Thu, 01 Dec 2022

Package qtl updated to version 1.54 with previous version 1.52 dated 2022-07-09

Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes (called quantitative trait loci, QTLs) contributing to variation in quantitative traits. Broman et al. (2003) <doi:10.1093/bioinformatics/btg112>.
Author: Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wol [...truncated...]
Maintainer: Karl W Broman <broman@wisc.edu>

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Package jtools updated to version 2.2.1 with previous version 2.2.0 dated 2022-04-25

Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools for more efficiently understanding and sharing the results of (primarily) regression analyses. There are also a number of miscellaneous functions for statistical and programming purposes. Support for models produced by the survey and lme4 packages are points of emphasis.
Author: Jacob A. Long [aut, cre]
Maintainer: Jacob A. Long <jacob.long@sc.edu>

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Package infer updated to version 1.0.4 with previous version 1.0.3 dated 2022-08-22

Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.
Author: Andrew Bray [aut], Chester Ismay [aut] , Evgeni Chasnovski [aut] , Simon Couch [aut, cre] , Ben Baumer [aut] , Mine Cetinkaya-Rundel [aut] , Ted Laderas [ctb] , Nick Solomon [ctb], Johanna Hardin [ctb], Albert Y. Kim [ctb] , Neal Fultz [ctb], Doug Fr [...truncated...]
Maintainer: Simon Couch <simonpatrickcouch@gmail.com>

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Package moderndive updated to version 0.5.5 with previous version 0.5.4 dated 2022-05-13

Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] , Chester Ismay [aut] , Andrew Bray [ctb] , Delaney Moran [ctb], Evgeni Chasnovski [ctb] , Will Hopper [ctb] , Benjamin S. Baumer [ctb] , Marium Tapal [ctb] , Wayne Ndlovu [ctb], Catherine Peppers [ctb], Annah Mutaya [ctb], A [...truncated...]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>

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Package OneArm2stage updated to version 1.1.5 with previous version 1.1.4 dated 2022-09-07

Title: Optimal One-Arm Two-Stage Phase II Design with Survival Endpoint
Description: The proposed two-stage design can be used for single-arm phase II trial designs with time-to-event endpoints, which is desirable for clinical trials on immunotherapies among cancer patients. There're two advantages of the proposed approach: 1) It provides flexible choices of four underlying survival distributions and 2) the power of the design is more accurately calculated using exact variance in one-sample log-rank test. The package can be used for 1) planning the sample size; 2) conducting the interim and final analyses for the Go/No-go decisions. More details about the design method can be found in the paper: Wu, J, Chen L, Wei J, Weiss H, Chauhan A. (2020). <doi:10.1002/pst.1983>.
Author: Xiaomeng Yuan [aut, cre], Haitao Pan [aut], Jianrong Wu [aut]
Maintainer: Xiaomeng Yuan <xiaomeng.yuan@stjude.org>

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Package PNADcIBGE updated to version 0.7.1 with previous version 0.7.0 dated 2021-11-30

Title: Downloading, Reading and Analyzing PNADC Microdata
Description: Provides tools for downloading, reading and analyzing the PNADC, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package 'survey'.
Author: Douglas Braga [aut], Gabriel Assuncao [aut, cre], Luna Hidalgo [ctb]
Maintainer: Gabriel Assuncao <pacotesipd@ibge.gov.br>

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Package NNS updated to version 0.9.4 with previous version 0.9.3 dated 2022-11-03

Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole [aut, cre], Roberto Spadim [ctb]
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>

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Package canvasXpress updated to version 1.40.6-2 with previous version 1.40.6-1 dated 2022-11-11

Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.
Author: Isaac Neuhaus [aut], Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>

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Package portalr updated to version 0.3.11 with previous version 0.3.10 dated 2022-07-14

Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahua desert. The raw data files can be found at <https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] , Hao Ye [aut] , Erica M. Christensen [aut] , Juniper L. Simonis [aut] , Ellen K. Bledsoe [aut] , Renata M. Diaz [aut] , Shawn D. Taylor [aut] , Ethan P, White [aut] , S.K. Morgan Ernest [aut] , Weecology [cph]
Maintainer: Glenda M. Yenni <glenda@weecology.org>

