Somehow my RMarkdown document is not crossreferencing tables or figures. Here is a stripped down version of my document.
---
title: "Test"
author: "Me"
date: "01/04/2022"
output: bookdown::pdf_document2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
var1<-sample(LETTERS)
tab1<-table(var1)
My table is in Table \#ref{tab:tab1}
library(knitr)
kable(tab1, caption="my table")
AS we see in Figure \#ref{fig:plot1}
plot(seq(1,10,1))
You should call your tab1 in the code chunk like this {r tab1}. And use () instead of {} for your #ref. In that case it reference to your figures and tables. You can use the following code:
---
title: "Test"
author: "Me"
date: "01/04/2022"
output: bookdown::pdf_document2
---
My table is in Table \#ref(tab:tab1)
```{r tab1, echo =FALSE}
var1<-sample(LETTERS)
tab1<-table(var1)
library(knitr)
kable(tab1, caption="my table")
```
\newpage
AS we see in Figure \#ref(fig:plot1)
```{r plot1, fig.cap ="plot", echo=FALSE}
par(mar = c(4, 4, .2, .1))
plot(seq(1,10,1))
```
Output:
As you can see on the image, when you click on 1 in will go to your table.
Related
I want to create dynamic sections in my R markdown document. For this, I use R chunks with the asis output type. The chunks contain tables created by the reactable package.
I cannot get the tables to print when I create them in a for-loop. I know that one usually must wrap plots or the like within print() in loops, but that had no effect in my case.
How can I get the tables to print?
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
print(reactable(data.frame(test = rnorm(3)))) ## shows nothing
}
```
I just found out, that reactable uses htmlwidgets under the hood. So one can wrap the result in shiny::tagList() to display it in a loop.
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
print(shiny::tagList(reactable(data.frame(test = rnorm(3))))) ## now it works
}
```
You could try to export your react-tables as temporary html-files that you then import as text and delete afterwards.
Here is a solution that worked for me:
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
htmlwidgets::saveWidget(reactable(data.frame(test = rnorm(3))),
file = 'temp.html')
cat(readr::read_lines('temp.html')[-1])
file.remove('temp.html')
}
```
When I want to print some tables in html report from knitr, sometime I use knitr::kable(), and other times I use htmltable::htmltable.
When I use bookdown::html_document2 in the YAML numbering of tables from kable is automatic. However, it is not for htmltable, and I need to use options(table_counter = TRUE), which generates another numbering mechanism. Is there a way to unify it?
Example:
---
title: "Untitled"
author: "Guilherme"
date: "10/26/2020"
output:
bookdown::html_document2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(table_counter = TRUE)
```
```{r cars}
library(htmlTable)
htmlTable(mtcars[1:5,1:5],
caption = "XX")
```
```{r}
htmlTable(mtcars[1:5,1:5],
caption = "XX")
```
```{r}
library(knitr)
kable(mtcars[1:5,1:5],
caption = "XX")
```
Outputs:
Thanks!
How can one create a full width figure when using the twocolumn class option in knitr / R / RMarkdown / LaTex?
Based on the Knitr documentation, I've tried two approaches. Nothing short of editing the .tex file has worked for me so far.
This:
---
output: pdf_document
classoption: twocolumn
header-includes:
- \usepackage{lipsum}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\lipsum[1-2]
```{r fig.env = "figure*", fig.cap = "Test"}
plot(runif(10))
```
\lipsum[3-5]
```{r fig.fullwidth = T}
plot(runif(10))
```
Results in this:
Yihui has fixed this in the development version of knitr. Yihui's response:
The option fig.env = 'figure*' should be respected now (in the dev version of knitr). But the plot will float to a new page. I guess that is a LaTeX issue orthogonal to knitr. Thanks!
Don't forget that you must include a caption for this to work.
---
output: pdf_document
classoption: twocolumn
header-includes:
- \usepackage{lipsum}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\lipsum[1-3]
```{r fig.env = "figure*"}
plot(runif(10))
```
\lipsum[2]
```{r fig.env = "figure*", fig.cap = ""}
plot(runif(10))
```
\lipsum[2]
I want to have table in 'one line' instead of dividing it. In the second picture is what I get and in the first picture is what I want to get. Thanks for your help.
1) https://i.stack.imgur.com/uwfZ5.png
2) https://i.stack.imgur.com/6nUJ2.png
my code
title: "Bundesliga - raport"
author: "aa aak"
date: "3 stycznia 2018"
output: html_document
---
```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(fig.width=12, fig.height=8, fig.path='Figs/',
echo=FALSE, warning=FALSE, message=FALSE)
library(vcd)
```
## Bundesliga
a
```{r echo=FALSE}
head(Bundesliga)
```
Use the width option. This works on your example:
```{r echo=FALSE}
options(width = 100)
head(Bundesliga)
```
I'm trying to produce a flexdashboard with R and want to show code in my presentation, but this seems not to work.
Here a little example:
---
title: "Test"
output:
flexdashboard::flex_dashboard
---
```{r setup, include=FALSE}
library(flexdashboard)
```
### Code
```{r, eval=FALSE, include=TRUE}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
### Output
```{r, fig.align='center', echo = FALSE}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
Even other chuck options like fig.show = 'hide' will not work.
Is it possible to show code in a R-chuck in flexdashboard?
The code highlights would be a benefit instead of a plain text.
If you want both the code and plot to show set the chunk options to: echo = true
If you just want code set it to: echo=TRUE, eval=FALSE
---
title: "Test"
output:
flexdashboard::flex_dashboard
---
```{r setup, include=FALSE}
library(flexdashboard)
```
### Code
```{r, echo=TRUE, eval=FALSE}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
### Code and Plot
```{r, echo=TRUE}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
### Plot
```{r, fig.align='center', echo = FALSE}
plot(iris$Sepal.Length, iris$Sepal.Width)
```
It won't show as a panel in your presentation, but to add a </> Source Code button to your dashboard, include source_code: embed in your YAML.
---
title: "Example"
output:
flexdashboard::flex_dashboard:
source_code: embed
---