Fri, 01 Apr 2022

Package btergm updated to version 1.10.6 with previous version 1.10.3 dated 2021-06-25

Title: Temporal Exponential Random Graph Models by Bootstrapped Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs. As described in Leifeld, Cranmer and Desmarais (2018), JStatSoft <doi:10.18637/jss.v083.i06>.
Author: Philip Leifeld [aut, cre], Skyler J. Cranmer [ctb], Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@essex.ac.uk>

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Package MLVSBM updated to version 0.2.3 with previous version 0.2.2 dated 2021-06-10

Title: A Stochastic Block Model for Multilevel Networks
Description: Simulation, inference and clustering of multilevel networks using a Stochastic Block Model framework as described in Chabert-Liddell, Barbillon, Donnet and Lazega (2021) <doi:10.1016/j.csda.2021.107179>. A multilevel network is defined as the junction of two interaction networks, the upper level or inter-organizational level and the lower level or inter-individual level. The inter-level represents an affiliation relationship.
Author: Saint-Clair Chabert-Liddell [aut, cre]
Maintainer: Saint-Clair Chabert-Liddell <academic@chabert-liddell.com>

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New package iq with initial version 1.9.3
Package: iq
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Version: 1.9.3
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Description: An implementation of the maximal peptide ratio extraction module of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Depends: R (>= 2.10)
License: BSD_3_clause + file LICENSE
Imports: Rcpp (>= 1.0.5)
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/tvpham/iq
BugReports: https://github.com/tvpham/iq/issues
NeedsCompilation: yes
Packaged: 2022-03-31 23:17:56 UTC; t.pham
Author: Thang Pham [aut, cre, cph, ctb] , Alex Henneman [ctb]
Repository: CRAN
Date/Publication: 2022-04-01 23:40:02 UTC

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Package flimo updated to version 0.1.1 with previous version 0.1.0 dated 2022-03-30

Title: Fixed Landscape Inference MethOd
Description: Likelihood-free inference method for stochastic models. Uses a deterministic optimizer on simple simulations of the model that are performed with a prior drawn randomness by applying the inverse transform method. Is designed to work on its own and also by using the Julia package Jflimo. See the git page of the project : <https://metabarcoding.org/flimo>.
Author: Sylvain Moinard
Maintainer: Sylvain Moinard <sylvain.moinard@univ-grenoble-alpes.fr>

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Package dynaTree updated to version 1.2-12 with previous version 1.2-11 dated 2022-03-31

Title: Dynamic Trees for Learning and Design
Description: Inference by sequential Monte Carlo for dynamic tree regression and classification models with hooks provided for sequential design and optimization, fully online learning with drift, variable selection, and sensitivity analysis of inputs. Illustrative examples from the original dynamic trees paper (Gramacy, Taddy & Polson (2011); <doi:10.1198/jasa.2011.ap09769>) are facilitated by demos in the package; see demo(package="dynaTree").
Author: Robert B. Gramacy <rbg@vt.edu>, Matt A. Taddy and Christoforos Anagnostopoulos
Maintainer: Robert B. Gramacy <rbg@vt.edu>

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Package dodgr updated to version 0.2.13 with previous version 0.2.12 dated 2021-10-18

Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre], Andreas Petutschnig [aut], Robin Lovelace [ctb], Andrew Smith [ctb], Malcolm Morgan [ctb], Shane Saunders [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package BayesMallows updated to version 1.1.1 with previous version 1.1.0 dated 2021-12-03

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 spacejamr updated to version 0.2.1 with previous version 0.2 dated 2022-02-03

Title: Simulate Spatial Bernoulli Networks
Description: Social network analysis is becoming commonplace in many social science disciplines, but access to useful network data, especially among marginalized populations, still remains a formidable challenge. This package mitigates that problem by providing tools to simulate spatial Bernoulli networks as proposed in Carter T. Butts (2002, ISBN:978-0-493-72676-2), "Spatial models of large-scale interpersonal networks." Using this package, network analysts can simulate a spatial point process or sequence with a given number of nodes inside a geographical boundary and estimate the probability of a tie formation between all node pairs. When simulating a network, an analyst can choose between five spatial interaction functions. The package also enables quick comparison of summary statistics for simulated networks and provides simple to use plotting methods for its classes that return plots which can be further refined with the 'ggplot2' package.
Author: Darren Colby [aut, cre]
Maintainer: Darren Colby <dscolby17@gmail.com>

