The hivscore package is an implementation of the VACS Index 1, the VACS Index 2 and the Dat’AIDS score.
Installation
You can install the development version of the hivscore package like so:
remotes::install_github("jaromilfrossard/hivscore")Computing the scores
You can compute the VACS Index 1:
library(hivscore)
data("vacs1")
vacs1$score_vacs1 <- score_vacsindex1(
age = vacs1$age, cd4_count = vacs1$cd4, hiv1_rna = vacs1$hiv1_rna,
hgb = vacs1$hgb, fib4 = vacs1$fib4, egfr = vacs1$egfr,
hepc = vacs1$hepc)
head(vacs1)
#> age cd4 log_hiv1_rna hgb fib4 egfr hepc alb wbc bmi hiv1_rna vacs1 vacs2
#> 1 52 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 23 51.11143
#> 2 30 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 11 38.98529
#> 3 35 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 11 44.19800
#> 4 40 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 11 47.50081
#> 5 45 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 11 49.47464
#> 6 50 435 1.7 14 1.34 90 TRUE 4 5.5 25 50 23 50.70043
#> score_vacs1
#> 1 23
#> 2 11
#> 3 11
#> 4 11
#> 5 11
#> 6 23For the VACS Index 2, you will use:
data("vacs2")
vacs2$score_vacs2 <- score_vacsindex2(
age = vacs2$AGE, cd4_count = vacs2$CD4,vl_log = vacs2$VL_LOG,
hgb = vacs2$HGB,fib4 = vacs2$FIB4,egfr = vacs2$EGFR,
hepc = vacs2$HEPC==1, alb = vacs2$ALB, bmi = vacs2$BMI,
wbc = vacs2$WBC)
head(vacs2)
#> PARAM SET AGE CD4 VL_LOG HGB FIB4 EGFR HEPC ALB WBC BMI SCORE_V2
#> 1 98 98 75 10 5.0 9 7.50 0 1 2 11.0 15.0 173.467
#> 2 99 99 75 1000 1.3 9 7.50 0 1 2 11.0 15.0 136.322
#> 3 0 50 52 435 1.7 14 1.34 90 0 4 5.5 25.3 44.419
#> 4 1 1 30 435 1.7 14 1.34 90 0 4 5.5 25.3 32.293
#> 5 1 2 35 435 1.7 14 1.34 90 0 4 5.5 25.3 37.506
#> 6 1 3 40 435 1.7 14 1.34 90 0 4 5.5 25.3 40.808
#> score_vacs2
#> 1 173.46689
#> 2 136.32164
#> 3 44.41904
#> 4 32.29290
#> 5 37.50561
#> 6 40.80842The Dat’AIDS score can be computed using:
data("dataids")
dataids$dataids <- score_dataids(
age = dataids$age,cd4_count = dataids$cd4_count, nonhiv_cancer = dataids$nonhiv_cancer,
cardio_disease = dataids$cardio_disease,egfr = dataids$egfr, cirrhosis = dataids$cirrhosis,
low_bmi = dataids$low_bmi,anemia = dataids$anemia)
head(dataids)
#> age cd4_count nonhiv_cancer cardio_disease egfr cirrhosis low_bmi anemia
#> 1 62 550 FALSE FALSE 70 FALSE FALSE FALSE
#> 2 62 550 FALSE FALSE 70 FALSE FALSE TRUE
#> 3 62 550 FALSE FALSE 70 FALSE TRUE FALSE
#> 4 62 550 FALSE FALSE 70 FALSE TRUE TRUE
#> 5 62 550 FALSE FALSE 70 TRUE FALSE FALSE
#> 6 62 550 FALSE FALSE 70 TRUE FALSE TRUE
#> SCORE_DATAIDS dataids
#> 1 0 0
#> 2 6 6
#> 3 10 10
#> 4 16 16
#> 5 13 13
#> 6 19 19Predicting survival probabilities
Using the Dat’AIDS score, you can predict survival probabilities after 1 year:
dataids$surv_prob1 <- surv_dataids(1, score = dataids$dataids)
head(dataids)
#> age cd4_count nonhiv_cancer cardio_disease egfr cirrhosis low_bmi anemia
#> 1 62 550 FALSE FALSE 70 FALSE FALSE FALSE
#> 2 62 550 FALSE FALSE 70 FALSE FALSE TRUE
#> 3 62 550 FALSE FALSE 70 FALSE TRUE FALSE
#> 4 62 550 FALSE FALSE 70 FALSE TRUE TRUE
#> 5 62 550 FALSE FALSE 70 TRUE FALSE FALSE
#> 6 62 550 FALSE FALSE 70 TRUE FALSE TRUE
#> SCORE_DATAIDS dataids surv_prob1
#> 1 0 0 0.9938032
#> 2 6 6 0.9886812
#> 3 10 10 0.9831056
#> 4 16 16 0.9692791
#> 5 13 13 0.9772061
#> 6 19 19 0.9586541References
For the VACS Index 1:
- Tate, J. P., Justice, A. C., Hughes, M. D., Bonnet, F., Reiss, P., Mocroft, A., … & Sterne, J. A. (2013). An internationally generalizable risk index for mortality after one year of antiretroviral therapy. AIDS (London, England), 27(4), 563.
- Bebu, I., Tate, J., Rimland, D., Mesner, O., Macalino, G. E., Ganesan, A., … & Infectious Disease Clinical Research Program HIV Working Group. (2014). The VACS index predicts mortality in a young, healthy HIV population starting highly active antiretroviral therapy. Journal of acquired immune deficiency syndromes (1999), 65(2), 226.
- Justice, A. C., Modur, S., Tate, J. P., Althoff, K. N., Jacobson, L. P., Gebo, K., … & Gange, S. J. (2013). Predictive accuracy of the Veterans Aging Cohort Study (VACS) index for mortality with HIV infection: a north American cross cohort analysis. Journal of acquired immune deficiency syndromes (1999), 62(2), 149.
For the VACS Index 2:
- Tate, J. P., Sterne, J. A., Justice, A. C., Study, V. A. C., & Antiretroviral Therapy Cohort Collaboration (ART-CC. (2019). Albumin, white blood cell count, and body mass index improve discrimination of mortality in HIV-positive individuals. AIDS (London, England), 33(5),
- McGinnis, K. A., Justice, A. C., Moore, R. D., Silverberg, M. J., Althoff, K. N., Karris, M., … & Study, V. A. C. (2021). Discrimination And Calibration Of The Vacs Index 2.0 For Predicting Mortality Among People With Hiv In North America. Clinical Infectious Diseases: an Official Publication of the Infectious Diseases Society of America.
For the Dat’AIDS score:
- Hentzien M, Delpierre C, Pugliese P, Allavena C, Jacomet C, Valantin M-A, et al. (2018) Derivation and internal validation of a mortality risk index for aged people living with HIV: The Dat’AIDS score. PLoS ONE 13(4): e0195725. https://doi.org/10.1371/journal.pone.0195725
- Hentzien, M., Frossard, J., Kouyos, R., Prendki, V., Damas, J., Hofmann, E., … & Swiss HIV Cohort Study. (2024). External validation of the Dat’AIDS score: A risk score for predicting 5‐year overall mortality in people living with HIV aged 60 years or older. HIV medicine, 25(1), 72-82. https://doi.org/10.1111/hiv.13534