Sat, 24 Jun 2017

Package R2MLwiN updated to version 0.8-4 with previous version 0.8-3 dated 2016-09-07

Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel modelling software package.
Author: Zhengzheng Zhang [aut, cre], Chris Charlton [aut], Richard Parker [aut], George Leckie [aut], William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>

Diff between R2MLwiN versions 0.8-3 dated 2016-09-07 and 0.8-4 dated 2017-06-24

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Package ggiraph updated to version 0.4.0 with previous version 0.3.3 dated 2017-03-24

Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre], Mike Bostock [cph] (d3.js), Speros Kokenes [cph] (d3-lasso)
Maintainer: David Gohel <david.gohel@ardata.fr>

Diff between ggiraph versions 0.3.3 dated 2017-03-24 and 0.4.0 dated 2017-06-24

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Package ggExtra updated to version 0.7 with previous version 0.6 dated 2016-11-11

Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main function is ggMarginal(), which can be used to add marginal histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre], Christopher Baker [ctb]
Maintainer: Dean Attali <daattali@gmail.com>

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Package aSPU updated to version 1.48 with previous version 1.47 dated 2017-05-21

Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single nucleotide polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended 'Simes' procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits- single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>

Diff between aSPU versions 1.47 dated 2017-05-21 and 1.48 dated 2017-06-24

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Package sys updated to version 1.4 with previous version 1.3 dated 2017-04-20

Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior across platforms. Supports interruption, background tasks, and full control over 'STDOUT' / 'STDERR' binary or text streams. On Unix systems the package also has functions for evaluating expressions inside a temporary fork. Such evaluations have no side effects on the main R process, and support reliable interrupts and timeouts. This provides the basis for a 'sandboxing' mechanism.
Author: Jeroen Ooms [aut, cre], Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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More information about sys at CRAN
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Package stacomirtools updated to version 0.5.2 with previous version 0.5.0 dated 2016-08-20

Title: 'ODBC' Connection Class for Package stacomiR
Description: S4 class wrappers for the 'ODBC' connection, also provides some utilities to paste small datasets to clipboard, rename columns. It is used by the package 'stacomiR' for connections to the database. Development versions of 'stacomiR' are available in R-forge.
Author: Cedric Briand [aut, cre]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>

Diff between stacomirtools versions 0.5.0 dated 2016-08-20 and 0.5.2 dated 2017-06-24

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Package spind updated to version 2.1.0 with previous version 2.0.1 dated 2017-04-07

Title: Spatial Methods and Indices
Description: Functions for spatial methods based on generalized estimating equations (GEE) and wavelet-revised methods (WRM), functions for scaling by wavelet multiresolution regression (WMRR), conducting multi-model inference, and stepwise model selection. Further, contains functions for spatially corrected model accuracy measures.
Author: Gudrun Carl [cre, aut], Ingolf Kuehn [aut], Sam Levin [aut]
Maintainer: Sam Levin <levisc8@gmail.com>

Diff between spind versions 2.0.1 dated 2017-04-07 and 2.1.0 dated 2017-06-24

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Package PRIMsrc updated to version 0.7.1 with previous version 0.7.0 dated 2017-05-29

Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>

Diff between PRIMsrc versions 0.7.0 dated 2017-05-29 and 0.7.1 dated 2017-06-24

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Package MultiSkew updated to version 1.1.1 with previous version 1.1 dated 2017-06-14

Title: Measures, Tests and Removes Multivariate Skewness
Description: Computes the third multivariate cumulant of either the raw, centered or standardized data. Computes the main measures of multivariate skewness, together with their bootstrap distributions. Finally, computes the least skewed linear projections of the data.
Author: Cinzia Franceschini, Nicola Loperfido
Maintainer: Cinzia Franceschini <cinziafranceschini@msn.com>

Diff between MultiSkew versions 1.1 dated 2017-06-14 and 1.1.1 dated 2017-06-24

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Package micompr updated to version 1.0.2 with previous version 1.0.1 dated 2016-08-04

Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with different groups. It uses principal component analysis to convert multivariate observations into a set of linearly uncorrelated statistical measures, which are then compared using a number of statistical methods. The procedure is independent of the distributional properties of samples and automatically selects features that best explain their differences, avoiding manual selection of specific points or summary statistics. It is appropriate for comparing samples of time series, images, spectrometric measures or similar multivariate observations.
Author: Nuno Fachada [aut, cre]
Maintainer: Nuno Fachada <faken@fakenmc.com>

