CRANberries

Wed, 04 Dec 2024

New package iClusterVB with initial version 0.1.3
Package: iClusterVB
Title: Fast Integrative Clustering and Feature Selection for High Dimensional Data
Version: 0.1.3
Author: Abdalkarim Alnajjar [aut, cre, cph] , Zihang Lu [aut]
Maintainer: Abdalkarim Alnajjar <abdalkarim.alnajjar@queensu.ca>
Description: A variational Bayesian approach for fast integrative clustering and feature selection, facilitating the analysis of multi-view, mixed type, high-dimensional datasets with applications in fields like cancer research, genomics, and more.
License: MIT + file LICENSE
URL: https://github.com/AbdalkarimA/iClusterVB
BugReports: https://github.com/AbdalkarimA/iClusterVB/issues
Depends: R (>= 4.0.0)
Imports: cluster, clustMixType, cowplot, ggplot2, graphics, grDevices, mclust, MCMCpack, mvtnorm, pheatmap, poLCA, R.utils, Rcpp (>= 1.0.12), stats, utils, VarSelLCM
Suggests: knitr, rmarkdown, survival, survminer
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-12-04 06:06:26 UTC; Abdalkarim
Repository: CRAN
Date/Publication: 2024-12-04 08:20:07 UTC

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Tue, 03 Dec 2024

New package aphylo with initial version 0.3-4
Package: aphylo
Title: Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Version: 0.3-4
Description: Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
Depends: R (>= 3.5.0), ape (>= 5.0)
LazyData: true
Imports: Rcpp (>= 0.12.1), Matrix, methods, coda, fmcmc, utils, MASS, xml2
Suggests: covr, knitr, tinytest, AUC, rmarkdown,
VignetteBuilder: knitr
LinkingTo: Rcpp
Encoding: UTF-8
URL: https://github.com/USCbiostats/aphylo
BugReports: https://github.com/USCbiostats/aphylo/issues
Classification/MSC: 90C35, 90B18, 91D30
License: MIT + file LICENSE
NeedsCompilation: yes
Packaged: 2024-12-03 16:29:02 UTC; u6039184
Author: George Vega Yon [aut, cre] , National Cancer Institute [fnd] , USC Biostatistics [cph]
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-03 23:00:10 UTC

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New package extractox with initial version 0.1.0
Package: extractox
Title: Extract Tox Info from Various Databases
Version: 0.1.0
Description: Extract toxicological and chemical information from databases maintained by scientific agencies and resources, including the Comparative Toxicogenomics Database <https://ctdbase.org/>, the Integrated Chemical Environment <https://ice.ntp.niehs.nih.gov/>, the Integrated Risk Information System <https://cfpub.epa.gov/ncea/iris/>, the CompTox Chemicals Dashboard Resource Hub <https://www.epa.gov/comptox-tools/comptox-chemicals-dashboard-resource-hub>, and PubChem <https://pubchem.ncbi.nlm.nih.gov/>.
License: MIT + file LICENSE
URL: https://github.com/c1au6i0/extractox, https://c1au6i0.github.io/extractox/
BugReports: https://github.com/c1au6i0/extractox/issues
Depends: R (>= 4.1)
Imports: cli, httr2, janitor, pingr, readxl, rvest, webchem
Suggests: openxlsx, testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-12-03 03:11:03 UTC; heverz
Author: Claudio Zanettini [aut, cre, cph] , Lucio Queiroz [aut]
Maintainer: Claudio Zanettini <claudio.zanettini@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-03 21:40:02 UTC

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New package csmGmm with initial version 0.3.0
Package: csmGmm
Title: Conditionally Symmetric Multidimensional Gaussian Mixture Model
Version: 0.3.0
Description: Implements the conditionally symmetric multidimensional Gaussian mixture model (csmGmm) for large-scale testing of composite null hypotheses in genetic association applications such as mediation analysis, pleiotropy analysis, and replication analysis. In such analyses, we typically have J sets of K test statistics where K is a small number (e.g. 2 or 3) and J is large (e.g. 1 million). For each one of the J sets, we want to know if we can reject all K individual nulls. Please see the vignette for a quickstart guide. The paper describing these methods is "Testing a Large Number of Composite Null Hypotheses Using Conditionally Symmetric Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw Z, & Lin X (2024, <doi:10.1080/01621459.2024.2422124>). The paper is accepted and published online (but not yet in print) in the Journal of the American Statistical Association as of Dec 1 2024.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, mvtnorm, rlang, magrittr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-02 20:45:12 UTC; rsun3
Author: Ryan Sun [aut, cre]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-03 19:30:02 UTC

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New package basicspace with initial version 0.25
Package: basicspace
Title: Recovering a Basic Space from Issue Scales
Version: 0.25
Date: 2024-12-02
Author: Royce Carroll [aut], Christopher Hare [aut, cre], Jeffrey B. Lewis [aut], James Lo [aut], Keith T. Poole [aut], Howard Rosenthal [aut]
Maintainer: Christopher Hare <cdhare@ucdavis.edu>
Description: Provides functions to estimate latent dimensions of choice and judgment using Aldrich-McKelvey and Blackbox scaling methods, as described in Poole et al. (2016, <doi:10.18637/jss.v069.i07>). These techniques allow researchers (particularly those analyzing political attitudes, public opinion, and legislative behavior) to recover spatial estimates of political actors' ideal points and stimuli from issue scale data, accounting for perceptual bias, multidimensional spaces, and missing data. The package uses singular value decomposition and alternating least squares (ALS) procedures to scale self-placement and perceptual data into a common latent space for the analysis of ideological or evaluative dimensions. Functionality also include tools for assessing model fit, handling complex survey data structures, and reproducing simulated datasets for methodological validation.
License: GPL-2
Depends: R (>= 3.0.0), tools
URL: https://CRAN.R-project.org/package=basicspace
NeedsCompilation: yes
Packaged: 2024-12-02 16:53:42 UTC; chare
Repository: CRAN
Date/Publication: 2024-12-03 19:10:01 UTC

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New package sshicm with initial version 0.1.0
Package: sshicm
Title: Information Consistency-Based Measures for Spatial Stratified Heterogeneity
Version: 0.1.0
Description: Spatial stratified heterogeneity (SSH) denotes the coexistence of within-strata homogeneity and between-strata heterogeneity. Information consistency-based methods provide a rigorous approach to quantify SSH and evaluate its role in spatial processes, grounded in principles of geographical stratification and information theory (Bai, H. et al. (2023) <doi:10.1080/24694452.2023.2223700>; Wang, J. et al. (2024) <doi:10.1080/24694452.2023.2289982>).
License: GPL-3
Encoding: UTF-8
URL: https://stscl.github.io/sshicm/, https://github.com/stscl/sshicm
BugReports: https://github.com/stscl/sshicm/issues
Depends: R (>= 4.1.0)
LinkingTo: Rcpp, RcppThread
Imports: dplyr, purrr, sdsfun (>= 0.5.0), sf
Suggests: gdverse, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-12-02 16:04:56 UTC; dell
Author: Wenbo Lv [aut, cre, cph]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-03 19:00:02 UTC

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New package resourcecode with initial version 0.2.1
Package: resourcecode
Title: Access to the 'RESOURCECODE' Hindcast Database
Version: 0.2.1
Date: 2024-11-29
Description: Utility functions to download data from the 'RESOURCECODE' hindcast database of sea-states, time series of sea-state parameters and time series of 1D and 2D wave spectra. See <https://resourcecode.ifremer.fr> for more details about the available data. Also provides facilities to plot and analyse downloaded data, such as computing the sea-state parameters from both the 1D and 2D surface elevation variance spectral density.
License: GPL (>= 3)
URL: https://github.com/Resourcecode-project/r-resourcecode, https://resourcecode-project.github.io/r-resourcecode/
BugReports: https://github.com/Resourcecode-project/r-resourcecode/issues
Depends: R (>= 3.6)
Imports: abind, curl, geosphere, ggplot2, jsonlite, ncdf4, pracma, Rcpp, rlang, sf, stats, tibble, tidyr
Suggests: knitr, rmarkdown, resourcecodedata, testthat, vdiffr
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
Additional_repositories: https://resourcecode-project.github.io/drat/
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: yes
Packaged: 2024-12-02 14:54:43 UTC; nraillar
Author: Nicolas Raillard [aut, cre]
Maintainer: Nicolas Raillard <nicolas.raillard@ifremer.fr>
Repository: CRAN
Date/Publication: 2024-12-03 19:00:05 UTC

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New package RCNA with initial version 1.0
Package: RCNA
Title: Robust Copy Number Alteration Detection (RCNA)
Version: 1.0
Description: Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
Imports: doParallel, methods, utils, modeest, data.table, foreach, R.utils
Suggests: knitr, rmarkdown, usethis
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2024-12-02 13:13:50 UTC; mbradley
Author: Matt Bradley [aut, cre]
Maintainer: Matt Bradley <mbradley@emmes.com>
Repository: CRAN
Date/Publication: 2024-12-03 18:40:06 UTC

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New package messy with initial version 0.1.0
Package: messy
Title: Create Messy Data from Clean Data Frames
Version: 0.1.0
Description: For the purposes of teaching, it is often desirable to show examples of working with messy data and how to clean it. This R package creates messy data from clean, tidy data frames so that students have a clean example to work towards.
Depends: R (>= 4.1)
Imports: dplyr, rlang, stringr
License: CC BY 4.0
Suggests: lubridate, testthat (>= 3.0.0)
Encoding: UTF-8
URL: https://nrennie.rbind.io/messy/, https://github.com/nrennie/messy
BugReports: https://github.com/nrennie/messy/issues
NeedsCompilation: no
Packaged: 2024-12-02 13:54:12 UTC; rennien2
Author: Nicola Rennie [aut, cre, cph]
Maintainer: Nicola Rennie <nrennie35@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-03 18:50:02 UTC

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Mon, 02 Dec 2024

New package gtfs2emis with initial version 0.1.1
Package: gtfs2emis
Title: Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data
Version: 0.1.1
Description: A bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification (GTFS) data. The package requires two main inputs: i) Public transport data in the GTFS standard format; and ii) Some basic information on fleet characteristics such as fleet age, technology, fuel and Euro stage. As it stands, the package estimates several pollutants at high spatial and temporal resolutions. Pollution levels can be calculated for specific transport routes, trips, time of the day or for the transport system as a whole. The output with emission estimates can be extracted in different formats, supporting analysis on how emission levels vary across space, time and by fleet characteristics. A full description of the methods used in the 'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; Andrade, P. R. (2022) <doi:10.31219/osf.io/8m2cy>.
URL: https://ipeagit.github.io/gtfs2emis/ , https://github.com/ipeaGIT/gtfs2emis
BugReports: https://github.com/ipeaGIT/gtfs2emis/issues
License: MIT + file LICENSE
Depends: R (>= 3.6)
Imports: checkmate, data.table, furrr, future, gtfs2gps, methods, sf (>= 0.9-0), sfheaders, terra, units
Suggests: gtfstools, ggplot2, knitr, lwgeom, progressr, rmarkdown, testthat (>= 2.1.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-12-02 15:20:51 UTC; joao
Author: Joao Bazzo [aut, cre] , Rafael H. M. Pereira [aut] , Pedro R. Andrade [aut] , Sergio Ibarra-Espinosa [ctb] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Joao Bazzo <joao.bazzo@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-02 15:40:12 UTC

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New package atime with initial version 2024.11.29
Package: atime
Title: Asymptotic Timing
Version: 2024.11.29
Description: Computing and visualizing comparative asymptotic timings of different algorithms and code versions. Also includes functionality for comparing empirical timings with expected references such as linear or quadratic, <https://en.wikipedia.org/wiki/Asymptotic_computational_complexity> Also includes functionality for measuring asymptotic memory and other quantities.
License: GPL-3
URL: https://github.com/tdhock/atime
BugReports: https://github.com/tdhock/atime/issues
Imports: data.table, bench, lattice, git2r, utils, stats, grDevices
Suggests: directlabels, ggplot2, testthat, knitr, markdown, stringi, re2, binsegRcpp, wbs, fpop, changepoint, LOPART, cumstats, PeakSegDisk, callr, readr, dplyr, tidyr, nc, RColorBrewer, tibble, Matrix
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-12-02 14:59:47 UTC; hoct2726
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Repository: CRAN
Date/Publication: 2024-12-02 15:40:21 UTC

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New package wdiEF with initial version 1.0.2
Package: wdiEF
Title: Calculation of the Water Deficit Index (WDI) and the Evaporative Fraction (EF) on Rasters
Version: 1.0.2
Description: Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) using geospatial data, such as fractional vegetation cover (FVC) and surface-air temperature difference (TS-TA). Terms like "raster", "CRS" are part of standard geospatial terminology.
License: GPL-3
Encoding: UTF-8
Imports: dplyr, stats, terra
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-12-01 14:55:12 UTC; hamelin
Author: Gaelle Hamelin [aut, cre]
Maintainer: Gaelle Hamelin <gaelle.hamelin@institut-agro.fr>
Repository: CRAN
Date/Publication: 2024-12-02 12:40:06 UTC

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New package twc with initial version 0.0.1
Package: twc
Title: Terrestrial Water Cycle
Version: 0.0.1
Description: An open-access tool/framework that constitutes the core functions to analyze terrestrial water cycle data across various spatio-temporal scales.
Depends: R (>= 4.0.0)
License: GPL-3
Encoding: UTF-8
Imports: data.table, doParallel, foreach, lubridate, magrittr, methods, ncdf4, parallel, raster, sf, sp,utils
URL: https://github.com/imarkonis/twc
BugReports: https://github.com/imarkonis/twc/issues
SystemRequirements: PROJ (>= 6, https://proj.org/download.html), GDAL (>= 3, https://gdal.org/download.html), NetCDF(>= 4, https://www.unidata.ucar.edu/software/netcdf/).
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-29 15:53:34 UTC; mirovago
Author: Mijael Rodrigo Vargas Godoy [aut, cre] , Yannis Markonis [aut]
Maintainer: Mijael Rodrigo Vargas Godoy <mirovago@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-02 12:40:31 UTC

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New package sffdr with initial version 1.0.0
Package: sffdr
Title: Surrogate Functional False Discovery Rates for Genome-Wide Association Studies
Version: 1.0.0
Maintainer: Andrew Bass <ab3105@cam.ac.uk>
Description: Pleiotropy-informed significance analysis of genome-wide association studies (GWAS) with surrogate functional false discovery rates (sfFDR). The sfFDR framework adapts the fFDR to leverage informative data from multiple sets of GWAS summary statistics to increase power in study while accommodating for linkage disequilibrium. sfFDR provides estimates of key FDR quantities in a significance analysis such as the functional local FDR and q-value, and uses these estimates to derive a functional p-value for type I error rate control and a functional local Bayes' factor for post-GWAS analyses (e.g., fine mapping and colocalization). The sfFDR framework is described in Bass and Wallace (2024) <doi:10.1101/2024.09.24.24314276>.
URL: https://github.com/ajbass/sffdr
License: LGPL
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
Depends: R (>= 3.5.0)
Imports: locfit, splines, dplyr, ggplot2 (>= 3.5.1), patchwork (>= 1.3.0), gam, qvalue, tibble, tidyr, Rcpp
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-11-29 14:22:57 UTC; andrewbass
Author: Andrew Bass [aut, cre], Chris Wallace [aut]
Repository: CRAN
Date/Publication: 2024-12-02 12:30:08 UTC

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New package scR with initial version 0.1.0
Package: scR
Title: Estimate Vapnik-Chervonenkis Dimension and Sample Complexity
Version: 0.1.0
Description: We provide a suite of tools for estimating the sample complexity of a chosen model through theoretical bounds and simulation. The package incorporates methods for estimating the Vapnik-Chervonenkis dimension (VCD) of a chosen algorithm, which can be used to estimate its sample complexity. Alternatively, we provide simulation methods to estimate sample complexity directly. For more details, see Carter, P & Choi, D (2024). "Learning from Noise: Applying Sample Complexity for Political Science Research" <doi:10.31219/osf.io/evrcj>.
Encoding: UTF-8
URL: https://github.com/pjesscarter/scR
BugReports: https://github.com/pjesscarter/scR/issues
Imports: parallel, pbapply, caret, dplyr, tidyr, ggplot2, plotly
Suggests: rmarkdown
Depends: R (>= 2.10)
LazyData: true
LazyDataCompression: xz
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2024-11-29 10:31:52 UTC; pjc504
Author: Perry Carter [aut, cre] , Dahyun Choi [aut]
Maintainer: Perry Carter <pjc504@nyu.edu>
Repository: CRAN
Date/Publication: 2024-12-02 12:20:07 UTC

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New package SAKERNAS with initial version 0.1.0
Package: SAKERNAS
Title: A National Labor Force Survey of Indonesia
Version: 0.1.0
Author: Fadhlul Mubarak [aut, cre], Nurniswah [aut], Vinny Yuliani Sundara [aut], Arsyad Lubis [aut], Ahmad Syukron Prasaja [aut]
Maintainer: Fadhlul Mubarak <mubarakfadhlul@gmail.com>
Description: Surveys to collect employment data so as to obtain data estimates on the number of employed people, the number of unemployed, and other employment indicators.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: readxl
NeedsCompilation: no
Packaged: 2024-11-29 22:29:32 UTC; HP
Repository: CRAN
Date/Publication: 2024-12-02 12:51:04 UTC

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New package RCMsize with initial version 1.0.0
Package: RCMsize
Title: Sample Size Calculation in Reversible Catalytic Models
Version: 1.0.0
Maintainer: Marcia Graca <marcia_da_graca@hotmail.com>
Description: Sample size and confidence interval calculations in reversible catalytic models, with applications in malaria research. Further details can be found in the paper by Sepúlveda and Drakeley (2015, <doi:10.1186/s12936-015-0661-z>).
License: GPL (>= 3)
Encoding: UTF-8
Imports: binom, stats
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, tools
URL: https://github.com/marciagraca/RCMsize , https://marciagraca.github.io/RCMsize/
BugReports: https://github.com/marciagraca/RCMsize/issues
NeedsCompilation: no
Packaged: 2024-11-29 16:29:42 UTC; Visitante
Author: Marcia Graca [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-12-02 12:41:41 UTC

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New package pipeflow with initial version 0.1.1
Package: pipeflow
Title: Implement Data Analysis Workflows with Pipelines
Version: 0.1.1
Description: A lightweight yet powerful framework for creating data analysis pipelines. You build your pipelines simply by defining a sequence of R functions and 'pipeflow' takes care of tracking dependencies among steps and managing all the analysis parameters. The framework is easy to get started with for the typical R user, but also provides advanced features to enable complex workflows.
License: GPL-3
Imports: data.table, jsonlite, lgr, methods, R6, stats, utils
Suggests: ggplot2, knitr, mockery, rmarkdown, testthat, visNetwork
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Packaged: 2024-12-01 12:41:00 UTC; Roman
Author: Roman Pahl [aut, cre]
Repository: CRAN
Date/Publication: 2024-12-02 12:40:56 UTC

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New package MEDesigns with initial version 1.0.0
Package: MEDesigns
Title: Mating Environmental Designs
Version: 1.0.0
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Description: In breeding experiments, mating environmental (ME) designs are very popular as mating designs are directly implemented in the field environment using block or row-column designs. Here, three functions are given related to three new methods which will generate mating diallel cross designs (Hinkelmann and Kempthorne, 1963<doi:10.2307/2333899>) or mating environmental (ME) designs along with design parameters, C matrix, eigenvalues (EVs), degree of fractionations (DF) and canonical efficiency factor (CEF). Another one function is added to check the properties of a given ME diallel cross design.
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-30 13:09:06 UTC; Ashutosh
Author: Ashutosh Dalal [aut, cre], Cini Varghese [aut, ctb], Rajender Parsad [aut, ctb], Mohd Harun [aut, ctb]
Repository: CRAN
Date/Publication: 2024-12-02 12:31:07 UTC

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New package ldmppr with initial version 1.0.3
Package: ldmppr
Title: Estimate and Simulate from Location Dependent Marked Point Processes
Version: 1.0.3
Maintainer: Lane Drew <lanetdrew@gmail.com>
Description: A suite of tools for estimating, assessing model fit, simulating from, and visualizing location dependent marked point processes characterized by regularity in the pattern. You provide a reference marked point process, a set of raster images containing location specific covariates, and select the estimation algorithm and type of mark model. 'ldmppr' estimates the process and mark models and allows you to check the appropriateness of the model using a variety of diagnostic tools. Once a satisfactory model fit is obtained, you can simulate from the model and visualize the results. Documentation for the package 'ldmppr' is available in the form of a vignette.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 1.0.12), terra, doParallel, xgboost, ranger, parsnip, dials, bundle, recipes, rsample, tune, workflows, magrittr, hardhat, ggplot2, spatstat.geom, spatstat.explore, nloptr, GET, progress, dplyr, future, furrr, yardstick
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/lanedrew/ldmppr
BugReports: https://github.com/lanedrew/ldmppr/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: yes
Packaged: 2024-11-29 19:39:14 UTC; lanedrew
Author: Lane Drew [aut, cre, cph] , Andee Kaplan [aut]
Repository: CRAN
Date/Publication: 2024-12-02 12:41:19 UTC

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New package ILRCM with initial version 0.1.0
Package: ILRCM
Title: Convert Irregular Longitudinal Data to Regular Intervals and Perform Clustering
Version: 0.1.0
Maintainer: Atanu Bhattacharjee <atanustat@gmail.com>
Description: Convert irregularly spaced longitudinal data into regular intervals for further analysis, and perform clustering using advanced machine learning techniques. The package is designed for handling complex longitudinal datasets, optimizing them for research in healthcare, demography, and other fields requiring temporal data modeling.
Imports: ggplot2, scales
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-11-29 23:11:06 UTC; Atanu Bhattacharjee
Author: Atanu Bhattacharjee [aut, cre, ctb], Tanmoy Majumdar [aut, ctb]
Repository: CRAN
Date/Publication: 2024-12-02 12:51:13 UTC

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New package IDLFM with initial version 0.0.1
Package: IDLFM
Title: Individual Dynamic Latent Factor Model
Version: 0.0.1
Maintainer: Siyang Liu <liusiyang.lucia@gmail.com>
Description: A personalized dynamic latent factor model (Zhang et al. (2024) <doi:10.1093/biomet/asae015>) for irregular multi-resolution time series data, to interpolate unsampled measurements from low-resolution time series.
Depends: R (>= 4.4.0)
Imports: stats, methods, splines, SparseArray
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-12-01 18:45:28 UTC; 24952
Author: Siyang Liu [aut, cre], Jiuchen Zhang [aut]
Repository: CRAN
Date/Publication: 2024-12-02 13:00:04 UTC

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New package gfoRmulaICE with initial version 0.1.0
Package: gfoRmulaICE
Title: Parametric Iterative Conditional Expectation G-Formula
Version: 0.1.0
Description: Implements iterative conditional expectation (ICE) estimators of the plug-in g-formula (Wen, Young, Robins, and Hernán (2020) <doi: 10.1111/biom.13321>). Both singly robust and doubly robust ICE estimators based on parametric models are available. The package can be used to estimate survival curves under sustained treatment strategies (interventions) using longitudinal data with time-varying treatments, time-varying confounders, censoring, and competing events. The interventions can be static or dynamic, and deterministic or stochastic (including threshold interventions). Both prespecified and user-defined interventions are available.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: data.table, ggplot2, nnet, doParallel, parallel, foreach, stringr, magrittr, dplyr, rlang, reshape2, speedglm, methods, Hmisc, splines
Suggests: testthat (>= 3.0.0)
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-12-01 17:39:16 UTC; carriecheng
Author: Zhaoxi Cheng [aut, cre], Jing Li [aut], Sophia Rein [aut], Ryan O'Dea [aut], Sean McGrath [aut], Lan Wen [aut], Miguel A. Hernan [aut], 2024 The President and Fellows of Harvard College [cph]
Maintainer: Zhaoxi Cheng <zcheng@hsph.harvard.edu>
Repository: CRAN
Date/Publication: 2024-12-02 12:50:08 UTC

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New package crimedatasets with initial version 0.1.0
Package: crimedatasets
Title: A Comprehensive Collection of Crime-Related Datasets
Version: 0.1.0
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Description: A comprehensive collection of datasets exclusively focused on crimes, criminal activities, and related topics. This package serves as a valuable resource for researchers, analysts, and students interested in crime analysis, criminology, social and economic studies related to criminal behavior. Datasets span global and local contexts, with a mix of tabular and spatial data.
License: GPL-3
URL: https://github.com/lightbluetitan/crimedatasets
BugReports: https://github.com/lightbluetitan/crimedatasets/issues
Encoding: UTF-8
LazyData: true
Suggests: ggplot2, dplyr, knitr, rmarkdown, sf, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-29 19:56:52 UTC; renzocrossi
Author: Renzo Caceres Rossi [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-12-02 12:50:37 UTC

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New package orthGS with initial version 0.1.6
Package: orthGS
Title: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants
Version: 0.1.6
Description: Tools to analyze and infer orthology and paralogy relationships between glutamine synthetase proteins in seed plants.
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 4.0)
LazyData: true
Imports: ape, bio3d, castor, igraph, phangorn, phytools, seqinr, TreeTools
Suggests: BiocManager, Biostrings, knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-30 10:08:12 UTC; jcaledo
Author: Elena Aledo [aut, cre, cph], Juan-Carlos Aledo [aut]
Maintainer: Elena Aledo <elenaaledoesteban@gmail.com>
Repository: CRAN
Date/Publication: 2024-12-02 10:00:07 UTC

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New package antaresViz with initial version 0.18.3
Package: antaresViz
Title: Antares Visualizations
Version: 0.18.3
Description: Visualize results generated by Antares, a powerful open source software developed by RTE to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions that create interactive charts to help 'Antares' users visually explore the results of their simulations.
URL: https://github.com/rte-antares-rpackage/antaresViz
BugReports: https://github.com/rte-antares-rpackage/antaresViz/issues
License: GPL (>= 3)
Encoding: UTF-8
Depends: antaresRead (>= 2.2.9), antaresProcessing (>= 0.13.0), spMaps (>= 0.5.0)
Imports: dygraphs (>= 1.1.1.6), shiny (>= 0.13.0), plotly (>= 4.5.6), htmltools, htmlwidgets (>= 0.7.0), manipulateWidget (>= 0.10.0), leaflet (>= 1.1.0), sp (>= 2.0-0), sf, webshot, data.table, methods, lubridate, geojsonio, graphics, stats, leaflet.minicharts (>= 0.5.3), assertthat, rAmCharts, utils, lifecycle
Suggests: testthat, covr, ggplot2, knitr, visNetwork, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-29 14:01:10 UTC; berthetcle
Author: Tatiana Vargas [aut, cre], Jalal-Edine Zawam [ctb], Francois Guillem [ctb], Benoit Thieurmel [ctb], Titouan Robert [ctb], Paul Plessiez [ctb], Baptiste Seguinot [ctb], RTE [cph]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Repository: CRAN
Date/Publication: 2024-12-02 10:00:19 UTC

