctb], Jun Yan [ctb]
Maintainer: Wenjie Wang <wang@wwenjie.org>

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Package proffer updated to version 0.1.5 with previous version 0.1.3 dated 2021-06-28

Title: Profile R Code and Visualize with 'Pprof'
Description: Like similar profiling tools, the 'proffer' package automatically detects sources of slowness in R code. The distinguishing feature of 'proffer' is its utilization of 'pprof', which supplies interactive visualizations that are efficient and easy to interpret. Behind the scenes, the 'profile' package converts native Rprof() data to a protocol buffer that 'pprof' understands. For the documentation of 'proffer', visit <https://r-prof.github.io/proffer/>. To learn about the implementations and methodologies of 'pprof', 'profile', and protocol buffers, visit <https://github.com/google/pprof>. <https://developers.google.com/protocol-buffers>, and <https://github.com/r-prof/profile>, respectively.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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Package landsepi updated to version 1.1.0 with previous version 1.0.2 dated 2020-11-30

Title: Landscape Epidemiology and Evolution
Description: A stochastic, spatially-explicit, demo-genetic model simulating the spread and evolution of a plant pathogen in a heterogeneous landscape to assess resistance deployment strategies. It is based on a spatial geometry for describing the landscape and allocation of different cultivars, a dispersal kernel for the dissemination of the pathogen, and a SEIR ('Susceptible-Exposed-Infectious-Removed’) structure with a discrete time step. It provides a useful tool to assess the performance of a wide range of deployment options with respect to their epidemiological, evolutionary and economic outcomes. Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G Barrett, Peter H Thrall (2018) <doi:10.1371/journal.pcbi.1006067>.
Author: Loup Rimbaud [aut], Julien Papaix [aut], Jean-François Rey [aut, cre] (<https://orcid.org/0000-0003-3281-6701>), Jean-Loup Gaussen [ctb]
Maintainer: Jean-François Rey <jean-francois.rey@inrae.fr>

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Package twang updated to version 2.4 with previous version 2.3 dated 2021-06-10

Title: Toolkit for Weighting and Analysis of Nonequivalent Groups
Description: Provides functions for propensity score estimating and weighting, nonresponse weighting, and diagnosis of the weights.
Author: Matthew Cefalu <Matthew_Cefalu@rand.org>, Greg Ridgeway, Dan McCaffrey, Andrew Morral, Beth Ann Griffin, and Lane Burgette
Maintainer: Matthew Cefalu <Matthew_Cefalu@rand.org>

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Package statgenGWAS updated to version 1.0.6 with previous version 1.0.5 dated 2020-09-29

Title: Genome Wide Association Studies
Description: Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Author: Bart-Jan van Rossum [aut, cre] (<https://orcid.org/0000-0002-8673-2514>), Willem Kruijer [aut] (<https://orcid.org/0000-0001-7179-1733>), Fred van Eeuwijk [ctb] (<https://orcid.org/0000-0003-3672-2921>), Martin Boer [ctb], Marcos Malosetti [ctb] (<https://orcid.org/0000-0002-8150-1397>), Daniela Bustos-Korts [ctb] (<https://orcid.org/0000-0003-3827-6726>), Emilie Millet [ctb] (<https://orcid.org/0000-0002-2913-4892>), Joao Paulo [ctb] (<https://orcid.org/0000-0002-4180-0763>), Maikel Verouden [ctb] (<https://orcid.org/0000-0002-4893-3323>), Ron Wehrens [ctb] (<https://orcid.org/0000-0002-8798-5599>), Choazhi Zheng [ctb] (<https://orcid.org/0000-0001-6030-3933>)
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Package fritools updated to version 2.2.0 with previous version 2.1.0 dated 2021-07-14

Title: Utilities for the Forest Research Institute of the State Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper functions for finding and searching files on disk, searching for and removing R objects from the workspace. These are utilities for packages <https://CRAN.R-project.org/package=cleanr>, <https://CRAN.R-project.org/package=document>, <https://CRAN.R-project.org/package=fakemake>, <https://CRAN.R-project.org/package=packager> and <https://CRAN.R-project.org/package=rasciidoc>. Does not import or depend on any third party package, but on core R only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

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Package fusen updated to version 0.2.3 with previous version 0.2.2 dated 2021-07-09

Title: Build a Package from Rmarkdown File
Description: Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.
Author: Sebastien Rochette [aut, cre] (<https://orcid.org/0000-0002-1565-9313>), ThinkR [cph]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>

