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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Package rpartScore updated to version 1.0-2 with previous version 1.0-1 dated 2012-12-08

Title: Classification Trees for Ordinal Responses
Description: Recursive partitioning methods to build classification trees for ordinal responses within the CART framework. Trees are grown using the Generalized Gini impurity function, where the misclassification costs are given by the absolute or squared differences in scores assigned to the categories of the response. Pruning is based on the total misclassification rate or on the total misclassification cost.
Author: Giuliano Galimberti, Gabriele Soffritti, Matteo Di Maso
Maintainer: Giuliano Galimberti <giuliano.galimberti@unibo.it>

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Package MapGAM updated to version 1.2-6 with previous version 1.2-5 dated 2019-07-27

Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai, Scott Bartell, Robin Bliss, and Veronica Vieira
Maintainer: Scott Bartell <sbartell@uci.edu>

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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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Package dcurves updated to version 0.3.0 with previous version 0.2.0 dated 2021-07-20

Title: Decision Curve Analysis for Model Evaluation
Description: Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes, but often require collection of additional information may be cumbersome to apply to models that yield a continuous result. Decision curve analysis is a method for evaluating and comparing prediction models that incorporates clinical consequences, requires only the data set on which the models are tested, and can be applied to models that have either continuous or dichotomous results. See the following references for details on the methods: Vickers (2006) <doi:10.1177/0272989X06295361>, Vickers (2008) <doi:10.1186/1472-6947-8-53>, and Pfeiffer (2020) <doi:10.1002/bimj.201800240>.
Author: Daniel D. Sjoberg [aut, cre, cph], Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>

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Package catIrt updated to version 0.5.1 with previous version 0.5-0 dated 2014-10-05

Title: Simulate IRT-Based Computerized Adaptive Tests
Description: Functions designed to simulate data that conform to basic unidimensional IRT models (for now 3-parameter binary response models and graded response models) along with Post-Hoc CAT simulations of those models given various item selection methods, ability estimation methods, and termination criteria. See Wainer (2000) <doi:10.4324/9781410605931>, van der Linden & Pashley (2010) <doi:10.1007/978-0-387-85461-8_1>, and Eggen (1999) <doi:10.1177/01466219922031365> for more details.
Author: Steven Nydick [cre, aut]
Maintainer: Steven Nydick <swnydick@gmail.com>

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Package usethis updated to version 2.1.6 with previous version 2.1.5 dated 2021-12-09

Title: Automate Package and Project Setup
Description: Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.
Author: Hadley Wickham [aut] , Jennifer Bryan [aut, cre] , Malcolm Barrett [aut] , RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>

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Package hapassoc updated to version 1.2-9 with previous version 1.2-8 dated 2015-05-10

Title: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
Description: The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.
Author: K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J. Graham <jgraham@stat.sfu.ca>, with code for case-control data contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>
Maintainer: K. Burkett <kburkett@uottawa.ca>

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Package vetiver updated to version 0.1.5 with previous version 0.1.4 dated 2022-04-28

Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to version, share, deploy, and monitor a trained model. Functions handle both recording and checking the model's input data prototype, and predicting from a remote API endpoint. The 'vetiver' package is extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] , RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>

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Package tidypredict updated to version 0.4.9 with previous version 0.4.8 dated 2020-10-28

Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula in 'Tidy Eval' code that calculates the predictions. It works with several databases back-ends because it leverages 'dplyr' and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.
Author: Max Kuhn [aut, cre], Edgar Ruiz [aut]
Maintainer: Max Kuhn <max@rstudio.com>

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Package swCRTdesign updated to version 3.2 with previous version 3.1 dated 2019-10-25

Title: Stepped Wedge Cluster Randomized Trial (SW CRT) Design
Description: A set of tools for examining the design and analysis aspects of stepped wedge cluster randomized trials (SW CRT) based on a repeated cross-sectional sampling scheme (Hussey MA and Hughes JP (2007) Contemporary Clinical Trials 28:182-191. <doi:10.1016/j.cct.2006.05.007>).
Author: Jim Hughes, Navneet R. Hakhu, Emily Voldal, and Fan Xia
Maintainer: Jim Hughes <jphughes@uw.edu>

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Package PUPAIM updated to version 0.3.1 with previous version 0.3.0 dated 2022-05-12

Title: A Collection of Physical and Chemical Adsorption Isotherm Models
Description: The PUPAIM R package can generally fit any adsorption experimental data to any of the 55 available adsorption isotherm models - 32 nonlinear models and 23 linear models. This package provides parameter estimation, model accuracy analysis, model error analysis, and adsorption plot created using the package 'ggplot2'. This package will help the users for a much easier way of adsorption model data fitting.
Author: Keith T. Ostan [aut] , Paul Angelo C. Manlapaz [aut] , Jemimah Christine L. Mesias [aut] , Chester C. Deocaris [aut, ths, cre]
Maintainer: Chester C. Deocaris <ccdeocaris@pup.edu.ph>

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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

More information about traitdataform at CRAN
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Package StereoMorph updated to version 1.6.7 with previous version 1.6.5 dated 2022-05-12

Title: Stereo Camera Calibration and Reconstruction
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen <aarolsen@gmail.com>

Diff between StereoMorph versions 1.6.5 dated 2022-05-12 and 1.6.7 dated 2022-05-25

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Package pogit updated to version 1.3.0 with previous version 1.2.0 dated 2019-01-17

Title: Bayesian Variable Selection for a Poisson-Logistic Model
Description: Bayesian variable selection for regression models of under-reported count data as well as for (overdispersed) Poisson, negative binomal and binomial logit regression models using spike and slab priors.
Author: Michaela Dvorzak [aut, cre], Helga Wagner [aut]
Maintainer: Michaela Dvorzak <m.dvorzak@gmx.at>

Diff between pogit versions 1.2.0 dated 2019-01-17 and 1.3.0 dated 2022-05-25

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Package habCluster updated to version 1.0.5 with previous version 1.0.3 dated 2022-05-18

Title: Detecting Spatial Clustering Based on Connection Cost Between Grids
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>.
Author: Qiang Dai
Maintainer: Qiang Dai <daiqiang@cib.ac.cn>

Diff between habCluster versions 1.0.3 dated 2022-05-18 and 1.0.5 dated 2022-05-25

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Package GeneralizedUmatrix updated to version 1.2.4 with previous version 1.2.2 dated 2021-01-12

Title: Credible Visualization for Two-Dimensional Projections of Data
Description: Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) <DOI:10.1007/978-3-658-20540-9> and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.
Author: Michael Thrun [aut, cre, cph] , Felix Pape [ctb, ctr], Tim Schreier [ctb, ctr], Luis Winckelman [ctb, ctr], Quirin Stier [ctb, ctr], Alfred Ultsch [ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>

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Permanent link

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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Package bpr updated to version 1.0.5 with previous version 1.0.4 dated 2021-09-22

Title: Fitting Bayesian Poisson Regression
Description: Posterior sampling and inference for Bayesian Poisson regression models. The model specification makes use of Gaussian (or conditionally Gaussian) prior distributions on the regression coefficients. Details on the algorithm are found in D'Angelo and Canale (2021) <arXiv:2109.09520>.
Author: Laura D'Angelo
Maintainer: Laura D'Angelo <laura.dangelo@live.com>

Diff between bpr versions 1.0.4 dated 2021-09-22 and 1.0.5 dated 2022-05-25

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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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Package radmixture (with last version 0.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2017-03-13 0.0.1

Permanent link
Package RFpredInterval updated to version 1.0.6 with previous version 1.0.5 dated 2022-01-20

Title: Prediction Intervals with Random Forests and Boosted Forests
Description: Implements various prediction interval methods with random forests and boosted forests. The package has two main functions: pibf() produces prediction intervals with boosted forests (PIBF) as described in Alakus et al. (2021) <arXiv:2106.08217> and rfpi() builds 15 distinct variations of prediction intervals with random forests (RFPI) proposed by Roy and Larocque (2020) <doi:10.1177/0962280219829885>.
Author: Cansu Alakus [aut, cre], Denis Larocque [aut], Aurelie Labbe [aut], Hemant Ishwaran [ctb] , Udaya B. Kogalur [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>

