Thu, 12 Dec 2019

Package ALTopt updated to version 0.1.2 with previous version 0.1.1 dated 2015-08-27

Title: Optimal Experimental Designs for Accelerated Life Testing
Description: Creates the optimal (D, U and I) designs for the accelerated life testing with right censoring or interval censoring. It uses generalized linear model (GLM) approach to derive the asymptotic variance-covariance matrix of regression coefficients. The failure time distribution is assumed to follow Weibull distribution with a known shape parameter and log-linear link functions are used to model the relationship between failure time parameters and stress variables. The acceleration model may have multiple stress factors, although most ALTs involve only two or less stress factors. ALTopt package also provides several plotting functions including contour plot, Fraction of Use Space (FUS) plot and Variance Dispersion graphs of Use Space (VDUS) plot. For more details, see Seo and Pan (2015) <doi:10.32614/RJ-2015-029>.
Author: Kangwon Seo [aut, cre], Rong Pan [aut]
Maintainer: Kangwon Seo <seoka@missouri.edu>

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More information about ALTopt at CRAN
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Package TDAstats updated to version 0.4.1 with previous version 0.4.0 dated 2018-11-05

Title: Pipeline for Topological Data Analysis
Description: A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa et al. (2018) <doi:10.21105/joss.00860>. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>. This package has been published as Wadhwa et al. (2018) <doi:10.21105/joss.00860>.
Author: Raoul Wadhwa [aut, cre], Andrew Dhawan [aut], Drew Williamson [aut], Jacob Scott [aut], Jason Cory Brunson [ctb], Shota Ochi [ctb]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>

Diff between TDAstats versions 0.4.0 dated 2018-11-05 and 0.4.1 dated 2019-12-12

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Permanent link

Package spsur updated to version 1.0.0.4 with previous version 1.0.0.3 dated 2019-03-23

Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly Unrelated Regression (usually called SUR) models, with spatial structure, by maximum likelihood and three-stage least squares. The package estimates the most common spatial specifications, that is, SUR with Spatial Lag of X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM), SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM), SUR with Spatial Durbin Error Model (called SUR-SDEM), SUR with Spatial Autoregressive terms and Spatial Autoregressive Disturbances (called SUR-SARAR) and SUR with Spatially Independent Model (called SUR-SIM). The methodology of these models can be found in next references Mur, J., Lopez, F., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443> Lopez, F.A., Mur, J., and Angulo, A. (2014) <doi:10.1007/s00168-014-0624-2>.
Author: Ana Angulo [aut], Fernando A Lopez [aut], Roman Minguez [aut, cre], Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>

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More information about spsur at CRAN
Permanent link

Package Seurat updated to version 3.1.2 with previous version 3.1.1 dated 2019-10-03

Title: Tools for Single Cell Genomics
Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
Author: Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)
Maintainer: Paul Hoffman <nygcSatijalab@nygenome.org>

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More information about Seurat at CRAN
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Package rtika updated to version 1.23 with previous version 1.22 dated 2019-08-02

Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre], The Apache Software Foundation [aut, cph], Julia Silge [rev] (Reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/191), David Gohel [rev] (Reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>

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Package metricTester updated to version 1.3.6 with previous version 1.3.4 dated 2017-10-31

Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and statistical performance of 13 pre-defined phylogenetic metrics and 11 null models, and of user-defined metrics and null models, as detailed in Miller et al. (2017) <doi:10.1111/ecog.02070>.
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>

Diff between metricTester versions 1.3.4 dated 2017-10-31 and 1.3.6 dated 2019-12-12

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Package EpiILMCT updated to version 1.1.5 with previous version 1.1.4 dated 2019-10-13

Title: Continuous Time Distance-Based and Network-Based Individual Level Models for Epidemics
Description: Provides tools for simulating from continuous-time individual level models of disease transmission, and carrying out infectious disease data analyses with the same models. The epidemic models considered are distance-based and/or contact network-based models within Susceptible-Infectious-Removed (SIR) or Susceptible-Infectious-Notified-Removed (SINR) compartmental frameworks.
Author: Waleed Almutiry [aut, cre], Rob Deardon [aut, ths], Vineetha Warriyar K. V. [ctb]
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>

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Package caretEnsemble updated to version 2.0.1 with previous version 2.0.0 dated 2016-02-07

Title: Ensembles of Caret Models
Description: Functions for creating ensembles of caret models: caretList() and caretStack(). caretList() is a convenience function for fitting multiple caret::train() models to the same dataset. caretStack() will make linear or non-linear combinations of these models, using a caret::train() model as a meta-model, and caretEnsemble() will make a robust linear combination of models using a GLM.
Author: Zachary A. Deane-Mayer [aut, cre], Jared E. Knowles [aut]
Maintainer: Zachary A. Deane-Mayer <zach.mayer@gmail.com>

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More information about caretEnsemble at CRAN
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Package ppcong updated to version 0.0.2 with previous version 0.0.1 dated 2019-11-28

Title: Interfacing with ProPublica's 'Congress' API
Description: A simple interface for interacting with ProPublica's 'Congress' API, which provides data about current and former members of both chambers of the U.S. Congress and can be found at the following URL: <https://projects.propublica.org/api-docs/congress-api/>.
Author: Michael W. Kearney [aut, cre] (<https://orcid.org/0000-0002-0730-4694>), Lingshu Hu [ctb] (<https://orcid.org/0000-0003-0304-882X>), Alieva Iuliia [ctb] (<https://orcid.org/0000-0001-6270-8985>)
Maintainer: Michael W. Kearney <kearneymw@missouri.edu>

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Package polymapR updated to version 1.0.20 with previous version 1.0.19 dated 2019-02-01