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Fri, 29 Nov 2024

New package vaccineff with initial version 1.0.0
Package: vaccineff
Title: Estimate Vaccine Effectiveness Based on Different Study Designs
Version: 1.0.0
Description: Provides tools for estimating vaccine effectiveness and related metrics. The 'vaccineff_data' class manages key features for preparing, visualizing, and organizing cohort data, as well as estimating vaccine effectiveness. The results and model performance are assessed using the 'vaccineff' class.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/vaccineff, https://epiverse-trace.github.io/vaccineff/
BugReports: https://github.com/epiverse-trace/vaccineff/issues
Depends: R (>= 4.0.0)
Imports: checkmate, ggplot2, linelist, MatchIt, rlang, scales, stats, survival
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-28 15:34:19 UTC; dsquevedovega
Author: David Santiago Quevedo [aut] , Zulma M. Cucunuba [aut, cre] , International Development Research Center [fnd], Geraldine Gomez Millan [ctb] , Pratik Gupte [ctb] , Erika J Cantor [ctb] , Santiago Loaiza [ctb] , Jaime Pavlich-Mariscal [ctb] , Hugo Gru [...truncated...]
Maintainer: Zulma M. Cucunuba <tracelacdev@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-29 09:30:02 UTC

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New package STATcubeR with initial version 1.0.0
Package: STATcubeR
Title: R Interface for the 'STATcube' REST API and Open Government Data
Version: 1.0.0
Date: 2024-11-29
Description: Import data from the 'STATcube' REST API or from the open data portal of Statistics Austria. This package includes a client for API requests as well as parsing utilities for data which originates from 'STATcube'. Documentation about 'STATcubeR' is provided by several vignettes included in the package as well as on the public 'pkgdown' page at <https://statistikat.github.io/STATcubeR/>.
License: GPL (>= 2)
URL: https://statistikat.github.io/STATcubeR/, https://github.com/statistikat/STATcubeR
BugReports: https://github.com/statistikat/STATcubeR/issues
Depends: R (>= 3.5.0)
Imports: cli (>= 3.4.1), httr, jsonlite, pillar (>= 1.5.0), vctrs (>= 0.5.2)
Suggests: magrittr, spelling, data.tree, rappdirs, xml2, reactable, markdown
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-29 05:30:06 UTC; meindl
Author: Bernhard Meindl [ctb, cre], Alexander Kowarik [ctb] , Gregor de Cillia [aut]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Repository: CRAN
Date/Publication: 2024-11-29 09:50:02 UTC

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New package PolisheR with initial version 1.0.0
Package: PolisheR
Title: Interfacing 'NaileR' with 'Shiny'
Version: 1.0.0
Description: A very small package for more convenient use of 'NaileR'. You provide a data set containing a latent variable you want to understand. It generates a description and an interpretation of this latent variable using a Large Language Model. For perceptual data, it describes the stimuli used in the experiment.
License: GPL (>= 2)
Encoding: UTF-8
Imports: dplyr, NaileR, shiny
Depends: R (>= 3.5.0)
Suggests: SensoMineR
NeedsCompilation: no
Packaged: 2024-11-28 13:10:28 UTC; sebastienle
Author: Sebastien Le [aut, cre]
Maintainer: Sebastien Le <sebastien.le@institut-agro.fr>
Repository: CRAN
Date/Publication: 2024-11-29 09:20:06 UTC

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New package PivotalP with initial version 0.1.2
Package: PivotalP
Title: Prediction for Future Data from Mixture Distributions Gamma, Beta, Weibull and Normal
Version: 0.1.2
Author: O. M. Khaled [aut], K. S. Khalil [aut, cre], M. H. Harby [aut]
Maintainer: K. S. Khalil <kekox38@gmail.com>
Description: Functions to get prediction intervals and prediction points of future observations from mixture distributions like gamma, beta, Weibull and normal.
License: GPL (>= 2)
Encoding: UTF-8
Imports: stats, zipfR
NeedsCompilation: no
Packaged: 2024-11-28 12:49:09 UTC; Karim
Repository: CRAN
Date/Publication: 2024-11-29 09:20:10 UTC

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New package PaRe with initial version 0.1.14
Package: PaRe
Title: A Way to Perform Code Review or QA on Other Packages
Version: 0.1.14
Language: en-US
Description: Reviews other packages during code review by looking at their dependencies, code style, code complexity, and how internally defined functions interact with one another.
URL: https://github.com/darwin-eu-dev/PaRe
BugReports: https://github.com/darwin-eu-dev/PaRe/issues
License: Apache License (>= 2)
Encoding: UTF-8
Imports: cli (>= 3.6.0), cyclocomp (>= 1.1.0), desc (>= 1.4.2), DiagrammeR (>= 1.0.9), DiagrammeRsvg (>= 0.1), dplyr (>= 1.1.0), glue (>= 1.6.2), lintr (>= 3.0.2), magrittr (>= 2.0.3), pak (>= 0.2.0), rmarkdown (>= 2.20), rsvg (>= 2.4.0), stringr (>= 1.5.0), igraph (>= 1.3.5), utils, R6 (>= 2.5.1), git2r (>= 0.31.0), checkmate (>= 2.1.0), parallel
Suggests: ggplot2, plotly, ggraph, DT, magick, withr, cowplot, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-28 15:02:16 UTC; mvankessel
Author: Maarten van Kessel [aut, cre]
Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
Repository: CRAN
Date/Publication: 2024-11-29 09:30:10 UTC

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New package nzilbb.vowels with initial version 0.3.1
Package: nzilbb.vowels
Title: Vowel Covariation Tools
Version: 0.3.1
Description: Tools to support research on vowel covariation. Methods are provided to support Principal Component Analysis workflows (as in Brand et al. (2021) <doi:10.1016/j.wocn.2021.101096> and Wilson Black et al. (2023) <doi:10.1515/lingvan-2022-0086>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1), patchwork
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vdiffr
Imports: dplyr, ggplot2, magrittr, rlang, rstudioapi, tibble, tidyr, forcats, glue, purrr, tidyselect, rsample, stringr, ggrepel, gghalves, smacof, Rdpack, lifecycle
URL: https://nzilbb.github.io/nzilbb_vowels/, https://github.com/nzilbb/nzilbb_vowels
BugReports: https://github.com/nzilbb/nzilbb_vowels/issues/
NeedsCompilation: no
Packaged: 2024-11-28 21:13:09 UTC; jbl91
Author: Joshua Wilson Black [aut, cre, cph] , James Brand [aut]
Maintainer: Joshua Wilson Black <joshua@wilsonblack.nz>
Repository: CRAN
Date/Publication: 2024-11-29 09:40:03 UTC

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New package greta.censored with initial version 0.1.0
Package: greta.censored
Title: Censored Distributions for 'greta'
Version: 0.1.0
Description: Provides additional censored distributions for use with 'greta', a probabilistic programming framework for Bayesian modeling. Includes censored versions of Normal, Log-Normal, Student's T, Gamma, Exponential, Weibull, Pareto, and Beta distributions with support for right, left, and interval censoring. For details on 'greta', see Golding (2019) <doi:10.21105/joss.01601>. The methods are implemented using 'TensorFlow' and 'TensorFlow Probability' for efficient computation.
License: Apache License 2.0
URL: https://github.com/mtwesley/greta.censored
BugReports: https://github.com/mtwesley/greta.censored/issues
Depends: greta (>= 0.4.2), R (>= 3.1.0)
Imports: glue, reticulate, tensorflow (>= 2.7.0)
Suggests: devtools, VGAM, knitr, rmarkdown, testthat (>= 3.1.0), roxygen2, styler, pkgdown
Encoding: UTF-8
Language: en-GB
SystemRequirements: Python (>= 3.7.0) with header files and shared library; TensorFlow (>= v2.0.0; https://www.tensorflow.org/); TensorFlow Probability (v0.8.0; https://www.tensorflow.org/probability/)
NeedsCompilation: no
Packaged: 2024-11-28 15:02:55 UTC; mtwesley
Author: Mlen-Too Wesley [aut, cre]
Maintainer: Mlen-Too Wesley <mlen.too.wesley@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-29 09:30:06 UTC

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New package banditsCI with initial version 1.0.0
Package: banditsCI
Title: Bandit-Based Experiments and Policy Evaluation
Version: 1.0.0
Description: Frequentist inference on adaptively generated data. The methods implemented are based on Zhan et al. (2021) <doi:10.48550/arXiv.2106.02029> and Hadad et al. (2021) <doi:10.48550/arXiv.1911.02768>. For illustration, several functions for simulating non-contextual and contextual adaptive experiments using Thompson sampling are also supplied.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/UChicago-pol-methods/banditsCI, https://uchicago-pol-methods.github.io/banditsCI/
BugReports: https://github.com/UChicago-pol-methods/banditsCI/issues
Suggests: knitr (>= 1.43), rmarkdown (>= 2.23), testthat (>= 3.0.0)
Imports: glmnet (>= 4.1-6), MASS (>= 7.3-56), mvtnorm (>= 1.2-2), Rdpack (>= 2.6)
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-11-26 14:18:18 UTC; moffer
Author: Molly Offer-Westort [aut, cre, cph] , Yinghui Zhou [aut] , Ruohan Zhan [aut]
Maintainer: Molly Offer-Westort <mollyow@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-29 09:20:02 UTC

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Thu, 28 Nov 2024

New package rsofun with initial version 5.0.0
Package: rsofun
Title: The P-Model and BiomeE Modelling Framework
Version: 5.0.0
Description: Implements the Simulating Optimal FUNctioning framework for site-scale simulations of ecosystem processes, including model calibration. It contains 'Fortran 90' modules for the P-model (Stocker et al. (2020) <doi:10.5194/gmd-13-1545-2020>), SPLASH (Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>) and BiomeE (Weng et al. (2015) <doi:10.5194/bg-12-2655-2015>).
URL: https://github.com/geco-bern/rsofun
BugReports: https://github.com/geco-bern/rsofun/issues
License: GPL-3
Depends: R (>= 4.1.0)
Imports: dplyr, purrr, tidyr, magrittr, GenSA, BayesianTools, multidplyr, stats, utils
LazyData: true
LazyDataCompression: xz
ByteCompile: true
NeedsCompilation: yes
Suggests: covr, rcmdcheck, testthat, rmarkdown, ggplot2, knitr, sensitivity
VignetteBuilder: knitr
Encoding: UTF-8
Packaged: 2024-11-28 13:06:16 UTC; mmarcadella
Author: Benjamin Stocker [aut, cre] , Koen Hufkens [aut] , Josefa Aran Paredes [aut] , Laura Marques [ctb] , Mayeul Marcadella [ctb] , Ensheng Weng [ctb] , Fabian Bernhard [aut] , Geocomputation and Earth Observation, University of Bern [cph, fnd]
Maintainer: Benjamin Stocker <benjamin.stocker@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-28 23:10:02 UTC

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New package TAD with initial version 1.0.0
Package: TAD
Title: Realize the Trait Abundance Distribution
Version: 1.0.0
Description: This analytical framework is based on an analysis of the shape of the trait abundance distributions to better understand community assembly processes, and predict community dynamics under environmental changes. This framework mobilized a study of the relationship between the moments describing the shape of the distributions: the skewness and the kurtosis (SKR). The SKR allows the identification of commonalities in the shape of trait distributions across contrasting communities. Derived from the SKR, we developed mathematical parameters that summarise the complex pattern of distributions by assessing (i) the R², (ii) the Y-intercept, (iii) the slope, (iv) the functional stability of community (TADstab), and, (v) the distance from specific distribution families (i.e., the distance from the skew-uniform family a limit to the highest degree of evenness: TADeve).
License: BSD_3_clause + file LICENSE
URL: https://forgemia.inra.fr/urep/data_processing/tad
BugReports: https://forgemia.inra.fr/urep/data_processing/tad/-/issues
Encoding: UTF-8
Depends: R (>= 3.5)
Imports: doFuture, foreach, mblm (>= 0.12), methods, stats
Suggests: Cairo, covr, dplyr, devtools, future (>= 1.33), ggplot2 (>= 3.5), ggpubr (>= 0.6), knitr, Matrix (>= 1.6), pkgdown, rlang, rmarkdown, roxygen2, testthat (>= 3.0), tinytex
Language: en-US
VignetteBuilder: knitr
LazyData: true
LazyDataCompression: bzip2
NeedsCompilation: no
Packaged: 2024-11-28 09:59:57 UTC; lain
Author: Nathan Rondeau [aut], Yoann Le Bagousse-Pinguet [aut] , Raphael Martin [aut] , Lain Pavot [aut, cre], Pierre Liancourt [aut] , Nicolas Gross [aut] , INRAe/UREP [cph]
Maintainer: Lain Pavot <lain.pavot@inrae.fr>
Repository: CRAN
Date/Publication: 2024-11-28 12:20:02 UTC

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New package qVarSel with initial version 1.1
Package: qVarSel
Title: Select Variables for Optimal Clustering
Version: 1.1
Date: 2024-11-24
Description: Finding hidden clusters in structured data can be hindered by the presence of masking variables. If not detected, masking variables are used to calculate the overall similarities between units, and therefore the cluster attribution is more imprecise. The algorithm q-vars implements an optimization method to find the variables that most separate units between clusters. In this way, masking variables can be discarded from the data frame and the clustering is more accurate. Tests can be found in Benati et al.(2017) <doi:10.1080/01605682.2017.1398206>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.13), lpSolveAPI
Suggests: mclust
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-11-28 08:01:14 UTC; stefanobenati
Author: Stefano Benati [aut, cre]
Maintainer: Stefano Benati <stefano.benati@unitn.it>
Repository: CRAN
Date/Publication: 2024-11-28 12:10:02 UTC

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New package samplezoo with initial version 1.1.0
Package: samplezoo
Title: Generate Samples with a Variety of Probability Distributions
Version: 1.1.0
Maintainer: Nicholas Vietto <nicholasvietto@gmail.com>
Description: The 'samplezoo' package streamlines the process of generating samples from various probability distributions, enabling users to quickly create data frames for demonstrations, troubleshooting, or teaching. By prioritizing simplicity and efficiency,'samplezoo' reduces the need for repetitive code, making it particularly useful for beginners or anyone seeking to save time. The package implements standard methods for generating random samples from probability distributions commonly available in base R, with no specific external references. For more details, visit the package documentation.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
URL: https://github.com/nvietto/samplezoo, https://nvietto.github.io/samplezoo/
BugReports: https://github.com/nvietto/samplezoo/issues
NeedsCompilation: no
Packaged: 2024-11-27 16:30:58 UTC; nicholasvietto
Author: Nicholas Vietto [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-28 11:40:03 UTC

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New package saeHB.twofold with initial version 0.1.2
Package: saeHB.twofold
Title: Hierarchical Bayes Twofold Subarea Level Model SAE
Version: 0.1.2
Maintainer: Reyhan Saadi <reyhansaadi335@gmail.com>
Description: We designed this package to provides several functions for area and subarea level of small area estimation under Twofold Subarea Level Model using hierarchical Bayesian (HB) method with Univariate Normal distribution for variables of interest. Some dataset simulated by a data generation are also provided. The 'rjags' package is employed to obtain parameter estimates using Gibbs Sampling algorithm. Model-based estimators involves the HB estimators which include the mean, the variation of mean, and the quantile. For the reference, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Torabi and Rao (2014) <doi:10.1016/j.jmva.2014.02.001>, Leyla Mohadjer et al.(2007) <http://www.asasrms.org/Proceedings/y2007/Files/JSM2007-000559.pdf>, and Erciulescu et al.(2019) <doi:10.1111/rssa.12390>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: rjags, coda, stringr, stats, grDevices, graphics, data.table, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
VignetteBuilder: knitr
URL: https://github.com/reymath99/saeHB.twofold
BugReports: https://github.com/reymath99/saeHB.twofold/issues
NeedsCompilation: no
Packaged: 2024-11-27 10:39:18 UTC; USER10
Author: Reyhan Saadi [aut, cre], Azka Ubaidillah [aut]
Repository: CRAN
Date/Publication: 2024-11-28 11:20:03 UTC

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New package LLIC with initial version 3.0.0
Package: LLIC
Title: Likelihood Criterion (LIC) Analysis for Laplace Regression Model
Version: 3.0.0
Date: 2024-11-23
Description: Performs likelihood criterion analysis using the Laplace regression model to determine its optimal subset of variables. The methodology is based on Guo et al. (2023), LIC criterion for optimal subset selection in distributed interval estimation <doi:10.1080/02331888.2020.1823979>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, VGAM, dplyr, LaplacesDemon, relliptical, ggplot2, rlang
NeedsCompilation: no
Packaged: 2024-11-23 10:48:14 UTC; Lenovo
Author: Guangbao Guo [aut, cre], Yaxuan Wang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-11-28 12:00:02 UTC

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New package interpret with initial version 0.1.34
Package: interpret
Title: Fit Interpretable Machine Learning Models
Version: 0.1.34
Date: 2024-11-28
Description: Package for training interpretable machine learning models. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
URL: https://github.com/interpretml/interpret
BugReports: https://github.com/interpretml/interpret/issues
License: MIT + file LICENSE
Depends: R (>= 3.0.0)
NeedsCompilation: yes
SystemRequirements: C++17
Packaged: 2024-11-28 10:45:55 UTC; runner
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], The InterpretML Contributors [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>
Repository: CRAN
Date/Publication: 2024-11-28 11:40:08 UTC

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New package HTSeedGLM with initial version 0.1.0
Package: HTSeedGLM
Title: Hydro Thermal Time Analysis of Seed Germination Using Generalised Linear Model
Description: Seed germinates through the physical process of water uptake by dry seed driven by the difference in water potential between the seed and the water. There exists seed-to-seed variability in the base seed water potential. Hence, there is a need for a distribution such that a viable seed with its base seed water potential germinates if and only if the soil water potential is more than the base seed water potential. This package estimates the stress tolerance and uniformity parameters of the seed lot for germination under various temperatures by using the hydro-time model of counts of germinated seeds under various water potentials. The distribution of base seed water potential has been considered to follow Normal, Logistic and Extreme value distribution. The estimated proportion of germinated seeds along with the estimates of stress and uniformity parameters are obtained using a generalised linear model. The significance test of the above parameters for within and between temperatures is [...truncated...]
Author: Dr. Himadri Ghosh [aut, cre], Mr. Saikath Das [aut], Dr. Debopam Rakshit [aut]
Maintainer: Dr. Himadri Ghosh <hghosh@gmail.com>
Imports: stats
Version: 0.1.0
Encoding: UTF-8
License: GPL-3
NeedsCompilation: no
Packaged: 2024-11-27 14:50:58 UTC; Debopam
Repository: CRAN
Date/Publication: 2024-11-28 11:30:21 UTC

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New package epiparameterDB with initial version 0.1.0
Package: epiparameterDB
Title: Database of Epidemiological Parameters
Version: 0.1.0
Description: A data package containing a database of epidemiological parameters. It stores the data for the 'epiparameter' R package. Epidemiological parameter estimates are extracted from the literature.
License: CC0
URL: https://github.com/epiverse-trace/epiparameterDB/
BugReports: https://github.com/epiverse-trace/epiparameterDB/issues
Depends: R (>= 4.0.0)
Suggests: DT, jsonlite, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-GB
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-27 15:57:54 UTC; lshjl15
Author: Joshua W. Lambert [cre, aut, cph] , Adam Kucharski [aut] , Carmen Tamayo [aut]
Maintainer: Joshua W. Lambert <joshua.lambert@lshtm.ac.uk>
Repository: CRAN
Date/Publication: 2024-11-28 11:40:11 UTC

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New package bayeslist with initial version 0.0.1.4
Package: bayeslist
Title: Bayesian Analysis of List Experiments with Prior Information
Version: 0.0.1.4
Author: Xiao Lu [aut, cre], Richard Traunmueller [aut]
Maintainer: Xiao Lu <xiao.lu.research@gmail.com>
Description: Estimates Bayesian models of list experiments with informative priors. It includes functionalities to estimate different types of list experiment models with varying prior information. See Lu and Traunmüller (2021) <doi:10.2139/ssrn.3871089> for examples and details of estimation.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Biarch: true
Depends: R (>= 3.5.0)
Imports: methods, Formula, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>= 2.1.1), ggplot2 (>= 3.3.3)
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2024-11-27 15:23:45 UTC; xiao
Repository: CRAN
Date/Publication: 2024-11-28 11:30:05 UTC

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Wed, 27 Nov 2024

New package OmopViewer with initial version 0.2.0
Package: OmopViewer
Title: Visualise OMOP Results using 'shiny' Applications
Version: 0.2.0
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Description: Visualise results obtained from analysing data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model using 'shiny' applications.
License: Apache License (>= 2)
Encoding: UTF-8
URL: https://ohdsi.github.io/OmopViewer/
Depends: R (>= 2.10)
Imports: bslib, cli, dplyr, DT, glue, gt, lifecycle, markdown, omopgenerics (>= 0.4.0), purrr, rlang, shiny, snakecase, stringr, styler, tidyr, usethis, visOmopResults (>= 0.5.0), yaml
Suggests: CDMConnector, CodelistGenerator (>= 3.2.0), CohortCharacteristics (>= 0.3.0), CohortConstructor, DiagrammeR, DrugUtilisation (>= 0.7.1), duckdb, ggplot2, here, htmlwidgets, IncidencePrevalence (>= 0.8.0), knitr, omock (>= 0.3.0), OmopSketch, PatientProfiles, plotly, rmarkdown, RPostgres, shinycssloaders, shinyWidgets, sortable, testthat (>= 3.1.5), utils, webshot2, zip
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-27 20:12:14 UTC; martics
Author: Marti Catala [aut, cre] , Yuchen Guo [aut] , Edward Burn [ctb] , Nuria Mercade-Besora [ctb] , Elin Rowlands [ctb] , Cecilia Campanile [ctb]
Repository: CRAN
Date/Publication: 2024-11-27 23:20:09 UTC

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New package antaresProcessing with initial version 0.18.3
Package: antaresProcessing
Title: 'Antares' Results Processing
Version: 0.18.3
Description: Process results generated by 'Antares', a powerful open source software developed by RTE (Réseau de Transport d’Électricité) to simulate and study electric power systems (more information about 'Antares' here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>). This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.
URL: https://github.com/rte-antares-rpackage/antaresProcessing
BugReports: https://github.com/rte-antares-rpackage/antaresProcessing/issues
License: GPL (>= 3)
Depends: antaresRead (>= 1.1.5)
Imports: data.table, methods, stats
Suggests: parallel, testthat, knitr, rmarkdown, covr
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-27 09:11:16 UTC; berthetcle
Author: Tatiana Vargas [aut, cre], Jalal-Edine ZAWAM [ctb], Francois Guillem [ctb], Benoit Thieurmel [ctb], Titouan Robert [ctb], RTE [cph]
Maintainer: Tatiana Vargas <tatiana.vargas@rte-france.com>
Repository: CRAN
Date/Publication: 2024-11-27 13:20:11 UTC

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New package VICatMix with initial version 1.0
Package: VICatMix
Title: Variational Mixture Models for Clustering Categorical Data
Version: 1.0
Date: 2024-11-25
Maintainer: Jackie Rao <jackie.rao@mrc-bsu.cam.ac.uk>
Description: A variational Bayesian finite mixture model for the clustering of categorical data, and can implement variable selection and semi-supervised outcome guiding if desired. Incorporates an option to perform model averaging over multiple initialisations to reduce the effects of local optima and improve the automatic estimation of the true number of clusters. For further details, see the paper by Rao and Kirk (2024) <doi:10.48550/arXiv.2406.16227>.
License: GPL (>= 3)
URL: https://github.com/j-ackierao/VICatMix
BugReports: https://github.com/j-ackierao/VICatMix/issues
Imports: klaR, matrixStats, mcclust, Rcpp, stats, gtools
Suggests: doParallel, doRNG, foreach, parallel
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Depends: R (>= 2.10)
NeedsCompilation: yes
Packaged: 2024-11-26 15:24:01 UTC; jackie
Author: Jackie Rao [aut, cre], Paul D.W Kirk [ths], Sara Wade [ctb], Colin Starr [ctb], John Maddock [cph] .)
Repository: CRAN
Date/Publication: 2024-11-27 12:40:06 UTC

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New package strata with initial version 1.0.1
Package: strata
Title: Simple Framework for Simple Automation
Version: 1.0.1
Description: A tool suite for building project frameworks for users with access to only the most basic of automation tools.
License: MIT + file LICENSE
URL: https://github.com/asenetcky/strata, https://asenetcky.github.io/strata/
BugReports: https://github.com/asenetcky/strata/issues
Imports: checkmate (>= 2.3.2), dplyr (>= 1.1.0), fs (>= 1.6.4), glue (>= 1.8.0), lifecycle (>= 1.0.0), purrr (>= 1.0.2), readr (>= 2.0.0), rlang (>= 1.1.4), stringr (>= 1.5.1), tibble (>= 3.2.1)
Suggests: testthat (>= 3.0.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-22 19:02:52 UTC; alex
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-27 13:00:02 UTC

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New package fastVoteR with initial version 0.0.1
Package: fastVoteR
Title: Efficient Voting Methods for Committee Selection
Version: 0.0.1
Description: A fast 'Rcpp'-based implementation of polynomially-computable voting theory methods for committee ranking and scoring. The package includes methods such as Approval Voting (AV), Satisfaction Approval Voting (SAV), sequential Proportional Approval Voting (PAV), and sequential Phragmen's Rule. Weighted variants of these methods are also provided, allowing for differential voter influence.
License: LGPL (>= 3)
URL: https://bblodfon.github.io/fastVoteR/
Imports: checkmate, data.table, Rcpp
Suggests: mlr3misc (>= 0.15.1), testthat (>= 3.0.0)
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-11-26 15:25:04 UTC; john
Author: John Zobolas [cre, aut] , Anne-Marie George [ctb]
Maintainer: John Zobolas <bblodfon@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-27 12:40:02 UTC

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New package evolved with initial version 1.0.0
Package: evolved
Title: Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries
Version: 1.0.0
Description: "Evolutionary Virtual Education" - 'evolved' - provides multiple tools to help educators (especially at the graduate level or in advanced undergraduate level courses) apply inquiry-based learning in general evolution classes. In particular, the tools provided include functions that simulate evolutionary processes (e.g., genetic drift, natural selection within a single locus) or concepts (e.g. Hardy-Weinberg equilibrium, phylogenetic distribution of traits). More than only simulating, the package also provides tools for students to analyze (e.g., measuring, testing, visualizing) datasets with characteristics that are common to many fields related to evolutionary biology. Importantly, the package is heavily oriented towards providing tools for inquiry-based learning - where students follow scientific practices to actively construct knowledge. For additional details, see package's vignettes.
License: GPL (>= 3)
Encoding: UTF-8
Imports: ape, diversitree, phytools
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), LSD, paleobioDB, BAMMtools, plot3D
Depends: R (>= 2.10)
LazyData: true
VignetteBuilder: knitr
URL: <https://github.com/Auler-J/evolved>
BugReports: https://github.com/Auler-J/evolved/issues
NeedsCompilation: no
Packaged: 2024-11-26 15:47:16 UTC; matheus
Author: Matheus Januario [aut, cph, cre] , Jennifer Auler [aut] , Andressa Viol [aut], Daniel Rabosky [aut]
Maintainer: Matheus Januario <januarioml.eco@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-27 12:50:02 UTC

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New package DiscreteFWER with initial version 1.0.0
Package: DiscreteFWER
Title: FWER-Based Multiple Testing Procedures with Adaptation for Discrete Tests
Version: 1.0.0
Date: 2024-11-26
Description: Implementations of several multiple testing procedures that control the family-wise error rate (FWER) designed specifically for discrete tests. Included are discrete adaptations of the Bonferroni, Holm, Hochberg and Šidák procedures as described in the papers Döhler (2010) "Validation of credit default probabilities using multiple-testing procedures" <doi:10.21314/JRMV.2010.062> and Zhu & Guo (2019) "Family-Wise Error Rate Controlling Procedures for Discrete Data" <doi:10.1080/19466315.2019.1654912>. The main procedures of this package take as input the results of a test procedure from package 'DiscreteTests' or a set of observed p-values and their discrete support under their nulls. A shortcut function to apply discrete procedures directly to data is also provided.
License: GPL (>= 2)
Language: en-GB
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: Rcpp (>= 1.0.13), checkmate, DiscreteFDR (>= 2.0.0)
LinkingTo: Rcpp, RcppArmadillo
Suggests: DiscreteDatasets, DiscreteTests (>= 0.2.1)
URL: https://github.com/DISOhda/DiscreteFWER
BugReports: https://github.com/DISOhda/DiscreteFWER/issues
NeedsCompilation: yes
Packaged: 2024-11-26 19:49:39 UTC; fjunge
Author: Sebastian Doehler [aut, ctb] , Florian Junge [aut, ctb, cre]
Maintainer: Florian Junge <diso.fbmn@h-da.de>
Repository: CRAN
Date/Publication: 2024-11-27 13:00:05 UTC

