Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-04 13.03.04
2013-02-04 13.02.04
2013-01-08 13.01.07
2012-12-03 12.12.03
2012-11-05 12.11.05
2012-10-01 12.10.01
2012-09-03 12.09.03
2012-08-06 12.08.06
2012-07-02 12.07.02
2012-06-04 12.06.04
2012-05-08 12.05.07
2012-04-02 12.04.02
2012-03-05 12.03.05
2012-01-02 12.01.02
2011-12-05 11.12.05
2011-11-03 11.11.03
2011-10-03 11.10.03
2011-09-26 11.09.26
2011-09-19 11.09.19
2011-09-12 11.09.12
2011-09-05 11.09.05
2011-08-22 11.08.22
2011-08-15 11.08.15
2011-08-08 11.08.08
2011-07-26 11.07.27
2011-07-23 11.07.15
2011-07-05 11.07.05
2011-06-27 11.06.27
2011-06-15 11.06.13
2011-06-07 11.06.05
2011-04-11 11.04.10
2011-04-04 11.04.04
2011-03-28 11.03.27
2011-03-21 11.03.20
2011-03-14 11.03.14
2011-03-07 11.03.06
2011-02-28 11.03.01
2011-02-22 11.02.21
2011-02-14 11.02.14
2011-02-07 11.02.07
2011-02-01 11.02.01
2011-01-28 11.01.27
2011-01-24 11.01.23
2011-01-19 11.01.18
2011-01-14 11.01.13
2011-01-09 11.01.08
2011-01-08 11.01.07
2011-01-06 11.01.05
2011-01-03 10.12.30
Title: Fuzzy Rank Tests and Confidence Intervals
Diff between fuzzyRankTests versions 0.3-4 dated 2013-03-31 and 0.3-5 dated 2013-07-15
More information about fuzzyRankTests at CRAN
Description: see title
Author: Charles J. Geyer
Maintainer: Charles J. Geyer
ChangeLog | 5
DESCRIPTION | 8 -
MD5 | 7 -
inst/doc/design.pdf |only
inst/doc/design.tex | 348 +++++++++++++++++++++++++++++++++++++++++++++-------
5 files changed, 319 insertions(+), 49 deletions(-)
Permanent link
Title: R Interface to the Protocol Buffers API
Diff between RProtoBuf versions 0.2.6 dated 2012-10-04 and 0.3 dated 2013-07-15
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal RPC protocols and file formats.
Author: Romain Francois, Dirk Eddelbuettel and Murray Stokely
Maintainer: Dirk Eddelbuettel
ChangeLog | 109
DESCRIPTION | 18
MD5 | 110
NAMESPACE | 3
R/00classes.R | 33
R/completion.R | 3
R/extensions.R |only
R/has.R | 5
R/set.R | 3
R/wrapper_EnumValueDescriptor.R | 6
R/wrapper_FieldDescriptor.R | 3
R/zzz.R | 6
TODO | 18
configure | 4635 ++++++++-----------
configure.in | 9
inst/NEWS.Rd | 37
inst/doc/RProtoBuf-intro.R |only
inst/doc/RProtoBuf-intro.pdf |binary
inst/doc/RProtoBuf-quickref.R |only
inst/doc/RProtoBuf-quickref.pdf |binary
inst/doc/RProtoBuf-unitTests.R |only
inst/doc/RProtoBuf-unitTests.Rnw | 2
inst/doc/RProtoBuf-unitTests.pdf |binary
inst/unitTests/runit.addressbook.R | 8
inst/unitTests/runit.enums.R | 4
inst/unitTests/runit.extensions.R |only
man/Descriptor-class.Rd | 4
man/EnumDescriptor-class.Rd | 17
man/EnumValueDescriptor-class.Rd | 13
man/FieldDescriptor-class.Rd | 46
man/FileDescriptor-class.Rd | 14
man/Message-class.Rd | 12
man/P.Rd | 4
man/RProtoBuf-package.Rd | 2
man/aslist.Rd | 10
man/clone.Rd | 5
man/has.Rd | 24
man/is_extension.Rd | 5
man/label.Rd | 4
man/number.Rd | 9
man/type.Rd | 3
man/with.Rd | 3
src/DescriptorPoolLookup.cpp | 8
src/S4_classes.h | 10
src/extensions.cpp |only
src/extractors.cpp | 8
src/lookup.cpp | 52
src/mutators.cpp | 2
src/rprotobuf.cpp | 9
src/rprotobuf.h | 8
src/wrapper_EnumDescriptor.cpp | 13
src/wrapper_EnumValueDescriptor.cpp | 4
src/wrapper_FileDescriptor.cpp | 17
vignettes/RProtoBuf-quickref/RProtoBuf-quickref.Rnw | 6
vignettes/RProtoBuf-unitTests.Rnw | 2
vignettes/RProtoBuf-unitTests.tex | 32
vignettes/RProtoBuf/RProtoBuf.Rnw | 165
vignettes/unitTests-results/RProtoBuf-unitTests.html | 48
vignettes/unitTests-results/RProtoBuf-unitTests.txt | 30
59 files changed, 2832 insertions(+), 2769 deletions(-)
Title: Data visualisation on maps
Diff between mapplots versions 1.2 dated 2012-12-19 and 1.4 dated 2013-07-15
Description: Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.
