Thu, 21 Oct 2021

Package grates updated to version 0.3.0 with previous version 0.2.0 dated 2021-05-28

Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating grouped date classes. This package is part of the RECON (<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>

Diff between grates versions 0.2.0 dated 2021-05-28 and 0.3.0 dated 2021-10-21

 DESCRIPTION                    |    8 
 MD5                            |   44 +--
 NAMESPACE                      |    5 
 NEWS.md                        |   10 
 R/int_period.R                 |    6 
 R/month.R                      |    6 
 R/period.R                     |   16 -
 R/seq.R                        |only
 R/year.R                       |    1 
 R/yearweek.R                   |    2 
 README.md                      |   23 -
 build/vignette.rds             |binary
 inst/doc/introduction.html     |  576 ++++++++++++-----------------------------
 man/as_month.Rd                |   17 -
 man/as_period.Rd               |   17 -
 man/as_quarter.Rd              |   17 -
 man/as_year.Rd                 |   17 -
 man/as_yearweek.Rd             |   17 -
 tests/testthat/test-month.R    |    4 
 tests/testthat/test-period.R   |    4 
 tests/testthat/test-quarter.R  |    4 
 tests/testthat/test-seq.R      |only
 tests/testthat/test-year.R     |    4 
 tests/testthat/test-yearweek.R |    6 
 24 files changed, 316 insertions(+), 488 deletions(-)

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Package biocompute updated to version 1.1.0 with previous version 1.0.6 dated 2021-09-29

Title: Create and Manipulate BioCompute Objects
Description: Tools to create, validate, and export BioCompute Objects described in King et al. (2019) <doi:10.17605/osf.io/h59uh>. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.
Author: Jeffrey Grover [aut, cre] (<https://orcid.org/0000-0001-6246-1767>), Soner Koc [aut] (<https://orcid.org/0000-0002-0772-6600>), Nan Xiao [aut] (<https://orcid.org/0000-0002-0250-5673>), Dennis Dean [aut] (<https://orcid.org/0000-0002-7621-9717>), Seven Bridges Genomics [cph, fnd]
Maintainer: Jeffrey Grover <jeffrey.grover@sevenbridges.com>

Diff between biocompute versions 1.0.6 dated 2021-09-29 and 1.1.0 dated 2021-10-21

 biocompute-1.0.6/biocompute/inst/bco/BCO_Example_CNVs.json              |only
 biocompute-1.1.0/biocompute/DESCRIPTION                                 |    6 
 biocompute-1.1.0/biocompute/MD5                                         |  109 ++-
 biocompute-1.1.0/biocompute/NAMESPACE                                   |   29 
 biocompute-1.1.0/biocompute/NEWS.md                                     |    9 
 biocompute-1.1.0/biocompute/R/compose-description.R                     |   14 
 biocompute-1.1.0/biocompute/R/compose-error.R                           |   10 
 biocompute-1.1.0/biocompute/R/compose-execution.R                       |   12 
 biocompute-1.1.0/biocompute/R/compose-extension-fhir.R                  |    8 
 biocompute-1.1.0/biocompute/R/compose-extension-scm.R                   |    8 
 biocompute-1.1.0/biocompute/R/compose-extension.R                       |    8 
 biocompute-1.1.0/biocompute/R/compose-io.R                              |    8 
 biocompute-1.1.0/biocompute/R/compose-parametric.R                      |   10 
 biocompute-1.1.0/biocompute/R/compose-provenance.R                      |    8 
 biocompute-1.1.0/biocompute/R/compose-top-level-fields.R                |   26 
 biocompute-1.1.0/biocompute/R/compose-usability.R                       |   10 
 biocompute-1.1.0/biocompute/R/compose.R                                 |   14 
 biocompute-1.1.0/biocompute/R/export-docs.R                             |    6 
 biocompute-1.1.0/biocompute/R/export-sevenbridges.R                     |    2 
 biocompute-1.1.0/biocompute/R/read-bco.R                                |only
 biocompute-1.1.0/biocompute/R/utils-compose.R                           |    2 
 biocompute-1.1.0/biocompute/R/validate-checksum.R                       |   16 
 biocompute-1.1.0/biocompute/R/validate-schema.R                         |   42 -
 biocompute-1.1.0/biocompute/R/version.R                                 |    4 
 biocompute-1.1.0/biocompute/README.md                                   |    4 
 biocompute-1.1.0/biocompute/inst/bco/HCV1a.json                         |  303 +++++-----
 biocompute-1.1.0/biocompute/inst/bco/HIVE_metagenomics.json             |   27 
 biocompute-1.1.0/biocompute/inst/bco/README                             |    2 
 biocompute-1.1.0/biocompute/inst/bco/UVP.json                           |   25 
 biocompute-1.1.0/biocompute/inst/bco/glycosylation-sites-UniCarbKB.json |   46 -
 biocompute-1.1.0/biocompute/inst/doc/case-study.html                    |   28 
 biocompute-1.1.0/biocompute/inst/doc/intro.html                         |   61 --
 biocompute-1.1.0/biocompute/inst/schemas/1.4.2                          |only
 biocompute-1.1.0/biocompute/man/compose.Rd                              |   10 
 biocompute-1.1.0/biocompute/man/compose_description.Rd                  |   16 
 biocompute-1.1.0/biocompute/man/compose_error.Rd                        |   10 
 biocompute-1.1.0/biocompute/man/compose_execution.Rd                    |   12 
 biocompute-1.1.0/biocompute/man/compose_extension.Rd                    |   10 
 biocompute-1.1.0/biocompute/man/compose_fhir.Rd                         |   10 
 biocompute-1.1.0/biocompute/man/compose_io.Rd                           |    8 
 biocompute-1.1.0/biocompute/man/compose_parametric.Rd                   |   10 
 biocompute-1.1.0/biocompute/man/compose_provenance.Rd                   |   10 
 biocompute-1.1.0/biocompute/man/compose_scm.Rd                          |   10 
 biocompute-1.1.0/biocompute/man/compose_tlf.Rd                          |   18 
 biocompute-1.1.0/biocompute/man/compose_usability.Rd                    |   10 
 biocompute-1.1.0/biocompute/man/export_html.Rd                          |    2 
 biocompute-1.1.0/biocompute/man/export_pdf.Rd                           |    2 
 biocompute-1.1.0/biocompute/man/export_sevenbridges.Rd                  |    2 
 biocompute-1.1.0/biocompute/man/export_word.Rd                          |    2 
 biocompute-1.1.0/biocompute/man/read_bco.Rd                             |only
 biocompute-1.1.0/biocompute/man/validate_checksum.Rd                    |   12 
 biocompute-1.1.0/biocompute/man/validate_schema.Rd                      |   12 
 52 files changed, 543 insertions(+), 480 deletions(-)