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New package autoslider.core with initial version 0.1.0
Package: autoslider.core
Title: Slide Automation for Tables, Listings and Figures
Version: 0.1.0
Description: The normal process of creating clinical study slides is that a statistician manually type in the numbers from outputs and a separate statistician to double check the typed in numbers. This process is time consuming, resource intensive, and error prone. Automatic slide generation is a solution to address these issues. It reduces the amount of work and the required time when creating slides, and reduces the risk of errors from manually typing or copying numbers from the output to slides. It also helps users to avoid unnecessary stress when creating large amounts of slide decks in a short time window.
License: Apache License 2.0
URL: https://github.com/insightsengineering/autoslider.core
BugReports: https://github.com/insightsengineering/autoslider.core/issues
Depends: flextable (>= 0.9.4), officer (>= 0.3.18), R (>= 2.10)
Imports: assertthat, checkmate, cli, dplyr, filters (>= 0.3.1), forcats, formatters (>= 0.5.9), ggplot2, ggpubr, glue, googlesheets4, grid, gridExtra, lubridate, magrittr, methods, purrr, readxl, rlang, rlistings (>= 0.2.9), rtables (>= 0.6.10), rvg (>= 0.2.5), stringr, survival, tern (>= 0.9.6), tidyr, yaml
Suggests: devtools, googledrive, htmltools, httr, knitr, mime, nestcolor, rmarkdown (>= 2.23), rsvg, styler (>= 1.10.2), svglite (>= 2.1.2), testthat (>= 3.2.0), withr
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-11-26 17:01:59 UTC; rstudio
Author: Joe Zhu [cre, aut], Heng Wang [aut], Yinqi Zhao [aut], Bo Ci [aut], Liming Li [aut], Laura Wang [ctb], Xiaoli Duan [aut], Stefan Pascal Thoma [aut], Thomas Neitmann [ctb], Miles Almond [aut], Mahdi About [ctb], Kai Lim [ctb], Nolan Steed [ctb], Daoli [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Repository: CRAN
Date/Publication: 2024-11-27 12:50:06 UTC

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Tue, 26 Nov 2024

New package MultiTraits with initial version 0.1.0
Package: MultiTraits
Title: Analyzing and Visualizing Multidimensional Plant Traits
Version: 0.1.0
Date: 2024-11-25
Maintainer: Yan He <heyan@njfu.edu.cn>
Description: Implements analytical methods for multidimensional plant traits, including Competitors-Stress tolerators-Ruderals strategy analysis using leaf traits, Leaf-Height-Seed strategy analysis, Niche Periodicity Table analysis, and Trait Network analysis. Provides functions for data analysis, visualization, and network metrics calculation. Methods are based on Grime (1974) <doi:10.1038/250026a0>, Pierce et al. (2017) <doi:10.1111/1365-2435.12882>, Westoby (1998) <doi:10.1023/A:1004327224729>, Yang et al. (2022) <doi:10.1016/j.foreco.2022.120540>, Winemiller et al. (2015) <doi:10.1111/ele.12462>, He et al. (2020) <doi:10.1016/j.tree.2020.06.003>.
Imports: ggtern,igraph,Hmisc,corrplot,scatterplot3d,vegan,ggrepel
Depends: R (>= 4.0.0), ggplot2
Suggests: knitr,rmarkdown,testthat (>= 3.0.0),devtools
License: GPL-3
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-26 13:53:13 UTC; Administrator
Author: Yan He [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-26 14:40:02 UTC

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New package DIRMR with initial version 0.5.0
Package: DIRMR
Version: 0.5.0
Date: 2024-11-22
Title: Distributed Imputation for Random Effects Models with Missing Responses
Description: By adding over-relaxation factor to PXEM (Parameter Expanded Expectation Maximization) method, the MOPXEM (Monotonically Overrelaxed Parameter Expanded Expectation Maximization) method is obtained. Compare it with the existing EM (Expectation-Maximization)-like methods. Then, distribute and process five methods and compare them, achieving good performance in convergence speed and result quality.The philosophy of the package is described in Guo G. (2022) <doi:10.1007/s00180-022-01270-z>.
License: GPL-2
Imports: MASS,lava,mvtnorm
Encoding: UTF-8
NeedsCompilation: no
Author: Guangbao Guo [aut, cre] , Yaping Li [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Repository: CRAN
Packaged: 2024-11-25 12:13:49 UTC; A
Depends: R (>= 3.5.0)
Date/Publication: 2024-11-26 14:10:02 UTC

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New package tern.rbmi with initial version 0.1.4
Package: tern.rbmi
Title: Create Interface for 'RBMI' and 'tern'
Version: 0.1.4
Date: 2024-11-18
Description: 'RBMI' implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). This package provides an interface for 'RBMI' uses the 'tern' <https://cran.r-project.org/package=tern> framework by Zhu et al. (2023) and tabulate results easily using 'rtables' <https://cran.r-project.org/package=rtables> by Becker et al. (2023).
License: Apache License 2.0
URL: https://github.com/insightsengineering/tern.rbmi, https://insightsengineering.github.io/tern.rbmi/
BugReports: https://github.com/insightsengineering/tern.rbmi/issues
Depends: R (>= 3.6), rbmi (>= 1.2.5), tern (>= 0.9.4)
Imports: broom (>= 0.5.4), checkmate (>= 2.1.0), formatters (>= 0.5.6), lifecycle (>= 0.2.0), magrittr (>= 1.5), rtables (>= 0.6.7)
Suggests: BH, dplyr (>= 1.0.3), knitr (>= 1.42), Matrix, RcppEigen, rmarkdown (>= 2.23), rstan, testthat (>= 3.0.4), tidyr (>= 0.8.3)
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-25 15:37:40 UTC; rstudio
Author: Joe Zhu [aut, cre], Jana Stoilova [aut], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Repository: CRAN
Date/Publication: 2024-11-26 12:50:02 UTC

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New package SUSENAS with initial version 0.1.0
Package: SUSENAS
Title: National Socio-Economic Survey Data Collection Indonesia
Version: 0.1.0
Author: Fadhlul Mubarak [aut, cre], Nurniswah [aut], Vinny Yuliani Sundara [aut], Yusma Damayanti [aut], Ahmad Syukron Prasaja [aut]
Maintainer: Fadhlul Mubarak <mubarakfadhlul@gmail.com>
Description: Survey to collect data about the social and economic conditions of Indonesian society. This activity aims to include: As a data source for planning and evaluating national, sectoral development programs, and providing indicators for Sustainable Development Goals (TPB), National Medium Term Development Plan (RPJMN), and Nawacita, GDP/GRDP and annual Integrated Institutional Balance Sheet.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: readxl
NeedsCompilation: no
Packaged: 2024-11-25 05:07:01 UTC; HP
Repository: CRAN
Date/Publication: 2024-11-26 12:40:02 UTC

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New package SMNlmec with initial version 0.1.0
Package: SMNlmec
Title: Scale Mixture of Normal Distribution in Linear Mixed-Effects Model
Version: 0.1.0
Maintainer: Kelin Zhong <kelin.zhong@uconn.edu>
Description: Bayesian analysis of censored linear mixed-effects models that replace Gaussian assumptions with a flexible class of distributions, such as the scale mixture of normal family distributions, considering a damped exponential correlation structure which was employed to account for within-subject autocorrelation among irregularly observed measures. For more details, see Zhong et al. (2025, forthcoming in Statistics in Medicine).
Depends: R (>= 4.2)
Imports: rstan (>= 2.26.23), StanHeaders (>= 2.26.28), MASS (>= 7.3-60), tmvtnorm (>= 1.5), mvtnorm (>= 1.2-3), mnormt (>= 2.1.1), methods, stats, LaplacesDemon (>= 16.1.6), TruncatedNormal (>= 2.2.2), numDeriv (>= 2016.8-1.1)
URL: https://github.com/KelinZhong/SMNlmec
BugReports: https://github.com/KelinZhong/SMNlmec/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-25 14:10:55 UTC; Colin
Author: Kelin Zhong [aut, cre], Fernanda L. Schumacher [aut], Luis M. Castro [aut], Victor H. Lachos [aut], Jalmar M.F. Carrasco [aut]
Repository: CRAN
Date/Publication: 2024-11-26 12:50:06 UTC

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New package RMFM with initial version 1.1.0
Package: RMFM
Title: Robust Matrix Factor Model
Version: 1.1.0
Date: 2024-11-23
Author: Wei Liu [aut, cre]
Maintainer: Wei Liu <liuwei8@scu.edu.cn>
Description: We introduce a robust matrix factor model that explicitly incorporates tail behavior and employs a mean-shift term to avoid efficiency losses through pre-centering of observed matrices. More details on the methods related to our paper are currently under submission. A full reference to the paper will be provided in future versions once the paper is published.
License: GPL-3
Depends: irlba, R (>= 3.5.0)
Imports: stats, LaplacesDemon, MixMatrix, COAP, Rcpp (>= 1.0.10)
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-11-25 12:23:13 UTC; 10297
Repository: CRAN
Date/Publication: 2024-11-26 12:50:09 UTC

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New package PurpleAirAPI with initial version 0.1.0
Package: PurpleAirAPI
Title: Historical Data Retrieval from 'PurpleAir' Sensors via API
Version: 0.1.0
Description: Provides tools for retrieving and analyzing air quality data from 'PurpleAir' sensors through their API. Functions enable downloading historical measurements, accessing sensor metadata, and managing API request limitations through chunked data retrieval. For more information about the 'PurpleAir' API, see <https://api.purpleair.com/>.
License: MIT + file LICENSE
URL: https://github.com/heba-razzak/PurpleAirAPI
Imports: httr, jsonlite
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-25 05:10:58 UTC; heba
Author: Heba Abdelrazzak [aut, cre]
Maintainer: Heba Abdelrazzak <hebaarazzak@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-26 12:40:05 UTC

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New package PGaGEV with initial version 0.1.0
Package: PGaGEV
Title: Power Garima-Generalized Extreme Value Distribution
Version: 0.1.0
Language: en-US
Maintainer: Kittipong Klinjan <kittipong_k@rmutt.ac.th>
Description: Density, distribution function, quantile function, and random generation function based on Kittipong Klinjan,Tipat Sottiwan and Sirinapa Aryuyuen (2024)<DOI:10.28919/cmbn/8833>.
License: GPL-3
Encoding: UTF-8
Imports: LambertW,stats
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-25 04:00:26 UTC; ThinkPad X1
Author: Kittipong Klinjan [cre, aut], Tipat Sottiwan [aut], Sirinapa Aryuyuen [aut]
Repository: CRAN
Date/Publication: 2024-11-26 12:40:08 UTC

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Mon, 25 Nov 2024

New package scatterbar with initial version 0.1.0
Package: scatterbar
Title: Scattered Stacked Bar Chart Plots
Version: 0.1.0
Imports: magrittr, dplyr, tidyr, ggplot2
URL: https://github.com/JEFworks-Lab/scatterbar, http://jef.works/scatterbar/
BugReports: https://github.com/JEFworks-Lab/scatterbar/issues
Description: Provides a powerful and flexible tool for visualizing proportional data across spatially resolved contexts. By combining the concepts of scatter plots and stacked bar charts, 'scatterbar' allows users to create scattered bar chart plots, which effectively display the proportions of different categories at each (x, y) location. This visualization is particularly useful for applications where understanding the distribution of categories across spatial coordinates is essential. This package features automatic determination of optimal scaling factors based on data, customizable scaling and padding options for both x and y axes, flexibility to specify custom colors for each category, options to customize the legend title, and integration with 'ggplot2' for robust and high-quality visualizations. For more details, see Velazquez et al. (2024) <doi:10.1101/2024.08.14.606810>.
License: GPL-3
Encoding: UTF-8
LazyData: FALSE
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, patchwork
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-22 22:47:37 UTC; deev
Author: Dee Velazquez [aut, cre] , Jean Fan [aut, rev]
Maintainer: Dee Velazquez <dvelazq5@jhu.edu>
Repository: CRAN
Date/Publication: 2024-11-25 11:50:02 UTC

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New package MaxWiK with initial version 1.0.5
Package: MaxWiK
Title: Machine Learning Method Based on Isolation Kernel Mean Embedding
Version: 1.0.5
Description: Incorporates Approximate Bayesian Computation to get a posterior distribution and to select a model optimal parameter for an observation point. Additionally, the meta-sampling heuristic algorithm is realized for parameter estimation, which requires no model runs and is dimension-independent. A sampling scheme is also presented that allows model runs and uses the meta-sampling for point generation. A predictor is realized as the meta-sampling for the model output. All the algorithms leverage a machine learning method utilizing the maxima weighted Isolation Kernel approach, or 'MaxWiK'. The method involves transforming raw data to a Hilbert space (mapping) and measuring the similarity between simulated points and the maxima weighted Isolation Kernel mapping corresponding to the observation point. Comprehensive details of the methodology can be found in the papers Iurii Nagornov (2024) <doi:10.1007/978-3-031-66431-1_16> and Iurii Nagornov (2023) <doi:10.1007/978-3-031-29168-5_18& [...truncated...]
License: GPL (>= 3)
Depends: R (>= 3.3.0)
Imports: methods, stats, utils, scales, parallel, abc, ggplot2
Suggests: rmarkdown, knitr
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-22 22:13:56 UTC; nagornov
Author: Yuri Nagornov [aut, cre, cph]
Maintainer: Yuri Nagornov <nagornov.yuri@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-25 11:40:13 UTC

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New package ecostate with initial version 0.2.0
Package: ecostate
Title: State-Space Mass-Balance Model for Marine Ecosystems
Version: 0.2.0
Date: 2024-11-15
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Description: Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from 'Ecopath with Ecosim' <https://ecopath.org/> while fitting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. Package 'ecostate' fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.
License: GPL-3
Depends: R (>= 4.1.0), RTMB (>= 1.5.0),
Imports: TMB, MASS, checkmate, ggplot2, ggnetwork, igraph
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
LazyData: true
URL: https://james-thorson-noaa.github.io/ecostate/
BugReports: https://github.com/James-Thorson-NOAA/ecostate/issues
NeedsCompilation: no
Packaged: 2024-11-22 15:10:37 UTC; James.Thorson
Author: James T. Thorson [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-25 11:50:14 UTC

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New package ClinTrialPredict with initial version 0.0.4
Package: ClinTrialPredict
Title: Predicting and Simulating Clinical Trial with Time-to-Event Endpoint
Version: 0.0.4
Description: Predict the course of clinical trial with a time-to-event endpoint for both two-arm and single-arm design. Each of the four primary study design parameters (the expected number of observed events, the number of subjects enrolled, the observation time, and the censoring parameter) can be derived analytically given the other three parameters. And the simulation datasets can be generated based on the design settings.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2024-11-22 14:58:20 UTC; YDing29
Author: Yang Ding [aut, cre]
Maintainer: Yang Ding <tomding.biostat@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-25 11:40:18 UTC

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New package Blend with initial version 0.1.0
Package: Blend
Title: Bayesian Longitudinal Regularized Semiparametric Quantile Mixed Models
Version: 0.1.0
Date: 2024-11-21
Description: Our recently developed fully Bayesian semiparametric quantile mixed-effect model for high-dimensional longitudinal studies with heterogeneous observations can be implemented through this package. This model can distinguish between time-varying interactions and constant-effect-only cases to avoid model misspecifications. Facilitated by spike-and-slab priors, this model leads to superior performance in estimation, identification and statistical inference. In particular, robust Bayesian inferences in terms of valid Bayesian credible intervals on both parametric and nonparametric effects can be validated on finite samples. The Markov chain Monte Carlo algorithms of the proposed and alternative models are efficiently implemented in 'C++'.
Depends: R (>= 4.2.0)
License: GPL-2
Encoding: UTF-8
URL: https://github.com/kunfa/Blend
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp, splines, stats, ggplot2
NeedsCompilation: yes
Packaged: 2024-11-22 16:32:46 UTC; kunfan
Author: Kun Fan [aut, cre], Cen Wu [aut]
Maintainer: Kun Fan <kfan@ksu.edu>
Repository: CRAN
Date/Publication: 2024-11-25 11:40:22 UTC

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Fri, 22 Nov 2024

New package saeHB.spatial with initial version 0.1.1
Package: saeHB.spatial
Title: Small Area Estimation Hierarchical Bayes For Spatial Model
Version: 0.1.1
Description: Provides several functions and datasets for area level of Small Area Estimation under Spatial Model using Hierarchical Bayesian (HB) Method. Model-based estimators include the HB estimators based on a Spatial Fay-Herriot model with univariate normal distribution for variable of interest.The 'rjags' package is employed to obtain parameter estimates. For the reference, see Rao and Molina (2015) <doi:10.1002/9781118735855>.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/arinams/saeHB.spatial
BugReports: https://github.com/arinams/saeHB.spatial/issues
Imports: stringr, coda, rjags, stats, grDevices, graphics
SystemRequirements: JAGS (http://mcmc-jags.sourceforge.net)
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-22 08:41:08 UTC; User
Author: Arina Mana Sikana [aut, cre], Azka Ubaidillah [aut]
Maintainer: Arina Mana Sikana <sikanaradrianan@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-22 09:40:02 UTC

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New package GWlasso with initial version 1.0.1
Package: GWlasso
Title: Geographically Weighted Lasso
Version: 1.0.1
Description: Performs geographically weighted Lasso regressions. Find optimal bandwidth, fit a geographically weighted lasso or ridge regression, and make predictions. These methods are specially well suited for ecological inferences. Bandwidth selection algorithm is from A. Comber and P. Harris (2018) <doi:10.1007/s10109-018-0280-7>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, ggplot2, ggside, glmnet, GWmodel, lifecycle, magrittr, methods, progress, rlang, sf, tidyr
NeedsCompilation: no
Packaged: 2024-11-22 07:51:01 UTC; nibor
Author: Matthieu Mulot [aut, cre, cph] , Sophie Erb [aut]
Maintainer: Matthieu Mulot <matthieu.mulot@gmail.com>
Suggests: knitr, maps, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
LazyData: true
URL: https://github.com/nibortolum/GWlasso, https://nibortolum.github.io/GWlasso/
BugReports: https://github.com/nibortolum/GWlasso/issues
Repository: CRAN
Date/Publication: 2024-11-22 09:30:07 UTC

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New package exametrika with initial version 1.1.0
Package: exametrika
Title: Test Theory Analysis and Biclustering
Version: 1.1.0
Description: Implements comprehensive test data engineering methods as described in Shojima (2022, ISBN:978-9811699856). Provides statistical techniques for engineering and processing test data: Classical Test Theory (CTT) with reliability coefficients for continuous ability assessment; Item Response Theory (IRT) including Rasch, 2PL, and 3PL models with item/test information functions; Latent Class Analysis (LCA) for nominal clustering; Latent Rank Analysis (LRA) for ordinal clustering with automatic determination of cluster numbers; Biclustering methods including infinite relational models for simultaneous clustering of examinees and items without predefined cluster numbers; and Bayesian Network Models (BNM) for visualizing inter-item dependencies. Features local dependence analysis through LRA and biclustering, parameter estimation, dimensionality assessment, and network structure visualization for educational, psychological, and social science research.
License: MIT + file LICENSE
Language: en-US
Encoding: UTF-8
LazyData: true
BuildVignettes: true
Suggests: testthat (>= 3.0.0)
Depends: R (>= 3.5.0), mvtnorm, igraph
NeedsCompilation: no
Packaged: 2024-11-22 07:42:59 UTC; napier3
Author: Koji Kosugi [aut, cre]
Maintainer: Koji Kosugi <kosugitti@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-22 09:30:02 UTC

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New package anominate with initial version 0.7
Package: anominate
Title: Alpha-NOMINATE Ideal Point Estimator
Version: 0.7
Date: 2024-11-21
Author: Royce Carroll [aut], Christopher Hare [aut, cre], Jeffrey B. Lewis [aut], James Lo [aut], Keith T. Poole [aut], Howard Rosenthal [aut], Carlos Algara [aut], Samuel Fuller [aut]
Maintainer: Christopher Hare <cdhare@ucdavis.edu>
Description: Provides functions to estimate and interpret the alpha-NOMINATE ideal point model developed in Carroll et al. (2013, <doi:10.1111/ajps.12029>). alpha-NOMINATE extends traditional spatial voting frameworks by allowing for a mixture of Gaussian and quadratic utility functions, providing flexibility in modeling political actors' preferences. The package uses Markov Chain Monte Carlo (MCMC) methods for parameter estimation, supporting robust inference about individuals' ideological positions and the shape of their utility functions. It also contains functions to simulate data from the model and to calculate the probability of a vote passing given the ideal points of the legislators/voters and the estimated location of the choice alternatives.
License: GPL-2
Depends: stats, coda, wnominate, pscl, MCMCpack
URL: https://CRAN.R-project.org/package=anominate
NeedsCompilation: yes
Packaged: 2024-11-21 22:20:12 UTC; chare
Repository: CRAN
Date/Publication: 2024-11-22 09:20:02 UTC

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New package topics with initial version 0.20.0
Package: topics
Title: Creating and Significance Testing Language Features for Visualisation
Version: 0.20.0
Description: Implements differential language analysis with statistical tests and offers various language visualization techniques for n-grams and topics. It also supports the 'text' package. For more information, visit <https://r-topics.org/> and <https://www.r-text.org/>.
License: GPL-3
URL: https://r-topics.org/
BugReports: https://github.com/theharmonylab/topics/issues
Encoding: UTF-8
Archs: x64
SystemRequirements: Python (>= 3.6.0)
LazyData: true
BuildVignettes: true
Imports: text, textmineR, ggplot2, dplyr, mallet, rJava, ggwordcloud, effsize, purrr, tibble, methods, readr, stopwords, Matrix, ngram, stringr, rlang, tidyr
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
Depends: R (>= 4.00)
NeedsCompilation: no
Packaged: 2024-11-21 18:13:35 UTC; oscarkjell
Author: Leon Ackermann [aut] , Zhuojun Gu [aut] , Oscar Kjell [aut, cre]
Maintainer: Oscar Kjell <oscar.kjell@psy.lu.se>
Repository: CRAN
Date/Publication: 2024-11-22 09:00:02 UTC

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New package super with initial version 0.0.3
Package: super
Title: Interpreted String Literals
Version: 0.0.3
Description: An implementation of interpreted string literals. Based on the 'glue' package by Hester & Bryan (2024) <doi:10.32614/CRAN.package.glue> but with a focus on efficiency and simplicity at a cost of flexibility.
License: MIT + file LICENSE
URL: https://timtaylor.github.io/super/
BugReports: https://github.com/TimTaylor/super/issues
Depends: R (>= 3.6)
Suggests: glue, litedown, microbenchmark, tinytest
VignetteBuilder: litedown
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-11-21 18:25:33 UTC; tim
Author: Tim Taylor [aut, cre] , Jim Hester [aut] , Jennifer Bryan [aut] , Posit Software, PBC [cph, fnd]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Repository: CRAN
Date/Publication: 2024-11-22 09:00:06 UTC

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Thu, 21 Nov 2024

New package table.glue with initial version 0.0.5
Package: table.glue
Title: Make and Apply Customized Rounding Specifications for Tables
Version: 0.0.5
Description: Translate double and integer valued data into character values formatted for tabulation in manuscripts or other types of academic reports.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat, covr, knitr, rmarkdown, magrittr, dplyr, tidyr, tibble, gt
Imports: glue, stringi
URL: https://github.com/bcjaeger/table.glue
BugReports: https://github.com/bcjaeger/table.glue/issues
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-21 19:34:44 UTC; bjaeger
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Repository: CRAN
Date/Publication: 2024-11-21 21:20:02 UTC

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New package xpose.xtras with initial version 0.0.2
Package: xpose.xtras
Title: Extra Functionality for the 'xpose' Package
Version: 0.0.2
Description: Adding some at-present missing functionality, or functions unlikely to be added to the base 'xpose' package. This includes some diagnostic plots that have been missing in translation from 'xpose4', but also some useful features that truly extend the capabilities of what can be done with 'xpose'. These extensions include the concept of a set of 'xpose' objects, and diagnostics for likelihood-based models.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: assertthat, cli, colorspace, conflicted, dplyr (>= 1.1.2), forcats (>= 1.0.0), GGally, ggplot2 (>= 3.4.2), glue, lifecycle, magrittr, pmxcv, purrr (>= 1.0.1), readr (>= 2.1.4), rlang, stats, stringr (>= 1.5.0), tibble (>= 3.2.1), tidyr (>= 1.3.0), tidyselect, utils, vctrs, xpose
Suggests: DiagrammeR, grDevices, knitr, rmarkdown, testthat (>= 3.0.0), vdiffr
Depends: R (>= 2.10)
LazyData: true
VignetteBuilder: knitr
URL: https://jprybylski.github.io/xpose.xtras/, https://github.com/jprybylski/xpose.xtras
NeedsCompilation: no
Packaged: 2024-11-20 19:03:45 UTC; PRYBYJ
Author: John Prybylski [aut, cre]
Maintainer: John Prybylski <john.prybylski@pfizer.com>
Repository: CRAN
Date/Publication: 2024-11-21 17:20:02 UTC

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New package transDA with initial version 1.0.0
Package: transDA
Title: Transformation Discriminant Analysis
Date: 2024-11-05
Version: 1.0.0
Maintainer: Jing Li <jli178@crimson.ua.edu>
Author: Jing Li [aut, cre], Yana Melnykov [aut]
Description: Performs transformation discrimination analysis and non-transformation discrimination analysis. It also includes functions for Linear Discriminant Analysis, Quadratic Discriminant Analysis, and Mixture Discriminant Analysis. In the context of mixture discriminant analysis, it offers options for both common covariance matrix (common sigma) and individual covariance matrices (uncommon sigma) for the mixture components.
License: GPL (>= 2)
Encoding: UTF-8
Repository: CRAN
ByteCompile: true
NeedsCompilation: yes
Imports: mvtnorm
Packaged: 2024-11-21 16:11:59 UTC; jingli
Date/Publication: 2024-11-21 18:00:02 UTC

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New package TimeDepFrail with initial version 0.0.0.9
Package: TimeDepFrail
Title: Time Dependent Shared Frailty Cox Model
Version: 0.0.0.9
Description: Fits time-dependent shared frailty Cox model (specifically the adapted Paik et al.'s Model) based on the paper "Centre-Effect on Survival After Bone Marrow Transplantation: Application of Time-Dependent Frailty Models", by C.M. Wintrebert, H. Putter, A.H. Zwinderman and J.C. van Houwelingen (2004) <doi:10.1002/bimj.200310051>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports:
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-21 12:47:56 UTC; alessandragni
Author: Alessandra Ragni [aut, cre] , Giulia Romani [aut], Chiara Masci [ctb]
Maintainer: Alessandra Ragni <alessandra.ragni@polimi.it>
Repository: CRAN
Date/Publication: 2024-11-21 17:40:16 UTC

