Sun, 03 May 2015

Package RcppAnnoy updated to version 0.0.6 with previous version 0.0.5 dated 2015-01-24

Title: 'Rcpp' Bindings for 'Annoy', a Library for Approximate Nearest Neighbors
Description: 'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between RcppAnnoy versions 0.0.5 dated 2015-01-24 and 0.0.6 dated 2015-05-03

 ChangeLog               |   26 +++++++++++-
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 MD5                     |   12 ++---
 README.md               |   13 +++---
 cleanup                 |    2 
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 7 files changed, 124 insertions(+), 65 deletions(-)

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Package parboost updated to version 0.1.4 with previous version 0.1.3 dated 2014-03-02

Title: Distributed Model-Based Boosting
Description: Distributed gradient boosting based on the mboost package. The parboost package is designed to scale up component-wise functional gradient boosting in a distributed memory environment by splitting the observations into disjoint subsets, or alternatively using bootstrap samples (bagging). Each cluster node then fits a boosting model to its subset of the data. These boosting models are combined in an ensemble, either with equal weights, or by fitting a (penalized) regression model on the predictions of the individual models on the complete data.
Author: Ronert Obst
Maintainer: Ronert Obst

Diff between parboost versions 0.1.3 dated 2014-03-02 and 0.1.4 dated 2015-05-03

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Package mvMORPH updated to version 1.0.5 with previous version 1.0.4 dated 2015-03-22

Title: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees.
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel

Diff between mvMORPH versions 1.0.4 dated 2015-03-22 and 1.0.5 dated 2015-05-03

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Package MAINT.Data updated to version 0.4 with previous version 0.3 dated 2014-10-24

Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data, considering appropriate parameterizations of the variance-covariance matrix that take into account the intrinsic nature of interval data, and lead to five different possible configuration structures.
Author: Pedro Duarte Silva Paula Brito
Maintainer: Pedro Duarte Silva

Diff between MAINT.Data versions 0.3 dated 2014-10-24 and 0.4 dated 2015-05-03

 CHANGELOG         |    5 +++++
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 6 files changed, 26 insertions(+), 16 deletions(-)

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New package ivmodel with initial version 1.0
Package: ivmodel
Type: Package
Title: Statistical Inference and Diagnostics for Instrumental Variables Model
Version: 1.0
Date: 2015-04-30
Author: Yang Jiang, Hyunseung Kang, and Dylan Small
Maintainer: Hyunseung Kang
Description: Contains functions for carrying out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics.
Depends: Matrix
License: GPL-2
Packaged: 2015-05-03 17:56:46 UTC; khyuns
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-05-04 01:31:33

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Package discreteRV updated to version 1.2.1 with previous version 1.2 dated 2015-04-10

Title: Create and Manipulate Discrete Random Variables
Description: Create, manipulate, transform, and simulate from discrete random variables. The syntax is modeled after that which is used in mathematical statistics and probability courses, but with powerful support for more advanced probability calculations. This includes the creation of joint random variables, and the derivation and manipulation of their conditional and marginal distributions.
Author: Andreas Buja [aut], Eric Hare [aut, cre], Heike Hofmann [aut]
Maintainer: Eric Hare

Diff between discreteRV versions 1.2 dated 2015-04-10 and 1.2.1 dated 2015-05-03

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Package rcbalance updated to version 1.5 with previous version 1.4 dated 2015-03-24

