Wed, 29 Apr 2015

New package ssizeRNA with initial version 1.1.1
Package: ssizeRNA
Type: Package
Title: Sample Size Calculation for RNA-Seq Data
Version: 1.1.1
Date: 2015-04-05
Author: Ran Bi , Peng Liu
Maintainer: Ran Bi
Description: We propose a procedure for sample size calculation while controlling false discovery rate for RNA-seq experimental design. Our procedure depends on the Voom method proposed for RNA-seq data analysis by Law et al. (2014) and the sample size calculation method proposed for microarray experiments by Liu and Hwang (2007). We develop a set of functions that calculates appropriate sample sizes for two-sample t-test for RNA-seq experiments with fixed or varied set of parameters. The outputs also contain a plot of power versus sample size, a table of power at different sample sizes, and a table of critical test values at different sample sizes.
Depends: R (>= 3.1.2)
Imports: MASS, Biobase, edgeR, limma, qvalue, ssize.fdr
License: GPL (>= 2)
Packaged: 2015-04-29 22:02:37 UTC; Ran
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-30 02:28:30

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Package Rchoice updated to version 0.3 with previous version 0.2 dated 2014-12-17

Title: Discrete Choice (Binary, Poisson and Ordered) Models with Random Parameters
Description: An implementation of simulated maximum likelihood method for the estimation of Binary (Probit and Logit), Ordered (Probit and Logit) and Poisson models with random parameters for cross-sectional and longitudinal data.
Author: Mauricio Sarrias
Maintainer: Mauricio Sarrias

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Package plotmo updated to version 3.0.0 with previous version 2.2.1 dated 2015-01-07

Title: Plot a Model's Response and Residuals
Description: Plot a model's response when varying one or two predictors while holding the other predictors constant. A poor man's partial dependence plot. Also plot model residuals.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

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Package markovchain updated to version 0.2 with previous version 0.1.1 dated 2015-02-21

Title: Easy Handling Discrete Time Markov Chains
Description: Functions and S4 methods to create and manage discrete time Markov chains (DTMC) more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of DTMC proprieties) analysis are provided.
Author: Giorgio Alfredo Spedicato [aut,cre], Tae Seung Kang [aut], Mildenberger Thoralf [ctb]
Maintainer: Giorgio Alfredo Spedicato

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Package dfmta updated to version 1.3-2 with previous version 1.3-1 dated 2015-04-26

Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper "Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere

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Package dfcomb updated to version 2.1-3 with previous version 2.1-1 dated 2015-04-26

Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere

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Package TeachingSampling updated to version 3.2.2 with previous version 3.2.1 dated 2014-03-27

Title: Selection of Samples and Parameter Estimation in Finite Population
Description: Allows the user to draw probabilistic samples and make inferences from a finite population based on several sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas

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Package samplesize4surveys updated to version 2.2.0 with previous version 2.1.0 dated 2014-09-21

Title: Sample Size Calculations for Complex Surveys
Description: Computes the required sample size for estimation of totals, means and proportions under complex sampling designs.
Author: Hugo Andres Gutierrez Rojas
Maintainer: Hugo Andres Gutierrez Rojas

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New package BCRA with initial version 1.0
Package: BCRA
Type: Package
Title: Breast Cancer Risk Assessment
Version: 1.0
Date: 2015-04-28
Author: Fanni Zhang
Maintainer: Fanni Zhang
Description: Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals.
License: GPL (>= 2)
Packaged: 2015-04-29 15:09:23 UTC; zhangf10
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-29 18:01:22