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New package scoutbaR with initial version 0.0.1
Package: scoutbaR
Title: A Spotlight 'React' Widget for 'shiny' Apps
Version: 0.0.1
Description: Creates a contextual menu that can be triggered with keyboard shortcuts or programmatically. This can replace traditional sidebars or navigation bars, thereby enhancing the user experience with lighter user interfaces.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: htmltools, reactR, shiny
Suggests: testthat (>= 3.0.0), shinytest2
NeedsCompilation: no
Packaged: 2024-11-21 11:12:07 UTC; davidgranjon
Author: David Granjon [aut, cre], Adenekan Wonderful [cph]
Maintainer: David Granjon <dgranjon@ymail.com>
Repository: CRAN
Date/Publication: 2024-11-21 17:40:02 UTC

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New package roxy.shinylive with initial version 1.0.0
Package: roxy.shinylive
Title: A 'roxygen2' Extension for 'Shinylive'
Version: 1.0.0
Description: An extension for 'roxygen2' to embed 'Shinylive' applications in the package documentation.
License: Apache License 2.0
URL: https://github.com/insightsengineering/roxy.shinylive/
BugReports: https://github.com/insightsengineering/roxy.shinylive/issues
Depends: R (>= 4.0)
Imports: glue, jsonlite (>= 1.8.6), lzstring (>= 0.1.3), roxygen2 (>= 7.2.0), stringr (>= 0.4)
Suggests: pkgdown (>= 2.0.0), testthat (>= 3.1.5), withr (>= 2.4.3)
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-21 10:51:44 UTC; ruckip
Author: Pawel Rucki [aut, cre], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Pawel Rucki <pawel.rucki@roche.com>
Repository: CRAN
Date/Publication: 2024-11-21 17:40:06 UTC

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New package mlms with initial version 1.0.2
Package: mlms
Title: Multilevel Monitoring System Data for Wells in the USGS INL Aquifer Monitoring Network
Version: 1.0.2
Description: Analysis-ready datasets detailing the Multilevel Monitoring System (MLMS) wells within the U.S. Geological Survey's (USGS) aquifer-monitoring network at the Idaho National Laboratory (INL) in Idaho, and the data collected within these wells. Supported by the U.S. Department of Energy (DOE), the USGS collected discrete measurements of hydraulic head at various depths from wells in the eastern Snake River Plain (ESRP) aquifer over several years. These measurements were derived from data on fluid pressure, fluid temperature, and atmospheric pressure. Each well was equipped with an MLMS, which included valved measurement ports, packer bladders, casing segments, and couplers. The MLMS facilitated monitoring at multiple hydraulically isolated depth intervals, reaching significant depths below the land surface. Additionally, groundwater samples were collected from these wells over multiple years and analyzed for various chemical and physical parameters.
Depends: R (>= 4.1)
Imports: checkmate, graphics, grDevices, jsonlite, plotrix, readxl, stats, sf, stringi, tools, utils
Suggests: connectapi, covr, dm, DiagrammeR, DiagrammeRsvg, fontawesome, htmltools, htmlwidgets, inldata, knitr, pkgbuild, pkgdown, pkgload, rcmdcheck, reactable, renv, rmarkdown, roxygen2, tinytest, V8, webmap
License: CC0
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey (USGS), an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
URL: https://code.usgs.gov/inl/mlms
BugReports: https://code.usgs.gov/inl/mlms/-/issues
NeedsCompilation: no
Packaged: 2024-11-20 22:40:52 UTC; jfisher
Author: Jason C. Fisher [aut, cre] , Brian V. Twining [aut]
Maintainer: Jason C. Fisher <jfisher@usgs.gov>
Repository: CRAN
Date/Publication: 2024-11-21 17:30:02 UTC

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New package matchedcc with initial version 0.1.1
Package: matchedcc
Title: 'Stata'-Like Matched Case-Control Analysis
Version: 0.1.1
Date: 2024-11-19
Maintainer: Simon R Parker <simon.parker.24@ucl.ac.uk>
Description: Calculate multiple statistics with confidence intervals for matched case-control data including risk difference, risk ratio, relative difference, and the odds ratio. Results are equivalent to those from 'Stata', and you can choose how to format your input data. Methods used are those described on page 56 the 'Stata' documentation for "Epitab - Tables for Epidemologists" <https://www.stata.com/manuals/repitab.pdf>.
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/simpar1471/matchedcc/, https://simpar1471.github.io/matchedcc/
BugReports: https://github.com/simpar1471/matchedcc/issues
Depends: R (>= 4.1.0)
Imports: checkmate, stats, cli, binom
Suggests: testthat (>= 3.0.0), readr, vctrs, stringr, purrr, knitr, rmarkdown, RStata
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-20 17:22:43 UTC; tadeo
Author: Simon R Parker [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-21 17:10:02 UTC

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New package kendallknight with initial version 0.4.0
Package: kendallknight
Title: Efficient Implementation of Kendall's Correlation Coefficient Computation
Version: 0.4.0
Imports: stats
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Depends: R(>= 3.5.0)
Description: The computational complexity of the implemented algorithm for Kendall's correlation is O(n log(n)), which is faster than the base R implementation with a computational complexity of O(n^2). For small vectors (i.e., less than 100 observations), the time difference is negligible. However, for larger vectors, the speed difference can be substantial and the numerical difference is minimal. The references are Knight (1966) <doi:10.2307/2282833>, Abrevaya (1999) <doi:10.1016/S0165-1765(98)00255-9>, Christensen (2005) <doi:10.1007/BF02736122> and Emara (2024) <https://learningcpp.org/>. This implementation is described in Vargas Sepulveda (2024) <doi:10.48550/arXiv.2408.09618>.
License: Apache License (>= 2)
BugReports: https://github.com/pachadotdev/capybara/issues
URL: https://pacha.dev/capybara/, https://github.com/pachadotdev/capybara
Encoding: UTF-8
NeedsCompilation: yes
LinkingTo: cpp11
VignetteBuilder: knitr
Language: en-US
LazyData: true
Packaged: 2024-11-20 15:49:09 UTC; pacha
Author: Mauricio Vargas Sepulveda [aut, cre] , Loader Catherine [ctb] ), Ross Ihaka [ctb] )
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2024-11-21 17:10:06 UTC

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New package eva3dm with initial version 0.99
Package: eva3dm
Title: Evaluation of 3D Meteorological and Air Quality Models
Version: 0.99
Date: 2024-11-19
Description: Provides tools for post-process, evaluate and visualize results from 3d Meteorological and Air Quality models against point observations (i.e. surface stations) and grid (i.e. satellite) observations.
Maintainer: Daniel Schuch <underschuch@gmail.com>
License: MIT + file LICENSE
Imports: terra, ncdf4, utils
Suggests: riem, testthat (>= 3.0.0)
Encoding: UTF-8
BugReports: https://github.com/Schuch666/eva3dm/issues/
Depends: R (>= 3.5.0)
URL: https://schuch666.github.io/eva3dm/
NeedsCompilation: no
Packaged: 2024-11-21 05:25:28 UTC; under
Author: Daniel Schuch [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-21 17:40:11 UTC

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New package covalchemy with initial version 1.0.0
Package: covalchemy
Title: Constructing Joint Distributions with Control Over Statistical Properties
Version: 1.0.0
Description: Synthesizing joint distributions from marginal densities, focusing on controlling key statistical properties such as correlation for continuous data, mutual information for categorical data, and inducing Simpson's Paradox. Generate datasets with specified correlation structures for continuous variables, adjust mutual information between categorical variables, and manipulate subgroup correlations to intentionally create Simpson's Paradox. Joe (1997) <doi:10.1201/b13150> Sklar (1959) <https://en.wikipedia.org/wiki/Sklar%27s_theorem>.
Encoding: UTF-8
Imports: dplyr, ggplot2, mvtnorm, interp, clue, ggExtra, gridExtra, DescTools, MASS
Depends: R (>= 3.5.0)
License: GPL-3
BugReports: https://github.com/namanlab/covalchemy/issues
URL: https://github.com/namanlab/covalchemy
NeedsCompilation: no
Packaged: 2024-11-20 14:57:15 UTC; namanagrawal
Author: Naman Agrawal [aut, cre]
Maintainer: Naman Agrawal <naman.agr03@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-21 17:10:11 UTC

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New package cohetsurr with initial version 1.0
Package: cohetsurr
Title: Assessing Complex Heterogeneity in Surrogacy
Version: 1.0
Date: 2024-11-20
Description: Provides functions to assess and test for complex heterogeneity in the utility of a surrogate marker with respect to multiple baseline covariates, using both a parametric model and a semiparametric two-step model. More details will be available in the future in: Knowlton, R., Tian, L., Parast, L. (2024) ``A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker."
License: GPL
Imports: stats, matrixStats, mvtnorm
NeedsCompilation: no
Packaged: 2024-11-20 18:08:26 UTC; rkkno
Author: Rebecca Knowlton [aut, cre]
Maintainer: Rebecca Knowlton <rknowlton@utexas.edu>
Repository: CRAN
Date/Publication: 2024-11-21 17:20:07 UTC

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New package chooseGCM with initial version 1.0.1
Package: chooseGCM
Title: Selecting General Circulation Models for Species Distribution Modeling
Version: 1.0.1
Maintainer: Luiz Esser <luizesser@gmail.com>
Description: Methods to help selecting General Circulation Models (GCMs) in the context of projecting models to future scenarios. It is provided clusterization algorithms, distance and correlation metrics, as well as a tailor-made algorithm to detect the optimum subset of GCMs that recreate the environment of all GCMs.
License: MIT + file LICENSE
Imports: checkmate, cluster, cowplot, factoextra, ggcorrplot, ggplot2, graphics, httr, methods, reshape2, stats, terra, usedist, utils
Encoding: UTF-8
Suggests: tictoc, testthat, sf, knitr, raster, rmarkdown, stars
URL: https://luizesser.github.io/chooseGCM/, https://github.com/luizesser/chooseGCM
VignetteBuilder: knitr
BugReports: https://github.com/luizesser/chooseGCM/issues
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-20 20:10:59 UTC; luizesser
Author: Dayani Baili [aut] , Reginaldo Re [aut] , Marcos Lima [aut] , Luiz Esser [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-21 17:20:11 UTC

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New package dhis2r with initial version 0.3.0
Package: dhis2r
Title: Client for the 'DHIS2' Web API
Version: 0.3.0
Description: Connect and pull data from a 'DHIS2 (District Health Information Software 2)' instance into R.
License: MIT + file LICENSE
URL: https://github.com/amanyiraho/dhis2r
BugReports: https://github.com/amanyiraho/dhis2r/issues
Imports: attempt (>= 0.3.1), curl (>= 4.3.3), dplyr (>= 1.0.10), httr2 (>= 0.2.2), R6 (>= 2.5.1)
Suggests: covr, httptest2, knitr, rmarkdown, testthat
Depends: R (>= 4.1.0)
Encoding: UTF-8
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-21 10:53:15 UTC; am
Author: Robinson Amanyiraho [cre, aut, cph]
Maintainer: Robinson Amanyiraho <amanyiraho@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-21 11:30:06 UTC

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New package scregclust with initial version 0.1.10
Package: scregclust
Title: Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data
Version: 0.1.10
Description: Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3> which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: Matrix, stats, methods, utils, reshape, igraph, graphics, grid, cli, prettyunits, ggplot2, rlang, Rcpp (>= 1.0.8)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), Seurat (>= 5.0.0), glmGamPoi, hdf5r
LinkingTo: Rcpp, RcppEigen
VignetteBuilder: knitr
License: GPL (>= 3)
URL: https://scmethods.github.io/scregclust/, https://github.com/scmethods/scregclust/
BugReports: https://github.com/scmethods/scregclust/issues
NeedsCompilation: yes
Packaged: 2024-11-20 09:16:53 UTC; felixheld
Author: Felix Held [aut, cre] , Ida Larsson [aut] , Sven Nelander [aut]
Maintainer: Felix Held <felix.held@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-21 07:30:02 UTC

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New package OutcomeWeights with initial version 0.1.0
Package: OutcomeWeights
Title: Outcome Weights of Treatment Effect Estimators
Version: 0.1.0
Description: Many treatment effect estimators can be written as weighted outcomes. These weights have established use cases like checking covariate balancing via packages like 'cobalt'. This package takes the original estimator objects and outputs these outcome weights. It builds on the general framework of Knaus (2024) <doi:10.48550/arXiv.2411.11559>. This version is compatible with the 'grf' package and provides an internal implementation of Double Machine Learning.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/MCKnaus/OutcomeWeights
BugReports: https://github.com/MCKnaus/OutcomeWeights/issues
Imports: ggplot2, grf, methods
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-11-20 13:34:23 UTC; Michael
Author: Michael C. Knaus [aut, cre] , Henri Pfleiderer [ctb]
Maintainer: Michael C. Knaus <michael.knaus@uni-tuebingen.de>
Repository: CRAN
Date/Publication: 2024-11-21 08:00:10 UTC

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New package CTTvis with initial version 0.1.0
Package: CTTvis
Title: Visualize Item Metrics of the Classical Test Theory Framework
Version: 0.1.0
Description: Visualizes results of item analysis such as item difficulty, item discrimination, and coefficient alpha for ease of result communication.
License: GPL-3
URL: https://github.com/TaridWong/CTTvis
Depends: R (>= 4.3)
Imports: CTT (>= 2.3.3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-20 06:38:06 UTC; tarid
Author: Tarid Wongvorachan [aut, cre, cph]
Maintainer: Tarid Wongvorachan <taridwongvorachan@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-21 07:30:07 UTC

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New package consrq with initial version 1.0
Package: consrq
Title: Constrained Quantile Regression
Version: 1.0
Date: 2024-11-20
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Depends: R (>= 4.0)
Suggests: Rfast2, cols
Imports: quantreg, Rfast
Description: Constrained quantile regression is performed. One constraint is that all beta coefficients (including the constant) cannot be negative, they can be either 0 or strictly positive. Another constraint is that the beta coefficients lie within an interval. References: Koenker R. (2005) Quantile Regression, Cambridge University Press. <doi:10.1017/CBO9780511754098>.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-11-20 13:44:36 UTC; mtsag
Repository: CRAN
Date/Publication: 2024-11-21 08:00:03 UTC

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New package cisp with initial version 0.1.0
Package: cisp
Title: A Correlation Indicator Based on Spatial Patterns
Version: 0.1.0
Description: Use the spatial association marginal contributions derived from spatial stratified heterogeneity to capture the degree of correlation between spatial patterns.
License: GPL-3
Encoding: UTF-8
URL: https://stscl.github.io/cisp/, https://github.com/stscl/cisp
BugReports: https://github.com/stscl/cisp/issues
Depends: R (>= 4.1.0)
Imports: dplyr, forcats, gdverse (>= 1.3), ggplot2, ggraph, igraph, magrittr, parallel, purrr, RColorBrewer, sdsfun (>= 0.4.3), sf, tibble, tidyr
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-20 13:40:22 UTC; dell
Author: Wenbo Lv [aut, cre, cph] , Yongze Song [aut] , Nan Jia [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-21 08:00:06 UTC

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New package AnomalyScore with initial version 0.1
Package: AnomalyScore
Title: Anomaly Scoring for Multivariate Time Series
Version: 0.1
Description: Compute an anomaly score for multivariate time series based on the k-nearest neighbors algorithm. Different computations of distances between time series are provided.
License: GPL (>= 3)
Imports: dtw, class, astsa, transport, marima, TSA, RANN, MASS, mvLSW, stats
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-20 14:21:40 UTC; guillermocgg
Author: Guillermo Granados [aut, cre]
Maintainer: Guillermo Granados <guillermo.granadosgarcia@outlook.com>
Repository: CRAN
Date/Publication: 2024-11-21 08:00:13 UTC

More information about AnomalyScore at CRAN
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Wed, 20 Nov 2024

New package quantsig with initial version 0.1.0
Package: quantsig
Title: Sigmoidal Quantile Function Estimator
Version: 0.1.0
Maintainer: Han Yu <han.yu@roswellpark.org>
Description: A sigmoidal quantile function estimator based on a newly defined generalized expectile function. The generalized sigmoidal quantile function can estimate quantiles beyond the range of the data, which is important for certain applications given smaller sample sizes. The package is based on the method introduced in Hutson (2024) <doi:10.1080/03610918.2022.2032161>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-20 01:33:30 UTC; ha31006
Author: Alan Hutson [aut], Han Yu [cre]
Repository: CRAN
Date/Publication: 2024-11-20 19:30:02 UTC

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New package gerda with initial version 0.1.0
Package: gerda
Title: German Election Database (GERDA)
Version: 0.1.0
Description: Provides tools to download comprehensive datasets of local, state, and federal election results in Germany from 1990 to 2021. The package facilitates access to data on turnout, vote shares for major parties, and demographic information across different levels of government (municipal, state, and federal). It offers access to geographically harmonized datasets that account for changes in municipal boundaries over time and incorporate mail-in voting districts. Users can easily retrieve, clean, and standardize German electoral data, making it ready for analysis. Data is sourced from <http://www.german-elections.com>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: stringdist, dplyr, readr, knitr, tibble
Suggests: rmarkdown, testthat (>= 3.0.0)
URL: https://github.com/hhilbig/gerda
BugReports: https://github.com/hhilbig/gerda/issues
VignetteBuilder: knitr
Maintainer: Hanno Hilbig <hhilbig@ucdavis.edu>
NeedsCompilation: no
Packaged: 2024-11-19 16:38:56 UTC; hanno
Author: Hanno Hilbig [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-20 19:10:01 UTC

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New package cellularautomata with initial version 0.1.0
Package: cellularautomata
Title: Cellular Automata
Version: 0.1.0
Maintainer: Vlad Tarko <vladtarko@gmail.com>
Description: Create cellular automata from 'Wolfram' rules. Allows the creation of 'Wolfram' style plots, as well as of animations. Easy to create multiple plots, for example the output of a rule with different initial states, or the output of many different rules from the same state. The output of a cellular automaton is given as a matrix, making it easy to try to explore the possibility of predicting its time evolution using various statistical tools available in R. Wolfram S. (2002, ISBN:1579550088) "A New Kind of Science".
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Imports: gganimate, ggplot2, patchwork, purrr, rlang
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-11-19 16:03:48 UTC; vladtarko
Author: Vlad Tarko [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-20 19:10:06 UTC

More information about cellularautomata at CRAN
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New package sampledatasets with initial version 0.1.0
Package: sampledatasets
Title: A Collection of Sample Datasets
Version: 0.1.0
Maintainer: Renzo Caceres Rossi <arenzocaceresrossi@gmail.com>
Description: Provides a collection of sample datasets on various fields such as automotive performance and safety data to historical demographics and socioeconomic indicators, as well as recreational data. It serves as a resource for researchers and analysts seeking to perform analyses and derive insights from classic data sets in R.
License: GPL-3
URL: https://github.com/lightbluetitan/sampledatasets
Encoding: UTF-8
LazyData: true
Suggests: ggplot2, dplyr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-19 15:43:53 UTC; renzorossiv
Author: Renzo Caceres Rossi [aut, cre]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-11-20 19:00:02 UTC

More information about sampledatasets at CRAN
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New package Certara.RsNLME with initial version 3.0.1
Package: Certara.RsNLME
Title: Pharmacometric Modeling
Version: 3.0.1
Description: Facilitate Pharmacokinetic (PK) and Pharmacodynamic (PD) modeling and simulation with powerful tools for Nonlinear Mixed-Effects (NLME) modeling. The package provides access to the same advanced Maximum Likelihood algorithms used by the NLME-Engine in the Phoenix platform. These tools support a range of analyses, from parametric methods to individual and pooled data analysis <https://www.certara.com/app/uploads/2020/06/BR_PhoenixNLME-v4.pdf>. Execution is supported both locally or on remote machines.
Depends: R (>= 4.0)
License: LGPL-3
URL: https://certara.github.io/R-RsNLME/
Encoding: UTF-8
LazyData: true
Suggests: rlang, knitr, rmarkdown, testthat, magrittr
Imports: xml2, assertthat, Certara.NLME8, data.table, jsonlite, methods, utils, ssh
NeedsCompilation: no
Packaged: 2024-11-19 15:11:50 UTC; jcraig
Author: James Craig [aut, cre], Michael Tomashevskiy [aut], Vitalii Nazarov [aut], Shuhua Hu [ctb], Soltanshahi Fred [aut], Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Repository: CRAN
Date/Publication: 2024-11-20 11:20:02 UTC

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New package SVEMnet with initial version 1.0.3
Package: SVEMnet
Title: Self-Validated Ensemble Models with Elastic Net Regression
Version: 1.0.3
Date: 2024-11-18
Maintainer: Andrew T. Karl <akarl@asu.edu>
Description: Implements Self-Validated Ensemble Models (SVEM, Lemkus et al. (2021) <doi:10.1016/j.chemolab.2021.104439>) using Elastic Net regression via 'glmnet' (Friedman et al. <doi:10.18637/jss.v033.i01>). SVEM averages predictions from multiple models fitted to fractionally weighted bootstraps of the data, tuned with anti-correlated validation weights. Also implements the randomized permutation whole model test for SVEM (Karl (2024) <doi:10.1016/j.chemolab.2024.105122>). Code for the whole model test was taken from the supplementary material of Karl (2024). Development of this package was assisted by 'GPT o1-preview' for code structure and documentation.
Depends: R (>= 3.5.0)
Imports: glmnet, stats, gamlss, gamlss.dist, ggplot2, lhs
License: GPL-2 | GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-19 10:06:13 UTC; andre
Author: Andrew T. Karl [cre, aut]
Repository: CRAN
Date/Publication: 2024-11-20 10:30:02 UTC

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New package psc with initial version 1.0.0
Package: psc
Title: Personalised Synthetic Controls
Version: 1.0.0
Maintainer: Richard Jackson <richJ23@liverpool.ac.uk>
Description: Allows the comparison of data cohorts (DC) against a Counter Factual Model (CFM) and measures the difference in terms of an efficacy parameter. Allows the application of Personalised Synthetic Controls.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/richjjackson/psc/
BugReports: https://github.com/richJJackson/psc/issues
Depends: R (>= 3.5.0)
Imports: mvtnorm, survival, enrichwith, stats, flexsurv
Suggests: knitr, rmarkdown, devtools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-19 10:15:28 UTC; richardjackson
Author: Richard Jackson [cre, aut]
Repository: CRAN
Date/Publication: 2024-11-20 10:40:02 UTC

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New package OpeNoise with initial version 0.2-18
Package: OpeNoise
Title: Environmental Noise Pollution Data Analysis
Version: 0.2-18
Maintainer: Pasquale Scordino <scordino.pasquale@gmail.com>
Imports: tidyr, lubridate, ggplot2, pracma
Description: Provides analyse, interpret and understand noise pollution data. Data are typically regular time series measured with sound meter. The package is partially described in Fogola, Grasso, Masera and Scordino (2023, <DOI:10.61782/fa.2023.0063>).
Depends: R (>= 3.5.0)
License: GPL (>= 3)
URL: https://arpapiemonte.github.io/openoise-analysis/, https://github.com/Arpapiemonte/openoise-analysis/
BugReports: https://github.com/Arpapiemonte/openoise-analysis/issues/
Encoding: UTF-8
LazyData: TRUE
Suggests: rmarkdown, htmltools, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-19 12:49:48 UTC; pakosko
Author: Pasquale Scordino [aut, cre], Simone Sperotto [ctb], Stefano Masera [ctb], Daniele Grasso [ctb], Jacopo Fogola [ctb]
Repository: CRAN
Date/Publication: 2024-11-20 10:40:10 UTC

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New package lwc2022 with initial version 1.0.0
Package: lwc2022
Title: Langa-Weir Classification of Cognitive Function for 2022 HRS Data
Version: 1.0.0
URL: https://github.com/C-Monaghan/lwc2022, https://c-monaghan.github.io/lwc2022/
BugReports: https://github.com/C-Monaghan/lwc2022/issues
Language: en-US
Description: Generates the Langa-Weir classification of cognitive function for the 2022 Health and Retirement Study (HRS) cognition data. It is particularly useful for researchers studying cognitive aging who wish to work with the most recent release of HRS data. The package provides user-friendly functions for data preprocessing, scoring, and classification allowing users to easily apply the Langa-Weir classification system. For details regarding the; HRS <https://hrsdata.isr.umich.edu/> and Langa-Weir classifications <https://hrsdata.isr.umich.edu/data-products/langa-weir-classification-cognitive-function-1995-2020>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: dplyr
Suggests: knitr
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-19 12:25:48 UTC; corma
Author: Cormac Monaghan [cph, aut, cre] , Rafael de Andrade Moral [aut] , Joanna McHugh Power [aut]
Maintainer: Cormac Monaghan <cormacmonaghan@protonmail.com>
Repository: CRAN
Date/Publication: 2024-11-20 10:40:07 UTC

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New package BioVizSeq with initial version 0.1.0
Package: BioVizSeq
Title: Visualizing the Elements Within Bio-Sequences
Version: 0.1.0
Maintainer: Shiqi Zhao <zhaosq89@163.com>
Description: Visualizing the types and distribution of elements within bio-sequences. At the same time, We have developed a geom layer, geom_rrect(), that can generate rounded rectangles. No external references are used in the development of this package.
License: Artistic-2.0
Encoding: UTF-8
Language: en-US
Imports: dplyr, ggplot2, httr, RColorBrewer, seqinr, stringr, tidyr, magrittr
NeedsCompilation: no
Packaged: 2024-11-19 10:08:10 UTC; zhaoshiqi
Author: Shiqi Zhao [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-20 10:40:14 UTC

More information about BioVizSeq at CRAN
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New package cbioportalR with initial version 1.1.1
Package: cbioportalR
Title: Browse and Query Clinical and Genomic Data from cBioPortal
Version: 1.1.1
Description: Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly functions that wrap 'cBioPortal's' existing API endpoints <https://www.cbioportal.org/api/swagger-ui/index.html>. Users can browse and query genomic data on mutations, copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'), microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study). See <https://www.cbioportal.org/> and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.1.4), knitr (>= 1.39), rmarkdown (>= 2.14), covr (>= 3.5.1), spelling
Depends: R (>= 2.10)
Imports: httr (>= 1.4.3), tibble (>= 3.1.7), purrr (>= 0.3.4), magrittr (>= 2.0.3), rlang (>= 1.0.3), glue (>= 1.6.2), jsonlite (>= 1.8.0), tidyr (>= 1.2.0), dplyr (>= 1.0.9), stringr (>= 1.4.0), cli (>= 3.3.0)
VignetteBuilder: knitr
URL: https://github.com/karissawhiting/cbioportalR, https://www.karissawhiting.com/cbioportalR/
BugReports: https://github.com/karissawhiting/cbioportalR/issues
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-19 21:02:33 UTC; kwhiting
Author: Karissa Whiting [aut, cre, cph]
Maintainer: Karissa Whiting <karissa.whiting@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-20 09:30:02 UTC

More information about cbioportalR at CRAN
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Tue, 19 Nov 2024

New package pseudobibeR with initial version 1.2
Package: pseudobibeR
Title: Aggregate Counts of Linguistic Features
Version: 1.2
Date: 2024-11-18
Description: Calculates the lexicogrammatical and functional features described by Biber (1985) <doi:10.1515/ling.1985.23.2.337> and widely used for text-type, register, and genre classification tasks.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: dplyr, purrr, quanteda, quanteda.textstats, rlang, stringr, tibble, magrittr
Suggests: testthat (>= 3.0.0), udpipe
NeedsCompilation: no
Packaged: 2024-11-18 19:20:40 UTC; alexreinhart
Author: David Brown [aut, cre] , Alex Reinhart [aut]
Maintainer: David Brown <dwb2@andrew.cmu.edu>
Repository: CRAN
Date/Publication: 2024-11-19 12:20:06 UTC

