Quickly read Excel worksheets into R (Windows only…sorry)

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I suppose most companies use the Microsoft Office suite of programs, and my office is no exception. It easy to import data from an API or a database into R, but importing data from an Excel workbook is a different story. There are a few R packages for reading Excel files, but I’ve had problems with all of them:

  • `read.xlsx` (`gdata` package): pretty convenient to run in R, but requires Perl which for some reason I have a hard time installing on my Windows machine…that might just be an issue with me, not the machine.
  • `odbcConnectExcel2007` (`RODBC` package): from what I’ve seen on the listservs, this one has a hard time reading xlsx files because of a driver mismatch – you have to access the files through 32-bit R, which is annoying.
  • `readWorksheetFromFile` (`XLConnect` package): uses Java, easy to install, and has tons of functionality to write in addition to read, but I don’t really need the write functionality and for large files especially XLConnect is very slow.

So I set off in search of a faster way to pull information out of an Excel file. The gist below shows what I came up with. Excel already has Visual Basic capabilities built in. So I stole a little VB script from here and stuck it in a function that writes the script to a temporary file, calls the script from the command line, and then outputs the contents of the formerly-Excel file.

The function takes the following inputs:

  • file_path: the full path of the Excel file
  • keep_sheets: the names of the sheets you want to keep; extracts all sheets if NULL
  • target_dir: the directory to which you want to output the excel sheets; defaults to the directory where the Excel sheet is kept. If set to FALSE, it doesn’t output any files – rather, it reads them all into R as a list of data frames.

Unfortunately, this only works on Windows. I had hoped it would work on a Mac where Excel was installed, but I haven’t had any luck getting it to work on my home computer.

# The MIT License (MIT)
#
# Copyright (c) 2012 Schaun Jacob Wheeler
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
excelToCsv <- function(file_path, keep_sheets = NULL, target_dir = NULL, ...) {
temp_already <- list.files(tempdir())
if(is.null(target_dir)) {
file_root <- gsub("([[:print:]]+(/|\\\\))[[:print:]]+", "\\1", file_path)
} else if(!is.null(target_dir) & target_dir != FALSE) {
file_root <- target_dir
}
file_name <- gsub("[[:print:]]+(/|\\\\)", "", file_path)
file_ext <- gsub("[[:print:]]+(.xls.?)", "\\1", file_path)
converter_file <- file(paste0(tempdir(),"/", "converter.vbs"))
writeLines(
c('rem XLS_To_CSV.vbs',
'rem =============================================================',
'rem convert all NON-empty worksheets in an Excel file to csv',
'rem CSV file names will default to Sheet names',
'rem output folder defaults to the folder where the script resides or',
'rem if path is specified with the input file, that path is used',
'rem ',
'rem input parameter 1: Excel path\\file in argument 1 ',
'rem (if path is not specified, the current path is defaulted)',
'rem ',
'rem ============================================================',
'',
'Dim strExcelFileName',
'Dim strCSVFileName',
'',
'strExcelFileName = WScript.Arguments.Item(0)',
'',
'rem get path where script is running',
'Set fso = CreateObject ("Scripting.FileSystemObject")',
'strScript = Wscript.ScriptFullName',
'strScriptPath = fso.GetAbsolutePathName(strScript & "\\..")',
'',
'rem If the Input file is NOT qualified with a path, default the current path',
'LPosition = InStrRev(strExcelFileName, "\\") ',
'if LPosition = 0 Then ',
' strExcelFileName = strScriptPath & "\\" & strExcelFileName',
'strScriptPath = strScriptPath & "\\" ',
'else ',
'strScriptPath = Mid(strExcelFileName, 1, LPosition) ',
'End If',
'rem msgbox LPosition & " - " & strExcelFileName & " - " & strScriptPath',
'',
'Set objXL = CreateObject("Excel.Application")',
'Set objWorkBook = objXL.Workbooks.Open(strExcelFileName)',
'objXL.DisplayAlerts = False',
'',
'rem loop over worksheets',
' For Each sheet In objWorkBook.Sheets ',
'if objXL.Application.WorksheetFunction.CountA(sheet.Cells) <> 0 Then ',
'rem sheet.Rows(1).delete',
'sheet.SaveAs strScriptPath & sheet.Name & ".csv", 6',
' End If',
' Next',
'',
'rem clean up ',
'objWorkBook.Close ',
'objXL.quit',
'Set objXL = Nothing ',
'Set objWorkBook = Nothing',
'Set fso = Nothing',
'',
'rem end script'),
con = converter_file)
close(converter_file)
file.copy(file_path, tempdir())
orig_wd <- getwd()
setwd(tempdir())
file.rename(file_name, paste0("filetoconvert", file_ext))
shell(paste("converter.vbs",
paste0("filetoconvert", file_ext)), intern = TRUE)
setwd(orig_wd)
if(is.null(keep_sheets)) {
keep_sheets <- gsub("\\.csv", "", list.files(tempdir(), pattern = "\\.csv"))
}
file_flags <- paste0(keep_sheets, ".csv")
if(is.null(target_dir) | (!is.null(target_dir) & target_dir != FALSE)) {
for(i in 1:length(file_flags)) {
file.copy(
paste0(tempdir(), "/", file_flags[i]), file_root, overwrite = TRUE)
}
} else {
all_files <- lapply(file_flags, function(x) {
csv_file <- read.csv(paste0(tempdir(), "/", x),
as.is = TRUE, na.strings = c("#N/A", "NA", "N/A", "?", ""))
csv_file[,sapply(csv_file, function(y) mean(is.na(y), na.rm = TRUE)) < 1]
})
if(length(all_files) == 1) {
all_files <- all_files[[1]]
} else {
names(all_files) <- keep_sheets
}
}
suppressWarnings(file.remove(
paste0(tempdir(),
"/",
list.files(tempdir())[!(list.files(tempdir()) %in% temp_already)])))
if(!is.null(target_dir) & target_dir == FALSE) {
all_files
}
}
view raw excelToCsv.R hosted with ❤ by GitHub

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