Author: Hans Gerritsen
Maintainer: Hans Gerritsen
mapplots-1.2/mapplots/R/geoTiff.R |only
mapplots-1.2/mapplots/man/geoTiff.Rd |only
mapplots-1.4/mapplots/DESCRIPTION | 16 +++-----
mapplots-1.4/mapplots/MD5 | 50 ++++++++++++--------------
mapplots-1.4/mapplots/R/legend.grid.R | 11 +++--
mapplots-1.4/mapplots/R/progressMsg.R | 8 ++--
mapplots-1.4/mapplots/R/write.grid.R | 39 ++++++++++++++------
mapplots-1.4/mapplots/man/add.pie.Rd | 6 +--
mapplots-1.4/mapplots/man/basemap.Rd | 10 ++---
mapplots-1.4/mapplots/man/draw.barplot2D.Rd | 12 +++---
mapplots-1.4/mapplots/man/draw.bubble.Rd | 10 ++---
mapplots-1.4/mapplots/man/draw.grid.Rd | 6 +--
mapplots-1.4/mapplots/man/draw.pie.Rd | 10 ++---
mapplots-1.4/mapplots/man/draw.rect.Rd | 2 -
mapplots-1.4/mapplots/man/draw.shape.Rd | 2 -
mapplots-1.4/mapplots/man/draw.xy.Rd | 20 +++++-----
mapplots-1.4/mapplots/man/ices.rect.Rd | 2 -
mapplots-1.4/mapplots/man/legend.box.Rd | 6 +--
mapplots-1.4/mapplots/man/legend.bubble.Rd | 12 +++---
mapplots-1.4/mapplots/man/legend.grid.Rd | 16 ++++----
mapplots-1.4/mapplots/man/legend.pie.Rd | 12 +++---
mapplots-1.4/mapplots/man/make.grid.Rd | 15 +++++--
mapplots-1.4/mapplots/man/make.multigrid.Rd | 4 +-
mapplots-1.4/mapplots/man/make.xyz.Rd | 10 ++---
mapplots-1.4/mapplots/man/mapplots-package.Rd | 2 -
mapplots-1.4/mapplots/man/progressMsg.Rd | 17 +++++---
mapplots-1.4/mapplots/man/write.grid.Rd | 25 +++++++------
27 files changed, 174 insertions(+), 149 deletions(-)
Title: Pedigree functions
Diff between kinship2 versions 1.5.0 dated 2013-06-06 and 1.5.4 dated 2013-07-15
Description: Routines to handle family data with a pedigree object. The
initial purpose was to create correlation structures that describe
family relationships such as kinship and identity-by-descent, which
can be used to model family data in mixed effects models, such as in the
coxme function. Also includes a tool for pedigree drawing which is
focused on producing compact layouts without intervention. Recent additions
include utilities to trim the pedigree object with various criteria, and
kinship for the X chromosome
Author: Terry Therneau, Elizabeth Atkinson, Jason Sinnwell, Daniel Schaid, Shannon McDonnell
Maintainer: Jason Sinnwell
kinship2-1.5.0/kinship2/R/pedtrim.R |only
kinship2-1.5.4/kinship2/DESCRIPTION | 30 ++++-----
kinship2-1.5.4/kinship2/MD5 | 20 +++---
