Thu, 14 Dec 2017

Package propr updated to version 3.1.2 with previous version 3.1.1 dated 2017-11-13

Title: Calculating Proportionality Between Vectors of Compositional Data
Description: The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, this approach lacks statistical validity when applied to relative data. This includes, for example, biological count data generated by high-throughput RNA-sequencing, chromatin immunoprecipitation (ChIP), ChIP-sequencing, Methyl-Capture sequencing, and other techniques. This package implements several metrics for proportionality, including phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also implements several metrics for differential proportionality. Unlike correlation, these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre], David Lovell [aut], Ionas Erb [aut], Anders Bilgrau [ctb], Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>

Diff between propr versions 3.1.1 dated 2017-11-13 and 3.1.2 dated 2017-12-14

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Package exprso updated to version 0.2.7 with previous version 0.2.6 dated 2017-11-30

Title: Rapid Deployment of Machine Learning Algorithms
Description: Supervised machine learning has an increasingly important role in data analysis. This package introduces a framework for rapidly building and deploying supervised machine learning in a high-throughput manner. This package provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, as well as regression, with minimal programming experience necessary.
Author: Thomas Quinn [aut, cre], Daniel Tylee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>

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Package RSNPset updated to version 0.5.3 with previous version 0.5.2 dated 2017-02-21

Title: Efficient Score Statistics for Genome-Wide SNP Set Analysis
Description: An implementation of the use of efficient score statistics in genome-wide SNP set analysis with complex traits. Three standard score statistics (Cox, binomial, and Gaussian) are provided, but the package is easily extensible to include others. Code implementing the inferential procedure is primarily written in C++ and utilizes parallelization of the analysis to reduce runtime. A supporting function offers simple computation of observed, permutation, and FWER and FDR adjusted p-values.
Author: Chanhee Yi, Alexander Sibley, and Kouros Owzar
Maintainer: Alexander Sibley <alexander.sibley@dm.duke.edu>

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Package spAddins updated to version 0.2.0 with previous version 0.1.7 dated 2017-01-03

Title: A Set of RStudio Addins
Description: A set of RStudio addins that are designed to be used in combination with user-defined RStudio keyboard shortcuts. These addins either: 1) insert text at a cursor position (e.g. insert operators %>%, <<-, %$%, etc.), 2) replace symbols in selected pieces of text (e.g., convert backslashes to forward slashes which results in stings like "c:\data\" converted into "c:/data/") or 3) enclose text with special symbols (e.g., converts "bold" into "**bold**") which is convenient for editing R Markdown files.
Author: Vilmantas Gegzna [aut, cre, cph]
Maintainer: Vilmantas Gegzna <GegznaV@gmail.com>

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Package mizer updated to version 0.4 with previous version 0.2 dated 2014-04-16

Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multispecies, trait based and community size spectrum ecological models, focussed on the marine environment.
Author: Finlay Scott [aut, cph], Julia Blanchard [aut, cph], Ken Andersen [aut, cph], Gustav Delius [ctb, cre], Richard Southwell [ctb]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>

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Package wrapr updated to version 1.0.2 with previous version 1.0.1 dated 2017-11-17

Title: Wrap R Functions for Debugging and Parametric Programming
Description: Powerful tools for writing and debugging R code. Provides: 'let()' which converts non-standard evaluation interfaces to parametric standard evaluation interface, 'DebugFnW()' to capture function context on error for debugging, and ':=' named map builder, and lambda-abstraction.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package utf8 updated to version 1.1.2 with previous version 1.1.1 dated 2017-11-29

Title: Unicode Text Processing
Description: Processing and printing 'UTF-8' encoded international text (Unicode). Functions to input, validate, normalize, encode, format, and display.
Author: Patrick O. Perry [aut, cph, cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>

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Package tweedie updated to version 2.3.2 with previous version 2.3.1 dated 2017-11-16

Title: Evaluation of Tweedie Exponential Family Models
Description: Maximum likelihood computations for Tweedie families, including the series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>), and related methods.
Author: Peter K. Dunn [cre, aut]
Maintainer: Peter K. Dunn <pdunn2@usc.edu.au>

Diff between tweedie versions 2.3.1 dated 2017-11-16 and 2.3.2 dated 2017-12-14

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Package treespace updated to version 1.0.1 with previous version 1.0.0 dated 2017-03-17

Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer().
Author: Thibaut Jombart [aut], Michelle Kendall [aut, cre], Jacob Almagro-Garcia [aut], Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>

Diff between treespace versions 1.0.0 dated 2017-03-17 and 1.0.1 dated 2017-12-14

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More information about treespace at CRAN
Permanent link

New package tidytree with initial version 0.1.5
Package: tidytree
Title: A Tidy Tool for Phylogenetic Tree Data Manipulation
Version: 0.1.5
Authors@R: c( person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")), person("Bradley", "Jones", email = "brj1@sfu.ca", role = "ctb"), person("Zebulun", "Arendsee", email = "zbwrnz@gmail.com", role = "ctb") )
Description: Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.
Depends: R (>= 3.4.0)
Imports: ape, dplyr, lazyeval, magrittr, methods, tibble
Suggests: ggtree, knitr, prettydoc, testthat, treeio
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
URL: https://github.com/GuangchuangYu/tidytree
BugReports: https://github.com/GuangchuangYu/tidytree/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-14 13:42:55 UTC; guangchuangyu
Author: Guangchuang Yu [aut, cre, cph] (0000-0002-6485-8781), Bradley Jones [ctb], Zebulun Arendsee [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Repository: CRAN
Date/Publication: 2017-12-14 16:23:00 UTC

More information about tidytree at CRAN
Permanent link

Package syuzhet updated to version 1.0.4 with previous version 1.0.1 dated 2017-03-06

Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs from text using a variety of sentiment dictionaries conveniently packaged for consumption by R users. Implemented dictionaries include "syuzhet" (default) developed in the Nebraska Literary Lab "afinn" developed by Finn {\AA}rup Nielsen, "bing" developed by Minqing Hu and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D. Applicable references are available in README.md and in the documentation for the "get_sentiment" function. The package also provides a hack for implementing Stanford's coreNLP sentiment parser. The package provides several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>

Diff between syuzhet versions 1.0.1 dated 2017-03-06 and 1.0.4 dated 2017-12-14

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Package multipanelfigure updated to version 0.10.6 with previous version 0.10.5 dated 2017-08-31

Title: Infrastructure to Assemble Multi-Panel Figures (from Grobs)
Description: Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, and PNG, JPEG, SVG and TIFF images.
Author: Johannes Graumann [cre, aut], Richard Cotton [ctb]
Maintainer: Johannes Graumann <jog2030@qatar-med.cornell.edu>

Diff between multipanelfigure versions 0.10.5 dated 2017-08-31 and 0.10.6 dated 2017-12-14

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More information about multipanelfigure at CRAN
Permanent link

New package humanleague with initial version 2.0.2
Package: humanleague
Type: Package
Title: Synthetic Population Generator
Version: 2.0.2
Description: Generates high-entropy integer synthetic populations from marginal and (optionally) seed data using quasirandom sampling, in arbitrary dimensionality (Smith, Lovelace and Birkin (2017) <doi:10.18564/jasss.3550>). The package also provides an implementation of the Iterative Proportional Fitting (IPF) algorithm (Zaloznik (2011) <doi:10.13140/2.1.2480.9923>).
Authors@R: c( person("Andrew", "Smith", email="a.p.smith@leeds.ac.uk", role=c("aut", "cre")), person("Steven", "Johnson", role=c("ctb"), comment="Sobol sequence generator implementation"), person("Massachusetts Institute of Technology", role=c("cph"), comment="Sobol sequence generator implementation"), person("John", "Burkhardt", role=c("ctb","cph"), comment="C++ implementation of incomplete gamma function"), person("G", "Bhattacharjee", role=c("ctb"), comment="Original FORTRAN implementation of incomplete gamma function"))
License: MIT + file LICENCE
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.8), curl
LinkingTo: Rcpp
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2017-12-14 13:39:34 UTC; az
Author: Andrew Smith [aut, cre], Steven Johnson [ctb] (Sobol sequence generator implementation), Massachusetts Institute of Technology [cph] (Sobol sequence generator implementation), John Burkhardt [ctb, cph] (C++ implementation of incomplete gamma function), G Bhattacharjee [ctb] (Original FORTRAN implementation of incomplete gamma function)
Maintainer: Andrew Smith <a.p.smith@leeds.ac.uk>
Repository: CRAN
Date/Publication: 2017-12-14 16:10:31 UTC