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Package argparse updated to version 2.1.2 with previous version 2.1.1 dated 2021-09-08

Title: Command Line Optional and Positional Argument Parser
Description: A command line parser to be used with Rscript to write "#!" shebang scripts that gracefully accept positional and optional arguments and automatically generate usage.
Author: Trevor L Davis [aut, cre], Allen Day [ctb] (Some documentation and examples ported from the getopt package.), Python Software Foundation [ctb] (Some documentation from the optparse Python module.), Paul Newell [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>

Diff between argparse versions 2.1.1 dated 2021-09-08 and 2.1.2 dated 2021-10-21

 DESCRIPTION                    |    6 ++---
 MD5                            |   16 ++++++++------
 NEWS.md                        |    9 +++++++-
 R/argparse.R                   |   20 +++++++++++++++--
 README.md                      |   11 +++++----
 build/vignette.rds             |binary
 inst/doc/argparse.html         |   46 ++++++++++++++++++++---------------------
 man/figures                    |only
 tests/testthat/test-argparse.R |   14 +++++++++++-
 9 files changed, 79 insertions(+), 43 deletions(-)

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Package relations updated to version 0.6-10 with previous version 0.6-9 dated 2019-10-26

Title: Data Structures and Algorithms for Relations
Description: Data structures and algorithms for k-ary relations with arbitrary domains, featuring relational algebra, predicate functions, and fitters for consensus relations.
Author: David Meyer [aut], Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>), Christian Buchta [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

Diff between relations versions 0.6-9 dated 2019-10-26 and 0.6-10 dated 2021-10-21

 DESCRIPTION                                        |    6 ++--
 MD5                                                |   30 ++++++++++-----------
 build/partial.rdb                                  |binary
 build/vignette.rds                                 |binary
 data/Cetacea.rda                                   |binary
 data/Felines.rda                                   |binary
 data/SVM_Benchmarking_Classification.rda           |binary
 data/SVM_Benchmarking_Classification_Consensus.rda |binary
 data/SVM_Benchmarking_Regression.rda               |binary
 data/SVM_Benchmarking_Regression_Consensus.rda     |binary
 inst/NEWS.Rd                                       |   12 ++++++++
 inst/doc/relations.R                               |    1 
 inst/doc/relations.pdf                             |binary
 man/consensus.Rd                                   |    2 -
 man/dissimilarity.Rd                               |    2 -
 vignettes/relations.bib                            |    4 +-
 16 files changed, 34 insertions(+), 23 deletions(-)

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Package rasciidoc updated to version 3.1.4 with previous version 3.1.3 dated 2021-08-22

Title: Create Reports Using R and 'asciidoc'
Description: Inspired by Karl Broman`s reader on using 'knitr' with 'asciidoc' (<https://kbroman.org/knitr_knutshell/pages/asciidoc.html>), this is merely a wrapper to 'knitr' and 'asciidoc'.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>

Diff between rasciidoc versions 3.1.3 dated 2021-08-22 and 3.1.4 dated 2021-10-21

 DESCRIPTION                                |    8 -
 MD5                                        |   10 -
 NEWS.md                                    |    4 
 inst/NEWS.rd                               |    6 
 inst/doc/An_Introduction_to_rasciidoc.html |  178 ++++++-----------------------
 inst/runit_tests/runit-render.R            |    5 
 6 files changed, 60 insertions(+), 151 deletions(-)