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Package statgenSTA updated to version 1.0.10 with previous version 1.0.9 dated 2022-06-24

Title: Single Trial Analysis (STA) of Field Trials
Description: Phenotypic analysis of field trials using mixed models with and without spatial components. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (<https://vsni.co.uk/software/asreml-r>).
Author: Bart-Jan van Rossum [aut, cre] , Fred van Eeuwijk [ctb] , Martin Boer [ctb] , Marcos Malosetti [ctb] , Daniela Bustos-Korts [ctb] , Emilie J. Millet [ctb] , Joao Paulo [ctb] , Maikel Verouden [ctb] , Willem Kruijer [ctb] , Ron Wehrens [ctb] , Choazhi [...truncated...]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>

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Package ssaBSS updated to version 0.1.1 with previous version 0.1 dated 2021-04-12

Title: Stationary Subspace Analysis
Description: Stationary subspace analysis (SSA) is a blind source separation (BSS) variant where stationary components are separated from non-stationary components. Several SSA methods for multivariate time series are provided here (Flumian et al. (2021); Hara et al. (2010) <doi:10.1007/978-3-642-17537-4_52>) along with functions to simulate time series with time-varying variance and autocovariance (Patilea and Raissi(2014) <doi:10.1080/01621459.2014.884504>).
Author: Markus Matilainen [cre, aut] , Lea Flumian [aut], Klaus Nordhausen [aut] , Sara Taskinen [aut]
Maintainer: Markus Matilainen <markus.matilainen@outlook.com>

Diff between ssaBSS versions 0.1 dated 2021-04-12 and 0.1.1 dated 2022-12-01

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Package gpboost updated to version 0.8.0 with previous version 0.7.10 dated 2022-11-14

Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2022, JMLR) <https://www.jmlr.org/papers/v23/20-322.html> and Sigrist (2022, TPAMI) <doi:10.1109/TPAMI.2022.3168152> for more information on the methodology.
Author: Fabio Sigrist [aut, cre], Benoit Jacob [cph], Gael Guennebaud [cph], Nicolas Carre [cph], Pierre Zoppitelli [cph], Gauthier Brun [cph], Jean Ceccato [cph], Jitse Niesen [cph], Other authors of Eigen for the included version of Eigen [ctb, cph], Timot [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>

Diff between gpboost versions 0.7.10 dated 2022-11-14 and 0.8.0 dated 2022-12-01

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Package DPQ updated to version 0.5-3 with previous version 0.5-2 dated 2022-06-10

Title: Density, Probability, Quantile ('DPQ') Computations
Description: Computations for approximations and alternatives for the 'DPQ' (Density (pdf), Probability (cdf) and Quantile) functions for probability distributions in R. Primary focus is on (central and non-central) beta, gamma and related distributions such as the chi-squared, F, and t. -- This is for the use of researchers in these numerical approximation implementations, notably for my own use in order to improve standard R pbeta(), qgamma(), ..., etc: {'"dpq"'-functions}.
Author: Martin Maechler [aut, cre] , Morten Welinder [ctb] ), Wolfgang Viechtbauer [ctb] , 2002), Ross Ihaka [ctb] , Marius Hofert [ctb] , lssum), R-core [ctb] , R Foundation [cph]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>

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Package rintcal updated to version 0.5.2 with previous version 0.5.0 dated 2022-10-04

Title: Radiocarbon Calibration Curves
Description: The IntCal20 radiocarbon calibration curves (Reimer et al. 2020 <doi:10.1017/RDC.2020.68>) are provided as a data package, together with previous IntCal curves (IntCal13, IntCal09, IntCal04, IntCal98) and postbomb curves. Also provided are functions to copy the curves into memory, to plot the curves and their underlying data, to calibrate radiocarbon dates and to transform between different radiocarbon 'domains'.
Author: Maarten Blaauw [aut, cre]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package ndi updated to version 0.1.3 with previous version 0.1.2 dated 2022-09-30

