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tamilyn/helper.R Secret

Created November 17, 2016 19:56
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plot_ly barchart, hover not displaying on negative values
Raw
helper.R
helper.setpar = function() {
par(oma = c(1, 4, 1, 2)) # outside margins, bot,l,top,right
par(mar = c(1, 1, 1, 1)) # margins
par(las = 1) #label axis always perpendicular to the axis
par(mgp=c(5,1,0))
}
#make the method a parameter
# get aux by applying the method, order by aux
helper.data_by_auc = function(otut,f, method='fdr') {
res = table.wilcox.auc(otut, f)
res = rbind(res, p.adjust = p.adjust(res["p.value",], method=method))
ordered <- order(res["auc",])
res <- res[,ordered,drop=F]
}
Raw
manifest.json
{
"version" : 1,
"locale" : "en_US",
"platform" : "3.3.1",
"metadata" : {
"appmode" : "shiny",
"primary_rmd" : null,
"primary_html" : null,
"content_category" : null,
"has_parameters" : false
},
"packages" : {
"BH" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "BH",
"Type" : "Package",
"Title" : "Boost C++ Header Files",
"Version" : "1.60.0-2",
"Date" : "2016-05-06",
"Author" : "Dirk Eddelbuettel, John W. Emerson and Michael J. Kane",
"Maintainer" : "Dirk Eddelbuettel <edd@debian.org>",
"Description" : "Boost provides free peer-reviewed portable C++ source \n libraries. A large part of Boost is provided as C++ template code\n which is resolved entirely at compile-time without linking. This \n package aims to provide the most useful subset of Boost libraries \n for template use among CRAN package. By placing these libraries in \n this package, we offer a more efficient distribution system for CRAN \n as replication of this code in the sources of other packages is \n avoided.\n\n As of release 1.60.0-2, the following Boost libraries are included:\n 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer' 'concept' 'config'\n 'container' 'date'_'time' 'detail' 'dynamic_bitset' 'exception'\n 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion' 'geometry'\n 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io'\n 'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision'\n 'numeric' 'pending' 'phoenix' 'preprocessor' 'random' 'range'\n 'smart_ptr' 'spirit' 'tuple' 'type_trains' 'typeof' 'unordered'\n 'utility' 'uuid'.",
"License" : "BSL-1.0",
"BugReports" : "https://github.com/eddelbuettel/bh/issues",
"NeedsCompilation" : "no",
"Packaged" : "2016-05-06 11:25:19.922404 UTC; edd",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-07 01:13:43",
"Built" : "R 3.3.0; ; 2016-05-07 10:08:26 UTC; unix"
}
},
"DBI" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "DBI",
"Version" : "0.4-1",
"Date" : "2016-05-07",
"Title" : "R Database Interface",
"Description" : "A database interface definition for communication\n between R and relational database management systems. All\n classes in this package are virtual and need to be extended by\n the various R/DBMS implementations.",
"Authors@R" : "c(\n person(\"R Special Interest Group on Databases (R-SIG-DB)\", role = \"aut\"),\n person(\"Hadley\", \"Wickham\", role = \"aut\"),\n person(\"Kirill\", \"Müller\", email = \"krlmlr+r@mailbox.org\", role = c(\"aut\", \"cre\"))\n )",
"Depends" : "R (>= 2.15.0), methods",
"Suggests" : "testthat, RSQLite, knitr, covr",
"Encoding" : "UTF-8",
"License" : "LGPL (>= 2)",
"URL" : "https://github.com/rstats-db/DBI",
"BugReports" : "https://github.com/rstats-db/DBI/issues",
"Collate" : "'DBObject.R' 'DBDriver.R' 'DBConnection.R' 'ANSI.R'\n'DBResult.R' 'data-types.R' 'data.R' 'deprecated.R'\n'interpolate.R' 'quote.R' 'rownames.R' 'table-create.R'\n'table-insert.R' 'table.R' 'transactions.R' 'util.R'",
"VignetteBuilder" : "knitr",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "no",
"Packaged" : "2016-05-07 13:24:22 UTC; muelleki",
"Author" : "R Special Interest Group on Databases (R-SIG-DB) [aut],\n Hadley Wickham [aut],\n Kirill Müller [aut, cre]",
"Maintainer" : "Kirill Müller <krlmlr+r@mailbox.org>",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-08 09:53:30",
"Built" : "R 3.3.0; ; 2016-05-09 08:49:23 UTC; unix"
}
},
"Formula" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "Formula",
"Version" : "1.2-1",
"Date" : "2015-04-07",
"Title" : "Extended Model Formulas",
"Description" : "Infrastructure for extended formulas with multiple parts on the\n right-hand side and/or multiple responses on the left-hand side.",
"Authors@R" : "c(person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\"),\n person(given = \"Yves\", family = \"Croissant\", role = \"aut\", email = \"Yves.Croissant@univ-reunion.fr\"))",
"Depends" : "R (>= 2.0.0), stats",
"License" : "GPL-2 | GPL-3",
"Packaged" : "2015-04-07 14:58:46 UTC; zeileis",
"Author" : "Achim Zeileis [aut, cre],\n Yves Croissant [aut]",
"Maintainer" : "Achim Zeileis <Achim.Zeileis@R-project.org>",
"NeedsCompilation" : "no",
"Repository" : "CRAN",
"Date/Publication" : "2015-04-07 18:42:14",
"Built" : "R 3.3.0; ; 2016-05-04 14:02:49 UTC; unix"
}
},
"Hmisc" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "Hmisc",
"Version" : "3.17-4",
"Date" : "2016-05-02",
"Title" : "Harrell Miscellaneous",
"Author" : "Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with\n contributions from Charles Dupont and many others.",
"Maintainer" : "Frank E Harrell Jr <f.harrell@vanderbilt.edu>",
"Depends" : "lattice, survival (>= 2.37-6), Formula, ggplot2 (>= 2.0)",
"Imports" : "methods, latticeExtra, cluster, rpart, nnet, acepack, foreign,\ngtable, grid, gridExtra, data.table",
"Suggests" : "chron, rms, mice, tables, knitr, ff, ffbase, htmltools",
"Description" : "Contains many functions useful for data\n\tanalysis, high-level graphics, utility operations, functions for\n\tcomputing sample size and power, importing and annotating datasets,\n\timputing missing values, advanced table making, variable clustering,\n\tcharacter string manipulation, conversion of R objects to LaTeX code,\n\tand recoding variables.",
"License" : "GPL (>= 2)",
"LazyLoad" : "Yes",
"URL" : "http://biostat.mc.vanderbilt.edu/Hmisc,\nhttps://github.com/harrelfe/Hmisc",
"NeedsCompilation" : "yes",
"Packaged" : "2016-05-02 14:10:51 UTC; harrelfe",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-02 17:28:19",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-05 16:21:13 UTC; unix"
}
},
"MASS" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "MASS",
