add PK KRI options. fix #1919 #1911

R/util-MakeBounds.R

@@ -60,6 +60,9 @@ MakeBounds <- function(
         as.list()
       vThreshold <- ParseThreshold(strThreshold = lMetric$Threshold)
       if (!is.null(lMetric$AnalysisType) &&
+        tolower(unique(lMetric$AnalysisType)) %in% c("identity")) {
+        dfBounds <- NULL 
+      } else if (!is.null(lMetric$AnalysisType) &&
         tolower(unique(lMetric$AnalysisType)) %in% c("poisson")) {
         dfBounds <- Analyze_Poisson_PredictBounds(
           dfResult,

inst/examples/pk_kri.R

@@ -0,0 +1,76 @@
+devtools::load_all()
+library(tidyr)
+set.seed(1234)
+
+# Step 0 - Simulate PK data for clindata participants
+mapped_pk <- tidyr::crossing(
+    subjid = unique(clindata::rawplus_dm$subjid),
+    pktpt = c( 
+        "Cycle 1 Day 1",
+        "Cycle 1 Day 1",
+        "Cycle 1 Day 1",
+        "Cycle 1 Day 15",
+        "Cycle 1 Day 2",
+        "Cycle 1 Day 4",
+        "Cycle 1 Day 8"
+    )
+)
+mapped_pk$pkperf <- sample(c("Yes","No"), prob=c(0.95,0.05),nrow(mapped_pk), replace = TRUE)
+
+pk_data <-list(
+  Mapped_SUBJ= clindata::rawplus_dm,
+  Mapped_PK= mapped_pk
+)
+
+# Example 1 - Standard KRI with normal approximation
+pk_kri <- gsm::RunWorkflows(
+  lWorkflow = MakeWorkflowList(strName = "kri0013.yaml"), 
+  lData = pk_data
+)
+Widget_BarChart(dfResults = pk_kri$Analysis_kri0013$Analysis_Summary)
+
+# Example 2 - KRI with custom flagging based on 90% threshold
+
+pk_kri_alt <- gsm::RunWorkflows(
+  lWorkflow = MakeWorkflowList(strName = "kri0013a.yaml"), 
+  lData = pk_data
+)
+Widget_BarChart(dfResults = pk_kri_alt$Analysis_kri0013a$Analysis_Summary)
+
+
+# Example 3 - Run Reports with other KRIs
+lSource <- list(
+    Source_SUBJ = clindata::rawplus_dm,
+    Source_AE = clindata::rawplus_ae,
+    Source_PD = clindata::ctms_protdev,
+    Source_LB = clindata::rawplus_lb,
+    Source_STUDCOMP = clindata::rawplus_studcomp,
+    Source_SDRGCOMP = clindata::rawplus_sdrgcomp %>% dplyr::filter(.data$phase == 'Blinded Study Drug Completion'),
+    Source_DATACHG = clindata::edc_data_points,
+    Source_DATAENT = clindata::edc_data_pages,
+    Source_QUERY = clindata::edc_queries,
+    Source_ENROLL = clindata::rawplus_enroll,
+    Source_SITE = clindata::ctms_site,
+    Source_STUDY = clindata::ctms_study,
+    Source_PK = pk_data$Mapped_PK # only new line
+)
+
+# Step 0 - Data Ingestion - standardize tables/columns names
+mappings_wf <- MakeWorkflowList(strPath = "workflow/1_mappings")
+mappings_spec <- CombineSpecs(mappings_wf)
+lRaw <- Ingest(lSource, mappings_spec)
+
+# Step 1 - Create Mapped Data Layer - filter, aggregate and join raw data to create mapped data layer
+mapped <- RunWorkflows(mappings_wf, lRaw)
+
+# Step 2 - Create Metrics - calculate metrics using mapped data
+metrics_wf <- MakeWorkflowList(strPath = "workflow/2_metrics")
+analyzed <- RunWorkflows(metrics_wf, mapped)
+
+# Step 3 - Create Reporting Layer - create reports using metrics data
+reporting_wf <- MakeWorkflowList(strPath = "workflow/3_reporting")
+reporting <- RunWorkflows(reporting_wf, c(mapped, list(lAnalyzed = analyzed, lWorkflows = metrics_wf)))
+
+# Step 4 - Create KRI Report - create KRI report using reporting data
+module_wf <- MakeWorkflowList(strPath = "workflow/4_modules")
+lReports <- RunWorkflows(module_wf, reporting)

inst/workflow/1_mappings/PK.yaml

@@ -0,0 +1,23 @@
+meta:
+  Type: Mapped
+  ID: PK
+  Description: PK Data Mapping 
+  Priority: 1
+spec: 
+ Raw_PK:
+    subjid:
+      required: true
+      type: character
+    pktpt:
+      required: true
+      type: character
+    pkperf:
+      required: true
+      type: character
+steps:
+  - output: Mapped_PK
+    name: =
+    params:
+      lhs: Mapped_PK
+      rhs: Raw_PK
+

