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According to pandoc tricks, you may first download the task-list.lua file and save it in $DATADIR/pandoc/filters/, so it will be visible to pandoc system-wide, then run pandoc --lua-filter=task-list.lua -o filename.html filename.md
Source: https://stackoverflow.com/questions/28628903/to-do-list-in-rmarkdown
This is linked to issue #18
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