Title: 3D visualization device system (OpenGL)
Diff between rgl versions 0.92.880 dated 2012-05-08 and 0.92.891 dated 2012-07-17
Description: 3D visualization device (OpenGL)
Author: Daniel Adler
Maintainer: Duncan Murdoch
rgl-0.92.880/rgl/src/AGL |only
rgl-0.92.880/rgl/src/osx/osxgui.o |only
rgl-0.92.880/rgl/src/osx/osxlib.o |only
rgl-0.92.891/rgl/DESCRIPTION | 8
rgl-0.92.891/rgl/MD5 | 44 +--
rgl-0.92.891/rgl/R/cylinder3d.R | 65 +++++
rgl-0.92.891/rgl/R/enum.R | 3
rgl-0.92.891/rgl/R/r3d.rgl.R | 17 +
rgl-0.92.891/rgl/R/scene.R | 22 +
rgl-0.92.891/rgl/R/webGL.R | 437 ++++++++++++++++++++++---------------
rgl-0.92.891/rgl/inst/NEWS | 15 +
rgl-0.92.891/rgl/man/attributes.Rd | 4
rgl-0.92.891/rgl/man/cylinder3d.Rd | 30 +-
rgl-0.92.891/rgl/man/sprites.Rd | 36 ++-
rgl-0.92.891/rgl/src/SceneNode.hpp | 10
rgl-0.92.891/rgl/src/Shape.cpp | 20 +
rgl-0.92.891/rgl/src/Shape.hpp | 17 +
rgl-0.92.891/rgl/src/SpriteSet.cpp | 133 ++++++++---
rgl-0.92.891/rgl/src/SpriteSet.hpp | 14 +
rgl-0.92.891/rgl/src/api.cpp | 82 +++---
rgl-0.92.891/rgl/src/api.h | 2
rgl-0.92.891/rgl/src/scene.cpp | 48 ++--
rgl-0.92.891/rgl/src/scene.h | 12 -
rgl-0.92.891/rgl/src/types.h | 2
24 files changed, 682 insertions(+), 339 deletions(-)
Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.4.0 dated 2012-06-13 and 1.4.1 dated 2012-07-17
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
DESCRIPTION | 8 -
MD5 | 22 ++--
R/GetGeneTable.r | 136 +------------------------
R/check.package.r | 20 ++-
R/getListFromXML.r | 47 +++++---
R/getSNPInfo.master.docset.r | 2
R/getSNPInfo.singlebatch.trimmednames.docset.r | 13 +-
R/showMessages.r | 48 ++++++--
man/AdjustRangeAroundGene.Rd | 7 -
man/AnnotateDataframe.Rd | 6 -
man/AnnotateSNPFile.Rd | 4
man/MergeSNPsGenes.Rd | 4
12 files changed, 124 insertions(+), 193 deletions(-)
Title: Gaussian Processes for Poisson-noised Data
Diff between gppois versions 0.2-0 dated 2012-07-16 and 0.2-1 dated 2012-07-17
Description: Analyzes data using Gaussian processes. Supported noise
models include Gaussian or Poisson; the latter is handled using
the Anscombe transform to turn it into Gaussian noise.
Author: Charles R. Hogg III
Maintainer: Charles R. Hogg III
gppois-0.2-0/gppois/data/.RData |only
gppois-0.2-0/gppois/data/.Rhistory |only
gppois-0.2-0/gppois/extras |only
gppois-0.2-1/gppois/DESCRIPTION | 6 +++---
gppois-0.2-1/gppois/MD5 | 10 +++++-----
gppois-0.2-1/gppois/NEWS | 5 +++++
gppois-0.2-1/gppois/data/simXrayAu2nm.rda |binary
gppois-0.2-1/gppois/data/steelStrain.rda |binary
gppois-0.2-1/gppois/data/xrayTiO2np20nm.rda |binary
9 files changed, 13 insertions(+), 8 deletions(-)
Title: Zendesk API Wrapper
Diff between zendeskR versions 0.1 dated 2012-07-15 and 0.2 dated 2012-07-17
Description: This package provides an R wrapper for the Zendesk API
Author: Tanya Cashorali
Maintainer: Tanya Cashorali
DESCRIPTION | 9 +++++----
MD5 | 16 ++++++++--------
R/getAllTickets.R | 4 +---
R/getAllUsers.R | 3 ---
R/getOrganizations.R | 3 ---
R/getTicket.R | 3 ---
R/getTicketAudits.R | 3 ---
R/getTickets.R | 3 ---
README.md | 18 +++++++++++++++++-
9 files changed, 31 insertions(+), 31 deletions(-)
Title: Univariate Stratification of Survey Populations
Diff between stratification versions 2.1-1 dated 2012-06-30 and 2.1-2 dated 2012-07-17
More information about stratification at CRAN
Description: This package performs univariate stratification of survey
populations. The main function implements a generalization of
the Lavallee-Hidiroglou method of stratum construction. The
generalized method takes into account a discrepancy between the
stratification variable and the survey variable. The
determination of the optimal boundaries also incorporate, if
desired, an anticipated non-response, a take-all stratum for
large units, and a take-none stratum for small units. The well
known cumulative root frequency rule of Dalenius and Hodges and
the geometric rule of Gunning and Horgan are also implemented.