inst/workflow/2_metrics/kri0013.yaml

@@ -0,0 +1,81 @@
+meta:
+  Type: Analysis
+  ID: kri0013
+  GroupLevel: Site
+  Abbreviation: PK
+  Metric: PK Rate
+  Numerator: PK Measures Completed
+  Denominator: PK Measures Expected
+  Model: Normal Approximation
+  Score: Adjusted Z-Score
+  AnalysisType: binary
+  Threshold: -3,-2,2,3
+  nMinDenominator: 10
+spec:
+  Mapped_SUBJ:
+    subjid:
+      required: true
+      type: character
+    invid:
+      required: true
+      type: character
+  Mapped_PK: 
+    subjid:
+      required: true
+      type: character
+    pktpt:
+      required: true
+      type: character
+    pkperf:
+      required: true
+      type: character
+steps:
+  - output: vThreshold
+    name: ParseThreshold
+    params:
+      strThreshold: Threshold
+  - output: Temp_PK_Complete
+    name: RunQuery
+    params:
+      df: Mapped_PK
+      strQuery: "SELECT * FROM df WHERE pkperf = 'Yes'"
+  - output: Analysis_Input
+    name: Input_Rate
+    params:
+      dfSubjects: Mapped_SUBJ
+      dfNumerator: Temp_PK_Complete
+      dfDenominator: Mapped_PK
+      strSubjectCol: subjid
+      strGroupCol: invid
+      strGroupLevel: GroupLevel
+      strNumeratorMethod: Count
+      strDenominatorMethod: Count
+  - output: Analysis_Transformed
+    name: Transform_Rate
+    params:
+      dfInput: Analysis_Input
+  - output: Analysis_Analyzed
+    name: Analyze_NormalApprox
+    params:
+      dfTransformed: Analysis_Transformed
+      strType: AnalysisType
+  - output: Analysis_Flagged
+    name: Flag_NormalApprox
+    params:
+      dfAnalyzed: Analysis_Analyzed
+      vThreshold: vThreshold
+  - output: Analysis_Summary
+    name: Summarize
+    params:
+      dfFlagged: Analysis_Flagged
+      nMinDenominator: nMinDenominator
+  - output: lAnalysis
+    name: list
+    params:
+      ID: ID
+      Analysis_Input: Analysis_Input
+      Analysis_Transformed: Analysis_Transformed
+      Analysis_Analyzed: Analysis_Analyzed
+      Analysis_Flagged: Analysis_Flagged
+      Analysis_Summary: Analysis_Summary
+

inst/workflow/2_metrics/kri0013a.yaml

@@ -0,0 +1,80 @@
+meta:
+  Type: Analysis
+  ID: kri0013a
+  GroupLevel: Site
+  Abbreviation: PKi
+  Metric: PK Rate - Identity
+  Numerator: PK Measures Completed
+  Denominator: PK Measures Expected
+  Model: Identity
+  Score: Percent Complete
+  AnalysisType: identity
+  Threshold: "0.9,1.0"
+  nMinDenominator: 10
+spec:
+  Mapped_SUBJ:
+    subjid:
+      required: true
+      type: character
+    invid:
+      required: true
+      type: character
+  Mapped_PK: 
+    subjid:
+      required: true
+      type: character
+    pktpt:
+      required: true
+      type: character
+    pkperf:
+      required: true
+      type: character
+steps:
+  - output: vThreshold
+    name: ParseThreshold
+    params:
+      strThreshold: Threshold
+  - output: Temp_PK_Complete
+    name: RunQuery
+    params:
+      df: Mapped_PK
+      strQuery: "SELECT * FROM df WHERE pkperf = 'Yes'"
+  - output: Analysis_Input
+    name: Input_Rate
+    params:
+      dfSubjects: Mapped_SUBJ
+      dfNumerator: Temp_PK_Complete
+      dfDenominator: Mapped_PK
+      strSubjectCol: subjid
+      strGroupCol: invid
+      strGroupLevel: GroupLevel
+      strNumeratorMethod: Count
+      strDenominatorMethod: Count
+  - output: Analysis_Transformed
+    name: Transform_Rate
+    params:
+      dfInput: Analysis_Input
+  - output: Analysis_Analyzed
+    name: Analyze_Identity
+    params:
+      dfTransformed: Analysis_Transformed
+  - output: Analysis_Flagged
+    name: Flag
+    params:
+      dfAnalyzed: Analysis_Analyzed
+      vThreshold: vThreshold
+  - output: Analysis_Summary
+    name: Summarize
+    params:
+      dfFlagged: Analysis_Flagged
+      nMinDenominator: nMinDenominator
+  - output: lAnalysis
+    name: list
+    params:
+      ID: ID
+      Analysis_Input: Analysis_Input
+      Analysis_Transformed: Analysis_Transformed
+      Analysis_Analyzed: Analysis_Analyzed
+      Analysis_Flagged: Analysis_Flagged
+      Analysis_Summary: Analysis_Summary
+