From 73d3cf9575f75b48fb19324e6ec7b3b31071e0ed Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 31 Dec 2021 16:56:47 -0600
Subject: [PATCH] Add configuration section

ref #5
---
 .../report-templates/rmarkdown-1/report-1.Rmd | 23 +++++
 .../rmarkdown-1/report-1.html                 | 91 ++++++++++++++++-
 inst/report-templates/rmarkdown-1/report-1.md | 98 ++++++++++++++++++-
 3 files changed, 206 insertions(+), 6 deletions(-)

diff --git a/inst/report-templates/rmarkdown-1/report-1.Rmd b/inst/report-templates/rmarkdown-1/report-1.Rmd
index 653328e..57e61bf 100644
--- a/inst/report-templates/rmarkdown-1/report-1.Rmd
+++ b/inst/report-templates/rmarkdown-1/report-1.Rmd
@@ -286,3 +286,26 @@ cat(sprintf("1. %s;", checks$smells_inactive$check_name), sep = "\n")
 
 To enable/disable a smell, set the `active` element in the yaml checks file to "true" or "false".
 </div>
+
+Configuration {.tabset .tabset-fade}
+=============================
+
+For the sake of documentation and reproducibility, the current report was rendered in the following environment.  Click the line below to expand.
+
+<details>
+  <summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>
+```{r session-info, echo=FALSE}
+if( requireNamespace("sessioninfo", quietly = TRUE) ) {
+  sessioninfo::session_info()
+} else {
+  sessionInfo()
+}
+```
+</details>
+
+```{r session-duration, echo=FALSE}
+report_render_duration_in_seconds <- as.integer(difftime(Sys.time(), report_render_start_time, units="secs"))
+```
+
+Report rendered by `r Sys.info()["user"]` at `r strftime(Sys.time(), "%Y-%m-%d, %H:%M %z")` in `r report_render_duration_in_seconds` seconds.
+
diff --git a/inst/report-templates/rmarkdown-1/report-1.html b/inst/report-templates/rmarkdown-1/report-1.html
index 5b14bf4..f08aef3 100644
--- a/inst/report-templates/rmarkdown-1/report-1.html
+++ b/inst/report-templates/rmarkdown-1/report-1.html
@@ -254,7 +254,7 @@
 
 
 <h1 class="title toc-ignore">Trawler Report</h1>
-<h4 class="date">Date: 2021-12-31 15:54:07</h4>
+<h4 class="date">Date: 2021-12-31 16:56:22</h4>
 