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New package ArArRedux with initial version 0.1
Package: ArArRedux
Title: Rigorous Data Reduction and Error Propagation of '40Ar/39Ar' Data
Version: 0.1
Authors@R: person("Pieter", "Vermeesch", , "p.vermeesch@ucl.ac.uk", role = c("aut", "cre"))
Description: Processes noble gas mass spectrometer data to determine the isotopic composition of argon (comprised of 36Ar, 37Ar, 38Ar, 39Ar and 40Ar) released from neutron-irradiated potassium-bearing minerals. Then uses these compositions to calculate precise and accurate geochronological ages for multiple samples as well as the covariances between them. Error propagation is done in matrix form, which jointly treats all samples and all isotopes simultaneously at every step of the data reduction process. The package includes methods for regression of the time-resolved mass spectrometer signals to t=0 ('time zero') for both single- and multi-collector instruments, blank correction, mass fractionation correction, detector intercalibration, decay corrections, interference corrections, interpolation of the irradiation parameter between neutron fluence monitors, and (weighted mean) age calculation. All operations are performed on the logs of the ratios between the different argon isotopes so as to properly treat them as 'compositional data', sensu Aitchison [1986, The Statistics of Compositional Data, Chapman and Hall].
Depends: R (>= 3.0.2)
License: GPL-2
LazyData: true
Packaged: 2015-04-29 15:08:07 UTC; root
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-04-29 18:01:19

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Package XBRL updated to version 0.99.16 with previous version 0.99.15 dated 2015-02-13

Title: Extraction of Business Financial Information from 'XBRL' Documents
Description: Functions to extract business financial information from an Extensible Business Reporting Language ('XBRL') instance file and the associated collection of files that defines its 'Discoverable' Taxonomy Set ('DTS').
Author: Roberto Bertolusso and Marek Kimmel
Maintainer: Roberto Bertolusso

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Package TSdbi updated to version 2015.1-1 with previous version 2013.9-1 dated 2013-09-29

Title: Time Series Database Interface
Description: Provides a common interface to time series databases. The objective is to define a standard interface so users can retrieve time series data from various sources with a simple, common, set of commands, and so programs can be written to be portable with respect to the data source. The SQL implementations also provide a database table design, so users needing to set up a time series database have a reasonably complete way to do this easily. The interface provides for a variety of options with respect to the representation of time series in R. The interface, and the SQL implementations, also handle vintages of time series data (sometime called editions or realtime data). There is also a (not yet well tested) mechanism to handle multilingual data documentation. Comprehensive examples of all the TS* packages is provided in the vignette Guide.pdf with the TSdata package.
Author: Paul Gilbert
Maintainer: Paul Gilbert

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New package replicatedpp2w with initial version 0.1-1
Package: replicatedpp2w
Type: Package
Title: Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns
Version: 0.1-1
Date: 2015-04-17
Author: Marcelino de la Cruz Rot
Maintainer: Marcelino de la Cruz
Description: Test for effects of both individual factors and their interaction on replicated spatial patterns in a two factorial design.
Imports: spatstat
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2015-04-29 13:28:58 UTC; marcelino
Repository: CRAN
Date/Publication: 2015-04-29 16:23:35

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Package PHENIX updated to version 1.2 with previous version 1.1 dated 2015-01-27

Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares

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Package KFAS updated to version 1.1.1 with previous version 1.1.0 dated 2015-04-18

Title: Kalman Filter and Smoother for Exponential Family State Space Models
Description: Functions for Kalman filtering, smoothing, forecasting and simulation of multivariate exponential family state space models with exact diffuse initialization and sequential processing.
Author: Jouni Helske
Maintainer: Jouni Helske

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Permanent link

Package ForeCA updated to version 0.2.2 with previous version 0.2.0 dated 2015-02-20

Title: Forecastable Component Analysis
Description: Implementation of Forecastable Component Analysis ('ForeCA'), including main algorithms and auxiliary function (summary, plotting, etc.) to apply 'ForeCA' to multivariate time series data. 'ForeCA' is a novel dimension reduction (DR) technique for temporally dependent signals. Contrary to other popular DR methods, such as 'PCA' or 'ICA', 'ForeCA' takes time dependency explicitly into account and searches for the most ''forecastable'' signal. The measure of forecastability is based on the Shannon entropy of the spectral density of the transformed signal.
Author: Georg M. Goerg
Maintainer: Georg M. Goerg

