diff --git a/.Rbuildignore b/.Rbuildignore index e13c405..fadfb40 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,7 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ +^vignettes/articles$ diff --git a/.gitignore b/.gitignore index c066a39..31d5365 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ inst/doc +docs diff --git a/DESCRIPTION b/DESCRIPTION index 3661db1..0d7d51b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,15 +32,18 @@ Imports: openxlsx, ospsuite.utils (>= 1.7.0), readxl -Remotes: +Remotes: ospsuite=Open-Systems-Pharmacology/OSPSuite-R@*release, ospsuite.utils=Open-Systems-Pharmacology/OSPSuite.RUtils@*release Suggests: devtools, + gt, knitr, rmarkdown, - testthat (>= 3.0.0) + testthat (>= 3.0.0), + tidyxl Config/testthat/edition: 3 VignetteBuilder: knitr Depends: R (>= 4.1.0) +Config/Needs/website: rmarkdown diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..b8aae29 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: https://www.open-systems-pharmacology.org/OSPSuite.QualificationPlanEditor/ +template: + bootstrap: 5 + diff --git a/inst/excel-display.R b/inst/excel-display.R new file mode 100644 index 0000000..64b9161 --- /dev/null +++ b/inst/excel-display.R @@ -0,0 +1,74 @@ +#' @title displayExcel +#' @description +#' A function that displays an Excel file with its styling +#' for pkgdown html format using `gt` and `tidyxl` packages +#' @param excelFile path of Excel file +#' @param level Section level for the displayed tab +#' @return Character string +displayExcel <- function(excelFile, level = 2) { + htmlContent <- paste( + paste0(rep("#", level), collapse = ""), + "Excel Content {.tabset .tabset-pills} \n\n" + ) + + excelSheets <- readxl::excel_sheets(excelFile) + excelFormats <- tidyxl::xlsx_formats(excelFile) + excelCells <- tidyxl::xlsx_cells(excelFile) + for (excelSheet in excelSheets) { + excelData <- openxlsx::readWorkbook(xlsxFile = excelFile, sheet = excelSheet, check.names = FALSE) + # Select content for the specific Excel sheet + dataCells <- excelCells |> + dplyr::filter(.data[["sheet"]] %in% excelSheet) |> + dplyr::filter(.data[["col"]] == 1) + # Create a list to define font and background styles for each row + dataStyles <- data.frame( + row = dataCells$row - 1, + color = excelFormats$local$font$color$rgb[dataCells$local_format_id], + fill = excelFormats$local$fill$patternFill$fgColor$rgb[dataCells$local_format_id] + ) |> + dplyr::mutate( + color = paste0("#", substr(.data[["color"]], 3, nchar(.data[["color"]]))), + fill = paste0("#", substr(.data[["fill"]], 3, nchar(.data[["fill"]]))), + color = ifelse(.data[["color"]] %in% "#NA", "#000000", .data[["color"]]), + fill = ifelse(.data[["fill"]] %in% "#NA", "#ffffff", .data[["fill"]]) + ) + dataStyles <- split(tail(dataStyles, -1), 1:(nrow(dataStyles) - 1)) + excelTable <- styleExcelData(excelData, dataStyles) + + htmlContent <- c( + htmlContent, + paste( + paste0(rep("#", level + 1), collapse = ""), + excelSheet, + "\n\n", + gt::as_raw_html(excelTable), + "\n\n" + ) + ) + } + return(htmlContent) +} + +#' @title styleExcelData +#' @description +#' A function to apply Excel styles in each row of a data.frame +#' @param data A data.frame +#' @param styles A list of `color`, `fill` styles mapped to a `row` +#' @return A `gt` table +styleExcelData <- function(data, styles) { + gtTable <- gt::gt(data) + if (nrow(data) == 0) { + return(gtTable) + } + for (style in styles) { + gtTable <- gtTable |> + gt::tab_style( + style = list( + gt::cell_fill(color = style$fill), + gt::cell_text(color = style$color) + ), + locations = gt::cells_body(rows = style$row) + ) + } + return(gtTable) +} diff --git a/vignettes/articles/.gitignore b/vignettes/articles/.gitignore new file mode 100644 index 0000000..097b241 --- /dev/null +++ b/vignettes/articles/.gitignore @@ -0,0 +1,2 @@ +*.html +*.R diff --git a/vignettes/articles/Verapamil-Model.json b/vignettes/articles/Verapamil-Model.json 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(n=6)", + "McAllister 1982 - Verapamil 10 mg IV - Verapamil - IV - 10 mg - Plasma - agg. (n=20)", + "Streit 2005 - intravenous verapamil during normoxia (5 mg) - Verapamil - IV - 5 mg - Plasma - agg. (n=10)", + "Eichelbaum 1984 - Subject 4 - R-Verapamil - IV - 5 mg - Plasma - indiv.", + "Eichelbaum 1984 - Subject 4 - R-Verapamil - IV - 25 mg - Plasma - indiv.", + "Eichelbaum 1984 - Subject 4 - R-Verapamil - IV - 50 mg - Plasma - indiv.", + "Eichelbaum 1984 - Subject 4 - S-Verapamil - IV - 5 mg - Plasma - indiv.", + "Eichelbaum 1984 - Subject 4 - S-Verapamil - IV - 7.5 mg - Plasma - indiv.", + "Eichelbaum 1984 - Subject 4 - S-Verapamil - IV - 10 mg - Plasma - indiv.", + "Streit et al. 2005 - intravenous verapamil during normoxia (5 mg) - Norverapamil - IV - 5 mg - Plasma - agg. (n=10)", + "Abernethy et al. 1985 - 10mg Verapamil without cimetidine, IV - Verapamil - IV - 10 mg - Plasma - indiv.", + "Freedman et al. 1981 - Control Subject (Subject number 4) - Verapamil - IV - 13.1 mg - Plasma - indiv.", + "Abernethy et al. 1993 - Representative younger subject - Verapamil - IV - 20 mg - Plasma - indiv.", + "Abernethy et al. 1993 - Representative younger subject - R-Verapamil - IV - 20 mg - Plasma - indiv.", + "Abernethy et al. 1993 - Representative younger subject - S-Verapamil - IV - 20 mg - Plasma - indiv.", + "Johnston 1981 - Verapamil IV - Verapamil - IV - 0.1 mg/kg - Plasma - agg. (n=6)", + "Mooy et al. 1985 - Normal volunteers, 3mg IV - Verapamil - IV - 3 mg - Plasma - agg. (n=5)", + "Smith 1984 - IV 10 mg Verapamil control - Verapamil - IV - 10 mg - Plasma - agg. (n=8)", + "Wing et al. 1985 - 10mg Verapamil without cimetidine, IV - Verapamil - IV - 10 mg - Plasma - indiv." + ] + }, + { + "Name": "po SD", + "Classifiables": [ + "Barbarash 1988 - Verapamil PO control - Verapamil - PO - 120 mg - Serum - agg. (n=6)", + "McAllister 1982 - Verapamil 80 mg PO - Verapamil - PO - 80 mg - Plasma - agg. (n=20)", + "McAllister 1982 - Verapamil 120 mg PO - Verapamil - PO - 120 mg - Plasma - agg. (n=20)", + "McAllister 1982 - Verapamil 160 mg PO - Verapamil - PO - 160 mg - Plasma - agg. (n=20)", + "Hla 1987 - conventional Verapamil 120mg once daily (day 1) - Verapamil - PO - 120 mg - Plasma - agg. (n=10)", + "Karim 1995 - Verapamil total IR fasting - Verapamil - PO - 240 mg - Plasma - agg. (n=12)", + "Karim 1995 - Verapamil total SR fed - Verapamil - PO - 240 mg - Plasma - agg. (n=12)", + "Abernethy et al. 1985 - 120mg Verapamil without cimetidine, PO - Verapamil - PO - 120 mg - Plasma - indiv.", + "Vogelgesang et al. 1984 - Healthy volunteers - R-Verapamil - PO - 250 mg - Plasma - indiv.", + "Choi et al. 2008 - 60mg Verapamil in absence of oral atorvastatin - Verapamil - PO - 60 mg - Arterial Plasma - agg. (n=12)", + "Choi et al. 2008 - 60mg Verapamil in absence of oral atorvastatin - Norverapamil - PO - 60 mg - Arterial Plasma - agg. (n=12)", + "Ratiopharm 1988 - Unknown - Verapamil - PO - 80 mg - Plasma - agg. (n=16)", + "Ratiopharm 1988 - Unknown - Norverapamil - PO - 80 mg - Plasma - agg. (n=16)", + "Ratiopharm 1989 - Unknown - Verapamil - PO - 80 mg - Plasma - agg. (n=16)", + "Ratiopharm 1989 - Unknown - Norverapamil - PO - 80 mg - Plasma - agg. (n=16)", + "Boehringer 2018 - Unknown - R-Verapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Boehringer 2018 - Unknown - S-Verapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Boehringer 2018 - Unknown - R-Norverapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Boehringer 2018 - Unknown - S-Norverapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Härtter et al. 2012 - 120mg po SD - R-Verapamil - PO - 120 mg - Plasma - agg. (n=19)", + "Härtter et al. 2012 - 120mg po SD - S-Verapamil - PO - 120 mg - Plasma - agg. (n=19)", + "Härtter et al. 2012 - 120mg po SD - R-Norverapamil - PO - 120 mg - Plasma - agg. (n=19)", + "Härtter et al. 2012 - 120mg po SD - S-Norverapamil - PO - 120 mg - Plasma - agg. (n=19)", + "Blume, Mutschler 1983 - Verapamil - Verapamil - PO - 40 mg - Plasma - agg. (n=12)", + "Blume, Mutschler 1990 - Verapamil - Verapamil - PO - 40 mg - Plasma - agg. (n=24)", + "Blume, Mutschler 1989 - Verapamil - Verapamil - PO - 80 mg - Plasma - agg. (n=18)", + "Blume, Mutschler 1987 - Verapamil - Verapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Maeda 2011 - Verapamil 16 mg - Verapamil - PO - 16 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 16 mg - Norverapamil - Norverapamil - PO - 16 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 0.1 mg - Verapamil - PO - 0.1 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 0.1 mg - Norverapamil - Norverapamil - PO - 0.1 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 3 mg - Verapamil - PO - 3 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 3 mg - Norverapamil - Norverapamil - PO - 3 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 80 mg - Verapamil - PO - 80 mg - Plasma - agg. (n=8)", + "Maeda 2011 - Verapamil 80 mg - Norverapamil - Norverapamil - PO - 80 mg - Plasma - agg. (n=8)", + "Sawicki, Janicki 2002 - Healthy volunteers; conventional tablets - Verapamil - PO - 40 mg - Plasma - agg. (n=12)", + "Sawicki, Janicki 2002 - Healthy volunteers; conventional tablets - Norverapamil - PO - 40 mg - Plasma - agg. (n=12)", + "John et al. 1992 - Healthy volunteers - Verapamil - PO - 40 mg - Plasma - agg. (n=6)", + "Johnston 1981 - Verapamil PO - Verapamil - PO - 120 mg - Plasma - agg. (n=6)", + "Johnston 1981 - Verapamil PO - Norverapamil - PO - 120 mg - Plasma - agg. (n=6)", + "Mooy et al. 1985 - Normal volunteers, 80mg PO - Verapamil - PO - 80 mg - Plasma - agg. (n=6)", + "Mooy et al. 1985 - Normal volunteers, 80mg PO - Norverapamil - PO - 80 mg - Plasma - agg. (n=6)", + "Smith 1984 - PO 120 mg Verapamil control - Verapamil - PO - 120 mg - Plasma - agg. (n=8)", + "Wing et al. 1985 - 80mg Verapamil without cimetidine, PO - Verapamil - PO - 80 mg - Plasma - indiv.", + "Mikus et al. 1990 - 160mg verapamil without cimetidine, PO - R-Verapamil - PO - 160 mg - Plasma - indiv.", + "Mikus et al. 1990 - 160mg verapamil without cimetidine, PO - S-Verapamil - PO - 160 mg - Plasma - indiv." + ] + }, + { + "Name": "po MD", + "Classifiables": [ + "Backman 1994 - Verapamil - Verapamil - PO - 80 mg - Plasma - agg. (n=9)", + "Hla 1987 - conventional Verapamil 120mg twice daily (day 10) - Verapamil - PO - 120 mg - Plasma - agg. (n=10)", + "Jorgensen 1988 - Conventional Verapamil 120 mg BID (day 1 - 5 and 8) - Verapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Jorgensen 1988 - Conventional Verapamil 120 mg BID (day 8) - Verapamil - PO - 120 mg - Plasma - agg. (n=12)", + "Jorgensen 1988 - Sustained release Verapamil 240 mg OD (day 1 - 5 and 8) - Verapamil - PO - 240 mg - Plasma - agg. (n=12)", + "Jorgensen 1988 - Sustained release Verapamil 240 mg OD (day 8) - Verapamil - PO - 240 mg - Plasma - agg. (n=12)", + "Shand 1981 - Verapamil day 1 - Verapamil - PO - 120 mg - Plasma - agg. (n=6)", + "Shand 1981 - Verapamil day 3 (after 7th dose) - Verapamil - PO - 120 mg - Plasma - agg. (n=6)", + "Johnson 2001 - Verapamil Steady State - Verapamil - PO - 80 mg - Plasma - agg. (n=12)", + "Härtter et al. 2012 - 120mg po bid - R-Verapamil - PO - 120 mg - Plasma - agg. (n=20)", + "Härtter et al. 2012 - 120mg po bid - S-Verapamil - PO - 120 mg - Plasma - agg. (n=20)", + "Härtter et al. 2012 - 120mg po bid - R-Norverapamil - PO - 120 mg - Plasma - agg. (n=20)", + "Härtter et al. 2012 - 120mg po bid - S-Norverapamil - PO - 120 mg - Plasma - agg. (n=20)", + "van Haarst et al. 2009 - Verapamil only - Verapamil - PO - 180 mg - Plasma - agg. (n=10)", + "van Haarst et al. 2009 - Verapamil only - Norverapamil - PO - 180 mg - Plasma - agg. (n=10)", + "Blume, Mutschler 1994 - Verapamil - Verapamil - PO - 240 mg - Plasma - agg. (n=24)", + "Johnson 2001 - Verapamil Steady State - Norverapamil - PO - 80 mg - Plasma - agg. (n=12)" + ] + } + ], + "SimulationClassifications": [ + { + "Name": "IV SD", + "Classifiables": [ + "iv_R-Verapamil 50 mg (5 min), Eichelbaum 1984, n=1", + "iv_Verapamil 3 mg SD (5min), Mooy 1985, n=5", + "iv_Verapamil 5 mg SD (5min), Streit 2005, n=10", + "iv_Verapamil 0.1 mg/kg SD (5min), Johnston 1981, n=6", + "iv_Verapamil 10mg SD (10min), Abernethy 1985, n=1", + "iv_Verapamil 10mg SD (10min), Barbarash 1988, n=6", + "iv_Verapamil 10mg SD (5min), McAllister, Kirsten 1982, n=20", + "iv_Verapamil 13.1 mg SD (13min), Freedman 1981, n=1", + "iv_Verapamil 20mg SD (30min), Abernethy 1993, n=1", + "iv_R-Verapamil 5 mg (5 min), Eichelbaum 1984, n=1", + "iv_R-Verapamil 25 mg (5 min), Eichelbaum 1984, n=1", + "iv_S-Verapamil 5 mg SD (5min), Eichelbaum 1984, n=1", + "iv_S-Verapamil 7.5 mg SD (5min), Eichelbaum 1984, n=1", + "iv_S-Verapamil 10 mg SD (5min), Eichelbaum 1984, n=1", + "iv_Verapamil 10 mg (bol), Smith 1984, n=8", + "iv_Verapamil 10mg SD (10min), Wing 1985, n=1" + ] + }, + { + "Name": "PO SD", + "Classifiables": [ + "po_Verapamil 120 mg SD (IR), Haertter 2012, n=19", + "po_Verapamil 16 mg SD (sol), Maeda 2011, n=8", + "po_Verapamil 80 mg SD, Mooy 1985, n=6", + "po_Verapamil 120 mg SD, Johnston 1981, n=6", + "po_Verapamil 120mg SD, Abernethy 1985, n=1", + "po_R-Verapamil 250mg SD, Vogelgesang 1984, n=1", + "po_Verapamil 0.1 mg SD (sol), Maeda 2011, n=8", + "po_Verapamil 3 mg SD (sol), Maeda 2011, n=8", + "po_Verapamil 80 mg SD (sol), Maeda 2011, n=8", + "po_Verapamil 40 mg SD, John 1992, n=6", + "po_Verapamil 40 mg SD, Sawicki, Janicki 2002, n=12", + "po_Verapamil 60 mg SD, Choi 2008, n=12", + "po_Verapamil 80 mg SD, Ratiopharm 1988, n=16", + "po_Verapamil 80 mg (2 40mg tab) SD, Ratiopharm 1989, n=16", + "po_Verapamil 120 mg (IR tab) SD, Boehringer 2018, n=12", + "po_Verapamil 120 mg SD, Hla 1987, n=10", + "po_Verapamil 80 mg SD, Blume, Mutschler 1989, n=18", + "po_Verapamil 120 mg SD, Blume, Mutschler 1987, n=12", + "po_Verapamil 40 mg SD, Blume, Mutschler 1990, n=24", + "po_Verapamil 40 mg SD, Blume, Mutschler 1983, n=12", + "po_Verapamil 120 mg SD, Barbarash 1988, n=6", + "po_Verapamil 80mg SD, McAllister, Kirsten 1982, n=20", + "po_Verapamil 120mg SD, McAllister, Kirsten 1982, n=20", + "po_Verapamil 160mg SD, McAllister, Kirsten 1982, n=20", + "po_Verapamil 240 mg SD, Karim 1995, n=12", + "po_Verapamil 120 mg SD, Smith 1984, n=8", + "po_Verapamil 80mg SD, Wing 1985, n=1", + "po_Verapamil 160 mg SD, Mikus 1990, n=1" + ] + }, + { + "Name": "PO MD", + "Classifiables": [ + "po_Verapamil 240 mg QD (SR), Blume, Mutschler 1994, n=24", + "po_Verapamil 80 mg tid 7rep, Johnson 2001, n=12", + "po_Verapamil 120 mg (IR) bid 3days, Haertter 2012, n=20", + "po_Verapamil 120 mg MD, Hla 1987, n=10", + "po_Verapamil 180mg PO BID 3days,van Haarst 2009, n=10", + "po_Verapamil 80mg PO TID 5rep, Backman 1994, n=9", + "po_Verapamil 120mg PO BID 8days, Jorgensen 1988, n=12", + "po_Verapamil 240mg PO OD 8days sustained realese, Jorgensen 1988, n=12", + "po_Verapamil 120mg PO TID 7rep, Shand 1981, n=6" + ] + } + ] +} \ No newline at end of file diff --git a/vignettes/articles/excel-template.Rmd b/vignettes/articles/excel-template.Rmd new file mode 100644 index 0000000..e33b6d6 --- /dev/null +++ b/vignettes/articles/excel-template.Rmd @@ -0,0 +1,152 @@ +--- +title: "Excel Template" +output: + rmarkdown::html_vignette: + tabset: true +vignette: > + %\VignetteIndexEntry{Excel Template} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +``` + +```{r setup} +library(ospsuite.qualificationplaneditor) +``` + +## Context + +This article describes the Excel template to be edited to create or update a qualification plan. + +## Color convention + +In the Excel template, many cells are filled with colors that follows the convention defined below: + +### Header + +Two background colors are used for headers: + +- Blue: data was found and corresponding Excel sheet was filled with project snapshots, observed datasets and/or qualification plan information +- Yellow: no data was found to fill corresponding sheet + +### Table rows + +- Green: project or observed dataset is not present in current qualification plan and assumed as to be **Added** to the qualification +- Grey: project or observed dataset is present in current qualification plan and
either not present in the list of added snapshots/observed dataset
or present but version/path is the same as in the qualification plan +- Yellow: project or observed dataset is present in current qualification plan and present in the list of added snapshots/observed dataset
