Thu, 05 May 2016

Package sitar updated to version 1.0.6 with previous version 1.0.5 dated 2016-04-12

Title: Super Imposition by Translation and Rotation Growth Curve Analysis
Description: Functions for fitting and plotting SITAR (Super Imposition by Translation And Rotation) growth curve models. SITAR is a shape-invariant model with a regression B-spline mean curve and subject-specific random effects on both the measurement and age scales.
Author: Tim Cole
Maintainer: Tim Cole <tim.cole@ucl.ac.uk>

Diff between sitar versions 1.0.5 dated 2016-04-12 and 1.0.6 dated 2016-05-05

 sitar-1.0.5/sitar/man/funcall.Rd       |only
 sitar-1.0.5/sitar/man/xaxsd.Rd         |only
 sitar-1.0.6/sitar/DESCRIPTION          |    8 +-
 sitar-1.0.6/sitar/MD5                  |   18 ++--
 sitar-1.0.6/sitar/NEWS                 |   16 ++++
 sitar-1.0.6/sitar/R/plot.sitar.R       |   37 +++-------
 sitar-1.0.6/sitar/R/predict.sitar.R    |  120 ++++++++++++++++++++-------------
 sitar-1.0.6/sitar/R/xyadj.R            |   10 --
 sitar-1.0.6/sitar/man/funcall.rd       |only
 sitar-1.0.6/sitar/man/predict.sitar.Rd |   19 ++---
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 12 files changed, 132 insertions(+), 107 deletions(-)

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Package RcppArmadillo updated to version 0.6.700.6.0 with previous version 0.6.700.3.0 dated 2016-04-06

Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the header files from the templated 'Armadillo' library. Thus users do not need to install 'Armadillo' itself in order to use 'RcppArmadillo'. 'Armadillo' is licensed under the MPL 2.0, while 'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois and Doug Bates
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppArmadillo versions 0.6.700.3.0 dated 2016-04-06 and 0.6.700.6.0 dated 2016-05-05

 ChangeLog                                          |   18 ++++++++
 DESCRIPTION                                        |    8 +--
 MD5                                                |   46 ++++++++++-----------
 build/vignette.rds                                 |binary
 inst/NEWS.Rd                                       |   18 ++++++++
 inst/doc/RcppArmadillo-intro.pdf                   |binary
 inst/doc/RcppArmadillo-unitTests.pdf               |binary
 inst/include/RcppArmadilloAs.h                     |   33 ++++++---------
 inst/include/RcppArmadilloConfig.h                 |    5 +-
 inst/include/armadillo_bits/Mat_meat.hpp           |   20 ++++-----
 inst/include/armadillo_bits/arma_ostream_bones.hpp |   18 ++++----
 inst/include/armadillo_bits/arma_ostream_meat.hpp  |    8 +++
 inst/include/armadillo_bits/arma_version.hpp       |    4 -
 inst/include/armadillo_bits/compiler_setup.hpp     |   23 ++--------
 inst/include/armadillo_bits/fn_clamp.hpp           |    1 
 inst/include/armadillo_bits/fn_kron.hpp            |   45 ++++++++++++++++++++
 inst/include/armadillo_bits/fn_reshape.hpp         |    8 +++
 inst/include/armadillo_bits/fn_resize.hpp          |    8 +++
 inst/include/armadillo_bits/fn_trunc_exp.hpp       |    4 -
 inst/include/armadillo_bits/fn_trunc_log.hpp       |    6 +-
 inst/include/armadillo_bits/glue_kron_meat.hpp     |    8 +++
 inst/include/armadillo_bits/op_find_meat.hpp       |   20 ++++-----
 inst/unitTests/cpp/sparse.cpp                      |   19 ++++++++
 inst/unitTests/runit.sparse.R                      |   17 +++++++
 24 files changed, 232 insertions(+), 105 deletions(-)

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Package parsec updated to version 1.1.2 with previous version 1.1.1 dated 2016-04-28

Title: Partial Orders in Socio-Economics
Description: Implements basic partial order tools for multidimensional poverty evaluation with ordinal variables. Its main goal is to provide socio-economic scholars with an integrated set of elementary functions for multidimensional poverty evaluation, based on ordinal information. The package is organized in four main parts. The first two comprise functions for data management and basic partial order analysis; the third and the fourth are devoted to evaluation and implement both the poset-based approach and a more classical counting procedure.
Author: Alberto Arcagni [aut, cre], Marco Fattore [ctb]
Maintainer: Alberto Arcagni <alberto.arcagni@unimib.it>

