Title: Copy Number Estimation from Tumor Genome Sequencing Data
Description: Tools to analyze genomic sequencing data from
paired normal-tumor samples, including cellularity and ploidy estimation; mutation
and copy number (allele-specific and total copy number) detection, quantification
and visualization.
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero <favero@cbs.dtu.dk>
Diff between sequenza versions 2.1.1 dated 2015-01-27 and 2.1.2 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NAMESPACE | 46 +++++++++++++++++++++++++++++++++++++++++++++- NEWS | 4 ++++ R/next.R | 12 +++++++++++- build/vignette.rds |binary data/CP.example.RData |binary data/example.seqz.rda |binary inst/doc/sequenza.pdf |binary 9 files changed, 72 insertions(+), 14 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.8 dated 2015-08-30 and 0.8.1 dated 2015-10-09
rmarkdown-0.8.1/rmarkdown/DESCRIPTION | 8 - rmarkdown-0.8.1/rmarkdown/MD5 | 32 +++-- rmarkdown-0.8.1/rmarkdown/R/html_dependencies.R | 55 ++-------- rmarkdown-0.8.1/rmarkdown/R/html_resources.R | 24 ++-- rmarkdown-0.8.1/rmarkdown/R/output_format.R | 12 +- rmarkdown-0.8.1/rmarkdown/R/render.R | 3 rmarkdown-0.8.1/rmarkdown/R/word_document.R | 12 +- rmarkdown-0.8.1/rmarkdown/inst/NEWS |only rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/default.html | 2 rmarkdown-0.8.1/rmarkdown/inst/rmd/ioslides/ioslides-13.5.1/js/slide-deck.js | 2 rmarkdown-0.8.1/rmarkdown/man/knitr_options.Rd | 8 + rmarkdown-0.8.1/rmarkdown/man/word_document.Rd | 10 + rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/csvs |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/directory-refs.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/empty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/nonempty |only rmarkdown-0.8.1/rmarkdown/tests/testthat/resources/resource-files.Rmd |only rmarkdown-0.8.1/rmarkdown/tests/testthat/test-resources.R | 45 ++++++++ rmarkdown-0.8/rmarkdown/NEWS |only 19 files changed, 132 insertions(+), 81 deletions(-)
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between paco versions 0.2.1 dated 2015-07-18 and 0.2.2 dated 2015-10-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/PACo.r | 8 +++++--- R/add_pcoord.r | 16 ++++++++-------- R/paco_links.r | 1 + man/PACo.Rd | 4 +++- man/add_pcoord.Rd | 4 +++- 7 files changed, 29 insertions(+), 22 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-62 dated 2015-08-24 and 0.1-63 dated 2015-10-09
Surrogate-0.1-62/Surrogate/R/SummaryTrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/R/plot.TrialLevelContCont.R |only Surrogate-0.1-62/Surrogate/man/TrialLevelContCont.Rd |only Surrogate-0.1-62/Surrogate/man/plot.TrialLevelContCont.Rd |only Surrogate-0.1-63/Surrogate/DESCRIPTION | 8 Surrogate-0.1-63/Surrogate/MD5 | 80 +++-- Surrogate-0.1-63/Surrogate/NAMESPACE | 27 + Surrogate-0.1-63/Surrogate/NEWS | 6 Surrogate-0.1-63/Surrogate/R/FixedBinBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedBinContIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContBinIT.r |only Surrogate-0.1-63/Surrogate/R/FixedContContIT.r | 27 - Surrogate-0.1-63/Surrogate/R/ICABinBin.R | 142 ++++------ Surrogate-0.1-63/Surrogate/R/MarginalProbs.R | 2 Surrogate-0.1-63/Surrogate/R/Pred.TrialT.ContCont.R |only Surrogate-0.1-63/Surrogate/R/Prentice.R |only Surrogate-0.1-63/Surrogate/R/SummaryITContCont.R | 4 Surrogate-0.1-63/Surrogate/R/SummaryTrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/TwoStageSurvSurv.R | 14 Surrogate-0.1-63/Surrogate/R/UnifixedContCont.R | 4 Surrogate-0.1-63/Surrogate/R/UnimixedContCont.R | 7 Surrogate-0.1-63/Surrogate/R/plot.BinContCombnIT.R |only Surrogate-0.1-63/Surrogate/R/plot.InfoTheoretic.R | 1 Surrogate-0.1-63/Surrogate/R/plot.