Using table caption on R markdown file using knitr to use in pandoc to convert to pdf

Question

I am wondering if it is possible to use the table captions like figure captions using knitr in .Rmd file ?

I saw options for figure caption but I couldn't see the option for the table caption. I also want to remove the message such as "% latex table generated in R 2.15.2 by xtable 1.7-0 package % Wed Mar 06 15:02:11 2013" .

I used X table to create the table: The sample code I used is as follows:

```{r table2, results='asis', message=FALSE} 
library(xtable) 
print(xtable(head(iris))) 
``` 

The table I got after processing through pandoc is as follows:

I tried to use message=FALSE in Rmd file to get rid of the message shown above. I also want to know if it is possible to automatically add the caption for table in Rmd ?

By caption I mean something like below (this is for the figure) and the figure number is automatically updated.

This output is a snapshot from the pdf generated by pdf using the markdown file created by knitr.

Thank you.

Lumberjack

I think that much of the answers you seek are through using ?xtable and ?print.xtable. Look at type and caption – Cartload

for the LaTeX comment, the issue has been solved in xtable; see github.com/yihui/knitr-book/issues/3 (the new version of xtable is on CRAN now) – Luna

@ Yihui: I upgraded my xtable from CRAN and now I have latest version and I am still getting the same output. I used the code <pre>{r table2, results='asis', message=FALSE,echo=FALSE} library(xtable) print(xtable(head(iris))) </pre>. Did I do anything wrong ? – Lumberjack

@Jdbaba read the documentation ?print.xtable and see the comment argument – Luna

@Jdbaba. I guess you have solved now the problem with the xtable showing the "% latex table generated in R 2.15.2 by xtable". I can not find the solution even by looking on print.xtable. Thanks. – Bequeath

So, here is the solution: print(xtable(yourtable, comment = getOption("xtable.comment", FALSE)) – Bequeath

Answer 1

If you do not insist on using a LaTeX/HTML-only solution with the otherwise awesome xtable package, you might achieve the same with Pandoc's markdown. One option is to add the caption manually below the table, or use my R Pandoc writer package:

> library(pander)                         # load pkg
> panderOptions('table.split.table', Inf) # not to split table
> set.caption('Hello Fisher!')            # add caption
> pander(head(iris))                      # show (almost) any R object in markdown
-------------------------------------------------------------------
 Sepal.Length   Sepal.Width   Petal.Length   Petal.Width   Species 
-------------- ------------- -------------- ------------- ---------
     5.1            3.5           1.4            0.2       setosa  

     4.9            3.0           1.4            0.2       setosa  

     4.7            3.2           1.3            0.2       setosa  

     4.6            3.1           1.5            0.2       setosa  

     5.0            3.6           1.4            0.2       setosa  

     5.4            3.9           1.7            0.4       setosa  
-------------------------------------------------------------------

Table: Hello Fisher!

Then use Pandoc to convert this markdown file to HTML, LaTeX, docx, odt or any other popular document formats.

Mythomania

I'm trying to use your nice pander package, but couldn't find an option to control the position of a table's caption (by default, the position is below the table, but I need above). I looked through documentation and on the Web, but to no avail. Any advice? (I understand that I can produce caption independently as R Markdown text, but then there is an issue of margin between the caption and the table. It would be nice to be able to specify both the position (above/below) and the margin.) – Rhadamanthus

@AleksandrBlekh having the caption above the table is not a valid markdown syntax, it should stay below the table. On the other hand, you can render that to be above the table/image in e.g. HTML or LaTeX. For the prior, use JavaScript, for the latter, I suggest the caption and floatrow LaTeX packages, like \floatsetup[table]{capposition=top} – Mythomania

Thanks for fast reply and nice suggestions! One of the reasons I'm trying to use pander and R Markdown format is to be able to produce multi-format output, as needed. Going the format-specific route is not optimal in this regard (no single codebase); I actually implemented some stuff in a LaTeX-specific way and it took a while just for that. Can't imagine spending more time to support HMTL, etc. Actually, I found a solution: I need pandoc 1.13+, which contains this fix (caption should be on top): search for "table captions above tables" here: johnmacfarlane.net/pandoc/releases.html. – Rhadamanthus