Title: Linkage Analysis in Outcrossing Polyploids
Description: Creation of linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>.
Author: Peter Bourke [aut, cre], Geert van Geest [aut], Roeland Voorrips [ctb]
Maintainer: Peter Bourke <pbourkey@gmail.com>

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Package gluvarpro updated to version 2.0 with previous version 1.0 dated 2019-04-09

Title: Glucose Variability Measures from Continuous Glucose Monitoring Data
Description: Calculate different glucose variability measures, including average measures of glycemia, measures of glycemic variability and measures of glycemic risk, from continuous glucose monitoring data. Boris P. Kovatchev, Erik Otto, Daniel Cox, Linda Gonder-Frederick, and William Clarke (2006) <doi:10.2337/dc06-1085>. Jean-Pierre Le Floch, Philippe Escuyer, Eric Baudin, Dominique Baudon, and Leon Perlemuter (1990) <doi:10.2337/diacare.13.2.172>. C.M. McDonnell, S.M. Donath, S.I. Vidmar, G.A. Werther, and F.J. Cameron (2005) <doi:10.1089/dia.2005.7.253>. Everitt, Brian (1998) <doi:10.1111/j.1751-5823.2011.00149_2.x>. Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) <doi:10.2307/2234167>. Dougherty, R. L., Edelman, A. and Hyman, J. M. (1989) <doi:10.1090/S0025-5718-1989-0962209-1>. Tukey, J. W. (1977) <doi:10.1016/0377-2217(86)90209-2>. F. John Service (2013) <doi:10.2337/db12-1396>. Edmond A. Ryan, Tami Shandro, Kristy Green, Breay W. Paty, Peter A. Senior, David Bigam, A.M. James Shapiro, and Marie-Christine Vantyghem (2004) <doi:10.2337/diabetes.53.4.955>. Seniz Sevimer Tuncan, Mehmet Uzunlulu, Ozge telci caklili, Hasan Huseyin Mutlu, and Aytekin Oguz (2016) <doi:10.5152/cjms.2016.109>. Sarah E. Siegelaar, Frits Holleman, Joost B. L. Hoekstra, and J. Hans DeVries (2010) <doi:10.1210/er.2009-0021>. Gabor Marics, Zsofia Lendvai, Csaba Lodi, Levente Koncz, David Zakarias, Gyorgy Schuster, Borbala Mikos, Csaba Hermann, Attila J. Szabo, and Peter Toth-Heyn (2015) <doi:10.1186/s12938-015-0035-3>.
Author: Sergio Contador
Maintainer: Sergio Contador <scontador@ucm.es>

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Package ecotox updated to version 1.4.1 with previous version 1.4.0 dated 2019-03-26

Title: Analysis of Ecotoxicology
Description: A simple approach to using a probit or logit analysis to calculate lethal concentration (LC) or time (LT) and the appropriate fiducial confidence limits desired for selected LC or LT for ecotoxicology studies (Finney 1971; Wheeler et al. 2006; Robertson et al. 2007). The simplicity of 'ecotox' comes from the syntax it implies within its functions which are similar to functions like glm() and lm(). In addition to the simplicity of the syntax, a comprehensive data frame is produced which gives the user a predicted LC or LT value for the desired level and a suite of important parameters such as fiducial confidence limits and slope. Finney, D.J. (1971, ISBN: 052108041X); Wheeler, M.W., Park, R.M., and Bailer, A.J. (2006) <doi:10.1897/05-320R.1>; Robertson, J.L., Savin, N.E., Russell, R.M., and Preisler, H.K. (2007, ISBN: 0849323312).
Author: Benjamin L Hlina [aut, cre]
Maintainer: Benjamin L Hlina <benjamin.hlina@gmail.com>

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Package rmarkdown updated to version 2.0 with previous version 1.18 dated 2019-11-27

Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut], Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Jonathan McPherson [aut], Javier Luraschi [aut], Kevin Ushey [aut], Aron Atkins [aut], Hadley Wickham [aut], Joe Cheng [aut], Winston Chang [aut], Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>), Andrew Dunning [ctb], Atsushi Yasumoto [ctb] (<https://orcid.org/0000-0002-8335-495X>), Barret Schloerke [ctb], Christophe Dervieux [ctb], Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>), Jeff Allen [ctb], Malcolm Barrett [ctb], Rob Hyndman [ctb], Romain Lesur [ctb], Roy Storey [ctb], Ruben Arslan [ctb], Sergio Oller [ctb], RStudio, Inc. [cph], jQuery Foundation [cph] (jQuery library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/rmd/h/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/rmd/h/jqueryui-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Alexander Farkas [ctb, cph] (html5shiv library), Scott Jehl [ctb, cph] (Respond.js library), Ivan Sagalaev [ctb, cph] (highlight.js library), Greg Franko [ctb, cph] (tocify library), John MacFarlane [ctb, cph] (Pandoc templates), Google, Inc. [ctb, cph] (ioslides library), Dave Raggett [ctb] (slidy library), W3C [cph] (slidy library), Dave Gandy [ctb, cph] (Font-Awesome), Ben Sperry [ctb] (Ionicons), Drifty [cph] (Ionicons), Aidan Lister [ctb, cph] (jQuery StickyTabs), Benct Philip Jonsson [ctb, cph] (pagebreak lua filter), Albert Krewinkel [ctb, cph] (pagebreak lua filter)
Maintainer: Yihui Xie <xie@yihui.name>

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Package lazytrade updated to version 0.3.8 with previous version 0.3.7 dated 2019-12-03

