Importing Excel files into R, xlsx or xls

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.

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.

You may also want to try the XLConnect package. I've had better luck with it than xlsx (plus it can read .xls files too).

library(XLConnect)
theData <- readWorksheet(loadWorkbook("C:/AB_DNA_Tag_Numbers.xlsx"),sheet=1)

also, if you are having trouble with your file not being found, try selecting it with file.choose().

I would definitely try the read.xls function in the gdata package, which is considerably more mature than the xlsx package. It may require Perl ...

Update

As the Answer below is now somewhat outdated, I'd just draw attention to the readxl package. If the Excel sheet is well formatted/lain out then I would now use readxl to read from the workbook. If sheets are poorly formatted/lain out then I would still export to CSV and then handle the problems in R either via read.csv() or plain old readLines().

Original

My preferred way is to save individual Excel sheets in comma separated value (CSV) files. On Windows, these files are associated with Excel so you don't loose the double-click-open-in-Excel "feature".

CSV files can be read into R using read.csv(), or, if you are in a location or using a computer set up with some European settings (where , is used as the decimal place), using read.csv2().

These functions have sensible defaults that makes reading appropriately formatted files simple. Just keep any labels for samples or variables in the first row or column.

Added benefits of storing files in CSV are that as the files are plain text they can be passed around very easily and you can be confident they will open anywhere; one doesn't need Excel to look at or edit the data.

Example 2012:

library("xlsx")
FirstTable <- read.xlsx("MyExcelFile.xlsx", 1 , stringsAsFactors=F)
SecondTable <- read.xlsx("MyExcelFile.xlsx", 2 , stringsAsFactors=F)

• I would try 'xlsx' package for it is easy to handle and seems mature enough
• worked fine for me and did not need any additionals like Perl or whatever

Example 2015:

library("readxl")
FirstTable  <- read_excel("MyExcelFile.xlsx", 1)
SecondTable <- read_excel("MyExcelFile.xlsx", 2)

• nowadays I use readxl and have made good experience with it.
• no extra stuff needed
• good performance