Diff between RFpredInterval versions 1.0.5 dated 2022-01-20 and 1.0.6 dated 2022-05-25

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Package GAIPE updated to version 1.1 with previous version 1.0 dated 2013-04-17

Title: Graphical Extension with Accuracy in Parameter Estimation (GAIPE)
Description: Implements graphical extension with accuracy in parameter estimation (AIPE) on RMSEA for sample size planning in structural equation modeling based on Lin, T.-Z. & Weng, L.-J. (2014) <doi: 10.1080/10705511.2014.915380>. And, it can also implement AIPE on RMSEA and power analysis on RMSEA.
Author: Tzu-Yao Lin
Maintainer: Yao Lin <zaiyaolin@gmail.com>

Diff between GAIPE versions 1.0 dated 2013-04-17 and 1.1 dated 2022-05-25

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More information about GAIPE at CRAN
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Package RcppAPT updated to version 0.0.9 with previous version 0.0.8 dated 2021-12-04

Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and Debian-derived Linux systems with a powerful system to resolve package dependencies. This package offers access directly from R. This can only work on a system with a suitable 'libapt-pkg-dev' installation so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppAPT versions 0.0.8 dated 2021-12-04 and 0.0.9 dated 2022-05-25

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Package monotone updated to version 0.1.2 with previous version 0.1.1 dated 2022-05-25

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

Diff between monotone versions 0.1.1 dated 2022-05-25 and 0.1.2 dated 2022-05-25

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More information about monotone at CRAN
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Package MLGL updated to version 0.6.7 with previous version 0.6.5 dated 2020-11-28

Title: Multi-Layer Group-Lasso
Description: It implements a new procedure of variable selection in the context of redundancy between explanatory variables, which holds true with high dimensional data (Grimonprez et al. (2018) <https://hal.inria.fr/hal-01857242>).
Author: Quentin Grimonprez [aut, cre], Samuel Blanck [ctb], Alain Celisse [ths], Guillemette Marot [ths], Yi Yang [ctb], Hui Zou [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>

Diff between MLGL versions 0.6.5 dated 2020-11-28 and 0.6.7 dated 2022-05-25

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Package mlr3viz updated to version 0.5.9 with previous version 0.5.8 dated 2022-04-04

Title: Visualizations for 'mlr3'
Description: Provides visualizations for 'mlr3' objects such as tasks, predictions, resample results or benchmark results via the autoplot() generic of 'ggplot2'. The returned 'ggplot' objects are intended to provide sensible defaults, yet can easily be customized to create camera-ready figures. Visualizations include barplots, boxplots, histograms, ROC curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] , Patrick Schratz [aut] , Raphael Sonabend [aut] , Marc Becker [aut] , Jakob Richter [aut] , Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3viz versions 0.5.8 dated 2022-04-04 and 0.5.9 dated 2022-05-25

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Package mlr3learners updated to version 0.5.3 with previous version 0.5.2 dated 2022-01-22

Title: Recommended Learners for 'mlr3'
Description: Recommended Learners for 'mlr3'. Extends 'mlr3' with interfaces to essential machine learning packages on CRAN. This includes, but is not limited to: (penalized) linear and logistic regression, linear and quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support vector machines, and gradient boosting.
Author: Michel Lang [cre, aut] , Quay Au [aut] , Stefan Coors [aut] , Patrick Schratz [aut]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between mlr3learners versions 0.5.2 dated 2022-01-22 and 0.5.3 dated 2022-05-25

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More information about mlr3learners at CRAN
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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

More information about africamonitor at CRAN
Permanent link

Package seqHMM updated to version 1.2.1-1 with previous version 1.2.0 dated 2021-10-18

Title: Mixture Hidden Markov Models for Social Sequence Data and Other Multivariate, Multichannel Categorical Time Series
Description: Designed for fitting hidden (latent) Markov models and mixture hidden Markov models for social sequence data and other categorical time series. Also some more restricted versions of these type of models are available: Markov models, mixture Markov models, and latent class models. The package supports models for one or multiple subjects with one or multiple parallel sequences (channels). External covariates can be added to explain cluster membership in mixture models. The package provides functions for evaluating and comparing models, as well as functions for visualizing of multichannel sequence data and hidden Markov models. Models are estimated using maximum likelihood via the EM algorithm and/or direct numerical maximization with analytical gradients. All main algorithms are written in C++ with support for parallel computation. Documentation is available via several vignettes in this page, and the paper by Helske and Helske (2019, <doi:10.18637/jss.v088.i03>).
Author: Jouni Helske [aut, cre] , Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>

Diff between seqHMM versions 1.2.0 dated 2021-10-18 and 1.2.1-1 dated 2022-05-25

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Package r2spss updated to version 0.3.2 with previous version 0.3.1 dated 2022-03-23

Title: Format R Output to Look Like SPSS
Description: Create plots and LaTeX tables that look like SPSS output for use in teaching materials. Rather than copying-and-pasting SPSS output into documents, R code that mocks up SPSS output can be integrated directly into dynamic LaTeX documents with tools such as knitr. Functionality includes statistical techniques that are typically covered in introductory statistics classes: descriptive statistics, common hypothesis tests, ANOVA, and linear regression, as well as box plots, histograms, scatter plots, and line plots (including profile plots).
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package list updated to version 9.2.2 with previous version 9.2.1 dated 2022-05-10

Title: Statistical Methods for the Item Count Technique and List Experiment
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.
Author: Graeme Blair [aut, cre], Winston Chou [aut], Kosuke Imai [aut], Bethany Park [ctb], Alexander Coppock [ctb]
Maintainer: Graeme Blair <graeme.blair@gmail.com>

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Package GMSE updated to version 1.0.0.1 with previous version 0.7.0.0 dated 2021-08-02

Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] , Adrian Bach [aut], Nils Bunnefeld [aut, fnd] , Jeremy Cusack [ctb] , Isabel Jones [ctb] , Jeroen Minderman [aut] , Erlend Nilsen [ctb] , Ochoa Gabriela [aut] , Rocio Pozo [ctb] , Sarobidy Rakotonarivo [ctb] , Bram Van M [...truncated...]
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>

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Package eurlex updated to version 0.4.2 with previous version 0.4.1 dated 2022-03-31

Title: Retrieve Data on European Union Law
Description: Access to data on European Union laws and court decisions made easy with pre-defined 'SPARQL' queries and 'GET' requests.
Author: Michal Ovadek [aut, cre, cph]
Maintainer: Michal Ovadek <michal.ovadek@gmail.com>

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Package binGroup2 updated to version 1.2.4 with previous version 1.2.3 dated 2022-05-16

Title: Identification and Estimation using Group Testing
Description: Methods for the group testing identification problem: 1) Operating characteristics (e.g., expected number of tests) for commonly used hierarchical and array-based algorithms, and 2) Optimal testing configurations for these same algorithms. Methods for the group testing estimation problem: 1) Estimation and inference procedures for an overall prevalence, and 2) Regression modeling for commonly used hierarchical and array-based algorithms.
Author: Brianna Hitt [aut, cre] , Christopher Bilder [aut] , Frank Schaarschmidt [aut] , Brad Biggerstaff [aut] , Christopher McMahan [aut] , Joshua Tebbs [aut] , Boan Zhang [ctb], Michael Black [ctb], Peijie Hou [ctb], Peng Chen [ctb]
Maintainer: Brianna Hitt <brianna.hitt@afacademy.af.edu>

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Package monotone updated to version 0.1.1 with previous version 0.1.0 dated 2021-03-10

