CRANberries

Mon, 25 Jul 2022

New package raptr with initial version 0.2.1
Package: raptr
Title: Representative and Adequate Prioritization Toolkit in R
Version: 0.2.1
Description: Biodiversity is in crisis. The overarching aim of conservation is to preserve biodiversity patterns and processes. To this end, protected areas are established to buffer species and preserve biodiversity processes. But resources are limited and so protected areas must be cost-effective. This package contains tools to generate plans for protected areas (prioritizations), using spatially explicit targets for biodiversity patterns and processes. To obtain solutions in a feasible amount of time, this package uses the commercial 'Gurobi' software (obtained from <https://www.gurobi.com/>). For more information on using this package, see Hanson et al. (2018) <doi:10.1111/2041-210X.12862>.
Imports: utils, methods, stats, graphics, grDevices, parallel, Matrix (>= 1.4.1), assertthat (>= 0.2.1), boot (>= 1.3.28), PBSmapping (>= 2.73.0), scales (>= 1.2.0), shape (>= 1.4.6), adehabitatHR (>= 0.4.19), RColorBrewer (>= 1.1.3), ggplot2 (>= 3.3.5), plyr (>= 1.8.7), doParallel (>= 1.0.17), rgeos (>= 0.5.9), rgdal (>= 1.5.30), hypervolume (>= 2.0.7), ks (>= 1.13.5), mvtnorm (>= 1.1.3), withr (>= 2.5.0),
Depends: R (>= 3.5.0), sp (>= 1.4.6), raster (>= 3.5.15)
LinkingTo: Rcpp, RcppEigen, BH
LazyData: true
License: GPL-3
Encoding: UTF-8
Language: en-US
URL: https://jeffrey-hanson.com/raptr/, https://github.com/jeffreyhanson/raptr
BugReports: https://github.com/jeffreyhanson/raptr/issues
VignetteBuilder: knitr
Suggests: knitr, roxygen2, rmarkdown, testthat, RgoogleMaps (>= 1.4.5.3), dplyr (>= 1.0.8), vegan (>= 2.6.2), gurobi (>= 8.0.0), gridExtra (>= 2.3), rgl (>= 0.108.3),
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2022-07-25 05:58:21 UTC; jeff
Author: Jeffrey O Hanson [aut, cre], Jonathan R Rhodes [aut], Hugh P Possingham [aut], Richard A Fuller [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Repository: CRAN
Date/Publication: 2022-07-25 14:10:02 UTC

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Thu, 21 Jul 2022

New package video with initial version 0.1.0
Package: video
Title: 'Shiny' Extension of 'video.js'
Version: 0.1.0
Description: Video interactivity within 'shiny' applications using 'video.js'. Enables the status of the video to be sent from the UI to the server, and allows events such as playing and pausing the video to be triggered from the server.
License: Apache License (>= 2)
URL: https://github.com/ashbaldry/video, https://github.com/videojs/video.js
BugReports: https://github.com/ashbaldry/video/issues
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: shiny, htmlwidgets, jsonlite
Suggests: rmarkdown, knitr, shinytest2, globals, testthat (>= 3.0.0)
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 17:11:08 UTC; arbal
Author: Ashley Baldry [aut, cre], Steve Heffernan [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-21 17:50:02 UTC

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New package rGV with initial version 0.0.1
Package: rGV
Version: 0.0.1
Date: 2022-07-21
Title: Analysis of Continuous Glucose Monitor Data
Author: Evan Olawsky [aut, cre], Yuan Zhang [ctb], Lynn Eberly [ctb]
Maintainer: Evan Olawsky <evanolawsky@gmail.com>
Depends: R (>= 3.2.0), chron
Description: Reads in continuous glucose monitor data of many different formats, calculates a host of glycemic variability metrics, and plots glucose over time.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: pastecs, zoo
NeedsCompilation: no
Packaged: 2022-07-21 15:50:48 UTC; overlord
Repository: CRAN
Date/Publication: 2022-07-21 17:40:02 UTC

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New package netcom with initial version 2.1.6
Package: netcom
Title: NETwork COMparison Inference
Version: 2.1.6
Date: 2022-7-19
Description: Infer system functioning with empirical NETwork COMparisons. These methods are part of a growing paradigm in network science that uses relative comparisons of networks to infer mechanistic classifications and predict systemic interventions. They have been developed and applied in Langendorf and Burgess (2021) <doi:10.1038/s41598-021-99251-7>, Langendorf (2020) <doi:10.1201/9781351190831-6>, and Langendorf and Goldberg (2019) <arXiv:1912.12551>.
URL: https://github.com/langendorfr/netcom
Repository: CRAN
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.1.0)
Imports: stats, dplyr, tibble, clue, expm, igraph, Matrix, pdist, pracma, vegan, magrittr, foreach, parallel, doParallel, optimx, GenSA, rlang, ggfortify, ggplot2, ggraph, reshape2
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 16:08:26 UTC; ryan
Author: Ryan Langendorf [aut, cre], Debra Goldberg [ctb], Matthew Burgess [ctb]
Maintainer: Ryan Langendorf <ryan.langendorf@colorado.edu>
Date/Publication: 2022-07-21 17:40:06 UTC

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New package howler with initial version 0.2.0
Package: howler
Title: 'Shiny' Extension of 'howler.js'
Version: 0.2.0
Description: Audio interactivity within 'shiny' applications using 'howler.js'. Enables the status of the audio player to be sent from the UI to the server, and events such as playing and pausing the audio can be triggered from the server.
License: MIT + file LICENSE
URL: https://github.com/ashbaldry/howler, https://github.com/goldfire/howler.js
BugReports: https://github.com/ashbaldry/howler/issues
Encoding: UTF-8
Imports: shiny, htmlwidgets
Suggests: rmarkdown, knitr, shinytest2, globals, testthat (>= 3.0.0)
Language: en-GB
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 17:06:04 UTC; arbal
Author: Ashley Baldry [aut, cre], James Simpson [aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-21 17:50:05 UTC

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New package robustmeta with initial version 1.1-1
Package: robustmeta
Title: Robust Inference for Meta-Analysis with Influential Outlying Studies
Version: 1.1-1
Date: 2022-07-09
Maintainer: Hisashi Noma <noma@ism.ac.jp>
Description: Robust inference methods for fixed-effect and random-effects models of meta-analysis are implementable. The robust methods are developed using the density power divergence that is a robust estimating criterion developed in machine learning theory, and can effectively circumvent biases and misleading results caused by influential outliers. The density power divergence is originally introduced by Basu et al. (1998) <doi:10.1093/biomet/85.3.549>, and the meta-analysis methods are developed by Noma et al. (2022) <forthcoming>.
Depends: R (>= 3.5.0)
Imports: stats, metafor
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-21 09:34:00 UTC; Hisashi
Author: Hisashi Noma [aut, cre], Shonosuke Sugasawa [aut], Toshi A. Furukawa [aut]
Repository: CRAN
Date/Publication: 2022-07-21 12:50:02 UTC

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New package rgrass with initial version 0.3-2
Package: rgrass
Version: 0.3-2
Date: 2022-07-21
Title: Interface Between 'GRASS' Geographical Information System and 'R'
Description: An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Depends: R (>= 3.3.0), XML
Imports: stats, utils, methods
Suggests: terra, sp (>= 0.9), knitr, rmarkdown, sf, stars, raster
VignetteBuilder: knitr
SystemRequirements: GRASS (>= 7)
License: GPL (>= 2)
URL: https://rsbivand.github.io/rgrass/, https://grass.osgeo.org/, https://github.com/rsbivand/rgrass, https://lists.osgeo.org/mailman/listinfo/grass-stats
BugReports: https://github.com/rsbivand/rgrass/issues/
NeedsCompilation: no
Packaged: 2022-07-21 09:19:06 UTC; rsb
Author: Roger Bivand [cre, aut] , Rainer Krug [ctb] , Markus Neteler [ctb] , Sebastian Jeworutzki [ctb] , Floris Vanderhaeghe [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Repository: CRAN
Date/Publication: 2022-07-21 12:50:05 UTC

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New package normalizeH with initial version 1.0.0
Package: normalizeH
Version: 1.0.0
Date: 2022-07-20
Title: Normalize Hadamard Matrix
Author: Baidya Nath Mandal [aut, cre]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Depends: R (>= 4.2.0)
Suggests: HadamardR
Description: Normalize a given Hadamard matrix. A Hadamard matrix is said to be normalized when its first row and first column entries are all 1, see Hedayat, A. and Wallis, W. D. (1978) "Hadamard matrices and their applications. The Annals of Statistics, 1184-1238." <doi:10.1214/aos/1176344370>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-07-20 05:27:10 UTC; b
Repository: CRAN
Date/Publication: 2022-07-21 12:30:02 UTC

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New package htmcglm with initial version 0.0.1
Package: htmcglm
Title: Hypothesis Testing for McGLMs
Version: 0.0.1
Author: Lineu Alberto Cavazani de Freitas [aut, cre], Wagner Hugo Bonat [ctb], Walmes Marques Zeviani [ctb]
Maintainer: Lineu Alberto Cavazani de Freitas <lineuacf@gmail.com>
Description: Performs hypothesis testing for multivariate covariance generalized linear models (McGLMs). McGLM is a general framework for non-normal multivariate data analysis, designed to handle multivariate response variables, along with a wide range of temporal and spatial correlation structures defined in terms of a covariance link function combined with a matrix linear predictor involving known matrices. The models take non-normality into account in the conventional way by means of a variance function, and the mean structure is modelled by means of a link function and a linear predictor. The models are fitted using an efficient Newton scoring algorithm based on quasi-likelihood and Pearson estimating functions, using only second-moment assumptions. This provides a unified approach to a wide variety of different types of response variables and covariance structures, including multivariate extensions of repeated measures, time series, longitudinal, spatial and spatio-temporal structures. The package offers a user-friendly interface for fitting McGLMs similar to the glm() R function.
License: MIT + file LICENSE
URL: https://github.com/lineu96/htmcglm
Encoding: UTF-8
Imports: stats, doBy, Matrix, mcglm, sjmisc, stringr
NeedsCompilation: no
Packaged: 2022-07-20 20:13:15 UTC; lacf14
Repository: CRAN
Date/Publication: 2022-07-21 12:10:06 UTC

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New package ensModelVis with initial version 0.1.0
Package: ensModelVis
Title: Visualisations for Model Ensembles
Version: 0.1.0
Description: Displays for model fits of multiple models and their ensembles. For classification models, the plots are heatmaps, for regression, scatterplots.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, forcats, ggplot2, magrittr, rlang, tidyr
URL: https://github.com/domijan/ensModelVis
BugReports: https://github.com/domijan/ensModelVis/issues
Suggests: discrim, glmnet, kernlab, knitr, MASS, nnet, ranger, rmarkdown, stacks, stringr, tidymodels
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 06:36:40 UTC; katarina
Author: Katarina Domijan [aut, cre]
Maintainer: Katarina Domijan <domijank@tcd.ie>
Repository: CRAN
Date/Publication: 2022-07-21 12:40:02 UTC

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New package connectapi with initial version 0.1.1.1
Package: connectapi
Title: Utilities for Interacting with the 'RStudio Connect' Server API
Version: 0.1.1.1
Description: Provides a helpful 'R6' class and methods for interacting with the 'RStudio Connect' Server API along with some meaningful utility functions for regular tasks. API documentation varies by 'RStudio Connect' installation and version, but the latest documentation is also hosted publicly at <https://docs.rstudio.com/connect/api/>.
License: MIT + file LICENSE
URL: https://github.com/rstudio/connectapi
Imports: config, dplyr, fs, glue, httr, lifecycle, magrittr, progress, purrr, R6, rlang (>= 0.4.2), tibble, uuid, vctrs (>= 0.3.0), yaml, bit64, jsonlite
Suggests: crayon, flexdashboard, ggplot2, gridExtra, htmltools, knitr, lubridate, processx, rmarkdown, rprojroot, spelling, testthat, rsconnect, webshot2, covr, mockery, devtools
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-20 20:50:15 UTC; r124525
Author: Sean Lopp [aut], Cole Arendt [aut, cre], RStudio PBC [cph, fnd]
Maintainer: Cole Arendt <cole@rstudio.com>
Repository: CRAN
Date/Publication: 2022-07-21 12:20:02 UTC

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New package amapro with initial version 0.1.0
Package: amapro
Title: Thin Wrapper for Mapping Library 'AMap' by 'AutoNavi'
Date: 2022-07-20
Version: 0.1.0
Author: Larry Helgason [aut, cre, cph]
Maintainer: Larry Helgason <larry@helgasoft.com>
Description: Build and control interactive 2D and 3D maps with 'R/Shiny'. Lean set of powerful commands wrapping native calls to 'AMap' <https://lbs.amap.com/api/jsapi-v2/summary/>. Deliver rich mapping functionality with minimal overhead.
URL: https://github.com/helgasoft/amapro/
BugReports: https://github.com/helgasoft/amapro/issues/
Depends: R (>= 4.1.0)
Imports: htmlwidgets, shiny (>= 1.7.0), tcltk (>= 4.2.0)
Suggests: knitr, rmarkdown
License: Apache License (>= 2)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-21 03:31:33 UTC; gugu
Repository: CRAN
Date/Publication: 2022-07-21 12:30:04 UTC

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New package nextGenShinyApps with initial version 1.5
Package: nextGenShinyApps
Title: Advanced Tools for Building the Next Generation of 'Shiny' Applications and Dashboards
Version: 1.5
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Description: Responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts and style sheets are based on 'jQuery' <https://jquery.com/> and 'Bootstrap' <https://getbootstrap.com/>.
License: MIT + file LICENSE
URL: https://github.com/oobianom/nextGenShinyApps
BugReports: https://github.com/oobianom/nextGenShinyApps
Depends: R (>= 3.4)
Imports: utils, shiny, htmltools
Suggests: rmarkdown, knitr, qpdf
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2022-07-20 17:15:30 UTC; in198
Repository: CRAN
Date/Publication: 2022-07-21 12:00:02 UTC

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New package EnrichIntersect with initial version 0.1
Package: EnrichIntersect
Title: Enrichment Analysis and Intersecting Sankey Diagram
Version: 0.1
Date: 2022-07-20
Description: A flexible tool for enrichment analysis based on user-defined sets is provided. It allows users to perform over-representation analysis of the custom sets among any specified ranked feature list, hence making enrichment analysis applicable to various types of data from different scientific fields. 'EnrichIntersect' also enables an interactive means to visualize identified associations based on, for example, the mix-lasso model (Zhao et al. (2022) <doi:10.1016/j.isci.2022.104767>) or similar methods.
License: MIT + file LICENSE
Depends: R (>= 4.0)
Encoding: UTF-8
Imports: ggplot2, dplyr, networkD3, jsonlite, htmlwidgets, webshot2, grDevices, methods
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-20 18:24:36 UTC; zhiz
Author: Zhi Zhao [aut, cre], Manuela Zucknick [aut], Tero Aittokallio [ctb]
Maintainer: Zhi Zhao <zhi.zhao@medisin.uio.no>
Repository: CRAN
Date/Publication: 2022-07-21 12:00:15 UTC

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New package autohrf with initial version 1.0.3
Package: autohrf
Title: Automated Generation of Data-Informed GLM Models in Task-Based fMRI Data Analysis
Version: 1.0.3
Maintainer: Jure Demsar <jure.demsar@fri.uni-lj.si>
Description: Analysis of task-related functional magnetic resonance imaging (fMRI) activity at the level of individual participants is commonly based on general linear modelling (GLM) that allows us to estimate to what extent the blood oxygenation level dependent (BOLD) signal can be explained by task response predictors specified in the GLM model. The predictors are constructed by convolving the hypothesised timecourse of neural activity with an assumed hemodynamic response function (HRF). To get valid and precise estimates of task response, it is important to construct a model of neural activity that best matches actual neuronal activity. The construction of models is most often driven by predefined assumptions on the components of brain activity and their duration based on the task design and specific aims of the study. However, our assumptions about the onset and duration of component processes might be wrong and can also differ across brain regions. This can result in inappropriate or suboptimal models, bad fitting of the model to the actual data and invalid estimations of brain activity. Here we present an approach in which theoretically driven models of task response are used to define constraints based on which the final model is derived computationally using the actual data. Specifically, we developed 'autohrf' — a package for the 'R' programming language that allows for data-driven estimation of HRF models. The package uses genetic algorithms to efficiently search for models that fit the underlying data well. The package uses automated parameter search to find the onset and duration of task predictors which result in the highest fitness of the resulting GLM based on the fMRI signal under predefined restrictions. We evaluate the usefulness of the 'autohrf' package on publicly available datasets of task-related fMRI activity. Our results suggest that by using 'autohrf' users can find better task related brain activity models in a quick and efficient manner.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cowplot (>= 1.1.1), doParallel (>= 1.0.17), dplyr (>= 1.0.8), foreach (>= 1.5.2), ggplot2 (>= 3.3.5), gtools (>= 3.9.2), lubridate (>= 1.8.0), magrittr (>= 2.0.2), RColorBrewer (>= 1.1)
Suggests: knitr (>= 1.38), testthat (>= 3.1.3)
VignetteBuilder: knitr
URL: https://github.com/demsarjure/autohrf
BugReports: https://github.com/demsarjure/autohrf/issues
NeedsCompilation: no
Packaged: 2022-07-20 17:50:56 UTC; jure
Author: Jure Demsar [cre, aut], Nina Purg [aut], Grega Repovs [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-07-21 12:00:11 UTC

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New package MetaSKAT with initial version 0.82
Package: MetaSKAT
Title: Meta Analysis for SNP-Set (Sequence) Kernel Association Test
Version: 0.82
Date: 2022-07-21
Author: Seunggeun Lee [aut, cre]
Maintainer: Seunggeun (Shawn) Lee <lee7801@snu.ac.kr>
Description: Functions for Meta-analysis Burden Test, Sequence Kernel Association Test (SKAT) and Optimal SKAT (SKAT-O) by Lee et al. (2013) <doi:10.1016/j.ajhg.2013.05.010>. These methods use summary-level score statistics to carry out gene-based meta-analysis for rare variants.
License: GPL (>= 2)
SystemRequirements: Little Endian
Depends: R (>= 2.13.0)
Imports: SKAT (>= 2.0.1)
NeedsCompilation: yes
Packaged: 2022-07-21 07:06:00 UTC; LEE7801
Repository: CRAN
Date/Publication: 2022-07-21 09:20:02 UTC

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New package did2s with initial version 0.7.0
Package: did2s
Title: Two-Stage Difference-in-Differences Following Gardner (2021)
Version: 0.7.0
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the approach proposed by Gardner (2021). To avoid the problems caused by OLS estimation of the Two-way Fixed Effects model, this function first estimates the fixed effects and covariates using untreated observations and then in a second stage, estimates the treatment effects.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), fixest (>= 0.10.1)
Imports: data.table, ggplot2, glue, stats, stringr, rlang, cli, Matrix, Rcpp, did, broom, methods, staggered, didimputation, boot
URL: http://kylebutts.com/did2s/
Suggests: rmarkdown, knitr, haven, testthat (>= 3.0.0)
VignetteBuilder: knitr
LinkingTo: RcppArmadillo, Rcpp
NeedsCompilation: yes
Packaged: 2022-07-20 22:53:14 UTC; kylebutts
Author: Kyle Butts [aut, cre] , John Gardner [aut] , Grant McDermott [ctb] , Laurent Berge [ctb]
Maintainer: Kyle Butts <kyle.butts@colorado.edu>
Repository: CRAN
Date/Publication: 2022-07-21 09:40:02 UTC

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Wed, 20 Jul 2022

New package promor with initial version 0.1.0
Package: promor
Title: Proteomics Data Analysis and Modeling Tools
Version: 0.1.0
Description: A comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from 'MaxQuant' can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).
License: LGPL (>= 2.1)
Encoding: UTF-8
Language: en-US
VignetteBuilder: knitr
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
URL: https://github.com/caranathunge/promor, https://caranathunge.github.io/promor/
Imports: reshape2, ggplot2, ggrepel, gridExtra, limma, statmod, pcaMethods, VIM, missForest, caret, kernlab, xgboost, viridis, pROC
LazyData: true
BugReports: https://github.com/caranathunge/promor/issues
NeedsCompilation: no
Packaged: 2022-07-19 20:40:22 UTC; ranathca
Author: Chathurani Ranathunge [aut, cre, cph]
Maintainer: Chathurani Ranathunge <caranathunge86@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-20 17:30:02 UTC

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New package lnmCluster with initial version 0.3.1
Package: lnmCluster
Title: Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data
Version: 0.3.1
Maintainer: Wangshu Tu <wangshu.tu@carleton.ca>
Description: An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <arXiv:2011.06682>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022) <doi:10.1002/sam.11555>.
License: GPL (>= 2)
Encoding: UTF-8
Imports: mclust, foreach, MASS, stringr, gtools, pgmm, utils
Suggests: knitr, rmarkdown, testthat, mvtnorm
VignetteBuilder: knitr
Depends: R (>= 3.50)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-07-19 19:53:07 UTC; wangshutu
Author: Wangshu Tu [aut, cre], Sanjeena Dang [aut], Yuan Fang [aut]
Repository: CRAN
Date/Publication: 2022-07-20 17:50:02 UTC

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New package giedata with initial version 0.1.0
Package: giedata
Title: API Wrapper for GIE's AGSI+/ALSI+ Natural Gas Storage Transparency Platform
Version: 0.1.0
Description: Functions to access the API for Gas Infrastructure Europe's (GIE) AGSI+/ALSI+ natural gas storage transparency platform (<https://agsi.gie.eu/> and <https://alsi.gie.eu/>). Lets the user easily download metadata on companies and gas storage units covered by the API as well as the respective data on regional, country, company or facility level.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, httr, lubridate, magrittr, purrr
Suggests: vcr (>= 0.6.0), testthat
NeedsCompilation: no
Packaged: 2022-07-20 15:53:29 UTC; Nutzer
Author: Yannik Buhl [aut, cre]
Maintainer: Yannik Buhl <ybuhl@posteo.de>
Repository: CRAN
Date/Publication: 2022-07-20 17:50:04 UTC

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New package cito with initial version 1.0.0
Package: cito
Date: 2022-07-17
Title: Building and Training Neural Networks
Version: 1.0.0
Description: Building and training custom neural networks in the typical R syntax. The 'torch' package is used for numerical calculations, which allows for training on CPU as well as on a graphics card.
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: coro, checkmate, torch
License: GPL (>= 3)
Suggests: rmarkdown, knitr, testthat, plotly, ggraph, igraph, ggplot2
VignetteBuilder: knitr
BugReports: https://github.com/citoverse/cito/issues
NeedsCompilation: no
Packaged: 2022-07-19 06:32:03 UTC; chris
Author: Christian Amesoeder [aut, cre], Maximilian Pichler [aut]
Maintainer: Christian Amesoeder <Christian.Amesoeder@stud.uni-regensburg.de>
Repository: CRAN
Date/Publication: 2022-07-20 17:10:02 UTC

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New package activAnalyzer with initial version 1.0.4
Package: activAnalyzer
Title: A 'Shiny' App to Analyze Accelerometer-Measured Daily Physical Behavior Data
Version: 1.0.4
Description: A tool to analyse 'ActiGraph' accelerometer data and to implement the use of the PROactive Physical Activity in COPD (chronic obstructive pulmonary disease) instruments. Once analysis is completed, the app allows to export results to .csv files and to generate a report of the measurement. All the configured inputs relevant for interpreting the results are recorded in the report. In addition to the existing 'R' packages that are fully integrated with the app, the app uses some functions from the 'actigraph.sleepr' package developed by Petkova (2021) <https://github.com/dipetkov/actigraph.sleepr/>.
License: GPL (>= 3)
Imports: dbplyr (>= 2.1.1), dplyr (>= 1.0.7), flextable (>= 0.6.10), forcats (>= 0.5.1), ggplot2 (>= 3.3.5), golem (>= 0.3.1), hms (>= 1.1.1), lubridate (>= 1.8.0), magrittr, modelr (>= 0.1.8), patchwork (>= 1.1.1), PhysicalActivity, reactable (>= 0.2.3), rmarkdown (>= 2.11), RSQLite, shiny (>= 1.6.0), shinycssloaders (>= 1.0.0), shinydashboard (>= 0.7.2), shinydashboardPlus (>= 2.0.3), shinyFeedback (>= 0.4.0), shinyjs (>= 2.0.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), zoo
Encoding: UTF-8
URL: https://pydemull.github.io/activAnalyzer/, https://github.com/pydemull/activAnalyzer
BugReports: https://github.com/pydemull/activAnalyzer/issues
Suggests: shinytest, covr, knitr, spelling, testthat (>= 3.0.0), processx, globals, config, tidyselect, DBI, assertthat, htmltools, officer, pkgload, scales, tibble, rlang, tinytex
Language: en-US
Depends: R (>= 3.4.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-19 15:35:14 UTC; pydemullenheim
Author: Pierre-Yves de Muellenheim [cre, aut]
Maintainer: Pierre-Yves de Muellenheim <pydemull@uco.fr>
Repository: CRAN
Date/Publication: 2022-07-20 17:20:02 UTC

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New package RadOnc with initial version 1.1.7
Package: RadOnc
Title: Analytical Tools for Radiation Oncology
Version: 1.1.7
Date: 2022-07-19
Author: Reid F. Thompson <reid.thompson@gmail.com>
Maintainer: Reid F. Thompson <reid.thompson@gmail.com>
Imports: stats, utils
Depends: R (>= 3.0.0), graphics, grDevices, methods, oro.dicom (>= 0.5.0), ptinpoly
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
License: GPL (>= 2)
LazyData: yes
LazyLoad: yes
NeedsCompilation: no
Packaged: 2022-07-19 22:53:12 UTC; thompsre
Repository: CRAN
Date/Publication: 2022-07-20 15:50:08 UTC