Title: Neighborhood Deprivation Indices
Description: Computes various metrics of socio-economic deprivation and disparity in the United States. Some metrics are considered "spatial" because they consider the values of neighboring (i.e., adjacent) census geographies in their computation, while other metrics are "aspatial" because they only consider the value within each census geography. Two types of aspatial neighborhood deprivation indices (NDI) are available: including: (1) based on Messer et al. (2006) <doi:10.1007/s11524-006-9094-x> and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066> and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002> who use variables chosen by Roux and Mair (2010) <doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple demographic characteristics from the U.S. Census Bureau American Community Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5 (2005-2009 onward), the package can also (1) compute the spatial Racial Iso [...truncated...]
Author: Ian D. Buller [aut, cre, cph] , NCI [cph, fnd]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

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Package geodata updated to version 0.5-3 with previous version 0.4-13 dated 2022-11-15

Title: Download Geographic Data
Description: Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Author: Robert J. Hijmans [cre, aut], Aniruddha Ghosh [ctb], Alex Mandel [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>

Diff between geodata versions 0.4-13 dated 2022-11-15 and 0.5-3 dated 2022-12-01

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Package gdm updated to version 1.5.0-9.1 with previous version 1.5.0-3 dated 2022-04-05

Title: Generalized Dissimilarity Modeling
Description: A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.
Author: Matt Fitzpatrick [aut, cre] , Karel Mokany [aut] , Glenn Manion [aut], Diego Nieto-Lugilde [aut] , Simon Ferrier [aut] , Matthew Lisk [ctb], Chris Ware [ctb], Skip Woolley [ctb], Tom Harwood [ctb]
Maintainer: Matt Fitzpatrick <mfitzpatrick@umces.edu>

Diff between gdm versions 1.5.0-3 dated 2022-04-05 and 1.5.0-9.1 dated 2022-12-01

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Package gateR updated to version 0.1.12 with previous version 0.1.11 dated 2022-08-26

Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
Description: Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.
Author: Ian D. Buller [aut, cre, cph] , Elena Hsieh [ctb] , Debashis Ghosh [ctb] , Lance A. Waller [ctb] , NCI [cph]
Maintainer: Ian D. Buller <ian.buller@alumni.emory.edu>

Diff between gateR versions 0.1.11 dated 2022-08-26 and 0.1.12 dated 2022-12-01

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New package dcortools with initial version 0.1.4
Package: dcortools
Title: Providing Fast and Flexible Functions for Distance Correlation Analysis
Description: Provides methods for distance covariance and distance correlation (Szekely, et al. (2007) <doi:10.1214/009053607000000505>), generalized version thereof (Sejdinovic, et al. (2013) <doi:10.1214/13-AOS1140>) and corresponding tests (Berschneider, Bottcher (2018) <arXiv:1808.07280>. Distance standard deviation methods (Edelmann, et al. (2020) <doi:10.1214/19-AOS1935>) and distance correlation methods for survival endpoints (Edelmann, et al. (2021) <doi:10.1111/biom.13470>) are also included.
Version: 0.1.4
Depends: Rdpack, R (>= 3.3.3), Rcpp (>= 0.11.0), Rfast
Imports: ggplot2, pheatmap, Hmisc, stats
LinkingTo: RcppArmadillo, Rcpp, RcppEigen
License: GPL-3
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-12-01 12:59:25 UTC; edelmand
Author: Dominic Edelmann [aut, cre], Jochen Fiedler [aut]
Maintainer: Dominic Edelmann <dominic.edelmann@dkfz-heidelberg.de>
Repository: CRAN
Date/Publication: 2022-12-01 15:30:05 UTC

