add subject disposition

R/Report_StudyInfo.R

@@ -35,7 +35,7 @@ Report_StudyInfo <- function(
     "ParticipantEnrollment"
   )
   show_table <- study_status_table %>%
-    dplyr::filter(.data$Param %in% subcols) %>%
+    dplyr::filter(tolower(.data$Param) %in% tolower(subcols)) %>%
     gt_StudyInfo(id = strId)
 
   strId_hide <- paste0(strId, "_hide")

inst/examples/3_ReportingWorkflow.R

@@ -7,7 +7,8 @@ lSource <- list(
     Source_PD = clindata::ctms_protdev,
     Source_LB = clindata::rawplus_lb,
     Source_STUDCOMP = clindata::rawplus_studcomp,
-    Source_SDRGCOMP = clindata::rawplus_sdrgcomp %>% dplyr::filter(.data$phase == 'Blinded Study Drug Completion'),
+    Source_SDRGCOMP = clindata::rawplus_sdrgcomp %>%
+      dplyr::filter(.data$phase == 'Blinded Study Drug Completion'),
     Source_DATACHG = clindata::edc_data_points,
     Source_DATAENT = clindata::edc_data_pages,
     Source_QUERY = clindata::edc_queries,
@@ -23,7 +24,8 @@ lRaw <- list(
     Raw_PD = lSource$Source_PD %>%
       rename(subjid = subjectenrollmentnumber),
     Raw_LB = lSource$Source_LB,
-    Raw_STUDCOMP = lSource$Source_STUDCOMP,
+    Raw_STUDCOMP = lSource$Source_STUDCOMP %>%
+      select(subjid, compyn),
     Raw_SDRGCOMP = lSource$Source_SDRGCOMP,
     Raw_DATACHG = lSource$Source_DATACHG %>%
       rename(subject_nsv = subjectname),
@@ -39,7 +41,8 @@ lRaw <- list(
       rename(InvestigatorLastName = pi_last_name) %>%
       rename(City = city) %>%
       rename(State = state) %>%
-      rename(Country = country),
+      rename(Country = country) %>%
+      rename(Status = site_status),
     Raw_STUDY = lSource$Source_STUDY %>%
       rename(studyid = protocol_number) %>%
       rename(Status = status)

inst/workflow/1_mappings/COUNTRY.yaml

@@ -16,9 +16,25 @@ steps:
     name: RunQuery
     params:
       df: Mapped_SUBJ
-      strQuery: "SELECT country as GroupID, COUNT(DISTINCT subjid) as ParticipantCount, COUNT(DISTINCT invid) as SiteCount FROM df GROUP BY country"
+      strQuery: |
+        SELECT
+          country as GroupID,
+          COUNT(DISTINCT subjid) as ParticipantCount,
+          SUM(CASE WHEN Status == 'Active' THEN 1 ELSE 0 END) as ActiveParticipantCount,
+          COUNT(DISTINCT invid) as SiteCount
+        FROM df
+        GROUP BY country
+  - output: Temp_CountryCountsWide_ActiveParticipants
+    name: CalculatePercentage
+    params:
+      data: Temp_CountryCountsWide
+      strCurrentCol: ActiveParticipantCount
+      strTargetCol: ParticipantCount
+      strPercVal: PercentParticipantsActive
+      strPercStrVal: ActiveParticipants
   - output: Mapped_COUNTRY
     name: MakeLongMeta
     params:
-      data: Temp_CountryCountsWide
+      data: Temp_CountryCountsWide_ActiveParticipants
       strGroupLevel: "Country"
+

inst/workflow/1_mappings/SITE.yaml

@@ -17,8 +17,9 @@ spec:
     InvestigatorLastName:
       type: character
       source_col: pi_last_name
-    site_status:
+    Status:
       type: character
+      source_col: site_status
     City:
       type: character
       source_col: city
@@ -35,6 +36,8 @@ spec:
       type: character
     subjid:
       type: character
+    Status:
+      type: character
 steps:
   - output: Temp_CTMSSiteWide
     name: RunQuery
@@ -50,11 +53,26 @@ steps:
     name: RunQuery
     params:
       df: Mapped_SUBJ
-      strQuery: "SELECT invid as GroupID, COUNT(DISTINCT subjid) as ParticipantCount, COUNT(DISTINCT invid) as SiteCount FROM df GROUP BY invid"
+      strQuery: |
+        SELECT
+          invid as GroupID,
+          COUNT(DISTINCT subjid) as ParticipantCount,
+          SUM(CASE WHEN Status == 'Active' THEN 1 ELSE 0 END) as ActiveParticipantCount,
+          COUNT(DISTINCT invid) as SiteCount
+        FROM df
+        GROUP BY invid
+  - output: Temp_SiteCountsWide_ActiveParticipants
+    name: CalculatePercentage
+    params:
+      data: Temp_SiteCountsWide
+      strCurrentCol: ActiveParticipantCount
+      strTargetCol: ParticipantCount
+      strPercVal: PercentParticipantsActive
+      strPercStrVal: ActiveParticipants
   - output: Temp_SiteCounts
     name: MakeLongMeta
     params:
-      data: Temp_SiteCountsWide
+      data: Temp_SiteCountsWide_ActiveParticipants
       strGroupLevel: "Site"
   - output: Mapped_SITE
     name: bind_rows

