basic rendering function

ref #5

NAMESPACE

@@ -2,4 +2,5 @@
 
 export(execute_checks)
 export(load_checks)
+export(render_rmarkdown)
 importFrom(rlang,.data)

R/execute-checks.R

@@ -1,5 +1,4 @@
-#' @title Load and parse checks in a yaml file, and return a list
-#' of useful objects.
+#' @title Execute the checks against a dataset to return a nested list.
 #' @param ds The [data.frame] to be checked.  Required.
 #' @param checks The [list] describing the check.  Is the output of
 #' [trawler::load_checks()].  Required.

R/render-rmarkdown.R

@@ -0,0 +1,55 @@
+#' @title Render (executed) checks to an html document with [R Markdown](https://rmarkdown.rstudio.com/)
+#' @param path_checks The file path of the output of
+#' [trawler::execute_checks()].  Required.
+#' @param 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.
+#' @param path_template The
+#' [rmd file](https://rmarkdown.rstudio.com/articles_intro.html),
+#' which serves as the report template.  Defaults to the
+#' [standard template](https://github.com/OuhscBbmc/trawler/tree/main/inst/report-templates/rmarkdown-1/report-1.Rmd)
+#' 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)
+#'
+#' # Step 2: execute the checks and save to an rds file
+#' execute_checks(ds_pt_event, checks) |>
+#'   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)
+#'
+#' @export
+render_rmarkdown <- function (
+  path_checks,
+  directory_output,
+  path_template = system.file("report-templates/rmarkdown-1/report-1.Rmd", package = "trawler")
+) {
+  checkmate::assert_file_exists(path_checks)
+
+  rmarkdown::render(
+    input       = path_template,
+    params      = list(path_checks = path_checks),
+    output_dir  = directory_output
+  )
+}