From 74ae0e87dc6a962e405b7772f43649f393ee3995 Mon Sep 17 00:00:00 2001
From: mattkorb <123395522+mattkorb@users.noreply.github.com>
Date: Mon, 19 Aug 2024 12:13:10 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Boehring?=
 =?UTF-8?q?er-Ingelheim/dv.edish@8430d03485710373a19aa4b744f0d10a0fbed8ab?=
 =?UTF-8?q?=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                            |  2 +-
 LICENSE-text.html                   |  2 +-
 articles/disp.html                  |  2 +-
 articles/index.html                 |  2 +-
 articles/qc.html                    | 38 ++++++++++++++---------------
 authors.html                        |  6 ++---
 index.html                          |  2 +-
 news/index.html                     |  5 +++-
 pkgdown.yml                         |  2 +-
 reference/derive_req_vars.html      |  2 +-
 reference/edish_UI.html             |  2 +-
 reference/edish_server.html         |  2 +-
 reference/filter_data.html          |  2 +-
 reference/generate_plot.html        |  2 +-
 reference/index.html                |  2 +-
 reference/mock_edish_app.html       |  2 +-
 reference/mock_edish_mm.html        |  2 +-
 reference/mod_edish.html            |  2 +-
 reference/pack_of_constants.html    |  2 +-
 reference/pipe.html                 |  2 +-
 reference/prepare_initial_data.html |  2 +-
 search.json                         |  2 +-
 22 files changed, 45 insertions(+), 42 deletions(-)

diff --git a/404.html b/404.html
index 7422fda..677c361 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 923e9dd..f6538ae 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/disp.html b/articles/disp.html
index 8adcb4e..790346d 100644
--- a/articles/disp.html
+++ b/articles/disp.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 6137255..a521a00 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/qc.html b/articles/qc.html
index b64ebb8..54d912b 100644
--- a/articles/qc.html
+++ b/articles/qc.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -92,9 +92,9 @@
 }
 </style>
 <div class="section level3">
-<h3 id="dv-edish-1-0-3">✅ dv.edish 1.0.3<a class="anchor" aria-label="anchor" href="#dv-edish-1-0-3"></a>
+<h3 id="dv-edish-1-0-4">✅ dv.edish 1.0.4<a class="anchor" aria-label="anchor" href="#dv-edish-1-0-4"></a>
 </h3>
-<p>Date: 2024-Jul-05 08:12:19</p>
+<p>Date: 2024-Aug-19 12:13:03</p>
 <p>The following document generates a report for R packages, to satisfy the criteria of a “Released” status under the <strong>Non-GxP</strong> project. The QC report contains the following information:</p>
 <ul>
 <li>
@@ -123,39 +123,39 @@ <h2 id="traceability-matrix">Traceability matrix<a class="anchor" aria-label="an
 <div class="section level3">
 <h3 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-f2f6518d3c716184e004" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-f2f6518d3c716184e004">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/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=\"0\" data-max=\"18\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["Yes","Yes","Yes","Yes","No"],["Pass","Failed","Skipped","No Test","NA"],[18,0,0,0,0],["white","green","green","green","green"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Spec.Exists<\/th>\n      <th>Test<\/th>\n      <th>Count<\/th>\n      <th>color<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"visible":false,"targets":3},{"className":"dt-right","targets":2},{"name":"Spec.Exists","targets":0},{"name":"Test","targets":1},{"name":"Count","targets":2},{"name":"color","targets":3}],"dom":"tp","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"rowCallback":"function(row, data, displayNum, displayIndex, dataIndex) {\nvar value=data[3]; $(this.api().cell(row, 2).node()).css({'background-color':value});\n}"},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-3713995158077c0b1330" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-3713995158077c0b1330">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/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=\"0\" data-max=\"18\"><\/div>\n      <span style=\"float: left;\"><\/span>\n      <span style=\"float: right;\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["Yes","Yes","Yes","Yes","No"],["Pass","Failed","Skipped","No Test","NA"],[18,0,0,0,0],["white","green","green","green","green"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Spec.Exists<\/th>\n      <th>Test<\/th>\n      <th>Count<\/th>\n      <th>color<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"columnDefs":[{"visible":false,"targets":3},{"className":"dt-right","targets":2},{"name":"Spec.Exists","targets":0},{"name":"Test","targets":1},{"name":"Count","targets":2},{"name":"color","targets":3}],"dom":"tp","order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"rowCallback":"function(row, data, displayNum, displayIndex, dataIndex) {\nvar value=data[3]; $(this.api().cell(row, 2).node()).css({'background-color':value});\n}"},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
 </div>
 <div class="section level3">
 <h3 id="passed-tests">Passed tests<a class="anchor" aria-label="anchor" href="#passed-tests"></a>
 </h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-9d36eb1da1fc90e19a75" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-9d36eb1da1fc90e19a75">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["19","16","6","7","2","14","12","1","8","9","11","17","15","4","3","10","5","13"],["framework_specs$bookmarking","input_menu_specs$default_vals$arm\ninput_menu_specs$default_vals$param","plot_specs$arm","plot_specs$arm\nplot_specs$param","plot_specs$arm\nplot_specs$param\nplot_specs$normalization","plot_specs$arm_coloring","plot_specs$axis_labels","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$hovering","plot_specs$multiple_vals","plot_specs$normalization","plot_specs$normalization","plot_specs$param","plot_specs$ref_lines"],["The app's state gets restored correctly after bookmarking.","The input menu shows the pre-specified arm values at app launch.\nThe input menu shows the pre-specified parameter values at app launch.","The plot displays data only of subjects corresponding to the selected arm(s).","The plot displays data only of subjects corresponding to the selected arm(s).\nThe plot displays data according to the parameter selection.","The plot displays data only of subjects corresponding to the selected arm(s).\nThe plot displays data according to the parameter selection.\nThe plot displays data normalized according to the selected method.","The plot shows data coloring according to arm information.","The plot's axis are labelled according to the parameter selection and normalization method.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot shows details when hovering over a data point.","In case of multiple values per subject, visit, and lab test, only the maximum value should be shown.","The plot displays data normalized according to the selected method.","The plot displays data normalized according to the selected method.","The plot displays data according to the parameter selection.","The plot displays the specified reference lines."],["(#19): the app's state is restored when bookmarking__spec_ids{framework_specs$bookmarking}","(#16): the default values are correct at app launch__spec_ids{input_menu_specs$default_vals$arm;input_menu_specs$default_vals$param}","(#6): the resulting dataset contains only data corresponding to the desired arms__spec_ids{plot_specs$arm}","(#7): the resulting dataset contains only data corresponding to the desired arms and lab tests__spec_ids{plot_specs$arm;plot_specs$param}","(#2): the kept variables are taken over correctly__spec_ids{plot_specs$arm;plot_specs$param;plot_specs$normalization}","(#14): the resulting plot object includes the correct coloring__spec_ids{plot_specs$arm_coloring}","(#12): the resulting plot object includes the correct axis labels__spec_ids{plot_specs$axis_labels}","(#1): the function returns a single dataset with the expected variables__spec_ids{plot_specs$data}","(#8): the function returns a single dataset with the expected variables__spec_ids{plot_specs$data}","(#9): the kept variables are taken over correctly__spec_ids{plot_specs$data}","(#11): the resulting plot object includes the correct data__spec_ids{plot_specs$data}","(#17): the app displays the correct plot at app launch (snapshot test)__spec_ids{plot_specs$data}","(#15): the resulting plot object includes the correct hovertext (snapshot test)__spec_ids{plot_specs$hovering}","(#4): the maximum values are used in case of multiple values__spec_ids{plot_specs$multiple_vals}","(#3): the new BASE variable contains the correct baseline values__spec_ids{plot_specs$normalization}","(#10): the new variables contain the correct normalized values__spec_ids{plot_specs$normalization}","(#5): the resulting dataset contains only data corresponding to the desired lab tests__spec_ids{plot_specs$param}","(#13): the resulting plot object includes the correct reference lines__spec_ids{plot_specs$ref_lines}"],["test-05-mod_edish.R","test-05-mod_edish.R","test-02-filter_data.R","test-02-filter_data.R","test-01-prepare_initial_data.R","test-04-generate_plot.R","test-04-generate_plot.R","test-01-prepare_initial_data.R","test-03-derive_req_vars.R","test-03-derive_req_vars.R","test-04-generate_plot.R","test-05-mod_edish.R","test-04-generate_plot.R","test-01-prepare_initial_data.R","test-01-prepare_initial_data.R","test-03-derive_req_vars.R","test-02-filter_data.R","test-04-generate_plot.R"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-fe99239e115dd452ef4b" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-fe99239e115dd452ef4b">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["19","16","6","7","2","14","12","1","8","9","11","17","15","4","3","10","5","13"],["framework_specs$bookmarking","input_menu_specs$default_vals$arm\ninput_menu_specs$default_vals$param","plot_specs$arm","plot_specs$arm\nplot_specs$param","plot_specs$arm\nplot_specs$param\nplot_specs$normalization","plot_specs$arm_coloring","plot_specs$axis_labels","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$data","plot_specs$hovering","plot_specs$multiple_vals","plot_specs$normalization","plot_specs$normalization","plot_specs$param","plot_specs$ref_lines"],["The app's state gets restored correctly after bookmarking.","The input menu shows the pre-specified arm values at app launch.\nThe input menu shows the pre-specified parameter values at app launch.","The plot displays data only of subjects corresponding to the selected arm(s).","The plot displays data only of subjects corresponding to the selected arm(s).\nThe plot displays data according to the parameter selection.","The plot displays data only of subjects corresponding to the selected arm(s).\nThe plot displays data according to the parameter selection.\nThe plot displays data normalized according to the selected method.","The plot shows data coloring according to arm information.","The plot's axis are labelled according to the parameter selection and normalization method.