More information about humanleague at CRAN
Permanent link

Package hsdar updated to version 0.7.0 with previous version 0.6.0 dated 2017-10-22

Title: Manage, Analyse and Simulate Hyperspectral Data
Description: Transformation of reflectance spectra, calculation of vegetation indices and red edge parameters, spectral resampling for hyperspectral remote sensing, simulation of reflectance and transmittance using the leaf reflectance model PROSPECT and the canopy reflectance model PROSAIL.
Author: Lukas W. Lehnert [cre, aut], Hanna Meyer [aut], Joerg Bendix [aut]
Maintainer: Lukas W. Lehnert <lukaslehnert@googlemail.com>

Diff between hsdar versions 0.6.0 dated 2017-10-22 and 0.7.0 dated 2017-12-14

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Package gravity updated to version 0.6 with previous version 0.5 dated 2017-11-14

Title: Estimation Methods for Gravity Models
Description: Gravity models are used to explain bilateral flows related to the sizes of bilateral partners, a measure of distance between them and other influences on interaction costs. The underlying idea is rather simple. The greater the masses of two bodies and the smaller the distance between them, the stronger their attraction. This concept is applied to several research topics such as trade, migration or foreign direct investment. Even though their basic idea is rather simple, gravity models can become complex regarding the choice of models or estimation methods. As especially for gravity beginners it is difficult to get an overview of the different methods and implement them in R, the package provides a wrapper of different standard estimation methods for gravity models. By considering the descriptions and codes of the estimation methods, users get a comprehensive and application-oriented overview of the different methods, see which method may be suitable for a certain research question or type of data and extend the code available to their research projects. The package contains two types of estimation methods: those estimating gravity models in their log-log form, such as Ordinary Least Squares (OLS), Fixed Effects, Double Demeaning (DDM), Bonus vetus OLS with simple averages (BVU) and with GDP-weights (BVW), Structural Iterated Least Squares (SILS), Tetrads, and different Tobit models (Tobit, ET-Tobit, EK-Tobit). These methods are partly complex to understand and program and thus a comparison of them is not straightforward, wherefore the package aims at easing an overview of the different methods combined with a direct application. A second type of estimation methods utilizes the gravity model in its multiplicative form with a log-link and different families of distributions. They are relatively easy to compute, added for completeness and contain the methods Poisson Pseudo Maximum Likelihood (PPML), Gamma Pseudo Maximum Likelihood (GPML), Negative Binomial Pseudo Maximum Likelihood (NBPML), and Nonlinear Least Squares (NLS). All functions named estimate gravity models, but they differ in whether they estimate them in their multiplicative or additive form, their requirements and assumptions with respect to data, their handling of Multilateral Resistance terms as well as their possibilities concerning the inclusion of unilateral independent variables. Therefore, they normally lead to different estimation results. We refer the user to the Gravity Cookbook website (<https://sites.google.com/site/hiegravity/>) for more information on gravity models in general. Head, K. and Mayer, T. (2014) <DOI:10.1016/B978-0-444-54314-1.00003-3> provide a comprehensive and accessible overview of the theoretical and empirical development of the gravity literature as well as the use of gravity models and the various estimation methods, especially their merits and potential problems regarding applicability as well as different datasets. In order to have a straightforward application of all methods, the package comes with two example dataset, one including and the other one excluding zero trade flows. Examples utilizing these dataset are included in the description of the methods. As the range of gravity models and their suitable estimation methods is huge and specific to data and research question at hand, the functions are kept simple such that researchers can utilize them as a starting point of their research and get familiar with them. On the Gravity Cookbook website (<https://sites.google.com/site/hiegravity/>) Keith Head and Thierry Mayer provide Stata code for most methods. Where possible, the functions are tested to lead the same results as the Stata code when choosing the option of robust variance estimation. However, compared to the Stata code available, the functions presented in this package provide users with more flexibility regarding the type of estimation, the number and type of independent variables as well as the possible data. Furthermore, additional functions are added. The functions of the package include distance as an independent variable. If a panel model is used time-invariant effects, such as geographical distance, may have to be excluded; see the respective descriptions. Therefore, it is up to the user to ensure that the functions can be applied to panel data. Depending on the panel dataset and the variables - specifically the type of fixed effects - included in the model, it may easily occur that the model is not computable. Depending on the specific model, the code of the respective function may has to be changed in order to exclude the distance variable from the estimation. For a comprehensive overview of gravity models for panel data see Egger, P., & Pfaffermayr, M. (2003) <DOI:10.1007/s001810200146>, Gomez-Herrera, E. (2013) <DOI:10.1007/s00181-012-0576-2> and Head, K., Mayer, T., & Ries, J. (2010) <DOI:10.1016/j.jinteco.2010.01.002> as well as the references therein (see also the references included in the descriptions of the different functions). At the very least, the user should take special care with respect to the meaning of the estimated coefficients and variances as well as the decision about which effects to include in the estimation. As, to our knowledge at the moment, there is no explicit literature covering the estimation of a gravity equation by Double Demeaning, Structural Iterated Least Squares or Bonus vetus OLS using panel data, we do not recommend to apply these methods in this case. Contributions, extensions and error corrections are very welcome. Please do not hesitate to contact us. We thank Martin Bresslein for valuable comments and advice on early versions of the package.
Author: Anna-Lena Woelwer <woelwer@uni-trier.de>, Jan Pablo Burgard <burgardj@uni-trier.de>
Maintainer: Anna-Lena Woelwer <woelwer@uni-trier.de>