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/plot.TrialLevelMA.R |only Surrogate-0.1-63/Surrogate/R/summary.SurvSurv.R |only Surrogate-0.1-63/Surrogate/R/summary.TrialLevelIT.R |only Surrogate-0.1-63/Surrogate/R/summary.TwoStageSurvSurv.R | 6 Surrogate-0.1-63/Surrogate/R/summaryBinContCombnIT.R |only Surrogate-0.1-63/Surrogate/data/Schizo.rda |binary Surrogate-0.1-63/Surrogate/man/FixedBinBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedBinContIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContBinIT.Rd |only Surrogate-0.1-63/Surrogate/man/FixedContContIT.Rd | 13 Surrogate-0.1-63/Surrogate/man/ICABinBin.Rd | 32 +- Surrogate-0.1-63/Surrogate/man/MixedContContIT.Rd | 5 Surrogate-0.1-63/Surrogate/man/Plot.PredTrialTContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Pred.TrialT.ContCont.Rd |only Surrogate-0.1-63/Surrogate/man/Prentice.Rd |only Surrogate-0.1-63/Surrogate/man/Schizo.Rd | 7 Surrogate-0.1-63/Surrogate/man/SurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/TwoStageSurvSurv.Rd | 6 Surrogate-0.1-63/Surrogate/man/UnifixedContCont.Rd | 5 Surrogate-0.1-63/Surrogate/man/UnimixedContCont.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticBinCombn.Rd |only Surrogate-0.1-63/Surrogate/man/plot.InformationTheoreticSurvSurv.Rd |only Surrogate-0.1-63/Surrogate/man/plot.MetaAnalytic.Rd | 3 Surrogate-0.1-63/Surrogate/man/plot.TrialLevelIT.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TrialLevelMA.Rd |only Surrogate-0.1-63/Surrogate/man/plot.TwoStageSurvSurv.Rd | 12 Surrogate-0.1-63/Surrogate/man/summary.gen.Rd | 20 + 58 files changed, 261 insertions(+), 173 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information: http://upwell.pfeg.noaa.gov/erddap/information.html.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.2.0 dated 2015-07-01 and 0.3.0 dated 2015-10-09
rerddap-0.2.0/rerddap/R/cache.R |only rerddap-0.2.0/rerddap/tests/testthat/test-griddap.R |only rerddap-0.3.0/rerddap/DESCRIPTION | 6 rerddap-0.3.0/rerddap/MD5 | 62 ++++--- rerddap-0.3.0/rerddap/NAMESPACE | 20 ++ rerddap-0.3.0/rerddap/NEWS | 20 ++ rerddap-0.3.0/rerddap/R/cache_delete.R |only rerddap-0.3.0/rerddap/R/cache_details.R |only rerddap-0.3.0/rerddap/R/cache_list.R |only rerddap-0.3.0/rerddap/R/convert_time.R | 2 rerddap-0.3.0/rerddap/R/convert_units.R | 2 rerddap-0.3.0/rerddap/R/fipscounty.R | 2 rerddap-0.3.0/rerddap/R/grid.R | 19 +- rerddap-0.3.0/rerddap/R/info.R | 3 rerddap-0.3.0/rerddap/R/keywords.R | 2 rerddap-0.3.0/rerddap/R/ncdf_helpers.R | 20 ++ rerddap-0.3.0/rerddap/R/rerddap-package.r | 6 rerddap-0.3.0/rerddap/R/search_adv.R | 1 rerddap-0.3.0/rerddap/R/table.R | 8 - rerddap-0.3.0/rerddap/README.md | 2 rerddap-0.3.0/rerddap/build/vignette.rds |binary rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.Rmd | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/doc/rerddap_vignette.html | 148 +++++++++---------- rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.Rmd | 15 + rerddap-0.3.0/rerddap/inst/vign/rerddap_vignette.md | 148 +++++++++---------- rerddap-0.3.0/rerddap/man/cache_delete.Rd |only rerddap-0.3.0/rerddap/man/cache_details.Rd |only rerddap-0.3.0/rerddap/man/cache_list.Rd | 29 +-- rerddap-0.3.0/rerddap/man/convert_time.Rd | 2 rerddap-0.3.0/rerddap/man/convert_units.Rd | 2 rerddap-0.3.0/rerddap/man/fipscounty.Rd | 2 rerddap-0.3.0/rerddap/man/griddap.Rd | 10 + rerddap-0.3.0/rerddap/man/key_words.Rd | 2 rerddap-0.3.0/rerddap/man/tabledap.Rd | 5 rerddap-0.3.0/rerddap/tests/testthat/test-griddap.r |only rerddap-0.3.0/rerddap/vignettes/rerddap_vignette.Rmd | 148 +++++++++---------- 36 files changed, 456 insertions(+), 378 deletions(-)
Title: Gene-Level Statistics for Pedigree Data
Description: Gene-level association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 2.7 dated 2015-08-03 and 2.9 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/pedgene.R | 25 ++++++++++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 5 +++++ tests/test.pedgene.expanded.R | 5 +++++ tests/test.pedgene.expanded.Rout.save | 25 +++++++++++++++++-------- 7 files changed, 53 insertions(+), 27 deletions(-)
