I use updated quarto and Rmarkdown and vtree ‘5.4.6’:
In the same project and same session:
Rmarkdown does what quarto does not:
Rmarkdown renders vtree(iris, "Species") and quarto not (allthough quarto renders inline)
What could be the problem for this?
See here a reproducible example:
1. Rmarkdown
---
title: "test"
author: "Me"
date: '2022-06-18'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(vtree)
```
## R Markdown
```{r cars}
vtree(iris, "Species")
```
2. Quarto
---
title: "Untitled"
format: html
editor: visual
---
## Quarto
```{r}
library(vtree)
vtree(iris, "Species")
```
When I click the Render button: -> it is NOT renderred:
When I render inline: -> it is renderred:
Quarto works a bit differently than R Markdown as it will run R only for the knitting process, and not for the conversion to output format, here HTML.
From the error message, vtree is writing to file the output in the R session temp folder. This folder is not persistent after the R session is closed, which happens once Quarto have run all the computation output. This means that the png file does not exists anymore when converting to HTML, hence the no image shown in HTML.
(regarding knitr warning, I believe it is knitr version matter, but that does not change the output).
Looking at vtree::vtree() function, it seems when knitting to HTML is detected R temp folder is used if none provided. IMO this should ne behave that way and it is an issue in vtree package.
To overcome the issue, you need to not let vtree do the default provide yourself a path. You can do that with folder argument. So this should work
---
title: "Untitled"
format: html
keep-md: true
---
## Quarto
```{r}
library(vtree)
if (!dir.exists("vtree_save")) dir.create("vtree_save")
vtree(iris, "Species", folder = "vtree_save")
```
I would report an issue in vtree repo about this behavior.
I am the author of the vtree package. I have just made a change to the code which I believe fixes the problem. See https://github.com/nbarrowman/vtree where there are instructions for downloading version 5.5.8 of the vtree package, which includes the fix.
Related
I have two RMarkdown files. main.Rmd which is the main file which is rendered as well as example.Rmd which holds a longer example and is used elsewhere (hence it lives in its own document).
I want to include example.Rmd in the main.Rmd file with code highlighting of its RMarkdown code but the code of example.Rmd does not need to be executed, as if I set eval=FALSE and copied all code into the chunk by hand.
An example MWE is
main.Rmd
---
title: This is main.rmd
output: html_document
---
```{r}
# attempt that doesnt work
cat(readLines("example.Rmd"), sep = "\n")
```
and in example.Rmd
---
title: This is example.rmd
output: html_document
---
```{r}
# code that is not executed but shown in main.Rmd
data <- ...
```
Set eval=FALSE in the example.Rmd file and then include it in main.Rmd using child chunk option.
example.Rmd
---
title: This is example.Rmd
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(eval = FALSE)
```
```{r}
# This is from example.Rmd
x <- rnorm(10)
y <- rnorm(10)
lm(y ~ x)
```
```{r}
# some comments
print("This is from example.Rmd")
```
main.Rmd
---
title: This is main.Rmd
output:
html_document:
highlight: haddock
---
```{r example, child="example.Rmd"}
```
Edit
To show full source-code of the Rmarkdown file, one possible option could be reading that Rmd file and then cat it with chunk option comment="".
Now about the syntax highlighting; there's a chunk option class.output with which it is possible to specify a language name for which pandoc supports syntax highlighting.
You can get the list of language names for which pandoc has syntax highlighting support by running the following,
pandoc --list-highlight-languages
(Note, if you don't have pandoc installed separately, you can also use the pandoc installed with Rstudio itself. Run rmarkdown::pandoc_exec() to get the pandoc executable path)
Now, the file we are trying to include actually contains not just R code, but also markdown and yaml syntaxes. So it's a kind of mixed thing and pandoc has no syntax highlighting support out of the box for this. Still I have chosen c as syntax highlighting language just to show the possibility. (Also tried r, but syntax-highlighting is not so distinctive)
---
title: This is main.Rmd
output:
html_document:
highlight: tango
---
## Rmarkdown
```{r example, echo=FALSE, class.output="c", comment=""}
cat(readLines("example.Rmd"), sep = "\n")
```
But still if you want a specific syntax-highlighting for Rmarkdown, you can actually create one. See here from the pandoc documentation itself and also this answer on SO about this.
does the button to copy to cliboard exist with R markdown?
It exists in Quarto (with the code-copy option)
and with pkgdown websites
but is it possible to add it to a R markdown or R notebook document?
You could use the package klippy to insert a copy to clipboard button in Rmarkdown HTML documents. To only thing you need to do is add this code somewhere in your document:
```{r klippy, echo=FALSE, include=TRUE}
klippy::klippy()
```
To install the package, you can use the following code:
remotes::install_github("rlesur/klippy")
library(klippy)
Here is a reproducible example:
---
title: "Copy code to clipboard"
date: "2022-10-31"
output: html_document
---
```{r klippy, echo=FALSE, include=TRUE}
klippy::klippy()
```
Some example code:
```{r}
# Summary of mtcars dataset:
summary(mtcars)
```
Output:
As you can see a copy to clipboard button in the top left of the code chunk.
