Similarity Regression Functions


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Documentation for package ‘SimReg’ version 1.4

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SimReg-package Similarity Regression Functions
acceptance_traces Get boolean vectors indicating whether proposed values in 'sim_reg' Markov chain were accepted
as.data.frame.sim_reg_summary Convert 'sim_reg_summary' object to 'data.frame'
as_row_leaves Get leaf matrix
final_sample Get final sample from 'sim_reg_samples' object
full_names Replace term ID names of vector/array with full term names
log_odds_trace Get trace of log odds of observing the rare genotype (y = 1) for individual cases from the output of 'sim_reg'
multi_sim_reg Similarity regression on multiple 'y' vectors
P(gamma=1) Extract the estimated posterior probability of gamma = 1
phi_plot Create 'ontology_plot' of phi
plot.sim_reg_samples Plot SimReg output
plot.sim_reg_summary Plot 'sim_reg_summary' object
print.sim_reg_samples Print 'sim_reg_samples' object
print.sim_reg_summary Print 'sim_reg_summary' object
prune_sim_mat Prune between-term similarity matrix
P_y_given_x Get probabilities y_i given ontological term sets x_i ('term_sets') based on SimReg parameter values sampled with 'sim_reg'
s Evaluate asymmetric similarity function
SimReg Similarity Regression Functions
sim_reg Similarity regression
sim_reg_mc Gets summarised output of multiple 'sim_reg' chains
sim_reg_summary Create grid of SimReg output plots
subset_sim_reg_samples Subset 'sim_reg_samples' object
summary.sim_reg_samples Get summary of 'sim_reg_samples' object.
s_phi Evaluate function s_phi
s_x Evaluate function s_x
term_marginals Get marginal frequencies of single terms in phi
term_marginals_from_phi_vec Get marginal frequencies of single terms in phi
term_pair_marginals Get matrix of presence of term pairs
term_pair_marginals_plot Plot marginal distribution of term-pair inclusion in phi