Nothing
R/ReadWriteSEERSTAT.R
In SEER2R: reading and writing SEER*STAT data files
#' SEER2R is a package used for reading data from and writing data to SEET*STAT data format
#' SEER*STAT plain data are represented in two files: dic and txt files. The dic file contains
#' variable information and the txt file contains data in columns.
NA;
#' This package is used for
#' @rdname SEER2-package
#roxygen();
######################
# private functions
######################
#' accessory functions
.string.trimleadingtrailing <- function(string){
# input see the parameter list
# return result
result <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", string, perl=TRUE)
}
.string.cutSubStringFileExtension <- function(FileName){
# input see the parameter list
# return result
ExtRegularExpr <- c("[.][^.]*$");
result <- sub(ExtRegularExpr, "", FileName, perl=TRUE);
result;
}
.catStr=function(myStr, ...,sep=""){
result=paste(
paste(myStr,collapse="",sep=sep),
...,
sep=sep
);
}
.create.emptyDataFrame.string=function(ColNames){
TableContentData=data.frame();
NumCols=length(ColNames);
if(NumCols>0)
for(ColIndex in 1:NumCols){
TableContentData=cbind(TableContentData,data.frame(numeric(0)));
}
colnames(TableContentData)=ColNames;
TableContentData;
}
.is.empty=function(x){
if(class(x) == "data.frame"){
result=(dim(x)[1]*dim(x)[2] == 0)
}else{
result=(length(as.vector(x)) == 0);
}
result;
}
.removeACharAll = function(char, string){
result <- gsub(char, "\\1", as.character(string), perl=TRUE)
}
.removeQuoteAll = function(string){
result <- .removeACharAll("\"",string);
}
.addQuoteIfSpaceAtEnd = function(string){
string = as.character(string);
Pattern1 = "^[[:space:]]+";
Pattern2 = "[[:space:]]+$";
ReturnedStr = string;
SpaceAtEnd = (length(grep(Pattern1, string)) == 1) || (length(grep(Pattern2, string)) == 1);
if(SpaceAtEnd){
ReturnedStr = .catStr("\"",string,"\"");
}
return(ReturnedStr);
}
.is.substring = function(x, string){
return(length(grep(x, string,ignore.case = TRUE)) == 1);
}
.substituteColNames = function(ByVarNamesInF, ByVarsDataColNamesInF, ColNamesInF){
NumNamesInF = length(ColNamesInF);
NumByVarNamesInF = length(ByVarNamesInF);
ColIndexByVar = numeric(NumByVarNamesInF);
if(NumNamesInF > 0 && NumByVarNamesInF > 0)
for(VInd in 1:NumByVarNamesInF){
for(NameInd in 1:NumNamesInF){
# if(.is.substring(ByVarNamesInF[VInd], gsub("_"," ", ColNamesInF[NameInd]))){
if(.is.substring(ByVarNamesInF[VInd], ColNamesInF[NameInd])){
ColNamesInF[NameInd] = ByVarsDataColNamesInF[VInd];
ColIndexByVar[VInd] = NameInd;
break;
}
}
}
return(list(ColNamesInF = ColNamesInF,ColIndexByVar = ColIndexByVar));
}
.assignColNames = function(data,ColNames = NULL){
OldColNames = colnames(data);
if(!is.null(ColNames)){
NewColNameInfo = .substituteColNames(ColNames, ColNames, OldColNames);
colnames(data) = NewColNameInfo$ColNamesInF;
attr(data,"NewColNameInfo") = NewColNameInfo;
}
return(data);
}
.getSubDataByVarName = function(data,ColNames = NULL){
TempData = .assignColNames(data,ColNames = ColNames);
NewColNameInfo = attr(TempData,"NewColNameInfo");
GoodColIndics = NewColNameInfo$ColIndexByVar[NewColNameInfo$ColIndexByVar>0];
NumByVars = length(GoodColIndics);
if(NumByVars > 0){
TempData1 = TempData[,GoodColIndics];
#attr(TempData1,"DICInfo") = attr(TempData,"DICInfo");
}else{
TempData1 = TempData;
}
return(TempData1);
}
#############################
# package specific functions
#############################
.replaceLabOrNum = function(VarFormatSecListInF, dataInF, LabReplaced = TRUE){
#LabReplaced = TRUE: means that current values are Labels, and will be replaced with numeric values
#columns of VarFormatSecListInF[[VarIndex]]: Numeric, Labels
NumVars = length(VarFormatSecListInF);
if(NumVars > 0){
for(VarIndex in 1:NumVars){
cntSection = VarFormatSecListInF[[VarIndex]];
if(!.is.empty(cntSection)){
NumLabels = dim(cntSection)[1];
for(LabIndex in 1:NumLabels){
ValueOnCheck = as.character(cntSection[LabIndex,1]);
ValueAssigned = .removeQuoteAll(cntSection[LabIndex,2]);
if(LabReplaced){
ValueOnCheck = .removeQuoteAll(as.character(cntSection[LabIndex,2]));
ValueAssigned = cntSection[LabIndex,1];
}
dataInF[as.character(dataInF[,VarIndex]) == ValueOnCheck,VarIndex] = ValueAssigned;
}
}
}
}
return(dataInF);
}
#' @include myLib.r
#' @callGraph
.read.SeerStatDIC = function(DICfileName){
# input:
# DICfileName:
# returned: (see the end of the function definition)
DicFileInF = DICfileName;
lines = readLines(DicFileInF);
#function for reading a section
findSectionInfo = function(lines,Pattern,splitchar="=",addedToName="",IsPatternStr=FALSE) {
#if IsPatternStr=FALSE, Pattern is regular expression
ItemInfo=data.frame("ItemNameInDic"=numeric(0),"ItemValueInDic"=numeric(0));
SectionName=character();
if(length(lines)>0)
for(LineInd in 1:length(lines)){
if(length(grep(Pattern, lines[LineInd], fixed=IsPatternStr)) == 1){
ItemInd = 1;
ItemLineInd=1;
SectionName=.string.trimleadingtrailing(lines[LineInd]);
while(lines[LineInd + ItemLineInd] != "" ){
if(length(grep(splitchar, lines[LineInd + ItemLineInd])) == 1){
ItemNames = unlist(strsplit(lines[LineInd + ItemLineInd], split=splitchar));
if(length(ItemNames) == 2){
ItemInfo[ItemInd,] = c(paste(as.character(ItemNames[1]),addedToName,sep=""),as.character(ItemNames[2]));
}else{
ItemInfo[ItemInd,1] = paste(as.character(ItemNames[1]),addedToName,sep="");
}
ItemInd = ItemInd + 1;
}
ItemLineInd = ItemLineInd + 1;
}
}
}
attr(ItemInfo, "SectionNameInDIC") = SectionName;
return(ItemInfo);
}
#read sections:
# System
SystemInfo = findSectionInfo(lines,Pattern="System[]]",splitchar="=",addedToName="");
# Session Options
SessionOptionInfo = findSectionInfo(lines,Pattern="Session Options[]]",splitchar="=",addedToName="");
# Export Options
ExportOptionInfo = findSectionInfo(lines,Pattern="Export Options[]]",splitchar="=",addedToName="");
