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AnalysisSession.R
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##################################################################################################
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#
####################################################################################################
cat("\nAnalysisSession version: 2018-11-27")
cat("\n\nFirst thing is to load data:")
cat("\n GetData(\"Proj_####_Data_yyymmdd_hhmm.xlsx\", 0)")
cat("\n\nThen run analyses and make plots and \"Send\" them:")
cat("\n p1 <- qplot(iris$Sepal.Length, iris$Petal.Length)")
cat("\n SendPlot(p1)")
## Sys.setenv("R_ZIPCMD" = "C:\\Rtools\\bin\\zip.exe")
## Load various packages ##
library(openxlsx)
library(readxl)
library(httr)
#library(XLConnect)
## ANALYSIS SESSION: Helpers to access data and document analyses -----------------------------
LaunchAnalysisSession <- function( usr, pwd, pk, debug=F)
{
require(httr)
if(debug)
{
myurl <- paste("http://localhost:60094/DataProject/AnalysisSession.aspx?pk=",pk,"&file="
, mysession$datafile, sep="")
}
else
{
myurl <- paste("https://uwac.autism.washington.edu/research/DataProject/AnalysisSession.aspx?pk="
, mysession$pk,"&file="
, mysession$datafile, sep="")
}
if(pk==0)
{
cat("\nLaunching new analysis session...\n")
cat("\nNEED TO GET THE SESSION PK HERE...\n")
} else if (pk > 0) {
cat(paste("\nLoading analysis session #",pk,"...\n"))
cat(paste("\n\nSession #",mysession$pk, " has been launched.\nAdd results as desired using the SendPlot() & SendOutput() functions.", sep=""))
}
BROWSE(myurl )
}
GetData <- function(datafile, pk = -1)
{
require(getPass)
require(httr)
usr <- getPass(msg = "Enter your UW NETID: ", noblank = FALSE, forcemask = FALSE)
pwd <- getPass(msg = "Enter your password: ", noblank = FALSE, forcemask = FALSE)
# initialize a new environment within which we keep track of indices, etc.
mysession <- new.env()
mysession$datafile <- datafile
mysession$filenamebody <- paste(gsub(".xlsx","", datafile), "_", usr,sep="")
mysession$user <- usr
mysession$pwd <- pwd
mysession$plotnum <- 0
mysession$tablenum <- 0
mysession$pk <- pk
assign("mysession", mysession, envir = .GlobalEnv)
cat("\nInitiating Analysis Session")
cat(paste("\nfile: ", datafile))
cat(paste("\nuser: ", usr,"\n"))
myurl <- paste("https://uwac.autism.washington.edu//research//stats//DataFileHandler.ashx?file="
, mysession$datafile, sep="")
r <- GET(myurl
, authenticate(user = mysession$user, password = mysession$pwd, type = "ntlm")
, write_disk(datafile, overwrite=TRUE) )
datafileinfo <- file.info(datafile)
if(datafileinfo$size > 1000)
{
cat("\n\nLoading Excel File...\n\n")
mysession$xlsx <- XLinfo(datafile)
if(pk >= 0)
{
LaunchAnalysisSession(usr, pwd, pk)
}
if(pk==0)
{
#Here I need to look up the session pk, number of plots and number of tables
newpk <- getPass(msg = "Enter the Session # from the new webpage: ", noblank = FALSE, forcemask = FALSE)
mysession$pk <- newpk
}
datarows <- nrow(mysession$xlsx$data[["Data"]])
datacols <- ncol(mysession$xlsx$data[["Data"]])
nsubj <- length(unique(mysession$xlsx$data[["Data"]]$id))
ntimept <- length(unique(mysession$xlsx$data[["Data"]]$timept))
cat(paste("\n\n'Data' worksheet contains: ",datarows, " rows and ", datacols, " variables.", sep=""))
cat(paste("\n\n'Data' worksheet contains: ", nsubj, " unique subjects across ", ntimept, " time points.", sep=""))
cat(paste("\n\nLoad the 'Data' worksheet into a data.frame like this:\n df <- mysession$xldata$data[[\"Data\"]]", sep=""))