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel

Diff between rcbalance versions 1.4 dated 2015-03-24 and 1.5 dated 2015-05-03

 DESCRIPTION              |    8 +--
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New package QCAfalsePositive with initial version 0.11
Package: QCAfalsePositive
Title: Tests for Type I Error in Qualitative Comparative Analysis (QCA)
Version: 0.11
Author: Bear Braumoeller
Maintainer: Bear Braumoeller
Description: Implements tests for Type I error in Qualitative Comparative Analysis (QCA) that take into account the multiple hypothesis tests inherent in the procedure. Tests can be carried out on three variants of QCA: crisp-set QCA (csQCA), multi-value QCA (mvQCA) and fuzzy-set QCA (fsQCA). For fsQCA, the fsQCApermTest() command implements a permutation test that provides 95% confidence intervals for the number of counterexamples and degree of consistency, respectively. The distributions of permuted values can be plotted against the observed values. For csQCA and mvQCA, simple binomial tests are implemented in csQCAbinTest() and mvQCAbinTest(), respectively.
Depends: R (>= 3.2.0)
License: GPL-3
LazyData: true
Note: For details and derivation, see Braumoeller, Bear F. "Guarding Against False Positives in Qualitative Comparative Analysis." Forthcoming, Political Analysis.
NeedsCompilation: no
Packaged: 2015-05-02 19:18:50 UTC; bfbraum
Repository: CRAN
Date/Publication: 2015-05-03 07:07:31

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Package NAM updated to version 1.3.2 with previous version 1.3 dated 2015-04-22

Title: Nested Association Mapping Analysis
Description: Designed for association studies in nested association mapping (NAM) panels, also handling biparental and random panels. It includes functions for genome-wide associations mapping of multiple populations, marker quality control, solving mixed models and finding variance components through REML and Gibbs sampling.
Author: Alencar Xavier, William Muir, Katy Rainey, Tiago Pimenta, Qishan Wang, Shizhong Xu.
Maintainer: Alencar Xavier

Diff between NAM versions 1.3 dated 2015-04-22 and 1.3.2 dated 2015-05-03

 DESCRIPTION        |   10 +-
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 20 files changed, 408 insertions(+), 241 deletions(-)

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New package neotoma with initial version 1.2-0
Package: neotoma
Type: Package
Title: Access to the Neotoma Paleoecological Database Through R
Version: 1.2-0
Date: 2015-05-01
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Authors@R: c(person(given = c("Simon", "J."), family = "Goring", role = c("aut", "cre"), email = "goring@wisc.edu"), person(given = c("Gavin", "L."), family = "Simpson", role = "aut"), person(given = c("Jeremiah", "P."), family = "Marsicek", role = "ctb"), person(given = "Karthik", family = "Ram", role = "aut"), person(given = "Luke", family = "Sosalla", role = "ctb"))
Maintainer: Simon J. Goring
Description: Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (http://api.neotomadb.org/). The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.
License: MIT + file LICENSE
URL: https://github.com/ropensci/neotoma
BugReports: https://github.com/ropensci/neotoma/issues
Depends: R (>= 2.10)
Imports: RJSONIO, RCurl (>= 1.6), plyr, reshape2
Suggests: testthat, knitr
NeedsCompilation: no
Packaged: 2015-05-02 15:11:25 UTC; Simon Goring
Repository: CRAN
Date/Publication: 2015-05-03 07:07:39

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Package MapGAM updated to version 0.7-5 with previous version 0.7-4 dated 2014-12-10

Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting for confounding variables, using methods described by Kelsall and Diggle (1998) and Webster at al. (2006). Includes convenient functions for mapping, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Veronica Vieira, Scott Bartell, and Robin Bliss
Maintainer: Scott Bartell

Diff between MapGAM versions 0.7-4 dated 2014-12-10 and 0.7-5 dated 2015-05-03

 ChangeLog             |   10 ++++++++++
 DESCRIPTION           |    8 ++++----
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 R/colormap.R          |   19 +++++++++++++++----
 R/trimdata.R          |    2 +-
 man/MAdata.Rd         |    2 +-
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 9 files changed, 47 insertions(+), 26 deletions(-)

