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#The base version on 9/23/2013 still dies on WUA_yldata_for TRB_contest Sep 10 2013.xlsx as a file name | |
xlsxToR <- function(file, keep_sheets = NULL, header = FALSE) { | |
require(XML) | |
require(plyr) | |
require(pbapply) | |
suppressWarnings(file.remove(tempdir())) | |
file.copy(file, tempdir()) | |
new_file <- list.files(tempdir(), full.name = TRUE, pattern = basename(file)) | |
new_file_rename <- gsub("xlsx$", "zip", new_file) | |
file.rename(new_file, new_file_rename) | |
unzip(new_file_rename, exdir = tempdir()) | |
# Get OS | |
mac <- xmlToList(xmlParse(list.files( | |
paste0(tempdir(), "/docProps"), full.name = TRUE, pattern = "app.xml"))) | |
mac <- grepl("Macintosh", mac$Application) | |
if(mac) { | |
os_origin <- "1899-12-30" # documentation says should be "1904-01-01" | |
} else { | |
os_origin <- "1899-12-30" | |
} | |
# Get names of sheets | |
sheet_names <- xmlToList(xmlParse(list.files( | |
paste0(tempdir(), "/xl"), full.name = TRUE, pattern = "workbook.xml"))) | |
sheet_names <- do.call("rbind", sheet_names$sheets) | |
rownames(sheet_names) <- NULL | |
sheet_names <- as.data.frame(sheet_names,stringsAsFactors = FALSE) | |
sheet_names$id <- gsub("\\D", "", sheet_names$id) | |
# Get column classes | |
styles <- xmlToList(xmlParse(list.files( | |
paste0(tempdir(), "/xl"), full.name = TRUE, pattern = "styles.xml"))) | |
styles <- styles$cellXfs[ | |
sapply(styles$cellXfs, function(x) any(names(x) == "applyNumberFormat"))] | |
styles <- do.call("rbind", lapply(styles, | |
function(x) as.data.frame(as.list(x[c("applyNumberFormat", "numFmtId")]), | |
stringsAsFactors = FALSE))) | |
if(!is.null(keep_sheets)) { | |
sheet_names <- sheet_names[sheet_names$name %in% keep_sheets,] | |
} | |
worksheet_paths <- list.files( | |
paste0(tempdir(), "/xl/worksheets"), | |
full.name = TRUE, | |
pattern = paste0( | |
"sheet(", | |
paste(sheet_names$id, collapse = "|"), | |
")\\.xml$")) | |
worksheets <- lapply(worksheet_paths, function(x) xmlRoot(xmlParse(x))[["sheetData"]]) | |
worksheets <- pblapply(seq_along(worksheets), function(i) { | |
x <- xpathApply(worksheets[[i]], "//x:c", namespaces = "x", function(node) { | |
c("v" = xmlValue(node[["v"]]), xmlAttrs(node)) | |
}) | |
if(length(x) > 0) { | |
x_rows <- unlist(lapply(seq_along(x), function(i) rep(i, length(x[[i]])))) | |
x <- unlist(x) | |
x <- reshape( | |
data.frame( | |
"row" = x_rows, | |
"ind" = names(x), | |
"value" = x, | |
stringsAsFactors = FALSE), | |
idvar = "row", timevar = "ind", direction = "wide") | |
x$sheet <- sheet_names[sheet_names$id == i, "name"] | |
colnames(x) <- gsub("^value\\.", "", colnames(x)) | |
} | |
x | |
}) | |
worksheets <- do.call("rbind.fill", | |
worksheets[sapply(worksheets, class) == "data.frame"]) | |
entries <- xmlParse(list.files(paste0(tempdir(), "/xl"), full.name = TRUE, | |
pattern = "sharedStrings.xml$")) | |
entries <- xpathSApply(entries, "//x:t", namespaces = "x", xmlValue) | |
names(entries) <- seq_along(entries) - 1 | |
entries_match <- entries[match(worksheets$v, names(entries))] | |
worksheets$v[worksheets$t == "s" & !is.na(worksheets$t)] <- | |
entries_match[worksheets$t == "s"& !is.na(worksheets$t)] | |
worksheets$cols <- match(gsub("\\d", "", worksheets$r), LETTERS) | |
worksheets$rows <- as.numeric(gsub("\\D", "", worksheets$r)) | |
if(!any(grepl("^s$", colnames(worksheets)))) { | |
worksheets$s <- NA | |
} | |
workbook <- lapply(unique(worksheets$sheet), function(x) { | |
y <- worksheets[worksheets$sheet == x,] | |
y_style <- as.data.frame(tapply(y$s, list(y$rows, y$cols), identity), | |
stringsAsFactors = FALSE) | |
y <- as.data.frame(tapply(y$v, list(y$rows, y$cols), identity), | |
stringsAsFactors = FALSE) | |
if(header) { | |
colnames(y) <- y[1,] | |
y <- y[-1,] | |
y_style <- y_style[-1,] | |
} | |
y_style <- sapply(y_style, | |
function(x) ifelse(length(unique(x)) == 1, unique(x), NA)) | |
if(length(styles) > 0) { | |
y_style <- styles$numFmtId[match(y_style, styles$applyNumberFormat)] | |
} | |
y_style[y_style %in% 14:17] <- "date" | |
y_style[y_style %in% c(18:21, 45:47)] <- "time" | |
y_style[y_style %in% 22] <- "datetime" | |
y_style[is.na(y_style) & !sapply(y, function(x)any(grepl("\\D", x)))] <- "numeric" | |
y_style[is.na(y_style)] <- "character" | |
y[] <- lapply(seq_along(y), function(i) { | |
switch(y_style[i], | |
character = y[,i], | |
numeric = as.numeric(y[,i]), | |
date = as.Date(as.numeric(y[,i]), origin = os_origin), | |
time = strftime(as.POSIXct(as.numeric(y[,i]), origin = os_origin), format = "%H:%M:%S"), | |
datetime = as.POSIXct(as.numeric(y[,i]), origin = os_origin)) | |
}) | |
y | |
}) | |
if(length(workbook) == 1) { | |
workbook <- workbook[[1]] | |
} | |
workbook | |
} |
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