params established for rds

ref #5
OuhscBbmc · Dec 29, 2021 · d1f03a8 · d1f03a8
1 parent a786faa
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Showing 3 changed files with 16 additions and 12 deletions.
diff --git a/for-developers/sandbox/report-1.Rmd b/for-developers/sandbox/report-1.Rmd
@@ -8,6 +8,8 @@ output:
     toc_float: true
     number_sections: true
     # css: ../analysis/common/styles-1.css
+params:
+  path_checks: "not-set"
 ---
 
 
@@ -50,16 +52,20 @@ requireNamespace("DT")
 
 <!-- Load any global functions and variables declared in the R file.  Suppress the output. -->
 ```{r declare-globals, echo=echo_chunks, results='show', message=FALSE}
-```
-
-<!-- Declare any global functions specific to a Rmd output.  Suppress the output. -->
-```{r, echo=echo_chunks, message=FALSE}
-  #Put presentation-specific code in here.  It doesn't call a chunk in the codebehind file.
+path_checks <- 
+  if (params$path_checks == "not-set") {
+    system.file("derived/biochemical.rds", package = "trawler")
+  } else {
+    params$path_checks
+  }
+
+checkmate::assert_character(path_checks, any.missing = FALSE, len = 1)
+checkmate::assert_file_exists(path_checks, extension = "rds")
 ```
 
 <!-- Load the datasets.   -->
 ```{r load-data, echo=echo_chunks, results='show', message=FALSE}
-checks <- readRDS(system.file("derived/biochemical.rds", package = "trawler"))
+checks <- readRDS(path_checks)
 ```
 
 <!-- Tweak the datasets.   -->

diff --git a/for-developers/sandbox/report-1.html b/for-developers/sandbox/report-1.html
@@ -242,7 +242,7 @@
 
 
 <h1 class="title toc-ignore">REDCapR Validator Example 1</h1>
-<h4 class="date">Date: 2021-12-29 17:13:59</h4>
+<h4 class="date">Date: 2021-12-29 17:49:10</h4>
 
 </div>
 
@@ -251,7 +251,6 @@ <h4 class="date">Date: 2021-12-29 17:13:59</h4>
 <!-- Set the report-wide options, and point to the external code file. -->
 <!-- Load 'sourced' R files.  Suppress the output when loading packages. -->
 <!-- Load any global functions and variables declared in the R file.  Suppress the output. -->
-<!-- Declare any global functions specific to a Rmd output.  Suppress the output. -->
 <!-- Load the datasets.   -->
 <!-- Tweak the datasets.   -->
 <div id="smells" class="section level1 tabset tabset-fade" number="1">

diff --git a/for-developers/sandbox/report-1.md b/for-developers/sandbox/report-1.md
@@ -1,13 +1,15 @@
 ---
 title: REDCapR Validator Example 1     # Change this value for new validators.
-date: "Date: 2021-12-29 17:13:59"
+date: "Date: 2021-12-29 17:49:10"
 output:
   html_document:
     keep_md: yes
     toc: yes
     toc_float: true
     number_sections: true
     # css: ../analysis/common/styles-1.css
+params:
+  path_checks: "not-set"
 ---
 
 
@@ -23,9 +25,6 @@ output:
 <!-- Load any global functions and variables declared in the R file.  Suppress the output. -->
 
 
-<!-- Declare any global functions specific to a Rmd output.  Suppress the output. -->
-
-
 <!-- Load the datasets.   -->