}
else
{
return(NA)
}
}
SendPlot <- function(p)
{
if(mysession$pk == -1)
{
cat("\n\nThere is no active Analysis Session.\n\n")
}
else
{
require(mime)
if(is.ggplot(p))
{
mysession$plotnum <- mysession$plotnum + 1
pname <- paste("PK",mysession$pk ,"_" , mysession$filenamebody,"_PN", mysession$plotnum, sep="")
fil <- paste( pname, ".png", sep="")
cat(paste("\n\nSaving ggplot object:\n",fil,"\n"))
ggsave(fil, p)
myurl <- "https://uwac.autism.washington.edu/research/Documents/WebDocFileHandler.ashx"
POST(myurl
, authenticate(user = mysession$user, password = mysession$pwd, type = "ntlm")
, body = list(y = upload_file(fil)))
}
else {
cat("\n\nNot a ggplot object!\n")
}
}
}
SendOutput <- function(obj, mytitle = "My Title", stargaze=T)
{
if(mysession$pk == -1)
{
cat("\n\nThere is no active Analysis Session.\n\n")
}
else
{
if(stargaze)
{
output <- stargazer(obj, title=mytitle, align=TRUE, type="html", no.space=TRUE)
}
else
{
output <- obj
}
mysession$tablenum <- mysession$tablenum + 1
tname <- paste("PK",mysession$pk ,"_" , mysession$filenamebody,"_TN", mysession$tablenum, sep="")
suffix <- ifelse(stargaze==T, ".html", ".txt")
fil <- paste( tname, suffix, sep="")
cat(paste("\n\nSaving output object:\n",fil,"\n"))
myurl <- "https://uwac.autism.washington.edu/research/Documents/WebDocFileHandler.ashx"
sink(fil)
cat(output)
sink()
POST(myurl
, authenticate(user = mysession$user, password = mysession$pwd, type = "ntlm")
, body = list(y = upload_file(fil)))
}
}
## EXCEL: Functions to handle the importing of Excel files and process their contents -----------------------------
XLquik <- function(df, path )
{
dfname <- deparse(substitute(df))
require(openxlsx)
q_xl <- createWorkbook("xl")
addWorksheet(q_xl, dfname)
writeData(q_xl, sheet=1, df )
saveWorkbook(q_xl, file=paste(path,"\\",dfname,".xlsx",sep=""), overwrite=T)
}
XLinfo <- function(xlfile, startrow=1, hasheader=TRUE, keepdata=TRUE, mergedata=FALSE
,onlysheets=NULL, printflag=FALSE, showColUsedInfo=FALSE)
{ ###################################################################################
# This function takes a "workbook" object (read from the openxlsx or XLConnect package)
# and provdies summary information about its contents.
###################################################################################
# returns a list object with the following named elements:
# sheets (data frame): Info regarding the worksheets in the workbook
# - sheet (string) name of the worksheet
# - nrows (numeric) # of rows of data in the worksheet
# - ncols (numeric) # of columns of data in the worksheet
###################################################################################
require(openxlsx)
#require(XLConnect)
require(sqldf)
require(reshape)
require(readxl)
last4 <- tolower(substr(xlfile, nchar(xlfile)-3, nchar(xlfile)))
sheets <- list(); col_names <- list(); data<-list()
if(printflag) print(paste("##### last4 =", last4))
if (last4 == "xlsx")
{
print("Using 'openxlsx' package for .xlsx file")
if(printflag) print("##### 01a #####")
wb <- openxlsx::loadWorkbook(xlfile) ## load the Excel file
s <- names(wb) ## get list of worksheets
} else if (last4 == ".xls") {
print("Using 'readxl' package for .xls file")
s <- excel_sheets(xlfile)
#if(printflag) print("##### 01b1 #####")
#wb <- XLConnect::loadWorkbook(xlfile) ## load the Excel file
#s <- getSheets(wb) ## get list of worksheets
}
else {
if(printflag) print("##### 1 #####")
print("##ERROR: file not .xlsx or .xls format.")
return("##ERROR: file not .xlsx or .xls format.")