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Package matsbyname updated to version 0.5.0 with previous version 0.4.25 dated 2021-10-12

Title: An Implementation of Matrix Mathematics
Description: An implementation of matrix mathematics wherein operations are performed "by name."
Author: Matthew Heun [aut, cre]
Maintainer: Matthew Heun <matthew.heun@me.com>

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Package SSBtools updated to version 1.3.0 with previous version 1.2.2 dated 2021-09-07

Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included (Langsrud, 2020) <doi:10.13140/RG.2.2.27313.61283>. The hierarchy specification functions are useful within statistical disclosure control.
Author: Oyvind Langsrud [aut, cre], Daniel Lupp [aut], Bjoern-Helge Mevik [cph]
Maintainer: Oyvind Langsrud <oyl@ssb.no>

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Package future.callr updated to version 0.8.0 with previous version 0.7.0 dated 2021-11-21

Title: A Future API for Parallel Processing using 'callr'
Description: Implementation of the Future API on top of the 'callr' package. This allows you to process futures, as defined by the 'future' package, in parallel out of the box, on your local (Linux, macOS, Windows, ...) machine. Contrary to backends relying on the 'parallel' package (e.g. 'future::multisession') and socket connections, the 'callr' backend provided here can run more than 125 parallel R processes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package FDRestimation updated to version 1.0.1 with previous version 1.0.0 dated 2020-11-14

Title: Estimate, Plot, and Summarize False Discovery Rates
Description: The user can directly compute and display false discovery rates from inputted p-values or z-scores under a variety of assumptions. p.fdr() computes FDRs, adjusted p-values and decision reject vectors from inputted p-values or z-values. get.pi0() estimates the proportion of data that are truly null. plot.p.fdr() plots the FDRs, adjusted p-values, and the raw p-values points against their rejection threshold lines.
Author: Megan Murray [aut, cre], Jeffrey Blume [aut]
Maintainer: Megan Murray <megan.c.hollister@vanderbilt.edu>

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Package feisr updated to version 1.3.0 with previous version 1.2.0 dated 2021-02-25

Title: Estimating Fixed Effects Individual Slope Models
Description: Provides the function feis() to estimate fixed effects individual slope (FEIS) models. The FEIS model constitutes a more general version of the often-used fixed effects (FE) panel model, as implemented in the package 'plm' by Croissant and Millo (2008) <doi:10.18637/jss.v027.i02>. In FEIS models, data are not only person demeaned like in conventional FE models, but detrended by the predicted individual slope of each person or group. Estimation is performed by applying least squares lm() to the transformed data. For more details on FEIS models see Bruederl and Ludwig (2015, ISBN:1446252442); Frees (2001) <doi:10.2307/3316008>; Polachek and Kim (1994) <doi:10.1016/0304-4076(94)90075-2>; Ruettenauer and Ludwig (2020) <doi:10.1177/0049124120926211>; Wooldridge (2010, ISBN:0262294354). To test consistency of conventional FE and random effects estimators against heterogeneous slopes, the package also provides the functions feistest() for an artificial regression test and bsfeistest() for a bootstrapped version of the Hausman test.
Author: Tobias Ruettenauer [aut, cre] , Volker Ludwig [aut]
Maintainer: Tobias Ruettenauer <ruettenauer@sowi.uni-kl.de>

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Package dail updated to version 1.3 with previous version 1.1 dated 2022-01-17

Title: Data from Access to Information Law
Description: Downloads the public data available from the Brazilian Access to Information Law and and performs a search on information requests and appeals made since 2015.
Author: Igor Laltuf [aut, cre]
Maintainer: Igor Laltuf <igorlaltuf@gmail.com>

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Package BE updated to version 0.2.0 with previous version 0.1.5 dated 2021-12-15

Title: Bioequivalence Study Data Analysis
Description: Analyze bioequivalence study data with industrial strength. Sample size could be determined for various crossover designs, such as 2x2 design, 2x4 design, 4x4 design, Balaam design, Two-sequence dual design, and William design. Reference: Chow SC, Liu JP. Design and Analysis of Bioavailability and Bioequivalence Studies. 3rd ed. (2009, ISBN:978-1-58488-668-6).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>

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Package Rlabkey updated to version 2.8.4 with previous version 2.8.3 dated 2022-02-25

Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to load live data from a 'LabKey' Server, <https://www.labkey.com/>, into the R environment for analysis, provided users have permissions to read the data. It also enables R users to insert, update, and delete records stored on a 'LabKey' Server, provided they have appropriate permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>

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Package ptmixed updated to version 1.1.2 with previous version 1.1.1 dated 2021-12-01

Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed model described in Signorelli et al. (2021, <doi:10.1177/1471082X20936017>). Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre, cph] , Pietro Spitali [ctb], Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>

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Package NIMAA updated to version 0.2.0 with previous version 0.1.0 dated 2021-09-13

Title: Nominal Data Mining Analysis
Description: Functions for nominal data mining based on bipartite graphs, which build a pipeline for analysis and missing values imputation. Methods are mainly from the paper: Jafari, Mohieddin, et al. (2021) <doi:10.1101/2021.03.18.436040>, some new ones are also included.
Author: Mohieddin Jafari [aut, cre], Cheng Chen [aut]
Maintainer: Mohieddin Jafari <mohieddin.jafari@helsinki.fi>

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Package yorkr updated to version 0.0.32 with previous version 0.0.31 dated 2022-02-05

Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>

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Package VARSEDIG updated to version 2.1 with previous version 1.9 dated 2018-12-07

Title: An Algorithm for Morphometric Characters Selection and Statistical Validation in Morphological Taxonomy
Description: An algorithm which identifies the morphometric features that significantly discriminate two taxa and validates the morphological distinctness between them via a Monte-Carlo test, polar coordinates and overlap of the area under the density curve.

Permanent link

Package RInside updated to version 0.2.17 with previous version 0.2.16 dated 2020-03-12

Title: C++ Classes to Embed R in C++ (and C) Applications
Description: C++ classes to embed R in C++ (and C) applications A C++ class providing the R interpreter is offered by this package making it easier to have "R inside" your C++ application. As R itself is embedded into your application, a shared library build of R is required. This works on Linux, OS X and even on Windows provided you use the same tools used to build R itself. Numerous examples are provided in the nine subdirectories of the examples/ directory of the installed package: standard, 'mpi' (for parallel computing), 'qt' (showing how to embed 'RInside' inside a Qt GUI application), 'wt' (showing how to build a "web-application" using the Wt toolkit), 'armadillo' (for 'RInside' use with 'RcppArmadillo'), 'eigen' (for 'RInside' use with 'RcppEigen'), and 'c_interface' for a basic C interface and 'Ruby' illustration. The examples use 'GNUmakefile(s)' with GNU extensions, so a GNU make is required (and will use the 'GNUmakefile' automatically). 'Doxygen'-generated documentation of the C++ classes is available at the 'RInside' website as well.
Author: Dirk Eddelbuettel, Romain Francois, and Lance Bachmeier
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package mpm updated to version 1.0-23 with previous version 1.0-22 dated 2011-11-25

Title: Multivariate Projection Methods
Description: Exploratory graphical analysis of multivariate data, specifically gene expression data with different projection methods: principal component analysis, correspondence analysis, spectral map analysis.
Author: Luc Wouters [aut], Tobias Verbeke [ctb], Laure Cougnaud [cre]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>

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New package KODAMA with initial version 1.9
Package: KODAMA
Version: 1.9
Date: 2022-03-29
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>
Title: Knowledge Discovery by Accuracy Maximization
Description: An unsupervised and semi-supervised learning algorithm that performs feature extraction from noisy and high-dimensional data. It facilitates identification of patterns representing underlying groups on all samples in a data set. Based on Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705> and Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>.
Depends: R (>= 2.10.0), stats, minerva
Imports: Rcpp (>= 0.12.4)
LinkingTo: Rcpp, RcppArmadillo
Suggests: rgl, knitr, rmarkdown
VignetteBuilder: knitr
SuggestsNote: No suggestions
License: GPL (>= 2)
Packaged: 2022-03-29 13:44:07 UTC; User
NeedsCompilation: yes
Repository: CRAN
Author: Stefano Cacciatore [aut, trl, cre] , Leonardo Tenori [aut]
Date/Publication: 2022-04-01 12:10:12 UTC

More information about KODAMA at CRAN
Permanent link

Package ebirdst updated to version 0.3.5 with previous version 0.3.4 dated 2022-03-16