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New package CDMConnector with initial version 0.3.1
Package: CDMConnector
Title: Connect to an OMOP Common Data Model
Version: 0.3.1
Description: Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.
License: Apache License (>= 2)
Encoding: UTF-8
Depends: R (>= 4.0)
Imports: dplyr, DBI (>= 0.3.0), checkmate, magrittr, dbplyr, pillar, cli, purrr, rlang, tidyselect, readr, glue, waldo, arrow, methods, withr, lifecycle, jsonlite, tibble, SqlRender, pkgfilecache
Suggests: covr, knitr, rmarkdown, duckdb (>= 0.6.0), RPostgres, odbc, ggplot2, testthat (>= 3.0.0), DatabaseConnector, lubridate
Enhances: CirceR
VignetteBuilder: knitr
Additional_repositories: https://OHDSI.github.io/drat
NeedsCompilation: no
Packaged: 2022-12-01 13:51:32 UTC; adamblack
Author: Adam Black [aut, cre]
Maintainer: Adam Black <black@ohdsi.org>
Repository: CRAN
Date/Publication: 2022-12-01 15:30:09 UTC

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Package ALassoSurvIC updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-16

Title: Adaptive Lasso for the Cox Regression with Interval Censored and Possibly Left Truncated Data
Description: Penalized variable selection tools for the Cox proportional hazards model with interval censored and possibly left truncated data. It performs variable selection via penalized nonparametric maximum likelihood estimation with an adaptive lasso penalty. The optimal thresholding parameter can be searched by the package based on the profile Bayesian information criterion (BIC). The asymptotic validity of the methodology is established in Li et al. (2019 <doi:10.1177/0962280219856238>). The unpenalized nonparametric maximum likelihood estimation for interval censored and possibly left truncated data is also available.
Author: Chenxi Li, Daewoo Pak and David Todem
Maintainer: Daewoo Pak <heavyrain.pak@gmail.com>

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Package VeryLargeIntegers updated to version 0.1.9 with previous version 0.1.8 dated 2020-01-29

Title: Store and Operate with Arbitrarily Large Integers
Description: Multi-precision library that allows to store and operate with arbitrarily big integers without loss of precision. It includes a large list of tools to work with them, like: - Arithmetic and logic operators - Modular-arithmetic operators - Computer Number Theory utilities - Probabilistic primality tests - Factorization algorithms - Random generators of diferent types of integers.
Author: Javier Leiva Cuadrado
Maintainer: Javier Leiva Cuadrado <jleivacuadrado@gmail.com>

Diff between VeryLargeIntegers versions 0.1.8 dated 2020-01-29 and 0.1.9 dated 2022-12-01

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Package spdl updated to version 0.0.2 with previous version 0.0.1 dated 2022-11-22

Title: Wrapper for 'RcppSpdlog' Functions
Description: Logging functions in 'RcppSpdlog' provide access to the logging functionality from the 'spdlog' 'C++' library. This package offers shorter convenience wrappers for the 'R' functions which match the 'C++' functions, namely via, say, 'spdl::debug()' at the debug level. The actual formatting is done by the 'fmt::format()' function from the 'fmtlib' library (that is also 'std::format()' in 'C++20' or later).
Author: Dirk Eddelbuettel [aut, cre]
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between spdl versions 0.0.1 dated 2022-11-22 and 0.0.2 dated 2022-12-01

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Package ROpenCVLite updated to version 4.60.3 with previous version 4.60.2 dated 2022-07-17

Title: Helper Package for Installing OpenCV with R
Description: Installs 'OpenCV' for use by other packages. 'OpenCV' <https://opencv.org/> is library of programming functions mainly aimed at real-time computer vision. This 'Lite' version installs the stable base version of 'OpenCV' and some of its experimental externally contributed modules. It does not provide R bindings directly.
Author: Simon Garnier [aut, cre] , Muschelli John [ctb]
Maintainer: Simon Garnier <garnier@njit.edu>

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Package Patterns updated to version 1.4 with previous version 1.3 dated 2021-03-21

Title: Deciphering Biological Networks with Patterned Heterogeneous Measurements
Description: A modeling tool dedicated to biological network modeling (Bertrand and others 2020, <doi:10.1093/bioinformatics/btaa855>). It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks (Jung and others 2014, <doi:10.1093/bioinformati [...truncated...]
Author: Frederic Bertrand [cre, aut] , Myriam Maumy-Bertrand [aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>