kinship2-1.5.4/kinship2/R/kinship.R | 2
kinship2-1.5.4/kinship2/inst/NEWS.Rd | 8 ++
kinship2-1.5.4/kinship2/inst/doc/pedigree.pdf |binary
kinship2-1.5.4/kinship2/inst/doc/pedigree.snw | 2
kinship2-1.5.4/kinship2/noweb/all.nw | 2
kinship2-1.5.4/kinship2/noweb/kinship.Rnw | 2
kinship2-1.5.4/kinship2/tests/test.kinX.R | 27 +++++++-
kinship2-1.5.4/kinship2/tests/test.kinX.Rout.save | 73 ++++++++++++++++++++--
kinship2-1.5.4/kinship2/vignettes |only
12 files changed, 129 insertions(+), 37 deletions(-)
Title: R wrappers for EXPOKIT; other matrix functions
Diff between rexpokit versions 0.24 dated 2013-02-16 and 0.24.1 dated 2013-07-15
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 | 31 +++++----------
MD5 | 37 +++++++++---------
NEWS |only
R/rexpokit-package.R | 19 +++++----
R/rexpokit_v1.R | 74 ++++++++++++++++++++++++-------------
man/SparseM_coo_to_REXPOKIT_coo.Rd | 3 +
man/coo2mat.Rd | 3 +
man/expokit_dgexpv_Qmat.Rd | 6 ++-
man/expokit_dgexpv_wrapper.Rd | 6 ++-
man/expokit_dgpadm_Qmat.Rd | 3 +
man/expokit_dmexpv_Qmat.Rd | 3 +
man/expokit_dmexpv_wrapper.Rd | 6 ++-
man/expokit_mydgexpv_wrapper.Rd | 6 ++-
man/expokit_mydmexpv_wrapper.Rd | 6 ++-
man/expokit_wrapalldgexpv_tvals.Rd | 6 ++-
man/expokit_wrapalldmexpv_tvals.Rd | 6 ++-
man/findrows_w_all_zeros.Rd | 6 ++-
man/mat2coo_forloop.Rd | 3 +
man/rexpokit-package.Rd | 26 +++++++------
man/row_allzero_TF.Rd | 6 ++-
20 files changed, 149 insertions(+), 107 deletions(-)
Title: Rcmdr Plug-In for Business and Customer Analytics
Diff between RcmdrPlugin.BCA versions 0.9-5 dated 2013-02-28 and 0.9-6 dated 2013-07-15
More information about RcmdrPlugin.BCA at CRAN
Description: This package provides an Rcmdr "plug-in" to accompany the
book Customer and Business Analytics: Applied Data Mining for
Business Decision Making Using R by Daniel S. Putler and Robert
E. Krider.
Author: Dan Putler
Maintainer: Dan Putler
DESCRIPTION | 8 +++----
MD5 | 6 ++---
R/RcmdrPlugin.BCA.R | 45 ++++++++++++++++++++++++++++++++++++-----
man/RcmdrPlugin.BCA-package.Rd | 2 -
4 files changed, 48 insertions(+), 13 deletions(-)
Permanent link
Title: Log-concave Density Estimation in Arbitrary Dimensions
Diff between LogConcDEAD versions 1.5-5 dated 2012-06-12 and 1.5-6 dated 2013-07-15
Description: Computes a log-concave (maximum likelihood) estimator for
i.i.d. data in any number of dimensions.
