Good morning everybody,
as stated above, I’m trying to render multiple Rmarkdown reports with different parameters for each report. Basically I have a folder of .csv files, which I have to clean up. I have packed all the steps in an .Rmd file, because this way the data gets cleaned and a short report is generated documenting the results. Some figures, some stats, nothing very dramatic, just an overview of how the cleaning went.
As each .csv file is slightly different, I have to tweak some parameters. This is the easy part. I have found some nice code in the “R for Data Science” book, which you can find here. https://r4ds.had.co.nz/r-markdown.html#parameters
This is my version:
library(dplyr)
library(stringr)
library(purrr)
# Create a vector with names
files <- c("dataframe", "datatable")
# Create a tibble with filenames and lists of parameters
reports <- tibble(
filename = str_c(files, ".html"),
params = map(files, ~ list(name = .,
factor = if_else(. == "dataframe", 2.5, 5))))
#-------------------------------------------------------------------
# make reports
reports <- reports %>%
select(output_file = filename, params) %>%
purrr::pwalk(rmarkdown::render, input = "template_datatable.Rmd")
Everything runs fine, when the .Rmd file uses data.frames. As my .csv are about 1 GB each, I would use data.table to speed things up. But as soon as my .Rmd file contains some data.table code I get this error message:
Error: `:=` can only be used within a quasiquoted argument
If I just render one file with rmarkdown::render(input = "template_datatable.Rmd", output_file = "test.html", params = list(name = "datatable", carat = 5)), the .Rmd with the data.table code works fine.
My questions are. What is causing this error? And is there a way to fix it?
Here is my code for the .Rmd using data.frames:
---
title: "A report for `r params$name`"
params:
name: "name"
factor: 1
output:
bookdown::html_document2:
fig_caption: yes
toc: yes
toc_float: true
code_folding: "hide"
---
```{r setup, include=FALSE}
# Setup Chunk
# Some knitr options
knitr::opts_chunk$set(echo = FALSE)
# Packages
library(dplyr)
library(ggplot2)
```
```{r dataImport}
df <- data.frame(A = seq(1, 100), B = seq(1, 100))
df <- df %>%
mutate(C = B * params$factor)
```
```{r makePlot}
ggplot(df, aes(A, C)) +
geom_line()
```
And my code for the .Rmd using data.tables:
```
---
title: "A report for `r params$name`"
params:
name: "name"
factor: 1
output:
bookdown::html_document2:
fig_caption: yes
toc: yes
toc_float: true
code_folding: "hide"
---
```{r setup, include=FALSE}
# Setup Chunk
# Some knitr options
knitr::opts_chunk$set(echo = FALSE)
# Packages
library(data.table)
library(ggplot2)
```
```{r dataImport}
dt <- data.table(A = seq(1, 100), B = seq(1, 100))
dt <- dt[, C := B*params$factor]
```
```{r makePlot}
ggplot(dt, aes(A, C)) +
geom_line()
```
Thanks for your help.
