Package index • eppasm

All functions

agemx(<spec>): Age-specific mortality
agepregartcov(): Age-specific ART coverage among pregnant women
agepregprev(): Age-specific prevalence among pregnant women
ageprev(): Prevalence by arbitrary age groups
ancsite_pred_df(): Prepare design matrix indices for ANC prevalence predictions
calc_infections_eppspectrum(): Annualized number of new infections
create_spectrum_fixpar(): Create simulation inputs fixed parameters
get_proj_years(): Get vector of years spanned by projections
hivpop_singleage(): Convert aggregate HIV population to single year
imis(): Incremental Mixture Importance Sampling (IMIS)
incid(): Incidence rate among adults age 15-49 years
incid15to49_eppinput_specres(): Incidence rate age 15-49 using previous-year susceptible population
ll_ancsite_conditional(): Pointwise likelihood for site-level ANC observations given site-level effects
ll_hhsage(): Log likelihood for age-specific household survey prevalence
ll_hhsage_binom(): Log likelihood for age-specific household survey prevalence using binomial approximation
ll_hhsartcov(): Log likelihood for age-specific household survey prevalence
ll_hhsincid(): Log-likelhood for direct incidence estimate from household survey
melt_ancsite_data(): Melt ANC-SS and site-level ANC-RT to long dataset
mod_dimnames(): Add dimnames to spec model output
natagemx(<spec>): Non-HIV age-specific mortality
prepare_ancsite_likdat(): Prepare site-level ANC prevalence data for EPP random-effects likelihood
prepare_directincid(): Prepare direct incidence input EPP simulation
prepare_hhsageprev_likdat(): Prepare age-specific HH survey prevalence likelihood data
prepare_hhsartcov_likdat(): ## Household survey ART coverage likelihood
prepare_hhsincid_likdat(): Prepare household survey incidence likelihood data
prepare_rhybrid(): Setup the r-hybrid model
prepare_spec_fit(): Prepare fit by EPP regions
read_csavr_data(): Read CSAVR input data
read_dp(): Read Spectrum internal files file from PJNZ
read_incid_input(): Read annual incidence input
read_pop1(): Read Spectrum _pop1.xlsx export file
sample_ancsite_pred(): Sample posterior predictions for site-level ANC observations
sample_b_site(): Sample from posterior ditribution for ANC site level random effects
sample_invgamma_post(): Sample from conditional posterior distribution for variance parameter
simmod(): Simulate model
spec_add_dimnames(): Add dimnames to EPP-ASM model output