}
if(class(wb)!="Workbook" & class(wb)!="workbook" ) {
if(printflag) print("##### 2 #####")
print("##ERROR: input not of class\"workbook\"")
}
else {
if(printflag) cat("#### XLinfo 0 ####\n")
### Loop through worksheets
sheets <- list(); col_names <- list(); data<-list()
if(printflag) cat("#### XLinfo 0 #### names(wb):\n")
if(!is.null(onlysheets))
{
s <- s[which(s %in% onlysheets)]
}
if(printflag) cat("#### XLinfo 1 ####\n")
for (i in 1:length(s))
{
## Read the data on the worksheet
if (last4 == "xlsx") {
if(printflag) cat("#### XLinfo 1a xlsx ####\n")
tmp <- readWorkbook(xlfile, sheet=s[i], startRow=startrow )
} else if (last4 == ".xls") {
if(printflag) cat("#### XLinfo 1a xls ####\n")
#tmp <- XLConnect::readWorksheet(wb, sheet=s[i], startRow=startrow )
tmp <- read_excel(xlfile, i)
}
##tmp <- readWorksheet(wb, sheet = s[i], startRow=startrow, header=hasheader)
if(printflag) cat("#### XLinfo 1b ####\n")
if(printflag) cat(paste("s[i]=", s[i],"\n"))
if(printflag) cat(paste("nrow(tmp)=",nrow(tmp),"\n"))
if(printflag) cat(paste("ncol(tmp)=", ncol(tmp),"\n"))
if(printflag) print(str(tmp))
tmpnrow <- ifelse(is.null(tmp), 0, nrow(tmp))
tmpncol <- ifelse(is.null(tmp), 0, ncol(tmp))
sheets[[i]] <- data.frame(cbind(s[i], tmpnrow, tmpncol), stringsAsFactors=FALSE)
if(printflag) cat("#### XLinfo 1c ####\n")
col_names[[i]] <- data.frame(cbind(s[i],names(tmp)), stringsAsFactors=FALSE)
if(printflag) cat("#### XLinfo 1d ####\n")
if(tmpnrow>0 | tmpncol>0)
{
data[[i]] <- data.frame(tmp, stringsAsFactors=FALSE)
if(printflag) cat("#### XLinfo 1e ####\n")
if(printflag) cat(paste("#### XLinfo 1e #### nrows=", nrow(data[[i]]) ,"\n"))
if(nrow(data[[i]])>0)
{
print(paste("...sheet #", i))
data[[i]]$sheet <- s[i]
if(printflag) cat("#### XLinfo 1f ####\n")
data[[i]]$rownum <- as.numeric(rownames(data[[i]])) ## create a var to hold the rownumber of the data
names(data)[i] <- s[i] ## name the list element
}
}
}
if(printflag) cat("#### XLinfo 2 ####\n")
if(printflag) cat("#### sheets ####\n")
if(printflag) print(sheets)
## Loop through sheets and drop those with no rows,cols
sheets <- merge_all(sheets)
names(sheets) <- c("sheet","nrows","ncols")
sheets$nrows <- as.numeric(sheets$nrows)
sheets$ncols <- as.numeric(sheets$ncols)
sheets$sheetnum <- as.numeric(rownames(sheets))
cols <- merge_all(col_names)
names(cols) <- c("sheet", "colname")
if(printflag) cat("#### XLSXinfo 3 ####\n")
####### CHECK COLUMN USAGE ######
## Test to see if the column names vary across worksheets
cols_used <- sqldf("select colname, count(*) as n_used from cols group by colname")
if(printflag) cat("#### XLSXinfo 4 ####\n")
if(length(s) > 1)
{
## List columns used fewer than the max:
maxused <- max(cols_used$n_used)
n_cols_LTmax <- nrow(cols_used[ which(cols_used$n_used < maxused), ])
if(n_cols_LTmax > 0)
{
if(printflag) cat("#### XLSXinfo 5 ####\n")
if(showColUsedInfo)
{
cat(paste("## CHECK COLUMN USAGE ##","\n"))
cat("## NOTICE: The following columns are used less than others.\n")
print(cols_used[ which(cols_used$n_used < maxused), ])
}
}
else
{
if(printflag) cat("#### XLSXinfo 6 ####\n")
cat("## OK: All columns are used the same number of times.\n")
if(mergedata)
{
mergeddata <- merge_all(data)
mergeddata <- mergeddata[order(mergeddata$sheet, mergeddata$rownum),]
}
}
}
if(mergedata)
{
if(keepdata)
{
if(printflag) cat("#### XLSXinfo 7a ####\n")
out <- list(sheets = sheets, cols = cols, cols_used = cols_used
