[R-gregmisc-commits] r2135 - in pkg: SASxport SASxport/.Rproj.user SASxport/.Rproj.user/632EB997 SASxport/.Rproj.user/632EB997/pcs SASxport/.Rproj.user/632EB997/sdb SASxport/.Rproj.user/632EB997/sdb/mt SASxport/.Rproj.user/632EB997/sdb/per SASxport/.Rproj.user/632EB997/sdb/per/t SASxport/.Rproj.user/632EB997/sdb/per/t/42c64b18 SASxport/.Rproj.user/632EB997/sdb/per/u SASxport/.Rproj.user/632EB997/sdb/prop SASxport/.Rproj.user/shared fork fork/.Rproj.user fork/.Rproj.user/632EB997 fork/.Rproj.user/632EB997/pcs fork/.Rproj.user/632EB997/sdb fork/.Rproj.user/632EB997/sdb/per fork/.Rproj.user/632EB997/sdb/per/t fork/.Rproj.user/632EB997/sdb/per/u fork/.Rproj.user/shared gplots gplots/.Rproj.user gplots/.Rproj.user/632EB997 gplots/.Rproj.user/632EB997/pcs gplots/.Rproj.user/632EB997/sdb gplots/.Rproj.user/632EB997/sdb/mt gplots/.Rproj.user/632EB997/sdb/per gplots/.Rproj.user/632EB997/sdb/per/t gplots/.Rproj.user/632EB997/sdb/per/t/a31943ab gplots/.Rproj.user/632EB997/sdb/per/t/d9524f0f gplots/.Rproj.user/632EB997/sdb/per/t/edc438ca gplots/.Rproj.user/632EB997/sdb/per/u gplots/.Rproj.user/632EB997/sdb/prop gplots/.Rproj.user/shared
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 12 19:38:14 CEST 2016
Author: warnes
Date: 2016-08-12 19:38:13 +0200 (Fri, 12 Aug 2016)
New Revision: 2135
Added:
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pkg/SASxport/.Rproj.user/632EB997/
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Log:
Add RStudio files
Added: pkg/SASxport/.Rproj.user/632EB997/build_options
===================================================================
--- pkg/SASxport/.Rproj.user/632EB997/build_options (rev 0)
+++ pkg/SASxport/.Rproj.user/632EB997/build_options 2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,4 @@
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===================================================================
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+++ pkg/SASxport/.Rproj.user/632EB997/persistent-state 2016-08-12 17:38:13 UTC (rev 2135)
@@ -0,0 +1,9 @@
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+build-last-errors-base-dir="~/src/r-gregmisc/SASxport/"
+build-last-outputs="[{\"output\":\"==> R CMD INSTALL --no-multiarch --with-keep.source SASxport\\n\\n\",\"type\":0},{\"output\":\"\\n\",\"type\":1},{\"output\":\" Welcome to BI enhanced R!\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing to library '/home/gwarnes1/Rlib'\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* installing *source* package 'SASxport' ...\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** libs\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"make: Nothing to be done for `all'.\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"installing to /home/gwarnes1/Rlib/SASxport/libs\\n\",\"type\":1},{\"output\":\"** R\\n\",\"type\":1},{\"output\":\"** data\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** inst\\n\",\"type\":1},{\"output\":\"** preparing package for lazy loading\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** help\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"*** installing help indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\" converting help for package 'SASxport'\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\" finding HTML links ...\",\"type\":1},{\"output\":\" Alfalfa html \",\"type\":1},{\"output\":\" done\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" SASformat html \\n\",\"type\":1},{\"output\":\" SASxport-package html \\n\",\"type\":1},{\"output\":\" lookup.xport html \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" makeSASNames html \\n\",\"type\":1},{\"output\":\" read.xport html \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" finding level-2 HTML links ...\",\"type\":1},{\"output\":\" done\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" toSAS html \\n\",\"type\":1},{\"output\":\" write.xport html \",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** building package indices\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"** testing if installed package can be loaded\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" Welcome to BI enhanced R!\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"Loaded SASxport version 1.5.4 (2016-03-25).\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\" Type `?SASxport' for usage information.\\n\",\"type\":1},{\"output\":\"\\n\",\"type\":1},{\"output\":\"\",\"type\":1},{\"output\":\"* DONE (SASxport)\\n\",\"type\":1},{\"output\":\"\",\"type\":1}]"