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Package appler updated to version 0.1.2 with previous version 0.1.1 dated 2021-05-24

Title: 'Apple App Store' and 'iTunes' Data Extraction
Description: Using 'Apple App Store' <https://www.apple.com/app-store/> web scraping and 'iTunes' API <https://affiliate.itunes.apple.com/resources/documentation/itunes-store-web-service-search-api/> to extract content information, app ratings and reviews.
Author: Ashley Baldry [aut, cre]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>

Diff between appler versions 0.1.1 dated 2021-05-24 and 0.1.2 dated 2021-10-21

 DESCRIPTION                 |   10 +++++-----
 MD5                         |    8 ++++----
 NEWS.md                     |    5 +++++
 R/reviews.R                 |    6 +++++-
 tests/testthat/test-chart.R |   15 ---------------
 5 files changed, 19 insertions(+), 25 deletions(-)

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New package rcbayes with initial version 0.1.0
Package: rcbayes
Title: Estimate Rogers-Castro Migration Age Schedules with Bayesian Models
Version: 0.1.0
Description: A collection of functions to estimate Rogers-Castro migration age schedules using 'Stan'. This model which describes the fundamental relationship between migration and age in the form of a flexible multi-exponential migration model was most notably proposed in Rogers and Castro (1978) <doi:10.1068/a100475>.
License: MIT + file LICENSE
Encoding: UTF-8
Biarch: true
Depends: R (>= 3.4.0)
Imports: methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.1.1), Rdpack, dplyr, rlang, stats, tibble, tidybayes, magrittr, shiny, shinythemes
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests: knitr, rmarkdown, ggplot2
SystemRequirements: GNU make
VignetteBuilder: knitr
RdMacros: Rdpack
NeedsCompilation: yes
Packaged: 2021-10-21 02:40:57 UTC; jessieyeung
Author: Jessie Yeung [aut, cre], Monica Alexander [aut] (<https://orcid.org/0000-0002-8135-3435>)
Maintainer: Jessie Yeung <jessieyeung1@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 17:10:02 UTC

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New package jenga with initial version 1.0.0
Package: jenga
Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Version: 1.0.0
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: purrr, abind, ggplot2, readr, stringr, lubridate, narray, imputeTS, scales, tictoc, modeest, moments, philentropy
URL: https://rpubs.com/giancarlo_vercellino/jenga
NeedsCompilation: no
Packaged: 2021-10-21 12:38:26 UTC; gvercellino
Repository: CRAN
Date/Publication: 2021-10-21 17:40:02 UTC

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New package GCPBayes with initial version 3.1.0
Package: GCPBayes
Title: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure
Version: 3.1.0
Author: Taban Baghfalaki
Maintainer: Taban Baghfalaki <t.baghfalaki@gmail.com>
Description: Run a Gibbs sampler for a multivariate Bayesian sparse group selection model with Dirac, continuous and hierarchical spike prior for detecting pleiotropy on the traits. This package is designed for summary statistics containing estimated regression coefficients and its estimated covariance matrix. The methodology is available from: Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021) <doi:10.1002/sim.8855>.
License: GPL (>= 2.0)
Encoding: UTF-8
Imports: MASS, arm, mvtnorm, invgamma, gdata, truncnorm, postpack, wiqid, usethis, Rcpp
LazyData: true
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2021-09-29 10:00:12 UTC; t_baghfalaki
Repository: CRAN
Date/Publication: 2021-10-21 17:30:02 UTC

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New package fdaMocca with initial version 0.1-0
Encoding: UTF-8
Package: fdaMocca
Version: 0.1-0
Author: Natalya Pya Arnqvist[aut, cre], Per Arnqvist [aut, cre], Sara Sjöstedt de Luna [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Title: Model-Based Clustering for Functional Data with Covariates
Date: 2021-10-21
Description: Routines for model-based functional cluster analysis for functional data with optional covariates. The idea is to cluster functional subjects (often called functional objects) into homogenous groups by using spline smoothers (for functional data) together with scalar covariates. The spline coefficients and the covariates are modelled as a multivariate Gaussian mixture model, where the number of mixtures corresponds to the number of clusters. The parameters of the model are estimated by maximizing the observed mixture likelihood via an EM algorithm (Arnqvist and Sjöstedt de Luna, 2019) <arXiv:1904.10265>. The clustering method is used to analyze annual lake sediment from lake Kassjön (Northern Sweden) which cover more than 6400 years and can be seen as historical records of weather and climate.
Depends: R (>= 3.6.0)
Imports: stats, graphics, Matrix, parallel, foreach, doParallel, mvtnorm, fda, grDevices
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2021-10-21 12:24:46 UTC; natalya
Repository: CRAN
Date/Publication: 2021-10-21 17:40:04 UTC

