|
binary_likelihood_profs()
|
Return likelihood profiles for binary covariates special case |
|
binary_loglike_wrapper()
|
Wrapper to optimize over a single variable for likelihood profiling |
|
bootstrap_clusters()
|
Resample clusters from an observed data set |
|
bp_loglike_binary_cov()
|
Calculate the likelihood for binary covariate MC trees |
|
calculate_transmission_prob()
|
Get the probability of transmission given a set of covariates |
|
compute_A_infects_B()
|
Compute probability from samples that person A infects person B |
|
covariate_df_to_mat()
|
Take data frame and turn it into matrix for logistic regression |
|
draw_covariate_rows()
|
Randomly sample covariate rows |
|
draw_features()
|
Draw the features for the tree people |
|
general_cluster_like()
|
Get the likelihood for a single cluster |
|
general_cluster_like.dt()
|
Get the likelihood for a single cluster |
|
general_generation_infection()
|
Infect the current generation given the previous generation |
|
general_loglike()
|
Calculate the estimated general loglikelihood |
|
general_loglike_mc_trees()
|
Calculate the log likelihood for a set of data, averaged by n |
|
general_tree_sampler()
|
Generate trees of certain size |
|
likelihood_profs()
|
Return likelihood profiles |
|
loglike_wrapper()
|
Wrapper to optimize over a single variable for likelihood profiling |
|
mc_trees_to_A_infects_B()
|
Looks at most likely transmissions from A to B for a cluster |
|
sample_connections()
|
Sample connections and form a tree |
|
sample_gen_out_cond()
|
Sample trees with same features as original but permuted through the trees |
|
sample_general_cond_trees()
|
Sample general conditional trees |
|
sample_general_tree_perm()
|
Sample the actual tree for given permutation |
|
sample_mc_binary_cov()
|
Sample binary covariate transmission trees |
|
sample_mc_binary_cov_inner()
|
Innfer function to sample MC trees with binary covariates |
|
sample_mc_trees()
|
Sample trees with same features as original but permuted through the trees |
|
sample_single_gen_out_cond()
|
Make the sampled clusters for a single cluster |
|
sample_trees_fixed_g()
|
Sample trees with given generation sizes |
|
sample_unif_trees_no_features()
|
Sample trees |
|
sample_unique_perms()
|
Sample unique permutations from a partition space |
|
simulate_bp()
|
Simulate the branching process of flipping until failure for K clusters |
|
simulate_general_outbreak_inner()
|
Generate a single cluster of infections |
|
summarize_binary_clusters()
|
Summarize binary covariate clusters |
|
summarize_binary_cov_trees()
|
Condense trees into a smaller format |
|
tb_clean
|
Subset of Tuberculosis data |