Difference in PDFs when manually generated with Knit-Button vs rmarkdown::render() - e.g. section numbers not always included - r-markdown

Question

I try to generate multiple reports (1 per group) with rmarkdown::render(), but it produces no section numbers.
I use the following file-structure for this in case you want to reproduce the sample (I tried to simplify each file and use only necessary code to reproduce the error):
*) groups.R: defines groups and subgroups in a nested list (all groups stored in a list and each group is a list itself)
groups <- list(
list(c("subgroup1","subgroup2"),"maingroup1"),
list(c("subgroup3","subgroup4"),"maingroup2")
)
*) main.Rmd: template for the reports
---
output:
pdf_document:
number_sections: true
classoption: a4paper
geometry: left=2cm,right=1cm,top=1.5cm,bottom=1cm,includeheadfoot
fontfamily: helvet
fontsize: 11pt
lang: en
header-includes:
- \usepackage{lastpage}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhf{}
- \fancyhead[R]{\fontsize{9}{11} \selectfont \leftmark}
- \fancyhead[L]{\fontsize{9}{11} \selectfont Special report xxx}
- \fancyfoot[R]{\fontsize{9}{0} \selectfont Page \thepage\ of
\pageref{LastPage}}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(echo =
FALSE,comment=NA,warning=FALSE,message=FALSE)
```
\thispagestyle{empty}
\tableofcontents
\newpage
\setcounter{page}{1}
# Introduction
Some text...
```{r results="asis"}
source("graphics.R")
```
*) graphics.R: generates graphics for each subgroup (sections/section numbers are produced with cat() for each subgroup)
load("actgroup.RData")
source("template_graphics.R")
for (g in 1:length(act.group[[1]][[1]])) {
subgroup.name <- act.group[[1]][[1]][g]
cat("\\clearpage")
cat("\n# ",subgroup.name, "\n")
template_graphics(cars)
cat("\n\n")
cat("\\clearpage")
template_graphics(iris)
cat("\n\n")
cat("\\clearpage")
template_graphics(airquality)
cat("\n\n")
cat("\\clearpage")
cat("\n")
}
*) template_graphics.R: template for plotting
template_graphics <- function(data) {
plot(data)
}
*) loop.R: used for generating all reports as PDF - 1 per group
setwd("YOUR DIRECTORY HERE")
library(rmarkdown)
source("groups.R")
for(i in 1:length(groups)) {
act.group = list(groups[[i]])
save(act.group,file="actgroup.RData")
rmarkdown::render("main.Rmd",
output_format=pdf_document(),
output_file=paste0("Special Report ",act.group[[1]][[2]],".pdf"),
output_dir="~/Reports")
}
The problem is, that the final documents do not show the section numbers. When I knit manually in main.Rmd (pressing knit-Button), the section numbers are printed.
Version rmarkdown::render
Version knit-Button
I thought that pressing the knit-Button also starts the rendering-process with rmarkdown::render()? So it's surprising that the reports are not identical?
In advance I installed tinytex::install_tinytex(). The used latex-packages in main.Rmd were automatically installed during the first time rendering.
I am not sure what the problem is. I use R 4.1.0 and RStudio 2022.02.2.
Thanks for your help!!

Answer 1

The behaviour of pdf_document() as the output-format in rmarkdown::render caused the missing section-numbers.
In my YAML-header in main.Rmd I chose to keep the section numbers with number_sections: true. If this should also be rendered when using rmarkdown::render, it has to be an argument in the function:
pdf_document(number_sections=TRUE)
The code of loop.R produces now pdfs with section numbers:
library(rmarkdown)
source("groups.R")
for(i in 1:length(groups)) {
act.group = list(groups[[i]])
save(act.group,file="actgroup.RData")
rmarkdown::render("main.Rmd",
output_format=pdf_document(number_sections=TRUE),
output_file=paste0("Special Report ",act.group[[1]][[2]],".pdf"),
output_dir="~/Reports")
}
More information on pdf_document() can be found here:
https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html
Alternatively, fill in just a text-reference as output-format: output_format="pdf_document". When set like this, the options of the YAML-Header are not overwritten and the numbers are also included.