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New package CoordinateCleaner with initial version 2.0-20
Package: CoordinateCleaner
Title: Automated Cleaning of Occurrence Records from Biological Collections
Version: 2.0-20
Description: Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Language: en-gb
Encoding: UTF-8
License: GPL-3
URL: https://ropensci.github.io/CoordinateCleaner/
BugReports: https://github.com/ropensci/CoordinateCleaner/issues
Depends: R (>= 3.5.0)
Imports: dplyr, geosphere, ggplot2, graphics, grDevices, methods, raster, rgbif, rgeos, rgdal, rnaturalearth, stats, sp, tidyselect, utils
LazyData: true
Suggests: covr, countrycode, knitr, maps, magrittr, paleobioDB, rmarkdown, rnaturalearthdata, testthat, viridis
SystemRequirements: GDAL (>= 2.0.1)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-20 18:24:55 UTC; az64mycy
Author: Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)
Maintainer: Alexander Zizka <zizka.alexander@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 17:10:05 UTC

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New package scatterPlotMatrix with initial version 0.1.0
Package: scatterPlotMatrix
Title: 'Htmlwidget' for a Scatter Plot Matrix & Multiple Scatter Plot
Version: 0.1.0
Description: Create a scatter plot matrix, using 'htmlwidgets' package and 'd3.js'.
URL: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix
BugReports: https://ifpen.gitlabfr.com/detocs/scatterplotmatrix/-/issues
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: htmlwidgets
Suggests: testthat, shiny, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2021-10-20 17:07:25 UTC; chazalviel
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib, http://d3js.org), David Chazalviel [aut, cre], Harry Stevens [cph] (d3-regression library in htmlwidgets/lib, https://github.com/HarryStevens/d3-regression)
Maintainer: David Chazalviel <david.chazalviel@club-internet.fr>
Repository: CRAN
Date/Publication: 2021-10-21 17:00:02 UTC

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New package supernova with initial version 2.4.4
Package: supernova
Title: Judd, McClelland, & Ryan Formatting for ANOVA Output
Version: 2.4.4
Date: 2021-10-20
Encoding: UTF-8
LazyData: yes
Description: Produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.
License: GPL-3
Depends: R (>= 3.4.0)
Suggests: car, covr, lintr, lme4, testthat (>= 2.1.0), vdiffr, tidyr
Imports: ggplot2, tibble, cli, magrittr, purrr, rlang, stringr, vctrs, pillar (>= 1.5.0), methods, backports
URL: https://github.com/UCLATALL/supernova
BugReports: https://github.com/UCLATALL/supernova/issues
NeedsCompilation: no
Packaged: 2021-10-20 17:07:39 UTC; Adam
Author: Adam Blake [cre, aut] (<https://orcid.org/0000-0001-7881-8652>), Jeff Chrabaszcz [aut], Ji Son [aut] (<https://orcid.org/0000-0002-4258-4791>), Jim Stigler [aut] (<https://orcid.org/0000-0001-6107-7827>)
Maintainer: Adam Blake <adamblake@g.ucla.edu>
Repository: CRAN
Date/Publication: 2021-10-21 15:50:02 UTC

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New package shinyr with initial version 0.3.0
Package: shinyr
Title: Data Insights Through Inbuilt R Shiny App
Version: 0.3.0
Description: It builds dynamic R shiny based dashboards to analyze any CSV files. It provides simple dashboard design to subset the data, perform exploratory data analysis and preliminary machine learning (supervised and unsupervised). It also provides filters based on columns of interest.
Depends: R (>= 3.1.0),
Imports: dplyr, shiny, shinydashboard, tm, wordcloud, corrplot, randomForest, RColorBrewer, caret, nnet, plotly, e1071, knitr
Maintainer: Jayachandra N <itsjay510@gmail.com>
License: GPL-3
Encoding: UTF-8
Suggests: testthat
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2021-10-20 10:50:11 UTC; JJJN
Author: Jayachandra N [aut, cre], Pushker Ravindra [aut]
Repository: CRAN
Date/Publication: 2021-10-21 15:30:02 UTC

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New package repairData with initial version 0.1.0
Package: repairData
Title: Open Repair Alliance Datasets 2021
Version: 0.1.0
Description: The complete data set of open repair data, full compliant with the Open Repair Data Standards (ORDS). It combines the datasets contributed by partner organizations of the Open Repair Alliance (ORA). Last updated: 2021-02-22. The package also contains via quests enriched datasets on batteries, printer, mobiles, and tablets.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
URL: https://github.com/petzi53/repairData
BugReports: https://github.com/petzi53/repairData/issues
NeedsCompilation: no
Packaged: 2021-10-20 09:15:29 UTC; petzi
Author: Peter Baumgartner [aut, cre] (<https://orcid.org/0000-0003-4526-8791>)
Maintainer: Peter Baumgartner <petzi53@gmail.com>
Repository: CRAN
Date/Publication: 2021-10-21 15:20:02 UTC

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Package RALSA updated to version 1.0.2 with previous version 1.0.1 dated 2021-05-28

Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with complex sampling and assessment design (see 'Rutkowski', 2010 <doi:10.3102/0013189X10363170>). Such studies are, for example, international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical interface is available for the non-technical user.The package includes functions to covert the original data from 'SPSS' into 'R' data sets keeping the user-defined missing values, merge data from different respondents and/or countries, generate variable dictionaries, modify data, produce descriptive statistics (percentages, means, percentiles, benchmarks) and multivariate statistics (correlations, linear regression, binary logistic regression). The number of supported studies and analysis types will increase in future. For a general presentation of the package, see 'Mirazchiyski', 2021a (<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the package, see 'Mirazchiyski', 2021b (<doi:10.3390/psych3020018>).
Author: Plamen V. Mirazchiyski [aut, cre], INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>

