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jacob-long / jtools

Tools for summarizing/visualizing regressions and other helpful stuff
https://jtools.jacob-long.com
GNU General Public License v3.0
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Rmarkdown pdf does not compile #58

Closed nlpaces closed 2 years ago

nlpaces commented 5 years ago

< Mac OS; latest versions RStudio/R

Poisson glm model.

Call jtools functions summ() and effect_plot().

All chunks returns expected output in Console.

Knitting to PDF fails.

/Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS Enrolled.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output Enrolled.tex --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/latex/default-1.17.0.2.tex --highlight-style tango --latex-engine pdflatex --variable graphics=yes --variable 'compact-title:yes' output file: Enrolled.knit.md

This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode ! Package inputenc Error: Unicode character χ (U+3C7) (inputenc) not set up for use with LaTeX.

Try other LaTeX engines instead (e.g., xelatex) if you are using pdflatex. For R Markdown users, see https://bookdown.org/yihui/rmarkdown/pdf-document.html Error: Failed to compile Enrolled.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Enrolled.log for more info. Execution halted

Have done all suggested debugging Enrolled.Rmd.txt

Knitting successful to MS word.

If chunks with jtools function calls set to eval = F, PDF compiles.

Data files attached.

.Rmd file attached in txt format.

Nathan ForNathanFig1eligible_20190418.xlsx ForNathanFig1enrolled_20190418.xlsx

Enrolled.Rmd.txt

jacob-long commented 5 years ago

Thanks a lot for including all of this info to help me.

This is an interesting problem and bear in mind that I'm troubleshooting on Windows. I can't quite replicate the error. I can't get it to compile even if I drop all the jtools stuff. Interestingly, when I set keep_tex = TRUE in the YAML header, I can compile the .tex file it produces.

Since there's probably some weird Windows stuff going on with my machine, I wonder what kind of TeX output you're getting. Can you change the relevant part of the YAML header to include this:

output:
  pdf_document: 
    keep_tex: true

instead of this

output: 
  pdf_document: default

And then send me the .tex file that it creates?