Title: A general-purpose package for dynamic report generation in R
Diff between knitr versions 1.0.5 dated 2013-01-21 and 1.1 dated 2013-02-16
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
knitr-1.0.5/knitr/Makefile |only
knitr-1.0.5/knitr/man/run_chunk.Rd |only
knitr-1.1/knitr/DESCRIPTION | 39 +++++-----
knitr-1.1/knitr/FAQ.md | 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 +
knitr-1.1/knitr/README.md | 4 -
knitr-1.1/knitr/inst/doc/Makefile | 9 +-
knitr-1.1/knitr/inst/doc/knitr-intro.Rnw | 1
knitr-1.1/knitr/inst/doc/knitr-intro.lyx | 1
knitr-1.1/knitr/inst/doc/knitr-intro.pdf |binary
knitr-1.1/knitr/inst/doc/knitr-markdown.Rmd |only
knitr-1.1/knitr/inst/doc/knitr-markdown.html |only
knitr-1.1/knitr/inst/doc/knitr-refcard.Rnw | 1
knitr-1.1/knitr/inst/doc/knitr-refcard.lyx | 1
knitr-1.1/knitr/inst/doc/knitr-refcard.pdf |binary
knitr-1.1/knitr/inst/examples/knitr-manual.Rnw | 2
knitr-1.1/knitr/inst/examples/knitr-manual.lyx | 2
knitr-1.1/knitr/inst/examples/knitr-packages.bib | 2
knitr-1.1/knitr/inst/shiny/ui.R | 2
knitr-1.1/knitr/inst/tests/test-parser.R | 6 -
knitr-1.1/knitr/man/chunk_hook.Rd | 8 ++
knitr-1.1/knitr/man/dep_auto.Rd | 6 -
knitr-1.1/knitr/man/imgur_upload.Rd | 15 +---
knitr-1.1/knitr/man/knit2html.Rd | 7 -
knitr-1.1/knitr/man/knit2pdf.Rd | 8 +-
knitr-1.1/knitr/man/knit2wp.Rd |only
knitr-1.1/knitr/man/spin.Rd | 6 -
45 files changed, 335 insertions(+), 219 deletions(-)
Title: Create cryptographic hash digests of R objects
Diff between digest versions 0.6.2 dated 2013-01-25 and 0.6.3 dated 2013-02-16
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
ftp://ftp.rocksoft.com/cliens/rocksoft/papers/crc_v3.txt.
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
Maintainer: Dirk Eddelbuettel
ChangeLog | 10 ++++++++
DESCRIPTION | 9 ++++---
MD5 | 10 ++++----
R/hmac.R | 23 ++++++++++++++-----
tests/hmacTest.R | 40 ++++++++++++++++++++++++++++++++++
tests/hmacTest.Rout.save | 55 +++++++++++++++++++++++++++++++++++++++++++----
6 files changed, 128 insertions(+), 19 deletions(-)
Title: R wrappers for EXPOKIT; other matrix functions
Diff between rexpokit versions 0.23 dated 2013-02-11 and 0.24 dated 2013-02-16
Description: This package wraps some of the matrix exponentiation
utilities from EXPOKIT (http://www.maths.uq.edu.au/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
DESCRIPTION | 9 ++--
MD5 | 13 +++----
R/rexpokit-package.R | 33 ++++++++++++------
inst/REFERENCES.bib | 29 +++++++++++++++
man/rexpokit-package.Rd | 86 ++++++++++++++++++++++++++++++-----------------
src/Makevars | 28 ---------------
src/blas_mod.f |only
src/expokit_wrappers.cpp | 4 +-
8 files changed, 120 insertions(+), 82 deletions(-)
Title: Robust Estimation of Overdispersed Multinomial Regression Models
Diff between multinomRob versions 1.8-6 dated 2012-09-29 and 1.8-6.1 dated 2013-02-16
Description: MNL and overdispersed multinomial regression using robust
(LQD and tanh) estimation
Author: Walter R. Mebane, Jr.
Maintainer: Jasjeet Singh Sekhon
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(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Diff between Matching versions 4.8-1 dated 2012-09-28 and 4.8-1.2 dated 2013-02-16
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
ChangeLog | 7 +++
DESCRIPTION | 9 ++--
MD5 | 22 +++++------
R/AI.R | 6 +--
R/GenMatching.R | 42 ++++++++++-----------
R/Matchby.R | 4 +-
R/Matching.R | 84 +++++++++++++++++++++----------------------
data/lalonde.rda |binary
tests/AbadieImbens.Rout.save | 10 ++---
tests/DehejiaWahba.Rout.save | 10 ++---
tests/GenMatch.Rout.save | 14 +++----
tests/Matchby.Rout.save | 10 ++---
12 files changed, 113 insertions(+), 105 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 1.7.3 dated 2013-01-29 and 1.7.4 dated 2013-02-16
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
lmomco-1.7.3/lmomco/inst/legacy |only
lmomco-1.7.4/lmomco/ChangeLog | 6 +++++
lmomco-1.7.4/lmomco/DESCRIPTION | 9 ++++----
lmomco-1.7.4/lmomco/MD5 | 42 +---------------------------------------
4 files changed, 13 insertions(+), 44 deletions(-)
Title: Multivariate Chebyshev interpolation
Diff between chebpol versions 1.0-832 dated 2013-02-13 and 1.1-856 dated 2013-02-16
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
DESCRIPTION | 17 +-
MD5 | 35 ++--
NAMESPACE | 2
R/chebpol.R | 68 ++++++---
configure | 10 +
configure.ac | 8 -
inst/doc/CHANGELOG | 99 +++++++++++++
man/chebappx.Rd | 25 +--
man/chebappxf.Rd | 2
man/chebappxg.Rd | 18 +-
man/chebcoef.Rd | 2
man/chebknots.Rd | 12 -
man/chebpol-package.Rd | 32 ++--
man/evalongrid.Rd | 42 ++++-
man/mlappx.Rd |only
src/Makevars.in | 5
src/chebpol.c | 354 +++++++++++++++++++++++++++++++++++++++----------
tests/all.R | 15 +-
tests/all.Rout.save | 38 ++++-
19 files changed, 598 insertions(+), 186 deletions(-)
Title: Sensitivity of the Bayesian Adjustment for Confounding (BAC)
algorithm to the choice of hyperparameter omega.
Diff between BACprior versions 1.2 dated 2012-11-17 and 1.2.1 dated 2013-02-16
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
ChangeLog |only
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(-)