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New package org with initial version 2022.7.21
Package: org
Title: Organising Projects
Version: 2022.7.21
Description: A system to help you organize projects. Most analyses have three (or more) main sections: code, results, and data, each with different requirements (version control/sharing/encryption). You provide folder locations and 'org' helps you take care of the details.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
URL: https://docs.sykdomspulsen.no/org/, https://github.com/sykdomspulsen-org/org
BugReports: https://github.com/sykdomspulsen-org/org/issues
Encoding: UTF-8
Suggests: testthat, knitr, rmarkdown, rstudioapi, glue
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-20 05:11:25 UTC; RIWH
Author: Richard Aubrey White [aut, cre] , Folkehelseinstituttet [cph]
Maintainer: Richard Aubrey White <hello@rwhite.no>
Repository: CRAN
Date/Publication: 2022-07-20 15:50:02 UTC

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New package mallet with initial version 1.3.0
Package: mallet
Title: An R Wrapper for the Java Mallet Topic Modeling Toolkit
Version: 1.3.0
Date: 2022-07-19
Maintainer: Måns Magnusson <mons.magnusson@gmail.com>
Description: An R interface for the Java Machine Learning for Language Toolkit (mallet) <http://mallet.cs.umass.edu/> to estimate probabilistic topic models, such as Latent Dirichlet Allocation. We can use the R package to read textual data into mallet from R objects, run the Java implementation of mallet directly in R, and extract results as R objects. The Mallet toolkit has many functions, this wrapper focuses on the topic modeling sub-package written by David Mimno. The package uses the rJava package to connect to a JVM.
License: MIT + file LICENSE
URL: https://github.com/mimno/RMallet
BugReports: https://github.com/mimno/RMallet/issues
SystemRequirements: java
Encoding: UTF-8
Depends: R (>= 3.6.3)
Imports: rJava, checkmate
Suggests: knitr, rmarkdown, dplyr, testthat
VignetteBuilder: rmarkdown, knitr
LazyData: TRUE
NeedsCompilation: no
Packaged: 2022-07-19 14:10:22 UTC; mansmagnusson
Author: Måns Magnusson [cre, aut] , David Mimno [aut, cph]
Repository: CRAN
Date/Publication: 2022-07-20 15:50:05 UTC

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New package geneticae with initial version 0.4.0
Package: geneticae
Title: Statistical Tools for the Analysis of Multi Environment Agronomic Trials
Version: 0.4.0
Description: Data from multi environment agronomic trials, which are often carried out by plant breeders, can be analyzed with the tools offered by this package such as the Additive Main effects and Multiplicative Interaction model or 'AMMI' ('Gauch' 1992, ISBN:9780444892409) and the Site Regression model or 'SREG' ('Cornelius' 1996, <doi:10.1201/9780367802226>). Since these methods present a poor performance under the presence of outliers and missing values, this package includes robust versions of the 'AMMI' model ('Rodrigues' 2016, <doi:10.1093/bioinformatics/btv533>), and also imputation techniques specifically developed for this kind of data ('Arciniegas-Alarcón' 2014, <doi:10.2478/bile-2014-0006>).
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stats, GGEBiplots, ggforce, ggplot2, scales, MASS, pcaMethods, rrcov, dplyr, missMDA, calibrate, graphics, reshape2, matrixStats, tidyr, prettydoc, rlang
Suggests: agridat, spelling, knitr, rmarkdown, testthat
VignetteBuilder: knitr
Depends: R (>= 2.12.0)
URL: https://jangelini.github.io/geneticae/
BugReports: https://github.com/jangelini/geneticae/issues
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-20 12:32:08 UTC; julia-fedora
Author: Julia Angelini [aut, cre] , Marcos Prunello [aut] , Gerardo Cervigni [aut]
Maintainer: Julia Angelini <jangelini_93@hotmail.com>
Repository: CRAN
Date/Publication: 2022-07-20 15:40:06 UTC

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New package did with initial version 2.1.2
Package: did
Title: Treatment Effects with Multiple Periods and Groups
Version: 2.1.2
URL: https://bcallaway11.github.io/did/, https://github.com/bcallaway11/did/
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences setups with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2021) <doi:10.1016/j.jeconom.2020.12.001>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
Depends: R (>= 3.5),
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: BMisc (>= 1.4.4), Matrix, pbapply, ggplot2, ggpubr, DRDID, generics, methods, tidyr
VignetteBuilder: knitr
Suggests: rmarkdown, plm, here, knitr, covr
NeedsCompilation: no
Packaged: 2022-07-20 03:09:38 UTC; brant
Author: Brantly Callaway [aut, cre], Pedro H. C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Repository: CRAN
Date/Publication: 2022-07-20 16:00:05 UTC

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New package PRSPGx with initial version 0.3.0
Package: PRSPGx
Title: Construct PGx PRS
Version: 0.3.0
Maintainer: Song Zhai <zsviolet1993@gmail.com>
Description: Construct pharmacogenomics (PGx) polygenic risk score (PRS) with PRS-PGx-Unadj (unadjusted), PRS-PGx-CT (clumping and thresholding), PRS-PGx-L, -GL, -SGL (penalized regression), PRS-PGx-Bayes (Bayesian regression). Package is based on ''Pharmacogenomics Polyenic Risk Score for Drug Response Prediction Using PRS-PGx Methods'' by Zhai, S., Zhang, H., Mehrotra, D.V., and Shen, J., 2021 (submitted).
License: GPL (>= 2)
Depends: R (>= 4.0.0)
Imports: gglasso (>= 1.5.0), SGL (>= 1.3.0), glmnet (>= 4.0.2), bigsnpr (>= 1.5.2), Matrix (>= 1.2.18), GIGrvg (>= 0.5.0), MCMCpack (>= 1.4.6), bdsmatrix (>= 1.3.4), bigsparser (>= 0.4.0), lmtest (>= 0.9.37), mvtnorm (>= 1.1.0), propagate (>= 1.0.6), bigparallelr (>= 0.2.3), methods (>= 3.6.3), bigstatsr (>= 1.2.3), Rfast (>= 1.9.9), matrixcalc (>= 1.0-3)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2022-07-19 15:16:57 UTC; zhaiso
Author: Song Zhai [aut, cre]
Repository: CRAN
Date/Publication: 2022-07-20 15:00:02 UTC

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Tue, 19 Jul 2022

New package DRDID with initial version 1.0.4
Package: DRDID
Title: Doubly Robust Difference-in-Differences Estimators
Version: 1.0.4
Description: Implements the locally efficient doubly robust difference-in-differences (DiD) estimators for the average treatment effect proposed by Sant'Anna and Zhao (2020) <doi:10.1016/j.jeconom.2020.06.003>. The estimator combines inverse probability weighting and outcome regression estimators (also implemented in the package) to form estimators with more attractive statistical properties. Two different estimation methods can be used to estimate the nuisance functions.
URL: https://psantanna.com/DRDID/, https://github.com/pedrohcgs/DRDID
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0)
Imports: stats, trust, BMisc (>= 1.4.1)
Suggests: knitr, rmarkdown, spelling, testthat
Date: 2022-07-19
Language: en-US
BugReports: https://github.com/pedrohcgs/DRDID/issues
NeedsCompilation: no
Packaged: 2022-07-19 20:55:52 UTC; psantanna
Author: Pedro H. C. Sant'Anna [aut, cre], Jun Zhao [aut]
Maintainer: Pedro H. C. Sant'Anna <pedro.h.santanna@vanderbilt.edu>
Repository: CRAN
Date/Publication: 2022-07-19 21:40:02 UTC

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New package imputeREE with initial version 0.0.1
Package: imputeREE
Title: Impute Missing Rare Earth Element Data Using a Lattice-Strain Derived Method
Version: 0.0.1
Description: Set of functions that fit a linear regression to calculate missing Rare Earth Element (REE) in zircon based on a method derived from the lattice strain theory of Blundy and Wood (1994)<doi:10.1038/372452a0>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0)
Imports: tibble, dplyr, magrittr, tidyr, stringr, purrr, rlang, broom
Depends: R (>= 4.0)
NeedsCompilation: no
Packaged: 2022-07-18 04:56:34 UTC; ccarr
Author: Carlos Carrasco Godoy [aut, cre]
Maintainer: Carlos Carrasco Godoy <carlos.Carrasco@anu.edu.au>
Repository: CRAN
Date/Publication: 2022-07-19 14:50:01 UTC

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New package climetrics with initial version 1.0-5
Package: climetrics
Title: Climate Change Metrics
Version: 1.0-5
Date: 2022-07-18
Depends: methods, sp (>= 1.2-0), R (>= 3.5.0), rts
Imports: raster, terra, zoo, yaImpute, xts
Suggests: R.rsp
VignetteBuilder: R.rsp
Description: A framework that facilitates spatio-temporal analysis of climate dynamics through exploring and measuring different dimensions of climate change in space and time.
License: GPL (>= 3)
Encoding: UTF-8
URL: http://r-gis.net
BugReports: https://github.com/shirintaheri/climetrics/issues/
NeedsCompilation: no
Packaged: 2022-07-18 12:06:32 UTC; babak
Author: Shirin Taheri [cre, aut] , Babak Naimi [aut] , Miguel Araujo [aut]
Maintainer: Shirin Taheri <taheri.shi@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-19 15:00:05 UTC

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New package bartcs with initial version 0.1.1
Package: bartcs
Title: Bayesian Additive Regression Trees for Confounder Selection
Version: 0.1.1
Description: Fit Bayesian Regression Additive Trees (BART) models to select relevant confounders among a large set of potential confounders and to estimate average treatment effect. For more information, see Kim et al. (2022) <doi:10.48550/arXiv.2203.11798>.
License: GPL (>= 3)
URL: https://github.com/yooyh/bartcs
BugReports: https://github.com/yooyh/bartcs/issues
Depends: R (>= 2.10)
Imports: ggcharts, ggplot2, invgamma, MCMCpack, Rcpp, rlang, rootSolve, stats
Suggests: knitr, microbenchmark, rmarkdown
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2022-07-18 05:52:07 UTC; yhoon
Author: Yeonghoon Yoo [aut, cre]
Maintainer: Yeonghoon Yoo <yooyh.stat@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-19 14:50:05 UTC

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New package bursts with initial version 1.0-2
Package: bursts
Title: Markov Model for Bursty Behavior in Streams
Version: 1.0-2
Date: 2022-07-14
Author: Jeff Binder [aut, cre]
Maintainer: Jeff Binder <extruded@gmail.com>
Imports: graphics
Description: An implementation of Jon Kleinberg's burst detection algorithm (Kleinberg (2003) <doi:10.1023/A:1024940629314>). Uses an infinite Markov model to detect periods of increased activity in a series of discrete events with known times, and provides a simple visualization of the results.
License: MIT + file LICENSE
Copyright: (c) 2012 NYU School of Medicine; (c) 2012-22 Jeff Binder
Packaged: 2022-07-18 21:44:48 UTC; jechk
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-07-19 11:30:02 UTC

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Mon, 18 Jul 2022

New package nplyr with initial version 0.1.0
Package: nplyr
Title: A Grammar of Nested Data Manipulation
Version: 0.1.0
Description: Provides functions for manipulating nested data frames in a list-column using 'dplyr' <https://dplyr.tidyverse.org/> syntax. Rather than unnesting, then manipulating a data frame, 'nplyr' allows users to manipulate each nested data frame directly. 'nplyr' is a wrapper for 'dplyr' functions that provide tools for common data manipulation steps: filtering rows, selecting columns, summarising grouped data, among others.
License: MIT + file LICENSE
URL: https://github.com/markjrieke/nplyr, https://markjrieke.github.io/nplyr/
BugReports: https://github.com/markjrieke/nplyr/issues
Depends: dplyr, R (>= 2.10)
Imports: assertthat, purrr, rlang
Encoding: UTF-8
Suggests: gapminder, knitr, readr, rmarkdown, stringr, testthat (>= 3.0.0), tibble, tidyr
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-17 12:56:12 UTC; E1735399
Author: Mark Rieke [aut, cre]
Maintainer: Mark Rieke <markjrieke@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-18 12:10:02 UTC

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New package datadictionary with initial version 0.1.0
Package: datadictionary
Title: Create a Data Dictionary
Version: 0.1.0
Description: Creates a data dictionary from any dataset in your R environment. You can opt to add variable labels. You can write the object directly to Excel.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-GB
Imports: chron, data.table, dplyr, haven, Hmisc, lubridate, magrittr, openxlsx, stats, tibble, tidyr, tidyselect,
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-07-17 03:11:30 UTC; BJ
Author: Bethany Jones [aut, cre]
Maintainer: Bethany Jones <r.data.nerd@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-18 12:10:08 UTC

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New package codebookr with initial version 0.1.4
Package: codebookr
Title: Create Codebooks from Data Frames
Version: 0.1.4
Maintainer: Brad Cannell <brad.cannell@gmail.com>
Description: Quickly and easily create codebooks (i.e. data dictionaries) directly from a data frame.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/brad-cannell/codebookr, https://brad-cannell.github.io/codebookr/
BugReports: https://github.com/brad-cannell/codebookr/issues
Depends: R (>= 2.10)
LazyData: true
Suggests: hms, testthat
Imports: haven (>= 2.5.0), flextable, dplyr, officer, purrr, rlang, stringr, tibble, tidyr
NeedsCompilation: no
Packaged: 2022-07-16 21:30:07 UTC; bradcannell
Author: Brad Cannell [aut, cre, cph]
Repository: CRAN
Date/Publication: 2022-07-18 12:10:11 UTC

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New package binaryTimeSeries with initial version 1.0.2
Package: binaryTimeSeries
Title: Analyzes a Binary Variable During a Time Series
Version: 1.0.2
Description: A procedure to create maps, pie charts, and stacked bar plots showing the trajectory of a binary variable during a time series. You provide a time series of data sets as a stack of raster files or a data frame and call the various functions in 'binaryTimeSeries' to create your desired graphics.For more information please consult: Pontius Jr, R. G. (2022). "Metrics That Make a Difference: How to Analyze Change and Error" Springer Nature Switzerland AG <doi:10.1007/978-3-030-70765-1> and Bilintoh, T.M., (2022). "Intensity Analysis to Study the Dynamics of reforestation in the Rio Doce Water Basin, Brazil". Frontiers in Remote Sensing, 3 (873341), 13. <doi:10.3389/frsen.2022.873341>.
License: AGPL (>= 3)
Depends: R (>= 3.3.0), rgdal
Imports: dplyr, ggnewscale, ggplot2, graphics, grDevices, magrittr, mice, prettymapr, raster, reshape2, stats, terra, utils
Suggests: knitr, maptools, rmarkdown, spelling
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-16 23:36:56 UTC; TBilintoh
Author: Thomas Mumuni Bilintoh [aut, cre] , Robert Gilmore Pontius Jr [aut]
Maintainer: Thomas Mumuni Bilintoh <tbilintoh@clarku.edu>
Repository: CRAN
Date/Publication: 2022-07-18 12:10:15 UTC

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New package POSSA with initial version 0.5.5
Package: POSSA
Title: Power Simulation for Sequential Analysis and Multiple Hypotheses
Version: 0.5.5
Date: 2022-07-14
Description: Calculates, via simulation, power and appropriate "stopping" alpha boundaries (and/or futility bounds) for sequential analyses (i.e., "group sequential design") as well as for multiple hypotheses (multiple tests included in an analysis), given any specified global error rate. This enables the sequential use of practically any significance test, as long as the underlying data can be simulated in advance to a reasonable approximation.
URL: https://github.com/gasparl/possa
Depends: R (>= 3.6.0)
Imports: data.table, methods
License: BSD_2_clause + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), faux, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-14 13:42:45 UTC; gaspar
Author: Gaspar Lukacs [aut, cre]
Maintainer: Gaspar Lukacs <lkcsgaspar@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-18 12:00:05 UTC

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New package LDABiplots with initial version 0.1.2
Package: LDABiplots
Title: Biplot Graphical Interface for LDA Models
Version: 0.1.2
Maintainer: Luis Pilacuan-Bonete <luis.pilacuanb@ug.edu.ec>
Description: Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Biplots representations from a scraping of news from digital newspapers under the Bayesian approach of Latent Dirichlet Assignment (LDA) and machine learning algorithms. Contains LDA methods described by Blei , David M., Andrew Y. Ng and Michael I. Jordan (2003) <https://jmlr.org/papers/volume3/blei03a/blei03a.pdf>, and Biplot methods described by Gabriel K.R(1971) <doi:10.1093/biomet/58.3.453> and Galindo-Villardon P(1986) <https://diarium.usal.es/pgalindo/files/2012/07/Questiio.pdf>.
License: GPL-3
Encoding: UTF-8
Imports: shiny, shinyBS, shinydashboard, shinyWidgets, shinyalert, shinybusy, shinyjs, shinycssloaders, dplyr, ggplot2, rvest, DT, highcharter, tidyr, SnowballC, ldatuning, topicmodels, textmineR, chinese.misc, stringr, htmlwidgets, ggrepel, textplot, glasso, qgraph, Matrix, utils, factoextra, quanteda
Suggests: rmarkdown, knitr, beepr, readxl
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-15 19:13:01 UTC; luisp
Author: Luis Pilacuan-Bonete [cre, aut] , Purificacion Galindo-Villardon [aut] , Javier De La Hoz Maestre [aut] , Francisco Javier Delgado-Álvarez [aut]
Repository: CRAN
Date/Publication: 2022-07-18 12:00:08 UTC

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New package geneset with initial version 0.2.6
Package: geneset
Title: Get Gene Sets for Gene Enrichment Analysis
Version: 0.2.6
Maintainer: Yunze Liu <jieandze1314@gmail.com>
URL: https://github.com/GangLiLab/geneset
BugReports: https://github.com/GangLiLab/geneset/issues
Description: Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) <doi:10.1093/nar/gkh036>), 'KEGG' (Minoru et al. (2000) <doi:10.1093/nar/28.1.27>), 'WikiPathway' (Marvin et al. (2020) <doi:10.1093/nar/gkaa1024>), 'MsigDb' (Arthur et al. (2015) <doi:10.1016/j.cels.2015.12.004>), 'Reactome' (David et al. (2011) <doi:10.1093/nar/gkq1018>), 'MeSH' (Ish et al. (2014) <doi:10.4103/0019-5413.139827>), 'DisGeNET' (Janet et al. (2017) <doi:10.1093/nar/gkw943>), 'Disease Ontology' (Lynn et al. (2011) <doi:10.1093/nar/gkr972>), 'Network of Cancer Genes' (Dimitra et al. (2019) <doi:10.1186/s13059-018-1612-0>) and 'COVID-19' (Maxim et al. (2020) <doi:10.21203/rs.3.rs-28582/v1>). Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'. The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of terms ID and term description.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: dplyr, RCurl, fst, stringi, stringr
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-07-16 02:07:25 UTC; reedliu1
Author: Yunze Liu [aut, cre]
Repository: CRAN
Date/Publication: 2022-07-18 12:00:02 UTC

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New package stacomiR with initial version 0.6.0.7
Package: stacomiR
Version: 0.6.0.7
Date: 2022-07-16
Title: Fish Migration Monitoring
Description: Graphical outputs and treatment for a database of fish pass monitoring. It is a part of the 'STACOMI' open source project developed in France by the French Office for Biodiversity institute to centralize data obtained by fish pass monitoring. This version is available in French and English. See <http://stacomir.r-forge.r-project.org/> for more information on 'STACOMI'.
License: GPL (>= 2)
URL: http://stacomir.r-forge.r-project.org/
BugReports: https://github.com/MarionLegrandLogrami/stacomiR/issues
LazyLoad: yes
LazyData: true
Depends: R (>= 4.0.0), methods, stacomirtools (>= 0.6.0.1)
Imports: magrittr, intervals, RColorBrewer, stringr, RPostgres, ggplot2, reshape2, graphics, utils, stats, lattice, grDevices, Hmisc (>= 4.1-1), lubridate, dplyr, xtable, mgcv, rlang, pool, withr, scales
Suggests: testthat, viridis, knitr, rmarkdown
Author: Cedric Briand [aut, cre], Marion Legrand [aut], Beaulaton Laurent [ctb], Boulenger Clarisse [ctb], Lafage Denis [ctb], Grall Sebastien [ctb]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2022-07-18 07:48:09 UTC; cedric.briand
Repository: CRAN
Date/Publication: 2022-07-18 09:20:02 UTC

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New package zerotradeflow with initial version 0.1.0
Package: zerotradeflow
Title: An Implementation for the Gravitational Models of Trade
Version: 0.1.0
Maintainer: Alexandre Loures <alexandre.loures@protonmail.com>
Description: A system for creating the bilateral trade flow between a country pair equal to zero. You provide the data, tell get_zerotradeflow() which variables are of interest and it expands the base by creating the bilateral zero trade flow. The bases on the flow of trade between countries only report positive trade (greater than zero), however, for some analyzes of gravitacional models, data on zero flow is also necessary. Some examples for Gravity Model: Figueiredo and Loures (2016) <doi:10.5935/0034-7140.20160015> and Yotov, Piermartini, Monteiro and Larch <https://vi.unctad.org/tpa/web/docs/vol2/book.pdf>.
License: MIT + file LICENSE
Encoding: UTF-8
Language: English
LazyData: true
LazyDataCompression: xz
Depends: R (>= 3.5.0)
Imports: magrittr, tidyverse, rlang, dplyr, tidyr, purrr, cli
Suggests: testthat (>= 2.1.0)
URL: https://github.com/AlexandreLoures/zerotradeflow
BugReports: https://github.com/AlexandreLoures/zerotradeflow/issues
Repository: CRAN
NeedsCompilation: no
Packaged: 2022-07-16 15:14:30 UTC; alexa
Author: Alexandre Loures [aut, cre]
Date/Publication: 2022-07-18 08:20:02 UTC

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New package tsintermittent with initial version 1.10
Package: tsintermittent
Title: Intermittent Time Series Forecasting
Version: 1.10
Date: 2022-07-15
Description: Time series methods for intermittent demand forecasting. Includes Croston's method and its variants (Moving Average, SBA), and the TSB method. Users can obtain optimal parameters on a variety of loss functions, or use fixed ones (Kourenztes (2014) <doi:10.1016/j.ijpe.2014.06.007>). Intermittent time series classification methods and iMAPA that uses multiple temporal aggregation levels are also provided (Petropoulos & Kourenztes (2015) <doi:10.1057/jors.2014.62>).
LazyData: yes
License: GPL (>= 2)
Imports: MAPA, parallel
URL: https://kourentzes.com/forecasting/2014/06/23/intermittent-demand-forecasting-package-for-r/
NeedsCompilation: no
Packaged: 2022-07-17 10:15:29 UTC; Nikos
Author: Nikolaos Kourentzes [cre, aut] , Fotios Petropoulos [ctb]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Repository: CRAN
Date/Publication: 2022-07-18 08:10:05 UTC

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New package RPANDA with initial version 2.1
Package: RPANDA
Version: 2.1
Date: 2022-07-07
Title: Phylogenetic ANalyses of DiversificAtion
Depends: R (>= 2.14.2), ape, picante, methods
Suggests: testthat
Imports: bipartite, cluster, coda, deSolve, fields, fpc, glassoFast, graphics, grDevices, igraph, Matrix, mvMORPH (>= 1.1.6), parallel, phytools, pspline, pvclust, raster, Rmpfr, stats, TESS, utils
Encoding: UTF-8
Author: Helene Morlon [aut, cre, cph], Eric Lewitus [aut, cph], Fabien Condamine [aut, cph], Marc Manceau [aut, cph], Julien Clavel [aut, cph], Jonathan Drury [aut, cph], Olivier Billaud [aut, cph], Odile Maliet [aut, cph], Leandro Aristide [aut, cph]
Maintainer: Helene Morlon <helene.morlon@bio.ens.psl.eu>
Description: Implements macroevolutionary analyses on phylogenetic trees. See Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011) <DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>, Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>, Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>, Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>, Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>, Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>, Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>, Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592> and Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>.
License: GPL-2
URL: https://github.com/hmorlon/PANDA
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-07-08 07:59:35 UTC; morlon
Date/Publication: 2022-07-18 08:40:09 UTC

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New package long2lstmarray with initial version 0.0.1
Package: long2lstmarray
Title: Longitudinal Dataframes into Arrays for Machine Learning Training
Version: 0.0.1
Maintainer: Luis Garcez <luis_garcez_ferreira@alunos.fc.ul.pt>
Description: An easy tool to transform 2D longitudinal data into 3D arrays suitable for Long short-term memory neural networks training. The array output can be used by the 'keras' package. Long short-term memory neural networks are described in: Hochreiter, S., & Schmidhuber, J. (1997) <doi:10.1162/neco.1997.9.8.1735>.
Imports: abind, dplyr
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
URL: https://github.com/luisgarcez11/long2lstmarray
BugReports: https://github.com/luisgarcez11/long2lstmarray/issues
Suggests: knitr, rmarkdown, testthat
Depends: R (>= 2.10)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-16 16:35:37 UTC; jjferreira-admin
Author: Luis Garcez [aut, cre, cph]
Repository: CRAN
Date/Publication: 2022-07-18 08:30:02 UTC

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New package highMLR with initial version 0.1.1
Title: Feature Selection for High Dimensional Survival Data
Package: highMLR
Version: 0.1.1
Date: 2022-07-17
Depends: R (>= 3.5.0)
Imports: mlr3, mlr3learners, survival, gtools, tibble, dplyr, utils, coxme, missForest, R6
LazyData: Yes
LazyDataCompression: xz
ByteCompile: Yes
Description: Perform high dimensional Feature Selection in the presence of survival outcome. Based on Feature Selection method and different survival analysis, it will obtain the best markers with optimal threshold levels according to their effect on disease progression and produce the most consistent level according to those threshold values. The functions' methodology is based on by Sonabend et al (2021) <doi:10.1093/bioinformatics/btab039> and Bhattacharjee et al (2021) <arXiv:2012.02102>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Packaged: 2022-07-16 22:31:58 UTC; atanu
Author: Atanu Bhattacharjee [aut, cre, ctb], Gajendra K. Vishwakarma [aut, ctb], Souvik Banerjee [aut, ctb]
Repository: CRAN
Date/Publication: 2022-07-18 08:10:08 UTC

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New package common with initial version 1.0.1
Package: common
Title: Solutions for Common Problems in Base R
Version: 1.0.1
Maintainer: David Bosak <dbosak01@gmail.com>
Description: Contains functions for solving commonly encountered problems while programming in R. This package is intended to provide a lightweight supplement to Base R, and will be useful for almost any R user.
License: CC0
Encoding: UTF-8
Depends: R (>= 3.6.0)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: this.path
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-16 11:25:12 UTC; dbosa
Author: David Bosak [aut, cre], Andrew Simmons [aut], Duong Tran [ctb]
Repository: CRAN
Date/Publication: 2022-07-18 08:10:11 UTC

