CRANberries

Wed, 25 May 2022

New package mixedCCA with initial version 1.5.2
Package: mixedCCA
Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed Data
Version: 1.5.2
Date: 2022-05-25
Maintainer: Irina Gaynanova <irinag@stat.tamu.edu>
Description: Semi-parametric approach for sparse canonical correlation analysis which can handle mixed data types: continuous, binary and truncated continuous. Bridge functions are provided to connect Kendall's tau to latent correlation under the Gaussian copula model. The methods are described in Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007> and Yoon, Mueller and Gaynanova (2020) <doi:10.1080/10618600.2021.1882468>.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.0.1), stats, MASS
Imports: Rcpp, pcaPP, Matrix, fMultivar, mnormt, irlba
NeedsCompilation: yes
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2022-05-25 18:16:48 UTC; irinag
Author: Grace Yoon [aut] , Mingze Huang [ctb] , Irina Gaynanova [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-25 23:10:02 UTC

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New package scar with initial version 0.2-2
Package: scar
Version: 0.2-2
Date: 2022-05-25
Title: Shape-Constrained Additive Regression: a Maximum Likelihood Approach
Author: Yining Chen and Richard Samworth
Maintainer: Yining Chen <y.chen101@lse.ac.uk>
Depends: R (>= 3.0.0)
Suggests: gam, mgcv, scam
Description: Computes the maximum likelihood estimator of the generalised additive and index regression with shape constraints. Each additive component function is assumed to obey one of the nine possible shape restrictions: linear, increasing, decreasing, convex, convex increasing, convex decreasing, concave, concave increasing, or concave decreasing. For details, see Chen and Samworth (2016) <doi:10.1111/rssb.12137>.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-25 16:13:43 UTC; chen
Repository: CRAN
Date/Publication: 2022-05-25 22:50:02 UTC

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New package markovchain with initial version 0.8.9
Package: markovchain
Title: Easy Handling Discrete Time Markov Chains
Version: 0.8.9
Date: 2022-05-24
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Description: Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>.
License: GPL-2
Depends: R (>= 4.0.0), methods
Imports: igraph, Matrix, expm, stats4, parallel, Rcpp (>= 1.0.2), RcppParallel, utils, stats, grDevices
Suggests: knitr, testthat, diagram, DiagrammeR, msm, Rsolnp, rmarkdown, ctmcd, bookdown, rticles
Enhances: etm
VignetteBuilder: utils, knitr
LinkingTo: Rcpp, RcppParallel, RcppArmadillo (>= 0.9.600.4.0)
SystemRequirements: GNU make
LazyLoad: yes
ByteCompile: yes
Encoding: UTF-8
BugReports: https://github.com/spedygiorgio/markovchain/issues
URL: https://github.com/spedygiorgio/markovchain/
NeedsCompilation: yes
Packaged: 2022-05-25 18:16:37 UTC; giorgio
Author: Giorgio Alfredo Spedicato [aut, cre] , Tae Seung Kang [aut], Sai Bhargav Yalamanchi [aut], Mildenberger Thoralf [ctb] , Deepak Yadav [aut], Ignacio Cordon [aut] , Vandit Jain [ctb], Toni Giorgino [ctb] , Richel J.C. Bilderbeek [ctb] , Daniel Ebbert [ [...truncated...]
Repository: CRAN
Date/Publication: 2022-05-25 22:50:05 UTC

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New package GLIDE with initial version 1.0.5
Package: GLIDE
Title: Global and Individual Tests for Direct Effects
Version: 1.0.5
Date: 2022-05-20
Author: James Dai [aut, cre], Xiaoyu Wang [aut]
Maintainer: James Dai <jdai@fredhutch.org>
Description: Global and individual tests for pleiotropy and direct effects in Mendelian randomization studies. Refer to J. Y. Dai, U. Peters, X. Wang, J. Kocarnik et al. AJE (2018) <doi:10.1093/aje/kwy177>.
Depends: R (>= 2.10)
Imports: MASS,foreach,parallel,doParallel
LazyLoad: no
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-25 21:53:18 UTC; xwang234
Repository: CRAN
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
Date/Publication: 2022-05-25 23:00:02 UTC

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New package traitdataform with initial version 0.6.8
Package: traitdataform
Title: Formatting and Harmonizing Ecological Trait-Data
Version: 0.6.8
Date: 2022-05-25
Description: Assistance for handling ecological trait data and applying the Ecological Trait-Data Standard terminology (Schneider et al. 2019 <doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of own trait datasets for publication, and (2) harmonizing trait datasets from different sources by re-formatting them into a unified format. See 'traitdataform' website for full documentation.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 2.10)
Imports: data.table, stats, reshape2, taxize, getPass, units, suppdata, curl, XML, RCurl, plyr
URL: https://ecologicaltraitdata.github.io/traitdataform/, https://github.com/ecologicaltraitdata/traitdataform
BugReports: https://github.com/ecologicaltraitdata/traitdataform/issues
VignetteBuilder: knitr
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat
NeedsCompilation: no
Packaged: 2022-05-25 14:26:48 UTC; Flo
Author: Florian D. Schneider [aut, cre] , Caterina Penone [ctb] , Andreas Ostrowski [ctb] , Dennis Heimann [ctb], Felix Neff [ctb], Markus J. Ankenbrand [ctb], Jessica Burnett [ctb], Inaki Ucar [ctb], Matthias Grenie [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-25 15:10:02 UTC

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New package discnorm with initial version 0.2.1
Package: discnorm
Title: Test for Discretized Normality in Ordinal Data
Version: 0.2.1
Description: Tests whether multivariate ordinal data may stem from discretizing a multivariate normal distribution. The test is described by Foldnes and Grønneberg (2019) <doi:10.1080/10705511.2019.1673168>. In addition, an adjusted polychoric correlation estimator is provided that takes marginal knowledge into account, as described by Grønneberg and Foldnes (2022) <doi:10.1037/met0000495>.
License: GPL (>= 2)
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Imports: lavaan (>= 0.6.10), arules, sirt, MASS, pbivnorm, cubature, copula, mnormt, GoFKernel
NeedsCompilation: no
Packaged: 2022-05-25 10:00:38 UTC; njaalfoldnes
Author: Njål Foldnes [aut, cre], Steffen Groenneberg [aut]
Maintainer: Njål Foldnes <njal.foldnes@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-25 15:20:02 UTC

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New package cdcatR with initial version 1.0.6
Package: cdcatR
Title: Cognitive Diagnostic Computerized Adaptive Testing
Version: 1.0.6
Date: 2022-05-25
Description: Provides a set of functions for conducting cognitive diagnostic computerized adaptive testing applications (Chen, 2009) <DOI:10.1007/s11336-009-9123-2>). It includes different item selection rules such us the global discrimination index (Kaplan, de la Torre, and Barrada (2015) <DOI:10.1177/0146621614554650>) and the nonparametric selection method (Chang, Chiu, and Tsai (2019) <DOI:10.1177/0146621618813113>), as well as several stopping rules. Functions for generating item banks and responses are also provided. To guide item bank calibration, model comparison at the item level can be conducted using the two-step likelihood ratio test statistic by Sorrel, de la Torre, Abad and Olea (2017) <DOI:10.1027/1614-2241/a000131>.
License: GPL-3
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports: cdmTools (>= 1.0.1), GDINA (>= 2.2.0), ggplot2 (>= 3.3.0), cowplot, foreach, doSNOW, NPCD, stats
Suggests: CDM
URL: https://github.com/miguel-sorrel/cdcatR
BugReports: https://github.com/miguel-sorrel/cdcatR/issues
Encoding: UTF-8
Author: Miguel A. Sorrel [aut, cre, cph], Pablo Najera [aut, cph], Francisco J. Abad [aut, cph]
Maintainer: Miguel A. Sorrel <miguel.sorrel@uam.es>
NeedsCompilation: no
Packaged: 2022-05-25 09:44:50 UTC; msorr
Repository: CRAN
Date/Publication: 2022-05-25 15:10:08 UTC

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New package alookr with initial version 0.3.6
Package: alookr
Title: Model Classifier for Binary Classification
Version: 0.3.6
Description: A collection of tools that support data splitting, predictive modeling, and model evaluation. A typical function is to split a dataset into a training dataset and a test dataset. Then compare the data distribution of the two datasets. Another feature is to support the development of predictive models and to compare the performance of several predictive models, helping to select the best model.
Depends: R (>= 3.2.0), ggplot2 (>= 3.0.0), randomForest
Imports: caTools, cli (>= 1.1.0), dlookr, dplyr (>= 0.7.6), future, ggmosaic, MASS, MLmetrics, methods, party, purrr, ROCR, ranger, rlang, rpart, stats, tibble, tidyr, tidyselect, xgboost, glmnet
Suggests: knitr, ISLR, mice, mlbench, rmarkdown, stringi
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
BugReports: https://github.com/choonghyunryu/alookr/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-25 07:14:47 UTC; choonghyunryu
Repository: CRAN
Date/Publication: 2022-05-25 15:20:05 UTC

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New package africamonitor with initial version 0.1.2
Package: africamonitor
Title: Africa Macroeconomic Monitor Database API
Version: 0.1.2
Description: An R API providing access to a relational database with macroeconomic data for Africa. The database is maintained at the Kiel Institute for the World Economy. See <https://africamonitor.ifw-kiel.de/>.
URL: https://africamonitor.ifw-kiel.de/
License: GPL-3
Encoding: UTF-8
Imports: DBI, RMySQL, data.table, collapse
Depends: R (>= 3.3.0)
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-24 21:19:17 UTC; sebastiankrantz
Author: Sebastian Krantz [aut, cre]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Repository: CRAN
Date/Publication: 2022-05-25 12:00:02 UTC

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New package SynDI with initial version 0.1.0
Package: SynDI
Title: Synthetic Data Integration
Version: 0.1.0
Description: Regression inference for multiple populations by integrating summary-level data using stacked imputations. Gu, T., Taylor, J.M.G. and Mukherjee, B. (2021) A synthetic data integration framework to leverage external summary-level information from heterogeneous populations <arXiv:2106.06835>.
License: GPL-2
URL: https://github.com/umich-biostatistics/SynDI
BugReports: https://github.com/umich-biostatistics/SynDI/issues
Depends: R (>= 3.6.0)
Imports: mice, magrittr, dplyr, StackImpute, arm, boot, broom, mvtnorm, randomForest, MASS, knitr
Suggests: markdown
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-24 15:19:44 UTC; mk
Author: Tian Gu [aut], Jeremy M.G. Taylor [aut], Bhramar Mukherjee [aut], Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Repository: CRAN
Date/Publication: 2022-05-25 07:50:05 UTC

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New package OPTS with initial version 0.1
Package: OPTS
Title: Optimization via Subsampling (OPTS)
Version: 0.1
Date: 2022-05-20
Maintainer: Mihai Giurcanu <giurcanu@uchicago.edu>
Author: Mihai Giurcanu [aut, cre], Marinela Capanu [aut, ctb], Colin Begg [aut], Mithat Gonen [aut]
Imports: MASS, cvTools, changepoint
Description: Subsampling based variable selection for low dimensional generalized linear models. The methods repeatedly subsample the data minimizing an information criterion (AIC/BIC) over a sequence of nested models for each subsample. Marinela Capanu, Mihai Giurcanu, Colin B Begg, Mithat Gonen, Subsampling based variable selection for generalized linear models.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-05-24 14:16:53 UTC; mgiurcanu
Repository: CRAN
Date/Publication: 2022-05-25 07:50:08 UTC

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New package nimbleNoBounds with initial version 1.0.1
Package: nimbleNoBounds
Title: Transformed Distributions for Improved MCMC Efficiency
Version: 1.0.1
Encoding: UTF-8
Date: 2022-05-24
Maintainer: David Pleydell <david.pleydell@inrae.fr>
Author: David Pleydell [aut, cre, cph]
URL: https://github.com/DRJP/nimbleNoBounds
Description: A collection of common univariate bounded probability distributions transformed to the unbounded real line, for the purpose of increased MCMC efficiency.
License: BSD_3_clause + file LICENSE
Copyright: See COPYRIGHTS file.
Depends: R (>= 3.1.2), nimble
Imports: methods
Suggests: knitr, rmarkdown, coda
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-24 14:27:37 UTC; pleydell
Repository: CRAN
Date/Publication: 2022-05-25 07:50:02 UTC

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New package multifunc with initial version 0.9.4
Package: multifunc
Version: 0.9.4
Date: 2022-05-23
Title: Analysis of Ecological Drivers on Ecosystem Multifunctionality
Description: Methods for the analysis of how ecological drivers affect the multifunctionality of an ecosystem based on methods of Byrnes et al. 2016 <doi:10.1111/2041-210X.12143> and Byrnes et al. 2022 <doi:10.1101/2022.03.17.484802>. Most standard methods in the literature are implemented (see vignettes) in a tidy format.
URL: https://jebyrnes.github.io/multifunc/, https://github.com/jebyrnes/multifunc
BugReports: https://github.com/jebyrnes/multifunc/issues
Imports: stats, dplyr, purrr, broom, MASS, utils, magrittr
Suggests: ggplot2, forcats, tidyr, gridExtra, knitr, patchwork, car
License: MIT + file LICENSE
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 16:01:35 UTC; jebyrnes
Author: Jarrett Byrnes [aut, cre, cph]
Maintainer: Jarrett Byrnes <jarrett.byrnes@umb.edu>
Repository: CRAN
Date/Publication: 2022-05-25 07:30:09 UTC

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New package lacrmr with initial version 1.0.5
Package: lacrmr
Title: Connect to the 'Less Annoying CRM' API
Version: 1.0.5
Description: Connect to the 'Less Annoying CRM' API with ease to get your crm data in a clean and tidy format. 'Less Annoying CRM' is a simple CRM built for small businesses, more information is available on their website <https://www.lessannoyingcrm.com/>.
License: GPL-3
URL: https://ixpantia.github.io/lacrmr/
BugReports: https://github.com/ixpantia/lacrmr/issues
Encoding: UTF-8
Depends: R (>= 3.6), magrittr
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, httptest, mockery
VignetteBuilder: knitr
Imports: dplyr, httr, jsonlite, janitor, sjmisc, stringr
NeedsCompilation: no
Packaged: 2022-05-25 00:23:47 UTC; frans
Author: ixpantia, family = SRL [cph], Ronny Hernandez Mora [aut] , Frans van Dunne [cre, aut]
Maintainer: Frans van Dunne <frans@ixpantia.com>
Repository: CRAN
Date/Publication: 2022-05-25 07:30:16 UTC

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New package GeoModels with initial version 1.0.0
Package: GeoModels
Title: Procedures for Gaussian and Non Gaussian Geostatistical (Large) Data Analysis
Version: 1.0.0
Date: 2022-05-01
Maintainer: Moreno Bevilacqua <moreno.bevilacqua89@gmail.com>
Description: Functions for Gaussian and Non Gaussian (bivariate) spatial and spatio-temporal data analysis are provided for a) simulation and inference for random fields using standard likelihood and a likelihood approximation method called weighted composite likelihood based on pairs and b) prediction using (local) best linear unbiased prediction. Weighted composite likelihood can be very efficient for estimating massive datasets. Both regression and spatial (temporal) dependence analysis can be jointly performed. Covariance functions for spatial and spatial-temporal data on Euclidean domains and spheres are provided. There are also many useful functions for plotting and performing diagnostic analysis. Different non Gaussian random fields can be considered in the analysis. Among them, random fields with marginal distributions such as Skew-Gaussian, Student-t, Tukey-h, Sin-Arcsin, Two-piece, Weibull, Gamma, Log-Gaussian, Binomial, Negative Binomial and Poisson. See the URL for the papers associated with this package, as for instance, Bevilacqua and Gaetan (2015) <doi:10.1007/s11222-014-9460-6>, Bevilacqua et al. (2016) <doi:10.1007/s13253-016-0256-3>, Vallejos et al. (2020) <doi:10.1007/978-3-030-56681-4>, Bevilacqua et al. (2022) <doi:10.1016/j.jmva.2022.104949>, Bevilacqua et al. (2022) <doi:10.1007/s11749-021-00797-5>, Blasi et al. (2022) <doi:10.1016/j.spasta.2022.100596>, Morales-Navarrete et al. (2022) <arXiv:2105.03734>, and a large class of examples and tutorials.
Depends: R (>= 4.1.0), GPvecchia,fields, mapproj, plot3D, shape
License: GPL (>= 3)
Encoding: UTF-8
Imports: methods, spam, scatterplot3d, dfoptim, dotCall64, optimParallel, parallel, plotrix, pracma, pbivnorm, zipfR, sn, nabor, numDeriv, hypergeo, ucminf, lamW, GpGp,VGAM, data.table
Suggests: actuar, GoFKernel, sphereplot
Repository: CRAN
URL: https://vmoprojs.github.io/GeoModels-page/
BugReports: https://github.com/vmoprojs/GeoModels/issues
NeedsCompilation: yes
Packaged: 2022-05-24 12:55:45 UTC; morenobevilacqua
Author: Moreno Bevilacqua [aut, cre] , Victor Morales-Onate [aut] , Christian Caamano-Carrillo [aut]
Date/Publication: 2022-05-25 07:40:05 UTC

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New package ClusROC with initial version 1.0.1
Package: ClusROC
Title: ROC Analysis in Three-Class Classification Problems for Clustered Data
Date: 2022-05-12
Version: 1.0.1
Author: Duc-Khanh To [aut, cre] , with contributions from Gianfranco Adimari and Monica Chiogna
Maintainer: Duc-Khanh To <toduc@stat.unipd.it>
Description: Statistical methods for ROC surface analysis in three-class classification problems for clustered data and in presence of covariates. In particular, the package allows to obtain covariate-specific point and interval estimation for: (i) true class fractions (TCFs) at fixed pairs of thresholds; (ii) the ROC surface; (iii) the volume under ROC surface (VUS); (iv) the optimal pairs of thresholds. Methods considered in points (i), (ii) and (iv) are proposed and discussed in To et al. (2022) <doi:10.1177/09622802221089029>. Referring to point (iv), three different selection criteria are implemented: Generalized Youden Index (GYI), Closest to Perfection (CtP) and Maximum Volume (MV). Methods considered in point (iii) are proposed and discussed in Xiong et al. (2018) <doi:10.1177/0962280217742539>. Visualization tools are also provided. We refer readers to the articles cited above for all details.
License: GPL (>= 2)
Depends: R (>= 3.5.0), stats, utils, graphics, nlme
Imports: rgl, car, numDeriv, ggplot2, ggpubr, snow, doSNOW, foreach
Encoding: UTF-8
LazyData: true
LazyLoad: yes
ByteCompile: yes
URL: https://github.com/toduckhanh/ClusROC
BugReports: https://github.com/toduckhanh/ClusROC/issues
NeedsCompilation: no
Packaged: 2022-05-24 13:54:48 UTC; duckh
Repository: CRAN
Date/Publication: 2022-05-25 07:40:11 UTC

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New package tvmediation with initial version 1.1.0
Package: tvmediation
Date: 2022-05-13
Version: 1.1.0
Title: Time Varying Mediation Analysis
Description: Provides functions for estimating mediation effects that vary over time as described in Cai X, Coffman DL, Piper ME, Li R. Estimation and inference for the mediation effect in a time-varying mediation model. BMC Med Res Methodol. 2022;22(1):1-12.
Depends: R (>= 4.0.0)
Imports: stats (>= 4.0.2), dplyr (>= 1.0.2), ggplot2 (>= 3.3.2), locpol (>= 0.7-0)
Suggests: knitr, rmarkdown
License: GPL-3
URL: https://github.com/dcoffman/tvmediation/wiki
BugReports: https://github.com/dcoffman/tvmediation/issues
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-21 15:38:02 UTC; yajna
Author: Donna Coffman [aut, cre] , Xizhen Cai [aut] , Yajnaseni Chakraborti [aut] , Harry Zobel [ctb]
Maintainer: Donna Coffman <dcoffman@temple.edu>
Repository: CRAN
Date/Publication: 2022-05-25 06:40:02 UTC

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Tue, 24 May 2022

New package nlmixr2 with initial version 2.0.6
Package: nlmixr2
Title: Nonlinear Mixed Effects Models in Population PK/PD
Version: 2.0.6
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
License: GPL (>= 3)
Encoding: UTF-8
Imports: nlmixr2est, nlmixr2extra, rxode2, nlmixr2plot, magrittr
Depends: nlmixr2data
Suggests: rmarkdown, knitr, devtools, withr, ggplot2, testthat
VignetteBuilder: knitr
BugReports: https://github.com/nlmixr2/nlmixr2/issues/
URL: https://nlmixr2.github.io/nlmixr2/, https://github.com/nlmixr2/nlmixr2/
NeedsCompilation: no
Packaged: 2022-05-23 15:42:00 UTC; matt
Author: Matthew Fidler [aut, cre] , Yuan Xiong [ctb], Rik Schoemaker [ctb] , Justin Wilkins [ctb] , Wenping Wang [aut], Mirjam Trame [ctb], Huijuan Xu [ctb], John Harrold [ctb], Bill Denney [ctb] , Theodoros Papathanasiou [ctb], Teun Post [ctb], Richard Hooi [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:50:02 UTC

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New package ggisotonic with initial version 0.1.2
Package: ggisotonic
Title: 'ggplot2' Friendly Isotonic or Monotonic Regression Curves
Version: 0.1.2
Description: Provides stat_isotonic() to add weighted univariate isotonic regression curves.
License: GPL-3
Encoding: UTF-8
Imports: ggplot2 (>= 3.0.0), dplyr (>= 1.0.0), fdrtool (>= 1.2.17),
URL: https://github.com/talegari/ggisotonic
BugReports: https://github.com/talegari/ggisotonic/issues
NeedsCompilation: no
Packaged: 2022-05-23 16:29:35 UTC; dattachidambara
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:50:06 UTC

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New package FuzzyClass with initial version 0.1.0
Package: FuzzyClass
Title: Fuzzy and Non-Fuzzy Classifiers
Version: 0.1.0
Description: Provides classifiers that can be used for discrete variables and for continuous variables based on the idea of Naive Bayes and Fuzzy Naive Bayes considering some statistical distributions of articles published in the literature developed in the LabTEVE and LEAPIG research laboratories. Among the proposed classification methods is a with the Gamma distribution, proposed by Moraes, Soares and Machado (2018) <doi:10.1142/9789813273238_0088>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: caTools, datasets, doParallel, e1071, EnvStats, foreach, MASS, mlbench, parallel, Rdpack, rootSolve, trapezoid
Depends: R (>= 2.10)
Suggests: testthat (>= 3.0.0)
URL: https://github.com/Jodavid/FuzzyClass
BugReports: https://github.com/Jodavid/FuzzyClass/issues
NeedsCompilation: no
Packaged: 2022-05-23 14:48:09 UTC; hartbjf
Author: Jodavid Ferreira [aut, cre] , Ronei Moraes [ctb] , Arthur Ricardo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 15:40:01 UTC

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New package tidyterra with initial version 0.1.0
Package: tidyterra
Title: 'tidyverse' Methods and 'ggplot2' Utils for 'terra' Objects
Version: 0.1.0
Description: Extension of the 'tidyverse' for 'SpatRaster' and 'SpatVector' objects of the 'terra' package. It includes also new 'geom_' functions that provide a convenient way of visualizing 'terra' objects with 'ggplot2'.
License: MIT + file LICENSE
URL: https://dieghernan.github.io/tidyterra/, https://github.com/dieghernan/tidyterra
BugReports: https://github.com/dieghernan/tidyterra/issues
Depends: R (>= 3.6.0)
Imports: cli (>= 3.0.0), crayon, data.table, dplyr, ggplot2 (>= 3.1.0), magrittr, rlang, scales, sf (>= 1.0.0), terra (>= 1.5-12), tibble, tidyr
Suggests: isoband, knitr, lifecycle, maptiles, rmarkdown, s2, testthat (>= 3.0.0), vdiffr
VignetteBuilder: knitr
Config/testthat/parallel: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 14:34:35 UTC; diego
Author: Diego Hernangomez [aut, cre, cph] , Dewey Dunnington [ctb]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 11:00:02 UTC

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New package subscore with initial version 3.3
Package: subscore
Title: Computing Subscores in Classical Test Theory and Item Response Theory
Version: 3.3
Author: Shenghai Dai [aut, cre], Xiaolin Wang [aut], Dubravka Svetina [aut]
Maintainer: Shenghai Dai <s.dai@wsu.edu>
Description: Functions for computing test subscores using different methods in both classical test theory (CTT) and item response theory (IRT). This package enables three types of subscoring methods within the framework of CTT and IRT, including (1) Wainer's augmentation method (Wainer et. al., 2001) <doi:10.4324/9781410604729>, (2) Haberman's subscoring methods (Haberman, 2008) <doi:10.3102/1076998607302636>, and (3) Yen's objective performance index (OPI; Yen, 1987) <https://www.ets.org/research/policy_research_reports/publications/paper/1987/hrap>. It also includes functions to compute Proportional Reduction of Mean Squared Errors (PRMSEs) in Haberman's methods which are used to examine whether test subscores are of added value. In addition, the package includes a function to assess the local independence assumption of IRT with Yen's Q3 statistic (Yen, 1984 <doi:10.1177/014662168400800201>; Yen, 1993 <doi:10.1111/j.1745-3984.1993.tb00423.x>).
Depends: R (>= 3.4.0), CTT, stats, irtoys, sirt, ltm
Imports: cocor, boot
NeedsCompilation: no
LazyData: true
Encoding: UTF-8
License: GPL (>= 2)
Packaged: 2022-05-20 15:33:36 UTC; daish
Repository: CRAN
Date/Publication: 2022-05-24 11:00:07 UTC

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New package spNNGP with initial version 0.1.8
Package: spNNGP
Title: Spatial Regression Models for Large Datasets using Nearest Neighbor Gaussian Processes
Version: 0.1.8
Date: 2022-05-19
Maintainer: Andrew Finley <finleya@msu.edu>
Author: Andrew Finley [aut, cre], Abhirup Datta [aut], Sudipto Banerjee [aut]
Depends: R (>= 3.5.0), coda, Formula, RANN
Description: Fits univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Finley, Datta, Banerjee (2020) <arXiv:2001.09111>, and Finley, Datta, Cook, Morton, Andersen, and Banerjee (2019) <doi:10.1080/10618600.2018.1537924> and Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091>.
License: GPL (>= 2)
Encoding: UTF-8
URL: https://www.finley-lab.com/
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-05-19 13:39:04 UTC; andy
Date/Publication: 2022-05-24 11:00:09 UTC
Imports: methods

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New package SDLfilter with initial version 2.2.1
Package: SDLfilter
Title: Filtering and Assessing the Sample Size of Tracking Data
Version: 2.2.1
Date: 2022-05-15
Author: Takahiro Shimada
Maintainer: Takahiro Shimada <taka.shimada@gmail.com>
Description: Functions to filter GPS/Argos locations, as well as assessing the sample size for the analysis of animal distributions. The filters remove temporal and spatial duplicates, fixes located at a given height from estimated high tide line, and locations with high error as described in Shimada et al. (2012) <doi:10.3354/meps09747> and Shimada et al. (2016) <doi:10.1007/s00227-015-2771-0>. Sample size for the analysis of animal distributions can be assessed by the conventional area-based approach or the alternative probability-based approach as described in Shimada et al. (2021) <doi:10.1111/2041-210X.13506>.
Depends: R (>= 3.5.0), ggplot2
Imports: geosphere, data.table, gridExtra, ggsn, ggmap, maps, pracma, lubridate, dplyr, emmeans, utils, sf, stars
License: GPL-2 | file LICENSE
URL: https://github.com/TakahiroShimada/SDLfilter
BugReports: https://github.com/TakahiroShimada/SDLfilter/issues
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 21:31:05 UTC; taka
Repository: CRAN
Date/Publication: 2022-05-24 10:10:11 UTC