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Package SOMEnv updated to version 1.1.2 with previous version 1.1.1 dated 2021-03-02

Title: SOM Algorithm for the Analysis of Multivariate Environmental Data
Description: Analysis of multivariate environmental high frequency data by Self-Organizing Map and k-means clustering algorithms. By means of the graphical user interface it provides a comfortable way to elaborate by self-organizing map algorithm rather big datasets (txt files up to 100 MB ) obtained by environmental high-frequency monitoring by sensors/instruments. The functions present in the package are based on 'kohonen' and 'openair' packages implemented by functions embedding Vesanto et al. (2001) <http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf> heuristic rules for map initialization parameters, k-means clustering algorithm and map features visualization. Cluster profiles visualization as well as graphs dedicated to the visualization of time-dependent variables Licen et al. (2020) <doi:10.4209/aaqr.2019.08.0414> are provided.
Author: Sabina Licen [aut, cre], Marco Franzon [aut], Tommaso Rodani [aut], Pierluigi Barbieri [aut]
Maintainer: Sabina Licen <slicen@units.it>

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Package sf updated to version 1.0-2 with previous version 1.0-1 dated 2021-06-29

Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection conversions and datum transformations. Uses by default the 's2' package for spherical geometry operations on ellipsoidal (long/lat) coordinates.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>), Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>), Etienne Racine [ctb], Michael Sumner [ctb], Ian Cook [ctb], Tim Keitt [ctb], Robin Lovelace [ctb], Hadley Wickham [ctb], Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>), Kirill Müller [ctb], Thomas Lin Pedersen [ctb], Dan Baston [ctb], Dewey Dunnington [ctb] (<https://orcid.org/0000-0002-9415-4582>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

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Package sdcMicro updated to version 5.6.1 with previous version 5.6.0 dated 2021-01-27

Title: Statistical Disclosure Control Methods for Anonymization of Data and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly confidential. This package (see also Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>) can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>. Various risk estimation and anonymisation methods are included. Note that the package includes a graphical user interface (Meindl and Templ, 2019 <doi:10.3390/a12090191>) that allows to use various methods of this package.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>), Bernhard Meindl [aut], Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Matthias Templ <matthias.templ@gmail.com>

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Package finbif updated to version 0.6.1 with previous version 0.6.0 dated 2021-07-22

Title: Interface for the 'Finnish Biodiversity Information Facility' API
Description: A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph], William K. Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>

Diff between finbif versions 0.6.0 dated 2021-07-22 and 0.6.1 dated 2021-07-26

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Package selection.index updated to version 1.1.2 with previous version 1.1.1 dated 2021-06-03

Title: Analysis of Selection Index in Plant Breeding
Description: The aim of most plant breeding programmes is simultaneous improvement of several characters. An objective method involving simultaneous selection for several attributes then becomes necessary. It has been recognised that most rapid improvements in the economic value is expected from selection applied simultaneously to all the characters which determine the economic value of a plant, and appropriate assigned weights to each character according to their economic importance, heritability and correlations between characters. So the selection for economic value is a complex matter. If the component characters are combined together into an index in such a way that when selection is applied to the index, as if index is the character to be improved, most rapid improvement of economic value is expected. Such an index was first proposed by Smith (1937 <doi:10.1111/j.1469-1809.1936.tb02143.x>) based on the Fisher's (1936 <doi:10.1111/j.1469-1809.1936.tb02137.x>) "discriminant function" Dabholkar (1999 <https://books.google.co.in/books?id=mlFtumAXQ0oC&lpg=PA4&ots=Xgxp1qLuxS&dq=elements%20of%20biometrical%20genetics&lr&pg=PP1#v=onepage&q&f=false>). In this package selection index is calculated based on the Smith (1937) selection index method.
Author: Zankrut Goyani [aut, cre, cph], Alok Shrivasatva [aut], Yogesh Garde [aut], Arvind Chaudhary [aut], Kaushal Modha [aut]
Maintainer: Zankrut Goyani <zankrut20@gmail.com>

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Package rvest updated to version 1.0.1 with previous version 1.0.0 dated 2021-03-09

Title: Easily Harvest (Scrape) Web Pages
Description: Wrappers around the 'xml2' and 'httr' packages to make it easy to download, then manipulate, HTML and XML.
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package pubmed.mineR updated to version 1.0.18 with previous version 1.0.17 dated 2021-01-07

Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <https://pubmed.ncbi.nlm.nih.gov/>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>