"Priority" : "recommended",
"Version" : "7.3-45",
"Date" : "2015-11-10",
"Revision" : "$Rev: 3453 $",
"Depends" : "R (>= 3.1.0), grDevices, graphics, stats, utils",
"Imports" : "methods",
"Suggests" : "lattice, nlme, nnet, survival",
"Authors@R" : "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"),\n email = \"ripley@stats.ox.ac.uk\"),\n\t person(\"Bill\", \"Venables\", role = \"ctb\"),\n\t person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"),\n\t person(\"Kurt\", \"Hornik\", role = \"trl\",\n comment = \"partial port ca 1998\"),\n\t person(\"Albrecht\", \"Gebhardt\", role = \"trl\",\n comment = \"partial port ca 1998\"),\n\t person(\"David\", \"Firth\", role = \"ctb\"))",
"Description" : "Functions and datasets to support Venables and Ripley,\n \"Modern Applied Statistics with S\" (4th edition, 2002).",
"Title" : "Support Functions and Datasets for Venables and Ripley's MASS",
"LazyData" : "yes",
"ByteCompile" : "yes",
"License" : "GPL-2 | GPL-3",
"URL" : "http://www.stats.ox.ac.uk/pub/MASS4/",
"NeedsCompilation" : "yes",
"Packaged" : "2016-04-21 09:06:13 UTC; ripley",
"Author" : "Brian Ripley [aut, cre, cph],\n Bill Venables [ctb],\n Douglas M. Bates [ctb],\n Kurt Hornik [trl] (partial port ca 1998),\n Albrecht Gebhardt [trl] (partial port ca 1998),\n David Firth [ctb]",
"Maintainer" : "Brian Ripley <ripley@stats.ox.ac.uk>",
"Repository" : "CRAN",
"Date/Publication" : "2016-04-21 11:13:45",
"Built" : "R 3.3.1; x86_64-apple-darwin13.4.0; 2016-06-24 18:37:19 UTC; unix"
}
},
"Matrix" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "Matrix",
"Version" : "1.2-6",
"Date" : "2016-04-28",
"Priority" : "recommended",
"Title" : "Sparse and Dense Matrix Classes and Methods",
"Author" : "Douglas Bates <bates@stat.wisc.edu> and Martin Maechler",
"Maintainer" : "Martin Maechler <mmaechler+Matrix@gmail.com>",
"Contact" : "Doug and Martin <Matrix-authors@R-project.org>",
"Description" : "Classes and methods for dense and sparse matrices and\n operations on them using 'LAPACK' and 'SuiteSparse'.",
"Depends" : "R (>= 3.0.1)",
"Imports" : "methods, graphics, grid, stats, utils, lattice",
"Suggests" : "expm, MASS",
"Enhances" : "MatrixModels, graph, SparseM, sfsmisc",
"Encoding" : "UTF-8",
"LazyData" : "no",
"LazyDataNote" : "not possible, since we use data/*.R *and* our classes",
"ByteCompile" : "yes",
"BuildResaveData" : "no",
"License" : "GPL (>= 2) | file LICENCE",
"URL" : "http://Matrix.R-forge.R-project.org/",
"NeedsCompilation" : "yes",
"Packaged" : "2016-04-28 14:49:36 UTC; maechler",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-02 15:51:43",
"Built" : "R 3.3.1; x86_64-apple-darwin13.4.0; 2016-06-24 18:37:32 UTC; unix"
}
},
"R6" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "R6",
"Title" : "Classes with Reference Semantics",
"Version" : "2.1.2",
"Authors@R" : "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")",
"Description" : "The R6 package allows the creation of classes with reference\n semantics, similar to R's built-in reference classes. Compared to reference\n classes, R6 classes are simpler and lighter-weight, and they are not built\n on S4 classes so they do not require the methods package. These classes\n allow public and private members, and they support inheritance, even when\n the classes are defined in different packages.",
"Depends" : "R (>= 3.0)",
"Suggests" : "knitr, microbenchmark, pryr, testthat, ggplot2, scales",
"License" : "MIT + file LICENSE",
"URL" : "https://github.com/wch/R6/",
"LazyData" : "true",
"VignetteBuilder" : "knitr",
"NeedsCompilation" : "no",
"Packaged" : "2016-01-25 18:40:15 UTC; winston",
"Author" : "Winston Chang [aut, cre]",
"Maintainer" : "Winston Chang <winston@stdout.org>",
"Repository" : "CRAN",
"Date/Publication" : "2016-01-26 00:30:15",
"Built" : "R 3.3.0; ; 2016-05-04 13:59:37 UTC; unix"
}
},
"RColorBrewer" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "RColorBrewer",
"Version" : "1.1-2",
"Date" : "2014-12-07",
"Title" : "ColorBrewer Palettes",
"Authors@R" : "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\",\n \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))",
"Author" : "Erich Neuwirth [aut, cre]",
"Maintainer" : "Erich Neuwirth <erich.neuwirth@univie.ac.at>",
"Depends" : "R (>= 2.0.0)",
"Description" : "Provides color schemes for maps (and other graphics)\n designed by Cynthia Brewer as described at http://colorbrewer2.org",
"License" : "Apache License 2.0",
"Packaged" : "2014-12-06 23:59:42 UTC; neuwirth",
"NeedsCompilation" : "no",
"Repository" : "CRAN",
"Date/Publication" : "2014-12-07 08:28:55",
"Built" : "R 3.3.0; ; 2016-05-04 14:03:36 UTC; unix"
}
},
"Rcpp" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "Rcpp",
"Title" : "Seamless R and C++ Integration",
"Version" : "0.12.7",
"Date" : "2016-09-04",
"Author" : "Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey,\n Qiang Kou, Douglas Bates and John Chambers",
"Maintainer" : "Dirk Eddelbuettel <edd@debian.org>",
"Description" : "The 'Rcpp' package provides R functions as well as C++ classes which\n offer a seamless integration of R and C++. Many R data types and objects can be\n mapped back and forth to C++ equivalents which facilitates both writing of new\n code as well as easier integration of third-party libraries. Documentation \n about 'Rcpp' is provided by several vignettes included in this package, via the \n 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and \n Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see \n 'citation(\"Rcpp\")' for details on these last two.",
"Depends" : "R (>= 3.0.0)",
"Imports" : "methods, utils",
"Suggests" : "RUnit, inline, rbenchmark, highlight, pkgKitten (>= 0.1.2)",
"VignetteBuilder" : "highlight",
"URL" : "http://www.rcpp.org, http://dirk.eddelbuettel.com/code/rcpp.html,\nhttps://github.com/RcppCore/Rcpp",
"License" : "GPL (>= 2)",
"BugReports" : "https://github.com/RcppCore/Rcpp/issues",
"MailingList" : "Please send questions and comments regarding Rcpp to\nrcpp-devel@lists.r-forge.r-project.org",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "yes",
"Packaged" : "2016-09-04 13:44:21.29814 UTC; edd",
"Repository" : "CRAN",
"Date/Publication" : "2016-09-05 02:31:01",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-09-05 09:49:42 UTC; unix",
"RemoteType" : "cran",
"RemoteSha" : "0.12.7",
"RemoteRepos" : "structure(\"https://cran.rstudio.com/\", .Names = \"CRAN\")",