Title: Performs Monotone Regression
Description: The monotone package contains a fast up-and-down-blocks implementation for the pool-adjacent-violators algorithm for simple linear ordered monotone regression, including two spin-off functions for unimodal and bivariate monotone regression (see <doi:10.18637/jss.v102.c01>).
Author: Frank Busing [aut, cre], Juan Claramunt Gonzalez [aut]
Maintainer: Frank Busing <busing@fsw.leidenuniv.nl>

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Package epiR updated to version 2.0.48 with previous version 2.0.46 dated 2022-03-31

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

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Package SoilHyP updated to version 0.1.6 with previous version 0.1.5 dated 2021-01-08

Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7]. Main references: [1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>, [2] Mualem (1976) <doi:10.1029/WR012i003p00513>, [3] Peters (2013) <doi:10.1002/wrcr.20548>, [4] Iden and Durner (2013) <doi:10.1002/2014WR015937>, [5] Peters (2014) <doi:10.1002/2014WR015937>, [6] Wind G. P. (1966), [7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and [8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre], Felix Andrews [ctb] which is not on r-cran . The SCEoptim function is adapted, and substantially revised from Brecht Donckels MATLAB code which is in turn adopted from Qingyun Duans MATLAB code), Brecht Donckels [ctb] , [...truncated...]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

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Package SecDim updated to version 2.2 with previous version 1.3 dated 2022-05-02

Title: The Second Dimension of Spatial Association
Description: Most of the current methods explore spatial association using observations at sample locations, which are defined as the first dimension of spatial association (FDA). The proposed concept of the second dimension of spatial association (SDA) aims to extract in-depth information about the geographical environment from locations outside sample locations for exploring spatial association.
Author: Yongze Song [aut, cre]
Maintainer: Yongze Song <yongze.song@postgrad.curtin.edu.au>

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Package radiant.model updated to version 1.4.4 with previous version 1.4.3 dated 2021-12-21

Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic regression, naive Bayes, neural networks, classification and regression trees, model evaluation, collaborative filtering, decision analysis, and simulation. The application extends the functionality in 'radiant.data'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

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Package radiant.data updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-12

Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant.data versions 1.4.1 dated 2021-11-12 and 1.4.2 dated 2022-05-25

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Package ORKM updated to version 0.1.1.1 with previous version 0.0.2.1 dated 2022-04-25

Title: The Online Regularized K-Means Clustering Algorithm
Description: Algorithm of online regularized k-means to deal with online multi(single) view data. The philosophy of the package is described in Guo G. (2020) <doi:10.1080/02331888.2020.1823979>.
Author: Guangbao Guo [aut, cre] , Miao Yu [aut], Haoyue Song [aut], Ruiling Niu [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>

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Package MeTo updated to version 0.1.1 with previous version 0.1.0 dated 2019-01-11

Title: Meteorological Tools
Description: Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1]. Functions for calculating: reference evapotranspiration (ETref), extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure (satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more. [1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9).
Author: Ullrich Dettmann [aut, cre], R. Grima [aut]
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>

Diff between MeTo versions 0.1.0 dated 2019-01-11 and 0.1.1 dated 2022-05-25

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Package basefun updated to version 1.1-3 with previous version 1.1-2 dated 2022-01-14

Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between basefun versions 1.1-2 dated 2022-01-14 and 1.1-3 dated 2022-05-25

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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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Package shadowr updated to version 0.0.2 with previous version 0.0.1 dated 2022-04-22

Title: Selenium Plugin to Manage Multi Level Shadow Elements on Web Page
Description: Shadow Document Object Model is a web standard that offers component style and markup encapsulation. It is a critically important piece of the Web Components story as it ensures that a component will work in any environment even if other CSS or JavaScript is at play on the page. Custom HTML tags can't be directly identified with selenium tools, because Selenium doesn't provide any way to deal with shadow elements. Using this plugin you can handle any custom HTML tags.
Author: Ricardo Landolt [cre, aut], Sushil Gupta [ctb]
Maintainer: Ricardo Landolt <ricardo.landolt1@gmail.com>

Diff between shadowr versions 0.0.1 dated 2022-04-22 and 0.0.2 dated 2022-05-25

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Package relliptical updated to version 1.2.0 with previous version 1.1.0 dated 2022-01-07

Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions. References used for this package: Galarza, C. E., Matos, L. A., Castro, L. M., & Lachos, V. H. (2022). Moments of the doubly truncated selection elliptical distributions with emphasis on the unified multivariate skew-t distribution. Journal of Multivariate Analysis, 189, 104944 <doi:10.1016/j.jmva.2021.104944>; Ho, H. J., Lin, T. I., Chen, H. Y., & Wang, W. L. (2012). Some results on the truncated multivariate t distribution. Journal of Statistical Planning and Inference, 142(1), 25-40 <doi:10.1016/j.jspi.2011.06.006>; Valeriano, K. A., Galarza, C. E., & Matos, L. A. (2021). Moments and random number generation for the truncated elliptical family of distributions. arXiv preprint <arXiv:2112.09319>.
Author: Katherine A. L. Valeriano [aut, cre] , Larissa Avila Matos [ctb] , Christian Galarza Morales [ctb]
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>

Diff between relliptical versions 1.1.0 dated 2022-01-07 and 1.2.0 dated 2022-05-25

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Package radiant updated to version 1.4.2 with previous version 1.4.1 dated 2021-11-22

Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business analytics in R, based on the shiny package. The application combines the functionality of 'radiant.data', 'radiant.design', 'radiant.basics', 'radiant.model', and 'radiant.multivariate'.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>

Diff between radiant versions 1.4.1 dated 2021-11-22 and 1.4.2 dated 2022-05-25

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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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Package meteospain updated to version 0.0.4 with previous version 0.0.3 dated 2021-11-05

Title: Access to Spanish Meteorological Stations Services
Description: Access to different Spanish meteorological stations data services and APIs (AEMET, SMC, MG, Meteoclimatic...).
Author: Victor Granda [aut, cre] , Miquel de Caceres [ctb] , Aitor Ameztegui [ctb]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>

Diff between meteospain versions 0.0.3 dated 2021-11-05 and 0.0.4 dated 2022-05-25

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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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Package ergm.count updated to version 4.1.1 with previous version 4.0.2 dated 2021-06-18

Title: Fit, Simulate and Diagnose Exponential-Family Models for Networks with Count Edges
Description: A set of extensions for the 'ergm' package to fit weighted networks whose edge weights are counts. See Krivitsky (2012) <doi:10.1214/12-EJS696> and Krivitsky, Hunter, Morris, and Klumb (2021) <arXiv:2106.04997>.
Author: Pavel N. Krivitsky [aut, cre] , Mark S. Handcock [ctb], David R. Hunter [ctb], Joyce Cheng [ctb]
Maintainer: Pavel N. Krivitsky <pavel@statnet.org>

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Package dycdtools updated to version 0.4.2 with previous version 0.4.1 dated 2022-05-08

Title: Tools for DYRESM-CAEDYM Model Development: Calibration Assistant and Post-Processing
Description: Tools for DYRESM-CAEDYM model development, including assisting with calibrating selected model parameters and visualising model output through time series plot, profile plot, contour plot, and scatter plot.
Author: Songyan Yu [aut, cre] , Christopher McBride [ctb], Marieke Frassl [ctb]
Maintainer: Songyan Yu <sunny.yu@griffith.edu.au>

Diff between dycdtools versions 0.4.1 dated 2022-05-08 and 0.4.2 dated 2022-05-25

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 dycdtools-0.4.2/dycdtools/NAMESPACE                                |    1 
 dycdtools-0.4.2/dycdtools/NEWS.md                                  |    5 
 dycdtools-0.4.2/dycdtools/R/Fun_Calib-assist.R                     |  261 ++++++----
 dycdtools-0.4.2/dycdtools/R/Fun_Change-input-file.R                |    8 
 dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim.R                 |  107 ++--
 dycdtools-0.4.2/dycdtools/R/Fun_Contour-plot_sim_obs.R             |  171 +++---
 dycdtools-0.4.2/dycdtools/R/Fun_Extract-simulation.R               |   64 +-
 dycdtools-0.4.2/dycdtools/R/Fun_Interpol.R                         |   48 +
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 dycdtools-0.4.2/dycdtools/R/obs_temp.R                             |    6 
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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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Package AlgDesign updated to version 1.2.1 with previous version 1.2.0 dated 2019-11-29

