Sat, 04 Jul 2015

Package spocc updated to version 0.3.0 with previous version 0.2.4 dated 2015-01-22

Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources, including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics' Engine 'eBird', and 'AntWeb'. Includes functionality for retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

Diff between spocc versions 0.2.4 dated 2015-01-22 and 0.3.0 dated 2015-07-04

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Package RedditExtractoR updated to version 1.1.1 with previous version 1.0.0 dated 2015-06-16

Title: Reddit Data Extraction Toolkit
Description: Reddit is an online bulletin board and a social networking website where registered users can submit and discuss content. This package uses Reddit API to extract Reddit data using Reddit API. The retrieved data has flat structure, i.e. the relationship between comments is not preserved.This may be addressed in the next update of this package. Note that due to the API limitations, the number of comments that can extracted is limited to 500 per thread. The package consists of 3 functions, one for extracting relevant URLS, one for extracting features out of given URLs and one that does both together.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>

Diff between RedditExtractoR versions 1.0.0 dated 2015-06-16 and 1.1.1 dated 2015-07-04

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Package curl updated to version 0.9.1 with previous version 0.9 dated 2015-06-19

Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption (https://, ftps://), 'gzip' compression, authentication, and other 'libcurl' goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr' package which builds on this package with HTTP specific tools and logic.
Author: Jeroen Ooms [cre, aut], Hadley Wickham [ctb], RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>

Diff between curl versions 0.9 dated 2015-06-19 and 0.9.1 dated 2015-07-04

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Package trust updated to version 0.1-7 with previous version 0.1-6 dated 2014-03-29

Title: Trust Region Optimization
Description: Does local optimization using two derivatives and trust regions. Guaranteed to converge to local minimum of objective function.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>

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Package smoothtail updated to version 2.0.4 with previous version 2.0.3 dated 2014-02-06

Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma in [-1,0], offers several estimates to compute estimates of gamma. The estimates are based on the principle of replacing the order statistics by quantiles of a distribution function based on a log--concave density function. This procedure is justified by the fact that the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Ru{f}{i}bach <kaspar.rufibach@gmail.com> and Samuel Mueller <samuel.mueller@sydney.edu.au>
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

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Package reporttools updated to version 1.1.2 with previous version 1.1.1 dated 2013-11-06

Title: Generate LaTeX Tables of Descriptive Statistics
Description: These functions are especially helpful when writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between reporttools versions 1.1.1 dated 2013-11-06 and 1.1.2 dated 2015-07-04

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Package RcppRedis updated to version 0.1.4 with previous version 0.1.3 dated 2014-12-10

Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the C-language client library 'hiredis'.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppRedis versions 0.1.3 dated 2014-12-10 and 0.1.4 dated 2015-07-04

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Package OrdFacReg updated to version 1.0.6 with previous version 1.0.5 dated 2014-09-06

Title: Least Squares, Logistic, and Cox-Regression with Ordered Predictors
Description: In biomedical studies, researchers are often interested in assessing the association between one or more ordinal explanatory variables and an outcome variable, at the same time adjusting for covariates of any type. The outcome variable may be continuous, binary, or represent censored survival times. In the absence of a precise knowledge of the response function, using monotonicity constraints on the ordinal variables improves efficiency in estimating parameters, especially when sample sizes are small. This package implements an active set algorithm that efficiently computes such estimators.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@gmail.com>

Diff between OrdFacReg versions 1.0.5 dated 2014-09-06 and 1.0.6 dated 2015-07-04

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Package patchSynctex updated to version 0.1-3 with previous version 0.1-2 dated 2015-05-01

Title: Communication Between Editor and Viewer for Literate Programs
Description: This utility eases the debugging of literate documents ('noweb' files) by patching the synchronization information (the '.synctex(.gz)' file) produced by 'pdflatex' with concordance information produced by 'Sweave' or 'knitr' and 'Sweave' or 'knitr' ; this allows for bilateral communication between a text editor (visualizing the 'noweb' source) and a viewer (visualizing the resultant 'PDF'), thus bypassing the intermediate 'TeX' file.
Author: Jan Gleixner [aut], Daniel Hicks [ctb], Emmanuel Charpentier [aut, cre]
Maintainer: Emmanuel Charpentier <emm.charpentier@free.fr>

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Package nat.utils updated to version 0.5.1 with previous version 0.5 dated 2015-07-02

Title: File System Utility Functions for 'NeuroAnatomy Toolbox'
Description: Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.
Author: Gregory Jefferis
Maintainer: Gregory Jefferis <jefferis@gmail.com>