"RemotePkgType" : "binary"
}
},
"acepack" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "acepack",
"Maintainer" : "Jonathan Baron <baron@psych.upenn.edu>",
"Version" : "1.3-3.3",
"Author" : "Phil Spector, Jerome Friedman, Robert Tibshirani, Thomas Lumley",
"Description" : "ACE and AVAS methods for choosing regression\n transformations.",
"Title" : "ace() and avas() for selecting regression transformations",
"License" : "MIT + file LICENSE",
"Packaged" : "2014-11-24 11:35:02 UTC; baron",
"Repository" : "CRAN",
"Date/Publication" : "2014-11-24 12:48:55",
"NeedsCompilation" : "yes",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-04 14:05:19 UTC; unix"
}
},
"assertthat" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "assertthat",
"Title" : "Easy pre and post assertions.",
"Version" : "0.1",
"Authors@R" : "'Hadley Wickham <h.wickham@gmail.com> [aut,cre]'",
"Description" : "assertthat is an extension to stopifnot() that makes it\n easy to declare the pre and post conditions that you code should\n satisfy, while also producing friendly error messages so that your\n users know what they've done wrong.",
"License" : "GPL-3",
"Suggests" : "testthat",
"Collate" : "'assert-that.r' 'on-failure.r' 'assertions-file.r'\n'assertions-scalar.R' 'assertions.r' 'base.r'\n'base-comparison.r' 'base-is.r' 'base-logical.r' 'base-misc.r'\n'utils.r' 'validate-that.R'",
"Roxygen" : "list(wrap = FALSE)",
"Packaged" : "2013-12-05 18:46:37 UTC; hadley",
"Author" : "'Hadley Wickham' [aut, cre]",
"Maintainer" : "'Hadley Wickham' <h.wickham@gmail.com>",
"NeedsCompilation" : "no",
"Repository" : "CRAN",
"Date/Publication" : "2013-12-06 00:51:10",
"Built" : "R 3.3.0; ; 2016-05-04 14:08:19 UTC; unix"
}
},
"base64enc" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "base64enc",
"Version" : "0.1-3",
"Title" : "Tools for base64 encoding",
"Author" : "Simon Urbanek <Simon.Urbanek@r-project.org>",
"Maintainer" : "Simon Urbanek <Simon.Urbanek@r-project.org>",
"Depends" : "R (>= 2.9.0)",
"Enhances" : "png",
"Description" : "This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.",
"License" : "GPL-2 | GPL-3",
"URL" : "http://www.rforge.net/base64enc",
"NeedsCompilation" : "yes",
"Packaged" : "2015-02-04 20:31:00 UTC; svnuser",
"Repository" : "CRAN",
"Date/Publication" : "2015-07-28 08:03:37",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-04 14:14:52 UTC; unix"
}
},
"chron" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "chron",
"Version" : "2.3-47",
"Title" : "Chronological Objects which can Handle Dates and Times",
"Description" : "Chronological objects which can handle dates and times.",
"Authors@R" : "c(person(\"David\", \"James\", role = \"aut\",\n comment = \"S original\"),\n person(\"Kurt\", \"Hornik\", role = c(\"aut\", \"trl\", \"cre\"),\n email = \"Kurt.Hornik@R-project.org\"),\n person(\"Gabor\", \"Grothendieck\", role = \"ctb\",\n email = \"ggrothendieck@gmail.com\"))",
"Depends" : "R (>= 2.12.0)",
"Imports" : "graphics, stats",
"Suggests" : "scales, ggplot2",
"Enhances" : "zoo",
"License" : "GPL-2",
"NeedsCompilation" : "yes",
"Packaged" : "2015-06-24 15:58:52 UTC; hornik",
"Author" : "David James [aut] (S original),\n Kurt Hornik [aut, trl, cre],\n Gabor Grothendieck [ctb]",
"Maintainer" : "Kurt Hornik <Kurt.Hornik@R-project.org>",
"Repository" : "CRAN",
"Date/Publication" : "2015-06-24 18:01:27",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-04 14:01:54 UTC; unix"
}
},
"cluster" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "cluster",
"Version" : "2.0.4",
"Date" : "2016-04-16",
"Priority" : "recommended",
"Title" : "\"Finding Groups in Data\": Cluster Analysis Extended Rousseeuw et\nal.",
"Description" : "Methods for Cluster analysis. Much extended the original from\n\tPeter Rousseeuw, Anja Struyf and Mia Hubert,\n\tbased on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".",
"Maintainer" : "Martin Maechler <maechler@stat.math.ethz.ch>",
"Authors@R" : "c(person(\"Martin\",\"Maechler\", role=c(\"aut\",\"cre\"), email=\"maechler@stat.math.ethz.ch\")\n ,person(\"Peter\", \"Rousseeuw\", role=\"aut\", email=\"rousse@uia.ua.ac.be\",\n comment = \"Fortran original\")\n ,person(\"Anja\", \"Struyf\", role=\"aut\", comment= \"S original\")\n ,person(\"Mia\", \"Hubert\", role=\"aut\", email= \"Mia.Hubert@uia.ua.ac.be\", comment= \"S original\")\n ,person(\"Kurt\", \"Hornik\", role=c(\"trl\", \"ctb\"),\n \temail=\"Kurt.Hornik@R-project.org\", comment=\"port to R; maintenance(1999-2000)\")\n ,person(\"Matthias\", \"Studer\", role=\"ctb\")\n ,person(\"Pierre\", \"Roudier\", role=\"ctb\")\n )",
"Depends" : "R (>= 3.0.1)",
"Imports" : "graphics, grDevices, stats, utils",
"Suggests" : "MASS",
"SuggestsNote" : "two small examples using MASS' cov.rob() and mvrnorm()",
"LazyLoad" : "yes",
"LazyData" : "yes",
"ByteCompile" : "yes",
"BuildResaveData" : "no",
"License" : "GPL (>= 2)",
"NeedsCompilation" : "yes",
"Packaged" : "2016-04-16 20:54:33 UTC; maechler",
"Author" : "Martin Maechler [aut, cre],\n Peter Rousseeuw [aut] (Fortran original),\n Anja Struyf [aut] (S original),\n Mia Hubert [aut] (S original),\n Kurt Hornik [trl, ctb] (port to R; maintenance(1999-2000)),\n Matthias Studer [ctb],\n Pierre Roudier [ctb]",
"Repository" : "CRAN",
"Date/Publication" : "2016-04-18 08:11:05",
"Built" : "R 3.3.1; x86_64-apple-darwin13.4.0; 2016-06-24 18:37:29 UTC; unix"
}
},
"colorspace" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "colorspace",
"Version" : "1.2-6",
"Date" : "2015-03-10",
"Title" : "Color Space Manipulation",
"Authors@R" : "c(person(given = \"Ross\", family = \"Ihaka\", role = \"aut\", email = \"ihaka@stat.auckland.ac.nz\"),\n person(given = \"Paul\", family = \"Murrell\", role = \"aut\", email = \"paul@stat.auckland.ac.nz\"),\n person(given = \"Kurt\", family = \"Hornik\", role = \"aut\", email = \"Kurt.Hornik@R-project.org\"),\n person(given = c(\"Jason\", \"C.\"), family = \"Fisher\", role = \"aut\", email = \"jfisher@usgs.gov\"),\n person(given = \"Achim\", family = \"Zeileis\", role = c(\"aut\", \"cre\"), email = \"Achim.Zeileis@R-project.org\"))",
"Description" : "Carries out mapping between assorted color spaces including\n RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV),\n\t CIELAB and polar CIELAB. Qualitative, sequential, and\n\t diverging color palettes based on HCL colors are provided.",