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Package alfred updated to version 0.2.0 with previous version 0.1.12 dated 2021-05-12

Title: Downloading Time Series from ALFRED Database for Various Vintages
Description: Provides direct access to the ALFRED (<https://alfred.stlouisfed.org>) and FRED (<https://fred.stlouisfed.org>) databases. Its functions return tidy data frames for different releases of the specified time series. Note that this product uses the FRED© API but is not endorsed or certified by the Federal Reserve Bank of St. Louis.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>

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Package pryr updated to version 0.1.5 with previous version 0.1.4 dated 2018-02-17

Title: Tools for Computing on the Language
Description: Useful tools to pry back the covers of R and understand the language at a deeper level.
Author: Hadley Wickham [aut, cre], R Core team [ctb] (Some code extracted from base R)
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package memoiR updated to version 1.1-0 with previous version 1.0-0 dated 2021-06-07

Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem. 'memoiR' makes it easy. It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>

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Package GWRM updated to version 2.1.0.4 with previous version 2.1.0.3 dated 2017-07-31

Title: Generalized Waring Regression Model for Count Data
Description: Statistical functions to fit, validate and describe a Generalized Waring Regression Model (GWRM).
Author: Silverio Vilchez-Lopez [aut, cre], Antonio Jose Saez-Castillo [aut], Maria Jose Olmo-Jimenez [aut], Jose Rodriguez-Avi [aut], Antonio Conde-Sanchez [aut], Ana Maria Martinez-Rodriguez [aut]
Maintainer: Silverio Vilchez-Lopez <svilchez@ujaen.es>

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Package ClusTorus updated to version 0.1.3 with previous version 0.1.1 dated 2021-06-30

Title: Prediction and Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular data on the torus. The package provides angular adaptations of usual clustering methods such as the k-means clustering, pairwise angular distances, which can be used as an input for distance-based clustering algorithms, and implements clustering based on the conformal prediction framework. Options for the conformal scores include scores based on a kernel density estimate, multivariate von Mises mixtures, and naive k-means clusters. Moreover, the package provides some basic data handling tools for angular data.
Author: Sungkyu Jung [aut, cph], Seungki Hong [aut, cre], Kiho Park [ctb], Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>

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Package bayestestR updated to version 0.10.5 with previous version 0.10.0 dated 2021-05-31

Title: Understand and Describe Bayesian Models and Posterior Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>, @Dom_Makowski), Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>, @strengejacke), Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>, @mattansb), Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets), Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>), Paul-Christian Bürkner [rev], Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>), Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>), Sam Crawley [ctb] (<https://orcid.org/0000-0002-7847-0411>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>

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Package springer updated to version 0.1.4 with previous version 0.1.3 dated 2021-07-24

Title: Sparse Group Variable Selection for Gene-Environment Interactions in the Longitudinal Study
Description: Recently, regularized variable selection has emerged as a powerful tool to identify and dissect gene-environment interactions. Nevertheless, in longitudinal studies with high dimensional genetic factors, regularization methods for G×E interactions have not been systematically developed. In this package, we provide the implementation of sparse group variable selection, based on both the quadratic inference function (QIF) and generalized estimating equation (GEE), to accommodate the bi-level selection for longitudinal G×E studies with high dimensional genomic features. Alternative methods conducting only the group or individual level selection have also been included. The core modules of the package have been developed in C++.
Author: Fei Zhou, Xi Lu, Jie Ren, Cen Wu
Maintainer: Fei Zhou <feiz@ksu.edu>

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Package tidytreatment updated to version 0.2.1 with previous version 0.2.0 dated 2021-06-23

Title: Tidy Methods for Bayesian Treatment Effect Models
Description: Functions for extracting tidy data from Bayesian treatment effect models, in particular BART, but extensions are possible. Functionality includes extracting tidy posterior summaries as in 'tidybayes' <https://github.com/mjskay/tidybayes>, estimating (average) treatment effects, common support calculations, and plotting useful summaries of these.
Author: Joshua J Bon [aut, cre] (<https://orcid.org/0000-0003-2313-2949>)
Maintainer: Joshua J Bon <joshuajbon@gmail.com>

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Package hesim updated to version 0.5.1 with previous version 0.5.0 dated 2021-02-17