Title: Algorithmic Experimental Design
Description: Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.
Author: Bob Wheeler <bwheelerg@gmail.com>
Maintainer: Jerome Braun <jvbraun.statistics@gmail.com>

Diff between AlgDesign versions 1.2.0 dated 2019-11-29 and 1.2.1 dated 2022-05-25

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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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Package hibayes updated to version 1.1.0 with previous version 1.0.1 dated 2022-01-13

Title: Individual-Level, Summary-Level and Single-Step Bayesian Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including: (1) fixed effects and coefficients of covariates, (2) environmental random effects, and its corresponding variance, (3) genetic variance, (4) residual variance, (5) heritability, (6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals, (7) SNP effect size, (8) phenotype/genetic variance explained (PVE) for single or multiple SNPs, (9) posterior probability of association of the genomic window (WPPA), (10) posterior inclusive probability (PIP). The functions are not limited, we will keep on going in enriching it with more features. References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph], Haohao Zhang [aut, cph], Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>

Diff between hibayes versions 1.0.1 dated 2022-01-13 and 1.1.0 dated 2022-05-25

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Package AzureStor updated to version 3.7.0 with previous version 3.6.1 dated 2022-02-03

Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/en-us/product-categories/storage/>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS). Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi73@gmail.com>

Diff between AzureStor versions 3.6.1 dated 2022-02-03 and 3.7.0 dated 2022-05-25

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2018-03-02 0.1.2
2017-11-06 0.1.1
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2017-09-19 0.0.90
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2012-12-03 0.9.6
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Package HARtools (with last version 0.0.5) was removed from CRAN

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2016-11-09 0.0.5

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Package SpaTimeClus (with last version 1.0.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-10-14 1.0.1
2016-12-21 1.0

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Package EcoHydRology (with last version 0.4.12.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-09-24 0.4.12.1
2014-04-04 0.4.12
2013-10-19 0.4.11
2013-04-04 0.4.9
2013-01-16 0.4.7
2013-01-14 0.4.6
2012-08-01 0.4.5
2012-07-16 0.4.3
2012-05-23 0.4.1
2011-06-20 0.3.8
2011-06-17 0.3.7

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Package baggedcv (with last version 1.0) was removed from CRAN

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2019-07-26 1.0

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Package DoE.multi.response (with last version 0.1.0) was removed from CRAN

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2019-08-22 0.1.0

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Package Clustering (with last version 1.7.6) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-04-19 1.7.6
2021-12-14 1.7.5
2021-12-08 1.7.4
2021-09-22 1.7.3

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Package advclust (with last version 0.4) was removed from CRAN

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2016-09-04 0.4

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Package CityWaterBalance (with last version 0.1.0) was removed from CRAN

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2017-06-16 0.1.0

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Tue, 24 May 2022

Package timedeppar updated to version 1.0.2 with previous version 1.0.1 dated 2020-10-01

Title: Infer Constant and Stochastic, Time-Dependent Model Parameters
Description: Infer constant and stochastic, time-dependent parameters to consider intrinsic stochasticity of a dynamic model and/or to analyze model structure modifications that could reduce model deficits. The concept is based on inferring time-dependent parameters as stochastic processes in the form of Ornstein-Uhlenbeck processes jointly with inferring constant model parameters and parameters of the Ornstein-Uhlenbeck processes. The package also contains functions to sample from and calculate densities of Ornstein-Uhlenbeck processes. References: Tomassini, L., Reichert, P., Kuensch, H.-R. Buser, C., Knutti, R. and Borsuk, M.E. (2009), A smoothing algorithm for estimating stochastic, continuous-time model parameters and its application to a simple climate model, Journal of the Royal Statistical Society: Series C (Applied Statistics) 58, 679-704, <doi:10.1111/j.1467-9876.2009.00678.x> Reichert, P., and Mieleitner, J. (2009), Analyzing input and structural uncertainty of nonlinear dynamic models with stochastic, time-dependent parameters. Water Resources Research, 45, W10402, <doi:10.1029/2009WR007814> Reichert, P., Ammann, L. and Fenicia, F. (2021), Potential and challenges of investigating intrinsic uncertainty of hydrological models with time-dependent, stochastic parameters. Water Resources Research 57(8), e2020WR028311, <doi:10.1029/2020WR028311> Reichert, P. (2022), timedeppar: An R package for inferring stochastic, time-dependent model parameters, in preparation.
Author: Peter Reichert <peter.reichert@eawag.ch>
Maintainer: Peter Reichert <peter.reichert@eawag.ch>

Diff between timedeppar versions 1.0.1 dated 2020-10-01 and 1.0.2 dated 2022-05-24

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Package sleev updated to version 1.0.2 with previous version 1.0.1 dated 2022-02-01

Title: Semiparametric Likelihood Estimation with Errors in Variables
Description: Efficient regression analysis under general two-phase sampling, where Phase I includes error-prone data and Phase II contains validated data on a subset.
Author: Sarah Lotspeich [aut], Ran Tao [aut, cre], Joey Sherrill [prg]
Maintainer: Ran Tao <r.tao@vanderbilt.edu>

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Package omu updated to version 1.0.5 with previous version 1.0.4 dated 2020-05-18

Title: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Description: Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.
Author: Connor Tiffany [aut, cre]
Maintainer: Connor Tiffany <crtiffany@ucdavis.edu>

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Package IFC updated to version 0.1.5 with previous version 0.1.2 dated 2021-10-13

Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre], Gautier Stoll [ctb], Guido Kroemer [ldr], Jean-Pierre Marolleau [ldr], Loïc Garcon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>

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Permanent link

Package gtfstools updated to version 1.1.0 with previous version 1.0.0 dated 2021-11-16

Title: General Transit Feed Specification (GTFS) Editing and Analysing Tools
Description: Utility functions to read, manipulate, analyse and write transit feeds in the General Transit Feed Specification (GTFS) data format.
Author: Daniel Herszenhut [aut, cre] , Rafael H. M. Pereira [aut] , Pedro R. Andrade [aut] , Joao Bazzo [aut] , Mark Padgham [ctb], Marcus Saraiva [ctb] , Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Daniel Herszenhut <dhersz@gmail.com>

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Package GeoWeightedModel updated to version 1.0.2 with previous version 1.0.0 dated 2022-05-11

Title: User-Friendly Interface for Geographically-Weighted Models
Description: Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Techniques from a subset of spatial statistics known as geographically weighted (GW) models. Contains methods described by Brunsdon et al., 1996 <doi:10.1111/j.1538-4632.1996.tb00936.x>, Brunsdon et al., 2002 <doi:10.1016/s0198-9715(01)00009-6>, Harris et al., 2011 <doi:10.1080/13658816.2011.554838>, Brunsdon et al., 2007 <doi:10.1111/j.1538-4632.2007.00709.x>.
Author: Javier De La Hoz Maestre [cre, aut] , Maria Jose Fernandez Gomez [aut] , Susana Mendez [aut]
Maintainer: Javier De La Hoz Maestre <jdelahozmaestre@gmail.com>

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Package composits updated to version 0.1.1 with previous version 0.1.0 dated 2020-09-30

Title: Compositional, Multivariate and Univariate Time Series Outlier Ensemble
Description: A compositional, multivariate and univariate time series outlier ensemble. It uses the four R packages 'forecast', 'tsoutliers', 'otsad' and 'anomalize' to detect time series outliers (Kandanaarachchi, Menendez 2020) <doi:10.13140/RG.2.2.32217.95845>.
Author: Sevvandi Kandanaarachchi [aut, cre] , Patricia Menendez [aut] , Ursula Laa [aut] , Ruben Loaiza-Maya [aut]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>

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Package clusterSim updated to version 0.50-1 with previous version 0.49-2 dated 2021-01-06

Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data). (MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>, HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>, RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>, JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>, MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>, JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>, DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>, CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>, HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>, TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>, BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>, WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>

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Package bcdata updated to version 0.3.1 with previous version 0.3.0 dated 2021-10-28

Title: Search and Retrieve Data from the BC Data Catalogue
Description: Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.
Author: Andy Teucher [aut, cre] , Sam Albers [aut, ctb] , Stephanie Hazlitt [aut, ctb] , Province of British Columbia [cph]
Maintainer: Andy Teucher <andy.teucher@gov.bc.ca>

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Package BayesMallows updated to version 1.2.0 with previous version 1.1.2 dated 2022-04-11

Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] , Valeria Vitelli [aut] , Marta Crispino [aut], Qinghua Liu [aut], Cristina Mollica [aut], Luca Tardella [aut], Anja Stein [aut], Waldir Leoncio [ctr]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>

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Package nanostringr updated to version 0.3.0 with previous version 0.2.0 dated 2021-02-06

Title: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data
Description: Provides quality control (QC), normalization, and batch effect correction operations for 'NanoString nCounter' data, Talhouk et al. (2016) <doi:10.1371/journal.pone.0153844>. Various metrics are used to determine which samples passed or failed QC. Gene expression should first be normalized to housekeeping genes, before a reference-based approach is used to adjust for batch effects. Raw NanoString data can be imported in the form of Reporter Code Count (RCC) files.
Author: Derek Chiu [aut, cre], Aline Talhouk [aut], Samuel Leung [aut]
Maintainer: Derek Chiu <dchiu@bccrc.ca>

Diff between nanostringr versions 0.2.0 dated 2021-02-06 and 0.3.0 dated 2022-05-24

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Package TBEST updated to version 5.2 with previous version 5.0 dated 2014-12-29

Title: Tree Branches Evaluated Statistically for Tightness
Description: Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.
Author: Guoli Sun, Alex Krasnitz
Maintainer: Guoli Sun <guolisun87@gmail.com>

Diff between TBEST versions 5.0 dated 2014-12-29 and 5.2 dated 2022-05-24

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Package ZetaSuite updated to version 1.0.1 with previous version 1.0.0 dated 2022-03-31

Title: Analyze High-Dimensional High-Throughput Dataset and Quality Control Single-Cell RNA-Seq
Description: The advent of genomic technologies has enabled the generation of two-dimensional or even multi-dimensional high-throughput data, e.g., monitoring multiple changes in gene expression in genome-wide siRNA screens across many different cell types (E Robert McDonald 3rd (2017) <doi: 10.1016/j.cell.2017.07.005> and Tsherniak A (2017) <doi: 10.1016/j.cell.2017.06.010>) or single cell transcriptomics under different experimental conditions. We found that simple computational methods based on a single statistical criterion is no longer adequate for analyzing such multi-dimensional data. We herein introduce 'ZetaSuite', a statistical package initially designed to score hits from two-dimensional RNAi screens.We also illustrate a unique utility of 'ZetaSuite' in analyzing single cell transcriptomics to differentiate rare cells from damaged ones (Vento-Tormo R (2018) <doi: 10.1038/s41586-018-0698-6>). In 'ZetaSuite', we have the following steps: QC of input datasets, normalization using Z-transformation, Zeta score calculation and hits selection based on defined Screen Strength.
Author: Yajing Hao [aut] , Shuyang Zhang [ctb] , Junhui Li [cre], Guofeng Zhao [ctb], Xiang-Dong Fu [cph, fnd]
Maintainer: Junhui Li <ljh.biostat@gmail.com>

Diff between ZetaSuite versions 1.0.0 dated 2022-03-31 and 1.0.1 dated 2022-05-24

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Package wTO updated to version 2.0.1 with previous version 2.0 dated 2022-05-10

Title: Computing Weighted Topological Overlaps (wTO) & Consensus wTO Network
Description: Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <arXiv:1711.04702>.
Author: Deisy Morselli Gysi, Andre Voigt, Tiago Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy.ccnr@gmail.com>

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Package VineCopula updated to version 2.4.4 with previous version 2.4.3 dated 2021-10-07

Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of regular vine copula models, see Aas et al. (2009) <doi:10.1016/j.insmatheco.2007.02.001> and Dissman et al. (2013) <doi:10.1016/j.csda.2012.08.010>. The package includes tools for parameter estimation, model selection, simulation, goodness-of-fit tests, and visualization. Tools for estimation, selection and exploratory data analysis of bivariate copula models are also provided.
Author: Thomas Nagler [aut, cre], Ulf Schepsmeier [aut], Jakob Stoeber [aut], Eike Christian Brechmann [aut], Benedikt Graeler [aut], Tobias Erhardt [aut], Carlos Almeida [ctb], Aleksey Min [ctb, ths], Claudia Czado [ctb, ths], Mathias Hofmann [ctb], Matthia [...truncated...]
Maintainer: Thomas Nagler <mail@tnagler.com>

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Package TreeTools updated to version 1.7.2 with previous version 1.7.1 dated 2022-03-25

Title: Create, Modify and Analyse Phylogenetic Trees
Description: Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2021) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013) <doi:10.1016/j.mbs.2012.10.005>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <http://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Author: Martin R. Smith [aut, cre, cph] , Emmanuel Paradis [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>

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Package shinyFiles updated to version 0.9.2 with previous version 0.9.1 dated 2021-11-10

Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of the server side file system in shiny apps. In case the app is running locally this gives the user direct access to the file system without the need to "download" files to a temporary location. Both file and folder selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut] , Vincent Nijs [aut], Thomas Schaffner [aut], Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between shinyFiles versions 0.9.1 dated 2021-11-10 and 0.9.2 dated 2022-05-24

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Package Rdsdp updated to version 1.0.5.2 with previous version 1.0.5.1 dated 2021-11-02

Title: R Interface to DSDP Semidefinite Programming Library
Description: R interface to DSDP semidefinite programming library. The DSDP software is a free open source implementation of an interior-point method for semidefinite programming. It provides primal and dual solutions, exploits low-rank structure and sparsity in the data, and has relatively low memory requirements for an interior-point method.
Author: Zhisu Zhu, Yinyu Ye
Maintainer: Zhisu Zhu <zhuzhisu@alumni.stanford.edu>

Diff between Rdsdp versions 1.0.5.1 dated 2021-11-02 and 1.0.5.2 dated 2022-05-24

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Package RcppXPtrUtils updated to version 0.1.2 with previous version 0.1.1 dated 2019-01-21

Title: XPtr Add-Ons for 'Rcpp'
Description: Provides the means to compile user-supplied C++ functions with 'Rcpp' and retrieve an 'XPtr' that can be passed to other C++ components.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>

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Package parameters updated to version 0.18.0 with previous version 0.17.0 dated 2022-03-10

Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Luedecke [aut, cre] , Dominique Makowski [aut] , Mattan S. Ben-Shachar [aut] , Indrajeet Patil [aut] , Soeren Hoejsgaard [aut], Brenton M. Wiernik [aut] , Zen J. Lau [ctb], Vincent Arel-Bundock [ctb] , Jeffrey Girard [ctb] , Christina Maimone [re [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>

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More information about parameters at CRAN
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Package openssl updated to version 2.0.2 with previous version 2.0.1 dated 2022-05-14

Title: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers. Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public key) encryption or EC for Diffie Hellman. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and 'bignum' math methods for manually performing crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] , Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Permanent link

Package dexter updated to version 1.2.1 with previous version 1.1.5 dated 2022-02-19

Title: Data Management and Analysis of Tests
Description: A system for the management, assessment, and psychometric analysis of data from educational and psychological tests.
Author: Gunter Maris [aut], Timo Bechger [aut], Jesse Koops [aut, cre], Ivailo Partchev [aut]
Maintainer: Jesse Koops <jesse.koops@cito.nl>

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Package Andromeda updated to version 0.6.1 with previous version 0.6.0 dated 2022-01-25

