In my Rmarkdownfile I want to download my .rmd as a html file but I get the following error.
Warning: Error in file. Cannot open the connection.
I think it's because of the external file included by source(...), but I don't know why. In the external file I make a connection to a db.
---
output:
flexdashboard::flex_dashboard:
orientation: columns
vertical_layout: fill
runtime: shiny
---
```{r setup, include=FALSE}
library(flexdashboard)
library(rmarkdown)
source('R/load_data.R')
```
```{r}
output$export_btn<- downloadHandler(
filename = "report.html",
content = function(file) {
tempReport <- file.path(tempdir(), "test.Rmd")
file.copy("test.Rmd", tempReport, overwrite = TRUE)
out<-render(tempReport, html_document())
file.rename(out,file)
}
)
```
You are passing file to your function content = function(file). file is a default R function. Did you mean to pass filename to the function instead?
output$export_btn<- downloadHandler(
filename = "report.html",
content = function(filename) {
tempReport <- file.path(tempdir(), "test.Rmd")
file.copy("test.Rmd", tempReport, overwrite = TRUE)
out<-render(tempReport, html_document())
file.rename(out,filename)
}
)
Related
I build a shiny app that can filter data and automatically render .docx reports. As I want to customize my reports I would like to use the reference_docx function in the YAML header. I have the shiny app, the markdown document and the template.docx all in one folder. However, the shiny app does not automatically "use" the template.docx as markdown usually does. I assume that I have to load the template in a tempdir() or something like this, but I couldn't quite figure out how. What do I have to do to load the reference docx into the shiny app?
Thank you for your help!
Keep your rmarkdown and word template in app folder.
In your downloadhandler:
output$your_output <- downloadHandler(
filename = function() {
'output_title.docx'
},
content = function(file) {
tempReport <- file.path(temp_folder,
"rmarkdown_template.Rmd")
tempTemplate <- file.path(temp_folder, "template.docx")
file.copy("rmarkdown_template.Rmd", tempReport, overwrite = TRUE)
file.copy("template.docx", tempTemplate, overwrite = TRUE)
# Params
)
rmarkdown::render(tempReport, output_file = file, output_format = 'word_document',
params = params,
envir = new.env(parent = globalenv())
)
}
)
Then in your yaml:
output:
word_document:
reference_docx: template.docx
I have a parameterized RMarkdown PDF report that I am running from a Shiny dashboard (after copying it to a temporary directory).
Example code:
Shiny dashboard:
---
title: "Company Report Frontend"
output:
flexdashboard::flex_dashboard:
orientation: columns
vertical_layout: fill
runtime: shiny
---
```{r global, include=FALSE}
library(flexdashboard)
library(shiny)
```
### Select Company
```{r}
textInput('name', label ='Firm')
```
### Report
```{r}
uiOutput("downloadUI")
# Create the actual downloadButton
output$downloadUI <- renderUI( {
downloadButton("downBtn", "Download Report")
})
# Add download handling
output$downBtn <- downloadHandler(
filename = "full_report.pdf",
content = function(file) {
tempReport <- file.path(tempdir())
file.copy("test_report.Rmd", paste0(tempReport, "/test_report.Rmd"), overwrite = TRUE)
rmarkdown::render(paste0(tempReport, "/test_report.Rmd"), output_file = file,
params = list(input=input),
envir = new.env(parent = globalenv()), clean = FALSE,
knit_root_dir = tempReport,
)
}
)
```
test_report.RMD:
---
title: "Report"
header-includes:
\usepackage{graphicx}
params:
input: NA
output:
pdf_document:
latex_engine: xelatex
---
```{r}
input <- params$input
data(mtcars)
plot(mtcars$hp, mtcars$mpg)
title(input$name)
```
When I run it, it successfully produces the .tex file but then can't compile it. When I try to compile the .tex file directly in a LaTeX editor, I get undefined control sequence and Missing endcsname defined errors on any \includegraphics lines like this one:
\includegraphics{C:/User/LONGUS~1/Temp/file5b381fa967c8_files/figure-latex/unnamed-chunk-1-1.pdf}
where LONGUS~1 is a shortened folder name from the actual Windows username LONGUSERNAME.
The error goes away, and the PDF compiles, if I replace LONGUS~1 with LONGUSERNAME, or just point it to the relative filepath. LaTeX does tend to get finicky about filepaths sometimes.
How can I instruct RMarkdown to either avoid shortening folder names, or skip the absolute filepath and just use the relative? test_report.RMD compiles fine if I run it by itself (and specify a default input), so I'd guess this is something to do with the use of tempdir() or at least something in the render() function. But I really should keep the tempdir() stuff in the case of multiple simultaneous users of the shiny app. I did try removing the knit_root_dir option but that didn't fix it.
Any suggestions welcome. Thank you!
title: File Reading
output: html_document
params:
user1: "C:/Users/myDir/Desktop/apples.jpeg"
user2: "C:/Users/myDir/Desktop/oranges.jpeg"
Lets say I have the following file paths set in params in a Rmardown file. Now I set a separate chunk for each file as follows:
```{r}
image_read(params$user1)
```
```{r}
image_read(params$user2)
```
Now lets say I want to knit the document but the path I have specified for user2 is not available. So I updated my chunks and added the following so if path is not available or correct, the chunk is not evaluated.