Diff between gravity versions 0.5 dated 2017-11-14 and 0.6 dated 2017-12-14

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Package gge updated to version 1.3 with previous version 1.2 dated 2017-05-25

Title: Genotype Plus Genotype-by-Environment Biplots
Description: Create biplots for GGE (genotype plus genotype-by-environment) and GGB (genotype plus genotype-by-block-of-environments) models.
Author: Kevin Wright [aut, cre], Jean-Louis Laffont [aut]
Maintainer: Kevin Wright <kw.stat@gmail.com>

Diff between gge versions 1.2 dated 2017-05-25 and 1.3 dated 2017-12-14

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Package elo updated to version 1.0.1 with previous version 1.0.0 dated 2017-11-20

Title: Elo Ratings
Description: A flexible framework for calculating Elo ratings and resulting rankings of any two-team-per-matchup system (chess, sports leagues, 'Go', etc.). This implementation is capable of evaluating a variety of matchups, Elo rating updates, and win probabilities, all based on the basic Elo rating system.
Author: Ethan Heinzen [aut, cre]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>

Diff between elo versions 1.0.0 dated 2017-11-20 and 1.0.1 dated 2017-12-14

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Package digest updated to version 0.6.13 with previous version 0.6.12 dated 2017-01-27

Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen, Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, Michel Lang and Viliam Simko.
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package antaresProcessing updated to version 0.13 with previous version 0.12 dated 2017-12-07

Title: Antares Results Processing
Description: Process results generated by Antares, a powerful software developed by RTE to simulate and study electric power systems (more information about Antares here: <https://antares.rte-france.com>). This package provides functions to create new columns like net load, load factors, upward and downward margins or to compute aggregated statistics like economic surpluses of consumers, producers and sectors.
Author: Jalal-Edine ZAWAM [aut, cre], Francois Guillem [aut], Benoit Thieurmel [aut], Titouan Robert [aut], RTE [cph]
Maintainer: Jalal-Edine ZAWAM <jalal-edine.zawam@rte-france.com>

Diff between antaresProcessing versions 0.12 dated 2017-12-07 and 0.13 dated 2017-12-14

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Package rbacon updated to version 2.3.1 with previous version 2.3.0 dated 2017-12-13

Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre], J. Andres Christen [aut], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

