Mon, 19 May 2014

Package sharx updated to version 1.0-4 with previous version 1.0-3 dated 2012-08-09

Title: Models and Data Sets for the Study of Species-Area Relationships
Description: Data sets and SAR, SARX, HSAR and HSARX models as described in Solymos and Lele (2012, GEB 21, 109-120).
Author: Peter Solymos
Maintainer: Peter Solymos

Diff between sharx versions 1.0-3 dated 2012-08-09 and 1.0-4 dated 2014-05-19

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 NAMESPACE      |    3 +++
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 inst/ChangeLog |    3 +++
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 man/sardata.Rd |   21 ++++++++++++++-------
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 8 files changed, 56 insertions(+), 32 deletions(-)

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Package PVAClone updated to version 0.1-2 with previous version 0.1-1 dated 2012-08-25

Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the presence of observation error and missing data. The package can be used to fit, compare, predict, and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos

Diff between PVAClone versions 0.1-1 dated 2012-08-25 and 0.1-2 dated 2014-05-19

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 R/ricker.R              |   52 ++++++++++++++++++++++++----------
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 21 files changed, 309 insertions(+), 147 deletions(-)

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Package mwa updated to version 0.3 with previous version 0.2 dated 2014-05-03

Title: MWA package for causal inference in spatiotemporal event data
Description: MWA grants insights into causal relationships in spatiotemporal event data.
Author: Sebastian Schutte and Karsten Donnay
Maintainer: Sebastian Schutte

Diff between mwa versions 0.2 dated 2014-05-03 and 0.3 dated 2014-05-19

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New package DNAprofiles with initial version 0.1.1
Package: DNAprofiles
Type: Package
Title: DNA profiling evidence analysis
Version: 0.1.1
Date: 2014-01-01
Author: Maarten Kruijver
Maintainer: Maarten Kruijver
Description: Methods for studying forensic DNA profiling, in particular familial database searches.
License: GPL (>= 2)
Imports: Rcpp (>= 0.10.3), bit
Depends: RcppProgress
LinkingTo: Rcpp, RcppProgress
Suggests: DNAtools
Packaged: 2014-05-19 14:47:01 UTC; maartenkruijver
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-19 17:34:22

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Package yhatr updated to version 0.9.0 with previous version 0.8.1 dated 2014-03-13

Title: R binder for the Yhat API
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat REST API.
Author: Greg Lamp , Eric Chiang
Maintainer: Greg Lamp

Diff between yhatr versions 0.8.1 dated 2014-03-13 and 0.9.0 dated 2014-05-19

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New package rbitcoinchartsapi with initial version 1.0.0
Package: rbitcoinchartsapi
Type: Package
Title: R Package for the BitCoinCharts.com API
Version: 1.0.0
Date: 2014-09-04
Author: Thomas P. Fuller
Maintainer: Thomas P. Fuller
Description: An R package for the BitCoinCharts.com API. Note that this package is an independent effort and not affiliated with the bitcoincharts.com website.
Depends: R (>= 3.0.3), RJSONIO, RCurl
SystemRequirements:
LazyLoad: yes
License: LGPL-3
Copyright: (C) 2014 Coherent Logic Limited
URL: http://www.r-project.org, http://www.coherentlogic.com/wordpress/?page_id=3580&source=cran
Repository: CRAN
Archs: i386, x64
Packaged: 2014-05-19 13:59:11 UTC; thospfuller
NeedsCompilation: no
Date/Publication: 2014-05-19 16:36:47

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Package ODMconverter updated to version 2.0 with previous version 1.2 dated 2013-10-24

Title: tools to convert ODM files
Description: Transformation of ODM files into R format, office format, CDA format and vice versa. CDISC ODM format is commonly used in clinical trials. Semantic annotation (such as UMLS, SNOMED or LOINC codes) are transformed accordingly.
Author: Martin Dugas
Maintainer: Martin Dugas

Diff between ODMconverter versions 1.2 dated 2013-10-24 and 2.0 dated 2014-05-19

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Package hawkes updated to version 0.0-4 with previous version 0.0-3 dated 2014-03-31

