Sat, 16 Feb 2013

Package knitr updated to version 1.1 with previous version 1.0.5 dated 2013-01-21

Title: A general-purpose package for dynamic report generation in R
Description: This package provides a general-purpose tool for dynamic report generation in R, which can be used to deal with any type of (plain text) files, including Sweave, HTML, Markdown and reStructuredText. The patterns of code chunks and inline R expressions can be customized. R code is evaluated as if it were copied and pasted in an R terminal thanks to the evaluate package (e.g. we do not need to explicitly print() plots from ggplot2 or lattice). R code can be reformatted by the formatR package so that long lines are automatically wrapped, with indent and spaces being added, and comments being preserved. A simple caching mechanism is provided to cache results from computations for the first time and the computations will be skipped the next time. Almost all common graphics devices, including those in base R and add-on packages like Cairo, cairoDevice and tikzDevice, are built-in with this package and it is straightforward to switch between devices without writing any special functions. The width and height as well as alignment of plots in the output document can be specified in chunk options (the size of plots for graphics devices is still supported as usual). Multiple plots can be recorded in a single code chunk, and it is also allowed to rearrange plots to the end of a chunk or just keep the last plot. Warnings, messages and errors are written in the output document by default (can be turned off). Currently LaTeX, HTML, Markdown and reST are supported, and other output formats can be supported by hook functions. The large collection of hooks in this package makes it possible for the user to control almost everything in the R code input and output. Hooks can be used either to format the output or to run a specified R code fragment before or after a code chunk. The language in code chunks is not restricted to R only (there is simple support to Python and Awk, etc). Many features are borrowed from or inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Author: Yihui Xie
Maintainer: Yihui Xie

Diff between knitr versions 1.0.5 dated 2013-01-21 and 1.1 dated 2013-02-16

 knitr-1.0.5/knitr/Makefile                       |only
 knitr-1.0.5/knitr/man/run_chunk.Rd               |only
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 knitr-1.1/knitr/                           |   15 +---
 knitr-1.1/knitr/MD5                              |   82 +++++++++++------------
 knitr-1.1/knitr/NAMESPACE                        |    4 -
 knitr-1.1/knitr/NEWS                             |   80 ++++++++++++++++++++++
 knitr-1.1/knitr/R/block.R                        |    7 +
 knitr-1.1/knitr/R/cache.R                        |    9 --
 knitr-1.1/knitr/R/defaults.R                     |    2 
 knitr-1.1/knitr/R/engine.R                       |    7 -
 knitr-1.1/knitr/R/hooks-extra.R                  |   22 +++++-
 knitr-1.1/knitr/R/hooks-html.R                   |    2 
 knitr-1.1/knitr/R/output.R                       |   21 ++---
 knitr-1.1/knitr/R/parser.R                       |   28 +++----
 knitr-1.1/knitr/R/spin.R                         |    9 +-
 knitr-1.1/knitr/R/template.R                     |    2 
 knitr-1.1/knitr/R/utils-conversion.R             |   53 ++++++++++++--
 knitr-1.1/knitr/R/utils-sweave.R                 |    9 +-
 knitr-1.1/knitr/R/utils-upload.R                 |   33 ++++-----
 knitr-1.1/knitr/R/utils-vignettes.R              |only
 knitr-1.1/knitr/R/utils.R                        |   45 +++---------
 knitr-1.1/knitr/R/zzz.R                          |    4 +
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 knitr-1.1/knitr/inst/doc/Makefile                |    9 +-
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 knitr-1.1/knitr/inst/tests/test-parser.R         |    6 -
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 45 files changed, 335 insertions(+), 219 deletions(-)

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Package digest updated to version 0.6.3 with previous version 0.6.2 dated 2013-01-25

Title: Create cryptographic hash digests of R objects
Description: The digest package provides a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256 and crc32 algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code. The md5 algorithm by Ron Rivest is specified in RFC 1321, the sha-1 and sha-256 algorithms are specified in FIPS-180-1 and FIPS-180-2, and the crc32 algorithm is described in For md5, sha-1, sha-256 and aes, this package uses a small standalone implementations that were provided by Christophe Devine. For crc32, code from the zlib library is used. For sha-512, an implementation by Aaron D. Gifford is used. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.
Author: Dirk Eddelbuettel with contributions by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek, Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen and Duncan Murdoch.
Maintainer: Dirk Eddelbuettel