while version/path is **Changed** between them + +## How to edit Excel sheets + +### MetaInfo + +Defines the version of the Qualification Plan Schema. The value should be formatted as `vX.Y`. + +You can check version tags on GitHub in [QualificationPlan](https://github.com/Open-Systems-Pharmacology/QualificationPlan/tags) repository. + +### Projects + +List project identifiers (`Id`) and their paths. +The background use the color convention defined above. + +This Excel sheet should not be edited. + +### Simulations_Outputs + +List simulations and outputs for each project. +The background use the color convention defined above. + +This Excel sheet should not be edited. + +### Simulations_ObsData + +List simulations and observed data for each project. +The background use the color convention defined above. + +This Excel sheet should not be edited. + +### ObsData + +List Observed dataset identifiers (`Id`), their paths and Type. +The background use the color convention defined above. + +You can edit the Type of Observed data. + +### BB + +List Building Blocks potential inheritance. +Fill the **Parent-Project** column for a project to inherit the corresponding building block from a parent project. + +An Excel data validation is set up to select from available projects. + +### SimParam + +List Simulated Parameters potential inheritance. +Fill the **Parent Project**, **Parent Simulation**, **Path** and **Target Simulation** columns for a project to inherit the corresponding simulated parameters from a parent project. + +Excel data validations are set up to select from available projects and simulations. + +### All_Plots + +List all plots evaluations for each project and simulation. + +Fill the **Section Reference** column to include the evaluation in the corresponding section. +Excel data validations are set up to select from available sections. + +### CT_Plots and CT_Mapping + +Define and list Comparison Time Profile (CT) plots. + +Excel data validations are set up to select from available sections, projects, simulations, observed data, etc. + +### GOF_Plots and GOF_Mapping + +Define and list Goodness of Fit (GOF) plots. + +Excel data validations are set up to select from available sections, projects, simulations, observed data, etc. + +### DDIRatio_Plots and DDIRatio_Mapping + +Define and list DDI Ratio plots. + +Excel data validations are set up to select from available sections, projects, simulations, observed data, etc. + +### PKRatio_Plots and PKRatio_Mapping + +Define and list PK Ratio plots. + +Excel data validations are set up to select from available sections, projects, simulations, observed data, etc. + +### Sections + +Define and list Qualification Report sections. + +Fill **Section Reference** tag to identify a section. +If section is a sub-section, fill the **Parent Section** column, Excel data validations are set up to select from available sections. + +### Intro + +Define the path of the markdown file used as introduction of your qualification report. + +### Inputs + +Fill the **Project**, **BB-Type**, **BB-Name** and **Section Reference** to include the Building Block definitions into the corresponding section of your qualification report. +Excel data validations are set up to select from available building blocks and sections. + +### GlobalPlotSettings + +Define the global settings of the exported figures including the size of the figure in pixels. + +### GlobalAxesSettings + +Define the global axes settings of the exported figures corresponding to dimensions, units and scales of the plots. + +### Lookup + +Look up table defining allowed values for qualification plan properties. + diff --git a/vignettes/articles/no-qualification.Rmd b/vignettes/articles/no-qualification.Rmd new file mode 100644 index 0000000..f9dc18b --- /dev/null +++ b/vignettes/articles/no-qualification.Rmd @@ -0,0 +1,68 @@ +--- +title: "Snapshot without a Qualification Plan" +output: + rmarkdown::html_vignette: + tabset: true +vignette: > + %\VignetteIndexEntry{Snapshot without a Qualification Plan} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +source(system.file("excel-display.R", package = "ospsuite.qualificationplaneditor")) +``` + +```{r setup} +library(ospsuite.qualificationplaneditor) +``` + +## Context + +This article shows how to create a Qualification Plan from scratch using a project snapshot. +The example used here is the [Verapamil-Model](https://github.com/Open-Systems-Pharmacology/Verapamil-Model) available on GitHub. + + +```{r} +snapshotPaths <- "Verapamil-Model.json" +qualificationPlan <- "qualification-verapamil.json" +excelFile <- "qualification-verapamil.xlsx" +``` + +## Conversion to Excel + +In order to assess and edit the qualification plan, the function `toExcelEditor()` will convert it into Excel format as illustrated below. + +```{r} +toExcelEditor( + fileName = excelFile, + snapshotPaths = snapshotPaths + ) +``` + +Users can then open and edit the Excel file converted from the Qualification Plan. +The code below will open the file using the default software reading `xlsx` files (such as Excel or Libre Office Calc). + +```r +utils::browseURL(excelFile) +``` + +The Excel file should include the content displayed below: + +```{r, results='asis',echo=FALSE} +cat(displayExcel(excelFile), sep = "\n") +``` + +## Convert back to json + +```r +excelToQualificationPlan( + excelFile = excelFile, + qualificationPlan = qualificationPlan +) +``` + diff --git a/vignettes/articles/qualification-verapamil.xlsx b/vignettes/articles/qualification-verapamil.xlsx new file mode 100644 index 0000000..317abcc Binary files /dev/null and b/vignettes/articles/qualification-verapamil.xlsx differ diff --git a/vignettes/articles/qualification_ugt.json b/vignettes/articles/qualification_ugt.json new file mode 100644 index 0000000..64e7fbe --- /dev/null +++ b/vignettes/articles/qualification_ugt.json @@ -0,0 +1,538 @@ +{ + "$schema": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/QualificationPlan/v3.3/schemas/OSP_Qualification_Plan_Schema.json", + "Projects": [ + { + "Id": "Mefenamic_acid", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Mefenamic-acid-Model/v2.0/Mefenamic_acid-Model.json", + "BuildingBlocks": [] + }, + { + "Id": "Dapagliflozin", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Dapagliflozin-Model/v2.0/Dapagliflozin-Model.json", + "BuildingBlocks": [] + }, + { + "Id": "Raltegravir", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Raltegravir-Model/v2.0/Raltegravir-Model.json", + "BuildingBlocks": [] + }, + { + "Id": "Atazanavir", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Atazanavir-Model/v2.0/Atazanavir-Model.json", + "BuildingBlocks": [] + }, + { + "Id": "Mefenamic_acid-Dapagliflozin-DDI", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Mefenamic_acid-Dapagliflozin-DDI/v1.2/Mefenamic_acid-Dapagliflozin-DDI.json", + "BuildingBlocks": [ + { + "Type": "Individual", + "Name": "Standard_Adult_UGT", + "Project": "Dapagliflozin" + }, + { + "Type": "Compound", + "Name": "Mefenamic acid", + "Project": "Mefenamic_acid" + }, + { + "Type": "Compound", + "Name": "Dapagliflozin", + "Project": "Dapagliflozin" + }, + { + "Type": "Formulation", + "Name": "Ponstan capsule", + "Project": "Mefenamic_acid" + } + ], + "SimulationParameters": [ + { + "Project": "Dapagliflozin", + "Simulation": "PO SD 10 mg (perm)", + "Path": "Dapagliflozin|logP (veg.oil/water)", + "TargetSimulations": [ + "DDI Control - Dapagliflozin - Kasichayanula 2013a", + "DDI Treatment - Mefenamic acid/Dapagliflozin - Kasichayanula 2013a" + ] + }, + { + "Project": "Dapagliflozin", + "Simulation": "PO SD 10 mg (perm)", + "Path": "Dapagliflozin|Blood/Plasma concentration ratio", + "TargetSimulations": [ + "DDI Control - Dapagliflozin - Kasichayanula 2013a", + "DDI Treatment - Mefenamic acid/Dapagliflozin - Kasichayanula 2013a" + ] + } + ] + }, + { + "Id": "Atazanavir-Raltegravir-DDI", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Atazanavir-Raltegravir-DDI/v1.1/Atazanavir-Raltegravir-DDI.json", + "BuildingBlocks": [ + { + "Type": "Compound", + "Name": "Raltegravir", + "Project": "Raltegravir" + }, + { + "Type": "Compound", + "Name": "Atazanavir", + "Project": "Atazanavir" + }, + { + "Type": "Formulation", + "Name": "Reyataz capsule", + "Project": "Atazanavir" + }, + { + "Type": "Formulation", + "Name": "filmcoated tablet (original Merck formulation)", + "Project": "Raltegravir" + } + ] + } + ], + "ObservedDataSets": [ + { + "Id": "DDI Ratios", + "Path": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Database-for-observed-data/v1.7/DDI.csv", + "Type": "DDIRatio" + } + ], + "Plots": { + "PlotSettings": { + "ChartWidth": 500, + "ChartHeight": 400, + "Fonts": { + "AxisSize": 11, + "LegendSize": 9, + "OriginSize": 9, + "FontFamilyName": "Arial", + "WatermarkSize": 40 + } + }, + "AxesSettings": { + "ComparisonTimeProfile": [ + { + "Unit": "h", + "Dimension": "Time", + "Type": "X", + "GridLines": false, + "Scaling": "Linear" + }, + { + "Unit": "ng/ml", + "Dimension": "Concentration (mass)", + "Type": "Y", + "GridLines": false, + "Scaling": "Log" + } + ], + "DDIRatioPlotsPredictedVsObserved": [ + { + "Unit": "", + "Dimension": "Dimensionless", + "Type": "X", + "GridLines": false, + "Scaling": "Log" + }, + { + "Unit": "", + "Dimension": "Dimensionless", + "Type": "Y", + "GridLines": false, + "Scaling": "Log" + } + ], + "DDIRatioPlotsResidualsVsObserved": [ + { + "Unit": "", + "Dimension": "Dimensionless", + "Type": "X", + "GridLines": false, + "Scaling": "Log" + }, + { + "Unit": "", + "Dimension": "Dimensionless", + "Type": "Y", + "GridLines": false, + "Scaling": "Log" + } + ] + }, + "AllPlots": [{ + "Project": "Raltegravir", + "Simulation": "tralala", + "SectionReference": "introduction" + }], + "ComparisonTimeProfilePlots": [ + { + "SectionReference": "atazanavir-raltegravir-ddi", + "Title": "Iwamoto 2008", + "SimulationDuration": 176, + "TimeUnit": "h", + "OutputMappings": [ + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Iwamoto2008_Raltegravir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Iwamoto 2008 - Study I, Period 1 (control) - Raltegravir - PO - 100 mg - Plasma - agg. (n=10)", + "StartTime": 0, + "TimeUnit": "h", + "Color": "#2166ac", + "Caption": "Control (without atazanavir)", + "Symbol": "Circle" + }, + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Iwamoto2008_Raltegravir+Atazanavir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Iwamoto 2008 - Study I, Period 2 (ATV treatment) - Raltegravir - PO - 100 mg - Plasma - agg. (n=10)", + "StartTime": 144, + "TimeUnit": "h", + "Color": "#b2182b", + "Caption": "Treatment (with atazanavir)", + "Symbol": "Square" + } + ] + }, + { + "SectionReference": "atazanavir-raltegravir-ddi", + "Title": "Krishna 2016", + "SimulationDuration": 216, + "TimeUnit": "h", + "OutputMappings": [ + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Krishna2016_Raltegravir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Krishna 2016 - Period 1, Day 1 (1200 mg raltegravir SD) - Raltegravir - PO - 1200 mg - Plasma - agg. (n=14)", + "StartTime": 0, + "TimeUnit": "h", + "Color": "#2166ac", + "Caption": "Control (without atazanavir)", + "Symbol": "Circle" + }, + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Krishna2016_Raltegravir+Atazanavir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Krishna 2016 - Period 2, Day 7 (1200 mg raltegravir SD with OD doses of 400 mg ATV) - Raltegravir - PO - 1200 mg - Plasma - agg. (n=12)", + "StartTime": 144, + "TimeUnit": "h", + "Color": "#b2182b", + "Caption": "Treatment (with atazanavir)", + "Symbol": "Square" + } + ] + }, + { + "SectionReference": "atazanavir-raltegravir-ddi", + "Title": "Neely 2010", + "SimulationDuration": 192, + "TimeUnit": "h", + "OutputMappings": [ + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Neely2010_Raltegravir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Neely 2010 - Study arm A (Raltegravir 400mg BID) - Raltegravir - PO - 400 mg - Plasma - agg. (n=20)", + "StartTime": 168, + "TimeUnit": "h", + "Color": "#2166ac", + "Caption": "Control (without atazanavir)", + "Symbol": "Circle" + }, + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Neely2010_Raltegravir+Atazanavir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Neely 2010 - Study arm B (Raltegravir 400mg OD + Atazanavir 400 mg OD) - Raltegravir - PO - 400 mg - Plasma - agg. (n=19)", + "StartTime": 168, + "TimeUnit": "h", + "Color": "#b2182b", + "Caption": "Treatment (with atazanavir)", + "Symbol": "Square" + } + ] + }, + { + "SectionReference": "atazanavir-raltegravir-ddi", + "Title": "Zhu 2010", + "SimulationDuration": 612, + "TimeUnit": "h", + "OutputMappings": [ + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Zhu2010_Raltegravir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Zhu 2010 - Raltegravir 400 mg twice daily - Raltegravir - PO - 400 mg - Plasma - agg. (n=22)", + "StartTime": 96, + "TimeUnit": "h", + "Color": "#2166ac", + "Caption": "Control (without atazanavir)", + "Symbol": "Circle" + }, + { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Zhu2010_Raltegravir+Atazanavir", + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "Zhu 2010 - Raltegravir 400 mg twice daily plus atazanavir 300 mg twice daily - Raltegravir - PO - 400 mg - Plasma - agg. (n=19)", + "StartTime": 600, + "TimeUnit": "h", + "Color": "#b2182b", + "Caption": "Treatment (with atazanavir)", + "Symbol": "Square" + } + ] + }, + { + "SectionReference": "mefenamic-acid-dapagliflozin-ddi", + "Title": "Kasichayanula 2013a", + "SimulationDuration": 48, + "TimeUnit": "h", + "OutputMappings": [ + { + "Project": "Mefenamic_acid-Dapagliflozin-DDI", + "Simulation": "DDI Control - Dapagliflozin - Kasichayanula 2013a", + "Output": "Organism|PeripheralVenousBlood|Dapagliflozin|Plasma (Peripheral Venous Blood)", + "ObservedData": "Kasichayanula 2013a - Study 2: Control (Perpetrator Placebo) - Dapagliflozin - PO - 10 mg - Plasma - agg. (n=16)", + "StartTime": 0, + "TimeUnit": "h", + "Color": "#2166ac", + "Caption": "Control (without mefenamic acid)", + "Symbol": "Circle" + }, + { + "Project": "Mefenamic_acid-Dapagliflozin-DDI", + "Simulation": "DDI Treatment - Mefenamic acid/Dapagliflozin - Kasichayanula 2013a", + "Output": "Organism|PeripheralVenousBlood|Dapagliflozin|Plasma (Peripheral Venous Blood)", + "ObservedData": "Kasichayanula 2013a - Study 2: with Perpetrator (Mefenamic Acid) - Dapagliflozin - PO - 10 mg - Plasma - agg. (n=16)", + "StartTime": 24, + "TimeUnit": "h", + "Color": "#b2182b", + "Caption": "Treatment (with mefenamic acid)", + "Symbol": "Square" + } + ] + } + ], + "DDIRatioPlots": [ + { + "SectionReference": "qualification-of-ugt-mediated-ddi", + "Title": "UGT1A1 and UGT1A9 Inhibition DDI", + "PKParameters": [ + "AUC", + "CMAX" + ], + "PlotTypes": [ + "predictedVsObserved", + "residualsVsObserved" + ], + "Artifacts": [ + "Plot", + "GMFE", + "Measure", + "Table" + ], + "Groups": [ + { + "Caption": "Atazanavir + Raltegravir", + "Color": "#b2182b", + "Symbol": "Circle", + "DDIRatios": [ + { + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "DDI Ratios", + "ObservedDataRecordId": 571, + "SimulationControl": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Iwamoto2008_Raltegravir", + "StartTime": 0, + "EndTime": 9999, + "TimeUnit": "h" + }, + "SimulationDDI": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Iwamoto2008_Raltegravir+Atazanavir", + "StartTime": 144, + "EndTime": 9999, + "TimeUnit": "h" + } + }, + { + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "DDI Ratios", + "ObservedDataRecordId": 575, + "SimulationControl": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Krishna2016_Raltegravir", + "StartTime": 0, + "EndTime": 9999, + "TimeUnit": "h" + }, + "SimulationDDI": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Krishna2016_Raltegravir+Atazanavir", + "StartTime": 144, + "EndTime": 9999, + "TimeUnit": "h" + } + }, + { + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "DDI Ratios", + "ObservedDataRecordId": 573, + "SimulationControl": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Neely2010_Raltegravir", + "StartTime": 168, + "EndTime": 180, + "TimeUnit": "h" + }, + "SimulationDDI": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Neely2010_Raltegravir+Atazanavir", + "StartTime": 168, + "EndTime": 192, + "TimeUnit": "h" + } + }, + { + "Output": "Organism|PeripheralVenousBlood|Raltegravir|Plasma (Peripheral Venous Blood)", + "ObservedData": "DDI Ratios", + "ObservedDataRecordId": 579, + "SimulationControl": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Zhu2010_Raltegravir", + "StartTime": 96, + "EndTime": 108, + "TimeUnit": "h" + }, + "SimulationDDI": { + "Project": "Atazanavir-Raltegravir-DDI", + "Simulation": "Zhu2010_Raltegravir+Atazanavir", + "StartTime": 600, + "EndTime": 612, + "TimeUnit": "h" + } + } + ] + }, + { + "Caption": "Mefenamic acid + Dapagliflozin", + "Color": "#2166ac", + "Symbol": "Square", + "DDIRatios": [ + { + "Output": "Organism|PeripheralVenousBlood|Dapagliflozin|Plasma (Peripheral Venous Blood)", + "ObservedData": "DDI Ratios", + "ObservedDataRecordId": 642, + "SimulationControl": { + "Project": "Mefenamic_acid-Dapagliflozin-DDI", + "Simulation": "DDI Control - Dapagliflozin - Kasichayanula 2013a", + "StartTime": 0, + "EndTime": 9999, + "TimeUnit": "h" + }, + "SimulationDDI": { + "Project": "Mefenamic_acid-Dapagliflozin-DDI", + "Simulation": "DDI Treatment - Mefenamic acid/Dapagliflozin - Kasichayanula 