Diff between Patterns versions 1.3 dated 2021-03-21 and 1.4 dated 2022-12-01

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Package cppRouting updated to version 3.1 with previous version 3.0 dated 2022-11-28

Title: Algorithms for Routing and Solving the Traffic Assignment Problem
Description: Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm. Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>), bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://archive.siam.org/meetings/alenex05/papers/03agoldberg.pdf>), A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>), new bidirectional A* (Pijls & Post (2009) <https://repub.eur.nl/pub/16100/ei2009-10.pdf>), Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>), PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>). Algorithms for solving the traffic assignment problem are All-or-Nothing assignment, Method of Successive Averages, Frank-Wolfe algorithm (M. Fukushima (1984) <doi:10.1016/0191-2615(84 [...truncated...]
Author: Vincent Larmet
Maintainer: Vincent Larmet <larmet.vincent@gmail.com>

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Package TraMineR updated to version 2.2-6 with previous version 2.2-5 dated 2022-08-30

Title: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences
Description: Toolbox for the manipulation, description and rendering of categorical sequences, and more generally the mining of sequence data in the field of social sciences. Although this sequence analysis toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph] , Nicolas Mueller [aut], Reto Buergin [aut] , Pierre-Alexandre Fonta [aut], Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

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Package paws.common updated to version 0.5.2 with previous version 0.5.1 dated 2022-10-02

Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services <https://aws.amazon.com>. The functions handle building, signing, and sending requests, and receiving responses. They are designed to help build higher-level interfaces to individual services, such as Simple Storage Service (S3).
Author: David Kretch [aut], Adam Banker [aut], Dyfan Jones [cre], Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>

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New package ppmlasso with initial version 1.3
Package: ppmlasso
Title: Point Process Models with LASSO-Type Penalties
Version: 1.3
Date: 2022-11-21
Author: Ian Renner
Maintainer: Ian Renner <Ian.Renner@newcastle.edu.au>
Description: Toolkit for fitting point process models with sequences of LASSO penalties ("regularisation paths"), as described in Renner, I.W. and Warton, D.I. (2013) <doi:10.1111/j.1541-0420.2012.01824.x>. Regularisation paths of Poisson point process models or area-interaction models can be fitted with LASSO, adaptive LASSO or elastic net penalties. A number of criteria are available to judge the bias-variance tradeoff.
License: GPL-3
Depends: R (>= 4.0.0), spatstat (>= 3.0-0)
Imports: methods, data.table, lattice, stats, plyr, spatstat.explore, spatstat.model, spatstat.geom
NeedsCompilation: no
Packaged: 2022-12-01 01:12:57 UTC; iwr478
Repository: CRAN
Date/Publication: 2022-12-01 12:50:02 UTC

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Package hsrecombi updated to version 0.5.1 with previous version 0.5.0 dated 2022-11-29

Title: Estimation of Recombination Rate and Maternal LD in Half-Sibs
Description: Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. The implementation relies on paternal half-sib families. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. For parameter estimation, at least one sire has to be double heterozygous at the investigated pairs of SNPs. Based on recombination rates, genetic distances between markers can be estimated. Markers with unusually large recombination rate to markers in close proximity (i.e. putatively misplaced markers) shall be discarded in this derivation. A workflow description is attached as vignette. *A pipeline is available at GitHub* <https://github.com/wittenburg/hsrecombi> Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" <doi [...truncated...]
Author: Doerte Wittenburg [aut, cre]
Maintainer: Doerte Wittenburg <wittenburg@fbn-dummerstorf.de>

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Package CorMID updated to version 0.1.7 with previous version 0.1.6 dated 2022-05-03

Title: Correct Mass Isotopologue Distribution Vectors
Description: In metabolic flux experiments tracer molecules (often glucose containing labelled carbon) are incorporated in compounds measured using mass spectrometry. The mass isotopologue distributions of these compounds needs to be corrected for natural abundance of labelled carbon and other effects, which are specific on the compound and ionization technique applied. This package provides functions to correct such effects in gas chromatography atmospheric pressure chemical ionization mass spectrometry analyses.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>

