Release v1.1.0 prep

DESCRIPTION

@@ -2,7 +2,7 @@ Package: Strategus
 Type: Package
 Title: Coordinate and Execute OHDSI HADES Modules
 Version: 1.1.0
-Date: 2024-11-12
+Date: 2024-11-26
 Authors@R: c(
 	person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")),
 	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),

NEWS.md

@@ -1,3 +1,9 @@
+Strategus 1.1.0
+===============
+- Inject cohort schema and table into `createCohortBasedCovariateSettings` (#181)
+- Provide hook to optimize cohort SQL construction (#179)
+- Fixes broken links in R6 class documentation (#183)
+
 Strategus 1.0.0
 ===============
 

R/Module-PatientLevelPrediction.R

@@ -156,10 +156,9 @@ PatientLevelPredictionModule <- R6::R6Class(
     }
   ),
   private = list(
-    .setCovariateSchemaTable = function(
-        modelDesignList,
-        cohortDatabaseSchema,
-        cohortTable) {
+    .setCovariateSchemaTable = function(modelDesignList,
+                                        cohortDatabaseSchema,
+                                        cohortTable) {
       if (inherits(modelDesignList, "modelDesign")) {
         modelDesignList <- list(modelDesignList)
       }

R/Settings.R

@@ -62,7 +62,7 @@ addModuleSpecifications <- function(analysisSpecifications, moduleSpecifications
 #' Add Characterization module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications   Created by the \href{../../docs/reference/CharacterizationModule.html#method-CharacterizationModule-createModuleSpecifications}{\code{CharacterizationModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications   Created by the \href{../reference/CharacterizationModule.html#method-CharacterizationModule-createModuleSpecifications}{\code{CharacterizationModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -81,7 +81,7 @@ addCharacterizationModuleSpecifications <- function(analysisSpecifications, modu
 #' Add Cohort Diagnostics module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/CohortDiagnosticsModule.html#method-CohortDiagnosticsModule-createModuleSpecifications}{\code{CohortDiagnosticsModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/CohortDiagnosticsModule.html#method-CohortDiagnosticsModule-createModuleSpecifications}{\code{CohortDiagnosticsModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -100,7 +100,7 @@ addCohortDiagnosticsModuleSpecifications <- function(analysisSpecifications, mod
 #' Add Cohort Generator module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/CohortGeneratorModule.html#method-CohortGeneratorModule-createModuleSpecifications}{\code{CohortGeneratorModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/CohortGeneratorModule.html#method-CohortGeneratorModule-createModuleSpecifications}{\code{CohortGeneratorModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -119,7 +119,7 @@ addCohortGeneratorModuleSpecifications <- function(analysisSpecifications, modul
 #' Add Cohort Incidence module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/CohortIncidenceModule.html#method-CohortIncidenceModule-createModuleSpecifications}{\code{CohortIncidenceModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/CohortIncidenceModule.html#method-CohortIncidenceModule-createModuleSpecifications}{\code{CohortIncidenceModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -138,7 +138,7 @@ addCohortIncidenceModuleSpecifications <- function(analysisSpecifications, modul
 #' Add Cohort Method module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/CohortMethodModule.html#method-CohortMethodModule-createModuleSpecifications}{\code{CohortMethodModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/CohortMethodModule.html#method-CohortMethodModule-createModuleSpecifications}{\code{CohortMethodModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -157,7 +157,7 @@ addCohortMethodeModuleSpecifications <- function(analysisSpecifications, moduleS
 #' Add Evidence Synthesis module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/EvidenceSynthesisModule.html#method-EvidenceSynthesisModule-createModuleSpecifications}{\code{EvidenceSynthesisModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/EvidenceSynthesisModule.html#method-EvidenceSynthesisModule-createModuleSpecifications}{\code{EvidenceSynthesisModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -176,7 +176,7 @@ addEvidenceSynthesisModuleSpecifications <- function(analysisSpecifications, mod
 #' Add Patient Level Prediction module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/PatientLevelPredictionModule.html#method-PatientLevelPredictionModule-createModuleSpecifications}{\code{PatientLevelPredictionModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/PatientLevelPredictionModule.html#method-PatientLevelPredictionModule-createModuleSpecifications}{\code{PatientLevelPredictionModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.
@@ -195,7 +195,7 @@ addPatientLevelPredictionModuleSpecifications <- function(analysisSpecifications
 #' Add Self Controlled Case Series Module module specifications to analysis specifications
 #'
 #' @template analysisSpecifications
-#' @param moduleSpecifications  Created by the \href{../../docs/reference/SelfControlledCaseSeriesModule.html#method-SelfControlledCaseSeriesModule-createModuleSpecifications}{\code{SelfControlledCaseSeriesModule$createModuleSpecifications()}} function.
+#' @param moduleSpecifications  Created by the \href{../reference/SelfControlledCaseSeriesModule.html#method-SelfControlledCaseSeriesModule-createModuleSpecifications}{\code{SelfControlledCaseSeriesModule$createModuleSpecifications()}} function.
 #'
 #' @return
 #' Returns the `analysisSpecifications` object with the module specifications added.