I can't find pandoc binary for that release or higher for Ubuntu/Debian anywhere. I think nobody has it yet. I've read on some mailing list that even Yihui can't find it. If you will find it, please let me know. – Rhadamanthus

@AleksandrBlekh This fix sounds great, but it seems to be LaTeX-only to me. RStudio has released some binaries: s3.amazonaws.com/rstudio-buildtools/pandoc-1.13.1.zip Anyway, you can still use markdown with multiple output formats and "captions above tables/images", but this way you have to develop your custom templates for HTML, PDF etc. This is a one-time investment, that you can use for all future reports, so besides the above mentioned one-liner LaTeX call, you'd need also another one-liner JavaScript call in your custom HTML template to move caption above the objects. – Mythomania

I appreciate your comments and link to the binary. I'm not sure I understand the need for developing templates (unless you meant that in context of using older versions of pandoc without the fix). If I don't need something fancy, aren't the default ones good enough? Sorry, if my question sounds stupid, but I'm not yet fluent in under-the-hood complexities of reproducible research tools (but willing and doing my best to learn as much as I can). P.S. Why do you think that fix is LaTeX-only? – Rhadamanthus

@AleksandrBlekh the changelog you linked above has the quote part below the "LaTeX writer" section, so I think this update has nothing to do with the other output formats. Also, I think the markdown specification of captions (to have it below the table) has not changed either. About "templates": probably I should have written "stylesheets" instead, see e.g. --template and -H at johnmacfarlane.net/pandoc/README.html#general-writer-options In short: you can override the bundled design of Pandoc created documents. – Mythomania

Answer 2

You can insert tables with automatically numbered captions in markdown for processing with pandoc using straight knitr code. Insert this code snippet at the top of your .rmd file:

```{r setup, echo=FALSE}
tn = local({
  i = 0
  function(x) {
    i <<- i + 1
    paste('\n\n:Table ', i, ': ', x, sep = '')
    # The : before Table tells pandoc to wrap your caption in <caption></caption>
  }
})
knit_hooks$set(tab.cap = function(before, options, envir) {
  if(!before)
    tn(options$tab.cap)
})
default_output_hook = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
  if (is.null(options$tab.cap) == F)  
    x
  else
    default_output_hook(x,options)
})
```

To insert a numbered table caption:

```{r myirischunk, tab.cap="This is the head of the Iris table"}
kable(head(iris))
```

By overriding the output hook and using tab.cap you don't need to clutter your chunk options with results='asis'.

Thanks Knitr!

PS: If you want to convert to latex/pdf you would probably want latex to number the tables for you. In that case you could change tn(options$tab.cap) to paste('\n\n:', options$tab.cap, sep='') - but I haven't tested this.

Pulmonate

I tried this with RStudio running rmarkdown_0.3.3; I did not need the : after \n\n. Because the : was printing. However, I cannot figure out how to get the caption BEFORE (ABOVE) the table. How could I revise the hook to make that work? For figures, I can do it with knit_hooks$set(plot = function(x, options) { paste('<figure><figcaption>', options$fig.cap, '</figcaption><img src="', opts_knit$get('base.url'), paste(x, collapse = '.'), '"></figure>', sep = '') – Barbaresi

I changed: paste('\n\n:Table ', i, ': ', x, sep = '') to paste('\n\n<caption>Table ', i, ': ', x, sep = '','</caption><p></p>') to add space after the caption, remove the : which was printed, and retain the caption formatting – Abscission

@DeanK: any recommendations on how this would look like if I want to add a short version of the caption to the TOC, i.e. tab.scap? See also github.com/yihui/knitr/issues/1679 – Stoup

Answer 3

You can accomplish this with xtable. Add caption to xtable and comment=FALSE to the print function.

print(
  xtable(
    head(iris),
    caption = 'Iris data'
  ),
  comment = FALSE,
  type = 'latex'
)

See the xtable and print.xtable documentation.

Prehension

Answer 4

I know this is since many years ago, but if there is someone like me who arrived here looking for an answer I'll tell you the answer that I found to the same problem.

It was really simply, we just need to put:

```{r mostrarSerie,results='asis',echo=FALSE}
library(xtable)
options(xtable.floating = TRUE)
print(xtable(AP, digits = 0,caption = "Serie de tiempo"),comment = FALSE)
```

The important step is to put into the options xtable.floating = TRUE because so LaTeX will recognize the table.

Deimos