Prepare Trio metric metadata for submission

This helper aligns the new submission workflow with the older writeCTD() metric handling. Internal package metrics are recorded directly. Custom metrics can optionally be uploaded to a GitHub gist and linked from the resulting Metric table rows.

Usage

prepareTrioSubmissionMetrics(
  trio,
  name = trio$name,
  uploadCustom = FALSE,
  githubPat = NULL,
  gistPublic = TRUE
)

Arguments

trio

A Trio object.

name

Dataset name used for the gist filename. Defaults to trio$name.

uploadCustom

Logical; if TRUE, custom metrics are uploaded to a GitHub gist.

githubPat

Optional GitHub personal access token with gist scope.

gistPublic

Logical; whether the created gist should be public.

Value

A list with entries Metric, gist, and custom_metric_lines.

Examples

data <- data.frame(feature = c(1, 2, 3), row.names = paste0("sample", 1:3))
labels <- factor(c("A", "B", "A"))
names(labels) <- rownames(data)
trio <- Trio$new(
  data = data,
  evidence = list(class_labels = list(
    evidence = labels,
    metrics = "macroF1Metric"
  )),
  metrics = list(macroF1Metric = macroF1Metric),
  name = "example_dataset",
  description = "A small example dataset."
)
prepareTrioSubmissionMetrics(trio)
#> $Metric
#>               metricID    metricName     wrapper_r metricType metricSourceType
#> macroF1Metric     <NA> macroF1Metric macroF1Metric       <NA>             gist
#>               metricKey wrapper_py gist_url
#> macroF1Metric      <NA>       <NA>     <NA>
#> 
#> $gist
#> NULL
#> 
#> $custom_metric_lines
#> [1] "macroF1Metric <- function (evidence, predicted) "                                    
#> [2] "{"                                                                                   
#> [3] "    2 * macroPrecMetric(evidence, predicted) * macroRecMetric(evidence, "            
#> [4] "        predicted)/(macroPrecMetric(evidence, predicted) + macroRecMetric(evidence, "
#> [5] "        predicted))"                                                                 
#> [6] "}"                                                                                   
#> [7] "macroF1MetricArgs <- NULL"                                                           
#>