Title: Performs Regularization on Structural Equation Models
Description: Uses both ridge and lasso penalties (and extensions) to penalize
specific parameters in structural equation models. The package offers additional
cost functions, cross validation, and other extensions beyond traditional SEM.
Author: Ross Jacobucci[aut,cre], Kevin J. Grimm [ctb]
Maintainer: Ross Jacobucci <rcjacobuc@gmail.com>
Diff between regsem versions 0.2.0 dated 2016-08-11 and 0.4.0 dated 2016-09-19
DESCRIPTION | 8 - MD5 | 25 ++-- NAMESPACE | 3 R/coord_desc.R | 245 +++++++++++++++++++++++++++++++++++++++---- R/cv_regsem.R | 67 +++++++++-- R/extractMatrices.R | 129 ++++++++++++++++++---- R/fiml_calc2.R |only R/multi_optim.R | 89 ++++++++++++--- R/plot.R |only R/regsem.R | 230 ++++++++++++++++++++++++++-------------- man/cv_regsem.Rd | 21 ++- man/multi_optim.Rd | 20 +++ man/plot.regsem.Rd |only man/regsem.Rd | 25 +++- src/regsem_rcpp_grad_ram.cpp | 8 - 15 files changed, 684 insertions(+), 186 deletions(-)
Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre],
Kouros Owzar [aut],
Gregory D. Sempowski [aut],
Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between permPATH versions 0.9 dated 2016-07-18 and 1.0 dated 2016-09-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/permPATHmanual.pdf |binary src/permPATH.cpp | 3 ++- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Memory Estimation Utilities
Description: How much ram do you need to store a 100,000 by 100,000 matrix?
How much ram is your current R session using? How much ram do you even have?
Learn the scintillating answer to these and many more such questions with
the 'memuse' package.
Author: Drew Schmidt [aut, cre],
Christian Heckendorf [ctb] (FreeBSD improvements to meminfo),
Wei-Chen Chen [ctb] (Windows build fixes),
Dan Burgess [ctb] (donation of a Mac for development and testing)
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between memuse versions 3.0-0 dated 2016-09-12 and 3.0-1 dated 2016-09-19
ChangeLog | 6 + DESCRIPTION | 6 - MD5 | 47 ++++++------ README.md | 11 +- cleanup | 2 configure |only configure.ac |only configure.win |only inst/doc/memuse-guide.Rnw | 2 inst/doc/memuse-guide.pdf |binary src/Makevars | 18 ++-- src/meminfo/src/cacheinfo.c | 109 ++++++++++++++++++----------- src/meminfo/src/conf.h.in |only src/meminfo/src/fileinfo.c | 86 +++++++++++++++-------- src/meminfo/src/getpid.c | 38 +++++++--- src/meminfo/src/main.c | 31 ++++++-- src/meminfo/src/meminfo.h | 35 +++++++-- src/meminfo/src/os.h |only src/meminfo/src/platform.c | 43 ++++++++++- src/meminfo/src/platform.h | 45 ++++++++---- src/meminfo/src/print.c | 33 ++++++-- src/meminfo/src/procinfo.c | 57 +++++++++------ src/meminfo/src/raminfo.c | 164 ++++++++++++++++++++++++-------------------- src/meminfo/src/swapinfo.c | 125 +++++++++++++++++++-------------- vignettes/build_pdf.sh | 11 ++ vignettes/cover/cover.pdf |binary vignettes/memuse-guide.Rnw | 2 27 files changed, 565 insertions(+), 306 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 1.9-0 dated 2015-10-09 and 1.10-0 dated 2016-09-19
fishmethods-1.10-0/fishmethods/DESCRIPTION | 10 fishmethods-1.10-0/fishmethods/MD5 | 54 +++-- fishmethods-1.10-0/fishmethods/NAMESPACE | 4 fishmethods-1.10-0/fishmethods/R/M.empirical.R | 16 + fishmethods-1.10-0/fishmethods/R/agesurv.R | 53 ++++- fishmethods-1.10-0/fishmethods/R/alkD.R | 2 fishmethods-1.10-0/fishmethods/R/bheq.R |only fishmethods-1.10-0/fishmethods/R/bhnoneq.R | 8 fishmethods-1.10-0/fishmethods/R/catch.select.R |only fishmethods-1.10-0/fishmethods/R/fm_checkdesign.R |only fishmethods-1.10-0/fishmethods/R/fm_model_avg.R |only fishmethods-1.10-0/fishmethods/R/fm_telemetry.R |only fishmethods-1.10-0/fishmethods/R/growhamp.R |only