I have a problem with R Markdown. In the Markdown file, I start by loading the necessary packages (including tidyverse) in a code chunk. But in the last code chunk, an error pops up which says
"could not find function %>% Calls: ...withVisible ->
eval_with_user_handlers -> eval -> eval Execution halted"
Can you please explain why this occurs and how I can fix it?
Thanks!
As requested:
This is the first code chunk where I load the packages:
library(tidyverse)
library(readxl)
library(psych)
options(scipen = 999)
And, this is the code chunk where the error occurs:
DE_GDP_1965_2020 <- DE_GDP_1965_1969 %>%
full_join(DE_GDP_1970_2020)
model <- lm(GDP ~ Period, data = DE_GDP_1965_2020)
summary(model)
Thanks!
Related
I am writing my thesis using a Quarto book in HTML, which has some dynamic content (leaflet maps, plotly dynamic graphs). However, eventually, I will need to export the book in PDF/LaTeX, or at least Word (and then I can copy and paste into LaTeX).
When I try to export to PDF I of course run into this error:
Functions that produce HTML output found in document targeting pdf
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: true
Note however that the HTML output will not be visible in non-HTML
formats.
I did try to add the always_allow_html: true in my YAML file, but I get the same exact error. I also tried the conditional rendering with {.content-hidden unless-format="pdf"}, but I can't seem to get it working.
Has anyone experienced the same issue?
Using .content-visible when-format="html" and .content-visible when-format="pdf" works very smoothly.
---
title: "Conditional Rendering"
format:
html: default
pdf: default
---
## Conditional Content in Quarto
::: {.content-visible when-format="html"}
```{r}
#| message: false
library(plotly)
library(ggplot2)
p <- ggplot(mtcars, aes(wt, mpg))
p <- p + geom_point(aes(colour = factor(cyl)))
ggplotly(p)
```
```{r}
#| message: false
#| fig-pos: "H"
#| fig-width: 4
#| fig-height: 3
library(leaflet)
# took this example from leaflet docs
m <- leaflet() %>%
addTiles() %>% # Add default OpenStreetMap map tiles
addMarkers(lng=174.768, lat=-36.852, popup="The birthplace of R")
m # Print the map
```
:::
::: {.content-visible when-format="pdf"}
```{r}
library(plotly)
library(ggplot2)
p <- ggplot(mtcars, aes(wt, mpg))
p <- p + geom_point(aes(colour = factor(cyl)))
p
```
:::
I use constructs like below
p <- ggplot()
if (interactive() || opts_knit$get("rmarkdown.pandoc.to") == "html") {
ggplotly(p)
} else {
p
}
Stumbled across this one too. I'm currently checking the output format of pandoc globally
```{r, echo = F}
output <- knitr::opts_knit$get("rmarkdown.pandoc.to")
```
and then evaluate chunks conditionally:
(leaflet example from here.)
```{r, echo = F, eval = output != "latex"}
library(leaflet)
leaflet() %>%
addTiles() %>% # Add default OpenStreetMap map tiles
addMarkers(lng=174.768, lat=-36.852, popup="The birthplace of R")
```
This is optional if you want a note on a missing component in the PDF version:
```{r, echo = F, eval = output == "latex", results = "asis"}
cat("\\textit{Please see the HTML version for interactive content.}")
```
Edit
I just checked, this also works with Quarto documents for me using the below YAML header.
---
title: "Untitled"
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
---
I´m trying to put my code, which runs perfectly, in an R markdown but I keep getting the row_to_name error when I knit, but no when I run the chunk. Honestly I don´t know how to fix it.
The code:
homicidios<-read.csv("/Users/julia/Documents/rdoctorado/tasa estatal homicidios.csv",header = TRUE)
#Transform the vector to data frame
thomicidios<-data.frame(homicidios)
# transpose the matrix To compute stats
th<-t(homicidios)
#delete first row and set it as header
thomicidios<-row_to_names(th,1,remove_row = TRUE)
#Transform the vector to data frame
thomicidios2<-data.frame(thomicidios)
#Convert string to integer
thomicidios2[c(1:33)] <- lapply(thomicidios2[c(1:33)], as.integer)
#Summary of the data
summary(thomicidios2)
The error is:
Error in row_to_names(th, 1, remove_row = TRUE) :
could not find funtion "row_to_names"
Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval
I believe you need to add library(janitor) within "this" code chunk.
I am trying to render the syntax for chunks of code in RMarkdown to a pdf. The final output should look like
```{r}
#some code
```
Rather than just
#some code
The best options to answer this can be found on the RStudio website. See the article on getting verbatim R chunks into rmarkdown http://rmarkdown.rstudio.com/articles_verbatim.html
My preferred solution is to add an inline R code at the end of the first line to make the chunk appear correctly in the output like so:
```{r eval=TRUE}` r ''`
seq(1, 10)
```
Which produces
```{r eval=TRUE}
seq(1:10)
```
Rather than
## [1] 1 2 3 4 5 6 7 8 9 10
Another way to do the same thing is treat the code chunk as a string (I don't usually use the -> operator but in this case I think this improves readability):
```{r comment = ""}
"{r eval=TRUE}
seq(1, 10)
" -> my_code_string
cat("```", my_code_string, "```", sep = "")
```
Which outputs:
```{r eval=TRUE}
seq(1, 10)
```
This question is also a possible duplicate of How to embed and escape R Markdown code in a R Markdown document
I am trying to publish a table with 1000 separators and I am not having any luck with it. I followed the link here: Set global thousand separator on knitr but am not having much success.
