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Auto-numbering and cross-referencing of figures and tables in rmarkdown
---
title: "Auto-numbering and cross-referencing of figures and tables in rmarkdown"
output: html_document
---
NOTE: I recommend using the bookdown package and `output: html_document2` to make captions and cross-references more easily than the method described below.
TODO: check this out: https://github.com/adletaw/captioner
Here's how to use:
1. Copy and paste the first two code chunks in this document to the top of your document
2. Make sure you have knitr and kfigr installed, use `devtools::install_github("github mkoohafkan/kfigr")` to install kfigr
3. For chunks in your doc that produce a figure or table for which you want a caption, be sure to include a label in the chuck options line. For example, the first chunk is this doc has the label `number_figures`
4. Also in the chunk options line, you need to specify the anchor type and the caption, for example `anchor="figure", fig.cap="Here is a nice figure"`, see the examples below. That will auto-generate the caption and give you auto-numering. See the example below for using with tables.
5. When you want to refer to the figure or table in your text, use a bit of in-line code like so `r figr('my-label', TRUE, type="figure")` which will generate a cross-reference like 'figure 3' or whatever the correct number is for the figure produced by the chunk that has the label 'my-label'
6. Other similar methods:
- http://rmflight.github.io/posts/2012/10/papersinRmd.html & https://gist.github.com/rmflight/3858973
- http://galahad.well.ox.ac.uk/repro/
- http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-iii/
```{r number_figures, echo=FALSE}
# This is a knitr hook to enable figure and table captions
# number figures
# from http://stackoverflow.com/a/18672268/1036500
library("knitr")
tn = local({
i = 0
function(x) {
i <<- i + 1
paste("<table><caption>", 'Figure ', i, ': ', x, "</caption><colgroup><col width='100'></col></colgroup><thead><tr class='header'></tr></thead><tbody></tbody></table><p>", sep = '')
}
})
knit_hooks$set(fig.cap = function(before, options, envir) {
if(!before)
tn(options$fig.cap)
})
default_output_hook = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
if (is.null(options$fig.cap) == F)
x
else
default_output_hook(x,options)
})
# number tables
# from http://stackoverflow.com/a/18672268/1036500
to = local({
i = 0
function(x) {
i <<- i + 1
paste("<table><caption>", 'Table ', i, ': ', x, "</caption><colgroup><col width='100'></col></colgroup><thead><tr class='header'></tr></thead><tbody></tbody></table><p>", sep = '')
}
})
knit_hooks$set(tab.cap = function(before, options, envir) {
if(!before)
to(options$tab.cap)
})
default_output_hook = knit_hooks$get("output")
knit_hooks$set(output = function(x, options) {
if (is.null(options$tab.cap) == F)
x
else
default_output_hook(x,options)
})
```
```{r setup, echo=FALSE, message=FALSE}
require(knitr)
require(kfigr) # devtools::install_github("github mkoohafkan/kfigr")
opts_chunk$set(message=FALSE, warning=FALSE)
```
# My document starts here
We can embed plots, for example:
```{r first, anchor="figure", fig.cap="Rather small sample", fig.align='center'}
require(ggplot2)
qplot(rnorm(10), geom="histogram")
```
Note that for `r figr('first', TRUE, type="figure")` we can refer to the figure by the chunck label and that will generate an auto-numbered reference in the text that also links to the figure.
```{r second, anchor="figure", fig.cap="Look at this nice big sample", fig.align='center'}
require(ggplot2)
qplot(rnorm(1000), geom="histogram")
```
Note that for `r figr('second', TRUE, type="figure")` we can do the same thing, numbering is taken care of for us.
```{r mytable, anchor="table", tab.cap="my table about cars", tab.align='center'}
kable(mtcars)
```
And we can have a table, see `r figr('mytable', TRUE, type="table")` we can refer to the table with a numbered reference in the text that also links to the table.
We can refer to the figures and tables multiple times in the text with no problems: `r figr('first', TRUE, type="figure")`, `r figr('second', TRUE, type="figure")`, `r figr('mytable', TRUE, type="table")`
@amm03

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commented Aug 15, 2018

This works great for me with word so far. Modified it so i get Figure S#. instead of figure #. However, in the in line text reference i get Figure S # instead of the desired Figure S#. How can i remove the space between S and # in the cross reference in the text? Thank you in advance for your help and contribution with this.

@BroVic

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commented Aug 27, 2018

This is great. Thanks for the contribution!

@nmolanog

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commented Sep 23, 2018

For figures the title in fig.cap appears twice in the document:

screenshot from 2018-09-23 09-55-55

@nmolanog

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commented Sep 23, 2018

I found an issue: if you add the following chunck to your document

summary(mtcars)

you get the following error

Error: C stack usage  7969380 is too close to the limit
Execution halted 

I found this issue working on my own documents using your functions and took me a while to find this.

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