Title: Learn Computer and Data Science using Algorithmic Trading
Description: Provide sets of functions and methods to learn and practice data science using idea of algorithmic trading. Main goal is to process information within "Decision Support System" to come up with analysis or predictions. There are several utilities such as dynamic and adaptive risk management using reinforcement learning and even functions to generate predictions of price changes using pattern recognition deep regression learning.
Author: Vladimir Zhbanko
Maintainer: Vladimir Zhbanko <vladimir.zhbanko@gmail.com>

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Package conStruct updated to version 1.0.4 with previous version 1.0.3 dated 2019-01-03

Title: Models Spatially Continuous and Discrete Population Genetic Structure
Description: A method for modeling genetic data as a combination of discrete layers, within each of which relatedness may decay continuously with geographic distance. This package contains code for running analyses (which are implemented in the modeling language 'rstan') and visualizing and interpreting output. See the paper for more details on the model and its utility.
Author: Gideon Bradburd [aut, cre]
Maintainer: Gideon Bradburd <bradburd@msu.edu>

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Package SEERaBomb updated to version 2019.2 with previous version 2019.1 dated 2019-05-07

Title: SEER and Atomic Bomb Survivor Data Analysis Tools
Description: Creates SEER (Surveillance, Epidemiology and End Results) and A-bomb data binaries from ASCII sources and provides tools for estimating SEER second cancer risks. Methods are described in <doi:10.1038/leu.2015.258>.
Author: Tomas Radivoyevitch [aut, cre], R. Molenaar [ctb]
Maintainer: Tomas Radivoyevitch <radivot@ccf.org>

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Package PCMBase updated to version 1.2.11 with previous version 1.2.10 dated 2019-09-11

Title: Simulation and Likelihood Calculation of Phylogenetic Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for ML and Bayesian fit of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph] (<a href="https://venelin.github.io">venelin.github.io</a>), Krzysztof Bartoszek [ctb], Georgios Asimomitis [ctb], Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>

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Package amap updated to version 0.8-18 with previous version 0.8-17 dated 2019-05-13

Title: Another Multidimensional Analysis Package
Description: Tools for Clustering and Principal Component Analysis (With robust methods, and parallelized functions).
Author: Antoine Lucas
Maintainer: Antoine Lucas <antoinelucas@gmail.com>

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Package treeHMM updated to version 0.1.1 with previous version 0.1.0 dated 2019-10-13

Title: Tree Structured Hidden Markov Model
Description: Used for Inference, Prediction and Parameter learning for tree structured Hidden Markov Model. The package propose a new architecture of Hidden Markov Model(HMM) known as Tree Structured HMM which could be used in various applications which involves graphs, trees etc.
Author: Prajwal Bende [aut, cre], Russ Greiner [ths], Pouria Ramazi [ths]
Maintainer: Prajwal Bende <pbende@ualberta.ca>

Diff between treeHMM versions 0.1.0 dated 2019-10-13 and 0.1.1 dated 2019-12-12

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Package miWQS updated to version 0.2.0 with previous version 0.1.0 dated 2019-07-31

Title: Multiple Imputation Using Weighted Quantile Sum Regression
Description: The `miWQS` package handles the uncertainty due to below the detection limit in a correlated component mixture problem. Researchers want to determine if a set/mixture of continuous and correlated components/chemicals is associated with an outcome and if so, which components are important in that mixture. These components share a common outcome but are interval-censored between zero and low thresholds, or detection limits, that may be different across the components. The `miWQS` package applies the multiple imputation (MI) procedure to the weighted quantile sum regression (WQS) methodology for continuous, binary, or count outcomes. The imputation models are: bootstrapping imputation (Lubin et.al (2004) <doi:10.1289/ehp.7199>) and Bayesian imputation.
Author: Paul M. Hargarten [aut, cre], David C. Wheeler [aut, rev, ths]
Maintainer: Paul M. Hargarten <hargartenp@vcu.edu>

Diff between miWQS versions 0.1.0 dated 2019-07-31 and 0.2.0 dated 2019-12-12

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Package datasets.load updated to version 1.0.0 with previous version 0.3.0 dated 2018-09-10

Title: Interfaces for Loading Datasets
Description: Visual interface for loading datasets in RStudio from all installed (unloaded) packages, also includes command line interfaces.
Author: Bastiaan quast [aut, cre]
Maintainer: Bastiaan quast <bquast@gmail.com>

Diff between datasets.load versions 0.3.0 dated 2018-09-10 and 1.0.0 dated 2019-12-12

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Package spam64 updated to version 2.5-1 with previous version 2.4-0 dated 2019-11-02

Title: 64-Bit Extension of the SPArse Matrix R Package 'spam'
Description: Provides the Fortran code of the R package 'spam' with 64-bit integers. Loading this package together with the R package spam enables the sparse matrix class spam to handle huge sparse matrices with more than 2^31-1 non-zero elements. Documentation is provided in Gerber, Moesinger and Furrer (2017) <doi:10.1016/j.cageo.2016.11.015>.
Author: Reinhard Furrer [aut, cre], Florian Gerber [aut], Roman Flury [aut], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

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 21 files changed, 1038 insertions(+), 1746 deletions(-)

More information about spam64 at CRAN
Permanent link

Package spam updated to version 2.5-1 with previous version 2.5-0 dated 2019-12-06