Author: Sophie Baillargeon
Maintainer: Sophie Baillargeon
DESCRIPTION | 8 -
MD5 | 25 ++-
NEWS | 18 ++
R/internals.R | 60 +++++----
R/strata.LH.R | 8 -
R/strata.bh.R | 2
R/strata.cumrootf.R | 4
R/strata.geo.R | 2
inst |only
man/SHS.Rd | 64 ++++-----
man/strata.LH.Rd | 273 ++++++++++++++++++++++--------------------
man/strata.rule.Rd | 10 -
man/stratification-package.Rd | 4
tests |only
14 files changed, 263 insertions(+), 215 deletions(-)
Permanent link
Title: functions for mixed stock analysis
Diff between mixstock versions 0.9.5 dated 2012-03-21 and 0.9.5.1 dated 2012-07-17
Description: mixed stock analysis functions
Author: Ben Bolker
Maintainer: Ben Bolker
mixstock-0.9.5.1/mixstock/DESCRIPTION | 8 ++++----
mixstock-0.9.5.1/mixstock/MD5 | 9 ++++-----
mixstock-0.9.5.1/mixstock/inst/NEWS.Rd | 7 ++++++-
mixstock-0.9.5.1/mixstock/inst/doc/mixstock.pdf |binary
mixstock-0.9.5.1/mixstock/vignettes/wbugs_cache.RData |binary
mixstock-0.9.5/mixstock/tests/.RData |only
mixstock-0.9.5/mixstock/vignettes/.Rhistory |only
mixstock-0.9.5/mixstock/vignettes/NEWS.Rd |only
8 files changed, 14 insertions(+), 10 deletions(-)
Title: Tools for general maximum likelihood estimation
Diff between bbmle versions 1.0.4.1 dated 2012-01-28 and 1.0.5.1 dated 2012-07-17
Description: Methods and functions for fitting maximum likelihood
models in R. This package modifies and extends the mle classes
in the stats4 package.
Author: Ben Bolker
Maintainer: Ben Bolker
bbmle-1.0.4.1/bbmle/NEWS |only
bbmle-1.0.4.1/bbmle/tests/.RData |only
bbmle-1.0.4.1/bbmle/tests/.Rhistory |only
bbmle-1.0.4.1/bbmle/vignettes/.Rhistory |only
bbmle-1.0.4.1/bbmle/vignettes/mle2-basegraphprofplot.pdf |only
bbmle-1.0.4.1/bbmle/vignettes/mle2-gg1plot.pdf |only
bbmle-1.0.4.1/bbmle/vignettes/mle2-ggplotprof.pdf |only
bbmle-1.0.4.1/bbmle/vignettes/mle2-latticeprof.pdf |only
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bbmle-1.0.4.1/bbmle/vignettes/mle2-profplotsigma.pdf |only
bbmle-1.0.4.1/bbmle/vignettes/mle2-profplottheta.pdf |only
bbmle-1.0.5.1/bbmle/DESCRIPTION | 14
bbmle-1.0.5.1/bbmle/MD5 | 80 ++-
bbmle-1.0.5.1/bbmle/NAMESPACE | 22
bbmle-1.0.5.1/bbmle/R/confint.R | 31 -
bbmle-1.0.5.1/bbmle/R/dists.R | 9
bbmle-1.0.5.1/bbmle/R/mle.R | 194 ++------
bbmle-1.0.5.1/bbmle/R/mle2-methods.R | 4
bbmle-1.0.5.1/bbmle/R/profile.R | 50 +-
bbmle-1.0.5.1/bbmle/R/slice.R |only
bbmle-1.0.5.1/bbmle/TODO | 1
bbmle-1.0.5.1/bbmle/inst/NEWS.Rd | 30 +
bbmle-1.0.5.1/bbmle/inst/doc/mle2.Rnw | 283 ++++++------
bbmle-1.0.5.1/bbmle/inst/doc/mle2.pdf |binary
bbmle-1.0.5.1/bbmle/inst/doc/quasi.pdf |binary
bbmle-1.0.5.1/bbmle/man/mle-class.Rd | 34 +
bbmle-1.0.5.1/bbmle/man/mle2.Rd | 4
bbmle-1.0.5.1/bbmle/man/profile-methods.Rd | 2
bbmle-1.0.5.1/bbmle/man/profile.mle-class.Rd | 76 ++-
