From 10ae65bb318029b0953dc74a4fa59cd90bed4c70 Mon Sep 17 00:00:00 2001 From: Juri Solodenko Date: Fri, 23 Aug 2024 13:51:06 +0200 Subject: [PATCH] Fixes #7 Adjust used observed data (#9) * Fixes #7 Adjust used observed data * fix evaluation plan --------- Co-authored-by: Yuri05 --- .github/workflows/Check_utf8.yml | 4 +- .github/workflows/ValidateEvaluationPlan.yml | 13 + Digoxin.json | 16573 ++++++++++------ ...luation_plan.json => evaluation_plan.json} | 2 +- Evaluation/workflow.R | 325 +- 5 files changed, 10807 insertions(+), 6110 deletions(-) create mode 100644 .github/workflows/ValidateEvaluationPlan.yml rename Evaluation/Input/{Evaluation_plan.json => evaluation_plan.json} (99%) diff --git a/.github/workflows/Check_utf8.yml b/.github/workflows/Check_utf8.yml index f035ce9..62f9fdf 100644 --- a/.github/workflows/Check_utf8.yml +++ b/.github/workflows/Check_utf8.yml @@ -10,4 +10,6 @@ jobs: utf8check: uses: Open-Systems-Pharmacology/Workflows/.github/workflows/UTF8Check.yml@main with: - file-extensions: 'R\|json\|md' + file-extensions: 'R\|json\|md' #File extension(s) to check separated by \| Examples: + #R + #R\|json diff --git a/.github/workflows/ValidateEvaluationPlan.yml b/.github/workflows/ValidateEvaluationPlan.yml new file mode 100644 index 0000000..63aacc9 --- /dev/null +++ b/.github/workflows/ValidateEvaluationPlan.yml @@ -0,0 +1,13 @@ +name: Validate Evaluation Plan + +on: + [push, pull_request] + +permissions: + contents: read + +jobs: + Validate-Evaluation-Plan: + uses: Open-Systems-Pharmacology/Workflows/.github/workflows/ValidateQualificationPlan.yml@main + with: + qualification-plan: 'Evaluation/Input/evaluation_plan.json' diff --git a/Digoxin.json b/Digoxin.json index 47d4fea..395932e 100644 --- a/Digoxin.json +++ b/Digoxin.json @@ -1838,7 +1838,7 @@ "Model": "4Comp", "ObservedData": [ "Eckermann 2012 - 0.25mg po - Digoxin - PO - 250 µg - Plasma - agg. (n=16)", - "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)" + "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)" ], "Solver": {}, "OutputSchema": [ @@ -2004,9 +2004,9 @@ } }, { - "Name": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|Time", - "Y": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|Time", + "Y": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 10, @@ -2092,9 +2092,9 @@ } }, { - "Name": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|Time", - "Y": "Gurley 2008 - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|Time", + "Y": "Gurley 2008b - Control (Perpetrator Placebo) - Digoxin - PO - 0.25 mg - Serum - agg. (n=18)|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 9, @@ -2129,15 +2129,15 @@ "Name": "Digoxin colon, 0.5 mg", "Model": "4Comp", "ObservedData": [ - "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)", - "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv." + "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)", + "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv." ], "Solver": {}, "OutputSchema": [ @@ -2296,9 +2296,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)-Digoxin-Kidney-Urine-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)|Time", - "Y": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)|ObservedData|Kidney|Urine|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)-Digoxin-Kidney-Urine-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)|Time", + "Y": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)|ObservedData|Kidney|Urine|Digoxin|ArithmeticMean", "CurveOptions": { "yAxisType": "Y2", "Color": "#8080FF", @@ -2308,9 +2308,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 13, @@ -2319,9 +2319,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 14, @@ -2330,9 +2330,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 15, @@ -2341,9 +2341,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 16, @@ -2352,9 +2352,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 17, @@ -2363,9 +2363,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 18, @@ -2374,9 +2374,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 19, @@ -2385,9 +2385,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 1 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 20, @@ -2474,9 +2474,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)-Digoxin-Kidney-Urine-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)|Time", - "Y": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - IV - 0.5 mg - Urine - agg. (n=8)|ObservedData|Kidney|Urine|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)-Digoxin-Kidney-Urine-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)|Time", + "Y": "Ochs 