Wed, 31 Oct 2018

Package fds updated to version 1.8 with previous version 1.7 dated 2013-08-22

Title: Functional Data Sets
Description: Functional data sets.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>

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Package arkdb updated to version 0.0.5 with previous version 0.0.4 dated 2018-09-27

Title: Archive and Unarchive Databases Using Flat Files
Description: Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
Author: Carl Boettiger [aut, cre, cph] (<https://orcid.org/0000-0002-1642-628X>), Richard FitzJohn [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>

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Package restriktor updated to version 0.1-80.911 with previous version 0.1-80.811 dated 2018-09-28

Title: Restricted Statistical Estimation and Inference for Linear Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre], Yves Rosseel [ctb]
Maintainer: Leonard Vanbrabant <Leonard.Vanbrabant@Ugent.be>

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Package logisticRR updated to version 0.2.0 with previous version 0.1.0 dated 2018-10-08

Title: Adjusted Relative Risk from Logistic Regression
Description: Adjusted odds ratio conditional on potential confounders can be directly obtained from logistic regression. However, those adjusted odds ratios have been widely incorrectly interpreted as a relative risk. As relative risk is often of interest in public health, we provide a simple code to return adjusted relative risks from logistic regression model under potential confounders.
Author: Youjin Lee
Maintainer: Youjin Lee <ylee160@jhu.edu>

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Package RATest updated to version 0.1.3 with previous version 0.1.2 dated 2018-01-22

Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on two testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package.
Author: Mauricio Olivares-Gonzalez [aut, cre], Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares-Gonzalez <maurice.olivares@gmail.com>

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Package HMP updated to version 1.6 with previous version 1.5.1 dated 2017-12-20

Title: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP
Description: Using Dirichlet-Multinomial distribution to provide several functions for formal hypothesis testing, power and sample size calculations for human microbiome experiments.
Author: Patricio S. La Rosa, Elena Deych, Sharina Carter, Berkley Shands, Dake Yang, William D. Shannon
Maintainer: Berkley Shands <rpackages@biorankings.com>

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Package automultinomial updated to version 2.0.0 with previous version 1.0.0 dated 2016-10-05

Title: Models for Spatially Correlated Data
Description: Fits the autologistic model described in Besag's famous 1974 paper on auto- models <http://www.jstor.org/stable/2984812>. Fits a multicategory generalization of the autologistic model when there are more than 2 response categories. Provides support for both asymptotic and bootstrap confidence intervals. For full model descriptions and a guide to the use of this package, please see the vignette.
Author: Stephen Berg [aut, cre], Rao Fu [aut], Jun Zhu [ths]
Maintainer: Stephen Berg <saberg2@wisc.edu>

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Package congressbr (with last version 0.1.3) was removed from CRAN

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

2018-06-01 0.1.3
2018-05-16 0.1.2
2017-06-20 0.1.1
2017-04-30 0.1.0

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Package gibble updated to version 0.1.2 with previous version 0.0.2 dated 2018-02-05

Title: Geometry Decomposition
Description: Build a map of path-based geometry, this is a simple description of the number of parts in an object and their basic structure. Translation and restructuring operations for planar shapes and other hierarchical types require a data model with a record of the underlying relationships between elements. The gibble() function creates a geometry map, a simple record of the underlying structure in path-based hierarchical types. There are methods for the planar shape types in the 'sf' and 'sp' packages and for types in the the 'trip' and in-development 'silicate' packages.
Author: Michael Sumner [aut, cre] (<https://orcid.org/0000-0002-2471-7511>)
Maintainer: Michael Sumner <mdsumner@gmail.com>

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Package flextable updated to version 0.4.6 with previous version 0.4.5 dated 2018-08-27

Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents. Functions are provided to let users create tables, modify and format their content. It extends package 'officer' that does not contain any feature for customized tabular reporting and can be used within R markdown documents when rendering to HTML and to 'Microsoft Word' documents.
Author: David Gohel [aut, cre], Maxim Nazarov [ctb] (rmarkdown for docx output)
Maintainer: David Gohel <david.gohel@ardata.fr>

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Package textmineR updated to version 3.0.1 with previous version 2.1.3 dated 2018-09-11

Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that should be familiar to experienced R users. Provides a wrapper for several topic models that take similarly-formatted input and give similarly-formatted output. Has additional functionality for analyzing and diagnostics for topic models.
Author: Thomas Jones [aut, cre], William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>