"Depends" : "R (>= 2.13.0), methods",
"Imports" : "graphics",
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"Author" : "Thomas Lumley [aut, cre], Ken Knoblauch [ctb], Scott Waichler\n [ctb], Achim Zeileis [ctb]",
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"Author" : "Dirk Eddelbuettel <edd@debian.org> with contributions \n by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,\n Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,\n Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx, \n Michel Lang and Viliam Simko.",
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"Description" : "A powerful and elegant high-level data visualization\n system inspired by Trellis graphics, with an emphasis on\n multivariate data. Lattice is sufficient for typical graphics needs,\n and is also flexible enough to handle most nonstandard requirements.\n See ?Lattice for an introduction.",
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"Maintainer" : "Yihui Xie <xie@yihui.name>",
"Description" : "Provides R bindings to the 'Sundown' 'Markdown' rendering library\n (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting\n syntax that can be converted to 'XHTML' or other formats. See\n http://en.wikipedia.org/wiki/Markdown for more information about 'Markdown'.",
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"Description" : "Provides easy access to, and manipulation of, the Munsell \n colours. Provides a mapping between Munsell's \n original notation (e.g. \"5R 5/10\") and hexadecimal strings suitable \n for use directly in R graphics. Also provides utilities \n to explore slices through the Munsell colour tree, to transform \n Munsell colours and display colour palettes.",
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"License" : "MIT + file LICENSE",
"Description" : "Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.",
"URL" : "https://plot.ly/r, https://cpsievert.github.io/plotly_book/,\nhttps://github.com/ropensci/plotly",
"BugReports" : "https://github.com/ropensci/plotly/issues",
"Depends" : "R (>= 3.2.0), ggplot2 (> 2.1.0)",
"Imports" : "scales, httr, jsonlite, magrittr, digest, viridisLite,\nbase64enc, htmlwidgets, tidyr, dplyr, tibble, hexbin, lazyeval\n(>= 0.2.0), purrr",
"Suggests" : "MASS, maps, ggthemes, GGally, testthat, knitr, devtools,\nshiny (>= 0.14), htmltools, curl, rmarkdown, RColorBrewer,\nRserve, RSclient, broom, webshot, listviewer",
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"RoxygenNote" : "5.0.1",
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"Packaged" : "2016-11-11 18:58:50 UTC; cpsievert",
"Author" : "Carson Sievert [aut, cre],\n Chris Parmer [aut, cph],\n Toby Hocking [aut],\n Scott Chamberlain [aut],\n Karthik Ram [aut],\n Marianne Corvellec [aut],\n Pedro Despouy [aut]",
"Maintainer" : "Carson Sievert <cpsievert1@gmail.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-11-12 00:14:36",
"Built" : "R 3.3.2; ; 2016-11-13 11:11:35 UTC; unix"
}
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"description" : {
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"Version" : "1.8.4",
"Title" : "Tools for Splitting, Applying and Combining Data",
"Description" : "A set of tools that solves a common set of problems: you\n need to break a big problem down into manageable pieces, operate on each\n piece and then put all the pieces back together. For example, you might\n want to fit a model to each spatial location or time point in your study,\n summarise data by panels or collapse high-dimensional arrays to simpler\n summary statistics. The development of 'plyr' has been generously supported\n by 'Becton Dickinson'.",
"Authors@R" : "person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\"))",
"URL" : "http://had.co.nz/plyr, https://github.com/hadley/plyr",
"BugReports" : "https://github.com/hadley/plyr/issues",
"Depends" : "R (>= 3.1.0)",
"Imports" : "Rcpp (>= 0.11.0)",
"LinkingTo" : "Rcpp",
"Suggests" : "abind, testthat, tcltk, foreach, doParallel, itertools,\niterators, covr",
"License" : "MIT + file LICENSE",
"LazyData" : "true",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "yes",
"Packaged" : "2016-06-07 19:58:36 UTC; hadley",
"Author" : "Hadley Wickham [aut, cre]",
"Maintainer" : "Hadley Wickham <hadley@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-06-08 10:40:15",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-06-09 09:08:22 UTC; unix"
}
},
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"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "purrr",
"Title" : "Functional Programming Tools",
"Version" : "0.2.2",
"Authors@R" : "c(\n person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\")),\n person(\"Lionel\", \"Henry\", , \"lionel.hry@gmail.com\", \"ctb\"),\n person(\"RStudio\", role = \"cph\")\n )",
"Description" : "Make your pure functions purr with the 'purrr' package. This\n package completes R's functional programming tools with missing features\n present in other programming languages.",
"License" : "GPL-3 | file LICENSE",
"LazyData" : "true",
"Imports" : "magrittr (>= 1.5), dplyr (>= 0.4.3), Rcpp, lazyeval (>= 0.2.0)",
"Suggests" : "testthat, covr",
"LinkingTo" : "Rcpp, dplyr, BH",
"URL" : "https://github.com/hadley/purrr",
"BugReports" : "https://github.com/hadley/purrr/issues",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "yes",
"Packaged" : "2016-06-17 22:17:44 UTC; hadley",
"Author" : "Hadley Wickham [aut, cre],\n Lionel Henry [ctb],\n RStudio [cph]",
"Maintainer" : "Hadley Wickham <hadley@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-06-18 10:05:18",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-06-19 10:14:43 UTC; unix"
}
},
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"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "reshape2",
"Title" : "Flexibly Reshape Data: A Reboot of the Reshape Package.",
"Version" : "1.4.1",
"Author" : "Hadley Wickham <h.wickham@gmail.com>",
"Maintainer" : "Hadley Wickham <h.wickham@gmail.com>",
"Description" : "Flexibly restructure and aggregate data using just two\n functions: melt and dcast (or acast).",
"URL" : "https://github.com/hadley/reshape",
"BugReports" : "https://github.com/hadley/reshape/issues",
"LinkingTo" : "Rcpp",
"Imports" : "plyr (>= 1.8.1), stringr, Rcpp",
"Suggests" : "testthat (>= 0.8.0), lattice",
"License" : "MIT + file LICENSE",
"LazyData" : "true",
