How do I convert markdown equations to pdf using pandoc

Question

I have a markdown document with lots of equations (mathjax I think) which renders fine with the application Marked 2. When I try to convert it to pdf with pandoc to create the bibliography, I get an error.

For example, with

\\[ \mu_{s,h,d,y} = \left\{
  \begin{array}{1 1}
    \omega_{s,h,d,y} + \delta_{s}(t_{s,h,d-1,y} - \omega_{s,h,d-1,y}) & \quad  \text{for $t_{s,h,d-1,y}$ is real} \\
    \omega_{s,h,d,y} & \quad  \text{for $t_{s,h,d-1,y}$ is not real}
  \end{array} \right.
 \\]

It looks like

However, when I run

pandoc -H format.sty -V fontsize=12pt --bibliography northeast_temperature_refs.bib --csl=american-geophysical-union.csl northeast_temperature_ms2.md -o northeast_temperature_ms.pdf --mathjax

with or without --mathjax I get the following error

! Missing $ inserted.
<inserted text> 
                $
l.268 \textbackslash{}{[} \mu

pandoc: Error producing PDF from TeX source

If I try to use $$ instead of \\\\[ like:

$$
\mu_{s,h,d,y} = \left\{
  \begin{array}
    \omega_{s,h,d,y} + \delta_{s}(t_{s,h,d-1,y} - \omega_{s,h,d-1,y}) & \quad  \text{for $$t_{s,h,d-1,y}$$ is real} \\
    \omega_{s,h,d,y} & \quad  \text{for $$t_{s,h,d-1,y}$$ is not real}
  \end{array} \right.
 $$

I get the following error:

! LaTeX Error: Illegal character in array arg.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              

l.278   \begin{array}{1 1}

pandoc: Error producing PDF from TeX source

This is my first time ever trying to write equations outside a canned program so any help would be appreciated. I thought I was doing such a good job when I did quick checks with Marked but apparently it doesn't work with pandoc the way I have it.

I am on a Mac with Yosemite and have MacTex installed.

Answer 1

Marked uses a different markdown processor under the hood (MultiMarkdown) than Pandoc, which has different syntax for equations ( \\\\[ \\\\] instead of $$ ). If you want to write in a single format for both Marked previewing/HTML and pandoc PDF/anything else output, you can change Marked's processor to Pandoc (directions here ). This way you can use $$ syntax for everything.

Answer 2

I think that pandoc doesn't cover the array command, as your command doesn't work for me in an IPython notebook. However, replacing the array command with a cases statement does work for me:

\\[ \mu_{s,h,d,y} = \begin{cases}
    \omega_{s,h,d,y} + \delta_{s}(t_{s,h,d-1,y} - \omega_{s,h,d-1,y}) & \quad  \text{for $t_{s,h,d-1,y}$ is real} \\
    \omega_{s,h,d,y} & \quad  \text{for $t_{s,h,d-1,y}$ is not real}
  \end{cases}
 \\]