Package: eppasm 0.7.6

Jeff Eaton

eppasm: Age-structured EPP Model for HIV Epidemic Estimates

What the package does (one paragraph).

Authors:Jeff Eaton [aut, cre]

eppasm_0.7.6.tar.gz
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eppasm.pdf |eppasm.html✨
eppasm/json (API)
NEWS

# Install 'eppasm' in R:
install.packages('eppasm', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mrc-ide/eppasm/issues

On CRAN:

49 exports 6 stars 1.85 score 39 dependencies 3 dependents 34 scripts

Last updated 3 months agofrom:52688b2c77 (on master). Checks:OK: 1 ERROR: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 14 2024
R-4.5-win-x86_64ERRORAug 14 2024
R-4.5-linux-x86_64ERRORAug 14 2024
R-4.4-win-x86_64ERRORAug 14 2024
R-4.4-mac-x86_64ERRORAug 14 2024
R-4.4-mac-aarch64ERRORAug 14 2024
R-4.3-win-x86_64ERRORAug 14 2024
R-4.3-mac-x86_64ERRORAug 14 2024
R-4.3-mac-aarch64ERRORAug 14 2024

Exports:agepregartcovagepregprevageprevageprev.specresaggr_specresaidsdeaths.specresancsite_pred_dfartcov15plusartcov15to49calc_incid15to49calc_pregprevcalc_prev15to49create_spectrum_fixparfitmodfnCreateParamfnPregPrevhivpop_singleageincidincid15to49_eppinput_specresllll_ancrtcensll_ancsitell_hhsagell_hhsage_binomlpriormod_dimnamesprepare_directincidprepare_likdatprepare_rhybridprepare_spec_fitprevread_countryread_csavr_dataread_demog_paramread_dpread_epp_perc_urbanread_epp_t0read_hivproj_outputread_hivproj_paramread_incid_inputread_iso3read_pjnread_pop1read_regionread_specdp_demog_paramread_subp_filesimmodspec_add_dimnamestidy_output

Dependencies:abindanclikBHbinombitbit64cellrangerclicpp11crayoneppfansifastmatchgluehmslifecyclemagrittrmvtnormpillarpkgconfigplyrprettyunitsprogressR6Rcppreadxlrematchreshape2rlangstringistringrtibbletidyselecttzdbutf8vctrsvroomwithrxml2

Readme and manuals

Help Manual

Help pageTopics
Age-specific mortalityagemx.spec
Age-specific ART coverage among pregnant womenagepregartcov
Age-specific prevalence among pregnant womenagepregprev
Prevalence by arbitrary age groupsageprev
Prepare design matrix indices for ANC prevalence predictionsancsite_pred_df
Annualized number of new infectionscalc_infections_eppspectrum
Create simulation inputs fixed parameterscreate_spectrum_fixpar
Get vector of years spanned by projectionsget_proj_years
Convert aggregate HIV population to single yearhivpop_singleage
Incremental Mixture Importance Sampling (IMIS)imis
Incidence rate among adults age 15-49 yearsincid
Incidence rate age 15-49 using previous-year susceptible populationincid15to49_eppinput_specres
Pointwise likelihood for site-level ANC observations given site-level effectsll_ancsite_conditional
Log likelihood for age-specific household survey prevalencell_hhsage
Log likelihood for age-specific household survey prevalence using binomial approximationll_hhsage_binom
Log likelihood for age-specific household survey prevalencell_hhsartcov
Log-likelhood for direct incidence estimate from household surveyll_hhsincid
Melt ANC-SS and site-level ANC-RT to long datasetmelt_ancsite_data
Add dimnames to spec model outputmod_dimnames
Non-HIV age-specific mortalitynatagemx.spec
Prepare site-level ANC prevalence data for EPP random-effects likelihoodprepare_ancsite_likdat
Prepare direct incidence input EPP simulationprepare_directincid
Prepare age-specific HH survey prevalence likelihood dataprepare_hhsageprev_likdat
## Household survey ART coverage likelihoodprepare_hhsartcov_likdat
Prepare household survey incidence likelihood dataprepare_hhsincid_likdat
Setup the r-hybrid modelprepare_rhybrid
Prepare fit by EPP regionsprepare_spec_fit
Read CSAVR input dataread_csavr_data
Read Spectrum internal files file from PJNZread_dp
Read annual incidence inputread_incid_input
Read Spectrum _pop1.xlsx export fileread_pop1
Sample posterior predictions for site-level ANC observationssample_ancsite_pred
Sample from posterior ditribution for ANC site level random effectssample_b_site
Sample from conditional posterior distribution for variance parametersample_invgamma_post
Simulate modelsimmod
Add dimnames to EPP-ASM model outputspec_add_dimnames