posterior_prediction: Predicted probability of 'y' given 'x' conditional on...

In SimReg: Similarity Regression

Description

Predicted probability of y given x conditional on association and given data.

Usage

posterior_prediction(
  ontology,
  x,
  y,
  sim_reg_out,
  x_new = x,
  information_content = get_term_info_content(ontology, x),
  sim_params = list(ontology = ontology, information_content = information_content),
  two_way = TRUE,
  prediction_fn = SimReg:::fg_step_tab_pp(N = length(y)),
  min_ratio = 0.001,
  ...
)

Arguments

ontology	ontology_index object.
x	list of character vectors of ontological terms.
y	logical response vector.
sim_reg_out	Object of class sim_reg_output.
x_new	New list of ontological term sets to perform prediction on. Defaults to x.
information_content	Numeric vector of information contents of terms named by term ID. Defaults to information content based on frequencies of annotation in x.
sim_params	List of arguments to pass to get_asym_sim_grid.
two_way	Boolean value determining whether to calculate semantic similarity ‘in both directions’ (i.e. compute s_x and s_phi or just s_phi).
prediction_fn	Function for computing predicted probabilities for y[i]=TRUE.
min_ratio	Threshold for fraction of posterior probability which sampled phi must hold in order to be included in sum.
...	Additional arguments to pass to prediction_fn.

Value

Vector of predicted probabilities corresponding to term sets in x_new.

SimReg documentation built on Feb. 15, 2021, 5:10 p.m.