# VarAllInfo
VarAllInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="=",addedToName="");
# Variables of non-survival data, Page Variables of survival data
VarInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Name=",addedToName="Name");
VarBaseInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Base=",addedToName="Base");
VarFormatSecList = list();
VarDimInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Dimension=",addedToName="Dimension");
VarDimList = list();
findVarFormatSecList = function(lines,VarBaseInfoInF,VarInfoInF){
NumBases = dim(VarBaseInfoInF)[1];
PageVar="Page type";
NumVars = dim(VarInfoInF)[1];
VarFormatSecListInF = list();
if(NumVars > 0)
for(VarInd in NumVars:1){
cntVar = as.character(VarInfoInF[VarInd,"ItemNameInDic"]);
cntVarItemValueInDic = as.character(VarInfoInF[VarInd,"ItemValueInDic"]);
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
if(.is.empty(VarFormatSecListInF[[VarInd]]))
VarFormatSecListInF[[VarInd]] = NULL;
comments = function(){
#if the variable is Page type, then handle it
if(length(grep(PageVar, cntVarItemValueInDic)) == 1){
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
}
if(NumBases > 0)
for(BaseInd in 1:NumBases){
cntBase = as.character(VarBaseInfoInF[BaseInd,"ItemNameInDic"]);
cntBase = unlist(strsplit(cntBase,"Base"))[1];
if(length(grep(cntBase, cntVar)) == 1){
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
}
}
}
}
return(VarFormatSecListInF)
}
VarFormatSecList = findVarFormatSecList(lines,VarBaseInfo,VarInfo);
PageVarNameInReadData = gsub("[,:()<>={}!@#$%^&*+-]", "", VarInfo[,"ItemValueInDic"]);
PageVarNameInReadData = gsub("[[:space:]]+", "_", PageVarNameInReadData);
Vars = data.frame(
"VarSymbolInDic" = VarInfo[,"ItemNameInDic"],
"VarNameInReadData" = PageVarNameInReadData,
"VarNameInTXT" = VarInfo[,"ItemValueInDic"]
);
attr(Vars, "SectionNameInDIC") = attr(VarInfo, "SectionNameInDIC");
attr(Vars, "VarBaseInfo") = VarBaseInfo;
attr(Vars, "VarFormatSecList") = VarFormatSecList;
attr(Vars, "VarDimInfo") = VarDimInfo;
attr(Vars, "VarDimList") = VarDimList;
returned=list(
SystemInfo=SystemInfo,
SessionOptionInfo = SessionOptionInfo,
ExportOptionInfo = ExportOptionInfo,
VarAllInfo = VarAllInfo,
Vars = Vars,
VarBaseInfo = VarBaseInfo,
VarFormatSecList = VarFormatSecList,
VarDimInfo = VarDimInfo,
VarDimList = VarDimList
);
}
####
##
.getReadingOptionFromExportOption = function(ExportOptionInfoInF){
# header = FALSE, sep = "", quote = "\"'",
# na.strings = "NA"
# gzfile("file.text.gz")
rownames(ExportOptionInfoInF)=ExportOptionInfoInF$ItemNameInDic;
GZipped = FALSE;
if("GZipped" %in% ExportOptionInfoInF$ItemNameInDic){
GZipped = ifelse(ExportOptionInfoInF["GZipped",2] == "true", TRUE, FALSE);
}
VariableformatNum = FALSE;
quotedlabels = TRUE;
if("Variable format" %in% ExportOptionInfoInF$ItemNameInDic){
VariableformatNum = !(length(grep("label", ExportOptionInfoInF["Variable format",2])) == 1);
quotedlabels = ifelse(ExportOptionInfoInF["Variable format",2] == "quotedlabels", TRUE, FALSE);
}
FileformatIsDOS = TRUE;
if("File format" %in% ExportOptionInfoInF$ItemNameInDic){
FileformatIsDOS = ifelse(ExportOptionInfoInF["File format",2] == "DOS/Windows", TRUE, FALSE);
}
Fielddelimiter = "\t";
if("Field delimiter" %in% ExportOptionInfoInF$ItemNameInDic){
Fielddelimiter = ifelse(ExportOptionInfoInF["Field delimiter",2] == "space", " ",
ifelse(ExportOptionInfoInF["Field delimiter",2] == "comma", ",",
ifelse(ExportOptionInfoInF["Field delimiter",2] == "semi-colon", ";", "\t")
));
}
MissingCh = ".";
if("Missing character" %in% ExportOptionInfoInF$ItemNameInDic){
MissingCh = ifelse(ExportOptionInfoInF["Missing character",2] == "period", ".", " ");
}
FieldsValuewithdelimiterinquotes = FALSE;
if("Fields with delimiter in quotes" %in% ExportOptionInfoInF$ItemNameInDic){
FieldsValuewithdelimiterinquotes = ifelse(ExportOptionInfoInF["Fields with delimiter in quotes",2] == "true", TRUE, FALSE);
}
VarNameIncluded = TRUE;
if("Variable names included" %in% ExportOptionInfoInF$ItemNameInDic){
VarNameIncluded = ifelse(ExportOptionInfoInF["Variable names included",2] == "true", TRUE, FALSE);
}
return(list(
GZipped = GZipped,
VariableformatNum = VariableformatNum,
quotedlabels = quotedlabels,
FileformatIsDOS = FileformatIsDOS,
Fielddelimiter = Fielddelimiter,
MissingCh = MissingCh,
FieldsValuewithdelimiterinquotes = FieldsValuewithdelimiterinquotes,
VarNameIncluded = VarNameIncluded
));
}
#' @include myLib.r
#' @callGraph
.read.SeerStatTXT = function(DICfileName, TXTfileName, UseVarLabelsInData=FALSE,ReadHeaderOnly=FALSE,...){
# input:
# DICfileName, TXTfileName
# returned: (see the end of the function definition)
InfoFromDIC=.read.SeerStatDIC(DICfileName);
ReadingOptionInfo = .getReadingOptionFromExportOption(InfoFromDIC$ExportOptionInfo);
NumVars = length(InfoFromDIC$VarFormatSecList);
if(NumVars == 0)
UseVarLabelsInData = TRUE;
DICInfo = list(
SystemInfo = InfoFromDIC$SystemInfo,
SessionOptionInfo = InfoFromDIC$SessionOptionInfo,
ExportOptionInfo = InfoFromDIC$ExportOptionInfo,
VarAllInfo = InfoFromDIC$VarAllInfo,
VarFormatSecList = InfoFromDIC$VarFormatSecList,
UseVarLabelsInData = UseVarLabelsInData
)
#DataFile
if(!ReadHeaderOnly){
if(ReadingOptionInfo$GZipped){
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".gz",sep="");
}
DataFile = gzfile(TXTfileName);
}else{
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
DataFile = TXTfileName;
}
#cntquote
cntquote = ifelse(!ReadingOptionInfo$VariableformatNum && ReadingOptionInfo$quotedlabels || ReadingOptionInfo$VarNameIncluded, "\"", "");
NumSkippedLines = ifelse(ReadingOptionInfo$VarNameIncluded,1,0);
TXTData = read.table(DataFile, skip = NumSkippedLines, #header = ReadingOptionInfo$VarNameIncluded,
sep = ReadingOptionInfo$Fielddelimiter, na.strings = ReadingOptionInfo$MissingCh,
quote = cntquote, ...