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New package RImpact with initial version 1.0
Package: RImpact
Type: Package
Title: Calculates Measures of Scholarly Impact
Version: 1.0
Author: John Ruscio
Maintainer: John Ruscio <ruscio@tcnj.edu>
Description: The metrics() function calculates measures of scholarly impact. These include conventional measures, such as the number of publications and the total citations to all publications, as well as modern and robust metrics based on the vector of citations associated with each publication, such as the h index and many of its variants or rivals. These methods are described in Ruscio et al. (2012) <DOI: 10.1080/15366367.2012.711147>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2018-10-26 21:46:14 UTC; oliviaortelli
Repository: CRAN
Date/Publication: 2018-10-31 12:40:03 UTC

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Permanent link

Package RcppTOML updated to version 0.1.5 with previous version 0.1.4 dated 2018-10-23

Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to "Tom's Obvious Markup Language") specifies an excellent format (described at <https://github.com/toml-lang/toml>) suitable for both human editing as well as the common uses of a machine-readable format. This package uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package idealstan updated to version 0.5.0 with previous version 0.2.7 dated 2018-02-09

Title: Generalized IRT Ideal Point Models with 'Stan'
Description: Offers item-response theory (IRT) ideal-point estimation for binary, ordinal, counts and continuous responses with time-varying and missing-data inference. Full and approximate Bayesian sampling with 'Stan' (www.mc-stan.org).
Author: Robert Kubinec [aut, cre], Jonah Gabry [ctb], Ben Goodrich [ctb], Trustees of Columbia University [cph]
Maintainer: Robert Kubinec <rmk7@nyu.edu>

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Package psych updated to version 1.8.10 with previous version 1.8.4 dated 2018-05-06

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A general purpose toolbox for personality, psychometric theory and experimental psychology. Functions are primarily for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for analyzing data at multiple levels include within and between group statistics, including correlations and factor analysis. Functions for simulating and testing particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometric theory as well as publications in personality research. For more information, see the <https://personality-project.org/r> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>

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Package MDFS updated to version 1.0.2 with previous version 1.0.1 dated 2018-06-26

Title: MultiDimensional Feature Selection
Description: Functions for MultiDimensional Feature Selection (MDFS): calculating multidimensional information gains, scoring variables, finding important variables, plotting selection results. This package includes an optional CUDA implementation that speeds up information gain calculation using NVIDIA GPGPUs.
Author: Radosław Piliszek [aut, cre], Krzysztof Mnich [aut], Paweł Tabaszewski [aut], Szymon Migacz [aut], Andrzej Sułecki [aut], Witold Remigiusz Rudnicki [aut]
Maintainer: Radosław Piliszek <r.piliszek@uwb.edu.pl>

Diff between MDFS versions 1.0.1 dated 2018-06-26 and 1.0.2 dated 2018-10-31

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Package ijtiff updated to version 1.5.0 with previous version 1.4.2 dated 2018-10-07

Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Kent Johnson [aut], Simon Urbanek [ctb], Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>), Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>), Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between ijtiff versions 1.4.2 dated 2018-10-07 and 1.5.0 dated 2018-10-31

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New package ViSiElse with initial version 1.2.1
Package: ViSiElse
Type: Package
Version: 1.2.1
Title: A Visual Tool for Behavior Analysis
Authors@R: c( person("Nastasia", "Fouret", , "nastasia.fouret@gmail.com", c("aut", "cph")), person( "Mederic", "Descoins", , "mederic.descoins@chu-reunion.fr", role=, c("aut", "cph")), person("Elodie", "Garnier", , "elodie.garnier@chu-reunion.fr", c("aut", "cre", "cph")), person( "CEPOI - EA 7388", role="cph" ) )
Description: A graphical tool designed to visualize and to give an overview of behavioral observations realized on individuals or groups. Visualization of raw data during experimental observations of the realization of a procedure. It graphically presents an overview of individuals and group actions usually acquired from timestamps during video recorded sessions. Options of the package allow adding graphical information as statistical indicators (mean, standard deviation, quantile or statistical test) but also for each action green or black zones providing visual information about the accuracy of the realized actions.
URL: https://github.com/CEPOI/ViSiElse
Author: Nastasia Fouret [aut, cph], Mederic Descoins [aut, cph], Elodie Garnier [aut, cre, cph], CEPOI - EA 7388 [cph]
Maintainer: Elodie Garnier <elodie.garnier@chu-reunion.fr>
License: AGPL-3
Depends: R (>= 3.2.0), methods (>= 3.2.0), grid (>= 3.2.0), chron (>= 2.3-46), Matrix (>= 1.2-0), colorspace (>= 1.2-6), stringr (>= 1.0.0)
Suggests: knitr, rmarkdown
LazyData: true
RoxygenNote: 6.1.0
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-10-31 06:56:07 UTC; 097200
Repository: CRAN
Date/Publication: 2018-10-31 10:20:22 UTC