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot displays the underlying data.","The plot shows details when hovering over a data point.","In case of multiple values per subject, visit, and lab test, only the maximum value should be shown.","The plot displays data normalized according to the selected method.","The plot displays data normalized according to the selected method.","The plot displays data according to the parameter selection.","The plot displays the specified reference lines."],["(#19): the app's state is restored when bookmarking__spec_ids{framework_specs$bookmarking}","(#16): the default values are correct at app launch__spec_ids{input_menu_specs$default_vals$arm;input_menu_specs$default_vals$param}","(#6): the resulting dataset contains only data corresponding to the desired arms__spec_ids{plot_specs$arm}","(#7): the resulting dataset contains only data corresponding to the desired arms and lab tests__spec_ids{plot_specs$arm;plot_specs$param}","(#2): the kept variables are taken over correctly__spec_ids{plot_specs$arm;plot_specs$param;plot_specs$normalization}","(#14): the resulting plot object includes the correct coloring__spec_ids{plot_specs$arm_coloring}","(#12): the resulting plot object includes the correct axis labels__spec_ids{plot_specs$axis_labels}","(#1): the function returns a single dataset with the expected variables__spec_ids{plot_specs$data}","(#8): the function returns a single dataset with the expected variables__spec_ids{plot_specs$data}","(#9): the kept variables are taken over correctly__spec_ids{plot_specs$data}","(#11): the resulting plot object includes the correct data__spec_ids{plot_specs$data}","(#17): the app displays the correct plot at app launch (snapshot test)__spec_ids{plot_specs$data}","(#15): the resulting plot object includes the correct hovertext (snapshot test)__spec_ids{plot_specs$hovering}","(#4): the maximum values are used in case of multiple values__spec_ids{plot_specs$multiple_vals}","(#3): the new BASE variable contains the correct baseline values__spec_ids{plot_specs$normalization}","(#10): the new variables contain the correct normalized values__spec_ids{plot_specs$normalization}","(#5): the resulting dataset contains only data corresponding to the desired lab tests__spec_ids{plot_specs$param}","(#13): the resulting plot object includes the correct reference lines__spec_ids{plot_specs$ref_lines}"],["test-05-mod_edish.R","test-05-mod_edish.R","test-02-filter_data.R","test-02-filter_data.R","test-01-prepare_initial_data.R","test-04-generate_plot.R","test-04-generate_plot.R","test-01-prepare_initial_data.R","test-03-derive_req_vars.R","test-03-derive_req_vars.R","test-04-generate_plot.R","test-05-mod_edish.R","test-04-generate_plot.R","test-01-prepare_initial_data.R","test-01-prepare_initial_data.R","test-03-derive_req_vars.R","test-02-filter_data.R","test-04-generate_plot.R"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level3">
 <h3 id="failed-tests">Failed tests<a class="anchor" aria-label="anchor" href="#failed-tests"></a>
 </h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-65e11060615a80707497" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-65e11060615a80707497">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-ff27d859386ac9db92b9" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-ff27d859386ac9db92b9">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level3">
 <h3 id="skipped-tests">Skipped tests<a class="anchor" aria-label="anchor" href="#skipped-tests"></a>
 </h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-0f941c1652ff200d5809" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-0f941c1652ff200d5809">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-9965997c3f77eff5b29d" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-9965997c3f77eff5b29d">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level3">
 <h3 id="uncovered-specifications">Uncovered specifications<a class="anchor" aria-label="anchor" href="#uncovered-specifications"></a>
 </h3>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-2371e744532b72338cb1" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-2371e744532b72338cb1">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Uncovered.Specifications<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Uncovered.Specifications","targets":1}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-469b1253e46351799b3f" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-469b1253e46351799b3f">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Uncovered.Specifications<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Uncovered.Specifications","targets":1}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
 <div class="section level3">
 <h3 id="undeclared-specifications">Undeclared specifications<a class="anchor" aria-label="anchor" href="#undeclared-specifications"></a>
 </h3>
 <p>This should always be empty, as non existant specs are controlled during test execution.</p>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-49ec56462a4b89c0f7a9" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-49ec56462a4b89c0f7a9">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-e52c00747b62609934dd" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-e52c00747b62609934dd">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" 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%;\" disabled=\"\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","data":[[],[],[],[],[]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>Spec ID<\/th>\n      <th>Spec<\/th>\n      <th>Test Desc<\/th>\n      <th>File<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"orderable":false,"targets":0},{"name":" ","targets":0},{"name":"Spec ID","targets":1},{"name":"Spec","targets":2},{"name":"Test Desc","targets":3},{"name":"File","targets":4}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
 </div>
 <div class="section level2">
@@ -171,7 +171,7 @@ <h2 id="session-info-and-system-configuration">Session Info and System Configura
 <span><span class="co">#&gt;  collate  en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  ctype    en_US.UTF-8</span></span>
 <span><span class="co">#&gt;  tz       Etc/UTC</span></span>
-<span><span class="co">#&gt;  date     2024-07-05</span></span>
+<span><span class="co">#&gt;  date     2024-08-19</span></span>
 <span><span class="co">#&gt;  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB; font-weight: bold;">─ Packages ───────────────────────────────────────────────────────────────────</span></span></span>
@@ -227,7 +227,7 @@ <h2 id="session-info-and-system-configuration">Session Info and System Configura
 <span><span class="co">#&gt;  xtable        1.8-4   <span style="color: #555555;">2019-04-21</span> <span style="color: #555555;">[2]</span> <span style="color: #BB00BB; font-weight: bold;">RSPM</span></span></span>
 <span><span class="co">#&gt;  yaml          2.3.8   <span style="color: #555555;">2023-12-11</span> <span style="color: #555555;">[2]</span> <span style="color: #BB00BB; font-weight: bold;">RSPM</span></span></span>
 <span><span class="co">#&gt; </span></span>
-<span><span class="co">#&gt; <span style="color: #555555;"> [1] /tmp/RtmpX3dbvK/temp_libpath376e1a1382</span></span></span>
+<span><span class="co">#&gt; <span style="color: #555555;"> [1] /tmp/RtmpcdDNtt/temp_libpath3936afad658</span></span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [2] /usr/local/lib/R/site-library</span></span></span>
 <span><span class="co">#&gt; <span style="color: #555555;"> [3] /usr/local/lib/R/library</span></span></span>
 <span><span class="co">#&gt; </span></span>
@@ -236,8 +236,8 @@ <h2 id="session-info-and-system-configuration">Session Info and System Configura
 <div class="section level2">
 <h2 id="list-of-specifications">List of specifications<a class="anchor" aria-label="anchor" href="#list-of-specifications"></a>
 </h2>
-<div class="datatables html-widget html-fill-item" id="htmlwidget-3e5ea53521bdbdba3969" style="width:100%;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-3e5ea53521bdbdba3969">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["input_menu_specs$default_vals$arm","input_menu_specs$default_vals$param","plot_specs$data","plot_specs$arm","plot_specs$arm_coloring","plot_specs$param","plot_specs$normalization","plot_specs$axis_labels","plot_specs$ref_lines","plot_specs$hovering","plot_specs$multiple_vals","framework_specs$bookmarking"],["The input menu shows the pre-specified arm values at app launch.","The input menu shows the pre-specified parameter values at app launch.","The plot displays the underlying data.","The plot displays data only of subjects corresponding to the selected arm(s).","The plot shows data coloring according to arm information.","The plot displays data according to the parameter selection.","The plot displays data normalized according to the selected method.","The plot's axis are labelled according to the parameter selection and normalization method.","The plot displays the specified reference lines.","The plot shows details when hovering over a data point.","In case of multiple values per subject, visit, and lab test, only the maximum value should be shown.","The app's state gets restored correctly after bookmarking."]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>spec_id<\/th>\n      <th>spec<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"name":"spec_id","targets":0},{"name":"spec","targets":1}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
+<div class="datatables html-widget html-fill-item" id="htmlwidget-824b220e06faff8fc984" style="width:100%;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-824b220e06faff8fc984">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td data-type=\"character\" 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  <\/td>\n  <td data-type=\"character\" 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  <\/td>\n<\/tr>","data":[["input_menu_specs$default_vals$arm","input_menu_specs$default_vals$param","plot_specs$data","plot_specs$arm","plot_specs$arm_coloring","plot_specs$param","plot_specs$normalization","plot_specs$axis_labels","plot_specs$ref_lines","plot_specs$hovering","plot_specs$multiple_vals","framework_specs$bookmarking"],["The input menu shows the pre-specified arm values at app launch.","The input menu shows the pre-specified parameter values at app launch.","The plot displays the underlying data.","The plot displays data only of subjects corresponding to the selected arm(s).","The plot shows data coloring according to arm information.","The plot displays data according to the parameter selection.","The plot displays data normalized according to the selected method.","The plot's axis are labelled according to the parameter selection and normalization method.","The plot displays the specified reference lines.","The plot shows details when hovering over a data point.","In case of multiple values per subject, visit, and lab test, only the maximum value should be shown.","The app's state gets restored correctly after bookmarking."]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>spec_id<\/th>\n      <th>spec<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"dom":"ltp","columnDefs":[{"name":"spec_id","targets":0},{"name":"spec","targets":1}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true},"selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":[],"jsHooks":[]}</script>
 </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside>
diff --git a/authors.html b/authors.html
index e2575a7..1146d19 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,13 +63,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Glauss I (2024).
