simplify rmd a little

There are a lot of options useful in [RAnalysisSkeleton](https://github.com/wibeasley/RAnalysisSkeleton/tree/main/analysis) that are unnecessary here. ref #5
OuhscBbmc · Dec 30, 2021 · 18283b4 · 18283b4
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diff --git a/inst/report-templates/rmarkdown-1/report-1.Rmd b/inst/report-templates/rmarkdown-1/report-1.Rmd
@@ -1,5 +1,5 @@
 ---
-title: REDCapR Validator Example 1     # Change this value for new validators.
+title: Trawler Report
 date: "Date: `r Sys.time()`"
 output:
   html_document:
@@ -12,46 +12,28 @@ params:
   path_checks: "not-set"
 ---
 
-
-<!--  Set the working directory to the repository's base directory; this assumes the report is nested inside of three directories.-->
-```{r, echo=F, message=F}
-# cat("Working directory: ", getwd())
-library(knitr)
-# Change this value for new validators.
-# opts_knit$set(root.dir='../')  #Don't combine this call with any other chunk -especially one that uses file paths.
-```
-
 <!-- Set the report-wide options, and point to the external code file. -->
 ```{r set-options, echo=F}
+library(knitr)
+
 # cat("Working directory: ", getwd())
 report_render_start_time <- Sys.time()
 opts_chunk$set(
   results    = 'show',
-  warning    = FALSE,
-  comment    = NA,
-  tidy       = FALSE,
-  fig.width  = 6.5,
-  fig.height = 4,
-  fig.path   = 'figure-png/'
+  warning    = TRUE
 )
-# dpi = 400,
-# out.width = "650px", #This affects only the markdown, not the underlying png file.  The height will be scaled appropriately.
 
 echo_chunks <- FALSE
-options(width=100) #So the output is 25% wider than the default.
-
-# Change this value for new validators.
-# read_chunk("./analysis/validator-1.R") #This allows knitr to call chunks tagged in the underlying *.R file.
 ```
 
-<!-- Load 'sourced' R files.  Suppress the output when loading packages. -->
-```{r load-packages, echo=echo_chunks, message=FALSE, warning=FALSE}
+<!-- Suppress the output when loading packages. -->
+```{r load-packages, echo = echo_chunks, message = FALSE}
 requireNamespace("dplyr")
 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}
+```{r declare-globals, echo = echo_chunks}
 path_checks <- 
   if (params$path_checks == "not-set") {
     system.file("derived/biochemical.rds", package = "trawler")
@@ -64,12 +46,12 @@ checkmate::assert_file_exists(path_checks, extension = "rds")
 ```
 
 <!-- Load the datasets.   -->
-```{r load-data, echo=echo_chunks, results='show', message=FALSE}
-checks <- readRDS(path_checks)
+```{r load-data, echo = echo_chunks}
+checks <- base::readRDS(path_checks)
 ```
 
 <!-- Tweak the datasets.   -->
-```{r tweak-data, echo=echo_chunks, results='show', message=TRUE}
+```{r tweak-data, echo = echo_chunks}
 ```
 
 
@@ -80,7 +62,7 @@ A *smell* test won't validate a specific record (like the rules below), but it w
 
 Smell Summary
 -----------------------------
-```{r table-smell-summary, echo=echo_chunks, message=TRUE}
+```{r table-smell-summary, echo = echo_chunks}
 palette_summary <- list(warm = "#fde0ef", hot = "#f1b6da", header = "#555") #http://colrd.com/palette/18841/
 
 ds_smell_result_pretty <-

diff --git a/inst/report-templates/rmarkdown-1/report-1.html b/inst/report-templates/rmarkdown-1/report-1.html
diff --git a/inst/report-templates/rmarkdown-1/report-1.md b/inst/report-templates/rmarkdown-1/report-1.md
@@ -0,0 +1,147 @@
+---
+title: Trawler Report
+date: "Date: 2021-12-30 13:10:56"
+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"
+---
+
+<!-- Set the report-wide options, and point to the external code file. -->
+
+
+<!-- Suppress the output when loading packages. -->
+
+
+<!-- Load any global functions and variables declared in the R file.  Suppress the output. -->
+
+
+<!-- Load the datasets.   -->
+
+
+<!-- Tweak the datasets.   -->
+
+
+
+Smells {.tabset .tabset-fade}
+=============================
+
+A *smell* test won't validate a specific record (like the rules below), but it will make sure the dataset overall smells correct.
+
+Smell Summary
+-----------------------------
+<table class="table table-hover table-condensed table-responsive" style="width: auto !important; ">
+ <thead>
+  <tr>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Smell Name </th>
+   <th style="text-align:right;font-weight: bold;color: white !important;background-color: #555 !important;"> Priority </th>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Proportion of... </th>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Legal Boundaries </th>
+   <th style="text-align:right;font-weight: bold;color: white !important;background-color: #555 !important;"> Value </th>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Pass </th>
+  </tr>
+ </thead>
+<tbody>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> average bmi at baseline </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Average BMI is between 18 and 24 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [18.00, 24.00] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 24.8500 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> average serum ferritin levels at baseline </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Mean serum ferritin levels are in the recommended range of &gt; 500ng/dl-1200ng/dl </td>
+   <td style="text-align:left;color: #555 !important;"> [501, 1200] </td>
+   <td style="text-align:right;color: #555 !important;"> 589.12 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> definitive diagnosis </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> A 100 percent of study participants were diagnosed with malnutrition associated with Chronic Renal Disease </td>
+   <td style="text-align:left;color: #555 !important;"> [1.00, 1.00] </td>
+   <td style="text-align:right;color: #555 !important;"> 1.0000 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> dialysis adequacy </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Normal range for Kt/V values are between 1.2 and 5 </td>
+   <td style="text-align:left;color: #555 !important;"> [1.20, 5.00] </td>
+   <td style="text-align:right;color: #555 !important;"> 1.9167 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> mean age </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Mean age of participants is between 18 years to 20 years </td>
+   <td style="text-align:left;color: #555 !important;"> [20.00, 80.00] </td>
+   <td style="text-align:right;color: #555 !important;"> 44.3889 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> mean serum cholesterol levels at baseline </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Average Cholesterol levels range is between 100mg/dl-140mg/dl at baseline level </td>
+   <td style="text-align:left;color: #555 !important;"> [100.00, 140.00] </td>
+   <td style="text-align:right;color: #555 !important;"> 134.1176 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> mean serum creatinine level at baseline </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Mean serum creatinine levels at baseline are between 3mg/dl and 15mg/dl </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [3.00, 15.00] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 23.1687 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> mean serum prealbumin level at baseline </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Mean serum pre-albumin levels at baseline are between 31mg/dl and 39mg/dl </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [32.00, 39.00] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 23.6667 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> normalized protein catabolic rate </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Average Normalized Protein Catabolic Rate is &lt; 1.2g/kg/day </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [0.00, 0.12] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 0.9313 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> nutritional counseling </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Most patients agreed to receiving nutritional counseling </td>
+   <td style="text-align:left;color: #555 !important;"> [0.85, 0.99] </td>
+   <td style="text-align:right;color: #555 !important;"> 0.8889 </td>
+   <td style="text-align:left;color: #555 !important;"> TRUE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> proportion female participants </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Proportion female participants is half the participants till study conclusion </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [0.50, 0.50] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 0.4444 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> proportion male participants </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Proportion male participants is half the participants till study conclusion </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> [0.50, 0.50] </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 0.5556 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> FALSE </td>
+  </tr>
+</tbody>
+</table>