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with other sparse matrix packages are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within G(M)RF. (4) and it is fast and scalable (with the extension package spam64). Documentation about 'spam' is provided by vignettes included in this package, see also Furrer and Sain (2010) <doi:10.18637/jss.v036.i10>; see 'citation("spam")' for details.
Author: Reinhard Furrer [aut, cre], Florian Gerber [aut], Roman Flury [aut], Daniel Gerber [ctb], Kaspar Moesinger [ctb], Youcef Saad [ctb] (SPARSEKIT http://www-users.cs.umn.edu/~saad/software/SPARSKIT/), Esmond G. Ng [ctb] (Fortran Cholesky routines), Barry W. Peyton [ctb] (Fortran Cholesky routines), Joseph W.H. Liu [ctb] (Fortran Cholesky routines), Alan D. George [ctb] (Fortran Cholesky routines), Lehoucq B. Rich [ctb] (ARPACK), Maschhoff Kristi [ctb] (ARPACK), Sorensen C. Danny [ctb] (ARPACK), Yang Chao [ctb] (ARPACK)
Maintainer: Reinhard Furrer <reinhard.furrer@math.uzh.ch>

Diff between spam versions 2.5-0 dated 2019-12-06 and 2.5-1 dated 2019-12-12

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 spam-2.5-1/spam/MD5                                       |   35 ++++++--------
 spam-2.5-1/spam/NEWS.md                                   |    7 ++
 spam-2.5-1/spam/inst/doc/spam.R                           |   26 +++++-----
 spam-2.5-1/spam/inst/doc/spam.pdf                         |binary
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 spam-2.5-1/spam/src/spamown.f                             |   10 +---
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More information about spam at CRAN
Permanent link

New package metaboGSE with initial version 1.2.2
Package: metaboGSE
Type: Package
Title: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data
Version: 1.2.2
Depends: R (>= 3.4.0), sybil (>= 2.0.4), ape (>= 3.3)
Suggests: glpkAPI (>= 1.3.0), clpAPI (>= 1.2.7), topGO (>= 2.24.0), unix, KernSmooth, KEGGREST, survival, ctc, knitr, rmarkdown
Imports: utils, stats, methods, parallel, grDevices, graphics, Matrix, AnnotationDbi (>= 1.32.3)
Packaged: 2019-12-12 08:22:16 UTC; ttran
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
VignetteBuilder: knitr
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2019-12-12 16:30:02 UTC

More information about metaboGSE at CRAN
Permanent link

Package idiogramFISH updated to version 1.11.1 with previous version 1.9.1 dated 2019-11-29

Title: Idiograms with Marks and Karyotype Indices
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>

Diff between idiogramFISH versions 1.9.1 dated 2019-11-29 and 1.11.1 dated 2019-12-12

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 45 files changed, 2818 insertions(+), 2342 deletions(-)

More information about idiogramFISH at CRAN
Permanent link

Package rpact updated to version 2.0.6 with previous version 2.0.5 dated 2019-11-08

Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut], Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>

Diff between rpact versions 2.0.5 dated 2019-11-08 and 2.0.6 dated 2019-12-12

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 rpact-2.0.6/rpact/DESCRIPTION                                                |   16 
 rpact-2.0.6/rpact/MD5                                                        |  302 +--
 rpact-2.0.6/rpact/NAMESPACE                                                  |    2 
 rpact-2.0.6/rpact/NEWS.md                                                    |   11 
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More information about rpact at CRAN
Permanent link

Package RandomFields updated to version 3.3.7 with previous version 3.3.6 dated 2019-03-06

Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields. Main geostatistical parts are based on the books by Christian Lantuejoul <doi:10.1007/978-3-662-04808-5>, Jean-Paul Chiles and Pierre Delfiner <doi:10.1002/9781118136188> and Noel A. Cressie <doi:10.1002/9781119115151>. For the extreme value random fields see Oesting, Schlather, Schillings (2019) <doi.org/10.1002/sta4.228> and Schlather (2002) <doi.org/10.1023/A:1020977924878>.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.3.6 dated 2019-03-06 and 3.3.7 dated 2019-12-12

 DESCRIPTION                |    8 ++++----
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More information about RandomFields at CRAN
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Package phylin updated to version 2.0.2 with previous version 2.0.1 dated 2019-11-19

Title: Spatial Interpolation of Genetic Data
Description: The spatial interpolation of genetic distances between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.
Author: Pedro Tarroso, Guillermo Velo-Anton, Silvia Carvalho
Maintainer: Pedro Tarroso <ptarroso@cibio.up.pt>

Diff between phylin versions 2.0.1 dated 2019-11-19 and 2.0.2 dated 2019-12-12

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 MD5                              |   18 +++++++++---------
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 10 files changed, 25 insertions(+), 23 deletions(-)

More information about phylin at CRAN
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Package OncoBayes2 updated to version 0.5-8 with previous version 0.5-4 dated 2019-11-19

Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive oncology Phase I dose-escalation trials which involve an arbitrary number of drugs. Please refer to Neuenschwander et al. (2008) <doi:10.1002/sim.3230> and Neuenschwander et al. (2016) <doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph], Sebastian Weber [aut, cre], Andrew Bean [aut], Lukas A. Widmer [aut], Trustees of Columbia University [cph] (R/stanmodels.R, configure, configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>

Diff between OncoBayes2 versions 0.5-4 dated 2019-11-19 and 0.5-8 dated 2019-12-12

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 23 files changed, 1204 insertions(+), 860 deletions(-)

More information about OncoBayes2 at CRAN
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Package virtualspecies updated to version 1.5.1 with previous version 1.5 dated 2019-05-06

Title: Generation of Virtual Species Distributions
Description: Provides a framework for generating virtual species distributions, a procedure increasingly used in ecology to improve species distribution models. This package integrates the existing methodological approaches with the objective of generating virtual species distributions with increased ecological realism.
Author: Boris Leroy [cre, aut], Christine N. Meynard [ctb], Celine Bellard [ctb], Franck Courchamp [ctb], Robin Delsol [ctb], Willson Gaul [ctb]
Maintainer: Boris Leroy <leroy.boris@gmail.com>

