Including 'abstract' into yaml header causes a bunch of various errors about thesisdown HOT 14 CLOSED

I dunno if this was solved, but, for me the issue was solved when I removed the first space before "`":

abstract: |
 `r if(knit .....

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Wow, I thought that commenting those lines would fix the "[WARNING] This document format requires a nonempty <title> element." issue.
Now, I have tried it again, and I'm getting the cites correctly.
thanks @ismayc , great package! ;)

from thesisdown.

Thanks for reporting, Christian. I'm still digging into what might be causing this change and hope to have an answer for you this week.

from thesisdown.

My comment on line 20 does suggest that one doesn't try to build the gitbook with the lines below it "on", but that's not necessarily clear. I think it's probably best that I switch to having specific files be used for the PDF and gitbook versions similar to what I did with the ModernDive book here. If you think that makes sense as well, let me know and I can get to working on changing it over.

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Thanks for tackling my issue.

For me it feels a bit redundant to specify almost exactly the same files for the different output types, but if this is working I am happy to use it.

My only concern is about the pdf output. So far some files (e.g. abstract, acknowledgement, prefect, etc...) are passed from the yaml header in index.Rmd to preamble.txt where they are integrated in their respective Latex environment:

preface: |
  This is an example of a thesis setup to use the reed thesis document class
  (for LaTeX) and the R bookdown package, in general.

to

\Preface{
$preface$
}

How will this work when you specify all files in _bookdown.yml? Will you still be able to pass them to the preamble.txt?

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The setup that you mentioned only really works with the PDF version, so the HTML version will need to include 00--prelim.Rmd as a file to use before index.Rmd in _bookdown.yml. If we can figure out a way to have the Preface and other non-main matter content work nicely with both HTML and LaTeX in the YAML, that's the best case scenario. Unfortunately, I couldn't figure out such a way in the past to incorporate the YAML to work with both.

One alternative is to remove the YAML specifying of this intro content and force everything to appear in their own Rmd files or we could just put the content in the index.Rmd file to force it to appear in the correct spot and that will also work with both the HTML and LaTeX versions. (This could also make using the _bookdown.yml file not be necessary.)

Complicated stuff 😄

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I found a repo that uses an adapted version of your thesisdown package (https://github.com/lazappi/phd-thesis; https://github.com/lazappi/unimelbdown). Checking the gitbook version of the thesis (https://lazappi.github.io/phd-thesis/) indicates that @lazappi might have found a way to make it work. At least title, author and date appear correctly. Maybe @lazappi is willing to help

PS: Does tagging work across repositories?

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I'm not sure if I came up with a different solution. I used the YAML fields for the PDF version and have this file which adds them to the HTML/DOCX versions https://github.com/lazappi/phd-thesis/blob/master/0-frontmatter/00-frontmatter.Rmd.

Not sure if that is useful or not. I'm a bit rusty on how this all works now but happy to help if I can.

from thesisdown.

Thanks, @lazappi. It doesn't seem that there is a clean solution here. Maybe it's best to just remove the YAML introductory content for the {thesisdown} template? That way specifying them as unnumbered in the index.Rmd file will transfer nicely over to all the various output formats (PDF, Gitbook, Word, etc.) to have them appear just before the Introduction unnumbered chapter?

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Hi, sorry I come with another issue, but by googling I note that @christianholland is having the same (other) issue as me:

pandoc-citeproc: reference Molina1994 not found
pandoc-citeproc: reference reedweb2007 not found
pandoc-citeproc: reference noble2002 not found

there is no way I can get references for the gitbook version, however for the pdf version it is working like a charm. This is happening with the fresh thesisdown example, and also with my repo https://github.com/jcrodriguez1989/tesis_doctoral/

Any idea?
thanks!

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Hi @jcrodriguez1989. I think it's probably best that I just remove the option to include the introductory material in YAML as I suggested in the comment above. I'll try to get this figured out over the next few weeks if that's OK with you.

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Yep. The most up-to-date version of the package template removes the extra line all together:

from thesisdown.

Yep. The most up-to-date version of the package template removes the extra line all together:

thesisdown/inst/rmarkdown/templates/thesis/skeleton/skeleton.Rmd

Line 32 in 2f14a72

abstract: '`r if(knitr:::is_latex_output()) paste(readLines(here::here("prelims", "00-abstract.Rmd")), collapse = "\n ")`'

Of note, the above removes line breaks, whereas the single space solution above does not. This was a VERY helpful thread.

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This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org whenever possible) and link to this issue. If a reprex is not applicable, recording a short Loom video showing what you are seeing can go a long way in helping to diagnose problems.

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