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.

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.

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.