Diff between ForeCA versions 0.2.0 dated 2015-02-20 and 0.2.2 dated 2015-04-29

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New package CorrMixed with initial version 0.1-1
Package: CorrMixed
Type: Package
Title: Estimate Correlations Between Repeatedly Measured Endpoints (E.g., Reliability) Based on Linear Mixed-Effects Models
Version: 0.1-1
Date: 2015-04-29
Author: Wim Van der Elst, Geert Molenberghs, Dieter Hilgers, & Nicole Heussen
Maintainer: Wim Van der Elst
Description: In clinical practice and research settings in medicine and the behavioral sciences, it is often of interest to quantify the correlation of a continuous endpoint that was repeatedly measured (e.g., test-retest correlations, ICC, etc.). This package allows for estimating these correlations based on mixed-effects models. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Depends: nlme
Imports: psych
License: GPL (>= 2)
BugReports: Wim Van der Elst
Repository: CRAN
NeedsCompilation: no
Packaged: 2015-04-29 13:55:31 UTC; lucp7687
Date/Publication: 2015-04-29 16:23:26

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Package stepR updated to version 1.0-2 with previous version 1.0-1 dated 2015-03-04

Title: Fitting Step-Functions
Description: Allows to fit step-functions to univariate serial data where neither the number of jumps nor their positions is known.
Author: Thomas Hotz [aut, cre], Hannes Sieling [aut], Pein Florian [ctb]
Maintainer: Thomas Hotz

Diff between stepR versions 1.0-1 dated 2015-03-04 and 1.0-2 dated 2015-04-29

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Package sdprisk updated to version 1.1-0 with previous version 1.0-3 dated 2013-12-30

Title: Measures of Risk for the Compound Poisson Risk Process with Diffusion
Description: The main purpose of this package is to provide saddlepoint approximations to some measures of risk, based on the compound Poisson risk process that is perturbed by a Brownian motion. Various approximation methods for the probability of ruin are also included. Furthermore, exact values of both the risk measures as well as the probability of ruin are available if the individual claims follow a hypo-exponential distribution (i. e., if it can be represented as a sum of independent exponentially distributed random variables with different rate parameters).
Author: Benjamin Baumgartner [aut, cre], Riccardo Gatto [ctb, ths], Sebastian Szugat [ctb]
Maintainer: Benjamin Baumgartner

Diff between sdprisk versions 1.0-3 dated 2013-12-30 and 1.1-0 dated 2015-04-29

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Package NPMLEcmprsk updated to version 2.1 with previous version 2.0 dated 2014-12-09

Title: Type-Specific Failure Rate and Hazard Rate on Competing Risks Data
Description: Given a failure type, the function computes covariate-specific probability of failure over time and covariate-specific conditional hazard rate based on possibly right-censored competing risk data. Specifically, it computes the non-parametric maximum-likelihood estimates of these quantities and their asymptotic variances in a semi-parametric mixture model for competing-risks data, as described in Chang et al. (2007a).
Author: Chung-Hsing Chen, I-Shou Chang and Chao A. Hsiung
Maintainer: Chung-Hsing Chen

Diff between NPMLEcmprsk versions 2.0 dated 2014-12-09 and 2.1 dated 2015-04-29

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Package evmix updated to version 2.5 with previous version 2.4 dated 2015-01-23

Title: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation
Description: The usual distribution functions, maximum likelihood inference and model diagnostics for univariate stationary extreme value mixture models are provided. Kernel density estimation including various boundary corrected kernel density estimation methods and a wide choice of kernels, with cross-validation likelihood based bandwidth estimator. Reasonable consistency with the base functions in the evd package is provided, so that users can safely interchange most code.
Author: Carl Scarrott and Yang Hu, University of Canterbury
Maintainer: Carl Scarrott

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Package synbreedData updated to version 1.5 with previous version 1.4 dated 2013-12-12