Author: Madeleine Cule, Robert Gramacy, Richard Samworth, Yining Chen
Maintainer: Yining Chen
LogConcDEAD-1.5-5/LogConcDEAD/LICENSE |only
LogConcDEAD-1.5-5/LogConcDEAD/R/zzz.R |only
LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/algorithm.intRnw |only
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LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/intro.intRnw |only
LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/logconcdead.bib |only
LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/rglfig.png |only
LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/rgllog.png |only
LogConcDEAD-1.5-5/LogConcDEAD/inst/doc/usage.intRnw |only
LogConcDEAD-1.5-6/LogConcDEAD/DESCRIPTION | 13
LogConcDEAD-1.5-6/LogConcDEAD/MD5 | 39
LogConcDEAD-1.5-6/LogConcDEAD/NEWS | 3
LogConcDEAD-1.5-6/LogConcDEAD/R/plot.LogConcDEAD.R | 6
LogConcDEAD-1.5-6/LogConcDEAD/inst/doc/LogConcDEAD.R |only
LogConcDEAD-1.5-6/LogConcDEAD/inst/doc/LogConcDEAD.Rnw | 830 ++++++++++++++-
LogConcDEAD-1.5-6/LogConcDEAD/man/LogConcDEAD-package.Rd | 4
LogConcDEAD-1.5-6/LogConcDEAD/man/dslcd.Rd | 4
LogConcDEAD-1.5-6/LogConcDEAD/man/getinfolcd.Rd | 3
LogConcDEAD-1.5-6/LogConcDEAD/man/hatA.Rd | 4
LogConcDEAD-1.5-6/LogConcDEAD/man/interactive2D.Rd | 23
LogConcDEAD-1.5-6/LogConcDEAD/man/rslcd.Rd | 4
LogConcDEAD-1.5-6/LogConcDEAD/src/Makevars | 2
LogConcDEAD-1.5-6/LogConcDEAD/vignettes |only
26 files changed, 872 insertions(+), 63 deletions(-)
Title: A general-purpose package for dynamic report generation in R
Diff between knitr versions 1.2 dated 2013-04-11 and 1.3 dated 2013-07-15
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, reStructuredText and AsciiDoc. 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-1.2/knitr/inst/doc/knitr-intro.lyx |only
knitr-1.2/knitr/inst/doc/knitr-refcard.lyx |only
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knitr-1.2/knitr/inst/themes/eclipse.brew |only
knitr-1.2/knitr/inst/themes/highlight3.brew |only
knitr-1.3/knitr/DESCRIPTION | 124 +++----
knitr-1.3/knitr/FAQ.md | 6
knitr-1.3/knitr/MD5 | 370 +++++++++++-----------
knitr-1.3/knitr/NAMESPACE | 6
knitr-1.3/knitr/NEWS | 170 ++++++++++
knitr-1.3/knitr/R/block.R | 69 ++--
knitr-1.3/knitr/R/cache.R | 4
knitr-1.3/knitr/R/citation.R | 2
knitr-1.3/knitr/R/concordance.R | 6
knitr-1.3/knitr/R/defaults.R | 13
knitr-1.3/knitr/R/engine.R | 102 ++++--
knitr-1.3/knitr/R/header.R | 23 -
knitr-1.3/knitr/R/highlight-renderer.R | 6
knitr-1.3/knitr/R/highlight.R | 62 +--
knitr-1.3/knitr/R/hooks-asciidoc.R |only
knitr-1.3/knitr/R/hooks-extra.R | 10
knitr-1.3/knitr/R/hooks-html.R | 10
knitr-1.3/knitr/R/hooks-latex.R | 105 ++++--
knitr-1.3/knitr/R/hooks-md.R | 8
knitr-1.3/knitr/R/hooks-rst.R | 14
knitr-1.3/knitr/R/hooks.R | 2
knitr-1.3/knitr/R/output.R | 116 ++++--
knitr-1.3/knitr/R/pandoc.R | 19 -
knitr-1.3/knitr/R/parser.R | 50 +-
knitr-1.3/knitr/R/pattern.R | 68 ++--
knitr-1.3/knitr/R/plot.R | 88 +----
knitr-1.3/knitr/R/spin.R | 25 -
knitr-1.3/knitr/R/table.R |only
knitr-1.3/knitr/R/template.R | 39 --
knitr-1.3/knitr/R/themes-eclipse.R | 63 +--
knitr-1.3/knitr/R/themes.R | 74 +++-
knitr-1.3/knitr/R/utils-base64.R | 12
knitr-1.3/knitr/R/utils-conversion.R | 27 -
knitr-1.3/knitr/R/utils-sweave.R | 22 -
knitr-1.3/knitr/R/utils-vignettes.R | 2
knitr-1.3/knitr/R/utils.R | 27 -
knitr-1.3/knitr/R/zzz.R | 4
knitr-1.3/knitr/README.md | 104 +++++-
