Rename 'trunk' to 'pkg' for compatibility with R-forge

Author: warnes

.Rinstignore

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+doc/.*\.tex$
+doc/.*\.sty$
+doc/.*\.dtx$
+\.svn

ChangeLog

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+inst/ChangeLog

DESCRIPTION

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+Package: gdata
+Title: Various R Programming Tools for Data Manipulation
+Description: Various R programming tools for data manipulation, including:
+   - medical unit conversions ('ConvertMedUnits', 'MedUnits'),
+   - combining objects ('bindData', 'cbindX', 'combine', 'interleave'),
+   - character vector operations ('centerText', 'startsWith', 'trim'),
+   - factor manipulation ('levels', 'reorder.factor', 'mapLevels'),
+   - obtaining information about R objects ('object.size', 'elem', 'env',
+     'humanReadable', 'is.what', 'll', 'keep', 'ls.funs',
+     'Args','nPairs', 'nobs'),
+   - manipulating MS-Excel formatted files ('read.xls',
+     'installXLSXsupport', 'sheetCount', 'xlsFormats'),
+   - generating fixed-width format files ('write.fwf'),
+   - extricating components of date & time objects ('getYear', 'getMonth',
+     'getDay', 'getHour', 'getMin', 'getSec'),
+   - operations on columns of data frames  ('matchcols', 'rename.vars'),
+   - matrix operations ('unmatrix', 'upperTriangle', 'lowerTriangle'),
+   - operations on vectors ('case', 'unknownToNA', 'duplicated2', 'trimSum'),
+   - operations on data frames ('frameApply', 'wideByFactor'),
+   - value of last evaluated expression ('ans'), and
+   - wrapper for 'sample' that ensures consistent behavior for both
+     scalar and vector arguments ('resample').
+Depends: R (>= 2.3.0)
+SystemRequirements: perl (>= 5.10.0)
+Imports: gtools
+Version: 2.16.1
+Date: 2015-04-28
+Author: Gregory R. Warnes, Ben Bolker, Gregor Gorjanc, Gabor
+        Grothendieck, Ales Korosec, Thomas Lumley, Don MacQueen, Arni
+        Magnusson, Jim Rogers, and others
+Maintainer: Gregory R. Warnes <greg@warnes.net>
+License: GPL-2
+NeedsCompilation: no
+Suggests: RUnit

INSTALL

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+
+Windows
+=======
+
+The instructions below relate to Windows only and are not relevant to other
+platforms.
+
+On Windows, the perl based routines (read.xls, xls2sep, xls2csv, xls2tab,
+xls2tsv, sheetNames, sheetCount) will work with ActiveState perl but not with
+Rtools perl.
+
+If you have ActiveState perl installed and the pl extension is associated with
+it (which the ActiveState installer associates automatically) then read.xls and
+other perl based routines in gdata will automatically locate ActiveState perl
+if you omit the perl= argument on these commands even if Rtools perl is ahead 
+of it on your path. e.g.
+
+	read.xls("mysheet.xls")
+
+Alternately you can use the perl= argument with a path to ActiveState perl to
+ensure it uses the right one. e.g.
+
+	read.xls("mysheet.xls", perl = "C:\\Perl\\bin\\perl.exe")
+
+Also ensure that gdata was built with ActiveState Perl and not Rtools perl.
+This may require rebuilding gdata yourself like this:
+
+1. Download and install the following (which all have automatic Windows 
+   installers and are therefore very easy to install):
+
+   R (you likely already have R so you can likely skip this one)
+   http://www.r-project.org
+
+   Rtools
+   http://www.murdoch-sutherland.com/Rtools/
+
+   ActiveState perl (ActivePerl)
+   http://www.activestate.com/activeperl/
+
+2. If simply installing gdata in the usual way from within R results in
+   read.xls and associated perl-based routines not working then re-install
+   gdata yourself like this:
+
+   Download gdata_*.tar.gz from:
+   http://cran.r-project.org/web/packages/gdata/index.html
+
+   and install it at the Windows console (not from within R):
+   Rcmd INSTALL --build gdata_*.tar.gz
+
+   Note: Rcmd is normally found in C:\Program Files\R\R-*\bin and if that 
+   is not on your path the above command should be written:
+   "C:\Program Files\R\R-*\bin\Rcmd.exe" INSTALL --build gdata_*.tar.gz
+
+   where the the path to Rcmd.exe should be replaced with the output of this 
+   R command:
+	   normalizePath(file.path(R.home(), "bin", "Rcmd.exe"))
+
+   Note: On Vista and above you may need to run Rcmd as Administrator.
+
+   Note: In the above the * in gdata_*.tar.gz should be replaced with the 
+   current version of gdata as found on:
+   http://cran.r-project.org/web/packages/gdata/index.html
+