, wbname=xlfile, startrow=startrow, hasheader=hasheader
, data=data, mergeddata=mergeddata )
}
else
{
if(printflag) cat("#### XLSXinfo 7b ####\n")
out <- list(sheets = sheets, cols = cols, cols_used = cols_used
, wbname=xlfile, startrow=startrow, hasheader=hasheader
, mergeddata=mergeddata )
}
}
else
{
if(keepdata)
{
if(printflag) cat("#### XLSXinfo 8a ####\n")
out <- list(sheets = sheets, cols = cols, cols_used = cols_used
, wbname=xlfile, startrow=startrow, hasheader=hasheader
, data=data)
}
else
{
if(printflag) cat("#### XLSXinfo 8b ####\n")
out <- list(sheets = sheets, cols = cols, cols_used = cols_used
, wbname=xlfile, startrow=startrow, hasheader=hasheader )
}
}
}
class(out) <- "XLinfo"
return (out)
}
print.XLinfo <- function(xlinfo)
{
cat("#######################################################\n")
cat("File Information for: ")
cat(paste(xlinfo$wbname,"\n"))
cat(paste(" --> starting row for reading data =", xlinfo$startrow,"\n"))
cat(paste(" --> assume data includes column header =", xlinfo$hasheader,"\n\n"))
####### SUMMARY INFO #######
cat("### SUMMARY INFO ###\n")
cat(paste("# of sheets:", nrow(xlinfo$sheets), "\n"))
if(nrow(xlinfo$sheets) > 1) {
cat(paste("Min/Max # rows:", min(xlinfo$sheets$nrows), max(xlinfo$sheets$nrows),
ifelse(min(xlinfo$sheets$nrows) != max(xlinfo$sheets$nrows), " ==> number of rows vary","") ,"\n"))
cat(paste("Min/Max # cols:", min(xlinfo$sheets$ncols), max(xlinfo$sheets$ncols),
ifelse(min(xlinfo$sheets$ncols) != max(xlinfo$sheets$ncols), " ==> number of columns vary","") ,"\n"))
} else {
cat(paste("# rows:", min(xlinfo$sheets$nrows), "\n"))
cat(paste("# cols:", min(xlinfo$sheets$ncols), "\n"))
}
cat("\n")
####### SHEET INFO #######
cat("### SHEET INFO ###\n")
print(xlinfo$sheets[order(as.numeric(rownames(xlinfo$sheets))),])
cat("\n")
####### DATA INFO #######
cat("### DATA INFO ###\n")
if("data" %in% names(xlinfo))
{
for(d in 1: length(xlinfo$data))
{
if(is.na(xlinfo$sheets$ncols[d] ) )
{
cat("#----------------------------------------------------------------------------------------\n")
cat(paste("# SHEET: ", xlinfo$data[[d]]$sheet[1],"\n"))
nchars <- nchar(xlinfo$data[[d]]$sheet[1])
cat(paste("# -------- NO ROW OR COLUMNS ", collapse=""),"\n",sep="",collapse="")
}
else if(xlinfo$sheets$ncols[d] == 0 )
{
cat("#----------------------------------------------------------------------------------------\n")
cat(paste("# SHEET: ", xlinfo$data[[d]]$sheet[1],"\n"))
nchars <- nchar(xlinfo$data[[d]]$sheet[1])
cat(paste("# -------- NO COLUMNS ", collapse=""),"\n",sep="",collapse="")
}
else if(xlinfo$sheets$nrows[d] == 0 )
{
cat("#----------------------------------------------------------------------------------------\n")
cat(paste("# SHEET: ", xlinfo$data[[d]]$sheet[1],"\n"))
nchars <- nchar(xlinfo$data[[d]]$sheet[1])
cat(paste("# -------- NO ROWS ", collapse=""),"\n",sep="",collapse="")
print(head(xlinfo$data[[d]],1))
}
else
{
cat("#----------------------------------------------------------------------------------------\n")
cat(paste("# SHEET: ", xlinfo$sheets$sheet[d],"\n"))
nchars <- nchar(xlinfo$sheets$sheet[d])
cat(paste("# --------",paste(rep("-",nchars), collapse=""),"\n",sep="",collapse=""))
print(head(xlinfo$data[[d]],3))
}
}
}
else
{
cat("### ==> NONE: Data from worksheets not retained. ###\n")
}
####### MERGED DATA #######
cat("\n### MERGED DATA INFO ###\n")
if(nrow(xlinfo$sheets) == 1) {
cat("### ==> NONE: Only 1 worksheet.")