Diff between parsec versions 1.1.1 dated 2016-04-28 and 1.1.2 dated 2016-05-05

 DESCRIPTION           |    8 ++++----
 MD5                   |    6 +++---
 R/pop2prof.R          |    2 +-
 man/parsec-package.Rd |    4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

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Package MetaLandSim updated to version 0.5.1 with previous version 0.5 dated 2016-04-11

Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change).
Author: Frederico Mestre, Fernando Canovas, Ricardo Pita, Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>

Diff between MetaLandSim versions 0.5 dated 2016-04-11 and 0.5.1 dated 2016-05-05

 DESCRIPTION                       |    8 
 MD5                               |   24 +-
 R/MetaLandSim.GUI.R               |   24 +-
 R/matrix.graph.R                  |    2 
 R/range_expansion.R               |  351 ++++++++++++--------------------------
 R/range_raster.R                  |   37 ++--
 R/span.graph.R                    |   10 -
 R/species.graph.R                 |    2 
 inst/doc/MetaLandSim.pdf          |binary
 inst/doc/landscape_simulation.pdf |binary
 inst/doc/parametrization.pdf      |binary
 inst/doc/range_expansion.pdf      |binary
 man/MetaLandSim-package.Rd        |    4 
 13 files changed, 171 insertions(+), 291 deletions(-)

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New package norm2 with initial version 2.0.0
Package: norm2
Type: Package
Title: Analysis of Incomplete Multivariate Data under a Normal Model
Version: 2.0.0
Date: 2016-05-05
Author: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Maintainer: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Description: Functions for parameter estimation, Bayesian posterior simulation and multiple imputation from incomplete multivariate data under a normal model.
Depends: R (>= 3.1.0)
Imports: stats
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-05 16:44:14 UTC; schaf310
Repository: CRAN
Date/Publication: 2016-05-06 00:12:51

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New package lmem.qtler with initial version 0.1.0
Package: lmem.qtler
Type: Package
Title: Linear Mixed Effects Models for QTL Mapping for Multienvironment and Multitrait Analysis
Version: 0.1.0
Authors@R: c(person("Lucia", "Gutierrez", role = "aut", email = "gutierrezcha@wisc.edu"), person("Gaston", "Quero",role =c("aut","cre"), email = "gastonquero@gmail.com"), person("Schubert", "Fernandez",role ="aut", email = "sfernandez@inia.org.uy"), person("Sofia", "Brandariz",role ="aut", email = "brandarizsofia@gmail.com"), person("Sebastian", "Simondi",role ="ctb", email = "sebastian.simondi@gmail.com"))
Author: Lucia Gutierrez [aut], Gaston Quero [aut, cre], Schubert Fernandez [aut], Sofia Brandariz [aut], Sebastian Simondi [ctb]
Maintainer: Gaston Quero <gastonquero@gmail.com>
Description: Performs QTL mapping analysis for balanced and for multi-environment and multi-trait analysis using mixed models. Balanced population, single trait, single environment QTL mapping is performed through marker-regression (Haley and Knott (1992) <DOI:10.1038/hdy.1992.131>, Martinez and Curnow (1992) <DOI:10.1007/BF00222330>, while multi-environment and multi-trait QTL mapping is performed through linear mixed models. These functions could use any of the following populations: double haploid, F2, recombinant inbred lines, back-cross, and 4-way crosses. Performs a Single Marker Analysis, a Single Interval Mapping, or a Composite Interval Mapping analysis, and then constructs a final model with all of the relevant QTL.
License: GPL-3
Depends: R (>= 2.10)
LazyData: TRUE
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Imports: qtl, lme4, lattice, pastecs, stringr, graphics, utils, grDevices, stats
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-05 15:16:20 UTC; GQ
Repository: CRAN
Date/Publication: 2016-05-06 00:09:50

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Package IsoplotR updated to version 0.2 with previous version 0.1 dated 2016-04-21

