Fri, 21 Dec 2012

Package tsDyn updated to version 0.9-2 with previous version 0.9-1 dated 2012-11-08

Title: Nonlinear time series models with regime switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut, cre], Jose Luis Aznarte [ctb], Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler

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Package sna updated to version 2.2-1 with previous version 2.2-0 dated 2010-11-22

Title: Tools for Social Network Analysis
Description: A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, p* modeling, random graph generation, and 2D/3D network visualization.
Author: Carter T. Butts
Maintainer: ORPHANED

Diff between sna versions 2.2-0 dated 2010-11-22 and 2.2-1 dated 2012-12-21

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Package ReadImages updated to version 0.1.3.3 with previous version 0.1.3.2 dated 2012-04-19

Title: Image Reading Module for R
Description: This package provides functions for reading JPEG and PNG files.
Author: Markus Loecher, Nikon Systems Inc, Nikon Digital Technologies Co., Ltd.
Maintainer: ORPHANED

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Package ReCiPa updated to version 3.0 with previous version 2.2 dated 2012-11-21

Title: Redundancy Control in Pathways databases
Description: Pathways in a database could have many redundancies among them. This package allows the user to set a maximum value for the proportion of these redundancies.
Author: Juan C. Vivar
Maintainer: Juan C. Vivar

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Package maxlike updated to version 0.1-2 with previous version 0.1-1 dated 2012-02-18

Title: Model species distributions by estimating the probability of occurrence using presence-only data.
Description: Provides a likelihood-based approach to modeling species distributions using presence-only data. In contrast to the popular software program MAXENT, this approach yields estimates of the probability of occurrence, which is a natural descriptor of a species' distribution.
Author: Richard Chandler and Andy Royle
Maintainer: Richard Chandler

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Package mvnmle updated to version 0.1-11 with previous version 0.1-10 dated 2011-06-30

Title: ML estimation for multivariate normal data with missing values.
Description: Finds the maximum likelihood estimate of the mean vector and variance-covariance matrix for multivariate normal data with missing values.
Author: Kevin Gross, with help from Douglas Bates
Maintainer: ORPHANED

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Package forensim updated to version 3.2.1 with previous version 3.2 dated 2012-08-07

Title: Statistical tools for the interpretation of forensic DNA mixtures
Description: Statistical methods and simulation tools for the interpretation of forensic DNA mixtures
Author: Hinda Haned
Maintainer: Hinda Haned

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Package caTools updated to version 1.14 with previous version 1.13 dated 2012-05-23

Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off error free sum and cumsum, etc.
Author: Jarek Tuszynski
Maintainer: ORPHANED

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New package BurStMisc with initial version 1.00
Package: BurStMisc
Title: Burns Statistics miscellaneous
Version: 1.00
Author: Burns Statistics
Description: corner, genetic optimization, permutation tests
Maintainer: Pat Burns
License: Unlimited
Packaged: Fri Dec 21 17:01:34 2012; pat
Repository: CRAN
Date/Publication: 2012-12-21 19:45:14

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Package agricolae updated to version 1.1-3 with previous version 1.1-2 dated 2012-07-06

Title: Statistical Procedures for Agricultural Research
Description: Agricolae was presented in the thesis "A statistical analysis tool for agricultural research" to obtain the degree of Master on science, mention Systems Engineering, Faculty of Industrial and Systems Engineering, National Engineering University (UNI), Lima-Peru Agricolae offers extensive functionality on experimental design especially for agricultural and plant breeding experiments, which can also be useful for other purposes. It supports planning of lattice, Alpha, Cyclic, Complete Block, Latin Square, Graeco-Latin Squares, augmented block, split and strip plot designs. There are also various analysis facilities for experimental data, e.g. treatment comparison procedures and several non-parametric tests comparison, biodiversity indexes and consensus cluster.
Author: Felipe de Mendiburu
Maintainer: Felipe de Mendiburu

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Package cclust (with last version 0.6-16) was removed from CRAN

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2009-09-18 0.6-16
2009-01-06 0.6-15
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Package crawl (with last version 1.3-4) was removed from CRAN

