Importing Excel files into R, xlsx or xls

Question

Please can someone help me on the best way to import an excel 2007 (.xlsx) file into R. I have tried several methods and none seems to work. I have upgraded to 2.13.1, windows XP, xlsx 0.3.0, I don't know why the error keeps coming up. I tried:

AB<-read.xlsx("C:/AB_DNA_Tag_Numbers.xlsx","DNA_Tag_Numbers")

OR

AB<-read.xlsx("C:/AB_DNA_Tag_Numbers.xlsx",1)

but I get the error:

 Error in .jnew("java/io/FileInputStream", file) : 
  java.io.FileNotFoundException: C:\AB_DNA_Tag_Numbers.xlsx (The system cannot find the file specified)

Thank you.

Answer 1

For a solution that is free of fiddly external dependencies*, there is now readxl:

The readxl package makes it easy to get data out of Excel and into R. Compared to many of the existing packages (e.g. gdata, xlsx, xlsReadWrite) readxl has no external dependencies so it's easy to install and use on all operating systems. It is designed to work with tabular data stored in a single sheet.

Readxl supports both the legacy .xls format and the modern xml-based .xlsx format. .xls support is made possible the with libxls C library, which abstracts away many of the complexities of the underlying binary format. To parse .xlsx, we use the RapidXML C++ library.

It can be installed like so:

install.packages("readxl") # CRAN version

or

devtools::install_github("hadley/readxl") # development version

Usage

library(readxl)

# read_excel reads both xls and xlsx files
read_excel("my-old-spreadsheet.xls")
read_excel("my-new-spreadsheet.xlsx")

# Specify sheet with a number or name
read_excel("my-spreadsheet.xls", sheet = "data")
read_excel("my-spreadsheet.xls", sheet = 2)

# If NAs are represented by something other than blank cells,
# set the na argument
read_excel("my-spreadsheet.xls", na = "NA")

* not strictly true, it requires the Rcpp package, which in turn requires Rtools (for Windows) or Xcode (for OSX), which are dependencies external to R. But they don't require any fiddling with paths, etc., so that's an advantage over Java and Perl dependencies.

Update There is now the rexcel package. This promises to get Excel formatting, functions and many other kinds of information from the Excel file and into R.