Man pages for skgallagher/InfectionTrees
Sample, Analyze, and Plot Infection Trees
| binary_likelihood_profs | Return likelihood profiles for binary covariates special case |
| binary_loglike_wrapper | Wrapper to optimize over a single variable for likelihood... |
| 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... |
| covariate_df_to_mat | Take data frame and turn it into matrix for logistic... |
| 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... |
| mc_trees_to_A_infects_B | Looks at most likely transmissions from A to B for a cluster |
| pipe | Pipe operator |
| sample_connections | Sample connections and form a tree |
| sample_general_cond_trees | Sample general conditional trees |
| sample_general_tree_perm | Sample the actual tree for given permutation |
| sample_gen_out_cond | Sample trees with same features as original but permuted... |
| 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... |
| 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... |
| 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 |