} else if(is.null(xlinfo$mergeddata))
{
cat("### ==> NONE: Column names vary across worksheets.")
}
else
{
cat(paste(" # rows:", nrow(xlinfo$mergeddata),"\n"))
cat(paste(" # cols:", ncol(xlinfo$mergeddata)," (including new columns: sheet & rownum) \n"))
cat("# ==> first 3 rows of merged data:\n")
print(head(xlinfo$mergeddata,3))
cat("\n\n")
}
}
loadXLfiles_in_folder <- function(path)
{
### Read the Excel files from a folder into a list
### and save the contents to a text file
require(XLConnect)
xlfiles <- list.files(path)
xlfiles <- xlfiles[grepl(".xls", xlfiles)]
x<-list()
for(i in 1:length(xlfiles)) {
x[[i]] <- XLinfo(paste(path,xlfiles[[i]], sep=""))
}
sink(paste(path, "XLcontents.txt", sep=""))
#### Display the contents of all the sheets
cat("##################\n")
cat(paste("Excel files from '", path,"'\n",sep=""))
cat("##################\n")
for(i in 1:length(x)) {
cat(paste("\n\n#################",x[[i]]$wbname,"#################\n"))
print(x[[i]]$sheets)
for(j in 1:length(x[[i]]$data)) {
cat(paste("\n\n# ============",x[[i]]$sheets$sheet[j],"============ #\n",sep=""))
info(x[[i]]$data[[j]])
}
}
sink()
cat(paste("\nFile contents saved to: ",path,"XLcontents.txt",sep=""))
return(x)
}
fixXLdatetime <- function(x)
{
newdate <- as.POSIXct(as.Date(x,origin="1899-12-30"))
return(newdate)
}
fixXLdate <- function(x)
{
newdate <- as.Date(x,origin="1899-12-30")
return (newdate)
}
writeInfoToXL <- function(wb, sh="", df, starting_row=1, starting_col=1)
{
actual_dfname <- deparse(substitute(df))
info <- info(df, mode="xl")
if(sh=="")
{
sh <- paste("info",actual_dfname)
addWorksheet(wb,sh)
}
writeTextToXL(wb, sh = sh, starting_row=starting_row, starting_col=starting_col, paste("Summary Info for the Data Frame:", actual_dfname))
if(info$dfinfo$levelinfo != "")
{
writeData(wb, sheet = sh, startRow=starting_row+1, startCol = starting_col, paste("Level Info:",info$dfinfo$levelinfo))
}
writeData(wb, sheet=sh, startRow=starting_row+1, startCol = starting_col, paste("N rows:",info$dfinfo$nrows))
writeData(wb, sheet=sh, startRow=starting_row+1, startCol = starting_col+3, paste("N cols:",info$dfinfo$ncols))
row_dates <- starting_row + 3
row_nums <- row_dates + 3 + nrow(info$dates)
row_txts <- row_dates + 3 + nrow(info$dates) + 3 + nrow(info$nums)
writeData(wb, sheet = sh, startRow= row_dates, startCol = starting_col, "DATE fields")
writeDataTable(wb, sheet = sh, startRow= row_dates+1, startCol = starting_col, info$dates, colNames=T, rowNames=F, withFilter=F)
writeData(wb, sheet = sh, startRow= row_nums, startCol = starting_col, "NUMERIC fields")
writeDataTable(wb, sheet = sh, startRow= row_nums + 1, startCol = starting_col, info$nums, colNames=T, rowNames=F, withFilter=F)
writeData(wb, sheet = sh, startRow= row_txts, startCol = starting_col, "TEXT fields")
writeDataTable(wb, sheet = sh, startRow= row_txts + 1, startCol = starting_col, info$txts, colNames=T, rowNames=F, withFilter=F)
return(wb)
}