Diff between RALSA versions 1.0.1 dated 2021-05-28 and 1.0.2 dated 2021-10-21

 DESCRIPTION             |   19 
 MD5                     |   38 
 NAMESPACE               |    2 
 NEWS.md                 |   25 
 R/RALSA.r               |   11 
 R/common.r              |  685 +++-----
 R/lsa.bench.r           |  365 +---
 R/lsa.bin.log.reg.r     |  244 --
 R/lsa.convert.data.r    |  658 --------
 R/lsa.corr.r            |  139 -
 R/lsa.data.diag.r       |  187 --
 R/lsa.lin.reg.r         |  278 ---
 R/lsa.merge.data.r      | 1237 ++++++---------
 R/lsa.pcts.means.r      |  104 -
 R/lsa.prctls.r          |  113 -
 R/lsa.recode.vars.r     |   77 
 R/lsa.vars.dict.r       |  265 +--
 inst/shiny/GUI/server.r | 2419 +++--------------------------
 inst/shiny/GUI/ui.r     | 3941 +++++++++++++++++++++---------------------------
 man/RALSA.Rd            |    6 
 20 files changed, 3219 insertions(+), 7594 deletions(-)

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New package pixelclasser with initial version 1.0.0
Package: pixelclasser
Title: Classifies Image Pixels by Colour
Version: 1.0.0
Description: Contains functions to classify the pixels of an image file by its colour. It implements a simple form of the techniques known as Support Vector Machine adapted to this particular problem.
Encoding: UTF-8
License: GPL-3
LazyData: false
Imports: graphics, grDevices, jpeg, tiff,
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr, rmarkdown
URL: https://github.com/ropensci/pixelclasser
BugReports: https://github.com/ropensci/pixelclasser
Language: en-GB
NeedsCompilation: no
Packaged: 2021-10-20 15:08:15 UTC; mnium
Author: Carlos Real [aut, cre] (<https://orcid.org/0000-0002-5433-6728>), Quentin Read [rev]
Maintainer: Carlos Real <carlos.real@usc.es>
Repository: CRAN
Date/Publication: 2021-10-21 15:40:02 UTC

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New package opGMMassessment with initial version 0.1.0
Package: opGMMassessment
Title: Optimized Automated Gaussian Mixture Assessment
Version: 0.1.0
Author: Jorn Lotsch [aut,cre] (<https://orcid.org/0000-0002-5818-6958>), Sebastian Malkusch [aut] (<https://orcid.org/0000-0001-6766-140X>)
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Description: Necessary functions for optimized automated evaluation of the number and parameters of Gaussian mixtures in one-dimensional data. Various methods are available for parameter estimation and for determining the number of modes in the mixture.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: AdaptGauss, DataVisualizations, DistributionOptimization, cluster, mixtools, grDevices, methods, foreach, stats, utils, rlang, ggplot2, parallel, caTools, dplyr, mclust, mixAK, multimode, NbClust, ClusterR, doParallel
NeedsCompilation: no
Packaged: 2021-10-20 12:01:08 UTC; joern
Repository: CRAN
Date/Publication: 2021-10-21 15:30:05 UTC

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Package OAIHarvester updated to version 0.3-3 with previous version 0.3-2 dated 2021-05-03

Title: Harvest Metadata Using OAI-PMH Version 2.0
Description: Harvest metadata using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) version 2.0 (for more information, see <https://www.openarchives.org/OAI/openarchivesprotocol.html>).
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>

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Package DCSmooth updated to version 1.1.2 with previous version 1.0.2 dated 2021-08-25

Title: Nonparametric Regression and Bandwidth Selection for Spatial Models
Description: Nonparametric smoothing techniques for data on a lattice and functional time series. Smoothing is done via kernel regression or local polynomial regression, a bandwidth selection procedure based on an iterative plug-in algorithm is implemented. This package allows for modeling a dependency structure of the error terms of the nonparametric regression model. Methods used in this paper are described in Feng/Schaefer (2021) <https://ideas.repec.org/p/pdn/ciepap/144.html>, Schaefer/Feng (2021) <https://ideas.repec.org/p/pdn/ciepap/143.html>.
Author: Bastian Schaefer [aut, cre], Sebastian Letmathe [ctb], Yuanhua Feng [ths]
Maintainer: Bastian Schaefer <bastian.schaefer@uni-paderborn.de>

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Package APCI updated to version 1.0.3 with previous version 1.0.2 dated 2021-10-01

Title: A New Age-Period-Cohort Model for Describing and Investigating Inter-Cohort Differences and Life Course Dynamics
Description: It implemented Age-Period-Interaction Model (APC-I Model) proposed in the paper of Liying Luo and James S. Hodges in 2019. A new age-period-cohort model for describing and investigating inter-cohort differences and life course dynamics.
Author: Jiahui Xu [aut, cre], Liying Luo [aut]
Maintainer: Jiahui Xu <jpx5053@psu.edu>