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2012-04-10 1.3-4
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2011-10-28 1.3-1
2011-05-25 1.3
2011-01-21 1.2
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2009-12-13 1.1-0
2009-05-06 1.0-4
2009-02-03 1.0-3
2009-01-09 1.0-1
2008-12-18 1.0

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Package rrBLUP updated to version 4.1 with previous version 4.0 dated 2012-09-18

Title: Ridge regression and other kernels for genomic selection
Description: Software for genomic prediction with the RR-BLUP mixed model. One application is to estimate marker effects by ridge regression; alternatively, BLUPs can be calculated based on an additive relationship matrix or a Gaussian kernel.
Author: Jeffrey Endelman
Maintainer: Jeffrey Endelman

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Package NestedCohort (with last version 1.1-2) was removed from CRAN

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Package EMA (with last version 1.3.2) was removed from CRAN

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2012-03-21 1.3.2
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Package sperich updated to version 1.5-5 with previous version 1.4-0 dated 2012-07-17

Title: Auxiliary functions to estimate centers of biodiversity
Description: Provides some easy-to-use functions to interpolate species range based on species occurrences and to estimate centers of biodiversity
Author: Maximilian Lange, Sven Lautenbach, Claudia Raedig
Maintainer: Maximilian Lange

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Package sp updated to version 1.0-5 with previous version 1.0-4 dated 2012-12-18

Title: classes and methods for spatial data
Description: A package that provides classes and methods for spatial data. The classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre], Roger Bivand [aut], Barry Rowlingson [ctb], Virgilio Gomez-Rubio [ctb]
Maintainer: Edzer Pebesma

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Package Rcpp updated to version 0.10.2 with previous version 0.10.1 dated 2012-11-27

Title: Seamless R and C++ Integration
Description: The Rcpp package provides R functions as well as a C++ library which facilitate the integration of R and C++. R data types (SEXP) are matched to C++ objects in a class hierarchy. All R types are supported (vectors, functions, environment, etc ...) and each type is mapped to a dedicated class. For example, numeric vectors are represented as instances of the Rcpp::NumericVector class, environments are represented as instances of Rcpp::Environment, functions are represented as Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good entry point to Rcpp. Conversion from C++ to R and back is driven by the templates Rcpp::wrap and Rcpp::as which are highly flexible and extensible, as documented in the "Rcpp-extending" vignette. Rcpp also provides Rcpp modules, a framework that allows exposing C++ functions and classes to the R level. The "Rcpp-modules" vignette details the current set of features of Rcpp-modules. Rcpp includes a concept called Rcpp sugar that brings many R functions into C++. Sugar takes advantage of lazy evaluation and expression templates to achieve great performance while exposing a syntax that is much nicer to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette gives an overview of the feature. Rcpp attributes provide a high-level syntax for declaring C++ functions as callable from R and automatically generating the code required to invoke them. Attributes are intended to facilitate both interactive use of C++ within R sessions as well as to support R package development. Attributes are built on top of Rcpp modules and their implementation is based on previous work in the inline package. Many examples are included, and over 870 unit tests in over 390 unit test functions provide additional usage examples. An earlier version of Rcpp, containing what we now call the 'classic Rcpp API' was written during 2005 and 2006 by Dominick Samperi. This code has been factored out of Rcpp into the package RcppClassic, and it is still available for code relying on the older interface. New development should always use this Rcpp package instead.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by Douglas Bates, John Chambers and JJ Allaire
Maintainer: Dirk Eddelbuettel

Diff between Rcpp versions 0.10.1 dated 2012-11-27 and 0.10.2 dated 2012-12-21

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Package postCP updated to version 1.6.2 with previous version 1.6.1 dated 2012-10-26

Title: A package to estimate posterior probabilities and perform model selection in change-point models using constrained HMM.
Description: The functions are used for change-point problems, after an initial set of change-points within the data has already been obtained. The function postCP obtains estimates of posterior probabilities of change-point and hidden states for each observation, and confidence intervals for the positions of the change-point. The function postCPsample obtains random samples of sets of change-points using the output of the postCP function. Model selection may be performed using function postCPmodelsel through criteria obtained from function postCPcrit.
Author: Gregory Nuel and The Minh Luong
Maintainer: The Minh Luong