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+ "contents" : "Package: SASxport\nType: Package\nTitle: Read and Write SAS XPORT Files\nVersion: 1.5.4\nDate: 2016-03-25\nDescription: Functions for reading, listing\n the contents of, and writing SAS xport format files.\n The functions support reading and writing of either\n individual data frames or sets of data frames. Further,\n a mechanism has been provided for customizing how\n variables of different data types are stored.\nAuthor:\n Unless otherwise noted, the contents of this package were written by\n Gregory R. Warnes <greg at warnes.net> and are provided under the\n terms of the GNU General Public License, version 2.0 or later.\n --\n The files 'src/ieee2ibm.c' and 'src/ibm2ieee.c' were extracted from\n BRL-CAD file /brlcad/src/libbu/htond.c written by Michael John\n Muuss, Copyright (c) 2004-2007 United States Government as\n represented by the U.S. Army Research Laboratory, and is utilized\n and redistributed under the terms of the GNU Lesser General Public\n License, version 2.1.\n --\n The files 'R/AFirst.lib.s', 'R/all.is.numeric.R',\n 'R/importConvertDateTime.R', 'R/in.opererator.R', 'R/makeNames.R',\n 'R/read.xport.R', and 'R/testDateTime.R' are copied or adapted from the\n 'Hmisc' package created by Frank E. Harrell, Jr.\n <f.harrell at vanderbilt.edu>, and are utilized and redistributed under\n the terms of the GNU General Public License, version 2.0 or later.\n --\n The files 'R/xport.R', 'src/SASxport.c', 'src/SASxport.h', and\n 'src/foreign.h' are copied or adapted from the R 'foreign' package\n created by Douglas M. Bates <bates at stat.wisc.edu> and Saikat DebRoy\n <saikat at stat.wisc.edu>, and are utilized and redistributed under the\n terms of the GNU General Public License, version 2.0 or later.\n --\n The creation of this package was partially funded by Metrum Institute\n <http://metruminstitute.org>.\nMaintainer: Gregory R. Warnes <greg at warnes.net>\nLicense: GPL-2\nDepends: R (>= 2.4.0), chron, Hmisc\nURL: http://www.warnes.net, http://metruminstitute.org\n",
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+ "contents" : "\\name{read.xport}\n\\alias{read.xport}\n\\title{Import a SAS XPORT File}\n\\description{\n Read a SAS XPORT format file and return the contained dataset(s).\n}\n\\usage{\nread.xport(file,\n force.integer=TRUE,\n formats=NULL,\n name.chars=NULL,\n names.tolower=FALSE,\n keep=NULL,\n drop=NULL,\n as.is=0.95,\n verbose=FALSE,\n as.list=FALSE,\n include.formats=FALSE\n )\n}\n\\arguments{\n \\item{file}{Character string specifying the name or URL of a SAS XPORT\n file.\n }\n \\item{force.integer}{Logical flag indicating whether integer-valued\n variables should be returned as integers (\\code{TRUE}) or doubles\n (\\code{FALSE}). Variables outside the supported integer range\n (\\code{.Machine$integer.max}) will always be converted to\n doubles.\n }\n \\item{formats}{a data frame or list (like that created by\n \\code{foreign:::read.xport}) containing \\code{PROC FORMAT}\n output, if such output is not stored in the main transport\n file.\n }\n \\item{name.chars}{Vector of additional characters permissible in\n variable names. By default, only the alpha and numeric\n characters ([A-Za-z0-9]) and periods ('.') are permitted. All\n other characters are converted into periods ('.').\n }\n \\item{names.tolower}{Logical indicating whether variable and dataset\n names should be converted to lowercase (\\code{TRUE}) or left\n uppercase (\\code{FALSE})\n }\n \\item{keep}{a vector of names of SAS datasets to process. This list\n must include \\code{PROC FORMAT} dataset if it is present for\n datasets to use use any of its value label formats.