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New package mvvg with initial version 0.1.0
Package: mvvg
Title: Matrix-Variate Variance-Gamma Distribution
Version: 0.1.0
Description: Rudimentary functions for sampling and calculating density from the matrix-variate variance-gamma distribution.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: MixMatrix, nlme, psych
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-11-18 20:58:53 UTC; soonsk
Author: Samuel Soon [aut, cre]
Maintainer: Samuel Soon <samksoon2@gmail.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-11-19 12:20:27 UTC

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New package LFM with initial version 0.1.0
Package: LFM
Title: Laplace Factor Model Analysis and Evaluation
Date: 2024-11-18
Version: 0.1.0
Description: Enables the generation of Laplace factor models across diverse Laplace distributions and facilitates the application of Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Parallel Principal Component (PPC), Sparse Approximate Principal Component (SAPC), Standard Principal Component (SPC), and Farm Test methods to these models. Evaluates the efficacy of these methods within the context of Laplace factor models by scrutinizing parameter estimation accuracy, mean square error, and the degree of sparsity.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: stats, FarmTest, MASS, SOPC, LaplacesDemon, matrixcalc, relliptical
NeedsCompilation: no
Language: en-US
Author: Guangbao Guo [aut, cre], Siqi Liu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Depends: R (>= 3.5.0)
BuildManual: yes
Suggests: testthat (>= 3.0.0)
Packaged: 2024-11-18 10:54:04 UTC; R7000
Repository: CRAN
Date/Publication: 2024-11-19 12:30:09 UTC

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New package GRIN2 with initial version 1.0
Package: GRIN2
Title: Genomic Random Interval (GRIN)
Version: 1.0
Description: Improved version of 'GRIN' software that streamlines its use in practice to analyze genomic lesion data, accelerate its computing, and expand its analysis capabilities to answer additional scientific questions including a rigorous evaluation of the association of genomic lesions with RNA expression. Pounds, Stan, et al. (2013) <DOI:10.1093/bioinformatics/btt372>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: biomaRt, circlize, ComplexHeatmap, data.table, dplyr, EnsDb.Hsapiens.v75, ensembldb, forcats, GenomeInfoDb, ggplot2, graphics, grDevices, grid, gridGraphics, Gviz, magrittr, stats, stringr, survival, tibble, tidyselect, utils, writexl
Suggests: knitr, rmarkdown
NeedsCompilation: no
Maintainer: Abdelrahman Elsayed <aelsayed@stjude.org>
Depends: R (>= 4.2.0)
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/abdel-elsayed87/GRIN2
BugReports: https://github.com/abdel-elsayed87/GRIN2/issues
Packaged: 2024-11-18 22:39:09 UTC; aelsa
Author: Abdelrahman Elsayed [aut, cre, cph] , Xueyuan Cao [aut], Lakshmi Anuhya patibandla [aut], Stanley Pounds [aut, cph]
Repository: CRAN
Date/Publication: 2024-11-19 12:30:36 UTC

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New package forestdynR with initial version 0.0.1
Package: forestdynR
Title: Calculate Forest Dynamics
Version: 0.0.1
Maintainer: Pedro Higuchi <higuchip@gmail.com>
Description: Determines the dynamics of tree species communities (mortality rates, recruitment, loss and gain in basal area, net changes and turnover). Important notes are a) The 'forest_df' argument (data) must contain the columns 'plot' (plot identification), 'spp' (species identification), DBH_1 (Diameter at breast height in first year of measure) and DBH_2 (Diameter at breast height in second year of measure). DBH_1 and DBH_2 must be numeric values; b) example input file in 'data(forest_df_example)'; c) The argument 'inv_time' represents the time between inventories, in years; d) The 'coord' argument must be of the type 'c(longitude, latitude)', with decimal degree values; e) Argument 'add_wd' represents a dataframe with wood density values (g cm-3) format with three columns ('genus', 'species', 'wd'). This argument is set to NULL by default, and if isn't provided, the wood density will be estimated with the getWoodDensity() function from the 'BIOMASS' package.
License: GPL (>= 2)
URL: https://github.com/higuchip/forestdynR
BugReports: https://github.com/higuchip/forestdynR/issues
Depends: R (>= 4.3.0)
Imports: BIOMASS (>= 2.1.11), tcltk (>= 1.0.0),
Suggests: covr, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-18 20:37:29 UTC; optimus-prime
Author: Pedro Higuchi [cre, aut], Ana Carolina Silva [aut], Adam Slabadack [aut]
Repository: CRAN
Date/Publication: 2024-11-19 12:20:41 UTC

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New package talkr with initial version 0.1.3
Package: talkr
Title: Plotting Conversation Data
Version: 0.1.3
Description: Visualisation, analysis and quality control of conversational data. Rapid and visual insights into the nature, timing and quality of time-aligned annotations in conversational corpora. For more details, see Dingemanse et al., (2022) <doi:10.18653/v1/2022.acl-long.385>.
License: Apache License (>= 2)
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Imports: cowplot, dplyr, ggplot2, ggthemes, knitr, stats, stringr, tidyr, tidyselect
Suggests: rmarkdown, testthat (>= 3.0.0), pkgdown, ggrepel, utils
NeedsCompilation: no
Packaged: 2024-11-15 13:53:36 UTC; pablo
Author: Mark Dingemanse [aut, cre], Barbara Vreede [aut], Eva Viviani [aut], Pablo Rodriguez-Sanchez [aut], Andreas Liesenfeld [ctb], Netherlands eScience Center [cph, fnd]
Maintainer: Mark Dingemanse <mark.dingemanse@ru.nl>
Repository: CRAN
Date/Publication: 2024-11-19 11:50:03 UTC

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New package ecdata with initial version 1.1.1
Package: ecdata
Title: Loads Data from the Executive Communications Dataset
Version: 1.1.1
Description: A minimal package for downloading data from 'GitHub' repositories of the Executive Communications Database.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
URL: https://github.com/Executive-Communications-Dataset/ecdata,https://executive-communications-dataset.github.io/ecdata/
BugReports: https://github.com/Executive-Communications-Dataset/ecdata/issues
Depends: R (>= 4.0)
Imports: arrow (>= 16.1.0), cli (>= 3.6.3), rlang (>= 1.1.0), glue (>= 1.4.0), piggyback (>= 0.1.5), utils, tools, cachem (>= 1.0.0), memoise (>= 2.0.0), vctrs, curl
Suggests: duckplyr, testthat (>= 3.0.0), data.table, dplyr, altdoc, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-18 18:12:34 UTC; josh
Author: Joshua Allen [aut, cre, cph] , Ryan Carlin [ctb], Juan Gomez-Gomez-Cruces [ctb], Will Horne [aut, ctb], Jamie Lindh [ctb], Cecilia Martinez-Gallardo [ctb], Miles Massesy [ctb]
Maintainer: Joshua Allen <joshua.f.allen@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-19 12:00:10 UTC

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New package CSTE with initial version 3.0.0
Package: CSTE
Version: 3.0.0
Date: 2024-11-16
Title: Covariate Specific Treatment Effect (CSTE) Curve
Description: A uniform statistical inferential tool in making individualized treatment decisions, which implements the methods of Ma et al. (2017)<DOI:10.1177/0962280214541724> and Guo et al. (2021)<DOI:10.1080/01621459.2020.1865167>. It uses a flexible semiparametric modeling strategy for heterogeneous treatment effect estimation in high-dimensional settings and can gave valid confidence bands. Based on it, one can find the subgroups of patients that benefit from each treatment, thereby making individualized treatment selection.
License: GPL (>= 2)
Encoding: UTF-8
Imports: Rcpp (>= 1.0.4), fda, splines, survival, locpol, dfoptim
LinkingTo: Rcpp
Suggests: mvtnorm, sigmoid
NeedsCompilation: yes
Packaged: 2024-11-18 16:47:21 UTC; wenjiehu
Author: Peng Wu [aut], Wenjie Hu [aut, cre], Yuhao Deng [aut], Haoxiang Wang [aut], Xiaohua Zhou [aut]
Maintainer: Wenjie Hu <huwenjie@pku.edu.cn>
Repository: CRAN
Date/Publication: 2024-11-19 12:00:15 UTC

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New package where with initial version 1.0.0
Package: where
Title: Vectorised Substitution and Evaluation
Version: 1.0.0
Description: Provides a clean syntax for vectorising the use of Non-Standard Evaluation (NSE), for example in 'ggplot2', 'dplyr', or 'data.table'.
License: MIT + file LICENSE
URL: https://github.com/KiwiMateo/where
BugReports: https://github.com/KiwiMateo/where/issues
Suggests: data.table, dplyr, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-18 06:45:14 UTC; OEM
Author: Matt Hendtlass [aut, cre]
Maintainer: Matt Hendtlass <m.hendtlass@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-19 09:40:02 UTC

More information about where at CRAN
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New package OutSeekR with initial version 1.0.0
Package: OutSeekR
Title: Statistical Approach to Outlier Detection in RNA-Seq and Related Data
Version: 1.0.0
Date: 2024-11-15
Description: An approach to outlier detection in RNA-seq and related data based on five statistics. 'OutSeekR' implements an outlier test by comparing the distributions of these statistics in observed data with those of simulated null data.
Depends: R (>= 2.10)
Imports: future.apply, gamlss, gamlss.dist, lsa, truncnorm
Suggests: future, knitr, rmarkdown, testthat (>= 3.0.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-15 23:56:34 UTC; danknight
Author: Jee Yun Han [aut], John Sahrmann [aut], Jaron Arbet [ctb], Paul Boutros [aut, cre, cph]
Maintainer: Paul Boutros <pboutros@mednet.ucla.edu>
Repository: CRAN
Date/Publication: 2024-11-19 09:10:05 UTC

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New package multiDoE with initial version 0.9.2
Package: multiDoE
Title: Multi-Criteria Design of Experiments for Optimal Design
Version: 0.9.2
Maintainer: Andrea Melloncelli <andrea.melloncelli@vanlog.it>
Description: Multi-criteria design of experiments algorithm that simultaneously optimizes up to six different criteria ('I', 'Id', 'D', 'Ds', 'A' and 'As'). The algorithm finds the optimal Pareto front and, if requested, selects a possible symmetrical design on it. The symmetrical design is selected based on two techniques: minimum distance with the Utopia point or the 'TOPSIS' approach.
License: CC BY 4.0
URL: https://github.com/andreamelloncelli/multiDoE
Imports: ggplot2, magrittr, plotly, pracma
Suggests: devtools, here, knitr, logr, markdown, rgl, rmarkdown, testthat (>= 3.0.0), usethis
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-18 08:46:59 UTC; daco
Author: Francesca Cucchi [aut], Andrea Melloncelli [aut, cre], Francesco Sambo [aut], Kalliopi Mylona [aut], Matteo Borrotti [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-11-19 09:50:02 UTC

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New package deident with initial version 1.0.0
Package: deident
Title: Persistent Data Anonymization Pipeline
Version: 1.0.0
Description: A framework for the replicable removal of personally identifiable data (PID) in data sets. The package implements a suite of methods to suit different data types based on the suggestions of Garfinkel (2015) <doi:10.6028/NIST.IR.8053> and the ICO "Guidelines on Anonymization" (2012) <https://ico.org.uk/media/1061/anonymisation-code.pdf>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), checkmate, knitr, rmarkdown, roxygen2
Imports: R6, dplyr, openssl, tidyselect, rlang (>= 0.4.11), glue, purrr, stringr, yaml, readr, openxlsx, lemon, withr, fs
Depends: R (>= 2.10)
VignetteBuilder: knitr
Language: en-GB
NeedsCompilation: no
Packaged: 2024-11-18 11:36:38 UTC; rzc1
Author: Robert Cook [aut, cre] , Md Assaduzaman [aut] , Sarahjane Jones [aut]
Maintainer: Robert Cook <robert.cook@staffs.ac.uk>
Repository: CRAN
Date/Publication: 2024-11-19 09:50:06 UTC

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Mon, 18 Nov 2024

New package tsmarch with initial version 1.0.0
Package: tsmarch
Title: Multivariate ARCH Models
Description: Feasible Multivariate Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models including Dynamic Conditional Correlation (DCC), Copula GARCH and Generalized Orthogonal GARCH with Generalized Hyperbolic distribution. A review of some of these models can be found in Boudt, Galanos, Payseur and Zivot (2019) <doi:10.1016/bs.host.2019.01.001>.
Version: 1.0.0
Maintainer: Alexios Galanos <alexios@4dscape.com>
Depends: R (>= 3.5.0), methods, tsmethods (>= 1.0.2)
LinkingTo: Rcpp (>= 0.10.6), RcppArmadillo, RcppParallel, RcppBessel
SystemRequirements: GNU make
Imports: Rcpp, RcppParallel, tsgarch (>= 1.0.3), tsdistributions (>= 1.0.2), RcppBessel, Rsolnp, nloptr, numDeriv, abind, shape, Rdpack, xts, zoo, lubridate, sandwich, future.apply, future, stats, utils, data.table
License: GPL-2
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/tsmodels/tsmarch/issues
ByteCompile: true
URL: https://github.com/tsmodels/tsmarch, https://www.nopredict.com
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), tstests
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-11-15 10:33:37 UTC; alexios
Author: Alexios Galanos [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-18 13:30:02 UTC

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New package effectplots with initial version 0.1.0
Package: effectplots
Title: Effect Plots
Version: 0.1.0
Description: High-performance implementation of various effect plots useful for regression and probabilistic classification tasks. The package includes partial dependence plots (Friedman, 2021, <doi:10.1214/aos/1013203451>), accumulated local effect plots and M-plots (both from Apley and Zhu, 2016, <doi:10.1111/rssb.12377>), as well as plots that describe the statistical associations between model response and features. It supports visualizations with either 'ggplot2' or 'plotly', and is compatible with most models, including 'Tidymodels', models wrapped in 'DALEX' explainers, or models with case weights.
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Encoding: UTF-8
Imports: collapse, ggplot2, grDevices, patchwork, plotly, Rcpp, stats
Suggests: testthat (>= 3.0.0)
URL: https://github.com/mayer79/effectplots
BugReports: https://github.com/mayer79/effectplots/issues
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2024-11-15 11:30:14 UTC; mayer
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-18 13:50:04 UTC

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New package CareDensity with initial version 0.1.0
Package: CareDensity
Title: Calculate the Care Density or Fragmented Care Density Given a Patient-Sharing Network
Version: 0.1.0
Maintainer: Robin Denz <robin.denz@rub.de>
Description: Given a patient-sharing network, calculate either the classic care density as proposed by Pollack et al. (2013) <doi:10.1007/s11606-012-2104-7> or the fragmented care density as proposed by Engels et al. (2024) <doi:10.1186/s12874-023-02106-0>. By utilizing the 'igraph' and 'data.table' packages, the provided functions scale well for very large graphs.
License: GPL (>= 3)
URL: https://github.com/RobinDenz1/CareDensity, https://robindenz1.github.io/CareDensity/
BugReports: https://github.com/RobinDenz1/CareDensity/issues
Depends: MatrixExtra
Imports: data.table, igraph (>= 2.0.0), utils
Suggests: knitr, rmarkdown, testthat (>= 3.2.1), covr
VignetteBuilder: knitr
Contact: <robin.denz@rub.de>
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-15 12:09:25 UTC; Robin Denz
Author: Robin Denz [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-18 13:50:11 UTC

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New package bfboinet with initial version 0.1.0
Package: bfboinet
Title: Backfill Bayesian Optimal Interval Design Using Efficacy and Toxicity
Version: 0.1.0
Description: The backfill Bayesian optimal interval design using efficacy and toxicity outcomes for dose optimization (BF-BOIN-ET) design is a novel clinical trial design to allow patients to be backfilled at lower doses during a dose-finding trial while prioritizing the dose-escalation cohort to explore a higher dose. The advantages compared to the other designs in terms of the percentage of correct optimal dose (OD) selection, reducing the sample size, and shortening the duration of the trial, in various realistic setting.
License: GPL-3
Encoding: UTF-8
Imports: Iso, copula, dplyr, tidyselect, magrittr
NeedsCompilation: no
Packaged: 2024-11-15 08:59:14 UTC; A4021579
Author: Jing Zhu [cre, aut], Kentaro Takeda [aut]
Maintainer: Jing Zhu <zhujing716@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-18 13:30:09 UTC

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Sat, 16 Nov 2024

New package dfr with initial version 0.1.1
Package: dfr
Title: Dual Feature Reduction for SGL
Version: 0.1.1
Date: 2024-11-16
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Description: Implementation of the Dual Feature Reduction (DFR) approach for the Sparse Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a feature reduction approach that applies strong screening to reduce the feature space before optimisation, leading to speed-up improvements for fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear and logistic SGL models supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported.
Imports: sgs, caret, MASS, methods, stats, grDevices, graphics, Matrix
Suggests: SGL, gglasso, glmnet, testthat
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/ff1201/dfr
BugReports: https://github.com/ff1201/dfr/issues
NeedsCompilation: no
Packaged: 2024-11-16 10:32:08 UTC; ff120
Author: Fabio Feser [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-16 16:20:01 UTC

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New package sgs with initial version 0.3.1
Package: sgs
Title: Sparse-Group SLOPE: Adaptive Bi-Level Selection with FDR Control
Version: 0.3.1
Date: 2024-11-16
Maintainer: Fabio Feser <ff120@ic.ac.uk>
Description: Implementation of Sparse-group SLOPE (SGS) (Feser and Evangelou (2023) <doi:10.48550/arXiv.2305.09467>) models. Linear and logistic regression models are supported, both of which can be fit using k-fold cross-validation. Dense and sparse input matrices are supported. In addition, a general Adaptive Three Operator Splitting (ATOS) (Pedregosa and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) implementation is provided. Group SLOPE (gSLOPE) (Brzyski et al. (2019) <doi:10.1080/01621459.2017.1411269>) and group-based OSCAR models (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) are also implemented. All models are available with strong screening rules (Feser and Evangelou (2024) <doi:10.48550/arXiv.2405.15357>) for computational speed-up.
Imports: Matrix, MASS, caret, grDevices, graphics, methods, stats, SLOPE, Rlab, Rcpp (>= 1.0.10)
LinkingTo: Rcpp, RcppArmadillo
Suggests: SGL, gglasso, glmnet, testthat, knitr, grpSLOPE, rmarkdown
License: GPL (>= 3)
Encoding: UTF-8
URL: https://github.com/ff1201/sgs
BugReports: https://github.com/ff1201/sgs/issues
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-11-16 10:33:20 UTC; ff120
Author: Fabio Feser [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-16 14:20:02 UTC

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Fri, 15 Nov 2024

New package GeoTox with initial version 0.2.0
Package: GeoTox
Title: Spatiotemporal Mixture Risk Assessment
Version: 0.2.0
Description: Connecting spatiotemporal exposure to individual and population-level risk via source-to-outcome continuum modeling. The package, methods, and case-studies are described in Messier, Reif, and Marvel (2024) <doi:10.1101/2024.09.23.24314096> and Eccles et al. (2023) <doi:10.1016/j.scitotenv.2022.158905>.
License: MIT + file LICENSE
URL: https://niehs.github.io/GeoTox/, https://github.com/NIEHS/GeoTox
Depends: R (>= 4.4.0)
Imports: dplyr, ggplot2, ggridges, rlang, sf, stats, stringr, tibble, tidyr, tidyselect, truncnorm, utils
Suggests: ggpubr, httk, httr2, knitr, purrr, readr, readxl, rmarkdown, scales, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/NIEHS/GeoTox/issues
NeedsCompilation: no
Packaged: 2024-11-14 17:29:09 UTC; marvelsw
Author: Skylar Marvel [aut] , David Reif [aut] , Kyle Messier [cre, aut] , Spatiotemporal Exposures and Toxicology Group [cph]
Maintainer: Kyle Messier <kyle.messier@nih.gov>
Repository: CRAN
Date/Publication: 2024-11-15 14:20:02 UTC

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New package OPTeCD with initial version 1.0.0
Package: OPTeCD
Title: Optimal Partial Tetra-Allele Cross Designs
Version: 1.0.0
Maintainer: Ashutosh Dalal <ashutosh.dalal97@gmail.com>
Description: Tetra-allele cross often referred as four-way cross or double cross or four-line cross are those type of mating designs in which every cross is obtained by mating amongst four inbred lines. A tetra-allele cross can be obtained by crossing the resultant of two unrelated diallel crosses. A common triallel cross involving four inbred lines A, B, C and D can be symbolically represented as (A X B) X (C X D) or (A, B, C, D) or (A B C D) etc. Tetra-allele cross can be broadly categorized as Complete Tetra-allele Cross (CTaC) and Partial Tetra-allele Crosses (PTaC). Rawlings and Cockerham (1962)<doi:10.2307/2527461> firstly introduced and gave the method of analysis for tetra-allele cross hybrids using the analysis method of single cross hybrids under the assumption of no linkage. The set of all possible four-way mating between several genotypes (individuals, clones, homozygous lines, etc.) leads to a CTaC. If there are N number of inbred lines involved in a CTaC, the the total number of [...truncated...]
License: GPL (>= 2)
Encoding: UTF-8
Repository: CRAN
NeedsCompilation: no
Packaged: 2024-11-15 06:17:26 UTC; Ashutosh
Author: Mohd Harun [aut, ctb], Cini Varghese [aut, ctb], Seema Jaggi [ctb], Eldho Varghese [ctb], Ashutosh Dalal [aut, cre]
Date/Publication: 2024-11-15 09:10:02 UTC

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New package wbids with initial version 0.1.0
Package: wbids
Title: Seamless Access to World Bank International Debt Statistics (IDS)
Version: 0.1.0
Description: Access and analyze the World Bank’s International Debt Statistics (IDS) <https://datacatalog.worldbank.org/search/dataset/0038015>. IDS provides creditor-debtor relationships between countries, regions, and institutions. 'wbids' enables users to download, process and work with IDS series across multiple geographies, counterparts, and time periods.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: cli, withr, httr2 (>= 1.0.0), dplyr (>= 1.0.0), purrr (>= 1.0.0), tidyr (>= 1.0.0), rlang (>= 1.0.0)
Suggests: curl, jsonlite, tibble, lintr (>= 3.1.2), quarto, readxl (>= 1.0.0), rmarkdown, testthat (>= 3.0.0), languageserver (>= 0.3.16)
URL: https://teal-insights.github.io/r-wbids/, https://github.com/teal-insights/r-wbids/
BugReports: https://github.com/teal-insights/r-wbids/issues
VignetteBuilder: quarto
NeedsCompilation: no
Packaged: 2024-11-14 15:55:27 UTC; teal_emery
Author: Teal Emery [aut, cre], Teal Insights [cph], Christoph Scheuch [aut] , Christopher Smith [ctb]
Maintainer: Teal Emery <lte@tealinsights.com>
Repository: CRAN
Date/Publication: 2024-11-15 09:00:02 UTC

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New package ReportSubtotal with initial version 0.1
Package: ReportSubtotal
Title: Adds Subtotals to Data Reports
Version: 0.1
Description: Adds subtotal rows / sections (a la the SAS "Proc Tabulate" "All" option) to a Group By output by running a series of Group By functions with partial sets of the same variables and combining the results with the original. Can be used to add comprehensive information to a data report or to quickly aggregate Group By outputs used to gain a greater understanding of data.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: dplyr, tidyselect, utils, magrittr
NeedsCompilation: no
Packaged: 2024-11-14 17:36:27 UTC; yonia
Author: Yoni Aboody [aut, cre, cph]
Maintainer: Yoni Aboody <yoniaboody@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-15 09:00:13 UTC

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New package quicR with initial version 1.0.2
Package: quicR
Title: RT-QuIC Data Formatting and Analysis
Version: 1.0.2
Description: Designed for the curation and analysis of data generated from real-time quaking-induced conversion (RT-QuIC) assays first described by Atarashi et al. (2011) <doi:10.1038/nm.2294>. 'quicR' calculates useful metrics such as maxpoint ratio: Rowden et al. (2023) <doi:10.1099/vir.0.069906-0>; time-to-threshold: Shi et al. (2013) <doi:10.1186/2051-5960-1-44>; and maximum slope. Integration with the output from plate readers allows for seamless input of raw data into the R environment.
Imports: dplyr, ggplot2, openxlsx, readxl, reshape2, slider, stats, stringr, tidyr
License: GPL-3
Encoding: UTF-8
Suggests: testthat (>= 3.1.0)
NeedsCompilation: no
Packaged: 2024-11-14 18:14:24 UTC; rowde002
Author: Gage Rowden [aut, cre]
Maintainer: Gage Rowden <gage.rowden1145@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-15 09:00:05 UTC

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New package necountries with initial version 0.1-1
Package: necountries
Version: 0.1-1
Date: 2024-11-14
Title: Countries of the World
Depends: R (>= 4.0.0)
Imports: Rdpack, tibble, ggplot2, sf, dplyr, ggrepel, rlang, classInt, stringr, magrittr, stringi
Description: Based on Natural Earth <https://www.naturalearthdata.com/>, a subset of countries can easily be selected with their administrative boundaries, joined with an external data frame and plotted as a thematic map.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://www.R-project.org
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
LazyData: true
NeedsCompilation: no
Suggests: knitr, tidyr, purrr, quarto
VignetteBuilder: quarto
Packaged: 2024-11-14 12:12:10 UTC; yves
Repository: CRAN
Date/Publication: 2024-11-15 09:00:10 UTC

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New package HMMRel with initial version 0.1.0
Package: HMMRel
Title: Hidden Markov Models for Reliability and Maintenance
Version: 0.1.0
Author: M.L. Gamiz [aut, cre, cph], N. Limnios [aut, cph], M.C. Segovia-Garcia [aut, cph]
Maintainer: M.L. Gamiz <mgamiz@ugr.es>
Description: Reliability Analysis and Maintenance Optimization using Hidden Markov Models (HMM). The use of HMMs to model the state of a system which is not directly observable and instead certain indicators (signals) of the true situation are provided via a control system. A hidden model can provide key information about the system dependability, such as the reliability of the system and related measures. An estimation procedure is implemented based on the Baum-Welch algorithm. Classical structures such as K-out-of-N systems and Shock models are illustrated. Finally, the maintenance of the system is considered in the HMM context and two functions for new preventive maintenance strategies are considered. Maintenance efficiency is measured in terms of expected cost. Maintenance efficiency is measured in terms of expected cost. Methods are described in Gamiz, Limnios, and Segovia-Garcia (2023) <doi:10.1016/j.ejor.2022.05.006>.
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-14 19:44:04 UTC; Usuario
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2024-11-15 09:00:17 UTC

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New package redatam with initial version 2.0.4
Package: redatam
Title: Import 'REDATAM' Files
Version: 2.0.4
Imports: data.table, janitor, stringi, stringr, tibble
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R(>= 3.5.0)
Description: Import 'REDATAM' formats into R via the 'Open REDATAM' C++ library <https://github.com/litalbarkai/open-redatam> based on De Grande (2016) <https://www.jstor.org/stable/24890658>.
License: Apache License (>= 2)
URL: https://github.com/litalbarkai/open-redatam
BugReports: https://github.com/litalbarkai/open-redatam/issues
Encoding: UTF-8
NeedsCompilation: yes
VignetteBuilder: knitr
LinkingTo: cpp11
Packaged: 2024-11-15 02:58:01 UTC; pacha
Author: Mauricio Vargas Sepulveda [aut, cre] , Lital Barkai [aut], Ivan Krylov [ctb], Arseny Kapoulkine [ctb] , Oriental Republic of Uruguay [dtc]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2024-11-15 07:30:02 UTC