1975 - 0.5mg Patients with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Urine - agg. (n=8)|ObservedData|Kidney|Urine|Digoxin|ArithmeticMean", "CurveOptions": { "yAxisType": "Y2", "Color": "#8080FF", @@ -2486,9 +2486,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 13, @@ -2497,9 +2497,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 14, @@ -2508,9 +2508,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 15, @@ -2519,9 +2519,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 16, @@ -2530,9 +2530,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 17, @@ -2541,9 +2541,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 18, @@ -2552,9 +2552,9 @@ } }, { - "Name": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", - "X": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|Time", - "Y": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", + "Name": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.-Digoxin-Peripheral Venous Blood-Plasma-ArithmeticMean", + "X": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|Time", + "Y": "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.|ObservedData|Peripheral Venous Blood|Plasma|Digoxin|ArithmeticMean", "CurveOptions": { "Color": "#FF0000", "LegendIndex": 19, @@ -2563,9 +2563,9 @@ } }, { - 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(n=12)", - "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", - "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - IV - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 2 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 3 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 4 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 5 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 6 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 7 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", + "Ochs 1975 - 0.5mg Patient 8 with normal colon mucosa - Digoxin - Intracolonic - 0.5 mg - Plasma - indiv.", "Wagner 1981 - 0.5mg iv 1h - Digoxin - IV - 0.5 mg - Urine - agg. (n=6)", "Wagner 1981 - 0.5mg iv 3h - Digoxin - IV - 0.5 mg - Urine - agg. (n=6)", "Wagner 1981 - 0.5mg iv bolus - Digoxin - IV - 0.5 mg - Urine - agg. (n=6)", @@ -23714,7 +28397,7 @@ "Ochs 1978 - 1mg - Digoxin - IV - 1 mg - Urine - agg. (n=9)", "Greiner 1999 - iv Control (Perpetrator Placebo) - Digoxin - IV - 1 mg - Plasma - agg. (n=8)", "Greiner 1999 - iv with Perpetrator (Rifampicin) - Digoxin - IV - 1 mg - Plasma - agg. (n=8)", - "Kramer 1979 - 1mg iv bolus - Digoxin - IV - 1 mg - Serum - agg. (n=12)", + "Kramer 1979 - 1mg iv bolus - Digoxin - IV - 1 mg - Plasma - agg. (n=12)", "Ochs 1978 - 1mg - Digoxin - IV - 1 mg - Plasma - agg. (n=9)" ] }, diff --git a/Evaluation/Input/Evaluation_plan.json b/Evaluation/Input/evaluation_plan.json similarity index 99% rename from Evaluation/Input/Evaluation_plan.json rename to Evaluation/Input/evaluation_plan.json index 10d23ee..2274d84 100644 --- a/Evaluation/Input/Evaluation_plan.json +++ b/Evaluation/Input/evaluation_plan.json @@ -1,4 +1,4 @@ -{ +{ "$schema": "https://github.com/Open-Systems-Pharmacology/QualificationPlan/releases/download/v3.0/OSP_Qualification_Plan_Schema.json", "Projects": [ { diff --git a/Evaluation/workflow.R b/Evaluation/workflow.R index c69933a..215fda5 100644 --- a/Evaluation/workflow.R +++ b/Evaluation/workflow.R @@ -1,163 +1,162 @@ -#' @title Digoxin Evaluation report -#' @description Run a qualification workflow to create a qualification report. -#' @param qualificationRunnerFolder Folder where QualificationRunner.exe is located -#' @param pkSimPortableFolder Folder where PK-Sim is located. -#' If not specified, installation path will be read from the registry (available only in case of full **non-portable** installation). -#' This option is **MANDATORY** for the portable version of PK-Sim. -#' @param createWordReport Logical defining if a `docx` version of the report should also be created. -#' Note that `pandoc` installation is required for this feature -#' [https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/wiki/Installing-pandoc] -#' @param maxSimulationsPerCore An integer that set the maximimum number of simulations per core -#' @param versionInfo A `QualificationVersionInfo` object to update title page with Qualification Version Information -#' @param wordConversionTemplate File name of docx template document passed to Pandoc for the conversion of the md report into docx -#' Default template is available using `system.file("extdata", "reference.docx", package = "ospsuite.reportingengine")` -#' @examples -#' # Create a Qualification Report without any option and running v9.1.1 of Qualification Runner -#' createQualificationReport("C:/Software/QualificationRunner9.1.1") -#' -#' # Create a Qualification Report and turn of the creation of a doc version -#' createQualificationReport("C:/Software/QualificationRunner9.1.1", createWordReport = FALSE) -#' -#' # Create a Qualification Report and set the number of simulations to be run per core -#' createQualificationReport("C:/Software/QualificationRunner9.1.1", maxSimulationsPerCore = 8) -#' -#' # Create a Qualification Report and update Qualification Version Information on title page -#' versionInfo <- QualificationVersionInfo$new("1.1", "2.2","3.3") -#' createQualificationReport("C:/Software/QualificationRunner9.1.1", versionInfo = versionInfo) -#' - -createQualificationReport <- function(qualificationRunnerFolder, - pkSimPortableFolder = NULL, - createWordReport = TRUE, - maxSimulationsPerCore = NULL, - versionInfo = NULL, - wordConversionTemplate = NULL) { - library(ospsuite.reportingengine) - - #-------- STEP 1: Define workflow settings --------# - #' replace `workingDirectory` and `qualificationPlanName` with your paths - #' - #' The directories are assumed the following structure - #' `workingDirectory` - #' - `input` - #' - `qualificationPlanName` - #' - `re_input` - #' - `configurationPlanFile` - #' - `re_output` - #' - `report` - #' - #' In case your folder structure is different from assumed above, - #' the paths below must be adjusted as well: - #' - `qualificationPlanFile`: path of qualification plan file run by Qualification Runner - #' - `reInputFolder`: input path for the Reporting engine - #' - `reOutputFolder`: outputs of the Reporting Engine will be created here - #' - `reportName`: path of final report - #' - #' **Template parameters to be replaced below** - - #' `workingDirectory`: current directory is used as default working directory - workingDirectory <- getwd() - - qualificationPlanName <- "Evaluation_plan.json" - qualificationPlanFile <- file.path(workingDirectory, "Input", qualificationPlanName) - - #' The default outputs of qualification runner should be generated under `/re_input` - reInputFolder <- file.path(workingDirectory, "re_input") - #' The default outputs or RE should be generated under `/re_output` - reOutputFolder <- file.path(workingDirectory, "re_output") - - #' Configuration Plan created from the Qualification Plan by the Qualification Runner - configurationPlanName <- "report-configuration-plan" - configurationPlanFile <- file.path(reInputFolder, paste0(configurationPlanName, ".json")) - - #' Option to record the time require to run the workflow. - #' The timer will calculate calculation time form internal `Sys.time` function - recordWorkflowTime <- TRUE - - #' Set watermark that will appear in all generated plots - #' Default is no watermark. `Label` objects from `tlf` package can be used to specifiy watermark font. - watermark <- "" - - #' If not set, report created will be named `report.md` and located in the worflow folder namely `reOutputFolder` - reportFolder <- file.path(workingDirectory, "report") - reportPath <- file.path(reportFolder, "report.md") - - #----- Optional parameters for the Qualification Runner -----# - #' If not null, `logFile` is passed internally via the `-l` option - logFile <- NULL - #' If not null, `logLevel` is passed internally via the `--logLevel` option - logLevel <- NULL - #' If `overwrite` is set to true, eventual results from the previous run of the QualiRunner/RE will be removed first - overwrite <- TRUE - - #-------- STEP 2: Qualification Runner --------# - #' Start timer to track time if option `recordWorkflowTime` is set to TRUE - if (recordWorkflowTime) { - tic <- as.numeric(Sys.time()) - } - - #' Start Qualification Runner to generate inputs for the reporting engine - startQualificationRunner( - qualificationRunnerFolder = qualificationRunnerFolder, - qualificationPlanFile = qualificationPlanFile, - outputFolder = reInputFolder, - # pkSimPortableFolder = , - configurationPlanName = configurationPlanName, - overwrite = overwrite, - logFile = logFile, - logLevel = logLevel - ) - - #' Print timer tracked time if option `recordWorkflowTime` is set to TRUE - if (recordWorkflowTime) { - toc <- as.numeric(Sys.time()) - print(paste0("Qualification Runner Duration: ", round((toc - tic) / 60, 1), " minutes")) - } - - #-------- STEP 3: Run Qualification Workflow --------# - # If version info