NAMESPACE

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+
+export(
+       .onAttach,
+       ans,
+       Args,
+       bindData,
+       case,
+       cbindX,
+       centerText,
+       combine,
+       ConvertMedUnits,
+       drop.levels,
+       duplicated2,
+       elem,
+       env,
+       first,
+       frameApply,
+       installXLSXsupport,
+       interleave,
+       is.what,
+       keep,
+       last,
+       left,
+       ll,
+       ls.funs,
+       lowerTriangle,
+       "lowerTriangle<-",
+       matchcols,
+       nobs,  # default method now provided by stats package
+       nPairs,
+       read.xls,
+       rename.vars,
+       remove.vars,
+       reorder.factor,
+       resample,
+       right,
+       sheetCount,
+       sheetNames,
+       startsWith,
+       trim,
+       trimSum,
+       unmatrix,
+       upperTriangle,
+       "upperTriangle<-",
+       wideByFactor,
+       write.fwf,
+       xls2csv,
+       xls2tab,
+       xls2tsv,
+       xls2sep,
+       xlsFormats,
+
+       ## Object size stuff
+       object.size, as.object_sizes, is.object_sizes, humanReadable,
+
+       ## getDateTime stuff
+       getYear, getMonth, getDay, getHour, getMin, getSec,
+
+       ## mapLevels stuff
+       mapLevels, as.levelsMap, as.listLevelsMap, is.levelsMap, is.listLevelsMap, "mapLevels<-",
+
+       ## unknown stuff
+       isUnknown, unknownToNA, NAToUnknown
+)
+
+importFrom(stats, reorder)
+importFrom(stats, nobs)
+importFrom(gtools, mixedsort)
+
+S3method(reorder, factor)
+
+S3method(summary, nPairs)
+
+## drop.levels stuff
+S3method(drop.levels, default)
+S3method(drop.levels, factor)
+S3method(drop.levels, list)
+S3method(drop.levels, data.frame)
+
+## getDateTime stuff
+S3method(getYear, default)
+S3method(getYear, Date)
+S3method(getYear, POSIXct)
+S3method(getYear, POSIXlt)
+
+S3method(getMonth, default)
+S3method(getMonth, Date)
+S3method(getMonth, POSIXct)
+S3method(getMonth, POSIXlt)
+
+S3method(getDay, default)
+S3method(getDay, Date)
+S3method(getDay, POSIXct)
+S3method(getDay, POSIXlt)
+
+S3method(getHour, default)
+
+S3method(getMin, default)
+
+S3method(getSec, default)
+
+## mapLevels stuff
+S3method(mapLevels, default)
+S3method(mapLevels, character)
+S3method(mapLevels, factor)
+S3method(mapLevels, list)
+S3method(mapLevels, data.frame)
+
+S3method("mapLevels<-", default)
+S3method("mapLevels<-", list)
+S3method("mapLevels<-", data.frame)
+
+S3method(print, levelsMap)
+S3method(print, listLevelsMap)
+
+S3method("[", levelsMap)
+S3method("[", listLevelsMap)
+
+S3method(c, levelsMap)
+S3method(c, listLevelsMap)
+
+S3method(unique, levelsMap)
+S3method(sort, levelsMap)
+
+## nobs stuff
+S3method(nobs, data.frame)
+S3method(nobs, default)
+S3method(nobs, lm)      # now provided by stats package
+
+## Object size stuff
+S3method(c,      object_sizes)
+S3method(format, object_sizes)
+S3method(print,  object_sizes)
+
+## unknown stuff
+S3method(isUnknown, default)
+S3method(isUnknown, POSIXlt)
+S3method(isUnknown, list)
+S3method(isUnknown, data.frame)
+S3method(isUnknown, matrix)
+
+S3method(unknownToNA, default)
+S3method(unknownToNA, factor)
+S3method(unknownToNA, list)
+S3method(unknownToNA, data.frame)
+
+S3method(NAToUnknown, default)
+S3method(NAToUnknown, factor)
+S3method(NAToUnknown, list)
+S3method(NAToUnknown, data.frame)
+
+## trim stuff
+S3method(trim, character)
+S3method(trim, default)
+S3method(trim, factor)
+S3method(trim, list)
+S3method(trim, data.frame)
+
+## left, right
+S3method(left,  data.frame)
+S3method(left,  matrix)
+S3method(right, data.frame)
+S3method(right, matrix)