\n }\n \\item{drop}{a vector of names of SAS datasets to ignore (original SAS\n upper case names)\n }\n \\item{as.is}{\n Either a logical flag indicating whether SAS character variables should\n be preserved as character objects (\\code{TRUE}) or factor\n objects (\\code{FALSE}), or a fractional cutoff between 0 and 1.\n\n When a fractional cutoff is provided, character variables\n containing a more than this fraction of unique values will be\n stored as a character variables. This is done in order to\n preserve space, since factors must store both the integer factor\n codes and the character factor labels.\n }\n \\item{verbose}{Logical indicating whether progress should be printed\n during the data loading and conversion process.}\n \\item{as.list}{Logical indicating whether to return a list even if\n the SAS xport file contains only only one dataset.}\n \\item{include.formats}{Logical indicating whether to include SAS\n format information (if present) in the returned list}\n}\n\\value{\n If only a single dataset is present (after removing \\code{PROC FORMAT}\n data when \\code{include.formats=FALSE}), the return value is a single\n dataframe object. Otherwise the return is a list of dataframe objects.\n\n Note that if \\code{include.formats=TRUE}, the returned list will\n contain a dataframe named \"FORMATS\" containing any available 'PROC FORMAT'\n information.\n}\n\\details{\n\n \\itemize{\n \\item SAS date, time, and date/time variables are converted respectively to \\code{Date},\n POSIX, or \\code{chron} objects\n\n \\item SAS labels are stored in \"label\" attributes on each variable,\n and are accessible using the \\code{\\link{label}} function.\n\n \\item SAS formats are stored in \"SASformat\" attributes on each\n variable, and are accessable using \\code{\\link{SASformat}}\n\n \\item SAS iformats are stored in \"SASiformat\" attributes on each\n variable, and are accessable using \\code{\\link{SASiformat}}\n\n \\item SAS integer variables are stored as integers unless\n \\code{force.integer} is \\code{FALSE}\n }\n\n If the file includes the output of \\code{PROC FORMAT CNTLOUT=},\n variables having customized label formats will be converted to \\code{factor}\n objects with appropriate labels.\n\n If a datasets in the original file has a label or type, these will be\n stored in the corresponding 'lable' and 'SAStype' attributes, which\n can be accessed by the \\code{\\link{label}} and \\code{\\link{SAStype}}\n functions.\n}\n\\author{ Gregory R. Warnes \\email{greg at warnes.net}\n based on \\code{Hmisc:::sasxport.get} by Frank E. Harrell, Jr.}\n\\section{Note}{\n This code provides a subset of the functionality of the\n \\code{sasxport.get} function in the Hmisc library.\n}\n\\seealso{\n \\code{\\link[foreign]{read.xport}},\n \\code{\\link{label}},\n \\code{\\link[Hmisc]{sas.get}},\n \\code{\\link[Hmisc]{sasxport.get}},\n \\code{\\link{Dates}},\n \\code{\\link{DateTimeClasses}},\n \\code{\\link[chron]{chron}},\n \\code{\\link[foreign]{lookup.xport}},\n \\code{\\link[Hmisc]{contents}},\n \\code{\\link[Hmisc]{describe}},\n \\code{\\link{label}},\n \\code{\\link{SASformat}},\n \\code{\\link{SASiformat}}, and\n \\code{\\link{SAStype}}\n}\n\\examples{\n\n## -------\n## SAS code to generate test dataset:\n## -------\n## libname y SASV5XPT \"test2.xpt\";\n##\n## PROC FORMAT; VALUE race 1=green 2=blue 3=purple; RUN;\n## PROC FORMAT CNTLOUT=format;RUN; * Name, e.g. 