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New package arabicStemR with initial version 1.3
Package: arabicStemR
Title: Arabic Stemmer for Text Analysis
Version: 1.3
Date: 2022-07-14
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>
Description: Allows users to stem Arabic texts for text analysis.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-07-16 13:13:46 UTC; rich
Repository: CRAN
Date/Publication: 2022-07-18 08:20:09 UTC

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New package and with initial version 0.1.1
Package: and
Title: Construct Natural-Language Lists with Internationalization
Version: 0.1.1
Description: Construct language-aware lists. Make "and"-separated and "or"-separated lists that automatically conform to the user's language settings.
License: MIT + file LICENSE
URL: http://and.rossellhayes.com, https://github.com/rossellhayes/and
BugReports: https://github.com/rossellhayes/and/issues
Depends: R (>= 2.10)
Imports: glue, rlang (>= 1.0.0)
Suggests: covr, knitr, mockery, stringi, testthat (>= 3.0.0), withr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-16 18:57:22 UTC; alex
Author: Alexander Rossell Hayes [aut, cre, cph] , Unicode, Inc. [dtc]
Maintainer: Alexander Rossell Hayes <alexander@rossellhayes.com>
Repository: CRAN
Date/Publication: 2022-07-18 08:30:05 UTC

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New package gcmr with initial version 1.0.3
Package: gcmr
Version: 1.0.3
Priority: optional
Title: Gaussian Copula Marginal Regression
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin <cristiano.varin@unive.it>
Description: Likelihood inference in Gaussian copula marginal regression models.
Depends: R (>= 4.0.0)
Imports: graphics, grDevices, stats, utils, betareg, car, Formula, lmtest, nlme, sandwich, sp
License: GPL (>= 2)
NeedsCompilation: yes
Repository: CRAN
Packaged: 2022-07-17 21:41:25 UTC; cristianovarin
Date/Publication: 2022-07-18 07:40:02 UTC

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New package flipr with initial version 0.3.2
Package: flipr
Title: Flexible Inference via Permutations in R
Version: 0.3.2
Description: A flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing, on any kind of data, be it univariate, multivariate, or more complex such as network-valued data, topological data, functional data or density-valued data.
License: GPL (>= 3)
Encoding: UTF-8
Imports: purrr, rlang, magrittr, cli, ggplot2, tibble, withr, viridisLite, Rcpp, R6, pbapply, dials, usethis, optimParallel, rgenoud
Suggests: rmarkdown, knitr, covr, tidyverse, plotly, htmlwidgets, htmltools, testthat (>= 3.0.0), interp
VignetteBuilder: knitr
URL: https://LMJL-Alea.github.io/flipr/, https://github.com/LMJL-Alea/flipr/
BugReports: https://github.com/LMJL-Alea/flipr/issues/
Depends: R (>= 2.10)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-07-17 21:05:43 UTC; stamm-a
Author: Alessia Pini [aut], Aymeric Stamm [aut, cre] , Simone Vantini [aut], Juliette Chiapello [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@math.cnrs.fr>
Repository: CRAN
Date/Publication: 2022-07-18 07:40:05 UTC

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New package FFTrees with initial version 1.6.5
Package: FFTrees
Title: Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees
Version: 1.6.5
Date: 2022-07-17
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Description: Create, visualize, and test fast-and-frugal decision trees (FFTs) using methods described in Phillips, Neth, Woike & Gaissmaier. (2017). FFTs are very simple decision trees for binary classification problems. FFTs can be preferable to more complex algorithms because they are easy to communicate, require very little information, and are robust against overfitting.
LazyData: TRUE
Depends: R(>= 3.5.0)
Imports: rpart, graphics, randomForest, e1071, crayon, scales, tibble, stringr, progress, caret, dplyr, testthat, magrittr, tidyselect
License: CC0
BugReports: https://github.com/ndphillips/FFTrees/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-17 17:36:12 UTC; nathanielphillips
Author: Nathaniel Phillips [aut, cre], Hansjoerg Neth [aut], Jan Woike [aut], Wolfgang Gaissmaer [aut]
Repository: CRAN
Date/Publication: 2022-07-18 07:20:04 UTC

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New package ammistability with initial version 0.1.3
Package: ammistability
Title: Additive Main Effects and Multiplicative Interaction Model Stability Parameters
Version: 0.1.3
Description: Computes various stability parameters from Additive Main Effects and Multiplicative Interaction (AMMI) analysis results such as Modified AMMI Stability Value (MASV), Sums of the Absolute Value of the Interaction Principal Component Scores (SIPC), Sum Across Environments of Genotype-Environment Interaction Modelled by AMMI (AMGE), Sum Across Environments of Absolute Value of Genotype-Environment Interaction Modelled by AMMI (AV_(AMGE)), AMMI Stability Index (ASI), Modified ASI (MASI), AMMI Based Stability Parameter (ASTAB), Annicchiarico's D Parameter (DA), Zhang's D Parameter (DZ), Averages of the Squared Eigenvector Values (EV), Stability Measure Based on Fitted AMMI Model (FA), Absolute Value of the Relative Contribution of IPCs to the Interaction (Za). Further calculates the Simultaneous Selection Index for Yield and Stability from the computed stability parameters. See the vignette for complete list of citations for the methods implemented.
Copyright: 2017-2022, ICAR-DGR
License: GPL-2 | GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
Imports: agricolae, ggcorrplot, ggplot2, methods, reshape2, stats, Rdpack, mathjaxr
Suggests: knitr, rmarkdown, pander, XML, httr, RCurl
URL: https://github.com/ajaygpb/ammistability/ https://CRAN.R-project.org/package=ammistability https://ajaygpb.github.io/ammistability/ https://doi.org/10.5281/zenodo.1344756
BugReports: https://github.com/ajaygpb/ammistability/issues
NeedsCompilation: no
Packaged: 2022-07-17 21:51:39 UTC; J. Aravind
Author: B. C. Ajay [aut, cre] , J. Aravind [aut] , R. Abdul Fiyaz [aut] , ICAR [cph]
Maintainer: B. C. Ajay <ajaygpb@yahoo.co.in>
Repository: CRAN
Date/Publication: 2022-07-18 07:40:09 UTC

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New package ACEP with initial version 0.0.1
Package: ACEP
Title: Análisis Computacional de Eventos de Protesta
Version: 0.0.1
Description: La librería 'ACEP' contiene funciones específicas para desarrollar análisis computacional de eventos de protesta. Asimismo, contiene base de datos con colecciones de notas sobre protestas y diccionarios de palabras conflictivas. Colección de diccionarios que reúne diccionarios de diferentes orígenes. The 'ACEP' library contains specific functions to perform computational analysis of protest events. It also contains a database with collections of notes on protests and dictionaries of conflicting words. Collection of dictionaries that brings together dictionaries from different sources.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
Language: es
LazyData: true
URL: https://github.com/agusnieto77/ACEP
BugReports: https://github.com/agusnieto77/ACEP/issues
Imports: graphics, stats
Suggests: covr, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-07-14 21:27:36 UTC; agust
Author: Agustin Nieto [aut, cre]
Maintainer: Agustin Nieto <agustin.nieto77@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-18 08:00:05 UTC

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Sat, 16 Jul 2022

New package tramvs with initial version 0.0-1
Package: tramvs
Title: Optimal Subset Selection for Transformation Models
Version: 0.0-1
Description: Greedy optimal subset selection for transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to models from packages 'tram' and 'cotram'.
Depends: R (>= 4.0), tram (>= 0.6-1)
Imports: stats, variables, methods
Suggests: abess, tramnet, colorspace, knitr, cotram, mlt, TH.data, survival, ordinal
License: GPL-3
Encoding: UTF-8
URL: http://ctm.R-forge.R-project.org
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-15 14:42:44 UTC; stigler
Author: Lucas Kook [aut, cre], Sandra Siegfried [ctb], Torsten Hothorn [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@uzh.ch>
Repository: CRAN
Date/Publication: 2022-07-16 09:10:02 UTC

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New package ptools with initial version 1.0.0
Package: ptools
Title: Tools for Poisson Data
Version: 1.0.0
Maintainer: Andrew Wheeler <apwheele@gmail.com>
Description: Functions used for analyzing count data, mostly crime counts. Includes checking difference in two Poisson counts (e-test), checking the fit for a Poisson distribution, small sample tests for counts in bins (Wheeler, ????) <doi:10.1002/jip.1449>, Weighted Displacement Difference test (Wheeler and Ratcliffe, 2018) <doi:10.1186/s40163-018-0085-5>, to evaluate crime changes over time in treated/control areas. Additionally includes functions for aggregating spatial data and spatial feature engineering.
License: MIT + file LICENSE
URL: https://github.com/apwheele/ptools
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Imports: partitions, sp, raster, igraph, RANN, spatstat.geom, rgeos, maptools, stats, methods
Depends: R (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-15 23:28:28 UTC; andre
Author: Andrew Wheeler [aut, cre]
Repository: CRAN
Date/Publication: 2022-07-16 09:50:02 UTC

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New package DySS with initial version 1.0
Package: DySS
Title: Dynamic Screening Systems
Version: 1.0
Date: 2022-07-04
Maintainer: Lu You <Lu.You@epi.usf.edu>
Description: In practice, we will encounter problems where the longitudinal performance of processes needs to be monitored over time. Dynamic screening systems (DySS) are methods that aim to identify and give signals to processes with poor performance as early as possible. This package is designed to implement dynamic screening systems and the related methods. References: Qiu, P. and Xiang, D. (2014) <doi:10.1080/00401706.2013.822423>; Qiu, P. and Xiang, D. (2015) <doi:10.1002/sim.6477>; Li, J. and Qiu, P. (2016) <doi:10.1080/0740817X.2016.1146423>; Li, J. and Qiu, P. (2017) <doi:10.1002/qre.2160>; You, L. and Qiu, P. (2019) <doi:10.1080/00949655.2018.1552273>; Qiu, P., Xia, Z., and You, L. (2020) <doi:10.1080/00401706.2019.1604434>; You, L., Qiu, A., Huang, B., and Qiu, P. (2020) <doi:10.1002/bimj.201900127>; You, L. and Qiu, P. (2021) <doi:10.1080/00224065.2020.1767006>.
License: GPL-2 | GPL-3
Imports: Rcpp (>= 1.0.0), utils, stats, graphics, ggplot2, gridExtra
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: yes
Packaged: 2022-07-15 23:39:41 UTC; luyou
Author: Lu You [aut, cre], Peihua Qiu [aut]
Repository: CRAN
Date/Publication: 2022-07-16 09:50:05 UTC

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New package detectnorm with initial version 1.0.0
Package: detectnorm
Title: Detect Nonnormality in Meta-Analysis without Raw Data
Version: 1.0.0
Maintainer: Rongwei Sun <irissun_s@hotmail.com>
Description: Non-normality could greatly distort the meta-analytic results, according to the simulation in Sun and Cheung (2020) <doi: 10.3758/s13428-019-01334-x>. This package aims to detect non-normality for two independent groups with only limited descriptive statistics, including mean, standard deviation, minimum, and maximum.
License: MIT + file LICENSE
URL: https://github.com/irissun/detectnorm
BugReports: https://github.com/irissun/detectnorm/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: nleqslv, ggplot2, truncnorm, Rdpack, psych
Suggests: knitr, metafor (>= 3.4-0), rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-15 13:29:16 UTC; iris
Author: Rongwei Sun [aut, cre, cph] , Shu Fai Cheung [aut, ctb, cph]
Repository: CRAN
Date/Publication: 2022-07-16 09:10:05 UTC

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New package ino with initial version 0.1.0
Package: ino
Title: Initialization of Numerical Optimization
Version: 0.1.0
Description: Implementation of several initialization strategies for the numerical optimization of real-valued functions, in particular likelihood functions of statistical models.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Imports: ggplot2, rlang, RprobitB, mvtnorm, evd, crayon, progress, dplyr, foreach, doSNOW
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), purrr, pracma
URL: https://github.com/loelschlaeger/ino
BugReports: https://github.com/loelschlaeger/ino/issues
VignetteBuilder: knitr
Depends: R (>= 4.0.0)
NeedsCompilation: no
Packaged: 2022-07-15 12:24:03 UTC; loelschlaeger
Author: Lennart Oelschlaeger [aut, cre] , Marius Ötting [aut]
Maintainer: Lennart Oelschlaeger <oelschlaeger.lennart@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-16 08:40:02 UTC

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New package ganDataModel with initial version 1.0.2
Package: ganDataModel
Title: Create a Hierarchical, Categorical Data Model for a Data Source
Version: 1.0.2
Date: 2022-07-14
Author: Werner Mueller
Maintainer: Werner Mueller <werner.mueller5@chello.at>
Description: Neural networks are applied to create a density value function which approximates density values for a data source. The trained neural network is analysed for different levels. For each level subspaces with density values above a level are determined. The obtained set of subspaces categorizes the data source hierarchically. A prerequisite is the definition of a data source, the generation of generative data and the calculation of density values. These tasks are executed using package 'ganGenerativeData' <https://cran.r-project.org/package=ganGenerativeData>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.3), tensorflow (>= 2.0.0)
LinkingTo: Rcpp
SystemRequirements: TensorFlow (https://www.tensorflow.org)
NeedsCompilation: yes
Packaged: 2022-07-14 20:03:21 UTC; rstudio
Repository: CRAN
Date/Publication: 2022-07-16 08:20:02 UTC

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New package etree with initial version 0.1.0
Package: etree
Title: Classification and Regression with Structured and Mixed-Type Data
Version: 0.1.0
Description: Implementation of Energy Trees, a statistical model to perform classification and regression with structured and mixed-type data. The model has a similar structure to Conditional Trees, but brings in Energy Statistics to test independence between variables that are possibly structured and of different nature. Currently, the package covers functions and graphs as structured covariates. It builds upon 'partykit' to provide functionalities for fitting, printing, plotting, and predicting with Energy Trees. Energy Trees are described in Giubilei et al. (2022) <arXiv:2207.04430>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.7.0)
Imports: brainGraph, cluster, energy, fda.usc (>= 2.0.0), igraph, NetworkDistance, parallel, partykit, survival, TDA, usedist
Suggests: knitr, MLmetrics, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/ricgbl/etree
BugReports: https://github.com/ricgbl/etree/issues
NeedsCompilation: no
Packaged: 2022-07-15 09:53:19 UTC; ricca
Author: Riccardo Giubilei [aut, cre] , Tullia Padellini [aut], Pierpaolo Brutti [aut], Marco Brandi [ctb], Gabriel Nespoli [ctb], Torsten Hothorn [ctb] ), Achim Zeileis [ctb] )
Maintainer: Riccardo Giubilei <riccardogbl@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-16 08:30:02 UTC

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Fri, 15 Jul 2022

New package text2sdg with initial version 0.1.4
Package: text2sdg
Version: 0.1.4
Date: 2022-07-13
Title: Detecting UN Sustainable Development Goals in Text
Description: The United Nations’ Sustainable Development Goals (SDGs) have become an important guideline for organisations to monitor and plan their contributions to social, economic, and environmental transformations. The 'text2sdg' package is an open-source analysis package that identifies SDGs in text using scientifically developed query systems, opening up the opportunity to monitor any type of text-based data, such as scientific output or corporate publications.
Maintainer: Dominik S. Meier <dominikmeier@outlook.com>
URL: https://github.com/dwulff/text2sdg
BugReports: https://github.com/dwulff/text2sdg/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: magrittr, dplyr, corpustools (>= 0.4.2), tidyr, tibble, stringr, ggplot2
Suggests: testthat, knitr, rmarkdown
LazyData: TRUE
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-13 11:50:09 UTC; dominik
Author: Dirk U. Wulff [aut] , Dominik S. Meier [aut, cre] , Rui Mata [ctb]
Repository: CRAN
Date/Publication: 2022-07-15 15:20:02 UTC

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New package multiocc with initial version 0.1.0
Package: multiocc
Title: Fits Multivariate Spatio-Temporal Occupancy Model
Version: 0.1.0
Depends: R (>= 4.1.0)
Description: Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.
License: GPL-2
Imports: MASS, truncnorm, tmvtnorm, fields, interp, MCMCpack, stats
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-14 15:05:11 UTC; erhardrj
Author: Staci Hepler [aut, cre], Rob Erhardt [aut]
Maintainer: Staci Hepler <heplersa@wfu.edu>
Repository: CRAN
Date/Publication: 2022-07-15 16:10:02 UTC

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New package InteRD with initial version 0.1.0
Package: InteRD
Title: The Integrated and Robust Deconvolution
Version: 0.1.0
Description: We developed the Integrated and Robust Deconvolution algorithm to infer cell-type proportions from target bulk RNA-seq data. This package is able to effectively integrate deconvolution results from multiple scRNA-seq datasets and calibrates estimates from reference-based deconvolution by taking into account extra biological information as priors. Moreover, the proposed algorithm is robust to inaccurate external information imposed in the deconvolution system.
License: Artistic-2.0
Encoding: UTF-8
URL: https://github.com/chencxxy28/InteRD
BugReports: https://github.com/chencxxy28/InteRD/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports: Rcpp (>= 0.11.0), L1pack, limSolve, cowplot, ggplot2, pheatmap, stats,DescTools, mgcv, reshape2, Biobase
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-07-13 23:46:21 UTC; chixiang.chen
Author: Chixiang Chen [cre, aut], Yuk Yee Leung [aut], Matei Lonita [aut], Li-San Wang [aut], Mingyao Li [aut]
Maintainer: Chixiang Chen <chencxxy@hotmail.com>
Repository: CRAN
Date/Publication: 2022-07-15 16:00:05 UTC

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New package ExposR with initial version 1.0
Package: ExposR
Title: Models Topographic Exposure to Hurricane Winds
Version: 1.0
Date: 2022-07-14
Description: The EXPOS model uses a digital elevation model (DEM) to estimate exposed and protected areas for a given hurricane wind direction and inflection angle. The resulting topographic exposure maps can be combined with output from the HURRECON model to estimate hurricane wind damage across a region. For details on the original version of the EXPOS model written in 'Borland Pascal', see: Boose, Foster, and Fluet (1994) <doi:10.2307/2937142>, Boose, Chamberlin, and Foster (2001) <doi:10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2>, and Boose, Serrano, and Foster (2004) <doi:10.1890/02-4057>.
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
Imports: graphics, grDevices, raster, rgdal, utils
Suggests: knitr, qpdf, testthat (>= 3.0.0), rmarkdown
URL: https://github.com/expos-model/ExposR
BugReports: https://github.com/expos-model/ExposR/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-14 12:23:51 UTC; erb709
Author: Emery Boose [aut, cre], President and Fellows of Harvard College [cph]
Maintainer: Emery Boose <boose@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-07-15 16:10:04 UTC

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New package dcifer with initial version 1.0.1

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New package cgaim with initial version 1.0.0
Package: cgaim
Title: Constrained Groupwise Additive Index Models
Version: 1.0.0
Description: Fits constrained groupwise additive index models and provides functions for inference and interpretation of these models. The method is described in Masselot, Chebana, Campagna, Lavigne, Ouarda, Gosselin (2022) "Constrained groupwise additive index models" <doi:10.1093/biostatistics/kxac023>.
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 2.1.0)
Imports: graphics, stats, scam, scar, quadprog, osqp, limSolve, Matrix, grDevices, methods, MASS, cgam, mgcv, gratia, doParallel, coneproj, TruncatedNormal, foreach
NeedsCompilation: no
Packaged: 2022-07-13 20:59:06 UTC; PierreMasselot
Author: Pierre Masselot [aut, cre]
Maintainer: Pierre Masselot <pierre.masselot@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2022-07-15 15:50:02 UTC

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New package subniche with initial version 1.5
Package: subniche
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Version: 1.5
Date: 2022-07-14
BugReports: https://github.com/KarasiewiczStephane/WitOMI/issues
Description: Complementary indexes calculation to the Outlying Mean Index analysis to explore niche shift of a community and biological constraint within an Euclidean space, with graphical displays. For details see Karasiewicz et al. (2017) <doi:10.7717/Peerj.3364>.
Suggests: adegraphics, ape, CircStats, deldir, lattice, maptools, MASS, pixmap, spdep, splancs, waveslim
Depends: ade4, SIBER, polyclip, wordcloud
License: GPL (>= 2)
NeedsCompilation: no
LazyData: true
Packaged: 2022-07-15 09:49:56 UTC; frenc
Author: Stephane Karasiewicz [aut, cre]
Maintainer: Stephane Karasiewicz <skaraz.science@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-15 12:50:02 UTC

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New package tlars with initial version 0.0.1
Package: tlars
Title: The T-LARS Algorithm: Early-Terminated Forward Variable Selection
Version: 0.0.1
Date: 2022-07-11
Description: Computes the solution path of the Terminating-LARS (T-LARS) algorithm. The T-LARS algorithm is a major building block of the T-Rex selector (see R package 'trex'). The package is based on the papers Machkour, Muma, and Palomar (2021) <arXiv:2110.06048>, Efron, Hastie, Johnstone, and Tibshirani (2004) <doi:10.1214/009053604000000067>, and Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>.
Maintainer: Jasin Machkour <jasin.machkour@tu-darmstadt.de>
URL: https://github.com/jasinmachkour/tlars, https://arxiv.org/abs/2110.06048
BugReports: https://github.com/jasinmachkour/tlars/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, ggplot2, patchwork, testthat (>= 3.0.0)
Imports: Rcpp, methods, stats, graphics
Depends: R (>= 2.10)
LinkingTo: RcppArmadillo, Rcpp
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-07-11 17:53:53 UTC; phd
Author: Jasin Machkour [aut, cre], Simon Tien [aut], Daniel P. Palomar [aut], Michael Muma [aut]
Repository: CRAN
Date/Publication: 2022-07-15 08:40:02 UTC

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New package dots with initial version 0.0.2
Package: dots
Title: Dot Density Maps
Version: 0.0.2
Description: Generate point data for representing people within spatial data. This collects a suite of tools for creating simple dot density maps. Several functions from different spatial packages are standardized to take the same arguments so that they can be easily substituted for each other.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, magrittr, rlang, rmapshaper, sf, terra, purrr, dplyr, sp
URL: https://github.com/christopherkenny/dots, http://christophertkenny.com/dots/
BugReports: https://github.com/christopherkenny/dots/issues
Depends: R (>= 4.1)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), wacolors
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-11 16:33:36 UTC; chris
Author: Christopher T. Kenny [aut, cre]
Maintainer: Christopher T. Kenny <christopherkenny@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-07-15 08:40:07 UTC

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Thu, 14 Jul 2022

New package FactorCopula with initial version 0.8.1
Package: FactorCopula
Version: 0.8.1
Date: 2022-06-14
Title: Factor, Bi-Factor and Second-Order Copula Models
Author: Sayed H. Kadhem [aut, cre], Aristidis K. Nikoloulopoulos [aut]
Maintainer: Sayed H. Kadhem <s.kadhem@uea.ac.uk>
Depends: R (>= 3.5.0), statmod, abind, utils, polycor, VineCopula, matlab
Description: Estimation, model selection and goodness-of-fit of (1) factor copula models for mixed continuous and discrete data in Kadhem and Nikoloulopoulos (2021) <doi:10.1111/bmsp.12231>; (2) bi-factor and second-order copula models for item response data in Kadhem and Nikoloulopoulos (2021) <arXiv:2102.10660>.
License: GPL (>= 2)
Packaged: 2022-07-14 11:44:45 UTC; sayedhasan
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2022-07-14 13:00:02 UTC

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New package TrafficBDE with initial version 0.1.1
Package: TrafficBDE
Title: Traffic Predictions Using Neural Networks
Version: 0.1.1
Date: 2022-07-12
Description: Estimate and return either the traffic speed or the car entries in the city of Thessaloniki using historical traffic data. It's used in transport pilot of the 'BigDataEurope' project. There are functions for processing these data, training a neural network, select the most appropriate model and predict the traffic speed or the car entries for a selected time date.
Author: Kleanthis Koupidis [aut, cre], Aikaterini Chatzopoulou [aut], Charalampos Bratsas [aut], Panagiotis Tzenos [dtc], Josep Maria Salanova [dtc]
Maintainer: Kleanthis Koupidis <koupidis.okfgr@gmail.com>
URL: https://github.com/okgreece/TrafficBDE
BugReports: https://github.com/okgreece/TrafficBDE/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: caret, data.table, DescriptiveStats.OBeu, dplyr, lubridate, RCurl, stats, zoo
Suggests: devtools, knitr, neuralnet, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-12 14:50:13 UTC; akis_
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-07-14 11:00:09 UTC

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New package tibblify with initial version 0.2.0
Package: tibblify
Title: Rectangle Nested Lists
Version: 0.2.0
Description: A tool to rectangle a nested list, that is to convert it into a tibble. This is done automatically or according to a given specification. A common use case is for nested lists coming from parsing JSON files or the JSON response of REST APIs. It is supported by the 'vctrs' package and therefore offers a wide support of vector types.
License: GPL-3
URL: https://github.com/mgirlich/tibblify
BugReports: https://github.com/mgirlich/tibblify/issues
Depends: R (>= 3.4.0)
Imports: cli (>= 3.3.0), lifecycle, purrr, rlang (>= 1.0.3), tibble, vctrs (>= 0.4.1), withr (>= 2.5.0)
Suggests: covr, jsonlite, knitr, rmarkdown, spelling, testthat (>= 3.1.4)
LinkingTo: cpp11 (>= 0.4.2), plogr, vctrs (>= 0.4.1)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: yes
SystemRequirements: C++11
Packaged: 2022-07-13 14:11:28 UTC; mgirlich
Author: Maximilian Girlich [aut, cre, cph], Kirill Mueller [ctb]
Maintainer: Maximilian Girlich <maximilian.girlich@outlook.com>
Repository: CRAN
Date/Publication: 2022-07-14 10:50:02 UTC