);
colnames(TXTData) = InfoFromDIC$Vars$VarNameInReadData;
if(UseVarLabelsInData && NumVars > 0){
TXTData = .replaceLabOrNum(InfoFromDIC$VarFormatSecList, TXTData, LabReplaced = FALSE);
}
}else{
return(DICInfo);
}
attr(TXTData, "DICInfo") = DICInfo;
attr(TXTData, "assignColNames") = .assignColNames;
attr(TXTData, "getSubDataByVarName") = .getSubDataByVarName;
return(TXTData);
}
.write.SeerStatDIC.section = function(DICSection, filename, append=TRUE){
#Assume that DICSection has very thing required ready
SectionNameInDIC = attr(DICSection, "SectionNameInDIC");
outputStr = .catStr(SectionNameInDIC,"\n");
NumRows = dim(DICSection)[1];
if(NumRows > 0)
for(RowIndex in 1:NumRows){
outputStr = .catStr(outputStr,
DICSection$ItemNameInDic[RowIndex],
"=",
DICSection$ItemValueInDic[RowIndex],
"\n"
);
}
write(outputStr, file=filename, sep="",append=append);
}
.assignItemValueToSecInfoVar = function(cntItemValue,cntItemName, cntSection){
SectionColNames = c("ItemNameInDic","ItemValueInDic");
if(cntItemName %in% cntSection$ItemNameInDic){
cntSection[cntItemName == cntSection$ItemNameInDic,2] = cntItemValue;
}else{
cntRow = .create.emptyDataFrame.string(SectionColNames);
cntRow[1,1] = cntItemName;
cntRow[1,2] = cntItemValue;
cntSectionNameInDIC = attr(cntSection, "SectionNameInDIC");
cntSection = rbind(cntRow, cntSection);
attr(cntSection, "SectionNameInDIC") = cntSectionNameInDIC;
}
return(cntSection);
}
.write.SeerStatDIC = function(DICInfo, DICfileName){
# input:
# DICfileName, TXTfileName
# returned:
# a list storing info in DICfileName
.write.SeerStatDIC.section(DICInfo$SystemInfo, DICfileName, append=FALSE)
.write.SeerStatDIC.section(DICInfo$SessionOptionInfo, DICfileName, append=TRUE)
.write.SeerStatDIC.section(DICInfo$ExportOptionInfo, DICfileName, append=TRUE)
.write.SeerStatDIC.section(DICInfo$VarAllInfo, DICfileName, append=TRUE)
NumMaxFormatSec = length(DICInfo$VarFormatSecList);
if(NumMaxFormatSec > 0)
for(VarCaseInd in 1:NumMaxFormatSec){
if(!.is.empty(DICInfo$VarFormatSecList[[VarCaseInd]]))
.write.SeerStatDIC.section(DICInfo$VarFormatSecList[[VarCaseInd]], DICfileName, append=TRUE);
}
return(DICInfo);
}
.write.SeerStatTXT = function(myData, DICInfo,...){
ReadingOptionInfo = .getReadingOptionFromExportOption(DICInfo$ExportOptionInfo);
#DataFile
TXTfileName = DICInfo$SystemInfo["Output filename" == DICInfo$SystemInfo$ItemNameInDic,2];
if(ReadingOptionInfo$GZipped){
DataFile = gzfile(TXTfileName);
}else{
DataFile = TXTfileName;
}
#cntquote
cntquote = (!ReadingOptionInfo$VariableformatNum && ReadingOptionInfo$quotedlabels);
outputColNames = colnames(myData);
if(!cntquote)
outputColNames = paste("\"",outputColNames,"\"",sep="");
if(!ReadingOptionInfo$VarNameIncluded){
outputColNames = FALSE;
}
write.table(myData, DataFile, col.names = outputColNames,
sep = ReadingOptionInfo$Fielddelimiter, na = ReadingOptionInfo$MissingCh,
quote = cntquote,
row.names = FALSE,...
