Mon, 13 Apr 2015

Package evaluate updated to version 0.6 with previous version 0.5.5 dated 2014-04-29

Title: Parsing and Evaluation Tools that Provide More Details than the Default
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham [aut], Yihui Xie [cre, ctb], Barret Schloerke [ctb]
Maintainer: Yihui Xie

Diff between evaluate versions 0.5.5 dated 2014-04-29 and 0.6 dated 2015-04-13

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 evaluate-0.6/evaluate/R/eval.r                  |    3 
 evaluate-0.6/evaluate/R/graphics.r              |   79 +++--------
 evaluate-0.6/evaluate/R/parse.r                 |  167 ++++++++++--------------
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 19 files changed, 151 insertions(+), 171 deletions(-)

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Package spartan updated to version 2.2.1 with previous version 2.2 dated 2015-03-23

Title: Simulation Parameter Analysis R Toolkit ApplicatioN: Spartan
Description: Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. SPARTAN, described in our 2013 publication in PLoS Computational Biology, provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust a simulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. Version 1.3 adds support for Netlogo simulations, aiding simulation developers who use Netlogo to build their simulations perform the same analyses. We have also added user support through the group spartan-group[AT]york[DOT]ac[DOT]uk. Version 2.0 added the ability to read all simulations in from a single CSV file in addition to the prescribed folder structure in previous versions.
Author: Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles
Maintainer: Kieran Alden

Diff between spartan versions 2.2 dated 2015-03-23 and 2.2.1 dated 2015-04-13

 spartan-2.2.1/spartan/DESCRIPTION                                          |    6 
 spartan-2.2.1/spartan/MD5                                                  |   65 +--
 spartan-2.2.1/spartan/R/aa_getATestResults.R                               |    8 
 spartan-2.2.1/spartan/R/aa_graphATestsForSampleSize.R                      |    8 
 spartan-2.2.1/spartan/R/aa_graphSampleSizeSummary.R                        |   17 
 spartan-2.2.1/spartan/R/aa_sampleSizeSummary.R                             |    7 
 spartan-2.2.1/spartan/R/aa_summariseReplicateRuns.R                        |    3 
 spartan-2.2.1/spartan/R/efast_generate_medians_for_all_parameter_subsets.R |    2 
 spartan-2.2.1/spartan/R/efast_get_overall_medians.R                        |    7 
 spartan-2.2.1/spartan/R/efast_graph_Results.R                              |    2 
 spartan-2.2.1/spartan/R/efast_netlogo_get_overall_medians.R                |    5 
 spartan-2.2.1/spartan/R/efast_netlogo_run_Analysis.R                       |    5 
 spartan-2.2.1/spartan/R/efast_process_netlogo_result.R                     |   15 
 spartan-2.2.1/spartan/R/efast_run_Analysis.R                               |    7 
 spartan-2.2.1/spartan/R/getMediansSubset.R                                 |   10 
 spartan-2.2.1/spartan/R/lhc_generateLHCSummary.R                           |    5 
 spartan-2.2.1/spartan/R/lhc_generatePRCoEffs.R                             |    5 
 spartan-2.2.1/spartan/R/lhc_generate_netlogo_PRCoEffs.R                    |    5 
 spartan-2.2.1/spartan/R/lhc_graphMeasuresForParameterChange.R              |    7 
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 spartan-2.2.1/spartan/R/lhc_plotCoEfficients.R                             |  197 ++++++----
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 spartan-2.2.1/spartan/R/lhc_process_sample_run_subsets.R                   |    5 
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 spartan-2.2.1/spartan/R/oat_graphATestsForSampleSize.R                     |   14 
 spartan-2.2.1/spartan/R/oat_plotResultDistribution.R                       |    5 
 spartan-2.2.1/spartan/R/oat_processParamSubsets.R                          |    3 
 spartan-2.2.1/spartan/R/oat_process_netlogo_result.R                       |   13 
 spartan-2.2.1/spartan/R/pcor.mat.R                                         |   12 
 spartan-2.2.1/spartan/R/pcor.rec.R                                         |   12 
 spartan-2.2.1/spartan/R/pcor.test.R                                        |    6 
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 34 files changed, 340 insertions(+), 255 deletions(-)

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Package settings updated to version 0.2.1 with previous version 0.1.1 dated 2014-10-28

Title: Software Option Settings Manager for R
Description: Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names and default values. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo

Diff between settings versions 0.1.1 dated 2014-10-28 and 0.2.1 dated 2015-04-13

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Package rstackdeque updated to version 1.1.1 with previous version 1.1 dated 2014-12-04

Title: Persistent Fast Amortized Stack and Queue Data Structures
Description: Provides fast, persistent (side-effect-free) stack, queue and deque (double-ended-queue) data structures. While deques include a superset of functionality provided by queues, in these implementations queues are more efficient in some specialized situations. See the documentation for rstack, rdeque, and rpqueue for details.
Author: Shawn T. O'Neil
Maintainer: Shawn T. O'Neil

Diff between rstackdeque versions 1.1 dated 2014-12-04 and 1.1.1 dated 2015-04-13

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Package rmaf updated to version 3.0 with previous version 2.0 dated 2014-03-10

Title: Refined Moving Average Filter
Description: Uses refined moving average filter based on the optimal and data-driven moving average lag q or smoothing spline to estimate trend and seasonal components, as well as irregularity (residuals) for univariate time series or data.
Author: Debin Qiu
Maintainer: Debin Qiu

Diff between rmaf versions 2.0 dated 2014-03-10 and 3.0 dated 2015-04-13

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Package retrosheet updated to version 1.0.2 with previous version 1.0.1 dated 2015-04-09

Title: Import Professional Baseball Data from 'Retrosheet'
Description: A collection of tools to import and structure the (currently) single-season event, game-log, roster, and schedule data available from http://www.retrosheet.org. In particular, the event (a.k.a. play-by-play) files can be especially difficult to parse. This package does the parsing on those files, returning the requested data in the most practical R structure to use for sabermetric or other analyses.
Author: Richard Scriven [aut, cre]
Maintainer: Richard Scriven

Diff between retrosheet versions 1.0.1 dated 2015-04-09 and 1.0.2 dated 2015-04-13

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 9 files changed, 59 insertions(+), 27 deletions(-)

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Package NbClust updated to version 3.0 with previous version 2.0.4 dated 2015-03-02

Title: Determining the Best Number of Clusters in a Data Set
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad

Diff between NbClust versions 2.0.4 dated 2015-03-02 and 3.0 dated 2015-04-13

 DESCRIPTION    |    8 +-
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 4 files changed, 131 insertions(+), 76 deletions(-)

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New package L1pack with initial version 0.3
Package: L1pack
Title: Routines for L1 Estimation
Version: 0.3
Date: 2015-04-13
Author: Felipe Osorio
Maintainer: Felipe Osorio
Description: L1 estimation for linear regression and random number generation for the multivariate Laplace distribution.
URL: http://www.ies.ucv.cl/l1pack/
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2015-04-13 21:11:54 UTC; ligges
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-13 23:11:54

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Package InvariantCausalPrediction updated to version 0.3 with previous version 0.1-4 dated 2014-12-12

Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen

Diff between InvariantCausalPrediction versions 0.1-4 dated 2014-12-12 and 0.3 dated 2015-04-13

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Package HiLMM updated to version 1.1 with previous version 1.0 dated 2014-04-15

Title: Estimation of Heritability in Linear Mixed Models
Description: Estimation of heritability with confidence intervals in linear mixed models.
Author: Anna Bonnet
Maintainer: Anna Bonnet

Diff between HiLMM versions 1.0 dated 2014-04-15 and 1.1 dated 2015-04-13

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Package GMCM updated to version 1.2 with previous version 1.1.1 dated 2014-10-06

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau

Diff between GMCM versions 1.1.1 dated 2014-10-06 and 1.2 dated 2015-04-13

 DESCRIPTION                           |   18 +--
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 NAMESPACE                             |    2 
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Package cancerTiming updated to version 3.0.0 with previous version 2.0.0 dated 2014-05-07

Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: This is a package with functions for timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom

Diff between cancerTiming versions 2.0.0 dated 2014-05-07 and 3.0.0 dated 2015-04-13

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Package ASMap updated to version 0.4 with previous version 0.3-3 dated 2015-02-02

Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).
Author: Julian Taylor , David Butler .
Maintainer: Julian Taylor

Diff between ASMap versions 0.3-3 dated 2015-02-02 and 0.4 dated 2015-04-13

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Package ramify updated to version 0.2.0 with previous version 0.1.0 dated 2015-03-23

Title: Additional Matrix Functionality
Description: Additional matrix functionality for R including: (1) wrappers for the base matrix function that allows matrices to be created from character strings and lists (the former is especially useful for creating block matrices), (ii) better default printing of large matrices, and (iii) a number of convenience functions for users more familiar with other scientific languages like Julia, Matlab/Octave, or Python.
Author: Brandon Greenwell [aut, cre]
Maintainer: Brandon Greenwell