Title: Asynchronous Disk-Based Representation of Massive Data
Description: Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.
Author: Adam Black [aut, cre], Martijn Schuemie [aut], Marc A. Suchard [aut], Observational Health Data Science and Informatics [cph]
Maintainer: Adam Black <black@ohdsi.org>

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Package HostSwitch updated to version 0.1.1 with previous version 0.1.0 dated 2021-09-27

Title: Simulate the Extent of Host Switching by Consumers
Description: Using a simulation-based approach, the 'HostSwitch' package provides functions to investigate host switches by consumers. The individual-based model is based on the concept of ecological fitting. The mockup model is published by Araujo et al. 2015. Understanding Host-Switching by Ecological Fitting (<doi:10.1371/journal.pone.0139225>). The package provides an R-friendly and modified version of this model which can be applied to different consumer-resource scenarios.
Author: Valeria Trivellone [aut], Sabrina B.L. Araujo [aut], Bernd Panassiti [cre, aut]
Maintainer: Bernd Panassiti <bernd.panassiti@gmail.com>

Diff between HostSwitch versions 0.1.0 dated 2021-09-27 and 0.1.1 dated 2022-05-24

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Package GaussSuppression updated to version 0.3.0 with previous version 0.2.0 dated 2022-04-05

Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression using the Gaussian elimination secondary suppression algorithm. Primary suppression functions for the minimum frequency rule, the dominance rule and a directly-disclosive rule are included. General primary suppression functions can be supplied as input. Suppressed frequencies can be replaced by synthetic decimal numbers as described in Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oyvind Langsrud [aut, cre], Daniel Lupp [aut], Hege Boevelstad [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>

Diff between GaussSuppression versions 0.2.0 dated 2022-04-05 and 0.3.0 dated 2022-05-24

 DESCRIPTION                            |    8 ++++----
 MD5                                    |    9 +++++----
 R/GaussSuppressDec.R                   |   29 +++++++++++++++++++++++------
 R/GaussSuppressionFromData.R           |    4 ++++
 R/SuppressDec.R                        |    4 +++-
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Package campfin updated to version 1.0.9 with previous version 1.0.8 dated 2021-09-02

Title: Wrangle Campaign Finance Data
Description: Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.
Author: Kiernan Nicholls [aut, cre, cph], Investigative Reporting Workshop [cph], Yanqi Xu [aut], Schuyler Erle [cph]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>

Diff between campfin versions 1.0.8 dated 2021-09-02 and 1.0.9 dated 2022-05-24

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 tests/testthat/test-diary.R        |    2 
 tests/testthat/test-normal-state.R |    6 
 23 files changed, 592 insertions(+), 274 deletions(-)

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Package POSetR updated to version 1.1.0 with previous version 1.0.4 dated 2021-11-24

Title: Partially Ordered Sets in R
Description: Provides a set of basic tools for generating, analyzing, summarizing and visualizing finite partially ordered sets. In particular, it implements flexible and very efficient algorithms for the extraction of linear extensions and for the computation of mutual ranking probabilities and other user-defined functionals, over them. The package is meant as a computationally efficient "engine", for the implementation of data analysis procedures, on systems of multidimensional ordinal indicators and partially ordered data, in the spirit of Fattore, M. (2016) "Partially ordered sets and the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-015-1059-6>, and Fattore M. and Arcagni, A. (2018) "A reduced posetic approach to the measurement of multidimensional ordinal deprivation", Social Indicators Research <DOI:10.1007/s11205-016-1501-4>.
Author: Alberto Arcagni [aut, cre], Alessandro Avellone [aut], Marco Fattore [aut]
Maintainer: Alberto Arcagni <alberto.arcagni@uniroma1.it>

Diff between POSetR versions 1.0.4 dated 2021-11-24 and 1.1.0 dated 2022-05-24

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Package audubon updated to version 0.2.0 with previous version 0.1.2 dated 2022-04-02

Title: Japanese Text Processing Tools
Description: A collection of Japanese text processing tools for filling Japanese iteration marks, Japanese character type conversions, segmentation by phrase, and text normalization which is based on rules for the 'Sudachi' morphological analyzer and the 'NEologd' (Neologism dictionary for 'MeCab'). These features are specific to Japanese and are not implemented in 'ICU' (International Components for Unicode).
Author: Akiru Kato [cre, aut], Koki Takahashi [cph] , Shuhei Iitsuka [cph] , Taku Kudo [cph]
Maintainer: Akiru Kato <paithiov909@gmail.com>

Diff between audubon versions 0.1.2 dated 2022-04-02 and 0.2.0 dated 2022-05-24

 DESCRIPTION                                     |   15 ++++---
 LICENSE.note                                    |    4 +-
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 NAMESPACE                                       |    1 
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 R/strj-fill.R                                   |    2 -
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 inst/WORDLIST                                   |    1 
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 tests/testthat/test_strj-tokenize-and-segment.R |   47 ++++++++++++++----------
 18 files changed, 97 insertions(+), 96 deletions(-)

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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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Package spcov (with last version 1.01) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-09-13 1.01
2012-02-19 1.0

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Package EntropyExplorer (with last version 1.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2015-06-11 1.1
2015-03-17 1.0

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Package ConnectednessApproach (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-03-22 1.0.0

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Package WeightedPortTest (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2012-05-24 1.0

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Package KOBT (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-02-20 0.1.0

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Package Keyboard (with last version 0.1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-07-07 0.1.0

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Package ri2 (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2020-12-07 0.2.0
2019-01-24 0.1.2

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Package RepeatedHighDim (with last version 2.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-08-21 2.0.0
2013-03-11 1.01
2011-03-14 1.0

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Package EvaluateCore (with last version 0.1.2) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2021-06-12 0.1.2
2020-06-03 0.1.1

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Package mpathsenser updated to version 1.0.2 with previous version 1.0.1 dated 2022-05-19

Title: Process and Analyse Data from m-Path Sense
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.
Author: Koen Niemeijer [aut, cre]
Maintainer: Koen Niemeijer <koen.niemeijer@kuleuven.be>

Diff between mpathsenser versions 1.0.1 dated 2022-05-19 and 1.0.2 dated 2022-05-24

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 9 files changed, 1252 insertions(+), 1182 deletions(-)

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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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Package npphen updated to version 1.5.0 with previous version 1.1.1 dated 2021-11-19

Title: Vegetation Phenological Cycle and Anomaly Detection using Remote Sensing Data
Description: Calculates phenological cycle and anomalies using a non-parametric approach applied to time series of vegetation indices derived from remote sensing data or field measurements. The package implements basic and high-level functions for manipulating vector data (numerical series) and raster data (satellite derived products). Processing of very large raster files is supported. For more information, please check the following paper: Estay, S., Chávez, R.O. (2018) <doi:10.1101/301143>.
Author: Roberto O. Chavez [cre, aut], Sergio A. Estay [cre, aut], Jose A. Lastra [cre,ctb] & Carlos G. Riquelme [ctb]
Maintainer: Jose A. Lastra <jose.lastra@pucv.cl>

Diff between npphen versions 1.1.1 dated 2021-11-19 and 1.5.0 dated 2022-05-24

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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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Package mand updated to version 1.1 with previous version 1.0 dated 2021-06-29

Title: Multivariate Analysis for Neuroimaging Data
Description: Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.
Author: Atsushi Kawaguchi [aut, cre]
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>

Diff between mand versions 1.0 dated 2021-06-29 and 1.1 dated 2022-05-24

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Package IPEC updated to version 1.0.3 with previous version 1.0.1 dated 2022-05-17

Title: Root Mean Square Curvature Calculation
Description: Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.
Author: Peijian Shi [aut, cre], Peter M. Ridland [aut], David A. Ratkowsky [aut], Yang Li [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>

Diff between IPEC versions 1.0.1 dated 2022-05-17 and 1.0.3 dated 2022-05-24

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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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Package cosinor updated to version 1.2.2 with previous version 1.1 dated 2014-07-28