Title: Work with 'GitHub' 'Gists'
Description: Work with 'GitHub' 'gists' from 'R' (e.g.,
http://en.wikipedia.org/wiki/GitHub#Gist,
https://help.github.com/articles/about-gists/). A 'gist' is simply one or
more files with code/text/images/etc. This package allows the user to
create new 'gists', update 'gists' with new files, rename files, delete files,
get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in
your default browser, get embed code for a 'gist', list 'gist' 'commits', and
get rate limit information when 'authenticated'. Some requests require
authentication and some do not. 'Gists' website: https://gist.github.com/.
Author: Ramnath Vaidyanathan [aut],
Karthik Ram [aut],
Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between gistr versions 0.3.0 dated 2015-07-03 and 0.3.4 dated 2015-10-09
gistr-0.3.0/gistr/tests/localtests/figure |only gistr-0.3.0/gistr/tests/testthat/figure |only gistr-0.3.4/gistr/DESCRIPTION | 8 - gistr-0.3.4/gistr/MD5 | 34 ++---- gistr-0.3.4/gistr/NAMESPACE | 2 gistr-0.3.4/gistr/R/gist_create.R | 19 ++- gistr-0.3.4/gistr/R/gist_create_git.R |only gistr-0.3.4/gistr/R/gist_create_obj.R | 2 gistr-0.3.4/gistr/R/gistr-package.R | 45 ++++++-- gistr-0.3.4/gistr/R/tabl.R | 90 ++++++++++++---- gistr-0.3.4/gistr/README.md | 2 gistr-0.3.4/gistr/build/vignette.rds |binary gistr-0.3.4/gistr/inst/ignore/gist_create_git.R | 21 +++ gistr-0.3.4/gistr/man/create_gists.Rd |only gistr-0.3.4/gistr/man/gist_create.Rd | 2 gistr-0.3.4/gistr/man/gist_create_git.Rd |only gistr-0.3.4/gistr/man/gist_create_obj.Rd | 2 gistr-0.3.4/gistr/man/tabl.Rd | 33 +++++ gistr-0.3.4/gistr/tests/testthat/test-gist_create_git.R |only 19 files changed, 198 insertions(+), 62 deletions(-)
Title: Fishery Science Methods and Models in R
Description: Fishery science methods and models from published literature and contributions from colleagues.
Author: Gary A. Nelson <gary.nelson@state.ma.us>
Maintainer: Gary A. Nelson <gary.nelson@state.ma.us>
Diff between fishmethods versions 1.8-0 dated 2015-05-28 and 1.9-0 dated 2015-10-09
DESCRIPTION | 10 - MD5 | 20 ++- NAMESPACE | 14 ++ R/agesurv.R | 25 ++++ R/astrocalc4r.R |only R/bhnoneq.R | 271 +++++++++++++++++++++++++++++------------------------ R/cpuekapp.R |only data/kappenman.rda |only man/agesurv.Rd | 12 +- man/astrocalc4r.Rd |only man/bheq2.Rd | 2 man/bhnoneq.Rd | 27 ++--- man/cpuekapp.Rd |only man/kappenman.Rd |only 14 files changed, 231 insertions(+), 150 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.31.3 dated 2015-07-09 and 1.31.4 dated 2015-10-09
DESCRIPTION | 8 +++--- MD5 | 22 ++++++++--------- R/CA.R | 9 +++--- R/FAMD.R | 3 +- R/HCPC.R | 4 +-- R/MCA.R | 7 +++-- R/MFA.R | 5 ++- R/PCA.R | 4 +-- R/plot.HCPC.R | 2 - R/plotellipses.r | 9 ++++-- inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary 12 files changed, 40 insertions(+), 33 deletions(-)
Title: Markov Model for the Online Multi-Channel Attribution Problem
Description: Advertisers use a variety of online marketing channels to reach consumers and they want to know the degree each channel contributes to their marketing success. It's called the online multi-channel attribution problem. This package contains a probabilistic algorithm for the attribution problem. The model uses a k-order Markov representation to identifying structural correlations in the customer journey data. The package also contains three heuristic algorithms (first-touch, last-touch and linear-touch approach) for the same problem. The algorithms are implemented in C++. For customizations or interest in other statistical methodologies for web data analysis please contact <davide.altomare@gmail.com>.