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Package googleVis updated to version 0.5.9 with previous version 0.5.8 dated 2015-01-21

Title: R Interface to Google Charts
Description: R interface to Google Charts API, allowing users to create interactive charts based on data frames. Charts are displayed locally via the R HTTP help server. A modern browser with Internet connection is required and for some charts a Flash player. The data remains local and is not uploaded to Google.
Author: Markus Gesmann [aut, cre], Diego de Castillo [aut], Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>

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Package GLDreg updated to version 1.0.3 with previous version 1.0.2 dated 2015-03-05

Title: Fit GLD Regression Model and GLD Quantile Regression Model to Empirical Data
Description: Owing to the rich shapes of GLDs, GLD standard/quantile regression is a competitive flexible model compared to standard/quantile regression. The proposed method has some major advantages: 1) it provides a reference line which is very robust to outliers with the attractive property of zero mean residuals and 2) it gives a unified, elegant quantile regression model from the reference line with smooth regression coefficients across different quantiles. The goodness of fit of the proposed model can be assessed via QQ plots and the Kolmogorov-Smirnov test, to ensure the appropriateness of the statistical inference under consideration. Statistical distributions of coefficients of the GLD regression line are obtained using simulation, and interval estimates are obtained directly from simulated data.
Author: Steve Su, with contributions from: R core team for qqgld.default function.
Maintainer: Steve Su <allegro.su@gmail.com>

Diff between GLDreg versions 1.0.2 dated 2015-03-05 and 1.0.3 dated 2015-07-04

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Package GLDEX updated to version 2.0.0.3 with previous version 2.0.0.2 dated 2014-12-22

Title: Fitting Single and Mixture of Generalised Lambda Distributions (RS and FMKL) using Various Methods
Description: The fitting algorithms considered in this package have two major objectives. One is to provide a smoothing device to fit distributions to data using the weight and unweighted discretised approach based on the bin width of the histogram. The other is to provide a definitive fit to the data set using the maximum likelihood and quantile matching estimation. Other methods such as moment matching, starship method, L moment matching are also provided. Diagnostics on goodness of fit can be done via qqplots, KS-resample tests and comparing mean, variance, skewness and kurtosis of the data with the fitted distribution.
Author: Steve Su, with contributions from: Diethelm Wuertz, Martin Maechler and Rmetrics core team members for low discrepancy algorithm, Juha Karvanen for L moments codes, Robert King for gld C codes and starship codes, Benjamin Dean for corrections and input in ks.gof code and R core team for histsu function.
Maintainer: Steve Su <allegro.su@gmail.com>

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Package forams updated to version 2.0-5 with previous version 2.0-4 dated 2014-02-18

Title: Foraminifera and Community Ecology Analyses
Description: SHE, FORAM Index and ABC Method analyses and custom plot functions for community data.
Author: Rodrigo Aluizio
Maintainer: Rodrigo Aluizio <r.aluizio@gmail.com>

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New package tseriesEntropy with initial version 0.5-12
Package: tseriesEntropy
Title: Entropy Based Analysis and Tests for Time Series
Date: 2015-07-02
Version: 0.5-12
Author: Simone Giannerini
Depends: R (>= 2.14.0)
Imports: cubature, methods, parallel, stats, graphics
Suggests:
Description: Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes.
Maintainer: Simone Giannerini <simone.giannerini@unibo.it>
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2015-07-03 15:19:31 UTC; Simone
Repository: CRAN
Date/Publication: 2015-07-04 09:52:03

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New package taber with initial version 0.0.1
Package: taber
Type: Package
Title: Split and Recombine Your Data
Version: 0.0.1
Date: 2015-07-02
Authors@R: person("Seth", "Wenchel", email = "seth@wenchel.com", role = c("aut", "cre", "cph"))
Description: Sometimes you need to split your data and work on the two chunks independently before bringing them back together. 'Taber' allows you to do that with its two functions.
License: BSD_3_clause + file LICENSE
LazyData: TRUE
Imports: magrittr, dplyr
URL: http://github.com/restonslacker/taber
BugReports: http://github.com/restonslacker/taber/issues
Twitter: @wenchel
Packaged: 2015-07-03 23:38:30 UTC; SWENCHEL
Author: Seth Wenchel [aut, cre, cph]
Maintainer: Seth Wenchel <seth@wenchel.com>
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-04 09:52:02

