Creating two table of contents with different depths in R Markdown - r-markdown

I created my lecture notes in pdf format using RMarkdown but it has many subheaders. Because of this, I want to create two different table of contents: first table of contents with 1 depth, then table of contents in 4 depth respectively.
Adding both toc_depth: 1 and toc_depth: 4 did not work.
My YAML header:
---
title: "Lecture Notes"
author: "x"
output:
pdf_document:
highlight: tango
toc: true
toc_depth: 4 #depth table of contents
number_sections: true
documentclass: article
classoption: a4paper
fontsize: 12pt
geometry: "right=1cm, left=1cm, top=1cm, bottom=3cm"
---

As far as I am aware, I don't believe two Table of Contents is possible. One thing you can try is if you don't want a certain heading numbered, you can do
## Including Plots {-}
Which heads it has a header, but doesn't number it in the TOC. Here is the two output differences
without {-}
with {-}
These can be used in places like the Preface, about the authors, etc.

This is not a perfect solution (maybe some with more knowledge could automate this).
The solution works if the intermediate latex file is kept and a short table of contents is manually added using the shorttoc package.
Adding shortdoc:
...
\documentclass[
]{book}
\usepackage{shorttoc}
...
And than adding it between title and TOC:
\shorttableofcontents{〈title 〉}{〈depth 〉}

Related

How to create own table in Bookdown and reference it within the text?

