As suggested in the comments, the problem is that the default LaTeX template for pandoc uses longtable (regular LaTeX tables are not paginated). If you donβt want to create your own template, you can simply change the default value.
Vanilla pandoc
You can use knitr to create a normal Markdown file. You can then use pandoc to create a PDF / TeX file using another LaTeX template using
pandoc --template=mytemplate.xex -o myfile.pdf myfile.md
The easiest way to set up a new template is to change the default value, which you can get pandoc to send to the console:
pandoc --print-default-template=latex
Then you need to change the line \usepackage{longtable,booktabs} to \usepackage{booktabs} .
If you are on OS X or Linux, you can use sed and redirect the output to directly create the template without longtable :
pandoc --print-default-template=latex | sed 's/longtable,//' > mytemplate.tex
Rstudio
If you are doing this from RStudio, the easiest option is to change the default template. (The latest releases of the RStudio pandoc package and therefore use things differently from the system pandoc.) If you look at the R Markdown build / status window, you will see something like this:
output file: rmarkdown.knit.md /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc rmarkdown.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output rmarkdown.pdf --template /Library/Frameworks/R.framework/Versions/3.0/Resources/library/rmarkdown/rmd/latex/default.tex --highlight-style tango --latex-engine /usr/texbin/pdflatex --variable 'geometry:margin=1in' Output created: rmarkdown.pdf
(I made this example on a Mac, on Windows or Linux, it will look different.) The template is specified in the command, which you can change as described above. This, of course, will change the behavior for all documents created through RStudio. As far as I know, there is currently no public option to change the template used, but this can change, since document templates seem to be an area of ββactive work in recent releases.
EDIT (2016-05-05):
It seems that using longtable hardcoded in recent versions of pandoc, so removing a longtable from the preamble will generate some errors. You can get around this using a filter .
Save the associated python script and
Vanilla pandoc
add the --filter path/to/filter.py to your pandoc call.
Rstudio
change your YAML block for additional pandoc arguments:
--- title : "Table" pandoc_args : --filter path/to/filter.py output : pdf_document ---
As noted in the link above, this will lead to the creation of simple LaTeX tables, which means there is no support for footnotes in the tables.