 <em>dv.edish: eDISH Plot Module for DILI assessment</em>.
-R package version 1.0.3. 
+R package version 1.0.4. 
 </p>
       <pre>@Manual{,
   title = {dv.edish: eDISH Plot Module for DILI assessment},
   author = {Isabel Glauss},
   year = {2024},
-  note = {R package version 1.0.3},
+  note = {R package version 1.0.4},
 }</pre>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/index.html b/index.html
index 7266697..43696c0 100644
--- a/index.html
+++ b/index.html
@@ -28,7 +28,7 @@
     
     <a class="navbar-brand me-2" href="index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index fd97683..2d4a3f4 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,6 +45,9 @@
       
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="1.0.4" id="dvedish-104">dv.edish 1.0.4<a class="anchor" aria-label="anchor" href="#dvedish-104"></a></h2>
+<ul><li>The module ignores now NA values when calculating the maximum value.</li></ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.0.3" id="dvedish-103">dv.edish 1.0.3<a class="anchor" aria-label="anchor" href="#dvedish-103"></a></h2>
 <ul><li>Initial release of dv.edish package to GitHub.</li></ul></div>
diff --git a/pkgdown.yml b/pkgdown.yml
index ebc5e3c..1b06400 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   disp: disp.html
   qc: qc.html
-last_built: 2024-07-05T08:12Z
+last_built: 2024-08-19T12:12Z
 
diff --git a/reference/derive_req_vars.html b/reference/derive_req_vars.html
index 8e02567..13d7d9b 100644
--- a/reference/derive_req_vars.html
+++ b/reference/derive_req_vars.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/edish_UI.html b/reference/edish_UI.html
index 575a2e8..2836c17 100644
--- a/reference/edish_UI.html
+++ b/reference/edish_UI.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/edish_server.html b/reference/edish_server.html
index a656cf5..304ca72 100644
--- a/reference/edish_server.html
+++ b/reference/edish_server.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/filter_data.html b/reference/filter_data.html
index 9d11ea4..645dd9c 100644
--- a/reference/filter_data.html
+++ b/reference/filter_data.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/generate_plot.html b/reference/generate_plot.html
index 6fc57ab..cafd43a 100644
--- a/reference/generate_plot.html
+++ b/reference/generate_plot.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 22b2d56..38f981a 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mock_edish_app.html b/reference/mock_edish_app.html
index 8ac051c..6bad1f9 100644
--- a/reference/mock_edish_app.html
+++ b/reference/mock_edish_app.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mock_edish_mm.html b/reference/mock_edish_mm.html
index 9c0d847..ec5484c 100644
--- a/reference/mock_edish_mm.html
+++ b/reference/mock_edish_mm.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mod_edish.html b/reference/mod_edish.html
index da4372f..3175aae 100644
--- a/reference/mod_edish.html
+++ b/reference/mod_edish.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pack_of_constants.html b/reference/pack_of_constants.html
index e1bfe88..64ccf8d 100644
--- a/reference/pack_of_constants.html
+++ b/reference/pack_of_constants.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pipe.html b/reference/pipe.html
index 0f4ffe9..421da59 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/prepare_initial_data.html b/reference/prepare_initial_data.html
index ebffb54..d184b31 100644
--- a/reference/prepare_initial_data.html
+++ b/reference/prepare_initial_data.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">dv.edish</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.3</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.4</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index ee66a75..e027a82 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"/articles/disp.html","id":"how-to-set-up-an-edish-module-using-dispatchers","dir":"Articles","previous_headings":"","what":"How to set up an eDISH module using dispatchers","title":"Usage of {dv.manager} dispatchers","text":"Dispatchers helper functions allow accessing data utility functions inside module manager dynamic way. Refer ?dv.manager::mm_dispatch information functionalities. , can find two examples can used set eDISH module. Note possible use arguments, dataset_names dataset_disp, time mod_edish() call.","code":""},{"path":"/articles/disp.html","id":"a--filtered-data","dir":"Articles","previous_headings":"How to set up an eDISH module using dispatchers","what":"a. Filtered data","title":"Usage of {dv.manager} dispatchers","text":"code piece produces essentially app behavior using dataset_names argument. , selection made user global filter menu affects module display.","code":"mod_edish(   module_id = \"edish_a\",   dataset_disp = dv.manager::mm_dispatch(     from = \"filtered_dataset\",     selection = c(\"dm\", \"lb\")   ) )"},{"path":"/articles/disp.html","id":"b--unfiltered-data","dir":"Articles","previous_headings":"How to set up an eDISH module using dispatchers","what":"b. Unfiltered data","title":"Usage of {dv.manager} dispatchers","text":"case undesirable global filter settings affect listings displayed eDISH module, possible define dispatcher delivers always unfiltered data. means global filter ignored!","code":"mod_edish(   module_id = \"edish_b\",   dataset_disp = dv.manager::mm_dispatch(     from = \"unfiltered_dataset\",     selection = c(\"dm\", \"lb\")   ) )"},{"path":"/articles/qc.html","id":"dv-edish-1-0-3","dir":"Articles","previous_headings":"","what":"✅ dv.edish 1.0.3","title":"Quality Control","text":"Date: 2024-Jul-05 08:12:19 following document generates report R packages, satisfy criteria “Released” status Non-GxP project. QC report contains following information: Specifications (specs): can attached every test user adds. Traceability matrix: Contains test cases passed, failed, skipped expectations. Uncovered undeclared specs Session Info System Configuration Please advised QC report generated module imply validation according GxP criteria. QC report satisfies internally developed quality checks non-GxP criteria. clinical reporting purposes, essential note outputs generated using module must checked verified within validated system adheres appropriate GxP guidelines.","code":""},{"path":"/articles/qc.html","id":"traceability-matrix","dir":"Articles","previous_headings":"","what":"Traceability matrix","title":"Quality Control","text":"traceability matrix tests point specification included. Test cases can contain several expectations test considered: passed expectations test pass. failed least one expectation test fails. skipped least one expectation test skipped. test can failed skipped.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"/articles/qc.html","id":"undeclared-specifications","dir":"Articles","previous_headings":"Traceability matrix","what":"Undeclared specifications","title":"Quality Control","text":"always empty, non existant specs controlled test execution.","code":""},{"path":"/articles/qc.html","id":"session-info-and-system-configuration","dir":"Articles","previous_headings":"","what":"Session Info and System Configuration","title":"Quality Control","text":"","code":"#> ─ Session info ─────────────────────────────────────────────────────────────── #>  setting  value #>  version  R version 4.3.2 (2023-10-31) #>  os       Ubuntu 22.04.4 LTS #>  system   x86_64, linux-gnu #>  ui       X11 #>  language en #>  collate  en_US.UTF-8 #>  ctype    en_US.UTF-8 #>  tz       Etc/UTC #>  date     2024-07-05 #>  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown) #>  #> ─ Packages ─────────────────────────────────────────────────────────────────── #>  package     * version date (UTC) lib source #>  bslib         0.6.1   2023-11-28 [2] RSPM #>  cachem        1.0.8   2023-05-01 [2] RSPM #>  cli           3.6.2   2023-12-11 [2] RSPM #>  crosstalk     1.2.1   2023-11-23 [2] RSPM #>  desc          1.4.3   2023-12-10 [2] RSPM #>  devtools      2.4.5   2022-10-11 [2] RSPM #>  digest        0.6.34  2024-01-11 [2] RSPM #>  DT            0.31    2023-12-09 [2] RSPM #>  ellipsis      0.3.2   2021-04-29 [2] RSPM #>  evaluate      0.23    2023-11-01 [2] RSPM #>  fastmap       1.1.1   2023-02-24 [2] RSPM #>  fs            1.6.3   2023-07-20 [2] RSPM #>  glue          1.7.0   2024-01-09 [2] RSPM #>  htmltools     0.5.7   2023-11-03 [2] RSPM #>  htmlwidgets   1.6.4   2023-12-06 [2] RSPM #>  httpuv        1.6.13  2023-12-06 [2] RSPM #>  jquerylib     0.1.4   2021-04-26 [2] RSPM #>  jsonlite      1.8.8   2023-12-04 [2] RSPM #>  knitr         1.45    2023-10-30 [2] RSPM #>  later         1.3.2   2023-12-06 [2] RSPM #>  lifecycle     1.0.4   2023-11-07 [2] RSPM #>  magrittr      2.0.3   2022-03-30 [2] RSPM #>  memoise       2.0.1   2021-11-26 [2] RSPM #>  mime          0.12    