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New package urbin with initial version 0.1-4
Package: urbin
Version: 0.1-4
Date: 2018-10-31
Title: Unifying Estimation Results with Binary Dependent Variables
Author: Arne Henningsen, Geraldine Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Depends: R (>= 2.14.0)
Suggests: sampleSelection (>= 0.7-0), maxLik (>= 1.1-2), mfx (>= 1.1), mlogit (>= 0.3-0), MASS (>= 7.3-50), mvProbit (>= 0.1-8)
Description: Calculate unified measures that quantify the effect of a covariate on a binary dependent variable (e.g., for meta-analyses). This can be particularly important if the estimation results are obtained with different models/estimators (e.g., linear probability model, logit, probit, ...) and/or with different transformations of the explanatory variable of interest (e.g., linear, quadratic, interval-coded, ...). The calculated unified measures are: (a) semi-elasticities of linear, quadratic, or interval-coded covariates and (b) effects of linear, quadratic, interval-coded, or categorical covariates when a linear or quadratic covariate changes between distinct intervals, the reference category of a categorical variable or the reference interval of an interval-coded variable needs to be changed, or some categories of a categorical covariate or some intervals of an interval-coded covariate need to be grouped together. Approximate standard errors of the unified measures are also calculated.
License: GPL (>= 2)
URL: http://r-forge.r-project.org/projects/urbin/
NeedsCompilation: no
Packaged: 2018-10-31 10:06:46 UTC; gsl324
Repository: CRAN
Date/Publication: 2018-10-31 10:50:04 UTC

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Package spatstat.utils updated to version 1.13-0 with previous version 1.12-0 dated 2018-10-29

Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre], Rolf Turner [aut], Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>

Diff between spatstat.utils versions 1.12-0 dated 2018-10-29 and 1.13-0 dated 2018-10-31

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New package scPDSI with initial version 0.1.2
Package: scPDSI
Type: Package
Title: Calculation of the Conventional and Self-Calibrating Palmer Drought Severity Index
Version: 0.1.2
Authors@R: c(person("Ruida", "Zhong", email = "zrd2017@163.com", role = c("aut", "cre")), person("Xiaohong", "Chen", email = "eescxh@mail.sysu.edu.cn", role = c("aut", "ctb")), person("Zhaoli", "Wang", email = "wangzhl@scut.edu.cn", role = c("aut", "ctb")), person("Chengguang", "Lai", email = "laichg@scut.edu.cn", role = c("aut", "ctb")), person("Steve", "Goddard", role = c("ctb")), person("Nathan", "Wells", role = c("ctb")), person("Mike", "Hayes", role = c("ctb")))
Description: Calculating the monthly conventional and self-calibrating Palmer Drought Severity Index (PDSI and scPDSI) using the precipitation and potential evapotranspiration data. The function to calculate PDSI is based on the C++ source codes developed by Nathan Wells, Steve Goddard and Michael J. Hayes, University of Nebraska-Lincoln. Reference: Palmer W. (1965). Meteorological drought. U.s.department of Commerce Weather Bureau Research Paper, <https://www.ncdc.noaa.gov/temp-and-precip/drought/docs/palmer.pdf>; Wells N., Goddard S., Hayes M. J. (2004). A Self-Calibrating Palmer Drought Severity Index. Journal of Climate, 17(12):2335-2351, <DOI:10.1175/1520-0442(2004)017%3C2335:ASPDSI%3E2.0.CO;2>.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: stats, Rcpp (>= 0.12.0)
URL: https://github.com/Sibada/scPDSI
BugReports: https://github.com/Sibada/scPDSI/issues
RoxygenNote: 5.0.1
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-10-31 02:16:20 UTC; vicerTi
Author: Ruida Zhong [aut, cre], Xiaohong Chen [aut, ctb], Zhaoli Wang [aut, ctb], Chengguang Lai [aut, ctb], Steve Goddard [ctb], Nathan Wells [ctb], Mike Hayes [ctb]
Maintainer: Ruida Zhong <zrd2017@163.com>
Repository: CRAN
Date/Publication: 2018-10-31 10:20:03 UTC