fishmethods-1.10-0/fishmethods/R/irm_cr.R | 77 +++---- fishmethods-1.10-0/fishmethods/R/irm_h.R | 191 +++++++++---------- fishmethods-1.10-0/fishmethods/data/Hightower.rda |only fishmethods-1.10-0/fishmethods/data/sblen.rda |only fishmethods-1.10-0/fishmethods/data/tanaka.rda |binary fishmethods-1.10-0/fishmethods/data/trout.rda |only fishmethods-1.10-0/fishmethods/man/Hightower.Rd |only fishmethods-1.10-0/fishmethods/man/M.empirical.Rd | 12 - fishmethods-1.10-0/fishmethods/man/agesurv.Rd | 6 fishmethods-1.10-0/fishmethods/man/bheq.Rd |only fishmethods-1.10-0/fishmethods/man/bhnoneq.Rd | 2 fishmethods-1.10-0/fishmethods/man/catch.select.Rd |only fishmethods-1.10-0/fishmethods/man/clus.lf.Rd | 5 fishmethods-1.10-0/fishmethods/man/fm_checkdesign.Rd |only fishmethods-1.10-0/fishmethods/man/fm_model_avg.Rd |only fishmethods-1.10-0/fishmethods/man/fm_telemetry.Rd |only fishmethods-1.10-0/fishmethods/man/grotag.Rd | 9 fishmethods-1.10-0/fishmethods/man/growhamp.Rd |only fishmethods-1.10-0/fishmethods/man/irm_cr.Rd | 16 - fishmethods-1.10-0/fishmethods/man/irm_h.Rd | 6 fishmethods-1.10-0/fishmethods/man/sblen.Rd |only fishmethods-1.10-0/fishmethods/man/trout.Rd |only fishmethods-1.9-0/fishmethods/R/bheq1.R |only fishmethods-1.9-0/fishmethods/R/bheq2.R |only fishmethods-1.9-0/fishmethods/man/bheq1.Rd |only fishmethods-1.9-0/fishmethods/man/bheq2.Rd |only 39 files changed, 274 insertions(+), 197 deletions(-)
Title: Distribution Function of Quadratic Forms in Normal Variables
Description: Computes the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.
Author: P. Lafaye de Micheaux
Maintainer: P. Lafaye de Micheaux <lafaye@dms.umontreal.ca>
Diff between CompQuadForm versions 1.4.1 dated 2013-06-16 and 1.4.2 dated 2016-09-19
DESCRIPTION | 14 ++---- MD5 | 29 +++++++------- NAMESPACE | 2 R/davies.R | 9 ++-- R/farebrother.R | 9 +--- R/imhof.R | 18 +++++--- R/liu.R | 37 +++++++++--------- TODO |only inst/HISTORY | 11 +++++ man/davies.Rd | 81 ++++++++++++++++++++++----------------- man/farebrother.Rd | 20 +++++++-- man/imhof.Rd | 15 +++---- man/liu.Rd | 27 ++++++------- src/imhof.cpp | 44 ++++++++++----------- src/qfc.cpp | 103 +++++++++++++++++++++++++------------------------- src/ruben.cpp | 108 ++++++++++++++++++++++++++--------------------------- 16 files changed, 283 insertions(+), 244 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.62-1 dated 2016-01-05 and 0.64-3 dated 2016-09-19
DESCRIPTION | 13 ++++--- MD5 | 80 +++++++++++++++++++++++++---------------------- NAMESPACE | 2 + R/brocolors.R | 40 +++++++++++++++++++++-- R/dotplot.R | 8 ++-- R/excel_fig.R | 27 +++++++-------- R/fisher.R | 2 - R/grayplot.R | 25 +++++--------- R/histlines.R | 6 +-- R/holmans_triangle.R | 5 -- R/jiggle.R | 7 ---- R/kbdate.R | 2 - R/manyboxplot.R | 4 +- R/normalize.R | 4 +- R/numbers.R |only R/objectsizes.R | 4 +- R/pushbullet.R | 18 +++++----- R/quantileSE.R | 4 +- R/runningmean.R | 16 ++++----- R/setRNGparallel.R |only data |only inst/README.md | 2 - inst/STATUS.txt | 11 ++++++ man/brocolors.Rd | 4 +- man/chisq.Rd | 2 - man/done.Rd | 4 +- man/dotplot.Rd | 2 - man/errors2pushbullet.Rd | 4 +- man/excel_fig.Rd | 17 +++++---- man/grayplot.Rd | 8 ++-- man/histlines.Rd | 4 +- man/jiggle.Rd | 2 - man/kbdate.Rd | 2 - man/normalize.Rd | 2 - man/note.Rd | 4 +- man/numbers.Rd |only man/objectsizes.Rd | 2 - man/quantileSE.Rd | 2 - man/runningmean.Rd | 8 ++-- man/runningratio.Rd | 6 +-- man/setRNGparallel.Rd |only man/triplot.Rd | 2 - src/compare_rows.c | 6 ++- 43 files changed, 202 insertions(+), 159 deletions(-)
Title: A Two-Stage Approach to Maximize Interpretability of Drug
Response Models Based on Multiple Molecular Data Types
Description: A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.