2021-09-28 [2] RSPM #>  miniUI        0.1.1.1 2018-05-18 [2] RSPM #>  pkgbuild      1.4.3   2023-12-10 [2] RSPM #>  pkgdown       2.0.7   2022-12-14 [2] RSPM #>  pkgload       1.3.3   2023-09-22 [2] RSPM #>  profvis       0.3.8   2023-05-02 [2] RSPM #>  promises      1.2.1   2023-08-10 [2] RSPM #>  purrr         1.0.2   2023-08-10 [2] RSPM #>  R6            2.5.1   2021-08-19 [2] RSPM #>  ragg          1.2.7   2023-12-11 [2] RSPM #>  Rcpp          1.0.12  2024-01-09 [2] RSPM #>  remotes       2.4.2.1 2023-07-18 [2] RSPM #>  rlang         1.1.3   2024-01-10 [2] RSPM #>  rmarkdown     2.25    2023-09-18 [2] RSPM #>  sass          0.4.8   2023-12-06 [2] RSPM #>  sessioninfo   1.2.2   2021-12-06 [2] RSPM #>  shiny         1.8.0   2023-11-17 [2] RSPM #>  stringi       1.8.3   2023-12-11 [2] RSPM #>  stringr       1.5.1   2023-11-14 [2] RSPM #>  systemfonts   1.0.5   2023-10-09 [2] RSPM #>  textshaping   0.3.7   2023-10-09 [2] RSPM #>  urlchecker    1.0.1   2021-11-30 [2] RSPM #>  usethis       2.2.2   2023-07-06 [2] RSPM #>  vctrs         0.6.5   2023-12-01 [2] RSPM #>  xfun          0.41    2023-11-01 [2] RSPM #>  xtable        1.8-4   2019-04-21 [2] RSPM #>  yaml          2.3.8   2023-12-11 [2] RSPM #>  #>  [1] /tmp/RtmpX3dbvK/temp_libpath376e1a1382 #>  [2] /usr/local/lib/R/site-library #>  [3] /usr/local/lib/R/library #>  #> ──────────────────────────────────────────────────────────────────────────────"},{"path":[]},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Boehringer-Ingelheim Pharma GmbH & Co.KG. Copyright holder, funder. Isabel Glauss. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Glauss (2024). dv.edish: eDISH Plot Module DILI assessment. R package version 1.0.3.","code":"@Manual{,   title = {dv.edish: eDISH Plot Module for DILI assessment},   author = {Isabel Glauss},   year = {2024},   note = {R package version 1.0.3}, }"},{"path":"/index.html","id":"edish-module","dir":"","previous_headings":"","what":"dv.edish","title":"dv.edish","text":"{dv.edish} package meant support assessment drug-induced liver injury means (modified) evaluation Drug-Induced Serious Hepatotoxicity plot.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dv.edish","text":"","code":"if (!require(\"remotes\")) install.packages(\"remotes\") remotes::install_github(\"Boehringer-Ingelheim/dv.edish\")"},{"path":"/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"dv.edish","text":"eDISH module shows scatter plot depicting correlations two lab parameters subject-level. parameter displayed axis can selected app user. Moreover, parameters can displayed multiples either upper limit normals (resulting eDISH plot) corresponding subject’s baseline values (resulting mDISH plot). Horizontal vertical lines indicating Hy’s law customizable well within input menu.","code":""},{"path":"/index.html","id":"creating-an-edish-application","dir":"","previous_headings":"","what":"Creating an eDISH application","title":"dv.edish","text":"following example shows set simple DaVinci app means {dv.manager}. app contains eDISH module display dummy data provided {pharmaverseadam} package: Note module expects two datasets: Demographics dataset (e.g. dm adsl) including, least, variables containing following information: Unique subject identifier (e.g. USUBJID) Arm (e.g. ACTARM) Laboratory Test Results dataset (e.g. lb adlb) including, least, variables containing following information: Unique subject identifier (e.g. USUBJID) Visit (e.g. VISIT) Lab test result name (e.g. LBTEST) Numeric lab test result (e.g. LBSTRESN) Lab test reference range upper limit (e.g. LBSTNRHI)","code":"dm <- pharmaverseadam::adsl lb <- pharmaverseadam::adlb    module_list <- list(   \"edish\" = dv.edish::mod_edish(     module_id = \"edish\",     dataset_names = c(\"dm\", \"lb\"),     arm_default_vals = c(\"Xanomeline Low Dose\", \"Xanomeline High Dose\"),     baseline_visit_val = \"SCREENING 1\"   ) )  dv.manager::run_app(   data = list(\"demo\" = list(\"dm\" = dm, \"lb\" = lb)),   module_list = module_list,   filter_data = \"dm\" )"},{"path":"/reference/derive_req_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive required variables — derive_req_vars","title":"Derive required variables — derive_req_vars","text":"derive_req_vars() restructures stated dataset include variables containing ratio lab result divided ULN baseline value. corresponding variable names shaped follows: \"r__.","code":""},{"path":"/reference/derive_req_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive required variables — derive_req_vars","text":"","code":"derive_req_vars(   dataset,   subjectid_var,   arm_var,   visit_var,   lb_test_var,   lb_result_var,   ref_range_upper_lim_var,   sel_x,   sel_y )"},{"path":"/reference/derive_req_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive required variables — derive_req_vars","text":"dataset [data.frame] dataframe containing variables listed columns. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. lb_test_var [character(1)] Name variable containing laboratory test information. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits. sel_x [character(1)] Character specifying laboratory test selected x-axis. sel_y [character(1)] Character specifying laboratory test selected y-axis.","code":""},{"path":"/reference/derive_req_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derive required variables — derive_req_vars","text":"restructured dataset.","code":""},{"path":"/reference/edish_UI.html","id":null,"dir":"Reference","previous_headings":"","what":"User Interface of the dv.edish module — edish_UI","title":"User Interface of the dv.edish module — edish_UI","text":"edish_UI() contains UI dv.edish module.","code":""},{"path":"/reference/edish_UI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User Interface of the dv.edish module — edish_UI","text":"","code":"edish_UI(module_id)"},{"path":"/reference/edish_UI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User Interface of the dv.edish module — edish_UI","text":"module_id [character(1)] unique ID string create namespace. Must match ID edish_server().","code":""},{"path":"/reference/edish_UI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User Interface of the dv.edish module — edish_UI","text":"shiny uiOutput element.","code":""},{"path":[]},{"path":"/reference/edish_server.html","id":null,"dir":"Reference","previous_headings":"","what":"Server of the dv.edish module — edish_server","title":"Server of the dv.edish module — edish_server","text":"edish_server() contains server dv.edish module.","code":""},{"path":"/reference/edish_server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server of the dv.edish module — edish_server","text":"","code":"edish_server(   module_id,   dataset_list,   subjectid_var = \"USUBJID\",   arm_var = \"ACTARM\",   arm_default_vals = NULL,   visit_var = \"VISIT\",   baseline_visit_val = \"VISIT 01\",   lb_test_var = \"LBTEST\",   lb_test_choices = c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\",     \"Aspartate Aminotransferase\", \"Bilirubin\"),   lb_test_default_x_val = \"Aspartate Aminotransferase\",   lb_test_default_y_val = \"Bilirubin\",   lb_result_var = \"LBSTRESN\",   ref_range_upper_lim_var = \"LBSTNRHI\" )"},{"path":"/reference/edish_server.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server of the dv.edish module — edish_server","text":"module_id [character(1)] unique ID string create namespace. Must match ID edish_UI(). dataset_list [shiny::reactive(list(data.frame))] reactive list named datasets. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. arm_default_vals [character(1+)] Vector specifying default value(s) arm selector. visit_var [character(1)] Name variable containing visit information. baseline_visit_val [character(1)] Character indicating visit used baseline visit. lb_test_var [character(1)] Name variable containing laboratory test information. lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. lb_test_default_x_val [character(1)] Character specifying default laboratory test choice plot's x-axis. lb_test_default_y_val [character(1)] Character specifying default laboratory test choice plot's y-axis. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits.","code":""},{"path":[]},{"path":"/reference/filter_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter data — filter_data","title":"Filter data — filter_data","text":"filter_data() filters dataset contain values sel_lb_test lb_test_var column values sel_arm arm_var column.","code":""},{"path":"/reference/filter_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter data — filter_data","text":"","code":"filter_data(dataset, arm_var, sel_arm, lb_test_var, sel_lb_test)"},{"path":"/reference/filter_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter data — filter_data","text":"dataset [data.frame] dataframe containing columns specified lb_test_var arm_var. arm_var [character(1)] Name variable containing arm/treatment information. sel_arm [character(1+)] Character vector specifying selection arms/treatments. lb_test_var [character(1)] Name variable containing laboratory test information. sel_lb_test [character(1+)] Character vector specifying selection laboratory tests.","code":""},{"path":"/reference/filter_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter data — filter_data","text":"filtered dataset.","code":""},{"path":"/reference/generate_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate plot — generate_plot","title":"Generate plot — generate_plot","text":"generate_plot() generates eDISH plot means plotly package.","code":""},{"path":"/reference/generate_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate plot — generate_plot","text":"","code":"generate_plot(   dataset,   subjectid_var,   arm_var,   visit_var,   sel_x,   sel_y,   x_plot_type,   y_plot_type,   x_ref_line_num,   y_ref_line_num )"},{"path":"/reference/generate_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate plot — generate_plot","text":"dataset [data.frame] dataframe containing variables listed columns. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. sel_x [character(1)] Character specifying laboratory test displayed x-axis. sel_y [character(1)] Character specifying laboratory test displayed y-axis. x_plot_type [character(1)] Character specifying plot type x-axis. leads using dataset's column \"r_<x_plot_type>_<x_sel>\" x-values. y_plot_type [character(1)] Character specifying plot type y-axis. leads using dataset's column \"r_<y_plot_type>_<y_sel>\" y-values.","code":""},{"path":"/reference/generate_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate plot — generate_plot","text":"plotly object specifying generated eDISH plot.","code":""},{"path":"/reference/mock_edish_app.html","id":null,"dir":"Reference","previous_headings":"","what":"Plain mock app without specific layout — mock_edish_app","title":"Plain mock app without specific layout — mock_edish_app","text":"mock_edish_app() launches mock app containing dv.edish shiny module.","code":""},{"path":"/reference/mock_edish_app.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plain mock app without specific layout — mock_edish_app","text":"","code":"mock_edish_app()"},{"path":"/reference/mock_edish_mm.html","id":null,"dir":"Reference","previous_headings":"","what":"Mock app integrated in the module manager framework — mock_edish_mm","title":"Mock app integrated in the module manager framework — mock_edish_mm","text":"mock_table_mm() launches mock app containing dv.edish shiny module means dv.manager.","code":""},{"path":"/reference/mock_edish_mm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mock app integrated in the module manager framework — mock_edish_mm","text":"","code":"mock_edish_mm()"},{"path":"/reference/mod_edish.html","id":null,"dir":"Reference","previous_headings":"","what":"eDISH module — mod_edish","title":"eDISH module — mod_edish","text":"mod_edish() displays (modified) evaluation Drug-Induced Serious Hepatotoxicity (eDISH/mDISH) plot support assessment drug-induced liver injury (DILI).","code":""},{"path":"/reference/mod_edish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"eDISH module — mod_edish","text":"","code":"mod_edish(   module_id,   dataset_names,   subjectid_var = \"USUBJID\",   arm_var = \"ACTARM\",   arm_default_vals = NULL,   visit_var = \"VISIT\",   baseline_visit_val = \"VISIT 01\",   lb_test_var = \"LBTEST\",   lb_test_choices = c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\",     \"Aspartate Aminotransferase\", \"Bilirubin\"),   lb_test_default_x_val = \"Aspartate Aminotransferase\",   lb_test_default_y_val = \"Bilirubin\",   lb_result_var = \"LBSTRESN\",   ref_range_upper_lim_var = \"LBSTNRHI\",   dataset_disp )"},{"path":"/reference/mod_edish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"eDISH module — mod_edish","text":"module_id [character(1)] unique module ID. dataset_names [character(1+)] Name(s) dataset(s) displayed. Can used together parameter dataset_disp. subjectid_var [character(1)] Name variable containing unique subject IDs. Defaults \"USUBJID\". arm_var [character(1)] Name variable containing arm/treatment information. Defaults \"ACTARM\". arm_default_vals [character(1+)] Vector specifying default value(s) arm selector. Defaults NULL. visit_var [character(1)] Name variable containing visit information. Defaults \"VISIT\". baseline_visit_val [character(1)] Character indicating visit used baseline visit. Defaults \"VISIT 01\". lb_test_var [character(1)] Name variable containing laboratory test information. Defaults \"LBTEST\". lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. Defaults c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\", \"Aspartate Aminotransferase\", \"Bilirubin\") lb_test_default_x_val [character(1)] Character specifying default laboratory test choice plot's x-axis. Defaults \"Aspartate Aminotransferase\". lb_test_default_y_val [character(1)] Character specifying default laboratory test choice plot's y-axis. Defaults \"Bilirubin\". lb_result_var [character(1)] Name variable containing results laboratory test. Defaults \"LBSTRESN\". case multiple values lb_result_var per subjectid_var, visit_var, lb_test_var, maximum value used. Note NA value considered values cause value NA returned maximum value. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits. Defaults \"LBSTNRHI\". dataset_disp [dv.manager::mm_dispatch()] advanced usage. mm_dispatch object. used together parameter dataset_names.","code":""},{"path":"/reference/mod_edish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"eDISH module — mod_edish","text":"list containing following elements used dv.manager: ui: UI function dv.edish module. server: server function dv.edish module. module_id: unique identifier.","code":""},{"path":"/reference/pack_of_constants.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a collection of named constants — pack_of_constants","title":"Build a collection of named constants — pack_of_constants","text":"Build collection named constants","code":""},{"path":"/reference/pack_of_constants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a collection of named constants — pack_of_constants","text":"","code":"pack_of_constants(...)"},{"path":"/reference/pack_of_constants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a collection of named constants — pack_of_constants","text":"... Named parameters collected constants","code":""},{"path":"/reference/pack_of_constants.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build a collection of named constants — pack_of_constants","text":"Shiny uses strings IDs link UI server elements. E.g: foo_UI(id = ns(\"foo\")) ... foo_server(id = \"foo\") pattern makes easy programmers fall trap modifying one instance string literal \"foo\" without modifying rest unaware problem bug hit. also easy mistakes uses \"foo\" identifier uses (text labels, ...) , often case, parameter explicitly named. One easy fix consists using global variables instead plain string literals. case previous example, mean: ID_FOO <- \"foo\" foo_UI(ns(ID_FOO)) ... foo_server(ID_FOO) simple addition makes purpose ID_FOO clear also fails gracefully ID_FOO instances updated synchronously along codebase. drawback polluting global namespace identifier variables. easily solved creating container constants, purpose pack_of_constants alias. ID <- pack_of_constants(FOO = \"foo\", BAR = \"bar\") ID$FOO \"foo\" ID$BA NULL","code":""},{"path":"/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"/reference/prepare_initial_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare initial data — prepare_initial_data","title":"Prepare initial data — prepare_initial_data","text":"prepare_initial_data() prepares data initially restructuring joining DM LB dataset one.","code":""},{"path":"/reference/prepare_initial_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare initial data — prepare_initial_data","text":"","code":"prepare_initial_data(   dataset_list,   subjectid_var,   arm_var,   visit_var,   baseline_visit_val,   lb_test_var,   lb_test_choices,   lb_result_var,   ref_range_upper_lim_var )"},{"path":"/reference/prepare_initial_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare initial data — prepare_initial_data","text":"dataset_list [list(data.frame))] list datasets, containing Demographics Lab Value dataset. [list(data.frame))]: R:list(data.frame)) subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. baseline_visit_val [character(1)] Character indicating visit used baseline visit. lb_test_var [character(1)] Name variable containing laboratory test information. lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits.","code":""},{"path":"/reference/prepare_initial_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare initial data — prepare_initial_data","text":"single dataframe including columns defined subjectid_var, arm_var, visit_var, lb_test_var, lb_result_var, ref_range_upper_lim_var, well column \"BASE\" containing corresponding baseline values. case multiple values lb_result_var per subjectid_var, visit_var, lb_test_var, maximum value used. Note NA value considered values cause value NA returned maximum value.","code":""},{"path":"/news/index.html","id":"dvedish-103","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.3","title":"dv.edish 1.0.3","text":"Initial release dv.edish package GitHub.","code":""},{"path":"/news/index.html","id":"dvedish-102","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.2","title":"dv.edish 1.0.2","text":"module now able deal multiple values per subject, visit, lab test using maximum value. data display, e.g., due filter settings, module provide meaningful output. module updated show commonly used default values reference lines. x-axis, default value 3, y-axis, default value 2.","code":""},{"path":"/news/index.html","id":"dvedish-101","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.1","title":"dv.edish 1.0.1","text":"Bugfix: Bookmarking app’s state failed arm parameter selection fixed now.","code":""},{"path":"/news/index.html","id":"dvedish-100","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.0","title":"dv.edish 1.0.0","text":"Initial version dv.edish.","code":""}]
+[{"path":"/articles/disp.html","id":"how-to-set-up-an-edish-module-using-dispatchers","dir":"Articles","previous_headings":"","what":"How to set up an eDISH module using dispatchers","title":"Usage of {dv.manager} dispatchers","text":"Dispatchers helper functions allow accessing data utility functions inside module manager dynamic way. Refer ?dv.manager::mm_dispatch information functionalities. , can find two examples can used set eDISH module. Note possible use arguments, dataset_names dataset_disp, time mod_edish() call.","code":""},{"path":"/articles/disp.html","id":"a--filtered-data","dir":"Articles","previous_headings":"How to set up an eDISH module using dispatchers","what":"a. Filtered data","title":"Usage of {dv.manager} dispatchers","text":"code piece produces essentially app behavior using dataset_names argument. , selection made user global filter menu affects module display.","code":"mod_edish(   module_id = \"edish_a\",   dataset_disp = dv.manager::mm_dispatch(     from = \"filtered_dataset\",     selection = c(\"dm\", \"lb\")   ) )"},{"path":"/articles/disp.html","id":"b--unfiltered-data","dir":"Articles","previous_headings":"How to set up an eDISH module using dispatchers","what":"b. Unfiltered data","title":"Usage of {dv.manager} dispatchers","text":"case undesirable global filter settings affect listings displayed eDISH module, possible define dispatcher delivers always unfiltered data. means global filter ignored!","code":"mod_edish(   module_id = \"edish_b\",   dataset_disp = dv.manager::mm_dispatch(     from = \"unfiltered_dataset\",     selection = c(\"dm\", \"lb\")   ) )"},{"path":"/articles/qc.html","id":"dv-edish-1-0-4","dir":"Articles","previous_headings":"","what":"✅ dv.edish 1.0.4","title":"Quality Control","text":"Date: 2024-Aug-19 12:13:03 following document generates report R packages, satisfy criteria “Released” status Non-GxP project. QC report contains following information: Specifications (specs): can attached every test user adds. Traceability matrix: Contains test cases passed, failed, skipped expectations. Uncovered undeclared specs Session Info System Configuration Please advised QC report generated module imply validation according GxP criteria. QC report satisfies internally developed quality checks non-GxP criteria. clinical reporting purposes, essential note outputs generated using module must checked verified within validated system adheres appropriate GxP guidelines.","code":""},{"path":"/articles/qc.html","id":"traceability-matrix","dir":"Articles","previous_headings":"","what":"Traceability matrix","title":"Quality Control","text":"traceability matrix tests point specification included. Test cases can contain several expectations test considered: passed expectations test pass. failed least one expectation test fails. skipped least one expectation test skipped. test can failed skipped.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"/articles/qc.html","id":"undeclared-specifications","dir":"Articles","previous_headings":"Traceability matrix","what":"Undeclared specifications","title":"Quality Control","text":"always empty, non existant specs controlled test execution.","code":""},{"path":"/articles/qc.html","id":"session-info-and-system-configuration","dir":"Articles","previous_headings":"","what":"Session Info and System Configuration","title":"Quality Control","text":"","code":"#> ─ Session info ─────────────────────────────────────────────────────────────── #>  setting  value #>  version  R version 4.3.2 (2023-10-31) #>  os       Ubuntu 22.04.4 LTS #>  system   x86_64, linux-gnu #>  ui       X11 #>  language en #>  collate  en_US.UTF-8 #>  ctype    en_US.UTF-8 #>  tz       Etc/UTC #>  date     2024-08-19 #>  pandoc   2.9.2.1 @ /usr/bin/ (via rmarkdown) #>  #> ─ Packages ─────────────────────────────────────────────────────────────────── #>  package     * version date (UTC) lib source #>  bslib         0.6.1   2023-11-28 [2] RSPM #>  cachem        1.0.8   2023-05-01 [2] RSPM #>  cli           3.6.2   2023-12-11 [2] RSPM #>  crosstalk     1.2.1   2023-11-23 [2] RSPM #>  desc          1.4.3   2023-12-10 [2] RSPM #>  devtools      2.4.5   2022-10-11 [2] RSPM #>  digest        0.6.34  2024-01-11 [2] RSPM #>  DT            0.31    2023-12-09 [2] RSPM #>  ellipsis      0.3.2   2021-04-29 [2] RSPM #>  evaluate      0.23    2023-11-01 [2] RSPM #>  fastmap       1.1.1   2023-02-24 [2] RSPM #>  fs            1.6.3   2023-07-20 [2] RSPM #>  glue          1.7.0   2024-01-09 [2] RSPM #>  htmltools     0.5.7   2023-11-03 [2] RSPM #>  htmlwidgets   1.6.4   2023-12-06 [2] RSPM #>  httpuv        1.6.13  2023-12-06 [2] RSPM #>  jquerylib     0.1.4   2021-04-26 [2] RSPM #>  jsonlite      1.8.8   2023-12-04 [2] RSPM #>  knitr         1.45    2023-10-30 [2] RSPM #>  later         1.3.2   2023-12-06 [2] RSPM #>  lifecycle     1.0.4   2023-11-07 [2] RSPM #>  magrittr      2.0.3   2022-03-30 [2] RSPM #>  memoise       2.0.1   2021-11-26 [2] RSPM #>  mime          0.12    2021-09-28 [2] RSPM #>  miniUI        0.1.1.1 2018-05-18 [2] RSPM #>  pkgbuild      1.4.3   2023-12-10 [2] RSPM #>  pkgdown       2.0.7   2022-12-14 [2] RSPM #>  pkgload       1.3.3   2023-09-22 [2] RSPM #>  profvis       0.3.8   2023-05-02 [2] RSPM #>  promises      1.2.1   2023-08-10 [2] RSPM #>  purrr         1.0.2   2023-08-10 [2] RSPM #>  R6            2.5.1   2021-08-19 [2] RSPM #>  ragg          1.2.7   2023-12-11 [2] RSPM #>  Rcpp          1.0.12  2024-01-09 [2] RSPM #>  remotes       2.4.2.1 2023-07-18 [2] RSPM #>  rlang         1.1.3   2024-01-10 [2] RSPM #>  rmarkdown     2.25    2023-09-18 [2] RSPM #>  sass          0.4.8   2023-12-06 [2] RSPM #>  sessioninfo   1.2.2   2021-12-06 [2] RSPM #>  shiny         1.8.0   2023-11-17 [2] RSPM #>  stringi       1.8.3   2023-12-11 [2] RSPM #>  stringr       1.5.1   2023-11-14 [2] RSPM #>  systemfonts   1.0.5   2023-10-09 [2] RSPM #>  textshaping   0.3.7   2023-10-09 [2] RSPM #>  urlchecker    1.0.1   2021-11-30 [2] RSPM #>  usethis       2.2.2   2023-07-06 [2] RSPM #>  vctrs         0.6.5   2023-12-01 [2] RSPM #>  xfun          0.41    2023-11-01 [2] RSPM #>  xtable        1.8-4   2019-04-21 [2] RSPM #>  yaml          2.3.8   2023-12-11 [2] RSPM #>  #>  [1] /tmp/RtmpcdDNtt/temp_libpath3936afad658 #>  [2] /usr/local/lib/R/site-library #>  [3] /usr/local/lib/R/library #>  #> ──────────────────────────────────────────────────────────────────────────────"},{"path":[]},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Boehringer-Ingelheim Pharma GmbH & Co.KG. Copyright holder, funder. Isabel Glauss. Author, maintainer.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Glauss (2024). dv.edish: eDISH Plot Module DILI assessment. R package version 1.0.4.","code":"@Manual{,   title = {dv.edish: eDISH Plot Module for DILI assessment},   author = {Isabel Glauss},   year = {2024},   note = {R package version 1.0.4}, }"},{"path":"/index.html","id":"edish-module","dir":"","previous_headings":"","what":"dv.edish","title":"dv.edish","text":"{dv.edish} package meant support assessment drug-induced liver injury means (modified) evaluation Drug-Induced Serious Hepatotoxicity plot.