Package: first90 1.7.1

Jeffrey Eaton

first90: The first90 model

Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.

Authors:Jeffrey Eaton [aut, cre], Mathieu Maheu-Giroux [aut], Katia Giguère [aut], Roma Bhatkoti [aut]

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first90.pdf |first90.html✨
first90/json (API)
NEWS

# Install 'first90' in R:
install.packages('first90', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mrc-ide/first90release/issues

Datasets:

    On CRAN:

    4.53 score 5 stars 3 packages 2 scripts 78 exports 29 dependencies

    Last updated 1 months agofrom:25494ecdca (on master). Checks:OK: 1 ERROR: 8. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKDec 18 2024
    R-4.5-win-x86_64ERRORDec 18 2024
    R-4.5-linux-x86_64ERRORDec 18 2024
    R-4.4-win-x86_64ERRORDec 18 2024
    R-4.4-mac-x86_64ERRORDec 18 2024
    R-4.4-mac-aarch64ERRORDec 18 2024
    R-4.3-win-x86_64ERRORDec 18 2024
    R-4.3-mac-x86_64ERRORDec 18 2024
    R-4.3-mac-aarch64ERRORDec 18 2024

    Exports:add_ss_indicesartcov15to49combine_inputscreate_hts_paramdenom_lifetablediagnosedend_of_yearevertestextract_pjnzfile_in_zipget_dp_srbget_dp_tfrget_dp_totpopget_out_artget_out_awareget_out_evertestget_out_nbawareget_out_nbtestget_out_nbtest_posget_out_nbtest_pos_sexget_out_nbtest_sexget_out_pregprevget_pjn_countryget_pjn_regionget_pjnz_summary_datall_evertestll_htsll_prgdatnumber_diagnosesnumber_retestsnumber_testsoptimized_parplot_input_ancposplot_input_anctotplot_input_totplot_input_totposplot_inputdataplot_outplot_out_90splot_out_evertestplot_out_evertest_fbyageplot_out_evertest_mbyageplot_out_evertestnegplot_out_evertestposplot_out_nbpostestplot_out_nbpostest_sexplot_out_nbtestplot_out_stratplot_pjnzplot_pjnz_incplot_pjnz_plhivplot_pjnz_popplot_pjnz_prvplot_prv_pos_yldplot_retest_test_negplot_retest_test_pospool_prb_dx_one_yrprb_dx_one_yrprepare_hts_likdatprepare_inputsprepare_inputs_from_extractsread_countryread_regionselect_htsselect_prgmdatasimmodsimul_pool_prb_dx_one_yrsimul.runsimul.samplesimul.testspectrum_output_tablesvy_hts_interfacetab_out_artcovtab_out_awaretab_out_evertesttab_out_nbawaretab_out_pregprevtotal_tests

    Dependencies:BHbitbit64clicpp11crayonfansifastmatchgluehmslatticelifecyclemagrittrMatrixmvtnormpillarpkgconfigprettyunitsprogressR6Rcpprlangtibbletidyselecttzdbutf8vctrsvroomwithr

    Readme and manuals

    Help Manual

    Help pageTopics
    Add incidences corresponding to state spaceadd_ss_indices
    ART coverage among age 15-49artcov15to49
    Calculate ASFR from TFR and fertility distributioncalc_asfr
    Combine PJNZ inputscombine_inputs
    Beers coefficients to distribute from 5-year to single-year of agecreate_beers
    Create HIV testing rates from parameter inputscreate_hts_param
    Proportion diagnosed among HIV+ by age, sex, or HIV statusdiagnosed
    Proportion ever tested by age, sex, or HIV statusevertest
    Internal helper functionsexists_dptag
    Extract outputs from PJNZ needed for first90 modelextract_pjnz
    Extract AIM module parametersget_dp_frr
    Get sex ratio at birthget_dp_srb
    Get mortality probability (Sx) from Spectrum DP fileget_dp_Sx
    Get age-specific fertility rate by single-yearget_dp_tfr
    Extract arrays from Spectrum DP fileget_dp_totpop
    Get country name from parsed PJNget_pjn_country
    Get subnational region from parsed PJNget_pjn_region
    Number of new diagnoses by age and sexnumber_diagnoses
    Calculate number adn proportion of retests conducted or number tested by year funtion based on number test in the outputs.R scriptnumber_retests
    Calculate number of tests conducted or number tested by yearnumber_tests
    Create model inputs from Spectrum PJNZprepare_inputs
    Create model inputs from aggregated Spectrum PJNZprepare_inputs_from_extracts
    Process survey data on hiv testing behaviorsselect_hts
    Process programmatic data on number of testsselect_prgmdata
    Simulate EPP-ASM modelsimmod
    Table to write CSV outputs for Spectrumspectrum_output_table
    Function to present the survey data on shinny interfacesvy_hts_interface