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 |