Diff between postCP versions 1.6.1 dated 2012-10-26 and 1.6.2 dated 2012-12-21

 DESCRIPTION           |   10 +++++-----
 MD5                   |   24 ++++++++++++------------
 R/postCP.modelsel.r   |   26 ++++++++++++++------------
 man/GreedySegmente.Rd |    4 ++--
 man/lesum.Rd          |    4 ++--
 man/mleNB.Rd          |    6 +++---
 man/plot.postCP.Rd    |    4 ++--
 man/postCP.Rd         |    4 ++--
 man/postCPcrit.Rd     |    6 +++---
 man/postCPmodelsel.Rd |    8 ++++----
 man/postCPsample.Rd   |    4 ++--
 man/viterbi.Rd        |    4 ++--
 src/postCP.cpp        |   21 +++++++++++++++++++--
 13 files changed, 72 insertions(+), 53 deletions(-)

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Package maptools updated to version 0.8-21 with previous version 0.8-20 dated 2012-11-12

Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHS shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko, Jonathan Callahan, German Carrillo, Stéphane Dray, David Forrest, Michael Friendly, Patrick Giraudoux, Duncan Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Karl Ove Hufthammer, Thomas Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai, Oscar Perpiñán Lamigueiro, Tom Short, Greg Snow, Ben Stabler and Rolf Turner
Maintainer: Roger Bivand

Diff between maptools versions 0.8-20 dated 2012-11-12 and 0.8-21 dated 2012-12-21

 ChangeLog        |   22 +++++++
 DESCRIPTION      |    9 +--
 MD5              |   16 ++---
 NAMESPACE        |    2 
 R/dotsinpolys.R  |    9 ++-
 R/lineLabel.R    |  155 +++++++++++++++++++++++++++++++++++++------------------
 inst/ChangeLog   |   22 +++++++
 man/lineLabel.Rd |   92 ++++++++++++++++++++++----------
 maptools-Ex.R    |   28 +++++++--
 9 files changed, 254 insertions(+), 101 deletions(-)

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New package mvinfluence with initial version 0.6
Package: mvinfluence
Type: Package
Title: Influence Measures and Diagnostic Plots for Multivariate Linear Models
Version: 0.6
Date: 2012-12-20
Author: Michael Friendly
Maintainer: Michael Friendly
Description: This package computes regression deletion diagnostics for multivariate linear models and provides some associated diagnostic plots.
Depends: car, heplots
Suggests:
License: GPL-2
URL: http://datavis.ca/R
Packaged: 2012-12-20 23:15:27 UTC; rforge
Repository: CRAN
Repository/R-Forge/Project: mvinfluence
Repository/R-Forge/Revision: 8
Repository/R-Forge/DateTimeStamp: 2012-12-20 21:36:50
Date/Publication: 2012-12-21 16:39:05

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New package tm.plugin.webmining with initial version 0.9
Package: tm.plugin.webmining
Imports: RJSONIO
License: GPL-3
Title: Retrieve structured, textual data from various web sources
Authors@R: c(person("Mario", "Annau", role = c("aut", "cre"), email = "mario.annau@gmail.com"))
Maintainer: Mario Annau
Description: tm.plugin.webmining facilitates text retrieval from feed formats like XML (RSS, ATOM) and JSON. Also direct retrieval from HTML is supported. As most (news) feeds only incorporate small fractions of the original text tm.plugin.webmining even retrieves and extracts the text of the original text source.
Version: 0.9
Date: 2012-12-13
Depends: R (>= 2.10), tm, RCurl, XML, boilerpipeR
Collate: 'corpus.R' 'feedquery.R' 'getLinkContent.R' 'reader.R' 'source.R' 'tm.plugin.webmining-package.R' 'trimWhiteSpaces.R' 'extract.R' 'auth.google.reader.R' 'transform.R' 'parser.R' 'getURL.R'
Packaged: 2012-12-19 04:15:48 UTC; mario
Author: Mario Annau [aut, cre]
Repository: CRAN
Date/Publication: 2012-12-21 12:12:30

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Package spdep updated to version 0.5-55 with previous version 0.5-53 dated 2012-11-09

Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross product statistic, Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G and multicoloured join count statistics, local Moran's I and Getis/Ord G, saddlepoint approximations and exact tests for global and local Moran's I; and functions for estimating spatial simultaneous autoregressive (SAR) lag and error models, impact measures for lag models, weighted and unweighted SAR and CAR spatial regression models, semi-parametric and Moran eigenvector spatial filtering, GM SAR error models, and generalized spatial two stage least squares models.
Author: Roger Bivand , with contributions by Micah Altman, Luc Anselin, Renato Assunção, Olaf Berke, Andrew Bernat, Guillaume Blanchet, Eric Blankmeyer, Marilia Carvalho, Bjarke Christensen, Yongwan Chun, Carsten Dormann, Stéphane Dray, Rein Halbersma, Elias Krainski, Pierre Legendre, Nicholas Lewin-Koh, Hongfei Li, Jielai Ma, Giovanni Millo, Werner Mueller, Hisaji Ono, Pedro Peres-Neto, Gianfranco Piras, Markus Reder, Michael Tiefelsdorf, and Danlin Yu.
Maintainer: Roger Bivand

Diff between spdep versions 0.5-53 dated 2012-11-09 and 0.5-55 dated 2012-12-21

 ChangeLog          |   34 +++++++++++++++++++++++++
 DESCRIPTION        |    8 ++---
 MD5                |   54 +++++++++++++++++++--------------------
 NAMESPACE          |    4 ++
 R/eigenw.R         |   57 +++++++++++++++++++++++++++++++++++++++++
 R/error.hessian.R  |    5 +--
 R/error.spsarlm.R  |    6 ++--
 R/impacts.R        |   72 ++++++++++++++++++++++++++++++++++++-----------------
 R/jacobian.R       |   17 ++++++++++++
 R/jacobian_setup.R |   10 +++++--
 R/lag.hessian.R    |    5 +--
 R/lag.spsarlm.R    |    6 ++--
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Package pedantics updated to version 1.04 with previous version 1.03 dated 2012-03-27

Title: Functions to facilitate power and sensitivity analyses for genetic studies of natural populations
Description: More to come
Author: Michael Morrissey
Maintainer: Michael Morrissey

Diff between pedantics versions 1.03 dated 2012-03-27 and 1.04 dated 2012-12-21

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New package gsg with initial version 1.0
Package: gsg
Type: Package
Title: Calculation of selection coefficients
Version: 1.0
Date: 2012-12-21
Author: Michael Morrissey, Krzysztof Sakrejda
Maintainer: Michael Morrissey
Depends: mgcv, mvtnorm, boot, numDeriv
Description: gsg (gam selection gradients) provides a unified approach to the regression analysis of selection from longitudinal data collected from natural populations.
License: GPL-2
LazyLoad: yes
Packaged: 2012-12-21 08:53:55 UTC; michael
Repository: CRAN
Date/Publication: 2012-12-21 12:01:50

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New package boilerpipeR with initial version 1.0
Package: boilerpipeR
Maintainer: Mario Annau
License: Apache License (== 2.0)
Title: Interface to the boilerpipe Java library by Christian Kohlschutter (http://code.google.com/p/boilerpipe/)
Authors@R: c(person("Mario", "Annau", role = c("aut", "cre"), email = "mario.annau@gmail.com"))
Description: Generic Extraction of main text content from HTML files; removal of ads, sidebars and headers using the boilerpipe Java library. The extraction heuristics from boilerpipe show a robust performance for a wide range of web site templates.
Version: 1.0
Date: 2012-12-13
Depends: rJava
Collate: 'Extractor.R' 'onload.R' 'boilerpipeR-package.R'
Packaged: 2012-12-19 04:15:40 UTC; mario
Author: Mario Annau [aut, cre]
Repository: CRAN
Date/Publication: 2012-12-21 09:27:52

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Package rpart.plot updated to version 1.4-3 with previous version 1.4-2 dated 2012-12-16

Title: Plot rpart models. An enhanced version of plot.rpart.
Description: Plot rpart models. Extends plot.rpart and text.rpart in the rpart package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow

Diff between rpart.plot versions 1.4-2 dated 2012-12-16 and 1.4-3 dated 2012-12-21

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Package ORMDR updated to version 1.3-2 with previous version 1.3-1 dated 2008-08-21

Title: ORMDR
Description: Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions
Author: Eun-Kyung Lee, Sung Gon Yi, Yoojin Jung, Junghyun Namkung, Taesung Park
Maintainer: Junghyun Namkung

Diff between ORMDR versions 1.3-1 dated 2008-08-21 and 1.3-2 dated 2012-12-21

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Package NSA updated to version 0.0.32 with previous version 0.0.31 dated 2012-10-04

Title: Post-normalization of total copy numbers
Description: Post-normalization of total copy-number estimates.
Author: Maria Ortiz-Estevez , Ander Aranburu , Angel Rubio
Maintainer: Maria Ortiz-Estevez

Diff between NSA versions 0.0.31 dated 2012-10-04 and 0.0.32 dated 2012-12-21

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Package lossDev updated to version 3.0.0-4 with previous version 3.0.0-3 dated 2012-07-03

Title: Robust Loss Development Using MCMC
Description: Loss Development for Insurance Triangles
Author: Christopher W. Laws, Frank A. Schmid
Maintainer: Christopher W. Laws

Diff between lossDev versions 3.0.0-3 dated 2012-07-03 and 3.0.0-4 dated 2012-12-21

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New package Lock5Data with initial version 2.6
Package: Lock5Data
Type: Package
Title: Datasets for "Statistics: UnLocking the Power of Data"
Version: 2.6
Date: 2012-08-20
Author: Robin Lock
Maintainer: Robin Lock
Description: Datasets for "Statistics:Unlocking the Power of Data" by Lock, Lock, Lock, Lock and Lock
License: GPL-2
LazyLoad: yes
Repository: CRAN
Repository/R-Forge/Project: stat2data
Repository/R-Forge/Revision: 60
Packaged: 2012-08-20 22:19:37 UTC; rforge
Depends: R (>= 2.10)
Date/Publication: 2012-12-21 08:05:02

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Package imputeMDR updated to version 1.1.2 with previous version 1.1.1 dated 2011-07-07

Title: The Multifactor Dimensionality Reduction (MDR) Analysis for Incomplete Data
Description: This package provides various approaches to handling missing values for the MDR analysis to identify gene-gene interactions using biallelic marker data in genetic association studies
Author: Junghyun Namkung, Taeyoung Hwang, MinSeok Kwon, Sunggon Yi and Wonil Chung
Maintainer: Junghyun Namkung

Diff between imputeMDR versions 1.1.1 dated 2011-07-07 and 1.1.2 dated 2012-12-21

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Package extrafont updated to version 0.13 with previous version 0.12 dated 2012-11-01

Title: Tools for using fonts
Description: Tools to using fonts other than the standard PostScript fonts. This package makes it easy to use system TrueType fonts and with PDF or PostScript output files, and with bitmap output files in Windows. extrafont can also be used with fonts packaged specifically to be used with, such as the fontcm package, which has Computer Modern PostScript fonts with math symbols. See https://github.com/wch/extrafont for instructions and examples.
Author: Winston Chang ,
Maintainer: Winston Chang

Diff between extrafont versions 0.12 dated 2012-11-01 and 0.13 dated 2012-12-21

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Package caret updated to version 5.15-048 with previous version 5.15-045 dated 2012-11-27

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn

Diff between caret versions 5.15-045 dated 2012-11-27 and 5.15-048 dated 2012-12-21

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Package bpkde updated to version 1.0-2 with previous version 1.0 dated 2012-04-29

Title: Back-Projected Kernel Density Estimation
Description: Nonparametric multivariate kernel density \ estimation using a back-projected kernel.
Author: Kjell Konis , Victor M. Panaretos .
Maintainer: Kjell Konis

Diff between bpkde versions 1.0 dated 2012-04-29 and 1.0-2 dated 2012-12-21

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Package aqp updated to version 1.4 with previous version 1.3 dated 2012-10-10

Title: Algorithms for Quantitative Pedology
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette , Pierre Roudier
Maintainer: Dylan Beaudette

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