Diff between virtualspecies versions 1.5 dated 2019-05-06 and 1.5.1 dated 2019-12-12

 DESCRIPTION                   |   13 
 MD5                           |   58 +--
 NAMESPACE                     |    2 
 NEWS                          |    8 
 R/convertToPA.R               |   10 
 R/generateRandomSp.R          |    9 
 R/generateSpFromFun.R         |    2 
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 30 files changed, 2190 insertions(+), 2110 deletions(-)

More information about virtualspecies at CRAN
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New package SCtools with initial version 0.3.0
Package: SCtools
Title: Extensions for Synthetic Controls Analysis
Version: 0.3.0
Authors@R: c( person(given = 'Bruno', family = 'Castanho Silva', role = c('aut', 'cre'), email = 'bcsilva@wiso.uni-koeln.de', comment = c(ORCID = '0000-0001-9363-4704')), person(given = 'Michael', family = 'DeWitt', role = c('aut'), email = 'me.dewitt.jr@gmail.com', comment = c(ORCID = '0000-0001-8940-1967')))
Description: Extensions to the synthetic controls analyses performed by the package 'Synth' as detailed in Abadie, Diamond, and Hainmueller (2011) <doi:10.18637/jss.v042.i13>. Includes generating and plotting placebos, post/pre-MSPE (mean squared prediction error) significance tests and plots, and calculating average treatment effects for multiple treated units. This package represents an implementation of those methods suggested in Abadie, Diamond,and Hainmueller (2010) <doi:10.1198/jasa.2009.ap08746> for use in synthetic control analysis.
BugReports: https://github.com/bcastanho/SCtools/issues
Maintainer: Bruno Castanho Silva <bcsilva@wiso.uni-koeln.de>
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.5), future (>= 1.6.2)
Imports: ggplot2, Synth, stringr, stats, cvTools, furrr, dplyr, purrr
Suggests: testthat, covr, knitr, tidyr, rmarkdown
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-12-03 16:00:23 UTC; 54011
Author: Bruno Castanho Silva [aut, cre] (<https://orcid.org/0000-0001-9363-4704>), Michael DeWitt [aut] (<https://orcid.org/0000-0001-8940-1967>)
Repository: CRAN
Date/Publication: 2019-12-12 13:40:02 UTC

More information about SCtools at CRAN
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Package APIS updated to version 1.0.0 with previous version 0.1.0 dated 2019-08-19

Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents
Description: Parentage assignment package. Parentage assignment is performed based on observed average Mendelian transmission probability distributions. The main function of this package is the function APIS(), which is the parentage assignment function.
Author: Ronan Griot, François Allal, Romain Morvezen, Sophie Brard-Fudulea, Pierrick Haffray, Florence Phocas and Marc Vandeputte
Maintainer: Ronan Griot <ronan.griot@gmail.com>

Diff between APIS versions 0.1.0 dated 2019-08-19 and 1.0.0 dated 2019-12-12

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More information about APIS at CRAN
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Package Rfast updated to version 1.9.8 with previous version 1.9.7 dated 2019-11-24

Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>

Diff between Rfast versions 1.9.7 dated 2019-11-24 and 1.9.8 dated 2019-12-12

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 Rfast-1.9.8/Rfast/DESCRIPTION                    |   10 +-
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 Rfast-1.9.8/Rfast/R/variable_selection.R         |   16 ++-
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Package paleotree updated to version 3.3.25 with previous version 3.3.0 dated 2019-06-04

Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.
Author: David W. Bapst, Peter J. Wagner
Maintainer: David W. Bapst <dwbapst@gmail.com>

Diff between paleotree versions 3.3.0 dated 2019-06-04 and 3.3.25 dated 2019-12-12

 CHANGELOG                                                     |  639 -
 DESCRIPTION                                                   |   23 
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 README.md                                                     |  110 
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 man/setRootAge.Rd                                             |  140 
 man/simFossilRecord.Rd                                        | 2402 +++---
 man/simFossilRecordMethods.Rd                                 |  369 
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 man/taxa2phylo.Rd                                             |  230 
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More information about paleotree at CRAN
Permanent link

Package mpr updated to version 1.0.5 with previous version 1.0.4 dated 2016-10-12

Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>

Diff between mpr versions 1.0.4 dated 2016-10-12 and 1.0.5 dated 2019-12-12

 DESCRIPTION           |    8 ++++----
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 3 files changed, 11 insertions(+), 9 deletions(-)

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Package FunnelPlotR updated to version 0.2.2 with previous version 0.2.1 dated 2019-10-09

Title: Funnel Plots for Indirectly-Standardised Ratios
Description: An implementation of the Spiegelhalter (2005) <doi:10.1002/sim.1970> Funnel plots for reporting standardised ratios, with overdispersion adjustment.
Author: Chris Mainey [aut, cre] (<https://orcid.org/0000-0002-3018-6171>), Matthew Bass [ctb]
Maintainer: Chris Mainey <chris.mainey@uhb.nhs.uk>

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Package clickR updated to version 0.4.40 with previous version 0.4.32 dated 2019-04-19

Title: Fix Data and Create Report Tables from Different Objects
Description: Tools for assessing data quality, performing exploratory analysis, fixing data errors in numerical, factor and date variables and creating report tables from models and summaries.
Author: Victoria Fornes Ferrer, David Hervas Marin
Maintainer: David Hervas Marin <ddhervas@yahoo.es>

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Package AID updated to version 2.5 with previous version 2.4 dated 2019-05-16

