Add case data source setting

ApexRMS · May 15, 2021 · 38096fe · 38096fe
1 parent 904c4e1
commit 38096fe
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Showing 2 changed files with 7 additions and 22 deletions.
diff --git a/src/model.R b/src/model.R
@@ -14,32 +14,16 @@ myScenario <- scenario()
 
 packagePath <- ssimEnvironment()$PackageDirectory
 
-pipeline <- datasheet(myScenario, "core_Pipeline", lookupsAsFactors = F)
 inputData <- datasheet(myScenario, name = "epi_DataSummary", lookupsAsFactors = F, optional = T) %>%
   replace_na(list(TransformerID = "Placeholder Transformer"))
 runSettings <- datasheet(myScenario, "epiModelVocVaccine_RunSettings", lookupsAsFactors = F, optional = T)
 jurisdictions <- datasheet(myScenario, "epiModelVocVaccine_RunJurisdictions", lookupsAsFactors = F, optional = T) %>% pull
 vaccinationRates <- datasheet(myScenario, "epiModelVocVaccine_VaccinationRates", lookupsAsFactors = F, optional = T)
 
-## Decide which source transformer to use ----
-
-# Find the position of the current transformer in the pipeline
-currentRunOrder <- pipeline %>%
-  filter(StageNameID == transformerName) %>%
-  pull(RunOrder)
-
-if(currentRunOrder > 1){
-  sourceTransformer <- pipeline %>%
-    filter(RunOrder == currentRunOrder - 1) %>%
-    pull(StageNameID)
-} else{
-  sourceTransformer <- inputData %>%
-    filter(Variable == "Cases - Daily") %>%
-    pull(TransformerID) %>%
-    tail(1)
-}
-
 ## Parse settings ----
+
+sourceTransformer <- ifelse(is.na(runSettings$CaseSource), "Placeholder Transformer", runSettings$CaseSource)
+
 if(length(jurisdictions) == 0)
   jurisdictions <- inputData %>%
     filter(TransformerID == sourceTransformer, Variable == "Cases - Daily") %>%

diff --git a/src/package.xml b/src/package.xml
@@ -30,11 +30,12 @@
                 <column name="MinimumIteration" dataType="Integer" isVisible="False" defaultValue="1" validationType="WholeNumber" validationCondition="GreaterEqual" formula1="1" format="d"/>                
                 <column name="MaximumIteration" dataType="Integer" displayName="Iterations" defaultValue="1" validationType="WholeNumber" validationCondition="GreaterEqual" formula1="1" format="d"/>
                 <column name="Breakpoints" dataType="Integer" displayName="Number of breakpoints" defaultValue="1" validationType="WholeNumber" validationCondition="GreaterEqual" formula1="1" format="d"/>
-                <column name="VaccineEfficacy" displayName="Vaccine efficacy" dataType="Double"/> validationType="Decimal" validationCondition="LessEqual" formula1="1" />
+                <column name="VaccineEfficacy" displayName="Vaccine efficacy" dataType="Double" validationType="Decimal" validationCondition="LessEqual" formula1="1" />
                 <column name="ImmunityDelay" dataType="Integer" displayName="Immunity delay" defaultValue="0" validationType="WholeNumber" validationCondition="GreaterEqual" formula1="0" format="d"/>
-                <column name="VocAdvantage" displayName="VOC advantage" dataType="Double"/> validationType="Decimal" validationCondition="LessEqual" formula1="1" />
-                <column name="VocShare" displayName="VOC case proportion" dataType="Double"/> validationType="Decimal" validationCondition="LessEqual" formula1="1" />
+                <column name="VocAdvantage" displayName="VOC advantage" dataType="Double" validationType="Decimal" validationCondition="LessEqual" formula1="1" />
+                <column name="VocShare" displayName="VOC case proportion" dataType="Double" validationType="Decimal" validationCondition="LessEqual" formula1="1" />
                 <column name="VocShareDate" displayName="VOC case proportion date (yyyy-mm-dd)" dataType="Date" validationType="Date"/>
+                <column name="CaseSource" displayName="Case data source" dataType="Integer" validationType="Datasheet" formula1="core_Transformer"/>
               </columns>
               <defaultRecords>
                 <record columns="MaximumIteration|Breakpoints|VaccineEfficacy|ImmunityDelay|VocAdvantage|VocShare|VocShareDate" values="20|3|0.8|10|0.07224557|0.1737582|2021-03-11"/>