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Package brif updated to version 1.2.0 with previous version 1.1 dated 2022-11-28

Title: A Tree and Forest Tool for Classification and Regression
Description: Build decision trees and random forests for classification and regression. The implementation strikes a balance between minimizing computing efforts and maximizing the expected predictive accuracy, thus scales well to large data sets. Multi-threading is available through 'OpenMP' <https://gcc.gnu.org/wiki/openmp>.
Author: Yanchao Liu [aut, cre]
Maintainer: Yanchao Liu <yanchaoliu@wayne.edu>

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Package pqrfe updated to version 1.1 with previous version 1.0 dated 2022-10-20

Title: Penalized Quantile Regression with Fixed Effects
Description: Quantile regression with fixed effects is a general model for longitudinal data. Here we proposed to solve it by several methods. The estimation methods include three loss functions as check, asymmetric least square and asymmetric Huber functions; and three structures as simple regression, fixed effects and fixed effects with penalized intercepts by LASSO.
Author: Ian Meneghel Danilevicz [aut, cre] , Valderio A Reisen [aut], Pascal Bondon [aut]
Maintainer: Ian Meneghel Danilevicz <iandanilevicz@gmail.com>

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Package this.path updated to version 1.1.0 with previous version 1.0.1 dated 2022-09-23

Title: Get Executing Script's Path, from 'RStudio', 'Rgui', 'VSCode', 'Rscript' (Shells Including Windows Command-Line / / Unix Terminal), and 'source'
Description: Determine the full path of the executing script. Works when running a line or selection from a script in 'RStudio', 'Rgui', and 'VSCode', when using 'source', 'sys.source', 'debugSource' in 'RStudio', 'testthat::source_file', and 'knitr::knit', and when running from a shell.
Author: Andrew Simmons
Maintainer: Andrew Simmons <akwsimmo@gmail.com>

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 82 files changed, 3209 insertions(+), 2469 deletions(-)

More information about this.path at CRAN
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Package deaR updated to version 1.3.2 with previous version 1.3.1 dated 2022-10-26

Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models.See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>