'format', unimportant;\n## data test;\n## LENGTH race 3 age 4;\n## age=30; label age=\"Age at Beginning of Study\";\n## race=2;\n## d1='3mar2002'd ;\n## dt1='3mar2002 9:31:02'dt;\n## t1='11:13:45't;\n## output;\n##\n## age=31;\n## race=4;\n## d1='3jun2002'd ;\n## dt1='3jun2002 9:42:07'dt;\n## t1='11:14:13't;\n## output;\n## format d1 mmddyy10. dt1 datetime. t1 time. race race.;\n## run;\n## data z; LENGTH x3 3 x4 4 x5 5 x6 6 x7 7 x8 8;\n## DO i=1 TO 100;\n## x3=ranuni(3);\n## x4=ranuni(5);\n## x5=ranuni(7);\n## x6=ranuni(9);\n## x7=ranuni(11);\n## x8=ranuni(13);\n## output;\n## END;\n## DROP i;\n## RUN;\n## PROC MEANS; RUN;\n## PROC COPY IN=work OUT=y;SELECT test format z;RUN; *Creates test2.xpt;\n## ------\n\n## Read this dataset from a local file:\ntestFile <- system.file('extdata', 'test2.xpt', package=\"SASxport\")\nw <- read.xport(testFile)\nclass(w)\nsapply(w, head)\n\n\\dontrun{\n## Or read a copy of test2.xpt available on the web:\nurl <- 'http://biostat.mc.vanderbilt.edu/wiki/pub/Main/Hmisc/test2.xpt'\nw <- read.xport(url)\n}\n\n## We can also get the dataset wrapped in a list\nw <- read.xport(testFile, as.list=TRUE)\nclass(w)\nsapply(w, head)\n\n## And we can ask for the format information to be included as well.\nw <- read.xport(testFile, as.list=TRUE, include.formats=TRUE)\nclass(w)\nsapply(w, head)\n\n\\dontshow{\nstopifnot( is.data.frame(w)==FALSE && is.list(w)==TRUE )\n}\n\n\n#### The Hmisc library provides many useful functions for interacting with\n#### data imported from SAS via read.xport()\nlibrary(Hmisc)\n\ndescribe(w$TEST) # see labels, format names for dataset test\nlapply(w, describe, \"\")# see descriptive stats in more detail for each variable\n\ncontents(w$TEST) # another way to see variable attributes\nlapply(w, contents)# show contents of individual items in more detail\n\noptions(digits=7) # compare the following matrix with PROC MEANS output\nt(sapply(w$Z, function(x)\n c(Mean=mean(x),SD=sqrt(var(x)),Min=min(x),Max=max(x))))\n\n}\n\\keyword{interface}\n\\keyword{manip}\n",
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Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/91BF8EB8
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+ "contents" : "\\name{write.xport}\n\\alias{write.xport}\n\\title{Write Data to a SAS XPORT File}\n\\description{\n This function writes one or more data frames into a SAS XPORT format\n library file.\n}\n\\usage{\nwrite.xport(...,\n list=base::list(),\n file = stop(\"'file' must be specified\"),\n verbose=FALSE,\n sasVer=\"7.00\",\n osType,\n cDate=Sys.time(),\n formats=NULL,\n autogen.formats=TRUE\n )\n}\n\\arguments{\n \\item{\\dots}{One or more data frames to be stored}\n \\item{list}{A list containing data frames to be stored.}\n \\item{file}{File name or connection object. Use \"\" to view the raw data}\n \\item{verbose}{Logical flag controlling whether status is reported\n during processing}\n \\item{sasVer}{SAS version string}\n \\item{osType}{Opererating system, defaults to \"R X.Y.Z\" for\n appropriate values of X, Y, and Z}\n \\item{cDate}{Date object specifying dataset creation date}\n \\item{formats}{Optional data frame containing SAS format information.}\n \\item{autogen.formats}{Logical indiciating whether SAS formats should be\n auto-generated for factor variables.}\n}\n\\details{\n The function creates a SAS XPORT data file (see reference) from one or\n more data frames. This file format imposes a number of constraints:\n \\itemize{\n \\item Data set and variable names are truncated to 8 characters and\n converted to upper case. All characters outside of the set A-Z,\n 0-9, and '\\_' are converted to '\\_'.\n \\item Character variables are stored as characters.\n \\item If \\code{autogen.formats=TRUE} (the default), factor variables\n are stored as numeric with an appropriate SAS format\n specification. If \\code{autogen.formats=FALSE}, factor variables\n are stored as characters.\n \\item All numeric variables are stored as double-precision floating\n point values utilizing the IBM mainframe double precision floating\n point format (see the reference).\n \\item Date and time variables are either converted to number of days since\n 1960-01-01 (date only), or number of seconds since\n 1960-01-01:00:00:00 GMT (date-time variables).\n \\item Missing values are converted to the standard SAS missing value\n '.'\n }\n\n The SAS XPORT format allows each dataset to have a label and a type\n (set via the \\code{\\link{label}} and \\code{\\link{SAStype}} functions).