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"dv.edish","text":"","code":"if (!require(\"remotes\")) install.packages(\"remotes\") remotes::install_github(\"Boehringer-Ingelheim/dv.edish\")"},{"path":"/index.html","id":"features","dir":"","previous_headings":"","what":"Features","title":"dv.edish","text":"eDISH module shows scatter plot depicting correlations two lab parameters subject-level. parameter displayed axis can selected app user. Moreover, parameters can displayed multiples either upper limit normals (resulting eDISH plot) corresponding subject’s baseline values (resulting mDISH plot). Horizontal vertical lines indicating Hy’s law customizable well within input menu.","code":""},{"path":"/index.html","id":"creating-an-edish-application","dir":"","previous_headings":"","what":"Creating an eDISH application","title":"dv.edish","text":"following example shows set simple DaVinci app means {dv.manager}. app contains eDISH module display dummy data provided {pharmaverseadam} package: Note module expects two datasets: Demographics dataset (e.g. dm adsl) including, least, variables containing following information: Unique subject identifier (e.g. USUBJID) Arm (e.g. ACTARM) Laboratory Test Results dataset (e.g. lb adlb) including, least, variables containing following information: Unique subject identifier (e.g. USUBJID) Visit (e.g. VISIT) Lab test result name (e.g. LBTEST) Numeric lab test result (e.g. LBSTRESN) Lab test reference range upper limit (e.g. LBSTNRHI)","code":"dm <- pharmaverseadam::adsl lb <- pharmaverseadam::adlb    module_list <- list(   \"edish\" = dv.edish::mod_edish(     module_id = \"edish\",     dataset_names = c(\"dm\", \"lb\"),     arm_default_vals = c(\"Xanomeline Low Dose\", \"Xanomeline High Dose\"),     baseline_visit_val = \"SCREENING 1\"   ) )  dv.manager::run_app(   data = list(\"demo\" = list(\"dm\" = dm, \"lb\" = lb)),   module_list = module_list,   filter_data = \"dm\" )"},{"path":"/reference/derive_req_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Derive required variables — derive_req_vars","title":"Derive required variables — derive_req_vars","text":"derive_req_vars() restructures stated dataset include variables containing ratio lab result divided ULN baseline value. corresponding variable names shaped follows: \"r__.","code":""},{"path":"/reference/derive_req_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derive required variables — derive_req_vars","text":"","code":"derive_req_vars(   dataset,   subjectid_var,   arm_var,   visit_var,   lb_test_var,   lb_result_var,   ref_range_upper_lim_var,   sel_x,   sel_y )"},{"path":"/reference/derive_req_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derive required variables — derive_req_vars","text":"dataset [data.frame] dataframe containing variables listed columns. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. lb_test_var [character(1)] Name variable containing laboratory test information. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits. sel_x [character(1)] Character specifying laboratory test selected x-axis. sel_y [character(1)] Character specifying laboratory test selected y-axis.","code":""},{"path":"/reference/derive_req_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derive required variables — derive_req_vars","text":"restructured dataset.","code":""},{"path":"/reference/edish_UI.html","id":null,"dir":"Reference","previous_headings":"","what":"User Interface of the dv.edish module — edish_UI","title":"User Interface of the dv.edish module — edish_UI","text":"edish_UI() contains UI dv.edish module.","code":""},{"path":"/reference/edish_UI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User Interface of the dv.edish module — edish_UI","text":"","code":"edish_UI(module_id)"},{"path":"/reference/edish_UI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User Interface of the dv.edish module — edish_UI","text":"module_id [character(1)] unique ID string create namespace. Must match ID edish_server().","code":""},{"path":"/reference/edish_UI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User Interface of the dv.edish module — edish_UI","text":"shiny uiOutput element.","code":""},{"path":[]},{"path":"/reference/edish_server.html","id":null,"dir":"Reference","previous_headings":"","what":"Server of the dv.edish module — edish_server","title":"Server of the dv.edish module — edish_server","text":"edish_server() contains server dv.edish module.","code":""},{"path":"/reference/edish_server.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Server of the dv.edish module — edish_server","text":"","code":"edish_server(   module_id,   dataset_list,   subjectid_var = \"USUBJID\",   arm_var = \"ACTARM\",   arm_default_vals = NULL,   visit_var = \"VISIT\",   baseline_visit_val = \"VISIT 01\",   lb_test_var = \"LBTEST\",   lb_test_choices = c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\",     \"Aspartate Aminotransferase\", \"Bilirubin\"),   lb_test_default_x_val = \"Aspartate Aminotransferase\",   lb_test_default_y_val = \"Bilirubin\",   lb_result_var = \"LBSTRESN\",   ref_range_upper_lim_var = \"LBSTNRHI\" )"},{"path":"/reference/edish_server.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Server of the dv.edish module — edish_server","text":"module_id [character(1)] unique ID string create namespace. Must match ID edish_UI(). dataset_list [shiny::reactive(list(data.frame))] reactive list named datasets. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. arm_default_vals [character(1+)] Vector specifying default value(s) arm selector. visit_var [character(1)] Name variable containing visit information. baseline_visit_val [character(1)] Character indicating visit used baseline visit. lb_test_var [character(1)] Name variable containing laboratory test information. lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. lb_test_default_x_val [character(1)] Character specifying default laboratory test choice plot's x-axis. lb_test_default_y_val [character(1)] Character specifying default laboratory test choice plot's y-axis. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits.","code":""},{"path":[]},{"path":"/reference/filter_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter data — filter_data","title":"Filter data — filter_data","text":"filter_data() filters dataset contain values sel_lb_test lb_test_var column values sel_arm arm_var column.","code":""},{"path":"/reference/filter_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter data — filter_data","text":"","code":"filter_data(dataset, arm_var, sel_arm, lb_test_var, sel_lb_test)"},{"path":"/reference/filter_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter data — filter_data","text":"dataset [data.frame] dataframe containing columns specified lb_test_var arm_var. arm_var [character(1)] Name variable containing arm/treatment information. sel_arm [character(1+)] Character vector specifying selection arms/treatments. lb_test_var [character(1)] Name variable containing laboratory test information. sel_lb_test [character(1+)] Character vector specifying selection laboratory tests.","code":""},{"path":"/reference/filter_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter data — filter_data","text":"filtered dataset.","code":""},{"path":"/reference/generate_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate plot — generate_plot","title":"Generate plot — generate_plot","text":"generate_plot() generates eDISH plot means plotly package.","code":""},{"path":"/reference/generate_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate plot — generate_plot","text":"","code":"generate_plot(   dataset,   subjectid_var,   arm_var,   visit_var,   sel_x,   sel_y,   x_plot_type,   y_plot_type,   x_ref_line_num,   y_ref_line_num )"},{"path":"/reference/generate_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate plot — generate_plot","text":"dataset [data.frame] dataframe containing variables listed columns. subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. sel_x [character(1)] Character specifying laboratory test displayed x-axis. sel_y [character(1)] Character specifying laboratory test displayed y-axis. x_plot_type [character(1)] Character specifying plot type x-axis. leads using dataset's column \"r_<x_plot_type>_<x_sel>\" x-values. y_plot_type [character(1)] Character specifying plot type y-axis. leads using dataset's column \"r_<y_plot_type>_<y_sel>\" y-values.","code":""},{"path":"/reference/generate_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate plot — generate_plot","text":"plotly object specifying generated eDISH plot.","code":""},{"path":"/reference/mock_edish_app.html","id":null,"dir":"Reference","previous_headings":"","what":"Plain mock app without specific layout — mock_edish_app","title":"Plain mock app without specific layout — mock_edish_app","text":"mock_edish_app() launches mock app containing dv.edish shiny module.","code":""},{"path":"/reference/mock_edish_app.