Title: Tools for Estimating and Predicting the Cosinor Model
Description: A set of simple functions that transforms longitudinal data to estimate the cosinor linear model as described in Tong (1976). Methods are given to summarize the mean, amplitude and acrophase, to predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs <sachsmc@gmail.com>
Maintainer: Michael Sachs <sachsmc@gmail.com>

Diff between cosinor versions 1.1 dated 2014-07-28 and 1.2.2 dated 2022-05-24

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Package CoOL updated to version 1.1.2 with previous version 1.0.3 dated 2021-07-16

Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. 2022. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. International Journal of Epidemiology <doi:10.1093/ije/dyac078>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre], Piotr Dworzynski [aut], Leila Arras [ctb], Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>

Diff between CoOL versions 1.0.3 dated 2021-07-16 and 1.1.2 dated 2022-05-24

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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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Package rspa updated to version 0.2.6 with previous version 0.2.5 dated 2019-06-19

Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such that each record satisfies a predefined set of equality and/or inequality constraints. The constraints can be defined using the 'validate' package. The core algorithms have recently been moved to the 'lintools' package, refer to 'lintools' for a more basic interface and access to a version of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>

Diff between rspa versions 0.2.5 dated 2019-06-19 and 0.2.6 dated 2022-05-24

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Package rsae updated to version 0.2 with previous version 0.1-5 dated 2014-02-13

Title: Robust Small Area Estimation
Description: Empirical best linear unbiased prediction (EBLUP) and robust prediction of the area-level means under the basic unit-level model. The model can be fitted by maximum likelihood or a (robust) M-estimator. Mean square prediction error is computed by a parametric bootstrap.
Author: Tobias Schoch [aut, cre] , Brent Richard [cph]
Maintainer: Tobias Schoch <tobias.schoch@fhnw.ch>

Diff between rsae versions 0.1-5 dated 2014-02-13 and 0.2 dated 2022-05-24

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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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Package languageserver updated to version 0.3.13 with previous version 0.3.12 dated 2021-10-19

Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol/> for details.
Author: Randy Lai [aut, cre], Kun Ren [ctb]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>

Diff between languageserver versions 0.3.12 dated 2021-10-19 and 0.3.13 dated 2022-05-24

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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>

More information about fanc at CRAN
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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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Package campsis (with last version 1.2.1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2022-05-03 1.2.1

Permanent link
Package wowa updated to version 1.0.2 with previous version 1.0.1 dated 2021-02-05

Title: Weighted Ordered Weighted Average
Description: Introduce weights into Ordered Weighted Averages and extend bivariate means based on n-ary tree construction. Please refer to the following: G. Beliakov, H. Bustince, and T. Calvo (2016, ISBN: 978-3-319-24753-3), G. Beliakov(2018) <doi:10.1002/int.21913>, G. Beliakov, J.J. Dujmovic (2016) <doi:10.1016/j.ins.2015.10.040>, J.J. Dujmovic and G. Beliakov (2017) <doi:10.1002/int.21828>.
Author: Gleb Beliakov [aut, cre], Daniela Calderon [aut]
Maintainer: Gleb Beliakov <gleb@deakin.edu.au>

Diff between wowa versions 1.0.1 dated 2021-02-05 and 1.0.2 dated 2022-05-24

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Package opdisDownsampling updated to version 0.8.2 with previous version 0.8.1 dated 2021-12-21

Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch [aut,cre] , Sebastian Malkusch [aut] , Alfred Ultsch [aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>

Diff between opdisDownsampling versions 0.8.1 dated 2021-12-21 and 0.8.2 dated 2022-05-24

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Package Directional updated to version 5.5 with previous version 5.4 dated 2022-05-15

Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>. d) Tsagris M. and Alenazi A. (2022). An investigation of hypothesis testing procedures for circular and spherical mean vectors. Communications in Statistics-Simulation and Computation (Accepted for publication). <doi:10.1080/03610918.2022.2045499>.
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>

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Package digitalDLSorteR updated to version 0.3.0 with previous version 0.2.0 dated 2022-03-10

Title: Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
Description: Deconvolution of bulk RNA-Seq data using context-specific deconvolution models based on Deep Neural Networks using scRNA-Seq data as input. These models are able to make accurate estimates of the cell composition of bulk RNA-Seq samples from the same context using the advances provided by Deep Learning and the meaningful information provided by scRNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> for more details.
Author: Diego Mananes [aut, cre] , Carlos Torroja [aut] , Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>

Diff between digitalDLSorteR versions 0.2.0 dated 2022-03-10 and 0.3.0 dated 2022-05-24

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Package campsismod updated to version 0.8.1 with previous version 0.8.0 dated 2022-02-14

Title: Generic Implementation of a PK/PD Model
Description: A generic, easy-to-use and expandable implementation of a pharmacokinetic (PK) / pharmacodynamic (PD) model based on the S4 class system. This package allows the user to read/write a pharmacometric model from/to files and adapt it further on the fly in the R environment. For this purpose, this package provides an intuitive API to add, modify or delete equations, ordinary differential equations (ODE's), model parameters or compartment properties (like infusion duration or rate, bioavailability and initial values). Finally, this package also provides a useful export of the model for use with simulation packages 'RxODE' and 'mrgsolve'. This package is designed and intended to be used with package 'campsis', a PK/PD simulation platform built on top of 'RxODE' and 'mrgsolve'.
Author: Nicolas Luyckx [aut, cre]
Maintainer: Nicolas Luyckx <nicolas.luyckx@calvagone.com>

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Package CausCor updated to version 0.1.2 with previous version 0.1.1 dated 2022-05-13

Title: Calculate Correlations and Estimate Causality
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.
Author: Tomomi Sugiyama [aut, cre]
Maintainer: Tomomi Sugiyama <sugiyama.t.am@m.titech.ac.jp>

Diff between CausCor versions 0.1.1 dated 2022-05-13 and 0.1.2 dated 2022-05-24

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Package nseval updated to version 0.4.2 with previous version 0.4 dated 2018-08-06

Title: Tools for Lazy and Non-Standard Evaluation
Description: Functions to capture, inspect, manipulate, and create lazy values (promises), "..." lists, and active calls.
Author: Peter Meilstrup <peter.meilstrup@gmail.com>
Maintainer: Peter Meilstrup <peter.meilstrup@gmail.com>

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Package gt updated to version 0.6.0 with previous version 0.5.0 dated 2022-04-21

Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.
Author: Richard Iannone [aut, cre] , Joe Cheng [aut], Barret Schloerke [aut] , RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>

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Package AntibodyTiters updated to version 0.1.24 with previous version 0.1.18 dated 2021-10-28

Title: Antibody Titer Analysis of Vaccinated Patients
Description: Visualization of antibody titer scores is valuable for examination of vaccination effects. 'AntibodyTiters' visualizes antibody titers of all or selected patients. This package also produces empty excel files in a specified format, in which users can fill in experimental data for visualization. Excel files with toy data can also be produced, so that users can see how it is visualized before obtaining real data. The data should contain titer scores at pre-vaccination, after-1st shot, after-2nd shot, and at least one additional sampling points. Patients with missing values can be included. The first two sampling points (pre-vaccination and after-1st shot) will be plotted discretely, whereas those following will be plotted on a continuous time scale that starts from the day of second shot. Half-life of titer can also be calculated for each pair of sampling points.
Author: Yuuki Mizumoto [aut], Hiroaki Kato [aut, cre] , Takeshi Urano [ctb]
Maintainer: Hiroaki Kato <hkato@med.shimane-u.ac.jp>

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Mon, 23 May 2022

Package support.BWS2 updated to version 0.4-0 with previous version 0.3-1 dated 2021-11-23

Title: Tools for Case 2 Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores. For details, see Aizaki and Fogarty (2019) <doi:10.1016/j.jocm.2019.100171>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>

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Package CNprep updated to version 2.2 with previous version 2.0 dated 2014-12-31