Title: Box-Cox Power Transformation
Description: Performs Box-Cox power transformation for different purposes, graphical approaches, assesses the success of the transformation via tests and plots, computes mean and confidence interval for back transformed data.
Author: Osman Dag [aut, cre], Ozgur Asar [aut], Ozlem Ilk [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>

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Package seminr updated to version 1.0.1 with previous version 1.0.0 dated 2019-09-27

Title: Domain-Specific Language for Building PLS Structural Equation Models
Description: A powerful, easy to write and easy to modify syntax for specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths], Nicholas Patrick Danks [aut, cre], Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>

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Package random.polychor.pa updated to version 1.1.4-3 with previous version 1.1.4-2 dated 2016-07-26

Title: A Parallel Analysis with Polychoric Correlation Matrices
Description: The Function performs a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from both the randomly generated and the real data polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. Random data sets are simulated assuming or a uniform or a multinomial distribution or via the bootstrap method of resampling (i.e., random permutations of cases). Also Multigroup Parallel analysis is made available for random (uniform and multinomial distribution and with or without difficulty factor) and bootstrap methods. An option to choose between default or full output is also available as well as a parameter to print Fit Statistics (Chi-squared, TLI, RMSEA, RMR and BIC) for the factor solutions indicated by the Parallel Analysis.
Author: Fabio Presaghi [aut, cre], Marta Desimoni [ctb]
Maintainer: Fabio Presaghi <fabio.presaghi@uniroma1.it>

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Package ProjectManagement updated to version 1.2.3 with previous version 1.2.1 dated 2019-04-08

Title: Management of Deterministic and Stochastic Projects
Description: Management problems of deterministic and stochastic projects. It obtains the duration of a project and the appropriate slack for each activity in a deterministic context. In addition it obtains a schedule of activities' time (Castro, Gómez & Tejada (2007) <doi:10.1016/j.orl.2007.01.003>). It also allows the management of resources. When the project is done, and the actual duration for each activity is known, then it can know how long the project is delayed and make a fair delivery of the delay between each activity (Bergantiños, Valencia-Toledo & Vidal-Puga (2018) <doi:10.1016/j.dam.2017.08.012>). In a stochastic context it can estimate the average duration of the project and plot the density of this duration, as well as, the density of the early and last times of the chosen activities. As in the deterministic case, it can make a distribution of the delay generated by observing the project already carried out.
Author: Juan Carlos Gonçalves Dosantos [aut, cre], Ignacio García Jurado [aut], Julián Costa Bouzas [aut]
Maintainer: Juan Carlos Gonçalves Dosantos <juan.carlos.goncalves@udc.es>

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Package mlr3misc updated to version 0.1.6 with previous version 0.1.5 dated 2019-09-28

Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>

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Package imagefluency updated to version 0.2.2 with previous version 0.2.1 dated 2019-09-27

Title: Image Statistics Based on Processing Fluency
Description: Get image statistics based on processing fluency theory. The functions provide scores for several basic aesthetic principles that facilitate fluent cognitive processing of images: contrast, complexity / simplicity, self-similarity, symmetry, and typicality. See Mayer & Landwehr (2018) <doi:10.1037/aca0000187> and Mayer & Landwehr (2018) <doi:10.31219/osf.io/gtbhw> for the theoretical background of the methods.
Author: Stefan Mayer [aut, cre] (<https://orcid.org/0000-0003-0034-7090>)
Maintainer: Stefan Mayer <stefan@mayer-de.com>

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Package congressbr updated to version 0.2.2 with previous version 0.2.1 dated 2019-05-08

Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <https://dadosabertos.camara.leg.br/> respectively.
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>

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Package BIOdry updated to version 0.7 with previous version 0.6 dated 2019-05-28

Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>

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Package tm updated to version 0.7-7 with previous version 0.7-6 dated 2018-12-21

Title: Text Mining Package
Description: A framework for text mining applications within R.
Author: Ingo Feinerer [aut, cre] (<https://orcid.org/0000-0001-7656-8338>), Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>), Artifex Software, Inc. [ctb, cph] (pdf_info.ps taken from GPL Ghostscript)
Maintainer: Ingo Feinerer <feinerer@logic.at>

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Package graph4lg updated to version 0.2.0 with previous version 0.1.1 dated 2019-07-23

Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of functions can be used to import and convert spatial and genetic data initially in different formats, import landscape graphs created with 'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>, make diagnosis plots of isolation by distance relationships in order to choose how to build genetic graphs, create graphs with a large range of pruning methods, weight their links with several genetic distances, plot and analyse graphs, compare them with other graphs. It uses functions from other packages such as 'adegenet' (Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi et Nepusz, 2006) <https://bit.ly/35a3V3H>. It also implements methods commonly used in landscape genetics to create graphs, described by Dyer et Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data (van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>

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Package CARBayesST updated to version 3.0.2 with previous version 3.0.1 dated 2019-01-08

Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, or Poisson, but for some models only the binomial and Poisson data likelihoods are available. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) style prior distributions. A number of different random effects structures are available, including Bernardinelli et al. (1995) <doi:10.1002/sim.4780142112>, Rushworth et al. (2014) <doi:10.1016/j.sste.2014.05.001> and Lee et al. (2016) <doi:10.1214/16-AOAS941>. Full details are given in the vignette accompanying this package. The creation of this package was supported by the Engineering and Physical Sciences Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee, Alastair Rushworth and Gary Napier
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

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Package sismonr updated to version 2.0.0 with previous version 1.1.4 dated 2019-07-21