Title: Hawkes process simulation and calibration toolkit
Description: The package allows to simulate Hawkes process both in univariate and multivariate settings. It gives functions to compute different moments of the number of jumps of the process on a given interval, such as mean, variance or autocorrelation of process jumps on time intervals separated by a lag.
Author: Riadh Zaatour
Maintainer: Riadh Zaatour

Diff between hawkes versions 0.0-3 dated 2014-03-31 and 0.0-4 dated 2014-05-19

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More information about hawkes at CRAN
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Package GRTo updated to version 1.2 with previous version 1.1 dated 2013-07-26

Title: Tools for the analysis of Gutenberg-Richter distributions of earthquake magnitudes
Description: This package offers functions for the comparison of Gutenberg-Richter b-values. Several functions in GRTo are helpful for the assessment of the quality of seismicity catalogs.
Author: Daniel Amorese, Paul A. Rydelek and Jean-Robert Grasso
Maintainer: Daniel C. Amorese

Diff between GRTo versions 1.1 dated 2013-07-26 and 1.2 dated 2014-05-19

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New package FLIM with initial version 1.1
Package: FLIM
Type: Package
Title: Farewell’s Linear Increments Model
Version: 1.1
Date: 2013-12-09
Author: Rune Hoff with contributions from Jon Michael Gran and Daniel Farewell
Maintainer: Rune Hoff
Description: FLIM fits linear models for the observed increments in a longitudinal dataset, and imputes missing values according to the models.
Depends: zoo, MASS
Encoding: UTF-8
License: GPL-2
Packaged: 2014-05-19 13:56:06 UTC; runehoff
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-19 16:33:10

More information about FLIM at CRAN
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Package dnet updated to version 1.0.3 with previous version 1.0.2 dated 2014-04-30

Title: an open-source R package for omics data integrative analysis in terms of network, evolution and ontology
Description: The 'dnet' package is initiated to fill in the need of an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for semantic similarity calculation between ontology terms (and genes), and network affinity calculation using Random Walk with Restart; both can be done via high-performance parallel computing. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang

Diff between dnet versions 1.0.2 dated 2014-04-30 and 1.0.3 dated 2014-05-19

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Package PopGenome updated to version 2.0.7 with previous version 2.0.6 dated 2014-04-16

Title: A swiss army knife for population genetic & genomic analysis
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer

Diff between PopGenome versions 2.0.6 dated 2014-04-16 and 2.0.7 dated 2014-05-19

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Package oce updated to version 0.9-14 with previous version 0.9-13 dated 2014-01-29

Title: Analysis of Oceanographic data
Description: Supports the analysis of Oceanographic data, including ADP measurements, CTD measurements, sectional data, sea-level time series, coastline files, etc. Provides functions for calculating seawater properties such as potential temperature and density, as well as derived properties such as buoyancy frequency and dynamic height.
Author: Dan Kelley
Maintainer: Dan Kelley

Diff between oce versions 0.9-13 dated 2014-01-29 and 0.9-14 dated 2014-05-19

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Package ggm updated to version 2.1 with previous version 2.0 dated 2014-03-21

Title: A package for Graphical Markov Models
Description: Functions for analyzing and fitting Graphical Markov models
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti

Diff between ggm versions 2.0 dated 2014-03-21 and 2.1 dated 2014-05-19

 DESCRIPTION      |    9 
 MD5              |   24 
 NAMESPACE        |    1 
 R/functions.R    |    3 
 R/kayvan.R       | 3012 +++++++++++++++++++++++++++----------------------------
 man/AG.Rd        |  178 +--
 man/MAG.Rd       |  200 +--
 man/MRG.Rd       |    6 
 man/MSG.Rd       |  208 +--
 man/RG.Rd        |  174 +--
 man/SG.Rd        |  171 +--
 man/ggm.Rd       |   10 
 man/isAcyclic.Rd |    3 
 13 files changed, 2012 insertions(+), 1987 deletions(-)

More information about ggm at CRAN
Permanent link

Package clickstream updated to version 1.1.1 with previous version 1.1.0 dated 2014-03-28