Title: Data for the Synbreed Package
Description: Data sets for the 'synbreed' package with three data sets from cattle, maize and mice to illustrate the functions in the 'synbreed' R package. All data sets are stored in the gpData format introduced in the 'synbreed' package. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Theresa Albrecht, Hans-Juergen Auinger, Chris-Carolin Schoen with contributions by Malena Erbe, Ulrike Ober and Christian Reimer
Maintainer: Valentin Wimmer

Diff between synbreedData versions 1.4 dated 2013-12-12 and 1.5 dated 2015-04-29

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Package sn updated to version 1.2-1 with previous version 1.2-0 dated 2015-03-25

Title: The Skew-Normal and Skew-t Distributions
Description: Define and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between sn versions 1.2-0 dated 2015-03-25 and 1.2-1 dated 2015-04-29

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More information about sn at CRAN
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New package quickpsy with initial version 0.1.0
Package: quickpsy
Type: Package
Title: Fits Psychometric Functions for Multiple Groups
Version: 0.1.0
Authors@R: c( person("Linares", "Daniel", email = "danilinares@gmail.com", role = c("aut","cre")), person("López-Moliner", "Joan", email = "j.lopezmoliner@gmail.com", role = "aut"))
URL: http://dlinares.org/quickpsy.html
Description: Quickly fits and plots psychometric functions (normal, logistic, Weibull or any or any function defined by the user) for multiple groups.
Depends: R (>= 3.1.1), boot, DEoptim, dplyr, ggplot2, tidyr
Imports: MPDiR
Encoding: UTF-8
License: MIT + file LICENSE
LazyData: true
NeedsCompilation: no
Packaged: 2015-04-29 09:41:56 UTC; daniellinares
Author: Linares Daniel [aut, cre], López-Moliner Joan [aut]
Maintainer: Linares Daniel
Repository: CRAN
Date/Publication: 2015-04-29 12:21:44

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Package jiebaR updated to version 0.5 with previous version 0.4 dated 2015-01-04

Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of CppJieba
Maintainer: Qin Wenfeng

Diff between jiebaR versions 0.4 dated 2015-01-04 and 0.5 dated 2015-04-29

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Package GWLelast updated to version 1.1 with previous version 1.0 dated 2015-04-20

Title: Geographically Weighted Logistic Elastic Net Regression
Description: Fit a geographically weighted logistic elastic net regression.
Author: Daisuke Yoneoka, Eiko Saito
Maintainer: Daisuke Yoneoka

Diff between GWLelast versions 1.0 dated 2015-04-20 and 1.1 dated 2015-04-29

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New package GlobalFit with initial version 1.0
Package: GlobalFit
Type: Package
Title: Bi-Level Optimization of Metabolic Network Models
Version: 1.0
Date: 2015-04-15
Author: Daniel Hartleb
Maintainer: Daniel Hartleb
Description: Initial metabolic networks often inaccurately predict in-silico growth or non-growth if compared to in-vivo data. This package refines metabolic network models by making networks changes (i.e., removing, adding, changing reversibility of reactions; adding and removing biomass metabolites) and simultaneously matching sets of experimental growth and non-growth data (e.g., KO-mutants, mutants grown under different media conditions,...)
License: GPL-3
Depends: R (>= 2.12.0), sybil (>= 1.1.7), methods
Suggests: cplexAPI (>= 1.2.1)
NeedsCompilation: no
Packaged: 2015-04-28 12:19:16 UTC; daniel
Repository: CRAN
Date/Publication: 2015-04-29 11:39:02

More information about GlobalFit at CRAN
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Package difR updated to version 4.6 with previous version 4.5 dated 2013-04-07

Title: Collection of Methods to Detect Dichotomous Differential Item Functioning (DIF)
Description: Collection of traditional methods to detect differential item functioning among dichotomously scored items.
Author: David Magis (U Liege), Sebastien Beland (UQAM) and Gilles Raiche (UQAM)
Maintainer: David Magis

Diff between difR versions 4.5 dated 2013-04-07 and 4.6 dated 2015-04-29

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Package dae updated to version 2.7-0 with previous version 2.4-0 dated 2014-12-10