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New package rr with initial version 1.4.1
Package: rr
Version: 1.4.1
Title: Statistical Methods for the Randomized Response Technique
Depends: R (>= 3.0.0), utils
Imports: MASS, arm, coda, magic
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Journal of the American Statistical Association <https://graemeblair.com/papers/randresp.pdf>.
LazyLoad: yes
LazyData: yes
License: GPL (>= 3)
Suggests: testthat
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-05-24 02:06:48 UTC; gdblair
Author: Graeme Blair [aut, cre], Yang-Yang Zhou [aut], Kosuke Imai [aut], Winston Chou [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 10:10:02 UTC

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New package nodeSub with initial version 1.2.4
Package: nodeSub
Title: Simulate DNA Alignments Using Node Substitutions
Version: 1.2.4
Author: Thijs Janzen
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Description: Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
URL: https://github.com/thijsjanzen/nodeSub
BugReports: https://github.com/thijsjanzen/nodeSub
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
LinkingTo: Rcpp
Depends: Rcpp, ape
Imports: apTreeshape, phangorn, tibble, DDD, Rmpfr, assertthat, pbapply, phylobase, geiger, babette, beautier, beastier, mauricer, tracerer, rappdirs, testit, stringr
Suggests: testthat, TreeSim, dplyr, knitr, rmarkdown, ggplot2, magrittr, tidyr
NeedsCompilation: yes
Packaged: 2022-05-23 11:14:43 UTC; p251362
Repository: CRAN
Date/Publication: 2022-05-24 10:10:04 UTC

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New package nLTT with initial version 1.4.8
Package: nLTT
Title: Calculate the NLTT Statistic
Version: 1.4.8
Description: Provides functions to calculate the normalised Lineage-Through- Time (nLTT) statistic, given two phylogenetic trees. The nLTT statistic measures the difference between two Lineage-Through-Time curves, where each curve is normalised both in time and in number of lineages.
License: GPL-2
Imports: ape, coda, testit
Suggests: TreeSim, DDD, ggplot2, Hmisc, knitr, lintr, microbenchmark, plyr, reshape2, rmarkdown, TESS, testthat, DAISIE
NeedsCompilation: no
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://github.com/thijsjanzen/nLTT
BugReports: https://github.com/thijsjanzen/nLTT/issues
Packaged: 2022-05-23 09:57:28 UTC; thijsjanzen
Author: Thijs Janzen [aut, cre], Richel J.C. Bilderbeek [aut] , Pedro Neves [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 11:00:12 UTC

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New package micompr with initial version 1.1.2
Package: micompr
Title: Multivariate Independent Comparison of Observations
Version: 1.1.2
Date: 2022-05-23
Maintainer: Nuno Fachada <faken@fakenmc.com>
Description: A procedure for comparing multivariate samples associated with different groups. It uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. The procedure is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. It is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.
Depends: R (>= 3.6.0)
Imports: utils, graphics, methods, stats
Suggests: biotools, MVN (>= 5.0), testthat (>= 0.8), knitr, roxygen2, devtools
License: MIT + file LICENSE
URL: https://github.com/nunofachada/micompr
BugReports: https://github.com/nunofachada/micompr/issues
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-23 18:22:17 UTC; nuno
Author: Nuno Fachada [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-24 10:10:07 UTC

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New package MBSP with initial version 2.0
Package: MBSP
Title: Multivariate Bayesian Model with Shrinkage Priors
Version: 2.0
Date: 2022-05-23
Author: Ray Bai, Malay Ghosh
Maintainer: Ray Bai <raybaistat@gmail.com>
Description: Gibbs sampler for fitting multivariate Bayesian linear regression with shrinkage priors (MBSP), using the three parameter beta normal family. The method is described in Bai and Ghosh (2018) <doi:10.1016/j.jmva.2018.04.010>.
License: GPL-3
Depends: R (>= 3.6.0)
Imports: stats, MCMCpack, GIGrvg, utils, MASS
NeedsCompilation: yes
Packaged: 2022-05-24 03:34:44 UTC; rayba
Repository: CRAN
Date/Publication: 2022-05-24 10:10:16 UTC

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New package file2meco with initial version 0.2.4
Package: file2meco
Title: Transform Files to 'microtable' Object with 'microeco' Package
Version: 0.2.4
Author: Chi Liu [aut, cre]
Maintainer: Chi Liu <liuchi0426@126.com>
Description: Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
URL: https://github.com/ChiLiubio/file2meco
Depends: R (>= 3.5.0)
Imports: microeco, ape, magrittr, dplyr, tidyr, yaml, rhdf5, Matrix
Suggests: Biostrings, seqinr, phyloseq
License: GPL-3
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-23 07:27:54 UTC; Chi
Repository: CRAN
Date/Publication: 2022-05-24 10:40:05 UTC

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New package eurodata with initial version 1.4.2
Package: eurodata
Title: Fast and Easy Eurostat Data Import and Search
Description: Interface to Eurostat’s Bulk Download Facility with fast data.table-based import of data, labels, and metadata. On top of the core functionality, data search and data description/comparison functions are also provided.
Version: 1.4.2
Date: 2022-05-20
License: GPL-2
URL: https://github.com/alekrutkowski/eurodata/
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: utils, Rcpp, magrittr, data.table, R.utils, xtable, memoise, stringr, rvest
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-05-23 09:50:56 UTC; Baieyu
Author: Aleksander Rutkowski [aut, cre]
Maintainer: Aleksander Rutkowski <alek.rutkowski@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-24 10:50:05 UTC

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New package cdmTools with initial version 1.0.2
Package: cdmTools
Title: Useful Tools for Cognitive Diagnosis Modeling
Version: 1.0.2
Date: 2022-05-20
Description: Provides useful tools for cognitive diagnosis modeling (CDM). The package includes functions for empirical Q-matrix estimation and validation, such as the Hull method (Nájera, Sorrel, de la Torre, & Abad, 2021, <doi:10.1111/bmsp.12228>) and the discrete factor loading method (Wang, Song, & Ding, 2018, <doi:10.1007/978-3-319-77249-3_29>). It also contains dimensionality assessment procedures for CDM, including parallel analysis and automated fit comparison as explored in Nájera, Abad, and Sorrel (2021, <doi:10.3389/fpsyg.2021.614470>). Other relevant methods and features for CDM applications, such as the general nonparametric classification method (Chiu et al., 2018; <doi:10.1007/s11336-017-9595-4>) and corrected estimation of the classification accuracy via multiple imputation (Kreitchmann et al., 2022) are also available. Lastly, the package provides some useful functions for CDM simulation studies, such as random Q-matrix generation and detection of complete/identified Q-matrices.
License: GPL-3
Depends: R (>= 3.6.0)
Imports: GDINA (>= 2.8.0), NPCD (>= 1.0-11), ggplot2 (>= 3.3.0), psych (>= 1.9.12), sirt (>= 3.9-4), parallel (>= 3.6.3), stats (>= 3.6.3), GPArotation (>= 2014.11-1), combinat (>= 0.0-8), foreach, doSNOW
URL: https://github.com/pablo-najera/cdmTools
BugReports: https://github.com/pablo-najera/cdmTools/issues
Encoding: UTF-8
Author: Pablo Najera [aut, cre, cph], Miguel A. Sorrel [aut, cph], Francisco J. Abad [aut, cph], Rodrigo S. Kreitchmann [ctb]
Maintainer: Pablo Najera <pablo.najera@uam.es>
NeedsCompilation: no
Packaged: 2022-05-20 07:28:17 UTC; Usuario
Repository: CRAN
Date/Publication: 2022-05-24 11:00:15 UTC

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New package spc4sts with initial version 0.6.3
Package: spc4sts
Title: Statistical Process Control for Stochastic Textured Surfaces
Version: 0.6.3
Author: Anh Tuan Bui [aut, cre] and Daniel W. Apley [ths]
Maintainer: Anh Tuan Bui <atbui@u.northwestern.edu>
Imports: rpart, gridExtra, parallel
Description: Provides statistical process control tools for stochastic textured surfaces. The current version supports the following tools: (1) generic modeling of stochastic textured surfaces. (2) local defect monitoring and diagnostics in stochastic textured surfaces, which was proposed by Bui and Apley (2018a) <doi:10.1080/00401706.2017.1302362>. (3) global change monitoring in the nature of stochastic textured surfaces, which was proposed by Bui and Apley (2018b) <doi:10.1080/00224065.2018.1507559>. (4) computation of dissimilarity matrix of stochastic textured surface images, which was proposed by Bui and Apley (2019b) <doi:10.1016/j.csda.2019.01.019>.
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-21 15:53:09 UTC; buiat2
Repository: CRAN
Date/Publication: 2022-05-24 09:50:02 UTC

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New package predictMe with initial version 0.1
Package: predictMe
Title: Visualize Individual Prediction Performance
Version: 0.1
Date/Publication: 2022-05-24 09:40:02 UTC
Author: Marcel Miche
Maintainer: Marcel Miche <marcel.miche.predictme@gmail.com>
Description: Enables researchers to visualize the prediction performance of any algorithm on the individual level (or close to it), given that the predicted outcome is either binary or continuous. Visual results are instantly comprehensible.
License: MIT + file LICENSE
Repository: CRAN
URL: https://github.com/mmiche/predictMe
Encoding: UTF-8
Imports: Rdpack, ggplot2, reshape2
Depends: R (>= 3.3.0)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-21 06:23:17 UTC; mmiche

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New package pasteAsComment with initial version 0.2.0
Package: pasteAsComment
Title: 'RStudio' Addin to Paste the Clipboard as a Comment Block or a 'roxygen' Block
Version: 0.2.0
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Description: Provides a 'RStudio' addin allowing to paste the content of the clipboard as a comment block or as 'roxygen' lines. This is very useful to insert an example in the 'roxygen' block.
License: GPL-3
Encoding: UTF-8
Imports: rstudioapi, clipr
URL: https://github.com/stla/pasteAsComment
BugReports: https://github.com/stla/pasteAsComment/issues
NeedsCompilation: no
Packaged: 2022-05-21 07:03:04 UTC; SDL96354
Repository: CRAN
Date/Publication: 2022-05-24 09:30:02 UTC

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New package fanc with initial version 2.3.5
Package: fanc
Title: Penalized Likelihood Factor Analysis via Nonconvex Penalty
Version: 2.3.5
Date: 2022-05-21
Depends: Matrix, ellipse, tcltk
Description: Computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used. This package also includes a new graphical tool which outputs path diagram, goodness-of-fit indices and model selection criteria for each regularization parameter. The user can change the regularization parameter by manipulating scrollbars, which is helpful to find a suitable value of regularization parameter.
License: GPL (>= 2)
URL: https://doi.org/10.1007/s11222-014-9458-0, https://doi.org/10.1016/j.csda.2014.05.011, https://doi.org/10.1007/s41237-016-0007-3, https://keihirose.com
Packaged: 2022-05-21 10:30:49 UTC; hirosekei
Repository: CRAN
Date/Publication: 2022-05-24 09:50:06 UTC
NeedsCompilation: yes
Author: Kei Hirose [aut, cre] , Michio Yamamoto [aut], Haruhisa Nagata [aut]
Maintainer: Kei Hirose <mail@keihirose.com>

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New package DWLS with initial version 0.1.0
Package: DWLS
Title: Gene Expression Deconvolution Using Dampened Weighted Least Squares
Version: 0.1.0
Maintainer: Adriana Sistig <adriana.sistig@icahn.mssm.edu>
Description: The rapid development of single-cell transcriptomic technologies has helped uncover the cellular heterogeneity within cell populations. However, bulk RNA-seq continues to be the main workhorse for quantifying gene expression levels due to technical simplicity and low cost. To most effectively extract information from bulk data given the new knowledge gained from single-cell methods, we have developed a novel algorithm to estimate the cell-type composition of bulk data from a single-cell RNA-seq-derived cell-type signature. Comparison with existing methods using various real RNA-seq data sets indicates that our new approach is more accurate and comprehensive than previous methods, especially for the estimation of rare cell types. More importantly,our method can detect cell-type composition changes in response to external perturbations, thereby providing a valuable, cost-effective method for dissecting the cell-type-specific effects of drug treatments or condition changes. As such, our method is applicable to a wide range of biological and clinical investigations. Dampened weighted least squares ('DWLS') is an estimation method for gene expression deconvolution, in which the cell-type composition of a bulk RNA-seq data set is computationally inferred. This method corrects common biases towards cell types that are characterized by highly expressed genes and/or are highly prevalent, to provide accurate detection across diverse cell types. See: <https://www.nature.com/articles/s41467-019-10802-z.pdf> for more information about the development of 'DWLS' and the methods behind our functions.
URL: https://github.com/sistia01/DWLS
BugReports: https://github.com/sistia01/DWLS/issues
Depends: R (>= 3.5.0)
Imports: quadprog, reshape, Seurat, ROCR, varhandle, dplyr, stats, utils, e1071, MAST, SummarizedExperiment
License: GPL-2
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
Suggests: testthat (>= 3.0.0), Matrix (>= 1.3.3)
NeedsCompilation: no
Packaged: 2022-05-19 13:37:17 UTC; adrianasistig
Author: Daphne Tsoucas [aut], Adriana Sistig [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-24 09:20:01 UTC

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New package copyseparator with initial version 1.0.0
Package: copyseparator
Title: Assembling Long Gene Copies from Short Read Data
Version: 1.0.0
Author: Lei Yang
Maintainer: Lei Yang <leiyangslu@gmail.com>
Description: Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.
License: GPL-2
URL: https://github.com/LeiYang-Fish/copyseparator
BugReports: https://github.com/LeiYang-Fish/copyseparator/issues
Depends: R (>= 3.5.0)
Encoding: UTF-8
Imports: ape, seqinr, stringr, kmer, DECIPHER, beepr, Biostrings, grDevices
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-21 00:55:18 UTC; lyang1
Repository: CRAN
Date/Publication: 2022-05-24 09:30:04 UTC

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Mon, 23 May 2022

New package mverse with initial version 0.1.0
Package: mverse
Title: Tidy Multiverse Analysis Made Simple
Version: 0.1.0
Maintainer: Michael Jongho Moon <michael.moon@mail.utoronto.ca>
Description: Extends 'multiverse' package (Sarma A., Kale A., Moon M., Taback N., Chevalier F., Hullman J., Kay M., 2021) <doi:10.31219/osf.io/yfbwm>, which allows users perform to create explorable multiverse analysis in R. This extension provides an additional level of abstraction to the 'multiverse' package with the aim of creating user friendly syntax to researchers, educators, and students in statistics. The 'mverse' syntax is designed to allow piping and takes hints from the 'tidyverse' grammar. The package allows users to define and inspect multiverse analysis using familiar syntax in R.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6), multiverse
Imports: magrittr (>= 1.5), rlang, dplyr, tidyr, tidyselect, stringr, stats, broom, grDevices, igraph, ggraph, ggplot2, cowplot
Suggests: tidyverse, scales, MASS, testthat (>= 2.1.0), pkgdown (>= 1.5.1), covr, knitr, rmarkdown, kableExtra
VignetteBuilder: knitr
URL: https://github.com/mverseanalysis/mverse/, https://mverseanalysis.github.io/mverse/
NeedsCompilation: no
Packaged: 2022-05-20 13:45:11 UTC; moon
Author: Michael Jongho Moon [aut, cre], Haoda Li [aut], Mingwei Xu [aut], Nathan Taback [aut], Fanny Chevalier [aut], Alison Gibbs [ctb]
Repository: CRAN
Date/Publication: 2022-05-23 08:10:02 UTC

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New package EUfootball with initial version 0.0.1
Package: EUfootball
Title: Football Match Data of European Leagues
Version: 0.0.1
Description: Contains match results from seven European men's football leagues, namely Premier League (England), Ligue 1 (France), Bundesliga (Germany), Serie A (Italy), Primera Division (Spain), Eredivisie (The Netherlands), Super Lig (Turkey). Includes Seasons 2010/2011 until 2019/2020 and a set of interesting covariates. Can be used all purposes.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-20 15:02:16 UTC; hendr
Author: Hendrik van der Wurp [aut, cre]
Maintainer: Hendrik van der Wurp <vanderwurp@statistik.tu-dortmund.de>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-05-23 08:30:02 UTC

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New package nlmixr2plot with initial version 2.0.6
Package: nlmixr2plot
Title: Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions
Version: 2.0.6
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.
License: GPL (>= 3)
URL: https://github.com/nlmixr2/nlmixr2plot
BugReports: https://github.com/nlmixr2/nlmixr2plot/issues/
Imports: ggplot2, nlmixr2est, nlmixr2extra, rxode2, utils, vpc, xgxr
Suggests: testthat (>= 3.0.0), dplyr, withr, nlmixr2data
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-20 10:51:58 UTC; FIDLEMA3
Author: Matthew Fidler [aut, cre] , Bill Denney [ctb] , Wenping Wang [aut], Vipul Mann [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-23 07:50:02 UTC

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New package pgmm with initial version 1.2.6
Package: pgmm
Title: Parsimonious Gaussian Mixture Models
Version: 1.2.6
Date: 2022-05-20
Author: Paul D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F. McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
License: GPL (>= 2)
LazyLoad: yes
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-05-20 15:21:23 UTC; paul
Date/Publication: 2022-05-21 23:00:08 UTC

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Sat, 21 May 2022

New package RankAggSIgFUR with initial version 0.1.0
Package: RankAggSIgFUR
Title: Polynomially Bounded Rank Aggregation under Kemeny's Axiomatic Approach
Version: 0.1.0
Description: Polynomially bounded algorithms to aggregate complete rankings under Kemeny's axiomatic framework. 'RankAggSIgFUR' (pronounced as rank-agg-cipher) contains two heuristics algorithms: FUR and SIgFUR. For details, please see Badal and Das (2018) <doi:10.1016/j.cor.2018.06.007>.
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
Imports: Rfast, combinat
Suggests: testthat (>= 3.0.0)
NeedsCompilation: yes
URL: https://github.com/prakashvs613/RankAggSIgFUR
BugReports: https://github.com/prakashvs613/RankAggSIgFUR/issues
Packaged: 2022-05-19 21:31:58 UTC; aprak
Author: Hannah Parker [aut], Rakhi Singh [cre, aut] , Prakash Singh Badal [aut]
Maintainer: Rakhi Singh <agrakhi@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-21 15:30:02 UTC

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New package gbifdb with initial version 0.1.2
Package: gbifdb
Version: 0.1.2
Title: High Performance Interface to 'GBIF'
Description: A high performance interface to the Global Biodiversity Information Facility, 'GBIF'. In contrast to 'rgbif', which can access small subsets of 'GBIF' data through web-based queries to a central server, 'gbifdb' provides enhanced performance for R users performing large-scale analyses on servers and cloud computing providers, providing full support for arbitrary 'SQL' or 'dplyr' operations on the complete 'GBIF' data tables (now over 1 billion records, and over a terabyte in size). 'gbifdb' accesses a copy of the 'GBIF' data in 'parquet' format, which is already readily available in commercial computing clouds such as the Amazon Open Data portal and the Microsoft Planetary Computer, or can be accessed directly without downloading, or downloaded to any server with suitable bandwidth and storage space. The high-performance techniques for local and remote access are described in <https://duckdb.org/why_duckdb> and <https://arrow.apache.org/docs/r/articles/fs.html> respectively.
License: Apache License (>= 2)
Encoding: UTF-8
ByteCompile: true
Depends: R (>= 4.0)
Imports: arrow (>= 6.0.1), duckdb (>= 0.2.9), DBI, dplyr
Suggests: spelling, dbplyr, testthat (>= 3.0.0), covr, knitr, rmarkdown, aws.s3
URL: https://docs.ropensci.org/gbifdb/, https://github.com/ropensci/gbifdb
BugReports: https://github.com/ropensci/gbifdb
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-19 21:02:47 UTC; cboettig
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-21 15:10:02 UTC

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New package CR2 with initial version 0.1.0
Package: CR2
Title: Compute Cluster Robust Standard Errors with Degrees of Freedom Adjustments
Version: 0.1.0
Date: 2022-05-19
Description: Estimate different types of cluster robust standard errors (CR0, CR1, CR2) with degrees of freedom adjustments. Standard errors are computed based on 'Liang and Zeger' (1986) <doi:10.1093/biomet/73.1.13> and Bell and 'McCaffrey' <https://www150.statcan.gc.ca/n1/en/pub/12-001-x/2002002/article/9058-eng.pdf?st=NxMjN1YZ>. Functions used in Huang and Li <doi:10.3758/s13428-021-01627-0> and Huang, 'Wiedermann', and 'Zhang' (forthcoming: Multivariate Behavioral Research).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/flh3/CR2
BugReports: https://github.com/flh3/CR2/issues
Depends: R (>= 2.10)
Imports: stats, lme4, nlme, Matrix, methods
NeedsCompilation: no
Packaged: 2022-05-19 21:53:43 UTC; flh3
Author: Francis Huang [aut, cre] , Bixi Zhang [aut]
Maintainer: Francis Huang <flhuang2000@yahoo.com>
Repository: CRAN
Date/Publication: 2022-05-21 15:30:05 UTC

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Fri, 20 May 2022

New package oscar with initial version 1.0.3
Package: oscar
Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the L0-Pseudonorm
Version: 1.0.3
Date: 2022-05-19
Description: Optimal Subset Cardinality Regression (OSCAR) models offer regularized linear regression using the L0-pseudonorm, conventionally known as the number of non-zero coefficients. The package estimates an optimal subset of features using the L0-penalization via cross-validation, bootstrapping and visual diagnostics. Effective Fortran implementations are offered along the package for finding optima for the DC-decomposition, which is used for transforming the discrete L0-regularized optimization problem into a continuous non-convex optimization task. These optimization modules include DBDC ('Double Bundle method for nonsmooth DC optimization' as described in Joki et al. (2018) <doi:10.1137/16M1115733>) and LMBM ('Limited Memory Bundle Method for large-scale nonsmooth optimization' as in Haarala et al. (2004) <doi:10.1080/10556780410001689225>). Multiple regression model families are supported: Cox, logistic, and Gaussian.
License: GPL-3
LazyData: true
URL: https://github.com/Syksy/oscar
BugReports: https://github.com/Syksy/oscar/issues
NeedsCompilation: yes
Depends: R (>= 3.6.0)
Imports: graphics, grDevices, hamlet, Matrix, methods, stats, survival, utils
Suggests: ePCR, glmnet, knitr, pROC, rmarkdown
VignetteBuilder: knitr
Encoding: UTF-8
Packaged: 2022-05-19 13:55:26 UTC; teemu
Author: Teemu Daniel Laajala [aut, cre] , Kaisa Joki [aut], Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>
Repository: CRAN
Date/Publication: 2022-05-20 18:20:01 UTC

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New package Yamm with initial version 1.3.2
Package: Yamm
Title: Multivariate Methods Based on Projections and Related Concepts
Version: 1.3.2
Date: 2022-04-19
Depends: R (>= 3.0), depth, robustX, interp
Suggests: animation
Maintainer: Guy Nason <g.nason@imperial.ac.uk>
Description: Functionality to compute the projection median via several algorithms. Also provides functions to plot different multivariate medians and multivariate quantiles in two-dimensional and three-dimensional data respectively. See Chen, F and Nason, G P (2020) "A new method for computing the projection median, its influence curve and techniques for the production of projected quantile plots." PLOS One <doi:10.1371/journal.pone.0229845>.
License: GPL-2
NeedsCompilation: yes
Packaged: 2022-05-19 13:54:12 UTC; guynason
Author: Fan Chen [aut], Guy Nason [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-20 12:50:09 UTC

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New package BootWPTOS with initial version 1.2.1
Package: BootWPTOS
Title: Test Stationarity using Bootstrap Wavelet Packet Tests
Version: 1.2.1
Date: 2022-05-19
Depends: R (>= 2.0), wavethresh, tseries
Description: Provides significance tests for second-order stationarity for time series using bootstrap wavelet packet tests. Provides functionality to visualize the time series with the results of the hypothesis tests superimposed. The methodology is described in Cardinali, A and Nason, G P (2016) "Practical powerful wavelet packet tests for second-order stationarity." Applied and Computational Harmonic Analysis, 44, 558-585 <doi:10.1016/j.acha.2016.06.006>.
License: GPL-2
NeedsCompilation: no
Packaged: 2022-05-19 17:47:06 UTC; guynason
Author: Guy Nason [aut, cre], Alessandro Cardinali [aut]
Maintainer: Guy Nason <g.nason@imperial.ac.uk>
Repository: CRAN
Date/Publication: 2022-05-20 12:40:02 UTC

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Thu, 19 May 2022

New package EMAS with initial version 0.1.0
Package: EMAS
Title: Epigenome-Wide Mediation Analysis Study
Version: 0.1.0
Date: 2022-05-17
Author: Xiuquan Nie [aut, cph, cre], Mengyi Wang [ctb, rev], Weihong Chen [fnd]
Maintainer: Xiuquan Nie <niexiuquan1995@foxmail.com>
Depends: R (>= 3.5.0)
Imports: mediation, parallel, minfi, qqman
Suggests: IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19
Description: DNA methylation is essential for human, and environment can change the DNA methylation and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide. For more information on the methods we used, please see the following references: Tingley, D. (2014) <doi:10.18637/jss.v059.i05>, Turner, S. D. (2018) <doi:10.21105/joss.00731>.
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-19 08:07:51 UTC; niexi
Repository: CRAN
Date/Publication: 2022-05-19 17:10:02 UTC

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New package ivaBSS with initial version 1.0.0
Package: ivaBSS
Title: Tools for Independent Vector Analysis
Version: 1.0.0
Date: 2022-05-03
Imports: stats, graphics, BSSprep
Suggests: LaplacesDemon
Encoding: UTF-8
Maintainer: Mika Sipilae <mika.e.sipila@student.jyu.fi>
Description: Independent vector analysis (IVA) is a blind source separation (BSS) model where several datasets are jointly unmixed. This package provides several methods for the unmixing together with some performance measures. For details, see Anderson et al. (2011) <doi:10.1109/TSP.2011.2181836> and Lee et al. (2007) <doi:10.1016/j.sigpro.2007.01.010>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2022-05-19 08:16:26 UTC; developer
Author: Mika Sipilae [aut, cre], Klaus Nordhausen [aut] , Sara Taskinen [aut]
Repository: CRAN
Date/Publication: 2022-05-19 17:00:02 UTC