writeInfoByToXL <- function(wb, infoby)
{
sheet <- paste("info",infoby[[2]]$dfinfo$dfname,"BY",infoby$byvar)
addWorksheet(wb,sheet)
for(i in 2:length(infoby))
{
if(i==2)
{
start_at=1
}
else
{
start_at = ((i-2) * (infoby[[2]]$dfinfo$ncols + 9 + 8 ))
# for(j in 2:(i-1))
# {
# ##add 9 for the blank rows between each var type
# starting_row = starting_row + 9 + nrow(infoby[[j]]$dates) + nrow(infoby[[j]]$nums) + nrow(infoby[[j]]$txts)
# }
}
wb = writeInfoToXL(wb, sh=sheet, df=infoby[[i]], starting_row=start_at)
}
return(wb)
}
writeInfoByToXL2 <- function(wb, df, byvar)
{
actual_dfname <- deparse(substitute(df))
sheet <- paste("info for [",actual_dfname,"] BY",byvar)
addWorksheet(wb,sheet)
infobyresults <- infoby(df, byvar, mode="xl")
for(i in 2:length(infobyresults))
{
if(i==2)
{
start_at=1
}
else
{
start_at = ((i-2) * (infobyresults[[i]]$dfinfo$ncols + 9 + 8 ))
# for(j in 2:(i-1))
# {
# ##add 9 for the blank rows between each var type
# starting_row = starting_row + 9 + nrow(infoby[[j]]$dates) + nrow(infoby[[j]]$nums) + nrow(infoby[[j]]$txts)
# }
}
wb = writeInfoByToXL2_subset(wb, sh=sheet, inforesults=infobyresults[[i]], starting_row=start_at)
}
return(wb)
}
writeInfoByToXL2_subset <- function(wb, sh="", inforesults, starting_row=1, starting_col=1)
{
actual_dfname <- deparse(substitute(df))
#info <- info(df, mode="xl")
if(sh=="")
{
sh <- paste("info",actual_dfname)
addWorksheet(wb,sh)
}
writeTextToXL(wb, sh = sh, starting_row=starting_row, starting_col=starting_col, paste("Summary Info for the Data Frame:", actual_dfname, inforesults[[1]]$levelinfo))
if(inforesults$dfinfo$levelinfo != "")
{
writeData(wb, sheet = sh, startRow=starting_row+1, startCol = starting_col, paste("Level Info:",inforesults$dfinfo$levelinfo))
}
writeData(wb, sheet=sh, startRow=starting_row+1, startCol = starting_col, paste("N rows:",inforesults$dfinfo$nrows))
writeData(wb, sheet=sh, startRow=starting_row+1, startCol = starting_col+3, paste("N cols:",inforesults$dfinfo$ncols))
row_dates <- starting_row + 3
row_nums <- row_dates + 3 + nrow(inforesults$dates)
row_txts <- row_dates + 3 + nrow(inforesults$dates) + 3 + nrow(inforesults$nums)
writeData(wb, sheet = sh, startRow= row_dates, startCol = starting_col, "DATE fields")
writeDataTable(wb, sheet = sh, startRow= row_dates+1, startCol = starting_col, inforesults$dates, colNames=T, rowNames=F, withFilter=F)
writeData(wb, sheet = sh, startRow= row_nums, startCol = starting_col, "NUMERIC fields")
writeDataTable(wb, sheet = sh, startRow= row_nums + 1, startCol = starting_col, inforesults$nums, colNames=T, rowNames=F, withFilter=F)
writeData(wb, sheet = sh, startRow= row_txts, startCol = starting_col, "TEXT fields")
writeDataTable(wb, sheet = sh, startRow= row_txts + 1, startCol = starting_col, inforesults$txts, colNames=T, rowNames=F, withFilter=F)
return(wb)
}
writeTextToXL <- function(wb, sh, text, starting_row=1, starting_col=1, hastitle=T)
{