);
}
.prepareDICInfoAndData = function(dataInF,DICfileName,TXTfileName=NULL,UseVarLabelsInTxtFile=TRUE,LabVarsNames=NULL){
DICInfo = attr(dataInF, "DICInfo");
SectionColNames = c("ItemNameInDic","ItemValueInDic");
if(is.null(DICInfo)){
DICInfo = list();
DICInfo$SystemInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$SystemInfo, "SectionNameInDIC") = "[System]";
DICInfo$SessionOptionInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$SessionOptionInfo, "SectionNameInDIC") = "[Session Options]";
DICInfo$ExportOptionInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$ExportOptionInfo, "SectionNameInDIC") = "[Export Options]";
DICInfo$VarAllInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$VarAllInfo, "SectionNameInDIC") = "[Life Page Variables]";
checkSurvData = function(ColNames){
IsSurvDataInF = FALSE;
NumNames = length(ColNames);
if(NumNames > 0)
for(NameIndex in 1:NumNames){
cntName = ColNames[NameIndex];
if( (length(grep("Page.*type", cntName)) == 1) ){
IsSurvDataInF = TRUE;
break;
}
}
return(IsSurvDataInF);
}
IsSurvData = checkSurvData(colnames(dataInF));
if( !IsSurvData )
attr(DICInfo$VarAllInfo, "SectionNameInDIC") = "[Variables]";
DICInfo$VarFormatSecList = list();
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
DICInfo$SystemInfo[1,1] = "Output filename";
DICInfo$SystemInfo[1,2] = TXTfileName;
#DICInfo$ExportOptionInfo
RowInd = 1;
DICInfo$ExportOptionInfo[RowInd,1] = "GZipped";
DICInfo$ExportOptionInfo[RowInd,2] = "false";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Variable format";
DICInfo$ExportOptionInfo[RowInd,2] = "quotedlabels";
if(!UseVarLabelsInTxtFile)
DICInfo$ExportOptionInfo[RowInd,2] = "numeric";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Field delimiter";
DICInfo$ExportOptionInfo[RowInd,2] = "tab";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Missing character";
DICInfo$ExportOptionInfo[RowInd,2] = "period";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Fields with delimiter in quotes";
DICInfo$ExportOptionInfo[RowInd,2] = "true";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Variable names included";
DICInfo$ExportOptionInfo[RowInd,2] = "false";
#DICInfo$VarAllInfo
NumVars = dim(dataInF)[2];
VarNames = colnames(dataInF);
if(NumVars > 0)
for(VarIndex in 1:NumVars){
DICInfo$VarAllInfo[VarIndex,1] = paste("Var",VarIndex,"Name",sep="");
DICInfo$VarAllInfo[VarIndex,2] = VarNames[VarIndex];
}
if(!UseVarLabelsInTxtFile){
NumVars = dim(dataInF)[2];
VarNames = colnames(dataInF);
if(!is.null(LabVarsNames)){
VarsNamesOnCheck = LabVarsNames;
}else{
VarsNamesOnCheck = VarNames;
}
NumLabVars = length(VarsNamesOnCheck);
if(NumVars > 0 && NumLabVars > 0)
for(VarIndex in 1:NumVars){
for(LabVIndex in 1:NumLabVars){
if(as.character(VarsNamesOnCheck[LabVIndex]) == as.character(VarNames[VarIndex]) &&
(class(dataInF[,VarIndex]) == "character" || class(dataInF[,VarIndex]) == "factor")){
DistinctValues = dataInF[,VarIndex];
DistinctValues = levels(factor(DistinctValues));
NumValues = length(DistinctValues);
if(NumValues > 0){
DICInfo$VarFormatSecList[[VarIndex]] = .create.emptyDataFrame.string(SectionColNames);
for(ValueIndex in 1:NumValues){
DICInfo$VarFormatSecList[[VarIndex]][ValueIndex,1] = ValueIndex -1;
DICInfo$VarFormatSecList[[VarIndex]][ValueIndex,2] = .addQuoteIfSpaceAtEnd(DistinctValues[ValueIndex]);
}
cntSectionName = paste("[Format=",VarsNamesOnCheck[LabVIndex],"]",sep="");
attr(DICInfo$VarFormatSecList[[VarIndex]], "SectionNameInDIC") = cntSectionName;
}
}
}
}
}
}else{
ReadingOptionInfo = .getReadingOptionFromExportOption(DICInfo$ExportOptionInfo);
if(ReadingOptionInfo$GZipped){
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".gz",sep="");
}
}else{
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
}
if("Output filename" %in% DICInfo$SystemInfo$ItemNameInDic){
DICInfo$SystemInfo["Output filename" == DICInfo$SystemInfo$ItemNameInDic,2] = TXTfileName;
}else{
cntRow = .create.emptyDataFrame.string(SectionColNames);
cntRow[1,1] = "Output filename";
cntRow[1,2] = TXTfileName;
cntSectionNameInDIC = attr(DICInfo$SystemInfo, "SectionNameInDIC");
DICInfo$SystemInfo = rbind(cntRow, DICInfo$SystemInfo);
attr(DICInfo$SystemInfo, "SectionNameInDIC") = cntSectionNameInDIC;
}
UseVarLabelsInDataWhenRead = DICInfo$UseVarLabelsInData;
if(is.null(UseVarLabelsInDataWhenRead)){
UseVarLabelsInTxtFile = TRUE;
DICInfo$VarFormatSecList = list();
}else{
if(UseVarLabelsInDataWhenRead){
if(UseVarLabelsInTxtFile){
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar("quotedlabels","Variable format", DICInfo$ExportOptionInfo);
DICInfo$VarFormatSecList = list();
}
}else{ #here numeric values in current data object
if(UseVarLabelsInTxtFile){
#replace labels for numeric values
dataInF = .replaceLabOrNum(DICInfo$VarFormatSecList, dataInF, LabReplaced = F)
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar("quotedlabels","Variable format", DICInfo$ExportOptionInfo);
DICInfo$VarFormatSecList = list();
}else{ #do nothing, just output DICInfo$VarFormatSecList and unchanged data object
}
#UseVarLabelsInTxtFile always true: because data is ready for output, no need of changes
UseVarLabelsInTxtFile = TRUE;
}
}
if(!UseVarLabelsInTxtFile){
cntItemValue = "numeric";
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar(cntItemValue,"Variable format", DICInfo$ExportOptionInfo);
}
}
NumVars = length(DICInfo$VarFormatSecList);
if(!UseVarLabelsInTxtFile && NumVars > 0){
dataInF = .replaceLabOrNum(DICInfo$VarFormatSecList, dataInF, LabReplaced = T);
}
attr(dataInF, "DICInfo") = DICInfo;
return(dataInF);
}
#############################
# exported functions
#############################
#' @export
read.SeerStat = function(DICfileName, TXTfileName=NULL, UseVarLabelsInData=FALSE,ReadHeaderOnly=FALSE,...){
# input:
# DICfileName, TXTfileName
# returned:
# an object of data.frame storing data in TXTfileName and info in DICfileName
if(!(length(grep("[.]dic$", DICfileName,ignore.case=TRUE)) == 1)){
DICfileName = paste(DICfileName, ".dic",sep="");
}
return(.read.SeerStatTXT(DICfileName, TXTfileName, UseVarLabelsInData=UseVarLabelsInData,ReadHeaderOnly=ReadHeaderOnly,...));
}
#' @export
write.SeerStat = function(myData, DICfileName, TXTfileName=NULL,UseVarLabelsInTxtFile=TRUE,LabVarsNames=NULL,...){
# input:
# DICfileName, TXTfileName
# returned:
# a list storing info in DICfileName
if(!(length(grep("[.]dic$", DICfileName,ignore.case=TRUE)) == 1)){
DICfileName = paste(DICfileName, ".dic",sep="");
}
#prepare DICInfo
myData = .prepareDICInfoAndData(myData,DICfileName,TXTfileName=TXTfileName,UseVarLabelsInTxtFile=UseVarLabelsInTxtFile,LabVarsNames=LabVarsNames);
DICInfo = attr(myData, "DICInfo");
.write.SeerStatDIC(DICInfo, DICfileName);
.write.SeerStatTXT(myData, DICInfo,...);
return(DICInfo);
}
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#' SEER2R is a package used for reading data from and writing data to SEET*STAT data format
#' SEER*STAT plain data are represented in two files: dic and txt files. The dic file contains
#' variable information and the txt file contains data in columns.