Diff between rbacon versions 2.3.0 dated 2017-12-13 and 2.3.1 dated 2017-12-14

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New package phmm with initial version 0.7-10
Package: phmm
Version: 0.7-10
Date: 2017-12-13
Title: Proportional Hazards Mixed-Effects Model (PHMM)
Authors@R: c(person(given="Michael", family="Donohue", role = c("aut", "cre"), email = "mdonohue@usc.edu"), person(given="Ronghui", family="Xu", role = "aut"))
Maintainer: Michael Donohue <mdonohue@usc.edu>
Depends: survival, lattice, Matrix
VignetteBuilder: knitr
Suggests: knitr, lme4 (>= 1.0)
Description: Fits proportional hazards model incorporating random effects using an EM algorithm using Markov Chain Monte Carlo at E-step. Vaida and Xu (2000) <doi:10.1002/1097-0258(20001230)19:24%3C3309::AID-SIM825%3E3.0.CO;2-9>.
License: GPL-3
Collate: 'phmm-package.R' 'formula.R' 'linear.predictors.R' 'phmm.R' 'pseudoPoisPHMM.R' 'traceHat.R'
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-12-14 00:36:47 UTC; mdonohue
Author: Michael Donohue [aut, cre], Ronghui Xu [aut]
Repository: CRAN
Date/Publication: 2017-12-14 15:38:06 UTC

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Package stopwords updated to version 0.9.0 with previous version 0.1.0 dated 2017-11-12

Title: Multilingual Stopword Lists
Description: Provides multiple sources of stopwords, for use in text analysis and natural language processing.
Author: Kenneth Benoit [aut], David Muhr [aut, cre], Kohei Watanabe [aut]
Maintainer: David Muhr <muhrdavid+github@gmail.com>

Diff between stopwords versions 0.1.0 dated 2017-11-12 and 0.9.0 dated 2017-12-14

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Package semtree updated to version 0.9.11 with previous version 0.9.10 dated 2017-04-05

Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision trees and forests to Structural Equation Models (SEM). SEM trees hierarchically split empirical data into homogeneous groups sharing similar data patterns with respect to a SEM by recursively selecting optimal predictors of these differences. SEM forests are an extension of SEM trees. They are ensembles of SEM trees each built on a random sample of the original data. By aggregating over a forest, we obtain measures of variable importance that are more robust than measures from single trees.
Author: Andreas M. Brandmaier [aut, cre], John J. Prindle [aut]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>

Diff between semtree versions 0.9.10 dated 2017-04-05 and 0.9.11 dated 2017-12-14

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New package sRDA with initial version 1.0.0
Package: sRDA
Title: Sparse Redundancy Analysis
Version: 1.0.0
Date: 2017-12-12
Authors@R: c(person("Attila", "Csala", role = c("aut", "cre"), email = "a@csala.me"), person("Koos", "Zwinderman", role = "ctb", email = "a.h.zwinderman@amc.uva.nl"))
Author: Attila Csala [aut, cre], Koos Zwinderman [ctb]
Maintainer: Attila Csala <a@csala.me>
Description: Sparse redundancy analysis for high dimensional (biomedical) data. Directional multivariate analysis to express the maximum variance in the predicted data set by a linear combination of variables of the predictive data set. Implemented in a partial least squares framework, for more details see Csala et al. (2017) <doi:10.1093/bioinformatics/btx374>.
Depends: R (>= 2.7), Matrix, doParallel, elasticnet, foreach, mvtnorm
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-14 10:24:28 UTC; acsala
Repository: CRAN
Date/Publication: 2017-12-14 13:36:54 UTC

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New package PooledMeanGroup with initial version 1.0
Package: PooledMeanGroup
Version: 1.0
Date: 2017-12-13
Title: Pooled Mean Group Estimation of Dynamic Heterogenous Panels
Authors@R: c(person("Piotr", "Zientara", role="aut", email="zientara@fest.pl"), person("Lech", "Kujawski", role=c("aut", "cre"), email = "lech.kujawski@ug.edu.pl"))
Author: Piotr Zientara [aut], Lech Kujawski [aut, cre]
Maintainer: Lech Kujawski <lech.kujawski@ug.edu.pl>
Depends: R (>= 3.2.3)
Description: Calculates the pooled mean group (PMG) estimator for dynamic panel data models, as described by Pesaran, Shin and Smith (1999) <doi:10.1080/01621459.1999.10474156>.
License: GPL (>= 2)
URL: https://www.r-project.org
NeedsCompilation: no
Packaged: 2017-12-14 08:45:00 UTC; Marcin
Repository: CRAN
Date/Publication: 2017-12-14 13:08:28 UTC

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Package CMplot updated to version 3.3.0 with previous version 3.2.1 dated 2017-07-08