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plain mock app without specific layout — mock_edish_app","text":"","code":"mock_edish_app()"},{"path":"/reference/mock_edish_mm.html","id":null,"dir":"Reference","previous_headings":"","what":"Mock app integrated in the module manager framework — mock_edish_mm","title":"Mock app integrated in the module manager framework — mock_edish_mm","text":"mock_table_mm() launches mock app containing dv.edish shiny module means dv.manager.","code":""},{"path":"/reference/mock_edish_mm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mock app integrated in the module manager framework — mock_edish_mm","text":"","code":"mock_edish_mm()"},{"path":"/reference/mod_edish.html","id":null,"dir":"Reference","previous_headings":"","what":"eDISH module — mod_edish","title":"eDISH module — mod_edish","text":"mod_edish() displays (modified) evaluation Drug-Induced Serious Hepatotoxicity (eDISH/mDISH) plot support assessment drug-induced liver injury (DILI).","code":""},{"path":"/reference/mod_edish.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"eDISH module — mod_edish","text":"","code":"mod_edish(   module_id,   dataset_names,   subjectid_var = \"USUBJID\",   arm_var = \"ACTARM\",   arm_default_vals = NULL,   visit_var = \"VISIT\",   baseline_visit_val = \"VISIT 01\",   lb_test_var = \"LBTEST\",   lb_test_choices = c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\",     \"Aspartate Aminotransferase\", \"Bilirubin\"),   lb_test_default_x_val = \"Aspartate Aminotransferase\",   lb_test_default_y_val = \"Bilirubin\",   lb_result_var = \"LBSTRESN\",   ref_range_upper_lim_var = \"LBSTNRHI\",   dataset_disp )"},{"path":"/reference/mod_edish.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"eDISH module — mod_edish","text":"module_id [character(1)] unique module ID. dataset_names [character(1+)] Name(s) dataset(s) displayed. Can used together parameter dataset_disp. subjectid_var [character(1)] Name variable containing unique subject IDs. Defaults \"USUBJID\". arm_var [character(1)] Name variable containing arm/treatment information. Defaults \"ACTARM\". arm_default_vals [character(1+)] Vector specifying default value(s) arm selector. Defaults NULL. visit_var [character(1)] Name variable containing visit information. Defaults \"VISIT\". baseline_visit_val [character(1)] Character indicating visit used baseline visit. Defaults \"VISIT 01\". lb_test_var [character(1)] Name variable containing laboratory test information. Defaults \"LBTEST\". lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. Defaults c(\"Alkaline Phosphatase\", \"Alanine Aminotransferase\", \"Aspartate Aminotransferase\", \"Bilirubin\") lb_test_default_x_val [character(1)] Character specifying default laboratory test choice plot's x-axis. Defaults \"Aspartate Aminotransferase\". lb_test_default_y_val [character(1)] Character specifying default laboratory test choice plot's y-axis. Defaults \"Bilirubin\". lb_result_var [character(1)] Name variable containing results laboratory test. Defaults \"LBSTRESN\". case multiple values lb_result_var per subjectid_var, visit_var, lb_test_var, maximum value used. Note NA value considered values cause value NA returned maximum value. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits. Defaults \"LBSTNRHI\". dataset_disp [dv.manager::mm_dispatch()] advanced usage. mm_dispatch object. used together parameter dataset_names.","code":""},{"path":"/reference/mod_edish.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"eDISH module — mod_edish","text":"list containing following elements used dv.manager: ui: UI function dv.edish module. server: server function dv.edish module. module_id: unique identifier.","code":""},{"path":"/reference/pack_of_constants.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a collection of named constants — pack_of_constants","title":"Build a collection of named constants — pack_of_constants","text":"Build collection named constants","code":""},{"path":"/reference/pack_of_constants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a collection of named constants — pack_of_constants","text":"","code":"pack_of_constants(...)"},{"path":"/reference/pack_of_constants.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a collection of named constants — pack_of_constants","text":"... Named parameters collected constants","code":""},{"path":"/reference/pack_of_constants.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build a collection of named constants — pack_of_constants","text":"Shiny uses strings IDs link UI server elements. E.g: foo_UI(id = ns(\"foo\")) ... foo_server(id = \"foo\") pattern makes easy programmers fall trap modifying one instance string literal \"foo\" without modifying rest unaware problem bug hit. also easy mistakes uses \"foo\" identifier uses (text labels, ...) , often case, parameter explicitly named. One easy fix consists using global variables instead plain string literals. case previous example, mean: ID_FOO <- \"foo\" foo_UI(ns(ID_FOO)) ... foo_server(ID_FOO) simple addition makes purpose ID_FOO clear also fails gracefully ID_FOO instances updated synchronously along codebase. drawback polluting global namespace identifier variables. easily solved creating container constants, purpose pack_of_constants alias. ID <- pack_of_constants(FOO = \"foo\", BAR = \"bar\") ID$FOO \"foo\" ID$BA NULL","code":""},{"path":"/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"/reference/prepare_initial_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare initial data — prepare_initial_data","title":"Prepare initial data — prepare_initial_data","text":"prepare_initial_data() prepares data initially restructuring joining DM LB dataset one.","code":""},{"path":"/reference/prepare_initial_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare initial data — prepare_initial_data","text":"","code":"prepare_initial_data(   dataset_list,   subjectid_var,   arm_var,   visit_var,   baseline_visit_val,   lb_test_var,   lb_test_choices,   lb_result_var,   ref_range_upper_lim_var )"},{"path":"/reference/prepare_initial_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare initial data — prepare_initial_data","text":"dataset_list [list(data.frame))] list datasets, containing Demographics Lab Value dataset. [list(data.frame))]: R:list(data.frame)) subjectid_var [character(1)] Name variable containing unique subject IDs. arm_var [character(1)] Name variable containing arm/treatment information. visit_var [character(1)] Name variable containing visit information. baseline_visit_val [character(1)] Character indicating visit used baseline visit. lb_test_var [character(1)] Name variable containing laboratory test information. lb_test_choices [character(1+)] Character vector specifying possible choices laboratory test. lb_result_var [character(1)] Name variable containing results laboratory test. ref_range_upper_lim_var [character(1)] Name variable containing reference range upper limits.","code":""},{"path":"/reference/prepare_initial_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare initial data — prepare_initial_data","text":"single dataframe including columns defined subjectid_var, arm_var, visit_var, lb_test_var, lb_result_var, ref_range_upper_lim_var, well column \"BASE\" containing corresponding baseline values. case multiple values lb_result_var per subjectid_var, visit_var, lb_test_var, maximum value used. Note NA value considered values cause value NA returned maximum value.","code":""},{"path":"/news/index.html","id":"dvedish-104","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.4","title":"dv.edish 1.0.4","text":"module ignores now NA values calculating maximum value.","code":""},{"path":"/news/index.html","id":"dvedish-103","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.3","title":"dv.edish 1.0.3","text":"Initial release dv.edish package GitHub.","code":""},{"path":"/news/index.html","id":"dvedish-102","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.2","title":"dv.edish 1.0.2","text":"module now able deal multiple values per subject, visit, lab test using maximum value. data display, e.g., due filter settings, module provide meaningful output. module updated show commonly used default values reference lines. x-axis, default value 3, y-axis, default value 2.","code":""},{"path":"/news/index.html","id":"dvedish-101","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.1","title":"dv.edish 1.0.1","text":"Bugfix: Bookmarking app’s state failed arm parameter selection fixed now.","code":""},{"path":"/news/index.html","id":"dvedish-100","dir":"Changelog","previous_headings":"","what":"dv.edish 1.0.0","title":"dv.edish 1.0.0","text":"Initial version dv.edish.","code":""}]