Tables from R into Word

A good looking table matters!
A good looking table matters!

This tutorial is on how to create a neat table in Word by combining knitr and R Markdown. I’ll be using my own function, htmlTable, from the Gmisc package.

Background: Because most journals that I submit to want the documents in Word and not LaTeX, converting my output into Word is essential. I used to rely on converting LaTeX into Word but this was tricky, full of bugs and still needed tweaking at the end. With R Markdown and LibreOffice it’s actually rather smooth sailing, although I must admit that I’m disappointed at how bad Word handles html.

The tutorial

We start with loading the package, and labeling the dataset. The labels and the units are from the Hmisc package:

?View Code RSPLUS
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library(Gmisc, verbose=FALSE)
 
data(mtcars)
 
label(mtcars$mpg) <- "Gas"
units(mtcars$mpg) <- "Miles/gal"
 
label(mtcars$wt) <- "Weight"
units(mtcars$wt) <- "10<sup>3</sup> lb"
 
mtcars$am <- factor(mtcars$am, 
                    levels=0:1, 
                    labels=c("Automatic", "Manual"))
label(mtcars$am) <- "Transmission"
 
mtcars$gear <- factor(mtcars$gear)
label(mtcars$gear) <- "Gears"
 
# Make up some data for making it slightly more interesting
mtcars$col <- factor(sample(c("red", "black", "silver"), 
                            size=NROW(mtcars), 
                            replace=TRUE))
label(mtcars$col) <- "Car color"

Now we calculate the statistics. The getDescriptionsStatsBy() is a more interesting alternative to just running table(). It can also run simple statistics that often are reported in table 1.

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mpg_data <- getDescriptionStatsBy(mtcars$mpg, mtcars$am, html=TRUE)
rownames(mpg_data) <- units(mtcars$mpg)
wt_data <- getDescriptionStatsBy(mtcars$wt, mtcars$am, html=TRUE)
rownames(wt_data) <- units(mtcars$wt)
 
gear_data <- getDescriptionStatsBy(mtcars$gear, mtcars$am, html=TRUE)
col_data <- getDescriptionStatsBy(mtcars$col, mtcars$am, html=TRUE)

Next we create the actual table with htmlTable. We can also have an internal reference to the table using the <a href=“#Table1” >, click here. The latex() function that I’ve used as a template for the parameters (to be able to quickly switch between the two) can feel a little overwhelming:

  • x – just the matrix with all the cells
  • caption – nothing fancy, just the table caption
  • label – this is transferred into an href anchor, <a name=“#label” ></a>
  • rowlabel – the contents of the top left cell
  • rgroup - the label of the groups, this is the unindented header of each group
  • n.rgroup – the number of rows that each group contains, note that this is not the position of the group but the number of elements in them, i.e. sum(n.rgroup) == nrow(x)
  • ctable – a formatting option from LaTeX that gives top/bottom border as single lines instead of double.
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htmlTable(
  x        = rbind(gear_data, col_data, mpg_data, wt_data),
  caption  = paste("My table 1. All continuous values are reported with",
                   "mean and standard deviation, x̄ (± SD), while categories",
                   "are reported in percentages, no (%)."),
  label    = "Table1",
  rowlabel = "Variables",
  rgroup   = c(label(gear_data),
               label(col_data),
               label(mpg_data),
               label(wt_data)),
  n.rgroup = c(NROW(gear_data),
               NROW(col_data),
               NROW(mpg_data),
               NROW(wt_data)),
  ctable   = TRUE)

Below is the table. Note: the table is formatted by this blog CSL, it will look different after running the Rmd document through knitr.

My table 1. All continuous values are reported with mean and standard deviation, x̄ (± SD), while categories are reported in percentages, no (%).
Variables Automatic Manual
Gears
  3 15 (78.9 %) 0 (0.0 %)
  4 4 (21.1 %) 8 (61.5 %)
  5 0 (0.0 %) 5 (38.5 %)
Car color
  black 6 (31.6 %) 4 (30.8 %)
  red 7 (36.8 %) 3 (23.1 %)
  silver 6 (31.6 %) 6 (46.2 %)
Gas
  Miles/gal 17.1 (± 3.8) 24.4 (± 6.2)
Weight
  103 lb 3.8 (± 0.8) 2.4 (± 0.6)

Now install and open in LibreOffice Writer the html document that knitr has created:

The table looks actually a little funny in Writer but don't worry, it'll be great!
The table looks actually a little funny in Writer but don’t worry, it’ll be great!

Now select the table, copy and paste into word, voila!

Now this looks better
Now this looks better!

flattr this!

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12 Responses to Tables from R into Word

  1. just thought you might like to see how I put gmisc htmlTable to use
    Tables Are Like Cockroaches

    thanks so much for a great post and a fine package

    • Max Gordon says:

      Thanks! Interesting post, it never stops amazing me how much tinkering one can do with a simple table. I’ll consider adding to the code options of super cgroups (not sure what to call them) and for styling each row. I just hope that people don’t find the options overwhelming. I’ve tried to document as much as I can but I know from my own experience that reading manuals is not that exciting…

  2. Chris says:

    I’ve copy and pasted your entire code into R Markdown and used Knitr. I get the following output:

    Reproducing example

    Variables
    Automatic
    Manual

    Gears

      3
    15 (78.9 %)
    0 (0.0 %)

      4
    4 (21.1 %)
    8 (61.5 %)

      5
    0 (0.0 %)
    5 (38.5 %)…

    I feel like I’m making a very silly and obvious mistake here, but I can’t for the life of me understand what it is. Your example looks amazing and I hope I can use it to create my own tables if I only figure out what’s going wrong. Any suggestions? Thanks.

  3. Hi, I’ve been using htmlTables for a while now and they are great…. but have you found a way to get them directly into word or pdf with pandoc or knitr, without copy-pasting from a compiled html file?

    • Max Gordon says:

      I tried pandoc a while ago but actually never with the htmlTables, I guess using pandoc’s --process-html option might be a worth a try. Let me know if it works.

  4. Chenguang says:

    Very cool! However, with the latest R version (3.0.1), your package cannot be loaded

    • Max Gordon says:

      Strange, works fine here. What errors do you get, what system are you using and how have you tried to install the package? I’ve uploaded a new version, although the previous should work OK.

  5. sjp says:

    Hi, great package.

    How would you get the column header “Transmission” to appear above “Automatic” and “Manual” in your htmlTable ?

    • sjp says:

      Whoops, found it in your package documentation! Awesome. (for others curious, the argument is cgroup=””)

  6. michael says:

    I like your package very much. Is it possible to allow more flexibility by allowing multiple levels of headings? The current “cgroup” and ‘n.cgroup’ only take a vector, it will be nice to allow a matrix so several layers of (nested) headings can be displayed. Thanks!

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