"Packaged" : "2014-12-05 16:34:10 UTC; hadley",
"NeedsCompilation" : "yes",
"Repository" : "CRAN",
"Date/Publication" : "2014-12-06 06:56:59",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-05 08:01:32 UTC; unix"
}
},
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"description" : {
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"Priority" : "recommended",
"Version" : "4.1-10",
"Date" : "2015-06-29",
"Authors@R" : "c(person(\"Terry\", \"Therneau\", role = \"aut\",\n\t email = \"therneau@mayo.edu\"),\n person(\"Beth\", \"Atkinson\", role = \"aut\",\t\n\t email = \"atkinson@mayo.edu\"),\n person(\"Brian\", \"Ripley\", role = c(\"aut\", \"trl\", \"cre\"),\n email = \"ripley@stats.ox.ac.uk\",\n\t\t comment = \"author of initial R port\"))",
"Description" : "Recursive partitioning for classification, \n regression and survival trees. An implementation of most of the \n functionality of the 1984 book by Breiman, Friedman, Olshen and Stone.",
"Title" : "Recursive Partitioning and Regression Trees",
"Depends" : "R (>= 2.15.0), graphics, stats, grDevices",
"Suggests" : "survival",
"License" : "GPL-2 | GPL-3",
"LazyData" : "yes",
"ByteCompile" : "yes",
"Note" : "Maintainers are not available to give advice on using a package\nthey did not author.",
"NeedsCompilation" : "yes",
"Packaged" : "2015-06-29 09:13:49 UTC; ripley",
"Author" : "Terry Therneau [aut],\n Beth Atkinson [aut],\n Brian Ripley [aut, trl, cre] (author of initial R port)",
"Maintainer" : "Brian Ripley <ripley@stats.ox.ac.uk>",
"Repository" : "CRAN",
"Date/Publication" : "2015-06-29 17:15:41",
"Built" : "R 3.3.1; x86_64-apple-darwin13.4.0; 2016-06-24 18:37:18 UTC; unix"
}
},
"scales" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "scales",
"Version" : "0.4.1",
"Authors@R" : "c(\n person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\")),\n person(\"RStudio\", role = \"cph\")\n )",
"Title" : "Scale Functions for Visualization",
"Description" : "Graphical scales map data to aesthetics, and provide\n methods for automatically determining breaks and labels\n for axes and legends.",
"URL" : "https://github.com/hadley/scales",
"BugReports" : "https://github.com/hadley/scales/issues",
"Depends" : "R (>= 2.13)",
"Imports" : "RColorBrewer, dichromat, plyr, munsell (>= 0.2), labeling,\nmethods, Rcpp",
"LinkingTo" : "Rcpp",
"Suggests" : "testthat (>= 0.8), covr, hms",
"License" : "MIT + file LICENSE",
"LazyLoad" : "yes",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "yes",
"Packaged" : "2016-11-08 19:11:18 UTC; hadley",
"Author" : "Hadley Wickham [aut, cre],\n RStudio [cph]",
"Maintainer" : "Hadley Wickham <hadley@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-11-09 18:28:56",
"Built" : "R 3.3.2; x86_64-apple-darwin13.4.0; 2016-11-10 10:44:34 UTC; unix"
}
},
"shiny" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "shiny",
"Type" : "Package",
"Title" : "Web Application Framework for R",
"Version" : "0.14",
"Authors@R" : "c(\n person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"),\n person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@rstudio.com\"),\n person(\"JJ\", \"Allaire\", role = \"aut\", email = \"jj@rstudio.com\"),\n person(\"Yihui\", \"Xie\", role = \"aut\", email = \"yihui@rstudio.com\"),\n person(\"Jonathan\", \"McPherson\", role = \"aut\", email = \"jonathan@rstudio.com\"),\n person(family = \"RStudio\", role = \"cph\"),\n person(family = \"jQuery Foundation\", role = \"cph\",\n comment = \"jQuery library and jQuery UI library\"),\n person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"),\n comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"),\n person(family = \"jQuery UI contributors\", role = c(\"ctb\", \"cph\"),\n comment = \"jQuery UI library; authors listed in inst/www/shared/jqueryui/1.10.4/AUTHORS.txt\"),\n person(\"Mark\", \"Otto\", role = \"ctb\",\n comment = \"Bootstrap library\"),\n person(\"Jacob\", \"Thornton\", role = \"ctb\",\n comment = \"Bootstrap library\"),\n person(family = \"Bootstrap contributors\", role = \"ctb\",\n comment = \"Bootstrap library\"),\n person(family = \"Twitter, Inc\", role = \"cph\",\n comment = \"Bootstrap library\"),\n person(\"Alexander\", \"Farkas\", role = c(\"ctb\", \"cph\"),\n comment = \"html5shiv library\"),\n person(\"Scott\", \"Jehl\", role = c(\"ctb\", \"cph\"),\n comment = \"Respond.js library\"),\n person(\"Stefan\", \"Petre\", role = c(\"ctb\", \"cph\"),\n comment = \"Bootstrap-datepicker library\"),\n person(\"Andrew\", \"Rowls\", role = c(\"ctb\", \"cph\"),\n comment = \"Bootstrap-datepicker library\"),\n person(\"Dave\", \"Gandy\", role = c(\"ctb\", \"cph\"),\n comment = \"Font-Awesome font\"),\n person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"),\n comment = \"selectize.js library\"),\n person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"),\n comment = \"es5-shim library\"),\n person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"),\n comment = \"es5-shim library\"),\n person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"),\n comment = \"ion.rangeSlider library\"),\n person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"),\n comment = \"Javascript strftime library\"),\n person(family = \"SpryMedia Limited\", role = c(\"ctb\", \"cph\"),\n comment = \"DataTables library\"),\n person(\"John\", \"Fraser\", role = c(\"ctb\", \"cph\"),\n comment = \"showdown.js library\"),\n person(\"John\", \"Gruber\", role = c(\"ctb\", \"cph\"),\n comment = \"showdown.js library\"),\n person(\"Ivan\", \"Sagalaev\", role = c(\"ctb\", \"cph\"),\n comment = \"highlight.js library\"),\n person(family = \"R Core Team\", role = c(\"ctb\", \"cph\"),\n comment = \"tar implementation from R\")\n )",
"Description" : "Makes it incredibly easy to build interactive web\n applications with R. Automatic \"reactive\" binding between inputs and\n outputs and extensive pre-built widgets make it possible to build\n beautiful, responsive, and powerful applications with minimal effort.",
"License" : "GPL-3 | file LICENSE",
"Depends" : "R (>= 3.0.0), methods",
"Imports" : "utils, httpuv (>= 1.3.3), mime (>= 0.3), jsonlite (>= 0.9.16),\nxtable, digest, htmltools (>= 0.3.5), R6 (>= 2.0), sourcetools",
"Suggests" : "datasets, Cairo (>= 1.5-5), testthat, knitr (>= 1.6),\nmarkdown, rmarkdown, ggplot2",
"URL" : "http://shiny.rstudio.com",
"BugReports" : "https://github.com/rstudio/shiny/issues",