Author: Davide Altomare and David Loris
Maintainer: Davide Altomare <davide.altomare@gmail.com>
Diff between ChannelAttribution versions 1.1 dated 2015-09-16 and 1.2 dated 2015-10-09
ChannelAttribution-1.1/ChannelAttribution/man/Dy.Rd |only ChannelAttribution-1.1/ChannelAttribution/vignettes |only ChannelAttribution-1.2/ChannelAttribution/DESCRIPTION | 10 ChannelAttribution-1.2/ChannelAttribution/MD5 | 21 ChannelAttribution-1.2/ChannelAttribution/R/ChannelAttribution.R | 21 ChannelAttribution-1.2/ChannelAttribution/data/PathData.rda |binary ChannelAttribution-1.2/ChannelAttribution/man/ChannelAttribution-package.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/man/Data.Rd |only ChannelAttribution-1.2/ChannelAttribution/man/heuristic_models.Rd | 16 ChannelAttribution-1.2/ChannelAttribution/man/markov_model.Rd | 33 ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.cpp | 1026 ++++++---- ChannelAttribution-1.2/ChannelAttribution/src/ChannelAttribution.h | 8 12 files changed, 741 insertions(+), 427 deletions(-)
More information about ChannelAttribution at CRAN
Permanent link
Title: Amdahl's Profiler, Directed Optimization Made Easy
Description: Assists the evaluation of whether and
where to focus code optimization, using Amdahl's law and visual aids
based on line profiling. Amdahl's profiler organises profiling output
files (including memory profiling) in a visually appealing way.
It is meant to help to balance development
vs. execution time by helping to identify the most promising sections
of code to optimize and projecting potential gains. The package is
an addition to R's standard profiling tools and is not a wrapper for them.
Author: Marco D. Visser
Maintainer: Marco D. Visser <marco.d.visser@gmail.com>
Diff between aprof versions 0.2.5 dated 2015-07-20 and 0.3.1 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 12 - R/aprof.R | 416 +++++++++++++++++++++++++++---------------------- man/aprof.Rd | 50 +++-- man/plot.Rd | 10 - man/print.Rd | 2 man/readLineDensity.Rd | 4 7 files changed, 283 insertions(+), 223 deletions(-)
Title: An R Package for Quantification of Pinned Microbial Culture
Description: The goal of this package is to allow users to robustly
and quickly grid and quantify sizes of pinned colonies in plate images.
gitter works by first finding the grid of colonies from a preprocessed image
and then locating the bounds of each colony separately.
It includes several image pre-processing techniques, such
as autorotation of plates, noise removal, contrast adjustment and image
resizing.
Author: Omar Wagih, Leopold Parts
Maintainer: Omar Wagih <wagih@ebi.ac.uk>
Diff between gitter versions 1.0.4 dated 2014-01-23 and 1.1 dated 2015-10-09
gitter-1.0.4/gitter/R/Help.R |only gitter-1.0.4/gitter/R/Main.R |only gitter-1.0.4/gitter/R/Peaks.R |only gitter-1.0.4/gitter/man/gitter-package.Rd |only gitter-1.1/gitter/DESCRIPTION | 20 ++-- gitter-1.1/gitter/MD5 | 29 +++--- gitter-1.1/gitter/NAMESPACE | 27 +++++- gitter-1.1/gitter/R/help.r |only gitter-1.1/gitter/R/io.r |only gitter-1.1/gitter/R/main.r |only gitter-1.1/gitter/R/peaks.r |only gitter-1.1/gitter/R/plot.r |only gitter-1.1/gitter/build/BUILD.R | 21 +++- gitter-1.1/gitter/man/gitter.Rd | 131 +++++++++--------------------- gitter-1.1/gitter/man/gitter.batch.Rd | 68 ++++----------- gitter-1.1/gitter/man/gitter.demo.Rd | 45 +--------- gitter-1.1/gitter/man/gitter.read.Rd | 46 ++-------- gitter-1.1/gitter/man/plate.warnings.Rd | 43 ++------- gitter-1.1/gitter/man/plot.gitter.Rd | 106 ++++++++---------------- gitter-1.1/gitter/man/summary.gitter.Rd | 47 ++-------- 20 files changed, 205 insertions(+), 378 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description:
We provide a set of functions to retrieve information about GIMMS NDVI3g
files currently available online; download and re-arrange the bi-monthly
datasets according to creation time; import downloaded files from native
binary (ENVI) format directly into R based on the widely applied 'raster'
package; and calculate monthly value composites (e.g. maximum value
composites, MVC) from the bi-monthly input data.