Title: Access and Analyze eBird Status and Trends Data
Description: Tools to download, map, plot and analyze eBird Status and Trends data (<https://ebird.org/science/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by citizen scientists. eBird Status and Trends uses these data to model continental bird abundances, range boundaries, habitat associations, and trends.
Author: Matthew Strimas-Mackey [aut, cre] , Shawn Ligocki [aut], Tom Auer [aut] , Daniel Fink [aut] , Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>

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Package chemCal updated to version 0.2.3 with previous version 0.2.2 dated 2021-04-17

Title: Calibration Functions for Analytical Chemistry
Description: Simple functions for plotting linear calibration functions and estimating standard errors for measurements according to the Handbook of Chemometrics and Qualimetrics: Part A by Massart et al. (1997) There are also functions estimating the limit of detection (LOD) and limit of quantification (LOQ). The functions work on model objects from - optionally weighted - linear regression (lm) or robust linear regression ('rlm' from the 'MASS' package).
Author: Johannes Ranke [aut, cre, cph]
Maintainer: Johannes Ranke <johannes.ranke@jrwb.de>

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Package spatstat.local updated to version 4.1-5 with previous version 4.1-4 dated 2022-02-23

Title: Extension to 'spatstat' for Local Composite Likelihood
Description: Extension to the 'spatstat' package, enabling the user to fit point process models to point pattern data by local composite likelihood ('geographically weighted regression').
Author: Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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Package projpred updated to version 2.1.0 with previous version 2.0.2 dated 2020-10-28

Title: Projection Predictive Feature Selection
Description: Performs projection predictive feature selection for generalized linear models and generalized linear and additive multilevel models (see Piironen, Paasiniemi and Vehtari, 2020, <doi:10.1214/20-EJS1711>; Catalina, Bürkner and Vehtari, 2020, <arXiv:2010.06994>). The package is compatible with the 'rstanarm' and 'brms' packages, but other reference models can also be used. See the documentation as well as the package vignette for more information and examples.
Author: Juho Piironen [aut], Markus Paasiniemi [aut], Alejandro Catalina [aut], Aki Vehtari [aut], Frank Weber [cre, aut], Jonah Gabry [ctb], Marco Colombo [ctb], Paul-Christian Buerkner [ctb], Hamada S. Badr [ctb]
Maintainer: Frank Weber <fweber144@protonmail.com>

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Package huito updated to version 0.1.3 with previous version 0.1.2 dated 2022-01-20

Title: Flexible and Reproducible Label Designs
Description: An open-source R package to deploys flexible and reproducible labels using layers. The 'huito' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] , Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>

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Package GJRM updated to version 0.2-6 with previous version 0.2-5.1 dated 2021-10-12

Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>

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Package conquestr updated to version 0.9.96 with previous version 0.8.5 dated 2020-08-10

Title: An R Package to Extend 'ACER ConQuest'
Description: Extends 'ACER ConQuest' through a family of functions designed to improve graphical outputs and help with advanced analysis (e.g., differential item functioning). Allows R users to call 'ACER ConQuest' from within R and read 'ACER ConQuest' System Files (generated by the command 'put'). Requires 'ACER ConQuest' version 5.19.5 or later. A demonstration version can be downloaded from <https://shop.acer.org/acer-conquest-5.html>.
Author: Dan Cloney [aut, cre] , Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>

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Package BGVAR updated to version 2.4.4 with previous version 2.4.3 dated 2021-11-06

Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available.
Author: Maximilian Boeck [aut, cre] , Martin Feldkircher [aut] , Florian Huber [aut] , Darjus Hosszejni [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@da-vienna.ac.at>

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Package baRcodeR updated to version 0.1.7 with previous version 0.1.5 dated 2020-03-07

Title: Label Creation for Tracking and Collecting Data from Biological Samples
Description: Tools to generate unique identifier codes and printable barcoded labels for the management of biological samples. The creation of unique ID codes and printable PDF files can be initiated by standard commands, user prompts, or through a GUI addin for R Studio. Biologically informative codes can be included for hierarchically structured sampling designs.
Author: Yihan Wu [aut] , Robert Colautti [aut, cre] , Emily Bao [ctb], Lluís Revilla Sancho [rev] , Rayna Harris [rev]
Maintainer: Robert Colautti <robert.colautti@queensu.ca>

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Package tram updated to version 0.7-0 with previous version 0.6-4 dated 2022-01-14