 </div>
 
@@ -515,8 +515,8 @@ <h2 number="2.1"><span class="header-section-number">2.1</span> Rule Summary</h2
 </div>
 <div id="rule-detail" class="section level2" number="2.2">
 <h2 number="2.2"><span class="header-section-number">2.2</span> Rule Detail</h2>
-<div id="htmlwidget-205d91dc155182c9cdb9" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-205d91dc155182c9cdb9">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;baseline prealbumin levels&quot;,&quot;hospitalization reason&quot;,&quot;missing serum marker levels&quot;,&quot;npcr&quot;,&quot;npcr comparison&quot;,&quot;optimal daily protein intake&quot;,&quot;recommended npcr range&quot;,&quot;serum prealbumin levels 1&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"integer\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1\" data-max=\"3\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit&quot;,&quot;Daily protein intake is optimal but one of the nutritional marker is not within the normal range&quot;,&quot;NPCR at completion is missing&quot;,&quot;NPCR at completion is not greater than npcr at baseline&quot;,&quot;NPCR values are not within the recommended range at completion&quot;,&quot;Patient was hospitalized but reason and the date of hospitalization is missing&quot;,&quot;Relevant nutritional serum markers are missing&quot;,&quot;Serum pre-albumin level of all enrolled patients do not meet the study criterion&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"integer\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1\" data-max=\"220\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;1&quot;,&quot;2&quot;,&quot;3&quot;,&quot;255&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"date\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1420156800000\" data-max=\"1427932800000\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","caption":"<caption>Violations at 2021-12-31 15:54:08<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50"],["baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","missing serum marker levels","missing serum marker levels","missing serum marker levels","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","hospitalization reason","hospitalization reason","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","npcr","npcr comparison","npcr comparison"],[1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3],["Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Patient was hospitalized but reason and the date of hospitalization is missing","Patient was hospitalized but reason and the date of hospitalization is missing","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR at completion is missing","NPCR at completion is not greater than npcr at baseline","NPCR at completion is not greater than npcr at baseline"],[1,2,3,8,9,12,13,14,15,100,7,10,11,1,2,3,4,5,6,8,9,12,13,14,15,16,100,220,8,14,5,6,7,8,11,15,100,1,6,7,8,12,13,14,16,100,220,10,1,12],["1","2","3","1","3","3","1","1","3","1","2","255","2","1","2","3","255","1","3","1","3","3","1","1","3","2","1","1",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["2015-01-02","2015-01-02","2015-01-05","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-04-02","2015-01-27","2015-02-13","2015-02-19","2015-01-02","2015-01-02","2015-01-05","2015-01-10","2015-01-13","2015-01-16","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-03-09","2015-04-02","2015-04-02",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Rule Name<\/th>\n      <th>Priority<\/th>\n      <th>Error Message<\/th>\n      <th>Record ID<\/th>\n      <th>Data Collector<\/th>\n      <th>Baseline Date<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":30,"dom":"tip","columnDefs":[{"className":"dt-center","targets":[5,6]},{"className":"dt-right","targets":[2,4]},{"orderable":false,"targets":0}],"initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'background-color': '#555', 'color': '#fff'});\n}","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[10,25,30,50,100]}},"evals":["options.initComplete"],"jsHooks":[]}</script>
+<div id="htmlwidget-a7777e8bdb5be5b1a3ad" style="width:100%;height:auto;" class="datatables html-widget"></div>
+<script type="application/json" data-for="htmlwidget-a7777e8bdb5be5b1a3ad">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;baseline prealbumin levels&quot;,&quot;hospitalization reason&quot;,&quot;missing serum marker levels&quot;,&quot;npcr&quot;,&quot;npcr comparison&quot;,&quot;optimal daily protein intake&quot;,&quot;recommended npcr range&quot;,&quot;serum prealbumin levels 1&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"integer\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1\" data-max=\"3\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit&quot;,&quot;Daily protein intake is optimal but one of the nutritional marker is not within the normal range&quot;,&quot;NPCR at completion is missing&quot;,&quot;NPCR at completion is not greater than npcr at baseline&quot;,&quot;NPCR values are not within the recommended range at completion&quot;,&quot;Patient was hospitalized but reason and the date of hospitalization is missing&quot;,&quot;Relevant nutritional serum markers are missing&quot;,&quot;Serum pre-albumin level of all enrolled patients do not meet the study criterion&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"integer\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1\" data-max=\"220\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;1&quot;,&quot;2&quot;,&quot;3&quot;,&quot;255&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"date\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"display: none;position: absolute;width: 200px;opacity: 1\">\n      <div data-min=\"1420156800000\" data-max=\"1427932800000\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","caption":"<caption>Violations at 2021-12-31 16:56:23<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50"],["baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","baseline prealbumin levels","missing serum marker levels","missing serum marker levels","missing serum marker levels","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","serum prealbumin levels 1","hospitalization reason","hospitalization reason","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","optimal daily protein intake","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","recommended npcr range","npcr","npcr comparison","npcr