Diff between micompr versions 1.0.1 dated 2016-08-04 and 1.0.2 dated 2017-06-24

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 vignettes/paper.Rnw                  |  258 +++++++++++++++++++++++------------
 53 files changed, 452 insertions(+), 296 deletions(-)

More information about micompr at CRAN
Permanent link

Package generalhoslem updated to version 1.2.5 with previous version 1.2.4 dated 2016-12-16

Title: Goodness of Fit Tests for Logistic Regression Models
Description: Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models. Included are the Hosmer-Lemeshow tests (binary, multinomial and ordinal) and the Lipsitz and Pulkstenis-Robinson tests (ordinal).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>

Diff between generalhoslem versions 1.2.4 dated 2016-12-16 and 1.2.5 dated 2017-06-24

 DESCRIPTION          |    8 ++++----
 MD5                  |   16 ++++++++--------
 R/lipsitz.test.R     |    2 +-
 R/logitgof.R         |    2 ++
 R/pulkrob.chisq.R    |    2 +-
 build/partial.rdb    |binary
 man/lipsitz.test.Rd  |    6 +++---
 man/logitgof.Rd      |    4 +++-
 man/pulkrob.chisq.Rd |    4 ++--
 9 files changed, 24 insertions(+), 20 deletions(-)

More information about generalhoslem at CRAN
Permanent link

Package RPostgreSQL updated to version 0.6-2 with previous version 0.4-1 dated 2016-05-08

Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'. This package provides a Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' database systems. In order to build and install this package from source, 'PostgreSQL' itself must be present your system to provide 'PostgreSQL' functionality via its libraries and header files. These files are provided as 'postgresql-devel' package under some Linux distributions. On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>

Diff between RPostgreSQL versions 0.4-1 dated 2016-05-08 and 0.6-2 dated 2017-06-24

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 RPostgreSQL-0.6-2/RPostgreSQL/NAMESPACE                                |    6 
 RPostgreSQL-0.6-2/RPostgreSQL/R/PostgreSQL.R                           |   34 
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 RPostgreSQL-0.6-2/RPostgreSQL/configure                                | 1892 ++++------
 RPostgreSQL-0.6-2/RPostgreSQL/configure.in                             |   29 
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 172 files changed, 8527 insertions(+), 5462 deletions(-)

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Package evaluate updated to version 0.10.1 with previous version 0.10 dated 2016-10-11

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Michael Lawrence [ctb], Thomas Kluyver [ctb], Barret Schloerke [ctb], Adam Ryczkowski [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

Diff between evaluate versions 0.10 dated 2016-10-11 and 0.10.1 dated 2017-06-24

 DESCRIPTION               |   10 +++++-----
 MD5                       |   32 ++++++++++++++++----------------
 NAMESPACE                 |    3 +++
 NEWS                      |    6 ++++++
 R/parse.r                 |   10 ++++++++++
 man/create_traceback.Rd   |    1 +
 man/evaluate.Rd           |    1 +
 man/flush_console.Rd      |    1 +
 man/inject_funs.Rd        |    1 +
 man/is.message.Rd         |   12 +++++++++---
 man/line_prompt.Rd        |    1 +
 man/new_output_handler.Rd |    1 +
 man/parse_all.Rd          |    1 +
 man/replay.Rd             |    1 +
 man/set_hooks.Rd          |    1 +
 man/try_capture_stack.Rd  |    1 +
 man/watchout.Rd           |    1 +
 17 files changed, 60 insertions(+), 24 deletions(-)

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New package aphid with initial version 1.0.0
Package: aphid
Type: Package
Title: Analysis with Profile Hidden Markov Models
Version: 1.0.0
Authors@R: person("Shaun", "Wilkinson", email = "shaunpwilkinson@gmail.com", role = c("aut", "cre"))
Author: Shaun Wilkinson [aut, cre]
Maintainer: Shaun Wilkinson <shaunpwilkinson@gmail.com>
Description: Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification.
License: GPL-3
URL: http://github.com/shaunpwilkinson/aphid
BugReports: http://github.com/shaunpwilkinson/aphid/issues
LazyData: TRUE
SystemRequirements: GNU make
Depends: R(>= 3.0.0)
Imports: graphics, openssl, phylogram (>= 1.0.0), Rcpp (>= 0.12.5), stats
Suggests: ape (>= 3.0), knitr, rmarkdown, testthat
LinkingTo: Rcpp
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-06-24 06:12:58 UTC; shaun
Repository: CRAN
Date/Publication: 2017-06-24 07:22:46 UTC