R/StrategusModule.R

@@ -334,8 +334,8 @@ StrategusModule <- R6::R6Class(
     if (inherits(s, "covariateSettings") && "fun" %in% names(attributes(s))) {
       if (attr(s, "fun") == "getDbCohortBasedCovariatesData") {
         # Set the covariateCohortDatabaseSchema & covariateCohortTable values
-        s$covariateCohortDatabaseSchema = executionSettings$workDatabaseSchema
-        s$covariateCohortTable = executionSettings$cohortTableNames$cohortTable
+        s$covariateCohortDatabaseSchema <- executionSettings$workDatabaseSchema
+        s$covariateCohortTable <- executionSettings$cohortTableNames$cohortTable
       }
     }
     return(s)
@@ -379,5 +379,3 @@ StrategusModule <- R6::R6Class(
   # Call the helper function on the input list
   return(replaceHelper(moduleSettings))
 }
-
-

extras/rdms/schema_meta.xml

@@ -1067,10 +1067,10 @@
     <table name="plp_model_designs" comments="PatientLevelPredictionModule: Model designs">
       <column name="model_design_id" comments="a unique identifier for the model design settings"/>
       <column name="target_id" comments="the  identifier for the target cohort id">
-        <foreignKey table="cg_cohort_definition" column="cohort_definition_id"/>
+        <foreignKey table="plp_cohorts" column="cohort_definition_id"/>
       </column>
       <column name="outcome_id" comments="the  identifier for the outcome cohort id">
-        <foreignKey table="cg_cohort_definition" column="cohort_definition_id"/>
+        <foreignKey table="plp_cohorts" column="cohort_definition_id"/>
       </column>
       <column name="tar_id" comments="the  identifier for the time at risk setting"/>
       <column name="plp_data_setting_id" comments="the  identifier for the plp data setting"/>

tests/testthat/test-Settings.R

@@ -453,8 +453,8 @@ test_that("Test internal function for modifying covariate settings", {
 
   testReplacedModuleSettings <- .replaceCovariateSettings(moduleSettings, executionSettings)
   # For visual inspection
-  #ParallelLogger::saveSettingsToJson(moduleSettings, "before_unit_test.json")
-  #ParallelLogger::saveSettingsToJson(testReplacedModuleSettings, "after_unit_test.json")
+  # ParallelLogger::saveSettingsToJson(moduleSettings, "before_unit_test.json")
+  # ParallelLogger::saveSettingsToJson(testReplacedModuleSettings, "after_unit_test.json")
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortDatabaseSchema, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortTable, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[2]]$covariateCohortDatabaseSchema, workDatabaseSchema)