comparison"],[1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,3,3],["Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Serum pre-albumin level of all enrolled patients do not meet the study criterion","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Patient was hospitalized but reason and the date of hospitalization is missing","Patient was hospitalized but reason and the date of hospitalization is missing","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR at completion is missing","NPCR at completion is not greater than npcr at baseline","NPCR at completion is not greater than npcr at baseline"],[1,2,3,8,9,12,13,14,15,100,7,10,11,1,2,3,4,5,6,8,9,12,13,14,15,16,100,220,8,14,5,6,7,8,11,15,100,1,6,7,8,12,13,14,16,100,220,10,1,12],["1","2","3","1","3","3","1","1","3","1","2","255","2","1","2","3","255","1","3","1","3","3","1","1","3","2","1","1",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["2015-01-02","2015-01-02","2015-01-05","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-04-02","2015-01-27","2015-02-13","2015-02-19","2015-01-02","2015-01-02","2015-01-05","2015-01-10","2015-01-13","2015-01-16","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-03-09","2015-04-02","2015-04-02",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Rule Name<\/th>\n      <th>Priority<\/th>\n      <th>Error Message<\/th>\n      <th>Record ID<\/th>\n      <th>Data Collector<\/th>\n      <th>Baseline Date<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":30,"dom":"tip","columnDefs":[{"className":"dt-center","targets":[5,6]},{"className":"dt-right","targets":[2,4]},{"orderable":false,"targets":0}],"initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'background-color': '#555', 'color': '#fff'});\n}","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[10,25,30,50,100]}},"evals":["options.initComplete"],"jsHooks":[]}</script>
 </div>
 <div id="inactive-rules" class="section level2" number="2.3">
 <h2 number="2.3"><span class="header-section-number">2.3</span> Inactive Rules</h2>
@@ -810,6 +810,91 @@ <h2 number="3.2"><span class="header-section-number">3.2</span> Inactive Smells<
 </div>
 </div>
 </div>
+<div id="configuration" class="section level1 tabset tabset-fade" number="4">
+<h1 class="tabset tabset-fade" number="4"><span class="header-section-number">4</span> Configuration</h1>
+<p>For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.</p>
+<details>
+<summary>
+Environment <span class="glyphicon glyphicon-plus-sign"></span>
+</summary>
+<pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
+##  setting  value
+##  version  R version 4.1.1 (2021-08-10)
+##  os       Ubuntu 21.10
+##  system   x86_64, linux-gnu
+##  ui       X11
+##  language (EN)
+##  collate  en_US.UTF-8
+##  ctype    en_US.UTF-8
+##  tz       America/Chicago
+##  date     2021-12-31
+##  pandoc   2.11.4 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
+## 
+## ─ Packages ───────────────────────────────────────────────────────────────────
+##  package     * version date (UTC) lib source
+##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
+##  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.1)
+##  bslib         0.3.1   2021-10-06 [1] CRAN (R 4.1.1)
+##  checkmate     2.0.0   2020-02-06 [1] CRAN (R 4.1.0)
+##  cli           3.1.0   2021-10-27 [1] CRAN (R 4.1.1)
+##  colorspace    2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
+##  crayon        1.4.2   2021-10-29 [1] CRAN (R 4.1.1)
+##  crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.1.1)
+##  DBI           1.1.1   2021-01-15 [1] CRAN (R 4.1.0)
+##  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.1)
+##  dplyr         1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
+##  DT            0.20    2021-11-15 [1] CRAN (R 4.1.1)
+##  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
+##  evaluate      0.14    2019-05-28 [1] CRAN (R 4.1.0)
+##  fansi         0.5.0   2021-05-25 [1] CRAN (R 4.1.0)
+##  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
+##  generics      0.1.1   2021-10-25 [1] CRAN (R 4.1.1)
+##  glue          1.6.0   2021-12-17 [1] CRAN (R 4.1.1)
+##  htmltools     0.5.2   2021-08-25 [1] CRAN (R 4.1.1)
+##  htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.1.1)
+##  httr          1.4.2   2020-07-20 [1] CRAN (R 4.1.0)
+##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.1.0)
+##  jsonlite      1.7.2   2020-12-09 [1] CRAN (R 4.1.0)
+##  kableExtra    1.3.4   2021-02-20 [1] CRAN (R 4.1.0)
+##  knitr       * 1.37    2021-12-16 [1] CRAN (R 4.1.1)
+##  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.1)
+##  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.1.0)
+##  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
+##  pillar        1.6.4   2021-10-18 [1] CRAN (R 4.1.1)
+##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
+##  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
+##  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.1)
+##  rlang         0.4.12  2021-10-18 [1] CRAN (R 4.1.1)
+##  rmarkdown     2.11    2021-09-14 [1] CRAN (R 4.1.1)
+##  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.0)
+##  rvest         1.0.2   2021-10-16 [1] CRAN (R 4.1.1)
+##  sass          0.4.0   2021-05-12 [1] CRAN (R 4.1.0)
+##  scales        1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
+##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.1)
+##  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.1)
+##  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
+##  svglite       2.0.0   2021-02-20 [1] CRAN (R 4.1.0)
+##  systemfonts   1.0.3   2021-10-13 [1] CRAN (R 4.1.1)
+##  tibble        3.1.6   2021-11-07 [1] CRAN (R 4.1.1)
+##  tidyr         1.1.4   2021-09-27 [1] CRAN (R 4.1.1)
+##  tidyselect    1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
+##  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
+##  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
+##  viridisLite   0.4.0   2021-04-13 [1] CRAN (R 4.1.0)
+##  webshot       0.5.2   2019-11-22 [1] CRAN (R 4.1.0)
+##  xfun          0.29    2021-12-14 [1] CRAN (R 4.1.1)
+##  xml2          1.3.3   2021-11-30 [1] CRAN (R 4.1.1)
+##  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.1.0)
+## 
+##  [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1
+##  [2] /usr/local/lib/R/site-library
+##  [3] /usr/lib/R/site-library
+##  [4] /usr/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────</code></pre>
+</details>
+<p>Report rendered by wibeasley at 2021-12-31, 16:56 -0600 in 1 seconds.</p>
+</div>
 