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New package STARTS with initial version 1.3-8
Package: STARTS
Title: Functions for the STARTS Model
Version: 1.3-8
Date: 2022-05-19 09:47:44
Author: Alexander Robitzsch [aut,cre] , Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Contains functions for estimating the STARTS model of Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>, <DOI:10.1037/10409-008>. Penalized maximum likelihood estimation and Markov Chain Monte Carlo estimation are also provided, see Luedtke, Robitzsch and Wagner (2018) <DOI:10.1037/met0000155>.
Depends: R (>= 3.1)
Imports: CDM (>= 7.1-19), graphics, LAM (>= 0.3-27), sirt (>= 2.3), Rcpp, stats, utils
Suggests: lavaan
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/alexanderrobitzsch/STARTS, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-19 07:48:19 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-19 11:20:02 UTC

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New package ModEstM with initial version 0.0.1
Package: ModEstM
Title: Mode Estimation, Even in the Multimodal Case
Version: 0.0.1
Description: Function ModEstM() is the only one of this package, it estimates the modes of an empirical univariate distribution. It relies on the stats::density() function, even for input control. Due to very good performance of the density estimation, computation time is not an issue. The multiple modes are handled using dplyr::group_by(). For conditions and rates of convergences, see Eddy (1980) <doi:10.1214/aos/1176345080>.
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
Imports: dplyr, rlang, stats
NeedsCompilation: no
Packaged: 2022-05-19 07:10:02 UTC; Jerome
Author: Jerome Collet [aut, cre]
Maintainer: Jerome Collet <jeromepcollet@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-19 08:10:02 UTC

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New package SoundShape with initial version 1.2.1
Package: SoundShape
Title: Sound Waves Onto Morphometric Data
Version: 1.2.1
Date: 2022-05-16
Description: Implement a promising, and yet little explored protocol for bioacoustical analysis, the eigensound method by MacLeod, Krieger and Jones (2013) <doi:10.4404/hystrix-24.1-6299>. Eigensound is a multidisciplinary method focused on the direct comparison between stereotyped sounds from different species. 'SoundShape', in turn, provide the tools required for anyone to go from sound waves to Principal Components Analysis, using tools extracted from traditional bioacoustics (i.e. 'tuneR' and 'seewave' packages), geometric morphometrics (i.e. 'geomorph' package) and multivariate analysis (e.g. 'stats' package). For more information, please see Rocha and Romano (2021) and check 'SoundShape' repository on GitHub for news and updates <https://github.com/p-rocha/SoundShape>.
Depends: R (>= 3.3.1)
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/p-rocha/SoundShape
BugReports: https://github.com/p-rocha/SoundShape/issues
Imports: abind, geomorph (>= 3.0.2), graphics, grDevices, plot3D, reshape2, seewave, stats, tuneR, utils
Suggests: vegan, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-16 23:49:44 UTC; Pedro
Author: Pedro Rocha [aut, cre]
Maintainer: Pedro Rocha <p.rocha1990@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-19 07:50:17 UTC

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New package FIESTA with initial version 3.4.0
Package: FIESTA
Title: Forest Inventory Estimation and Analysis
Version: 3.4.0
Date: 2022-05-13
Description: A research estimation tool for analysts that work with sample-based inventory data from the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) Program.
Depends: R (>= 4.0)
Imports: data.table, DBI, FIESTAutils (>= 1.1.1), grDevices, graphics, methods, rgdal, RSQLite, sf, sqldf, utils
Suggests: knitr, raster, rmarkdown
VignetteBuilder: knitr
License: GPL-3
Copyright: See file COPYRIGHTS for details.
LazyData: true
SystemRequirements: C++11
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-18 23:26:08 UTC; graysonwhite
Author: Tracey Frescino [aut], Gretchen Moisen [aut], Paul Patterson [aut], Chris Toney [aut], Grayson White [aut, cre]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-19 07:50:20 UTC

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New package chromatographR with initial version 0.4.1
Package: chromatographR
Title: Import and Analyze HPLC-DAD/UV Data
Version: 0.4.1
Maintainer: Ethan Bass <ethanbass@gmail.com>
Description: Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in alsace (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (ptw) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (VPdtw) (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <http://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.
License: GPL (>= 2)
URL: https://ethanbass.github.io/chromatographR/
BugReports: https://github.com/ethanbass/chromatographR/issues
Depends: R (>= 3.5.0)
Imports: chromConverter, dynamicTreeCut, fastcluster, graphics, grDevices, lattice, methods, minpack.lm, parallel, ptw, pvclust, scales, smoother, stats, utils
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0), VPdtw
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
LazyDataCompression: xz
Additional_repositories: https://ethanbass.github.io/drat/
NeedsCompilation: no
Packaged: 2022-05-18 21:26:28 UTC; ethanbass
Author: Ethan Bass [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-19 07:40:02 UTC

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New package BranchGLM with initial version 1.0.0
Package: BranchGLM
Title: Glm Fitting and Variable Selection using 'RcppArmadillo'
Version: 1.0.0
Date: 2022-5-16
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
URL: https://github.com/JacobSeedorff21/BranchGLM
BugReports: https://github.com/JacobSeedorff21/BranchGLM/issues
Description: Fits glms using 'RcppArmadillo', can use Fisher's scoring, BFGS, or L-BFGS. Can also make use of parallel computation to speed up fitting process via 'OpenMP'. Also can perform best subset selection with an efficient branch and bound algorithm that allows best subset selection for more variables.
License: Apache License (>= 2)
Depends: R (>= 3.3.0)
Imports: Rcpp (>= 1.0.7), methods
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-19 04:22:06 UTC; Jacob
Author: Jacob Seedorff [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-19 08:00:02 UTC

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New package sits with initial version 1.0.0
Package: sits
Version: 1.0.0
Title: Satellite Image Time Series Analysis for Earth Observation Data Cubes
Maintainer: Gilberto Camara <gilberto.camara.inpe@gmail.com>
Description: An end-to-end toolkit for land use and land cover classification using big Earth observation data, based on machine learning methods applied to satellite image data cubes, as described in Simoes et al (2021) <doi:10.3390/rs13132428>. Builds regular data cubes from collections in AWS, Microsoft Planetary Computer, Brazil Data Cube, and Digital Earth Africa using the STAC protocol <https://stacspec.org/> and the 'gdalcubes' R package <doi:10.3390/data4030092>. Supports visualization methods for images and time series and smoothing filters for dealing with noisy time series. Includes functions for quality assessment of training samples using self-organized maps as presented by Santos et al (2021) <doi:10.1016/j.isprsjprs.2021.04.014>. Provides machine learning methods including support vector machines, random forests, extreme gradient boosting, multi-layer perceptrons, temporal convolutional neural networks <doi:10.3390/rs11050523>, residual networks <arxiv:1809.04356>, and temporal attention encoders <arXiv:2007.00586>. Performs efficient classification of big Earth observation data cubes and includes functions for post-classification smoothing based on Bayesian inference, and methods for uncertainty assessment. Enables best practices for estimating area and assessing accuracy of land change as recommended by Olofsson et al(2014) <doi:10.1016/j.rse.2014.02.015>. Minimum recommended requirements: 16 GB RAM and 4 CPU dual-core.
Encoding: UTF-8
Language: en-US
Depends: R (>= 4.0.0)
URL: https://github.com/e-sensing/sits/, https://e-sensing.github.io/sitsbook/
BugReports: https://github.com/e-sensing/sits/issues
License: GPL-2
ByteCompile: true
LazyData: true
Imports: magrittr, yaml, data.table (>= 1.13), dplyr (>= 1.0.0), gdalUtilities, grDevices, ggplot2, graphics, lubridate, parallel (>= 4.0.5), purrr (>= 0.3.0), Rcpp, rstac (>= 0.9.1-5), sf (>= 1.0), slider (>= 0.2.0), stats, terra (>= 1.5-17), tibble (>= 3.1), tidyr (>= 1.2.0), torch (>= 0.7.0), utils
Suggests: caret, dendextend, dtwclust, dtwSat (>= 0.2.7), digest, e1071, FNN, gdalcubes (>= 0.6.0), geojsonsf, httr, jsonlite, kohonen(>= 3.0.11), leafem (>= 0.2.0), leaflet (>= 2.1.1), luz (>= 0.2.0), methods, mgcv, openxlsx, randomForest, RcppArmadillo (>= 0.11), scales, stars (>= 0.5), testthat (>= 3.1.3), torchopt(>= 0.1.1), xgboost, zoo
Config/testthat/parallel: false
Config/testthat/start-first: cube, raster, ml
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2022-05-19 00:09:17 UTC; gilbertocamara
Author: Rolf Simoes [aut], Gilberto Camara [aut, cre], Felipe Souza [aut], Lorena Santos [aut], Pedro Andrade [aut], Karine Ferreira [aut], Alber Sanchez [aut], Gilberto Queiroz [aut]
Repository: CRAN
Date/Publication: 2022-05-19 07:00:02 UTC

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New package DepCens with initial version 0.2.1
Package: DepCens
Title: Dependent Censoring Regression Models
Version: 0.2.1
Description: Dependent censoring regression models for survival multivariate data. These models are based on extensions of the frailty models, capable to accommodating the dependence between failure and censoring times, with Weibull and piecewise exponential marginal distributions. Theoretical details regarding the models implemented in the package can be found in Schneider et al. (2019) <doi:10.1002/bimj.201800391>.
License: GPL (>= 2)
URL: https://github.com/GabrielGrandemagne/DepCens
BugReports: https://github.com/GabrielGrandemagne/DepCens/issues
Depends: R (>= 2.10)
Imports: dlm, Formula, rootSolve, survival, matrixStats, stats
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-05-18 18:49:28 UTC; Gabriel-PC
Author: Silvana Schneider [aut, cre] , Gabriel Grandemagne dos Santos [ctb]
Maintainer: Silvana Schneider <silvana.schneider@ufrgs.br>
Repository: CRAN
Date/Publication: 2022-05-19 06:50:23 UTC

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New package cellpypes with initial version 0.1.3
Package: cellpypes
Title: Cell Type Pipes for Single-Cell RNA Sequencing Data
Version: 0.1.3
Description: Annotate single-cell RNA sequencing data manually based on marker gene thresholds. Find cell type rules (gene+threshold) through exploration, use the popular piping operator '%>%' to reconstruct complex cell type hierarchies. 'cellpypes' models technical noise to find positive and negative cells for a given expression threshold and returns cell type labels or pseudobulks. Cite this package as Frauhammer (2022) <doi:10.5281/zenodo.6555728> and visit <https://github.com/FelixTheStudent/cellpypes> for tutorials and newest features.
URL: https://github.com/FelixTheStudent/cellpypes
BugReports: https://github.com/FelixTheStudent/cellpypes/issues
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, Seurat, DESeq2, RcppAnnoy, tibble, SeuratObject
Imports: scUtils, ggplot2, Matrix, rlang, viridis, cowplot, dplyr, scales, methods, scattermore
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-18 20:33:14 UTC; felix
Author: Felix Frauhammer [aut, cre]
Maintainer: Felix Frauhammer <felixfrauhammer@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-19 07:00:08 UTC

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Wed, 18 May 2022

New package markets with initial version 1.0.2
Package: markets
Title: Estimation Methods for Markets in Equilibrium and Disequilibrium
Version: 1.0.2
Date: 2022-05-18
Description: Provides estimation methods for markets in equilibrium and disequilibrium. Supports the estimation of an equilibrium and four disequilibrium models with both correlated and independent shocks. Also provides post-estimation analysis tools, such as aggregation, marginal effect, and shortage calculations. The estimation methods are based on full information maximum likelihood techniques given in Maddala and Nelson (1974) <doi:10.2307/1914215>. They are implemented using the analytic derivative expressions calculated in Karapanagiotis (2020) <doi:10.2139/ssrn.3525622>. Standard errors can be estimated by adjusting for heteroscedasticity or clustering. The equilibrium estimation constitutes a case of a system of linear, simultaneous equations. Instead, the disequilibrium models replace the market-clearing condition with a non-linear, short-side rule and allow for different specifications of price dynamics.
Language: en-US
URL: https://github.com/pi-kappa-devel/markets/, https://markets.pikappa.eu/
BugReports: https://github.com/pi-kappa-devel/markets/issues
Depends: R (>= 3.5.0)
Imports: bbmle (>= 1.0.20), dplyr (>= 0.7.6), Formula, magrittr (>= 1.5), MASS (>= 7.3-50), methods, rlang (>= 0.2.1), systemfit (>= 1.1), tibble (>= 1.4.2), tidyr (>= 1.0.2), Rcpp, RcppGSL, RcppParallel
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Suggests: ggplot2 (>= 3.0.0), knitr (>= 1.20), numDeriv (>= 2016.8.1.1), rmarkdown (>= 1.10), testthat (>= 2.0.0)
VignetteBuilder: knitr
LinkingTo: Rcpp, RcppGSL
SystemRequirements: C++11
NeedsCompilation: yes
Packaged: 2022-05-18 11:24:28 UTC; ntelispak
Author: Pantelis Karapanagiotis [aut, cre]
Maintainer: Pantelis Karapanagiotis <pikappa.devel@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 19:10:02 UTC

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New package hgwrr with initial version 0.2-1
Package: hgwrr
Title: Hierarchical and Geographically Weighted Regression
Version: 0.2-1
Date: 2022-05-17
Author: Yigong Hu
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Description: This model divides coefficients into three types, i.e., local fixed effects, global fixed effects, and random effects. If data have spatial hierarchical structures (especially are overlapping on some locations), it is worth trying this model to reach better fitness.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.8)
LinkingTo: Rcpp, RcppArmadillo
Depends: R (>= 3.5.0), stats, utils
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2022-05-18 10:29:52 UTC; hpdell
Repository: CRAN
Date/Publication: 2022-05-18 19:10:07 UTC

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New package EpiInvert with initial version 0.1.0
Package: EpiInvert
Version: 0.1.0
Title: Estimation of Time Varying Reproduction Numbers and Restored Incidence Curves Using Variational Techniques
Maintainer: Luis Alvarez <lalvarez@ulpgc.es>
Description: Estimation, by inverting a renewal equation, of time-varying reproduction numbers and restored incidence curves with festive days and weekly biases corrected as described in Alvarez et al. (2021) <doi:10.1073/pnas.2105112118> and Alvarez et al. (2022) <doi:10.3390/biology11040540>.
URL: https://github.com/lalvarezmat/EpiInvert
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 1.0.8.3)
LinkingTo: Rcpp
Suggests: knitr, ggplot2, grid, dplyr, testthat (>= 3.0.0), rmarkdown
Depends: R (>= 2.10)
LazyLoad: yes
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-18 13:49:45 UTC; lalva
Author: Luis Alvarez [aut, cre] , Jean-David Morel [ctb] , Jean-Michel Morel [ctb]
Repository: CRAN
Date/Publication: 2022-05-18 19:10:09 UTC

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New package TSdisaggregation with initial version 2.0.0
Package: TSdisaggregation
Title: High-Dimensional Temporal Disaggregation
Version: 2.0.0
Description: First - Generates (potentially high-dimensional) high-frequency and low-frequency series for simulation studies in temporal disaggregation; Second - a toolkit utilizing temporal disaggregation and benchmarking techniques with a low-dimensional matrix of indicator series previously proposed in Dagum and Cholette (2006, ISBN:978-0-387-35439-2) ; and Third - novel techniques proposed by Mosley, Gibberd and Eckley (2021) <arXiv:2108.05783> for disaggregating low-frequency series in the presence of high-dimensional indicator matrices.
Imports: Rdpack, zoo, lars, Matrix, withr
License: GPL (>= 3)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-17 22:52:06 UTC; kaveh
Author: Luke Mosley [aut, cre], Kaveh S. Nobari [aut]
Maintainer: Luke Mosley <l.mosley@lancaster.ac.uk>
Repository: CRAN
Date/Publication: 2022-05-18 19:00:05 UTC

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New package smlmkalman with initial version 0.1.0
Package: smlmkalman
Title: Generation and Tracking of Super-Resolution Filamentous Datasets
Version: 0.1.0
Author: Andrew Buist [aut, cre]
Maintainer: Andrew Buist <ab1051@exeter.ac.uk>
Depends: R (>= 4.1.0), stats, spdep, pracma, scales, truncnorm
Description: A pair of functions that allow for the generation and tracking of coordinate data clouds without a time dimension, primarily for use in super-resolution plant micro-tubule image segmentation.
License: GPL-2
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-18 18:33:40 UTC; Andrew
Repository: CRAN
Date/Publication: 2022-05-18 19:00:02 UTC

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New package ThomasJeffersonUniv with initial version 0.1.0
Package: ThomasJeffersonUniv
Title: Handy Tools for TJU/TJUH Employees
Version: 0.1.0
Date: 2022-05-17
Author: Tingting Zhan [aut, cre, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Description: Functions for admin needs of employees of Thomas Jefferson University and Thomas Jefferson University Hospital, Philadelphia, PA.
License: GPL-2
Encoding: UTF-8
Imports: zoo, timeDate, lubridate
Language: en-US
Depends: R (>= 4.2.0)
NeedsCompilation: no
Packaged: 2022-05-17 16:51:34 UTC; txz003
Repository: CRAN
Date/Publication: 2022-05-18 16:40:11 UTC

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New package T2Qv with initial version 0.1.0
Package: T2Qv
Title: Control Qualitative Variables
Version: 0.1.0
Maintainer: Wilson Rojas-Preciado <wrojas@utmachala.edu.ec>
Description: Covers k-table control analysis using multivariate control charts for qualitative variables using fundamentals of multiple correspondence analysis and multiple factor analysis. The graphs can be shown in a flat or interactive way, in the same way all the outputs can be shown in an interactive shiny panel.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Imports: shiny, shinydashboardPlus, shinydashboard, shinycssloaders, dplyr, ca, highcharter, stringr, tables, purrr, tidyr, htmltools (>= 0.5.1.1)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-05-18 02:51:04 UTC; wilso
Author: Wilson Rojas-Preciado [aut, cre], Mauricio Rojas-Campuzano [aut, ctb], Purificacion Galindo-Villardon [aut, ctb], Omar Ruiz-Barzola [aut, ctb]
Repository: CRAN
Date/Publication: 2022-05-18 17:00:04 UTC

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New package shinybrowser with initial version 1.0.0
Package: shinybrowser
Title: Find Out Information About a User's Web Browser in 'Shiny'
Version: 1.0.0
Description: Sometimes it's useful to know some information about your user in a 'Shiny' app. The available information is: browser name (such as 'Chrome' or 'Safari') and version, device type (mobile or desktop), operating system (such as 'Windows' or 'Mac' or 'Android') and version, and browser dimensions.
URL: https://github.com/daattali/shinybrowser https://daattali.com/shiny/shinybrowser-demo/
BugReports: https://github.com/daattali/shinybrowser/issues
Depends: R (>= 3.1.0)
Imports: shiny (>= 1.0.4)
Suggests: shinydisconnect
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-17 16:25:04 UTC; Dean-X1C
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 16:40:02 UTC

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New package ScaleSpikeSlab with initial version 1.0
Package: ScaleSpikeSlab
Title: Scalable Spike-and-Slab
Version: 1.0
Date: 2022-05-13
Description: A scalable Gibbs sampling implementation for high dimensional Bayesian regression with the continuous spike-and-slab prior. Niloy Biswas, Lester Mackey and Xiao-Li Meng, "Scalable Spike-and-Slab" (2022) <arXiv:2204.01668>.
License: GPL (>= 2)
Imports: Rcpp, stats, TruncatedNormal
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2022-05-17 20:40:23 UTC; niloybiswas
Author: Niloy Biswas [aut, cre] , Lester Mackey [aut], Xiao-Li Meng [aut]
Maintainer: Niloy Biswas <niloy_biswas@g.harvard.edu>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-05-18 17:00:07 UTC

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New package qbr with initial version 1.0.0
Package: qbr
Title: Access the 'Quickbase' JSON API
Version: 1.0.0
Description: Programmatically access the 'Quickbase' JSON API <https://developer.quickbase.com>. You supply parameters for an API call, 'qbr' delivers an http request to the API endpoint and returns its response. Outputs follow 'tidyverse' philosophy.
URL: https://github.com/BHII-KSC/qbr
BugReports: https://github.com/BHII-KSC/qbr/issues
License: GPL (>= 3)
Encoding: UTF-8
Imports: dplyr (>= 1.0.9), httr (>= 1.4.3), jsonlite (>= 1.8.0), magrittr (>= 2.0.3), purrr (>= 0.3.4), stringr (>= 1.4.0), tibble (>= 3.1.7)
Suggests: testthat (>= 3.0.0), keyring
NeedsCompilation: no
Packaged: 2022-05-17 17:44:07 UTC; jae1028
Author: John Erdmann [aut, cre], Keene State College [cph, fnd]
Maintainer: John Erdmann <john.erdmann@keene.edu>
Repository: CRAN
Date/Publication: 2022-05-18 16:40:05 UTC

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New package protoshiny with initial version 0.1.0
Package: protoshiny
Title: Interactive Dendrograms for Visualizing Hierarchical Clusters with Prototypes
Version: 0.1.0
Description: Shiny app to interactively visualize hierarchical clustering with prototypes. For details on hierarchical clustering with prototypes, see Bien and Tibshirani (2011) <doi:10.1198/jasa.2011.tm10183>. This package currently launches the application.
License: GPL-3
Encoding: UTF-8
Imports: DT, dynamicTreeCut, methods, protoclust, rare, shiny, shinycssloaders, shinythemes, tools
Depends: R (>= 4.0.0)
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-05-17 16:03:30 UTC; andeek
Author: Andee Kaplan [aut, cre], Jacob Bien [aut], Mike Bostock [cph] , Brian Reavis [cph]
Maintainer: Andee Kaplan <andee.kaplan@colostate.edu>
Repository: CRAN
Date/Publication: 2022-05-18 16:30:08 UTC

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New package naive with initial version 1.0.0
Package: naive
Title: Empirical Extrapolation of Time Feature Patterns
Version: 1.0.0
Description: An application for the empirical extrapolation of time features selecting and summarizing the most relevant patterns in time sequences.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.1)
Imports: purrr (>= 0.3.4), ggplot2 (>= 3.3.5), readr (>= 2.1.2), lubridate (>= 1.7.10), imputeTS (>= 3.2), fANCOVA (>= 0.6-1), scales (>= 1.1.1), tictoc (>= 1.0.1), modeest (>= 2.4.0), moments (>= 0.14), greybox (>= 1.0.1), Rfast (>= 2.0.6)
URL: https://rpubs.com/giancarlo_vercellino/naive
NeedsCompilation: no
Packaged: 2022-05-18 07:30:24 UTC; gvercellino
Author: Giancarlo Vercellino [aut, cre, cph]
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 17:00:02 UTC

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New package grwat with initial version 0.0.2
Package: grwat
Title: River Hydrograph Separation and Analysis
Version: 0.0.2
Date: 2022-05-17
Description: River hydrograph separation and daily runoff time series analysis. Provides various filters to separate baseflow and quickflow using methods by Lyne and Hollick (1979) <https://www.researchgate.net/publication/272491803_Stochastic_Time-Variable_Rainfall-Runoff_Modeling>, Chapman (1991) <doi:10.1029/91WR01007>, Boughton (1993) <https://cir.nii.ac.jp/crid/1572543026556977024>, Jakeman and Hornberger (1993) <doi:10.1029/93WR00877>, Chapman and Maxwell (1996) <https://search.informit.org/doi/10.3316/informit.360361071346753>, and Kudelin (1960) <https://www.worldcat.org/title/printsipy-regionalnoi-otsenki-estestvennykh-resursov-podzemnykh-vod/>. Implements advanced separation technique by Rets et al. (2022) <doi:10.1134/S0097807822010146> which involves meteorological data to reveal genetic components of the runoff: ground, rain, thaw and spring (seasonal thaw). High-performance C++17 computation, annually aggregated variables, statistical testing and numerous plotting functions for high-quality visualization.
License: MIT + file LICENSE
URL: https://github.com/tsamsonov/grwat
BugReports: https://github.com/tsamsonov/grwat/issues
Encoding: UTF-8
Language: en-US
LinkingTo: Rcpp
SystemRequirements: pandoc
LazyData: true
VignetteBuilder: knitr
Depends: R (>= 3.3)
Imports: crayon, progress, Rcpp, magrittr, dplyr, tidyr, lubridate, stringr, rlang, grid, ggplot2, knitr, rmarkdown, kableExtra, zoo, trend, mblm
Suggests: ggridges, ggHoriPlot, ggthemes, ncdf4, sf, testthat, stringi
NeedsCompilation: yes
Packaged: 2022-05-17 16:27:50 UTC; tsamsonov
Author: Timofey Samsonov [aut, cre] , Ekaterina Retz [ctb] , Maria Kireeva [ctb]
Maintainer: Timofey Samsonov <iamste@yandex.ru>
Repository: CRAN
Date/Publication: 2022-05-18 16:40:08 UTC

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New package DLPCA with initial version 0.0.2
Package: DLPCA
Title: The Distributed Local PCA Algorithm
Version: 0.0.2
Date: 2022-05-18
Maintainer: Guangbao Guo <ggb11111111@163.com>
Description: Algorithm to handle with optimal subset selection for distributed local principal component analysis. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2022-05-18 07:39:17 UTC; s
Author: Guangbao Guo [aut, cre] , Guoqi Qian [aut], Yixiao Liu [aut], Haoyue Song [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-05-18 17:00:10 UTC

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New package REndo with initial version 2.4.5
Package: REndo
Title: Fitting Linear Models with Endogenous Regressors using Latent Instrumental Variables
Version: 2.4.5
Date: 2022-05-17
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches. The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized method of moment approach that deals with endogeneity in a multilevel setting. These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed. Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
License: GPL-3
URL: https://github.com/mmeierer/REndo
BugReports: https://github.com/mmeierer/REndo/issues
NeedsCompilation: yes
Depends: R (>= 3.4)
Imports: methods (>= 3.4), stats (>= 3.4), utils (>= 3.4), Formula (>= 1.2), optimx (>= 2013.8.7), mvtnorm (>= 1.0-8), AER (>= 1.2-5), Matrix (>= 1.2-14), lme4 (>= 1.1-18-1), data.table (>= 1.11.8), corpcor (>= 1.6.9), Rcpp (>= 1.0.3), lmtest (>= 0.9-35)
Suggests: testthat, covr, R.rsp
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
VignetteBuilder: R.rsp
Packaged: 2022-05-17 22:06:14 UTC; patrik
Author: Raluca Gui [cre, aut], Markus Meierer [aut], Rene Algesheimer [aut], Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 13:40:06 UTC

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New package rdataretriever with initial version 3.1.0
Package: rdataretriever
Title: R Interface to the Data Retriever
Description: Provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.
Version: 3.1.0
BugReports: https://github.com/ropensci/rdataretriever/issues
URL: https://docs.ropensci.org/rdataretriever/ (website), https://github.com/ropensci/rdataretriever/
Depends: R (>= 3.4.0)
Imports: reticulate (>= 1.16), semver
Suggests: testthat (>= 1.0.0), DBI, devtools, RSQLite, RPostgreSQL, knitr, rmarkdown, dbplyr, raster, ggplot2
VignetteBuilder: knitr
SystemRequirements: Python (>= 3.7), retriever (>= 3.0.0) (version must be listed to patch to allow parsing)
License: MIT + file LICENSE
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-14 06:33:59 UTC; henrysenyondo
Author: Henry Senyondo [aut, cre] , Daniel McGlinn [aut] , Pranita Sharma [aut] , David J Harris [aut] , Hao Ye [aut] , Shawn Taylor [aut] , Jeroen Ooms [aut] , Francisco Rodriguez-Sanchez Ooms [aut] , Karthik Ram [aut] , Apoorva Pandey [aut] , Harshit Bansa [...truncated...]
Maintainer: Henry Senyondo <henrykironde@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 14:00:02 UTC