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New package RBitly with initial version 0.6.1
Package: RBitly
Type: Package
Title: R Wrapper for the Bit.ly API
Description: Allows users accessing 'Bit.ly API' http://dev.bitly.com/ and retrieve many useful statistics.
Version: 0.6.1
Date: 2015-07-02
Authors@R: c( person("John", "Malc", email = "cincenko@outlook.com", role = c("aut", "cre"), comment = "@dmpe") )
Maintainer: John Malc <cincenko@outlook.com>
Depends: R (>= 3.2.0)
Imports: httr (>= 1.0.0), jsonlite (>= 0.9.16), stringr (>= 1.0.0)
Suggests: roxygen2 (>= 4.1.0), knitr (>= 1.10.5), testthat (>= 0.10.0)
VignetteBuilder: knitr
License: Apache License 2.0
URL: https://github.com/dmpe/rbitly
BugReports: https://github.com/dmpe/rbitly/issues
NeedsCompilation: no
Packaged: 2015-07-03 14:28:31 UTC; jm
Author: John Malc [aut, cre] (@dmpe)
Repository: CRAN
Date/Publication: 2015-07-04 09:51:54

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Package gdata updated to version 2.17.0 with previous version 2.16.1 dated 2015-05-01

Title: Various R Programming Tools for Data Manipulation
Description: Various R programming tools for data manipulation, including: - medical unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects ('bindData', 'cbindX', 'combine', 'interleave'), - character vector operations ('centerText', 'startsWith', 'trim'), - factor manipulation ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll', 'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel formatted files ('read.xls', 'installXLSXsupport', 'sheetCount', 'xlsFormats'), - generating fixed-width format files ('write.fwf'), - extricating components of date & time objects ('getYear', 'getMonth', 'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'), - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames ('frameApply', 'wideByFactor'), - value of last evaluated expression ('ans'), and - wrapper for 'sample' that ensures consistent behavior for both scalar and vector arguments ('resample').
Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni Magnusson, Jim Rogers, and others
Maintainer: Gregory R. Warnes <greg@warnes.net>

Diff between gdata versions 2.16.1 dated 2015-05-01 and 2.17.0 dated 2015-07-04

 gdata-2.16.1/gdata/ChangeLog                           |only
 gdata-2.16.1/gdata/NEWS                                |only
 gdata-2.17.0/gdata/DESCRIPTION                         |   10 
 gdata-2.17.0/gdata/MD5                                 |   28 
 gdata-2.17.0/gdata/NAMESPACE                           |    4 
 gdata-2.17.0/gdata/R/upperTriangle.R                   |   34 
 gdata-2.17.0/gdata/inst/ChangeLog                      | 1790 ++++++-----------
 gdata-2.17.0/gdata/inst/NEWS                           |   18 
 gdata-2.17.0/gdata/inst/doc/mapLevels.pdf              |binary
 gdata-2.17.0/gdata/inst/doc/unknown.pdf                |binary
 gdata-2.17.0/gdata/man/upperTriangle.Rd                |   39 
 gdata-2.17.0/gdata/tests/test.humanReadable.Rout.save  |    2 
 gdata-2.17.0/gdata/tests/test.read.xls.R               |   74 
 gdata-2.17.0/gdata/tests/test.read.xls.Rout.save       |   76 
 gdata-2.17.0/gdata/tests/test.reorder.factor.Rout.save |    2 
 gdata-2.17.0/gdata/tests/tests.write.fwf.Rout.save     |    2 
 16 files changed, 849 insertions(+), 1230 deletions(-)

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Package VTrack updated to version 1.11 with previous version 1.10 dated 2015-07-02

Title: A Collection of Tools for the Analysis of Remote Acoustic Telemetry Data
Description: Designed to facilitate the assimilation, analysis and synthesis of animal location and movement data collected by the VEMCO suite of acoustic transmitters and receivers. As well as database and geographic information capabilities the principal feature of VTrack is the qualification and identification of ecologically relevant events from the acoustic detection and sensor data. This procedure condenses the acoustic detection database by orders of magnitude, greatly enhancing the synthesis of acoustic detection data.
Author: Ross G. Dwyer, Mathew E. Watts, Hamish A. Campbell & Craig E. Franklin
Maintainer: Ross Dwyer <ross.dwyer@uq.edu.au>

Diff between VTrack versions 1.10 dated 2015-07-02 and 1.11 dated 2015-07-04

 DESCRIPTION                              |   12 ++++++------
 MD5                                      |   16 ++++++++--------
 R/GenerateAnimationKMLFile_Multitag.R    |   13 +++++++------
 man/ExtractRecSummary.Rd                 |   11 +++++++++++
 man/ExtractTagSummary.Rd                 |   12 ++++++++++++
 man/GenerateAnimationKMLFile_Multitag.Rd |   13 +++++++++++--
 man/GenerateAnimationKMLFile_Track.Rd    |   12 +++++++-----
 man/ReadInputData.Rd                     |    2 +-
 man/VTrack-package.Rd                    |    4 ++--
 9 files changed, 65 insertions(+), 30 deletions(-)

