How to knit markdown to PDF using R command? - r

Question

Trying to knit an Rmarkdown document to PDF from another R script. When I use the Rstudio interface, and hit Knit to PDF, it works perfectly fine and generates the PDF. But when I use the rmarkdown::render command, it gives me an error:
Markdown:
---
geometry: margin=0.75in
output:
pdf_document: default
params:
set_title:
value: "Sample"
editor_options:
chunk_output_type: console
header-includes:
\usepackage{fancyhdr}
\usepackage{graphicx}
---
---
title: `r params$set_title`
---
```{r load_libraries, include=FALSE, echo=FALSE}
suppressPackageStartupMessages({
library(knitr)
library(tidyverse)
library(kableExtra)
})
```
\addtolength{\headheight}{2.0cm}
\fancypagestyle{plain}{}
\pagestyle{fancy}
\renewcommand{\headrulewidth}{0pt}
```{r set_options, include = FALSE, echo = FALSE, warning = FALSE}
knitr::opts_chunk$set(comment = NA)
`%>%` <- dplyr::`%>%`
```
# 1. Table
```{r, echo = FALSE, message = FALSE, warning = FALSE}
# sample data frame
df <- data.frame(x = c("a", "b", "c"),
y = c("a", "b", "c"))
# print table
kableExtra::kable(df, booktabs = T) %>%
kable_styling(full_width = TRUE, font_size = 8) %>%
row_spec(0, bold = T) %>%
column_spec(1, width = "1cm") %>%
column_spec(2, width = "2cm")
```
This is how I am running it:
rmarkdown::render(input = "~/Projects/test.Rmd",
params = list(set_title = "TEMP"),
output_dir = "~/Desktop/",
output_file = "test.pdf")
Error:
! LaTeX Error: Environment tabu undefined.
Error: LaTeX failed to compile /Users/rathik/Projects/test.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See test.log for more info.
The error is due to using kableExtra::kable because when I remove that function call, the error goes away. Any ideas how to resolve it?

Answer 1

Thank you #Dirk, based on your suggestion and the LaTeX documentation, I added the following in the header and it seems to be working as expected:
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{array}
\usepackage{multirow}
\usepackage{wrapfig}
\usepackage{float}
\usepackage{colortbl}
\usepackage{pdflscape}
\usepackage{tabu}
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage[normalem]{ulem}
\usepackage{makecell}
\usepackage{xcolor}