Title: Transformation Models
Description: Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to transformation models for clustered data is provided (Hothorn, 2019, <arxiv:1910.09219>). Multivariate conditional transformation models (<arxiv:1906.03151>) can be fitted as well.
Author: Torsten Hothorn [aut, cre] , Luisa Barbanti [aut] , Brian Ripley [ctb], Bill Venables [ctb], Douglas M. Bates [ctb], Nadja Klein [ctb]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

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Package mombf updated to version 3.1.3 with previous version 3.0.7 dated 2021-11-03

Title: Bayesian Model Selection and Averaging for Non-Local and Local Priors
Description: Bayesian model selection and averaging for regression and mixtures for non-local and selected local priors.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck, Oriol Abril, Miquel Torrens
Maintainer: David Rossell <rosselldavid@gmail.com>

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Package ggfun updated to version 0.0.6 with previous version 0.0.5 dated 2022-01-20

Title: Miscellaneous Functions for 'ggplot2'
Description: Useful functions to edit 'ggplot' object (e.g., setting fonts for theme and layers, adding rounded rectangle as background for each of the legends).
Author: Guangchuang Yu [aut, cre, cph] , Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package spatstat updated to version 2.3-4 with previous version 2.3-3 dated 2022-02-20

Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images. Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported. Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

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New package PKPDsim with initial version 1.1.1
Package: PKPDsim
Title: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations
Version: 1.1.1
Date: 2022-03-31
Depends: R (>= 3.0.2)
Imports: Rcpp (>= 0.12.9), BH, data.table, stringr, MASS, randtoolbox, jsonlite, stats, parallel, magrittr
Suggests: httr, testthat (>= 3.0.0), mockery
LinkingTo: BH, Rcpp (>= 0.12.9)
Description: Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD) models described by differential equation (DE) systems. Simulation using ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015) <doi:10.1016/j.vascn.2015.03.004>).
License: MIT + file LICENSE
LazyData: TRUE
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2022-03-31 22:37:01 UTC; ron@insight-rx.com
Author: Ron Keizer [aut, cre], Jasmine Hughes [aut], Dominic Tong [aut], Kara Woo [aut], InsightRX [cph, fnd]
Maintainer: Ron Keizer <ron@insight-rx.com>
Repository: CRAN
Date/Publication: 2022-04-01 08:10:02 UTC

More information about PKPDsim at CRAN
Permanent link

Package TestDesign updated to version 1.3.1 with previous version 1.3.0 dated 2022-03-10

Title: Optimal Test Design Approach to Fixed and Adaptive Test Construction
Description: Uses the optimal test design approach by Birnbaum (1968, ISBN:9781593119348) and van der Linden (2018) <doi:10.1201/9781315117430> to construct fixed, adaptive, and parallel tests. Supports the following mixed-integer programming (MIP) solver packages: 'lpsymphony', 'Rsymphony', 'gurobi', 'lpSolve', and 'Rglpk'. The 'gurobi' package is not available from CRAN; see <https://www.gurobi.com/downloads/>.
Author: Seung W. Choi [aut, cre] , Sangdon Lim [aut]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>

Diff between TestDesign versions 1.3.0 dated 2022-03-10 and 1.3.1 dated 2022-04-01

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More information about TestDesign at CRAN
Permanent link

Package ssdtools updated to version 1.0.0 with previous version 0.3.7 dated 2021-10-27

Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and Weibull to censored and/or weighted data. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] , Carl Schwarz [aut, ctr], Rebecca Fisher [ctb], David Fox [ctb], Angeline Tillmanns [ctb], Ali Azizishirazi [ctb], Kathleen McTavish [ctb], Heather Thompson [ctb], Andy Teucher [ctb], Emilie Doussantousse [ctb], Stephanie [...truncated...]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>

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New package SPCompute with initial version 1.0.1
Package: SPCompute
Title: Compute Power or Sample Size for GWAS with Covariate Effect
Version: 1.0.1
Author: Ziang Zhang
Maintainer: Ziang Zhang <aguero.zhang@mail.utoronto.ca>
Description: Fast computation of the required sample size or the achieved power, for GWAS studies with different types of covariate effects and different types of covariate-gene dependency structure. For the detailed description of the methodology, see Zhang (2022) "Power and Sample Size Computation for Genetic Association Studies of Binary Traits: Accounting for Covariate Effects" <arXiv:2203.15641>.
License: GPL (>= 3)
Imports: Matrix, stats
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2022-03-31 15:01:42 UTC; ziangzhang
Repository: CRAN
Date/Publication: 2022-04-01 07:50:04 UTC