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New package skpr with initial version 1.1.6
Package: skpr
Title: Design of Experiments Suite: Generate and Evaluate Optimal Designs
Date: 2022-07-13
Version: 1.1.6
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.
Copyright: Institute for Defense Analyses
Depends: R (>= 3.0.2), shiny
License: GPL-3
Imports: utils, iterators, stats, lme4, Rcpp (>= 0.11.0), rintrojs, shinythemes, foreach, doParallel, survival, doRNG, future, promises, shinyjs, car, viridis, magrittr, lmerTest, methods, lazyeval, progress, gt, scales
LinkingTo: Rcpp, RcppEigen
Suggests: testthat, mbest
Encoding: UTF-8
URL: https://github.com/tylermorganwall/skpr
BugReports: https://github.com/tylermorganwall/skpr/issues
NeedsCompilation: yes
Packaged: 2022-07-13 20:11:25 UTC; tmorganw
Author: Tyler Morgan-Wall [aut, cre], George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-14 10:50:05 UTC

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New package Rrdap with initial version 1.0.6
Package: Rrdap
Title: RDAP Server Querying
Version: 1.0.6
Date: 2022-07-12
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Description: Queries data from RDAP servers.
Imports: curl, rjson, stringr, utils
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2022-07-13 03:49:41 UTC; lister
Repository: CRAN
Date/Publication: 2022-07-14 11:00:12 UTC

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New package PLRModels with initial version 1.2
Package: PLRModels
Title: Statistical Inference in Partial Linear Regression Models
Version: 1.2
Date: 2022-07-12
Author: German Aneiros Perez and Ana Lopez-Cheda
Maintainer: Ana Lopez-Cheda <ana.lopez.cheda@udc.es>
Description: Contains statistical inference tools applied to Partial Linear Regression (PLR) models. Specifically, point estimation, confidence intervals estimation, bandwidth selection, goodness-of-fit tests and analysis of covariance are considered. Kernel-based methods, combined with ordinary least squares estimation, are used and time series errors are allowed. In addition, these techniques are also implemented for both parametric (linear) and nonparametric regression models.
License: GPL-3
Imports: stats
NeedsCompilation: no
Packaged: 2022-07-13 15:05:22 UTC; Ana
Repository: CRAN
Date/Publication: 2022-07-14 10:40:02 UTC

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New package ncdfgeom with initial version 1.1.3
Package: ncdfgeom
Title: 'NetCDF' Geometry and Time Series
Version: 1.1.3
Date: 2022-07-13
Description: Tools to create time series and geometry 'NetCDF' files.
URL: https://code.usgs.gov/water/ncdfgeom
BugReports: https://github.com/USGS-R/ncdfgeom/issues
Imports: RNetCDF, ncmeta, sf, dplyr, methods, stars
Depends: R (>= 3.5)
Suggests: testthat, knitr, rmarkdown, pkgdown, geoknife, ncdf4, jsonlite, areal
License: CC0
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-13 14:07:53 UTC; dblodgett
Author: David Blodgett [aut, cre], Luke Winslow [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Repository: CRAN
Date/Publication: 2022-07-14 11:00:02 UTC

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New package ifultools with initial version 2.0-26
Package: ifultools
Title: Insightful Research Tools
Version: 2.0-26
Depends: R (>= 3.0.2)
Imports: MASS, methods, splus2R (>= 1.2-0)
Description: Insightful Research Tools is a collection of signal processing, image processing, and time series modeling routines written in the C language for speed and efficiency. The routines were originally developed at Insightful for use in S-PLUS.
License: GPL-2
URL: https://github.com/spkaluzny/ifultools
BugReports: https://github.com/spkaluzny/ifultools/issues
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-07-12 18:35:12 UTC; spk
Author: William Constantine [aut], Stephen Kaluzny [aut, cre], R Core Team [ctb]
Maintainer: Stephen Kaluzny <spkaluzny@gmail.com>
Date/Publication: 2022-07-14 11:00:05 UTC

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New package VPdtw with initial version 2.1-14
Package: VPdtw
Title: Variable Penalty Dynamic Time Warping
Version: 2.1-14
Date: 2022-07-03
Description: Variable Penalty Dynamic Time Warping (VPdtw) for aligning chromatographic signals. With an appropriate penalty this method performs good alignment of chromatographic data without deforming the peaks (Clifford, D., Stone, G., Montoliu, I., Rezzi S., Martin F., Guy P., Bruce S., and Kochhar S.(2009) <doi:10.1021/ac802041e>; Clifford, D. and Stone, G. (2012) <doi:10.18637/jss.v047.i08>).
License: GPL-2
URL: https://github.com/ethanbass/VPdtw/
BugReports: https://github.com/ethanbass/VPdtw/issues
NeedsCompilation: yes
Packaged: 2022-07-10 20:17:13 UTC; ethanbass
Author: David Clifford [aut], Glenn Stone [aut], Ethan Bass [ctb, cre]
Maintainer: Ethan Bass <ethanbass@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-14 09:50:02 UTC

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New package trouBBlme4SolveR with initial version 0.1
Package: trouBBlme4SolveR
Version: 0.1
Date: 2022-07-09
Title: Troubles Solver for 'lme4'
Description: The main function of the package aims to update 'lmer()'/'glmer()' models depending on their warnings, so trying to avoid convergence and singularity problems.
Depends: R (>= 4.0)
Imports: lme4 (>= 1.1-28)
Suggests: nlme (>= 3.1-123), ggplot2 (>= 2.0.0)
License: GPL-3
URL: https://gitlab.com/iagogv/trouBBlme4SolveR
BugReports: https://gitlab.com/iagogv/trouBBlme4SolveR/-/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-09 14:56:32 UTC; iago
Author: Iago Gine-Vazquez [aut, cre]
Maintainer: Iago Gine-Vazquez <iago.gin-vaz@protonmail.com>
Repository: CRAN
Date/Publication: 2022-07-14 09:20:02 UTC

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New package treePlotArea with initial version 1.0.0
Package: treePlotArea
Title: Correction Factors for Tree Plot Areas Intersected by Stand Boundaries
Version: 1.0.0
Description: The German national forest inventory uses angle count sampling, a sampling method first published as `Bitterlich, W.: Die Winkelzählmessung. Allgemeine Forst- und Holzwirtschaftliche Zeitung, 58. Jahrg., Folge 11/12 vom Juni 1947` and extended by Grosenbaugh (<https://academic.oup.com/jof/article-abstract/50/1/32/4684174>) as probability proportional to size sampling. When plots are located near stand boundaries, their sizes and hence their probabilities need to be corrected.
License: BSD_2_clause + file LICENSE
URL: https://gitlab.com/fvafrcu/treePlotArea.git
Depends: R (>= 4.0.0)
Imports: fritools, graphics, sf
Suggests: knitr, pkgload, plotrix, rmarkdown, rprojroot, RUnit, testthat, tinytest
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-09 22:20:39 UTC; qwer
Author: Andreas Dominik Cullmann [aut, cre], Bernhard Boesch [ctb], Gerald Kaendler [ctb]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Repository: CRAN
Date/Publication: 2022-07-14 09:30:06 UTC

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New package StrucDiv with initial version 0.1.0
Package: StrucDiv
Title: Spatial Structural Diversity Quantification in Raster Data
Version: 0.1.0
Maintainer: Leila Schuh <l.schuh@posteo.net>
Description: Spatial structural diversity refers to the spatial arrangement of landscape elements and can reveal itself as landscape features, such as patches and line features. The 'R' package 'StrucDiv' provides methods to quantify spatial structural diversity in continuous remote sensing data, or in other data in gridded field format. The methods are based on second-order texture metrics, considering the spatial arrangement of pixel pairs.
Depends: R (>= 3.5.0)
License: GPL (>= 3)
Imports: Rcpp (>= 1.0.4), raster (>= 3.1.5)
Suggests: testthat, knitr, rmarkdown
LinkingTo: Rcpp, RcppProgress
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-07-11 08:32:00 UTC; leila
Author: Leila Schuh [aut, cre] , Reinhard Furrer [aut] , Kalina Cherneva [ctb, ctr], Patrick Schratz [ctr], University Research Priority Progam Global Change and Biodiversity of the University of Zurich [fnd]
Repository: CRAN
Date/Publication: 2022-07-14 09:50:05 UTC

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New package portalr with initial version 0.3.10
Package: portalr
Title: Create Useful Summaries of the Portal Data
Version: 0.3.10
Description: Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahua desert. The raw data files can be found at <https://github.com/weecology/portaldata>.
License: MIT + file LICENSE
URL: https://weecology.github.io/portalr/, https://github.com/weecology/portalr
BugReports: https://github.com/weecology/portalr/issues
Depends: R (>= 3.2.3)
Imports: clipr, clisymbols, crayon, dplyr, forecast, httr, lubridate, lunar, magrittr, rlang, tidyr, tidyselect (>= 1.0.0), zoo
Suggests: covr, cowplot, ggplot2, httptest, knitr, pkgdown, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-14 05:35:39 UTC; GlendaYenni
Author: Glenda M. Yenni [aut, cre] , Hao Ye [aut] , Erica M. Christensen [aut] , Juniper L. Simonis [aut] , Ellen K. Bledsoe [aut] , Renata M. Diaz [aut] , Shawn D. Taylor [aut] , Ethan P, White [aut] , S.K. Morgan Ernest [aut] , Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Repository: CRAN
Date/Publication: 2022-07-14 09:40:02 UTC

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New package ggpackets with initial version 0.2.0
Package: ggpackets
Title: Package Plot Layers for Easier Portability and Modularization
Version: 0.2.0
Description: Create groups of 'ggplot2' layers that can be easily migrated from one plot to another, reducing redundant code and improving the ability to format many plots that draw from the same source 'ggpacket' layers.
Depends: R (>= 3.1.0), ggplot2
Imports: utils, methods, tibble, rlang, crayon
Suggests: testthat, dplyr, backports, knitr, rmarkdown, stringi, covr
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://dgkf.github.io/ggpackets/
NeedsCompilation: no
Packaged: 2022-07-09 03:39:22 UTC; root
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-14 09:10:02 UTC

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New package weightedRank with initial version 0.1.6
Package: weightedRank
Title: Sensitivity Analysis Using Weighted Rank Statistics
Version: 0.1.6
Description: Performs a sensitivity analysis using weighted rank tests in observational studies with I blocks of size J; see Rosenbaum (2018) <doi:10.1214/18-AOAS1153>. The package can perform adaptive inference in block designs; see Rosenbaum (2012) <doi:10.1093/biomet/ass032>. The main functions are wgtRank() and wgtRanktt().
License: GPL-2
Encoding: UTF-8
LazyData: true
Imports: stats, graphics, mvtnorm
Suggests: sensitivitymw, sensitivitymult
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-07-08 18:01:59 UTC; rosenbap
Author: Paul Rosenbaum [aut, cre]
Maintainer: Paul Rosenbaum <rosenbaum@wharton.upenn.edu>
Repository: CRAN
Date/Publication: 2022-07-14 09:00:02 UTC

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New package mildsvm with initial version 0.4.0
Package: mildsvm
Title: Multiple-Instance Learning with Support Vector Machines
Version: 0.4.0
Description: Weakly supervised (WS), multiple instance (MI) data lives in numerous interesting applications such as drug discovery, object detection, and tumor prediction on whole slide images. The 'mildsvm' package provides an easy way to learn from this data by training Support Vector Machine (SVM)-based classifiers. It also contains helpful functions for building and printing multiple instance data frames. The core methods from 'mildsvm' come from the following references: Kent and Yu (2022) <arXiv:2206.14704>; Xiao, Liu, and Hao (2018) <doi:10.1109/TNNLS.2017.2766164>; Muandet et al. (2012) <https://proceedings.neurips.cc/paper/2012/file/9bf31c7ff062936a96d3c8bd1f8f2ff3-Paper.pdf>; Chu and Keerthi (2007) <doi:10.1162/neco.2007.19.3.792>; and Andrews et al. (2003) <https://papers.nips.cc/paper/2232-support-vector-machines-for-multiple-instance-learning.pdf>. Many functions use the 'Gurobi' optimization back-end to improve the optimization problem speed; the 'gurobi' R package and associated software can be downloaded from <https://www.gurobi.com> after obtaining a license.
License: MIT + file LICENSE
URL: https://github.com/skent259/mildsvm
BugReports: https://github.com/skent259/mildsvm/issues
Depends: R (>= 3.5.0)
Imports: dplyr, e1071, kernlab, magrittr, mvtnorm, pillar, pROC, purrr, rlang, stats, tibble, tidyr, utils
Suggests: covr, gurobi, Matrix, testthat
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-08 22:49:54 UTC; spkent
Author: Sean Kent [aut, cre] , Yifei Liou [aut]
Maintainer: Sean Kent <skent259@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-14 09:00:04 UTC

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Wed, 13 Jul 2022

New package goodpractice with initial version 1.0.3
Package: goodpractice
Title: Advice on R Package Building
Version: 1.0.3
Description: Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
License: MIT + file LICENSE
URL: https://github.com/mangothecat/goodpractice
BugReports: https://github.com/mangothecat/goodpractice/issues
Imports: clisymbols, covr, crayon, cyclocomp (>= 1.1.0), desc, jsonlite, lintr (>= 3.0.0), praise, rcmdcheck, rstudioapi, tools, utils, whoami, withr, xml2, xmlparsedata (>= 1.0.1)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-13 08:08:50 UTC; karina.marks
Author: Ascent Digital Services UK Limited [cph] , Karina Marks [aut, cre] , Daniel de Bortoli [aut] , Gabor Csardi [aut], Hannah Frick [aut], Owen Jones [aut] , Hannah Alexander [aut], Ana Simmons [ctb] , Fabian Scheipl [ctb]
Maintainer: Karina Marks <karina.marks@ascent.io>
Repository: CRAN
Date/Publication: 2022-07-13 13:20:08 UTC

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New package FDboost with initial version 1.1-0
Package: FDboost
Title: Boosting Functional Regression Models
Version: 1.1-0
Date: 2022-06-14
Maintainer: David Ruegamer <david.ruegamer@gmail.com>
Description: Regression models for functional data, i.e., scalar-on-function, function-on-scalar and function-on-function regression models, are fitted by a component-wise gradient boosting algorithm. For a manual on how to use 'FDboost', see Brockhaus, Ruegamer, Greven (2017) <doi:10.18637/jss.v094.i10>.
Depends: R (>= 3.5.0), mboost (>= 2.9-0)
Imports: methods, graphics, grDevices, utils, stats, Matrix, gamboostLSS (>= 2.0-0), stabs, mgcv, MASS, zoo
Suggests: fda, fields, ggplot2, maps, mapdata, knitr, refund, testthat
License: GPL-2
Packaged: 2022-07-13 09:34:57 UTC; david
Encoding: UTF-8
BugReports: https://github.com/boost-R/FDboost/issues
URL: https://github.com/boost-R/FDboost
VignetteBuilder: knitr
NeedsCompilation: no
Author: Sarah Brockhaus [aut], David Ruegamer [aut, cre], Almond Stoecker [aut], Torsten Hothorn [ctb], with contributions by many others [ctb]
Repository: CRAN
Date/Publication: 2022-07-13 12:50:02 UTC

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New package ForagingOrg with initial version 0.1.0
Package: ForagingOrg
Title: Organization Measures for Visual Foraging
Version: 0.1.0
Author: Marcos Bella-Fernandez
Maintainer: Marcos Bella-Fernandez <marcosbellafernandez@gmail.com>
Description: Several functions to compute indicators for organization and efficiency in visual foraging, multi-target visual search, and cancellation tasks. The current version of this package includes the following indicators: best-r, mean Inter-target Distance, Percentage Above Optimal (PAO) scan path, and intersections in the scan path. For more detailed descriptions, see Mark et al. (2004) <doi:10.1212/01.WNL.0000131947.08670.D4>.
License: GPL-3
Encoding: UTF-8
Depends: PairViz, TSP
NeedsCompilation: no
Packaged: 2022-07-08 17:27:59 UTC; durie
Repository: CRAN
Date/Publication: 2022-07-13 08:20:02 UTC

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New package TrenchR with initial version 0.1.0
Package: TrenchR
Title: Tools for Microclimate and Biophysical Ecology
Description: Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.
Version: 0.1.0
Maintainer: Lauren Buckley <lbuckley@uw.edu>
License: MIT + file LICENSE
Date: 2022-07-07
URL: https://trenchproject.github.io/, https://github.com/trenchproject/TrenchR
BugReports: https://github.com/trenchproject/TrenchR/issues
VignetteBuilder: knitr
Depends: R (>= 3.3.1)
Imports: deSolve, msm, Rdpack (>= 0.7), stats, zoo
Suggests: covr, knitr, rmarkdown, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-07 20:32:39 UTC; lbuckley
Author: Lauren Buckley [aut, cre] , Bryan Briones Ortiz [aut], Isaac Caruso [aut], Aji John [aut] , Ofir Levy [aut] , Abigail Meyer [aut], Eric Riddell [aut] , Yutaro Sakairi [aut], Juniper Simonis [aut] , Brian Helmuth [ctb]
Repository: CRAN
Date/Publication: 2022-07-13 07:30:06 UTC

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New package renderthis with initial version 0.1.0
Package: renderthis
Title: Render Slides to Different Formats
Version: 0.1.0
Description: Render slides to different formats, including 'html', 'pdf', 'png', 'gif', 'pptx', and 'mp4', as well as a 'social' output, a 'png' of the first slide re-sized for sharing on social media.
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
Imports: cli (>= 3.0.0), digest, fs, jsonlite, magick (>= 2.7.1), pagedown, progress, rmarkdown, withr, xaringan, zip
Suggests: av, chromote, knitr, lifecycle, officer, pdftools, testthat (>= 3.0.0), webshot2
Config/Needs/website: xaringanExtra
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-07 15:36:56 UTC; jhelvy
Author: John Helveston [aut, cre, cph] , Garrick Aden-Buie [aut] , Bryan Shalloway [ctb]
Maintainer: John Helveston <john.helveston@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-13 07:30:02 UTC

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Tue, 12 Jul 2022

New package vprr with initial version 0.2.3
Package: vprr
Title: Processing and Visualization of Video Plankton Recorder Data
Version: 0.2.3
Maintainer: Emily O'Grady <vprrcontact@gmail.com>
Description: An oceanographic data processing package for analyzing and visualizing Video Plankton Recorder data. This package was developed at 'Bedford Institute of Oceanography'. Functions are designed to process automated image classification output and create organized and easily portable data products.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: ggplot2, oce, dplyr, interp, magick, gsw, tidyr, stringr, metR, gridExtra, lubridate, cmocean, withr, usethis
Suggests: knitr, rmarkdown, testthat, markdown
VignetteBuilder: knitr
BuildVignettes: true
URL: https://eogrady21.github.io/vprr/
NeedsCompilation: no
Packaged: 2022-07-12 12:14:19 UTC; ChisholmE
Author: Emily O'Grady [aut, cre, cph], Kevin Sorochan dev [aut], Catherine Johnson [aut]
Repository: CRAN
Date/Publication: 2022-07-12 14:20:02 UTC

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New package tipmap with initial version 0.1.7
Package: tipmap
Title: Tipping Point Analysis for Bayesian Dynamic Borrowing
Version: 0.1.7
Description: Tipping point analysis for clinical trials that employ Bayesian dynamic borrowing via robust meta-analytic predictive (MAP) priors. Mainly an implementation of an approach proposed by Best and colleagues (2021) is provided <doi:10.1002/pst.2093>. Intended use is the planning, analysis and interpretation of extrapolation studies in pediatric drug development, but applicability is generally wider.
License: GPL (>= 3)
Encoding: UTF-8
Imports: dplyr, ggplot2, RBesT
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-07-11 18:31:52 UTC; stockch
Author: Morten Dreher [aut], Christian Stock [aut, cre]
Maintainer: Christian Stock <christian.stock@boehringer-ingelheim.com>
Repository: CRAN
Date/Publication: 2022-07-12 10:50:02 UTC

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New package DSSP with initial version 0.1.1
Package: DSSP
Title: Implementation of the Direct Sampling Spatial Prior
Version: 0.1.1
Date: 2022-07-07
Maintainer: Gentry White <gentry.white@qut.edu.au>
Description: Draw samples from the direct sampling spatial prior model as described in G. White, D. Sun, P. Speckman (2019) <arXiv:1906.05575>. The basic model assumes a Gaussian likelihood and derives a spatial prior based on thin-plate splines.
License: GPL (>= 3)
URL: https://github.com/gentrywhite/DSSP
BugReports: https://github.com/gentrywhite/DSSP/issues
Imports: mcmcse, posterior, rust, sp
Suggests: cowplot, ggplot2, gstat, interp, knitr, rmarkdown, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-07-06 20:02:32 UTC; Rex
Author: Gentry White [aut, cre] , Rex Parsons [aut]
Repository: CRAN
Date/Publication: 2022-07-12 11:00:06 UTC

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Mon, 11 Jul 2022

New package RobustRankAggreg with initial version 1.2
Package: RobustRankAggreg
Title: Methods for Robust Rank Aggregation
Version: 1.2
Date: 2022-07-11
Maintainer: Raivo Kolde <rkolde@gmail.com>
Description: Methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation Kolde et al (2012) <doi:10.1093/bioinformatics/btr709> and some other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.
License: GPL-2
LazyLoad: yes
Depends: methods
NeedsCompilation: no
Packaged: 2022-07-11 19:56:04 UTC; raivokolde
Author: Raivo Kolde [aut, cre] , Sven Laur [ctb]
Repository: CRAN
Date/Publication: 2022-07-12 00:20:02 UTC

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New package asbio with initial version 1.8-1
Package: asbio
Title: A Collection of Statistical Tools for Biologists
Version: 1.8-1
Depends: R (>= 3.5.0), tcltk
Imports: scatterplot3d, pixmap, plotrix, mvtnorm, deSolve, lattice, multcompView, grDevices, graphics, stats, utils, gWidgets2, gWidgets2tcltk
Suggests: boot, tkrplot
Date: 2022-7-11
SystemRequirements: BWidget
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Packaged: 2022-07-11 20:10:18 UTC; ahoken
Repository: CRAN
Date/Publication: 2022-07-11 23:40:05 UTC

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New package idm with initial version 1.8.3
Package: idm
Title: Incremental Decomposition Methods
Version: 1.8.3
Date: 2022-07-11
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Depends: R (>= 2.10), ggplot2, animation
Imports: corpcor, ca, ggrepel
Suggests: caret
SystemRequirements: ImageMagick (http://imagemagick.org) or GraphicsMagick (http://www.graphicsmagick.org)
Description: Incremental Multiple Correspondence Analysis and Principal Component Analysis.
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Packaged: 2022-07-11 17:09:39 UTC; amarkos
Date/Publication: 2022-07-11 18:20:02 UTC

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New package BMisc with initial version 1.4.5
Package: BMisc
Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing Results
Version: 1.4.5
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Depends: R (>= 3.1.0)
Imports: data.table, Rcpp
License: GPL-2
Suggests: testthat (>= 3.0.0), plm, tibble
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
URL: https://bcallaway11.github.io/BMisc/, https://github.com/bcallaway11/BMisc
BugReports: https://github.com/bcallaway11/BMisc/issues
NeedsCompilation: yes
Packaged: 2022-07-11 13:33:20 UTC; brant
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Repository: CRAN
Date/Publication: 2022-07-11 18:30:10 UTC

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New package bbsBayes with initial version 2.5.0
Package: bbsBayes
Title: Hierarchical Bayesian Analysis of North American BBS Data
Version: 2.5.0
Date: 2022-07-11
Imports: progress, jagsUI, ggrepel, geofacet, ggplot2, stringr, grDevices, dplyr, sf, tools, rappdirs, sbtools, mgcv
Depends: R (>= 3.5)
SystemRequirements: JAGS 4.3.0 (https://sourceforge.net/projects/mcmc-jags/)
URL: https://github.com/BrandonEdwards/bbsBayes
NeedsCompilation: no
Description: The North American Breeding Bird Survey (BBS) is a long-running program that seeks to monitor the status and trends of the breeding birds in North America. Since its start in 1966, the BBS has accumulated over 50 years of data for over 500 species of North American Birds. Given the temporal and spatial structure of the data, hierarchical Bayesian models are used to assess the status and trends of these 500+ species of birds. 'bbsBayes' allows you to perform hierarchical Bayesian analysis of BBS data. You can run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for 'JAGS', or modelled. The functions provided here allow you to replicate analyses performed by the United State Geological Survey (USGS, see Link and Sauer (2011) <doi:10.1525/auk.2010.09220>) and Canadian Wildlife Service (CWS, see Smith and Edwards (2020) <doi:10.1101/2020.03.26.010215>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Packaged: 2022-07-11 13:00:59 UTC; brand
Author: Brandon P.M. Edwards [aut, cre], Adam C. Smith [aut]
Maintainer: Brandon P.M. Edwards <brandonedwards3@cmail.carleton.ca>
Repository: CRAN
Date/Publication: 2022-07-11 18:30:06 UTC

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New package glmmSeq with initial version 0.2.0
Package: glmmSeq
Title: General Linear Mixed Models for Gene-Level Differential Expression
Version: 0.2.0
Description: Using random and fixed effects to model expression at an individual gene level can highlight differences between sample groups over time. The most widely used differential gene expression tools are unable to fit linear mixed effect models, therefore do not capture interaction terms. This package uses negative binomial mixed effects models to fit gene expression with matched samples. This is particularly useful for investigating changes in gene expression between groups of individuals over time, as seen in: Rivellese F., Surace A.E.A., Goldmann K., Sciacca E., Giorli G., Cubuk C., John C.R., Nerviani A., Fossati-Jimack L., Thorborn G., Humby F., Bombardieri M., Lewis M.J., Pitzalis C. (2021) "Molecular Pathology Profiling of Synovial Tissue Predicts Response to Biologic Treatment in Rheumatoid Arthritis" [Manuscript in preparation].
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Language: en-gb
URL: https://github.com/KatrionaGoldmann/glmmSeq
BugReports: https://github.com/KatrionaGoldmann/glmmSeq/issues
Suggests: knitr, rmarkdown, kableExtra, edgeR
VignetteBuilder: knitr
Depends: R (>= 3.6.0)
Imports: MASS, car, stats, gghalves, ggplot2, ggpubr, graphics, lme4, methods, plotly, qvalue, pbapply, pbmcapply
NeedsCompilation: no
Packaged: 2022-07-11 09:57:39 UTC; phd
Author: Myles Lewis [aut] , Katriona Goldmann [aut, cre] , Elisabetta Sciacca [aut] , Cankut Cubuk [ctb] , Anna Surace [ctb]
Maintainer: Katriona Goldmann <k.goldmann@qmul.ac.uk>
Repository: CRAN
Date/Publication: 2022-07-11 12:40:02 UTC

