Fix 107 ae assessment qualification docs

DESCRIPTION

@@ -9,9 +9,10 @@ License: file LICENSE
 Encoding: UTF-8
 Imports:
     dplyr,
-    lubridate, 
+    broom,
+    lubridate,
     magrittr,
-    broom
+    valtools
 Suggests:
     testthat (>= 3.0.0),
     safetyData,

vignettes/validation/.gitignore

@@ -0,0 +1 @@
+!*

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

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.

vignettes/validation/validation.yml

@@ -0,0 +1,13 @@
+package: gsm
+working_dir: vignettes
+output_dir: inst
+report_rmd_name: qualification.Rmd
+report_naming_format: Qualification_Report_{package}_v{version}_{date}
+usernames:
+  nathan.kosiba:
+    name: Nathan Kosiba
+    title: Developer
+    role: Qualification Lead
+validation_files:
+- Specifications_for_AE_Assessment.md
+- Test_Cases_for_AE_Assessment.md