"Collate" : "'app.R' 'bookmark-state-local.R' 'stack.R' 'bookmark-state.R'\n'bootstrap-layout.R' 'conditions.R' 'map.R' 'globals.R'\n'utils.R' 'bootstrap.R' 'cache.R' 'diagnose.R' 'fileupload.R'\n'graph.R' 'hooks.R' 'html-deps.R' 'htmltools.R'\n'image-interact-opts.R' 'image-interact.R' 'imageutils.R'\n'input-action.R' 'input-checkbox.R' 'input-checkboxgroup.R'\n'input-date.R' 'input-daterange.R' 'input-file.R'\n'input-numeric.R' 'input-password.R' 'input-radiobuttons.R'\n'input-select.R' 'input-slider.R' 'input-submit.R'\n'input-text.R' 'input-textarea.R' 'input-utils.R' 'insert-ui.R'\n'jqueryui.R' 'middleware-shiny.R' 'middleware.R' 'modal.R'\n'modules.R' 'notifications.R' 'priorityqueue.R' 'progress.R'\n'react.R' 'reactive-domains.R' 'reactives.R' 'render-plot.R'\n'render-table.R' 'run-url.R' 'serializers.R'\n'server-input-handlers.R' 'server.R' 'shiny-options.R'\n'shiny.R' 'shinyui.R' 'shinywrappers.R' 'showcase.R' 'tar.R'\n'timer.R' 'update-input.R'",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "no",
"Packaged" : "2016-09-09 16:45:37 UTC; winston",
"Author" : "Winston Chang [aut, cre],\n Joe Cheng [aut],\n JJ Allaire [aut],\n Yihui Xie [aut],\n Jonathan McPherson [aut],\n RStudio [cph],\n jQuery Foundation [cph] (jQuery library and jQuery UI library),\n jQuery contributors [ctb, cph] (jQuery library; authors listed in\n inst/www/shared/jquery-AUTHORS.txt),\n jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in\n inst/www/shared/jqueryui/1.10.4/AUTHORS.txt),\n Mark Otto [ctb] (Bootstrap library),\n Jacob Thornton [ctb] (Bootstrap library),\n Bootstrap contributors [ctb] (Bootstrap library),\n Twitter, Inc [cph] (Bootstrap library),\n Alexander Farkas [ctb, cph] (html5shiv library),\n Scott Jehl [ctb, cph] (Respond.js library),\n Stefan Petre [ctb, cph] (Bootstrap-datepicker library),\n Andrew Rowls [ctb, cph] (Bootstrap-datepicker library),\n Dave Gandy [ctb, cph] (Font-Awesome font),\n Brian Reavis [ctb, cph] (selectize.js library),\n Kristopher Michael Kowal [ctb, cph] (es5-shim library),\n es5-shim contributors [ctb, cph] (es5-shim library),\n Denis Ineshin [ctb, cph] (ion.rangeSlider library),\n Sami Samhuri [ctb, cph] (Javascript strftime library),\n SpryMedia Limited [ctb, cph] (DataTables library),\n John Fraser [ctb, cph] (showdown.js library),\n John Gruber [ctb, cph] (showdown.js library),\n Ivan Sagalaev [ctb, cph] (highlight.js library),\n R Core Team [ctb, cph] (tar implementation from R)",
"Maintainer" : "Winston Chang <winston@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-09-10 01:54:32",
"Built" : "R 3.3.0; ; 2016-09-10 10:34:37 UTC; unix"
}
},
"shinydashboard" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "shinydashboard",
"Title" : "Create Dashboards with 'Shiny'",
"Version" : "0.5.3",
"Authors@R" : "c(\n person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@rstudio.com\"),\n person(family = \"RStudio\", role = \"cph\"),\n person(family = \"Almasaeed Studio\", role = c(\"ctb\", \"cph\"), comment = \"AdminLTE theme for Bootstrap\"),\n person(family = \"Adobe Systems Incorporated\", role = c(\"ctb\", \"cph\"), comment = \"Source Sans Pro font\")\n )",
"Description" : "Create dashboards with 'Shiny'. This package provides\n a theme on top of 'Shiny', making it easy to create attractive dashboards.",
"URL" : "http://rstudio.github.io/shinydashboard/",
"Depends" : "R (>= 3.0)",
"License" : "GPL-2 | file LICENSE",
"Imports" : "utils, shiny (>= 0.12.1), htmltools (>= 0.2.6)",
"BugReports" : "https://github.com/rstudio/shinydashboard",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "no",
"Packaged" : "2016-09-20 18:47:14 UTC; winston",
"Author" : "Winston Chang [aut, cre],\n RStudio [cph],\n Almasaeed Studio [ctb, cph] (AdminLTE theme for Bootstrap),\n Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font)",
"Maintainer" : "Winston Chang <winston@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2016-09-20 22:18:55",
"Built" : "R 3.3.0; ; 2016-09-21 11:35:15 UTC; unix"
}
},
"sourcetools" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "sourcetools",
"Type" : "Package",
"Title" : "Tools for Reading, Tokenizing and Parsing R Code",
"Version" : "0.1.5",
"Author" : "Kevin Ushey",
"Maintainer" : "Kevin Ushey <kevinushey@gmail.com>",
"Description" : "Tools for the reading and tokenization of R code. The\n 'sourcetools' package provides both an R and C++ interface for the tokenization\n of R code, and helpers for interacting with the tokenized representation of R\n code.",
"License" : "MIT + file LICENSE",
"LazyData" : "TRUE",
"Depends" : "R (>= 3.0.2)",
"Suggests" : "testthat",
"RoxygenNote" : "5.0.1",
"BugReports" : "https://github.com/kevinushey/sourcetools/issues",
"Encoding" : "UTF-8",
"NeedsCompilation" : "yes",
"Packaged" : "2016-09-14 22:38:37 UTC; kevin",
"Repository" : "CRAN",
"Date/Publication" : "2016-09-15 03:07:07",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-09-15 12:52:49 UTC; unix"
}
},
"stringi" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "stringi",
"Version" : "1.1.1",
"Date" : "2016-05-25",
"Title" : "Character String Processing Facilities",
"Description" : "Allows for fast, correct, consistent, portable,\n as well as convenient character string/text processing in every locale\n and any native encoding. Owing to the use of the ICU library,\n the package provides R users with platform-independent functions\n known to Java, Perl, Python, PHP, and Ruby programmers. Among available\n features there are: pattern searching (e.g., with ICU Java-like regular\n expressions or the Unicode Collation Algorithm), random string generation,\n case mapping, string transliteration, concatenation,\n Unicode normalization, date-time formatting and parsing, etc.",
"URL" : "http://www.gagolewski.com/software/stringi/\nhttp://site.icu-project.org/ http://www.unicode.org/",
"BugReports" : "http://github.com/gagolews/stringi/issues",
"SystemRequirements" : "ICU4C (>= 50, optional)",
"Type" : "Package",
"Depends" : "R (>= 2.13.1)",
"Imports" : "tools, utils, stats",
"Biarch" : "TRUE",
"License" : "file LICENSE",
"Author" : "Marek Gagolewski [aut, cre] and Bartek Tartanus [ctb] (stringi source code);\n IBM and other contributors (ICU4C 55.1 source code);\n Unicode, Inc. (Unicode Character Database)",
"Maintainer" : "Marek Gagolewski <gagolews@rexamine.com>",
"RoxygenNote" : "5.0.1",
"NeedsCompilation" : "yes",
