Man pages for thednainus/senegalHIVmodel
Analysis of HIV data from Senegal
| beast_phydyn | Convert tips of a phylogentic tree suitable to use with BEAST... |
| bindTree_for_phydynBeast | Merged phylogenetic trees for the 3 HIV-1 subtypes (B, C, and... |
| births_mq | Calculate median and quantiles when using processed object... |
| births_newCases | Organize the solved "births" objects and calculate new HIV... |
| births_pafs | Organizes the solved birth element and calculate pafs |
| calculate_newCases | Calculate the proportion of new cases |
| calculate_pafs | Calculate the proportion of population attributable fraction... |
| data_format | Reformat collection dates of HIV samples |
| deme2deme | Gets the proportion of infections in deme1 atributable to... |
| df_newCases | Create dataframe for new cases of HIV |
| df_pafs | Create dataframe for PAF |
| df_r0 | Create dataframe for basic reproduction number |
| df_sizes | Create dataframe for effective number of infections |
| df_sizes_prop | Create dataframe for the proportion of effective number of... |
| get_posterior | Get posterior distributions of MCMC runs |
| gpspline | Calculate the shape of the linear function for the general... |
| median_and_quantiles | Calculates the median and quantiles for each deme size |
| mq_prop | Calculates the proportion of each deme |
| mq_r0 | Calculates median and quantiles for basic reproduction number |
| msmspline | Calculate the shape of the linear function for msm |
| organize_metadata | Organize HIV metadata |
| organize_metadata_bySubtype | Organize metadata by HIV subtype. |
| posterior_trajectories | Get posterior distribution samples for the demographic model |
| post_traj | Calculates trajectories using the posterior distribution |
| post_traj_mx | Calculates trajectories using the posterior distrubution when... |
| prop_infected | Calculates the proportion of infected individuals |
| prPrevalenceStat | Density function for the prevalence statistics |
| read_mcmc_rds | Reads MCMC runs |
| reorganize_deme_sizes | Reorganize by deme size |
| replace_values | Replace tip names used in a phylogentic tree |
| root_drop_tips | Re-root and remove tips in a phylogenetic tree |
| set_prev_state_parameters | Set states for prevalence values |
| setup.model.equations | Setup Model Equations |
| tfgy2prevalenceStat | Converts size for point estimate 2010 to prevalence of males... |