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New package fheatmap with initial version 1.0.0
Package: fheatmap
Type: Package
Title: Draw Heatmaps with Colored Dendogram
Version: 1.0.0
Date: 2015-05-02
Author: Vaishali Tumulu and Sivasish Sindiri
Maintainer: Sivasish Sindiri
Depends: R (>= 3.0)
Description: R function to plot high quality, elegant heatmap using 'ggplot2' graphics . Some of the important features of this package are, coloring of row/column side tree with respect to the number of user defined cuts in the cluster, add annotations to both columns and rows, option to input annotation palette for tree and column annotations and multiple parameters to modify aesthetics (style, color, font) of texts in the plot.
License: GPL-3
LazyData: true
Imports: grid, RColorBrewer , gdata, ggplot2, reshape2, gplots
NeedsCompilation: no
Repository: CRAN
Packaged: 2015-05-02 17:21:10 UTC; sivasishsindiri
Date/Publication: 2015-05-03 07:07:38

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New package EW with initial version 1.1
Package: EW
Type: Package
Title: Edgeworth Expansion
Version: 1.1
Date: 2015-04-28
Author: H.R.Law
Maintainer: H.R.Law <4islands@gmail.com>
Description: Edgeworth Expansion calculation.
License: GPL
NeedsCompilation: no
Packaged: 2015-04-28 05:52:09 UTC; abc
Repository: CRAN
Date/Publication: 2015-05-03 07:07:26

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Package bnlearn updated to version 3.8 with previous version 3.7.1 dated 2015-01-23

Title: Bayesian Network Structure Learning, Parameter Learning and Inference
Description: Bayesian network structure learning, parameter learning and inference. This package implements constraint-based (GS, IAMB, Inter-IAMB, Fast-IAMB, MMPC, Hiton-PC), pairwise (ARACNE and Chow-Liu), score-based (Hill-Climbing and Tabu Search) and hybrid (MMHC and RSMAX2) structure learning algorithms for discrete, Gaussian and conditional Gaussian networks, along with many score functions and conditional independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also implemented. Some utility functions (model comparison and manipulation, random data generation, arc orientation testing, simple and advanced plots) are included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional probability queries and cross-validation. Development snapshots with the latest bugfixes are available from www.bnlearn.com.
Author: Marco Scutari
Maintainer: Marco Scutari

Diff between bnlearn versions 3.7.1 dated 2015-01-23 and 3.8 dated 2015-05-03

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 bnlearn-3.8/bnlearn/src/loss.c                             |    7 
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 bnlearn-3.8/bnlearn/src/mi.matrix.c                        |    7 
 bnlearn-3.8/bnlearn/src/mvber.c                            |    6 
 bnlearn-3.8/bnlearn/src/nparams.c                          |    3 
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 bnlearn-3.8/bnlearn/src/path.c                             |    5 
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 bnlearn-3.8/bnlearn/src/predict.c                          |    7 
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 bnlearn-3.8/bnlearn/src/sanitization.c                     |    2 
 bnlearn-3.8/bnlearn/src/score.delta.c                      |    4 
 bnlearn-3.8/bnlearn/src/shd.c                              |    4 
 bnlearn-3.8/bnlearn/src/shrinkage.c                        |    7 
 bnlearn-3.8/bnlearn/src/simulation.c                       |    2 
 bnlearn-3.8/bnlearn/src/strings.c                          |    2 
 bnlearn-3.8/bnlearn/src/subsets.c                          |    5 
 bnlearn-3.8/bnlearn/src/symmetric.c                        |    3 
 bnlearn-3.8/bnlearn/src/tabu.c                             |    6 
 bnlearn-3.8/bnlearn/src/test.counter.c                     |    2 
 bnlearn-3.8/bnlearn/src/tiers.c                            |    4 
 bnlearn-3.8/bnlearn/src/utest.c                            |    7 
 bnlearn-3.8/bnlearn/src/which.max.c                        |    3 
 bnlearn-3.8/bnlearn/src/wishart.posterior.c                |    8 
 103 files changed, 751 insertions(+), 455 deletions(-)

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