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New package FlickrAPI with initial version 0.1.0.1
Package: FlickrAPI
Title: Access to Flickr API
Version: 0.1.0.1
Description: Provides an interface to the Flickr API <https://www.flickr.com/services/api/> and allows R users to download data on Flickr.
Depends: R (>= 3.1)
License: GPL (>= 3)
Encoding: UTF-8
Imports: httr2, janitor, magrittr, rlang, utils
Suggests: sf, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-11 10:53:57 UTC; koki2
Author: Koki Ando [aut, cre], Eli Pousson [aut, ctb]
Maintainer: Koki Ando <koki.25.ando@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-11 12:40:10 UTC

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New package R2ucare with initial version 1.0.2
Package: R2ucare
License: GPL (>= 2)
Title: Goodness-of-Fit Tests for Capture-Recapture Models
Description: Performs goodness-of-fit tests for capture-recapture models as described by Gimenez et al. (2018) <doi:10.1111/2041-210X.13014>. Also contains several functions to process capture-recapture data.
Version: 1.0.2
URL: https://github.com/oliviergimenez/R2ucare
Depends: R (>= 3.3.0)
Suggests: knitr, rmarkdown, testthat
Imports: stringr, RMark, stats, utils
Encoding: UTF-8
VignetteBuilder: knitr
BugReports: https://github.com/oliviergimenez/R2ucare/issues
NeedsCompilation: no
Packaged: 2022-07-09 01:26:19 UTC; Murray
Author: Olivier Gimenez [aut, cre] , Jean-Dominique Lebreton [ctb], Remi Choquet [ctb], Roger Pradel [ctb]
Maintainer: Olivier Gimenez <olivier.gimenez@cefe.cnrs.fr>
Repository: CRAN
Date/Publication: 2022-07-11 08:10:12 UTC

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Fri, 08 Jul 2022

New package parcats with initial version 0.0.4
Package: parcats
Title: Interactive Parallel Categories Diagrams for 'easyalluvial'
Version: 0.0.4
URL: https://erblast.github.io/parcats/
BugReports: https://github.com/erblast/parcats/issues/
Description: Complex graphical representations of data are best explored using interactive elements. 'parcats' adds interactive graphing capabilities to the 'easyalluvial' package. The 'plotly.js' parallel categories diagrams offer a good framework for creating interactive flow graphs that allow manual drag and drop sorting of dimensions and categories, highlighting single flows and displaying mouse over information. The 'plotly.js' dependency is quite heavy and therefore is outsourced into a separate package.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.0.0)
Suggests: testthat, covr, randomForest, knitr, rmarkdown, spelling, plotly, shiny
Imports: easyalluvial (>= 0.2.1.0), tidyr (>= 1.0.0), dplyr, purrr, forcats, magrittr, tibble, htmlwidgets, stringr
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-08 07:19:14 UTC; koneswab
Author: Bjoern Koneswarakantha [aut, cre]
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-08 22:10:02 UTC

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New package ebirdst with initial version 1.2020.1
Package: ebirdst
Title: Access and Analyze eBird Status and Trends Data
Version: 1.2020.1
Description: Tools to download, load, plot, and analyze eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird abundances, range boundaries, and habitat associations at a high spatial and temporal resolution.
License: GPL-3
URL: https://github.com/CornellLabofOrnithology/ebirdst
BugReports: https://github.com/CornellLabofOrnithology/ebirdst/issues
Depends: R (>= 4.0.0)
Imports: DBI, dplyr (>= 1.0.0), gbm, ggplot2, grDevices, gridExtra, jsonlite, magrittr, mgcv, precrec, PresenceAbsence, raster (>= 3.1-5), rgdal, rlang, RSQLite, sf (>= 1.0-0), stats, stringr, tidyr (>= 1.0.0), tools, utils, viridisLite
Suggests: exactextractr, fields, knitr, rmarkdown, rnaturalearth, testthat, withr
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-08 13:20:32 UTC; mes335
Author: Matthew Strimas-Mackey [aut, cre] , Shawn Ligocki [aut], Tom Auer [aut] , Daniel Fink [aut] , Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Repository: CRAN
Date/Publication: 2022-07-08 22:50:02 UTC

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New package ExactCIdiff with initial version 2.1
Package: ExactCIdiff
Version: 2.1
Date: 2022-07-06
Title: Inductive Confidence Intervals for the Difference Between Two Proportions
Author: Guogen Shan <gshan@ufl.edu>, Weizhen Wang <weizhen.wang@wright.edu>
Maintainer: Guogen Shan <gshan@ufl.edu>
Depends: R (>= 1.8.0)
Description: This is a package for exact Confidence Intervals for the difference between two independent or dependent proportions.
License: GPL (>= 2)
URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org&d=DwICaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=u5749-0kOlGR1AfizUVmaw&m=qjJHLdipM5gUyXllZWH5kL0wENGFef6KuJ57hW5lHx14eZasfdmgFN_1geUbxk5J&s=VFf9h_9FOlJBpRMIjim8tGuVnJ7GlWc5qZkrA9kmoMM&e=, https://biostat.ufl.edu/profile/shan-guogen/
NeedsCompilation: no
Packaged: 2022-07-08 15:17:17 UTC; gshan
Repository: CRAN
Date/Publication: 2022-07-08 21:50:13 UTC

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New package xadmix with initial version 1.0.0
Package: xadmix
Title: Subsetting and Plotting Optimized for Admixture Data
Version: 1.0.0
Description: A few functions which provide a quick way of subsetting genomic admixture data and generating customizable stacked barplots.
License: GPL (>= 3)
URL: https://github.com/SpaceCowboy-71/xadmix
BugReports: https://github.com/SpaceCowboy-71/xadmix/issues
Depends: R (>= 2.10)
Imports: dplyr, forcats, ggplot2, magrittr, methods, rlang, stringr, tidyr, viridis
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-07 15:08:33 UTC; Austin
Author: Lukas Schoenmann [aut, cre]
Maintainer: Lukas Schoenmann <lukas.schoenmann@outlook.com>
Repository: CRAN
Date/Publication: 2022-07-08 15:20:02 UTC

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New package visaOTR with initial version 0.1.0
Package: visaOTR
Title: Valid Improved Sparsity A-Learning for Optimal Treatment Decision
Version: 0.1.0
Maintainer: Zishu Zhan <zishu927@hotmail.com>
Description: Valid Improved Sparsity A-Learning (VISA) provides a new method for selecting important variables involved in optimal treatment regime from a multiply robust perspective. The VISA estimator achieves its success by borrowing the strengths of both model averaging (ARM, Yuhong Yang, 2001) <doi:10.1198/016214501753168262> and variable selection (PAL, Chengchun Shi, Ailin Fan, Rui Song and Wenbin Lu, 2018) <doi:10.1214/17-AOS1570>. The package is an implementation of Zishu Zhan and Jingxiao Zhang. (2022+).
License: GPL-3
Encoding: UTF-8
Imports: Rglpk, e1071, kernlab, Matrix, mboost, randomForest, stats, xgboost
Depends: R (>= 3.5.0)
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-07 11:20:59 UTC; treer
Author: Zishu Zhan [aut, cre], Jingxiao Zhang [aut]
Repository: CRAN
Date/Publication: 2022-07-08 15:20:05 UTC

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New package ThresholdROCsurvival with initial version 1.0.1
Package: ThresholdROCsurvival
Title: Threshold and AUC Estimation with Right-Censored Data at a Fixed Time t
Version: 1.0.1
Date: 2022-07-06
Description: We focus on the estimation of optimal thresholds and AUCs when the outcome of interest is the status (alive or dead) of the subjects at a certain time-point t. This binary status is determined by right-censored times to event and it is missing for those subjects censored before t. Here we provide three methods (missing exclusion, imputation of censored times and using time-dependent ROC curves) to estimate optimal thresholds and AUCs in this context. Two references for the methods used here are Skaltsa et al. (2010) <doi:10.1002/bimj.200900294> and Heagerty et al. (2000) <doi:10.1111/j.0006-341x.2000.00337.x>.
License: GPL (>= 2)
Depends: R (>= 4.0.0)
Imports: boot, InformativeCensoring, pROC, psych, survival, survivalROC, ThresholdROC
LazyData: TRUE
NeedsCompilation: no
Packaged: 2022-07-06 14:23:30 UTC; sperezj
Author: Sara Perez-Jaume [aut, cre], Josep L Carrasco [aut]
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-08 14:20:05 UTC

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New package rKenyaForex with initial version 0.1.0
Package: rKenyaForex
Title: Historical Data for Kenya Foreign Exchange Prices
Version: 0.1.0
Author: Mutua Kilai
Maintainer: Mutua Kilai <kilaimutua@gmail.com>
Description: Exchange rate for Kenya Shilling against other currencies, US DOLLAR, EURO, STERLING POUND, Tanzania Shilling, Uganda Shilling.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-07-06 06:33:30 UTC; Mutua Sam
Repository: CRAN
Date/Publication: 2022-07-08 14:10:05 UTC

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New package ivgets with initial version 0.1.0
Package: ivgets
Title: General to Specific Modeling and Indicator Saturation in 2SLS Models
Version: 0.1.0
Description: Provides facilities of general to specific model selection for exogenous regressors in 2SLS models. Furthermore, indicator saturation methods can be used to detect outliers and structural breaks in the sample.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10), gets (>= 0.36), ivreg
Imports: stats, stringr
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/jkurle/ivgets
BugReports: https://github.com/jkurle/ivgets/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-06 09:38:54 UTC; jonas
Author: Kurle Jonas [aut, cre]
Maintainer: Kurle Jonas <mail@jonaskurle.com>
Repository: CRAN
Date/Publication: 2022-07-08 14:20:02 UTC

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New package HurreconR with initial version 1.0
Package: HurreconR
Title: Models Hurricane Wind Speed, Wind Direction, and Wind Damage
Version: 1.0
Date: 2022-07-06
Description: The HURRECON model estimates wind speed, wind direction, enhanced Fujita scale wind damage, and duration of EF0 to EF5 winds as a function of hurricane location and maximum sustained wind speed. Results may be generated for a single site or an entire region. Hurricane track and intensity data may be imported directly from the US National Hurricane Center's HURDAT2 database. For details on the original version of the model written in Borland Pascal, see: Boose, Chamberlin, and Foster (2001) <doi:10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2> and Boose, Serrano, and Foster (2004) <doi:10.1890/02-4057>.
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
Imports: graphics, grDevices, raster, rgdal, utils
Suggests: knitr, qpdf, testthat (>= 3.0.0), rmarkdown
URL: https://github.com/hurrecon-model/HurreconR
BugReports: https://github.com/hurrecon-model/hurreconR/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-06 21:30:15 UTC; erb709
Author: Emery Boose [aut, cre], President and Fellows of Harvard College [cph]
Maintainer: Emery Boose <boose@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-07-08 14:50:02 UTC

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New package fMRIscrub with initial version 0.11.2
Package: fMRIscrub
Title: Scrubbing and Other Data Cleaning Routines for fMRI
Version: 0.11.2
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Description: Data-driven fMRI denoising with projection scrubbing (Pham et al (2022) <arXiv:2108.00319>). Also includes routines for DVARS (Derivatives VARianceS) (Afyouni and Nichols (2018) <doi:10.1016/j.neuroimage.2017.12.098>), motion scrubbing (Power et al (2012) <doi:10.1016/j.neuroimage.2011.10.018>), aCompCor (anatomical Components Correction) (Muschelli et al (2014) <doi:10.1016/j.neuroimage.2014.03.028>), detrending, and nuisance regression. Projection scrubbing and DVARS are also applicable to other outlier detection tasks involving high-dimensional data.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
Imports: MASS, e1071, pesel, robustbase, stats, utils
Suggests: corpcor, cowplot, ciftiTools, gifti, knitr, rmarkdown, RNifti, ggplot2, gsignal, fastICA, oro.nifti, testthat (>= 3.0.0), covr
URL: https://github.com/mandymejia/fMRIscrub
BugReports: https://github.com/mandymejia/fMRIscrub/issues
LazyData: true
NeedsCompilation: no
Packaged: 2022-07-06 06:00:11 UTC; ddpham
Author: Amanda Mejia [aut, cre], John Muschelli [aut] , Damon Pham [aut] , Daniel McDonald [ctb]
Repository: CRAN
Date/Publication: 2022-07-08 14:30:02 UTC

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New package Families with initial version 1.0.1
Package: Families
Title: Kinship Ties in Virtual Populations
Version: 1.0.1
Depends: R (>= 3.5.0)
Imports: msm,reshape
Suggests: knitr, rmarkdown,ggplot2,lubridate,xml2
BuildResaveData: best
VignetteBuilder: knitr
LazyData: true
Date: 2022-07-06
Maintainer: Frans Willekens <willekens@nidi.nl>
Description: Tools to study kinship networks, grandparenthood, and double burden (presence of children and oldest old parents) in virtual population produced by 'VirtualPop'.
License: GPL-2
NeedsCompilation: no
Encoding: UTF-8
BugReports: https://github.com/willekens/VirtualPop/issues
Packaged: 2022-07-06 16:16:43 UTC; frans
Author: Frans Willekens [aut, cre]
Repository: CRAN
Date/Publication: 2022-07-08 14:30:06 UTC

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Thu, 07 Jul 2022

New package vdg with initial version 1.2.2
Package: vdg
Title: Variance Dispersion Graphs and Fraction of Design Space Plots
Version: 1.2.2
Date: 2022-07-06
Author: Pieter Schoonees [aut, cre, cph], Niel le Roux [ctb]
Maintainer: Pieter Schoonees <schoonees@gmail.com>
Depends: R (>= 4.2.0), parallel, ggplot2, quantreg
Imports: proxy, splines, gridExtra, grDevices, methods, stats, utils
Suggests: rsm, AlgDesign, knitr, lhs
Description: Facilities for constructing variance dispersion graphs, fraction- of-design-space plots and similar graphics for exploring the properties of experimental designs. The design region is explored via random sampling, which allows for more flexibility than traditional variance dispersion graphs. A formula interface is leveraged to provide access to complex model formulae. Graphics can be constructed simultaneously for multiple experimental designs and/or multiple model formulae. Instead of using pointwise optimization to find the minimum and maximum scaled prediction variance curves, which can be inaccurate and time consuming, this package uses quantile regression as an alternative.
VignetteBuilder: knitr
License: GPL (>= 2)
LazyData: yes
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2022-07-07 13:50:11 UTC; schoo
Repository: CRAN
Date/Publication: 2022-07-07 22:30:02 UTC

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New package nestedcv with initial version 0.2.3
Package: nestedcv
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Version: 0.2.3
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>.
Language: en-gb
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Boruta, caret, CORElearn, data.table, glmnet, hsstan, matrixTests, methods, parallel, pROC, randomForest, RcppEigen, Rfast
Suggests: mda, rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-05 22:15:57 UTC; myles
Author: Myles Lewis [aut, cre] , Athina Spiliopoulou [aut] , Katriona Goldmann [aut]
Repository: CRAN
Date/Publication: 2022-07-07 08:40:02 UTC

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New package distillML with initial version 0.1.0.9
Package: distillML
Title: Model Distillation and Interpretability Methods for Machine Learning Models
Version: 0.1.0.9
Maintainer: Theo Saarinen <theo_s@berkeley.edu>
BugReports: https://github.com/forestry-labs/distillML/issues
URL: https://github.com/forestry-labs/distillML
Description: Provides several methods for model distillation and interpretability for general black box machine learning models and treatment effect estimation methods. For details on the algorithms implemented, see <https://forestry-labs.github.io/distillML/index.html> Brian Cho, Theo F. Saarinen, Jasjeet S. Sekhon, Simon Walter.
License: GPL (>= 3)
Encoding: UTF-8
Imports: ggplot2, glmnet, Rforestry, MASS, dplyr, R6 (>= 2.0), checkmate, purrr, tidyr, data.table, mltools, gridExtra
Suggests: testthat, knitr, rmarkdown, mvtnorm
NeedsCompilation: no
Packaged: 2022-07-06 00:08:44 UTC; theosaa
Author: Brian Cho [aut], Theo Saarinen [aut, cre], Jasjeet Sekhon [aut], Simon Walter [aut]
Repository: CRAN
Date/Publication: 2022-07-07 08:50:06 UTC

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Wed, 06 Jul 2022

New package delaunay with initial version 1.0.0
Package: delaunay
Title: 2d, 2.5d, and 3d Delaunay Tessellations
Version: 1.0.0
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Description: Construction and visualization of 2d Delaunay triangulations, possibly constrained, 2.5d (i.e. elevated) Delaunay triangulations, and 3d Delaunay triangulations.
License: GPL-3
URL: https://github.com/stla/delaunay
BugReports: https://github.com/stla/delaunay/issues
Depends: R (>= 4.2.0)
Imports: gplots, graphics, randomcoloR, Rcpp (>= 1.0.8), rgl, Rvcg, utils
Suggests: uniformly
LinkingTo: Rcpp, RcppCGAL, RcppEigen
Encoding: UTF-8
SystemRequirements: C++ 14, gmp, mpfr
OS_type: windows
NeedsCompilation: yes
Packaged: 2022-07-05 09:30:14 UTC; SDL96354
Repository: CRAN
Date/Publication: 2022-07-06 05:40:02 UTC

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New package brpop with initial version 0.1.0
Package: brpop
Title: Brazilian Population Estimatives
Version: 0.1.0
Description: Datasets with yearly (2000 to 2021) Brazilian population estimates from DataSUS/Brazilian Health Ministry, aggregated by state, municipality, sex, and age groups. The data in this package is manually downloaded from the DataSUS website (<http://tabnet.datasus.gov.br/cgi/deftohtm.exe?popsvs/cnv/popbr.def>) and converted to tibbles.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
LazyDataCompression: xz
Suggests: testthat (>= 3.0.0)
Imports: dplyr, magrittr, rlang
NeedsCompilation: no
Packaged: 2022-07-05 14:52:00 UTC; raphaelsaldanha
Author: Raphael Saldanha [aut, cre]
Maintainer: Raphael Saldanha <raphael.saldanha@icict.fiocruz.br>
Repository: CRAN
Date/Publication: 2022-07-06 05:50:02 UTC

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Tue, 05 Jul 2022

New package r5r with initial version 0.7.1
Package: r5r
Title: Rapid Realistic Routing with 'R5'
Version: 0.7.1
Description: Rapid realistic routing on multimodal transport networks (walk, bike, public transport and car) using 'R5', the Rapid Realistic Routing on Real-world and Reimagined networks engine <https://github.com/conveyal/r5>. The package allows users to generate detailed routing analysis or calculate travel time matrices using seamless parallel computing on top of the R5 Java machine. While R5 is developed by Conveyal, the package r5r is independently developed by a team at the Institute for Applied Economic Research (Ipea) with contributions from collaborators. Apart from the documentation in this package, users will find additional information on R5 documentation at <https://docs.conveyal.com/>. Although we try to keep new releases of r5r in synchrony with R5, the development of R5 follows Conveyal's independent update process. Hence, users should confirm the R5 version implied by the Conveyal user manual (see <https://docs.conveyal.com/changelog>) corresponds with the R5 version that r5r depends on.
Date: 2022-07-05
URL: https://github.com/ipeaGIT/r5r
BugReports: https://github.com/ipeaGIT/r5r/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 3.6)
Suggests: interp, covr, dplyr, ggplot2 (>= 3.3.1), knitr, mapview, rmarkdown, rgdal, testthat
Imports: checkmate, curl, data.table, httr, methods, raster, rJava (>= 0.9-10), sf (>= 0.9-3), sfheaders, utils
SystemRequirements: Java JDK (>= 11.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-05 15:22:48 UTC; user
Author: Marcus Saraiva [aut] , Rafael H. M. Pereira [cre] , Rafael H. M. Pereira [aut] , Daniel Herszenhut [aut] , Carlos Kaue Vieira Braga [aut] , Matthew Wigginton Conway [aut] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-05 22:40:05 UTC

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New package riverconn with initial version 0.3.18
Package: riverconn
Title: Common Fragmentation and Connectivity Indices for Riverscapes
Version: 0.3.18
Maintainer: Damiano Baldan <damiano.baldan91@gmail.com>
Description: Indices for assessing riverscape fragmentation, including the Dendritic Connectivity Index, the Population Connectivity Index, the River Fragmentation Index, the Probability of Connectivity, and the Integral Index of connectivity. For a review, see Jumani et al. (2020) <doi:10.1088/1748-9326/abcb37>. Functions to calculate temporal indices improvement when fragmentation due to barriers is reduced are also included.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: doParallel, dplyr, foreach, igraph, magrittr, markdown, parallel, rlang, stats, tidyr, tidyselect, dodgr, reshape2
Suggests: knitr, ggnetwork, ggplot2, viridis, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-05 06:23:36 UTC; Damiano
Author: Damiano Baldan [aut, cre] , David Cunillera-Montcusi [ctb] , Andrea Funk [ctb]
Repository: CRAN
Date/Publication: 2022-07-05 21:10:02 UTC

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New package rtiddlywiki with initial version 0.1.0
Package: rtiddlywiki
Title: R Interface for 'TiddlyWiki'
Version: 0.1.0
Author: Bangyou Zheng
Maintainer: Bangyou Zheng <Bangyou.Zheng@csiro.au>
Description: 'TiddlyWiki' is a unique non-linear notebook for capturing, organising and sharing complex information. 'rtiddlywiki' is a R interface of 'TiddlyWiki' <https://tiddlywiki.com> to create new tiddler from Rmarkdown file, and then put into a local 'TiddlyWiki' node.js server if it is available.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://rtiddlywiki.bangyou.me/, https://github.com/byzheng/rtiddlywiki
BugReports: https://github.com/byzheng/rtiddlywiki/issues
Imports: settings, httr, rmarkdown, utils, jsonlite, bookdown, stringr
Suggests: covr, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-05 03:25:48 UTC; zhe00a
Repository: CRAN
Date/Publication: 2022-07-05 21:00:02 UTC

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New package dtrackr with initial version 0.2.4
Package: dtrackr
Title: Track your Data Pipelines
Version: 0.2.4
Description: Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.
License: MIT + file LICENSE
Language: en-GB
Imports: dplyr, glue, htmltools, magrittr, rlang, rsvg, stringr, tibble, tidyr, utils, V8, fs, purrr, base64enc
Suggests: here, knitr, magick, rmarkdown, staplr, tidyverse, devtools, testthat (>= 2.1.0), rstudioapi
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-07-04 21:38:31 UTC; terminological
Author: Robert Challen [aut, cre]
Maintainer: Robert Challen <rc538@exeter.ac.uk>
Repository: CRAN
Date/Publication: 2022-07-05 21:00:09 UTC

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New package sharpeRratio with initial version 1.4.3
Package: sharpeRratio
Title: Moment-Free Estimation of Sharpe Ratios
Version: 1.4.3
Date: 2022-07-25
Author: Damien Challet
Maintainer: Damien Challet <damien.challet@gmail.com>
Description: An efficient moment-free estimator of the Sharpe ratio, or signal-to-noise ratio, for heavy-tailed data (see <arXiv:1505.01333>).
License: GPL
Depends: R (>= 3.5.0), ghyp, methods
Imports: Rcpp (>= 0.12.4)
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-07-05 14:07:50 UTC; damien
Repository: CRAN
Date/Publication: 2022-07-05 14:20:02 UTC

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New package SCCS with initial version 1.6
Package: SCCS
Title: The Self-Controlled Case Series Method
Version: 1.6
Date: 2022-07-04
Author: Yonas Ghebremichael Weldeselassie, Heather Whitaker, Paddy Farrington
Maintainer: "Yonas Ghebremichael Weldeselassie" <yonas.weldeselassie@open.ac.uk>
Description: Various self-controlled case series models used to investigate associations between time-varying exposures such as vaccines or other drugs or non drug exposures and an adverse event can be fitted. Detailed information on the self-controlled case series method and its extensions with more examples can be found in Farrington, P., Whitaker, H., and Ghebremichael Weldeselassie, Y. (2018, ISBN: 978-1-4987-8159-6. Self-controlled Case Series studies: A modelling Guide with R. Boca Raton: Chapman & Hall/CRC Press) and <https://sccs-studies.info/index.html>.
License: GPL (>= 2)
Depends: R (>= 2.14.0)
Imports: survival, splines, corpcor, fda, R.methodsS3, gnm
LazyData: yes
Packaged: 2022-07-04 22:50:06 UTC; u1673493
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-07-05 14:20:09 UTC

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New package easyalluvial with initial version 0.3.1
Package: easyalluvial
Title: Generate Alluvial Plots with a Single Line of Code
Version: 0.3.1
URL: https://github.com/erblast/easyalluvial/
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for data exploration.
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R(>= 3.5)
Suggests: testthat, covr, ISLR, nycflights13, vdiffr (>= 0.3.1), pkgdown, mlbench, earth, workflows, future, furrr, e1071, caret, parsnip, vip, rpart, glmnet, xgboost
Imports: purrr , tidyr (>= 1.0.0) , dplyr , forcats , ggalluvial (>= 0.9.1) , ggplot2 (>= 3.2.0) , ggridges , RColorBrewer , recipes (>= 0.1.5) , rlang , stringr , magrittr , tibble , gridExtra , randomForest , progressr , progress
Language: en-US
NeedsCompilation: no
Packaged: 2022-07-05 06:01:51 UTC; koneswab
Author: Bjoern Koneswarakantha [aut, cre]
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-05 07:30:08 UTC

