Sun, 16 Apr 2017

Package splancs updated to version 2.01-40 with previous version 2.01-39 dated 2016-08-23

Title: Spatial and Space-Time Point Pattern Analysis
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre], Barry Rowlingson [aut], Peter Diggle [aut], Giovanni Petris [ctb], Stephen Eglen [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between splancs versions 2.01-39 dated 2016-08-23 and 2.01-40 dated 2017-04-16

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Package unmarked updated to version 0.12-0 with previous version 0.11-0 dated 2015-09-03

Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson
Maintainer: Andy Royle <aroyle@usgs.gov>

Diff between unmarked versions 0.11-0 dated 2015-09-03 and 0.12-0 dated 2017-04-16

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Package spgwr updated to version 0.6-30 with previous version 0.6-29 dated 2017-01-09

Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted regressions are provided, based on work by Chris Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut], Danlin Yu [aut], Tomoki Nakaya [ctb], Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between spgwr versions 0.6-29 dated 2017-01-09 and 0.6-30 dated 2017-04-16

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Package rotationForest updated to version 0.1.3 with previous version 0.1 dated 2015-05-17

Title: Fit and Deploy Rotation Forest Models
Description: Fit and deploy rotation forest models ("Rodriguez, J.J., Kuncheva, L.I., 2006. Rotation forest: A new classifier ensemble method. IEEE Trans. Pattern Anal. Mach. Intell. 28, 1619-1630 <doi:10.1109/TPAMI.2006.211>") for binary classification. Rotation forest is an ensemble method where each base classifier (tree) is fit on the principal components of the variables of random partitions of the feature set.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@gmail.com>

Diff between rotationForest versions 0.1 dated 2015-05-17 and 0.1.3 dated 2017-04-16

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New package mro with initial version 0.1.1
Package: mro
Type: Package
Title: Multiple Correlation
Version: 0.1.1
Author: Abirami S
Maintainer: Abirami S <abirami89@gmail.com>
Description: Computes multiple correlation coefficient when the data matrix is given and tests its significance.
Depends: R (>= 3.1.0), MASS,matrixcalc
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-04-16 15:29:21 UTC; Sampath
Repository: CRAN
Date/Publication: 2017-04-16 16:24:55 UTC

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Package forestmodel updated to version 0.4.3 with previous version 0.4.0 dated 2015-12-10

Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>

Diff between forestmodel versions 0.4.0 dated 2015-12-10 and 0.4.3 dated 2017-04-16

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Package classInt updated to version 0.1-24 with previous version 0.1-23 dated 2015-09-28

Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre], Hisaji Ono [ctb], Richard Dunlap [ctb], Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between classInt versions 0.1-23 dated 2015-09-28 and 0.1-24 dated 2017-04-16

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Package rpivotTable updated to version 0.2.0 with previous version 0.1.5.20 dated 2016-06-05

Title: Build Powerful Pivot Tables and Dynamically Slice & Dice your Data
Description: Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab) and dynamically slice & dice / drag 'n' drop your data. 'rpivotTable' is a wrapper of 'pivottable', a powerful open-source Pivot Table library implemented in 'JavaScript' by Nicolas Kruchten. Aligned to 'pivottable' v2.11.0.
Author: Enzo Martoglio [aut, cre] (R interface), Nicolas Kruchten [ctb, cph] (pivottable library), Kenton Russell [ctb]
Maintainer: Enzo Martoglio <enzo@smartinsightsfromdata.com>

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Package XGR updated to version 1.0.10 with previous version 1.0.9 dated 2017-03-14

Title: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>

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Package R.rsp updated to version 0.41.0 with previous version 0.40.0 dated 2016-12-06

Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>

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Package RandomFields updated to version 3.1.48 with previous version 3.1.36 dated 2016-12-25

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.
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], Christoph Berreth [ctr], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>

Diff between RandomFields versions 3.1.36 dated 2016-12-25 and 3.1.48 dated 2017-04-16

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More information about RandomFields at CRAN
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Package mcmc updated to version 0.9-5 with previous version 0.9-4 dated 2015-07-16

Title: Markov Chain Monte Carlo
Description: Simulates continuous distributions of random vectors using Markov chain Monte Carlo (MCMC). Users specify the distribution by an R function that evaluates the log unnormalized density. Algorithms are random walk Metropolis algorithm (function metrop), simulated tempering (function temper), and morphometric random walk Metropolis (Johnson and Geyer, 2012, <https://doi.org/10.1214/12-AOS1048>, function morph.metrop), which achieves geometric ergodicity by change of variable.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif T. Johnson <ltjohnson@google.com>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

Diff between mcmc versions 0.9-4 dated 2015-07-16 and 0.9-5 dated 2017-04-16

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More information about mcmc at CRAN
Permanent link

Package idm updated to version 1.8.1 with previous version 1.8.0 dated 2017-03-24

Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>

Diff between idm versions 1.8.0 dated 2017-03-24 and 1.8.1 dated 2017-04-16

 DESCRIPTION         |    8 +--
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More information about idm at CRAN
Permanent link

Package Epi updated to version 2.12 with previous version 2.11 dated 2017-04-14

Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multi state data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.
Author: Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>