NEWS

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+inst/NEWS

R/Args.R

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+Args <- function(name, sort=FALSE)
+{
+  a <- formals(get(as.character(substitute(name)), pos=1))
+  if(is.null(a))
+    return(NULL)
+  arg.labels <- names(a)
+  arg.values <- as.character(a)
+  char <- sapply(a, is.character)
+  arg.values[char] <- paste("\"", arg.values[char], "\"", sep="")
+
+  if(sort)
+  {
+    ord <- order(arg.labels)
+    if(any(arg.labels == "..."))
+      ord <- c(ord[-which(arg.labels[ord]=="...")],
+               which(arg.labels=="..."))
+    arg.labels <- arg.labels[ord]
+    arg.values <- arg.values[ord]
+  }
+
+  output <- data.frame(value=I(arg.values), row.names=arg.labels)
+  print(output, right=FALSE)
+
+  invisible(output)
+}

R/ConvertMedUnits.R

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+ConvertMedUnits <- function(x, measurement, abbreviation,
+                            to=c("Conventional","SI","US"),
+                            exact=!missing(abbreviation))
+  {
+    MedUnits <- NULL ## Define to avoid R CMD check warning
+    data(MedUnits,package='gdata', envir=environment())
+    
+    to=match.arg(to)
+    if(!missing(measurement) && missing(abbreviation))
+      {
+        if(exact)
+          matchUnits <- MedUnits[tolower(MedUnits$Measurement)==
+                                 tolower(measurement),]
+        else
+          matchUnits <- MedUnits[grep(measurement, MedUnits$Measurement,
+                                  ignore.case=TRUE),]
+      }
+    else if(missing(measurement) && !missing(abbreviation))
+      {
+        if(exact)
+          matchUnits <- MedUnits[tolower(MedUnits$Abbreviation)==
+                                 tolower(abbreviation),]
+    else
+      matchUnits <- MedUnits[grep(match, MedUnits$Abbrevation,
+                                  ignore.case=TRUE),]
+      }
+    else # both missing or both specified
+      stop("One of `measurement' or `abbreviation' must be specified.")
+
+
+    if(nrow(matchUnits)>1)
+      stop(
+           paste("More than one matching row.  Please use 'exact=TRUE' ",
+                 "and supply one of these matching strings:",
+                 paste('\t"',matchUnits$Measurement, '"', sep='', collapse="\n\t"),
+                 sep="\n\t"))
+   else if (nrow(matchUnits)<1)
+     stop("No match")
+
+    if (to %in% c("Convetional", "US"))
+      {
+        retval <- x / matchUnits$Conversion
+        attr(retval,"units") <- matchUnits$ConventionalUnits
+      }
+    else
+      {
+        retval <- x * matchUnits$Conversion
+        attr(retval,"units") <- matchUnits$SIUnits
+      }
+    retval
+  }
+      
+    
+
+    
+    

R/ans.R

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+ans <- function() .Last.value

R/bindData.R

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+### bindData.R
+###------------------------------------------------------------------------
+### What: Bind two data frames - code
+### $Id$
+### Time-stamp: <2008-12-30 22:01:00 ggorjan>
+###------------------------------------------------------------------------
+
+bindData <- function(x, y, common)
+{
+  ## --- Setup ---
+  if(!is.data.frame(x)) stop("'x' must be a data frame")
+  if(!is.data.frame(y)) stop("'y' must be a data frame")
+
+  ## --- New data frame ---
+
+  ## First add common column and a dataset indicator column
+  z <- rbind(x[common], y[common])
+
+  ## Other columns
+  ## - remove common columns in x and y
+  namesz <- names(z)
+  otherx <- names(x)
+  otherx <- otherx[!(otherx %in% namesz)]
+  othery <- names(y)
+  othery <- othery[!(othery %in% namesz)]
+
+  ## - add all other columns but as a set for each input data frame
+  rx <- nrow(x); cx <- length(otherx)
+  ry <- nrow(y); cy <- length(othery)
+  
+  z <- cbind(z, rbind(x[otherx], matrix(rep(NA, times=(ry * cx)), nrow=ry, ncol=cx, dimnames=list(NULL, otherx))))
+  z <- cbind(z, rbind(matrix(rep(NA, times=(rx * cy)), nrow=rx, ncol=cy, dimnames=list(NULL, othery)), y[othery]))
+
+  z
+}
+
+###------------------------------------------------------------------------
+### bindData.R ends here