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Thu, 14 Nov 2024

New package shinyMixR with initial version 0.5.0
Package: shinyMixR
Title: Interactive 'shiny' Dashboard for 'nlmixr2'
Version: 0.5.0
Description: An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package, designed to simplify the modeling process for users. Additionally, this package includes supplementary functions to further enhances the usage of 'nlmixr2'.
Depends: R (>= 3.5.0), shiny, ggplot2
Imports: gridExtra, collapsibleTree, shinyAce, DT, bs4Dash, shinyWidgets, stringi, R3port, whisker, plotly, patchwork, shinyjs, ps, xfun, fresh, nlmixr2, nlmixr2est, magrittr, cli
Suggests: xpose, xpose.nlmixr2, nlme, testthat, shinytest2, knitr, rmarkdown, rlang, miniUI, shinyFiles, rstudioapi
License: MIT + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-14 14:25:49 UTC; r.hooijmaijers
Author: Richard Hooijmaijers [aut, cre, cph], Teun Post [aut, cph], LAPP Consultants [fnd, cph], Matthew Fidler [ctb], Veerle van Leemput [ctb]
Maintainer: Richard Hooijmaijers <richardhooijmaijers@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-14 16:10:03 UTC

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New package mapindia with initial version 1.0.1
Package: mapindia
Title: Plot Map of the Indian Subcontinent
Version: 1.0.1
Maintainer: Shubham Dutta <shubhamdutta26@gmail.com>
Description: Get map data frames for the Indian subcontinent with different region levels (e.g., district, state). The package also offers convenience functions for plotting choropleths, visualizing spatial data, and handling state/district codes.
License: MIT + file LICENSE
URL: https://github.com/shubhamdutta26/mapindia, https://www.shubhamdutta.com/mapindia/
BugReports: https://github.com/shubhamdutta26/mapindia/issues
Depends: R (>= 2.10)
Imports: ggplot2, mapindiatools, rlang, sf, vdiffr
Suggests: knitr, patchwork, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-14 15:15:37 UTC; shubham
Author: Shubham Dutta [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-14 16:10:07 UTC

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New package EDCimport with initial version 0.5.2
Package: EDCimport
Version: 0.5.2
Title: Import Data from EDC Software
Description: A convenient toolbox to import data exported from Electronic Data Capture (EDC) software 'TrialMaster'.
License: GPL-3
URL: https://github.com/DanChaltiel/EDCimport, https://danchaltiel.github.io/EDCimport/
BugReports: https://github.com/DanChaltiel/EDCimport/issues
Depends: R (>= 3.1.0)
Imports: cli, dplyr, forcats, fs, glue, ggplot2, haven, purrr, readr, rlang, scales, stringr, tibble, tidyr, tidyselect, utils, lifecycle
Suggests: callr, crosstable, gtools, htmlwidgets, janitor, knitr, openxlsx, patchwork, plotly, quarto, rmarkdown, rstudioapi, testthat (>= 3.1.8), usethis, vdiffr, withr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-14 14:14:50 UTC; Dan
Author: Dan Chaltiel [aut, cre]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-14 16:10:11 UTC

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New package visvaR with initial version 1.0.0
Package: visvaR
Title: Shiny-Based Statistical Solutions for Agricultural Research
Version: 1.0.0
Description: Visualize Variance is an intuitive 'shiny' applications tailored for agricultural research data analysis, including one-way and two-way analysis of variance, correlation, and other essential statistical tools. Users can easily upload their datasets, perform analyses, and download the results as a well-formatted document, streamlining the process of data analysis and reporting in agricultural research.The experimental design methods are based on classical work by Fisher (1925) and Scheffe (1959). The correlation visualization approaches follow methods developed by Wei & Simko (2021) and Friendly (2002) <doi:10.1198/000313002533>.
License: AGPL (>= 3)
Encoding: UTF-8
URL: https://github.com/rameshram96/visvaR, https://rameshram96.github.io/visvaR/
BugReports: https://github.com/rameshram96/visvaR/issues
Imports: agricolae, bslib, corrplot, flextable, ggcorrplot, ggplot2, officer, patchwork, shiny, tibble, tidyr, rlang, dplyr, DT, readxl, htmltools, utils, stats, graphics, grDevices
Suggests: testthat (>= 3.0.0), writexl, shinytest2, extrafont
NeedsCompilation: no
Packaged: 2024-11-14 06:02:52 UTC; Ramesh_PhD
Author: Ramesh Ramasamy [aut, cre, cph] , Mathiyarasi Kulandaivadivel [ctb], Tamilselvan Arumugam [ctb]
Maintainer: Ramesh Ramasamy <ramesh.rahu96@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-14 15:50:02 UTC

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New package TFM with initial version 0.1.0
Package: TFM
Title: Sparse Online Principal Component for TFM
Version: 0.1.0
Description: The Truncated Factor Model is a statistical model designed to handle specific data structures in data analysis. This R package focuses on the Sparse Online Principal Component Estimation method, which is used to calculate data such as the loading matrix and specific variance matrix for truncated data, thereby better explaining the relationship between common factors and original variables. Additionally, the R package also provides other equations for comparison with the Sparse Online Principal Component Estimation method.The philosophy of the package is described in Guangbao Guo. (2023) <doi:10.1007/s00180-022-01270-z>.
License: MIT + file LICENSE
Suggests: rmarkdown, psych
Depends: R (>= 3.0)
Encoding: UTF-8
Language: en-US
Author: Beibei Wu [aut], Guangbao Guo [aut, cre]
NeedsCompilation: yes
Maintainer: Guangbao Guo <ggb11111111@163.com>
Imports: relliptical, SOPC, MASS, mvtnorm
Packaged: 2024-11-12 08:34:55 UTC; 14218
Repository: CRAN
Date/Publication: 2024-11-14 15:40:07 UTC

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New package sivirep with initial version 1.0.0
Package: sivirep
Title: Data Wrangling and Automated Reports from 'SIVIGILA' Source
Version: 1.0.0
Description: Data wrangling, pre-processing, and generating automated reports from Colombia's epidemiological surveillance system, 'SIVIGILA' <https://portalsivigila.ins.gov.co/>. It provides a customizable R Markdown template for analysis and automatic generation of epidemiological reports that can be adapted to local, regional, and national contexts. This tool offers a standardized and reproducible workflow that helps to reduce manual labor and potential errors in report generation, improving their efficiency and consistency.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: config, dplyr, ggplot2, httr2, stringr, xml2, epitrix, sf, readxl, rlang, tools, sysfonts, showtext, kableExtra
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
Depends: R (>= 4.0.0)
VignetteBuilder: knitr
Language: es_ES
URL: https://epiverse-trace.github.io/sivirep/, https://github.com/epiverse-trace/sivirep
BugReports: https://github.com/epiverse-trace/sivirep/issues
NeedsCompilation: no
Packaged: 2024-11-14 03:38:35 UTC; geral
Author: Geraldine Gomez-Millan [aut, cre, ctb] , Zulma M. Cucunuba [aut, ctb] , Jennifer A. Mendez-Romero [aut, ctb] , Claudia Huguett-Aragon [aut, ctb] , Hugo Gruson [ctb] , Juanita Romero-Garces [ctb] , Jaime Pavlich-Mariscal [ctb] , Laura Gomez Bermeo [ct [...truncated...]
Maintainer: Geraldine Gomez-Millan <geralidine.gomez@javeriana.edu.co>
Repository: CRAN
Date/Publication: 2024-11-14 15:50:05 UTC

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New package ReSurv with initial version 1.0.0
Package: ReSurv
Title: Machine Learning Models for Predicting Claim Counts
Version: 1.0.0
Description: Prediction of claim counts using the feature based development factors introduced in the manuscript Hiabu M., Hofman E. and Pittarello G. (2023) <doi:10.48550/arXiv.2312.14549>. Implementation of Neural Networks, Extreme Gradient Boosting, and Cox model with splines to optimise the partial log-likelihood of proportional hazard models.
URL: https://github.com/edhofman/ReSurv
BugReports: https://github.com/edhofman/ReSurv/issues
License: GPL (>= 2)
Depends: tidyverse
Imports: stats, dplyr, dtplyr, fastDummies, forecast, data.table, purrr, tidyr, tibble, ggplot2, survival, reshape2, bshazard, SynthETIC, rpart, reticulate, xgboost, SHAPforxgboost
SystemRequirements: Python (>= 3.8.0)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-11-14 08:40:52 UTC; gpitt
Author: Emil Hofman [aut, cre, cph], Gabriele Pittarello [aut, cph] , Munir Hiabu [aut, cph]
Maintainer: Emil Hofman <emil_hofman@hotmail.dk>
Repository: CRAN
Date/Publication: 2024-11-14 16:00:10 UTC

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New package powertools with initial version 0.1.0
Package: powertools
Title: Power and Sample Size Tools
Version: 0.1.0
Maintainer: Catherine M. Crespi <ccrespi@ucla.edu>
Description: Power and sample size calculations for a variety of study designs and outcomes. Methods include t tests, ANOVA (including tests for interactions, simple effects and contrasts), proportions, categorical data (chi-square tests and proportional odds), linear, logistic and Poisson regression, alternative and coprimary endpoints, power for confidence intervals, correlation coefficient tests, cluster randomized trials, individually randomized group treatment trials, multisite trials, treatment-by-covariate interaction effects and nonparametric tests of location. Utilities are provided for computing various effect sizes. Companion package to the book "Power and Sample Size in R", Crespi (2025, ISBN:9781138591622).
URL: https://github.com/powerandsamplesize/powertools
BugReports: https://github.com/powerandsamplesize/powertools/issues
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: testthat (>= 3.0.0)
Imports: mvtnorm, PowerTOST, Hmisc, stats, knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-13 21:22:52 UTC; zichenliu
Author: Catherine M. Crespi [aut, cre], Zichen Liu [aut], Kristen M. McGreevy [ctb]
Repository: CRAN
Date/Publication: 2024-11-14 14:00:07 UTC

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New package PerRegMod with initial version 4.4.1
Package: PerRegMod
Maintainer: Slimane Regui <slimaneregui111997@gmail.com>
Title: Fitting Periodic Coefficients Linear Regression Models
Version: 4.4.1
Description: Provides tools for fitting periodic coefficients regression models to data where periodicity plays a crucial role. It allows users to model and analyze relationships between variables that exhibit cyclical or seasonal patterns, offering functions for estimating parameters and testing the periodicity of coefficients in linear regression models. For simple periodic coefficient regression model see Regui et al. (2024) <doi:10.1080/03610918.2024.2314662>.
License: GPL
Encoding: UTF-8
Imports: expm, readxl, sn
URL: https://doi.org/10.1080/03610918.2024.2314662
Packaged: 2024-11-14 14:15:20 UTC; slima
NeedsCompilation: no
Author: Slimane Regui [aut, cre] , Abdelhadi Akharif [aut], Amal Mellouk [aut]
Repository: CRAN
Date/Publication: 2024-11-14 16:00:14 UTC

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New package lovecraftr with initial version 1.0.0
Package: lovecraftr
Title: A Collection of Lovecraftian Tales and Texts
Version: 1.0.0
Maintainer: Ruff Sergej <serijnh@gmail.com>
Description: A curated collection of Howard Phillips Lovecraft's complete stories, collected for the purpose of text analysis.
License: GPL (>= 3)
URL: https://github.com/SergejRuff/lovecraftr
BugReports: https://github.com/SergejRuff/lovecraftr/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-13 20:57:25 UTC; sergej
Author: Ruff Sergej [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-14 14:00:29 UTC

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New package VecDep with initial version 0.1.3
Package: VecDep
Title: Measuring Copula-Based Dependence Between Random Vectors
Version: 0.1.3
Description: Provides functions for estimation (parametric, semi-parametric and non-parametric) of copula-based dependence coefficients between a finite collection of random vectors, including phi-dependence measures and Bures-Wasserstein dependence measures. An algorithm for agglomerative hierarchical variable clustering is also implemented. Following the articles De Keyser & Gijbels (2024) <doi:10.1016/j.jmva.2024.105336>, De Keyser & Gijbels (2024) <doi:10.1016/j.ijar.2023.109090>, and De Keyser & Gijbels (2024) <doi:10.48550/arXiv.2404.07141>.
License: GPL-3
Encoding: UTF-8
URL: https://github.com/StevenDeKeyser98/VecDep
BugReports: https://github.com/StevenDeKeyser98/VecDep/issues
Depends: R (>= 4.4.0)
Imports: ElliptCopulas (>= 0.1.4.1), HAC (>= 1.1-1), hash (>= 2.2.6.3), sets (>= 1.0-25), covglasso (>= 1.0.3), expm (>= 1.0-0), magic (>= 1.6-1), pbapply (>= 1.7-2), Rmpfr (>= 0.9-5), reticulate (>= 1.39.0), gtools (>= 3.9.5)
Suggests: mvtnorm, ggplot2, extraDistr, fossil, dendextend, copula, knitr, rmarkdown, testthat (>= 3.0.0)
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-13 20:10:33 UTC; u0149189
Author: Steven De Keyser [aut, cre] , Irene Gijbels [ctb]
Maintainer: Steven De Keyser <steven.dekeyser@kuleuven.be>
Repository: CRAN
Date/Publication: 2024-11-14 13:50:19 UTC

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New package RobustPrediction with initial version 0.1.4
Package: RobustPrediction
Title: Robust Tuning and Training for Cross-Source Prediction
Version: 0.1.4
Maintainer: Yuting He <Yuting.He@campus.lmu.de>
Description: Provides robust parameter tuning and model training for predictive models across data sources. This package implements three primary tuning methods: cross-validation-based internal tuning, external tuning, and the 'RobustTuneC' method. It supports Lasso, Ridge, Random Forest, Boosting, and Support Vector Machine classifiers. The tuning methods are based on the paper by Nicole Ellenbach, Anne-Laure Boulesteix, Bernd Bischl, Kristian Unger, and Roman Hornung (2021) "Improved Outcome Prediction Across Data Sources Through Robust Parameter Tuning" <doi:10.1007/s00357-020-09368-z>.
License: GPL-3
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
Depends: R (>= 3.5.0)
Imports: glmnet, mboost, mlr, ranger, e1071, pROC
URL: https://github.com/Yuting-He/RobustPrediction
Packaged: 2024-11-13 16:25:05 UTC; yutin
Author: Yuting He [aut, cre], Nicole Ellenbach [ctb], Roman Hornung [ctb]
Repository: CRAN
Date/Publication: 2024-11-14 13:30:08 UTC

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New package RegrCoeffsExplorer with initial version 1.1.0
Package: RegrCoeffsExplorer
Title: Efficient Visualization of Regression Coefficients for lm(), glm(), and glmnet() Objects
Version: 1.1.0
Imports: dplyr, ggpubr, gridExtra, glmnet, ggplot2, magrittr, grDevices, rlang, stats
Description: The visualization tool offers a nuanced understanding of regression dynamics, going beyond traditional per-unit interpretation of continuous variables versus categorical ones. It highlights the impact of unit changes as well as larger shifts like interquartile changes, acknowledging the distribution of empirical data. Furthermore, it generates visualizations depicting alterations in Odds Ratios for predictors across minimum, first quartile, median, third quartile, and maximum values, aiding in comprehending predictor-outcome interplay within empirical data distributions, particularly in logistic regression frameworks.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: faraway, knitr, MASS, psych, rmarkdown, selectiveInference, survival
VignetteBuilder: knitr
URL: https://vadimtyuryaev.github.io/RegrCoeffsExplorer/
NeedsCompilation: no
Packaged: 2024-11-13 20:38:35 UTC; vadim
Author: Vadim Tyuryaev [aut, cre] , Aleksandr Tsybakin [aut], Jane Heffernan [aut], Hanna Jankowski [aut], Kevin McGregor [aut]
Maintainer: Vadim Tyuryaev <vadim.tyuryaev@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-14 13:50:49 UTC

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New package JANE with initial version 0.1.1
Package: JANE
Title: Just Another Latent Space Network Clustering Algorithm
Version: 0.1.1
Description: Fit and simulate latent space network cluster models using an expectation-maximization algorithm. Enables flexible modeling of unweighted network data, supporting both directed and undirected networks, with or without degree heterogeneity. Designed to handle large networks efficiently, it allows users to explore network structure through latent space representations, identify clusters within network data, and simulate models with varying clustering and connectivity patterns.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.1.0)
LinkingTo: Rcpp, RcppArmadillo
Imports: Rcpp (>= 1.0.10), Matrix, extraDistr, mclust, scales, aricode, stringdist, utils, splines, rlang, future.apply, future, progressr, progress, igraph, methods
URL: https://github.com/a1arakkal/JANE
BugReports: https://github.com/a1arakkal/JANE/issues
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-11-13 16:59:35 UTC; alanarakkal
Author: Alan Arakkal [aut, cre, cph] , Daniel Sewell [aut]
Maintainer: Alan Arakkal <alan-arakkal@uiowa.edu>
Repository: CRAN
Date/Publication: 2024-11-14 13:40:03 UTC

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New package HiGarrote with initial version 1.0
Package: HiGarrote
Title: Nonnegative Garrote Method Incorporating Hierarchical Relationships
Version: 1.0
Date: 2024-11-08
Author: Wei-Yang Yu [aut, cre], V. Roshan Joseph [aut]
Maintainer: Wei-Yang Yu <wyu322@gatech.edu>
Description: An implementation of the nonnegative garrote method that incorporates hierarchical relationships among variables. The core function, HiGarrote(), offers an automated approach for analyzing experiments while respecting hierarchical structures among effects. For methodological details, refer to Yu and Joseph (2024) <doi:10.48550/arXiv.2411.01383>. This work is supported by U.S. National Science Foundation grant DMS-2310637.
License: GPL (>= 2)
Imports: Matrix, MaxPro, nloptr, purrr, quadprog, Rcpp (>= 1.0.12), RcppArmadillo, rlist, scales, stringr
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: yes
Packaged: 2024-11-13 16:06:24 UTC; weiyang
Repository: CRAN
Date/Publication: 2024-11-14 13:30:37 UTC

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New package clustur with initial version 0.1.0
Package: clustur
Title: Clustering
Version: 0.1.0
Date: 2024-10-18
Maintainer: Patrick Schloss <pschloss@umich.edu>
Description: A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Matrix, methods, Rcpp (>= 1.0.12), utils
Depends: R (>= 3.5.0)
LinkingTo: Rcpp, testthat
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), xml2
VignetteBuilder: knitr
URL: http://www.schlosslab.org/clustur/, https://github.com/SchlossLab/clustur
BugReports: https://github.com/SchlossLab/clustur/issues
NeedsCompilation: yes
Packaged: 2024-11-13 18:38:22 UTC; grejoh
Author: Gregory Johnson [aut] , Sarah Westcott [aut], Patrick Schloss [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-14 13:50:05 UTC

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New package Bios2cor with initial version 2.2.2
Package: Bios2cor
Title: From Biological Sequences and Simulations to Correlation Analysis
Version: 2.2.2
Date: 2024-10-15
Author: Bruck Taddese [aut], Antoine Garnier [aut], Madeline Deniaud [aut], Julien Pele [ctb], Lea Bellenger [ctb], Jean-Michel Becu [ctb], Marie Chabbert [aut, cre]
Maintainer: Marie Chabbert <marie.chabbert@univ-angers.fr>
Depends: R (>= 3.5), bio3d, circular, bigmemory, parallel
Imports: igraph
Description: Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in side chain motions during molecular dynamics simulations. Features include the computation of correlation/covariation scores using a variety of scoring functions between either sequence positions in alignments or side chain dihedral angles in molecular dynamics simulations and utilities to analyze the correlation/covariation matrix through a variety of tools including network representation and principal components analysis. In addition, several utility functions are based on the R graphical environment to provide friendly tools for help in data interpretation. Examples of sequence covariation analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2) Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M (2018) <doi:10.1371/journal.pcbi.1006209>. An example of side chain cor [...truncated...]
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2024-11-13 18:29:12 UTC; root
Repository: CRAN
Date/Publication: 2024-11-14 13:40:23 UTC

More information about Bios2cor at CRAN
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New package autometric with initial version 0.1.1
Package: autometric
Title: Background Resource Logging
Description: Intense parallel workloads can be difficult to monitor. Packages 'crew.cluster', 'clustermq', and 'future.batchtools' distribute hundreds of worker processes over multiple computers. If a worker process exhausts its available memory, it may terminate silently, leaving the underlying problem difficult to detect or troubleshoot. Using the 'autometric' package, a worker can proactively monitor itself in a detached background thread. The worker process itself runs normally, and the thread writes to a log every few seconds. If the worker terminates unexpectedly, 'autometric' can read and visualize the log file to reveal potential resource-related reasons for the crash. The 'autometric' package borrows heavily from the methods of packages 'ps' <doi:10.32614/CRAN.package.ps> and 'psutil'.
Version: 0.1.1
License: MIT + file LICENSE
URL: https://wlandau.github.io/autometric/, https://github.com/wlandau/autometric
BugReports: https://github.com/wlandau/autometric/issues
Depends: R (>= 3.5.0)
Imports: graphics, utils
Suggests: grDevices, ps, tinytest
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2024-10-31 19:33:31 UTC; C240390
Author: William Michael Landau [aut, cre] , Eli Lilly and Company [cph, fnd], Posit Software, PBC [cph] , Jay Loden [cph] , Dave Daeschler [cph] , Giampaolo Rodola [cph]
Maintainer: William Michael Landau <will.landau.oss@gmail.com>
Repository: CRAN
Date/Publication: 2024-10-31 23:10:02 UTC

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Wed, 13 Nov 2024

New package shinyWGD with initial version 1.0.0
Package: shinyWGD
Title: 'Shiny' Application for Whole Genome Duplication Analysis
Version: 1.0.0
Maintainer: Jia Li <li081766@gmail.com>
Description: Provides a comprehensive 'Shiny' application for analyzing Whole Genome Duplication ('WGD') events. This package provides a user-friendly 'Shiny' web application for non-experienced researchers to prepare input data and execute command lines for several well-known 'WGD' analysis tools, including 'wgd', 'ksrates', 'i-ADHoRe', 'OrthoFinder', and 'Whale'. This package also provides the source code for experienced researchers to adjust and install the package to their own server. Key Features 1) Input Data Preparation This package allows users to conveniently upload and format their data, making it compatible with various 'WGD' analysis tools. 2) Command Line Generation This package automatically generates the necessary command lines for selected 'WGD' analysis tools, reducing manual errors and saving time. 3) Visualization This package offers interactive visualizations to explore and interpret 'WGD' results, facilitating in-depth 'WGD' analysis. 4) Comparative Genomics Users can study and [...truncated...]
License: GPL-3
Encoding: UTF-8
SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
Imports: shiny, shinyalert, stringr, vroom, fs, tidyr, data.table, dplyr, ape, ks, mclust, htmltools, seqinr, httr, jsonlite
Suggests: tidyverse, knitr, rmarkdown, DT, argparse, bslib, bsplus, english, fontawesome, igraph, shinyBS, shinyFiles, shinyWidgets, shinyjs, stringi, tools, testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-13 01:08:49 UTC; jiali
Author: Jia Li [aut, cre], Zhen Li [ctb], Arthur Zwaenepoel [ctb]
Repository: CRAN
Date/Publication: 2024-11-13 15:10:01 UTC

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New package cppcontainers with initial version 1.0.0
Package: cppcontainers
Title: 'C++' Standard Template Library Containers
Version: 1.0.0
Description: Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps, unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.
Encoding: UTF-8
URL: https://github.com/cdueben/cppcontainers
BugReports: https://github.com/cdueben/cppcontainers/issues
License: MIT + file LICENSE
Imports: base (>= 4.0.0), methods, Rcpp
LinkingTo: Rcpp
SystemRequirements: C++20
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-11-13 00:31:54 UTC; Christian
Author: Christian Dueben [aut, cre]
Maintainer: Christian Dueben <cdueben.ml+cran@proton.me>
Repository: CRAN
Date/Publication: 2024-11-13 15:10:05 UTC

More information about cppcontainers at CRAN
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New package CBRT with initial version 0.1.1
Package: CBRT
Title: CBRT Data on Turkish Economy
Version: 0.1.1
Maintainer: Erol Taymaz <etaymaz@metu.edu.tr>
Description: The Central Bank of the Republic of Turkey (CBRT) provides one of the most comprehensive time series databases on the Turkish economy. The 'CBRT' package provides functions for accessing the CBRT's electronic data delivery system <https://evds2.tcmb.gov.tr/>. It contains the lists of all data categories and data groups for searching the available variables (data series). As of November 3, 2024, there were 40,826 variables in the dataset. The lists of data categories and data groups can be updated by the user at any time. A specific variable, a group of variables, or all variables in a data group can be downloaded at different frequencies using a variety of aggregation methods.
License: GPL-3
URL: https://github.com/etaymaz/CBRT
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), data.table, curl
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-12 19:47:30 UTC; etaymaz
Author: Erol Taymaz [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-13 15:10:10 UTC

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New package RCognito with initial version 0.1.0
Package: RCognito
Title: A Simplified Interface for 'Amazon Cognito'
Version: 0.1.0
Maintainer: Sanjaya J Shetty <shettysanjaya01@gmail.com>
Description: Simplifies integration with 'Amazon Cognito' (<https://aws.amazon.com/cognito/>) for R developers, enabling easy management of user authentication, registration, and password flows.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: paws
Suggests: testthat (>= 3.0.0), mockery
NeedsCompilation: no
Packaged: 2024-11-12 14:26:18 UTC; sanjaya
Author: Sanjaya J Shetty [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-13 14:20:02 UTC

More information about RCognito at CRAN
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New package PlotFTIR with initial version 1.0.0
Package: PlotFTIR
Title: Plot FTIR Spectra
Version: 1.0.0
Description: The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions. L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: cli, rlang, scales
Depends: R (>= 3.3)
Suggests: testthat (>= 3.0.0), withr, ggplot2 (>= 3.0.0), ggthemes, knitr, rmarkdown, ir, ChemoSpec, R.utils
VignetteBuilder: knitr
BugReports: https://github.com/NRCan/PlotFTIR/issues
URL: https://github.com/NRCan/PlotFTIR
NeedsCompilation: no
Packaged: 2024-11-12 14:55:05 UTC; pbulsink
Author: Philip Bulsink [aut, cre] , Ulrich Makanda [trl] , His Majesty the King in Right of Canada, as represented by the Minister of Natural Resources [cph]
Maintainer: Philip Bulsink <philip.bulsink@nrcan-rncan.gc.ca>
Repository: CRAN
Date/Publication: 2024-11-13 14:20:06 UTC

More information about PlotFTIR at CRAN
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New package phylolm.hp with initial version 0.0-1
Package: phylolm.hp
Title: Hierarchical Partitioning of R2 for Phylogenetic Linear Regression
Version: 0.0-1
Date: 2024-11-12
Depends: R (>= 3.4.0),rr2,phylolm,ggplot2,vegan
Maintainer: Jiangshan Lai <lai@njfu.edu.cn>
Description: Conducts hierarchical partitioning to calculate individual contributions of phylogenetic tree and predictors towards total R2 for phylogenetic linear regression models.
License: GPL
Encoding: UTF-8
URL: https://github.com/laijiangshan/phylolm.hp
NeedsCompilation: no
Packaged: 2024-11-12 02:04:29 UTC; lai
Author: Jiangshan Lai [aut, cre] , Gang Wang [aut]
Repository: CRAN
Date/Publication: 2024-11-13 14:10:02 UTC