inst/workflow/1_mappings/STUDY.yaml

@@ -12,8 +12,9 @@ spec:
       type: character
     protocol_title:
       type: character
-    status:
+    Status:
       type: character
+      source_col: status
     num_plan_site:
       type: integer
     num_plan_subj:
@@ -41,6 +42,8 @@ spec:
       type: character
     subjid:
       type: character
+    Status:
+      type: character
 steps:
   - output: Temp_CTMSStudyWide
     name: RunQuery
@@ -61,7 +64,14 @@ steps:
     name: RunQuery
     params:
       df: Mapped_SUBJ
-      strQuery: "SELECT studyid as GroupID, COUNT(DISTINCT subjid) as ParticipantCount, COUNT(DISTINCT invid) as SiteCount FROM df GROUP BY studyid"
+      strQuery: |
+        SELECT
+          studyid as GroupID,
+          COUNT(DISTINCT subjid) as ParticipantCount,
+          SUM(CASE WHEN Status == 'Active' THEN 1 ELSE 0 END) as ActiveParticipantCount,
+          COUNT(DISTINCT invid) as SiteCount
+        FROM df
+        GROUP BY studyid
   - output: Temp_CountTargetsWide
     name: left_join
     params:
@@ -84,13 +94,22 @@ steps:
       strTargetCol: ParticipantTarget
       strPercVal: PercentParticipantsEnrolled
       strPercStrVal: ParticipantEnrollment
+  - output: Temp_CountTargetsWide_ActiveParticipants
+    name: CalculatePercentage
+    params:
+      data: Temp_CountTargetsWide_addsitepts
+      strCurrentCol: ActiveParticipantCount
+      strTargetCol: ParticipantCount
+      strPercVal: PercentParticipantsActive
+      strPercStrVal: ActiveParticipants
   - output: Temp_CountTargetsPercs
     name: MakeLongMeta
     params:
-      data: Temp_CountTargetsWide_addsitepts
+      data: Temp_CountTargetsWide_ActiveParticipants
       strGroupLevel: "Study"
   - output: Mapped_STUDY
     name: bind_rows
     params:
       Temp_CTMSStudy: Temp_CTMSStudy
       Temp_CountTargetsPercs: Temp_CountTargetsPercs
+

inst/workflow/1_mappings/SUBJ.yaml

@@ -19,9 +19,32 @@ spec:
       type: character
     timeonstudy:
       type: integer
+  Raw_STUDCOMP:
+    subjid:
+      type: character
+    compyn:
+      type: character
 steps:
+  - output: Temp_SUBJ
+    name: left_join
+    params:
+      x: Raw_SUBJ
+      "y": Raw_STUDCOMP
+      by: subjid
   - output: Mapped_SUBJ
     name: RunQuery
     params:
-      df: Raw_SUBJ
-      strQuery: "SELECT * FROM df WHERE enrollyn == 'Y'"
+      df: Temp_SUBJ
+      strQuery: |
+        SELECT *,
+        CASE
+          WHEN compyn == 'Y' THEN 'Completed'
+          WHEN compyn == 'N' THEN 'Discontinued'
+          WHEN enrollyn == 'Y' THEN 'Active'
+          WHEN enrollyn == 'N' THEN 'Screen Failure'
+          WHEN enrollyn == '' THEN 'In Screening'
+          ELSE 'Unknown'
+        END as Status
+        FROM df
+        WHERE enrollyn == 'Y'
+

tests/testthat/_snaps/Report_StudyInfo.md

@@ -467,6 +467,8 @@
         <tbody class="gt_table_body">
           <tr><td headers="Description" class="gt_row gt_left">Nickname</td>
       <td headers="Value" class="gt_row gt_right">Nickname</td></tr>
+          <tr><td headers="Description" class="gt_row gt_left">Status</td>
+      <td headers="Value" class="gt_row gt_right">Ongoing</td></tr>
         </tbody>