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New package SpatialPOP with initial version 0.1.0
Package: SpatialPOP
Title: Generation of Spatial Data with Spatially Varying Model Parameter
Version: 0.1.0
Author: Nobin Chandra Paul
Maintainer: Nobin Chandra Paul<ncp375@gmail.com>
Depends: R(>= 2.10)
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Description: A spatial population can be generated based on spatially varying regression model under the assumption that observations are collected from a uniform two-dimensional grid consist of (m * m) lattice points with unit distance between any two neighbouring points. For method details see Chao, Liu., Chuanhua, Wei. and Yunan, Su. (2018).<DOI:10.1080/10485252.2018.1499907>. This spatially generated data can be used to test different issues related to the statistical analysis of spatial data. This generated spatial data can be utilized in geographically weighted regression analysis for studying the spatially varying relationships among the variables.
License: GPL (>= 2.0)
Encoding: UTF-8
Imports: base,MASS,stats, qpdf, numbers
NeedsCompilation: no
Packaged: 2022-03-31 17:28:08 UTC; nobin ch paul
Repository: CRAN
Date/Publication: 2022-04-01 07:50:02 UTC

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New package QWDAP with initial version 1.1.17
Package: QWDAP
Title: Quantum Walk-Based Data Analysis and Prediction
Version: 1.1.17
Date: 2022-04-01
Author: Binghuang Pan [aut, cre], Zhaoyuan Yu [aut], Xu Hu [ctb], Yuhao Teng [ctb]
Maintainer: Binghuang Pan <bright1up@163.com>
Description: The modeling and prediction of graph-associated time series(GATS) based on continuous time quantum walk. This software is mainly used for feature extraction, modeling, prediction and result evaluation of GATS, including continuous time quantum walk simulation, feature selection, regression analysis, time series prediction, and series fit calculation.
Imports: pls, CORElearn, Rcpp, methods
LinkingTo: Rcpp,RcppEigen
License: GPL-2
Encoding: UTF-8
LazyData: true
LazyDataCompression: xz
Depends: R (>= 3.5.0)
NeedsCompilation: yes
SystemRequirements: C++11
Packaged: 2022-04-01 03:35:07 UTC; bright1
Repository: CRAN
Date/Publication: 2022-04-01 07:20:02 UTC

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New package pop.lion with initial version 1.0
Package: pop.lion
Title: Models for Simulating Lion Populations
Version: 1.0
Date: 2022-03-28
Author: Guillaume Chapron [aut, cre], Matthew Wijers [ctb], Andrew Loveridge [ctb], David Macdonald [ctb]
Maintainer: Guillaume Chapron <gchapron@carnivoreconservation.org>
Description: Simulate the dynamic of lion populations using a specific Individual-Based Model (IBM) compiled in C.
License: GPL-3
Depends: parallel, abind
NeedsCompilation: yes
Encoding: UTF-8
Packaged: 2022-03-31 20:10:49 UTC; guillaume
Repository: CRAN
Date/Publication: 2022-04-01 08:00:02 UTC

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Package MolgenisArmadillo updated to version 1.1.3 with previous version 1.0.3 dated 2021-10-12

Title: Armadillo Client for the Armadillo Service
Description: A set of functions to be able to manage data shared on a 'MOLGENIS Armadillo' storage server ('MinIO').
Author: Mariska Slofstra [aut, cre] , Sido Haakma [aut] , Tommy de Boer [aut] , Fleur Kelpin [aut] , Morris Swertz [aut]
Maintainer: Mariska Slofstra <m.k.slofstra@umcg.nl>

Diff between MolgenisArmadillo versions 1.0.3 dated 2021-10-12 and 1.1.3 dated 2022-04-01

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New package manydata with initial version 0.7.3
Package: manydata
Title: A Portal for Global Governance Data
Version: 0.7.3
Date: 2022-04-01
Description: This is the core package for the many packages universe. It includes functions to help researchers work with and contribute to event datasets on global governance.
License: CC BY 4.0
URL: https://github.com/globalgov/manydata
BugReports: https://github.com/globalgov/manydata/issues
Depends: R (>= 3.5.0)
Imports: covr, tibble, dplyr, messydates, lubridate, pkgdown, purrr, rlang, roxygen2, stringr, usethis, jsonlite, remotes, httr, progress, ggplot2
Suggests: testthat, anytime, mice, withr, haven, readxl, readr, knitr, rmarkdown
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-03-31 22:13:02 UTC; hollway
Author: James Hollway [cre, aut, ctb] , Henrique Sposito [ctb] , Bernhard Bieri [ctb] , Esther Peev [ctb] , Jael Tan [ctb]
Maintainer: James Hollway <james.hollway@graduateinstitute.ch>
Repository: CRAN
Date/Publication: 2022-04-01 08:00:05 UTC