Diff between digest versions 0.6.2 dated 2013-01-25 and 0.6.3 dated 2013-02-16

 ChangeLog                |   10 ++++++++
 DESCRIPTION              |    9 ++++---
 MD5                      |   10 ++++----
 R/hmac.R                 |   23 ++++++++++++++-----
 tests/hmacTest.R         |   40 ++++++++++++++++++++++++++++++++++
 tests/ |   55 +++++++++++++++++++++++++++++++++++++++++++----
 6 files changed, 128 insertions(+), 19 deletions(-)

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Package rexpokit updated to version 0.24 with previous version 0.23 dated 2013-02-11

Title: R wrappers for EXPOKIT; other matrix functions
Description: This package wraps some of the matrix exponentiation utilities from EXPOKIT (, a FORTRAN library that is widely recommended for matrix exponentiation (Sidje RB, 1998. "Expokit: A Software Package for Computing Matrix Exponentials." ACM Trans. Math. Softw. 24(1): 130-156). EXPOKIT includes functions for exponentiating both small, dense matrices, and large, sparse matrices (in sparse matrices, most of the cells have value 0). Rapid matrix exponentiation is useful in phylogenetics when we have a large number of states (as we do when we are inferring the history of transitions between the possible geographic ranges of a species), but is probably useful in other ways as well.
Author: Nicholas J. Matzke [aut, cre, cph], Roger B. Sidje [aut, cph]
Maintainer: Nicholas J. Matzke

Diff between rexpokit versions 0.23 dated 2013-02-11 and 0.24 dated 2013-02-16

 DESCRIPTION              |    9 ++--
 MD5                      |   13 +++----
 R/rexpokit-package.R     |   33 ++++++++++++------
 inst/REFERENCES.bib      |   29 +++++++++++++++
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Package multinomRob updated to version 1.8-6.1 with previous version 1.8-6 dated 2012-09-29

Title: Robust Estimation of Overdispersed Multinomial Regression Models
Description: MNL and overdispersed multinomial regression using robust (LQD and tanh) estimation
Author: Walter R. Mebane, Jr. , Jasjeet Singh Sekhon
Maintainer: Jasjeet Singh Sekhon

Diff between multinomRob versions 1.8-6 dated 2012-09-29 and 1.8-6.1 dated 2013-02-16

 DESCRIPTION     |    9 +++++----
 MD5             |   10 +++++-----
 R/genoudRob.R   |    7 +++----
 R/multinomLQD.R |   14 +++++++-------
 R/multinomRob.R |   14 +++++++-------
 R/resstd2.R     |    9 ++++-----
 6 files changed, 31 insertions(+), 32 deletions(-)

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Package Matching updated to version 4.8-1.2 with previous version 4.8-1 dated 2012-09-28

Title: Multivariate and Propensity Score Matching with Balance Optimization
Description: Provides functions for multivariate and propensity score matching and for finding optimal balance based on a genetic search algorithm. A variety of univariate and multivariate metrics to determine if balance has been obtained are also provided.
Author: Jasjeet Singh Sekhon
Maintainer: Jasjeet Singh Sekhon

Diff between Matching versions 4.8-1 dated 2012-09-28 and 4.8-1.2 dated 2013-02-16

 ChangeLog                    |    7 +++
 DESCRIPTION                  |    9 ++--
 MD5                          |   22 +++++------
 R/AI.R                       |    6 +--
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 12 files changed, 113 insertions(+), 105 deletions(-)

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Package lmomco updated to version 1.7.4 with previous version 1.7.3 dated 2013-01-29

Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments, and Many Distributions
Description: The package implements the statistical theory of L-moments in R including L-moment estimation, probability-weighted moment estimation, parameter estimation for numerous familiar and not-so-familiar distributions, and L-moment estimation for the same distributions from the parameters. L-moments are derived from the expectations of order statistics and are linear with respect to the probability-weighted moments; choice of either can be made by mathematical convenience. L-moments are directly analogous to the well-known product moments; however, L-moments have many advantages including unbiasedness, robustness, and consistency with respect to the product moments, and the method of L-moments can out perform the method of maximum likelihood. The lmomco package historically was originally oriented around canonical FORTRAN algorithms of Hosking's library, and the nomenclature for many of the functions parallels those of the Hosking library. Hosking's algorithms later became available in the lmom package. However, vast extensions, components, concepts, and other L-moment curiosities are added to lmomco to aid and expand the breadth of L-moment applications. Such extensions include venerable statistics as Sen weighted mean, Gini mean difference, plotting positions, and conditional probability adjustment. The plotting of L-moment ratio diagrams is directly supported in this package. Computations of L-moments for right-tail and left-tail censoring by known or unknown censoring threshold (Hosking) and also by indicator variable also are available. Trimmed L-moments are supported as is numerical integration of quantile functions to dynamically compute trajectories of select TL-moment ratios for the construction of TL-moment ratio diagrams. L-moments have been extended into multivariate space; the so-called sample L-comoments are implemented and might have considerable application in copula theory because they measure asymmetric correlation and higher comoments or comovements of variables. The package supports exact analytical boot strap estimates of order statistics, L-moments, and variances-covariances of L-moments. The package provides the Harri-Coble Tau34-squared Test for Normality that uses only the sample L-skew and L-kurtosis. The package supports the following distributions with moment type shown as "L" (L-moments) or "TL" (trimmed L-moments) and additional support for right-tail censoring ([RC]) include: Asymmetric Exponential Power (L), Cauchy (TL), Eta-Mu (L), Exponential (L), Gamma (L), Generalized Extreme Value (L), Generalized Lambda (L & TL), Generalized Logistic (L), Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel (L), Kappa (L), Kappa-Mu (L), Kumaraswamy (L), Laplace (L), Normal (L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L), Wakeby (L), and Weibull (L).
Author: William H. Asquith
Maintainer: William H. Asquith

Diff between lmomco versions 1.7.3 dated 2013-01-29 and 1.7.4 dated 2013-02-16

 lmomco-1.7.3/lmomco/inst/legacy |only
 lmomco-1.7.4/lmomco/ChangeLog   |    6 +++++
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 lmomco-1.7.4/lmomco/MD5         |   42 +---------------------------------------
 4 files changed, 13 insertions(+), 44 deletions(-)

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Package chebpol updated to version 1.1-856 with previous version 1.0-832 dated 2013-02-13

Title: Multivariate Chebyshev interpolation
Description: The package contains methods for creating multivariate Chebyshev polynomials for interpolation of functions.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research, Oslo, Norway
Maintainer: Simen Gaure

Diff between chebpol versions 1.0-832 dated 2013-02-13 and 1.1-856 dated 2013-02-16

 DESCRIPTION            |   17 +-
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 19 files changed, 598 insertions(+), 186 deletions(-)

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Package BACprior updated to version 1.2.1 with previous version 1.2 dated 2012-11-17

Title: Sensitivity of the Bayesian Adjustment for Confounding (BAC) algorithm to the choice of hyperparameter omega.
Description: The BACprior package provides an approximate sensitivity analysis of the Bayesian Adjustment for Confounding (BAC) algorithm (Wang et al., 2012) with regards to hyperparameter omega. The method is based on Lefebvre, Atherton and Talbot (2013).
Author: Denis jf Talbot, Geneviève Lefebvre, Juli Atherton
Maintainer: Denis jf Talbot

Diff between BACprior versions 1.2 dated 2012-11-17 and 1.2.1 dated 2013-02-16

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 DESCRIPTION             |   15 ++++++++-------
 MD5                     |    9 +++++----
 R/BACprior.lm.R         |   23 ++++++++++++++++-------
 man/BACprior-package.Rd |   11 +++++++----
 man/BACprior.lm.Rd      |    2 +-
 6 files changed, 37 insertions(+), 23 deletions(-)

More information about BACprior at CRAN
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