writeData(wb, sheet = sh, text, startRow=starting_row, startCol = starting_col)
boldStyle <- createStyle(textDecoration=c("BOLD","UNDERLINE"))
addStyle(wb, sheet=sh, style=boldStyle,
rows = starting_row, cols = starting_col, gridExpand = FALSE)
}
XLcols <- function(){
l2 <- c(" ","A","B","C", "D", "E", "F", "G")
l1 <- LETTERS #rep(LETTERS, 8)
l12 <- merge(l1,l2, all=T)
l12$col <- paste(l12$y,l12$x,sep="")
l3 <- sqldf("select col from l12 order by col")
l3$colnum <- seq(1:nrow(l3))
l3$col <- gsub(" ","",l3$col)
return(l3)
}
XLcol <- function(x)
{
if(is.numeric(x))
{
L1 <- trunc(x / 26, 0)
L2 <- x %% 26
if(L1 >= 1) col <- paste(LETTERS[L1], LETTERS[L2], sep="")
else col <- LETTERS[L2]
} else if (is.character(x)) {
if(nchar(x) == 1)
{
col <- which(LETTERS==toupper(x))
} else if(nchar(x) == 2) {
x1 <- substr(x,1,1)
x2 <- substr(x,2,2)
col <- (which(LETTERS==toupper(x1))*26) +
which(LETTERS==toupper(x2))
} else {
col = "Must be only 1 or 2 characters."
}
}
return(col)
}
XLcolindex <- function(y, debug=F)
{
foo <- strsplit(y,",")
if(debug==T) print(paste("foo =",foo))
colidx <- array()
counter <- 1
for(c in 1:length(foo[[1]]))
{
if(debug==T) print(paste("foo[c] =",foo[c]))
hascolon <- grep(":",foo[[1]][c])
if(debug==T) print(paste("hascolon =", hascolon))
if(length(hascolon)==0)
{ # not a range
colidx[counter] <- XLcolindex_single(foo[[1]][c])
counter <- counter + 1
} else {
newrange <- XLcolindex_range(foo[[1]][c])
if(debug==T) print("length(colidx)")
if(debug==T) print(length(colidx))
if(length(colidx)>1)
{
colidx <- c(colidx, newrange)
} else {
colidx <- newrange
}
counter <- length(colidx)
}
if(debug==T) print(paste(foo[c], colidx[c]))
}
return(colidx)
}
XLcolindex_range <- function(x)
{
foo <- strsplit(x,":")
idx1 <- XLcolindex_single(foo[[1]][1])
idx2 <- XLcolindex_single(foo[[1]][2])
idx_range <- c(idx1 : idx2)
return (idx_range)
}
XLcolindex_single <- function(x)
{
idx <- 0
for(i in 1:nchar(x))
{
digits_place <- nchar(x) - i
letteridx <- grep(tolower(substr(x,i,i)), letters)
tmpidx <- ifelse( digits_place==0, letteridx, (letteridx*(26^digits_place))) #+ letteridx
idx <- idx + tmpidx
#print(paste(substr(x,i,i)," i=",i," digits_place=",digits_place," letteridx=",letteridx," tmpidx=",tmpidx," idx=",idx,sep=""))
}
return (idx)
}
## Utilities ####
# Load Sheets into common dataframe of all
XLsheets_in_xllist <- function(xllist)
{
path_to_remove <- "C:\\\\Consulting\\\\TMDW\\\\SNC\\\\recd files\\\\"
datasheets <- NULL
dupsheets <- NULL
# Loop through all the XL files in the list
counter <- 0; dupcounter <- 0;
for(i in 1:length(xllist))
{
tmpsheets <- xllist[[i]]$sheets
tmpsheets <- tmpsheets[which(tmpsheets$nrows>0),]
#Look through each sheet and get the field names
# and column sums first and last columns of first and last 10 rows
# (this integer representation will help check
# for duplicate data)
for(s in 1:nrow(tmpsheets))
{
tmp <- tmpsheets[s, ]
tmp$filename <- gsub(path_to_remove,"",xllist[[i]]$wbname)