Diff between Epi versions 2.11 dated 2017-04-14 and 2.12 dated 2017-04-16

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More information about Epi at CRAN
Permanent link

New package corpus with initial version 0.2-0
Package: corpus
Version: 0.2-0
Date: 2017-04-15
Title: Text Corpus Analysis
Author: Patrick O. Perry
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Description: Text corpus data analysis, with full support for UTF8-encoded Unicode text. The package provides the ability to seamlessly read and process text from large JSON files without holding all of the data in memory simultaneously.
Suggests: testthat
LazyData: Yes
License: Apache License (== 2.0) | file LICENSE
URL: https://github.com/patperry/r-corpus
BugReports: https://github.com/patperry/r-corpus/issues
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2017-04-15 23:31:41 UTC; ptrck
Repository: CRAN
Date/Publication: 2017-04-16 10:09:37 UTC

More information about corpus at CRAN
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Package choroplethr updated to version 3.6.1 with previous version 3.6.0 dated 2017-04-09

Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut], Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>

Diff between choroplethr versions 3.6.0 dated 2017-04-09 and 3.6.1 dated 2017-04-16

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Package APfun updated to version 0.1.1 with previous version 0.1.0 dated 2017-01-15

Title: Geo-Processing Base Functions
Description: Base tools for facilitating the creation geo-processing functions in R.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>

Diff between APfun versions 0.1.0 dated 2017-01-15 and 0.1.1 dated 2017-04-16

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More information about APfun at CRAN
Permanent link

Package phantom updated to version 0.1.1 with previous version 0.1.0 dated 2017-04-13

Title: Gene Set Pareto Heterogeneity Analysis of Time-Course Gene Expression Data
Description: Pareto front based statistical tool for detecting heterogeneity in gene sets and biological modules from time-course data.
Author: Jinghua Gu [aut, cre], Xuan Wang [aut], Jinayn Chan [aut, cre], Nicole Baldwin [aut], Jacob Turner [aut]
Maintainer: Jinyan Chan <Jinyan.Chan@bswhealth.org>

Diff between phantom versions 0.1.0 dated 2017-04-13 and 0.1.1 dated 2017-04-16

 DESCRIPTION    |   16 +++++++-------
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More information about phantom at CRAN
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Package lingtypology updated to version 1.0.3 with previous version 1.0.2 dated 2017-02-23

Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://agricolamz.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>

Diff between lingtypology versions 1.0.2 dated 2017-02-23 and 1.0.3 dated 2017-04-16

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Package joint.Cox updated to version 2.11 with previous version 2.10 dated 2016-10-30

Title: Penalized Likelihood Estimation and Dynamic Prediction under the Joint Frailty-Copula Models Between Tumour Progression and Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction methods under the joint frailty-copula model between tumour progression and death for meta-analysis. A penalized likelihood is employed for estimating model parameters, where the baseline hazard functions are approximated by smoothing splines. The methods are applicable for meta-analytic data combining several studies. The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression). See Emura et al. (2015) <doi:10.1177/0962280215604510> and Emura et al. (2017) <doi:10.1177/0962280216688032> for details. Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

Diff between joint.Cox versions 2.10 dated 2016-10-30 and 2.11 dated 2017-04-16

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Permanent link

Package datarobot updated to version 2.6.0 with previous version 2.4.0 dated 2016-12-01

Title: DataRobot Predictive Modeling API
Description: For working with the DataRobot predictive modeling platform's <https://app.datarobot.com> API.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut]
Maintainer: Sergey Yurgenson <api-maintainer@datarobot.com>

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More information about datarobot at CRAN
Permanent link

Package curvHDR updated to version 1.2-0 with previous version 1.1-0 dated 2016-03-14

Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of flow cytometry samples using the curvHDR method, which is described in Naumann, U., Luta, G. and Wand, M.P. (2010) <DOI:10.1186/1471-2105-11-44>.
Author: Matt Wand [aut, cre], George Luta [aut], Ulrike Naumann [aut], Mathew W. McLean [ctb], Dai Feng [ctb], Luke Tierney [ctb], Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>

Diff between curvHDR versions 1.1-0 dated 2016-03-14 and 1.2-0 dated 2017-04-16

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More information about curvHDR at CRAN
Permanent link

Package childsds updated to version 0.6 with previous version 0.5 dated 2014-08-21

Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores adduced from different growth standards (WHO, UK, German). Therefore, the calculation for SDS-values for different measures like BMI, weight, height, head circumference, different ratios, etc. are easy to carry out. Also, references for laboratory values in children are available: serum lipids, iron-related blood parameters. In the new version, there are also functions combining the gamlss lms() function with resampling methods for using with repeated measurements and family dependencies.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>

Diff between childsds versions 0.5 dated 2014-08-21 and 0.6 dated 2017-04-16

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 48 files changed, 239 insertions(+), 204 deletions(-)

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2016-02-02 2.0.0
2015-06-04 1.2.1
2015-04-01 1.1.1
2015-03-11 1.1
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2014-08-23 1.0

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Package PGRdup (with last version 0.2.3.1) was removed from CRAN

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2017-03-15 0.2.3.1
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2016-03-09 0.2.2.1
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2015-04-14 0.2

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