My sample dataset is here: https://goo.gl/G7sZhr
The RMarkdown code is here:
---
title: "Table Example"
author: "Krishnan Viswanathan"
date: "August 4, 2015"
output: html_document
---
Load Data
{r, results='asis', message = FALSE, tidy=TRUE}
load("i75_from_flow.RData")
library(data.table)
{r, results='asis', echo=FALSE,message = FALSE, tidy=TRUE}
i75_from_flow <- i75_from_flow[order(-Tons),]
knitr::kable(i75_from_flow)
However, when I include this chunk of code (knit_hook$set) in the RMarkdown document, i get errors.
```{r, results='asis', echo=FALSE,message = FALSE, tidy=TRUE}
i75_from_flow <- i75_from_flow[order(-Tons),]
knit_hooks$set(inline = function(x) {
prettyNum(x, big.mark=",")
})
knitr::kable(i75_from_flow)
```
Error:
# object knit_hooks not found.
Any insights on what I am doing wrong and how to fix this is much appreciated.
Thanks,
Krishnan
The easiest is to use the format arguments of the kable() function itself, where you can specify the big number mark like so:
kable(df, format.args = list(big.mark = ","))
So your example would look like:
```{r, results='asis', echo=FALSE,message = FALSE, tidy=TRUE}
i75_from_flow <- i75_from_flow[order(-Tons),]
knitr::kable(i75_from_flow, format.args = list(big.mark = ","))
```
without any need for knitr hooks.
What about using pander with bunch of options to fine-tune your markdown table:
> pander::pander(i75_from_flow, big.mark = ',')
----------------------------
ORIGFIPS TERMFIPS Tons
---------- ---------- ------
12,023 12,117 5,891
12,119 12,105 4,959
12,001 12,057 3,585
12,001 12,113 3,083
12,047 12,047 1,517
----------------------------
The reason that the knit_hooks object is not found is that you either need to load the knitr package or use the knitr:: prefix in order to set the knit_hooks options. For example:
knitr::knit_hooks$set(inline = function(x) {
prettyNum(x, big.mark=",")
})
I am using RStudio to write my R Markdown files. How can I remove the hashes (##) in the final HTML output file that are displayed before the code output?
As an example:
---
output: html_document
---
```{r}
head(cars)
```
You can include in your chunk options something like
comment=NA # to remove all hashes
or
comment='%' # to use a different character
More help on knitr available from here: http://yihui.name/knitr/options
If you are using R Markdown as you mentioned, your chunk could look like this:
```{r comment=NA}
summary(cars)
```
If you want to change this globally, you can include a chunk in your document:
```{r include=FALSE}
knitr::opts_chunk$set(comment = NA)
```
Just HTML
If your output is just HTML, you can make good use of the PRE or CODE HTML tag.
Example
```{r my_pre_example,echo=FALSE,include=TRUE,results='asis'}
knitr::opts_chunk$set(comment = NA)
cat('<pre>')
print(t.test(mtcars$mpg,mtcars$wt))
cat('</pre>')
```
HTML Result:
Welch Two Sample t-test
data: mtcars$mpg and mtcars$wt
t = 15.633, df = 32.633, p-value < 0.00000000000000022
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
14.67644 19.07031
sample estimates:
mean of x mean of y
20.09062 3.21725
Just PDF
If your output is PDF, then you may need some replace function. Here what I am using:
```r
tidyPrint <- function(data) {
content <- paste0(data,collapse = "\n\n")
content <- str_replace_all(content,"\\t"," ")
content <- str_replace_all(content,"\\ ","\\\\ ")
content <- str_replace_all(content,"\\$","\\\\$")
content <- str_replace_all(content,"\\*","\\\\*")
content <- str_replace_all(content,":",": ")
return(content)
}
```
Example
The code also needs to be a little different:
```{r my_pre_example,echo=FALSE,include=TRUE,results='asis'}
knitr::opts_chunk$set(comment = NA)
resultTTest <- capture.output(t.test(mtcars$mpg,mtcars$wt))
cat(tidyPrint(resultTTest))
```
PDF Result
PDF and HTML
If you really need the page work in both cases PDF and HTML, the tidyPrint should be a little different in the last step.
```r
tidyPrint <- function(data) {
content <- paste0(data,collapse = "\n\n")
content <- str_replace_all(content,"\\t"," ")
content <- str_replace_all(content,"\\ ","\\\\ ")
content <- str_replace_all(content,"\\$","\\\\$")
content <- str_replace_all(content,"\\*","\\\\*")
content <- str_replace_all(content,":",": ")
return(paste("<code>",content,"</code>\n"))
}
```
Result
The PDF result is the same, and the HTML result is close to the previous, but with some extra border.
It is not perfect but maybe is good enough.