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Package MAFDash updated to version 0.2.1 with previous version 0.2.0 dated 2022-02-04

Title: Create an HTML Dashboard to Visualize Data from MAF File
Description: Mutation Annotation Format (MAF) is a tabular data format used for storing genetic mutation data. For example, The Cancer Genome Atlas (TCGA) project has made MAF files from each project publicly available. This package contains a set of tools to easily create an HTML dashboard to summarize and visualize data from MAF file. The resulting HTML file serves as a self-contained report that can be used to explore the result.
Author: Ashish Jain [aut, cre], Mayank Tandon [aut], Frederick National Laboratory For Cancer Research [cph]
Maintainer: Ashish Jain <jain.ashishjain1@gmail.com>

Diff between MAFDash versions 0.2.0 dated 2022-02-04 and 0.2.1 dated 2022-04-01

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New package hyperbrick with initial version 1.0
Package: hyperbrick
Title: Accessory Tools for Preprocessing Hyper-Spectral Images
Version: 1.0
Date: 2022-03-29
Description: Read and execute preprocessing procedures on hyper-spectral images. These type of sensor data are usually recorded in a raw format. This package contains some easy-to-use functions to promptly build the image with some basic radiometric calibrations, setting up the geographic information. Geometric correction can be done with band-to-band registration (translation and rotation). Further functionalities allow to compute sliding windows statistics over the image.
License: GPL (>= 2)
Author: Anderson Rodrigo da Silva [aut, cre]
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Encoding: UTF-8
LazyLoad: true
Depends: raster
Imports: rgdal, OpenImageR, caTools, dfoptim, pbapply
Suggests: knitr, rmarkdown, spelling
URL: https://github.com/arsilva87/hyperbrick
BugReports: https://github.com/arsilva87/hyperbrick/issues
Language: en-US
NeedsCompilation: no
Packaged: 2022-03-31 20:30:35 UTC; User
Repository: CRAN
Date/Publication: 2022-04-01 08:00:08 UTC

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New package Evacluster with initial version 0.1.0
Package: Evacluster
Title: Evaluation Clustering Methods for Disease Subtypes Diagnosis
Version: 0.1.0
Date: 2022-03-25
Author: Fahimeh Nezhadmoghadam,Jose Gerardo Tamez-Pena
Maintainer: Fahimeh Nezhadmoghadam <f.nejad.moghadam@gmail.com>
Description: Contains a set of clustering methods and evaluation metrics to select the best number of the clusters based on clustering stability. Two references describe the methodology: Fahimeh Nezhadmoghadam, and Jose Tamez-Pena (2021)<doi:10.1016/j.compbiomed.2021.104753>, and Fahimeh Nezhadmoghadam, et al.(2021)<doi:10.2174/1567205018666210831145825>.
License: LGPL (>= 2)
Encoding: UTF-8
Suggests: mlbench,EMCluster,inaparc,ppclust,FRESA.CAD,MASS,stats,class,NMF,cluster,Rtsne,proxy,uwot,mclust,graphics
Packaged: 2022-03-31 18:27:26 UTC; fneja
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2022-04-01 07:50:07 UTC

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New package DEM with initial version 0.0.0.1
Package: DEM
Title: The Distributed EM Algorithms in Multivariate Gaussian Mixture Models
Version: 0.0.0.1
Description: The distributed expectation maximization algorithms are used to solve parameters of multivariate Gaussian mixture models. The philosophy of the package is described in Guo, G. (2022) <doi:10.1080/02664763.2022.2053949>.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: mvtnorm
Suggests: testthat (>= 3.0.0)
NeedsCompilation: no
Packaged: 2022-03-31 15:05:23 UTC; GD
Author: Qian Wang [aut, cre], Guangbao Guo [aut], Guoqi Qian [aut]
Maintainer: Qian Wang <waqian0715@163.com>
Depends: R (>= 3.5.0)
Repository: CRAN
Date/Publication: 2022-04-01 07:50:10 UTC