is provided update title page - titlePageFile <- file.path(reInputFolder, "Intro/titlepage.md") - if(!is.null(versionInfo) & file.exists(titlePageFile)){ - adjustTitlePage(titlePageFile, qualificationVersionInfo = versionInfo) - } - - #' Load `QualificationWorkflow` object from configuration plan - workflow <- loadQualificationWorkflow( - workflowFolder = reOutputFolder, - configurationPlanFile = configurationPlanFile - ) - - #' Set the name of the final report - workflow$reportFilePath <- reportPath - workflow$createWordReport <- createWordReport - workflow$wordConversionTemplate <- wordConversionTemplate - - #' Set watermark. If set, it will appear in all generated plots - workflow$setWatermark(watermark) - - #' Set the maximimum number of simulations per core if defined - if(!is.null(maxSimulationsPerCore)){ - workflow$simulate$settings$maxSimulationsPerCore <- maxSimulationsPerCore - } - - #' Activate/Deactivate tasks of qualification workflow prior running - # workflow$inactivateTasks("simulate") - # workflow$inactivateTasks("calculatePKParameters") - # workflow$inactivateTasks("plotTimeProfiles") - # workflow$inactivateTasks("plotComparisonTimeProfile") - # workflow$inactivateTasks("plotGOFMerged") - # workflow$inactivateTasks("plotPKRatio") - # workflow$inactivateTasks("plotDDIRatio") - - #' Run the `QualificatitonWorklfow` - workflow$plotPKRatio$settings$units$C_max <- "ng/mL" - workflow$runWorkflow() - - - #' Print timer tracked time if option `recordWorkflowTime` is set to TRUE - if (recordWorkflowTime) { - toc <- as.numeric(Sys.time()) - print(paste0("Qualification Workflow Total Duration: ", round((toc - tic) / 60, 1), " minutes")) - } - return(invisible()) -} +#' @title createQualificationReport +#' @description Run a qualification workflow to create a qualification report. +#' @param qualificationRunnerFolder Folder where QualificationRunner.exe is located +#' @param pkSimPortableFolder Folder where PK-Sim is located. +#' If not specified, installation path will be read from the registry (available only in case of full **non-portable** installation). +#' This option is **MANDATORY** for the portable version of PK-Sim. +#' @param createWordReport Logical defining if a `docx` version of the report should also be created. +#' Note that `pandoc` installation is required for this feature +#' [https://github.com/Open-Systems-Pharmacology/OSPSuite.ReportingEngine/wiki/Installing-pandoc] +#' @param maxSimulationsPerCore An integer that set the maximimum number of simulations per core +#' @param versionInfo A `QualificationVersionInfo` object to update title page with Qualification Version Information +#' @param wordConversionTemplate File name of docx template document passed to Pandoc for the conversion of the md report into docx +#' Default template is available using `system.file("extdata", "reference.docx", package = "ospsuite.reportingengine")` +#' @examples +#' # Create a Qualification Report without any option and running v9.1.1 of Qualification Runner +#' createQualificationReport("C:/Software/QualificationRunner9.1.1") +#' +#' # Create a Qualification Report and turn of the creation of a doc version +#' createQualificationReport("C:/Software/QualificationRunner9.1.1", createWordReport = FALSE) +#' +#' # Create a Qualification Report and set the number of simulations to be run per core +#' createQualificationReport("C:/Software/QualificationRunner9.1.1", maxSimulationsPerCore = 8) +#' +#' # Create a Qualification Report and update Qualification Version Information on title page +#' versionInfo <- QualificationVersionInfo$new("1.1", "2.2","3.3") +#' createQualificationReport("C:/Software/QualificationRunner9.1.1", versionInfo = versionInfo) +#' +createQualificationReport <- function(qualificationRunnerFolder, + pkSimPortableFolder = NULL, + createWordReport = TRUE, + maxSimulationsPerCore = NULL, + versionInfo = NULL, + wordConversionTemplate = NULL) { + library(ospsuite.reportingengine) + + #-------- STEP 1: Define workflow settings --------# + #' replace `workingDirectory` and `qualificationPlanName` with your paths + #' + #' The directories are assumed the following structure + #' `workingDirectory` + #' - `input` + #' - `qualificationPlanName` + #' - `re_input` + #' - `configurationPlanFile` + #' - `re_output` + #' - `report` + #' + #' In case your folder structure is different from assumed above, + #' the paths below must be adjusted as well: + #' - `qualificationPlanFile`: path of qualification plan file run by Qualification Runner + #' - `reInputFolder`: input