More information about phylolm.hp at CRAN
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New package hmsidwR with initial version 1.1.2
Package: hmsidwR
Title: Health Metrics and the Spread of Infectious Diseases
Version: 1.1.2
Description: A collection of datasets and supporting functions accompanying Health Metrics and the Spread of Infectious Diseases by Federica Gazzelloni (2024). This package provides data for health metrics calculations, including Disability-Adjusted Life Years (DALYs), Years of Life Lost (YLLs), and Years Lived with Disability (YLDs), as well as additional tools for analyzing and visualizing health data. Federica Gazzelloni (2024) <doi:10.5281/zenodo.10818338>.
License: MIT + file LICENSE
URL: https://github.com/Fgazzelloni/hmsidwR, https://fgazzelloni.github.io/hmsidwR/
BugReports: https://github.com/Fgazzelloni/hmsidwR/issues
Depends: R (>= 2.10)
Imports: ggplot2, gstat, purrr, showtext, sysfonts, tibble
Suggests: devtools, dplyr, geomtextpath, ggthemes, httr, janitor, knitr, lubridate, maps, pkgdown, plotly, readr, readxl, rmarkdown, sessioninfo, sf, stats, testthat (>= 3.0.0), tidyr, tidyverse
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-12 17:20:52 UTC; federicagazzelloni
Author: Federica Gazzelloni [aut, cre]
Maintainer: Federica Gazzelloni <fede.gazzelloni@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-13 15:00:02 UTC

More information about hmsidwR at CRAN
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New package brickster with initial version 0.2.5
Package: brickster
Title: R Toolkit for 'Databricks'
Version: 0.2.5
Description: Collection of utilities that improve using 'Databricks' from R. Primarily functions that wrap specific 'Databricks' APIs (<https://docs.databricks.com/api>), 'RStudio' connection pane support, quality of life functions to make 'Databricks' simpler to use.
License: Apache License (>= 2)
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: arrow, base64enc, cli, curl, dplyr, glue, httr2, ini, jsonlite, purrr, reticulate, R6 (>= 2.4.0), rlang, tibble, utils
Suggests: testthat (>= 3.0.0), huxtable, htmltools, knitr, magick, rmarkdown, rstudioapi, withr
VignetteBuilder: knitr
URL: https://github.com/databrickslabs/brickster
NeedsCompilation: no
Packaged: 2024-11-12 07:54:34 UTC; zachary.davies
Author: Zac Davies [aut, cre], Rafi Kurlansik [aut], Databricks [cph, fnd]
Maintainer: Zac Davies <zac@databricks.com>
Repository: CRAN
Date/Publication: 2024-11-13 14:10:06 UTC

More information about brickster at CRAN
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New package rcprd with initial version 0.0.1
Package: rcprd
Title: Extraction and Management of Clinical Practice Research Datalink Data
Version: 0.0.1
Description: Simplify the process of extracting and processing Clinical Practice Research Datalink (CPRD) data in order to build datasets ready for statistical analysis. This process is difficult in 'R', as the raw data is very large and cannot be read into the R workspace. 'rcprd' utilises 'RSQLite' to create 'SQLite' databases which are stored on the hard disk. These are then queried to extract the required information for a cohort of interest, and create datasets ready for statistical analysis. The processes follow closely that from the 'rEHR' package, see Springate et al., (2017) <doi:10.1371/journal.pone.0171784>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: data.table
Imports: dplyr, fastmatch, RSQLite, stringr
URL: https://alexpate30.github.io/rcprd/
NeedsCompilation: no
Packaged: 2024-11-11 22:30:47 UTC; mbrxsap3
Author: Alexander Pate [aut, cre, cph]
Maintainer: Alexander Pate <alexander.pate@manchester.ac.uk>
Repository: CRAN
Date/Publication: 2024-11-13 14:00:02 UTC

More information about rcprd at CRAN
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New package PepMapViz with initial version 1.0.0
Package: PepMapViz
Title: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration
Version: 1.0.0
Description: A versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of 'PepMapViz' include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of major histocompatibility complex-presented peptides in different antibody regions predicting immunogenicity in antibody drug development.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ggplot2, stringr, ggforce, ggh4x, ggnewscale, data.table, rlang
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-11 21:36:29 UTC; zhouz45
Maintainer: Zhenru Zhou <zhou.zhenru@gene.com>
Note: The following words are correctly spelled domain-specific terms: MHC, 'PepMapViz', immunogenicity, linearized, spectrometry, translational. The package includes large datasets in the 'extdata' directory, which are essential for demonstrating the functionality and performance of the tools provided. These datasets are necessary for reproducibility and comprehensive testing.
Author: Zhenru Zhou [aut, cre], Qui Phung [ctb], Corey Bakalarski [aut], Genentech, Inc. [cph]
Repository: CRAN
Date/Publication: 2024-11-13 14:00:13 UTC

More information about PepMapViz at CRAN
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New package COveR with initial version 1.1.0
Package: COveR
Title: Clustering with Overlaps
Version: 1.1.0
Description: Provide functions for overlaps clustering, fuzzy clustering and interval-valued data manipulation. The package implement the following algorithms: OKM (Overlapping Kmeans) from Cleuziou, G. (2007) <doi:10.1109/icpr.2008.4761079> ; NEOKM (Non-exhaustive overlapping Kmeans) from Whang, J. J., Dhillon, I. S., and Gleich, D. F. (2015) <doi:10.1137/1.9781611974010.105> ; Fuzzy Cmeans from Bezdek, J. C. (1981) <doi:10.1007/978-1-4757-0450-1> ; Fuzzy I-Cmeans from de A.T. De Carvalho, F. (2005) <doi:10.1016/j.patrec.2006.08.014>.
Depends: R (>= 3.2.3)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Suggests: testthat
SystemRequirements: Gnu Scientific Library version >= 1.12
NeedsCompilation: yes
Packaged: 2024-11-13 11:02:19 UTC; hiot
Author: Guillaume Cleuziou [aut], Nicolas Hiot [cre]
Maintainer: Nicolas Hiot <nicolas.hiot@univ-orleans.fr>
Repository: CRAN
Date/Publication: 2024-11-13 13:00:22 UTC

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New package cia with initial version 1.0.0
Package: cia
Title: Learn and Apply Directed Acyclic Graphs for Causal Inference
Version: 1.0.0
Description: Causal Inference Assistance (CIA) for performing causal inference within the structural causal modelling framework. Structure learning is performed using partition Markov chain Monte Carlo (Kuipers & Moffa, 2017) and several additional functions have been added to help with causal inference. Kuipers and Moffa (2017) <doi:10.1080/01621459.2015.1133426>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.4.0)
Imports: bnlearn (>= 4.9), igraph, doParallel, parallel, foreach, arrangements, graphics, dplyr, rlang, fastmatch, methods, gRain, patchwork, tidyr
Suggests: rmarkdown, knitr, testthat (>= 3.0.0), gtools, gRbase, ggplot2, qgraph, dagitty
URL: https://spaceodyssey.github.io/cia/
BugReports: https://github.com/SpaceOdyssey/cia/issues
NeedsCompilation: no
Packaged: 2024-11-11 21:41:08 UTC; mvar0005
Author: Mathew Varidel [aut, cre, cph] , Victor An [ctb]
Maintainer: Mathew Varidel <mathew.varidel@sydney.edu.au>
Repository: CRAN
Date/Publication: 2024-11-13 14:00:07 UTC

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Tue, 12 Nov 2024

New package Virusparies with initial version 1.0.0
Package: Virusparies
Title: Visualize and Process Output from 'VirusHunterGatherer'
Version: 1.0.0
Maintainer: Ruff Sergej <serijnh@gmail.com>
Description: A collection of tools for downstream analysis of 'VirusHunterGatherer' output. Processing of hittables and plotting of results, enabling better interpretation, is made easier with the provided functions.
License: GPL (>= 3)
URL: https://github.com/SergejRuff/Virusparies, https://github.com/lauberlab/VirusHunterGatherer
BugReports: https://github.com/SergejRuff/Virusparies/issues
Encoding: UTF-8
Imports: chromote, cowplot, dplyr, ggplot2, gt, parallel, readr, rlang, scales, stats, stringr, tidyr, tools, utils
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-10 16:37:26 UTC; sergej
Author: Ruff Sergej [aut, cre] , Lauber Chris [ctb] , Chong Li Chuin [ctb]
Repository: CRAN
Date/Publication: 2024-11-12 14:10:06 UTC

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New package textAnnotatoR with initial version 0.1.4
Package: textAnnotatoR
Title: Interactive Text Annotation Tool with 'shiny' GUI
Version: 0.1.4
Date: 2024-10-25
Description: A comprehensive text annotation tool built with 'shiny'. Provides an interactive graphical user interface for coding text documents, managing code hierarchies, creating memos, and analyzing coding patterns. Features include code co-occurrence analysis, visualization of coding patterns, comparison of multiple coding sets, and export capabilities. Supports collaborative qualitative research through standardized annotation formats and analysis tools.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: shiny (>= 1.7.0), shinydashboard, shinyjs, shinyFiles, data.tree, jsonlite, DT, readtext, magrittr, tools, utils, stats, grDevices, graphics
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, covr, mockery
URL: https://github.com/chaoliu-cl/textAnnotatoR, http://liu-chao.site/textAnnotatoR/
BugReports: https://github.com/chaoliu-cl/textAnnotatoR/issues
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-11 19:23:25 UTC; chaoliu
Author: Chao Liu [aut, cre, cph]
Maintainer: Chao Liu <chaoliu@cedarville.edu>
Repository: CRAN
Date/Publication: 2024-11-12 14:40:01 UTC

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New package rOCEAN with initial version 1.0
Package: rOCEAN
Title: Two-Way Feature Set Testing for Multi-Omics
Version: 1.0
Maintainer: Mitra Ebrahimpoor <mitra.ebrahimpoor@gmail.com>
Description: For any two way feature-set from a pair of pre-processed omics data, 3 different true discovery proportions (TDP), namely pairwise-TDP, column-TDP and row-TDP are calculated. Due to embedded closed testing procedure, the choice of feature-sets can be changed infinite times and even after seeing the data without any change in type I error rate. For more details refer to Ebrahimpoor et al., (2024) <doi:10.48550/arXiv.2410.19523>.
License: GPL (>= 2)
Date: 2024-10-31
Encoding: UTF-8
Imports: ff
NeedsCompilation: no
Packaged: 2024-11-10 22:01:22 UTC; mitra
Author: Mitra Ebrahimpoor [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-12 14:10:02 UTC

More information about rOCEAN at CRAN
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New package fastml with initial version 0.1.0
Package: fastml
Title: Fast Machine Learning Model Training and Evaluation
Version: 0.1.0
Description: Streamlines the training, evaluation, and comparison of multiple machine learning models with minimal code by providing comprehensive data preprocessing and support for a wide range of algorithms with hyperparameter tuning. It offers performance metrics and visualization tools to facilitate efficient and effective machine learning workflows.
License: GPL (>= 2)
Encoding: UTF-8
Imports: caret, pROC, reshape2, ggplot2, foreach, doParallel
Suggests: knitr, rmarkdown, randomForest, kernlab, gbm, nnet, rpart, glmnet, xgboost, pls, C50, mboost, arm, ipred, caTools, e1071, MASS
NeedsCompilation: no
Packaged: 2024-11-11 13:28:27 UTC; selcukkorkmaz
Author: Selcuk Korkmaz [aut, cre] , Dincer Goksuluk [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-12 14:30:02 UTC

More information about fastml at CRAN
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New package bplsr with initial version 1.0.0
Package: bplsr
Title: Bayesian partial least squares regression
Version: 1.0.0
Maintainer: Szymon Urbas <szymon.urbas@mu.ie>
Description: Fits the Bayesian partial least squares regression model introduced in Urbas et al. (2024) <doi:10.1214/24-AOAS1947>. Suitable for univariate and multivariate regression with high-dimensional data.
License: GPL (>= 3)
Encoding: UTF-8
Language: eng
Depends: R (>= 2.10)
LazyData: true
Imports: coda, progress, statmod, stats, utils
NeedsCompilation: no
Packaged: 2024-11-11 20:55:25 UTC; surbas
Author: Szymon Urbas [aut, cre], Pierre Lovera [ctb], Robert Daly [ctb], Alan O'Riordan [ctb], Donagh Berry [ctb], Isobel Claire Gormley [ctb]
Repository: CRAN
Date/Publication: 2024-11-12 14:50:02 UTC

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New package BayesGP with initial version 0.1.3
Package: BayesGP
Title: Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models
Version: 0.1.3
Description: Implements Bayesian hierarchical models with flexible Gaussian process priors, focusing on Extended Latent Gaussian Models and incorporating various Gaussian process priors for Bayesian smoothing. Computations leverage finite element approximations and adaptive quadrature for efficient inference. Methods are detailed in Zhang, Stringer, Brown, and Stafford (2023) <doi:10.1177/09622802221134172>; Zhang, Stringer, Brown, and Stafford (2024) <doi:10.1080/10618600.2023.2289532>; Zhang, Brown, and Stafford (2023) <doi:10.48550/arXiv.2305.09914>; and Stringer, Brown, and Stafford (2021) <doi:10.1111/biom.13329>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LinkingTo: TMB (>= 1.9.7), RcppEigen
Imports: TMB (>= 1.9.7), numDeriv, rstan, sfsmisc, Matrix (>= 1.6.3), aghq (>= 0.4.1), fda, tmbstan, LaplacesDemon, methods
Depends: R (>= 3.6.0)
Suggests: rmarkdown, knitr, survival, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2024-11-10 22:31:24 UTC; ziangzhang
Author: Ziang Zhang [aut, cre], Yongwei Lin [aut], Alex Stringer [aut], Patrick Brown [aut]
Maintainer: Ziang Zhang <ziangzhang@uchicago.edu>
Repository: CRAN
Date/Publication: 2024-11-12 14:20:03 UTC

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New package SFM with initial version 0.1.0
Package: SFM
Title: A Package for Analyzing Skew Factor Models
Version: 0.1.0
Description: Generates Skew Factor Models data and applies Sparse Online Principal Component (SOPC) method to estimate model parameters. It includes capabilities for calculating mean squared error, relative error, and sparsity of the loading matrix. Additionally, it includes robust regression methods such as adaptive Huber regression.The philosophy of the package is described in Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: MASS, SOPC, matrixcalc, sn, stats
NeedsCompilation: no
Language: en-US
Author: Guangbao Guo [aut, cre], Yu Jin [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Suggests: testthat (>= 3.0.0), ggplot2, reshape2
Packaged: 2024-11-08 06:55:06 UTC; AIERXUAN
Repository: CRAN
Date/Publication: 2024-11-12 13:10:02 UTC

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New package CIMPLE with initial version 0.1.0
Package: CIMPLE
Title: Analysis of Longitudinal Electronic Health Record (EHR) Data with Possibly Informative Observational Time
Version: 0.1.0
Description: Analyzes longitudinal Electronic Health Record (EHR) data with possibly informative observational time. These methods are grouped into two classes depending on the inferential task. One group focuses on estimating the effect of an exposure on a longitudinal biomarker while the other group assesses the impact of a longitudinal biomarker on time-to-diagnosis outcomes. The accompanying paper is Du et al (2024) <doi:10.48550/arXiv.2410.13113>.
License: GPL (>= 3)
Depends: R (>= 2.10)
Imports: dplyr, JMbayes2, lme4, mice, nleqslv, nlme, statmod, stats, survival, utils
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-09 05:45:29 UTC; hb636
Author: Jiacong Du [aut] , Howard Baik [cre]
Maintainer: Howard Baik <howard.baik@yale.edu>
Repository: CRAN
Date/Publication: 2024-11-12 13:20:10 UTC

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New package forestGYM with initial version 1.0.0
Package: forestGYM
Title: Forest Growth and Yield Model Based on Clutter Model
Version: 1.0.0
Depends: R (>= 3.5.0)
Imports: gtools(>= 3.8.5),stats(>= 4.3.1)
Description: The Clutter model is a significant forest growth simulation tool. Grounded on individual trees and comprehensively considering factors such as competition among trees and the impact of environmental elements on growth, it can accurately reflect the growth process of forest stands. It can be applied in areas like forest resource management, harvesting planning, and ecological research. With the help of the Clutter model, people can better understand the dynamic changes of forests and provide a scientific basis for rational forest management and protecting the ecological environment. This R package can effectively realize the construction of forest growth and harvest models based on the Clutter model and achieve optimized forest management.References: Farias A, Soares C, Leite H et al(2021)<doi:10.1007/s10342-021-01380-1>. Guera O, Silva J, Ferreira R, et al(2019)<doi:10.1590/2179-8087.038117>.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-12 01:39:36 UTC; 78438
Author: Zongzheng Chai [aut, cre]
Maintainer: Zongzheng Chai <chaizz@126.com>
Repository: CRAN
Date/Publication: 2024-11-12 10:20:05 UTC

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Mon, 11 Nov 2024

New package semaphore with initial version 1.0.1
Package: semaphore
Title: Shared Memory Atomic Operations
Version: 1.0.1
Date: 2024-11-08
Description: Implements named semaphores from the 'boost' 'C++' library <https://www.boost.org/>. A semaphore object is shared amongst several processes. This integer value can be safely incremented or decremented by each processes. Processes can also wait (blocking) for the value to become non-zero.
URL: https://cmmr.github.io/semaphore/, https://github.com/cmmr/semaphore
BugReports: https://github.com/cmmr/semaphore/issues
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.2.0)
LinkingTo: Rcpp, BH
Imports: Rcpp
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-11-08 17:49:24 UTC; Daniel
Author: Daniel P. Smith [aut, cre] , Alkek Center for Metagenomics and Microbiome Research [cph, fnd]
Maintainer: Daniel P. Smith <dansmith01@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-11 20:40:02 UTC

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New package rjaf with initial version 0.1.0
Package: rjaf
Title: Regularized Joint Assignment Forest with Treatment Arm Clustering
Version: 0.1.0
URL: https://github.com/wustat/rjaf
BugReports: https://github.com/wustat/rjaf/issues
Description: Personalized assignment to one of many treatment arms via regularized and clustered joint assignment forests as described in Ladhania, Spiess, Ungar, and Wu (2023) <doi:10.48550/arXiv.2311.00577>. The algorithm pools information across treatment arms: it considers a regularized forest-based assignment algorithm based on greedy recursive partitioning that shrinks effect estimates across arms; and it incorporates a clustering scheme that combines treatment arms with consistently similar outcomes.
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: Rcpp, dplyr, tibble, magrittr, readr, randomForest, ranger, forcats, rlang (>= 1.1.0), tidyr, stringr, MASS
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
NeedsCompilation: yes
Packaged: 2024-11-08 00:31:37 UTC; xinyizhang
Author: Wenbo Wu [aut, cph] , Xinyi Zhang [aut, cre, cph] , Jann Spiess [aut, cph] , Rahul Ladhania [aut, cph]
Maintainer: Xinyi Zhang <zhang.xinyi@nyu.edu>
Repository: CRAN
Date/Publication: 2024-11-11 20:10:02 UTC

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New package RadEro with initial version 1.0.4
Package: RadEro
Title: Cs-137 Conversion Model
Version: 1.0.4
Date: 2024-10-30
Description: A straightforward model to estimate soil migration rates across various soil contexts. Based on the compartmental, vertically-resolved, physically-based mass balance model of Soto and Navas (2004) <doi:10.1016/j.jaridenv.2004.02.003> and Soto and Navas (2008) <doi:10.1016/j.radmeas.2008.02.024>. 'RadEro' provides a user-friendly interface in R, utilizing input data such as 137Cs inventories and parameters directly derived from soil samples (e.g., fine fraction density, effective volume) to accurately capture the 137Cs distribution within the soil profile. The model simulates annual 137Cs fallout, radioactive decay, and vertical diffusion, with the diffusion coefficient calculated from 137Cs reference inventory profiles. Additionally, it allows users to input custom parameters as calibration coefficients. This tool and its code are openly accessible, facilitating usage in soil erosion studies.
License: GPL (>= 2)
Depends: R (>= 4.3.0)
Imports: Rcpp (>= 1.0.11), dplyr (>= 1.1.4), roxygen2 (>= 7.2.3), usethis (>= 2.2.2), jsonlite (>= 1.8.7), data.table (>= 1.14.8), devtools (>= 2.4.5), ggplot2 (>= 3.4.4), patchwork (>= 1.1.3), utils (>= 4.3.1), stats (>= 4.3.1)
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2024-11-08 09:55:28 UTC; artur
Author: Arturo Catala [aut, cre], Borja Latorre [aut, ctb, cph], Leticia Gaspar [aut], Ana Navas [aut], Dave Gamble [ctb]
Maintainer: Arturo Catala <acatalae@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-11 20:20:01 UTC

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New package pannotator with initial version 1.0.0.4
Package: pannotator
Title: Visualisation and Annotation of 360 Degree Imagery
Version: 1.0.0.4
Description: Provides a customisable R 'shiny' app for immersively visualising, mapping and annotating panospheric (360 degree) imagery. The flexible interface allows annotation of any geocoded images using up to 4 user specified dropdown menus. The app uses 'leaflet' to render maps that display the geo-locations of images and panellum <https://pannellum.org/>, a lightweight panorama viewer for the web, to render images in virtual 360 degree viewing mode. Key functions include the ability to draw on & export parts of 360 images for downstream applications. Users can also draw polygons and points on map imagery related to the panoramic images and export them for further analysis. Downstream applications include using annotations to train Artificial Intelligence/Machine Learning (AI/ML) models and geospatial modelling and analysis of camera based survey data.
License: GPL (>= 3)
URL: https://github.com/NunzioKnerr/pannotator_package_source
BugReports: https://github.com/NunzioKnerr/pannotator_package_source/issues
Imports: bslib, colourpicker, config, configr, dplyr, exiftoolr, geojsonsf, ggplot2, golem, graphics, grDevices, htmlwidgets, jpeg, jsonify, jsonlite, leaflet, leaflet.extras, leafpm, magrittr, readr, scales, sf, shiny, shinyFiles, shinyhelper, shinyjs, shinythemes, shinyWidgets, stringr, tools, utils
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-08 11:56:18 UTC; kne01b
Author: Nunzio Knerr [aut, cre] , Robert Godfree [aut] , Matthew Petroff [ctb], CSIRO [cph]
Maintainer: Nunzio Knerr <Nunzio.Knerr@csiro.au>
Repository: CRAN
Date/Publication: 2024-11-11 20:30:02 UTC

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New package GTFSwizard with initial version 1.0.0
Package: GTFSwizard
Title: Exploring and Manipulating 'GTFS' Files
Version: 1.0.0
Date/Publication: 2024-11-11 20:40:05 UTC
URL: https://github.com/nelsonquesado/GTFSwizard
BugReports: https://github.com/nelsonquesado/GTFSwizard/issues
Description: Exploring, analyzing, and manipulating General Transit Feed Specification (GTFS) files, which represent public transportation schedules and geographic data. The package allows users to filter data by routes, trips, stops, and time, generate spatial visualizations, and perform detailed analyses of transit networks, including headway, dwell times, and route frequencies. Designed for transit planners, researchers, and data analysts, 'GTFSwizard' integrates functionalities from popular packages to enable efficient GTFS data manipulation and visualization.
Imports: gtfstools, tidytransit, lubridate, sf, tidyr, data.table, shiny, leaflet, checkmate, dplyr, ggplot2, gtfsio, purrr, rlang, crayon, forcats, hrbrthemes, stringr, tibble, plotly, leaflet.extras, geosphere, stplanr, glue, hms, sfnetworks
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-11-08 16:54:42 UTC; nelsonquesado
Author: Nelson de O. Quesado Filho [aut, cre], Caio G. C. Guimaraes [aut]
Maintainer: Nelson de O. Quesado Filho <nquesado@gmail.com>
Repository: CRAN

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New package FedData with initial version 4.1.0
Package: FedData
Title: Download Geospatial Data Available from Several Federated Data Sources
Version: 4.1.0
Date: 2024-11-06
Description: Download geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from nine datasets: The National Elevation Dataset digital elevation models (<https://www.usgs.gov/3d-elevation-program> 1 and 1/3 arc-second; USGS); The National Hydrography Dataset (<https://www.usgs.gov/national-hydrography/national-hydrography-dataset>; USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (<https://websoilsurvey.sc.egov.usda.gov/>; NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (<https://www.ncei.noaa.gov/products/land-based-station/global-historical-climatology-network-daily>; GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 4, available from the Oak Ridge [...truncated...]
License: MIT + file LICENSE
URL: https://docs.ropensci.org/FedData/, https://github.com/ropensci/FedData
BugReports: https://github.com/ropensci/FedData/issues
SystemRequirements: GDAL (>= 3.1.0)
Depends: R (>= 3.2.0)
Imports: curl, httr, dplyr, tibble, tidyr, stringr, igraph, xml2, lifecycle, lubridate, progress, purrr, readr, terra (>= 1.0), sf (>= 1.0), arcgislayers (>= 0.2.0), ggplot2, glue, magrittr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Repository: CRAN
Suggests: knitr, leaflet, mapview, ncdf4, rmapshaper, testthat, usethis
Packaged: 2024-11-07 23:20:08 UTC; kyle.bocinsky
Author: R. Kyle Bocinsky [aut, cre, cph] , Dylan Beaudette [ctb], Scott Chamberlain [ctb, rev], Jeffrey Hollister [ctb], Julia Gustavsen [rev]
Maintainer: R. Kyle Bocinsky <bocinsky@gmail.com>
Date/Publication: 2024-11-11 20:10:05 UTC

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New package betaselectr with initial version 0.1.0
Package: betaselectr
Title: Betas-Select in Structural Equation Models and Linear Models
Version: 0.1.0
Description: It computes betas-select, coefficients after standardization in structural equation models and regression models, standardizing only selected variables. Supports models with moderation, with product terms formed after standardization. It also offers confidence intervals that account for standardization, including bootstrap confidence intervals as proposed by Cheung et al. (2022) <doi:10.1037/hea0001188>.
License: GPL (>= 3)
Encoding: UTF-8
Suggests: testthat (>= 3.0.0), knitr, rmarkdown
Imports: boot, stats, lavaan, methods, numDeriv, manymome, pbapply, lavaan.printer
VignetteBuilder: knitr
URL: https://sfcheung.github.io/betaselectr/
BugReports: https://github.com/sfcheung/betaselectr/issues
Depends: R (>= 3.5.0)
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-08 11:26:51 UTC; shufa
Author: Shu Fai Cheung [aut, cre] , Rong Wei Sun [aut] , Florbela Chang [aut] , Wendie Yang [aut] , Sing-Hang Cheung [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-11 20:30:06 UTC

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New package forestSAS with initial version 2.0.4
Package: forestSAS
Title: Forest Spatial Structure Analysis Systems
Version: 2.0.4
Depends: R (>= 3.5.0)
Imports: spatstat, spatstat.data, spatstat.geom, spatstat.random
Description: Recent years have seen significant interest in neighborhood-based structural parameters that effectively represent the spatial characteristics of tree populations and forest communities, and possess strong applicability for guiding forestry practices. This package provides valuable information that enhances our understanding and analysis of the fine-scale spatial structure of tree populations and forest stands. Reference: Yan L, Tan W, Chai Z, et al (2019) <doi:10.13323/j.cnki.j.fafu(nat.sci.).2019.03.007>.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-06 14:06:51 UTC; 78438
Author: Zongzheng Chai [aut, cre]
Maintainer: Zongzheng Chai <chaizz@126.com>
Repository: CRAN
Date/Publication: 2024-11-11 16:50:02 UTC