Title: Analyzes clickstreams based on Markov chains
Description: This package allows modeling clickstreams with Markov chains. It supports to model clickstreams as zero-order, first-order or higher-order Markov chains.
Author: Michael Scholz
Maintainer: Michael Scholz

Diff between clickstream versions 1.1.0 dated 2014-03-28 and 1.1.1 dated 2014-05-19

 DESCRIPTION                        |    8 -
 MD5                                |   55 ++++---
 NAMESPACE                          |    2 
 NEWS                               |    7 +
 R/Clickstream.r                    |  259 ++++++++++++++++++++++++++++++++++++-
 R/Fitting.r                        |  146 +++++++++++++++-----
 R/MarkovChain.r                    |  206 +++++++++++++++++++++++++++++
 R/Pattern.r                        |   27 +++
 R/clickstream-package.R            |only
 man/MarkovChain-class.Rd           |   57 +-------
 man/Pattern-class.Rd               |   49 ++-----
 man/absorbingStates-methods.Rd     |   22 ++-
 man/clickstream-package.Rd         |   45 +++---
 man/clusterClickstreams.Rd         |   84 +++++-------
 man/fitMarkovChain.Rd              |   76 ++++++----
 man/predict-methods.Rd             |   73 ++++++----
 man/predict.ClickstreamClusters.Rd |   54 +++----
 man/print.ClickstreamClusters.Rd   |   39 ++---
 man/print.Clickstreams.Rd          |   35 ++---
 man/print.MarkovChainSummary.Rd    |   35 ++---
 man/randomClicks-methods.Rd        |   52 ++++---
 man/randomClickstreams.Rd          |   59 +++-----
 man/readClickstreams.Rd            |   55 ++++---
 man/states-methods.Rd              |   22 ++-
 man/summary-methods.Rd             |   44 ++++--
 man/summary.ClickstreamClusters.Rd |   41 ++---
 man/summary.Clickstreams.Rd        |   37 ++---
 man/transientStates-methods.Rd     |   23 ++-
 man/writeClickstreams.Rd           |   59 ++++----
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More information about clickstream at CRAN
Permanent link

Package conting updated to version 1.2 with previous version 1.1 dated 2013-08-13

Title: Bayesian analysis of contingency tables
Description: Bayesian analysis of complete and incomplete contingency tables.
Author: Antony M. Overstall
Maintainer: Antony M. Overstall

Diff between conting versions 1.1 dated 2013-08-13 and 1.2 dated 2014-05-19

 DESCRIPTION            |   11 +++++----
 MD5                    |   54 ++++++++++++++++++++++++-------------------------
 NAMESPACE              |    4 +++
 data/AOH.rda           |binary
 data/ScotPWID.rda      |binary
 data/heart.rda         |binary
 data/spina.rda         |binary
 man/AOH.Rd             |    4 +--
 man/RJ_update.Rd       |    4 +--
 man/ScotPWID.Rd        |   10 ++++-----
 man/bayespval.Rd       |   12 +++++-----
 man/bcct.Rd            |   25 ++++++++++------------
 man/bcct.fit.Rd        |    9 +++-----
 man/beta_mode.Rd       |   18 ++++++++--------
 man/bict.Rd            |   30 ++++++++++++---------------
 man/bict.fit.Rd        |   10 ++++-----
 man/conting-package.Rd |    8 +++----
 man/find_cens.Rd       |    8 +++----
 man/heart.Rd           |    9 +++-----
 man/index2model.Rd     |    2 -
 man/inter_probs.Rd     |    2 -
 man/inter_stats.Rd     |    2 -
 man/iwls_mh.Rd         |    4 +--
 man/mod_probs.Rd       |    2 -
 man/spina.Rd           |    4 +--
 man/sub_model.Rd       |   14 ++++++------
 man/summary.bcct.Rd    |   14 ++++++------
 man/total_pop.Rd       |    2 -
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More information about conting at CRAN
Permanent link