bbmle-1.0.5.1/bbmle/man/slice.Rd | 97 +++-
bbmle-1.0.5.1/bbmle/oldsave |only
bbmle-1.0.5.1/bbmle/tests/gradient_vecpar_profile.R |only
bbmle-1.0.5.1/bbmle/tests/gradient_vecpar_profile.Rout.save |only
bbmle-1.0.5.1/bbmle/tests/methods.R | 2
bbmle-1.0.5.1/bbmle/tests/profbound.R |only
bbmle-1.0.5.1/bbmle/vignettes/Makefile | 2
bbmle-1.0.5.1/bbmle/vignettes/mle2.Rnw | 283 ++++++------
37 files changed, 753 insertions(+), 465 deletions(-)
Title: Auxiliary functions to estimate centers of biodiversity
Diff between sperich versions 1.3-7 dated 2012-03-02 and 1.4-0 dated 2012-07-17
Description: Provides some easy-to-use functions to interpolate species
range based on species occurences and to estimate centers of
biodiversity
Author: Maximilian Lange
Maintainer: Maximilian Lange
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/species.range.R | 12 +++++++-----
R/species.richness.CV.R | 10 +++++-----
R/species.richness.R | 4 ++--
R/species.richness.main.R | 5 +----
man/species.richness.main.Rd | 7 +++----
7 files changed, 29 insertions(+), 31 deletions(-)
Title: Hourly interpolation of multiple temperature daily series
Diff between Interpol.T versions 1.0 dated 2012-02-01 and 2.0 dated 2012-07-17
Description: Hourly interpolation of daily minimum and maximum
temperature series. Carries out interpolation on multiple
series ad once. Requires some hourly series for calibration
(alternatively can use default calibration table).
Author: Emanuele Eccel & Emanuele Cordano
Maintainer:
Interpol.T-1.0/Interpol.T/00check.log |only
Interpol.T-1.0/Interpol.T/R/Interpol.T-package.R |only
Interpol.T-1.0/Interpol.T/inst/doc/hourly_interp_T_xmpls.R |only
Interpol.T-2.0/Interpol.T/DESCRIPTION | 14 -
Interpol.T-2.0/Interpol.T/MD5 | 29 +-
Interpol.T-2.0/Interpol.T/R/F_Mo.Th.Ra.R | 12 -
Interpol.T-2.0/Interpol.T/R/F_Th_int_series.R | 48 ++--
Interpol.T-2.0/Interpol.T/R/F_Th_interp.R | 74 +++---
Interpol.T-2.0/Interpol.T/R/F_par_calibration.R | 4
Interpol.T-2.0/Interpol.T/R/F_plot_meas_sim.R | 4
Interpol.T-2.0/Interpol.T/R/F_shape_calibration.R | 138 +------------
Interpol.T-2.0/Interpol.T/R/InterpolT-package.R |only
Interpol.T-2.0/Interpol.T/data/Trentino_hourly_T.rda |binary
Interpol.T-2.0/Interpol.T/inst/doc/examples |only
Interpol.T-2.0/Interpol.T/man/Interpol.T-package.Rd | 4
Interpol.T-2.0/Interpol.T/man/Th_int_series.Rd | 28 +-
Interpol.T-2.0/Interpol.T/man/Th_interp.Rd | 62 ++---
Interpol.T-2.0/Interpol.T/man/shape_calibration.Rd | 34 ---
18 files changed, 163 insertions(+), 288 deletions(-)
Title: Compound Poisson linear models
Diff between cplm versions 0.5-1 dated 2012-01-07 and 0.6-1 dated 2012-07-17
Description: Likelihood-based and Bayesian methods for various compound
Poisson linear models.