Author: Florian Detsch
Maintainer: Florian Detsch <admin@environmentalinformatics-marburg.de>
Diff between gimms versions 0.1 dated 2015-10-08 and 0.1.1 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/createHdr.R | 2 ++ man/createHdr.Rd | 2 ++ 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Utility Sparse Matrix Functions for Quantitative Language
Comparison
Description: Extension of the functionality of the Matrix package for using sparse matrices. Some of the functions are very general, while other are highly specific for special data format as used for quantitative language comparison (QLC).
Author: Michael Cysouw
Maintainer: Michael Cysouw <cysouw@mac.com>
Diff between qlcMatrix versions 0.9.4 dated 2015-04-27 and 0.9.5 dated 2015-10-09
DESCRIPTION | 9 +- MD5 | 28 ++++---- NAMESPACE | 5 + NEWS.md |only R/array.R |only R/assoc.R | 4 - R/base.R | 84 +++++++++++++----------- R/split.R | 7 +- R/utils.R | 42 ++++++++---- build/vignette.rds |binary inst/doc/transformingDataSparse.html | 19 ++++- man/array.Rd |only man/bibles.Rd | 6 - man/qlcMatrix-package.Rd | 6 - man/rowMax.Rd | 2 man/unfold.Rd | 118 ++++++++++++++++++++--------------- man/unfoldBlockMatrix.Rd |only 17 files changed, 196 insertions(+), 134 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative
discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences,
turns of talk, syllables and other assorted analysis tasks. The
package provides parsing tools for preparing transcript data.
Many functions enable the user to aggregate data by any number
of grouping variables, providing analysis and seamless
integration with other R packages that undertake higher level
analysis and visualization of text. This affords the user a
more efficient and targeted analysis. 'qdap' is designed for
transcript analysis, however, many functions are applicable to
other areas of Text Mining/Natural Language Processing.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.2.2 dated 2015-07-05 and 2.2.4 dated 2015-10-09
DESCRIPTION | 12 - MD5 | 44 ++--- NAMESPACE | 1 NEWS | 30 +++ R/add_s.R |only R/as.tdm.R | 2 R/automated_readability_index.R | 2 R/common.R | 3 R/formality.R | 3 R/lexical_classification.R | 28 ++- R/name2sex.R | 64 ++++++-- R/pos.R | 22 +- R/question_type.R | 4 R/word_cor.R | 15 + README.md | 3 inst/CITATION | 6 inst/Rmd_vignette/qdap_vignette.Rmd | 265 +++++++++++++++++----------------- inst/doc/cleaning_and_debugging.pdf |binary inst/doc/tm_package_compatibility.pdf |binary man/add_s.Rd |only man/as.tdm.Rd | 2 man/lexical_classification.Rd | 4 man/pos.Rd | 7 man/word_cor.Rd | 16 +- 24 files changed, 313 insertions(+), 220 deletions(-)
Title: Access to Open Street Map Raster Images
Description: Accesses high resolution raster maps using the OpenStreetMap protocol. Dozens of road, satellite,
and topographic map servers are directly supported, including CloudMade,
Mapnik, Bing, stamen, and MapQuest. Maps can be plotted using either base
graphics, or ggplot2. This package is not affiliated with the OpenStreetMap.org mapping project.
