Knitr misplaces the output graphics when output format is pdf and fig_caption is set to true. Could you reproduce this problem?
---
title: "Untitled"
author: "xxx"
date: "December 19, 2016"
output:
pdf_document:
fig_caption: true
---
# section 1
## sub 1
some text
```{r, fig.cap="caption2"}
plot(10:1)
```
# section 2
the plot draws under section 2.
I have also filed an issue on github repo but no answer yet.
Related
When I add the following lines to add table of content to a shiny document:
toc: true
toc_float: true
The document fails to run. It runs fine without them. I get the following error:
Error Scanner error: mapping values are not allowed in this context at line 5, column 8 (line 5 is toc: true)
How can I resolve this issue?
The code I ran:
---
title: "Untitled"
runtime: shiny
output:
html_document
toc: true
toc_float: true
---
### section 1
```{r, echo=FALSE}
sliderInput("slider", "Number of observations:", 1, 100, 50)
renderText({paste0(rep('blah', 100), collapse = '\n')})
```
### section 2
```{r, echo=FALSE}
renderPlot({hist(rnorm(500)[seq_len(input$slider)])})
```
You're just missing a : from html_document. It should be html_document:
---
title: "Untitled"
runtime: shiny
output:
html_document:
toc: true
toc_float: true
---
I am trying to make an R Markdown doc with tabs and a table of contents under each tab
Here is my header:
---
title: "Palliative/Comfort Care/Hospice Patients Report"
output:
html_document:
toc: true
toc_floating: true
theme: "cerulean"
date: "`r format(Sys.time(), '%B %d, %Y')`"
pdf_document: default
---
Followed by:
# {.tabset}
## tab1
## tab 2
I have seen people that are able to create an index based on the titles that you have on your R markdown document like in this picture
If somebody could let me know how would I have to modify this code so it creates that left index table?
---
title: "Untitled"
author: "Juan Lozano"
date: "October 19, 2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Title 1
Text Text Text Text Text
```{r cars}
summary(cars)
```
## Title 2
Text Text Text Text Text
As #hrbrmstr 's link indicates there are many YAML customisations possible:
This is the sort of thing I usually use:
---
title: "Untitled"
author: "john Smith"
date: "today ;)"
output:
html_notebook:
fig_caption: yes
number_sections: yes
toc: yes
toc_float: yes
html_document:
fig_caption: yes
number_sections: yes
toc: yes
toc_float: yes
df_print: paged
bibliography: /path/to/library.bib
---
Is is possible to hide some comments in code when kniting using knitr / R markdown? Example:
---
title: "SOSO"
author: "SO"
date: '2017-06-06'
output: pdf_document
---
```{r}
# Generate some data
rnorm(2)
## But keep this comment
```
When kniting I would like the first comment to disapear, but keep the second one somehow.
Here is a quick example of modifying the hook to change knitr behavior.
---
title: "SOSO"
author: "SO"
date: 2017-06-06
output: pdf_document
---
```{r setup-hook, echo=FALSE}
hook_in <- function(x, options) {
x <- x[!grepl("^#\\s+", x)]
paste0("```r\n",
paste0(x, collapse="\n"),
"\n```")
}
knitr::knit_hooks$set(source = hook_in)
```
```{r}
# Generate some data
# Lines that starts with `# ` will be removed from the rendered documents
rnorm(2)
## But keep this comment
## But lines that starts with `## ` will be kept
```
produces this
In fact, you can choose to show any lines of R code by passing numeric indices to the chunk option echo, e.g.
---
title: "SOSO"
author: "SO"
date: '2017-06-06'
output: pdf_document
---
```{r echo=4:7}
# Generate some data
rnorm(2)
## But keep this comment
```
See knitr documentation for more information.
Just wanted to insert two images in to the rmarkdown pdf document. When knitting it gives the error
pandoc.exe: Could not find image paste0(Figs,%20%22Fig1.png%22)',
skipping... pandoc.exe: Unable to convert
paste0(Figs,%20%22Fig1.png%22)' for use with pdflatex. ! Missing
\endcsname inserted.
Below is the code
---
title: "Some title"
author: Arvin
date: "October 20, 2016"
output: pdf_document
fig_caption: yes
---
```{r, echo=FALSE}
Figs <- 'C:/Users/arvin/Figs/'
```
)
I used knitr_1.14 and r_markdown_1.0.
It is clear, why your code does not work: you used the function paste outside the R-environment. So pandoc searches for paste0(Figs,%20%22Fig1.png%22) as a filename.
You can't do it in this way you wanna do this. The regular usage is
---
title: "Some title"
author: Arvin
date: "October 20, 2016"
output:
pdf_document:
fig_caption: yes
---
BUT there is another solution, where you have the full control of image size, and you can plot like a regular R plot, using grid.raster from the grid package. And here your approach will work, because we are in a R environment:
```{r fig.width=10, fig.height=10, echo=FALSE}
library(png)
library(grid)
Figs <- 'C:/Users/arvin/Figs/'
img <- readPNG(paste0(Figs, "Fig1.png"))
grid.raster(img)
```
Inline R code should be put in `r `:
---
title: "Some title"
author: Arvin
date: "October 20, 2016"
output:
pdf_document
fig_caption: yes
---
```{r, echo=FALSE}
Figs <- 'C:/Users/arvin/Figs/'
```
`)
BTW, an unsolicited pro-tip: Do not use absolute paths. Use relative paths.