Read an Excel file directly from a R script

Question

How can I read an Excel file directly into R? Or should I first export the data to a text- or CSV file and import that file into R?

Answer 1

Let me reiterate what @Chase recommended: Use XLConnect.

The reasons for using XLConnect are, in my opinion:

1. Cross platform. XLConnect is written in Java and, thus, will run on Win, Linux, Mac with no change of your R code (except possibly path strings)
2. Nothing else to load. Just install XLConnect and get on with life.
3. You only mentioned reading Excel files, but XLConnect will also write Excel files, including changing cell formatting. And it will do this from Linux or Mac, not just Win.

XLConnect is somewhat new compared to other solutions so it is less frequently mentioned in blog posts and reference docs. For me it's been very useful.

Answer 2

And now there is readxl:

The readxl package makes it easy to get data out of Excel and into R. Compared to the existing packages (e.g. gdata, xlsx, xlsReadWrite etc) 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 is built on top of the libxls C library, which abstracts away many of the complexities of the underlying binary format.

It supports both the legacy .xls format and .xlsx

readxl is available from CRAN, or you can install it from github with:

# install.packages("devtools")
devtools::install_github("hadley/readxl")

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")

Note that while the description says 'no external dependencies', it does require the Rcpp package, which in turn requires Rtools (for Windows) or Xcode (for OSX), which are dependencies external to R. Though many people have them installed for other reasons.

Answer 3

Yes. See the relevant page on the R wiki. Short answer: read.xls from the gdata package works most of the time (although you need to have Perl installed on your system -- usually already true on MacOS and Linux, but takes an extra step on Windows, i.e. see http://strawberryperl.com/). There are various caveats, and alternatives, listed on the R wiki page.

The only reason I see not to do this directly is that you may want to examine the spreadsheet to see if it has glitches (weird headers, multiple worksheets [you can only read one at a time, although you can obviously loop over them all], included plots, etc.). But for a well-formed, rectangular spreadsheet with plain numbers and character data (i.e., not comma-formatted numbers, dates, formulas with divide-by-zero errors, missing values, etc. etc. ..) I generally have no problem with this process.

Answer 4

EDIT 2015-October: As others have commented here the openxlsx and readxl packages are by far faster than the xlsx package and actually manage to open larger Excel files (>1500 rows & > 120 columns). @MichaelChirico demonstrates that readxl is better when speed is preferred and openxlsx replaces the functionality provided by the xlsx package. If you are looking for a package to read, write, and modify Excel files in 2015, pick the openxlsx instead of xlsx.

Pre-2015: I have used xlsxpackage. It changed my workflow with Excel and R. No more annoying pop-ups asking, if I am sure that I want to save my Excel sheet in .txt format. The package also writes Excel files.

However, I find read.xlsx function slow, when opening large Excel files. read.xlsx2 function is considerably faster, but does not quess the vector class of data.frame columns. You have to use colClasses command to specify desired column classes, if you use read.xlsx2 function. Here is a practical example:

read.xlsx("filename.xlsx", 1) reads your file and makes the data.frame column classes nearly useful, but is very slow for large data sets. Works also for .xls files.

read.xlsx2("filename.xlsx", 1) is faster, but you will have to define column classes manually. A shortcut is to run the command twice (see the example below). character specification converts your columns to factors. Use Dateand POSIXct options for time.

coln <- function(x){y <- rbind(seq(1,ncol(x))); colnames(y) <- colnames(x)
rownames(y) <- "col.number"; return(y)} # A function to see column numbers

data <- read.xlsx2("filename.xlsx", 1) # Open the file 

coln(data)    # Check the column numbers you want to have as factors

x <- 3 # Say you want columns 1-3 as factors, the rest numeric

data <- read.xlsx2("filename.xlsx", 1, colClasses= c(rep("character", x),
rep("numeric", ncol(data)-x+1)))

Answer 5

Given the proliferation of different ways to read an Excel file in R and the plethora of answers here, I thought I'd try to shed some light on which of the options mentioned here perform the best (in a few simple situations).

I myself have been using xlsx since I started using R, for inertia if nothing else, and I recently noticed there doesn't seem to be any objective information about which package works better.

Any benchmarking exercise is fraught with difficulties as some packages are sure to handle certain situations better than others, and a waterfall of other caveats.