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Package sodium updated to version 1.2.0 with previous version 1.1 dated 2017-03-31

Title: A Modern and Easy-to-Use Crypto Library
Description: Bindings to 'libsodium': a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. Sodium uses curve25519, a state-of-the-art Diffie-Hellman function by Daniel Bernstein, which has become very popular after it was discovered that the NSA had backdoored Dual EC DRBG.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package shrinkTVP updated to version 2.0.3 with previous version 2.0.2 dated 2021-05-13

Title: Efficient Bayesian Inference for Time-Varying Parameter Models with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006> and Cadonna et al. (2020) <doi:10.3390/econometrics8020020>.
Author: Peter Knaus [aut, cre] (<https://orcid.org/0000-0001-6498-7084>), Angela Bitto-Nemling [aut], Annalisa Cadonna [aut] (<https://orcid.org/0000-0003-0360-7628>), Sylvia Frühwirth-Schnatter [aut] (<https://orcid.org/0000-0003-0516-5552>), Daniel Winkler [ctb], Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>

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Package windex updated to version 2.0.3 with previous version 2.0.2 dated 2021-04-14

Title: Analysing Convergent Evolution using the Wheatsheaf Index
Description: Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other random but perhaps useful functions.
Author: Kevin Arbuckle and Amanda Minter
Maintainer: Kevin Arbuckle <kevin.arbuckle@swansea.ac.uk>

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Package RSC updated to version 2.0.1 with previous version 2.0 dated 2021-10-17

Title: Robust and Sparse Correlation Matrix
Description: Performs robust and sparse correlation matrix estimation. Robustness is achieved based on a simple robust pairwise correlation estimator, while sparsity is obtained based on thresholding. The optimal thresholding is tuned via cross-validation. See Serra, Coretto, Fratello and Tagliaferri (2018) <doi:10.1093/bioinformatics/btx642>.
Author: Luca Coraggio [cre, aut], Pietro Coretto [aut], Angela Serra [aut], Roberto Tagliaferri [ctb]
Maintainer: Luca Coraggio <luca.coraggio@unina.it>

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Package epicontacts updated to version 1.1.2 with previous version 1.1.0 dated 2017-11-21

Title: Handling, Visualisation and Analysis of Epidemiological Contacts
Description: A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.
Author: Finlay Campbell [aut, cre], Thibaut Jombart [aut], Nistara Randhawa [aut], Bertrand Sudre [aut], VP Nagraj [aut], Thomas Crellen [aut], Zhian N. Kamvar [aut]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>

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Package bRacatus updated to version 1.0.5 with previous version 1.0.4 dated 2021-05-28

Title: A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data
Description: Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Author: Eduardo Arlé [aut, cre], Alexander Zizka [aut], Patrick Weigelt [ctb], Sam Levin [ctb], Carsten Meyer [ths]
Maintainer: Eduardo Arlé <eduardo.arle@idiv.de>

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Package apexcharter updated to version 0.3.0 with previous version 0.2.0 dated 2021-05-11

Title: Create Interactive Chart with the JavaScript 'ApexCharts' Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'. 'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API. 'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre], Fanny Meyer [aut], Juned Chhipa [cph] (apexcharts.js library), Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>

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Package RandomFieldsUtils updated to version 0.5.6 with previous version 0.5.5 dated 2021-10-05

Title: Utilities for the Simulation and Analysis of Random Fields
Description: Various utilities are provided that might be used in spatial statistics and elsewhere. It delivers a method for solving linear equations that checks the sparsity of the matrix before any algorithm is used. Furthermore, it includes the Struve functions.
Author: Martin Schlather [aut, cre], Reinhard Furrer [ctb], Martin Kroll [ctb], Brian D. Ripley [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFieldsUtils versions 0.5.5 dated 2021-10-05 and 0.5.6 dated 2021-10-21

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Package IOHanalyzer updated to version 0.1.6.1 with previous version 0.1.5.2 dated 2021-05-31

Title: Data Analysis Part of 'IOHprofiler'
Description: The data analysis module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides statistical analysis methods for the benchmark data generated by optimization heuristics, which can be visualized through a web-based interface. The benchmark data is usually generated by the experimentation module, called 'IOHexperimenter'. 'IOHanalyzer' also supports the widely used 'COCO' (Comparing Continuous Optimisers) data format for benchmarking.
Author: Hao Wang [cre, aut], Diederick Vermetten [aut], Carola Doerr [aut], Thomas Bäck [aut]
Maintainer: Hao Wang <h.wang@liacs.leidenuniv.nl>

Diff between IOHanalyzer versions 0.1.5.2 dated 2021-05-31 and 0.1.6.1 dated 2021-10-21

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 IOHanalyzer-0.1.6.1/IOHanalyzer/R/IOHanalyzer-deprecated.R                                                     |  390 ++--
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More information about IOHanalyzer at CRAN
Permanent link

Package monobin updated to version 0.2.0 with previous version 0.1.1 dated 2021-08-02