"Packaged" : "2016-05-25 15:59:57 UTC; gagolews",
"License_is_FOSS" : "yes",
"Repository" : "CRAN",
"Date/Publication" : "2016-05-27 18:08:57",
"Built" : "R 3.3.0; x86_64-apple-darwin13.4.0; 2016-05-28 09:25:45 UTC; unix"
}
},
"stringr" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Package" : "stringr",
"Version" : "1.0.0",
"Title" : "Simple, Consistent Wrappers for Common String Operations",
"Description" : "A consistent, simple and easy to use set of wrappers around the\n fantastic 'stringi' package. All function and argument names (and positions)\n are consistent, all functions deal with \"NA\"'s and zero length vectors\n in the same way, and the output from one function is easy to feed into\n the input of another.",
"Authors@R" : "c(\n person(\"Hadley\", \"Wickham\", , \"hadley@rstudio.com\", c(\"aut\", \"cre\", \"cph\")),\n person(\"RStudio\", role = \"cph\")\n )",
"License" : "GPL-2",
"Depends" : "R (>= 2.14)",
"Imports" : "stringi (>= 0.4.1), magrittr",
"Suggests" : "testthat, knitr",
"VignetteBuilder" : "knitr",
"NeedsCompilation" : "no",
"Packaged" : "2015-04-29 12:46:34 UTC; hadley",
"Author" : "Hadley Wickham [aut, cre, cph],\n RStudio [cph]",
"Maintainer" : "Hadley Wickham <hadley@rstudio.com>",
"Repository" : "CRAN",
"Date/Publication" : "2015-04-30 11:48:24",
"Built" : "R 3.3.0; ; 2016-05-05 02:35:51 UTC; unix"
}
},
"survival" : {
"Source" : "CRAN",
"Repository" : "https://cran.rstudio.com/",
"description" : {
"Title" : "Survival Analysis",
"Maintainer" : "Terry M Therneau <therneau.terry@mayo.edu>",
"Priority" : "recommended",
"Package" : "survival",
"Version" : "2.39-4",
"Depends" : "R (>= 2.13.0)",
"Imports" : "graphics, Matrix, methods, splines, stats, utils",
"LazyData" : "Yes",
"LazyLoad" : "Yes",
"ByteCompile" : "Yes",
"Authors@R" : "c(person(c(\"Terry\", \"M\"), \"Therneau\",\n email=\"therneau.terry@mayo.edu\",\n\t role=c(\"aut\", \"cre\")),\n person(\"Thomas\", \"Lumley\", role=c(\"ctb\", \"trl\"),\n\t comment=\"original S->R port and maintainer until 2009\"))",
"Description" : "Contains the core survival analysis routines, including\n\t definition of Surv objects, \n\t Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,\n\t and parametric accelerated failure time models.",
"License" : "LGPL (>= 2)",
"NeedsCompilation" : "yes",
"Packaged" : "2016-05-10 20:07:43 UTC; therneau",
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Raw
overview.md

This is the overview

Some Stuff

  • Item
  • Item
  • Item
  • Blah
  • Blah
Raw
pesame.R
## 2013 Copyright Alexander V. Alekseyenko
library(Hmisc)
library(colorspace)
table.wilcox.auc = function(xx, f, alpha=0.05){
rnames = colnames(wilcox.auc(xx[,1], f))
wt = apply(xx, 2, function(z) wilcox.auc(z, f))
rownames(wt) = rnames
wt
}
wilcox.auc = function(x, f, alpha=0.05){
w = rcorr.cens(x, f)
auc = w['C Index']
se = w['S.D.']/2 # Dxy to AUC transformation
low = auc+qnorm(alpha)*se
high = auc+qnorm(1-alpha)*se
p.value = wilcox.test(x~f)$p.value
ns = tapply(f,f,length)
res=rbind(n1=ns[1], n2=ns[2], auc=auc, se=se, low=low, high=high, p.value=p.value)
colnames(res) = ""
t(res)
}
wilcox.auc.barplot = function(wt, f, ticks = 5){
oo = order(wt["auc",])
wt = wt[,oo, drop=F]
lims = round(min(0.5, max(abs(c(wt["high",], wt["low",])-0.5))), 2)
bar.lengths = wt["auc",,drop=F]-0.5
cols = c("red", "green")[(bar.lengths>0.0)+1]
ys = barplot(c(bar.lengths), horiz=T, axes=F, xlim=c(-lims, lims), col=cols, xlab="AUC", names.arg = colnames(bar.lengths))
ticks = seq(-lims, lims, length.out=ticks)
labels = format(ticks+0.5, digits=3)
axis(1, at= ticks, labels=labels)
legend("topleft", bty="n", legend=levels(f)[1], text.col='black', horiz=T)
legend("topright", bty="n", legend=levels(f)[2], text.col='black', horiz=T)
segments(wt["low",] - 0.5, ys, wt["high",] - 0.5, ys, col="gray")
abline(v=0, lwd=5)
}
auc.se = function(theta, n, p=0.5){
q1 = theta/(2-theta)
q2 = 2*theta^2/(1+theta)
na = n*p
nn = n*(1-p)
sqrt((theta * (1-theta) + (na-1)*(q1-theta^2) + (nn-1)*(q2-theta^2))/(nn*na))
}
# auc.se(.7, 10)
# Predictive Effect Size Analysis in Multivariate Ensembles (PESAME)
# x = matrix(runif(20*10), nrow=20, ncol=10)
# y = matrix(runif(19*10), nrow=19, ncol=10)
# f = factor(c(rep(0, dim(x)[1]), rep(1, dim(y)[1])))
# xx = rbind(x,y)
#rnames = colnames(wilcox.auc(xx[,1], f))
#wt = apply(xx, 2, function(z) wilcox.auc(z, f))
#rownames(wt) = rnames
#wilcox.auc.barplot(wt, f)
Raw
server.R
#
# This is the server logic of a Shiny web application. You can run the
# application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
library(shiny)
library(shinydashboard)
library(plotly)
library(dplyr)
# Define server logic required to draw a histogram
shinyServer(function(input, output) {
## keep track of elements inserted and not yet removed
inserted <- c()
# Load the functions
source('pesame.R')
load("example_data.RData") # creates data 'otut' and factor value 'f'
source('helper.R')
#sink("sink-example.txt")
helper.setpar() # set plot parameters
#####################################################################
#####################################################################
# Apply the selected adjustment method to the original data
baseData <- reactive({
print(paste("***** data with ADJ MEHTOD ", input$adj_method))
helper.data_by_auc(otut,f,input$adj_method) })
############################################################
############################################################
# filter the data and transpose
baseFilteredData <- reactive({
ft = baseData()
sf <- as.numeric(input$signficance_threshold)
filt = (ft["p.adjust",] < sf) & !is.na(ft["p.adjust",])
t(ft[,filt,drop=F]) })
############################################################
############################################################
# number of filtered rows
rowsDisplayed <- reactive({
b <- baseFilteredData()
nrow(b)
})
############################################################
############################################################
# number of rows in original data set (eg. before filters applied)
availableRows <- reactive({
ft = baseData()
nrow(t(ft))
})
############################################################
############################################################
# generates sequence for tick marks
generateTicks <- function(dd) {
tickMarkers = round(min(0.5, max(abs(c(dd$high, dd$low)-0.5))), 2)
seq(-tickMarkers, tickMarkers, length.out=5)