That said, I'm using a (reproducible) data set that I think is in a pretty common format (8 string fields, 3 numeric, 1 integer, 3 dates):

set.seed(51423)
data.frame(
  str1 = sample(sprintf("%010d", 1:NN)), #ID field 1
  str2 = sample(sprintf("%09d", 1:NN)),  #ID field 2
  #varying length string field--think names/addresses, etc.
  str3 = 
    replicate(NN, paste0(sample(LETTERS, sample(10:30, 1L), TRUE),
                         collapse = "")),
  #factor-like string field with 50 "levels"
  str4 = sprintf("%05d", sample(sample(1e5, 50L), NN, TRUE)),
  #factor-like string field with 17 levels, varying length
  str5 = 
    sample(replicate(17L, paste0(sample(LETTERS, sample(15:25, 1L), TRUE),
                                 collapse = "")), NN, TRUE),
  #lognormally distributed numeric
  num1 = round(exp(rnorm(NN, mean = 6.5, sd = 1.5)), 2L),
  #3 binary strings
  str6 = sample(c("Y","N"), NN, TRUE),
  str7 = sample(c("M","F"), NN, TRUE),
  str8 = sample(c("B","W"), NN, TRUE),
  #right-skewed integer
  int1 = ceiling(rexp(NN)),
  #dates by month
  dat1 = 
    sample(seq(from = as.Date("2005-12-31"), 
               to = as.Date("2015-12-31"), by = "month"),
           NN, TRUE),
  dat2 = 
    sample(seq(from = as.Date("2005-12-31"), 
               to = as.Date("2015-12-31"), by = "month"),
           NN, TRUE),
  num2 = round(exp(rnorm(NN, mean = 6, sd = 1.5)), 2L),
  #date by day
  dat3 = 
    sample(seq(from = as.Date("2015-06-01"), 
               to = as.Date("2015-07-15"), by = "day"),
           NN, TRUE),
  #lognormal numeric that can be positive or negative
  num3 = 
    (-1) ^ sample(2, NN, TRUE) * round(exp(rnorm(NN, mean = 6, sd = 1.5)), 2L)
)

I then wrote this to csv and opened in LibreOffice and saved it as an .xlsx file, then benchmarked 4 of the packages mentioned in this thread: xlsx, openxlsx, readxl, and gdata, using the default options (I also tried a version of whether or not I specify column types, but this didn't change the rankings).

I'm excluding RODBC because I'm on Linux; XLConnect because it seems its primary purpose is not reading in single Excel sheets but importing entire Excel workbooks, so to put its horse in the race on only its reading capabilities seems unfair; and xlsReadWrite because it is no longer compatible with my version of R (seems to have been phased out).

I then ran benchmarks with NN=1000L and NN=25000L (resetting the seed before each declaration of the data.frame above) to allow for differences with respect to Excel file size. gc is primarily for xlsx, which I've found at times can create memory clogs. Without further ado, here are the results I found:

1,000-Row Excel File

benchmark1k <-
  microbenchmark(times = 100L,
                 xlsx = {xlsx::read.xlsx2(fl, sheetIndex=1); invisible(gc())},
                 openxlsx = {openxlsx::read.xlsx(fl); invisible(gc())},
                 readxl = {readxl::read_excel(fl); invisible(gc())},
                 gdata = {gdata::read.xls(fl); invisible(gc())})

# Unit: milliseconds
#      expr       min        lq      mean    median        uq       max neval
#      xlsx  194.1958  199.2662  214.1512  201.9063  212.7563  354.0327   100
#  openxlsx  142.2074  142.9028  151.9127  143.7239  148.0940  255.0124   100
#    readxl  122.0238  122.8448  132.4021  123.6964  130.2881  214.5138   100
#     gdata 2004.4745 2042.0732 2087.8724 2062.5259 2116.7795 2425.6345   100

So readxl is the winner, with openxlsx competitive and gdata a clear loser. Taking each measure relative to the column minimum:

#       expr   min    lq  mean median    uq   max
# 1     xlsx  1.59  1.62  1.62   1.63  1.63  1.65
# 2 openxlsx  1.17  1.16  1.15   1.16  1.14  1.19
# 3   readxl  1.00  1.00  1.00   1.00  1.00  1.00
# 4    gdata 16.43 16.62 15.77  16.67 16.25 11.31

We see my own favorite, xlsx is 60% slower than readxl.