Diff between ramify versions 0.1.0 dated 2015-03-23 and 0.2.0 dated 2015-04-13

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More information about ramify at CRAN
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Package metacom updated to version 1.4.3 with previous version 1.4.2 dated 2014-12-11

Title: Analysis of the "Elements of Metacommunity Structure"
Description: Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.
Author: Tad Dallas
Maintainer: Tad Dallas

Diff between metacom versions 1.4.2 dated 2014-12-11 and 1.4.3 dated 2015-04-13

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Package drc updated to version 2.5-11 with previous version 2.3-96 dated 2013-11-29

Title: Analysis of Dose-Response Curves
Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
Author: Christian Ritz , Jens C. Strebig
Maintainer: Christian Ritz

Diff between drc versions 2.3-96 dated 2013-11-29 and 2.5-11 dated 2015-04-13

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Package subselect updated to version 0.12-5 with previous version 0.12-4 dated 2014-10-08

Title: Selecting Variable Subsets
Description: A collection of functions which (i) assess the quality of variable subsets as surrogates for a full data set, in either an exploratory data analysis or in the context of a multivariate linear model, and (ii) search for subsets which are optimal under various criteria.
Author: Jorge Orestes Cerdeira [aut], Pedro Duarte Silva [aut], Jorge Cadima [aut, cre], Manuel Minhoto [aut]
Maintainer: Jorge Cadima

Diff between subselect versions 0.12-4 dated 2014-10-08 and 0.12-5 dated 2015-04-13

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New package smds with initial version 1.0
Package: smds
Type: Package
Title: Symbolic Multidimensional Scaling
Version: 1.0
Date: 2015-04-10
Author: Yoshikazu Terada, Patrick J. F. Groenen
Maintainer: Yoshikazu Terada
Depends: R (>= 1.8.0), MASS
Description: Symbolic multidimensional scaling for interval-valued dissimilarities. The hypersphere model and the hyperbox model are available.
License: GPL (>= 2)
Packaged: 2015-04-13 08:12:52 UTC; terada
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-13 12:50:14

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Package lfe updated to version 2.2-1699 with previous version 2.1-1640 dated 2015-03-11

Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS. Useful for estimating linear models with multiple group fixed effects, and for estimating linear models which uses factors as pure control variables. Includes support for instrumental variables, conditional F statistics for weak instruments, robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure

Diff between lfe versions 2.1-1640 dated 2015-03-11 and 2.2-1699 dated 2015-04-13

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Package geeM updated to version 0.7.3 with previous version 0.7.2 dated 2014-12-03

Title: Fit Generalized Estimating Equations
Description: Allows generalized estimating equation fits with user-specified link and variance functions.
Author: Lee S. McDaniel and Nick Henderson
Maintainer: Lee S. McDaniel

Diff between geeM versions 0.7.2 dated 2014-12-03 and 0.7.3 dated 2015-04-13

 DESCRIPTION |    8 
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Package R2admb updated to version 0.7.13 with previous version 0.7.10 dated 2013-09-22

Title: 'ADMB' to R Interface Functions
Description: A series of functions to call AD Model Builder (i.e., compile and run models) from within R, read the results back into R as 'admb' objects, and provide standard accessors (i.e. coef(), vcov(), etc.)
Author: Ben Bolker, Hans Skaug, Jeff Laake
Maintainer: Ben Bolker

Diff between R2admb versions 0.7.10 dated 2013-09-22 and 0.7.13 dated 2015-04-13

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Package inline updated to version 0.3.14 with previous version 0.3.13 dated 2013-08-08

Title: Functions to Inline C, C++, Fortran Function Calls from R
Description: Functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel, Romain Francois, Karline Soetaert
Maintainer: Dirk Eddelbuettel

Diff between inline versions 0.3.13 dated 2013-08-08 and 0.3.14 dated 2015-04-13

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Package fCertificates updated to version 0.5-4 with previous version 0.5-3 dated 2014-03-02

Title: Basics of Certificates and Structured Products Valuation
Description: Collection of pricing by duplication methods for popular structured products ("Zertifikate").
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm

Diff between fCertificates versions 0.5-3 dated 2014-03-02 and 0.5-4 dated 2015-04-13

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Package apc updated to version 1.1 with previous version 1.0 dated 2014-08-30

Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen

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