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New package mlr3verse with initial version 0.2.5
Package: mlr3verse
Title: Easily Install and Load the 'mlr3' Package Family
Version: 0.2.5
Description: The 'mlr3' package family is a set of packages for machine-learning purposes built in a modular fashion. This wrapper package is aimed to simplify the installation and loading of the core 'mlr3' packages. Get more information about the 'mlr3' project at <https://mlr3book.mlr-org.com/>.
License: LGPL-3
URL: https://mlr3verse.mlr-org.com, https://github.com/mlr-org/mlr3verse
BugReports: https://github.com/mlr-org/mlr3verse/issues
Depends: mlr3 (>= 0.12.0), R (>= 3.1.0)
Imports: bbotk, data.table, mlr3cluster, mlr3data, mlr3filters, mlr3fselect (>= 0.6.0), mlr3hyperband, mlr3learners, mlr3misc, mlr3pipelines (>= 0.4.0), mlr3tuning (>= 0.9.0), mlr3tuningspaces (>= 0.1.1), mlr3viz, paradox (>= 0.6.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-18 12:45:36 UTC; michel
Author: Michel Lang [cre, aut] , Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 13:50:02 UTC

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New package LAM with initial version 0.6-19
Package: LAM
Title: Some Latent Variable Models
Version: 0.6-19
Date: 2022-05-17 14:14:12
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Includes some procedures for latent variable modeling with a particular focus on multilevel data. The 'LAM' package contains mean and covariance structure modelling for multivariate normally distributed data (mlnormal(); Longford, 1987; <doi:10.1093/biomet/74.4.817>), a general Metropolis-Hastings algorithm (amh(); Roberts & Rosenthal, 2001, <doi:10.1214/ss/1015346320>) and penalized maximum likelihood estimation (pmle(); Cole, Chu & Greenland, 2014; <doi:10.1093/aje/kwt245>).
Depends: R (>= 3.1)
Imports: CDM, graphics, Rcpp, sirt, stats, utils
Suggests: coda, expm, MASS, numDeriv, TAM
Enhances: lavaan, lme4
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/alexanderrobitzsch/LAM, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-17 12:15:23 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-18 13:40:10 UTC

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New package cinaR with initial version 0.2.3
Package: cinaR
Title: A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Version: 0.2.3
Description: Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/eonurk/cinaR/
BugReports: https://github.com/eonurk/cinaR/issues/
Depends: R (>= 4.0.0)
Imports: ChIPseeker, DESeq2, dplyr, edgeR, fgsea, GenomicRanges, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, ggplot2, ggrepel, grDevices, limma, utils, pheatmap, preprocessCore, RColorBrewer, sva, writexl
Suggests: knitr, rmarkdown, markdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-17 08:45:32 UTC; onur-lumc
Author: Onur Karakaslar [aut, cre], Duygu Ucar [aut]
Maintainer: Onur Karakaslar <eonurkara@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 14:00:09 UTC

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New package pathwayTMB with initial version 0.1.2
Package: pathwayTMB
Title: Pathway Based Tumor Mutational Burden
Version: 0.1.2
Maintainer: Junwei Han <hanjunwei1981@163.com>
Description: A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.
License: GPL (>= 2)
Depends: R (>= 4.1.0)
Encoding: UTF-8
LazyData: true
Imports: BiocGenerics, purrr, utils, glmnet, randomForest, stats, survival, survminer, caret, data.table, RColorBrewer, grDevices, pROC, graphics, maftools, clusterProfiler
VignetteBuilder: knitr,rmarkdown,qpdf
Suggests: stringi, knitr, rmarkdown, testthat, BiocManager, xfun, e1071, qpdf, tinytex, spelling
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-18 07:22:38 UTC; DELL
Author: Junwei Han [aut, cre, cph], Xiangmei Li [aut]
Repository: CRAN
Date/Publication: 2022-05-18 08:30:02 UTC

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New package mnlfa with initial version 0.2-4
Package: mnlfa
Title: Moderated Nonlinear Factor Analysis
Version: 0.2-4
Date: 2022-05-17 12:28:17
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Conducts moderated nonlinear factor analysis (e.g., Curran et al., 2014, <doi:10.1080/00273171.2014.889594>). Regularization methods are implemented for assessing non-invariant items. Currently, the package includes dichotomous items and unidimensional item response models. Extensions will be included in future package versions.
Depends: R (>= 3.1)
Imports: CDM (>= 7.0-4), stats, utils
LinkingTo: Rcpp, RcppArmadillo
Enhances: aMNLFA, GPCMlasso, sirt
URL: https://github.com/alexanderrobitzsch/mnlfa, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-17 10:28:51 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-18 08:10:05 UTC

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New package CACIMAR with initial version 1.0.0
Package: CACIMAR
Title: Cross-Species Analysis of Cell Identities, Markers and Regulations
Version: 1.0.0
Maintainer: Junyao Jiang <jiangjunyao789@163.com>
Author: Junyao Jiang <jiangjunyao789@163.com>
Description: A toolkit to perform cross-species analysis based on scRNA-seq data. This package contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotation (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: pheatmap, pbapply, psych, ROCR, reshape2, dplyr, grDevices, stats, methods, viridisLite
Depends: R (>= 4.0), Seurat
Suggests: knitr, testthat (>= 3.0.0)
URL: https://github.com/jiang-junyao/CACIMAR
BugReports: https://github.com/jiang-junyao/CACIMAR/issues
NeedsCompilation: no
Packaged: 2022-05-17 12:49:03 UTC; jiangjunyao
Repository: CRAN
Date/Publication: 2022-05-18 08:20:02 UTC

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New package rsolr with initial version 0.0.13
Package: rsolr
Title: R to Solr Interface
Version: 0.0.13
Author: Michael Lawrence, Gabe Becker, Jan Vogel
Maintainer: Michael Lawrence <michafla@gene.com>
Description: A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
License: Apache License (== 2.0)
VignetteBuilder: knitr
Imports: restfulr (>= 0.0.2), graph, S4Vectors (>= 0.14.3), rjson, XML, RCurl
Depends: R (>= 3.4.0), BiocGenerics (>= 0.15.1), methods
Suggests: nycflights13, RUnit, MASS, knitr
NeedsCompilation: no
Packaged: 2022-05-17 23:32:52 UTC; michafla
Repository: CRAN
Date/Publication: 2022-05-18 07:10:02 UTC

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New package habCluster with initial version 1.0.3
Package: habCluster
Title: Detecting Spatial Clustering Based on Connection Cost Between Grids
Version: 1.0.3
Date: 2022-04-21
Author: Qiang Dai
Maintainer: Qiang Dai <daiqiang@cib.ac.cn>
Description: Based on landscape connectivity, spatial boundaries were identified using community detection algorithm at grid level. Methods using raster as input and the value of each cell of the raster is the "smoothness" to indicate how easy the cell connecting with neighbor cells. Details about the 'habCluster' package methods can be found in Zhang et al. <bioRxiv:2022.05.06.490926>.
License: GPL (>= 3)
Depends: R (>= 4.0.0), igraph (>= 1.3.0), stars (>= 0.5-0), sf (>= 1.0.0), methods
Imports: Rcpp, raster
Suggests: knitr, rmarkdown, testthat (>= 3.1.0), spelling
LinkingTo: Rcpp
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-US
NeedsCompilation: yes
Packaged: 2022-05-17 08:00:26 UTC; qiang
Repository: CRAN
Date/Publication: 2022-05-18 08:00:02 UTC

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New package GEint with initial version 1.0
Package: GEint
Title: Misspecified Models for Gene-Environment Interaction
Version: 1.0
Date: 2022-05-17
Description: The first major functionality is to compute the bias in misspecified linear gene-environment interaction models. The most generalized function for this objective is GE_bias(). However GE_bias() requires specification of many higher order moments of covariates in the model. If users are unsure about how to calculate/estimate these higher order moments, it may be easier to use GE_bias_normal_squaredmis(). This function places many more assumptions on the covariates (most notably that they are all jointly generated from a multivariate normal distribution) and is thus able to automatically calculate many of the higher order moments automatically, necessitating only that the user specify some covariances. There are also functions to solve for the bias through simulation and non-linear equation solvers, these can be used to check your work. Second major functionality is to implement the Bootstrap Inference with Correct Sandwich (BICS) testing procedure, which we have found to provide better finite-sample performance than other inference procedures for testing GxE interaction. More details on these functions are available in Sun, Carroll, Christiani, and Lin (2018) <doi:10.1111/biom.12813>.
Imports: mvtnorm, bindata, nleqslv, pracma, speedglm, rje, geepack, stats
License: GPL-3
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-17 20:17:44 UTC; rsun3
Author: Ryan Sun [aut, cre], Richard Barfield [ctb]
Maintainer: Ryan Sun <ryansun.work@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-18 07:20:02 UTC

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New package webshot2 with initial version 0.1.0
Package: webshot2
Title: Take Screenshots of Web Pages
Version: 0.1.0
Description: Takes screenshots of web pages, including Shiny applications and R Markdown documents. 'webshot2' uses headless Chrome or Chromium as the browser back-end.
Imports: chromote (>= 0.1.0), later, promises, magrittr, callr
Suggests: shiny, httpuv, rmarkdown
Depends: R (>= 3.2)
License: GPL-2
Encoding: UTF-8
URL: https://github.com/rstudio/webshot2
BugReports: https://github.com/rstudio/webshot2/issues
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-13 19:54:06 UTC; barret
Author: Winston Chang [aut, cre], Barret Schloerke [ctb] , RStudio [cph, fnd]
Maintainer: Winston Chang <winston@rstudio.com>
Repository: CRAN
Date/Publication: 2022-05-18 06:00:02 UTC

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Tue, 17 May 2022

New package fctbases with initial version 1.1.1
Package: fctbases
Title: Functional Bases
Version: 1.1.1
Date: 2022-05-17
Author: Niels Olsen
Maintainer: Niels Olsen <nalo@dtu.dk>
Description: Easy-to-use, very fast implementation of various functional bases. Easily used together with other packages. A functional basis is a collection of basis functions [\phi_1, ..., \phi_n] that can represent a smooth function, i.e. $f(t) = \sum c_k \phi_k(t)$. First- and second-order derivatives are also included. These are the mathematically correct ones, no approximations applied. As of version 1.1, this package includes B-splines, Fourier bases and polynomials.
URL: https://github.com/naolsen/fctbases
License: GPL-3
Imports: Rcpp (>= 0.12.19)
Suggests: knitr, rmarkdown, microbenchmark
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2022-05-17 14:10:06 UTC; nalo
Repository: CRAN
Date/Publication: 2022-05-17 17:10:02 UTC

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New package designer with initial version 0.1.0
Package: designer
Title: 'Shiny' UI Prototype Builder
Version: 0.1.0
Description: A 'shiny' application that enables the user to create a prototype UI, being able to drag and drop UI components before being able to save or download the equivalent R code.
URL: https://github.com/ashbaldry/designer, https://ashbaldry.github.io/designer/
BugReports: https://github.com/ashbaldry/designer/issues
License: MIT + file LICENSE
Language: en-GB
Encoding: UTF-8
VignetteBuilder: knitr
Imports: config (>= 0.3.1), golem (>= 0.3.1), htmltools, shiny (>= 1.7.1), bslib, jsonlite, shinipsum, shinyscreenshot, cicerone
Suggests: covr, testthat (>= 3.0.0), shinytest2, globals, knitr, rmarkdown
NeedsCompilation: no
Packaged: 2022-05-16 09:55:48 UTC; arbal
Author: Ashley Baldry [cre, aut]
Maintainer: Ashley Baldry <arbaldry91@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-17 17:10:05 UTC

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New package loadshaper with initial version 1.1.1
Package: loadshaper
Title: Producing Load Shape with Target Peak and Load Factor
Version: 1.1.1
Date: 2022-05-08
Language: en-US
Description: Modifying a load shape to match specific peak and load factor is a fundamental component for various power system planning and operation studies. This package is an efficient tool to modify a reference load shape while matching the desired peak and load factor. The package offers both linear and non-linear method, described in <https://rpubs.com/riazakhan94/load_shape_match_peak_energy>. The user can control the shape of the final load shape by regulating certain parameters. The package provides validation metrics for assessing the derived load shape in terms of preserving time series properties. It also offers powerful graphics, that allows the user to visually assess the derived load shape.
Imports: stats, graphics
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-15 05:35:34 UTC; riaza
Author: Md Riaz Ahmed Khan [aut, cre]
Maintainer: Md Riaz Ahmed Khan <mdriazahmed.khan@jacks.sdstate.edu>
Repository: CRAN
Date/Publication: 2022-05-17 16:20:02 UTC

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New package iscoCrosswalks with initial version 1.0.0
Package: iscoCrosswalks
Title: Crosswalks Between Classifications of Occupations
Version: 1.0.0
Description: Allows the user to perform approximate matching between the occupational classifications using concordances provided by the Institute for Structural Research and Faculty of Economics, University of Warsaw, <doi:10.1111/ecot.12145>. The crosswalks offer a complete step-by-step mapping of Standard Occupational Classification (2010) data to the International Standard Classification of Occupations (2008). We propose a mapping method based on the aforementioned research that converts measurements to the smallest possible unit of the target taxonomy, and then performs an aggregation/estimate to the requested degree Occupational Hierarchical level.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/eworx-org/iscoCrosswalks
BugReports: https://github.com/eworx-org/iscoCrosswalks/issues
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 3.1.0)
Imports: data.table, labourR, Rdpack
NeedsCompilation: no
Packaged: 2022-05-15 21:37:54 UTC; ale
Author: Alexandros Kouretsis [aut, cre], Andreas Bampouris [aut]
Maintainer: Alexandros Kouretsis <ako@eworx.gr>
Repository: CRAN
Date/Publication: 2022-05-17 16:50:02 UTC

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New package geosimilarity with initial version 1.1
Package: geosimilarity
Title: Geographically Optimal Similarity
Date: 2022-05-13
Version: 1.1
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>
Description: Spatial prediction can be performed based on the geographical similarity theory. Geographically optimal similarity (GOS) model is a generalized model for accurate and reliable spatial prediction based on the geographical similarity theory.
Imports: stats, SecDim
Depends: R (>= 4.1.0)
License: GPL-2
LazyData: true
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-14 07:55:23 UTC; 268222H
Author: Yongze Song [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-17 16:20:06 UTC

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New package europeanaR with initial version 0.1.0
Package: europeanaR
Title: Interact with Metadata Records and Media on the Europeana Repository
Version: 0.1.0
Maintainer: Alexandros Kouretsis <akourets@ionio.gr>
Description: Interact with the Europeana Data Model via a variety of API endpoints that contains digital collections from thousands of institutions around Europe. This translates to millions of Cultural Heritage Objects in the form of image, text, video, sound and 3D, accompanied by rich metadata. The Data Model design principles are based on the core principles and best practices of the Semantic Web and Linked Data efforts to which Europeana contributes (see, e.g., Doerr, Martin, et al. The europeana data model (edm). World Library and Information Congress: 76th IFLA general conference and assembly. Vol. 10. 2010.). The package also provides methods for bulk downloads of specific subsets of items, including both their metadata and their associated media files.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/AleKoure/europeanaR
Imports: data.table, httr, jsonlite, magrittr, utils, Rdpack
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-15 20:53:17 UTC; ale
Author: Alexandros Kouretsis [aut, cre], Andreas Giannakoulopoulos [aut], Laida Limniati [aut]
Repository: CRAN
Date/Publication: 2022-05-17 16:40:02 UTC

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New package EMLI with initial version 0.1.0
Package: EMLI
Title: Efficient Maximum Likelihood Identification
Version: 0.1.0
Description: Provides implementations of computationally efficient maximum likelihood estimation algorithms for system identification tasks. Currently, one such algorithm is implemented which identifies the one-dimensional cumulative structural equation model with normality assumptions. The corresponding scientific paper is yet to be published, therefore the relevant reference is not available yet.
License: GPL-2
Copyright: Vilnius University Institute of Data Science and Digital Technologies
Imports: stats
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-15 14:52:25 UTC; milis
Author: Vytautas Dulskis [cre, aut], Leonidas Sakalauskas [aut]
Maintainer: Vytautas Dulskis <vytautas.dulskis@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-17 16:30:02 UTC

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New package CSCDRNA with initial version 1.0.1
Package: CSCDRNA
Title: Covariance Based Decomposition of Bulk Expression with Single-Cell Sequencing
Version: 1.0.1
Author: Ali Karimnezhad [aut, cre, ctb]
Maintainer: Ali Karimnezhad <ali.karimnezhad@gmail.com>
Description: Provides accurate cell type proportion estimation by incorporating covariance structure in both single-cell and bulk RNA-seq datasets into the analysis. For a related work, see Jew, B. et al. (2020) <dio:10.1038/s41467-020-15816-6>.
License: GPL-3
Encoding: UTF-8
Imports: nlshrink, limSolve, Biobase, BisqueRNA, methods, plyr, Seurat, MAST
Suggests: testthat (>= 3.0.0)
Depends: R (>= 2.10)
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-14 17:01:11 UTC; ali
Repository: CRAN
Date/Publication: 2022-05-17 16:20:08 UTC

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New package BayesMultMeta with initial version 0.1.0
Package: BayesMultMeta
Title: Bayesian Multivariate Meta-Analysis
Version: 0.1.0
Author: Ohla Bodnar [aut] , Taras Bodnar [aut] , Erik Thorsen [aut, cre]
Maintainer: Erik Thorsen <erik.thorsen@math.su.se>
Description: Objective Bayesian inference procedures for the parameters of the multivariate random effects model with application to multivariate meta-analysis. The posterior for the model parameters, namely the overall mean vector and the between-study covariance matrix, are assessed by constructing Markov chains based on the Metropolis-Hastings algorithms as developed in Bodnar and Bodnar (2021) (<arXiv:2104.02105>). The Metropolis-Hastings algorithm is designed under the assumption of the normal distribution and the t-distribution when the Berger and Bernardo reference prior and the Jeffreys prior are assigned to the model parameters. Convergence properties of the generated Markov chains are investigated by the rank plots and the split hat-R estimate based on the rank normalization, which are proposed in Vehtari et al. (2021) (<DOI:10.1214/20-BA1221>).
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Imports: assertthat, Rdpack
Suggests: mvmeta, gplots, testthat
NeedsCompilation: no
Packaged: 2022-05-16 08:22:13 UTC; ethor
Repository: CRAN
Date/Publication: 2022-05-17 16:50:05 UTC

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New package repoRter.nih with initial version 0.1.3
Package: repoRter.nih
Title: R Interface to the 'NIH RePORTER Project' API
Version: 0.1.3
Description: Methods to easily build requests in the non-standard JSON schema required by the National Institute of Health (NIH)'s 'RePORTER Project API' <https://api.reporter.nih.gov/#/Search/post_v2_projects_search>. Also retrieve and process result sets as either a ragged or flattened 'tibble'.
License: MIT + file LICENSE
URL: https://github.com/bikeactuary/repoRter.nih
BugReports: https://github.com/bikeactuary/repoRter.nih/issues
Depends: R (>= 4.1.0)
Imports: assertthat (>= 0.2.1), crayon (>= 1.4.1), dplyr (>= 1.0.7), httr (>= 1.4.2), janitor (>= 2.1.0), jsonlite (>= 1.7.2), lubridate (>= 1.7.10), magrittr (>= 2.0.1), purrr (>= 0.3.4), tibble (>= 3.1.3)
Suggests: devtools, ggplot2, ggrepel, knitr, tinytex, rmarkdown, scales, tufte, spelling
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-17 11:27:37 UTC; mbarr
Author: Michael Barr, ACAS, MAAA, CPCU [cre, aut]
Maintainer: "Michael Barr, ACAS, MAAA, CPCU" <mike@bikeactuary.com>
Repository: CRAN
Date/Publication: 2022-05-17 14:00:02 UTC

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New package mdmb with initial version 1.6-5
Package: mdmb
Title: Model Based Treatment of Missing Data
Version: 1.6-5
Date: 2022-05-17 12:12:29
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Contains model-based treatment of missing data for regression models with missing values in covariates or the dependent variable using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005; <doi:10.1198/016214504000001844>; Luedtke, Robitzsch, & West, 2020a, 2020b; <doi:10.1080/00273171.2019.1640104><doi:10.1037/met0000233>). The regression model can be nonlinear (e.g., interaction effects, quadratic effects or B-spline functions). Multilevel models with missing data in predictors are available for Bayesian estimation. Substantive-model compatible multiple imputation can be also conducted.
Depends: R (>= 3.1)
Imports: CDM, coda, graphics, miceadds (>= 3.2-23), Rcpp, sirt, stats, utils
Suggests: MASS
LinkingTo: miceadds, Rcpp, RcppArmadillo
Enhances: JointAI, jomo, mice, smcfcs
URL: https://github.com/alexanderrobitzsch/mdmb, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-17 10:13:57 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-17 14:00:05 UTC

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New package immer with initial version 1.3-3
Package: immer
Title: Item Response Models for Multiple Ratings
Version: 1.3-3
Date: 2022-05-17 12:00:59
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Implements some item response models for multiple ratings, including the hierarchical rater model, conditional maximum likelihood estimation of linear logistic partial credit model and a wrapper function to the commercial FACETS program. See Robitzsch and Steinfeld (2018) for a description of the functionality of the package. See Wang, Su and Qiu (2014; <doi:10.1111/jedm.12045>) for an overview of modeling alternatives.
Depends: R (>= 3.0-0)
Imports: CDM, coda, graphics, methods, psychotools, Rcpp, sirt, stats, TAM
Suggests: MASS
Enhances: eRm, lme4
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/alexanderrobitzsch/immer, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-17 10:03:29 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-17 14:00:08 UTC

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New package mpathsenser with initial version 1.0.0
Package: mpathsenser
Title: Process and Analyse Data from m-Path Sense
Version: 1.0.0
Description: Overcomes one of the major challenges in mobile (passive) sensing, namely being able to pre-process the raw data that comes from a mobile sensing app, specifically "m-Path Sense" <https://m-path.io>. The main task of 'mpathsenser' is therefore to read "m-Path Sense" JSON files into a database and provide several convenience functions to aid in data processing.
Depends: R (>= 4.0.0)
License: GPL (>= 3)
URL: https://gitlab.kuleuven.be/ppw-okpiv/researchers/u0134047/mpathsenser/
BugReports: https://gitlab.kuleuven.be/ppw-okpiv/researchers/u0134047/mpathsenser/-/issues
Encoding: UTF-8
Imports: DBI, dbplyr, dplyr, furrr, future, jsonlite, lubridate, magrittr, purrr, rjson, RSQLite, stats, tibble, tidyr
Suggests: curl, dbx, ggplot2, httr, lme4, lmerTest, progressr, rlang, rvest, sodium, testthat (>= 3.0.0), vroom
Config/Needs/website: tidyverse/tidytemplate
NeedsCompilation: no
Packaged: 2022-05-13 15:45:36 UTC; u0134047
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>
Repository: CRAN
Date/Publication: 2022-05-17 10:10:02 UTC

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New package ggbraid with initial version 0.2.2
Package: ggbraid
Title: Braid Ribbons in 'ggplot2'
Version: 0.2.2
Description: A new stat, stat_braid(), that extends the functionality of geom_ribbon() to correctly fill the area between two alternating lines (or steps) with two different colors, and a geom, geom_braid(), that wraps geom_ribbon() and uses stat_braid() by default.
URL: https://nsgrantham.github.io/ggbraid/, https://github.com/nsgrantham/ggbraid/
BugReports: https://github.com/nsgrantham/ggbraid/issues/
License: MIT + file LICENSE
Depends: R (>= 3.4.0)
Imports: ggplot2 (>= 3.0.0)
Suggests: rmarkdown, knitr, scales, readr, dplyr, tidyr, ggtext, glue, hms
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-14 06:14:44 UTC; neal
Author: Neal Grantham [aut, cre]
Maintainer: Neal Grantham <neal@nsgrantham.com>
Repository: CRAN
Date/Publication: 2022-05-17 10:40:02 UTC

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New package EATME with initial version 0.1.0
Package: EATME
Title: Exponentially Weighted Moving Average with Adjustments to Measurement Error
Version: 0.1.0
Description: The univariate statistical quality control tool aims to address measurement error effects when constructing exponentially weighted moving average p control charts. The method primarily focuses on binary random variables, but it can be applied to any continuous random variables by using sign statistic to transform them to discrete ones. With the correction of measurement error effects, we can obtain the corrected control limits of exponentially weighted moving average p control chart and reasonably adjusted exponentially weighted moving average p control charts. The methods in this package can be found in some relevant references, such as Chen and Yang (2022) <arXiv: 2203.03384>; Yang et al. (2011) <doi: 10.1016/j.eswa.2010.11.044>; Yang and Arnold (2014) <doi: 10.1155/2014/238719>; Yang (2016) <doi: 10.1080/03610918.2013.763980> and Yang and Arnold (2016) <doi: 10.1080/00949655.2015.1125901>.
License: GPL-3
Encoding: UTF-8
Imports: qcr, stats, graphics
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2022-05-13 17:03:38 UTC; KUAN
Author: Cheng-Kuan Lin Developer [aut, cre, cph], Li-Pang Chen Su-Fen Yang [aut]
Maintainer: Cheng-Kuan Lin Developer <zore2023852@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-17 10:10:06 UTC

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New package DrDimont with initial version 0.1.3
Package: DrDimont
Title: Drug Response Prediction from Differential Multi-Omics Networks
Version: 0.1.3
Description: While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. We present a novel network analysis pipeline, DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e., molecular differences that are the source of high differential drug scores can be retrieved. Our proposed pipeline leverages multi-omics data for differential predictions, e.g. on drug response, and includes prior information on interactions. The case study presented in the vignette uses data published by Krug (2020) <doi:10.1016/j.cell.2020.10.036>. The package license applies only to the software and explicitly not to the included data.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
VignetteBuilder: knitr
Imports: igraph, dplyr, stringr, WGCNA, Rfast, readr, tibble, tidyr, magrittr, rlang, utils, stats
Suggests: rmarkdown, knitr
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-05-13 18:59:09 UTC; kabaum
Author: Katharina Baum [cre] , Pauline Hiort [aut] , Julian Hugo [aut] , Spoorthi Kashyap [aut], Nataniel Mueller [aut] , Justus Zeinert [aut]
Maintainer: Katharina Baum <katharina.baum@hpi.de>
Repository: CRAN
Date/Publication: 2022-05-17 10:20:02 UTC

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New package xefun with initial version 0.1.0
Package: xefun
Version: 0.1.0
Title: X-Engineering or Supporting Functions
Description: Miscellaneous functions used for x-engineering (feature engineering) or for supporting in other packages maintained by 'Shichen Xie'.
Imports: data.table
License: MIT + file LICENSE
URL: https://github.com/ShichenXie/xefun
BugReports: https://github.com/ShichenXie/xefun/issues
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-13 11:27:05 UTC; jovyan
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Repository: CRAN
Date/Publication: 2022-05-17 09:50:02 UTC

