So I'm using RMarkdown with the Bookdown extension to take notes in math classes. Bookdown has several pre-defined math environments to include and auto-number theorems, definitions, proofs, etc.
These are implemented as special code chunks in RMarkdown; for example, this chunk with the {theorem} header renders the text as a theorem in the output
```{theorem}
Here is my theorem.
``\`
The issue I'm facing is that RMarkdown seems to be treating the text inside the body as code, and as a result, several convenient features of the RMarkdown editor do not work here. For instance, one cannot click on inline math to get a preview pop-up, and inserting a ' (like in variable names such as x') highlights the rest of the body in green (presumably because the editor thinks its the beginning of a string).
Is there a way to get the editor to treat the Bookdown math environments as regular text instead of code? Alternatively, is there a way to create special headers for math environments (like maybe # (thm) Pythagorean theorem)?
Any help will be appreciated.
Related
I am working on a scientific paper in R Markdown and it needs an abstract (with embedded results) at the start of the paper. Currently the paper has analyses interspersed before the paragraphs and/or tables and figures where I report the results. I can render the abstract at the end because all the parts have been calculated but I cant submit the paper like this. I hate to front load all the analysis code (out of context) so I have the numbers ready for the abstract.
Does anybody have a strategy for this?
I know I can manually cut and paste the abstract to the top after rendering the document but that wrecks an otherwise fully reproducible workflow.
The best idea I have come up with (but I have not tried yet) is to save the .md file that is generated as the Rmd is processed and then programmatically parse the file and feed the abstract then the body of the paper directly to pandoc.
Is there a good solution to this using Quarto?
Both rmarkdown (through {bookdown}) and {quarto} will allow you to assemble a series of rmd/qmd files into a single document and use a YAML file to specify the order in which they should be assembled.
I'm currently using something like this for developing a standard reporting format for some research on human/machine interfaces. Intended for an applied scientist/engineer audience, which is not so different from your academic journal application.
I am new to R and Rmd and trying to generate a report using Rmd. This report has several images inserted along with the text. I am able to insert an image by hardcoding the path of the image. I have no problems with that but I need the path as a variable because it varies with the project. Can anyone help me with the syntax for calling a variable within a path to the image?
"Project123" changes based on the project. Is there a way I can declare this variable and call it to define the path?
Help please.
Images can use online R code for dynamic paths and/or alt text. (Early adopters of rmarkdown often tried this method as the default method of including R plots in the reports, using png(filepath...); plot(...); dev.off() followed by what I recommend you use.)
This will allow you to do what you need:
as raw markdown (and not inside a traditional code chunk).
If you aren't familiar with inline code blocks, then know that you can put just about anything in an inline code block. This is handy for including dynamic content in a paragraph of text, for example "the variance of the sample is \r var(sample(99))``". (Often it is just a pre-created variable, if numeric it is often rounded or formated to control the display of significant figures.)
I know that three backticks ``` are used to indicate a code block in RMarkdown and if you put a language inside of braces R markdown will try to run it but what does it mean if the language is not in braces? I can see that Yihui uses ```yaml, ```r, ```bibtex to cause code blocks to appear with color highlighting in the RMarkdown book. Does anybody know a reference to what that is actually doing and best practices with the notation? I am thinking it means show (but don't execute) this code block (and indicate the language for anybody who bothers to look into the source). If that is right, where is it documented? Does anybody know how to set the color of the words that are rendered inside such a (language named but not braced) code block in a html and/or pdf document?
I am using .. [2] / [2]_ style footnotes in restructuredText. I would like them to be displayed on the end of the page where they occur rather than at the end of the document. How can I go about this? I need a solution that works with rst2latex.
/please refrain from classifying this as of topic. restructuredText is part of the PYTHON programming language.
The LaTeX writer in docutils uses \footnotetext to specify the page at the bottom of which the footnote text should appear. If you want the text to appear at the same page as its mark, you can try to put them close together.
If you want to directly use the \footnote command in LaTeX, you will have to create a new LaTeX writer, probably by extending the LaTeXTranslator class in docutils.writers.latex2e and overload the visit_footnote_reference function. There, search for the footnote content in self.document.footnotes, and write a \footnote command to the output. Also overload visit_footnote and do nothing there (raise nodes.SkipNode).
Alternatively, you can redefine some TeX command to generate the text at the correct position, probably in two passes to get the footnotes marks and contents at first.
I would like to enter several formulas into my Doxygen documentation. Is there any way to create a label of some type that automatically numbers each formula? Ideally, the automatic numbering will work both in HTML generated output and within Latex generated output from Doxygen. I am looking for something similar to the Caption feature in MS Word.
Example:
You can see the results of my example in Equation 1.1 below.
{Some Formula}
Equation 1.1
{Some other formula}
Equation 1.2
In the example above, the number after "Equation" gets automatically generated. And then I can reference it in the text.
The \anchor feature in Doxygen would allow me to link to the locations. But I don't think that it would generate the auto-numbering correctly.
The option I thought of was to modify my CSS that I use for Doxygen. Currently I already modified it to automatically number my headings. And Latex automatically numbers headings 1-4 already. I could change my CSS to format Heading 4 so that it looks like a right-justified equation label. But I don't know how I can get Latex to use the same formatting.
Any helpful suggestions?
Thanks.
From what I learned, this can not be done in Doxygen. I am now considering two authoring systems to do this:
Doxygen to document the code.
Open Office / Libre Office to document user manuals, which is where the bulk of the equations are.
Both authoring apps will write HTML output. And then I will combine the output with Qt Help Project system.