Title: Simulation of in Silico Multi-Omic Networks
Description: A tool for the simulation of gene expression profiles for in silico regulatory networks. The package generates gene regulatory networks, which include protein-coding and noncoding genes linked via different types of regulation: regulation of transcription, translation, RNA or protein decay, and post-translational modifications. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations, but is defined by the user. A choice of stochastic simulation algorithms allow us to simulate the expression profiles (RNA and if applicable protein abundance) of the genes in the in silico system for the different in silico individuals. A tutorial explaining how to use the package is available at <https://oliviaab.github.io/sismonr/>. Manuscript in preparation; see also Angelin-Bonnet O., Biggs P.J. and Vignes M. (2018) <doi:10.1109/BIBM.2018.8621131>. Note that sismonr relies on Julia code called internally by the functions. No knowledge of Julia is required in order to use sismonr, but Julia must be installed on the computer (instructions can be found in the tutorial, the GitHub page or the vignette of the package).
Author: Olivia Angelin-Bonnet [aut, cre] (<https://orcid.org/0000-0002-7708-2919>), Patrick Biggs [aut] (<https://orcid.org/0000-0002-0285-4101>), Matthieu Vignes [aut] (<https://orcid.org/0000-0001-8929-2975>), John M. Chambers [ctb]
Maintainer: Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>

Diff between sismonr versions 1.1.4 dated 2019-07-21 and 2.0.0 dated 2019-12-12

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More information about sismonr at CRAN
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Package rprev updated to version 1.0.3 with previous version 1.0.2 dated 2019-03-12

Title: Estimating Disease Prevalence from Registry Data
Description: Estimates disease prevalence for a given index date, using existing registry data extended with Monte Carlo simulations.
Author: Stuart Lacy [cre, aut], Simon Crouch [aut], Stephanie Lax [aut]
Maintainer: Stuart Lacy <stuart.lacy@york.ac.uk>

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Package RGCxGC updated to version 1.1.0 with previous version 1.0.0 dated 2019-01-20

Title: Preprocessing and Multivariate Analysis of Bidimensional Gas Chromatography Data
Description: Toolbox for chemometrics analysis of bidimensional gas chromatography data. This package import data for common scientific data format (NetCDF) and fold it to 2D chromatogram. Then, it can perform preprocessing and multivariate analysis. In the preprocessing algorithms, baseline correction, smoothing, and peak alignment are available. While in multivariate analysis, multiway principal component analysis is incorporated.
Author: Cristian Quiroz-Moreno [aut, cre], Guilherme L. Alexandrino [aut], Noroska G.S. Mogollón [aut]
Maintainer: Cristian Quiroz-Moreno <cristianquirozd1997@gmail.com>

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Package RclusTool updated to version 0.91.1 with previous version 0.91 dated 2019-11-06

Title: Graphical Toolbox for Clustering and Classification of Data Frames
Description: Graphical toolbox for clustering and classification of data frames. It proposes a graphical interface to process clustering and classification methods on features data-frames, and to view initial data as well as resulted cluster or classes. According to the level of available labels, different approaches are proposed: unsupervised clustering, semi-supervised clustering and supervised classification. To assess the processed clusters or classes, the toolbox can import and show some supplementary data formats: either profile/time series, or images. These added information can help the expert to label clusters (clustering), or to constrain data frame rows (semi-supervised clustering), using Constrained spectral embedding algorithm by Wacquet et al. (2013) <doi:10.1016/j.patrec.2013.02.003> and the methodology provided by Wacquet et al. (2013) <doi:10.1007/978-3-642-35638-4_21>.
Author: Guillaume Wacquet [aut], Pierre-Alexandre Hebert [aut, cre], Emilie Poisson [aut], Pierre Talon [aut]
Maintainer: Pierre-Alexandre Hebert <hebert@univ-littoral.fr>

Diff between RclusTool versions 0.91 dated 2019-11-06 and 0.91.1 dated 2019-12-12

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Package interpret updated to version 0.1.24 with previous version 0.1.25 dated 2019-12-12

Title: Fit Interpretable Machine Learning Models and Explain Blackbox Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretability. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>

Diff between interpret versions 0.1.25 dated 2019-12-12 and 0.1.24 dated 2019-12-12

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More information about interpret at CRAN
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Package ifaTools updated to version 0.20 with previous version 0.19 dated 2019-03-09

Title: Toolkit for Item Factor Analysis with 'OpenMx'
Description: Tools, tutorials, and demos of Item Factor Analysis using 'OpenMx'.
Author: Joshua N. Pritikin [cre, aut]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>

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Package geepack updated to version 1.3-0 with previous version 1.2-1 dated 2016-09-24

Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can also handle clustered categorical responses.
Author: Søren Højsgaard [aut, cre, cph], Ulrich Halekoh [aut, cph], Jun Yan [aut, cph], Claus Ekstrøm [ctb]
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>

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Package CARBayes updated to version 5.1.3 with previous version 5.1.2 dated 2019-06-21

Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al. (1991) <doi:10.1007/BF00116466>), the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>) and the localised model (Lee et al. (2015) <doi:10.1002/env.2348>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>

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Package texPreview updated to version 1.4.3 with previous version 1.4.2 dated 2019-12-05

Title: Compile and Preview Snippets of 'LaTeX'
Description: Compile snippets of 'LaTeX' directly into images from the R console to view in the 'RStudio' viewer pane, Shiny apps and 'RMarkdown' documents.
Author: Jonathan Sidi [aut, cre], Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>

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Package interpret updated to version 0.1.25 with previous version 0.1.23 dated 2019-11-03