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Mon, 04 Jul 2022

New package SensMap with initial version 0.7
Package: SensMap
Title: Sensory and Consumer Data Mapping
Version: 0.7
Date: 2022-06-29
Author: Ibtihel Rebhi [aut, cre], Dhafer Malouche [ctb]
Maintainer: Ibtihel Rebhi <ibtihel.rebhi@enit.utm.tn>
URL: https://github.com/IbtihelRebhi/SensMap
Description: Provides Sensory and Consumer Data mapping and analysis <doi:10.14569/IJACSA.2017.081266>. The mapping visualization is made available from several features : options in dimension reduction methods and prediction models ranging from linear to non linear regressions. A smoothed version of the map performed using locally weighted regression algorithm is available. A selection process of map stability is provided. A 'shiny' application is included. It presents an easy GUI for the implemented functions as well as a comparative tool of fit models using several criteria. Basic analysis such as characterization of products, panelists and sessions likewise consumer segmentation are also made available.
Depends: R (>= 4.0), stats, grDevices, graphics
Imports: doBy, lattice, FactoMineR, MCMCpack, factoextra, fields, ggdendro, glmulti, mgcv, plotly, shiny, ggplot2, reshape2
License: GPL (>= 2)
LazyData: TRUE
Suggests: testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-04 12:45:33 UTC; Ibtihel Rebhi
Repository: CRAN
Date/Publication: 2022-07-04 19:00:02 UTC

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New package RDSsamplesize with initial version 0.1.0
Package: RDSsamplesize
Title: RDS Sample Size Estimation and Power Calculation
Version: 0.1.0
Maintainer: Yibo Wang <wangyb@umich.edu>
Description: Provides functionality for carrying out sample size estimation and power calculation in Respondent-Driven Sampling.
License: GPL-3
Depends: R (>= 3.3.0)
Imports: Rcpp
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-07-03 19:21:34 UTC; Owner
Author: Yibo Wang [aut, cre], Michael R. Elliott [aut], Sunghee Lee [aut]
Suggests: knitr, rmarkdown, dplyr, ggplot2, latex2exp
VignetteBuilder: knitr
Repository: CRAN
Date/Publication: 2022-07-04 18:40:02 UTC

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New package MMINP with initial version 0.1.0
Package: MMINP
Title: Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor
Version: 0.1.0
Description: Implements a computational framework to predict microbial community-based metabolic profiles with 'O2PLS' model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.
Depends: R (>= 4.1.0)
Imports: magrittr (>= 2.0.1), OmicsPLS (>= 2.0.2), utils, stats
Suggests: rmarkdown, knitr, prettydoc, testthat (>= 3.0.0)
License: GPL (>= 3.0)
URL: https://github.com/YuLab-SMU/MMINP
BugReports: https://github.com/YuLab-SMU/MMINP/issues
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-04 03:45:54 UTC; Dell
Author: Wenli Tang [aut, cre] , Guangchuang Yu [aut, ths]
Maintainer: Wenli Tang <1071429394@qq.com>
Repository: CRAN
Date/Publication: 2022-07-04 18:50:05 UTC

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New package IntervalQuestionStat with initial version 0.1.0
Package: IntervalQuestionStat
Title: Tools to Deal with Interval-Valued Responses in Questionnaires
Version: 0.1.0
Date: 2022-07-04
Description: S4 classes, methods and functions to deal with interval-valued responses in questionnaires. They allow for computing any arithmetic and statistical operations with interval-valued data, preparing plots, transforming interval-valued responses into Likert-type and visual analogue scales responses, analysing respondents answers reliability and simulating interval-valued responses in a questionnaire.
License: LGPL (>= 3)
Author: Jose Garcia Garcia [aut, cre], Asun Lubiano [ctb]
Maintainer: Jose Garcia Garcia <garciagarjose@uniovi.es>
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
Depends: R (>= 3.5.0), methods, grDevices, graphics, stats
Packaged: 2022-07-04 12:06:58 UTC; crist
Repository: CRAN
Date/Publication: 2022-07-04 19:00:05 UTC

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New package ggseqplot with initial version 0.6.2
Package: ggseqplot
Title: Render Sequence Plots using 'ggplot2'
Version: 0.6.2
Description: A set of wrapper functions that mainly re-produces some of the sequence plots rendered with TraMineR::seqplot() and 'TraMineRextras'. Whereas 'TraMineR' uses base R to produce the plots this library draws on 'ggplot2'. The plots are produced on the basis of a sequence object defined with TraMineR::seqdef(). The package automates the reshaping and plotting of sequence data. Resulting plots are of class 'ggplot', i.e. components can be added and tweaked using '+' and regular 'ggplot2' functions.
URL: https://github.com/maraab23/ggseqplot
BugReports: https://github.com/maraab23/ggseqplot/issues
License: GPL (>= 3)
Encoding: UTF-8
Imports: colorspace, dplyr, forcats, ggh4x, ggplot2, ggrepel, ggtext, glue, patchwork, purrr, Rdpack, tidyr, TraMineR, usethis
Suggests: covr, ggthemes, hrbrthemes, knitr, rmarkdown, testthat (>= 3.0.0), TraMineRextras
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-04 11:44:24 UTC; ba3gh6
Author: Marcel Raab [aut, cre]
Maintainer: Marcel Raab <marcel.raab@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-04 18:50:01 UTC

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New package archetypal with initial version 1.3.0
Package: archetypal
Version: 1.3.0
Title: Finds the Archetypal Analysis of a Data Frame
Description: Performs archetypal analysis by using Principal Convex Hull Analysis under a full control of all algorithmic parameters. It contains a set of functions for determining the initial solution, the optimal algorithmic parameters and the optimal number of archetypes. Post run tools are also available for the assessment of the derived solution. Morup, M., Hansen, LK (2012) <doi:10.1016/j.neucom.2011.06.033>. Hochbaum, DS, Shmoys, DB (1985) <doi:10.1287/moor.10.2.180>. Eddy, WF (1977) <doi:10.1145/355759.355768>. Barber, CB, Dobkin, DP, Huhdanpaa, HT (1996) <doi:10.1145/235815.235821>. Christopoulos, DT (2016) <doi:10.2139/ssrn.3043076>. Falk, A., Becker, A., Dohmen, T., Enke, B., Huffman, D., Sunde, U. (2018), <doi:10.1093/qje/qjy013>. Christopoulos, DT (2015) <doi:10.1016/j.jastp.2015.03.009> . Murari, A., Peluso, E., Cianfrani, Gaudio, F., Lungaroni, M., (2019), <doi:10.3390/e21040394>.
Maintainer: Demetris Christopoulos <dchristop@econ.uoa.gr>
Depends: R (>= 3.1.0)
Imports: Matrix, geometry, inflection, doParallel, lpSolve, methods, plot3D, entropy
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
ByteCompile: true
NeedsCompilation: no
Packaged: 2022-07-04 10:21:26 UTC; demetris_ws
Author: Demetris Christopoulos [aut, cre], David Midgley [ctb], Sunil Venaik [ctb], INSEAD Fontainebleau France [fnd, cph]
Repository: CRAN
Date/Publication: 2022-07-04 12:30:02 UTC

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New package latrend with initial version 1.4.1
Package: latrend
Version: 1.4.1
Date: 2022-07-04
Title: A Framework for Clustering Longitudinal Data
Description: A framework for clustering longitudinal datasets in a standardized way. The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
Maintainer: Niek Den Teuling <niek.den.teuling@philips.com>
URL: https://github.com/philips-software/latrend
BugReports: https://github.com/philips-software/latrend/issues
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Language: en-US
Depends: R (>= 3.6.0)
Imports: stats, methods, Rdpack, R.utils, assertthat (>= 0.2.1), foreach, data.table (>= 1.12.0), magrittr, matrixStats, rlang, rmarkdown (>= 1.18)
Suggests: testthat (>= 3.0.0), roxygen2 (>= 7.1.0), knitr (>= 1.24), rcmdcheck, pkgdown, devtools, evaluate, lme4, covr, lintr, tinytex, longitudinalData (>= 2.4.1), kml (>= 2.4.1), lcmm (>= 1.9.3), mixtools, flexmix, fda, funFEM, gridExtra, igraph, crimCV, akmedoids (>= 1.3.0), dtwclust, mixAK, clusterCrit, mclust, mclustcomp, psych, qqplotr, doParallel, simTool, dplyr, ggplot2, caret, tibble
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-04 09:02:52 UTC; 310083353
Author: Niek Den Teuling [aut, cre] , Steffen Pauws [ctb], Edwin van den Heuvel [ctb], Copyright © 2022 Koninklijke Philips N.V. [cph]
Repository: CRAN
Date/Publication: 2022-07-04 11:50:02 UTC

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Sun, 03 Jul 2022

New package SurvivalPath with initial version 1.3.2
Package: SurvivalPath
Title: Construction and Visualization of Survival Path Tree using Time-Series Survival Data
Version: 1.3.2
Description: Facilitates building personalized survival path models. The function survivalpath() return tree structure results, which can be used to draw easily beautiful and ready-to-publish survival path tree. See Shen L, et al (2018) <doi:10.1038/s41467-018-04633-7> .
Depends: R (>= 3.6)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, ggtree, treeio, dplyr, rms, survival, survminer, survivalROC, Hmisc
Maintainer: Zhang Tao <nyy1920@163.com>
URL: https://github.com/zhangt369/SurvivalPath
NeedsCompilation: no
Packaged: 2022-07-03 08:51:44 UTC; lenovo
Author: Shen Lujun [aut, dtc], Zhang Tao [cre, cph]
Repository: CRAN
Date/Publication: 2022-07-03 18:30:05 UTC

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New package fst4pg with initial version 1.0.0
Package: fst4pg
Title: Genetic Distance Segmentation for Population Genetics
Version: 1.0.0
Date: 2022-06-15
Description: Provides efficient methods to compute local and genome wide genetic distances (corresponding to the so called Hudson Fst parameters) through moment method, perform chromosome segmentation into homogeneous Fst genomic regions, and selection sweep detection for multi-population comparison. When multiple profile segmentation is required, the procedure can be parallelized using the future package.
License: GPL (>= 2)
Depends: R (>= 2.10)
Imports: dplyr, fpopw, furrr, future, ggplot2, gplots, graphics, grDevices, purrr, rlang, scales, stats, stringr, tibble, tidyr, utils
LazyData: true
NeedsCompilation: no
Packaged: 2022-06-30 16:24:08 UTC; smoka
Author: Tristan Mary-Huard [aut, cre] , Guillem Rigaill [aut]
Maintainer: Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr>
Repository: CRAN
Date/Publication: 2022-07-03 18:20:02 UTC

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New package elastes with initial version 0.1.6
Package: elastes
Title: Elastic Full Procrustes Means for Sparse and Irregular Planar Curves
Version: 0.1.6
Description: Provides functions for the computation of functional elastic shape means over sets of open planar curves. The package is particularly suitable for settings where these curves are only sparsely and irregularly observed. It uses a novel approach for elastic shape mean estimation, where planar curves are treated as complex functions and a full Procrustes mean is estimated from the corresponding smoothed Hermitian covariance surface. This is combined with the methods for elastic mean estimation proposed in Steyer, Stöcker, Greven (2022) <doi:10.1111/biom.13706>. See Stöcker et. al. (2022) <arXiv:2203.10522> for details.
License: GPL (>= 3)
Encoding: UTF-8
Language: en-US
Imports: elasdics, utils, graphics, stats, splines, mgcv, sparseFLMM, orthogonalsplinebasis
Suggests: knitr, covr, testthat (>= 3.0.0), rmarkdown, shapes
VignetteBuilder: knitr
URL: https://mpff.github.io/elastes/
NeedsCompilation: no
Packaged: 2022-07-02 08:43:40 UTC; mnl
Author: Manuel Pfeuffer [aut, cre], Lisa Steyer [aut], Almond Stoecker [aut]
Maintainer: Manuel Pfeuffer <mnl.pfeuffer@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-03 18:20:05 UTC

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New package bsnsing with initial version 1.0.1
Package: bsnsing
Title: Build Decision Trees with Optimal Multivariate Splits
Version: 1.0.1
Author: Yanchao Liu
Maintainer: Yanchao Liu <yanchaoliu@wayne.edu>
Description: Functions for training an optimal decision tree classifier, making predictions and generating latex code for plotting. Works for two-class and multi-class classification problems. The algorithm seeks the optimal Boolean rule consisting of multiple variables to split a node, resulting in shorter trees. Use bsnsing() to build a tree, predict() to make predictions and plot() to plot the tree into latex and PDF. See Yanchao Liu (2022) <arXiv:2205.15263> for technical details. Source code and more data sets are at <https://github.com/profyliu/bsnsing/>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: methods, Rcpp (>= 1.0.3)
Suggests: C50, party, rpart, tree
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-07-03 15:16:04 UTC; gn0061
Repository: CRAN
Date/Publication: 2022-07-03 18:40:02 UTC

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New package EvaluateCore with initial version 0.1.3
Package: EvaluateCore
Title: Quality Evaluation of Core Collections
Version: 0.1.3
Description: Implements various quality evaluation statistics to assess the value of plant germplasm core collections using qualitative and quantitative phenotypic trait data according to Odong et al. (2015) <doi:10.1007/s00122-012-1971-y>.
Copyright: 2018-2022, ICAR-NBPGR
License: GPL-2 | GPL-3
Encoding: UTF-8
URL: https://github.com/aravind-j/EvaluateCore https://CRAN.R-project.org/package=EvaluateCore https://aravind-j.github.io/EvaluateCore/ https://doi.org/10.5281/zenodo.3875930
BugReports: https://github.com/aravind-j/EvaluateCore/issues
Depends: R (>= 3.5.0)
Imports: agricolae, boot, car, cluster, dplyr, entropy, ggcorrplot, ggplot2, grDevices, gridExtra, kSamples, mathjaxr, psych, reshape2, Rdpack, stats, vegan
Suggests: corehunter, pander, rJava (>= 0.9-8)
LazyData: true
NeedsCompilation: no
Packaged: 2022-06-30 12:06:32 UTC; J. Aravind
Author: J. Aravind [aut, cre] , Vikender Kaur [aut] , Dhammaprakash Pandhari Wankhede [aut] , Joghee Nanjundan [aut] , ICAR-NBGPR [cph]
Maintainer: J. Aravind <j.aravind@icar.gov.in>
Repository: CRAN
Date/Publication: 2022-07-03 12:50:02 UTC

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New package ergm.multi with initial version 0.1.0
Package: ergm.multi
Version: 0.1.0
Date: 2022-07-03
Title: Fit, Simulate and Diagnose Exponential-Family Models for Multiple or Multilayer Networks
Depends: R (>= 3.5.0), ergm (>= 4.2.2), network (>= 1.17)
Imports: statnet.common (>= 4.6.0), rlang, purrr (>= 0.2.4), tibble (>= 1.4.2), Matrix, methods, parallel, glue, rle, Rdpack (>= 0.8.2)
LinkingTo: ergm
Suggests: rmarkdown, knitr, dplyr, testthat
BugReports: https://github.com/statnet/ergm.multi/issues
Description: A set of extensions for the 'ergm' package to fit multilayer/multiplex/multirelational networks and samples of multiple networks. 'ergm.multi' is a part of the Statnet suite of packages for network analysis. See Krivitsky, Koehly, and Marcum (2020) <doi:10.1007/s11336-020-09720-7> and Krivitsky, Coletti, and Hens (2022) <doi:10.48550/arXiv.2202.03685>.
License: GPL-3 + file LICENSE
URL: https://statnet.org
VignetteBuilder: rmarkdown, knitr
Config/testthat/parallel: true
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-07-03 06:34:03 UTC; pavel
Author: Pavel N. Krivitsky [aut, cre] , Mark S. Handcock [ctb], David R. Hunter [ctb], Chad Klumb [ctb], Pietro Coletti [ctb], Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>
Repository: CRAN
Date/Publication: 2022-07-03 12:30:02 UTC

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New package woodValuationDE with initial version 1.0.1
Package: woodValuationDE
Title: Wood Valuation Germany
Version: 1.0.1
Description: Monetary valuation of wood in German forests (stumpage values), including estimations of harvest quantities, wood revenues, and harvest costs. The functions are sensitive to tree species, mean diameter of the harvested trees, stand quality, and logging method. The functions include estimations for the consequences of disturbances on revenues and costs. The underlying assortment tables are taken from Offer and Staupendahl (2018) with corresponding functions for salable and skidded volume derived in Fuchs et al. (in preparation). Wood revenue and harvest cost functions were taken from v. Bodelschwingh (2018). The consequences of disturbances refer to Dieter (2001), Moellmann and Moehring (2017), and Fuchs et al. (2022a, 2022b). For the full references see documentation of the functions, package README, and Fuchs et al. (in preparation). Apart from Dieter (2001) and Moellmann and Moehring (2017), all functions and factors are based on data from HessenForst, the forest administration of the Federal State of Hesse in Germany.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr (>= 1.0.0)
URL: https://github.com/Forest-Economics-Goettingen/woodValuationDE
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-07-02 21:26:06 UTC; Jasper Fuchs
Author: Jasper M. Fuchs [aut, cre] , Kai Husmann [aut] , Hilmar v. Bodelschwingh [ctb], Roman Koster [ctb] , Kai Staupendahl [ctb] , Armin Offer [ctb], Bernhard Moehring [ctb], Carola Paul [ctb]
Maintainer: Jasper M. Fuchs <jasper.fuchs@uni-goettingen.de>
Repository: CRAN
Date/Publication: 2022-07-03 09:10:02 UTC

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New package rdddr with initial version 1.0.0
Package: rdddr
Title: Companion Datasets and Functions for Blair, Coppock, and Humphreys (2022) "Research Design: Declare, Diagnose, Redesign"
Version: 1.0.0
Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design: Declare, Diagnose, Redesign" <https://book.declaredesign.org>. 'rdddr' includes datasets, helper functions, and plotting components to enable use and replication of the book.
Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, prediction, broom, purrr, fabricatr, estimatr, randomizr, DeclareDesign
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), rdrobust, DIDmultiplegt, broom.mixed, grf, CausalQueries, metafor, cjoint, lme4, rstanarm, spdep
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-07-03 02:40:47 UTC; gblair
Author: Graeme Blair [aut, cre] , Alexander Coppock [aut] , Macartan Humphreys [aut]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-03 09:20:02 UTC

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New package qPCRtools with initial version 0.1.1
Package: qPCRtools
Version: 0.1.1
Title: Tools for qPCR
Description: qPCR is a widely used method to detect the expression level of genes in biological research. A crucial step in processing qPCR data is to calculate the amplification efficiency of genes to determine which method should be used to calculate expression level of genes. This Package can do it easily. In addition to that, this package can calculate the expression level of genes based on three methods.
URL: https://github.com/lixiang117423/qPCRtools
BugReports: https://github.com/lixiang117423/qPCRtools/issues
License: MIT + file LICENSE
Imports: broom, data.table, dplyr, ggplot2, ggpmisc, ggthemes, magrittr, multcomp, readxl, reshape2, rstatix, sjmisc, stringr, tibble, tidyr, xlsx
NeedsCompilation: no
Packaged: 2022-07-02 17:20:39 UTC; xiang
Author: Xiang LI [cre, aut]
Maintainer: Xiang LI <lixiang117423@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-03 09:10:07 UTC

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New package ftaproxim with initial version 0.0.1
Package: ftaproxim
Title: Fault Tree Analysis Based on Proxel Simulation
Version: 0.0.1
Maintainer: Hossein Haghbin <haghbin@pgu.ac.ir>
Description: Calculation and plotting of instantaneous unavailabilities of basic events along with the top event of fault trees are issues important in reliability analysis of complex systems. Here, a fault tree is provided in terms of its minimal cut sets, along with reliability and maintainability distribution functions of the basic events. All the methods are derived from Horton (2002, ISBN: 3-936150-21-4), Niloofar and Lazarova-Molnar (2022).
License: GPL (>= 2)
Encoding: UTF-8
Imports: plyr, ggplot2
NeedsCompilation: no
Packaged: 2022-07-02 19:46:57 UTC; Hossein
Author: Parisa Niloofar [aut] , Sanja Lazarova-Molnar [aut], Hossein Haghbin [aut, cre]
Repository: CRAN
Date/Publication: 2022-07-03 09:10:09 UTC

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New package spatgeom with initial version 0.1.0
Package: spatgeom
Title: Geometric Spatial Point Analysis
Version: 0.1.0
Maintainer: Maikol Solis <maikol.solis@ucr.ac.cr>
Description: The implementation to perform the geometric spatial point analysis developed in Hernández & Solís (2022) <doi:10.1007/s00180-022-01244-1>. It estimates the geometric goodness-of-fit index for a set of variables against a response one based on the 'sf' package. The package has methods to print and plot the results.
License: MIT + file LICENSE
URL: https://github.com/maikol-solis/spatgeom
BugReports: https://github.com/maikol-solis/spatgeom/issues
Encoding: UTF-8
Imports: ggplot2, scales, sf, dplyr, lwgeom, cowplot, purrr
Depends: R (>= 3.6.0)
Suggests: rmarkdown, knitr, testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2022-07-02 11:47:40 UTC; maikol
Author: Maikol Solis [aut, cre], Alberto Hernandez [ctb], Carlos Pasquier [ctb]
Repository: CRAN
Date/Publication: 2022-07-03 09:00:02 UTC

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Sat, 02 Jul 2022

New package ANTs with initial version 0.0.16
Package: ANTs
Date: 2022-06-29
Title: Animal Network Toolkit Software
Version: 0.0.16
Description: How animals interact and develop social relationships in face of sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis (SNA), allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit 'ANTs' was developed with the aim of implementing in one package the different social network analysis techniques currently used in the study of animal social networks. Hence, ANT is a toolkit for animal research allowing among other things to: 1) measure global, dyadic and nodal networks metrics; 2) perform data randomization: pre- and post-network (node and link permutations); 3) perform statistical permutation tests as correlation test (<doi:10.2307/2332226>), t-test (<doi:10.1037/h0041412>), General Linear Model (<doi:10.2307/2346786>), General Linear Mixed Model (<doi:10.2307/2346786>), deletion simulation (<doi:10.1098/rsbl.2003.0057>), 'Matrix TauKr correlations' (<doi:10.1016/S0022-5193(05)80036-0>). The package is partially coded in C++ using the R package 'Rcpp' for an optimal coding speed. The package gives researchers a workflow from the raw data to the achievement of statistical analyses, allowing for a multilevel approach (<doi:10.1007/978-3-319-47829-6_1882-1>): from the individual's position and role within the network, to the identification of interaction patterns, and the study of the overall network properties. Furthermore, ANT also provides a guideline on the SNA techniques used: 1) from the appropriate randomization technique according to the data collected; 2) to the choice, the meaning, the limitations and advantages of the network metrics to apply, 3) and the type of statistical tests to run. The ANT project is multi-collaborative, aiming to provide access to advanced social network analysis techniques and to create new ones that meet researchers' needs in future versions. The ANT project is multi-collaborative, aiming to provide access to advanced social network analysis techniques and to create new ones that meet researchers' needs in future versions.
License: GPL (>= 3)
URL: www.s-sosa.com/softwares or https://github.com/SebastianSosa/ANTs
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
Imports: lme4,methods,Kendall,gtools,rstudioapi
LinkingTo: Rcpp,RcppArmadillo,RcppEigen
SystemRequirements: C++11
BugReports: https://github.com/SebastianSosa/ANTs
Suggests: testthat, knitr, rmarkdown, markdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-06-29 16:29:29 UTC; SSosa
Author: Sosa Sebastian [aut, cre], Puga-Gonzalez Ivan [aut], Hu Feng He [aut], Pansanel Jerome [aut], Xiaohua Xie [aut], Sueur Cedric [aut]
Maintainer: Sosa Sebastian <s.sosa@live.fr>
Repository: CRAN
Date/Publication: 2022-07-02 22:20:02 UTC

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New package vrtest with initial version 1.0
Package: vrtest
Title: Variance Ratio Tests and Other Tests for Martingale Difference Hypothesis
Version: 1.0
Date: 2022-06-29
Author: Jae H. Kim
Maintainer: Jae H. Kim <jaekim8080@gmail.com>
Description: A collection of statistical tests for martingale difference hypothesis, including automatic portmanteau test (Escansiano and Lobato, 2009) <doi:10.1016/j.jeconom.2009.03.001> and automatic variance ratio test (Kim, 2009) <doi:10.1016/j.frl.2009.04.003>.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-07-02 12:28:56 UTC; jh808
Repository: CRAN
Date/Publication: 2022-07-02 15:00:02 UTC

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New package WLogit with initial version 1.0
Package: WLogit
Title: Whitening Logistic Regression for Variable Selection
Version: 1.0
Date: 2022-07-01
Author: Wencan Zhu
Maintainer: Wencan Zhu <wencan.zhu@agroparistech.fr>
Description: It proposes a novel variable selection approach in classification problem that takes into account the correlations that may exist between the predictors of the design matrix in a high-dimensional logistic model. Our approach consists in rewriting the initial high-dimensional logistic model to remove the correlation between the predictors and in applying the generalized Lasso criterion. For further details we refer the reader to the paper Zhu et al. (2022) <arXiv:2206.14850>.
License: GPL-2
Imports: cvCovEst, genlasso, tibble, MASS, ggplot2, Matrix, glmnet, corpcor
VignetteBuilder: knitr
Suggests: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-07-02 06:05:53 UTC; mmip
Repository: CRAN
Date/Publication: 2022-07-02 12:20:02 UTC

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New package pedbp with initial version 1.0.0
Package: pedbp
Title: Pediatric Blood Pressure
Version: 1.0.0
Description: Data and utilities for estimating pediatric blood pressure percentiles by sex, age, and optionally height (stature). Blood pressure percentiles for children under one year of age come from Gemelli et.al. (1990) <doi:10.1007/BF02171556>. Estimates of blood pressure percentiles for children at least one year of age are informed by data from the National Heart, Lung, and Blood Institute (NHLBI) and the Centers for Disease Control and Prevention (CDC) <doi:10.1542/peds.2009-2107C> or from Lo et.al. (2013) <doi:10.1542/peds.2012-1292>. The flowchart for selecting the informing data source comes from Martin et.al. (2022) <doi:10.1542/hpeds.2021-005998>.
Depends: R (>= 3.5.0)
License: GPL-2
Encoding: UTF-8
URL: https://github.com/dewittpe/pedbp/
Language: en-us
LazyData: true
Imports: ggplot2, scales
Suggests: covr, data.table, DT, gridExtra, knitr, rmarkdown, shiny, shinydashboard
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-01 18:10:18 UTC; peterdewitt
Author: Peter DeWitt [aut, cre] , Blake Martin [ctb] , David Albers [ctb] , Tell Bennett [ctb]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Repository: CRAN
Date/Publication: 2022-07-02 10:10:02 UTC