New package sse with initial version 0.5-1
Package: sse
Type: Package
Title: Sample size estimation
Version: 0.5-1
Date: 2014-05-10
Author: Thomas Fabbro
Maintainer: Thomas Fabbro
Description: The sse package takes user-defined power functions, evaluates them for a parameter range, and draws a sensitivity plot. It also provides a resampling procedure for semi-parametric sample size estimation and methods for adding informations to a Sweave report.
License: GPL-3
LazyLoad: yes
Depends: R (>= 2.5.0), methods, grid, lattice, graphics, base, stats
Repository: CRAN
Repository/R-Forge/Project: power
Repository/R-Forge/Revision: 12
Repository/R-Forge/DateTimeStamp: 2014-05-14 07:39:06
Date/Publication: 2014-05-19 09:59:41
Packaged: 2014-05-14 08:15:36 UTC; rforge
NeedsCompilation: no

More information about sse at CRAN
Permanent link

Package MASSTIMATE updated to version 1.2 with previous version 1.1 dated 2013-11-13

Title: Body Mass Estimation Equations for Vertebrates
Description: Estimation equations are from a variety of sources but are, in general, based on regressions between skeletal measurements (e.g., femoral circumference) and body mass in living taxa.
Author: Nicolas E. Campione
Maintainer: Nicolas E. Campione

Diff between MASSTIMATE versions 1.1 dated 2013-11-13 and 1.2 dated 2014-05-19

 DESCRIPTION               |    8 +++----
 MD5                       |   50 +++++++++++++++++++++++++---------------------
 R/AHR1985.R               |    6 ++---
 R/CF2004.R                |    4 +--
 R/CM1992.R                |    4 +--
 R/MCF2004.R               |    4 +--
 R/MR.R                    |   22 ++++++++++----------
 R/QE.R                    |   22 ++++++++++----------
 R/bipeds.R                |only
 R/cQE.R                   |   24 +++++++++++-----------
 R/ppe.R                   |   12 ++++++++---
 R/quadrupeds.R            |only
 R/see.R                   |only
 data/dinosbip.csv.gz      |binary
 data/dinosbip.rda         |binary
 man/AHR1985.Rd            |   12 ++++++-----
 man/CF2004.Rd             |    7 +++---
 man/CM1992.Rd             |    7 +++---
 man/MASSTIMATE-package.Rd |    6 ++---
 man/MCF2004.Rd            |   14 +++++++-----
 man/MR.Rd                 |   17 ++++++++-------
 man/QE.Rd                 |   17 ++++++++-------
 man/bipeds.Rd             |only
 man/cQE.Rd                |   29 ++++++++++++++------------
 man/dinos.Rd              |    2 -
 man/dinosbip.Rd           |    6 ++---
 man/ppe.Rd                |   20 ++++++++++--------
 man/quadrupeds.Rd         |only
 man/see.Rd                |only
 29 files changed, 159 insertions(+), 134 deletions(-)

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Package hmm.discnp updated to version 0.2-2 with previous version 0.2-1 dated 2014-01-31

Title: Hidden Markov models with discrete non-parametric observation distributions.
Description: Fits hidden Markov models with discrete non-parametric observation distributions to data sets. Simulates data from such models. Finds most probable underlying hidden states, the most probable sequences of such states, and the log likelihood of a collection of observations given the parameters of the model.
Author: Rolf Turner and Limin Liu.
Maintainer: Rolf Turner

Diff between hmm.discnp versions 0.2-1 dated 2014-01-31 and 0.2-2 dated 2014-05-19