```{r, eval = file.exists(params$user2)}
image_read(params$user2)
What I want to do is to somehow specify if file does not exist then upload another image from a default path that I have specified in a separate chunk at the top of my file
```{r}
default_image <- "C:/Users/myDir/Desktop/default.jpeg"
```
So essentially whenever a file path is missing, I want to replace it with this default image. Any help would be appreciated
In this case a simple if-else statement would solve it. If you are going to run it multiple times it might be worth it packing it into a function.
---
title: "test conditional chunks"
output: html_document
params:
user1: "C:/Users/blah/Desktop/Discrete-event-simulation-concepts.png"
user2: "C:/Users/blah/Desktop/Discrete-event-simulation-concepts5.png"
default: "path_to_default"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(magick)
```
```{r}
# basic example
if (file.exists(params$user1)) {
image_read(params$user1)
} else {
image_read(params$default)
}
```
```{r}
# packing into a function
image_read_with_default <- function(path, ...) {
if (file.exists(params$user1)) {
img <- magick::image_read(params$user1, ...)
} else {
img <- magick::image_read(params$default, ...)
}
return(img)
}
```
```{r}
image_read_with_default(params$user1)
```
I am trying to create a downloadable report from a shiny app. The report shows a table in which there are images.
I am passing the table with the url in the table as a parameter to the report as follows:
server <- function(input, output,session) {
data <- reactive({
data <- data.frame(RV3$data[,input$Map_EndoscopistIn],
RV3$data[,input$Map_FindingsIn],
RV3$data[,input$Map_MicroscopicTextIn],
RV3$data$url)
names(data)<-c(input$Map_EndoscopistIn,input$Map_FindingsIn,input$Map_MicroscopicTextIn,"Image")
if(!is.null(input$EndoscopistChooserIn)){
data<-data%>%filter(get(input$Map_EndoscopistIn)==input$EndoscopistChooserIn)
}
data
})
}
output$report <- downloadHandler(
# For PDF output, change this to "report.pdf"
filename = "report.doc",
content = function(file) {
# Copy the report file to a temporary directory before processing it, in
# case we don't have write permissions to the current working dir (which
# can happen when deployed).
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
browser()
# Set up parameters to pass to Rmd document
params <- list(performanceTable=data()
)
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
rmarkdown::render(tempReport, output_file = file,
params = params,
envir = new.env(parent = globalenv())
)
}
)
the url column in data() contains the following path eg:
The report is as follows:
---
title: "Dynamic report"
always_allow_html: yes
output:
word_document:
fig_caption: true
params:
performanceTable: NA
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
```
```{r,echo=FALSE,warning=FALSE}
pander(params$performanceTable, justify='left',split.table=Inf,caption="Table 1: Cancer diagnoses")
```
The report is in the same folder as the Images folder.
With this I get the following error example:
[pandoc warning] Could not find image `img%20src='Images/Images%20Captured%20with%20Proc%20Data%20Audit.files/img2500.jpg'', skipping...
What am I doing wrong? Is this a reformatting in pander issue or a paths issue or what? Or could this be that the report root is the tmp directory whereas I am referring to images stored in anoter static directory. If it is the latter, what do I do to get paths relative to the temp directory so I can see the images?
The reason you couldn't locate your image file is because you render your report.Rmd from a temp directory where your image doesn't exist:
tempReport <- file.path(tempdir(), "report.Rmd")
file.copy("report.Rmd", tempReport, overwrite = TRUE)
The solution is that the image should also be copied to the same temp directory where markdown syntax  will pick up the file.
As in code change, you should be able to get it working by doing this:
assign a tempDir
tempDir <- tempdir()
Move Rmd as well as images to tempDir
file.copy(c("report.Rmd", "Images/Images Captured with Proc Data
Audit.files/img2527.jpg"), tempDir, overwrite = TRUE)
then render from temp dir
rmarkdown::render(file.path(tempDir, 'report.Rmd'), output_file = file,
params = params,
envir = new.env(parent = globalenv())
I try to create button for downloading with knitr package.
I have found some example which works a bit but I'm not able to change the name of the pdf. moreover it causes errors then.
enter image description here
second problem is that when I download the file , it is not a .pdf extension and I have to choose program to open it when I try to open. How can I download file as .pdf in default?
here are my codes (example from the internet):
server.R
library(knitr)
shinyServer(function(input, output) {
output$myreport = downloadHandler(
filename = "adads.pdf",
content = function(file) {
out = knit2pdf('input.Rnw', clean = TRUE )
file.rename(out, file) # move pdf to file for downloading
},
contentType = 'application/pdf'
)
})
ui.R
library(shiny)
shinyUI(basicPage(
textInput('firstname', 'First name', value = 'Jimmy'),
textInput('lastname', 'Last name', value = 'John'),
downloadButton('myreport')
))
and input.Rnw file
\documentclass{article}
\begin{document}
<<names>>=
input$firstname
input$lastname
#
\end{document}