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New package sirt with initial version 3.12-66
Package: sirt
Title: Supplementary Item Response Theory Models
Version: 3.12-66
Date: 2022-05-16 12:27:54
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Supplementary functions for item response models aiming to complement existing R packages. The functionality includes among others multidimensional compensatory and noncompensatory IRT models (Reckase, 2009, <doi:10.1007/978-0-387-89976-3>), MCMC for hierarchical IRT models and testlet models (Fox, 2010, <doi:10.1007/978-1-4419-0742-4>), NOHARM (McDonald, 1982, <doi:10.1177/014662168200600402>), Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>; Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>), faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011, <doi:10.1111/j.1745-3984.2011.00143.x>), ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>), DETECT statistic (Stout, Habing, Douglas & Kim, 1996, <doi:10.1177/014662169602000403>), local structural equation modeling (LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016, <doi:10.1080/00273171.2016.1142856>).
Depends: R (>= 3.5)
Imports: CDM, graphics, methods, Rcpp, stats, TAM, utils
Suggests: coda, igraph, lavaan, lavaan.survey, MASS, Matrix, miceadds, minqa, mirt, mvtnorm, nloptr, optimx, pbivnorm, pbv, psych, sfsmisc, sm, survey
LinkingTo: pbv, Rcpp, RcppArmadillo
URL: https://github.com/alexanderrobitzsch/sirt, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2022-05-16 10:37:36 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-17 09:10:05 UTC

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New package Rwclust with initial version 0.0.1
Package: Rwclust
Title: Random Walk Clustering on Weighted Graphs
Version: 0.0.1
Author: Carson Sprock [aut, cre]
Maintainer: Carson Sprock <csprock@gmail.com>
Description: Implements the random walk clustering algorithm for weighted graphs as found in Harel and Koren (2001) <https://link.springer.com/chapter/10.1007/3-540-45294-X_3>.
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: igraph, knitr, rmarkdown, testthat (>= 3.0.0)
Imports: Matrix
Depends: R (>= 3.5.0)
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-13 01:16:41 UTC; abc
Repository: CRAN
Date/Publication: 2022-05-17 09:50:05 UTC

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New package nlmixr2extra with initial version 2.0.6
Package: nlmixr2extra
Title: Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions
Version: 2.0.6
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.
License: GPL (>= 3)
URL: https://nlmixr2.github.io/nlmixr2extra/, https://github.com/nlmixr2/nlmixr2extra/
BugReports: https://github.com/nlmixr2/nlmixr2extra/issues/
Imports: checkmate, cli, crayon, data.table, digest, ggplot2, ggtext, lotri, nlme, nlmixr2est, Rcpp, rxode2, stats, symengine, utils
Suggests: nlmixr2data, testthat (>= 3.0.0), withr
LinkingTo: Rcpp, RcppArmadillo
Biarch: true
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-05-12 15:19:52 UTC; matt
Author: Matthew Fidler [aut, cre] , Vipul Mann [aut]
Repository: CRAN
Date/Publication: 2022-05-17 09:20:02 UTC

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New package marginaleffects with initial version 0.5.0
Package: marginaleffects
Title: Marginal Effects, Marginal Means, Predictions, and Contrasts
Version: 0.5.0
Description: Compute, summarize, and plot marginal effects, adjusted predictions, contrasts, and marginal means for a wide variety of models.
License: GPL (>= 3)
Copyright: inst/COPYRIGHTS
Encoding: UTF-8
URL: https://vincentarelbundock.github.io/marginaleffects/ https://github.com/vincentarelbundock/marginaleffects
BugReports: https://github.com/vincentarelbundock/marginaleffects/issues
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Imports: checkmate, data.table, generics, insight (>= 0.17.1), methods
Suggests: bench, brms, broom, datawizard, dplyr, emmeans, future, future.apply, ggdist, ggplot2, ggrepel, ggbeeswarm, haven, kableExtra, knitr, magrittr, margins, modelsummary, systemfonts, patchwork, quantreg, rlang, rmarkdown, testthat (>= 3.0.0), tidyverse, vdiffr, AER, aod, betareg, bife, BH, brglm2, brmsmargins, crch, estimatr, fixest (>= 0.10.1), gam, geepack, glmmTMB, glmx, itsadug, ivreg, lme4, lmerTest, MASS, mclogit, mgcv, mhurdle, mlogit, modelbased, nlme, nnet, ordinal, plm, pscl, RcppEigen, rms, robust, robustbase, robustlmm, rstantools, rstanarm, sampleSelection, sandwich, scam, speedglm, survey, survival, tobit1, truncreg, withr, covr, spelling
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-16 11:34:18 UTC; vincent
Author: Vincent Arel-Bundock [aut, cre, cph]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Repository: CRAN
Date/Publication: 2022-05-17 09:10:20 UTC

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New package lgcp with initial version 1.8
Package: lgcp
Maintainer: Benjamin M. Taylor <benjamin.taylor.software@gmail.com>
License: GPL-2 | GPL-3
Title: Log-Gaussian Cox Process
LazyLoad: yes
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma, Dominic Schumacher.
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo. See Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle (2015) <doi:10.18637/jss.v063.i07>.
Version: 1.8
Date: 2022-05-16
Imports: spatstat.geom, spatstat.core, spatstat.utils, sp, raster, tcltk, iterators, ncdf4, methods, rpanel (>= 1.1-3), fields, maptools, Matrix, rgeos
Suggests: sparr, rgdal, gpclib
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-16 19:31:32 UTC; taylorb7
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2022-05-17 09:20:05 UTC

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New package FLSSS with initial version 9.1.1
Package: FLSSS
Title: Mining Rigs for Problems in the Subset Sum Family
Version: 9.1.1
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to compressed 64-bit integer instance with user-controlled precision loss, which could yield substantial speedup due to the dimension reduction and efficient compressed integer arithmetic via bit-manipulations; (e) distributed computing infrastructure for multidimensional subset sum; (f) arbitrary-precision zero-margin-of-error multidimensional Subset Sum accelerated by a simplified Bloom filter. The package contains a copy of xxHash from <https://github.com/Cyan4973/xxHash>. Package vignette (<arXiv:1612.04484v3>) detailed a few historical updates. Functions prefixed with 'aux' (auxiliary) are independent implementations of published algorithms for solving optimization problems less relevant to Subset Sum.
License: GPL-3
Encoding: UTF-8
ByteCompile: true
Imports: Rcpp (>= 0.12.13), RcppParallel
LinkingTo: Rcpp, RcppParallel
SystemRequirements: GNU make
NeedsCompilation: yes
Packaged: 2022-05-14 15:12:28 UTC; i56087
Repository: CRAN
Date/Publication: 2022-05-17 09:10:33 UTC

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New package EvoPhylo with initial version 0.1
Package: EvoPhylo
Version: 0.1
Title: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Description: Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
Depends: R (>= 4.0.0)
Imports: ape (>= 1.16.2), cluster (>= 2.1.2), deeptime (>= 0.2.0), ggplot2 (>= 3.3.5), ggrepel (>= 0.9.1), ggtree (>= 3.1.4.992), patchwork, treeio (>= 1.16.2), Rtsne (>= 0.15), unglue (>= 0.1.0)
Suggests: kableExtra, knitr, rmarkdown
Encoding: UTF-8
LazyData: false
License: GPL (>= 2)
URL: https://github.com/tiago-simoes/EvoPhylo, https://tiago-simoes.github.io/EvoPhylo/
BugReports: https://github.com/tiago-simoes/EvoPhylo/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-12 22:25:17 UTC; tiago
Author: Tiago Simoes [cre, aut] , Noah Greifer [aut] , Stephanie Pierce [aut]
Maintainer: Tiago Simoes <tsimoes@fas.harvard.edu>
Repository: CRAN
Date/Publication: 2022-05-17 09:30:05 UTC

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New package epm with initial version 1.0.0
Package: epm
Title: EcoPhyloMapper
Version: 1.0.0
Depends: R (>= 4.0)
Imports: terra (>= 1.5.10), sf, ape, viridisLite, pbapply, methods, Rcpp (>= 0.12.9), RcppProgress
Suggests: tmap, data.table, spdep
Description: Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography.
License: GPL (>= 3)
URL: https://github.com/ptitle/epm
BugReports: https://github.com/ptitle/epm/issues
NeedsCompilation: yes
SystemRequirements: C++11
LinkingTo: Rcpp, RcppProgress
LazyData: true
ByteCompile: true
Encoding: UTF-8
Packaged: 2022-05-13 14:35:11 UTC; pascaltitle
Author: Pascal Title [aut, cre] , Donald Swiderski [aut], Miriam Zelditch [aut]
Maintainer: Pascal Title <pascal.title@stonybrook.edu>
Repository: CRAN
Date/Publication: 2022-05-17 10:00:02 UTC

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New package dimensionalAnalysis with initial version 0.1.0
Package: dimensionalAnalysis
Title: Dimensional Analysis
Version: 0.1.0
Maintainer: V. Vinothkumar <vinoth.agritech1115@gmail.com>
Depends: R (>= 3.5.0)
Imports: caracas, hash, reticulate
Description: Performs Rayleigh's method of dimensional analysis. This form of dimensional analysis expresses a functional relationship of some variables in the form of an exponential equation (Buckingham, (1914), <doi:10.1103/PhysRev.4.345>).
Config/reticulate: list( packages = list( list(package = "sympy") ) )
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-12 21:45:12 UTC; selcukkorkmaz
Author: V. Vinothkumar [aut, cre], M. Saravanakumar [aut], Namitha M.R. [aut], J. Ramachandran [aut]
Repository: CRAN
Date/Publication: 2022-05-17 09:40:02 UTC

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New package DEBBI with initial version 0.1.0
Package: DEBBI
Title: Differential Evolution-Based Bayesian Inference
Version: 0.1.0
Description: Bayesian inference algorithms based on the population-based "differential evolution" (DE) algorithm. Users can obtain posterior mode (MAP) estimates via DEMAP, posterior samples via DEMCMC, and variational approximations via DEVI.
License: MIT + file LICENSE
URL: https://github.com/bmgaldo/DEBBI
BugReports: https://github.com/bmgaldo/DEBBI
Encoding: UTF-8
Imports: stats, doParallel, randtoolbox, numDeriv
Depends: R (>= 3.5.0)
NeedsCompilation: no
Packaged: 2022-05-12 22:16:44 UTC; brendan
Author: Brendan Matthew Galdo [aut, cre]
Maintainer: Brendan Matthew Galdo <Brendan.m.galdo@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-17 09:30:09 UTC

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New package chronicler with initial version 0.2.0
Package: chronicler
Title: Add Logging to Functions
Version: 0.2.0
Description: Decorate functions to make them return enhanced output. The enhanced output consists in an object of type 'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function was run, what were its inputs, what were the errors (if the function failed to run) and other useful information. Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.
License: GPL (>= 3)
Encoding: UTF-8
BugReports: https://github.com/b-rodrigues/chronicler/issues
Depends: R (>= 4.1),
Imports: clipr, diffobj, dplyr, maybe, rlang, stringr, tibble
Suggests: knitr, lubridate, purrr, rmarkdown, testthat (>= 3.1.4), tidyr
VignetteBuilder: knitr
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-13 08:23:07 UTC; LLP685
Author: Bruno Rodrigues [aut, cre, cph]
Maintainer: Bruno Rodrigues <bruno@brodrigues.co>
Repository: CRAN
Date/Publication: 2022-05-17 09:40:04 UTC

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New package CEOdata with initial version 1.2.0.1
Package: CEOdata
Title: Datasets of the CEO (Centre d'Estudis d'Opinio) for Opinion Polls in Catalonia
Version: 1.2.0.1
Description: Easy and convenient access to the datasets of the "Centre d'Estudis d'Opinio", the Catalan institution for polling and public opinion. The package uses the data stored in the servers of the CEO and returns it in a tidy format.
Depends: R (>= 4.1.0), haven, dplyr (>= 1.0.0), urltools, stringr, jsonlite
Suggests: knitr, R.rsp, ggplot2, tidyr (> 1.1.1), curl, rmarkdown, vtable, compareGroups
License: GPL-3
URL: https://ceo.gencat.cat/ca/inici/, https://github.com/ceopinio/CEOdata/
BugReports: https://github.com/ceopinio/CEOdata/issues/
Encoding: UTF-8
VignetteBuilder: knitr, R.rsp
NeedsCompilation: no
Packaged: 2022-05-17 06:57:24 UTC; xavier
Author: Xavier Fernandez-i-Marin [aut, cre]
Maintainer: Xavier Fernandez-i-Marin <xavier.fim@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-17 09:20:16 UTC

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Mon, 16 May 2022

New package UBCRM with initial version 1.0.2
Package: UBCRM
Title: Functions to Simulate and Conduct Dose-Escalation Phase I Studies
Version: 1.0.2
Date: 2022-05-12
Author: Benjamin Esterni with contribution from Baboukar Mane
Maintainer: Christophe Zemmour <christophe.zemmour@gmail.com>
Description: Two Phase I designs are implemented in the package: the classical 3+3 and the Continual Reassessment Method. Simulations tools are also available to estimate the operating characteristics of the methods with several user-dependent options.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-05-13 13:30:27 UTC; ZEMMOURC
Repository: CRAN
Date/Publication: 2022-05-16 18:30:05 UTC

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New package robin with initial version 1.1.1
Package: robin
Title: ROBustness in Network
Version: 1.1.1
Maintainer: Valeria Policastro <valeria.policastro@gmail.com>
Description: Assesses the robustness of the community structure of a network found by one or more community detection algorithm to give indications about their reliability. It detects if the community structure found by a set of algorithms is statistically significant and compares the different selected detection algorithms on the same network. robin helps to choose among different community detection algorithms the one that better fits the network of interest. Reference in Policastro V., Righelli D., Carissimo A., Cutillo L., De Feis I. (2021) <https://journal.r-project.org/archive/2021/RJ-2021-040/index.html>.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/ValeriaPolicastro/robin
Depends: R (>= 3.5), igraph
Imports: ggplot2, networkD3, DescTools, fdatest, methods, gridExtra, parallel, spam, qpdf, Matrix
VignetteBuilder: knitr
Suggests: devtools, knitr, rmarkdown, testthat (>= 2.1.0)
NeedsCompilation: no
Packaged: 2022-05-16 18:01:35 UTC; valer
Author: Valeria Policastro [aut, cre], Dario Righelli [aut], Luisa Cutillo [aut], Italia De Feis [aut], Annamaria Carissimo [aut]
Repository: CRAN
Date/Publication: 2022-05-16 18:30:02 UTC

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New package cuRe with initial version 1.1.0
Package: cuRe
Title: Parametric Cure Model Estimation
Version: 1.1.0
Date: 2022-05-16
Maintainer: Lasse Hjort Jakobsen <lahja@math.aau.dk>
Description: Contains functions for estimating generalized parametric mixture and non-mixture cure models, loss of lifetime, mean residual lifetime, and crude event probabilities.
URL: https://github.com/LasseHjort/cuRe
BugReports: https://github.com/LasseHjort/cuRe/issues
License: GPL (>= 2)
Encoding: UTF-8
Depends: R (>= 3.5.0), survival, rstpm2, date
Imports: numDeriv, statmod, relsurv, reshape2
LazyData: Yes
NeedsCompilation: no
Packaged: 2022-05-16 09:20:05 UTC; sw1y
Author: Lasse Hjort Jakobsen [aut, cre], Mark Clements [cph], Rasmus Kuhr Jensen [ctb], Lars Klingen Gjærde [ctb]
Repository: CRAN
Date/Publication: 2022-05-16 18:20:02 UTC

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Sat, 14 May 2022

New package TAM with initial version 4.0-16
Package: TAM
Title: Test Analysis Modules
Version: 4.0-16
Date: 2022-05-13 13:23:23
Author: Alexander Robitzsch [aut,cre] , Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Includes marginal maximum likelihood estimation and joint maximum likelihood estimation for unidimensional and multidimensional item response models. The package functionality covers the Rasch model, 2PL model, 3PL model, generalized partial credit model, multi-faceted Rasch model, nominal item response model, structured latent class model, mixture distribution IRT models, and located latent class models. Latent regression models and plausible value imputation are also supported. For details see Adams, Wilson and Wang, 1997 <doi:10.1177/0146621697211001>, Adams, Wilson and Wu, 1997 <doi:10.3102/10769986022001047>, Formann, 1982 <doi:10.1002/bimj.4710240209>, Formann, 1992 <doi:10.1080/01621459.1992.10475229>.
Depends: R (>= 2.15.1), CDM (>= 6.4-19)
Imports: graphics, methods, Rcpp, stats, utils
Suggests: coda, GPArotation, grDevices, lattice, lavaan, MASS, miceadds, mvtnorm, plyr, psych, sfsmisc, splines, WrightMap
LinkingTo: Rcpp, RcppArmadillo
Enhances: LSAmitR
License: GPL (>= 2)
URL: http://www.edmeasurementsurveys.com/TAM/Tutorials/, https://github.com/alexanderrobitzsch/TAM, https://sites.google.com/site/alexanderrobitzsch2/software
NeedsCompilation: yes
Packaged: 2022-05-13 11:30:43 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-14 23:20:23 UTC

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New package gsloid with initial version 0.2.0
Package: gsloid
Title: Global Sea Level and Oxygen Isotope Data
Version: 0.2.0
Maintainer: Ben Marwick <benmarwick@gmail.com>
Description: Contains published data sets for global benthic d18O data for 0-5.3 Myr <doi:10.1029/2004PA001071> and global sea levels based on marine sediment core data for 0-800 ka <doi:10.5194/cp-12-1-2016>.
License: MIT + file LICENSE
BugReports: https://github.com/benmarwick/gsloid
URL: https://github.com/benmarwick/gsloid
Depends: R (>= 3.3.0)
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-13 23:09:58 UTC; bmarwick
Author: Ben Marwick [aut, cre], Lorraine Lisiecki [aut], Rachel Spratt [aut], Maureen Raymo [aut]
Repository: CRAN
Date/Publication: 2022-05-14 06:10:06 UTC

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Fri, 13 May 2022

New package PVplr with initial version 0.1.1
Package: PVplr
Title: Performance Loss Rate Analysis Pipeline
Version: 0.1.1
Description: The pipeline contained in this package provides tools used in the Solar Durability and Lifetime Extension Center (SDLE) for the analysis of Performance Loss Rates (PLR) in real world photovoltaic systems. Functions included allow for data cleaning, feature correction, power predictive modeling, PLR determination, and uncertainty bootstrapping through various methods <doi:10.1109/PVSC40753.2019.8980928>. The vignette "Pipeline Walkthrough" gives an explicit run through of typical package usage. This material is based upon work supported by the U.S Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) under Solar Energy Technologies Office (SETO) Agreement Number DE-EE-0008172. This work made use of the High Performance Computing Resource in the Core Facility for Advanced Research Computing at Case Western Reserve University.
Depends: R (>= 2.10)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr (>= 0.7.8), magrittr (>= 1.5), broom (>= 0.5.1), ggplot2 (>= 3.1.0), stlplus (>= 0.5.1), cluster (>= 2.0.7-1), purrr (>= 0.3.3), tidyr (>= 1.1.1), minpack.lm (>= 1.2-1), rlang (>= 0.3.1), segmented, forecast, scales, zoo
Suggests: testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-04-25 19:24:55 UTC; wco3
Author: Alan Curran [aut] , Tyler Burleyson [aut] , William Oltjen [aut] , Sascha Lindig [aut] , David Moser [aut] , Roger French [aut, cre] , Solar Durability and Lifetime Extension research center [cph, fnd]
Maintainer: Roger French <roger.french@case.edu>
Repository: CRAN
Date/Publication: 2022-05-13 21:10:02 UTC

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New package pepe with initial version 1.2.0
Package: pepe
Title: Data Manipulation
Version: 1.2.0
Author: Seyma Kalay
Maintainer: Seyma Kalay <seymakalay@hotmail.com>
Description: Is designed to make easier printing summary statistics (for continues and factor level) tables in Latex, and plotting by factor.
License: GPL-3
Encoding: UTF-8
LazyData: true
URL: https://github.com/seymakalay/pepe
BugReports: https://github.com/seymakalay/pepe/issues
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Depends: R (>= 2.10)
Imports: dplyr, ggplot2, psych, tidyr, utils
NeedsCompilation: no
Packaged: 2022-05-12 14:26:14 UTC; Seyma
Repository: CRAN
Date/Publication: 2022-05-13 16:40:02 UTC

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New package NiLeDAM with initial version 0.2
Package: NiLeDAM
Title: Monazite Dating for the NiLeDAM Team
Version: 0.2
Date: 2022-05-12
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Description: Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>.
License: GPL (>= 2)
Depends: R (>= 2.4.0)
Imports: dplyr, ggplot2, magrittr, methods, nleqslv, rlang, scales, shiny, shinyjs, shinythemes, stats, thematic, tidyr
Suggests: knitr, rmarkdown, spelling, testthat (>= 3.0.0)
VignetteBuilder: knitr
Encoding: UTF-8
Repository: CRAN
Language: en-US
NeedsCompilation: no
Packaged: 2022-05-12 10:29:00 UTC; nathalie
Author: Nathalie Vialaneix [aut, trl, cre], Aurelie Mercadie [aut], Jean-Marc Montel [aut], Anne-Magali Seydoux-Guillaume [ctb]
Date/Publication: 2022-05-13 16:10:02 UTC

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New package linelist with initial version 0.0.1
Package: linelist
Title: Tagging and Validating Epidemiological Data
Version: 0.0.1
Description: Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.
License: MIT + file LICENSE
URL: https://github.com/epiverse-trace/linelist
BugReports: https://github.com/epiverse-trace/linelist/issues
Encoding: UTF-8
Imports: checkmate
Suggests: callr, covr, dplyr, knitr, magrittr, outbreaks, rmarkdown, testthat, tibble
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-12 13:17:06 UTC; thibaut
Author: Thibaut Jombart [aut, cre]
Maintainer: Thibaut Jombart <thibaut@data.org>
Repository: CRAN
Date/Publication: 2022-05-13 16:30:02 UTC

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New package jgsbook with initial version 1.0
Package: jgsbook
Title: Package of the German Book "Statistik mit R und RStudio" by Joerg grosse Schlarmann
Author: Joerg grosse Schlarmann
Maintainer: Joerg grosse Schlarmann <schlarmann@produnis.de>
Description: All datasets and functions used in the german book "Statistik mit R und RStudio" by Joerg grosse Schlarmann. You can read it online at <https://www.produnis.de/R/> .
Version: 1.0
Date: 2022-05-12
Language: de-de
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Encoding: UTF-8
Imports: statip
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-12 10:09:42 UTC; produnis
Repository: CRAN
Date/Publication: 2022-05-13 16:00:02 UTC

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New package geomaroc with initial version 0.1.1
Package: geomaroc
Title: Easily Visualize Geographic Data of Morocco
Version: 0.1.1
Maintainer: Amine Andam <andamamine83@gmail.com>
Description: Tools to easily visualize geographic data of Morocco. This package interacts with data available through the 'geomarocdata' package, which is available in a 'drat' repository. The size of the 'geomarocdata' package is approximately 12 MB.
License: GPL
Imports: jsonlite , sf
Encoding: UTF-8
URL: https://github.com/AmineAndam04/R-geomaroc
Suggests: knitr, rmarkdown, testthat, geomarocdata
Additional_repositories: https://amineandam04.github.io/drat/
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-11 15:02:06 UTC; pc
Author: Amine Andam [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-13 16:00:06 UTC

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New package ycevo with initial version 0.1.0
Package: ycevo
Title: Nonparametric Estimation of the Yield Curve Evolution
Version: 0.1.0
Maintainer: Yangzhuoran Fin Yang <yangyangzhuoran@gmail.com>
Description: Nonparametric estimation of the discount rate and yield curve. Koo, B., La Vecchia, D., & Linton, O. B. (2021) <doi:10.1016/j.jeconom.2020.04.014> describe the application with the Center for Research in Security Prices (CRSP) Bond Data and document the methods of this package.
URL: https://github.com/bonsook/ycevo
BugReports: https://github.com/bonsook/ycevo/issues
License: GPL-3
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
Imports: dplyr, magrittr, Matrix, Rcpp (>= 0.12.18), rlang, stats
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat (>= 3.0.0), akima, knitr, plotly, rmarkdown, tidyverse
Language: en-AU
NeedsCompilation: yes
Packaged: 2022-05-12 06:36:07 UTC; fyan0012
Author: Bonsoo Koo [aut], Nathaniel Tomasetti [aut], Kai-Yang Goh [aut], Yangzhuoran Fin Yang [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-13 09:10:01 UTC

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New package terminaldigits with initial version 0.1.0
Package: terminaldigits
Title: Tests of Uniformity and Independence for Terminal Digits
Version: 0.1.0
Description: Implements simulated tests for the hypothesis that terminal digits are uniformly distributed (chi-squared goodness-of-fit) and the hypothesis that terminal digits are independent from preceding digits (several tests of independence for r x c contingency tables). Also, for a number of distributions, implements Monte Carlo simulations for type I errors and power for the test of independence.
License: MIT + file LICENSE
Depends: R (>= 2.10)
Imports: discretefit, Rcpp
Suggests: dplyr, gt, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0)
LinkingTo: Rcpp
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-12 06:54:28 UTC; Josh
Author: Josh McCormick [aut, cre]
Maintainer: Josh McCormick <josh.mccormick@aya.yale.edu>
Repository: CRAN
Date/Publication: 2022-05-13 09:10:12 UTC

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New package linea with initial version 0.0.1
Package: linea
Title: Linear Regression Interface
Version: 0.0.1
Description: An interface to accelerate linear regression (Ordinary least squares) modelling, which allows users to build models quickly, while automatically generating interactive visualizations of the results. Non-linear models specification (e.g. y = b1*x1 + b2*log(x2)) can be easily constructed using user-defined transformations. Functions for testing wide ranges of model specifications (e.g. y = b*log(x,10) , y = b*log(x,20) , ...), all at once, are also available. Finally, models can be imported and exported as Excel files where all the information necessary for re-running the models is stored in separate sheets.
License: GPL-3
Encoding: UTF-8
Imports: anytime, dplyr , gtrendsR, lubridate , magrittr , methods , openxlsx , plotly , purrr , RColorBrewer , readr , readxl , reshape2 , rlist, sjmisc , stringr , tibble , tidyr , tidyverse , tis , zoo
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-05-12 05:47:12 UTC; 44751
Author: Claudio Paladini [aut, cre]
Maintainer: Claudio Paladini <clode.paladini@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-13 09:10:15 UTC