Author: Wayne Zhang
Maintainer: Wayne Zhang
cplm-0.5-1/cplm/R/bcpglm.R |only
cplm-0.5-1/cplm/R/bcpglmm.R |only
cplm-0.5-1/cplm/data/fineroot.RData |only
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cplm-0.5-1/cplm/man/prior.Rd |only
cplm-0.5-1/cplm/src/bcpglm_lat.c |only
cplm-0.5-1/cplm/src/bcpglm_tw.c |only
cplm-0.5-1/cplm/src/bcpglmm_lat.c |only
cplm-0.5-1/cplm/src/bcpglmm_tw.c |only
cplm-0.5-1/cplm/src/cpglmm_lap.c |only
cplm-0.5-1/cplm/src/cplm.h |only
cplm-0.5-1/cplm/src/latent_sim.c |only
cplm-0.5-1/cplm/test/test_bcpglm.R |only
cplm-0.5-1/cplm/test/test_bcpglmm.R |only
cplm-0.5-1/cplm/test/test_cpglmm2.R |only
cplm-0.6-1/cplm/DESCRIPTION | 15
cplm-0.6-1/cplm/MD5 | 89 +-
cplm-0.6-1/cplm/NAMESPACE | 18
cplm-0.6-1/cplm/NEWS | 37
cplm-0.6-1/cplm/R/bcplm.R |only
cplm-0.6-1/cplm/R/classMethods.R | 1102 +++++++++++++---------------
cplm-0.6-1/cplm/R/cpglm.R | 111 +-
cplm-0.6-1/cplm/R/cpglmm.R | 346 ++++----
cplm-0.6-1/cplm/R/gini.R |only
cplm-0.6-1/cplm/R/spline.R | 334 ++++++++
cplm-0.6-1/cplm/R/utilities.R | 186 ++--
cplm-0.6-1/cplm/R/zcpglm.R |only
cplm-0.6-1/cplm/data/AutoClaim.RData |only
cplm-0.6-1/cplm/data/ClaimTriangle.RData |only
cplm-0.6-1/cplm/data/FineRoot.RData |only
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cplm-0.6-1/cplm/man/cpglm.Rd | 43 -
cplm-0.6-1/cplm/man/cpglmm.Rd | 51 -
cplm-0.6-1/cplm/man/cplm-package.Rd | 76 +
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cplm-0.6-1/cplm/man/getF.Rd |only
cplm-0.6-1/cplm/man/gini.Rd |only
cplm-0.6-1/cplm/man/zcpglm.Rd |only
cplm-0.6-1/cplm/src/Makevars | 2
cplm-0.6-1/cplm/src/bcplm.c |only
cplm-0.6-1/cplm/src/bcplm.h |only
cplm-0.6-1/cplm/src/common.h |only
cplm-0.6-1/cplm/src/cpglmm.c |only
cplm-0.6-1/cplm/src/cpglmm.h |only
cplm-0.6-1/cplm/src/init.c | 16
cplm-0.6-1/cplm/src/mh.c |only
cplm-0.6-1/cplm/src/mh.h |only
cplm-0.6-1/cplm/src/tweedie.c |only
cplm-0.6-1/cplm/src/tweedie.h |only
cplm-0.6-1/cplm/src/utilities.c | 1155 ++----------------------------
cplm-0.6-1/cplm/src/utilities.h |only
cplm-0.6-1/cplm/test/test_bcplm.R |only
cplm-0.6-1/cplm/test/test_cpglm.R | 23
cplm-0.6-1/cplm/test/test_cpglmm.R | 293 +++++++
cplm-0.6-1/cplm/test/test_gini.R |only
cplm-0.6-1/cplm/test/test_zcpglm.R |only
cplm-0.6-1/cplm/vignettes |only
63 files changed, 1805 insertions(+), 2092 deletions(-)
Title: A general-purpose package for dynamic report generation in R
Diff between knitr versions 0.6.3 dated 2012-06-22 and 0.7 dated 2012-07-17
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 or inspired by Sweave, cacheSweave,
pgfSweave, brew and decumar.