Author: Nanne Aben
Maintainer: Nanne Aben <nanne.aben@gmail.com>
Diff between TANDEM versions 0.9.3 dated 2016-07-13 and 1.0.0 dated 2016-09-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/my-vignette.Rmd | 5 ++++- inst/doc/my-vignette.html | 14 +++++++++----- vignettes/my-vignette.Rmd | 5 ++++- 5 files changed, 25 insertions(+), 15 deletions(-)
Title: 'Htmlwidget' for 'Kerry Rodden' 'd3.js' Sequence Sunburst
Description: Make interactive 'd3.js' sequence sunburst diagrams in R with the
convenience and infrastructure of an 'htmlwidget'.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kerry Rodden [aut, cph] (sequences library in htmlwidgets/lib,
https://gist.github.com/kerryrodden/7090426),
Kent Russell [aut, cre] (R interface),
Florian Breitwieser [ctb] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between sunburstR versions 0.6.0 dated 2016-08-25 and 0.6.2 dated 2016-09-19
DESCRIPTION | 8 ++--- MD5 | 25 +++++++++-------- NEWS.md | 18 ++++++++++++ R/shiny.R | 4 ++ inst/examples/example_baseball.Rmd |only inst/examples/example_ngram.R | 3 ++ inst/examples/example_replicate.R | 4 ++ inst/examples/example_shiny.R | 3 ++ inst/htmlwidgets/lib/d3/LICENSE | 52 ++++++++++++++++++------------------- inst/htmlwidgets/lib/d3/d3.min.js | 10 +++---- inst/htmlwidgets/sunburst.js | 13 +++++++-- inst/htmlwidgets/sunburst.yaml | 2 - man/add_shiny.Rd | 49 ++++++++++++++++++++++++++++++++++ man/sunburst.Rd | 7 ++++ 14 files changed, 146 insertions(+), 52 deletions(-)
Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes
from http://bootswatch.com/, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans font),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between shinythemes versions 1.0.1 dated 2015-03-02 and 1.1 dated 2016-09-19
shinythemes-1.0.1/shinythemes/NEWS |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/Lato.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/LatoBold.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/LatoItalic.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/NewsCycle.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/NewsCycleBold.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/OpenSans.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/OpenSansBold.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/OpenSansBoldItalic.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/OpenSansItalic.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/Raleway.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/RalewayBold.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/SourceSansPro.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/SourceSansProBold.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/SourceSansProLight.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/Ubuntu.ttf |only shinythemes-1.1/shinythemes/DESCRIPTION | 9 shinythemes-1.1/shinythemes/LICENSE | 2 shinythemes-1.1/shinythemes/MD5 | 83 + shinythemes-1.1/shinythemes/NAMESPACE | 2 shinythemes-1.1/shinythemes/NEWS.md |only shinythemes-1.1/shinythemes/R/shinythemes-package.r | 25 shinythemes-1.1/shinythemes/inst/shinythemes/css/cerulean.min.css | 10 shinythemes-1.1/shinythemes/inst/shinythemes/css/cosmo.min.css | 16 shinythemes-1.1/shinythemes/inst/shinythemes/css/cyborg.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/darkly.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/flatly.min.css | 16 shinythemes-1.1/shinythemes/inst/shinythemes/css/journal.min.css | 14 shinythemes-1.1/shinythemes/inst/shinythemes/css/lumen.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/paper.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/readable.min.css | 14 shinythemes-1.1/shinythemes/inst/shinythemes/css/sandstone.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/simplex.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/slate.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/spacelab.min.css | 18 shinythemes-1.1/shinythemes/inst/shinythemes/css/superhero.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/css/united.min.css | 12 shinythemes-1.1/shinythemes/inst/shinythemes/css/yeti.min.css |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Lato_300.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Lato_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Lato_400italic.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Lato_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/News_Cycle_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/News_Cycle_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_300.