Title: Health Economic Simulation Modeling and Decision Analysis
Description: A modular and computationally efficient R package for parameterizing, simulating, and analyzing health economic simulation models. The package supports cohort discrete time state transition models (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>, N-state partitioned survival models (Glasziou et al. 1990) <doi:10.1002/sim.4780091106>, and individual-level continuous time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>, encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is quantified with standard graphical and tabular summaries of a probabilistic sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table make individual-patient simulation, probabilistic sensitivity analysis, and incorporation of patient heterogeneity fast.
Author: Devin Incerti [aut, cre], Jeroen P. Jansen [aut], R Core Team [ctb] (hesim uses some slightly modified C functions from base R)
Maintainer: Devin Incerti <devin.incerti@gmail.com>

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 hesim-0.5.1/hesim/MD5                                                                                |  363 +--
 hesim-0.5.1/hesim/NAMESPACE                                                                          |   48 
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 hesim-0.5.1/hesim/R/bootstrap.R                                                                      |    8 
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 hesim-0.5.1/hesim/R/hesim.R                                                                          |    8 
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 hesim-0.5.1/hesim/man/as_array3.Rd                                                                   |   14 
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 hesim-0.5.1/hesim/man/ce.Rd                                                                          |    2 
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 hesim-0.5.1/hesim/man/costs.Rd                                                                       |    3 
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 hesim-0.5.1/hesim/man/define_model.Rd                                                                |   18 
 hesim-0.5.1/hesim/man/define_rng.Rd                                                                  |   27 
 hesim-0.5.1/hesim/man/disprog.Rd                                                                     |   14 
 hesim-0.5.1/hesim/man/hesim_data.Rd                                                                  |   11 
 hesim-0.5.1/hesim/man/hesim_survdists.Rd                                                             |    4 
 hesim-0.5.1/hesim/man/id_attributes.Rd                                                               |   16 
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 hesim-0.5.1/hesim/man/mstate3_exdata.Rd                                                              |    2 
 hesim-0.5.1/hesim/man/params_lm.Rd                                                                   |   35 
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 hesim-0.5.1/hesim/man/params_mlogit_list.Rd                                                          |   39 
 hesim-0.5.1/hesim/man/params_surv.Rd                                                                 |   40 
 hesim-0.5.1/hesim/man/params_surv_list.Rd                                                            |   35 
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Package VicmapR updated to version 0.1.7 with previous version 0.1.6 dated 2021-07-06

Title: Access Victorian Spatial Data Through Web File Services (WFS)
Description: Easily interfaces R to spatial datasets available through the Victorian Government's WFS (Web Feature Service): <https://services.land.vic.gov.au/catalogue/publicproxy/guest/dv_geoserver/wfs?request=getCapabilities>, which allows users to read in 'sf' data from these sources. VicmapR uses the lazy querying approach and code developed by Teucher et al. (2021) for the 'bcdata' R package <doi:10.21105/joss.02927>.
Author: Justin Cally [aut, cre] (<https://orcid.org/0000-0003-4584-2220>), Rachel Swain [ctb], Andy Teucher [aut] (<https://orcid.org/0000-0002-7840-692X>, bcdata author), Sam Albers [aut] (<https://orcid.org/0000-0002-9270-7884>, bcdata author), Stephanie Hazlitt [aut] (<https://orcid.org/0000-0002-3161-2304>, bcdata author), Province of British Columbia [cph] (bcdata copyright)
Maintainer: Justin Cally <justin.g.cally@gmail.com>

Diff between VicmapR versions 0.1.6 dated 2021-07-06 and 0.1.7 dated 2021-07-26

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Package sysfonts updated to version 0.8.4 with previous version 0.8.3 dated 2021-01-10

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

Diff between sysfonts versions 0.8.3 dated 2021-01-10 and 0.8.4 dated 2021-07-26

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Package showtext updated to version 0.9-3 with previous version 0.9-2 dated 2021-01-10

Title: Using Fonts More Easily in R Graphs
Description: Making it easy to use various types of fonts ('TrueType', 'OpenType', Type 1, web fonts, etc.) in R graphs, and supporting most output formats of R graphics including PNG, PDF and SVG. Text glyphs will be converted into polygons or raster images, hence after the plot has been created, it no longer relies on the font files. No external software such as 'Ghostscript' is needed to use this package.
Author: Yixuan Qiu and authors/contributors of the included software. See file AUTHORS for details.
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>