\n In addition, each variable may have a corresponding label, display\n format, and input format. To set these values, add the attribute\n 'label', 'SASformat', or 'SASiformat' to individual data frame. These\n attributes may be set using the \\code{\\link{label}},\n \\code{\\link{SASformat}}, and \\code{\\link{SASiformat}} functions. (See\n examples provided below.)\n\n The actual translation of R objects to objects appropriate for SAS is\n handled by the \\code{\\link{toSAS}} generic and associated methods,\n which can be (re)defined by the user to provide fine-grained control.\n}\n\\value{\n No return value\n}\n\\references{\n SAS Technical Support document TS-140: ``The Record Layout of a\n Data Set in SAS Transport (XPORT) Format'' available at\n \\url{https://support.sas.com/techsup/technote/ts140.pdf}.\n}\n\\author{Gregory R. Warnes \\email{greg at warnes.net}}\n\\note{\n This package was created with partial funding by Metrum Institute\n \\url{http://metruminstitute.org}.\n}\n\\seealso{\n \\code{\\link{toSAS}},\n \\code{\\link{lookup.xport}},\n \\code{\\link{read.xport}},\n \\code{\\link{label}},\n \\code{\\link{SAStype}},\n \\code{\\link{SASformat}},\n and \\code{\\link{SASiformat}}\n}\n\\examples{\n\n#####\n## R version of the example given in TS-140\n#####\n\n## manually create a data set\nabc <- data.frame( x=c(1, 2, NA, NA ), y=c('a', 'B', NA, '*' ) )\n\n## look at it\nabc\n\n## add a format specifier (not used by R)\nSASformat(abc$x) <- 'date7.'\n\n## add a variable label (not used by R)\nlabel(abc$y) <- 'character variable'\n\n## add a dataset label and type\nlabel(abc) <- 'Simple example'\nSAStype(abc) <- 'MYTYPE'\n\n## verify the additions\nstr(abc)\n\n# create a SAS XPORT file\nwrite.xport( abc, file=\"xxx.dat\" )\n\n# list the contents of the file\nlookup.xport(\"xxx.dat\")\n\n## reload the data\nxxx.abc <- read.xport(\"xxx.dat\")\n\n## and look at it\nxxx.abc\n\n## Check the label and type\nlabel(xxx.abc)\nSAStype(xxx.abc)\n\n## Note that the variable names and SAS dataset type have been converted\n## to uppercase\n\n}\n\\keyword{file}\n",
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Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF
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+++ pkg/SASxport/.Rproj.user/632EB997/sdb/mt/B97C53CF 2016-08-12 17:38:13 UTC (rev 2135)
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+ "contents" : "useDynLib(SASxport, .registration=TRUE)\n\nimportFrom(chron, chron, times)\nimportFrom(utils, packageDescription)\nimportFrom(Hmisc, label, label.default, \"label<-\", \"label<-.default\")\nimportFrom(utils, download.file)\n\nexport(\n toSAS,\n lookup.xport,\n read.xport,\n write.xport,\n ## \"label\",\n ## \"label<-\",\n\n makeSASNames,\n\n \"SASformat\",\n \"SASformat<-\",\n\n \"SASiformat\",\n \"SASiformat<-\",\n\n \"SAStype\",\n \"SAStype<-\"\n)\n\nS3method(toSAS, numeric)\nS3method(toSAS, logical)\nS3method(toSAS, character)\nS3method(toSAS, factor)\nS3method(toSAS, chron)\nS3method(toSAS, POSIXt)\nS3method(toSAS, Date)\nS3method(toSAS, default)\n\n## S3method(label, default)\nS3method(SASformat, default)\nS3method(SASiformat, default)\nS3method(SAStype, default)\n\n## S3method(label, data.frame)\nS3method(SASformat, data.frame)\nS3method(SASiformat, data.frame)\n##S3method(SAStype, data.frame)\n\n## S3method(\"label<-\", default)\nS3method(\"SASformat<-\", default)\nS3method(\"SASiformat<-\", default)\nS3method(\"SAStype<-\", default)\n\n## S3method(\"label<-\", data.frame)\nS3method(\"SASformat<-\", data.frame)\nS3method(\"SASiformat<-\", data.frame)\n##S3method(\"SAStype<-\", data.frame)\n\nS3method(print, lookup.xport)\nS3method(summary, lookup.xport)\nS3method(print, summary.lookup.xport)\n\n",
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Added: pkg/SASxport/.Rproj.user/632EB997/sdb/mt/EB1F71A0
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/r-gregmisc -r 2135
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