Bio_i-specific computation for dynamicPredictionBio() — compute_bio_marker

Internal helper for the part of dynamicPredictionBio()'s pipeline that does depend on which biomarker is being predicted: building the candidate-value grid Y_all, evaluating the numerator conditional density on it, and assembling/normalizing Y_density and Y_predict. Takes the output of compute_bio_shared_step() so the bio_i-independent pieces are not recomputed.

Usage

compute_bio_marker_step(
  shared,
  bio_i,
  long_fit_all,
  survival_fit_all,
  prediction_time,
  horizon,
  time_variable,
  survival_variable_all,
  survival_trans_function,
  bandcount3
)

Arguments

shared: Output of compute_bio_shared_step().
bio_i: See dynamicPredictionBio.
long_fit_all: See dynamicPredictionBio.
survival_fit_all: See dynamicPredictionBio.
prediction_time: See dynamicPredictionBio.
horizon: See dynamicPredictionBio.
time_variable: See dynamicPredictionBio.
survival_variable_all: See dynamicPredictionBio.
survival_trans_function: See dynamicPredictionBio.
bandcount3: See dynamicPredictionBio.

Value

A list with Y_predict, Y_density, Y_all (matching dynamicPredictionBio()'s return value fields). For an ordinal bio_i, Y_all/Y_predict hold integer category codes (1:K, in threshold order) rather than a numeric grid – see Details below – and Y_all additionally carries a "category_labels" attribute with the matching level-label strings.