Title: Pre-Process DNA Copy Number (CN) Data for Detection of CN Events
Description: DNA copy number data evaluation using both their initial form (copy number as a noisy function of genomic position) and their approximation by a piecewise-constant function (segmentation), for the purpose of identifying genomic regions where the copy number differs from the norm.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>

Diff between CNprep versions 2.0 dated 2014-12-31 and 2.2 dated 2022-05-23

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Package mlflow updated to version 1.26.0 with previous version 1.25.1 dated 2022-04-20

Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine learning life cycle, see <https://mlflow.org/>. This package supports installing 'MLflow', tracking experiments, creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre], Javier Luraschi [aut], Kevin Kuo [aut] , RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>

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Package CORE updated to version 3.2 with previous version 3.0 dated 2014-12-29

Title: Cores of Recurrent Events
Description: Given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.
Author: Alex Krasnitz, Guoli Sun
Maintainer: Guoli Sun <guolisun87@gmail.com>

Diff between CORE versions 3.0 dated 2014-12-29 and 3.2 dated 2022-05-23

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Package CMplot updated to version 4.1.0 with previous version 4.0.0 dated 2022-01-13

Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>

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Package disordR updated to version 0.0-9-1 with previous version 0.0-9 dated 2021-12-09

Title: Non-Ordered Vectors
Description: Functionality for manipulating values of associative maps. Ordinary R vectors are unsuitable for working with values of associative maps because elements of an R vector may be accessed by reference to their location in the vector, but associative maps are stored in arbitrary order. However, when associating keys with values one needs both parts to be in 1-1 correspondence, so one cannot dispense with the order entirely. The 'disordR' package includes a single S4 class, disord. This class allows one to perform only those operations appropriate for manipulating values of associative maps and prevents any other operation (such as accessing an element at a particular location). A useful heuristic is that one is only allowed to access or modify a disord object using a python list comprehension. The idea is to prevent ill-defined operations on values (or keys) of associative maps, whose order is undefined or at best implementation-specific, while allowing and facilitating sensible operations.
Author: Robin K. S. Hankin [aut, cre]
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>

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Package superml updated to version 0.5.5 with previous version 0.5.4 dated 2022-05-12

Title: Build Machine Learning Models Like Using Python's Scikit-Learn Library in R
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.
Author: Manish Saraswat [aut, cre]
Maintainer: Manish Saraswat <manish06saraswat@gmail.com>

Diff between superml versions 0.5.4 dated 2022-05-12 and 0.5.5 dated 2022-05-23

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Package santaR updated to version 1.2.3 with previous version 1.2.2 dated 2022-05-23

Title: Short Asynchronous Time-Series Analysis
Description: A graphical and automated pipeline for the analysis of short time-series in R ('santaR'). This approach is designed to accommodate asynchronous time sampling (i.e. different time points for different individuals), inter-individual variability, noisy measurements and large numbers of variables. Based on a smoothing splines functional model, 'santaR' is able to detect variables highlighting significantly different temporal trajectories between study groups. Designed initially for metabolic phenotyping, 'santaR' is also suited for other Systems Biology disciplines. Command line and graphical analysis (via a 'shiny' application) enable fast and parallel automated analysis and reporting, intuitive visualisation and comprehensive plotting options for non-specialist users.
Author: Arnaud Wolfer [aut, cre] , Timothy Ebbels [ctb], Joe Cheng [ctb]
Maintainer: Arnaud Wolfer <adwolfer@gmail.com>

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Package randtoolbox updated to version 2.0.0 with previous version 1.31.1 dated 2021-10-30

Title: Toolbox for Pseudo and Quasi Random Number Generation and Random Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators, multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some generator tests - the gap test, the serial test, the poker test. See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided without the rngWELL dependency on demand. Take a look at the Distribution task view of types and tests of random number generators. Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of the SFMT algorithm from M. Matsumoto and M. Saito, the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <dutangc@gmail.com>

Diff between randtoolbox versions 1.31.1 dated 2021-10-30 and 2.0.0 dated 2022-05-23

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Package oscar updated to version 1.0.4 with previous version 1.0.3 dated 2022-05-20

Title: Optimal Subset Cardinality Regression (OSCAR) Models Using the L0-Pseudonorm
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.
Author: Teemu Daniel Laajala [aut, cre] , Kaisa Joki [aut], Anni Halkola [aut]
Maintainer: Teemu Daniel Laajala <teelaa@utu.fi>

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Package shazam updated to version 1.1.1 with previous version 1.1.0 dated 2021-07-08

Title: Immunoglobulin Somatic Hypermutation Analysis
Description: Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
Author: Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut], Julian Zhou [aut], Nima Nouri [aut], Ang Cui [ctb], Jason Vander Heiden [aut, cre], Gur Yaari [aut], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@gmail.com>

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Package condGEE updated to version 0.2.0 with previous version 0.1-4 dated 2013-08-17

Title: Parameter Estimation in Conditional GEE for Recurrent Event Gap Times
Description: Solves for the mean parameters, the variance parameter, and their asymptotic variance in a conditional GEE for recurrent event gap times, as described by Clement and Strawderman (2009) in the journal Biostatistics. Makes a parametric assumption for the length of the censored gap time.
Author: David Clement
Maintainer: David Clement <dyc24@cornell.edu>

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Package ramchoice updated to version 2.1 with previous version 2.0 dated 2021-10-22

Title: Revealed Preference and Attention Analysis in Random Limited Attention Models
Description: It is widely documented in psychology, economics and other disciplines that socio-economic agent may not pay full attention to all available alternatives, rendering standard revealed preference theory invalid. This package implements the estimation and inference procedures of Cattaneo, Ma, Masatlioglu and Suleymanov (2020) <arXiv:1712.03448> and Cattaneo, Cheung, Ma, and Masatlioglu (2022) <arXiv:2110.10650>, which utilizes standard choice data to partially identify and estimate a decision maker's preference and attention. For inference, several simulation-based critical values are provided.
Author: Matias D. Cattaneo, Paul Cheung, Xinwei Ma, Yusufcan Masatlioglu, Elchin Suleymanov
Maintainer: Xinwei Ma <x1ma@ucsd.edu>

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Package miRtest updated to version 2.0 with previous version 1.8 dated 2014-11-26

Title: Combined miRNA- And mRNA-Testing
Description: Package for combined miRNA- and mRNA-testing.
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann <stephanartmann@gmx.net>

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Package robmed updated to version 0.11.0 with previous version 0.10.1 dated 2022-03-17

Title: (Robust) Mediation Analysis
Description: Perform mediation analysis via a (fast and robust) bootstrap test.
Author: Andreas Alfons [aut, cre] , Nufer Y. Ates [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>

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Package jenga updated to version 1.2.0 with previous version 1.1.0 dated 2022-04-16

Title: Fast Extrapolation of Time Features using K-Nearest Neighbors
Description: Fast extrapolation of univariate and multivariate time features using K-Nearest Neighbors. The compact set of hyper-parameters is tuned via grid or random search.
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>

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Package text2map updated to version 0.1.5 with previous version 0.1.4 dated 2022-04-12

Title: R Tools for Text Matrices, Embeddings, and Networks
Description: This is a collection of functions optimized for working with with various kinds of text matrices. Focusing on the text matrix as the primary object - represented either as a base R dense matrix or a 'Matrix' package sparse matrix - allows for a consistent and intuitive interface that stays close to the underlying mathematical foundation of computational text analysis. In particular, the package includes functions for working with word embeddings, text networks, and document-term matrices. Methods developed in Stoltz and Taylor (2019) <doi:10.1007/s42001-019-00048-6>, Taylor and Stoltz (2020) <doi:10.1007/s42001-020-00075-8>, Taylor and Stoltz (2020) <doi:10.15195/v7.a23>, and Stoltz and Taylor (2021) <doi:10.1016/j.poetic.2021.101567>.
Author: Dustin Stoltz [aut, cre] , Marshall Taylor [aut]
Maintainer: Dustin Stoltz <maintainers@textmapping.com>

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