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]

first90_1.7.1.tar.gz
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first90_1.7.1.tgz(r-4.6-x86_64)first90_1.7.1.tgz(r-4.6-arm64)first90_1.7.1.tgz(r-4.5-x86_64)first90_1.7.1.tgz(r-4.5-arm64)
first90_1.7.1.tar.gz(r-4.7-arm64)first90_1.7.1.tar.gz(r-4.7-x86_64)first90_1.7.1.tar.gz(r-4.6-arm64)first90_1.7.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
first90/json (API)
NEWS

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

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

On CRAN:

Conda:

3.95 score 5 stars 4 packages 9 scripts 78 exports 28 dependencies

Last updated from:25494ecdca (on master). Checks:11 ERROR, 1 OK, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR141
linux-devel-x86_64ERROR148
source / vignettesOK190
linux-release-arm64ERROR176
linux-release-x86_64ERROR147
macos-release-arm64ERROR86
macos-release-x86_64ERROR169
macos-oldrel-arm64ERROR89
macos-oldrel-x86_64ERROR234
windows-develERROR153
windows-releaseERROR119
windows-oldrelERROR116
wasm-releaseFAIL113

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:BHbitbit64clicpp11crayonfastmatchgluehmslatticelifecyclemagrittrMatrixmvtnormpillarpkgconfigprettyunitsprogressR6Rcpprlangtibbletidyselecttzdbutf8vctrsvroomwithr

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