 
 
diff --git a/inst/report-templates/rmarkdown-1/report-1.md b/inst/report-templates/rmarkdown-1/report-1.md
index 1c194d4..a227a61 100644
--- a/inst/report-templates/rmarkdown-1/report-1.md
+++ b/inst/report-templates/rmarkdown-1/report-1.md
@@ -1,6 +1,6 @@
 ---
 title: Trawler Report
-date: "Date: 2021-12-31 15:54:07"
+date: "Date: 2021-12-31 16:56:22"
 output:
   html_document:
     keep_md: yes
@@ -164,8 +164,8 @@ Rule Detail
 -----------------------------
 
 ```{=html}
-<div id="htmlwidget-205d91dc155182c9cdb9" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-205d91dc155182c9cdb9">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;baseline prealbumin levels&quot;,&quot;hospitalization reason&quot;,&quot;missing serum marker levels&quot;,&quot;npcr&quot;,&quot;npcr comparison&quot;,&quot;optimal daily protein intake&quot;,&quot;recommended npcr range&quot;,&quot;serum prealbumin levels 1&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"integer\" style=\"vertical-align: top;\">\n    <div 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visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Patient was hospitalized but reason and the date of hospitalization is missing","Patient 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of all enrolled patients do not meet the study criterion","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Relevant nutritional serum markers are missing","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Patient was hospitalized but reason and the date of hospitalization is missing","Patient was hospitalized but reason and the date of hospitalization is missing","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR values are not within the recommended range at completion","NPCR at completion is missing","NPCR at completion is not greater than npcr at baseline","NPCR at completion is not greater than npcr at baseline"],[1,2,3,8,9,12,13,14,15,100,7,10,11,1,2,3,4,5,6,8,9,12,13,14,15,16,100,220,8,14,5,6,7,8,11,15,100,1,6,7,8,12,13,14,16,100,220,10,1,12],["1","2","3","1","3","3","1","1","3","1","2","255","2","1","2","3","255","1","3","1","3","3","1","1","3","2","1","1",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],["2015-01-02","2015-01-02","2015-01-05","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-04-02","2015-01-27","2015-02-13","2015-02-19","2015-01-02","2015-01-02","2015-01-05","2015-01-10","2015-01-13","2015-01-16","2015-02-03","2015-02-08","2015-03-06","2015-03-15","2015-03-10","2015-03-03","2015-03-09","2015-04-02","2015-04-02",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Rule Name<\/th>\n      <th>Priority<\/th>\n      <th>Error Message<\/th>\n      <th>Record ID<\/th>\n      <th>Data Collector<\/th>\n      <th>Baseline Date<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":30,"dom":"tip","columnDefs":[{"className":"dt-center","targets":[5,6]},{"className":"dt-right","targets":[2,4]},{"orderable":false,"targets":0}],"initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'background-color': '#555', 'color': '#fff'});\n}","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[10,25,30,50,100]}},"evals":["options.initComplete"],"jsHooks":[]}</script>
 ```
 
