In OuhscBbmc/trawler: Inspect a dataset

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

trawler

The goal of trawler is to ...

Installation

You can install the development version of trawler from GitHub with:

# install.packages("devtools")
devtools::install_github("OuhscBbmc/trawler")

Standard Trawler Report

# 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       <- trawler::load_checks(path_defs, origin = "REDCap")

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

# Step 3: render checks as an html report with R Markdown
trawler::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)