NA;
#' This package is used for
#' @rdname SEER2-package
#roxygen();
######################
# private functions
######################
#' accessory functions
.string.trimleadingtrailing <- function(string){
# input see the parameter list
# return result
result <- sub("^[[:space:]]*(.*?)[[:space:]]*$", "\\1", string, perl=TRUE)
}
.string.cutSubStringFileExtension <- function(FileName){
# input see the parameter list
# return result
ExtRegularExpr <- c("[.][^.]*$");
result <- sub(ExtRegularExpr, "", FileName, perl=TRUE);
result;
}
.catStr=function(myStr, ...,sep=""){
result=paste(
paste(myStr,collapse="",sep=sep),
...,
sep=sep
);
}
.create.emptyDataFrame.string=function(ColNames){
TableContentData=data.frame();
NumCols=length(ColNames);
if(NumCols>0)
for(ColIndex in 1:NumCols){
TableContentData=cbind(TableContentData,data.frame(numeric(0)));
}
colnames(TableContentData)=ColNames;
TableContentData;
}
.is.empty=function(x){
if(class(x) == "data.frame"){
result=(dim(x)[1]*dim(x)[2] == 0)
}else{
result=(length(as.vector(x)) == 0);
}
result;
}
.removeACharAll = function(char, string){
result <- gsub(char, "\\1", as.character(string), perl=TRUE)
}
.removeQuoteAll = function(string){
result <- .removeACharAll("\"",string);
}
.addQuoteIfSpaceAtEnd = function(string){
string = as.character(string);
Pattern1 = "^[[:space:]]+";
Pattern2 = "[[:space:]]+$";
ReturnedStr = string;
SpaceAtEnd = (length(grep(Pattern1, string)) == 1) || (length(grep(Pattern2, string)) == 1);
if(SpaceAtEnd){
ReturnedStr = .catStr("\"",string,"\"");
}
return(ReturnedStr);
}
.is.substring = function(x, string){
return(length(grep(x, string,ignore.case = TRUE)) == 1);
}
.substituteColNames = function(ByVarNamesInF, ByVarsDataColNamesInF, ColNamesInF){
NumNamesInF = length(ColNamesInF);
NumByVarNamesInF = length(ByVarNamesInF);
ColIndexByVar = numeric(NumByVarNamesInF);
if(NumNamesInF > 0 && NumByVarNamesInF > 0)
for(VInd in 1:NumByVarNamesInF){
for(NameInd in 1:NumNamesInF){
# if(.is.substring(ByVarNamesInF[VInd], gsub("_"," ", ColNamesInF[NameInd]))){
if(.is.substring(ByVarNamesInF[VInd], ColNamesInF[NameInd])){
ColNamesInF[NameInd] = ByVarsDataColNamesInF[VInd];
ColIndexByVar[VInd] = NameInd;
break;
}
}
}
return(list(ColNamesInF = ColNamesInF,ColIndexByVar = ColIndexByVar));
}
.assignColNames = function(data,ColNames = NULL){
OldColNames = colnames(data);
if(!is.null(ColNames)){
NewColNameInfo = .substituteColNames(ColNames, ColNames, OldColNames);
colnames(data) = NewColNameInfo$ColNamesInF;
attr(data,"NewColNameInfo") = NewColNameInfo;
}
return(data);
}
.getSubDataByVarName = function(data,ColNames = NULL){
TempData = .assignColNames(data,ColNames = ColNames);
NewColNameInfo = attr(TempData,"NewColNameInfo");
GoodColIndics = NewColNameInfo$ColIndexByVar[NewColNameInfo$ColIndexByVar>0];
NumByVars = length(GoodColIndics);
if(NumByVars > 0){
TempData1 = TempData[,GoodColIndics];
#attr(TempData1,"DICInfo") = attr(TempData,"DICInfo");
}else{
TempData1 = TempData;
}
return(TempData1);
}
#############################
# package specific functions
#############################
.replaceLabOrNum = function(VarFormatSecListInF, dataInF, LabReplaced = TRUE){
#LabReplaced = TRUE: means that current values are Labels, and will be replaced with numeric values
#columns of VarFormatSecListInF[[VarIndex]]: Numeric, Labels
NumVars = length(VarFormatSecListInF);
if(NumVars > 0){
for(VarIndex in 1:NumVars){
cntSection = VarFormatSecListInF[[VarIndex]];
if(!.is.empty(cntSection)){
NumLabels = dim(cntSection)[1];
for(LabIndex in 1:NumLabels){
ValueOnCheck = as.character(cntSection[LabIndex,1]);
ValueAssigned = .removeQuoteAll(cntSection[LabIndex,2]);
if(LabReplaced){
ValueOnCheck = .removeQuoteAll(as.character(cntSection[LabIndex,2]));
ValueAssigned = cntSection[LabIndex,1];
}
dataInF[as.character(dataInF[,VarIndex]) == ValueOnCheck,VarIndex] = ValueAssigned;
}
}
}
}
return(dataInF);
}
#' @include myLib.r
#' @callGraph
.read.SeerStatDIC = function(DICfileName){
# input:
# DICfileName:
# returned: (see the end of the function definition)
DicFileInF = DICfileName;
lines = readLines(DicFileInF);
#function for reading a section
findSectionInfo = function(lines,Pattern,splitchar="=",addedToName="",IsPatternStr=FALSE) {
#if IsPatternStr=FALSE, Pattern is regular expression
ItemInfo=data.frame("ItemNameInDic"=numeric(0),"ItemValueInDic"=numeric(0));
SectionName=character();
if(length(lines)>0)
for(LineInd in 1:length(lines)){
if(length(grep(Pattern, lines[LineInd], fixed=IsPatternStr)) == 1){
ItemInd = 1;
ItemLineInd=1;
SectionName=.string.trimleadingtrailing(lines[LineInd]);
while(lines[LineInd + ItemLineInd] != "" ){
if(length(grep(splitchar, lines[LineInd + ItemLineInd])) == 1){
ItemNames = unlist(strsplit(lines[LineInd + ItemLineInd], split=splitchar));
if(length(ItemNames) == 2){
ItemInfo[ItemInd,] = c(paste(as.character(ItemNames[1]),addedToName,sep=""),as.character(ItemNames[2]));
}else{
ItemInfo[ItemInd,1] = paste(as.character(ItemNames[1]),addedToName,sep="");
}
ItemInd = ItemInd + 1;
}
ItemLineInd = ItemLineInd + 1;
}
}
}
attr(ItemInfo, "SectionNameInDIC") = SectionName;
return(ItemInfo);
}
#read sections:
# System
SystemInfo = findSectionInfo(lines,Pattern="System[]]",splitchar="=",addedToName="");
# Session Options
SessionOptionInfo = findSectionInfo(lines,Pattern="Session Options[]]",splitchar="=",addedToName="");
# Export Options
ExportOptionInfo = findSectionInfo(lines,Pattern="Export Options[]]",splitchar="=",addedToName="");
# VarAllInfo
VarAllInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="=",addedToName="");
# Variables of non-survival data, Page Variables of survival data
VarInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Name=",addedToName="Name");
VarBaseInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Base=",addedToName="Base");
VarFormatSecList = list();
VarDimInfo = findSectionInfo(lines,Pattern="Variables[]]",splitchar="Dimension=",addedToName="Dimension");
VarDimList = list();
findVarFormatSecList = function(lines,VarBaseInfoInF,VarInfoInF){
NumBases = dim(VarBaseInfoInF)[1];
PageVar="Page type";
NumVars = dim(VarInfoInF)[1];
VarFormatSecListInF = list();
if(NumVars > 0)
for(VarInd in NumVars:1){
cntVar = as.character(VarInfoInF[VarInd,"ItemNameInDic"]);
cntVarItemValueInDic = as.character(VarInfoInF[VarInd,"ItemValueInDic"]);
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
if(.is.empty(VarFormatSecListInF[[VarInd]]))
VarFormatSecListInF[[VarInd]] = NULL;
comments = function(){
#if the variable is Page type, then handle it
if(length(grep(PageVar, cntVarItemValueInDic)) == 1){
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
}
if(NumBases > 0)
for(BaseInd in 1:NumBases){
cntBase = as.character(VarBaseInfoInF[BaseInd,"ItemNameInDic"]);
cntBase = unlist(strsplit(cntBase,"Base"))[1];
if(length(grep(cntBase, cntVar)) == 1){
cntPattern = cntVarItemValueInDic;
cntPattern = paste(cntPattern,"]",sep="");
VarFormatSecListInF[[VarInd]] = findSectionInfo(lines,Pattern=cntPattern,splitchar="=",IsPatternStr=T);
}
}
}
}
return(VarFormatSecListInF)
}
VarFormatSecList = findVarFormatSecList(lines,VarBaseInfo,VarInfo);
PageVarNameInReadData = gsub("[,:()<>={}!@#$%^&*+-]", "", VarInfo[,"ItemValueInDic"]);
PageVarNameInReadData = gsub("[[:space:]]+", "_", PageVarNameInReadData);
Vars = data.frame(
"VarSymbolInDic" = VarInfo[,"ItemNameInDic"],
"VarNameInReadData" = PageVarNameInReadData,
"VarNameInTXT" = VarInfo[,"ItemValueInDic"]
);
attr(Vars, "SectionNameInDIC") = attr(VarInfo, "SectionNameInDIC");
attr(Vars, "VarBaseInfo") = VarBaseInfo;
attr(Vars, "VarFormatSecList") = VarFormatSecList;
attr(Vars, "VarDimInfo") = VarDimInfo;
attr(Vars, "VarDimList") = VarDimList;
returned=list(
SystemInfo=SystemInfo,
SessionOptionInfo = SessionOptionInfo,
ExportOptionInfo = ExportOptionInfo,
VarAllInfo = VarAllInfo,
Vars = Vars,
VarBaseInfo = VarBaseInfo,
VarFormatSecList = VarFormatSecList,
VarDimInfo = VarDimInfo,
VarDimList = VarDimList
);
}
####
##
.getReadingOptionFromExportOption = function(ExportOptionInfoInF){
# header = FALSE, sep = "", quote = "\"'",
# na.strings = "NA"
# gzfile("file.text.gz")
rownames(ExportOptionInfoInF)=ExportOptionInfoInF$ItemNameInDic;
GZipped = FALSE;
if("GZipped" %in% ExportOptionInfoInF$ItemNameInDic){
GZipped = ifelse(ExportOptionInfoInF["GZipped",2] == "true", TRUE, FALSE);
}
VariableformatNum = FALSE;
quotedlabels = TRUE;
if("Variable format" %in% ExportOptionInfoInF$ItemNameInDic){
VariableformatNum = !(length(grep("label", ExportOptionInfoInF["Variable format",2])) == 1);
quotedlabels = ifelse(ExportOptionInfoInF["Variable format",2] == "quotedlabels", TRUE, FALSE);
}
FileformatIsDOS = TRUE;
if("File format" %in% ExportOptionInfoInF$ItemNameInDic){
FileformatIsDOS = ifelse(ExportOptionInfoInF["File format",2] == "DOS/Windows", TRUE, FALSE);
}
Fielddelimiter = "\t";
if("Field delimiter" %in% ExportOptionInfoInF$ItemNameInDic){
Fielddelimiter = ifelse(ExportOptionInfoInF["Field delimiter",2] == "space", " ",
ifelse(ExportOptionInfoInF["Field delimiter",2] == "comma", ",",
ifelse(ExportOptionInfoInF["Field delimiter",2] == "semi-colon", ";", "\t")
));
}
MissingCh = ".";
if("Missing character" %in% ExportOptionInfoInF$ItemNameInDic){
MissingCh = ifelse(ExportOptionInfoInF["Missing character",2] == "period", ".", " ");
}
FieldsValuewithdelimiterinquotes = FALSE;
if("Fields with delimiter in quotes" %in% ExportOptionInfoInF$ItemNameInDic){
FieldsValuewithdelimiterinquotes = ifelse(ExportOptionInfoInF["Fields with delimiter in quotes",2] == "true", TRUE, FALSE);
}
VarNameIncluded = TRUE;
if("Variable names included" %in% ExportOptionInfoInF$ItemNameInDic){
VarNameIncluded = ifelse(ExportOptionInfoInF["Variable names included",2] == "true", TRUE, FALSE);
}
return(list(
GZipped = GZipped,
VariableformatNum = VariableformatNum,
quotedlabels = quotedlabels,
FileformatIsDOS = FileformatIsDOS,
Fielddelimiter = Fielddelimiter,
MissingCh = MissingCh,
FieldsValuewithdelimiterinquotes = FieldsValuewithdelimiterinquotes,
VarNameIncluded = VarNameIncluded
));
}
#' @include myLib.r
#' @callGraph
.read.SeerStatTXT = function(DICfileName, TXTfileName, UseVarLabelsInData=FALSE,ReadHeaderOnly=FALSE,...){
# input:
# DICfileName, TXTfileName
# returned: (see the end of the function definition)
InfoFromDIC=.read.SeerStatDIC(DICfileName);
ReadingOptionInfo = .getReadingOptionFromExportOption(InfoFromDIC$ExportOptionInfo);
NumVars = length(InfoFromDIC$VarFormatSecList);
if(NumVars == 0)
UseVarLabelsInData = TRUE;
DICInfo = list(
SystemInfo = InfoFromDIC$SystemInfo,
SessionOptionInfo = InfoFromDIC$SessionOptionInfo,
ExportOptionInfo = InfoFromDIC$ExportOptionInfo,
VarAllInfo = InfoFromDIC$VarAllInfo,
VarFormatSecList = InfoFromDIC$VarFormatSecList,
UseVarLabelsInData = UseVarLabelsInData
)
#DataFile
if(!ReadHeaderOnly){
if(ReadingOptionInfo$GZipped){
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".gz",sep="");
}
DataFile = gzfile(TXTfileName);
}else{
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
DataFile = TXTfileName;
}
#cntquote
cntquote = ifelse(!ReadingOptionInfo$VariableformatNum && ReadingOptionInfo$quotedlabels || ReadingOptionInfo$VarNameIncluded, "\"", "");
NumSkippedLines = ifelse(ReadingOptionInfo$VarNameIncluded,1,0);
TXTData = read.table(DataFile, skip = NumSkippedLines, #header = ReadingOptionInfo$VarNameIncluded,
sep = ReadingOptionInfo$Fielddelimiter, na.strings = ReadingOptionInfo$MissingCh,
quote = cntquote, ...
