createLearningCurve: createLearningCurve

In quinterpriest/PatientLevelPrediction: Developing patient level prediction using data in the OMOP Common Data Model

createLearningCurve

Description

Creates a learning curve object, which can be plotted using the plotLearningCurve() function.

Usage

createLearningCurve(
  plpData,
  outcomeId,
  parallel = T,
  cores = 4,
  modelSettings,
  saveDirectory = getwd(),
  analysisId = "learningCurve",
  populationSettings = createStudyPopulationSettings(),
  splitSettings = createDefaultSplitSetting(),
  trainFractions = c(0.25, 0.5, 0.75),
  trainEvents = c(500, 1000, 1500),
  sampleSettings = createSampleSettings(),
  featureEngineeringSettings = createFeatureEngineeringSettings(),
  preprocessSettings = createPreprocessSettings(minFraction = 0.001, normalize = T),
  logSettings = createLogSettings(),
  executeSettings = createExecuteSettings(runSplitData = T, runSampleData = F,
    runfeatureEngineering = F, runPreprocessData = T, runModelDevelopment = T,
    runCovariateSummary = F)
)

Arguments

plpData	An object of type plpData - the patient level prediction data extracted from the CDM.
outcomeId	(integer) The ID of the outcome.
parallel	Whether to run the code in parallel
cores	The number of computer cores to use if running in parallel
modelSettings	An object of class modelSettings created using one of the function: setLassoLogisticRegression() A lasso logistic regression model setGradientBoostingMachine() A gradient boosting machine setAdaBoost() An ada boost model setRandomForest() A random forest model setDecisionTree() A decision tree model setCovNN()) A convolutional neural network model setCIReNN() A recurrent neural network model setMLP() A neural network model setDeepNN() A deep neural network model setKNN() A KNN model
saveDirectory	The path to the directory where the results will be saved (if NULL uses working directory)
analysisId	(integer) Identifier for the analysis. It is used to create, e.g., the result folder. Default is a timestamp.
populationSettings	An object of type populationSettings created using createStudyPopulationSettings that specifies how the data class labels are defined and addition any exclusions to apply to the plpData cohort
splitSettings	An object of type splitSettings that specifies how to split the data into train/validation/test. The default settings can be created using createDefaultSplitSetting.
trainFractions	A list of training fractions to create models for. Note, providing trainEvents will override your input to trainFractions.
trainEvents	Events have shown to be determinant of model performance. Therefore, it is recommended to provide trainEvents rather than trainFractions. Note, providing trainEvents will override your input to trainFractions. The format should be as follows: c(500, 1000, 1500) - a list of training events
sampleSettings	An object of type sampleSettings that specifies any under/over sampling to be done. The default is none.
featureEngineeringSettings	An object of featureEngineeringSettings specifying any feature engineering to be learned (using the train data)
preprocessSettings	An object of preprocessSettings. This setting specifies the minimum fraction of target population who must have a covariate for it to be included in the model training and whether to normalise the covariates before training
logSettings	An object of logSettings created using createLogSettings specifying how the logging is done
executeSettings	An object of executeSettings specifying which parts of the analysis to run

Value

A learning curve object containing the various performance measures obtained by the model for each training set fraction. It can be plotted using plotLearningCurve.

Examples

## Not run: 
# define model
modelSettings = PatientLevelPrediction::setLassoLogisticRegression()

# create learning curve
learningCurve <- PatientLevelPrediction::createLearningCurve(population,
                                                             plpData,
                                                             modelSettings)
# plot learning curve
PatientLevelPrediction::plotLearningCurve(learningCurve)

## End(Not run)

quinterpriest/PatientLevelPrediction documentation built on April 20, 2022, 12:50 a.m.