Diff between deaR versions 1.3.1 dated 2022-10-26 and 1.3.2 dated 2022-12-01

 DESCRIPTION                     |    6 
 MD5                             |  210 ++++++++++++++++--------------
 NAMESPACE                       |    5 
 R/bootstrap_basic.R             |   11 -
 R/cross_efficiency.R            |   30 ++--
 R/cross_efficiency_fuzzy.R      |   10 -
 R/data_sets.R                   |  272 ++++++++++++++++++++--------------------
 R/eff_dmus.R                    |    6 
 R/efficiencies.dea.R            |    6 
 R/efficiencies.dea_fuzzy.R      |    6 
 R/is.friends.R                  |    6 
 R/lambdas.R                     |    6 
 R/make_deadata.R                |only
 R/make_deadata_fuzzy.R          |only
 R/make_malmquist.R              |only
 R/malmquist_index.R             |    8 -
 R/maximal_friends.R             |    6 
 R/model_additive.R              |   19 +-
 R/model_addsupereff.R           |    8 -
 R/model_basic.R                 |   26 +--
 R/model_deaps.R                 |    8 -
 R/model_fdh.R                   |   14 +-
 R/model_multiplier.R            |   14 +-
 R/model_nonradial.R             |    8 -
 R/model_profit.R                |   20 +-
 R/model_rdm.R                   |    2 
 R/model_sbmeff.R                |   16 +-
 R/model_sbmsupereff.R           |    8 -
 R/model_supereff.R              |   14 +-
 R/modelfuzzy_guotanaka.R        |   22 +--
 R/modelfuzzy_kaoliu.R           |   22 +--
 R/modelfuzzy_possibilistic.R    |   12 -
 R/multipliers.R                 |    6 
 R/plot.dea.R                    |    6 
 R/print.deadata.R               |only
 R/print.deadata_fuzzy.R         |only
 R/read_data.R                   |    2 
 R/read_data_fuzzy.R             |    2 
 R/read_malmquist.R              |    8 -
 R/references.R                  |    7 -
 R/rts.R                         |   12 +
 R/slacks.R                      |    6 
 R/summary.dea.R                 |   19 +-
 R/summary.deafuzzy.R            |   31 ++--
 R/targets.R                     |    6 
 R/undesirable_basic.R           |   22 +--
 build/partial.rdb               |binary
 man/Coelli_1998.Rd              |   10 -
 man/Coll_Blasco_2006.Rd         |   10 -
 man/Departments.Rd              |    8 -
 man/Doyle_Green_1994.Rd         |   10 -
 man/Economy.Rd                  |    4 
 man/EconomyLong.Rd              |    4 
 man/Electric_plants.Rd          |   10 -
 man/Fortune500.Rd               |   10 -
 man/Fried1993.Rd                |    8 -
 man/FuzzyExample.Rd             |   20 +-
 man/Golany_Roll_1989.Rd         |   10 -
 man/Grifell_Lovell_1999.Rd      |    4 
 man/Guo_Tanaka_2001.Rd          |   14 +-
 man/Hotels.Rd                   |   10 -
 man/Hua_Bian_2007.Rd            |   10 -
 man/Kao_Liu_2003.Rd             |   14 +-
 man/Leon2003.Rd                 |   14 +-
 man/Libraries.Rd                |   22 +--
 man/Lim_Zhu_2015.Rd             |   10 -
 man/PFT1981.Rd                  |   18 +-
 man/Power_plants.Rd             |   14 +-
 man/Ruggiero2007.Rd             |   10 -
 man/Supply_Chain.Rd             |   10 -
 man/Tone2001.Rd                 |    8 -
 man/Tone2003.Rd                 |   10 -
 man/bootstrap_basic.Rd          |    6 
 man/cross_efficiency.Rd         |   30 ++--
 man/cross_efficiency_fuzzy.Rd   |   10 -
 man/eff_dmus.Rd                 |    6 
 man/efficiencies.dea.Rd         |    6 
 man/efficiencies.dea_fuzzy.Rd   |    6 
 man/is.friends.Rd               |    4 
 man/lambdas.Rd                  |    6 
 man/make_deadata.Rd             |only
 man/make_deadata_fuzzy.Rd       |only
 man/make_malmquist.Rd           |only
 man/malmquist_index.Rd          |    6 
 man/maximal_friends.Rd          |    4 
 man/model_additive.Rd           |   17 +-
 man/model_addsupereff.Rd        |    6 
 man/model_basic.Rd              |   22 +--
 man/model_deaps.Rd              |    6 
 man/model_fdh.Rd                |   12 -
 man/model_multiplier.Rd         |   12 -
 man/model_nonradial.Rd          |    6 
 man/model_profit.Rd             |   18 +-
 man/model_sbmeff.Rd             |   14 +-
 man/model_sbmsupereff.Rd        |    6 
 man/model_supereff.Rd           |   12 -
 man/modelfuzzy_guotanaka.Rd     |   20 +-
 man/modelfuzzy_kaoliu.Rd        |   20 +-
 man/modelfuzzy_possibilistic.Rd |   10 -
 man/multipliers.Rd              |    6 
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 man/read_malmquist.Rd           |    3 
 man/references.Rd               |    6 
 man/rts.Rd                      |    8 -
 man/slacks.Rd                   |    6 
 man/summary.dea.Rd              |   19 +-
 man/summary.dea_fuzzy.Rd        |   25 +--
 man/targets.Rd                  |    6 
 man/undesirable_basic.Rd        |   16 +-
 111 files changed, 808 insertions(+), 758 deletions(-)

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New package VALIDICLUST with initial version 0.1.0
Package: VALIDICLUST
Title: VALID Inference for Clusters Separation Testing
Version: 0.1.0
Author: Benjamin Hivert
Maintainer: Benjamin Hivert <benjamin.hivert@u-bordeaux.fr>
Description: Given a partition resulting from any clustering algorithm, the implemented tests allow valid post-clustering inference by testing if a given variable significantly separates two of the estimated clusters. Methods are detailed in: Hivert B, Agniel D, Thiebaut R & Hejblum BP (2022). "Post-clustering difference testing: valid inference and practical considerations", <arXiv:2210.13172>.
Encoding: UTF-8
Imports: diptest, dplyr
Depends: R (>= 3.6)
License: MIT + file LICENSE
NeedsCompilation: no
Packaged: 2022-11-30 15:06:52 UTC; benjaminhivert
Repository: CRAN
Date/Publication: 2022-12-01 08:20:02 UTC