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New package windfarmGA with initial version 1.0
Package: windfarmGA
Type: Package
Title: Genetic Algorithm for Wind Farm Layout Optimization
Version: 1.0
Date: 2017-06-20
Author: Sebastian Gatscha
Maintainer: Sebastian Gatscha <sebastian_gatscha@gmx.at>
Description: The genetic algorithm is designed to optimize small wind farms up to 50 turbines. The algorithm works with a fixed amount of turbines, a fixed rotor radius and a mean wind speed value for every incoming wind direction. If required it can include a terrain effect model, which downloads an 'SRTM' elevation model automatically and loads a Corine Land Cover raster, which has to be downloaded previously. Further information can be found at the description of the function 'windfarmGA'. To start an optimization run, either the function 'windfarmGA' or 'genAlgo' can be used. The function 'windfarmGA' checks the user inputs interactively and then runs the function 'genAlgo'. If the input parameters are already known, an optimization can be run directly via the function 'genAlgo'. Their output is identical.
License: MIT + file LICENSE
LazyData: TRUE
Depends: R (>= 3.2.3)
Imports: rgdal (>= 1.0-4), raster (>= 2.5-2), sp (>= 1.2-2), dplyr (>= 0.5.0), data.table (>= 1.9.6), gtools (>= 3.5.0), maptools (>= 0.8-36), calibrate (>= 1.7.2), geoR (>= 1.7-5.1), gstat (>= 1.0-26), ggplot2 (>= 2.2.0), RColorBrewer (>= 1.1-2), rgeos (>= 0.3-11), RgoogleMaps (>= 1.2.0.7), googleVis (>= 0.5.9), rgl (>= 0.96.0), grDevices, graphics, stats, utils
Suggests: magrittr
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-06-23 20:08:54 UTC; Bobo
Repository: CRAN
Date/Publication: 2017-06-24 05:54:16 UTC

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New package DZEXPM with initial version 1.0
Package: DZEXPM
Type: Package
Title: Estimation and Prediction of Skewed Spatial Processes
Version: 1.0
Date: 2017-06-24
Author: Jiangyan Wang, Miao Yang and Anandamayee Majumdar
Maintainer: "Jiangyan Wang" <jiangyanwang@nau.edu.cn>
Description: A collection of functions designed to estimate and predict skewed spatial processes, and a real data set.
License: GPL (>= 2)
LazyData: true
NeedsCompilation: no
Packaged: 2017-06-24 04:41:05 UTC; Jiangyan
Repository: CRAN
Date/Publication: 2017-06-24 05:49:25 UTC

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Package ddpcr updated to version 1.8 with previous version 1.6 dated 2016-11-11

Title: Analysis and Visualization of Droplet Digital PCR in R and on the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>

Diff between ddpcr versions 1.6 dated 2016-11-11 and 1.8 dated 2017-06-24

 DESCRIPTION                           |    6 
 MD5                                   |   84 +++++++-----
 NEWS.md                               |   10 +
 R/aaa.R                               |    3 
 R/empty.R                             |   87 ++++++-------
 R/plate-utils.R                       |   30 +++-
 R/pnpp_experiment-classify.R          |  142 ++++++++++-----------
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More information about ddpcr at CRAN
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New package nlsrk with initial version 1.1
Package: nlsrk
Version: 1.1
Date: 2017-06-22
Title: Runge-Kutta Solver for Function nls()
Author: Jean-Sebastien Pierre <jean-sebastien.pierre@univ-rennes1.fr>
Maintainer: Jean-Sebastien Pierre <jean-sebastien.pierre@univ-rennes1.fr>
Depends: R (>= 3.0.0)
Description: Performs univariate or multivariate computation of a single ODE or of a set of ODE (ordinary differential equations).
License: GPL (>= 2)
URL: none
NeedsCompilation: no
Packaged: 2017-06-23 20:53:09 UTC; jpierre
Repository: CRAN
Date/Publication: 2017-06-23 23:01:24 UTC

More information about nlsrk at CRAN
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