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r – data.table::fread Read all worksheets in an Excel workbook

Posted by: admin May 14, 2020 Leave a comment

Questions:

My Excel document my.xlsx has two Sheets named Sheet1 and Sheet2. I want to read all worksheets in an Excel workbook using fread function from data.table R package. The following code just read the active worksheet. Wonder how to read all worksheets without knowing their names. Thanks

df3 <- data.table::fread("in2csv my.xlsx")
> names(df3)
[1] "A" "B"
> df3
   A  B
1: 1  2
2: 2  4
3: 3  6
4: 4  8
5: 5 10
How to&Answers:

I used openxlsx::read.xlsx the last time I needed to read many sheets from an XLSX.

#install.packages("openxlsx")
library(openxlsx)
#?openxlsx::read.xlsx

#using file chooser:
filename <- file.choose()
#or hard coded file name:
#filename <- "filename.xlsx"

#get all the sheet names from the workbook
SheetNames<-getSheetNames(filename)

# loop through each sheet in the workbook
for (i in SheetNames){

  #Read the i'th sheet
  tmp_sheet<-openxlsx::read.xlsx(filename, i)

  #if the input file exists, append the new data;; else use the first sheet to initialize the input file
  ifelse(exists("input"),
         input<-rbind(input, tmp_sheet),
         input<-tmp_sheet)
}

Note: This assumes each worksheet has identical column structure and data types. You may need to standardize\normalize the data (ex. tmp_sheet <- as.data.frame(sapply(tmp_sheet,as.character), stringsAsFactors=FALSE)), or load each sheet into it’s own dataframe and pre-process further before merging.