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New package PALMO with initial version 0.1.0
Package: PALMO
Title: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset
Version: 0.1.0
Maintainer: Suhas Vasaikar <suhas.vasaikar@alleninstitute.org>
Description: It is a platform for analyzing longitudinal data from bulk as well as single cell datasets. It allows to identify variations in molecular features within and across donors over longitudinal time points. The analysis can be done on bulk expression dataset without known cell type information or single cell with cell type/user-defined groups. It allows to infer stable and variable features in given donor and each cell type (or user defined group). The outlier analysis can be performed to identify technical/biological perturbed samples in donor/participant. Further, differential analysis can be performed to decipher time-wise changes in gene expression in a cell type.
Depends: R (>= 4.0), methods, grid, graphics, stats, grDevices
Imports: Seurat (>= 3.9), ggrepel (>= 0.9), pbapply (>= 1.4), lme4 (>= 1.1), ggforce (>= 0.3), MAST (>= 1.14), factoextra (>= 1.0), Rtsne (>= 0.15), knitr(>= 1.30), dplyr, ggplot2, reshape2, ComplexHeatmap, circlize, cowplot, pheatmap, tidyverse, utils
Suggests: ggpubr, rmarkdown
URL: https://github.com/aifimmunology/PALMO
BugReports: https://github.com/aifimmunology/PALMO/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-11 16:21:00 UTC; suhas.vasaikar
Author: Suhas Vasaikar [aut, cre], Aarthi Talla [aut, ctb], Xiaojun Li [aut, ctb]
Repository: CRAN
Date/Publication: 2022-05-13 08:40:06 UTC

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New package NovelDistns with initial version 0.1.0
Package: NovelDistns
Title: Computes PDF, CDF, Quantile, Random Numbers and Measures of Inference for 3 General Families of Distributions
Version: 0.1.0
Author: Mutua Kilai, Gichuhi Waititu, Wanjoya Kibira
Maintainer: Mutua Kilai <kilaimutua@gmail.com>
Description: Computes the probability density function, the cumulative density function, quantile function, random numbers and measures of inference for the following families exponentiated generalized gull alpha power family, exponentiated gull alpha powerfamily, gull alpha power family.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: AdequacyModel, gsl, rootSolve, stats
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-11 18:43:51 UTC; Mutua Sam
Repository: CRAN
Date/Publication: 2022-05-13 08:40:10 UTC

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New package diceR with initial version 1.2.0
Package: diceR
Title: Diverse Cluster Ensemble in R
Version: 1.2.0
Description: Performs cluster analysis using an ensemble clustering framework, Chiu & Talhouk (2018) <doi:10.1186/s12859-017-1996-y>. Results from a diverse set of algorithms are pooled together using methods such as majority voting, K-Modes, LinkCluE, and CSPA. There are options to compare cluster assignments across algorithms using internal and external indices, visualizations such as heatmaps, and significance testing for the existence of clusters.
License: MIT + file LICENSE
URL: https://github.com/AlineTalhouk/diceR/, https://alinetalhouk.github.io/diceR/
BugReports: https://github.com/AlineTalhouk/diceR/issues
Depends: R (>= 3.5)
Imports: abind, assertthat, class, clue, clusterCrit, clValid, dplyr (>= 0.7.5), ggplot2, infotheo, klaR, magrittr, mclust, methods, NMF, purrr (>= 0.2.3), RankAggreg, Rcpp, stringr, tidyr, yardstick
Suggests: apcluster, blockcluster, cluster, covr, dbscan, e1071, kernlab, knitr, kohonen, pander, poLCA, progress, RColorBrewer, rlang, rmarkdown, Rtsne, sigclust, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Packaged: 2022-05-11 19:21:18 UTC; derek
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Repository: CRAN
Date/Publication: 2022-05-13 08:50:11 UTC

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New package CDM with initial version 8.1-12
Package: CDM
Title: Cognitive Diagnosis Modeling
Version: 8.1-12
Date: 2022-05-12 13:47:57
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. This package enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model (de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992, <doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis (Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>). See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> or Robitzsch and George (2019, <doi:10.1007/978-3-030-05584-4_26>) for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).
Depends: R (>= 3.1), mvtnorm
Imports: graphics, grDevices, methods, polycor, Rcpp, stats, utils
Suggests: BIFIEsurvey, lattice, MASS, miceadds, ROI, sfsmisc
LinkingTo: Rcpp, RcppArmadillo
Enhances: dina, GDINA, mirt, rrum
LazyLoad: yes
LazyData: yes
URL: https://github.com/alexanderrobitzsch/CDM, https://sites.google.com/site/alexanderrobitzsch2/software
License: GPL (>= 2)
BugReports: https://github.com/alexanderrobitzsch/CDM/issues?state=open
NeedsCompilation: yes
Packaged: 2022-05-12 11:51:09 UTC; sunpn563
Repository: CRAN
Date/Publication: 2022-05-13 08:50:14 UTC

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New package ParallelDSM with initial version 0.3.2
Package: ParallelDSM
Title: Parallel Digital Soil Mapping using Machine Learning
Version: 0.3.2
Description: Parallel computing, multi-core CPU is used to efficiently compute and process multi-dimensional soil data.This package includes the parallelized 'Quantile Regression Forests' algorithm for Digital Soil Mapping and is mainly dependent on the package 'quantregForest' and 'snowfall'. Detailed references to the R package and the web site are described in the methods, as detailed in the method documentation.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), snowfall, raster, sp
Imports: methods, pryr, utils, caret, gstat, quantregForest, randomForest, stringr, rgdal, stats,
NeedsCompilation: no
Packaged: 2022-05-13 06:24:01 UTC; tpc
Author: Xiaodong Song [aut], Peicong Tang [aut, cre], Gaoqiang Ge [aut], Jun Zhu [aut], Ganlin Zhang [aut]
Maintainer: Peicong Tang <peicongtang0409@163.com>
Repository: CRAN
Date/Publication: 2022-05-13 07:30:06 UTC

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New package GLDreg with initial version 1.1.0
Package: GLDreg
Title: Fit GLD Regression/Quantile/AFT Model to Data
Version: 1.1.0
Date: 2022-05-04
Maintainer: Steve Su <allegro.su@gmail.com>
Depends: GLDEX (>= 2.0.0.5), ddst, grDevices, graphics, stats
Suggests: MASS, quantreg, mlr3proba
Description: Owing to the rich shapes of Generalised Lambda Distributions (GLDs), GLD standard/quantile/Accelerated Failure Time (AFT) regression is a competitive flexible model compared to standard/quantile/AFT regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. For AFT model, it also eliminates the needs to try several different AFT models, owing to the flexible shapes of GLD. The goodness of fit of the proposed model can be assessed via QQ plots and Kolmogorov-Smirnov tests and data driven smooth test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data. References include the following: Su (2015) "Flexible Parametric Quantile Regression Model" <doi:10.1007/s11222-014-9457-1>, Su (2021) "Flexible parametric accelerated failure time model"<doi:10.1080/10543406.2021.1934854>.
License: GPL (>= 3)
NeedsCompilation: no
Packaged: 2022-05-09 12:45:20 UTC; Allegro
Author: Steve Su [aut, cre, cph] , R Core Team [aut]
Repository: CRAN
Date/Publication: 2022-05-13 07:30:09 UTC

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New package metaplus with initial version 1.0-4
Package: metaplus
Title: Robust Meta-Analysis and Meta-Regression
Version: 1.0-4
Date: 2022-05-11
Maintainer: Ken Beath <ken@kjbeath.com.au>
Contact: Ken Beath <ken@kjbeath.com.au>
Author: Ken Beath [aut, cre], Ben Bolker [aut], R Development Core Team [aut]
Description: Performs meta-analysis and meta-regression using standard and robust methods with confidence intervals based on the profile likelihood. Robust methods are based on alternative distributions for the random effect, either the t-distribution (Lee and Thompson, 2008 <doi:10.1002/sim.2897> or Baker and Jackson, 2008 <doi:10.1007/s10729-007-9041-8>) or mixtures of normals (Beath, 2014 <doi:10.1002/jrsm.1114>).
Depends: R(>= 3.2.0)
Suggests: R.rsp
VignetteBuilder: R.rsp
Imports: bbmle, metafor, boot, methods, numDeriv, MASS, graphics, stats, fastGHQuad, lme4, Rfast, parallel, doParallel, foreach, doRNG
LazyData: yes
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-05-11 09:07:31 UTC; kjbeath1
Repository: CRAN
Date/Publication: 2022-05-13 05:40:02 UTC

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New package CausCor with initial version 0.1.1
Package: CausCor
Title: Calculate Correlations and Estimate Causality
Version: 0.1.1
Description: This tool performs pairwise correlation analysis and estimate causality. Particularly, it is useful for detecting the metabolites that would be altered by the gut bacteria.
URL: https://github.com/sugym/CausCor
License: MIT + file LICENSE
Language: en-US
Encoding: UTF-8
Imports: cowplot, dplyr, ggplot2, grDevices, magrittr, stats, WriteXLS
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-05-12 02:22:05 UTC; sugiyamatomomi
Author: Tomomi Sugiyama [aut, cre]
Maintainer: Tomomi Sugiyama <sugiyama.t.am@m.titech.ac.jp>
Repository: CRAN
Date/Publication: 2022-05-13 05:40:05 UTC

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Thu, 12 May 2022

New package subscreen with initial version 3.0.7
Package: subscreen
Title: Systematic Screening of Study Data for Subgroup Effects
Version: 3.0.7
Author: Bodo Kirsch, Steffen Jeske, Susanne Lippert, Thomas Schmelter, Christoph Muysers, Hermann Kulmann
Maintainer: Bodo Kirsch <bodo.kirsch@bayer.com>
Description: Identifying outcome relevant subgroups has now become as simple as possible! The formerly lengthy and tedious search for the needle in a haystack will be replaced by a single, comprehensive and coherent presentation. The central result of a subgroup screening is a diagram in which each single dot stands for a subgroup. The diagram may show thousands of them. The position of the dot in the diagram is determined by the sample size of the subgroup and the statistical measure of the treatment effect in that subgroup. The sample size is shown on the horizontal axis while the treatment effect is displayed on the vertical axis. Furthermore, the diagram shows the line of no effect and the overall study results. For small subgroups, which are found on the left side of the plot, larger random deviations from the mean study effect are expected, while for larger subgroups only small deviations from the study mean can be expected to be chance findings. So for a study with no conspicuous subgroup effects, the dots in the figure are expected to form a kind of funnel. Any deviations from this funnel shape hint to conspicuous subgroups. This approach was presented in Muysers (2020) <doi:10.1007/s43441-019-00082-6> and referenced in Ballarini (2020) <doi:10.1002/pst.2012>. New to version 3 is the Automatic Screening of one- or MUlti-factorial Subgroups (ASMUS) for documentation of the structured review of subgroup findings.
License: GPL-3
Encoding: UTF-8
Imports: utils, plyr, data.table, grDevices, graphics, shiny, DT, stats, shinyjs, bsplus, jsonlite, colourpicker, dplyr, ranger, purrr, shinyWidgets
Suggests: parallel, survival, knitr, rmarkdown
NeedsCompilation: no
VignetteBuilder: knitr
Packaged: 2022-05-12 09:01:40 UTC; SGFPJ
Repository: CRAN
Date/Publication: 2022-05-12 22:00:03 UTC

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New package lba with initial version 2.4.5
Package: lba
Title: Latent Budget Analysis for Compositional Data
Version: 2.4.5
Date: 2022-05-12
Author: Enio G. Jelihovschi <eniojelihovs@gmail.com> and Ivan Bezerra Allaman <iballaman@uesc.br>
Maintainer: Ivan Bezerra Allaman <iballaman@uesc.br>
Depends: R (>= 3.1.0), MASS, alabama, plotrix, scatterplot3d, rgl
Description: Latent budget analysis is a method for the analysis of a two-way contingency table with an exploratory variable and a response variable. It is specially designed for compositional data.
Encoding: latin1
License: GPL (>= 2)
URL: https://github.com/ivanalaman/lba
NeedsCompilation: no
Packaged: 2022-05-12 18:40:21 UTC; ivana
Repository: CRAN
Date/Publication: 2022-05-12 21:20:02 UTC

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New package pbANOVA with initial version 0.1.0
Package: pbANOVA
Title: Parametric Bootstrap for ANOVA Models
Version: 0.1.0
Maintainer: Sarah Alver <salver@unm.edu>
Description: Parametric bootstrap (PB) has been used for three-way ANOVA model with unequal group variances.
License: GPL-2 | GPL-3
Imports: MASS, Rmisc, plyr, DescTools, lmtest,dplyr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-10 17:56:58 UTC; luyan
Author: Sarah Alver [aut, cre], Guoyi Zhang [aut]
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-05-12 19:10:02 UTC

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New package mlr3fairness with initial version 0.3.0
Package: mlr3fairness
Title: Fairness Auditing and Debiasing for 'mlr3'
Version: 0.3.0
Description: Integrates fairness auditing and bias mitigation methods for the 'mlr3' ecosystem. This includes fairness metrics, reporting tools, visualizations and bias mitigation techniques such as "Reweighing" described in 'Kamiran, Calders' (2012) <doi:10.1007/s10115-011-0463-8> and "Equalized Odds" described in 'Hardt et al.' (2016) <https://papers.nips.cc/paper/2016/file/9d2682367c3935defcb1f9e247a97c0d-Paper.pdf>. Integration with 'mlr3' allows for auditing of ML models as well as convenient joint tuning of machine learning algorithms and debiasing methods.
URL: https://mlr3fairness.mlr-org.com, https://github.com/mlr-org/mlr3fairness
BugReports: https://github.com/mlr-org/mlr3fairness/issues
License: LGPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5.0), mlr3 (>= 0.13.0)
Imports: checkmate, R6 (>= 2.4.1), data.table (>= 1.13.6), paradox, mlr3measures, mlr3misc, mlr3pipelines, ggplot2
Suggests: mlr3viz, rmarkdown, knitr, rpart, testthat (>= 3.0.0), patchwork, ranger, mlr3learners, linprog, posterdown, kableExtra, fairml, iml
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-11 16:32:36 UTC; flo
Author: Florian Pfisterer [cre, aut] , Wei Siyi [aut], Michel Lang [aut]
Maintainer: Florian Pfisterer <pfistererf@googlemail.com>
Repository: CRAN
Date/Publication: 2022-05-12 19:30:02 UTC

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New package superml with initial version 0.5.4
Package: superml
Title: Build Machine Learning Models Like Using Python's Scikit-Learn Library in R
Version: 0.5.4
Maintainer: Manish Saraswat <manish06saraswat@gmail.com>
Description: The idea is to provide a standard interface to users who use both R and Python for building machine learning models. This package provides a scikit-learn's fit, predict interface to train machine learning models in R.
License: GPL-3 | file LICENSE
Encoding: UTF-8
LazyData: true
URL: https://github.com/saraswatmks/superml
BugReports: https://github.com/saraswatmks/superml/issues
Depends: R(>= 3.5), R6(>= 2.2)
Imports: data.table (>= 1.10), Rcpp (>= 1.0), assertthat (>= 0.2), Metrics (>= 0.1)
LinkingTo: Rcpp, BH, RcppArmadillo
Suggests: knitr, rlang, testthat, rmarkdown, naivebayes(>= 0.9), ClusterR(>= 1.1), FNN(>= 1.1), ranger(>= 0.10), caret(>= 6.0), xgboost(>= 0.6), glmnet(>= 2.0), e1071(>= 1.7)
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-10 10:06:00 UTC; m.saraswat
Author: Manish Saraswat [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-12 14:10:02 UTC

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New package BCT with initial version 1.2
Package: BCT
Title: Bayesian Context Trees for Discrete Time Series
Version: 1.2
Date: 2022-11-05
Author: Ioannis Papageorgiou, Valentinian Mihai Lungu, Ioannis Kontoyiannis
Maintainer: Valentinian Mihai Lungu <valentinian.mihai@gmail.com>
Description: An implementation of a collection of tools for exact Bayesian inference with discrete times series. This package contains functions that can be used for prediction, model selection, estimation, segmentation/change-point detection and other statistical tasks. Specifically, the functions provided can be used for the exact computation of the prior predictive likelihood of the data, for the identification of the a posteriori most likely (MAP) variable-memory Markov models, for calculating the exact posterior probabilities and the AIC and BIC scores of these models, for prediction with respect to log-loss and 0-1 loss and segmentation/change-point detection. Example data sets from finance, genetics, animal communication and meteorology are also provided. Detailed descriptions of the underlying theory and algorithms can be found in [Kontoyiannis et al. 'Bayesian Context Trees: Modelling and exact inference for discrete time series.' Journal of the Royal Statistical Society: Series B (Statistical Methodology), April 2022. Available at: <arXiv:2007.14900> [stat.ME], July 2020] and [Lungu et al. 'Change-point Detection and Segmentation of Discrete Data using Bayesian Context Trees' <arXiv:2203.04341> [stat.ME], March 2022].
License: GPL (>= 2)
LazyData: true
Encoding: UTF-8
SystemRequirements: C++11
Imports: Rcpp (>= 1.0.5), stringr, igraph, grDevices, graphics
LinkingTo: Rcpp
Depends: R (>= 4.0)
NeedsCompilation: yes
Packaged: 2022-05-12 13:30:53 UTC; Valentinian
Repository: CRAN
Date/Publication: 2022-05-12 14:00:05 UTC

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New package sspm with initial version 0.9.1
Package: sspm
Title: Spatial Surplus Production Model Framework for Northern Shrimp Populations
Version: 0.9.1
Description: Implement a gam-based spatial surplus production model, aimed at modeling northern shrimp population in Atlantic Canada but potentially to any stock in any location. The package is opinionated in its implementation of SPMs as it internally makes the choice to use penalized spatial gams with time lags. However, it also aims to provide options for the user to customize their model.
License: MIT + file LICENSE
BugReports: https://github.com/pedersen-fisheries-lab/sspm/issues
URL: https://pedersen-fisheries-lab.github.io/sspm/
Encoding: UTF-8
Depends: sf, mgcv, R (>= 3.5.0)
Imports: stats, methods, units, checkmate, cli, tibble, magrittr, tidyr, dplyr, purrr, stringr, rlang
Suggests: testthat (>= 3.0.0), covr, ggplot2, ggforce, lwgeom, tweedie, sfdct, knitr, rmarkdown
LazyData: True
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-10 22:27:20 UTC; vlucet
Author: Valentin Lucet [aut, cre, cph], Eric Pedersen [aut]
Maintainer: Valentin Lucet <valentin.lucet@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-12 08:10:02 UTC

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New package s3.resourcer with initial version 1.0.1
Package: s3.resourcer
Title: S3 Resource Resolver
Version: 1.0.1
Description: Resources are files in tidy or R data format stored in a S3 compatible system, such as Amazon Web Services S3 or Minio object stores. Resources can also be Parquet files, accessed through an Apache Spark service.
License: LGPL (>= 2.1)
Depends: R6, httr, resourcer (>= 1.2), aws.s3, sparklyr
Suggests: testthat, knitr
BugReports: https://github.com/obiba/s3.resourcer
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-11 07:18:32 UTC; yannick
Author: Yannick Marcon [aut, cre] , OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Repository: CRAN
Date/Publication: 2022-05-12 08:40:02 UTC

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New package robflreg with initial version 1.0
Package: robflreg
Title: Robust Functional Linear Regression
Version: 1.0
Date: 2022-05-11
Depends: R (>= 3.5.0), fda, MASS, robustbase
Imports: expm, fda.usc, goffda, mvtnorm, pcaPP, plot3D
LazyLoad: yes
ByteCompile: TRUE
Maintainer: Ufuk Beyaztas <ufukbeyaztas@gmail.com>
Description: Functions for implementing robust methods for functional linear regression. In the functional linear regression, we consider scalar-on-function linear regression and function-on-function linear regression. More details, see Beyaztas, U., and Shang, H. L. (2021) <arXiv:2111.01238> and Beyaztas, U., and Shang, H. L. (2022) <arXiv:2203.05065>.
License: GPL-3
NeedsCompilation: no
Packaged: 2022-05-10 23:30:45 UTC; mq20178348
Author: Ufuk Beyaztas [aut, cre, cph] , Han Lin Shang [aut]
Repository: CRAN
Date/Publication: 2022-05-12 08:20:02 UTC

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New package metrica with initial version 1.2.3
Package: metrica
Title: Prediction Performance Metrics
Version: 1.2.3
Date: 2022-05-10
Description: A compilation of more than 40 functions designed to evaluate prediction performance of point-forecast models accounting for different aspects of the agreement between predicted and observed values. It includes error metrics (e.g. MAE, RMSE), model efficiencies (e.g. NSE, KGE), indices of agreement (e.g. d, RAC), goodness of fit (e.g. r, R2), concordance correlation (e.g. CCC), error decomposition (e.g. lack of accuracy-precision), and plots the visualize agreement. For more details visit the vignettes <https://adriancorrendo.github.io/metrica/>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Suggests: covr, tidyverse, knitr, rmarkdown, apsimx, testthat (>= 3.0.0)
Imports: stats, ggplot2, dplyr, rlang, tidyr, viridis, utils, DBI, RSQLite, ggpp
VignetteBuilder: knitr
URL: https://adriancorrendo.github.io/metrica/
BugReports: https://github.com/adriancorrendo/metrica/issues
NeedsCompilation: no
Packaged: 2022-05-11 07:12:07 UTC; correndo
Author: Adrian A. Correndo [cre, cph] , Adrian A. Correndo [aut] , Luiz H. Moro Rosso [aut] , Rai Schwalbert [aut] , Carlos Hernandez [aut] , Leonardo M. Bastos [aut] , Dean Holzworth [aut], Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <correndo@ksu.edu>
Repository: CRAN
Date/Publication: 2022-05-12 08:40:05 UTC

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New package getwiki with initial version 0.9.0
Package: getwiki
Title: R Wrapper for Wikipedia Data
Version: 0.9.0
Description: A simple wrapper for 'Wikipedia' data. Specifically, this package looks to fill a gap in retrieving text data in a tidy format that can be used for Natural Language Processing.
Imports: jsonlite
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-11 00:16:09 UTC; corydonbaylor
Author: Corydon Baylor [aut, cre]
Maintainer: Corydon Baylor <cwbaylor1@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-12 08:20:05 UTC

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New package FloodFreqPlot with initial version 0.1.0
Package: FloodFreqPlot
Version: 0.1.0
Date: 2022-05-09
Title: Flood Probability Plotting and Graphical Frequency Analysis
Depends: R (>= 3.5.0)
Imports: stats, graphics, grDevices
Description: Plotting flood quantiles and their corresponding probabilities (return periods) on the probability papers. The details of relevant methods are available in Chow et al (1988, ISBN: 007070242X, 9780070702424), and Bobee and Ashkar (1991, ISBN: 0918334683, 9780918334688).
License: GPL (>= 3)
LazyData: yes
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-10 20:12:32 UTC; Ali
Author: Ali Ahani [aut, cre] , S. Saeid Mousavi Nadoushani [aut]
Maintainer: Ali Ahani <ali.ahani66@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-12 08:10:06 UTC

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New package CopSens with initial version 0.1.0
Package: CopSens
Title: Copula-Based Sensitivity Analysis for Observational Causal Inference
Version: 0.1.0
Description: Implements the copula-based sensitivity analysis method, as discussed in Copula-based Sensitivity Analysis for Multi-Treatment Causal Inference with Unobserved Confounding <arXiv:2102.09412>, with Gaussian copula adopted in particular.
URL: https://github.com/JiajingZ/CopSens
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.6.0)
Imports: pcaMethods (>= 1.78.0), CVXR (>= 1.0), MASS (>= 7.3-53), ggplot2 (>= 3.3.3), stats (>= 4.0.3), dplyr (>= 1.0.3), tidyr (>= 1.1.2), tidyverse (>= 1.3.0)
NeedsCompilation: no
Packaged: 2022-05-11 06:23:54 UTC; jiajing
Author: Jiajing Zheng [aut, cre], Alexander Franks [aut], Alex D'Amour [ctb]
Maintainer: Jiajing Zheng <carolinez6850@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-12 08:30:02 UTC

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New package biogeom with initial version 1.0.5
Package: biogeom
Title: Biological Geometries
Version: 1.0.5
Date: 2022-05-11
Author: Peijian Shi [aut, cre], Johan Gielis [aut], Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
Imports: spatstat.geom (>= 2.4-0)
Description: Is used to simulate and fit biological geometries. biogeom incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> was used to estimate model parameters. biogeom includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. biogeom can quantify the conspecific or interspecific similarity of natural outlines, and provides information with important ecological and evolutionary implications for the growth and form of living organisms.
Depends: R (>= 4.2.0)
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-05-11 07:01:26 UTC; PEIJIAN SHI
Repository: CRAN
Date/Publication: 2022-05-12 08:40:09 UTC

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New package simer with initial version 0.9.0.0
Package: simer
Title: Data Simulation for Life Science and Breeding
Version: 0.9.0.0
Date: 2022-5-1
Description: Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.
License: Apache License 2.0
URL: https://github.com/xiaolei-lab/SIMER
BugReports: https://github.com/xiaolei-lab/SIMER/issues
Imports: utils, stats, Matrix, methods, MASS, rMVP, Rcpp, rjson, igraph
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, BH, bigmemory
Depends: R (>= 3.5.0), bigmemory
Suggests: knitr
Encoding: UTF-8
SystemRequirements: C++11
NeedsCompilation: yes
Maintainer: Xiaolei Liu <xiaoleiliu@mail.hzau.edu.cn>
Packaged: 2022-05-10 00:04:33 UTC; Administrator
Author: Dong Yin [aut], Xuanning Zhang [aut], Lilin Yin [aut], Haohao Zhang [aut], Zhenshuang Tang [ctb], Jingya Xu [ctb], Xiaohui Yuan [ctb], Xinyun Li [ctb], Shuhong Zhao [ctb], Xiaolei Liu [cre, aut, cph]
Repository: CRAN
Date/Publication: 2022-05-12 07:10:02 UTC

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New package nlmixr2est with initial version 2.0.6
Package: nlmixr2est
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Depends: R (>= 4.0), nlmixr2data
Imports: Rcpp (>= 0.12.3), lbfgsb3c, dparser, methods, rex, minqa, Matrix, n1qn1 (>= 6.0.1-10), rxode2(>= 1.0.0), nlme, magrittr, backports, symengine
Suggests: Rvmmin, broom.mixed, crayon, knitr, data.table, devtools, digest, dplyr, lotri, nloptr, pkgdown, rmarkdown, testthat, ucminf, generics, tibble, checkmate, cli, qs, covr, vpc, withr, xgxr
Version: 2.0.6
Description: Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
License: GPL (>= 3)
NeedsCompilation: yes
LinkingTo: dparser(>= 0.1.8), rxode2(>= 1.0.0), RcppEigen (>= 0.3.3.3.0), lbfgsb3c, Rcpp, BH, StanHeaders(>= 2.18.0), RcppArmadillo (>= 0.5.600.2.0)
URL: https://github.com/nlmixr2/nlmixr2est
Biarch: true
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Encoding: UTF-8
Language: en-US
Packaged: 2022-05-10 14:19:53 UTC; matt
Author: Matthew Fidler [aut, cre] , Yuan Xiong [aut], Rik Schoemaker [aut] , Justin Wilkins [aut] , Wenping Wang [aut], Robert Leary [ctb], Mason McComb [ctb] , Vipul Mann [aut], Mirjam Trame [ctb], Mahmoud Abdelwahab [ctb], Teun Post [ctb], Richard Hooijmai [...truncated...]
Repository: CRAN
Date/Publication: 2022-05-12 07:50:02 UTC

