Man pages for thednainus/senegalHIVmodel
Analysis of HIV data from Senegal

beast_phydynConvert tips of a phylogentic tree suitable to use with BEAST...
bindTree_for_phydynBeastMerged phylogenetic trees for the 3 HIV-1 subtypes (B, C, and...
births_mqCalculate median and quantiles when using processed object...
births_newCasesOrganize the solved "births" objects and calculate new HIV...
births_pafsOrganizes the solved birth element and calculate pafs
calculate_newCasesCalculate the proportion of new cases
calculate_pafsCalculate the proportion of population attributable fraction...
data_formatReformat collection dates of HIV samples
deme2demeGets the proportion of infections in deme1 atributable to...
df_newCasesCreate dataframe for new cases of HIV
df_pafsCreate dataframe for PAF
df_r0Create dataframe for basic reproduction number
df_sizesCreate dataframe for effective number of infections
df_sizes_propCreate dataframe for the proportion of effective number of...
get_posteriorGet posterior distributions of MCMC runs
gpsplineCalculate the shape of the linear function for the general...
median_and_quantilesCalculates the median and quantiles for each deme size
mq_propCalculates the proportion of each deme
mq_r0Calculates median and quantiles for basic reproduction number
msmsplineCalculate the shape of the linear function for msm
organize_metadataOrganize HIV metadata
organize_metadata_bySubtypeOrganize metadata by HIV subtype.
posterior_trajectoriesGet posterior distribution samples for the demographic model
post_trajCalculates trajectories using the posterior distribution
post_traj_mxCalculates trajectories using the posterior distrubution when...
prop_infectedCalculates the proportion of infected individuals
prPrevalenceStatDensity function for the prevalence statistics
read_mcmc_rdsReads MCMC runs
reorganize_deme_sizesReorganize by deme size
replace_valuesReplace tip names used in a phylogentic tree
root_drop_tipsRe-root and remove tips in a phylogenetic tree
set_prev_state_parametersSet states for prevalence values
setup.model.equationsSetup Model Equations
tfgy2prevalenceStatConverts size for point estimate 2010 to prevalence of males...
thednainus/senegalHIVmodel documentation built on May 31, 2019, 1:54 a.m.