 hmm.discnp-0.2-1/hmm.discnp/R/mat2list.R               |only
 hmm.discnp-0.2-2/hmm.discnp/ChangeLog                  |   34 ++++++++++++++
 hmm.discnp-0.2-2/hmm.discnp/DESCRIPTION                |    9 ++-
 hmm.discnp-0.2-2/hmm.discnp/MD5                        |   40 +++++++++--------
 hmm.discnp-0.2-2/hmm.discnp/R/charList.R               |only
 hmm.discnp-0.2-2/hmm.discnp/R/check.yval.R             |   27 ++++++-----
 hmm.discnp-0.2-2/hmm.discnp/R/ffun.R                   |   23 ++++++---
 hmm.discnp-0.2-2/hmm.discnp/R/fitted.hmm.discnp.R      |    5 +-
 hmm.discnp-0.2-2/hmm.discnp/R/hmm.R                    |   18 +++++--
 hmm.discnp-0.2-2/hmm.discnp/R/logLikHmm.R              |    4 -
 hmm.discnp-0.2-2/hmm.discnp/R/mps.R                    |    4 -
 hmm.discnp-0.2-2/hmm.discnp/R/pr.R                     |    4 -
 hmm.discnp-0.2-2/hmm.discnp/R/revise.rho.R             |    4 +
 hmm.discnp-0.2-2/hmm.discnp/R/sp.R                     |   10 +---
 hmm.discnp-0.2-2/hmm.discnp/R/viterbi.R                |    4 -
 hmm.discnp-0.2-2/hmm.discnp/data                       |only
 hmm.discnp-0.2-2/hmm.discnp/man/colifCount.Rd          |only
 hmm.discnp-0.2-2/hmm.discnp/man/fitted.hmm.discnp.Rd   |   10 +++-
 hmm.discnp-0.2-2/hmm.discnp/man/hmm.Rd                 |   18 +++++--
 hmm.discnp-0.2-2/hmm.discnp/man/hmm.discnp-internal.Rd |    6 +-
 hmm.discnp-0.2-2/hmm.discnp/man/lesionCount.Rd         |only
 hmm.discnp-0.2-2/hmm.discnp/man/logLikHmm.Rd           |   12 +++--
 hmm.discnp-0.2-2/hmm.discnp/man/mps.Rd                 |   15 ++++--
 23 files changed, 165 insertions(+), 82 deletions(-)

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New package s2dverification with initial version 2.1
Package: s2dverification
Type: Package
Title: Set of common tools for model diagnostics.
Version: 2.1
Date: 2014-05-18
Author: Nicolau Manubens Gil , Virginie Guemas , Isabel Andreu-Burillo , Fabian Lienert , Javier Garcia-Serrano , Ludovic Auger
Maintainer: Nicolau Manubens
Description: Set of tools to assess the performance of a model through the computation of typical prediction scores against one or more observational datasets or reanalyses (a reanalysis being a physical extrapolation of observations that relies on the equations from a model, not a pure observational dataset).
License: GPL-3
Depends: R (>= 2.14.1), GEOmap, geomapdata, maps, mapproj
LazyData: yes
Encoding: UTF-8
Packaged: 2014-05-18 18:35:06 UTC; nmanubens
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-19 07:13:14

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Package qlcMatrix updated to version 0.9.2 with previous version 0.9.1 dated 2014-05-17

Title: Utility sparse matrix functions for Quantitative Language Comparison
Description: This package contains various functions that extend the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw

Diff between qlcMatrix versions 0.9.1 dated 2014-05-17 and 0.9.2 dated 2014-05-19

 DESCRIPTION              |    8 ++++----
 MD5                      |   11 ++++++-----
 README.md                |only
 man/qlcMatrix-package.Rd |    4 ++--
 man/rowMax.Rd            |   15 +++++++++++++--
 man/sim.nominal.Rd       |    6 +++---
 man/ttMatrix.Rd          |    2 +-
 7 files changed, 29 insertions(+), 17 deletions(-)

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Package peptider updated to version 0.1.4 with previous version 0.1.3 dated 2014-05-07

Title: Evaluation of diversity in nucleotide libraries
Description: Functions for evaluating diversity in peptide libraries, including NNN, NNB, NNK/S, and trimer schemes. This includes expected coverage, relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare

Diff between peptider versions 0.1.3 dated 2014-05-07 and 0.1.4 dated 2014-05-19

 DESCRIPTION                |    8 +++----
 MD5                        |   46 ++++++++++++++++++++++-----------------------
 NAMESPACE                  |    2 -
 R/tabulate.r               |   11 ++++------
 man/BLOSUM80.Rd            |    2 -
 man/codons.Rd              |    2 -
 man/coverage.Rd            |    2 -
 man/detect.Rd              |    2 -
 man/diversity.Rd           |    2 -
 man/efficiency.Rd          |    2 -
 man/encodingReduce.Rd      |    2 -
 man/generateCustom.Rd      |    2 -
 man/generateCustomLib.Rd   |    2 -
 man/generateCustomProbs.Rd |    2 -
 man/getChoices.Rd          |    2 -
 man/getCounts.Rd           |    2 -
 man/getNeighbors.Rd        |    2 -
 man/getNofNeighbors.Rd     |    2 -
 man/libBuild.Rd            |    2 -
 man/libscheme.Rd           |    2 -
 man/makowski.Rd            |    2 -
 man/ppeptide.Rd            |    2 -
 man/scheme.Rd              |    2 -
 man/schemes.Rd             |    2 -
 24 files changed, 53 insertions(+), 54 deletions(-)

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New package letsR with initial version 1.0
Package: letsR
Type: Package
Title: Tools for data handling and analysis in macroecology
Version: 1.0
Date: 2014-18-05
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
Description: R functions for handling and analyzing geographic data, mainly species' geographic distributions (in ESRI shapefile format) and environmental variables (in raster format), as well as species' information related to their description (e.g. taxonomy and year of description) and conservation status (e.g. category of threat, population trend) as provided by the IUCN's RedList database. The package includes functions to create presence-absence matrices based on species distributions and user-defined grid systems, from which several other functions could be applied to generate, for example, species richness rasters and maps, and geographical midpoints of species. In addition, it provides a function to create spatial correlograms of variables, based on the Moran's I index, under the equiprobable or equidistant criterion to define distance classes.
License: GPL-2
Imports: maps, raster, XML, geosphere, maptools, sp
Depends: R (>= 2.10)
Packaged: 2014-05-18 18:50:13 UTC; Bruno
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-19 07:10:39

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New package gset with initial version 1.0
Package: gset
Type: Package
Title: Group Sequential Design in Equivalence Studies
Version: 1.0
Date: 2014-05-14
Authors@R: c(person("Fang", "Liu", role = c("aut", "cre"), email = "fang.liu.131@nd.edu"))
Author: Fang Liu
Maintainer: Fang Liu
Depends: R (>= 3.0.2), Hmisc, mvtnorm, MCMCpack, graphics
Description: calculate equivalence and futility boundaries based on the exact bivariate $t$ test statistics for group sequential designs in studies with equivalence hypotheses.
URL: http://www.r-project.org, http://www3.nd.edu/~fliu2/
BugReports: http://www3.nd.edu/~fliu2/
License: GPL (>= 2)
Packaged: 2014-05-18 16:01:12 UTC; fliu2
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-05-19 07:10:43

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New package cubfits with initial version 0.1-0
Package: cubfits
Version: 0.1-0
Date: 2014-05-15
Title: Codon Usage Bias Fits
Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email = "wccsnow@gmail.com"), person("Russell", "Zaretzki", role = "aut"), person("William", "Howell", role = "aut"), person("Drew", "Schmidt", role = "aut"), person("Michael", "Gilchrist", role = "aut"), person("Students", "REU13", role = "ctb"))
Depends: R(>= 3.0.0), methods
Suggests: seqinr, VGAM, EMCluster
Enhances: pbdMPI (>= 0.2-2), parallel
LazyLoad: yes
LazyData: yes
Description: Estimating mutation and selection coefficients on synonymous codon bias usage based on models of ribosome overhead cost (ROC). Multinomial logistic regression and Markov Chain Monte Carlo are used to estimate and predict protein production rates with/without the presence of expressions and measurement errors. Work flows with examples for simulation, estimation and prediction processes are also provided with parallelization speedup. The whole framework is tested with yeast genome and gene expression data of Yassour (2009).
License: Mozilla Public License 2.0
URL: https://github.com/snoweye/cubfits
Packaged: 2014-05-18 19:08:04 UTC; snoweye
Author: Wei-Chen Chen [aut, cre], Russell Zaretzki [aut], William Howell [aut], Drew Schmidt [aut], Michael Gilchrist [aut], Students REU13 [ctb]
Maintainer: Wei-Chen Chen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-05-19 07:14:28

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