For more information check the documentation.
Trying to knit a doc into html, RStudio would hang on the conversion to html part. I looked around and it looked like this happened to other folks when they were using an out of date pandoc version. I updated pandoc to 2.8. I received the error in the title. Looking around again, it appeared that v 2.5 seemed stable. I installed that, restarted my computer, and still get the same error.
repex is the default example when you create an RMarkdown file in RStudio: file -> New file -> R Markdown -> html.
---
title: "repexpandocerror23"
author: "Adam Korejwa"
date: "11/22/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for
authoring HTML, PDF, and MS Word documents. For more details on using R
Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that
includes both content as well as the output of any embedded R code chunks
within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to
prevent printing of the R code that generated the plot.
I have fixed this issue two months ago. Please make sure your rmarkdown version is at least v1.16. Once again, when in doubt, consider updating your packages:
update.packages(ask = FALSE, checkBuilt = TRUE)
I'm getting started with rmarkdown and knitr. In the sample document provided by RStudio, I can successfully use render() to generate an HTML file that views fine in Chrome. However, when I click on the knit button, it generates a .markdown file and then returns the following error without rendering the preview:
Error generating HTML preview for ~/path/to/file/report.rmarkdown system error 2 (The system cannot find the file specified)
I think it's getting hung up at the pandoc stage. Is it possible that RStudio is looking for pandoc in the wrong place? Pandoc was already installed at C:\Program Files (x86)\Pandoc\pandoc.exe, but RStudio installed its own instance at C:\Program Files\RStudio\bin\pandoc\pandoc.exe, so maybe it's looking in the wrong place and/or confusing settings from one with the other?
Any help would be greatly appreciated. Thanks!
And just in case, here's the RMarkdown template I'm starting with:
---
title: "Monthly Report"
author: "Kris Shaffer"
date: "February 17, 2017"
output: html_document
---
```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
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:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
R version 3.3.2
RStudio 1.0.136
rmarkdown 1.3
knitr 1.15.1
pandoc 1.17.2 (both installations)
Turns out it was as simple as a file extension. I changed the filename from report.rmarkdown to report.Rmd. Knit works fine now.
The following Rmarkdown renders the plotly 3D graph in HTML, but not in PDF.
Testing plotly
```{r}
library(plotly)
p <- plot_ly(data=iris, x=~Sepal.Length, y=~Sepal.Width, z=~Petal.Length,
color=~Species, symbols=c(0,1), type="scatter3d", mode="markers")
p
```
A snapshot of the graph appears as follows:
According to the plotly help page:
If you are using rmarkdown with HTML output, printing a plotly object in a code chunk will result in an interactive HTML graph. When using rmarkdown with non-HTML output, printing a plotly object will result in a png screenshot of the graph.
Is there a way to render the plotly graph in a PDF?
Note: The error from rmarkdown::render() is:
Error: Functions that produce HTML output found in document targeting latex output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:
always_allow_html: yes
Note however that the HTML output will not be visible in non-HTML formats.
I have created a little workaround, which saves the plotly images locally as png-file and imports it back to the RMD file.
You need the package webshot, which you can load via:
install.packages("webshot")
Further more, you need to install phantomjs via
webshot::install_phantomjs()
Then (when phantomjs is in your PATH), you can create your RMD file:
---
title: "Untitled"
output: pdf_document
---
```{r}
library(plotly)
p <- plot_ly(economics, x = ~date, y = ~unemploy / pop)
tmpFile <- tempfile(fileext = ".png")
export(p, file = tmpFile)
```
This works for me .. perhaps it's a workaround for you, too!
As #hrbrmstr commented, export() previously didn't support WebGL at all, but more recent versions support exporting to png via RSelenium (see help(export, package = "plotly")). If you need pdf export, you'll have to pay for a cloud account -- https://plot.ly/products/cloud/
Same issue with R markdown compile error:. You need to choose what format you want to KNIT to, tried to look at mine.
---
title: "<img src='www/binary-logo.jpg' width='240'>"
subtitle: "[<span style='color:blue'>binary.com</span>](https://github.com/englianhu/binary.com-interview-question) Interview Question I"
author: "[<span style='color:blue'>®γσ, Lian Hu</span>](https://englianhu.github.io/) <img src='www/ENG.jpg' width='24'> <img src='www/RYO.jpg' width='24'>白戸則道®"
date: "`r Sys.Date()`"
output:
tufte::tufte_html:
toc: yes
tufte::tufte_handout:
citation_package: natbib
latex_engine: xelatex
tufte::tufte_book:
citation_package: natbib
latex_engine: xelatex
link-citations: yes
---
What I do so that rendering to PDF's work but you can still have the interactive plots in other knit types and in rmarkdown files in r studio is:
this goes in the setup block (or really, anywhere early in the file):
is_pdf <- try (("pdf_document" %in% rmarkdown::all_output_formats(knitr::current_input())), silent=TRUE)
is_pdf <- (is_pdf == TRUE)
then this is used to render any plotly plot based on what kind of document you are creating:
if (is_pdf) { export(base_plot) } else {base_plot}
in the example base_plot is the name of the plot.