knitr-1.3/knitr/inst/bin/knit | 23 -
knitr-1.3/knitr/inst/doc/datatables.R |only
knitr-1.3/knitr/inst/doc/datatables.Rmd |only
knitr-1.3/knitr/inst/doc/datatables.html |only
knitr-1.3/knitr/inst/doc/knit_expand.R |only
knitr-1.3/knitr/inst/doc/knit_expand.Rmd |only
knitr-1.3/knitr/inst/doc/knit_expand.html |only
knitr-1.3/knitr/inst/doc/knitr-html.R | 8
knitr-1.3/knitr/inst/doc/knitr-html.Rhtml | 7
knitr-1.3/knitr/inst/doc/knitr-html.html | 128 ++-----
knitr-1.3/knitr/inst/doc/knitr-intro.R | 2
knitr-1.3/knitr/inst/doc/knitr-intro.Rnw | 6
knitr-1.3/knitr/inst/doc/knitr-intro.pdf |binary
knitr-1.3/knitr/inst/doc/knitr-markdown.R | 16
knitr-1.3/knitr/inst/doc/knitr-markdown.Rmd | 16
knitr-1.3/knitr/inst/doc/knitr-markdown.html | 186 ++++++++---
knitr-1.3/knitr/inst/doc/knitr-refcard.R | 2
knitr-1.3/knitr/inst/doc/knitr-refcard.Rnw | 4
knitr-1.3/knitr/inst/doc/knitr-refcard.pdf |binary
knitr-1.3/knitr/inst/examples/knit-all.R | 6
knitr-1.3/knitr/inst/examples/knitr-beamer.Rnw | 10
knitr-1.3/knitr/inst/examples/knitr-graphics.Rnw | 2
knitr-1.3/knitr/inst/examples/knitr-listings.Rnw | 2
knitr-1.3/knitr/inst/examples/knitr-manual.Rnw | 23 -
knitr-1.3/knitr/inst/examples/knitr-manual.lyx | 17 -
knitr-1.3/knitr/inst/examples/knitr-minimal.Rnw | 2
knitr-1.3/knitr/inst/examples/knitr-packages.bib | 20 -
knitr-1.3/knitr/inst/examples/knitr-spin.html | 89 ++---
knitr-1.3/knitr/inst/examples/knitr-subfloats.Rnw | 2
knitr-1.3/knitr/inst/examples/knitr-themes.Rnw | 34 --
knitr-1.3/knitr/inst/examples/knitr-themes.lyx | 343 +++-----------------
knitr-1.3/knitr/inst/examples/knitr-twocolumn.Rnw | 2
knitr-1.3/knitr/inst/misc/datatables.txt |only
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knitr-1.3/knitr/inst/misc/vignette.css | 35 --
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knitr-1.3/knitr/inst/themes/aiseered.css | 56 +--
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knitr-1.3/knitr/inst/themes/anotherdark.css | 52 ---
knitr-1.3/knitr/inst/themes/autumn.css | 52 ---
knitr-1.3/knitr/inst/themes/baycomb.css | 55 +--
knitr-1.3/knitr/inst/themes/bclear.css | 52 ---
knitr-1.3/knitr/inst/themes/biogoo.css | 53 +--
knitr-1.3/knitr/inst/themes/bipolar.css | 61 +--
knitr-1.3/knitr/inst/themes/blacknblue.css | 57 +--
knitr-1.3/knitr/inst/themes/bluegreen.css | 57 +--
knitr-1.3/knitr/inst/themes/breeze.css | 52 ---
knitr-1.3/knitr/inst/themes/bright.css | 54 +--
knitr-1.3/knitr/inst/themes/camo.css | 52 ---
knitr-1.3/knitr/inst/themes/candy.css | 53 +--
knitr-1.3/knitr/inst/themes/clarity.css | 52 ---
knitr-1.3/knitr/inst/themes/dante.css | 52 ---
knitr-1.3/knitr/inst/themes/darkblue.css | 55 +--
knitr-1.3/knitr/inst/themes/darkbone.css | 54 +--
knitr-1.3/knitr/inst/themes/darkness.css | 56 +--
knitr-1.3/knitr/inst/themes/darkslategray.css | 54 +--
knitr-1.3/knitr/inst/themes/darkspectrum.css | 54 +--
knitr-1.3/knitr/inst/themes/default.css | 78 +---
knitr-1.3/knitr/inst/themes/denim.css | 52 ---
knitr-1.3/knitr/inst/themes/dusk.css | 52 ---
knitr-1.3/knitr/inst/themes/earendel.css | 55 +--
knitr-1.3/knitr/inst/themes/easter.css | 58 +--
knitr-1.3/knitr/inst/themes/edit-anjuta.css | 54 +--
knitr-1.3/knitr/inst/themes/edit-eclipse.css | 55 +--
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knitr-1.3/knitr/inst/themes/edit-flashdevelop.css | 51 ---