Title: Monotonic Binning for Credit Rating Models
Description: Performs monotonic binning of numeric risk factor in credit rating models (PD, LGD, EAD) development. All functions handle both binary and continuous target variable. Functions that use isotonic regression in the first stage of binning process have an additional feature for correction of minimum percentage of observations and minimum target rate per bin. Additionally, monotonic trend can be identified based on raw data or, if known in advance, forced by functions' argument. Missing values and other possible special values are treated separately from so-called complete cases.
Author: Andrija Djurovic [aut, cre]
Maintainer: Andrija Djurovic <djandrija@gmail.com>

Diff between monobin versions 0.1.1 dated 2021-08-02 and 0.2.0 dated 2021-10-21

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More information about monobin at CRAN
Permanent link

Package nominatimlite updated to version 0.1.3 with previous version 0.1.2 dated 2021-10-07

Title: Interface with 'Nominatim' API Service
Description: Lite interface for getting data from 'OSM' service 'Nominatim' <https://nominatim.org/release-docs/latest/>. Extract coordinates from addresses, find places near a set of coordinates, search for amenities and return spatial objects on 'sf' format.
Author: Diego Hernangómez [aut, cre, cph] (<https://orcid.org/0000-0001-8457-4658>), Jindra Lacko [ctb, rev]
Maintainer: Diego Hernangómez <diego.hernangomezherrero@gmail.com>

Diff between nominatimlite versions 0.1.2 dated 2021-10-07 and 0.1.3 dated 2021-10-21

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Package sociome updated to version 2.1.0 with previous version 2.0.0 dated 2021-02-24

Title: Operationalizing Social Determinants of Health Data for Researchers
Description: Accesses raw data via API and calculates social determinants of health measures for user-specified locations in the US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre], Jarrod Dalton [aut], Cindy Wang [aut], Adam Perzynski [aut], National Institutes of Health/National Institute on Aging [fnd] (The development of this software package was supported by a research grant from the National Institutes of Health/National Institute on Aging, (Principal Investigators: Jarrod E. Dalton, PhD and Adam T. Perzynski, PhD; Grant Number: 5R01AG055480-02). All of its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.)
Maintainer: Nik Krieger <nk@case.edu>

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Package RedditExtractoR updated to version 3.0.5 with previous version 3.0.3 dated 2021-09-03

Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

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Package tLagPropOdds updated to version 1.2 with previous version 1.1 dated 2021-10-20

Title: Proportional Odds Model with Censored, Time-Lagged Categorical Outcome
Description: Implements a semiparametric estimator for the odds ratio model with censored, time-lagged, ordered categorical outcome in a randomized clinical trial that incorporates baseline and time-dependent information. Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut], A. A. Tsiatis [aut], Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>

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Package rflexscan updated to version 1.0.0 with previous version 0.4.0 dated 2021-01-19

Title: The Flexible Spatial Scan Statistic
Description: Functions for the detection of spatial clusters using the flexible spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>. This package implements a wrapper for the C routine used in the FleXScan 3.1.2 <https://sites.google.com/site/flexscansoftware/home> developed by Takahashi, Yokoyama, and Tango. For details, see Otani et al. (2021) <doi:10.18637/jss.v099.i13>.
Author: Takahiro Otani, Kunihiko Takahashi
Maintainer: Takahiro Otani <otani@med.nagoya-cu.ac.jp>

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Package cancensus updated to version 0.4.6 with previous version 0.4.5 dated 2021-10-20

Title: Access, Retrieve, and Work with Canadian Census Data and Geography
Description: Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer), Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for correspondence), Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>

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Package tabxplor updated to version 1.0.2 with previous version 1.0.1 dated 2021-09-14

Title: User-Friendly Tables with Color Helpers for Data Exploration
Description: Make it easy to deal with multiple cross-tables in data exploration, by creating them, manipulating them, and adding color helpers to highlight important informations. All functions are "tidy", pipe-friendly, and render data frames which can be easily manipulated. Tables can be exported to Excel and in html with formats and colors.
Author: Brice Nocenti [aut, cre]
Maintainer: Brice Nocenti <brice.nocenti@gmail.com>

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Package textTinyR updated to version 1.1.6 with previous version 1.1.5 dated 2021-10-13

Title: Text Processing for Small or Big Data Files
Description: It offers functions for splitting, parsing, tokenizing and creating a vocabulary for big text data files. Moreover, it includes functions for building a document-term matrix and extracting information from those (term-associations, most frequent terms). It also embodies functions for calculating token statistics (collocations, look-up tables, string dissimilarities) and functions to work with sparse matrices. Lastly, it includes functions for Word Vector Representations (i.e. 'GloVe', 'fasttext') and incorporates functions for the calculation of (pairwise) text document dissimilarities. The source code is based on 'C++11' and exported in R through the 'Rcpp', 'RcppArmadillo' and 'BH' packages.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>

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Package VancouvR updated to version 0.1.7 with previous version 0.1.6 dated 2021-07-09

Title: Access the 'City of Vancouver' Open Data API
Description: Wrapper around the 'City of Vancouver' Open Data API <https://opendata.vancouver.ca/api/v2/console> to simplify and standardize access to 'City of Vancouver' open data. Functionality to list the data catalogue and access data and geographic records.
Author: Jens von Bergmann
Maintainer: Jens von Bergmann <jens@mountainmath.ca>