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_300italic.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_400italic.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Open_Sans_700italic.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/README.md |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Raleway_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Raleway_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Roboto_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Roboto_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Source_Sans_Pro_300.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Source_Sans_Pro_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Source_Sans_Pro_400italic.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Source_Sans_Pro_700.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/Ubuntu_400.ttf |only shinythemes-1.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.eot |binary shinythemes-1.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.svg | 487 +++++----- shinythemes-1.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.ttf |binary shinythemes-1.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.woff |binary shinythemes-1.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.woff2 |only shinythemes-1.1/shinythemes/man/shinytheme.Rd | 2 shinythemes-1.1/shinythemes/man/shinythemes.Rd | 27 67 files changed, 432 insertions(+), 305 deletions(-)
Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve
phylogenetic trees, information about studies used to assemble the synthetic
tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The
'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all
named species.
Author: Francois Michonneau [aut, cre],
Joseph Brown [aut],
David Winter [aut]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rotl versions 3.0.0 dated 2016-04-26 and 3.0.1 dated 2016-09-19
DESCRIPTION | 10 +- MD5 | 41 +++++----- NEWS.md | 10 ++ R/methods.R | 3 R/studies-utils.R | 2 R/studies.R | 5 - README.md | 24 +++++ build/vignette.rds |binary inst/CITATION |only inst/doc/data_mashups.html | 34 ++++---- inst/doc/how-to-use-rotl.R | 8 + inst/doc/how-to-use-rotl.Rmd | 19 +++- inst/doc/how-to-use-rotl.html | 153 +++++++++++++++++++++++--------------- inst/doc/meta-analysis.R | 12 +- inst/doc/meta-analysis.Rmd | 12 +- inst/doc/meta-analysis.html | 65 +++++++--------- man/tax_lineage.Rd | 3 tests/testthat/test-external.R | 21 +++-- tests/testthat/test-match_names.R | 21 ++--- tests/testthat/test-tol.R | 4 vignettes/how-to-use-rotl.Rmd | 19 +++- vignettes/meta-analysis.Rmd | 2 22 files changed, 281 insertions(+), 187 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
between compiled C and interpreted R code. Not to be confused with RNiftyReg,
which provides tools for image registration.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.1.0 dated 2016-09-01 and 0.2.0 dated 2016-09-19
DESCRIPTION | 8 - MD5 | 131 +++++++++++++++- NEWS |only R/nifti.R | 2 README.md | 2 inst/doxygen |only inst/include/RNifti.h | 8 + inst/include/RNiftiAPI.h | 214 +++++++++++++++----------- inst/include/lib/NiftiImage.h | 333 ++++++++++++++++++++++++++++++++++++------ 9 files changed, 559 insertions(+), 139 deletions(-)
Title: Multiscale Bernstein Polynomials for Densities
Description: Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).
Author: Antonio Canale
Maintainer: Antonio Canale <antonio.canale@unito.it>
Diff between msBP versions 1.1 dated 2016-04-20 and 1.2 dated 2016-09-19
ChangeLog | 1 + DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- src/auxGibbs.cpp | 10 +++++----- src/gibbs.cpp | 16 ++++++++-------- src/msBP.cpp | 54 +++++++++++++++++++++++++++--------------------------- 6 files changed, 50 insertions(+), 49 deletions(-)
Title: Multivariate Distance Matrix Regression
Description: Allows a user to conduct multivariate distance matrix regression using analytic p-values and compute measures of effect size.
Author: Daniel B. McArtor (dmcartor@nd.edu) [aut, cre]
Maintainer: Daniel B. McArtor <dmcartor@nd.edu>
Diff between MDMR versions 0.4.2 dated 2016-08-12 and 0.4.3 dated 2016-09-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/mdmr.R | 2 +- inst/doc/mdmr-vignette.html | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Estimate Global Clustering in Infectious Disease
Description: Implements various novel and standard
clustering statistics and other analyses useful for understanding the
spread of infectious disease.