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Package kinfit updated to version 1.1.14 with previous version 1.1.13 dated 2014-11-25

Title: Routines for Fitting Kinetic Models to Chemical Degradation Data
Description: The FOCUS Kinetics Report first published in 2006 describes mathematical models and recommends statistical methods for the evaluation of chemical degradation data. This package implements fitting the kinetic models suitable for observations of the decline of a single chemical compound (no metabolite formation/decline or multi-compartment kinetics). Please note that no warranty is implied for correctness of results or fitness for a particular purpose. 'kinfit' is maintained, but not actively developed at the moment. Please check the 'mkin' package for an actively developed package for kinetic evaluations of degradation data.
Author: Johannes Ranke [aut, cre, cph], Katrin Lindenberger [ctb]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>

Diff between kinfit versions 1.1.13 dated 2014-11-25 and 1.1.14 dated 2015-07-04

 DESCRIPTION                         |   42 +++++++++++++++++++-----------------
 MD5                                 |   30 ++++++++++++-------------
 NAMESPACE                           |    4 +++
 build/vignette.rds                  |binary
 data/FOCUS_2006_A.rda               |binary
 data/FOCUS_2006_B.rda               |binary
 data/FOCUS_2006_C.rda               |binary
 data/FOCUS_2006_D.rda               |binary
 data/FOCUS_2006_DFOP_ref_A_to_B.rda |binary
 data/FOCUS_2006_E.rda               |binary
 data/FOCUS_2006_F.rda               |binary
 data/FOCUS_2006_FOMC_ref_A_to_F.rda |binary
 data/FOCUS_2006_HS_ref_A_to_F.rda   |binary
 data/FOCUS_2006_SFO_ref_A_to_F.rda  |binary
 inst/doc/examples.pdf               |binary
 inst/doc/kinfit.pdf                 |binary
 16 files changed, 42 insertions(+), 34 deletions(-)

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Package ecespa updated to version 1.1-8 with previous version 1.1-7 dated 2013-03-13

Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on spatstat), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones".
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@upm.es>

Diff between ecespa versions 1.1-7 dated 2013-03-13 and 1.1-8 dated 2015-07-04

 DESCRIPTION             |   18 +++++--------
 MD5                     |   42 ++++++++++++++++----------------
 NAMESPACE               |    1 
 R/Kinhom.log.R          |    2 -
 R/Kmm.R                 |    2 -
 R/LF.gof.R              |only
 R/getis.R               |    2 -
 R/haz.ppp.R             |    2 -
 R/marksum.R             |    2 -
 R/plot.ecespa.getis.R   |    2 -
 R/plot.ecespa.marksum.R |    8 +++---
 R/rIPCP.R               |   63 ++++++++++++++++++------------------------------
 R/syrjala.test.R        |    6 ++--
 R/syrjala0.R            |    2 -
 man/Helianthemum.Rd     |    2 -
 man/K012.Rd             |    1 
 man/K1K2.rd             |    2 -
 man/LF.gof.Rd           |only
 man/dixon2002.Rd        |    4 ++-
 man/getis.rd            |    4 +--
 man/gypsophylous.rd     |    1 
 man/marksum.rd          |   17 ++++++++----
 man/seedlings.Rd        |    2 -
 23 files changed, 86 insertions(+), 99 deletions(-)

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New package hoa with initial version 2.1.1
Package: hoa
Version: 2.1.1
Date: 2015-07-03
Title: Higher Order Likelihood Inference
Author: R port by Alessandra R. Brazzale <alessandra.brazzale@unipd.it>, following earlier work by Douglas Bates. The function tem is based on work by Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Alex-Antoine Fortin <alex@fortin.bio>
Depends: R (>= 3.0.0)
Imports: graphics, statmod, stats, survival, utils
Suggests: boot, csampling
Description: Performs likelihood-based inference for a wide range of regression models. Provides higher-order approximations for inference based on extensions of saddlepoint type arguments as discussed in the book Applied Asymptotics: Case Studies in Small-Sample Statistics by Brazzale, Davison, and Reid (2007).
License: GPL (>= 2) | file LICENCE
URL: http://www.r-project.org, http://statwww.epfl.ch/AA/
LazyLoad: yes
LazyData: yes
Packaged: 2015-07-03 14:47:45 UTC; Alex
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-07-04 08:40:19

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