Title: Statistical Toolbox for Radiometric Geochronology
Description: An R implementation of Ken Ludwig's popular Isoplot add-in to Microsoft Excel. Currently plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams, taking into account error correlations. Future versions will include functionality for the Ar-Ar, Rb-Sr, Sm-Nd, Re-Os, U-Th-He, fission track and cosmogenic nuclide methods, including isochrons, age spectra, ternary diagrams, kernel density estimates, radial plots, banana diagrams and multidimensional scaling plots. A graphical user interface is provided as an RStudio Shiny app.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>

Diff between IsoplotR versions 0.1 dated 2016-04-21 and 0.2 dated 2016-05-05

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 IsoplotR-0.2/IsoplotR/R/UPb.R                  |  190 ++++++-------------------
 IsoplotR-0.2/IsoplotR/R/concordia.R            |  145 +++++++++++--------
 IsoplotR-0.2/IsoplotR/R/constants.R            |   87 ++++++++---
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 IsoplotR-0.2/IsoplotR/R/errorellipse.R         |   19 +-
 IsoplotR-0.2/IsoplotR/R/io.R                   |   91 +++++------
 IsoplotR-0.2/IsoplotR/R/toolbox.R              |   47 +++++-
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 33 files changed, 378 insertions(+), 366 deletions(-)

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New package imputeMulti with initial version 0.4.5
Package: imputeMulti
Title: Imputation Methods for Multivariate Multinomial Data
Version: 0.4.5
Authors@R: person("Alex", "Whitworth", , "whitworth.alex@gmail.com", c("aut", "cre"))
Description: Implements imputation methods using EM and Data Augmentation for multinomial data following the work of Schafer 1997 <ISBN: 978-0-412-04061-0>.
Depends: R (>= 3.2.1)
Imports: gtools (>= 3.3), methods, parallel, Rcpp
License: GPL-3
LazyData: true
Suggests: testthat
LinkingTo: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-05 15:34:54 UTC; awhitworth
Author: Alex Whitworth [aut, cre]
Maintainer: Alex Whitworth <whitworth.alex@gmail.com>
Repository: CRAN
Date/Publication: 2016-05-05 23:49:23

More information about imputeMulti at CRAN
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Package fields updated to version 8.4-1 with previous version 8.3-6 dated 2016-01-04

Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis on splines, spatial data and spatial statistics. The major methods include cubic, and thin plate splines, Kriging and compact covariances for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range). A major feature is that any covariance function implemented in R and following a simple fields format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details in addition to the manual pages. The commented source code can be viewed by expanding the source code file (ending in tar.gz) and looking in the R subdirectory. Please cite fields along with its DOI in your publications!
Author: Douglas Nychka [aut, cre], Reinhard Furrer [aut], John Paige [aut], Stephan Sain [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>

Diff between fields versions 8.3-6 dated 2016-01-04 and 8.4-1 dated 2016-05-05

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 fields-8.4-1/fields/R/Exponential.R                       |   36 
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 fields-8.4-1/fields/R/MLEfast.R                           |   22 
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 fields-8.4-1/fields/R/Matern.parameters.R                 |   20 
 fields-8.4-1/fields/R/QTps.R                              |   20 
 fields-8.4-1/fields/R/REMLtest.R                          |   26 
 fields-8.4-1/fields/R/RMprecip.R                          |   24 
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 fields-8.4-1/fields/R/cubic.cov.R                         |   24 
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Package epifit updated to version 0.1.0 with previous version 0.0.6 dated 2016-03-01

Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data analysis by a unified model specification, along with some data manipulation functions. This package covers fitting of variety models including Cox regression models, linear regression models, Poisson regression models, logistic models and others whose likelihood is expressed in negative binomial, gamma and Weibull distributions.
Author: Kazutaka Doi [aut,cre], Kei Sakabe [ctb], Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>

Diff between epifit versions 0.0.6 dated 2016-03-01 and 0.1.0 dated 2016-05-05

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Package survival updated to version 2.39-3 with previous version 2.39-2 dated 2016-04-16

Title: Survival Analysis
Description: Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>

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New package PResiduals with initial version 0.2-2
Package: PResiduals
Type: Package
Title: Probability-Scale Residuals and Residual Correlations
Version: 0.2-2
Date: 2015-07-21
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Charles Dupont <charles.dupont@vanderbilt.edu>
Description: Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data.
Imports: MASS, Formula, rms,
Suggests: survival
License: GPL (>= 2)
Collate: 'GKGamma.R' 'PResiduals-package.R' 'pgumbel.R' 'newPolr.R' 'diagn.R' 'cobot.R' 'cocobot.R' 'cocobot_orm.R' 'condis.R' 'corTS.R' 'countbot.R' 'getCI.R' 'lm.scores.R' 'megabot.R' 'nb.scores.R' 'orm.scores.R' 'poisson.scores.R' 'presid.R' 'print.cobot.R' 'print.cocobot.R'
NeedsCompilation: no
Packaged: 2015-07-22 14:26:21 UTC; dupontct
Repository: CRAN
Date/Publication: 2015-07-23 04:45:55

