My workflow for rendering and saving automated reports.

Workflow.Rmd

---
title: "Title"
subtitle: "Subtitle"
author: "Carlos Guio"
date: "`r Sys.Date()`"
knit: (function(inputFile, encoding) { 
      out_dir <- 'Subfolder_for_report';
      rmarkdown::render(input = inputFile,
                        encoding = encoding, 
                        output_file = file.path(
                                        here::here(), 
                                        out_dir, 
                                        'Report_name.html'))
                                        })
output:
  html_document:
    theme: journal
    highlight: tango
    keep_md: true
---

I modified the YAML above to render the outputs in a different directory than the `.Rmd`. The `.Rmd`will be stored in the `/R`folder, whereas the `.html`and `.md`will be stored in the `/Reports` folder.

The folders need to be previously created following the structure:

* Project folder/
      + R
      + Reports
      + Plots
      + Data

Next, use `r here::set_here()`  just one time, to tag the root directory with a .here file

Set chunk options, including graphic display.

```{r setup_chunks, warning = FALSE, message = FALSE}

knitr::opts_chunk$set(include = FALSE, echo = FALSE, warning = FALSE, message = FALSE, fig.align="center", fig.showtext = TRUE, fig.retina = 1, dpi = 300, out.width = "70%")

showtext_auto()
#Following the advice from here: https://cran.rstudio.com/web/packages/showtext/vignettes/introduction.html

```

To save the figures
```{r}

ggsave(file = "Figure_name.png", plot = object_in_R, device = "png", type = "cairo", path = here::here("Plots"), dpi = 300)

```

After having created de `.Rmd`, run in the console `r knitr::purl("File_name.Rmd", documentation = 0)`. This will create an .R file, simplefied, without turning the Markdown text to comments. To add comments, set documentation = 2.