add_1940_1950 | internal fucntion to add early years to population data |
calc_incidence_vac_general | calculate the first instance of vaccine coverage |
calc_pop_moments | calculate population moments |
calc_pop_moments_agg | calculate the population moments for aggregated data |
calc_t0_vac_africa | get time of first vaccination |
calculate_bootstrap_Bayes | Calculate Bayes factors and bootstrap for uncertainty |
calculate_hpd | Calculating the High probability density regions for all... |
create_pop30_agg_vc30_agg | get aggregated population and vaccination across observation... |
create_pop_at_survey | get the population at the survey times and places |
create_R0_lookup | function to calculate aggregated seroprevalence at survey in... |
fit_glm | fit the glm |
foi_calculate_seroprevalence | function to calculate aggregated seroprevalence at survey in... |
fun_calc_pdetect_multi_both | calculate the probability of detection for both models |
fun_calcPred | calculate predicitions from glm |
fun_calc_transmission_Africa | calculate the probability of detection for both models |
get_chains | Import and bind chains for estimation |
get_pop_data_3d | function to import and get pop data in array |
GLMlike | likelihood for the GLM parameters |
GLM_MCMC | mcmc for the GLM parameters |
GLM_MCMC_step | mcmc step for the GLM parameters |
GLMprior | Prior distributions for the GLM parameters |
GLMproposal | Proposal distribution for GLM |
hpd_out | Internal function to get hpd |
import_pop_data_LS2014 | old popualtion data import function |
import_pop_data_LS2017 | population data import function |
launch_env_dat | load environmental data from path |
Make_aggregate_pop_vc | aggregating population and vaccination data for serological... |
Make_aggregate_pop_vc_3d | Aggregate the population and vaccination data into an array |
Make_pop3d_Ptot2d_Pprop3d | function to reorganise population data |
mean_fun | Internal mean function |
plot_glm_map | plot a map of glm output alongside map of data |
plot_prior_post | Plot the prior and posterior deinsities |
plot_sero_predictions | plot the seroprevalence predictions with data and credible... |
plot_transmission_intensity | calculate and plot the transmission intensity across the... |
process_serology | extract key information from serological data |
R0_calculate_seroprevalence | function to calculate aggregated seroprevalence at survey in... |
R0_recurrence_seroprev | function to calculate seroprevalence by recurrence relation... |
R0_recurrence_seroprev_survey | function to calculate seroprevalence at survey by recurrence... |
R0_recurrence_seroprev_whole | function to calculate seroprevalence everywhere by recurrence... |
Sero_Gibbs_MCMC | MCMC for Sero |
Sero_Gibbs_MCMC_model_step | MCMC model step for Sero |
Sero_Gibbs_MCMC_parameter_step | MCMC parameter step for Sero |
Sero_Gibbs_MCMC_step | MCMC step for Sero |
SEROlike | Likelihood distribution for Sero |
SEROlike_onesurvey | likelihood for one serological survey in either model |
SEROprior | Prior distribution for Sero |
SEROproposal | Proposal distribution for Sero |
SEROpseudoprior | Pseudo prior probability |
setup_modelprior | function estimate a value for the model prior in order to... |
setup_pseudoprior | function estimate a value for the pseudo prior in order to... |
transform_into_vc3d | get vaccine data into an array |
YFestimation | YFestimation: Estimate ecological niche and two transmission... |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.