path for the Reporting engine + #' - `reOutputFolder`: outputs of the Reporting Engine will be created here + #' - `reportName`: path of final report + #' + #' **Template parameters to be replaced below** + + #' `workingDirectory`: current directory is used as default working directory + workingDirectory <- getwd() + + qualificationPlanName <- "evaluation_plan.json" + qualificationPlanFile <- file.path(workingDirectory, "Input", qualificationPlanName) + + #' The default outputs of qualification runner should be generated under `/re_input` + reInputFolder <- file.path(workingDirectory, "re_input") + #' The default outputs or RE should be generated under `/re_output` + reOutputFolder <- file.path(workingDirectory, "re_output") + + #' Configuration Plan created from the Qualification Plan by the Qualification Runner + configurationPlanName <- "report-configuration-plan" + configurationPlanFile <- file.path(reInputFolder, paste0(configurationPlanName, ".json")) + + #' Option to record the time require to run the workflow. + #' The timer will calculate calculation time form internal `Sys.time` function + recordWorkflowTime <- TRUE + + #' Set watermark that will appear in all generated plots + #' Default is no watermark. `Label` objects from `tlf` package can be used to specifiy watermark font. + watermark <- "" + + #' If not set, report created will be named `report.md` and located in the worflow folder namely `reOutputFolder` + reportFolder <- file.path(workingDirectory, "report") + reportPath <- file.path(reportFolder, "report.md") + + #----- Optional parameters for the Qualification Runner -----# + #' If not null, `logFile` is passed internally via the `-l` option + logFile <- NULL + #' If not null, `logLevel` is passed internally via the `--logLevel` option + logLevel <- NULL + #' If `overwrite` is set to true, eventual results from the previous run of the QualiRunner/RE will be removed first + overwrite <- TRUE + + #-------- STEP 2: Qualification Runner --------# + #' Start timer to track time if option `recordWorkflowTime` is set to TRUE + if (recordWorkflowTime) { + tic <- as.numeric(Sys.time()) + } + + #' Start Qualification Runner to generate inputs for the reporting engine + startQualificationRunner( + qualificationRunnerFolder = qualificationRunnerFolder, + qualificationPlanFile = qualificationPlanFile, + outputFolder = reInputFolder, + pkSimPortableFolder = pkSimPortableFolder, + configurationPlanName = configurationPlanName, + overwrite = overwrite, + logFile = logFile, + logLevel = logLevel + ) + + #' Print timer tracked time if option `recordWorkflowTime` is set to TRUE + if (recordWorkflowTime) { + toc <- as.numeric(Sys.time()) + print(paste0("Qualification Runner Duration: ", round((toc - tic) / 60, 1), " minutes")) + } + + #-------- STEP 3: Run Qualification Workflow --------# + # If version info is provided update title page + titlePageFile <- file.path(reInputFolder, "Intro/titlepage.md") + if(!is.null(versionInfo) & file.exists(titlePageFile)){ + adjustTitlePage(titlePageFile, qualificationVersionInfo = versionInfo) + } + + #' Load `QualificationWorkflow` object from configuration plan + workflow <- loadQualificationWorkflow( + workflowFolder = reOutputFolder, + configurationPlanFile = configurationPlanFile + ) + + #' Set the name of the final report + workflow$reportFilePath <- reportPath + workflow$createWordReport <- createWordReport + workflow$wordConversionTemplate <- wordConversionTemplate + + #' Set watermark. If set, it will appear in all generated plots + workflow$setWatermark(watermark) + + #' Set the maximimum number of simulations per core if defined + if(!is.null(maxSimulationsPerCore)){ + workflow$simulate$settings$maxSimulationsPerCore <- maxSimulationsPerCore + } + + #' Activate/Deactivate tasks of qualification workflow prior running + # workflow$inactivateTasks("simulate") + # workflow$inactivateTasks("calculatePKParameters") + # workflow$inactivateTasks("plotTimeProfiles") + # workflow$inactivateTasks("plotComparisonTimeProfile") + # workflow$inactivateTasks("plotGOFMerged") + # workflow$inactivateTasks("plotPKRatio") + # workflow$inactivateTasks("plotDDIRatio") + + workflow$plotPKRatio$settings$units$C_max <- "ng/mL" + + #' Run the `QualificatitonWorklfow` + workflow$runWorkflow() + + #' Print timer tracked time if option `recordWorkflowTime` is set to TRUE + if (recordWorkflowTime) { + toc <- as.numeric(Sys.time()) + print(paste0("Qualification Workflow Total Duration: ", round((toc - tic) / 60, 1), " minutes")) + } + return(invisible()) +}