knitr-1.3/knitr/inst/themes/edit-gedit.css | 53 +--
knitr-1.3/knitr/inst/themes/edit-jedit.css | 55 +--
knitr-1.3/knitr/inst/themes/edit-kwrite.css | 51 +--
knitr-1.3/knitr/inst/themes/edit-matlab.css | 52 ---
knitr-1.3/knitr/inst/themes/edit-msvs2008.css | 52 ---
knitr-1.3/knitr/inst/themes/edit-nedit.css | 55 +--
knitr-1.3/knitr/inst/themes/edit-vim-dark.css | 52 ---
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knitr-1.3/knitr/inst/themes/ekvoli.css | 58 +--
knitr-1.3/knitr/inst/themes/fine_blue.css | 57 +--
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knitr-1.3/knitr/inst/themes/kellys.css | 53 +--
knitr-1.3/knitr/inst/themes/leo.css | 53 +--
knitr-1.3/knitr/inst/themes/lucretia.css | 54 +--
knitr-1.3/knitr/inst/themes/manxome.css | 54 +--
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knitr-1.3/knitr/inst/themes/matrix.css | 52 +--
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knitr-1.3/knitr/inst/themes/navajo-night.css | 56 +--
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knitr-1.3/knitr/inst/themes/neon.css | 52 ---
knitr-1.3/knitr/inst/themes/night.css | 52 ---
knitr-1.3/knitr/inst/themes/nightshimmer.css | 52 ---
knitr-1.3/knitr/inst/themes/nuvola.css | 53 +--
knitr-1.3/knitr/inst/themes/olive.css | 53 +--
knitr-1.3/knitr/inst/themes/orion.css | 54 +--
knitr-1.3/knitr/inst/themes/oxygenated.css |only
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knitr-1.3/knitr/inst/themes/peaksea.css | 52 ---
knitr-1.3/knitr/inst/themes/print.css | 52 +--
knitr-1.3/knitr/inst/themes/rand01.css | 57 +--
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knitr-1.3/knitr/inst/themes/relaxedgreen.css | 52 ---
knitr-1.3/knitr/inst/themes/rootwater.css | 52 ---
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knitr-1.3/knitr/inst/themes/solarized-dark.css | 54 +--
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knitr-1.3/knitr/inst/themes/vampire.css | 57 +--
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knitr-1.3/knitr/man/Sweave2knitr.Rd | 4
knitr-1.3/knitr/man/all_patterns.Rd | 15
knitr-1.3/knitr/man/eclipse_theme.Rd | 2
knitr-1.3/knitr/man/hook_plot.Rd | 7
knitr-1.3/knitr/man/kable.Rd |only
knitr-1.3/knitr/man/knit.Rd | 40 +-
knitr-1.3/knitr/man/knit2html.Rd | 14
knitr-1.3/knitr/man/knit2pdf.Rd | 19 -
knitr-1.3/knitr/man/knit2wp.Rd | 4
knitr-1.3/knitr/man/knit_child.Rd | 9
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knitr-1.3/knitr/man/output_hooks.Rd | 10
knitr-1.3/knitr/man/pandoc.Rd | 5
knitr-1.3/knitr/man/pat_fun.Rd | 3
knitr-1.3/knitr/man/read_chunk.Rd | 16
knitr-1.3/knitr/man/read_rforge.Rd | 4
knitr-1.3/knitr/man/spin.Rd | 9
knitr-1.3/knitr/man/stitch.Rd | 2
knitr-1.3/knitr/man/wrap_rmd.Rd | 4
knitr-1.3/knitr/tests/run-all.R | 6
knitr-1.3/knitr/tests/testit |only
knitr-1.3/knitr/vignettes |only
183 files changed, 3093 insertions(+), 4341 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.8-3 dated 2013-06-14 and 0.8-4 dated 2013-07-15
Description: This package provides functions and a graphical user interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests, adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer
gMCP-0.8-3/gMCP/inst/doc/Makefile |only
gMCP-0.8-3/gMCP/inst/doc/figure |only
gMCP-0.8-3/gMCP/inst/doc/gMCP |only
gMCP-0.8-3/gMCP/inst/doc/literatur.bib |only
gMCP-0.8-3/gMCP/inst/doc/myIndex.ist |only