2013a", + "StartTime": 24, + "EndTime": 9999, + "TimeUnit": "h" + } + } + ] + } + ] + } + ] + }, + "Inputs": [], + "Sections": [ + { + "Reference": "introduction", + "Title": "Introduction", + "Sections": [ + { + "Reference": "objective", + "Title": "Objective", + "Content": "Content/Qualification_DDI_UGT_objective.md" + }, + { + "Reference": "ugt-ddi-network", + "Title": "UGT DDI Network", + "Content": "Content/Qualification_DDI_UGT_network_description.md", + "Sections": [ + { + "Reference": "network-atazanavir-raltegravir-ddi", + "Title": "Atazanavir - Raltegravir DDI", + "Content": "Content/ATV-RAL-DDI.md" + }, + { + "Reference": "network-mefenamic-acid-dapagliflozin-ddi", + "Title": "Mefenamic acid - Dapagliflozin DDI", + "Content": "Content/MEFA-Dapa-DDI.md" + } + ] + } + ] + }, + { + "Reference": "qualification-of-ugt-mediated-ddi", + "Title": "Qualification of Use Case UGT-mediated DDI", + "Content": "Content/Intro_evaluation_DDI_network.md" + }, + { + "Reference": "ct-profiles", + "Title": "Concentration-Time Profiles", + "Content": "Content/Intro_evaluation_CTprofiles.md", + "Sections": [ + { + "Reference": "atazanavir-raltegravir-ddi", + "Title": "Atazanavir - Raltegravir DDI" + }, + { + "Reference": "mefenamic-acid-dapagliflozin-ddi", + "Title": "Mefenamic acid - Dapagliflozin DDI" + } + ] + }, + { + "Reference": "main-references", + "Title": "References", + "Content": "Content/References.md", + "Sections": [] + }, + { + "Reference": "appendix", + "Title": "Appendix", + "Sections": [ + { + "Reference": "osp-introduction", + "Title": "Open Systems Pharmacology Suite (OSPS) Introduction", + "Content": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Qualification-text-modules/v1.3/OSPS_Introduction.md" + }, + { + "Reference": "mathematical-implementation-of-ddi", + "Title": "Mathematical Implementation of Drug-Drug Interactions", + "Content": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Qualification-text-modules/v1.3/Mathematical_Implementation_of_DDI.md" + }, + { + "Reference": "automatic-requalification-workflow", + "Title": "Automatic (re)-qualification workflow", + "Content": "https://raw.githubusercontent.com/Open-Systems-Pharmacology/Qualification-text-modules/v1.3/Qualification_Workflow.md" + } + ] + } + ], + "Intro": [ + { + "Path": "Content/titlepage.md" + } + ] +} \ No newline at end of file diff --git a/vignettes/articles/qualification_ugt.xlsx b/vignettes/articles/qualification_ugt.xlsx new file mode 100644 index 0000000..0f63401 Binary files /dev/null and b/vignettes/articles/qualification_ugt.xlsx differ diff --git a/vignettes/articles/snapshot-qualification.Rmd b/vignettes/articles/snapshot-qualification.Rmd new file mode 100644 index 0000000..76fd6db --- /dev/null +++ b/vignettes/articles/snapshot-qualification.Rmd @@ -0,0 +1,68 @@ +--- +title: "Add a Snapshot to my Qualification Plan" +output: + rmarkdown::html_vignette: + tabset: true +vignette: > + %\VignetteIndexEntry{Add a Snapshot to my Qualification Plan} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +source(system.file("excel-display.R", package = "ospsuite.qualificationplaneditor")) +``` + +```{r setup} +library(ospsuite.qualificationplaneditor) +``` + +## Context + +This article shows how to add and integrate a project Snapshot (json) into a Qualification Plan. +The example used here is the qualification plan for UGT1A1- and UGT1A9-mediated inhibition drug-drug interactions (DDI) available in the [Qualification-DDI-UGT](https://github.com/Open-Systems-Pharmacology/Qualification-DDI-UGT) GitHub repository and the project snapshot [Verapamil-Model](https://github.com/Open-Systems-Pharmacology/Verapamil-Model) also available on GitHub. + + +```{r} +snapshotPaths <- "Verapamil-Model.json" +qualificationPlan <- "qualification_ugt.json" +excelFile <- "qualification_ugt.xlsx" +``` + +## Conversion to Excel + +In order to assess and edit the qualification plan, the function `toExcelEditor()` will convert it into Excel format as illustrated below. + +```{r} +toExcelEditor( + fileName = excelFile, + snapshotPaths = snapshotPaths, + qualificationPlan = qualificationPlan + ) +``` + +Users can then open and edit the Excel file converted from the Qualification Plan. +The code below will open the file using the default software reading `xlsx` files (such as Excel or Libre Office Calc). + +```r +utils::browseURL(excelFile) +``` + +The Excel file should include the content displayed below: + +```{r, results='asis',echo=FALSE} +cat(displayExcel(excelFile), sep = "\n") +``` + +## Convert back to json + +```r +excelToQualificationPlan( + excelFile = excelFile, + qualificationPlan = paste0("updated-", qualificationPlan) +) +``` diff --git a/vignettes/articles/update-qualification.Rmd b/vignettes/articles/update-qualification.Rmd new file mode 100644 index 0000000..a30d406 --- /dev/null +++ b/vignettes/articles/update-qualification.Rmd @@ -0,0 +1,66 @@ +--- +title: "Update my Qualification Plan Evaluations" +output: + rmarkdown::html_vignette: + tabset: true +vignette: > + %\VignetteIndexEntry{Update my Qualification Plan Evaluations} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) +source(system.file("excel-display.R", package = "ospsuite.qualificationplaneditor")) +``` + +```{r setup} +library(ospsuite.qualificationplaneditor) +``` + +## Context + +This article shows how to check and update the evaluations of a qualification plan. +The example used here is the qualification plan for UGT1A1- and UGT1A9-mediated inhibition drug-drug interactions (DDI) available in the [Qualification-DDI-UGT](https://github.com/Open-Systems-Pharmacology/Qualification-DDI-UGT) GitHub