Diff between showtext versions 0.9-2 dated 2021-01-10 and 0.9-3 dated 2021-07-26

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Sun, 25 Jul 2021

Package carat updated to version 1.5 with previous version 1.4 dated 2020-09-26

Title: Covariate-Adaptive Randomization for Clinical Trials
Description: Provides functions and command-line user interface to generate allocation sequence by covariate-adaptive randomization for clinical trials. The package currently supports six covariate-adaptive randomization procedures. Three hypothesis testing methods that are valid and robust under covariate-adaptive randomization are also available in the package to facilitate the inference for treatment effect under the included randomization procedures. Additionally, the package provides comprehensive and efficient tools to allow one to evaluate and compare the performance of randomization procedures and tests based on various criteria.
Author: Fuyi Tu [aut], Xiaoqing Ye [aut, cre], Wei Ma [aut, ths], Feifang Hu [aut, ths]
Maintainer: Xiaoqing Ye <ye_xiaoq@163.com>

Diff between carat versions 1.4 dated 2020-09-26 and 1.5 dated 2021-07-25

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Package loon.tourr updated to version 0.1.2 with previous version 0.1.1 dated 2021-05-17

Title: Tour in 'Loon'
Description: Implement tour algorithms in interactive graphical system 'loon'.
Author: Zehao Xu [aut, cre], R. Wayne Oldford [aut]
Maintainer: Zehao Xu <z267xu@uwaterloo.ca>

Diff between loon.tourr versions 0.1.1 dated 2021-05-17 and 0.1.2 dated 2021-07-25

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Package BNPmix updated to version 0.2.9 with previous version 0.2.8 dated 2021-03-21

Title: Bayesian Nonparametric Mixture Models
Description: Functions to perform Bayesian nonparametric univariate and multivariate density estimation and clustering, by means of Pitman-Yor mixtures, and dependent Dirichlet process mixtures for partially exchangeable data.
Author: Riccardo Corradin [aut, cre], Antonio Canale [ctb], Bernardo Nipoti [ctb]
Maintainer: Riccardo Corradin <riccardo.corradin@gmail.com>

Diff between BNPmix versions 0.2.8 dated 2021-03-21 and 0.2.9 dated 2021-07-25

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Package set6 updated to version 0.2.3 with previous version 0.2.2 dated 2021-07-16

Title: R6 Mathematical Sets Interface
Description: An object-oriented package for mathematical sets, upgrading the current gold-standard {sets}. Many forms of mathematical sets are implemented, including (countably finite) sets, tuples, intervals (countably infinite or uncountable), and fuzzy variants. Wrappers extend functionality by allowing symbolic representations of complex operations on sets, including unions, (cartesian) products, exponentiation, and differences (asymmetric and symmetric).
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>), Franz Kiraly [aut]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>

Diff between set6 versions 0.2.2 dated 2021-07-16 and 0.2.3 dated 2021-07-25

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Package pointblank updated to version 0.8.0 with previous version 0.7.0 dated 2021-03-09

Title: Data Validation and Organization of Metadata for Local and Remote Tables
Description: Validate data in data frames, 'tibble' objects, 'Spark' 'DataFrames', and database tables. Validation pipelines can be made using easily-readable, consecutive validation steps. Upon execution of the validation plan, several reporting options are available. User-defined thresholds for failure rates allow for the determination of appropriate reporting actions. Many other workflows are available including an information management workflow, where the aim is to record, collect, and generate useful information on data tables.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>), Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>

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Package MGMM updated to version 0.4.0 with previous version 0.3.1 dated 2020-08-26

Title: Missingness Aware Gaussian Mixture Models
Description: Parameter estimation and classification for Gaussian Mixture Models (GMMs) in the presence of missing data. This package complements existing implementations by allowing for both missing elements in the input vectors and full (as opposed to strictly diagonal) covariance matrices. Estimating is performed using an expectation conditional maximization algorithm that accounts for missingness of both the cluster assignments and the vector components. The output includes the marginal cluster membership probabilities; the mean and covariance of each cluster; the posterior probabilities of cluster membership; and a completed version of the input data, with missing values imputed to their posterior expectations. For additional details, please see McCaw ZR, Julienne H, Aschard H. "MGMM: an R package for fitting Gaussian Mixture Models on Incomplete Data." <doi:10.1101/2019.12.20.884551>.
Author: Zachary McCaw [aut, cre] (<https://orcid.org/0000-0002-2006-9828>)
Maintainer: Zachary McCaw <zmccaw@alumni.harvard.edu>

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Package jstable updated to version 1.0.6 with previous version 1.0.5 dated 2021-07-20

Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>), Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>

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Package ffscrapr updated to version 1.4.5 with previous version 1.4.4 dated 2021-07-20