Author: Yihui Xie
Maintainer: Yihui Xie
knitr-0.6.3/knitr/R/eclipse.R |only
knitr-0.6.3/knitr/R/highlight-00_sizes.R |only
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knitr-0.7/knitr/DESCRIPTION | 28
knitr-0.7/knitr/MD5 | 140 +-
knitr-0.7/knitr/Makefile |only
knitr-0.7/knitr/NAMESPACE | 10
knitr-0.7/knitr/NEWS | 1105 ++++++++++++----------
knitr-0.7/knitr/NEWS.md |only
knitr-0.7/knitr/R/block.R | 42
knitr-0.7/knitr/R/cache.R | 95 +
knitr-0.7/knitr/R/citation.R | 9
knitr-0.7/knitr/R/concordance.R | 8
knitr-0.7/knitr/R/defaults.R | 74 -
knitr-0.7/knitr/R/engine.R | 73 +
knitr-0.7/knitr/R/header.R | 20
knitr-0.7/knitr/R/highlight-css.R | 184 +--
knitr-0.7/knitr/R/highlight-renderer.R | 432 --------
knitr-0.7/knitr/R/highlight.R | 40
knitr-0.7/knitr/R/hooks-extra.R | 39
knitr-0.7/knitr/R/hooks-html.R | 117 +-
knitr-0.7/knitr/R/hooks-latex.R | 66 -
knitr-0.7/knitr/R/hooks-md.R | 35
knitr-0.7/knitr/R/hooks-rst.R | 7
knitr-0.7/knitr/R/hooks.R | 2
knitr-0.7/knitr/R/output.R | 83 -
knitr-0.7/knitr/R/parser.R | 7
knitr-0.7/knitr/R/pattern.R | 7
knitr-0.7/knitr/R/plot.R | 183 ++-
knitr-0.7/knitr/R/spin.R | 12
knitr-0.7/knitr/R/themes-eclipse.R |only
knitr-0.7/knitr/R/themes.R | 8
knitr-0.7/knitr/R/utils-base64.R |only
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knitr-0.7/knitr/R/utils.R | 134 ++
knitr-0.7/knitr/inst/doc/knitr-intro.pdf |binary
knitr-0.7/knitr/inst/examples/knitr-beamer.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-graphics.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-lang.Rmd | 55 +
knitr-0.7/knitr/inst/examples/knitr-lang.md | 101 +-
knitr-0.7/knitr/inst/examples/knitr-listings.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-manual.Rnw | 18
knitr-0.7/knitr/inst/examples/knitr-manual.lyx | 20
knitr-0.7/knitr/inst/examples/knitr-minimal.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-minimal.Rrst | 2
knitr-0.7/knitr/inst/examples/knitr-minimal.rst | 12
knitr-0.7/knitr/inst/examples/knitr-packages.bib | 32
knitr-0.7/knitr/inst/examples/knitr-slides.md | 38
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knitr-0.7/knitr/inst/examples/knitr-subfloats.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-themes.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-twocolumn.Rnw | 2
knitr-0.7/knitr/inst/examples/knitr-upload.md | 17
knitr-0.7/knitr/inst/misc/knitr-template.Rhtml | 19
knitr-0.7/knitr/inst/misc/knitr-template.Rmd | 20
knitr-0.7/knitr/inst/misc/knitr-template.Rnw | 33
knitr-0.7/knitr/inst/misc/knitr.sty | 11
knitr-0.7/knitr/inst/opencpu/apps/index.html | 2
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knitr-0.7/knitr/inst/tests/test-parser.R | 5
knitr-0.7/knitr/inst/tests/test-patterns.R | 1
knitr-0.7/knitr/inst/tests/test-plot.R |only
knitr-0.7/knitr/inst/tests/test-utils.R | 21
knitr-0.7/knitr/man/chunk_hook.Rd | 10
knitr-0.7/knitr/man/dep_auto.Rd |only
knitr-0.7/knitr/man/dep_prev.Rd |only
knitr-0.7/knitr/man/fig_path.Rd | 6
knitr-0.7/knitr/man/hook_animation.Rd |only
knitr-0.7/knitr/man/hook_plot.Rd | 4
knitr-0.7/knitr/man/image_uri.Rd |only
knitr-0.7/knitr/man/knit.Rd | 15
knitr-0.7/knitr/man/knit2html.Rd | 17
knitr-0.7/knitr/man/knit2pdf.Rd | 22
knitr-0.7/knitr/man/knit_child.Rd | 4
knitr-0.7/knitr/man/knit_engines.Rd | 8
knitr-0.7/knitr/man/opts_template.Rd |only
knitr-0.7/knitr/man/rand_seed.Rd |only
knitr-0.7/knitr/man/rst2pdf.Rd |only
knitr-0.7/knitr/man/spin.Rd | 12
81 files changed, 1938 insertions(+), 1541 deletions(-)