# Adding Custom Sampling Functions

#### Jenna Reps

#### 2025-02-10

# Introduction

This vignette describes how you can add your own custom function for sampling the target population in the Observational Health Data Sciencs and Informatics (OHDSI) `PatientLevelPrediction` package. This vignette assumes you have read and are comfortable with building single patient level prediction models as described in the `vignette('BuildingPredictiveModels')`.

We invite you to share your new sample functions with the OHDSI community through our GitHub repository.

# Sample Function Code Structure

To make a sampling function that can be used within PatientLevelPrediction you need to write two different functions. The ‘create’ function and the ‘implement’ function.

The ‘create’ function, e.g., create<SampleFunctionName>, takes the parameters of the sample ‘implement’ function as input, checks these are valid and outputs these as a list of class ‘sampleSettings’ with the ‘fun’ attribute specifying the ‘implement’ function to call.

The ‘implement’ function, e.g., implement<SampleFunctionName>, must take as input: * trainData - a list containing: - covariateData: the plpData$covariateData restricted to the training patients - labels: a data frame that contain rowId (patient identifier) and outcomeCount (the class labels) - folds: a data.frame that contains rowId (patient identifier) and index (the cross validation fold) * sampleSettings - the output of your create<SampleFunctionName>

The ‘implement’ function can then do any manipulation of the trainData (such as undersampling or oversampling) but must output a trainData object containing the covariateData, labels and folds for the new training data sample.

# Example

Let’s consider the situation where we wish to take a random sample of the training data population. To make this custom sampling function we need to write the ‘create’ and ‘implement’ R functions.

## Create function

Our random sampling function will randomly sample `n` patients from the trainData. Therefore, the inputs for this are: * `n` an integer/double specifying the number of patients to sample * `sampleSeed` an integer/double specifying the seed for reproducibility

    createRandomSampleSettings <- function(n = 10000,
                                           sampleSeed = sample(10000, 1)) {
      # add input checks
      checkIsClass(n, c("numeric", "integer"))
      checkHigher(n, 0)
      checkIsClass(sampleSeed, c("numeric", "integer"))

      # create list of inputs to implement function
      sampleSettings <- list(
        n = n,
        sampleSeed = sampleSeed
      )

      # specify the function that will implement the sampling
      attr(sampleSettings, "fun") <- "implementRandomSampleSettings"

      # make sure the object returned is of class "sampleSettings"
      class(sampleSettings) <- "sampleSettings"
      return(sampleSettings)
    }

We now need to create the ‘implement’ function `implementRandomSampleSettings()`

## Implement function

All ‘implement’ functions must take as input the trainData and the sampleSettings (this is the output of the ‘create’ function). They must return a trainData object containing the covariateData, labels and folds.

In our example, the `createRandomSampleSettings()` will return a list with ‘n’ and ‘sampleSeed’. The sampleSettings therefore contains these.

    implementRandomSampleSettings <- function(trainData, sampleSettings) {
      n <- sampleSettings$n
      sampleSeed <- sampleSettings$sampleSeed

      if (n > nrow(trainData$labels)) {
        stop("Sample n bigger than training population")
      }

      # set the seed for the randomization
      set.seed(sampleSeed)

      # now implement the code to do your desired sampling

      sampleRowIds <- sample(trainData$labels$rowId, n)

      sampleTrainData <- list()

      sampleTrainData$labels <- trainData$labels %>%
        dplyr::filter(.data$rowId %in% sampleRowIds) %>%
        dplyr::collect()

      sampleTrainData$folds <- trainData$folds %>%
        dplyr::filter(.data$rowId %in% sampleRowIds) %>%
        dplyr::collect()

      sampleTrainData$covariateData <- Andromeda::andromeda()
      sampleTrainData$covariateData$covariateRef <- trainData$covariateData$covariateRef
      sampleTrainData$covariateData$covariates <- trainData$covariateData$covariates %>% dplyr::filter(.data$rowId %in% sampleRowIds)

      # update metaData$populationSize
      metaData <- attr(trainData$covariateData, "metaData")
      metaData$populationSize <- n
      attr(sampleTrainData$covariateData, "metaData") <- metaData

      # make the cocvariateData the correct class
      class(sampleTrainData$covariateData) <- "CovariateData"

      # return the updated trainData
      return(sampleTrainData)
    }

# Acknowledgments

Considerable work has been dedicated to provide the `PatientLevelPrediction` package.

    citation("PatientLevelPrediction")

    ## To cite PatientLevelPrediction in publications use:
    ##
    ##   Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek P (2018). "Design
    ##   and implementation of a standardized framework to generate and
    ##   evaluate patient-level prediction models using observational
    ##   healthcare data." _Journal of the American Medical Informatics
    ##   Association_, *25*(8), 969-975.
    ##   <https://doi.org/10.1093/jamia/ocy032>.
    ##
    ## A BibTeX entry for LaTeX users is
    ##
    ##   @Article{,
    ##     author = {J. M. Reps and M. J. Schuemie and M. A. Suchard and P. B. Ryan and P. Rijnbeek},
    ##     title = {Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data},
    ##     journal = {Journal of the American Medical Informatics Association},
    ##     volume = {25},
    ##     number = {8},
    ##     pages = {969-975},
    ##     year = {2018},
    ##     url = {https://doi.org/10.1093/jamia/ocy032},
    ##   }

Please reference this paper if you use the PLP Package in your work:

Reps JM, Schuemie MJ, Suchard MA, Ryan PB, Rijnbeek PR. Design and implementation of a standardized framework to generate and evaluate patient-level prediction models using observational healthcare data. J Am Med Inform Assoc. 2018;25(8):969-975.

This work is supported in part through the National Science Foundation grant IIS 1251151.