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New package Missplot with initial version 0.1.0
Package: Missplot
Title: Missing Plot Technique in Design of Experiment
Version: 0.1.0
Description: A system for testing differential effects among treatments in case of Randomised Block Design and Latin Square Design when there is one missing observation. Methods for this process are as described in A.M.Gun,M.K.Gupta and B.Dasgupta(2019,ISBN:81-87567-81-3).
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-07-01 19:07:07 UTC; USER
Author: Shantanu Nayek [cre, aut], Saheli Datta [aut]
Maintainer: Shantanu Nayek <shantanuashis@gmail.com>
Repository: CRAN
Date/Publication: 2022-07-02 10:10:06 UTC

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New package ixplorer with initial version 0.2.2
Package: ixplorer
Title: Easy DataOps for R Users
Version: 0.2.2
Description: Create and view tickets in 'gitea', a self-hosted git service <https://gitea.io>, using an 'RStudio' addin, and use helper functions to publish documentation and use git.
License: AGPL (>= 3)
Depends: R (>= 3.4)
Imports: dplyr (>= 0.8.1), gitear (>= 0.0.2), kableExtra (>= 1.1.0), lubridate (>= 1.7.4), miniUI (>= 0.1.1.1), RColorBrewer (>= 1.1.2), shiny.i18n (>= 0.2.0), shiny (>= 1.3.2), stringr (>= 1.4.0), shinyWidgets (>= 0.2.1), purrr (>= 0.3.4), gert (>= 1.5.0), keyring (>= 1.3.0), methods
Suggests: knitr (>= 1.23), git2r (>= 0.30.1), here (>= 1.0.1), tibble (>= 3.1.6), readr (>= 1.3.1), rmarkdown (>= 1.12), rstudioapi (>= 0.10), testthat (>= 3.0.0), tidyr (>= 0.8.3),
VignetteBuilder: knitr
Encoding: UTF-8
URL: https://github.com/ixpantia/ixplorer
BugReports: https://github.com/ixpantia/ixplorer/issues
NeedsCompilation: no
Packaged: 2022-07-01 19:54:01 UTC; frans
Author: ixpantia, SRL [cph], Frans van Dunne [cre, aut] , Ronny Hernandez Mora [aut] , Daniel Granados Campos [ctb], Nayib Vargas Zuniga [ctb]
Maintainer: Frans van Dunne <frans@ixpantia.com>
Repository: CRAN
Date/Publication: 2022-07-02 10:20:02 UTC

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New package GPCERF with initial version 0.1.0
Package: GPCERF
Title: Gaussian Processes for Estimating Causal Exposure Response Curves
Version: 0.1.0
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Description: Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <arXiv:2105.03454>.
License: GPL (>= 3)
Language: en-US
URL: https://github.com/NSAPH-Software/GPCERF
BugReports: https://github.com/NSAPH-Software/GPCERF/issues
Copyright: Harvard University
Imports: parallel, data.table, xgboost, stats, MASS, spatstat.geom, logger, Rcpp, ggplot2, rlang, Matrix
Encoding: UTF-8
Depends: R (>= 3.5.0)
Suggests: rmarkdown, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
LinkingTo: RcppArmadillo, Rcpp
NeedsCompilation: yes
Packaged: 2022-06-30 14:33:22 UTC; nak443
Author: Naeem Khoshnevis [aut, cre] , Boyu Ren [aut] , Tanujt Dey [ctb] , Danielle Braun [aut]
Repository: CRAN
Date/Publication: 2022-07-02 09:50:02 UTC

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Fri, 01 Jul 2022

New package VAR.etp with initial version 1.0
Package: VAR.etp
Title: VAR Modelling: Estimation, Testing, and Prediction
Version: 1.0
Date: 2022-06-29
Author: Jae. H. Kim
Maintainer: Jae H. Kim <jaekim8080@gmail.com>
Description: A collection of the functions for estimation, hypothesis testing, prediction for stationary vector autoregressive models.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-06-30 10:32:41 UTC; jh808
Repository: CRAN
Date/Publication: 2022-07-01 21:50:02 UTC

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New package GHap with initial version 3.0.0
Package: GHap
Title: Genome-Wide Haplotyping
Version: 3.0.0
Date: 2022-06-30
Author: Yuri Tani Utsunomiya, Andre Vieira do Nascimento, Marco Milanesi, Mario Barbato
Maintainer: Yuri Tani Utsunomiya <ytutsunomiya@gmail.com>
Description: Haplotype calling from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers. The package was first described in Bioinformatics by Utsunomiya et al. (2016, <doi:10.1093/bioinformatics/btw356>). Since the v2 release, the package provides functions for unsupervised and supervised detection of ancestry tracks. The methods implemented in these functions were described in an article published in Methods in Ecology and Evolution by Utsunomiya et al. (2020, <doi:10.1111/2041-210X.13467>). The source code for v3 was modified for improved performance and inclusion of new functionality, including analysis of unphased data, runs of homozygosity, sampling methods for virtual gamete mating, mixed model fitting and GWAS.
License: GPL (>= 2)
Imports: parallel (>= 3.4.4), Matrix (>= 1.2-16), methods (>= 3.4.4), pedigreemm (>= 0.3-3), sparseinv (>= 0.1.3), e1071 (>= 1.7-0.1), class (>= 7.3-15), data.table (>= 1.12.6), stringi (>= 1.7.6)
VignetteBuilder: R.rsp
Suggests: R.rsp
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-30 12:41:55 UTC; yuri
Repository: CRAN
Date/Publication: 2022-07-01 21:50:05 UTC

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New package RcppColors with initial version 0.1.0
Package: RcppColors
Title: 'C++' Header Files for Color Conversion and Color Mappings
Version: 0.1.0
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Description: Provides 'C++' header files to deal with color conversion from some color spaces to hexadecimal with 'Rcpp', and exports some color mapping functions for usage in R. Also exports functions to convert colors from the 'HSLuv' color space for usage in R. 'HSLuv' is a human-friendly alternative to HSL.
License: GPL-3
URL: https://github.com/stla/RcppColors
BugReports: https://github.com/stla/RcppColors/issues
Imports: Rcpp (>= 1.0.8)
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-06-30 07:46:03 UTC; SDL96354
Author: Stephane Laurent [cre, aut], Scott Spencer [aut]
Repository: CRAN
Date/Publication: 2022-07-01 16:10:05 UTC

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New package mapiso with initial version 0.1.1
Package: mapiso
Title: Create Contour Polygons from Regular Grids
Version: 0.1.1
Description: Regularly spaced grids containing continuous data are transformed to contour polygons. A grid can be defined by a data.frame (x, y, value), an 'sf' object or a raster from 'terra'.
URL: https://github.com/riatelab/mapiso
BugReports: https://github.com/riatelab/mapiso/issues/
Depends: R (>= 3.6.0)
Imports: sf, isoband
Suggests: covr, mapsf, terra, tinytest
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-30 14:13:52 UTC; tim
Author: Timothee Giraud [cre, aut]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Repository: CRAN
Date/Publication: 2022-07-01 16:10:02 UTC

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New package rfVarImpOOB with initial version 1.0.3
Package: rfVarImpOOB
Title: Unbiased Variable Importance for Random Forests
Version: 1.0.3
Date: 2022-06-30
Depends: R (>= 3.2.2), stats, randomForest
Imports: ggplot2, ggpubr, dplyr,titanic,magrittr,ranger
Suggests: knitr,rmarkdown
Author: Markus Loecher <Markus.Loecher@gmail.com>
Maintainer: Markus Loecher <Markus.Loecher@gmail.com>
Description: Computes a novel variable importance for random forests: Impurity reduction importance scores for out-of-bag (OOB) data complementing the existing inbag Gini importance, see also <doi: 10.1080/03610926.2020.1764042>. The Gini impurities for inbag and OOB data are combined in three different ways, after which the information gain is computed at each split. This gain is aggregated for each split variable in a tree and averaged across trees.
License: GPL (>= 2)
Repository: CRAN
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-07-01 08:16:57 UTC; loecherm
Date/Publication: 2022-07-01 14:40:02 UTC

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New package ParallelDSM with initial version 0.3.3
Package: ParallelDSM
Title: Parallel Digital Soil Mapping using Machine Learning
Version: 0.3.3
Description: Parallel computing, multi-core CPU is used to efficiently compute and process multi-dimensional soil data.This package includes the parallelized 'Quantile Regression Forests' algorithm for Digital Soil Mapping and is mainly dependent on the package 'quantregForest' and 'snowfall'. Detailed references to the R package and the web site are described in the methods, as detailed in the method documentation.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), snowfall, raster, sp
Imports: methods, pryr, utils, caret, gstat, quantregForest, randomForest, stringr, rgdal, stats,
NeedsCompilation: no
Packaged: 2022-07-01 10:28:11 UTC; tpc
Author: Xiaodong Song [aut], Peicong Tang [aut, cre], Wentao Zhu [aut], Gaoqiang Ge [aut], Jun Zhu [aut], Ganlin Zhang [aut]
Maintainer: Peicong Tang <peicongtang0409@163.com>
Repository: CRAN
Date/Publication: 2022-07-01 14:40:04 UTC

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New package tipmap with initial version 0.1.1
Package: tipmap
Title: Tipping Point Analysis for Bayesian Dynamic Borrowing
Version: 0.1.1
Description: Tipping point analysis for clinical trials that employ Bayesian dynamic borrowing via robust meta-analytic predictive (MAP) priors. Mainly an implementation of an approach proposed by Best and colleagues (2021) <doi:10.1002/pst.2093> is provided. Further functions facilitate the specification of the robust MAP prior via expert elicitation (using the roulette method) and computation of the posterior distribution of the treatment effect with either fixed or stochastic expert-elicited weights. Intended use is the planning, analysis and interpretation of extrapolation studies in pediatric drug development, but applicability is generally wider.
License: GPL (>= 3)
Encoding: UTF-8
Imports: dplyr, ggplot2, RBesT, SHELF, purrr
Suggests: knitr, meta, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-06-29 16:38:19 UTC; stockch
Author: Morten Dreher [aut], Christian Stock [cre]
Maintainer: Christian Stock <christian.stock@boehringer-ingelheim.com>
Repository: CRAN
Date/Publication: 2022-07-01 10:40:02 UTC

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New package scAnnotate with initial version 0.0.1
Package: scAnnotate
Title: An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data
Version: 0.0.1
Description: An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.
Depends: R(>= 4.0.0)
License: GPL-3
URL: https://doi.org/10.1101/2022.02.19.481159
Encoding: UTF-8
LazyData: true
Suggests: knitr, testthat (>= 3.0.0), rmarkdown
VignetteBuilder: knitr
Imports: glmnet, stats, MTPS, Seurat (>= 4.0.5), harmony
NeedsCompilation: no
Packaged: 2022-06-30 00:58:42 UTC; 54041
Author: Xiangling Ji [aut], Danielle Tsao [aut], Kailun Bai [ctb], Min Tsao [aut], Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Repository: CRAN
Date/Publication: 2022-07-01 11:00:02 UTC

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New package CREDS with initial version 0.1.0
Package: CREDS
Title: Calibrated Ratio Estimator under Double Sampling Design
Version: 0.1.0
Author: Dr. Sadikul Islam [aut, cre], Dr. Md Yeasin [aut], Dr. M. Muruganandam [aut], Dr. M. Madhu [aut]
Maintainer: Dr. Sadikul Islam <sadikul.islamiasri@gmail.com>
Description: Population ratio estimator (calibrated) under two-phase random sampling design has gained enormous popularity in the recent time. This package provides functions for estimation population ratio (calibrated) under two phase sampling design, including the approximate variance of the ratio estimator. The improved ratio estimator can be applicable for both the case, when auxiliary data is available at unit level or aggregate level (eg., mean or total) for first phase sampled. Calibration weight of each unit of the second phase sample was calculated. Single and combined inclusion probabilities were also estimated for both phases under two phase random [simple random sampling without replacement (SRSWOR)] sampling. The improved ratio estimator's percentage coefficient of variation was also determined as a measure of accuracy. This package has been developed based on the theoretical development of Islam et al. (2021) and Ozgul (2020) <doi:10.1080/00949655.2020.1844702>.
License: GPL-3
Encoding: UTF-8
Imports: MASS, stats
NeedsCompilation: no
Packaged: 2022-06-29 17:03:45 UTC; YEASIN
Repository: CRAN
Date/Publication: 2022-07-01 10:50:01 UTC

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Thu, 30 Jun 2022

New package VariantScan with initial version 1.1.9
Package: VariantScan
Version: 1.1.9
Date: 2022-06-25
Title: A Machine Learning Tool for Genetic Association Studies
Description: Portable, scalable and highly computationally efficient tool for genetic association studies."VariantScan" provides a set of machine learning methods (Linear, Local Polynomial Regression Fitting and Generalized Additive Model with Local Polynomial Smoothing) for genetic association studies that test for disease or trait association with genetic variants (biomarkers, e.g.,genomic (genetic loci), transcriptomic (gene expressions), epigenomic (methylations), proteomic (proteins), metabolomic (metabolites)). It is particularly useful when local associations and complex nonlinear associations exist.
Maintainer: Xinghu Qin <qin.xinghu@163.com>
Depends: R (>= 3.0)
License: GPL (>= 3)
SystemRequirements: GNU make
URL: https://github.com/xinghuq/VariantScan
BugReports: https://github.com/xinghuq/VariantScan/issues
Imports: stats,SNPRelate,caret,gam,ModelMetrics
VignetteBuilder: knitr
NeedsCompilation: no
Suggests: knitr,testthat,rmarkdown,ggplot2
Packaged: 2022-06-29 02:19:41 UTC; Qin_st_andrews
Author: Xinghu Qin [aut, cre, cph] , Tianzi Liu [aut], Peilin Jia [aut]
Repository: CRAN
Date/Publication: 2022-06-30 11:50:06 UTC

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New package TrendTM with initial version 2.0.14
Package: TrendTM
Title: Trend of High-Dimensional Time Series Matrix Estimation
Version: 2.0.14
Date: 2022-06-01
Author: Emilie Lebarbier [aut, cre], Nicolas Marie [aut], Amelie Rosier [aut, cre].
Maintainer: Emilie Lebarbier <emilie.lebarbier@parisnanterre.fr>
Description: Matrix factorization for multivariate time series with both low rank and temporal structures. The procedure is the one proposed by Alquier, P. and Marie, N. Matrix factorization for multivariate time series analysis. Electronic journal of statistics, 13(2), 4346-4366 (2019).
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: softImpute, capushe, fda
NeedsCompilation: no
Packaged: 2022-06-29 11:54:43 UTC; lebarbier
Repository: CRAN
Date/Publication: 2022-06-30 12:00:02 UTC

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New package TimeVarConcurrentModel with initial version 1.0
Package: TimeVarConcurrentModel
Title: Concurrent Multivariate Models with Time-Varying Coefficients
Version: 1.0
Date: 2022-06-23
Imports: Bolstad2, fda
Description: Provides a hypothesis test and variable selection algorithm for use in time-varying, concurrent regression models. The hypothesis test function is also accompanied by a plotting function which will show the estimated beta(s) and confidence band(s) from the hypothesis test. The hypothesis test function helps the user identify significant covariates within the scope of a time-varying concurrent model. The plots will show the amount of area that falls outside the confidence band(s) which is used for the test statistic within the hypothesis test.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-06-28 22:04:03 UTC; leave
Author: Adriano Zambom [aut], Chance Vandergeugten [aut, cre]
Maintainer: Chance Vandergeugten <leaveitalltochance@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-30 11:40:05 UTC

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New package rflashtext with initial version 0.1.0
Package: rflashtext
Title: FlashText Algorithm for Finding and Replacing Words
Version: 0.1.0
Description: Implementation of the FlashText algorithm, by Singh (2017) <arXiv:1711.00046>. It can be used to find and replace words in a given text with only one pass over the document.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
URL: https://github.com/AbrJA/rflashtext
BugReports: https://github.com/AbrJA/rflashtext/issues
Imports: R6
NeedsCompilation: no
Packaged: 2022-06-28 21:50:03 UTC; ajaimes
Author: Abraham Jaimes [aut, cre]
Maintainer: Abraham Jaimes <ajaimes@occ.com.mx>
Repository: CRAN
Date/Publication: 2022-06-30 11:40:02 UTC

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New package accessibility with initial version 0.1.0
Package: accessibility
Title: Transport Accessibility Metrics
Version: 0.1.0
Description: A set of fast and convenient functions to calculate multiple transport accessibility measures. Given a pre-computed travel cost matrix in long format combined with land-use data (e.g. location of jobs, healthcare, population), the package allows one to calculate active and passive accessibility levels using multiple accessibility metrics such as: cumulative opportunity measure (using either travel time cutoff or interval), minimum travel cost to closest N number of activities, gravitational measures and different floating catchment area methods.
License: MIT + file LICENSE
URL: https://github.com/ipeaGIT/accessibility
BugReports: https://github.com/ipeaGIT/accessibility/issues
Depends: R (>= 3.5.0)
Imports: checkmate, data.table, utils
Suggests: covr, ggplot2, knitr, r5r, rmarkdown, sf, stats, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-29 11:27:31 UTC; user
Author: Rafael H. M. Pereira [aut, cre] , Daniel Herszenhut [aut] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-30 11:50:02 UTC

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New package yfR with initial version 1.0.0
Package: yfR
Title: Downloads and Organizes Financial Data from Yahoo Finance
Version: 1.0.0
Description: Facilitates download of financial data from Yahoo Finance <https://finance.yahoo.com/>, a vast repository of stock price data across multiple financial exchanges. The package offers a local caching system and support for parallel computation.
URL: https://github.com/ropensci/yfR, https://docs.ropensci.org/yfR/
BugReports: https://github.com/ropensci/yfR/issues
Depends: R (>= 4.0.0)
Imports: stringr, curl, tidyr, lubridate, furrr, purrr, future, tibble, zoo, cli, readr, rvest, dplyr, quantmod (>= 0.4.20), magrittr, humanize, methods
License: MIT + file LICENSE
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, covr, spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-06-28 19:10:05 UTC; msperlin
Author: Marcelo Perlin [aut, cre], Nic Crane [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/523>), Alexander Fischer [rev] for rOpenSci, see <https://github.com/ropensci/software-review/issues/523>)
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-30 06:20:02 UTC

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New package scISR with initial version 0.1.1
Package: scISR
Title: Single-Cell Imputation using Subspace Regression
Version: 0.1.1
Maintainer: Duc Tran <duct@nevada.unr.edu>
Description: Provides an imputation pipeline for single-cell RNA sequencing data. The 'scISR' method uses a hypothesis-testing technique to identify zero-valued entries that are most likely affected by dropout events and estimates the dropout values using a subspace regression model (Tran et.al. (2022) <DOI:10.1038/s41598-022-06500-4>).
License: LGPL
Depends: R (>= 3.4)
Imports: cluster, entropy, stats, utils, parallel, irlba, PINSPlus, matrixStats, markdown
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Suggests: testthat, knitr, mclust
VignetteBuilder: knitr
URL: https://github.com/duct317/scISR
BugReports: https://github.com/duct317/scISR/issues
Packaged: 2022-06-28 19:32:08 UTC; dtran
Author: Duc Tran [aut, cre], Bang Tran [aut], Hung Nguyen [aut], Tin Nguyen [fnd]
Repository: CRAN
Date/Publication: 2022-06-30 06:20:08 UTC

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New package sciRmdTheme with initial version 0.1
Package: sciRmdTheme
Title: Upgraded 'Rmarkdown' Themes for Scientific Writing
Version: 0.1
Author: Obinna Obianom
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Description: A set of 'Rmarkdown' themes for creating scientific and professional documents. Simple interface with features to ease navigation across the page and sub-pages.
License: MIT + file LICENSE
URL: https://github.com/oobianom/sciRmdTheme
BugReports: https://github.com/oobianom/sciRmdTheme
Depends: R (>= 3.4)
Imports: utils
Suggests: rmarkdown, knitr
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2022-06-28 21:25:29 UTC; in198
Repository: CRAN
Date/Publication: 2022-06-30 06:20:06 UTC

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New package farr with initial version 0.2.27
Package: farr
Title: Data and Code for Financial Accounting Research
Version: 0.2.27
Description: Provides handy functions and data to support a course book for accounting research. Gow, Ian and Tongqing Ding (2022) "Accounting Research: An Introductory Course" <https://iangow.github.io/far_book/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dbplyr (>= 2.2.0), dplyr, magrittr, rlang, tidyr, tibble, readr, stringr, DBI, lubridate
Depends: R (>= 3.5.0)
Suggests: RPostgres, knitr, rmarkdown, testthat (>= 3.0.0), spelling
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-06-28 16:41:11 UTC; igow
Author: Ian Gow [aut, cre]
Maintainer: Ian Gow <iandgow@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-30 06:10:02 UTC

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New package extrafrail with initial version 1.0
Package: extrafrail
Title: Estimation and Additional Tools for Alternative Multivariate Frailty Models
Version: 1.0
Date: 2022-06-09
Author: Diego Gallardo [aut, cre], Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Description: Provide estimation and data generation tools for some new multivariate frailty models. This initial version includes only the weighted Lindley as the distribution for the frailty terms. For the basal model, it is considered a parametric approach based on the Weibull distribution and a semiparametric approach. For details, see Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Depends: R (>= 4.0.0), stats
Imports: survival, pracma
Suggests: frailtypack
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-06-28 16:49:30 UTC; Usuario
Repository: CRAN
Date/Publication: 2022-06-30 06:10:07 UTC

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Wed, 29 Jun 2022

New package BootPR with initial version 0.70
Package: BootPR
Title: Bootstrap Prediction Intervals and Bias-Corrected Forecasting
Version: 0.70
Date: 2022-06-29
Author: Jae. H. Kim <jaekim8080@gmail.com>
Maintainer: Jae H. Kim <jaekim8080@gmail.com>
Description: Contains functions for bias-Corrected Forecasting and Bootstrap Prediction Intervals for Autoregressive Time Series.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-06-29 13:11:15 UTC; jh808
Repository: CRAN
Date/Publication: 2022-06-29 16:10:16 UTC

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New package bandit with initial version 0.5.1
Package: bandit
Title: Functions for Simple a/B Split Test and Multi-Armed Bandit Analysis
Version: 0.5.1
Date: 2022-06-028
Imports: boot, gam (>= 1.09)
Author: Thomas Lotze and Markus Loecher
Maintainer: Markus Loecher <markus.loecher@gmail.com>
Description: A set of functions for doing analysis of A/B split test data and web metrics in general.
License: GPL-3
NeedsCompilation: no
Repository: CRAN
Packaged: 2022-06-28 16:06:35 UTC; loecherm
Date/Publication: 2022-06-29 11:20:12 UTC

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Tue, 28 Jun 2022

New package statcodelists with initial version 0.9.2
Package: statcodelists
Title: Use Standardized Statistical Codelists
Version: 0.9.2
Description: The goal of statcodelists is to promote the reuse and exchange of statistical information and related metadata with making the internationally standardized SDMX code lists available for the R user. SDMX has been published as an ISO International Standard (ISO 17369). The metadata definitions, including the codelists are updated regularly according to the standard. The authoritative version of the code lists made available in this package is <https://sdmx.org/?page_id=3215/>.
Language: en-US
License: CC0
URL: https://statcodelists.dataobservatory.eu, https://github.com/antaldaniel
BugReports: https://github.com/antaldaniel/statcodelists/issues
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Suggests: spelling
NeedsCompilation: no
Packaged: 2022-06-28 08:19:42 UTC; Daniel Antal
Author: Daniel Antal [aut, cre]
Maintainer: Daniel Antal <daniel.antal@dataobservatory.eu>
Repository: CRAN
Date/Publication: 2022-06-28 16:20:02 UTC

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New package spectralR with initial version 0.1.2
Package: spectralR
Title: Obtain and Visualize Spectral Reflectance Data for Earth Surface Polygons
Version: 0.1.2
Description: Tools for obtaining, processing, and visualizing spectral reflectance data for the user-defined land or water surface classes for visual exploring in which wavelength the classes differ. Input should be a shapefile with polygons of surface classes (it might be different habitat types, crops, vegetation, etc.). The Sentinel-2 L2A satellite mission optical bands pixel data are obtained through the Google Earth Engine service (<https://earthengine.google.com/>) and used as a source of spectral data.
Depends: R (>= 4.1.0)
Imports: rgee (>= 1.1.3), geojsonio (>= 0.9.4), sf (>= 1.0-7), dplyr (>= 1.0.9), ggplot2 (>= 3.3.5), reshape2 (>= 1.4.0), rlang (>= 1.0.0), tibble (>= 3.1.0), tidyr (>= 1.2.0)
Suggests: tinytest (>= 1.3.0)
License: GPL-3
URL: https://github.com/olehprylutskyi/spectralR/
BugReports: https://github.com/olehprylutskyi/spectralR/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-28 08:49:51 UTC; mik
Author: Oleh Prylutskyi [aut, cre], Dariia Shyriaieva [ctb], Vladimir Mikryukov [ctb]
Maintainer: Oleh Prylutskyi <oleh.prylutskyi@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-28 16:30:02 UTC

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New package segen with initial version 1.0.0
Package: segen
Title: Sequence Generalization Through Similarity Network
Version: 1.0.0
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Description: Proposes an application for sequence prediction generalizing the similarity within the network of previous sequences.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6)
Imports: purrr (>= 0.3.4), ggplot2 (>= 3.3.5), readr (>= 2.1.2), lubridate (>= 1.7.10), imputeTS (>= 3.2), fANCOVA (>= 0.6-1), scales (>= 1.1.1), tictoc (>= 1.0.1), modeest (>= 2.4.0), moments (>= 0.14), greybox (>= 1.0.1), philentropy (>= 0.5.0), entropy (>= 1.3.1), Rfast (>= 2.0.6), narray (>= 0.4.1.1)
URL: https://rpubs.com/giancarlo_vercellino/segen
NeedsCompilation: no
Packaged: 2022-06-28 08:08:25 UTC; gvercellino
Repository: CRAN
Date/Publication: 2022-06-28 16:20:05 UTC

