render_rmarkdown: Render (executed) checks to an html document with R Markdown

In OuhscBbmc/trawler: Inspect a dataset

Render (executed) checks to an html document with R Markdown

Description

Render (executed) checks to an html document with R Markdown

Usage

render_rmarkdown(
  path_checks,
  directory_output,
  report_file_name = "trawler.html",
  path_template = system.file("report-templates/rmarkdown-1/report-1.Rmd", package =
    "trawler")
)

Arguments

path_checks	The file path of the output of execute_checks(). Required.
directory_output	A writable directory to save the report outputs. The html file is the primary output. The markdown file is sometimes useful too. Required.
report_file_name	The name of the resulting html file. Defaults to "trawler.html".
path_template	The rmd file, which serves as the report template. Defaults to the standard template built into the trawler package.

Examples

# Step 0: define paths.
#   So this package example executes on every machine, temp files are used.

# Replace the two paths for your specific project
path_data    <- system.file("datasets/pt-event-biochemical.rds", package = "trawler")
path_defs    <- system.file("checks/checks-biochemical.yml", package = "trawler")

# In your real code, this will probably in a static directory.
# If PHI or sensitive info is contained, use a secure location.
directory_output <- file.path(tempdir(check = TRUE), "trawler")
if (!dir.exists(directory_output)) dir.create(directory_output)
path_checks <- tempfile("trawler-checks-", fileext = ".rds", tmpdir = directory_output)

# Step 1: load the check definitions and the dataset to test
ds_pt_event  <- readr::read_rds(path_data)
checks       <- load_checks(path_defs, origin = "REDCap")

# Step 2: execute the checks and save to an rds file
ds_pt_event |>
  execute_checks(checks, origin = "REDCap") |>
  readr::write_rds(path_checks)

# Step 3: render checks as an html report with R Markdown
render_rmarkdown(path_checks, directory_output)

# For the sake of this example, clean up temp files.
#    You probably do NOT want this line in your real code.
unlink(directory_output, recursive = TRUE)

OuhscBbmc/trawler documentation built on Oct. 8, 2024, 11:44 p.m.