get_stats function

Metrics for Predictive Performance

A function to return a variety metrics for predictions vs actual values. Works well when piped to straight from get_predictions().

get_stats(
  predictions,
  biomarker_values,
  model = "",
  threshold = 300,
  metrics = c("R", "AUPRC")
)

Arguments

• predictions: (list) A list with two elements, 'predictions' and 'panel_lengths', as produced by the function get_predictions().
• biomarker_values: (dataframe) A dataframe with two columns, 'Tumor_Sample_Barcode' and a column with the name of the biomarker in question containing values.
• model: (character) The name of the model type producing these predictions.
• threshold: (numeric) The threshold for biomarker high/low categorisation.
• metrics: (character) A vector of the names of metrics to calculate.

Returns

dataframe with 5 columns:

• panel_length: the length of each panel.
• model: the model that produced the predictions.
• biomarker: the name of the biomarker in question.
• stat: the metric values for each panel.
• metric: the name of the metric.

Examples

example_stat <- get_stats(predictions = get_predictions(example_refit_panel,
new_data = example_tables$val), biomarker_values = example_tmb_tables$val,
model = "Refitted T", threshold = 10)