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Package tpn updated to version 1.2 with previous version 1.1 dated 2021-10-13

Title: Truncated Positive Normal Model and Extensions
Description: Provide data generation and estimation tools for the truncated positive normal model discussed in Gomez, Olmos, Varela and Bolfarine (2018) <doi:10.1007/s11766-018-3354-x>, the slash truncated positive normal distribution discussed in Gomez, Gallardo and Santoro (2021) <doi:10.3390/sym13112164>, the bimodal truncated positive normal distribution discussed in Gomez et al. (2022) <doi:10.3390/sym14040665> and the flexible truncated positive normal model.
Author: Diego Gallardo [aut, cre], Hector J. Gomez [aut], Yolanda M. Gomez [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>

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Package inti updated to version 0.5.5 with previous version 0.5.4 dated 2022-02-22

Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and technical writing. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] , QuipoLab [ctb], Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flavjack@gmail.com>

Diff between inti versions 0.5.4 dated 2022-02-22 and 0.5.5 dated 2022-04-01

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Package igraph updated to version 1.3.0 with previous version 1.2.11 dated 2022-01-04

Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Tamas Nepusz <ntamas@gmail.com>

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More information about igraph at CRAN
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Package sos updated to version 2.1-4 with previous version 2.1-0 dated 2021-06-20

Title: Search Contributed R Packages, Sort by Package
Description: Search contributed R packages, sort by package.
Author: Spencer Graves [cre, aut, cph], Sundar Dorai-Raj [aut], and Romain Francois [ctb]
Maintainer: Spencer Graves <spencer.graves@prodsyse.com>

Diff between sos versions 2.1-0 dated 2021-06-20 and 2.1-4 dated 2022-04-01

 DESCRIPTION                              |   10 
 MD5                                      |  100 +-
 NAMESPACE                                |   62 -
 NEWS                                     |   57 -
 R/CRAN.R                                 |   76 +-
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 R/PackageSum2.R                          |  290 +++----
 R/PackageSummary.R                       |  108 +-
 R/back2ForwardSlash.R                    |    8 
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 R/findFn2.R                              |  182 ++---
 R/grepFn.R                               |   32 
 R/hits.R                                 |   14 
 R/installPackages.R                      |  115 +--
 R/intersectFindFn.R                      |  132 +--
 R/packageSum.R                           |  122 +--
 R/print.findFn.R                         |  549 +++++++--------
 R/print.packageSum.R                     |  558 +++++++--------
 R/sortFindFn.R                           |  108 +-
 R/summary.findFn.R                       |   94 +-
 R/unionFindFn.R                          |  130 +--
 R/writeFindFn2xls.R                      |  334 ++++-----
 README.md                                |  144 +--
 build/vignette.rds                       |binary
 inst/WORDLIST                            |  132 +--
 inst/brew/default/results.brew.html      |  232 +++---
 inst/brew/iframe/results.brew.html       |  190 ++---
 inst/doc/sos.R                           |  394 +++++-----
 inst/doc/sos.Rnw                         | 1124 +++++++++++++++----------------
 inst/doc/sos.pdf                         |binary
 inst/js/sorttable.js                     |  984 +++++++++++++--------------
 inst/tests/example_back2ForwardSlash.txt |    4 
 man/CRAN.Rd                              |  214 ++---
 man/Extract.findFn.Rd                    |  122 +--
 man/PackageSum2.Rd                       |  278 +++----
 man/PackageSummary.Rd                    |  176 ++--
 man/back2ForwardSlash.Rd                 |  160 ++--
 man/findFn.Rd                            |  485 ++++++-------
 man/grepFn.Rd                            |  122 +--
 man/hits.Rd                              |  102 +-
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 man/print.findFn.Rd                      |  154 ++--
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 man/sortFindFn.Rd                        |   96 +-
 man/summary.findFn.Rd                    |  198 ++---
 man/unionFindFn.Rd                       |  226 +++---
 man/writeFindFn2xls.Rd                   |  136 +--
 vignettes/RJournal.sty                   |  466 ++++++------
 vignettes/sos.Rnw                        | 1124 +++++++++++++++----------------
 51 files changed, 5837 insertions(+), 5784 deletions(-)

More information about sos at CRAN
Permanent link

Package dsims (with last version 0.2.2) was removed from CRAN

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

2022-03-31 0.2.2
2022-03-17 0.2.1
2021-09-01 0.2.0
2021-04-22 0.1.1

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