R/create_rmarkdown.R

In plnr: A System for Planing Analyses

#' Create example rmarkdown project
#' @param home Location of the 'home' directory
#' @export
create_rmarkdown <- function(home) {
  fs::dir_create(fs::path(home))
  fs::dir_create(fs::path(home, "R"))
  fs::dir_create(fs::path(home, "results"))
  fs::dir_create(fs::path(home, "paper"))
  fs::dir_create(fs::path(home, "raw"))

  # delete some files if not needed
  unlink(fs::dir_ls(home, regexp = "*Rproj$"))

  ############
  # run.R

  txt <- glue::glue('
# Initialize the project
org::initialize_project(
  home = "{home}",
  results = "{fs::path(home,"results")}",
  paper = "{fs::path(home,"paper")}",
  raw = "{fs::path(home,"raw")}",
  create_folders = TRUE
)

library(ggplot2)
library(data.table)

# info.txt
txt <- glue::glue("
{lubridate::today()}:
  Project initialized.
", .trim=FALSE)

org::write_text(
  txt = txt,
  file = fs::path(org::project$results, "info.txt")
)

# define a new plan
p <- plnr::Plan$new()

# adding data
p$add_data(
  name = "deaths",
  direct = data.table(deaths=1:4, year=2001:2004)
)

# adding analyses
p$add_analysis(
  name = "tab_1",
  fn_name = "table_death"
)

p$add_analysis(
  name = "fig_1",
  fn_name = "figure_death",
  year_max = 2004
)

# render the paper
rmarkdown::render(
  input = fs::path(org::project$paper,"paper.Rmd"),
  output_dir = org::project$results_today,
  quiet = F
)
',
    home = home
  )

  cat(txt, file = fs::path(home, "run.R"))

  ############
  # R/table_death.R

  txt <- glue::glue('
table_death <- function(data, argset){{
  # data <- p$get_data()
  # argset <- p$get_argset("tab_1")

  ht <- huxtable::hux(data$deaths, add_colnames = TRUE)
  ht <- huxtable::theme_article(ht)
  ht
}}
')

  cat(txt, file = fs::path(home, "R", "figure_death.R"))

  ############
  # R/figure_death.R

  txt <- glue::glue('
figure_death <- function(data, argset){{
  # data <- p$get_data()
  # argset <- p$get_argset("fig_1")

  plot_data <- data$deaths[year<= argset$year_max]

  q <- ggplot(plot_data, aes(x=year, y=deaths))
  q <- q + geom_line()
  q <- q + geom_point(size=3)
  q <- q + labs(title = glue::glue("Deaths from 2001 until {{argset$year_max}}"))
  q
}}
')

  cat(txt, file = fs::path(home, "R", "figure_death.R"))

  ############
  # paper/paper.Rmd

  txt <- glue::glue('
---
title: "Untitled"
output: html_document
editor_options:
  chunk_output_type: console
---

```{{r setup, include=FALSE}}
knitr::opts_chunk$set(echo = TRUE)
```

## Table

Here is a table:

```{{r, echo=FALSE, results="asis"}}
p$run_one("tab_1")
```

## Plot

Here is a plot:

```{{r, echo=FALSE}}
p$run_one("fig_1")
```

  ')

  cat(txt, file = fs::path(home, "paper", "paper.Rmd"))

  usethis::create_project(home)
}