}
#####################################################################
# Apply the filter to the base data.
# Get data with adjust method applied, then apply the p.value filter,
# transpose the result.
filteredData <- reactive({
b <- baseFilteredData()
if (nrow(b) == 0) {
return(data.frame())
}
dd = as.data.frame(b)
ticks = generateTicks(dd)
#print(paste("data frame", str(dd)))
#print(rownames(dd))
dd$Enriched = levels(f)[(dd$auc<.5) + 1]
dd$Names = factor(rownames(dd), levels=rownames(dd)[order(dd$auc)])
dd
})
############################################################
############################################################
# Generate plot using ggplot
generate_ggplot <- function(dd){
if(length(dd) > 0) {
ticks = generateTicks(dd)
dd$heights = dd$auc - 0.5
ggplot(data=dd, aes(y=heights, x=Names)) +
theme_bw() +
geom_bar(stat="identity", aes(fill=Enriched)) +
geom_errorbar(aes(ymax = high-0.5, ymin=low-0.5)) +
coord_flip() + xlab("") + ylab("") +
scale_y_continuous(breaks = ticks, labels = format(ticks+0.5, digits=3))
} else {
ggplot() # empty plot
}
}
############################################################
############################################################
# Render the plot
output$filteredPlot <- renderPlot({
generate_ggplot(filteredData())
})
############################################################
############################################################
# Informational message
output$informationMessage <- renderText({
msg <- paste("Displaying ", rowsDisplayed(), " of ", availableRows(), " total rows using ",
input$adj_method, " significance value ", input$signficance_threshold)
print(msg)
msg })
#####################################################################
#####################################################################
#
##############################################
##############################################
generatePlot_ly <- function(dd) {
print(paste("211: generatePlot_ly"))
if(length(dd) <= 0) {
print(paste("126: returning empty plot_ly,no rows"))
return(ggplot())
}
ticks = generateTicks(dd)
# the hover doesnot work on the ones that are negative
# Create lists for axis properties
f1 <- list(
family = "Arial, sans-serif",
size = 18,
color = "lightgrey")
f2 <- list(
family = "Old Standard TT, serif",
size = 14,
color = "#ff9999")
my.xaxis = list( title = "auc",
autotick = TRUE,
ticktextsrc = format(ticks+0.5, digits=3),
showticklabels = TRUE,
#titlefont = f1,
#tickfont = f2,
showline = TRUE,
linecolor = toRGB("gray"),
linewidth = 1,
ticktext = format(ticks+0.5, digits=3),
tickvals = ticks,
tickmode = "array"
)
my.error.bars = list(type = "data", symmetric = FALSE, color = '#333333',arrayminus = ~dd$low-0.5,array = ~dd$high-0.5)
#hovermode = "closest", source = "source"
my_text=paste(dd$Names, " Auc ",round(dd$auc,2)," high: ", round(dd$high,2), "low", round(dd$low,2))
ppxx <- dd %>%
plot_ly( x = ~dd$heights, y = ~dd$Names, color = ~dd$Enriched, type = "bar", orientaton = "h",
hoverinfo = "text", text = my_text ) %>%
#add_bars( orientation = 'h', color = ~dd$Enriched ) %>%
add_markers( x = ~dd$low - 0.5, y = ~dd$Names, marker = list(symbol=142, color="black"), showlegend = FALSE ) %>%
add_markers( x = ~dd$high - 0.5, y = ~dd$Names, marker = list(symbol=142, color="black"), showlegend = FALSE,
hoverinfo = "none" ) %>%
add_segments( x = ~dd$low - 0.5, xend = ~dd$high - 0.5, y = ~dd$Names, yend = ~dd$Names, color = toRGB("black"),
showlegend = FALSE, hoverinfo = "none") %>%
layout(title =NULL, xaxis = my.xaxis, margin = list(l=120,t=50,b=30,unit="pt",pad=2),
yaxis = list(title=""))
ppxx
}
#####################################################################
#####################################################################
#
output$filteredPlotly <- renderPlotly({
dd <- filteredData()
if(length(dd) == 0) {
return(NULL)
} else {
dd$heights = dd$auc - 0.5
dd$auc1 = dd$heights
dd$Enriched = levels(f)[(dd$auc<.5) + 1]
dd$Names = factor(rownames(dd), levels=rownames(dd)[order(dd$auc)])
generatePlot_ly(dd)
}
})
#####################################################################
#####################################################################
#
output$filterSummary <- renderTable({ data.frame(filteredData()) })
#####################################################################
#####################################################################
#
output$dataTable <- renderDataTable({
df = data.frame(filteredData())
if(length(df) > 0) {
c = colnames(df)
#print(paste("colnames ", c))
#print(paste("rownames ", rownames(df)))
df1 = df[c('Names','Enriched','auc','low','high','p.adjust',
'p.value', 'n1', 'n2')]
df1
} else {
df
}
}, options = list(orderClasses = TRUE))
### Update Citations when the method or adj method changes
observeEvent(input$adj_method, {
print(paste("adjust method changed ", input$adj_method))
btn <- input$adj_method
id <- paste0('txt', btn)
insertUI(
selector = '#placeholder',
## wrap element in a div with id for ease of removal
ui = tags$div(
tags$p(paste('Element number', btn)),
id = id
)
)
inserted <<- c(id, inserted)
})
#####################################################################
#####################################################################
#
summaryText <- reactive({
print("BLAH")
withTags({
div(class="header",
p("Specify a metadata file which contains a data.frame",
"(rownames must make the colnames of the data file)"),
p( paste("adjustment method: ", input$adj_method, " significant threshold: ", input$signficance_threshold,
"Suggested methodology wording:
References:
1.
2.
"))
)})
})
#####################################################################
#####################################################################
#
output$summary <- renderText({
paste("adjustment method: ", input$adj_method,
" significant threshold: ", input$signficance_threshold,
"<br/>Suggested methodology wording: References: 1. 2. ")})
})
Raw
ui.R
#
# This is the user-interface definition of a Shiny web application. You can
# run the application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
#
# http://shiny.rstudio.com/
#
library(shiny)
library(shinydashboard)
library(plotly)
library(markdown)
significance.options <- list(
"1.0" = 1.0,
"0.5" = 0.5,
"0.2" = 0.2,
"0.1" = 0.1,
"0.05" = 0.05,
"0.01" = 0.01,
"0.001" = 0.001,
"0.0001" = 0.0001,
"0.00001" = 0.00001,
"0.000001" = 0.000001,
"0.0000001" = 0.0000001,
"0.00000001" = 0.00000001,
"0.000000001" = 0.000000001)
significance.options.default = significance.options[3]
method.options = list("holm" = "holm", "hochberg" = "hochberg",
"hommel" = "hommel", "bonferroni" = "bonferroni",
"BH" = "BH","BY" = "BY", "fdr" = "fdr","none" = "none")
method.options.default = "fdr"
header <- dashboardHeader(
title = "PESAME Dashboard Header"
)
body <- dashboardBody(
fluidRow(verbatimTextOutput("informationMessage")),
fluidRow(
column( width = 9,
tabsetPanel(type="tabs",
tabPanel("Plotly",plotlyOutput("filteredPlotly")),
tabPanel("Plot",plotOutput("filteredPlot")),
# inside this tab put the citation and a markdown specific to this particular item
tabPanel("Citation",
textOutput("summary")),
tabPanel("Overview",
# maybe two rows, one the parameters output,
# then some details about the parameters
includeMarkdown("overview.md"))
)
),
column(width = 3,
selectInput("adj_method", label = h3("Comparison Method"),
choices = method.options,
selectize = FALSE,
size = 1,
selected = method.options.default),
selectInput(inputId = "signficance_threshold",
label=h3("Significance Threshold"),
selectize = FALSE,
size = 1,
choices = significance.options,
selected = significance.options.default ),
submitButton("Generate data")
)
)
#,
#fluidRow( tabPanel("Data", dataTableOutput("dataTable")))))
)
dashboardPage( header, dashboardSidebar(disable = TRUE), body)
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