gMCP-0.8-3/gMCP/inst/doc/pictures |only
gMCP-0.8-4/gMCP/.Rinstignore | 7
gMCP-0.8-4/gMCP/DESCRIPTION | 17
gMCP-0.8-4/gMCP/MD5 | 265 ++++++++--
gMCP-0.8-4/gMCP/NAMESPACE | 4
gMCP-0.8-4/gMCP/NEWS | 26
gMCP-0.8-4/gMCP/R/calcPower.R | 16
gMCP-0.8-4/gMCP/R/convertFromOldClassDefinition.R | 7
gMCP-0.8-4/gMCP/R/rqmvnorm.R | 66 +-
gMCP-0.8-4/gMCP/R/startGUIs.R | 2
gMCP-0.8-4/gMCP/TODO | 45 +
gMCP-0.8-4/gMCP/inst/classes |only
gMCP-0.8-4/gMCP/inst/doc/AQuickStart.pdf |binary
gMCP-0.8-4/gMCP/inst/doc/gMCP.pdf |binary
gMCP-0.8-4/gMCP/inst/doc/parametric.pdf |binary
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/CreateGraphGUI.java | 15
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/DebugTextConsole.java | 4
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/MenuBarMGraph.java | 19
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/RControl.java | 16
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/dialogs/DialogConfIntEstVar.java | 2
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/Edge.java | 5
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/LaTeXTool.java | 13
gMCP-0.8-4/gMCP/inst/java-src/org/af/gMCP/gui/graph/Node.java | 11
gMCP-0.8-4/gMCP/inst/java/gsrmtp.jar |binary
gMCP-0.8-4/gMCP/inst/unitTests/runit.LaTeX.R | 9
gMCP-0.8-4/gMCP/inst/unitTests/runit.cover.everything.R |only
gMCP-0.8-4/gMCP/inst/unitTests/runit.power.R | 2
gMCP-0.8-4/gMCP/man/calcPower.Rd | 8
gMCP-0.8-4/gMCP/man/exampleGraphs.Rd | 5
gMCP-0.8-4/gMCP/man/graph2latex.Rd | 3
gMCP-0.8-4/gMCP/tests/doRUnit.R | 6
gMCP-0.8-4/gMCP/vignettes |only
37 files changed, 437 insertions(+), 136 deletions(-)
Title: C++ implementations of phylogenetic calculations
Diff between cladoRcpp versions 0.14 dated 2013-06-22 and 0.14.2 dated 2013-07-15
Description: This package implements in C++/Rcpp various cladogenesis-related calculations that are slow in pure R. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations.
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke
DESCRIPTION | 29 --
MD5 | 44 +--
NEWS |only
R/cladoRcpp-package.R | 29 ++
R/cladoRcpp.R | 112 +++++++-
inst |only
man/Rcpp_combn_zerostart.Rd | 12
man/areas_list_to_states_list_old.Rd | 18 +
man/cladoRcpp-package.Rd | 58 ++++
man/numstates_from_numareas.Rd | 25 +
man/rcpp_areas_list_to_states_list.Rd | 29 ++
man/rcpp_calc_anclikes_sp.Rd | 19 +
man/rcpp_calc_anclikes_sp_COOprobs.Rd | 19 +
man/rcpp_calc_anclikes_sp_COOweights_faster.Rd | 19 +
man/rcpp_calc_anclikes_sp_prebyte.Rd | 19 +
man/rcpp_calc_anclikes_sp_rowsums.Rd | 19 +
man/rcpp_calc_anclikes_sp_using_COOprobs.Rd | 12
man/rcpp_calc_rowsums_for_COOweights_columnar.Rd | 12
man/rcpp_calc_splitlikes_using_COOweights_columnar.Rd | 12
man/rcpp_convolve.Rd | 8
man/rcpp_states_list_to_DEmat.Rd | 54 +++-
src/basics.cpp | 28 +-
src/basics.h | 2
src/calc_anclikes_sp.cpp | 234 +++++++++++++-----
24 files changed, 675 insertions(+), 138 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-05-15 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-21 1.5
2012-12-04 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-18 1.2
2012-12-04 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-04-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 1.1-9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-12-04 0.30
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-25 0.9.2
2013-02-07 0.9.1