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New package forestPSD with initial version 1.0.0
Package: forestPSD
Title: Forest Population Structure and Numeric Dynamics
Version: 1.0.0
Depends: R (>= 3.5.0)
Imports: ggplot2,reshape2,TTR,modelr,minpack.lm,stats,utils
Description: Analysis of forest population structure and quantitative dynamics is the research and evaluation of the composition, distribution, age structure and changes in quantity over time of various populations in the forest. By deeply understanding these characteristics of forest populations, scientific basis can be provided for the management, protection and sustainable utilization of forest resources. This R package conducts a systematic analysis of forest population structure and quantitative dynamics through analyzing age structure, compiling life tables, population quantitative dynamic change indices and time series models, in order to provide support for forest population protection and sustainable management. References: Zhang Y, Wang J, Wang X, et al(2024)<doi:10.3390/plants13070946>. Yuan G, Guo Q, Xie N, et al(2023)<doi:10.1007/s11629-022-7429-z>.
License: GPL-2
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-06 12:21:43 UTC; 78438
Author: Zongzheng Chai [aut, cre]
Maintainer: Zongzheng Chai <chaizz@126.com>
Repository: CRAN
Date/Publication: 2024-11-11 16:50:05 UTC

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New package seAMLess with initial version 0.1.1
Package: seAMLess
Title: A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia
Description: Given a bulk transcriptomic (RNA-seq) sample of an Myeloid Leukemia patient calculates immune composition and drug resistance for different small-molecule inhibitors. Published in <https://www.nature.com/articles/s41698-024-00596-9>.
Version: 0.1.1
Depends: R (>= 3.5.0)
Imports: Biobase, ggplot2, optparse, data.table,
Suggests: MuSiC, ggtern, seAMLessData, randomForest
Additional_repositories: https://eonurk.github.io/drat/
URL: https://github.com/eonurk/seAMLess
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-11 10:18:00 UTC; onur-lumc
Author: E Onur Karakaslar [aut, cre], Redmar van den Berg [ctb]
Maintainer: E Onur Karakaslar <eonurkara@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-11 12:50:02 UTC

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New package photon with initial version 0.3.1
Package: photon
Title: High-Performance Geocoding using 'photon'
Version: 0.3.1
Description: Features unstructured, structured and reverse geocoding using the 'photon' geocoding API <https://photon.komoot.io/>. Facilitates the setup of local 'photon' instances to enable offline geocoding.
License: Apache License (>= 2)
URL: https://github.com/jslth/photon/, https://jslth.github.io/photon/
BugReports: https://github.com/jslth/photon/issues
Encoding: UTF-8
Imports: utils, cli, countrycode, httr2, R6, sf, processx
Suggests: testthat (>= 3.0.0), tibble, knitr, rmarkdown, webfakes, ps
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 21:41:38 UTC; PC
Author: Jonas Lieth [aut, cre, cph]
Maintainer: Jonas Lieth <jonas.lieth@gesis.org>
Repository: CRAN
Date/Publication: 2024-11-11 12:20:02 UTC

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New package PakPC with initial version 0.2.0
Package: PakPC
Title: 'shiny' App to Analyze Pakistan's Population Census Data
Version: 0.2.0
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Provides tools for analyzing Pakistan's Population Censuses data via the 'PakPC2023' and 'PakPC2017' R packages. Designed for researchers, policymakers, and professionals, the app enables in-depth numerical and graphical analysis, including detailed cross-tabulations and insights. With diverse statistical models and visualization options, it supports informed decision-making in social and economic policy. This tool enhances users' ability to explore and interpret census data, providing valuable insights for effective planning and analysis across various fields.
URL: https://myaseen208.com/PakPC/ https://myaseen208.shinyapps.io/PakPC/ https://CRAN.R-project.org/package=PakPC
BugReports: https://github.com/myaseen208/PakPC/issues
Depends: R (>= 4.1)
Imports: DT, htmltools, magrittr, PakPC2017, PakPC2023, rpivotTable, shiny, shinydashboard, shinydashboardPlus
Suggests: shinytest2, testthat (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
Note: 1. School of Mathematical & Statistical Sciences, Clemson University, Clemson, South Carolina, USA 2. Department of Mathematics and Statistics, University of Agriculture Faisalabad, Pakistan
NeedsCompilation: no
Packaged: 2024-11-07 18:52:34 UTC; myaseen208
Author: Muhammad Yaseen [aut, cre, cph] , Muhammad Arfan Dilber [ctb], Zahid Asghar [ctb]
Repository: CRAN
Date/Publication: 2024-11-11 11:50:07 UTC

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New package PakNAcc with initial version 0.1.0
Package: PakNAcc
Title: 'shiny' App for National Accounts
Version: 0.1.0
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Description: Provides a comprehensive suite of tools for analyzing Pakistan's Quarterly National Accounts data. Users can gain detailed insights into Pakistan's economic performance, visualize quarterly trends, and detect patterns and anomalies in key economic indicators. Compare sector contributions—including agriculture, industry, and services—to understand their influence on economic growth or decline. Customize analyses by filtering and manipulating data to focus on specific areas of interest. Ideal for policymakers, researchers, and analysts aiming to make informed, data-driven decisions based on timely and detailed economic insights.
URL: https://myaseen208.com/PakNAcc/ https://myaseen208.shinyapps.io/PakNAcc/ https://CRAN.R-project.org/package=PakNAcc
BugReports: https://github.com/myaseen208/PakNAcc/issues
Depends: R (>= 4.1)
Imports: collapse, DT, htmltools, magrittr, rpivotTable, shiny, shinydashboard, shinydashboardPlus
Suggests: shinytest2, testthat (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
Note: School of Mathematical & Statistical Sciences, Clemson University, Clemson, South Carolina, USA
NeedsCompilation: no
Packaged: 2024-11-07 18:34:28 UTC; myaseen208
Author: Muhammad Yaseen [aut, cre, cph] , Zahid Asghar [ctb]
Repository: CRAN
Date/Publication: 2024-11-11 11:50:11 UTC

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New package JAGStree with initial version 1.0.1
Package: JAGStree
Title: Automatically Write 'JAGS' Code for Hierarchical Bayesian Models on Trees
Version: 1.0.1
Maintainer: Mallory J Flynn <mallory.flynn@stat.ubc.ca>
Description: When relationships between sources of data can be represented by a tree, the generation of appropriate Markov Chain Monte Carlo modeling code to be used with 'JAGS' to run a Bayesian hierarchical model can be automatically generated by this package. Any admissible tree-structured data can be used, under the assumption that node counts are multinomial and branching probabilities are Dirichlet among sibling groups. The methodological basis used to create this package can be found in Flynn (2023) <http://hdl.handle.net/2429/86174>.
License: GPL (>= 2)
URL: https://github.com/malfly/JAGStree
Depends: R (>= 4.3.0)
Imports: data.tree, gtools, mcmcplots, stats, R2jags, tidyverse, DiagrammeR, AutoWMM
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 18:58:12 UTC; mallory
Author: Mallory J Flynn [cre, aut]
Repository: CRAN
Date/Publication: 2024-11-11 12:00:13 UTC

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New package ig.degree.betweenness with initial version 0.1.0
Package: ig.degree.betweenness
Title: "Smith-Pittman Community Detection Algorithm for 'igraph' Objects (2024)"
Version: 0.1.0
Description: Implements the "Smith-Pittman" community detection algorithm for network analysis using 'igraph' objects. This algorithm combines node degree and betweenness centrality measures to identify communities within networks, with a gradient evident in social partitioning. The package provides functions for community detection, visualization, and analysis of the resulting community structure. Methods are based on results from Smith, Pittman and Xu (2024) <doi:10.48550/arXiv.2411.01394>.
License: MIT + file LICENSE
URL: https://github.com/benyamindsmith/ig.degree.betweenness
BugReports: https://github.com/benyamindsmith/ig.degree.betweenness/issues
Encoding: UTF-8
Imports: igraph, igraphdata, rlist, BBmisc, qgraph
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2024-11-07 19:17:21 UTC; ben29
Author: Benjamin Smith [aut, cre] , Tyler Pittman [aut] , Wei Xu [aut]
Maintainer: Benjamin Smith <benyamin.smith@mail.utoronto.ca>
Repository: CRAN
Date/Publication: 2024-11-11 12:00:01 UTC

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New package distfreereg with initial version 1.0
Package: distfreereg
Title: Distribution-Free Goodness-of-Fit Testing for Regression
Version: 1.0
Depends: R (>= 4.4)
Imports: clue, methods, numDeriv
Suggests: knitr, Matrix, mvtnorm, rmarkdown
VignetteBuilder: knitr
Date: 2024-11-04
Maintainer: Jesse Miller <mill9116@umn.edu>
Description: Implements distribution-free goodness-of-fit regression testing for the mean structure of parametric models introduced in Khmaladze (2021) <doi:10.1007/s10463-021-00786-3>.
License: GPL-3
NeedsCompilation: no
Packaged: 2024-11-07 18:52:22 UTC; Jesse
Author: Jesse Miller [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-11 12:00:04 UTC

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Sun, 10 Nov 2024

New package SegEnvIneq with initial version 1.2
Package: SegEnvIneq
Title: Environmental Inequality Indices Based on Segregation Measures
Version: 1.2
Date: 2024-11-07
Description: A set of segregation-based indices and randomization methods to make robust environmental inequality assessments, as described in Schaeffer and Tivadar (2019) "Measuring Environmental Inequalities: Insights from the Residential Segregation Literature" <doi:10.1016/j.ecolecon.2019.05.009>.
Depends: R (>= 4.4.0)
Imports: sf (>= 1.0-16), spdep (>= 1.3-6), OasisR (>= 3.1.1), outliers (>= 0.15)
License: GPL-2 | GPL-3
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-07 11:05:44 UTC; mtivadar
Author: Mihai Tivadar [aut, cre], Yves Schaeffer [aut]
Maintainer: Mihai Tivadar <mihai.tivadar@inrae.fr>
Repository: CRAN
Date/Publication: 2024-11-10 15:50:06 UTC

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New package maicplus with initial version 0.1.0
Title: Matching Adjusted Indirect Comparison
Package: maicplus
Version: 0.1.0
Date: 2024-10-29
Description: Facilitates performing matching adjusted indirect comparison (MAIC) analysis where the endpoint of interest is either time-to-event (e.g. overall survival) or binary (e.g. objective tumor response). The method is described by Signorovitch et al (2012) <doi:10.1016/j.jval.2012.05.004>.
License: Apache License 2.0
URL: https://github.com/hta-pharma/maicplus/, https://hta-pharma.github.io/maicplus/
BugReports: https://github.com/hta-pharma/maicplus/issues
Depends: R (>= 3.6)
Imports: graphics, grDevices, stats, survival, lubridate, DescTools, MASS, boot, stringr, lmtest, sandwich
Suggests: knitr, testthat (>= 2.0), ggplot2, rmarkdown, dplyr, survminer, flexsurv, tibble, vdiffr, checkmate
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2024-11-07 11:31:16 UTC; gravesti
Author: Gregory Chen [aut], Michael Seo [aut], Isaac Gravestock [aut, cre], Miranta Antoniou [ctb], Chrysostomos Kalyvas [ctb], MSD, Inc. [cph, fnd], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Repository: CRAN
Date/Publication: 2024-11-10 15:50:02 UTC

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New package laminr with initial version 0.1.0
Package: laminr
Title: Interface for 'LaminDB'
Version: 0.1.0
Description: Interact with 'LaminDB'. 'LaminDB' is an open-source data framework for biology. This package allows you to query and download data from 'LaminDB' instances.
License: Apache License (>= 2)
URL: https://laminr.lamin.ai, https://github.com/laminlabs/laminr
BugReports: https://github.com/laminlabs/laminr/issues
Depends: R (>= 4.0.0)
Imports: cli, httr, jsonlite, purrr, R6, rlang
Suggests: anndata, quarto, s3 (>= 1.1.0), testthat (>= 3.0.0), withr
VignetteBuilder: quarto
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-07 14:07:57 UTC; root
Author: Robrecht Cannoodt [aut, cre], Luke Zappia [aut], Data Intuitive [aut], Lamin Labs [aut, cph]
Maintainer: Robrecht Cannoodt <robrecht@data-intuitive.com>
Repository: CRAN
Date/Publication: 2024-11-10 16:00:02 UTC

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Fri, 08 Nov 2024

New package SimRDS with initial version 2.0.0
Package: SimRDS
Title: Simulation of Respondent Driven Samples
Version: 2.0.0
Maintainer: Ayesha Perera <gaayesha93@gmail.com>
Description: Simulate populations with desired properties and extract respondent driven samples. To better understand the usage of the package and the algorithm used, please refer to Perera, A., and Ramanayake, A. (2019) <https://www.aimr.tirdiconference.com/assets/images/portfolio/Conference-Proceeding-AIMR-19.pdf>.
License: GPL-2
Imports: RDS, e1071, stats
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
Suggests: knitr, rmarkdown
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2024-11-07 01:59:49 UTC; GPERERA
Author: Ayesha Perera [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-08 15:10:09 UTC

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New package lofifonts with initial version 0.1.3
Package: lofifonts
Title: Text Rendering with Bitmap and Vector Fonts
Version: 0.1.3
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Description: Alternate font rendering is useful when rendering text to novel graphics outputs where modern font rendering is not available or where bespoke text positioning is required. Bitmap and vector fonts allow for custom layout and rendering using pixel coordinates and line drawing. Formatted text is created as a data.frame of pixel coordinates (for bitmap fonts) or stroke coordinates (for vector fonts). All text can be easily previewed as a matrix or raster image. A selection of fonts is included with this package.
License: MIT + file LICENSE
Encoding: UTF-8
Copyright: The included 'spleen' font is BSD licensed and Copyright (c) 2018-2024, Frederic Cambus. The included 'Tamzen' font is free to distribute and Copyright 2011 Suraj N. Kurapati (it is based upon the 'Tamsyn' font which is also free to distribute Copyright 2010 Scott Fial) The included 'unifont' font is SIL Open Font Licensed, and is Copyright the GNU unifont authors. The included 'gridfont' is MIT licensed is Copyright (c) 2019 Anders Hoff. See 'COPYRIGHTS' file for more details.
URL: https://github.com/coolbutuseless/lofifonts
BugReports: https://github.com/coolbutuseless/lofifonts/issues
Depends: R (>= 2.10)
Suggests: knitr, rmarkdown, bittermelon, ggplot2, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 09:48:56 UTC; mike
Author: Mike Cheng [aut, cre, cph], June Choe [ctb] , Frederic Cambus [cph, tyd] , GNU Unifont authors [cph, tyd] , Suraj Kurapati [cph, tyd] , Scott Fial [cph, tyd] , Anders Hoff [cph, tyd]
Repository: CRAN
Date/Publication: 2024-11-08 15:20:02 UTC

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New package FGRepo with initial version 1.3.2.0
Package: FGRepo
Title: Functional Genomics Repository for POST-GWAS Analysis
Version: 1.3.2.0
Date: 2024-11-07
Author: Alireza Ani [aut, cre], Ahmad Vaez [aut]
Maintainer: Alireza Ani <a.ani@umcg.nl>
Depends: R (>= 3.5)
Description: A collection of datasets essential for functional genomic analysis. Gene names, gene positions, cytoband information, sourced from Ensembl and phenotypes association graph prepared from GWAScatalog are included. Data is available in both GRCh37 and 38 builds. These datasets facilitate a wide range of genomic studies, including the identification of genetic variants, exploration of genomic features, and post-GWAS functional analysis.
License: GPL-3
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2024-11-07 06:27:56 UTC; Alireza
Repository: CRAN
Date/Publication: 2024-11-08 15:10:12 UTC

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New package AIscreenR with initial version 0.1.0
Package: AIscreenR
Title: AI Screening Tools in R for Systematic Reviewing
Version: 0.1.0
Description: Provides functions to conduct title and abstract screening in systematic reviews using large language models, such as the Generative Pre-trained Transformer (GPT) models from 'OpenAI' <https://platform.openai.com/>. These functions can enhance the quality of title and abstract screenings while reducing the total screening time significantly. In addition, the package includes tools for quality assessment of title and abstract screenings, as described in Vembye, Christensen, Mølgaard, and Schytt (2024) <DOI:10.31219/osf.io/yrhzm>.
Depends: R (>= 4.1.0)
License: GPL (>= 3)
Encoding: UTF-8
Imports: dplyr, tibble, httr2, stringr, furrr, tidyr, tictoc, askpass, curl, purrr, lifecycle, jsonlite
Suggests: future, knitr, rmarkdown, usethis, testthat (>= 3.0.0)
URL: https://mikkelvembye.github.io/AIscreenR/, https://github.com/MikkelVembye/AIscreenR
BugReports: https://github.com/MikkelVembye/AIscreenR/issues
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-07 09:01:08 UTC; B199526
Author: Mikkel H. Vembye [aut, cre, cph]
Maintainer: Mikkel H. Vembye <mikkel.vembye@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:10:15 UTC

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New package tidyplots with initial version 0.1.2
Package: tidyplots
Title: Tidy Plots for Scientific Papers
Version: 0.1.2
Description: The goal of 'tidyplots' is to streamline the creation of publication-ready plots for scientific papers. It allows to gradually add, remove and adjust plot components using a consistent and intuitive syntax.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: cli, dplyr, forcats, ggbeeswarm, ggplot2, ggpubr, ggrastr, ggrepel, glue, Hmisc, htmltools, lifecycle, patchwork, purrr, rlang, scales, stringr, tidyr, tidyselect
Depends: R (>= 2.10)
LazyData: true
URL: https://github.com/jbengler/tidyplots, https://jbengler.github.io/tidyplots/
BugReports: https://github.com/jbengler/tidyplots/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-06 23:27:30 UTC; janbroderengler
Author: Jan Broder Engler [aut, cre, cph]
Maintainer: Jan Broder Engler <broder.engler@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:02 UTC

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New package redcas with initial version 0.1.1
Package: redcas
Depends: R (>= 3.5.0), methods
Title: An Interface to the Computer Algebra System 'REDUCE'
Version: 0.1.1
Date: 2024-11-05
Author: Martin Gregory [aut, cre]
Maintainer: Martin Gregory <mairtin.macghreagoir@gmail.com>
Description: 'REDUCE' is a portable general-purpose computer algebra system supporting scalar, vector, matrix and tensor algebra, symbolic differential and integral calculus, arbitrary precision numerical calculations and output in 'LaTeX' format. 'REDUCE' is based on 'Lisp' and is available on the two dialects 'Portable Standard Lisp' ('PSL') and 'Codemist Standard Lisp' ('CSL'). The 'redcas' package provides an interface for executing arbitrary 'REDUCE' code interactively from 'R', returning output as character vectors. 'R' code and 'REDUCE' code can be interspersed. It also provides a specialized function for calling the 'REDUCE' feature for solving systems of equations, returning the output as an 'R' object designed for the purpose. A further specialized function uses 'REDUCE' features to generate 'LaTeX' output and post-processes this for direct use in 'LaTeX' documents, e.g. using 'Sweave'.
License: GPL-3
SystemRequirements: 'REDUCE' <http://www.reduce-algebra.com>. At least one of the 'CSL' or 'PSL' dialects must be installed in order to use the package. Tested with 'REDUCE' releases 6860 and 6558 for both 'CSL' and 'PSL' on Linux, and 6558 and 6339 for 'CSL' on MacOS
NeedsCompilation: no
OS_type: unix
Packaged: 2024-11-05 16:30:11 UTC; mg
Repository: CRAN
Date/Publication: 2024-11-08 14:50:02 UTC

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New package metasnf with initial version 1.1.1
Package: metasnf
Title: Meta Clustering with Similarity Network Fusion
Version: 1.1.1
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
License: GPL (>= 3)
Encoding: UTF-8
Imports: cluster, digest, dplyr, ggplot2, grDevices, MASS, mclust, methods, progressr, purrr, rlang, SNFtool, stats, tidyr, utils
Suggests: circlize, ComplexHeatmap, InteractiveComplexHeatmap, clv, future, future.apply, knitr, rmarkdown, testthat (>= 3.0.0), ggalluvial, dbscan
Depends: R (>= 4.1.0)
LazyData: true
VignetteBuilder: knitr
URL: https://branchlab.github.io/metasnf/, https://github.com/BRANCHlab/metasnf/
BugReports: https://github.com/BRANCHlab/metasnf/issues
NeedsCompilation: no
Packaged: 2024-11-06 18:40:32 UTC; prashanth
Author: Prashanth S Velayudhan [aut, cre], Xiaoqiao Xu [aut], Prajkta Kallurkar [aut], Ana Patricia Balbon [aut], Maria T Secara [aut], Adam Taback [aut], Denise Sabac [aut], Nicholas Chan [aut], Shihao Ma [aut], Bo Wang [aut], Daniel Felsky [aut], Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:08 UTC

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New package ineAtlas with initial version 0.1.2
Package: ineAtlas
Title: Access to Spanish Household Income Distribution Atlas Data
Version: 0.1.2
Description: Provides access to granular socioeconomic indicators from the Spanish Statistical Office (INE) Household Income Distribution Atlas. The package downloads and processes data from a companion 'GitHub' repository (<https://github.com/pablogguz/ineAtlas.data/>) which contains processed versions of the official INE Atlas data. Functions are provided to fetch data at multiple geographic levels (municipalities, districts, and census tracts), including income indicators, demographic characteristics, and inequality metrics. The data repository is updated every year when new releases are published by INE.
License: MIT + file LICENSE
URL: https://github.com/pablogguz/ineAtlas, https://pablogguz.github.io/ineAtlas/
BugReports: https://github.com/pablogguz/ineAtlas/issues
Imports: dplyr, httr, readr, sf, stringr, utils, zip
Suggests: data.table, extrafont, ggplot2, ggtext, knitr, mapSpain, mockery, rmarkdown, spelling, testthat (>= 3.0.0), tidyr
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
NeedsCompilation: no
Packaged: 2024-11-06 19:31:47 UTC; pablo
Author: Pablo Garcia Guzman [aut, cre, cph]
Maintainer: Pablo Garcia Guzman <garciagp@ebrd.com>
Repository: CRAN
Date/Publication: 2024-11-08 15:00:17 UTC

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New package ILSAmerge with initial version 1.0.0
Package: ILSAmerge
Title: Merge and Download International Large-Scale Assessments (ILSA) Data
Version: 1.0.0
Maintainer: Andres Christiansen <andres.christiansen@iea-hamburg.de>
Description: Merges and downloads 'SPSS' data from different International Large-Scale Assessments (ILSA), including: Trends in International Mathematics and Science Study (TIMSS), Progress in International Reading Literacy Study (PIRLS), Programme for International Student Assessment (PISA), and others.
License: GPL (>= 3.0)
URL: https://github.com/dopatendo/ILSAmerge
Imports: haven
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-11-06 17:24:19 UTC; andreschristiansen
Author: Andres Christiansen [aut, cre]
Repository: CRAN
Date/Publication: 2024-11-08 14:50:06 UTC

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New package ife with initial version 0.1.0
Package: ife
Title: Influence Function Based Estimate Objects
Version: 0.1.0
Maintainer: Nicholas Williams <ntwilliams.personal@gmail.com>
Description: Implements an S7 class for estimates based on influence functions. Standard arithmetic operations are defined for the class.
License: GPL (>= 3)
Encoding: UTF-8
Imports: cli, generics, S7
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2024-11-06 19:03:21 UTC; nicholaswilliams
Author: Nicholas Williams [aut, cre, cph]
Repository: CRAN
Date/Publication: 2024-11-08 15:00:20 UTC

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New package epicmodel with initial version 0.1.1
Package: epicmodel
Title: Causal Modeling in Epidemiology
Version: 0.1.1
Description: Create causal models for use in epidemiological studies, including sufficient-component cause models as introduced by Rothman (1976) <doi:10.1093/oxfordjournals.aje.a112335>.
License: GPL (>= 3)
Encoding: UTF-8
Imports: checkmate, cli, dagitty, DiagrammeR, dplyr, DT, ggplot2, gtools, magrittr, methods, prompter, purrr, rlang, shiny, shinyalert, shinyjs, shinythemes, spsUtil, stringr, tibble, tidyr
Suggests: ggdag, ggforce, ggraph, knitr, rmarkdown, testthat (>= 3.0.0)
Depends: R (>= 3.5.0)
LazyData: true
VignetteBuilder: knitr
URL: https://forsterepi.github.io/epicmodel/, https://github.com/forsterepi/epicmodel
BugReports: https://github.com/forsterepi/epicmodel/issues
NeedsCompilation: no
Packaged: 2024-11-06 10:44:37 UTC; ffors
Author: Felix Forster [aut, cre, cph]
Maintainer: Felix Forster <felix.forster@med.uni-muenchen.de>
Repository: CRAN
Date/Publication: 2024-11-08 14:30:01 UTC

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New package DTSR with initial version 0.1.0
Package: DTSR
Version: 0.1.0
Date: 2024-10-22
Title: Distributed Trimmed Scores Regression for Handling Missing Data
Author: Guangbao Guo [aut, cre, cph] , Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Description: Provides functions for handling missing data using Distributed Trimmed Scores Regression and other imputation methods. It includes facilities for data imputation, evaluation metrics, and clustering analysis. It is designed to work in distributed computing environments to handle large datasets efficiently. The philosophy of the package is described in Guo G. (2024) <doi:10.1080/03610918.2022.2091779>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.5.0)
Repository: CRAN
Imports: stats, mvdalab, DMwR2, cluster, MASS
NeedsCompilation: no
Packaged: 2024-11-06 08:37:30 UTC; ASUS
Date/Publication: 2024-11-08 14:30:06 UTC

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Thu, 07 Nov 2024

New package WMAP with initial version 1.0.0
Package: WMAP
Title: Weighted Meta-Analysis with Pseudo-Populations
Version: 1.0.0
Description: Implementation of integrative weighting approaches for multiple observational studies and causal inferences. The package features three weighting approaches, each representing a special case of the unified weighting framework, introduced by Guha and Li (2024) <doi:10.1093/biomtc/ujae070>, which includes an extension of inverse probability weights for data integration settings.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: pkgcond, ggplot2, zeallot, caret, randomForest, forcats, utils, stats, grDevices
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2024-11-06 02:25:33 UTC; doggydoggy
Author: Subharup Guha [aut, cre], Mengqi Xu [aut], Kashish Priyam [aut], Yi Li [aut]
Maintainer: Subharup Guha <s.guha@ufl.edu>
Repository: CRAN
Date/Publication: 2024-11-07 18:40:02 UTC

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New package threeBrain with initial version 1.2.0
Package: threeBrain
Title: Your Advanced 3D Brain Visualization
Version: 1.2.0
Description: A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://openwetware.org/wiki/RAVE>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check 'citation("threeBrain")' for details.
License: MPL-2.0
Encoding: UTF-8
Language: en-US
URL: https://dipterix.org/threeBrain/, https://github.com/dipterix/threeBrain
BugReports: https://github.com/dipterix/threeBrain/issues
Imports: utils, grDevices, graphics, dipsaus, xml2, servr, png, knitr, shiny (>= 1.2.0), digest (>= 0.6.22), freesurferformats (>= 0.1.7), jsonlite (>= 1.5), stringr (>= 1.3.1), htmlwidgets (>= 1.3), R6 (>= 2.3.0), gifti (>= 0.7.5), oro.nifti (>= 0.9.1)
Suggests: rmarkdown, DT, ravetools, htmltools
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-11-05 16:10:27 UTC; dipterix
Author: Zhengjia Wang [aut, cre, cph], John Magnotti [ctb, res], Xiang Zhang [ctb, res], Brian Metzger [res], Elizabeth Nesbitt [res], Meng Li [ths], Michael Beauchamp [ths, ctb, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Repository: CRAN
Date/Publication: 2024-11-07 18:20:03 UTC

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