25,000-Row Excel File

Due to the amount of time it takes, I only did 20 repetitions on the larger file, otherwise the commands were identical. Here's the raw data:

# Unit: milliseconds
#      expr        min         lq       mean     median         uq        max neval
#      xlsx  4451.9553  4539.4599  4738.6366  4762.1768  4941.2331  5091.0057    20
#  openxlsx   962.1579   981.0613   988.5006   986.1091   992.6017  1040.4158    20
#    readxl   341.0006   344.8904   347.0779   346.4518   348.9273   360.1808    20
#     gdata 43860.4013 44375.6340 44848.7797 44991.2208 45251.4441 45652.0826    20

Here's the relative data:

#       expr    min     lq   mean median     uq    max
# 1     xlsx  13.06  13.16  13.65  13.75  14.16  14.13
# 2 openxlsx   2.82   2.84   2.85   2.85   2.84   2.89
# 3   readxl   1.00   1.00   1.00   1.00   1.00   1.00
# 4    gdata 128.62 128.67 129.22 129.86 129.69 126.75

So readxl is the clear winner when it comes to speed. gdata better have something else going for it, as it's painfully slow in reading Excel files, and this problem is only exacerbated for larger tables.

Two draws of openxlsx are 1) its extensive other methods (readxl is designed to do only one thing, which is probably part of why it's so fast), especially its write.xlsx function, and 2) (more of a drawback for readxl) the col_types argument in readxl only (as of this writing) accepts some nonstandard R: "text" instead of "character" and "date" instead of "Date".

Answer 6

I've had good luck with XLConnect: http://cran.r-project.org/web/packages/XLConnect/index.html

Answer 7

library(RODBC)
file.name <- "file.xls"
sheet.name <- "Sheet Name"

## Connect to Excel File Pull and Format Data
excel.connect <- odbcConnectExcel(file.name)
dat <- sqlFetch(excel.connect, sheet.name, na.strings=c("","-"))
odbcClose(excel.connect)

Personally, I like RODBC and can recommend it.

Answer 8

Just gave the package openxlsx a try today. It worked really well (and fast).

http://cran.r-project.org/web/packages/openxlsx/index.html

Answer 9

Another solution is the xlsReadWrite package, which doesn't require additional installs but does require you download the additional shlib before you use it the first time by :

require(xlsReadWrite)
xls.getshlib()

Forgetting this can cause utter frustration. Been there and all that...

On a sidenote : You might want to consider converting to a text-based format (eg csv) and read in from there. This for a number of reasons :

• whatever your solution (RODBC, gdata, xlsReadWrite) some strange things can happen when your data gets converted. Especially dates can be rather cumbersome. The HFWutils package has some tools to deal with EXCEL dates (per @Ben Bolker's comment).

• if you have large sheets, reading in text files is faster than reading in from EXCEL.

• for .xls and .xlsx files, different solutions might be necessary. EG the xlsReadWrite package currently does not support .xlsx AFAIK. gdata requires you to install additional perl libraries for .xlsx support. xlsx package can handle extensions of the same name.

Answer 10

As noted above in many of the other answers, there are many good packages that connect to the XLS/X file and get the data in a reasonable way. However, you should be warned that under no circumstances should you use the clipboard (or a .csv) file to retrieve data from Excel. To see why, enter =1/3 into a cell in excel. Now, reduce the number of decimal points visible to you to two. Then copy and paste the data into R. Now save the CSV. You'll notice in both cases Excel has helpfully only kept the data that was visible to you through the interface and you've lost all of the precision in your actual source data.

Answer 11

Expanding on the answer provided by @Mikko you can use a neat trick to speed things up without having to "know" your column classes ahead of time. Simply use read.xlsx to grab a limited number of records to determine the classes and then followed it up with read.xlsx2

Example

# just the first 50 rows should do...
df.temp <- read.xlsx("filename.xlsx", 1, startRow=1, endRow=50) 
df.real <- read.xlsx2("filename.xlsx", 1, 
                      colClasses=as.vector(sapply(df.temp, mode)))

Answer 12

An Excel file can be read directly into R as follows:

my_data <- read.table(file = "xxxxxx.xls", sep = "\t", header=TRUE)

Reading xls and xlxs files using readxl package

library("readxl")
my_data <- read_excel("xxxxx.xls")
my_data <- read_excel("xxxxx.xlsx")