Author: Justin Lessler <justin@jhu.edu>, Henrik Salje <hsalje@jhsph.edu>
Maintainer: Justin Lessler <justin@jhu.edu>
Diff between IDSpatialStats versions 0.2.1 dated 2016-05-10 and 0.2.2 dated 2016-09-19
DESCRIPTION | 6 ++-- MD5 | 52 +++++++++++++++++++-------------------- man/DengueSimR01.Rd | 3 +- man/DengueSimR02.Rd | 3 +- man/DengueSimRepresentative.Rd | 3 +- man/get.pi.Rd | 13 +++++---- man/get.pi.bootstrap.Rd | 14 ++++++---- man/get.pi.ci.Rd | 14 ++++++---- man/get.pi.permute.Rd | 14 ++++++---- man/get.pi.typed.Rd | 11 ++++---- man/get.pi.typed.bootstrap.Rd | 12 +++++---- man/get.pi.typed.permute.Rd | 12 +++++---- man/get.tau.Rd | 14 ++++++---- man/get.tau.bootstrap.Rd | 14 ++++++---- man/get.tau.ci.Rd | 14 ++++++---- man/get.tau.permute.Rd | 14 ++++++---- man/get.tau.typed.Rd | 11 ++++---- man/get.tau.typed.bootstrap.Rd | 12 +++++---- man/get.tau.typed.permute.Rd | 12 +++++---- man/get.theta.Rd | 15 ++++++----- man/get.theta.bootstrap.Rd | 14 ++++++---- man/get.theta.ci.Rd | 14 ++++++---- man/get.theta.permute.Rd | 14 ++++++---- man/get.theta.typed.Rd | 13 +++++---- man/get.theta.typed.bootstrap.Rd | 14 ++++++---- man/get.theta.typed.permute.Rd | 14 ++++++---- src/spatialfuncs.c | 8 +++--- 27 files changed, 197 insertions(+), 157 deletions(-)
More information about IDSpatialStats at CRAN
Permanent link
Title: Offers Various Swiss Maps as ggplot2 Objects
Description: Offers various swiss maps as ggplot2 objects and gives the
possibility to add layers of data on the maps. Data are publicly available
from the swiss federal statistical office.
Author: Sandro Petrillo Burri [aut, cre],
Eric Stephani [aut],
Lisa Bottinelli [ctb]
Maintainer: Sandro Petrillo Burri <gibo.gaf@gmail.com>
Diff between ggswissmaps versions 0.0.8 dated 2016-02-12 and 0.0.9 dated 2016-09-19
DESCRIPTION | 9 +- MD5 | 16 ++-- NEWS | 11 ++ README.md | 8 +- build/vignette.rds |binary inst/doc/ggswissmaps_intro.R | 20 ++++- inst/doc/ggswissmaps_intro.Rmd | 41 +++++++++- inst/doc/ggswissmaps_intro.html | 151 +++++++++++++++++++++++++++------------- vignettes/ggswissmaps_intro.Rmd | 41 +++++++++- 9 files changed, 224 insertions(+), 73 deletions(-)
Title: Join Tables Together on Inexact Matching
Description: Join tables together based not on whether columns
match exactly, but whether they are similar by some comparison.
Implementations include string distance and regular expression
matching.
