document specification creation function and fix list elements to new…

… validatExternal function in PLP

SettingsFunctions.R

@@ -1,26 +1,43 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+#' Create specifications for the PatientLevelPredictionValidationModule
+#'
+#' @param validationComponentList a list of the components neccesary for the validationDesigns
+#' to be created. Each component in the list is a list with the following list items:
+#' - restrictPlpDataSettings: created with `PatientLevelPrediction::createRestrictPlpDataSettings` or 
+#' a list of such objects
+#' - populationSettings: created with `PatientLevelPrediction::createStudyPopulationSettings` or a list
+#' of such objects
+#' - recalibrate: a string with the recalibration method to use, either `weakRecalibration` pr `calibrationInTheLarge`
+#' - runCovariateSummary: `TRUE`/`FALSE` indicating if the `covariateSummary` should be run
+#' 
+#' @return
+#' An object of type `PatientLevelPredictionValidationModuleSpecifications`.
+#'
+#' @export
 createPatientLevelPredictionValidationModuleSpecifications <- function(
     validationComponentsList = list(
       list(
-        targetId = 1,
-        oucomeId = 4,
-        restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(), # vector
-        validationSettings = PatientLevelPrediction::createValidationSettings(
-          recalibrate = "weakRecalibration"
-          ),
-        populationSettings = PatientLevelPrediction::createStudyPopulationSettings(
-          riskWindowStart = 90, 
-          riskWindowEnd = 360,
-          requireTimeAtRisk = F
-          )
+        restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(), 
+        populationSettings = PatientLevelPrediction::createStudyPopulationSettings(),
+        recalibrate = "weakRecalibration",
+        runCovariateSummary = TRUE
       ), 
       list(
-        targetId = 3,
-        oucomeId = 4,
-        restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(), # vector
-        validationSettings = PatientLevelPrediction::createValidationSettings(
-          recalibrate = "weakRecalibration"
-          )
-
+        restrictPlpDataSettings = PatientLevelPrediction::createRestrictPlpDataSettings(),
+        populationSettings = PatientLevelPrediction::createStudyPopulationSettings(),    
+        recalibrate = "calibrationInTheLarge",
+        runCovariateSummary = FALSE
       )
     )
 ) {
@@ -34,4 +51,5 @@ createPatientLevelPredictionValidationModuleSpecifications <- function(
   )
   class(specifications) <- c("PatientLevelPredictionValidationModuleSpecifications", "ModuleSpecifications")
   return(specifications)
-}
+}
+