 Inactive Rules
@@ -310,3 +310,95 @@ Inactive Smells
 
 To enable/disable a smell, set the `active` element in the yaml checks file to "true" or "false".
 </div>
+
+Configuration {.tabset .tabset-fade}
+=============================
+
+For the sake of documentation and reproducibility, the current report was rendered in the following environment.  Click the line below to expand.
+
+<details>
+  <summary>Environment <span class="glyphicon glyphicon-plus-sign"></span></summary>
+
+```
+## ─ Session info ───────────────────────────────────────────────────────────────
+##  setting  value
+##  version  R version 4.1.1 (2021-08-10)
+##  os       Ubuntu 21.10
+##  system   x86_64, linux-gnu
+##  ui       X11
+##  language (EN)
+##  collate  en_US.UTF-8
+##  ctype    en_US.UTF-8
+##  tz       America/Chicago
+##  date     2021-12-31
+##  pandoc   2.11.4 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
+## 
+## ─ Packages ───────────────────────────────────────────────────────────────────
+##  package     * version date (UTC) lib source
+##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.1.0)
+##  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.1)
+##  bslib         0.3.1   2021-10-06 [1] CRAN (R 4.1.1)
+##  checkmate     2.0.0   2020-02-06 [1] CRAN (R 4.1.0)
+##  cli           3.1.0   2021-10-27 [1] CRAN (R 4.1.1)
+##  colorspace    2.0-2   2021-06-24 [1] CRAN (R 4.1.0)
+##  crayon        1.4.2   2021-10-29 [1] CRAN (R 4.1.1)
+##  crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.1.1)
+##  DBI           1.1.1   2021-01-15 [1] CRAN (R 4.1.0)
+##  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.1)
+##  dplyr         1.0.7   2021-06-18 [1] CRAN (R 4.1.0)
+##  DT            0.20    2021-11-15 [1] CRAN (R 4.1.1)
+##  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
+##  evaluate      0.14    2019-05-28 [1] CRAN (R 4.1.0)
+##  fansi         0.5.0   2021-05-25 [1] CRAN (R 4.1.0)
+##  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
+##  generics      0.1.1   2021-10-25 [1] CRAN (R 4.1.1)
+##  glue          1.6.0   2021-12-17 [1] CRAN (R 4.1.1)
+##  htmltools     0.5.2   2021-08-25 [1] CRAN (R 4.1.1)
+##  htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.1.1)
+##  httr          1.4.2   2020-07-20 [1] CRAN (R 4.1.0)
+##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.1.0)
+##  jsonlite      1.7.2   2020-12-09 [1] CRAN (R 4.1.0)
+##  kableExtra    1.3.4   2021-02-20 [1] CRAN (R 4.1.0)
+##  knitr       * 1.37    2021-12-16 [1] CRAN (R 4.1.1)
+##  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.1)
+##  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.1.0)
+##  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.1.0)
+##  pillar        1.6.4   2021-10-18 [1] CRAN (R 4.1.1)
+##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.1.0)
+##  purrr         0.3.4   2020-04-17 [1] CRAN (R 4.1.0)
+##  R6            2.5.1   2021-08-19 [1] CRAN (R 4.1.1)
+##  rlang         0.4.12  2021-10-18 [1] CRAN (R 4.1.1)
+##  rmarkdown     2.11    2021-09-14 [1] CRAN (R 4.1.1)
+##  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.0)
+##  rvest         1.0.2   2021-10-16 [1] CRAN (R 4.1.1)
+##  sass          0.4.0   2021-05-12 [1] CRAN (R 4.1.0)
+##  scales        1.1.1   2020-05-11 [1] CRAN (R 4.1.0)
+##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.1.1)
+##  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.1)
+##  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.0)
+##  svglite       2.0.0   2021-02-20 [1] CRAN (R 4.1.0)
+##  systemfonts   1.0.3   2021-10-13 [1] CRAN (R 4.1.1)
+##  tibble        3.1.6   2021-11-07 [1] CRAN (R 4.1.1)
+##  tidyr         1.1.4   2021-09-27 [1] CRAN (R 4.1.1)
+##  tidyselect    1.1.1   2021-04-30 [1] CRAN (R 4.1.0)
+##  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
+##  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
+##  viridisLite   0.4.0   2021-04-13 [1] CRAN (R 4.1.0)
+##  webshot       0.5.2   2019-11-22 [1] CRAN (R 4.1.0)
+##  xfun          0.29    2021-12-14 [1] CRAN (R 4.1.1)
+##  xml2          1.3.3   2021-11-30 [1] CRAN (R 4.1.1)
+##  yaml          2.2.1   2020-02-01 [1] CRAN (R 4.1.0)
+## 
+##  [1] /home/wibeasley/R/x86_64-pc-linux-gnu-library/4.1
+##  [2] /usr/local/lib/R/site-library
+##  [3] /usr/lib/R/site-library
+##  [4] /usr/lib/R/library
+## 
+## ──────────────────────────────────────────────────────────────────────────────
+```
+</details>
+
+
+
+Report rendered by wibeasley at 2021-12-31, 16:56 -0600 in 1 seconds.
+