tmp$xllist <- deparse(substitute(xllist))
tmp$xllistnum <- i
tmp <- tmp[which(tmp$nrows>0),]
tmpdata <- xllist[[i]]$data[[tmp$sheet[1]]]
flds <- names(tmpdata)
fldscsv <- paste(flds, collapse=",")
tmp$flds <- fldscsv
tmp$colsums_third <- sum(XLcolumnsum(tmpdata, 3))
tmp$colsums_last <- sum(XLcolumnsum(tmpdata, ncol(tmpdata)))
#sheets_[[length(sheets_) + 1]] <- tmp
if(counter==0)
{
datasheets <- tmp
counter <- counter+1
}
else
{
#Check for dups
potdups <- sqldf("select *
from datasheets a
join tmp b ON a.nrows=b.nrows
and a.ncols=b.ncols
and a.colsums_third=b.colsums_third
and a.colsums_last=b.colsums_last")
if(nrow(potdups)>=1)
{
# Yes, this is a dup
if(dupcounter==0)
{
dupsheets <- tmp
dupcounter <- dupcounter + 1
}
else
{
dupsheets <- rbind(dupsheets, tmp)
dupcounter <- dupcounter + 1
}
}
else
{
# not a dup
datasheets <- rbind(datasheets, tmp)
counter <- counter+1
}
}
}
}
out <- list()
out[[1]] <- datasheets
if(!is.null(dupsheets))
{
out[[2]] <- dupsheets
}
else {
out[[2]] <- "No duplicate worksheets"
}
names(out) <- c("datasheets", "dupsheets")
return( out )
}
XLcommonsheets <- function(sheetslist, xllist)
{
# Combine worksheets that contain the same fields
# Returns a list of compiled dataframes
datasheets <- sheetslist$datasheets
datalist <- list()
commonflds <- unique(datasheets$flds)
commonflds <- commonflds[which(commonflds!="")]
for(i in 1:length(commonflds))
{
cat(paste("\n\n######",i,"\n"))
print(commonflds[i])
counter <- 1
for(j in 1:nrow(datasheets))
{
#Do the flds match this commonflds?
if(datasheets$flds[j] == commonflds[i])
{
print(paste(" -- match --", counter))
mysheet <- datasheets$sheet[j]
myxl <- datasheets$xllistnum[j]
#print(paste(mysheet, myxl))
tmpdata <- xllist[[myxl]]$data[[mysheet]]
tmpdata <- DATEtoTEXT(tmpdata)
tmpdata$filename <- xllist[[myxl]]$wbname
#print(head(tmpdata,1))
if(counter==1) {data <- tmpdata}
else {data <- rbind(data, tmpdata)}
counter <- counter+1
}
}
datalist[[i]] <- data
}
class(datalist) <- "XLdatalist"
return(datalist)
}
print.XLdatalist <- function(xldatalist){
for(i in 1:length(xldatalist))
{
nsheets <- nrow(sqldf())
cat(paste("\n\n####",i,"####\nnrows=",nrow(xldatalist[[i]])
," ncols=",ncol(xldatalist[[i]]),"\n\n"))
print(head(xldatalist[[i]],3))
}
}
XLcolumnsum <- function(df, columnidx)
{
if(nrow(df) > 40)
{
df <- df[c(1:20, (nrow(df)-20):nrow(df)), ]
}
colvals <- sapply(as.character(df[,columnidx]), function(x) sum(strtoi(charToRaw(x),16L)))
return(colvals)
}
XLsummarize_data_sets <- function(sheets, datalist, path, filename)
{
wb <- createWorkbook("wb")
addWorksheet(wb, "XLsheets")
writeData(wb, "XLsheets", "Data sheets"
, startRow = 1, startCol = 1)
writeData(wb, "XLsheets", sheets$datasheets[ , 1:5]
, startRow = 2, startCol = 1)
writeData(wb, "XLsheets", "Duplicate sheets"
, startRow = nrow(sheets$datasheets) + 5, startCol = 1)
writeData(wb, "XLsheets", sheets$dupsheets[ , 1:5]
, startRow = nrow(sheets$datasheets) + 6, startCol = 1)