repository. + + +```{r} +qualificationPlan <- "qualification_ugt.json" +excelFile <- "qualification_ugt.xlsx" +``` + +## Conversion to Excel + +In order to assess and edit the qualification plan, the function `toExcelEditor()` will convert it into Excel format as illustrated below. + +```{r} +toExcelEditor( + fileName = excelFile, + qualificationPlan = qualificationPlan + ) +``` + +Users can then open and edit the Excel file converted from the Qualification Plan. +The code below will open the file using the default software reading `xlsx` files (such as Excel or Libre Office Calc). + +```r +utils::browseURL(excelFile) +``` + +The Excel file should include the content displayed below: + +```{r, results='asis',echo=FALSE} +cat(displayExcel(excelFile), sep = "\n") +``` + +## Convert back to json + +```r +excelToQualificationPlan( + excelFile = excelFile, + qualificationPlan = paste0("updated-", qualificationPlan) +) +``` diff --git a/vignettes/ospsuite-qualificationplaneditor.Rmd b/vignettes/ospsuite-qualificationplaneditor.Rmd index 36beaf7..7c8d3cf 100644 --- a/vignettes/ospsuite-qualificationplaneditor.Rmd +++ b/vignettes/ospsuite-qualificationplaneditor.Rmd @@ -1,6 +1,8 @@ --- title: "Get Started" -output: rmarkdown::html_vignette +output: + rmarkdown::html_vignette: + tabset: true vignette: > %\VignetteIndexEntry{Get Started} %\VignetteEngine{knitr::rmarkdown} @@ -12,20 +14,73 @@ knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) +source(system.file("excel-display.R", package = "ospsuite.qualificationplaneditor")) ``` ```{r setup} -# library(ospsuite.qualificationplaneditor) +library(ospsuite.qualificationplaneditor) ``` - The OSPSuite.QualificationPlanEditor package is designed to help you convert qualification plans from/into Excel format for easier editing. The package provides functionality to parse project snapshots, extract simulation data, and generate Excel workbooks with structured data sheets that can be edited and converted back to qualification plans. -## Example +## Workflow + +To create or update a qualification plan, the workflow is: + +1. Define a list of project snapshots and/or observed datasets +2. Define a Qualification Plan +3. Convert them to Excel +4. Edit the Qualification Plan in Excel +5. Convert back Qualification Plan to json format +6. Run the updated Qualification + + +## Fetch latest release + +Steps 1 and 2 usually involve to use the latest release version of project snapshots, observed data and qualification plans. This can be done using the function `getLatestReleasedPaths()` as illustrated below: + +``` r +# Get latest released paths from a qualification plan +latestPaths <- getLatestReleasedPaths( + qualificationPlan = "path/to/qualification_plan.json", + includePreReleases = FALSE, + returnUpdatedOnly = TRUE +) + +# Access the updated project and observed data paths +latestProjectPaths <- latestPaths$projects +latestObservedDataPaths <- latestPaths$observedData + +# You can also ignore specific projects or observed data +latestPaths <- getLatestReleasedPaths( + qualificationPlan = "path/to/qualification_plan.json", + projectsToIgnore = c("ProjectA", "ProjectB"), + observedDataToIgnore = c("ObsData1") +) + +# Get all paths (not just updated ones) +allPaths <- getLatestReleasedPaths( + qualificationPlan = "path/to/qualification_plan.json", + returnUpdatedOnly = FALSE +) +``` + +## Excel file content + +The article [Excel Template](./excel-template.html) describes the content of the Excel template file, its color and data validation conventions and how to edit before converting back to json format. + +## Examples + +Below is a basic example with generic names showing how to include an updated project snapshot in your qualification plan: + +For more detailed examples, you can read the following articles: + +- [Update my Qualification Plan Evaluations](./update-qualification.html) +- [Add a Snapshot to my Qualification Plan](./snapshot-qualification.html) +- [Snapshot without a Qualification Plan](./no-qualification.html) -Here is a basic example showing how to include an updated project snapshot in your qualification plan: ``` r ## Load the ospsuite.qualificationplaneditor package @@ -62,33 +117,9 @@ utils::browseURL(excelQualification) ``` -## Automatically Get Latest Released Paths - -The `getLatestReleasedPaths()` function helps you automatically fetch the latest released versions of projects and observed data from your qualification plan: - -``` r -# Get latest released paths from a qualification plan -latestPaths <- getLatestReleasedPaths( - qualificationPlan = "path/to/qualification_plan.json", - includePreReleases = FALSE, - returnUpdatedOnly = TRUE -) - -# Access the updated project and observed data paths -latestProjectPaths <- latestPaths$projects -latestObservedDataPaths <- latestPaths$observedData - -# You can also ignore specific projects or observed data -latestPaths <- getLatestReleasedPaths( - qualificationPlan = "path/to/qualification_plan.json", - projectsToIgnore = c("ProjectA", "ProjectB"), - observedDataToIgnore = c("ObsData1") -) +## Testing of the converted Qualification Plan -# Get all paths (not just updated ones) -allPaths <- getLatestReleasedPaths( - qualificationPlan = "path/to/qualification_plan.json", - returnUpdatedOnly = FALSE -) -``` +To ensure that the converted qualification and evaluation plans provide appropriate evaluations, the following qualification plans are tested in the repo [RE-Test-Reports](https://github.com/Open-Systems-Pharmacology/RE-Test-Reports) +- [Qualification-DDI-UGT](https://github.com/Open-Systems-Pharmacology/Qualification-DDI-UGT) +- TBD