From d765fbb4c3f71894131fe630a16befa23c15ee8f Mon Sep 17 00:00:00 2001 From: Nathan Kosiba Date: Tue, 8 Feb 2022 16:32:18 +0000 Subject: [PATCH 1/2] Begin qualification documents for AE assessment pipeline --- DESCRIPTION | 5 ++-- vignettes/validation/.gitignore | 1 + .../Specifications_for_AE_Assessment.md | 21 +++++++++++++++ .../Test_Cases_for_AE_Assessment.md | 27 +++++++++++++++++++ vignettes/validation/validation.yml | 15 +++++++++++ 5 files changed, 67 insertions(+), 2 deletions(-) create mode 100644 vignettes/validation/.gitignore create mode 100644 vignettes/validation/requirements/Specifications_for_AE_Assessment.md create mode 100644 vignettes/validation/test_cases/Test_Cases_for_AE_Assessment.md create mode 100644 vignettes/validation/validation.yml diff --git a/DESCRIPTION b/DESCRIPTION index 42af4900d..7500f08b2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,8 +9,9 @@ License: file LICENSE Encoding: UTF-8 Imports: dplyr, - lubridate, - magrittr + lubridate, + magrittr, + valtools Suggests: testthat (>= 3.0.0), safetyData, diff --git a/vignettes/validation/.gitignore b/vignettes/validation/.gitignore new file mode 100644 index 000000000..f9be8dfe0 --- /dev/null +++ b/vignettes/validation/.gitignore @@ -0,0 +1 @@ +!* diff --git a/vignettes/validation/requirements/Specifications_for_AE_Assessment.md b/vignettes/validation/requirements/Specifications_for_AE_Assessment.md new file mode 100644 index 000000000..ea857f04d --- /dev/null +++ b/vignettes/validation/requirements/Specifications_for_AE_Assessment.md @@ -0,0 +1,21 @@ +#' @title Specifications for AE Assessment +#' @editor Nathan Kosiba +#' @editDate 2022-02-08 +#' @riskAssessment +#' 1.1: 1, High Risk, High Impact +#' 1.2: 1, High Risk, High Impact +#' 1.3: 3, Low Risk, High Impact +#' 1.4: 2, Medium Risk, High Impact +#' 1.5: 4, Low Risk, Medium Impact +#' 1.6: 3, Medium Risk, Medium Impact + ++ 1.1 Given correct input data an Adverse Event assessment can be done using +the poisson method ++ 1.2 Given correct input data an Adverse Event assessment can be done using +the wilcoxon method ++ 1.3 Assessments are correctly grouped by the site variable ++ 1.4 Given correct input data an flags will correctly be applied to records that +meet flagging criteria ++ 1.5 Assessment can return all data in the standard data pipeline +(`dfInput`, `dfTransformed`, `dfAnalyzed`, `dfFlagged`, and `dfSummary`) ++ 1.6 Ensure that missing and invalid data are handled correctly diff --git a/vignettes/validation/test_cases/Test_Cases_for_AE_Assessment.md b/vignettes/validation/test_cases/Test_Cases_for_AE_Assessment.md new file mode 100644 index 000000000..748dc5277 --- /dev/null +++ b/vignettes/validation/test_cases/Test_Cases_for_AE_Assessment.md @@ -0,0 +1,27 @@ +#' @title Test_Cases_for_AE_Assessment +#' @editor Nathan Kosiba +#' @editDate 2022-02-08 +#' @coverage +#' 1.1: 1.1, 1.3 +#' 1.2: 1.2, 1.3 +#' 1.3: 1.4 +#' 1.4: 1.4 +#' 1.5: 1.5 +#' 1.6: 1.6 +#' 1.7: 1.6 + + ++ Setup: DOCUMENT ANY SETUP THAT NEEDS TO BE DONE FOR TESTING + ++ 1.1 Test that the AE assessment can return a correctly assessed data frame +for the poisson test grouped by the study variable when given correct input data ++ 1.2 Test that the AE assessment can return a correctly assessed data frame +for the wilcoxon test grouped by the study variable when given correct input data ++ 1.3 Test that sites are flagged with -1 when AE rate is lower than expected ++ 1.4 Test that sites are flagged with +1 when AE rate is higher than expected ++ 1.5 Test that Assessment can return all data in the standard data pipeline +(`dfInput`, `dfTransformed`, `dfAnalyzed`, `dfFlagged`, and `dfSummary`) ++ 1.6 Test that (NA, NaN) in input exposure data throws a warning and +drops the person from the analysis. ++ 1.7 Test that (NA, NaN) in input count data throws a warning and +drops the person from the analysis. diff --git a/vignettes/validation/validation.yml b/vignettes/validation/validation.yml new file mode 100644 index 000000000..4d22bfa09 --- /dev/null +++ b/vignettes/validation/validation.yml @@ -0,0 +1,15 @@ +package: gsm +working_dir: vignettes +output_dir: inst +report_rmd_name: qualification.Rmd +report_naming_format: Validation_Report_{package}_v{version}_{date} +usernames: + nathan.kosiba: + name: Nathan Kosiba + title: Developer + role: Validation Lead +validation_files: +- Specification_001.md +- Specification_002.md +- Specifications_for_AE_Assessment.md +- Test_Cases_for_AE_Assessment.md From 55c99d54227ecec601ed86234305db931f3314f6 Mon Sep 17 00:00:00 2001 From: Nathan Kosiba Date: Tue, 8 Feb 2022 16:50:52 +0000 Subject: [PATCH 2/2] Update yaml --- vignettes/validation/validation.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/vignettes/validation/validation.yml b/vignettes/validation/validation.yml index 4d22bfa09..1222d5396 100644 --- a/vignettes/validation/validation.yml +++ b/vignettes/validation/validation.yml @@ -2,14 +2,12 @@ package: gsm working_dir: vignettes output_dir: inst report_rmd_name: qualification.Rmd -report_naming_format: Validation_Report_{package}_v{version}_{date} +report_naming_format: Qualification_Report_{package}_v{version}_{date} usernames: nathan.kosiba: name: Nathan Kosiba title: Developer - role: Validation Lead + role: Qualification Lead validation_files: -- Specification_001.md -- Specification_002.md - Specifications_for_AE_Assessment.md - Test_Cases_for_AE_Assessment.md