Author: Ian Fellows, using the JMapViewer library by Jan Peter Stotz
Maintainer: Ian Fellows <ian@fellstat.com>
Diff between OpenStreetMap versions 0.3.1 dated 2013-04-14 and 0.3.2 dated 2015-10-09
OpenStreetMap-0.3.1/OpenStreetMap/javasrc |only OpenStreetMap-0.3.1/OpenStreetMap/man/raster.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/DESCRIPTION | 24 - OpenStreetMap-0.3.2/OpenStreetMap/MD5 | 123 +++++----- OpenStreetMap-0.3.2/OpenStreetMap/NAMESPACE | 13 - OpenStreetMap-0.3.2/OpenStreetMap/R/OpenStreetMap-package.R | 4 OpenStreetMap-0.3.2/OpenStreetMap/R/autoplot.R | 23 - OpenStreetMap-0.3.2/OpenStreetMap/R/osm.R | 20 - OpenStreetMap-0.3.2/OpenStreetMap/R/zzz.R | 13 - OpenStreetMap-0.3.2/OpenStreetMap/inst/java/RTileController.jar |binary OpenStreetMap-0.3.2/OpenStreetMap/java |only OpenStreetMap-0.3.2/OpenStreetMap/man/LA_places.Rd | 5 OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.OpenStreetMap.Rd | 15 - OpenStreetMap-0.3.2/OpenStreetMap/man/autoplot.osmtile.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/getMapInfo.Rd | 7 OpenStreetMap-0.3.2/OpenStreetMap/man/launchMapHelper.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/longlat.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/openmap.Rd | 42 +-- OpenStreetMap-0.3.2/OpenStreetMap/man/openproj.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/osm.Rd | 6 OpenStreetMap-0.3.2/OpenStreetMap/man/osmtile.Rd | 16 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.OpenStreetMap.Rd | 19 - OpenStreetMap-0.3.2/OpenStreetMap/man/plot.osmtile.Rd | 18 - OpenStreetMap-0.3.2/OpenStreetMap/man/print.OpenStreetMap.Rd | 10 OpenStreetMap-0.3.2/OpenStreetMap/man/projectMercator.Rd | 13 - OpenStreetMap-0.3.2/OpenStreetMap/man/raster-OpenStreetMap-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/raster-osmtile-method.Rd |only OpenStreetMap-0.3.2/OpenStreetMap/man/setCloudMadeKey.Rd | 9 OpenStreetMap-0.3.2/OpenStreetMap/man/states.Rd | 5 29 files changed, 224 insertions(+), 206 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.2 dated 2015-06-29 and 1.2.3 dated 2015-10-09
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS | 7 +++++++ R/HelpersMG-package.R | 4 ++-- R/LD50.R | 4 ++-- R/MHalgoGen.R | 20 +++++++++----------- R/sun.info.R | 18 ++++++++---------- R/wget.R |only man/HelpersMG-package.Rd | 4 ++-- man/sun.info.Rd | 14 +++++++------- man/wget.Rd |only 12 files changed, 53 insertions(+), 47 deletions(-)
Title: Retrospective Noise Control for fMRI
Description: Useful functions for fMRI preprocessing.
Author: Tim Tierney
Maintainer: Tim Tierney <fiachmri@gmail.com>
Diff between FIACH versions 0.1.1 dated 2015-10-01 and 0.1.2 dated 2015-10-09
DESCRIPTION | 6 MD5 | 61 ++--- NAMESPACE | 22 - R/GUI.R | 11 R/RcppExports.R | 272 ++++++++++++------------ R/arrMat.R | 10 R/basisFunctions.R | 42 +-- R/boldContrast.R | 148 ++++++------- R/fd.R | 34 +-- R/fiach.R | 18 + R/gaussKernel.R | 20 - R/highBasis.R | 18 - R/highPass.R | 34 +-- R/kaiserWin.R | 48 ++-- R/kmeansMask.R | 14 - R/lowBasis.R | 22 - R/matArr.R | 6 R/naSpline.R | 82 +++---- R/quantMask.r | 18 - R/rawPeriodogram.R | 64 ++--- R/sinc.R | 30 +- R/spmHrf.R | 18 - R/spmOrth.R | 24 +- R/t2Grey.R | 12 - R/t2sGrey.R | 26 +- R/viewR.R | 531 +++++++++++------------------------------------- inst/extdata/mni.nii.gz |only man/GUI.Rd | 42 +-- man/rawPeriodogram.Rd | 108 ++++----- man/rp.Rd | 68 +++--- man/sinc.Rd | 86 +++---- man/viewR.Rd | 5 32 files changed, 827 insertions(+), 1073 deletions(-)