Author: David Robinson [aut, cre],
Joran Elias [ctb]
Maintainer: David Robinson <drobinson@stackoverflow.com>
Diff between fuzzyjoin versions 0.1.1 dated 2016-06-28 and 0.1.2 dated 2016-09-19
DESCRIPTION | 8 - MD5 | 12 - NEWS.md | 5 R/fuzzy_join.R | 10 + README.md | 71 +++++------ inst/doc/stringdist_join.html | 212 +++++++++++++++++----------------- tests/testthat/test_stringdist_join.R | 12 + 7 files changed, 179 insertions(+), 151 deletions(-)
More information about UCR.ColumnNames at CRAN
Permanent link
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.6.2 dated 2016-08-11 and 1.6.2.1 dated 2016-09-19
DESCRIPTION | 8 +++---- MD5 | 21 ++++++++++---------- data/rgbs.txt.gz |binary inst |only man/Rsomoclu.kohonen.Rd | 4 +-- src/Makefile.in | 6 +++++ src/Makefile.root.in | 2 - src/Makevars | 1 src/Makevars.win | 2 - src/configure | 18 ++++++++--------- src/somoclu.h | 13 ++++++++++++ src/training.cpp | 49 ++++++++++++++++++++++++++++++++++++++++++++++++ 12 files changed, 97 insertions(+), 27 deletions(-)
Title: Visualizing Asymmetric Data
Description: The slide-vector model is provided in this package together with functions for the analysis and graphical display of asymmetry. The slide vector model is a scaling model for asymmetric data. A distance model is fitted to the symmetric part of the data whereas the asymmetric part of the data is represented by projections of the coordinates onto the slide-vector. The slide-vector points in the direction of large asymmetries in the data. The distance is modified in such a way that the distance between two points that are parallel to the slide-vector is larger in the direction of this vector. The distance is smaller in the opposite direction. If the line connecting two points is perpendicular to the slide-vector the difference between the two projections is zero. In this case the distance between the two points is symmetric. The algorithm for fitting this model is derived from the majorization approach to multidimensional scaling.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 1.1 dated 2016-06-25 and 1.1.1 dated 2016-09-19
DESCRIPTION | 11 +++++------ MD5 | 10 ++++++---- NAMESPACE | 1 + R/decomposition.R |only build/partial.rdb |binary man/decomposition.Rd |only man/hmap.Rd | 6 +++--- 7 files changed, 15 insertions(+), 13 deletions(-)
Title: Fast Hierarchical Clustering Routines for R and Python
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical, agglomerative
clustering routines. Part of the functionality is designed as drop-in
replacement for existing routines: linkage() in the SciPy package
'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
'flashClust' package. It provides the same functionality with the
benefit of a much faster implementation. Moreover, there are
memory-saving routines for clustering of vector data, which go beyond
what the existing packages provide. For information on how to install
the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner [aut, cph, cre]
Maintainer: Daniel Müllner <daniel@danifold.net>
Diff between fastcluster versions 1.1.20 dated 2016-03-31 and 1.1.21 dated 2016-09-19
fastcluster-1.1.20/fastcluster/src/fastcluster_python.cpp |only fastcluster-1.1.20/fastcluster/src/python/test |only fastcluster-1.1.21/fastcluster/DESCRIPTION | 8 +- fastcluster-1.1.21/fastcluster/MD5 | 36 +++++----- fastcluster-1.1.21/fastcluster/NEWS | 4 + fastcluster-1.1.21/fastcluster/build/vignette.rds |binary fastcluster-1.1.21/fastcluster/inst/doc/fastcluster.Rtex | 4 - fastcluster-1.1.21/fastcluster/inst/doc/fastcluster.pdf |binary fastcluster-1.1.21/fastcluster/man/fastcluster.Rd | 4 - fastcluster-1.1.21/fastcluster/man/hclust.Rd | 2 fastcluster-1.1.21/fastcluster/man/hclust.vector.Rd | 2 fastcluster-1.1.21/fastcluster/src/fastcluster.cpp | 25 +----- fastcluster-1.1.21/fastcluster/src/fastcluster_R.cpp | 11 +-- fastcluster-1.1.21/fastcluster/src/python/fastcluster.py | 2 fastcluster-1.1.21/fastcluster/src/python/fastcluster_python.cpp |only fastcluster-1.1.21/fastcluster/src/python/setup.py | 3 fastcluster-1.1.21/fastcluster/src/python/tests |only fastcluster-1.1.21/fastcluster/vignettes/fastcluster.Rtex | 4 - 18 files changed, 49 insertions(+), 56 deletions(-)
Title: Rolling Statistics
Description: Parallel functions for computing rolling statistics of time-series
data.
Author: Jason Foster
Maintainer: Jason Foster <jason.j.foster@gmail.com>
Diff between roll versions 1.0.5 dated 2016-08-29 and 1.0.6 dated 2016-09-19
DESCRIPTION | 10 MD5 | 22 NEWS.md | 6 R/RcppExports.R | 10 R/roll.R | 18 man/roll_lm.Rd | 13 man/roll_pcr.Rd | 12 man/roll_vif.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 84 +-- src/roll.cpp | 1362 ++++++++++++++++++++++++++++++++++------------------ 12 files changed, 1008 insertions(+), 533 deletions(-)
Title: Multivariate Double Hierarchical Generalized Linear Models
Description: Allows various models for multivariate response variables where each response is assumed to follow double hierarchical generalized linear models. In double hierarchical generalized linear models, the mean, dispersion parameters for variance of random effects, and residual variance can be further modeled as random-effect models.