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New package fitPS with initial version 0.2
Package: fitPS
Title: Fit Zeta Distributions to Forensic Data
Version: 0.2
Date: 2022-11-30
Description: Fits zeta distributions (discrete power laws) to data that arises from forensic surveys of clothing on the presence of glass and paint in various populations. The general method is described to some extent in Coulson, S.A., Buckleton, J.S., Gummer, A.B., and Triggs, C.M. (2001) <doi:10.1016/S1355-0306(01)71847-3>, although the implementation differs.
License: GPL (>= 2)
Encoding: UTF-8
Depends: dplyr, VGAM, methods, readxl
URL: https://github.com/jmcurran/fitPS
BugReports: https://github.com/jmcurran/fitPS/issues
NeedsCompilation: no
Packaged: 2022-11-30 20:04:53 UTC; jcur002
Author: James Curran [aut, cre]
Maintainer: James Curran <j.curran@auckland.ac.nz>
Repository: CRAN
Date/Publication: 2022-12-01 08:10:02 UTC

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New package rapidphylo with initial version 0.1.0
Package: rapidphylo
Title: Rapidly Estimate Phylogeny from Large Allele Frequency Data Using Root Distances Method
Version: 0.1.0
Author: Arindam RoyChoudhury [aut, cre, cph], Jing Peng [aut], Ying Li [aut], Laura Kubatko [aut, ths]
Maintainer: Arindam RoyChoudhury <arr2014@med.cornell.edu>
Description: Rapidly estimates tree-topology from large allele frequency data using Root Distances Method, under a Brownian Motion Model. See Jing Peng et al. (2021) <doi:10.1016/j.ympev.2021.107142>.
License: AGPL-3
URL: https://github.com/ArindamRoyChoudhury/rapidphylo
BugReports: https://github.com/ArindamRoyChoudhury/rapidphylo/issues
Depends: R (>= 4.1.0)
Imports: ape, phangorn, stats
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2022-11-30 15:06:13 UTC; yil4013
Repository: CRAN
Date/Publication: 2022-12-01 08:00:02 UTC

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New package HTT with initial version 0.1.0
Package: HTT
Title: Hypothesis Testing Tree
Version: 0.1.0
Date: 2022-11-06
Author: Jiaqi Hu [cre, aut], Zhe Gao [aut], Bo Zhang [aut], Xueqin Wang [aut]
Maintainer: Jiaqi Hu <hujiaqi@mail.ustc.edu.cn>
Description: A novel decision tree algorithm in the hypothesis testing framework. The algorithm examines the distribution difference between two child nodes over all possible binary partitions. The test statistic of the hypothesis testing is equivalent to the generalized energy distance, which enables the algorithm to be more powerful in detecting the complex structure, not only the mean difference. It is applicable for numeric, nominal, ordinal explanatory variables and the response in general metric space of strong negative type. The algorithm has superior performance compared to other tree models in type I error, power, prediction accuracy, and complexity.
License: GPL-3
VignetteBuilder: knitr
Depends: R (>= 3.5.0)
Suggests: knitr, rmarkdown, MASS
Imports: Rcpp (>= 1.0.6), ggraph, igraph, ggplot2
LinkingTo: Rcpp
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-11-30 11:57:04 UTC; jqhu
Repository: CRAN
Date/Publication: 2022-12-01 08:00:05 UTC

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Package toRvik (with last version 1.1.1) was removed from CRAN

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

2022-11-08 1.1.1

Permanent link
Package mclustAddons (with last version 0.7) was removed from CRAN

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

2022-11-15 0.7
2021-12-17 0.6
2021-09-29 0.5

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