Title: Fit Interpretable Machine Learning Models and Explain Blackbox Machine Learning
Description: Package for training interpretable machine learning models and explaining blackbox systems. Historically, the most interpretable machine learning models were not very accurate, and the most accurate models were not very interpretable. Microsoft Research has developed an algorithm called the Explainable Boosting Machine (EBM) which has both high accuracy and interpretable characteristics. EBM uses machine learning techniques like bagging and boosting to breathe new life into traditional GAMs (Generalized Additive Models). This makes them as accurate as random forests and gradient boosted trees, and also enhances their intelligibility and editability. Details on the EBM algorithm can be found in the paper by Rich Caruana, Yin Lou, Johannes Gehrke, Paul Koch, Marc Sturm, and Noemie Elhadad (2015, <doi:10.1145/2783258.2788613>).
Author: Samuel Jenkins [aut], Harsha Nori [aut], Paul Koch [aut], Rich Caruana [aut, cre], Microsoft Corporation [cph]
Maintainer: Rich Caruana <interpretml@outlook.com>

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Package biomartr (with last version 0.9.1) was removed from CRAN

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

2019-12-10 0.9.1
2019-05-21 0.9.0

Permanent link
Package RMAWGEN updated to version 1.3.7 with previous version 1.3.6 dated 2019-11-15

Title: Multi-Site Auto-Regressive Weather GENerator
Description: S3 and S4 functions are implemented for spatial multi-site stochastic generation of daily time series of temperature and precipitation. These tools make use of Vector AutoRegressive models (VARs). The weather generator model is then saved as an object and is calibrated by daily instrumental "Gaussianized" time series through the 'vars' package tools. Once obtained this model, it can it can be used for weather generations and be adapted to work with several climatic monthly time series.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>

Diff between RMAWGEN versions 1.3.6 dated 2019-11-15 and 1.3.7 dated 2019-12-12

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Package partition updated to version 0.1.1 with previous version 0.1.0 dated 2019-05-17

Title: Agglomerative Partitioning Framework for Dimension Reduction
Description: A fast and flexible framework for agglomerative partitioning. 'partition' uses an approach called Direct-Measure-Reduce to create new variables that maintain the user-specified minimum level of information. Each reduced variable is also interpretable: the original variables map to one and only one variable in the reduced data set. 'partition' is flexible, as well: how variables are selected to reduce, how information loss is measured, and the way data is reduced can all be customized.
Author: Joshua Millstein [aut], Malcolm Barrett [aut, cre] (<https://orcid.org/0000-0003-0299-5825>)
Maintainer: Malcolm Barrett <malcolmbarrett@gmail.com>

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Package glmnetUtils updated to version 1.1.4 with previous version 1.1.3 dated 2019-11-18

Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for elasticnet regression, a method for cross-validating the alpha parameter, and other quality-of-life tools.
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi@microsoft.com>

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Package emojifont updated to version 0.5.3 with previous version 0.5.2 dated 2018-06-20

Title: Emoji and Font Awesome in Graphics
Description: An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>), Claus Thorn Ekstrøm [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

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Package StratifiedMedicine updated to version 0.2.1 with previous version 0.2.0 dated 2019-10-13

Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine. Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate models (counterfactual patient-level quantities, for example the individual treatment effect), (3) subgroup identification models (find subsets of patients with similar treatment effects), and (4) parameter estimation and inference (for the overall population and discovered subgroups). These tools can directly feed into stratified medicine algorithms including PRISM (patient response identifiers for stratified medicine; Jemielita and Mehrotra (2019) <arXiv:1912.03337>. PRISM is a flexible and general framework which accepts user-created models/functions. This package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>

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Package Rphylopars updated to version 0.2.12 with previous version 0.2.11 dated 2019-10-21

Title: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Description: Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data. Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
Author: Eric W. Goolsby, Jorn Bruggeman, Cecile Ane
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>

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Package RFishBC updated to version 0.2.3 with previous version 0.2.2 dated 2019-05-02

Title: Back-Calculation of Fish Length
Description: Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software (<https://fisheries.org/bookstore/all-titles/software/70317/>).
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between RFishBC versions 0.2.2 dated 2019-05-02 and 0.2.3 dated 2019-12-12

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Package MBHdesign updated to version 2.1.6 with previous version 2.1.5 dated 2019-10-17

Title: Spatial Designs for Ecological and Environmental Surveys
Description: Provides spatially balanced designs from a set of (contiguous) potential sampling locations in a study region for point-based and for transect-based surveys. Accommodates, without detrimental effects on spatial balance, sites that the researcher wishes to include in the survey for reasons other than the current randomisation (legacy sites).
Author: Scott D. Foster
Maintainer: Scott Foster <scott.foster@data61.csiro.au>

Diff between MBHdesign versions 2.1.5 dated 2019-10-17 and 2.1.6 dated 2019-12-12

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 R/MBHdesign4.R         |    6 ++++--
 inst/doc/MBHdesign.pdf |binary
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Package BHSBVAR updated to version 2.0.1 with previous version 2.0.0 dated 2019-10-28

Title: Structural Bayesian Vector Autoregression Models
Description: Provides a function for estimating the parameters of Structural Bayesian Vector Autoregression models with the method developed by Baumeister and Hamilton (2015) <doi:10.3982/ECTA12356>, Baumeister and Hamilton (2017) <doi:10.3386/w24167>, and Baumeister and Hamilton (2018) <doi:10.1016/j.jmoneco.2018.06.005>. Functions for plotting impulse responses, historical decompositions, and posterior distributions of model parameters are also provided.
Author: Paul Richardson
Maintainer: Paul Richardson <p.richardson.54391@gmail.com>

Diff between BHSBVAR versions 2.0.0 dated 2019-10-28 and 2.0.1 dated 2019-12-12

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 vignettes/fig/Dist_plots-1.pdf |binary
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More information about BHSBVAR at CRAN
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