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New package kmscv with initial version 0.1.0
Package: kmscv
Title: K-Means Based Stratified Resampling
Version: 0.1.0
Description: An 'rsample' extension to create cluster based stratified resamples for cross-validation.
License: GPL (>= 3)
Encoding: UTF-8
Imports: parsnip,rsample,tibble,purrr,dplyr
BugReports: https://github.com/sametsoekel/kmscv/issues
NeedsCompilation: no
Packaged: 2022-06-28 07:27:37 UTC; samet.sokel
Author: Samet Sokel [aut, cre]
Maintainer: Samet Sokel <a_s@eskisehir.edu.tr>
Repository: CRAN
Date/Publication: 2022-06-28 16:20:08 UTC

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New package xQTLbiolinks with initial version 1.0.0
Package: xQTLbiolinks
Title: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'GTEx'
Version: 1.0.0
Description: User can query, download, and visualize of molecular quantitative trait locus and gene expression data from public resources through the application programming interface <https://gtexportal.org/home/api-docs/index.html> of 'GTEx'.
URL: https://github.com/dingruofan/xQTLbiolinks
BugReports: https://github.com/dingruofan/xQTLbiolinks/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.00)
VignetteBuilder: knitr
Imports: BiocGenerics, cowplot (>= 1.1.1), curl (>= 4.3.2), data.table (>= 1.14.2), DBI, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.3.6), ggrepel, ggridges, httr, IRanges, jsonlite (>= 1.7.2), PupillometryR, RMySQL, scales, stringr (>= 1.4.0), SummarizedExperiment (>= 1.4.0), utils (>= 4.0.3), viridis
Suggests: coloc, knitr, rtracklayer, usethis
NeedsCompilation: no
Packaged: 2022-06-27 19:19:29 UTC; DELL
Author: Ruofan Ding [aut, cre], Xudong Zou [aut, ctb], Yangmei Qin [aut, ctb], Gao Wang [aut, ctb], Lei Li [aut, ctb, cph]
Maintainer: Ruofan Ding <dingruofan1@foxmail.com>
Repository: CRAN
Date/Publication: 2022-06-28 16:00:02 UTC

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New package WeibullR.ALT with initial version 0.7.2
Package: WeibullR.ALT
Title: Accelerated Life Testing Using 'WeibullR'
Version: 0.7.2
Date: 2022-6-27
Description: Graphical data analysis of accelerated life tests. Methods derived from Wayne Nelson (1990, ISBN: 9780471522775), William Q. Meeker and Lois A. Escobar (1998, ISBN: 1-471-14328-6).
License: GPL (>= 3)
Copyright: copyright (c) OpenReliability.org 2022
Author: David Silkworth [aut], Jacob Ormerod [cre], OpenReliability.org [cph]
Depends: R (>= 3.5.0), WeibullR, methods
URL: http://www.openreliability.org/weibull-r-weibull-analysis-on-r/
LazyLoad: yes
NeedsCompilation: no
Packaged: 2022-06-27 15:23:15 UTC; djsil
Maintainer: Jacob Ormerod <jake@openreliability.org>
Repository: CRAN
Date/Publication: 2022-06-28 15:50:06 UTC

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New package tcgaViz with initial version 1.0.0
Package: tcgaViz
Title: Visualization Tool for the Cancer Genome Atlas Program (TCGA)
Version: 1.0.0
Description: Differential analysis of tumor tissue immune cell type abundance based on RNA-seq gene-level expression from The Cancer Genome Atlas (TCGA; <https://pancanatlas.xenahubs.net>) database.
License: GPL-3
Depends: R (>= 2.10)
Imports: config, data.table, dplyr, DT, ggplot2, ggpubr, golem, grDevices, magrittr, methods, openxlsx, plotly, readr, reshape2, rlang, rstatix, shiny, shinyFeedback, shinyjs, stats, stringr, tidyr, tidyselect, utils
Suggests: BiocCheck, covr, knitr, rmarkdown, spelling, testthat
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: false
NeedsCompilation: no
Packaged: 2022-06-27 14:26:10 UTC; rstudio
Author: Etienne Camenen [aut, cre], Gilles Marodon [aut], Nicolas Aubert [aut]
Maintainer: Etienne Camenen <etienne.camenen@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-28 15:50:02 UTC

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New package qsplines with initial version 0.1.0
Package: qsplines
Title: Quaternions Splines
Version: 0.1.0
Description: Provides routines to create some quaternions splines: Barry-Goldman algorithm, De Casteljau algorithm, and Kochanek-Bartels algorithm. The implementations are based on the Python library 'splines'. Quaternions splines allow to construct spherical curves. References: Barry and Goldman <doi:10.1145/54852.378511>, Kochanek and Bartels <doi:10.1145/800031.808575>.
License: GPL-3
URL: https://github.com/stla/qsplines
BugReports: https://github.com/stla/qsplines/issues
Depends: onion
Imports: shiny, stats, utils
Suggests: rgl
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-27 08:54:43 UTC; SDL96354
Author: Stephane Laurent [aut, cre], Matthias Geier [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Repository: CRAN
Date/Publication: 2022-06-28 15:30:02 UTC

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New package OBL with initial version 0.1.0
Package: OBL
Title: Optimum Block Length
Version: 0.1.0
Maintainer: Daniel James <futathesis@gmail.com>
Description: Obtain optimum block from Non-overlapping Block Bootstrap method.
Depends: R (>= 4.2.0)
Imports: forecast, foreach, doParallel, parallel, future, utils, stats, tibble
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-06-27 18:13:56 UTC; economia
Author: Daniel James [cre, aut], Ayinde Kayode [aut]
Repository: CRAN
Date/Publication: 2022-06-28 16:00:05 UTC

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New package IDEAFilter with initial version 0.1.2
Package: IDEAFilter
Version: 0.1.2
Title: Agnostic, Idiomatic Data Filter Module for Shiny
Description: When added to an existing shiny app, users may subset any developer-chosen R data.frame on the fly. That is, users are empowered to slice & dice data by applying multiple (order specific) filters using the AND (&) operator between each, and getting real-time updates on the number of rows effected/available along the way. Thus, any downstream processes that leverage this data source (like tables, plots, or statistical procedures) will re-render after new filters are applied. The shiny module’s user interface has a 'minimalist' aesthetic so that the focus can be on the data & other visuals. In addition to returning a reactive (filtered) data.frame, 'IDEAFilter' as also returns 'dplyr' filter statements used to actually slice the data.
License: AGPL-3
URL: https://biogen-inc.github.io/IDEAFilter/
BugReports: https://github.com/Biogen-Inc/IDEAFilter/issues
Encoding: UTF-8
Imports: shiny, ggplot2, pillar (>= 1.5.0), crayon, RColorBrewer, shinyTime, purrr
Suggests: shinytest, shinytest2, testthat, knitr, rmarkdown, spelling, dplyr
Language: en-US
NeedsCompilation: no
Packaged: 2022-06-27 15:53:49 UTC; aclark5
Author: Aaron Clark [aut, cre] , Doug Kelkhoff [aut], Maya Gans [ctb], Jeff Thompson [ctb], Biogen [cph]
Maintainer: Aaron Clark <clark.aaronchris@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-28 15:50:08 UTC

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New package bentcableAR with initial version 0.3.1
Package: bentcableAR
Title: Bent-Cable Regression for Independent Data or Autoregressive Time Series
Version: 0.3.1
Date: 2022-06-27
Author: Grace Chiu <bentcable@gmail.com>, Virginia Institute of Marine Science, William & Mary PO Box 1346, Gloucester Point, VA 23062, USA
Maintainer: Grace Chiu <bentcable@gmail.com>
Description: Included are two main interfaces, bentcable.ar() and bentcable.dev.plot(), for fitting and diagnosing bent-cable regressions for autoregressive time-series data (Chiu and Lockhart 2010, <doi:10.1002/cjs.10070>) or independent data (time series or otherwise - Chiu, Lockhart and Routledge 2006, <doi:10.1198/016214505000001177>). Some components in the package can also be used as stand-alone functions. The bent cable (linear-quadratic-linear) generalizes the broken stick (linear-linear), which is also handled by this package. Version 0.2 corrected a glitch in the computation of confidence intervals for the CTP. References that were updated from Versions 0.2.1 and 0.2.2 appear in Version 0.2.3 and up. Version 0.3.0 improved robustness of the error-message producing mechanism. Version 0.3.1 improves the NAMESPACE file of the package. It is the author's intention to distribute any future updates via GitHub.
License: GPL (>= 3)
Packaged: 2022-06-28 02:13:33 UTC; gschiu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-06-28 10:40:02 UTC

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New package ecostats with initial version 1.1.10
Package: ecostats
Title: Code and Data Accompanying the Eco-Stats Text (Warton 2022)
Version: 1.1.10
Date: 2022-06-28
Description: Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.
License: LGPL (>= 2.1)
Imports: ecoCopula, GET, graphics, grDevices, MASS, mgcv, mvtnorm, stats
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), mvabund (>= 4.2)
Suggests: knitr, rmarkdown, ade4, caper, car, corrplot, DAAG, DHARMa, dplyr, ecomix, gclus, GGally, ggplot2, ggthemes, glmnet, gllvm, glmmTMB, GPArotation, grplasso, lattice, leaps, lme4, MCMCglmm, multcomp, nlme, ordinal, permute, pgirmess, phylobase, phylosignal, psych, reshape2, smatr, testthat, vegan, VGAM
Additional_repositories: https://dwarton.github.io/drat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-06-28 07:10:35 UTC; z3103495
Author: David Warton [aut, cre], Christopher Chung [ctb], Mark Donoghoe [ctb], Eve Slavich [ctb]
Maintainer: David Warton <david.warton@unsw.edu.au>
Repository: CRAN
Date/Publication: 2022-06-28 09:30:02 UTC

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New package VisualizeSimon2Stage with initial version 0.1.0
Package: VisualizeSimon2Stage
Title: Visualize Simon's Two-Stage Design
Version: 0.1.0
Date: 2022-06-26
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Description: Functions for visualizing the probabilities of early termination, fail and success of Simon's two-stage design. Functions for evaluating and visualizing the operating characteristics of Simon's two-stage design.
License: GPL-2
Imports: methods
Encoding: UTF-8
Language: en-US
Depends: R (>= 4.2.0),ggplot2
Suggests: clinfun
NeedsCompilation: no
Packaged: 2022-06-26 20:32:48 UTC; txz003
Repository: CRAN
Date/Publication: 2022-06-28 07:20:05 UTC

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New package odns with initial version 1.0.0
Package: odns
Title: Access Scottish Health and Social Care Open Data
Version: 1.0.0
Description: Allows potential users of Scottish Health and Social Care Open Data (<https://www.opendata.nhs.scot/>) to easily explore and extract the available data.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: glue, httr, utils, data.table, methods, jsonlite
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), mockery, digest
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-06-27 08:02:31 UTC; friday
Author: James Hardy [aut, cre]
Maintainer: James Hardy <jrh-dev@protonmail.com>
Repository: CRAN
Date/Publication: 2022-06-28 07:30:02 UTC

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New package hdtg with initial version 0.1.0
Package: hdtg
Title: Generate Samples from Multivariate Truncated Normal Distributions
Version: 0.1.0
Maintainer: Zhenyu Zhang <zhangzhenyusa@gmail.com>
Description: Efficient sampling from high-dimensional truncated Gaussian distributions (so comes the package name hdtg). Techniques include zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and Marc A. Suchard (2021) <arXiv:2104.07694>, and harmonic Hamiltonian Monte Carlo in Ari Pakman and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Rcpp, RcppParallel, RcppXsimd, mgcv, stats, Rdpack
LinkingTo: Rcpp, RcppEigen, RcppParallel, RcppXsimd
SystemRequirements: C++14
NeedsCompilation: yes
Packaged: 2022-06-26 21:02:33 UTC; zhenyuzhang
Author: Zhenyu Zhang [aut, cre], Andrew Chin [aut], Akihiko Nishimura [aut], Marc A. Suchard [aut], John W. Ratcliff et al. [cph, ctb]
Repository: CRAN
Date/Publication: 2022-06-28 07:20:02 UTC

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New package CondMVT with initial version 0.1.0
Package: CondMVT
Title: Conditional Multivariate t Distribution, Expectation Maximization Algorithm, and Its Stochastic Variants
Version: 0.1.0
Maintainer: Paul Kinyanjui <kinyanjui.access@gmail.com>
Description: Computes conditional multivariate t probabilities, random deviates, and densities. It can also be used to create missing values at random in a dataset, resulting in a missing at random (MAR) mechanism. Inbuilt in the package are the Expectation-Maximization (EM), Monte Carlo EM, and Stochastic EM algorithms for imputation of missing values in datasets assuming the multivariate t distribution. See Kinyanjui, Tamba, Orawo, and Okenye (2020)<doi:10.3233/mas-200493>, and Kinyanjui, Tamba, and Okenye(2021)<http://www.ceser.in/ceserp/index.php/ijamas/article/view/6726/0> for more details.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, mvtnorm
NeedsCompilation: no
Packaged: 2022-06-26 20:52:27 UTC; Lenovo
Author: Paul Kinyanjui [aut, cre], Cox Tamba [aut], Justin Okenye [aut], Luke Orawo [ctb]
Repository: CRAN
Date/Publication: 2022-06-28 07:20:08 UTC

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Mon, 27 Jun 2022

New package RcppCensSpatial with initial version 0.3.0
Package: RcppCensSpatial
Title: Spatial Estimation and Prediction for Censored/Missing Responses
Version: 0.3.0
Description: It provides functions to estimate parameters in linear spatial models with censored/missing responses via the Expectation-Maximization (EM), the Stochastic Approximation EM (SAEM), or the Monte Carlo EM (MCEM) algorithm. These algorithms are widely used to compute the maximum likelihood (ML) estimates in problems with incomplete data. The EM algorithm computes the ML estimates when a closed expression for the conditional expectation of the complete-data log-likelihood function is available. In the MCEM algorithm, the conditional expectation is substituted by a Monte Carlo approximation based on many independent simulations of the missing data. In contrast, the SAEM algorithm splits the E-step into simulation and integration steps. This package also approximates the standard error of the estimates using the Louis method. Moreover, it has a function that performs spatial prediction in new locations.
License: GPL (>= 2)
Encoding: UTF-8
Imports: ggplot2, gridExtra, MomTrunc, mvtnorm, Rcpp, Rdpack, relliptical, stats, StempCens
LinkingTo: RcppArmadillo, Rcpp, RcppProgress, roptim
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: yes
Packaged: 2022-06-27 22:27:04 UTC; 55199
Author: Katherine A. L. Valeriano [aut, cre] , Alejandro Ordonez Cuastumal [ctb] , Christian Galarza Morales [ctb] , Larissa Avila Matos [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-27 23:00:02 UTC

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New package PRIMME with initial version 3.2-3
Package: PRIMME
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Version: 3.2-3
Date: 2022-06-25
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Description: R interface to 'PRIMME' <https://www.cs.wm.edu/~andreas/software/>, a C library for computing a few eigenvalues and their corresponding eigenvectors of a real symmetric or complex Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute singular values and vectors of a square or rectangular matrix. 'PRIMME' finds largest, smallest, or interior singular/eigenvalues and can use preconditioning to accelerate convergence. General description of the methods are provided in the papers Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>). See 'citation("PRIMME")' for details.
URL: https://www.cs.wm.edu/~andreas/software/ https://github.com/primme/primme
BugReports: https://github.com/primme/primme/issues
Imports: Rcpp
LinkingTo: Rcpp, Matrix
Suggests: Matrix
SystemRequirements: A POSIX system. Currently Linux and OS X are known to work. GNU make.
NeedsCompilation: yes
License: GPL-3
Encoding: UTF-8
Packaged: 2022-06-25 14:32:55 UTC; eloy
Author: Eloy Romero [aut, cre], Andreas Stathopoulos [aut], Lingfei Wu [aut], College of William & Mary [cph]
Repository: CRAN
Date/Publication: 2022-06-27 23:00:06 UTC

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New package bayeslm with initial version 1.0.1
Package: bayeslm
Title: Efficient Sampling for Gaussian Linear Regression with Arbitrary Priors
Version: 1.0.1
Date: 2022-6-25
Maintainer: Jingyu He <jingyuhe@cityu.edu.hk>
Description: Efficient sampling for Gaussian linear regression with arbitrary priors, Hahn, He and Lopes (2018) <arXiv:1806.05738>.
License: LGPL (>= 2)
Imports: Rcpp (>= 0.12.7), stats, graphics, grDevices, coda, methods, RcppParallel
SystemRequirements: GNU make
Depends: R (>= 2.10)
URL: https://github.com/JingyuHe/bayeslm
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Packaged: 2022-06-27 02:09:32 UTC; jingyuhe
Author: Jingyu He [aut, cre], P. Richard Hahn [aut], Hedibert Lopes [aut], Andrew Herren [ctb]
Repository: CRAN
Date/Publication: 2022-06-27 22:50:02 UTC

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New package fangs with initial version 0.1.6
Package: fangs
Title: Feature Allocation Neighborhood Search Algorithm
Version: 0.1.6
Description: A neighborhood-based, greedy search algorithm is performed to estimate a feature allocation by minimizing the expected loss based on posterior samples from the feature allocation distribution.
License: MIT + file LICENSE | Apache License 2.0
Depends: R (>= 4.2.0)
Imports: cargo (>= 0.2.5)
SystemRequirements: Cargo (>= 1.61) for installation from sources: see INSTALL file
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-06-25 21:36:10 UTC; dahl
Author: David B. Dahl [aut, cre] , Jacob Andros [aut] , Devin J. Johnson [aut]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Repository: CRAN
Date/Publication: 2022-06-27 15:10:02 UTC

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New package scOntoMatch with initial version 0.1.0
Package: scOntoMatch
Title: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'
Version: 0.1.0
Author: Yuyao Song [aut, cre]
Maintainer: Yuyao Song <ysong@ebi.ac.uk>
Description: Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.
Imports: ontologyIndex, ontologyPlot, purrr
URL: https://github.com/YY-SONG0718/scOntoMatch
BugReports: https://github.com/YY-SONG0718/scOntoMatch/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R(>= 3.5)
Suggests: knitr, devtools, SeuratObject
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-06-25 18:04:53 UTC; ysong
Repository: CRAN
Date/Publication: 2022-06-27 15:00:08 UTC

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New package nparLD with initial version 2.1-1
Package: nparLD
Version: 2.1-1
Date: 2022-06-27
Title: Nonparametric Analysis of Longitudinal Data in Factorial Experiments
Author: Kimihiro Noguchi <kinoguchi@ucdavis.edu>, Mahbub Latif <mlatif@gwdg.de>, Karthinathan Thangavelu <kthanga@gwdg.de>, Frank Konietschke <fkoniet@gwdg.de>, Yulia R. Gel <ygl@math.uwaterloo.ca>, Edgar Brunner <brunner@ams.med.uni-goettingen.de>
Maintainer: ORPHANED
Depends: R (>= 2.6.0), MASS
License: GPL (>= 2)
Description: Performs nonparametric analysis of longitudinal data in factorial experiments. Longitudinal data are those which are collected from the same subjects over time, and they frequently arise in biological sciences. Nonparametric methods do not require distributional assumptions, and are applicable to a variety of data types (continuous, discrete, purely ordinal, and dichotomous). Such methods are also robust with respect to outliers and for small sample sizes.
NeedsCompilation: no
Packaged: 2022-06-27 09:43:39 UTC; ligges
Repository: CRAN
Date/Publication: 2022-06-27 11:43:39

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New package rTCRBCRr with initial version 0.1.0
Package: rTCRBCRr
Title: Repertoire Analysis of the Detected Clonotype
Version: 0.1.0
Description: The 'TRUST4' or 'MiXCR' is used to identify the clonotypes. The goal of 'rTCRBCRr' is to process the results from these clonotyping tools, and analyze the clonotype repertoire metrics based on chain names and IGH isotypes. The manuscript is still under preparation for publication for now. The references describing the methods in this package will be added later.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: magrittr, readr, tidyr, tidyselect
Depends: R (>= 2.10)
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-06-18 05:10:48 UTC; Andy
Author: Lizhong Ding [aut, cre]
Maintainer: Lizhong Ding <z82xh3f4r@mozmail.com>
Repository: CRAN
Date/Publication: 2022-06-27 07:20:02 UTC

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New package mmcif with initial version 0.1.0
Package: mmcif
Title: Mixed Multivariate Cumulative Incidence Functions
Version: 0.1.0
Description: Fits the mixed cumulative incidence functions model suggested by <doi:10.1093/biostatistics/kxx072> which decomposes within cluster dependence of risk and timing. The estimation method supports computation in parallel using a shared memory C++ implementation. A sandwich estimator of the covariance matrix is available. Natural cubic splines are used to provide a flexible model for the cumulative incidence functions.
License: GPL (>= 3)
URL: https://github.com/boennecd/mmcif
BugReports: https://github.com/boennecd/mmcif/issues
Encoding: UTF-8
Depends: R (>= 3.5.0)
VignetteBuilder: R.rsp
LinkingTo: Rcpp, RcppArmadillo, testthat, psqn
Imports: Rcpp, stats, alabama
Suggests: testthat (>= 3.0.0), xml2, mvtnorm, R.rsp, mets
SystemRequirements: C++17
NeedsCompilation: yes
Packaged: 2022-06-25 16:52:24 UTC; boennecd
Author: Benjamin Christoffersen [cre, aut] , Mark Clements [cph], Alan Genz [cph], Frank Bretz [cph], Torsten Hothorn [cph], R-core [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Repository: CRAN
Date/Publication: 2022-06-27 07:40:02 UTC

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New package lipidmapsR with initial version 1.0.4
Package: lipidmapsR
Title: Lipid Maps Rest Service
Version: 1.0.4
Date: 2022-06-17
Depends: R (>= 4.2.0)
Imports: httr (>= 1.3.1), RJSONIO (>= 1.3-0)
Description: Lipid Maps Rest service. Researchers can access the Lipid Maps Rest service programmatically and conveniently integrate it into the current workflow or packages.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-24 23:22:21 UTC; liyao
Author: Mingzhuo Tian [aut, cre], Yaoxiang Li [ctb], Amrita Cheema [ctb]
Maintainer: Mingzhuo Tian <tianmingzhuo@outlook.com>
Repository: CRAN
Date/Publication: 2022-06-27 07:30:02 UTC

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New package hydrorecipes with initial version 0.0.3
Package: hydrorecipes
Title: Hydrogeology Steps for the 'recipes' Package
Version: 0.0.3
Date: 2022-06-24
Maintainer: Jonathan Kennel <jkennel@uoguelph.ca>
Description: Additional steps to be used with the 'recipes' package. New steps were designed for regression deconvolution on datasets with millions of rows with applications to signal decomposition and response characterization. The methods in this package were developed as part of PhD thesis titled High Frequency Water Level Responses to Natural Signals <http://hdl.handle.net/10214/17890> by Jonathan Kennel in 2020.
BugReports: https://github.com/jkennel/hydrorecipes/issues
URL: https://github.com/jkennel/hydrorecipes
License: GPL-3
Depends: R (>= 4.1.0), recipes (>= 0.1.15)
Imports: Rcpp (>= 1.0.7), earthtide, generics, splines, tibble, dplyr, rlang, tidyr, fftw
LinkingTo: Rcpp, RcppArmadillo, RcppParallel
Encoding: UTF-8
Suggests: knitr, rmarkdown, ggplot2, scales, broom, glmnet, testthat (>= 3.0.0), covr, splines2
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: yes
SystemRequirements: C++11
Packaged: 2022-06-24 18:55:23 UTC; jonathankennel
Author: Jonathan Kennel [aut, cre], Beth Parker [ths]
Repository: CRAN
Date/Publication: 2022-06-27 07:30:04 UTC

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New package DEET with initial version 1.0.2
Package: DEET
Title: Differential Expression Enrichment Tool
Version: 1.0.2
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Description: A bio informatics R package for comparing a list of human genes to published RNA-Seq studies containing similar DE genes. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).
Depends: R (>= 3.5.0)
Imports: ActivePathways, pbapply, dplyr, ggplot2, glmnet, utils, stats, ggrepel, downloader
License: GPL-3
URL:
Encoding: UTF-8
LazyData: true
Packaged: 2022-06-24 18:57:18 UTC; djsok
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Author: Dustin Sokolowski [aut, cre], Jedid Ahn [aut], Lauren Erdman [aut], Huayun Hou [aut], Anna Goldenberg [aut], Michael Wilson [aut]
Repository: CRAN
Date/Publication: 2022-06-27 07:30:11 UTC

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New package acdcR with initial version 1.0.0
Package: acdcR
Title: Agro-Climatic Data by County
Version: 1.0.0
Date: 2022-06-14
Author: Seong D. Yun [aut, cre]
Maintainer: Seong D. Yun <seong.yun@msstate.edu>
Description: The functions are designed to calculate the most widely-used county-level variables in agricultural production or agricultural-climatic and weather analyses. To operate some functions in this package needs download of the bulk PRISM raster. See the examples, testing versions and more details from: <https://github.com/ysd2004/acdcR>.
Depends: R (>= 4.0.0), raster, data.table, stats
License: GPL (>= 2)
URL: https://github.com/ysd2004/acdcR
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-06-25 13:50:12 UTC; Seong Yun
Repository: CRAN
Date/Publication: 2022-06-27 07:40:05 UTC

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Sun, 26 Jun 2022

New package mined with initial version 1.0-3
Package: mined
Title: Minimum Energy Designs
Version: 1.0-3
Date: 2022-06-19
Author: Dianpeng Wang and V. Roshan Joseph
Maintainer: Dianpeng Wang <wdp@bit.edu.cn>
Description: This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2019) <DOI:10.1080/00401706.2018.1552203>. The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate. This research is supported by a U.S. National Science Foundation grant DMS-1712642.
License: LGPL-2.1
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2022-06-19 06:37:01 UTC; dpwang
Repository: CRAN
Date/Publication: 2022-06-26 21:30:02 UTC

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