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New package IPEDSuploadables with initial version 2.4.5
Package: IPEDSuploadables
Title: Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload
Version: 2.4.5
Description: Starting from user-supplied institutional data, these scripts transform, aggregate, and reshape the information to produce key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes. Final files are saved locally to a location of the user's choice. User-friendly readable files can also be produced for purposes of data review and validation.
Note: Because IPEDS requirements may change from year to year, having the most recent version of this package is highly recommended. Old versions can be found as GitHub branches. The package can also be used to convert any correctly-prepared data into a key-value pair format for any survey (IPEDS or non-IPEDS).
URL: https://github.com/AlisonLanski/IPEDSuploadables, https://alisonlanski.github.io/IPEDSuploadables/
BugReports: https://github.com/AlisonLanski/IPEDSuploadables/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, lubridate, magrittr, purrr, rlang, stringr, svDialogs, tidyr (>= 1.0.0), utils
Suggests: knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
VignetteBuilder: knitr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-10 19:42:23 UTC; alanski
Author: Alison Lanski [aut, cre], Shiloh Fling [aut]
Maintainer: Alison Lanski <alanski@nd.edu>
Repository: CRAN
Date/Publication: 2022-05-12 08:00:02 UTC

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New package gRim with initial version 0.2.9
Package: gRim
Version: 0.2.9
Title: Graphical Interaction Models
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Description: Provides the following types of models: Models for contingency tables (i.e. log-linear models) Graphical Gaussian models for multivariate normal data (i.e. covariance selection models) Mixed interaction models. Documentation about 'gRim' is provided by vignettes included in this package and the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>); see 'citation("gRim")' for details.
License: GPL (>= 2)
URL: https://people.math.aau.dk/~sorenh/software/gR/
Encoding: UTF-8
Depends: R (>= 3.6.0), methods, gRbase (>= 1.8.6)
Suggests: testthat (>= 2.1.0)
Imports: graph, Rgraphviz, igraph, stats4, gRain (>= 1.3.10), magrittr, Rcpp (>= 0.11.1)
ByteCompile: yes
LinkingTo: Rcpp (>= 0.11.1), RcppArmadillo, RcppEigen, gRbase (>= 1.8.6)
NeedsCompilation: yes
Packaged: 2022-05-12 03:37:25 UTC; sorenh
Repository: CRAN
Date/Publication: 2022-05-12 07:10:07 UTC

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New package FRESHD with initial version 1.0
Package: FRESHD
Title: Fast Robust Estimation of Signals in Heterogeneous Data
Version: 1.0
Date: 2022-05-09
Maintainer: Adam Lund <adam.lund@math.ku.dk>
Description: Procedure for solving the maximin problem for identical design across heterogeneous data groups. Particularly efficient when the design matrix is either orthogonal or has tensor structure. Orthogonal wavelets can be specified for 1d, 2d or 3d data simply by name. For tensor structured design the tensor components (two or three) may be supplied. The package also provides an efficient implementation of the generic magging estimator.
Imports: Rcpp (>= 0.12.12), glamlasso
License: GPL
LinkingTo: Rcpp, RcppArmadillo, RcppEigen
NeedsCompilation: yes
Packaged: 2022-05-10 18:35:57 UTC; adam
Author: Adam Lund [aut, cre, ctb, cph], Benjamin Stephens [ctb, cph], Gael Guennebaud [ctb, cph], Angelo Furfaro [ctb, cph], Luca Di Gaspero [ctb, cph], Brandon Whitcher [ctb, cph]
Repository: CRAN
Date/Publication: 2022-05-12 08:00:06 UTC

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New package causalDisco with initial version 0.9.1
Package: causalDisco
Title: Tools for Causal Discovery on Observational Data
Version: 0.9.1
Description: Various tools for inferring causal models from observational data. The package includes an implementation of the temporal Peter-Clark (TPC) algorithm. Petersen, Osler and Ekstrøm (2021) <doi:10.1093/aje/kwab087>. It also includes general tools for evaluating differences in adjacency matrices, which can be used for evaluating performance of causal discovery procedures.
Depends: R (>= 3.5.0)
License: GPL-2
Encoding: UTF-8
LazyData: true
URL: https://github.com/annennenne/causalDisco
BugReports: https://github.com/annennenne/causalDisco/issues
Imports: pcalg, igraph, RColorBrewer, gtools, clipr, methods, scales
NeedsCompilation: no
Packaged: 2022-05-10 16:40:10 UTC; root
Author: Anne Helby Petersen [aut, cre]
Maintainer: Anne Helby Petersen <ahpe@sund.ku.dk>
Repository: CRAN
Date/Publication: 2022-05-12 07:50:06 UTC

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New package APML with initial version 0.0.5
Package: APML
Title: An Approach for Machine-Learning Modelling
Version: 0.0.5
Description: We include 1) data cleaning including variable scaling, missing values and unbalanced variables identification and removing, and strategies for variable balance improving; 2) modeling based on random forest and gradient boosted model including feature selection, model training, cross-validation and external testing. For more information, please see Deng X (2021). <doi:10.1016/j.scitotenv.2020.144746>; H2O.ai (Oct. 2016). R Interface for H2O, R package version 3.10.0.8. <https://github.com/h2oai/h2o-3>; Zhang W (2016). <doi:10.1016/j.scitotenv.2016.02.023>.
License: GPL-3
Encoding: UTF-8
Imports: survival,h2o,performanceEstimation,fastDummies,dplyr,ggplot2,pROC
NeedsCompilation: no
Author: Xinlei Deng [aut, cre, cph], Wangjian Zhang [aut], Tianyue Mi [aut], Shao Lin [aut]
Maintainer: Xinlei Deng <xinlei.deng.apha@gmail.com>
Repository: CRAN
Packaged: 2022-05-12 04:10:18 UTC; Xinlei Deng
Date/Publication: 2022-05-12 07:10:11 UTC

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New package PMA2 with initial version 2.1
Package: PMA2
Title: Penalized Multivariate Analysis
Version: 2.1
Date: 2022-05-04
URL: https://github.com/Ali-Mahzarnia/PMA2
BugReports: https://github.com/Ali-Mahzarnia/PMA2
Author: Ali Mahzarnia
Maintainer: Ali Mhazarnia <ali.mahzarnia@duke.edu>
Description: A modified version of PMA. The CCA() and CCA.permute() functions can also compute the component-wise standard deviations of estimated U and V through permutations in addition to standardize them. Furthermore, it computes the non-parametric p-values for each components. Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in Ali Mahzarnia, Alexander Badea (2022), "Joint Estimation of Vulnerable Brain Networks and Alzheimer’s Disease Risk Via Novel Extension of Sparse Canonical Correlation" at bioRxiv.
Depends: R (>= 2.10)
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-05-09 13:26:36 UTC; ali
Repository: CRAN
Date/Publication: 2022-05-12 07:00:05 UTC

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New package GLDEX with initial version 2.0.0.8
Package: GLDEX
Version: 2.0.0.8
Date: 2022-04-28
Title: Fitting Single and Mixture of Generalised Lambda Distributions
Maintainer: Steve Su <allegro.su@gmail.com>
Depends: cluster, grDevices, graphics, stats, spacefillr
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution. References include the following: Karvanen and Nuutinen (2008) "Characterizing the generalized lambda distribution by L-moments" <doi:10.1016/j.csda.2007.06.021>, King and MacGillivray (1999) "A starship method for fitting the generalised lambda distributions" <doi:10.1111/1467-842X.00089>, Su (2005) "A Discretized Approach to Flexibly Fit Generalized Lambda Distributions to Data" <doi:10.22237/jmasm/1130803560>, Su (2007) "Nmerical Maximum Log Likelihood Estimation for Generalized Lambda Distributions" <doi:10.1016/j.csda.2006.06.008>, Su (2007) "Fitting Single and Mixture of Generalized Lambda Distributions to Data via Discretized and Maximum Likelihood Methods: GLDEX in R" <doi:10.18637/jss.v021.i09>, Su (2009) "Confidence Intervals for Quantiles Using Generalized Lambda Distributions" <doi:10.1016/j.csda.2009.02.014>, Su (2010) "Chapter 14: Fitting GLDs and Mixture of GLDs to Data using Quantile Matching Method" <doi:10.1201/b10159-3>, Su (2010) "Chapter 15: Fitting GLD to data using GLDEX 1.0.4 in R" <doi:10.1201/b10159-3>, Su (2015) "Flexible Parametric Quantile Regression Model" <doi:10.1007/s11222-014-9457-1>, Su (2021) "Flexible parametric accelerated failure time model"<doi:10.1080/10543406.2021.1934854>.
License: GPL (>= 3)
NeedsCompilation: yes
Packaged: 2022-05-09 12:47:23 UTC; Allegro
Author: Steve Su [aut, cre, cph] , Martin Maechler [aut], Juha Karvanen [aut], Robert King [aut], Benjamin Dean [ctb], R Core Team [aut]
Repository: CRAN
Date/Publication: 2022-05-12 07:00:08 UTC

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Wed, 11 May 2022

New package stdmod with initial version 0.1.7.1
Package: stdmod
Title: Standardized Moderation Effect and Its Confidence Interval
Version: 0.1.7.1
Description: Functions for computing a standardized moderation effect in moderated regression and forming its confidence interval by nonparametric bootstrapping as proposed in Cheung, Cheung, Lau, Hui, and Vong (2002) <doi:10.1037/hea0001188>. Also includes simple-to-use functions for computing conditional effects (unstandardized or standardized) and plotting moderation effects.
URL: https://sfcheung.github.io/stdmod/
BugReports: https://github.com/sfcheung/stdmod/issues
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: testthat, dplyr, knitr, rmarkdown, lavaan, visreg, lm.beta
Depends: R (>= 4.0.0)
Imports: boot, ggplot2, stats
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-10 15:11:13 UTC; sfcheung
Author: Shu Fai Cheung [aut, cre] , David Weng Ngai Vong [ctb]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-11 14:40:02 UTC

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New package MixGHD with initial version 2.3.7
Package: MixGHD
Title: Model Based Clustering, Classification and Discriminant Analysis Using the Mixture of Generalized Hyperbolic Distributions
Version: 2.3.7
Date: 2022-05-10
Maintainer: Cristina Tortora <grikris1@gmail.com>
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Donald D. Amos [ctb].
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015) <doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016) <doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD' is the mixture of multiple scaled generalized hyperbolic distributions, the 'cMSGHD' is a 'MSGHD' with convex contour plots and the 'MCGHD', mixture of coalesced generalized hyperbolic distributions is a new more flexible model (Tortora et al. (2019)<doi:10.1007/s00357-019-09319-3>. The paper related to the software can be found at <doi:10.18637/jss.v098.i03>.
Imports: Bessel,stats, mvtnorm, ghyp, numDeriv, mixture, e1071,cluster, methods
Depends: MASS, R (>= 3.1.3)
NeedsCompilation: no
License: GPL (>= 2)
Packaged: 2022-05-10 17:56:15 UTC; 011543324
Repository: CRAN
Date/Publication: 2022-05-11 11:50:07 UTC

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New package maskRangeR with initial version 1.1
Package: maskRangeR
Title: Mask Species Geographic Ranges
Version: 1.1
Description: Mask ranges based on expert knowledge or remote sensing layers. These tools can be combined to quantitatively and reproducibly generate a new map or to update an existing map. Methods include expert opinion and data-driven tools to generate thresholds for binary masks.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.4.0)
Imports: dplyr, e1071, lubridate, magrittr, raster, sp, stats, utils,
Suggests: dismo, testthat, knitr, rmarkdown, wallace
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-05-10 16:23:32 UTC; ctg
Author: Cory Merow [aut, cre], Peter J. Galante [aut], Jamie M. Kass [aut], Cecina Babich Morrow [aut], Valentina Grisales Betancur [aut]
Maintainer: Cory Merow <cory.merow@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-11 11:50:02 UTC

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New package rnetcarto with initial version 0.2.5
Package: rnetcarto
Title: Fast Network Modularity and Roles Computation by Simulated Annealing (Rgraph C Library Wrapper for R)
Version: 0.2.5
Description: Provides functions to compute the modularity and modularity-related roles in networks. It is a wrapper around the rgraph library (Guimera & Amaral, 2005, <doi:10.1038/nature03288>).
License: GPL (>= 2)
Encoding: UTF-8
LazyLoad: no
SystemRequirements: GNU GSL
NeedsCompilation: yes
Suggests: testthat, knitr, rmarkdown, igraph
VignetteBuilder: knitr
Packaged: 2022-05-11 02:22:49 UTC; stouffer
Author: Daniel B. Stouffer [cre, aut, ths] , Guilhem Doulcier [aut] , Roger Guimera [ctb]
Maintainer: Daniel B. Stouffer <daniel.stouffer@canterbury.ac.nz>
Repository: CRAN
Date/Publication: 2022-05-11 09:30:02 UTC

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New package LS2Wstat with initial version 2.1-4
Package: LS2Wstat
Title: A Multiscale Test of Spatial Stationarity for LS2W Processes
Version: 2.1-4
Date: 2022-05-09
Depends: LS2W(>= 1.3-1)
Imports: matrixStats, spdep
Description: Wavelet-based methods for testing stationarity and quadtree segmenting of images, see Taylor et al (2014) <doi:10.1080/00401706.2013.823890>.
License: GPL-2
Author: Sarah Taylor [aut], Matt Nunes [aut, cre], Idris Eckley [ctb, ths]
Maintainer: Matt Nunes <nunesrpackages@gmail.com>
LazyLoad: yes
Packaged: 2022-05-09 18:29:59 UTC; man54
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-05-11 09:40:08 UTC

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New package gamboostLSS with initial version 2.0-6
Package: gamboostLSS
Title: Boosting Methods for 'GAMLSS'
Version: 2.0-6
Date: 2022-05-05
Description: Boosting models for fitting generalized additive models for location, shape and scale ('GAMLSS') to potentially high dimensional data.
Depends: R (>= 2.10.0), mboost (>= 2.8-0), stabs (>= 0.5-0), parallel
Imports: graphics, grDevices, stats, utils
Suggests: gamlss, gamlss.dist, survival, BayesX, R2BayesX
LazyLoad: yes
LazyData: yes
License: GPL-2
URL: For source code, development versions and issue tracker see https://github.com/boost-R/gamboostLSS
NeedsCompilation: no
Packaged: 2022-05-05 14:59:30 UTC; Benjamin (PEI)
Author: Benjamin Hofner [aut, cre] , Andreas Mayr [aut], Nora Fenske [aut], Janek Thomas [aut], Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Repository: CRAN
Date/Publication: 2022-05-11 09:30:05 UTC

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New package camtrapR with initial version 2.2.0
Package: camtrapR
Title: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses
Version: 2.2.0
Date: 2022-05-05
Depends: R (>= 3.1.0)
Imports: methods, generics, sf, sp, overlap, secr, data.table, lubridate, ggplot2
Suggests: knitr, raster, rgdal, ritis, rmarkdown, taxize, testthat, tibble, unmarked, zip, RSQLite, lattice, magick, tesseract, snow, nimble, nimbleEcology, coda, rjags, snowfall, reshape2, R.rsp
VignetteBuilder: R.rsp
SystemRequirements: ExifTool (https://exiftool.org/)
Description: Management of and data extraction from camera trap data in wildlife studies. The package provides a workflow for storing and sorting camera trap photos (and videos), tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it can visualise species activity data and provides simple mapping functions with GIS export.
URL: https://github.com/jniedballa/camtrapR, https://jniedballa.github.io/camtrapR/, https://groups.google.com/forum/#!forum/camtrapr
BugReports: https://groups.google.com/forum/#!forum/camtrapr
Encoding: UTF-8
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2022-05-10 10:27:04 UTC; niedballa
Author: Juergen Niedballa [aut, cre] , Alexandre Courtiol [aut] , Rahel Sollmann [aut] , John Mathai [ctb], Seth Timothy Wong [ctb], An The Truong Nguyen [ctb] , Azlan bin Mohamed [ctb] , Andrew Tilker [ctb] , Roshan Guharajan [ctb] , Ioannis Alexiou [ctb] , [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-11 09:20:02 UTC

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New package fitHeavyTail with initial version 0.1.4
Package: fitHeavyTail
Title: Mean and Covariance Matrix Estimation under Heavy Tails
Version: 0.1.4
Date: 2022-5-11
Description: Robust estimation methods for the mean vector, scatter matrix, and covariance matrix (if it exists) from data (possibly containing NAs) under multivariate heavy-tailed distributions such as angular Gaussian (via Tyler's method), Cauchy, and Student's t distributions. Additionally, a factor model structure can be specified for the covariance matrix. The latest revision also includes the multivariate skewed t distribution. The package is based on the papers: Sun, Babu, and Palomar (2014), Sun, Babu, and Palomar (2015), Liu and Rubin (1995), and Zhou, Liu, Kumar, and Palomar (2019).
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
URL: https://CRAN.R-project.org/package=fitHeavyTail, https://github.com/dppalomar/fitHeavyTail, https://www.danielppalomar.com, https://doi.org/10.1109/TSP.2014.2348944, https://doi.org/10.1109/TSP.2015.2417513
BugReports: https://github.com/dppalomar/fitHeavyTail/issues
License: GPL-3
Encoding: UTF-8
Depends:
Imports: ICSNP, mvtnorm, ghyp, numDeriv, stats
Suggests: knitr, ggplot2, prettydoc, reshape2, rmarkdown, R.rsp, testthat
VignetteBuilder: knitr, rmarkdown, R.rsp
NeedsCompilation: no
Packaged: 2022-05-11 00:19:43 UTC; palomar
Author: Daniel P. Palomar [cre, aut], Rui Zhou [aut], Xiwen Wang [aut]
Repository: CRAN
Date/Publication: 2022-05-11 08:40:02 UTC

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New package soiltestcorr with initial version 2.1.1
Package: soiltestcorr
Title: Soil Test Correlation and Calibration
Version: 2.1.1
Date: 2022-05-10
Description: A compilation of functions designed to assist users on the correlation analysis of crop yield and soil test values. Functions to estimate response patterns to nutrient availability and critical soil test values using alternative approaches such as: 1) the modified arcsine-log calibration curve (Correndo et al. (2017) <doi:10.1071/CP16444>); 2) the graphical Cate-Nelson quadrants-analysis (Cate & Nelson (1965)), 3) the statistical Cate-Nelson quadrants-analysis (Cate & Nelson (1971) <doi:10.2136/sssaj1971.03615995003500040048x>), 4) the linear-plateau regression (Anderson & Nelson (1975) <doi:10.2307/2529422>), 5) the quadratic-plateau regression (Bullock & Bullock (1994) <doi:10.2134/agronj1994.00021962008600010033x>), and 6) the Mitscherlich regression (Melsted & Peck (1977) <doi:10.2134/asaspecpub29.c1>).
License: MIT + file LICENSE
Encoding: UTF-8
Suggests: smatr, covr, knitr, rmarkdown, testthat
Imports: stats, dplyr, rlang, tidyr, utils, purrr, data.table, ggplot2, ggpp, nlstools, minpack.lm, modelr, AICcmodavg
Depends: R (>= 2.10)
LazyData: true
VignetteBuilder: knitr
URL: https://adriancorrendo.github.io/soiltestcorr/
BugReports: https://github.com/adriancorrendo/soiltestcorr/issues
NeedsCompilation: no
Packaged: 2022-05-10 06:54:02 UTC; correndo
Author: Adrian A. Correndo [cre, cph] , Adrian A. Correndo [aut] , Austin Pearce [aut] , Ignacio A. Ciampitti [aut]
Maintainer: Adrian A. Correndo <correndo@ksu.edu>
Repository: CRAN
Date/Publication: 2022-05-11 05:50:02 UTC

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New package mnorm with initial version 1.0.0
Package: mnorm
Title: Multivariate Normal Distribution
Version: 1.0.0
Date: 2022-05-08
Description: Calculates and differentiates probabilities and density of (conditional) multivariate normal distribution using methods described in A. Genz (2004) <doi:10.1023/B:STCO.0000035304.20635.31>, A. Genz, F. Bretz (2009) <doi:10.1007/978-3-642-01689-9> and E. Kossova, B. Potanin (2018) <https:ideas.repec.org/a/ris/apltrx/0346.html>.
License: GPL (>= 2)
Imports: Rcpp (>= 1.0.6)
LinkingTo: Rcpp, RcppArmadillo
NeedsCompilation: yes
Packaged: 2022-05-09 21:55:50 UTC; bogda
Author: Bogdan Potanin [aut, cre, ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-11 05:40:02 UTC

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New package ccpsyc with initial version 0.2.6
Package: ccpsyc
Title: Methods for Cross-Cultural Psychology
Version: 0.2.6
Description: With the development of new cross-cultural methods this package is intended to combine multiple functions automating and simplifying functions providing a unified analysis approach for commonly employed methods.
License: GPL-3
Depends: R (>= 4.0.0)
Imports: magrittr, dplyr, lavaan, readr, MCMCpack, psych, ufs, xlsx, tibble, rlang, RcppAlgos, tidyr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-10 03:45:45 UTC; karljo
Author: Johannes Karl [aut, cre]
Maintainer: Johannes Karl <johannes.a.karl@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-11 05:50:06 UTC

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Tue, 10 May 2022

New package pwlmm with initial version 1.1.0
Package: pwlmm
Title: PWIGLS for Two-Level Multivariate and Multilevel Linear Models
Version: 1.1.0
Maintainer: Alinne Veiga <alinne.veiga@ibge.gov.br>
Description: Estimates two-level multilevel linear model and two-level multivariate linear multilevel model with weights following Probability Weighted Iterative Generalised Least Squares approach. For details see Veiga et al.(2014) <doi:10.1111/rssc.12020>.
License: GPL (>= 2)
Depends: R (>= 3.5.0)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppEigen
Imports: lme4, Matrix, Rcpp, RcppEigen
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-10 21:47:15 UTC; alinn
Author: Alinne Veiga [aut, cre] , Joao Messa [aut, trl, com]
Repository: CRAN
Date/Publication: 2022-05-10 22:20:02 UTC

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New package ZINARp with initial version 0.1.0
Package: ZINARp
Title: Simulate INAR/ZINAR(p) Models and Estimate Its Parameters
Version: 0.1.0
Maintainer: Tharso Augustus Rossiter Araujo Monteiro <tharso.augustus@ufpe.br>
Description: Simulation, exploratory data analysis and Bayesian analysis of the p-order Integer-valued Autoregressive (INAR(p)) and Zero-inflated p-order Integer-valued Autoregressive (ZINAR(p)) processes, as described in Garay et al. (2020) <doi:10.1080/00949655.2020.1754819>.
License: GPL (>= 3.0)
Encoding: UTF-8
LazyData: true
Imports: progress, stats, utils, graphics
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-06 14:57:02 UTC; tharso
Author: Aldo William Medina Garay [aut], Francyelle de Lima Medina [aut], Tharso Augustus Rossiter Araujo Monteiro [aut, cre]
Repository: CRAN
Date/Publication: 2022-05-09 11:30:02 UTC

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New package VARDetect with initial version 0.1.6
Package: VARDetect
Title: Multiple Change Point Detection in Structural VAR Models
Version: 0.1.6
Author: Yue Bai [aut, cre], Peiliang Bai [aut], Abolfazl Safikhani [aut], George Michailidis [aut]
Maintainer: Yue Bai <baiyue@ufl.edu>
Description: Implementations of Thresholded Block Segmentation Scheme (TBSS) and Low-rank plus Sparse Two Step Procedure (LSTSP) algorithms for detecting multiple changes in structural VAR models. The package aims to address the problem of change point detection in piece-wise stationary VAR models, under different settings regarding the structure of their transition matrices (autoregressive dynamics); specifically, the following cases are included: (i) (weakly) sparse, (ii) structured sparse, and (iii) low rank plus sparse. It includes multiple algorithms and related extensions from Safikhani and Shojaie (2020) <doi:10.1080/01621459.2020.1770097> and Bai, Safikhani and Michailidis (2020) <doi:10.1109/TSP.2020.2993145>.
License: GPL-2
LazyData: true
Depends: R (>= 3.5.0)
Imports: stats, MTS, igraph, pracma, graphics, mvtnorm, sparsevar, lattice, Rcpp (>= 1.0.7)
Encoding: UTF-8
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown
NeedsCompilation: yes
Packaged: 2022-05-09 16:46:10 UTC; yuebai
Repository: CRAN
Date/Publication: 2022-05-10 08:00:06 UTC

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New package usincometaxes with initial version 0.2.0
Package: usincometaxes
Title: Calculate Federal and State Income Taxes in the United States
Version: 0.2.0
Description: Calculates federal and state income taxes in the United States. It acts as a wrapper to the NBER's TAXSIM 35 (<http://taxsim.nber.org/taxsim35/>) tax simulator. TAXSIM 35 conducts the calculations, while `usincometaxes` prepares the data for TAXSIM 35, sends the data to TAXSIM 35's server, retrieves the data, and places it into a data frame. All without the user worrying about this process.
License: MIT + file LICENSE
URL: https://github.com/shanejorr/usincometaxes, https://shaneorr.io/r/usincometaxes
BugReports: https://github.com/shanejorr/usincometaxes/issues
Depends: R (>= 3.1)
Imports: datasets, vroom
Suggests: dplyr, ggplot2, knitr, rmarkdown, scales, testthat (>= 3.0.0), tidyr, tools
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2022-05-08 03:27:18 UTC; shane
Author: Shane Orr [aut, cre, cph]
Maintainer: Shane Orr <shane.j.orr@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 09:20:02 UTC

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New package thriftr with initial version 1.1.7
Package: thriftr
Title: Apache Thrift Client Server
Version: 1.1.7
Date: 2022-05-08
Author: Marek Jagielski [aut, cre, cph], Lixin Yu [aut, cph]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Description: Pure R implementation of Apache Thrift. This library doesn't require any code generation. To learn more about Thrift go to <https://thrift.apache.org>.
License: MIT + file LICENSE
URL: https://github.com/systemincloud/thriftr
BugReports: https://github.com/systemincloud/thriftr/issues
Suggests: testthat
Encoding: UTF-8
Imports: R6, rly (>= 1.7.4), stringi
NeedsCompilation: no
Packaged: 2022-05-08 13:49:04 UTC; lupus
Repository: CRAN
Date/Publication: 2022-05-10 10:00:02 UTC

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New package squashinformr with initial version 0.2.6
Package: squashinformr
Title: Politely Web Scrape Data from SquashInfo
Version: 0.2.6
Author: Hayden MacDonald [aut, cre]
Maintainer: Hayden MacDonald <hayden.macdonald.8778@gmail.com>
Description: Scrape SquashInfo <http://www.squashinfo.com/> for data on the Professional Squash Association World Tour and other squash events. 'squashinformr' functions scrape, parse, and clean data associated with players, tournaments, and rankings.
Depends: R (>= 4.0)
Imports: dplyr (>= 1.0.2), plyr (>= 1.8.6), tibble (>= 3.0.4), lubridate (>= 1.7.4), stringr (>= 1.4.0), tidyr (>= 1.1.2), rvest (>= 0.3.6), polite (>= 0.1.1), naniar (>= 0.5.0), janitor (>= 2.1.0), Hmisc (>= 4.4.2), rlang (>= 0.4.10)
Suggests: testthat, covr, knitr, rmarkdown
License: GPL-3
Encoding: UTF-8
URL: https://github.com/HaydenMacDonald/squashinformr
BugReports: https://github.com/HaydenMacDonald/squashinformr/issues
NeedsCompilation: no
Packaged: 2022-05-09 19:37:40 UTC; Hayden
Repository: CRAN
Date/Publication: 2022-05-10 16:30:02 UTC