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

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Package chicane updated to version 0.1.6 with previous version 0.1.5 dated 2021-06-10

Title: Capture Hi-C Analysis Engine
Description: Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Author: Erle Holgersen [aut, cre], Olivia Leavy [aut], Olivia Fletcher [aut], Frank Dudbridge [aut], Syed Haider [aut]
Maintainer: Erle Holgersen <erle.holgersen@gmail.com>

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Package serp updated to version 0.2.0 with previous version 0.1.8 dated 2021-01-29

Title: Smooth Effects on Response Penalty for 'CLM'
Description: A regularization method for the cumulative link models. The 'smooth-effect-on-response penalty' ('SERP') provides flexible modelling of the ordinal model by enabling the smooth transition from the general cumulative link model to a coarser form of the same model. In other words, as the tuning parameter goes from zero to infinity, the subject-specific effects associated with each variable in the model tend to a unique global effect. The parameter estimates of the general cumulative model are mostly unidentifiable or at least only identifiable within a range of the entire parameter space. Thus, by maximizing a penalized rather than the usual non-penalized log-likelihood, this and other numerical problems common with the general model are to a large extent eliminated. Fitting is via a modified Newton's method. Several standard model performance and descriptive methods are also available. For more details on the penalty implemented here, see, 'Ugba et al. (2021)' <doi:10.3390/stats4030037> and Tutz and Gertheiss (2016) <doi:10.1177/1471082X16642560>.
Author: Ejike R. Ugba [aut, cre, cph]
Maintainer: Ejike R. Ugba <ejike.ugba@outlook.com>

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Package qs updated to version 0.25.1 with previous version 0.24.1 dated 2021-03-07

Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd, lz4 and xxHash code), Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled zstd code), Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled code), Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd bundled code), Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled code), Romain Francois [ctb, cph] (Derived example/tutorials for ALTREP structures), Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc library), Bryce Chamberlain [ctb] (qsavem and qload functions)
Maintainer: Travers Ching <traversc@gmail.com>

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Package MetaStan updated to version 0.4.0 with previous version 0.2.0 dated 2020-04-09

Title: Bayesian Meta-Analysis via 'Stan'
Description: Performs Bayesian meta-analysis and model-based meta-analysis using 'Stan'. Includes binomial-normal hierarchical models and option to use weakly informative priors for the heterogeneity parameter and the treatment effect parameter which are described in Guenhan, Roever, and Friede (2020) <doi:10.1002/jrsm.1370>.
Author: Burak Kuersad Guenhan [aut, cre] (<https://orcid.org/0000-0002-7454-8680>), Trustees of Columbia University [cph] (src/init.cpp, tools/make_cpp.R, R/stanmodels.R)
Maintainer: Burak Kuersad Guenhan <burakgunhan@gmail.com>

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Package ggheatmap updated to version 2.1 with previous version 2.0 dated 2021-07-12

Title: Plot Heatmap
Description: The flexibility and excellence of 'ggplot2' is unquestionable, so many drawing tools basically need 'ggplot2' as the operating object. In order to develop a heatmap drawing system based on ggplot2, we developed this tool, mainly to solve the heatmap puzzle problem and the flexible connection between the heatmap and the 'ggplot2' object. The advantages of this tool are as follows: 1. More flexible label settings; 2. Realize the linkage of heatmap and 'ggplot2' drawing system, which is helpful for operations such as puzzles; 3. Simple and easy to operate; 4. Optimization of clustering tree visualization.
Author: Baiwei Luo [aut, cre]
Maintainer: Baiwei Luo <2734782653@qq.com>

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Package cvCovEst updated to version 1.0.0 with previous version 0.3.5 dated 2021-04-18

Title: Cross-Validated Covariance Matrix Estimation
Description: An efficient cross-validated approach for covariance matrix estimation, particularly useful in high-dimensional settings. This method relies upon the theory of loss-based estimator selection to identify the optimal estimator of the covariance matrix from among a prespecified set of candidates.
Author: Philippe Boileau [aut, cre, cph] (<https://orcid.org/0000-0002-4850-2507>), Nima Hejazi [aut] (<https://orcid.org/0000-0002-7127-2789>), Brian Collica [aut] (<https://orcid.org/0000-0003-1127-2557>), Jamarcus Liu [ctb], Mark van der Laan [ctb, ths] (<https://orcid.org/0000-0003-1432-5511>), Sandrine Dudoit [ctb, ths] (<https://orcid.org/0000-0002-6069-8629>)
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>

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