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Package multiwayvcov updated to version 1.2.3 with previous version 1.2.2 dated 2015-09-25

Title: Multi-Way Standard Error Clustering
Description: Exports two functions implementing multi-way clustering using the method suggested by Cameron, Gelbach, & Miller (2011) and cluster (or block) bootstrapping for estimating variance-covariance matrices. Normal one and two-way clustering matches the results of other common statistical packages. Missing values are handled transparently and rudimentary parallelization support is provided.
Author: Nathaniel Graham and Mahmood Arai and Björn Hagströmer
Maintainer: Nathaniel Graham <npgraham1@gmail.com>

Diff between multiwayvcov versions 1.2.2 dated 2015-09-25 and 1.2.3 dated 2016-05-05

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Package joint.Cox updated to version 2.5 with previous version 2.4 dated 2016-02-24

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 under the joint frailty-copula model between tumour progression and death for meta-analysis. The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>

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Package ENiRG updated to version 1.0 with previous version 0.1 dated 2014-10-09

Title: Ecological Niche in R and GRASS
Description: A set of tools for the analysis of ecological niche of species and calculation of habitat suitability maps.
Author: Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes Gonzalez-Wanguemert
Maintainer: Fernando Garcia Canovas <fcgarcia@ualg.pt>

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Package cba updated to version 0.2-16 with previous version 0.2-15 dated 2015-07-23

Title: Clustering for Business Analytics
Description: Implements clustering techniques such as Proximus and Rock, utility functions for efficient computation of cross distances and data manipulation.
Author: Christian Buchta and Michael Hahsler
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>

Diff between cba versions 0.2-15 dated 2015-07-23 and 0.2-16 dated 2016-05-05

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 4 files changed, 16 insertions(+), 7 deletions(-)

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Package arulesSequences updated to version 0.2-15 with previous version 0.2-14 dated 2016-03-26

Title: Mining Frequent Sequences
Description: Add-on for arules to handle and mine frequent sequences. Provides interfaces to the C++ implementation of cSPADE by Mohammed J. Zaki.
Author: Christian Buchta and Michael Hahsler, with contributions from Daniel Diaz
Maintainer: Christian Buchta <christian.buchta@wu.ac.at>

Diff between arulesSequences versions 0.2-14 dated 2016-03-26 and 0.2-15 dated 2016-05-05

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Package STPGA updated to version 2.0 with previous version 1.0 dated 2014-05-31

Title: Selection of Training Populations by Genetic Algorithm
Description: Can be utilized to select a test data calibrated training population in high dimensional prediction problems and assumes that the explanatory variables are observed for all of the individuals. Once a "good" training set is identified, the response variable can be obtained only for this set to build a model for predicting the response in the test set.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>

Diff between STPGA versions 1.0 dated 2014-05-31 and 2.0 dated 2016-05-05

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Package rnoaa updated to version 0.5.6 with previous version 0.5.2 dated 2016-01-25

Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre], Karthik Ram [ctb], Adam Erickson [ctb], Nicholas Potter [ctb], Joseph Stachelek [ctb], Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between rnoaa versions 0.5.2 dated 2016-01-25 and 0.5.6 dated 2016-05-05

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Package biwavelet updated to version 0.19.2 with previous version 0.19.1 dated 2016-05-01

Title: Conduct Univariate and Bivariate Wavelet Analyses
Description: This is a port of the WTC MATLAB package written by Aslak Grinsted and the wavelet program written by Christopher Torrence and Gibert P. Compo. This package can be used to perform univariate and bivariate (cross-wavelet, wavelet coherence, wavelet clustering) analyses.
Author: Tarik C. Gouhier, Aslak Grinsted, Viliam Simko
Maintainer: Tarik C. Gouhier <tarik.gouhier@gmail.com>

Diff between biwavelet versions 0.19.1 dated 2016-05-01 and 0.19.2 dated 2016-05-05

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