# Xpose 4
# An R-based population pharmacokinetic/
# pharmacodynamic model building aid for NONMEM.
# Copyright (C) 1998-2004 E. Niclas Jonsson and Mats Karlsson.
# Copyright (C) 2005-2008 Andrew C. Hooker, Justin J. Wilkins,
# Mats O. Karlsson and E. Niclas Jonsson.
# Copyright (C) 2009-2010 Andrew C. Hooker, Mats O. Karlsson and
# E. Niclas Jonsson.
# This file is a part of Xpose 4.
# Xpose 4 is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation, either version 3
# of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser General Public License
# along with this program. A copy can be cound in the R installation
# directory under \share\licenses. If not, see http://www.gnu.org/licenses/.
#' @describeIn add_transformed_columns Create a log transformation of an existing variable
#' @export
"add.log" <- function(object, listall=TRUE, classic=FALSE )
{
if(listall) db.names(object)
cat("Please type the names of the items to be log-transformed, one\n")
cat("per line, and finish with a blank line.\n")
items <- scan(what=character())
data <- object@Data
sdata <- object@SData
nams <- names(data)
for(i in items) {
if(is.na(match(i, nams))) {
cat("No match: ", i, "\n", sep="")
next
}
if(any(data[[i]] <=0)) {
cat(i,"contains entries which are less than or equal to zero!\n")
next
}
nam <- paste("log", i, sep="")
#cat(nam)
newit <- log(data[[i]])
newits <- log(sdata[[i]])
if(any((data[[i]]-newit) !=0)) {
data[[nam]] <- newit
#vname(data[,nam]) <- nam
}
if(any((sdata[[i]]-newits) !=0)) {
sdata[[nam]] <- newits
#vname(data[,nam]) <- nam
}
}
object@Data <- data
object@SData <- sdata
for (i in items) {
logitem <- paste("log", i, sep="")
object@Prefs@Labels[[logitem]] <- c(paste("log(", i, ")", sep=""))
}
if (classic==TRUE) {
#assign(paste("xpdb", object@Runno, sep = ""), object, immediate=T, envir = .GlobalEnv)
#assign(pos = 1, ".cur.db", eval(as.name(paste("xpdb", object@Runno, sep = ""))))
#return(cat(""))
## to avoid checks on global variable assignment in package building
c1<-call("assign",paste("xpdb", object@Runno, sep = ""),object,envir=.GlobalEnv)
eval(c1)
c2<-call("assign",pos = 1, ".cur.db", eval(as.name(paste("xpdb", object@Runno, sep = ""))))
eval(c2)
return(cat(""))
} else {
return(object)
}
}
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