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Package reinforcedPred updated to version 0.1.1 with previous version 0.1.0 dated 2018-10-26

Title: Reinforced Risk Prediction with Budget Constraint
Description: Traditional risk prediction only utilizes baseline factors known to be associated with the disease. Given that longitudinal information are routinely measured and documented for patients, it is worthwhile to make full use of these data. The available longitudinal biomarker data will likely improve prediction. However, repeated biomarker collection could be costly and inconvenient, and risk prediction for patients at a later time could delay necessary medical decisions. Thus, there is a trade-off between high quality prediction and cost. This package implements a cost-effective statistical procedure that recursively incorporates comprehensive longitudinal information into the risk prediction model, taking into account the cost of delaying the decision to a follow-up time when more information is available. The statistical methods are described in the following paper: Pan, Y., Laber, E., Smith, M., Zhao, Y. (2018). Reinforced risk prediction with budget constraint: application to electronic health records data. Manuscript submitted for publication.
Author: Yinghao Pan [aut, cre], Yingqi Zhao [aut], Eric Laber [aut]
Maintainer: Yinghao Pan <ypan8@uncc.edu>

Diff between reinforcedPred versions 0.1.0 dated 2018-10-26 and 0.1.1 dated 2018-10-31

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Package germinationmetrics updated to version 0.1.2 with previous version 0.1.1.1 dated 2018-10-16

Title: Seed Germination Indices and Curve Fitting
Description: Provides functions to compute various germination indices such as germinability, median germination time, mean germination time, mean germination rate, speed of germination, Timson's index, germination value, coefficient of uniformity of germination, uncertainty of germination process, synchrony of germination etc. from germination count data. Includes functions for fitting cumulative seed germination curves using four-parameter hill function and computation of associated parameters. See the vignette for more, including full list of citations for the methods implemented.
Author: J. Aravind [aut, cre] (<https://orcid.org/0000-0002-4791-442X>), S. Vimala Devi [aut], J. Radhamani [aut], Sherry Rachel Jacob [aut], Kalyani Srinivasan [aut], ICAR-NBGPR [cph] (www.nbpgr.ernet.in)
Maintainer: J. Aravind <j.aravind@icar.gov.in>

Diff between germinationmetrics versions 0.1.1.1 dated 2018-10-16 and 0.1.2 dated 2018-10-31

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Package mvord updated to version 0.3.3 with previous version 0.3.2 dated 2018-10-03

Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate ordinal regression models with composite likelihood methods.
Author: Rainer Hirk [aut, cre], Kurt Hornik [aut], Laura Vana [aut], Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>

Diff between mvord versions 0.3.2 dated 2018-10-03 and 0.3.3 dated 2018-10-31

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Package customLayout updated to version 0.3.0 with previous version 0.2.0 dated 2018-09-27

Title: Arrange Elements on the R's Drawing Area or Inside the PowerPoint's Slide
Description: Create complicated drawing areas for multiple elements by combining much simpler layouts. It is an extended version of layout function from the 'graphics' package, but it also works with 'grid' graphics. It also supports arranging elements inside 'PowerPoint' slides created using the 'officer' package.
Author: Zygmunt Zawadzki [aut, cre]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>

Diff between customLayout versions 0.2.0 dated 2018-09-27 and 0.3.0 dated 2018-10-31

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Package blavaan updated to version 0.3-3 with previous version 0.3-2 dated 2018-06-10

Title: Bayesian Latent Variable Analysis
Description: Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models.
Author: Edgar Merkle [aut, cre] (<https://orcid.org/0000-0001-7158-0653>), Yves Rosseel [aut], Mauricio Garnier-Villarreal [ctb], Terrence D. Jorgensen [ctb], Huub Hoofs [ctb], Rens van de Schoot [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>

Diff between blavaan versions 0.3-2 dated 2018-06-10 and 0.3-3 dated 2018-10-31

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