Author: Youngjo Lee, Marek Molas, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>
Diff between mdhglm versions 1.4 dated 2016-06-28 and 1.6 dated 2016-09-19
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- NAMESPACE | 4 +- R/IWLS_CorrZIP.R | 4 +- R/dhglmfit_run_joint.R | 97 ++++++++++++++++++++++++------------------------- R/hglmfit_corr.R | 1 R/jointfit_selection.R | 4 +- R/jointfit_shared.R | 1 man/mdhglm-package.Rd | 4 +- 9 files changed, 71 insertions(+), 68 deletions(-)
Title: Double Hierarchical Generalized Linear Models
Description: Double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.
Author: Youngjo Lee, Maengseok Noh
Maintainer: Maengseok Noh <msnoh@pknu.ac.kr>
Diff between dhglm versions 1.5 dated 2015-09-18 and 1.6 dated 2016-09-19
DESCRIPTION | 10 - MD5 | 12 - NAMESPACE | 4 R/dhglmfit_run.R | 343 +++++++++++++++++++++++++++++++++++++++++---------- R/plotdhglm.R | 32 +++- man/dhglm-package.Rd | 8 - man/dhglmfit.Rd | 12 - 7 files changed, 323 insertions(+), 98 deletions(-)
Title: Tools for Aquatic Sciences
Description: Datasets, constants, conversion factors, and utilities for 'MArine', 'Riverine',
'Estuarine', 'LAcustrine' and 'Coastal' science.
The package contains among others: (1) chemical and
physical constants and datasets, e.g. atomic weights, gas
constants, the earths bathymetry; (2) conversion factors
(e.g. gram to mol to liter, barometric units,
temperature, salinity); (3) physical functions, e.g. to
estimate concentrations of conservative substances, gas
transfer and diffusion coefficients, the Coriolis force
and gravity; (4) thermophysical properties of the
seawater, as from the UNESCO polynomial or from the more
recent derivation based on a Gibbs function.
Author: Karline Soetaert <karline.soetaert@nioz.nl>,
Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>,
Filip Meysman <filip.meysman@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between marelac versions 2.1.5 dated 2015-09-04 and 2.1.6 dated 2016-09-19
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ R/sw_alpha.R | 2 -- R/sw_beta.R | 2 -- R/sw_gibbs.R | 7 +++++++ build/vignette.rds |binary data/AtomicWeight.rda |binary data/Bathymetry.rda |binary data/Constants.rda |binary data/Oceans.rda |binary data/sw_sfac.rda |binary man/convert_T.Rd | 4 +++- src/gsw_AbsSal.f | 27 ++++++++++++++------------- 13 files changed, 43 insertions(+), 37 deletions(-)
Title: Family REGional Association Tests
Description: Fast regional association analysis of quantitative traits for family-based and population studies.
Author: Nadezhda M. Belonogova <belon@bionet.nsc.ru> and
Gulnara R. Svishcheva <gulsvi@mail.ru>,
with contributions from:
Seunggeun Lee (kernel functions), Pierre Lafaye de Micheaux ('davies' method),
Thomas Lumley ('kuonen' method), James O. Ramsay (functional data analysis functions),
David Clayton ('read.plink' function) and Brian Ripley ('ginv' function)
Maintainer: Nadezhda M. Belonogova <belon@bionet.nsc.ru>
Diff between FREGAT versions 1.0.1 dated 2016-04-12 and 1.0.2 dated 2016-09-19
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++--------- R/check.input.R | 8 ++++++- R/genotypes.R | 54 ++++++++++++++++++++++++++++++-------------------- man/FFBSKAT.rd | 2 - man/FREGAT-package.rd | 3 -- man/MLR.rd | 2 - man/famBT.rd | 2 - man/famFLM.rd | 4 --- src/ruben.cpp | 8 ++++++- src/uncertain.c | 3 +- 11 files changed, 66 insertions(+), 46 deletions(-)