Man pages for mrc-ide/eppasm
Age-structured EPP Model for HIV Epidemic Estimates
| 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... |
| ll_ancsite_conditional | Pointwise likelihood for site-level ANC observations given... |
| ll_hhsage | Log likelihood for age-specific household survey prevalence |
| ll_hhsage_binom | Log likelihood for age-specific household survey prevalence... |
| ll_hhsartcov | Log likelihood for age-specific household survey prevalence |
| ll_hhsincid | Log-likelhood for direct incidence estimate from household... |
| 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... |
| 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... |
| sample_invgamma_post | Sample from conditional posterior distribution for variance... |
| simmod | Simulate model |
| spec_add_dimnames | Add dimnames to EPP-ASM model output |