Title: Functions Useful in the Design and ANOVA of Experiments
Description: The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. A document 'daeDesignRandomization.pdf', available in the doc subdirectory of the installation directory for 'dae', describes the use of the package for generating randomized layouts for experiments. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'.
Author: Chris Brien .
Maintainer: Chris Brien

Diff between dae versions 2.4-0 dated 2014-12-10 and 2.7-0 dated 2015-04-29

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Package phytools updated to version 0.4-56 with previous version 0.4-45 dated 2015-02-05

Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis. This functionality is concentrated in the phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian and ML ancestral state estimation; visual simulation of trait evolution; fitting models of trait evolution with multiple Brownian rates and correlations; visualizing discrete and continuous character evolution using colors or projections into trait space; identifying the location of a change in the rate of character evolution on the tree; fast Brownian motion simulation and simulation under several other models of continuous trait evolution; fitting a model of correlated binary trait evolution; locating the position of a fossil or an recently extinct lineage on a tree using continuous character data with ML; plotting lineage accumulation through time, including across multiple trees (such as a Bayesian posterior sample); conducting an analysis called stochastic character mapping, in which character histories for a discrete trait are sampled from their posterior probability distribution under a model; conducting a multiple (i.e., partial) Mantel test; fitting a phylogenetic regression model with error in predictor and response variables; conducting a phylogenetic principal components analysis, a phylogenetic regression, a reduced major axis regression, a phylogenetic canonical correlation analysis, and a phylogenetic ANOVA; projecting a tree onto a geographic map; simulating discrete character histories on the tree; and fitting a model in which a discrete character evolves under the threshold model. In addition to this phylogenetic comparative method functionality, the package also contains functions for a wide range of other purposes in phylogenetic biology. For instance, functionality in this package includes (but is not restricted to): adding taxa to a tree (including randomly, everywhere, or automatically to genera); generating all bi- and multi-furcating trees for a set of taxa; reducing a phylogeny to its backbone tree; dropping tips or adding tips to special types of phylogenetic trees; exporting a tree as an XML file; converting a tree with a mapped character to a tree with singleton nodes and one character state per edge; estimating a phylogeny using the least squares method; simulating birth-death trees under a range of conditions; rerooting trees; a wide range of visualizations of trees; and a variety of other manipulations and analyses that phylogenetic biologists may find useful for their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell

Diff between phytools versions 0.4-45 dated 2015-02-05 and 0.4-56 dated 2015-04-29

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More information about phytools at CRAN
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Package prettyR updated to version 2.1-1 with previous version 2.1 dated 2015-01-20

Title: Pretty Descriptive Stats
Description: Functions for conventionally formatting descriptive stats, reshaping data frames and formatting R output as HTML.
Author: Jim Lemon , Philippe Grosjean
Maintainer: Jim Lemon

Diff between prettyR versions 2.1 dated 2015-01-20 and 2.1-1 dated 2015-04-29

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Package GEOmap updated to version 2.3-5 with previous version 2.2-2 dated 2014-01-05

Title: Topographic and Geologic Mapping
Description: Set of routines for making Map Projections (forward and inverse), Topographic Maps, Perspective plots, Geological Maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.
Author: Jonathan M. Lees
Maintainer: Jonathan M. Lees

Diff between GEOmap versions 2.2-2 dated 2014-01-05 and 2.3-5 dated 2015-04-29

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Package dcemriS4 updated to version 0.55 with previous version 0.51 dated 2013-12-30

Title: A Package for Image Analysis of DCE-MRI (S4 Implementation)
Description: A collection of routines and documentation that allows one to perform voxel-wise quantitative analysis of dynamic contrast-enhanced MRI (DEC-MRI) and diffusion-weighted imaging (DWI) data, with emphasis on oncology applications.
Author: Brandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [ctb]
Maintainer: Brandon Whitcher

Diff between dcemriS4 versions 0.51 dated 2013-12-30 and 0.55 dated 2015-04-29

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