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New package robmixglm with initial version 1.2-3
Package: robmixglm
Title: Robust Generalized Linear Models (GLM) using Mixtures
Version: 1.2-3
Date: 2022-05-08
Maintainer: Ken Beath <ken@kjbeath.com.au>
Contact: Ken Beath <ken@kjbeath.com.au>
Author: Ken Beath [aut, cre]
Description: Robust generalized linear models (GLM) using a mixture method, as described in Beath (2018) <doi:10.1080/02664763.2017.1414164>. This assumes that the data are a mixture of standard observations, being a generalised linear model, and outlier observations from an overdispersed generalized linear model. The overdispersed linear model is obtained by including a normally distributed random effect in the linear predictor of the generalized linear model.
Depends: R(>= 3.2.0)
Suggests: R.rsp, robustbase, lattice, forward
VignetteBuilder: R.rsp
Imports: fastGHQuad, stats, bbmle, VGAM, actuar, Rcpp (>= 0.12.15), methods, boot, numDeriv, parallel, doParallel, foreach, doRNG, MASS
LazyLoad: yes
LazyData: yes
NeedsCompilation: yes
License: GPL (>= 2)
LinkingTo: Rcpp
Packaged: 2022-05-09 05:49:03 UTC; kjbeath1
Repository: CRAN
Date/Publication: 2022-05-09 09:00:02 UTC

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New package RMM with initial version 0.1.0
Package: RMM
Title: Revenue Management Modeling
Version: 0.1.0
Date: 2022-04-29
Maintainer: Chul Kim <statkim7578@yonsei.ac.kr>
Description: The RMM fits Revenue Management Models using the RDE(Robust Demand Estimation) method introduced in the paper by <doi:10.2139/ssrn.3598259>, one of the customer choice-based Revenue Management Model. Furthermore, it is possible to select a multinomial model as well as a conditional logit model as a model of RDE.
License: GPL (>= 2.0)
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.1.0)
Imports: tibble, magrittr, rlang, dplyr, numDeriv, Rcpp
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-05-06 12:03:59 UTC; chulkim
Author: Chul Kim [aut, cre], Sanghoon Cho [aut], Jongho Im [aut]
Repository: CRAN
Date/Publication: 2022-05-09 11:30:05 UTC

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New package quantdr with initial version 1.2.2
Package: quantdr
Title: Dimension Reduction Techniques for Conditional Quantiles
Version: 1.2.2
Description: An implementation of dimension reduction techniques for conditional quantiles. Nonparametric estimation of conditional quantiles is also available.
License: GPL-2 | GPL-3
Encoding: UTF-8
Imports: dr, KernSmooth, mvtnorm, quantreg
Depends: R (>= 3.2.0)
Suggests: ggplot2, knitr, rmarkdown, testthat, pracma, MASS, PerformanceAnalytics, png
VignetteBuilder: knitr
SystemRequirements: GNU make
URL: https://github.com/elianachristou/quantdr
BugReports: https://github.com/elianachristou/quantdr/issues
NeedsCompilation: no
Packaged: 2022-05-06 21:30:33 UTC; echris15
Author: Eliana Christou [aut, cre]
Maintainer: Eliana Christou <echris15@uncc.edu>
Repository: CRAN
Date/Publication: 2022-05-09 09:10:02 UTC

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New package PopulationGrowthR with initial version 0.1.1
Package: PopulationGrowthR
Title: Linear Population Growth Scenarios
Version: 0.1.1
Maintainer: Biman Chakraborty <biman_c@yahoo.com>
Description: Fit linear splines to species time series to detect population growth scenarios based on Hyndman, R J and Mesgaran, M B and Cousens, R D (2015) <doi:10.1007/s10530-015-0962-8>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: dplyr
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-09 12:04:35 UTC; chakrabb
Author: Philipp Robeck [aut], Biman Chakraborty [cre]
Repository: CRAN
Date/Publication: 2022-05-10 10:40:06 UTC

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New package phers with initial version 0.0.2
Package: phers
Title: Calculate Phenotype Risk Scores
Version: 0.0.2
Description: Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and rare genetic variants. See Bastarache et al. 2018 <doi:10.1126/science.aal4043>.
URL: https://phers.hugheylab.org, https://github.com/hugheylab/phers
License: GPL-2
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5)
Imports: checkmate (>= 2.0.0), data.table (>= 1.5.0), foreach (>= 1.5.2), stats (>= 4.0.2), MASS (>= 7.3-55), iterators (>= 1.0.14), BEDMatrix (>= 2.0.3)
Suggests: doParallel (>= 1.0.17), knitr, rmarkdown, testthat (>= 3.1.0), ggplot2 (>= 3.3.5), qs (>= 0.25.2)
NeedsCompilation: no
Packaged: 2022-05-06 17:23:36 UTC; joshuaschoenbachler
Author: Jake Hughey [aut, cre], Layla Aref [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 09:10:06 UTC

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New package onlineforecast with initial version 1.0.1
Package: onlineforecast
Title: Forecast Modelling for Online Applications
Version: 1.0.1
Description: A framework for fitting adaptive forecasting models. Provides a way to use forecasts as input to models, e.g. weather forecasts for energy related forecasting. The models can be fitted recursively and can easily be setup for updating parameters when new data arrives. See the included vignettes, the website <https://onlineforecasting.org> and the pre-print paper "onlineforecast: An R package for adaptive and recursive forecasting" <arXiv:2109.12915>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0.0)
Imports: Rcpp (>= 0.12.18), R6 (>= 2.2.2), splines (>= 3.1.1), pbs, digest
LinkingTo: Rcpp, RcppArmadillo
Suggests: knitr, rmarkdown, R.rsp, testthat (>= 3.0.0), data.table, plotly
VignetteBuilder: knitr
URL: https://onlineforecasting.org
BugReports: https://lab.compute.dtu.dk/packages/onlineforecast/-/issues
NeedsCompilation: yes
Packaged: 2022-05-09 13:35:01 UTC; pbac
Author: Peder Bacher [cre], Hjorleifur G Bergsteinsson [aut]
Maintainer: Peder Bacher <pbac@dtu.dk>
Repository: CRAN
Date/Publication: 2022-05-10 09:30:05 UTC

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New package nbc4va with initial version 1.2
Package: nbc4va
Title: Bayes Classifier for Verbal Autopsy Data
Version: 1.2
Date: 2022-04-25
Maintainer: Richard Wen <rrwen.dev@gmail.com>
Description: An implementation of the Naive Bayes Classifier (NBC) algorithm used for Verbal Autopsy (VA) built on code from Miasnikof et al (2015) <DOI:10.1186/s12916-015-0521-2>.
Depends: R (>= 4.0.0)
Imports: graphics, methods, utils, shiny
Suggests: bookdown, knitr, rmarkdown, testthat
Enhances: openVA
License: GPL-3
LazyData: TRUE
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-09 12:05:12 UTC; rrwen
Author: Richard Wen [aut, cre], Pierre Miasnikof [ctb], Vasily Giannakeas [ctb], Mireille Gomes [ctb]
Repository: CRAN
Date/Publication: 2022-05-10 10:40:02 UTC

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New package list with initial version 9.2.1
Package: list
Version: 9.2.1
Title: Statistical Methods for the Item Count Technique and List Experiment
Depends: R (>= 3.2.0), utils, sandwich (>= 2.3-3)
Imports: VGAM (>= 0.9-8), magic (>= 1.5-6), gamlss.dist (>= 4.3-4), MASS (>= 7.3-40), quadprog (>= 1.5-5), corpcor (>= 1.6.7), mvtnorm (>= 1.0-2), coda (>= 0.17-1), stats, arm
Suggests: testthat (>= 0.9.1), knitr (>= 1.10.5)
VignetteBuilder: knitr
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011) <doi:10.1198/jasa.2011.ap10415>, Blair and Imai (2012) <doi:10.1093/pan/mpr048>, Blair, Imai, and Lyall (2013) <doi:10.1111/ajps.12086>, Imai, Park, and Greene (2014) <doi:10.1093/pan/mpu017>, Aronow, Coppock, Crawford, and Green (2015) <doi:10.1093/jssam/smu023>, Chou, Imai, and Rosenfeld (2017) <doi:10.1177/0049124117729711>, and Blair, Chou, and Imai (2018) <https://imai.fas.harvard.edu/research/files/listerror.pdf>. This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, a method for combining list experiments with direct questions, and methods for diagnosing and adjusting for response error. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
LazyLoad: yes
LazyData: yes
License: GPL (>= 2)
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-05-09 05:26:09 UTC; graeme
Author: Graeme Blair [aut, cre], Winston Chou [aut], Kosuke Imai [aut], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-09 09:10:05 UTC

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New package intccr with initial version 3.0.4
Package: intccr
Title: Semiparametric Competing Risks Regression under Interval Censoring
Version: 3.0.4
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jun.park@alumni.iu.edu>
Maintainer: Jun Park <jun.park@alumni.iu.edu>
Description: Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) /doi{10.1002/sim.7350} and the models with missing event types as described in Park, Bakoyannis, Zhang, & Yiannoutsos (2021) \doi{10.1093/biostatistics/kxaa052}. The proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Date: 2022-05-09
Imports: alabama, doParallel, foreach, MASS, parallel, splines2, stats, utils
Suggests: R.rsp
Depends: R (>= 3.5.0)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2022-05-09 18:05:22 UTC; Jun
Repository: CRAN
Date/Publication: 2022-05-10 08:00:02 UTC

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New package independenceWeights with initial version 0.0.1
Package: independenceWeights
Title: Estimates Weights for Confounding Control for Continuous-Valued Exposures
Version: 0.0.1
Description: Estimates weights to make a continuous-valued exposure statistically independent of a vector of pre-treatment covariates using the method proposed in Huling, Greifer, and Chen (2021) <arxiv:2107.07086>.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: osqp (>= 0.6.0.3)
Imports: locfit
Suggests: cobalt
NeedsCompilation: no
Packaged: 2022-05-09 18:31:38 UTC; huling
Author: Jared Huling [aut, cre] , Noah Greifer [aut]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 15:20:02 UTC

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New package graDiEnt with initial version 1.0.1
Package: graDiEnt
Title: Stochastic Quasi-Gradient Differential Evolution Optimization
Version: 1.0.1
Description: An optim-style implementation of the Stochastic Quasi-Gradient Differential Evolution (SQG-DE) optimization algorithm first published by Sala, Baldanzini, and Pierini (2018; <doi:10.1007/978-3-319-72926-8_27>). This optimization algorithm fuses the robustness of the population-based global optimization algorithm "Differential Evolution" with the efficiency of gradient-based optimization. The derivative-free algorithm uses population members to build stochastic gradient estimates, without any additional objective function evaluations. Sala, Baldanzini, and Pierini argue this algorithm is useful for 'difficult optimization problems under a tight function evaluation budget.' This package can run SQG-DE in parallel and sequentially.
License: MIT + file LICENSE
URL: https://github.com/bmgaldo/graDiEnt
BugReports: https://github.com/bmgaldo/graDiEnt
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: stats, doParallel
NeedsCompilation: no
Packaged: 2022-05-09 20:15:25 UTC; brendan
Author: Brendan Matthew Galdo [aut, cre]
Maintainer: Brendan Matthew Galdo <Brendan.m.galdo@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 16:40:02 UTC

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New package ghyp with initial version 1.6.2
Package: ghyp
Version: 1.6.2
Date: 2022-04-27
Title: Generalized Hyperbolic Distribution and Its Special Cases
Author: Marc Weibel, David Luethi, Wolfgang Breymann
Maintainer: Marc Weibel <marc.weibel@quantsulting.ch>
LazyData: no
Depends: R(>= 2.7), methods, numDeriv, graphics, stats, MASS
Description: Detailed functionality for working with the univariate and multivariate Generalized Hyperbolic distribution and its special cases (Hyperbolic (hyp), Normal Inverse Gaussian (NIG), Variance Gamma (VG), skewed Student-t and Gaussian distribution). Especially, it contains fitting procedures, an AIC-based model selection routine, and functions for the computation of density, quantile, probability, random variates, expected shortfall and some portfolio optimization and plotting routines as well as the likelihood ratio test. In addition, it contains the Generalized Inverse Gaussian distribution. See Chapter 3 of A. J. McNeil, R. Frey, and P. Embrechts. Quantitative risk management: Concepts, techniques and tools. Princeton University Press, Princeton (2005).
License: GPL (>= 2)
Encoding: latin1
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-05-09 09:54:08 UTC; marc
Date/Publication: 2022-05-09 10:10:02 UTC

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New package ggblanket with initial version 1.0.0
Package: ggblanket
Title: Wrappers to Make Beautiful 'ggplot2' Visualisation Simpler
Version: 1.0.0
Description: Wrapper functions around the amazing 'ggplot2' package with the objective to make beautiful 'ggplot2' visualisation simpler.
License: MIT + file LICENSE
URL: https://github.com/davidhodge931/ggblanket/, https://davidhodge931.github.io/ggblanket/
Encoding: UTF-8
Imports: dplyr, forcats, ggplot2, lubridate, magrittr, rlang, scales, snakecase, stringr, tidyr, tidyselect, viridis
Suggests: palmerpenguins, sf
NeedsCompilation: no
Packaged: 2022-05-09 20:14:05 UTC; david
Author: David Hodge [aut, cre]
Maintainer: David Hodge <davidhodge931@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 16:40:05 UTC

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New package FREG with initial version 1.1
Package: FREG
Title: Functional Regression Models
Version: 1.1
Description: Different regression models with functional features are implemented: for continuous response, categorical response and ordinal response. The model for ordinal response has been published in: 'Analyzing cycling sensors data through ordinal logistic regression with functional covariates, Jacques J. and Samardzic S., Journal of the Royal Statistical Society, Series C, 1-18, 2022'.
License: GPL-3
Encoding: UTF-8
LazyData: True
LazyDataCompression: xz
Suggests: knitr, rmarkdown
Imports: fda, graphics
Depends: R (>= 2.10)
NeedsCompilation: no
Packaged: 2022-05-07 15:20:28 UTC; julienjacques
Author: Sanja Samardzic [aut], Julien Jacques [cre, ctb]
Maintainer: Julien Jacques <julien.jacques@univ-lyon2.fr>
Repository: CRAN
Date/Publication: 2022-05-09 11:50:02 UTC

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New package fdacluster with initial version 0.1.1
Package: fdacluster
Title: Joint Clustering and Alignment of Functional Data
Version: 0.1.1
Description: Revisited clustering approaches to accommodate functional data by allowing to jointly align the data during the clustering process. Currently, shift, dilation and affine transformations only are available to perform alignment. The k-mean algorithm has been extended to integrate alignment and is fully parallelized. Hierarchical clustering will soon be available as well. References: Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment for curve clustering" <doi:10.1016/j.csda.2009.12.008>.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, nloptr
Suggests: testthat
Imports: Rcpp, magrittr, tibble, dplyr, tidyr, purrr, ggplot2, nloptr
Depends: R (>= 2.10)
URL: https://astamm.github.io/fdacluster/index.html, https://github.com/astamm/fdacluster
NeedsCompilation: yes
Packaged: 2022-05-04 16:13:01 UTC; stamm-a
Author: Laura Sangalli [aut], Piercesare Secchi [aut], Aymeric Stamm [cre, ctb] , Simone Vantini [aut], Valeria Vitelli [aut], Alessandro Zito [ctb]
Maintainer: Aymeric Stamm <aymeric.stamm@math.cnrs.fr>
Repository: CRAN
Date/Publication: 2022-05-09 12:10:11 UTC

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New package ExtremalDep with initial version 0.0.3-5
Package: ExtremalDep
Version: 0.0.3-5
Date: 2022-05-06
Title: Extremal Dependence Models
Author: Boris Beranger [aut] , Simone Padoan [cre, aut] , Giulia Marcon [aut], Steven G. Johnson [ctb]
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Imports: numDeriv, evd, sn, quadprog, copula, nloptr, gtools, mvtnorm, fda
Description: A set of procedures for modelling parametrically and non-parametrically the dependence structure of multivariate extreme-values is provided. The statistical inference is performed with non-parametric estimators, likelihood-based estimators and Bayesian techniques. Adapts the methodologies derived in Beranger et al. (2019) <arxiv:1904.08251>, Beranger et al. (2017) <doi:10.1111/sjos.12240>, Beranger and Padoan (2015) <arxiv:1508.05561>, Marcon et al. (2017) <doi:10.1002/sta4.145>, Marcon et al. (2017) <doi:10.1016/j.jspi.2016.10.004> and Marcon et al. (2016) <doi:10.1214/16-EJS1162>. It also refers to the works of Bortot (2010) <https://www.semanticscholar.org/paper/Tail-dependence-in-bivariate-skew-Normal-and-skew-t-Bortot/b0dc1cb608d35bf515c76e39aacc14b4de82e281?p2df>, Padoan (2011) <doi:10.1016/j.jmva.2011.01.014>, Cooley et al. (2010) <doi:10.1016/j.jmva.2010.04.007>, Husler and Reiss (1989) <doi:10.1016/0167-7152(89)90106-5>, Engelke et al. (2015) <doi:10.1111/rssb.12074>, Coles and Tawn (1991) <doi:10.1111/j.2517-6161.1991.tb01830.x>, Nikoloulopoulos et al. (2011) <doi:10.1007/s10687-008-0072-4>, Opitz (2013) <doi:10.1016/j.jmva.2013.08.008>, Tawn (1990) <doi:10.2307/2336802>, Azzalini and Capitanio (2014) <doi:10.1017/CBO9781139248891>, Azzalini (2003) <doi:10.1111/1467-9469.00322>, Azzalini and Capitanio (1999) <doi:10.1111/1467-9868.00194>, Azzalini and Dalla Valle (1996) <doi:10.1093/biomet/83.4.715>, Einmahl et al. (2013) <doi:10.1007/s10687-012-0156-z>, Naveau et al (2009) <doi:10.1093/biomet/asp001> and Heffernan and Tawn (2004) <doi:10.1111/j.1467-9868.2004.02050.x>.
License: GPL (>= 2)
LazyData: yes
NeedsCompilation: yes
Repository: CRAN
Repository/R-Forge/Project: extremaldep
Repository/R-Forge/Revision: 145
Repository/R-Forge/DateTimeStamp: 2022-05-09 06:25:17
Date/Publication: 2022-05-09 09:00:09 UTC
Packaged: 2022-05-09 06:31:20 UTC; rforge
Depends: R (>= 2.10)
URL: https://mypage.unibocconi.it/simonepadoan/

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New package EL with initial version 1.1
Package: EL
Version: 1.1
Date: 2022-05-03
Title: Two-Sample Empirical Likelihood
License: GPL (>= 2)
Description: Empirical likelihood (EL) inference for two-sample problems. The following statistics are included: the difference of two-sample means, smooth Huber estimators, quantile (qdiff) and cumulative distribution functions (ddiff), probability-probability (P-P) and quantile-quantile (Q-Q) plots as well as receiver operating characteristic (ROC) curves. EL calculations are based on J. Valeinis, E. Cers (2011) <http://home.lu.lv/~valeinis/lv/petnieciba/EL_TwoSample_2011.pdf>.
Author: Janis Valeinis [aut] , Edmunds Cers [aut], Janis Gredzens [cre]
Maintainer: Janis Gredzens <janis.gredzens@lu.lv>
Repository: CRAN
NeedsCompilation: yes
Packaged: 2022-05-07 15:58:37 UTC; jgredzens
Date/Publication: 2022-05-09 09:10:09 UTC

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New package dnapath with initial version 0.7.4
Package: dnapath
Title: Differential Network Analysis using Gene Pathways
Version: 0.7.4
Description: Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
Depends: R (>= 3.6)
License: GPL-2 | GPL-3
LazyData: true
Imports: Rcpp (>= 1.0.1), corpcor, igraph, ggplot2, SeqNet, Rdpack, dplyr, tibble, stats, methods, curl, graphics, grDevices, gtools, utils, wCorr, parallel
LinkingTo: Rcpp, RcppArmadillo
Encoding: UTF-8
SystemRequirements: C++11
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, markdown, xml2, readr, bc3net, DWLasso, huge, GENIE3, minet, AnnotationDbi, reactome.db, biomaRt
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-09 00:39:52 UTC; gregory
Author: Tyler Grimes [aut, cre], Somnath Datta [aut]
Maintainer: Tyler Grimes <tyler.grimes@unf.edu>
Repository: CRAN
Date/Publication: 2022-05-09 09:00:05 UTC

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New package COMIX with initial version 0.1.4
Package: COMIX
Title: Coarsened Mixtures of Hierarchical Skew Kernels
Version: 0.1.4
Description: Bayesian fit of a Dirichlet Process Mixture with hierarchical multivariate skew normal kernels and coarsened posteriors. For more information, see Gorsky, Chan and Ma (2020) <arXiv:2001.06451>.
License: CC0
Encoding: UTF-8
Imports: Rcpp (>= 0.12.18)
Suggests: sn, knitr
LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppNumerical
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2022-05-09 17:15:42 UTC; hhh
Author: S. Gorsky [aut, cre], C. Chan [ctb], L. Ma [ctb]
Maintainer: S. Gorsky <sgorsky@umass.edu>
Repository: CRAN
Date/Publication: 2022-05-10 15:10:02 UTC

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New package Canek with initial version 0.2.1
Package: Canek
Title: Batch Correction of Single Cell Transcriptome Data
Version: 0.2.1
Description: Non-linear/linear hybrid method for batch-effect correction that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
Depends: R (>= 2.10)
Imports: FNN, irlba, numbers, fpc, bluster, igraph, matrixStats
Suggests: testthat (>= 2.1.0), Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-04-18 07:52:49 UTC; martin
Author: Martin Loza [aut, cre] , Diego Diez [aut]
Maintainer: Martin Loza <martin.loza.lopez@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-10 10:50:02 UTC

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New package BayesRGMM with initial version 2.2
Package: BayesRGMM
Title: Bayesian Robust Generalized Mixed Models for Longitudinal Data
Version: 2.2
Depends: R (>= 3.5.0)
Date: 2022-05-06
Description: To perform model estimation using MCMC algorithms with Bayesian methods for incomplete longitudinal studies on binary and ordinal outcomes that are measured repeatedly on subjects over time with drop-outs. Details about the method can be found in the vignette or <https://sites.google.com/view/kuojunglee/r-packages/bayesrgmm>.
License: GPL-2
URL: https://sites.google.com/view/kuojunglee/r-packages
Encoding: UTF-8
Imports: Rcpp (>= 1.0.1), MASS, batchmeans, abind, reshape, msm, mvtnorm, plyr, Rdpack
LinkingTo: Rcpp, RcppArmadillo, RcppDist
Suggests: testthat
NeedsCompilation: yes
Packaged: 2022-05-09 15:03:10 UTC; kuojunglee
Author: Kuo-Jung Lee [aut, cre] , Hsing-Ming Chang [ctb], Ray-Bing Chen [ctb], Keunbaik Lee [ctb], Chanmin Kim [ctb]
Maintainer: Kuo-Jung Lee <kuojunglee@ncku.edu.tw>
Repository: CRAN
Date/Publication: 2022-05-10 12:30:13 UTC

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Mon, 09 May 2022

New package tdcmStan with initial version 1.0.0
Package: tdcmStan
Title: Automating the Creation of Stan Code for TDCMs
Version: 1.0.0
Description: A collection of functions for automatically creating 'Stan' code for transition diagnostic classification models (TDCMs) as they are defined by Madison and Bradshaw (2018) <DOI:10.1007/s11336-018-9638-5>. This package supports automating the creation of 'Stan' code for TDCMs, fungible TDCMs (i.e., TDCMs with item parameters constrained to be equal across all items), and multi-threaded TDCMs.
License: GPL (>= 2)
Imports: dplyr (>= 1.0.7), glue (>= 1.4.2), magrittr (>= 2.0.1), rlang (>= 0.4.11), stringr (>= 1.4.0), tibble (>= 3.1.5), tidyr (>= 1.1.4)
Suggests: readr (>= 2.0.0), testthat (>= 3.0.4)
Depends: R (>= 3.5.0)
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-05-06 21:30:31 UTC; jeff
Author: Jeffrey Hoover [aut, cre, cph] , W. Jake Thompson [aut]
Maintainer: Jeffrey Hoover <jeffrey.c.hoover@gmail.com>
Repository: CRAN
Date/Publication: 2022-05-09 07:50:02 UTC

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New package rxode2 with initial version 2.0.6
Package: rxode2
Version: 2.0.6
Title: Facilities for Simulating from ODE-Based Models
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Depends: R (>= 4.0.0)
Suggests: Matrix, DT, covr, crayon, curl, data.table (>= 1.12.4), digest, dplyr (>= 0.8.0), ggrepel, gridExtra, htmltools, knitr, learnr, microbenchmark, nlme, remotes, rlang, rmarkdown, scales, shiny, stringi, symengine, testthat, tidyr, usethis, vdiffr (>= 1.0), withr, xgxr, pillar, tibble, units (>= 0.6-0), rsconnect, devtools, patchwork, nlmixr2data
Imports: PreciseSums (>= 0.3), Rcpp (>= 0.12.3), assertthat, backports, checkmate, cli (>= 2.0.0), dparser (>= 0.1.8), ggplot2, inline, lotri (>= 0.4.0), magrittr, memoise, methods, rex, qs, sys, tools, utils
Description: Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
BugReports: https://github.com/nlmixr2/rxode2/issues/
NeedsCompilation: yes
VignetteBuilder: knitr
License: GPL (>= 3)
URL: https://nlmixr2.github.io/rxode2/, https://github.com/nlmixr2/rxode2/
Biarch: true
LinkingTo: dparser (>= 1.3.1-0), PreciseSums (>= 0.3), RcppEigen (>= 0.3.3.3.0), RcppArmadillo (>= 0.9.300.2.0), sitmo, StanHeaders (>= 2.21.0), BH
Encoding: UTF-8
LazyData: true
Language: en-US
Packaged: 2022-05-05 15:13:05 UTC; matt
Author: Matthew L. Fidler [aut, cre] , Melissa Hallow [aut], Wenping Wang [aut], Zufar Mulyukov [ctb], Alan Hindmarsh [ctb], Awad H. Al-Mohy [ctb], Matt Dowle [ctb], Cleve Moler [ctb], David Cooley [ctb], Drew Schmidt [ctb], Arun Srinivasan [ctb], Ernst Hair [...truncated...]
Repository: CRAN
Date/Publication: 2022-05-09 07:00:02 UTC

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New package primate with initial version 0.2.0
Package: primate
Version: 0.2.0
Date: 2022-05-05
Title: Tools and Methods for Primatological Data Science
Author: David Schruth [aut][cre], Marc Myers [ctb], Noel Rowe [aut]
Maintainer: David Schruth <data@anthropoidea.org>
Depends: R (>= 1.8.0), caroline
Suggests: RJDBC
Description: Data from All the World's Primates relational SQL database and other tabular datasets are made available via drivers and connection functions. Additionally we provide several functions and examples to facilitate the merging and aggregation of these tabular inputs.
License: Apache License
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2022-05-05 18:18:45 UTC; mint
Date/Publication: 2022-05-09 07:20:02 UTC

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