);
colnames(TXTData) = InfoFromDIC$Vars$VarNameInReadData;
if(UseVarLabelsInData && NumVars > 0){
TXTData = .replaceLabOrNum(InfoFromDIC$VarFormatSecList, TXTData, LabReplaced = FALSE);
}
}else{
return(DICInfo);
}
attr(TXTData, "DICInfo") = DICInfo;
attr(TXTData, "assignColNames") = .assignColNames;
attr(TXTData, "getSubDataByVarName") = .getSubDataByVarName;
return(TXTData);
}
.write.SeerStatDIC.section = function(DICSection, filename, append=TRUE){
#Assume that DICSection has very thing required ready
SectionNameInDIC = attr(DICSection, "SectionNameInDIC");
outputStr = .catStr(SectionNameInDIC,"\n");
NumRows = dim(DICSection)[1];
if(NumRows > 0)
for(RowIndex in 1:NumRows){
outputStr = .catStr(outputStr,
DICSection$ItemNameInDic[RowIndex],
"=",
DICSection$ItemValueInDic[RowIndex],
"\n"
);
}
write(outputStr, file=filename, sep="",append=append);
}
.assignItemValueToSecInfoVar = function(cntItemValue,cntItemName, cntSection){
SectionColNames = c("ItemNameInDic","ItemValueInDic");
if(cntItemName %in% cntSection$ItemNameInDic){
cntSection[cntItemName == cntSection$ItemNameInDic,2] = cntItemValue;
}else{
cntRow = .create.emptyDataFrame.string(SectionColNames);
cntRow[1,1] = cntItemName;
cntRow[1,2] = cntItemValue;
cntSectionNameInDIC = attr(cntSection, "SectionNameInDIC");
cntSection = rbind(cntRow, cntSection);
attr(cntSection, "SectionNameInDIC") = cntSectionNameInDIC;
}
return(cntSection);
}
.write.SeerStatDIC = function(DICInfo, DICfileName){
# input:
# DICfileName, TXTfileName
# returned:
# a list storing info in DICfileName
.write.SeerStatDIC.section(DICInfo$SystemInfo, DICfileName, append=FALSE)
.write.SeerStatDIC.section(DICInfo$SessionOptionInfo, DICfileName, append=TRUE)
.write.SeerStatDIC.section(DICInfo$ExportOptionInfo, DICfileName, append=TRUE)
.write.SeerStatDIC.section(DICInfo$VarAllInfo, DICfileName, append=TRUE)
NumMaxFormatSec = length(DICInfo$VarFormatSecList);
if(NumMaxFormatSec > 0)
for(VarCaseInd in 1:NumMaxFormatSec){
if(!.is.empty(DICInfo$VarFormatSecList[[VarCaseInd]]))
.write.SeerStatDIC.section(DICInfo$VarFormatSecList[[VarCaseInd]], DICfileName, append=TRUE);
}
return(DICInfo);
}
.write.SeerStatTXT = function(myData, DICInfo,...){
ReadingOptionInfo = .getReadingOptionFromExportOption(DICInfo$ExportOptionInfo);
#DataFile
TXTfileName = DICInfo$SystemInfo["Output filename" == DICInfo$SystemInfo$ItemNameInDic,2];
if(ReadingOptionInfo$GZipped){
DataFile = gzfile(TXTfileName);
}else{
DataFile = TXTfileName;
}
#cntquote
cntquote = (!ReadingOptionInfo$VariableformatNum && ReadingOptionInfo$quotedlabels);
outputColNames = colnames(myData);
if(!cntquote)
outputColNames = paste("\"",outputColNames,"\"",sep="");
if(!ReadingOptionInfo$VarNameIncluded){
outputColNames = FALSE;
}
write.table(myData, DataFile, col.names = outputColNames,
sep = ReadingOptionInfo$Fielddelimiter, na = ReadingOptionInfo$MissingCh,
quote = cntquote,
row.names = FALSE,...