I am currently writing my thesis in RMarkdown using the template Oxforddown (which is ultimately based on bookdown). I have been reading the documentation but I confess I am lost. I am trying to create a table that contains an overview of the experimental conditions and items I used in my empirical study, so it is not data that I can load into R and then use the kable function on. However, I do not understand how I could generate such a table. Generating RMarkdown tables outside code chunks seems to work, but then the captions and referencing are very different than the rest of the captions used so far, which I usually set up within code chunks. Example below:
{r pilot-short7, echo=FALSE, fig.scap="Pilot 2: ....", out.width="65%", message=FALSE, fig.pos='H', fig.align = 'center'}
When I am trying to include RMarkdown tables inside a code chunks, things go wrong. What would my options be?
Any help would be very much appreciated!
I prepared a markdown template for you.
Here I made a table with flextable library.
But you can use another, which you like, f.e.: kableExtra, gt etc.
As you can see, you should put \label{tab:caption} and after refer in the text by \ref{tab:caption}.
---
title: "Hello World"
header-includes:
- \usepackage{caption}
output:
pdf_document:
latex_engine: xelatex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, include = FALSE}
library(flextable)
library(dplyr)
table2 <- flextable(mtcars[1:5, 1:6])
```
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
\begin{table}[hbtp]
\captionof{table}{Text of the caption.}
\label{tab:caption}
`r table2`
\end{table}
Table \ref{tab:caption} is the baddest table in the World

How do I remove DOI from R-markdown bibliography?

I would like to remove the DOI from the bibliographic references in my markdown script. Is there a way I can do this?
Here is my markdown file:
---
title: "my paper"
author: "name"
date: \today
header-includes:
output:
pdf_document:
number_sections: yes
toc: yes
keep_tex: yes
fig_caption: yes
word_document:
toc: yes
latex_engine: xelatex
indent: yes
bibliography: library.bib
references:
link-citations: yes
linkcolor: blue
hyperfootnotes: yes
---
I would like to remove the DOI from this reference #Wallace2005
# Bibliography {-}
::: {#refs}
:::
The output of this file is the following:
And here is the .bib file
#article{Wallace2005,
abstract = {Constantly evolving, and with far-reaching implications, European Union policy-making is of central importance to the politics of the European Union. From defining the processes, institutions and modes through which policy-making operates, the text moves on to situate individual policieswithin these modes, detail their content, and analyse how they are implemented, navigating policy in all its complexities. The first part of the text examines processes, institutions, and the theoretical and analytical underpinnings of policy-making, while the second part considers a wide range of policy areas, from economics to the environment, and security to the single market. Throughout the text, theoreticalapproaches sit side by side with the reality of key events in the EU, including enlargement, the ratification of the Lisbon Treaty, and the financial crisis and resulting euro area crisis, exploring what determines how policies are made and implemented. In the final part, the editors consider trendsin EU policy-making and look at the challenges facing the EU. Exploring the link between the modes and mechanisms of EU policy-making and its implementation at national level, Policy-Making in the Europe Union helps students to engage with the key issues related to policy. Written by experts, for students and scholars alike, this is the most authoritative andin-depth guide to policy in the European Union.},
author = {Wallace, Helen and Wallace, William and Pollack, Mark A},
doi = {10.1177/0010414013516917},
file = {:Users/aguasti/Desktop/Mendely Organized Library/Wallace, Wallace, Pollack/Wallace, Wallace, Pollack - 2005 - Policy-Making in the European Union.pdf:pdf},
isbn = {0199689679},
issn = {0010-4140},
pages = {574},
pmid = {130137987},
title = {{Policy-Making in the European Union}},
url = {https://books.google.com/books?id=w6SbBQAAQBAJ&pgis=1},
year = {2005}
}
If anyone knows how I could remove the DOI from the bibliographic reference I would be extremely grateful
I am assuming that you want to have this done on the fly while knitting the PDF.
The way the references are rendered is controlled by the applied citation styles.
So, one way would be to change the citation style and in the YAML header to a style that does not include the DOI (note that for the PDF output you would need to add the natbib line).
bibliography: library.bib
citation_package: natbib
csl: somethingelse.csl
Alternatively, if you have to stick to a certain style, you could [modify the CSL-file] (https://www.zotero.org/support/dev/citation_styles/style_editing_step-by-step).
Example for elsevier-harvard.csl
You could just comment the relevant line in the CSL-file:
<if variable="DOI">
<!--<text variable="DOI" prefix="https://doi.org/"/> -->
</if>
Save this under a new name (e.g., elsevier-harvard_mod.csl)
and then re-run your example (here shortened)
---
title: "my paper"
author: "name"
date: \today
output: pdf_document
bibliography: library.bib
citation_package: natbib
csl: elsevier-harvard_mod.csl
---
I would like to remove the DOI from this reference #Wallace2005
# Bibliography {-}

Converting xtable of Markdown Equations to Word or .rtf

I've created tables in Rmarkdown using xtable.
I need to convert them to either .doc or .rtf in order to submit to a journal.
I can successfully convert to .html and .pdf but when I convert these formats to .doc or .rtf, the nice equation formatting disappears.
I've tried opening the files in word and converting to .rtf. Is there a way to do this without re-doing the tables entirely? I am fairly new to Markdown and Pandoc.
Here is the reproducible code.
---
title: ''
output:
html_document:
df_print: paged
pdf_document:
fig_caption: yes
keep_tex: yes
latex_engine: xelatex
header-includes:
- \usepackage{lineno}
- \linenumbers
---
```{r, results='asis', echo=FALSE}
library(xtable)
Parameter <- c("T","V","$i$")
Definition <- c("Temperature (C)","Velocity (cm/s)","Prey class within $I$ 1 mm bins")
Method <- c("Field data","Field data","$EC = SC + MC$","$NEI = GEI - EC$")
Reference <-c("","", [1,2]")
table1_df <- cbind.data.frame(Parameter, Definition,Method,Reference)
table1 <- xtable(table1_df, include.rownames=FALSE, caption="This should be a pretty table")
print(table1, comment=FALSE, include.rownames=FALSE, caption.placement="top",size="\\fontsize{9pt}{10pt}\\selectfont", sanitize.text.function=function(x){x}, type="html")
```

Bibtex in Rmarkdown - First and and last names of second author get swapped in citation

As the title says, I use Rmarkdown to write a document.
I use the following text at the top of the .Rmd document:
---
title: "Title"
author: "Me"
date: "September 10, 2018"
output:
pdf_document: default
html_document: default
bibliography: bibliography.bib
---
And then I use the following code in my bibliography.bib document, which, according to the document properties is a bibtex file:
#article{Brooks98,
author={ Brooks, S. P. and Gelman, A.},
title={Interface foundation of america general methods for monitoring convergence of iterative simulations general methods for monitoring convergence of iterative simulations},
year={1998},
journal={Journal of Computational and Graphical Statistics},
volume=7,
issue=4,
pages=434-455
}
I expect to get
Brooks, S. P. and Gelman, A. 1998
but instead I get
Brooks, S. P., and A. Gelman. 1998
My question is, what causes this and how do I solve the problem?
You have to change your citation style. One simple solution would be to use bibtex together with natbib and apalike:
---
title: "Title"
author: "Me"
date: "September 10, 2018"
output:
pdf_document:
citation_package: natbib
html_document: default
bibliography: bibliography.bib
biblio-style: apalike
---
(Note that you will have to use pages={434-455} for this to work.)
If there are other aspects of the citation style that do not fit, you can have a look at this answer for ways of finding other styles. Another alternative would be biblatex.
The default, which I am less familiar with, is to use pandoc-citeproc, which uses CSL files to define the style. See here for resources about additional CSL styles: https://citationstyles.org/

How to select the language (for captions) in a rmarkdown document

Is there a way to select the language for Rmarkdown? For example, I'm writing an assignment in portuguese, but table captions will come off as Table 1: something.
In latex files you can just add \usepackage[brazil]{babel}. Is there an equivalent option for rmarkdown?
I found the answer in the TeX SE site: https://tex.stackexchange.com/questions/171711/how-to-include-latex-package-in-r-markdown.
You can just include packages with a header-includes argument.
---
title: "Title"
author: "Me"
header-includes:
- \usepackage[brazil]{babel}
output:
pdf_document
---