Description Usage Arguments Details Value
Incindence from testing history
1 2 3 4 | testing_incidence(report_hiv_pos, biomarker_art, low_viral, hiv, last_hiv_lower,
last_hiv_upper, ever_hiv_test, weights = rep(1,
length(report_hiv_pos))/length(report_hiv_pos), distribution = "weibull",
ptruth = NULL, ptreated = NULL, non_tester_tid = 123.824)
|
report_hiv_pos |
A logical vector indicating whether each subject reported a positive hiv status |
biomarker_art |
A logical vector indicating whether ART antibodies are present. NA if test not done. |
low_viral |
A logical vector indicating whether viral load is <=1000 |
hiv |
A logical vector indicating hiv status |
last_hiv_lower |
A numeric vector indicating the lower bound of the months since last hiv test bin in months. |
last_hiv_upper |
A numeric vector indicating the upper bound of the months since last hiv test bin in months. |
ever_hiv_test |
A logical vector indicating whether the subject had eer had an hiv test. |
weights |
Survey weights |
distribution |
Either "weibull" or "gamma." This controls the family of distribution used to model time since last test. |
ptruth |
The proportion of the diagnosed hiv positive population that would report being hiv positive. If NULL, this is estimated using biomarker_art and low_viral. |
ptreated |
The proportion of hiv positive individuals with postive biomarker_art or low_viral. If NULL, this is estimated from the data. |
non_tester_tid |
mean nummber of months between infection and diagnosis for non_testers. |
last_hiv_upper should always be greater than last_hiv_lower, and may be infinite (e.g. test was > 24 months ago). Those with missing data or who never had an hiv test should be assigned NA for both their lower and upper bound.
A data.frame of class test_inc with elements: 'inc': the estimated incidence. 'pundiag': The estimated proportion of positive cases that are undiagnosed. 'psay_undiag': The proportion of positive cases that report being undiagnosed. 'pmiss_class': the proportion whose diagnosis status is incorrectly reported by the individual . 'phiv': The proportion with a positive diagnosis. 'ptester': The proportion who have ever been tested. 'mean_time_since_last_test': the mean tie since last test in years. 'tid': mean time between infection and diagnosis in years. 'ptruth' the proportion of positive individuals that correctly report their status. 'ptreated': the proportion of positive indivudals who are identified as treated by viral load or biomarker.
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