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

Diff between CMplot versions 3.2.1 dated 2017-07-08 and 3.3.0 dated 2017-12-14

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New package submax with initial version 1.1.1
Package: submax
Type: Package
Title: Effect Modification in Observational Studies Using the Submax Method
Version: 1.1.1
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>
Description: Effect modification occurs if a treatment effect is larger or more stable in certain subgroups defined by observed covariates. The submax or subgroup-maximum method of Lee et al. (2017) <arXiv:1702.00525> does an overall test and separate tests in subgroups, correcting for multiple testing using the joint distribution.
Imports: stats, mvtnorm, sensitivityfull
License: GPL-2
Encoding: UTF-8
LazyData: true
NeedsCompilation: no
Packaged: 2017-12-13 23:19:44 UTC; Rosenbaum
Repository: CRAN
Date/Publication: 2017-12-14 12:41:36 UTC

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Package polymapR updated to version 1.0.12 with previous version 1.0.11 dated 2017-12-05

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 autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. Methods are described in a preprint manuscript of Bourke et al. (2017) <doi:10.1101/228817>.
Author: Peter Bourke [aut, cre], Geert van Geest [aut]
Maintainer: Peter Bourke <pbourkey@gmail.com>

Diff between polymapR versions 1.0.11 dated 2017-12-05 and 1.0.12 dated 2017-12-14

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Package PBNPA updated to version 0.0.2 with previous version 0.0.1 dated 2016-12-20

Title: Permutation Based Non-Parametric Analysis of CRISPR Screen Data
Description: Permutation based non-parametric analysis of CRISPR screen data. Details about this algorithm are published in the following paper published on BMC genomics, Jia et al. (2017) <doi:10.1186/s12864-017-3938-5>: A permutation-based non-parametric analysis of CRISPR screen data. Please cite this paper if you use this algorithm for your paper.
Author: Gaoxiang Jia [aut, cre]
Maintainer: Gaoxiang Jia <GJia@SMU.edu>

Diff between PBNPA versions 0.0.1 dated 2016-12-20 and 0.0.2 dated 2017-12-14

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New package childhoodmortality with initial version 0.1.0
Package: childhoodmortality
Type: Package
Title: Calculating Childhood Mortality Rates
Version: 0.1.0
Author: Casey Breen
Depends: R(>= 2.10.0)
Maintainer: Casey Breen <cbreen@umn.edu>
Description: Calculates childhood (neonatal, postneonatal, infant, child, and under-five) mortality rates using Demographic and Health Survey (DHS) microdata. The 'childhoodmortality' package was developed in accordance to the methodology outlined in the "DHS Guide to Statistics" (Rutstein 2006, <http://dhsprogram.com/pubs/pdf/DHSG1/Guide_to_DHS_Statistics_29Oct2012_DHSG1.pdf>) Specifically, the package uses a synthetic cohort life table approach, combining mortality probabilities for age segments with actual cohort mortality experience into more common age segments. Standard errors for mortality estimates are computed using the jackknife repeated replication method outlined in the "Estimates of Sampling Errors" appendix of DHS Final Reports (DHS 2004, <http://dhsprogram.com/pubs/pdf/FR175/19AppendixB.pdf>). This methodology controls for sample design.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports: plyr, matrixStats
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-12-13 19:55:11 UTC; cbreen
Repository: CRAN
Date/Publication: 2017-12-14 12:38:30 UTC

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Package spatgraphs updated to version 3.2-1 with previous version 3.1-3 dated 2017-10-06

Title: Graph Edge Computations for Spatial Point Patterns
Description: Graphs (or networks) and graph component calculations for spatial locations in 1D, 2D, 3D etc.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>

Diff between spatgraphs versions 3.1-3 dated 2017-10-06 and 3.2-1 dated 2017-12-14

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Package clickstream updated to version 1.3.0 with previous version 1.2.1 dated 2017-05-18

Title: Analyzes Clickstreams Based on Markov Chains
Description: A set of tools to read, analyze and write lists of click sequences on websites (i.e., clickstream). A click can be represented by a number, character or string. Clickstreams can be modeled as zero- (only computes occurrence probabilities), first- or higher-order Markov chains.
Author: Michael Scholz, Theo van Kraay
Maintainer: Michael Scholz <michael.scholz@uni-passau.de>

Diff between clickstream versions 1.2.1 dated 2017-05-18 and 1.3.0 dated 2017-12-14

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 45 files changed, 168 insertions(+), 74 deletions(-)

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