);
}
.prepareDICInfoAndData = function(dataInF,DICfileName,TXTfileName=NULL,UseVarLabelsInTxtFile=TRUE,LabVarsNames=NULL){
DICInfo = attr(dataInF, "DICInfo");
SectionColNames = c("ItemNameInDic","ItemValueInDic");
if(is.null(DICInfo)){
DICInfo = list();
DICInfo$SystemInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$SystemInfo, "SectionNameInDIC") = "[System]";
DICInfo$SessionOptionInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$SessionOptionInfo, "SectionNameInDIC") = "[Session Options]";
DICInfo$ExportOptionInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$ExportOptionInfo, "SectionNameInDIC") = "[Export Options]";
DICInfo$VarAllInfo = .create.emptyDataFrame.string(SectionColNames);
attr(DICInfo$VarAllInfo, "SectionNameInDIC") = "[Life Page Variables]";
checkSurvData = function(ColNames){
IsSurvDataInF = FALSE;
NumNames = length(ColNames);
if(NumNames > 0)
for(NameIndex in 1:NumNames){
cntName = ColNames[NameIndex];
if( (length(grep("Page.*type", cntName)) == 1) ){
IsSurvDataInF = TRUE;
break;
}
}
return(IsSurvDataInF);
}
IsSurvData = checkSurvData(colnames(dataInF));
if( !IsSurvData )
attr(DICInfo$VarAllInfo, "SectionNameInDIC") = "[Variables]";
DICInfo$VarFormatSecList = list();
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
DICInfo$SystemInfo[1,1] = "Output filename";
DICInfo$SystemInfo[1,2] = TXTfileName;
#DICInfo$ExportOptionInfo
RowInd = 1;
DICInfo$ExportOptionInfo[RowInd,1] = "GZipped";
DICInfo$ExportOptionInfo[RowInd,2] = "false";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Variable format";
DICInfo$ExportOptionInfo[RowInd,2] = "quotedlabels";
if(!UseVarLabelsInTxtFile)
DICInfo$ExportOptionInfo[RowInd,2] = "numeric";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Field delimiter";
DICInfo$ExportOptionInfo[RowInd,2] = "tab";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Missing character";
DICInfo$ExportOptionInfo[RowInd,2] = "period";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Fields with delimiter in quotes";
DICInfo$ExportOptionInfo[RowInd,2] = "true";
RowInd = RowInd + 1;
DICInfo$ExportOptionInfo[RowInd,1] = "Variable names included";
DICInfo$ExportOptionInfo[RowInd,2] = "false";
#DICInfo$VarAllInfo
NumVars = dim(dataInF)[2];
VarNames = colnames(dataInF);
if(NumVars > 0)
for(VarIndex in 1:NumVars){
DICInfo$VarAllInfo[VarIndex,1] = paste("Var",VarIndex,"Name",sep="");
DICInfo$VarAllInfo[VarIndex,2] = VarNames[VarIndex];
}
if(!UseVarLabelsInTxtFile){
NumVars = dim(dataInF)[2];
VarNames = colnames(dataInF);
if(!is.null(LabVarsNames)){
VarsNamesOnCheck = LabVarsNames;
}else{
VarsNamesOnCheck = VarNames;
}
NumLabVars = length(VarsNamesOnCheck);
if(NumVars > 0 && NumLabVars > 0)
for(VarIndex in 1:NumVars){
for(LabVIndex in 1:NumLabVars){
if(as.character(VarsNamesOnCheck[LabVIndex]) == as.character(VarNames[VarIndex]) &&
(class(dataInF[,VarIndex]) == "character" || class(dataInF[,VarIndex]) == "factor")){
DistinctValues = dataInF[,VarIndex];
DistinctValues = levels(factor(DistinctValues));
NumValues = length(DistinctValues);
if(NumValues > 0){
DICInfo$VarFormatSecList[[VarIndex]] = .create.emptyDataFrame.string(SectionColNames);
for(ValueIndex in 1:NumValues){
DICInfo$VarFormatSecList[[VarIndex]][ValueIndex,1] = ValueIndex -1;
DICInfo$VarFormatSecList[[VarIndex]][ValueIndex,2] = .addQuoteIfSpaceAtEnd(DistinctValues[ValueIndex]);
}
cntSectionName = paste("[Format=",VarsNamesOnCheck[LabVIndex],"]",sep="");
attr(DICInfo$VarFormatSecList[[VarIndex]], "SectionNameInDIC") = cntSectionName;
}
}
}
}
}
}else{
ReadingOptionInfo = .getReadingOptionFromExportOption(DICInfo$ExportOptionInfo);
if(ReadingOptionInfo$GZipped){
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".gz",sep="");
}
}else{
if(is.null(TXTfileName)){
TXTfileName = paste(.string.cutSubStringFileExtension(DICfileName), ".txt",sep="");
}
}
if("Output filename" %in% DICInfo$SystemInfo$ItemNameInDic){
DICInfo$SystemInfo["Output filename" == DICInfo$SystemInfo$ItemNameInDic,2] = TXTfileName;
}else{
cntRow = .create.emptyDataFrame.string(SectionColNames);
cntRow[1,1] = "Output filename";
cntRow[1,2] = TXTfileName;
cntSectionNameInDIC = attr(DICInfo$SystemInfo, "SectionNameInDIC");
DICInfo$SystemInfo = rbind(cntRow, DICInfo$SystemInfo);
attr(DICInfo$SystemInfo, "SectionNameInDIC") = cntSectionNameInDIC;
}
UseVarLabelsInDataWhenRead = DICInfo$UseVarLabelsInData;
if(is.null(UseVarLabelsInDataWhenRead)){
UseVarLabelsInTxtFile = TRUE;
DICInfo$VarFormatSecList = list();
}else{
if(UseVarLabelsInDataWhenRead){
if(UseVarLabelsInTxtFile){
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar("quotedlabels","Variable format", DICInfo$ExportOptionInfo);
DICInfo$VarFormatSecList = list();
}
}else{ #here numeric values in current data object
if(UseVarLabelsInTxtFile){
#replace labels for numeric values
dataInF = .replaceLabOrNum(DICInfo$VarFormatSecList, dataInF, LabReplaced = F)
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar("quotedlabels","Variable format", DICInfo$ExportOptionInfo);
DICInfo$VarFormatSecList = list();
}else{ #do nothing, just output DICInfo$VarFormatSecList and unchanged data object
}
#UseVarLabelsInTxtFile always true: because data is ready for output, no need of changes
UseVarLabelsInTxtFile = TRUE;
}
}
if(!UseVarLabelsInTxtFile){
cntItemValue = "numeric";
DICInfo$ExportOptionInfo = .assignItemValueToSecInfoVar(cntItemValue,"Variable format", DICInfo$ExportOptionInfo);
}
}
NumVars = length(DICInfo$VarFormatSecList);
if(!UseVarLabelsInTxtFile && NumVars > 0){
dataInF = .replaceLabOrNum(DICInfo$VarFormatSecList, dataInF, LabReplaced = T);
}
attr(dataInF, "DICInfo") = DICInfo;
return(dataInF);
}
#############################
# exported functions
#############################
#' @export
read.SeerStat = function(DICfileName, TXTfileName=NULL, UseVarLabelsInData=FALSE,ReadHeaderOnly=FALSE,...){
# input:
# DICfileName, TXTfileName
# returned:
# an object of data.frame storing data in TXTfileName and info in DICfileName
if(!(length(grep("[.]dic$", DICfileName,ignore.case=TRUE)) == 1)){
DICfileName = paste(DICfileName, ".dic",sep="");
}
return(.read.SeerStatTXT(DICfileName, TXTfileName, UseVarLabelsInData=UseVarLabelsInData,ReadHeaderOnly=ReadHeaderOnly,...));
}
#' @export
write.SeerStat = function(myData, DICfileName, TXTfileName=NULL,UseVarLabelsInTxtFile=TRUE,LabVarsNames=NULL,...){
# input:
# DICfileName, TXTfileName
# returned:
# a list storing info in DICfileName
if(!(length(grep("[.]dic$", DICfileName,ignore.case=TRUE)) == 1)){
DICfileName = paste(DICfileName, ".dic",sep="");
}
#prepare DICInfo
myData = .prepareDICInfoAndData(myData,DICfileName,TXTfileName=TXTfileName,UseVarLabelsInTxtFile=UseVarLabelsInTxtFile,LabVarsNames=LabVarsNames);
DICInfo = attr(myData, "DICInfo");
.write.SeerStatDIC(DICInfo, DICfileName);
.write.SeerStatTXT(myData, DICInfo,...);
return(DICInfo);
}
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