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Package HDBRR updated to version 1.1.2 with previous version 1.1.1 dated 2021-09-22

Title: High Dimensional Bayesian Ridge Regression without MCMC
Description: The svd(singular value decomposition) or qr decomposition was using for the implementation, this avoid the recursion optimizing the time in the compute.
Author: Sergio Perez-Elizalde Developer [aut], Blanca Monroy-Castillo Developer [aut, cre], Paulino Perez-Rodriguez User [ctb], Jose Crossa User [ctb]
Maintainer: Blanca Monroy-Castillo Developer <blancamonroy.96@gmail.com>

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Package fasstr updated to version 0.3.3 with previous version 0.3.2 dated 2020-11-07

Title: Analyze, Summarize, and Visualize Daily Streamflow Data
Description: The Flow Analysis Summary Statistics Tool for R, 'fasstr', provides various functions to tidy and screen daily stream discharge data, calculate and visualize various summary statistics and metrics, and compute annual trending and volume frequency analyses. It features useful function arguments for filtering of and handling dates, customizing data and metrics, and the ability to pull daily data directly from the Water Survey of Canada hydrometric database (<https://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>).
Author: Jon Goetz [aut, cre] (<https://orcid.org/0000-0002-4993-1119>), Carl James Schwarz [aut], Robin Pike [ctb], Province of British Columbia [cph]
Maintainer: Jon Goetz <jon.goetz@gov.bc.ca>

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 tests/testthat/test-add_cumulative_volume.R          |   16 
 tests/testthat/test-add_cumulative_yield.R           |   18 
 tests/testthat/test-add_daily_volume.R               |    8 
 tests/testthat/test-add_daily_yield.R                |   12 
 tests/testthat/test-add_date_variables.R             |   28 
 tests/testthat/test-add_rolling_means.R              |   16 
 tests/testthat/test-add_seasons.R                    |   12 
 tests/testthat/test-calc_all_annual_stats.R          |   12 
 tests/testthat/test-calc_annual_cumulative_stats.R   |   12 
 tests/testthat/test-calc_annual_flow_timing.R        |   10 
 tests/testthat/test-calc_annual_lowflows.R           |   12 
 tests/testthat/test-calc_annual_outside_normal.R     |    8 
 tests/testthat/test-calc_annual_stats.R              |   20 
 tests/testthat/test-calc_daily_cumulative_stats.R    |   12 
 tests/testthat/test-calc_daily_stats.R               |   20 
 tests/testthat/test-calc_flow_percentile.R           |    6 
 tests/testthat/test-calc_longterm_daily_stats.R      |   20 
 tests/testthat/test-calc_longterm_mean.R             |   10 
 tests/testthat/test-calc_longterm_monthly_stats.R    |   20 
 tests/testthat/test-calc_longterm_percentile.R       |    8 
 tests/testthat/test-calc_monthly_cumulative_stats.R  |   12 
 tests/testthat/test-calc_monthly_stats.R             |   22 
 tests/testthat/test-compute_annual_frequencies.R     |    4 
 tests/testthat/test-compute_annual_trends.R          |   18 
 tests/testthat/test-compute_frequency_analysis.R     |    4 
 tests/testthat/test-compute_frequency_quantile.R     |    4 
 tests/testthat/test-compute_full_analysis.R          |    4 
 tests/testthat/test-compute_hydat_peak_frequencies.R |    6 
 tests/testthat/test-fill_missing_dates.R             |   20 
 tests/testthat/test-plot_annual_cumulative_stats.R   |    8 
 tests/testthat/test-plot_annual_flow_timing.R        |    4 
 tests/testthat/test-plot_annual_lowflows.R           |    6 
 tests/testthat/test-plot_annual_means.R              |    4 
 tests/testthat/test-plot_annual_outside_normal.R     |    6 
 tests/testthat/test-plot_annual_stats.R              |    4 
 tests/testthat/test-plot_daily_cumulative_stats.R    |    4 
 tests/testthat/test-plot_daily_stats.R               |    6 
 tests/testthat/test-plot_data_screening.R            |    6 
 tests/testthat/test-plot_flow_data.R                 |    6 
 tests/testthat/test-plot_flow_duration.R             |    6 
 tests/testthat/test-plot_longterm_daily_stats.R      |    4 
 tests/testthat/test-plot_longterm_monthly_stats.R    |    4 
 tests/testthat/test-plot_missing_dates.R             |    4 
 tests/testthat/test-plot_monthly_cumulative_stats.R  |    4 
 tests/testthat/test-plot_monthly_stats.R             |    8 
 tests/testthat/test-screen_flow_data.R               |   14 
 vignettes/fasstr_full_analysis.Rmd                   |    9 
 vignettes/fasstr_trending_analysis.Rmd               |   12 
 vignettes/fasstr_under_the_hood.Rmd                  |    3 
 vignettes/fasstr_users_guide.Rmd                     |    8 
 145 files changed, 6572 insertions(+), 8189 deletions(-)

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