PooledCohort

The goal of PooledCohort is to give researchers who study risk prediction for cardiovascular disease (CVD) a unified interface to implement the Pooled Cohort Equations, the PREVENT equations, and other contemporary CVD risk calculators

Why use these CVD risk calculators?

The 2017 American College of Cardiology and American Heart Association blood pressure guideline recommends using 10-year predicted atherosclerotic cardiovascular disease risk to guide the decision to initiate or intensify antihypertensive medication. The guideline recommends using the Pooled Cohort Risk prediction equations to predict 10-year atherosclerotic cardiovascular disease risk. Therefore, new methods for predicting atherosclerotic cardiovascular disease risk should be evaluated with reference to the Pooled Cohort Risk prediction equations.

Installation

You can install the released version of PooledCohort from CRAN with:

install.packages("PooledCohort")

and the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("bcjaeger/PooledCohort")

Example

A basic example below computes 10-year atherosclerotic cardiovascular risk using the original Pooled Cohort Risk equations for a person who is black/white and male/female with

  • 55 years of age
  • 213 mg/dL total cholesterol
  • 50 mg/dL high density lipoprotein (HDL) cholesterol
  • 120 mm Hg systolic blood pressure
  • no antihypertensive medication use
  • no current smoking
  • no prevalent diabetes

First we will use a dataset that requires no modification of any variable to be plugged into predict_10yr_ascvd_risk()


library(PooledCohort)
library(dplyr, warn.conflicts = FALSE)

example_data <- data.frame(
  sex = c('female', 'female', 'male', 'male'),
  race = c('black', 'white', 'black', 'white'),
  age_years = rep(55, times = 4),
  chol_total_mgdl = rep(213, times = 4),
  chol_hdl_mgdl = rep(50, times = 4),
  bp_sys_mmhg = rep(120, times = 4),
  bp_meds = rep('no', times = 4),
  smoke_current = rep('no', times = 4),
  diabetes = rep('no', times = 4),
  stringsAsFactors = FALSE
)

example_data
#>      sex  race age_years chol_total_mgdl chol_hdl_mgdl bp_sys_mmhg bp_meds
#> 1 female black        55             213            50         120      no
#> 2 female white        55             213            50         120      no
#> 3   male black        55             213            50         120      no
#> 4   male white        55             213            50         120      no
#>   smoke_current diabetes
#> 1            no       no
#> 2            no       no
#> 3            no       no
#> 4            no       no

A convenient way to use predict_10yr_ascvd_risk() is within dplyr::mutate():


example_risk <- example_data %>% 
  mutate(
    risk = predict_10yr_ascvd_risk(
      sex = sex,
      race = race,
      age_years = age_years,
      chol_total_mgdl = chol_total_mgdl,
      chol_hdl_mgdl = chol_hdl_mgdl,
      bp_sys_mmhg = bp_sys_mmhg,
      bp_meds = bp_meds,
      smoke_current = smoke_current,
      diabetes = diabetes
    )
  ) %>% 
  select(sex, race, risk)

example_risk
#>      sex  race       risk
#> 1 female black 0.02998196
#> 2 female white 0.02054450
#> 3   male black 0.06061116
#> 4   male white 0.05378606

Using the PREVENT equations

A similar interface is available for the PREVENT equations by setting the equation_version input to “Khan_2023”. Additionally,

  • the type of PREVENT equation to use is governed by the prevent_type input.

  • We no longer specify race as the PREVENT equations do not use race.

  • We add values for statin use, estimated glomerular filtration rate, and body mass index.


example_data %>% 
  mutate(
    risk = predict_10yr_ascvd_risk(
      sex = sex,
      age_years = age_years,
      chol_total_mgdl = chol_total_mgdl,
      chol_hdl_mgdl = chol_hdl_mgdl,
      bp_sys_mmhg = bp_sys_mmhg,
      bp_meds = bp_meds,
      smoke_current = smoke_current,
      diabetes = diabetes, 
      statin_meds = "no",
      egfr_mlminm2 = 100,
      bmi = 28,
      equation_version = "Khan_2023",
      prevent_type = 'base'
    )
  ) %>% 
  select(sex, race, risk)
#>      sex  race       risk
#> 1 female black 0.01910652
#> 2 female white 0.01910652
#> 3   male black 0.02778896
#> 4   male white 0.02778896

Data formatting

Data usually need to be modified slightly before being plugged into a Risk calculator. For example, instead of a race variable with values of black and white, the data may have a race variable with values of african_american, caucasian, and other.


example_data_granular <- data.frame(
  sex = c('female', 'female', 'male', 'male'),
  race = c('african_american', 'caucasian', 'african_american', 'other'),
  age_years = rep(55, times = 4),
  chol_total_mgdl = rep(213, times = 4),
  chol_hdl_mgdl = rep(50, times = 4),
  bp_sys_mmhg = rep(120, times = 4),
  bp_meds = rep('no', times = 4),
  smoke_current = rep('no', times = 4),
  diabetes = rep('no', times = 4),
  stringsAsFactors = FALSE
)

While you can always modify variables in your data so that they meet the same format as the variables in example_data above, you may prefer to let predict_10yr_ascvd_risk() modify those variables for you:


# a mapping from the current race categories to 
# the 'black' and 'white' categories used by the
# Pooled Cohort Risk equations.

race_levels <- list(
  black = 'african_american',
  white = c('caucasian', 'other')
)

example_risk_granular <- example_data_granular %>% 
  mutate(
    risk = predict_10yr_ascvd_risk(
      sex = sex,
      race = race,
      race_levels = race_levels,
      age_years = age_years,
      chol_total_mgdl = chol_total_mgdl,
      chol_hdl_mgdl = chol_hdl_mgdl,
      bp_sys_mmhg = bp_sys_mmhg,
      bp_meds = bp_meds,
      smoke_current = smoke_current,
      diabetes = diabetes
    )
  ) %>% 
  select(sex, race, risk)

example_risk_granular
#>      sex             race       risk
#> 1 female african_american 0.02998196
#> 2 female        caucasian 0.02054450
#> 3   male african_american 0.06061116
#> 4   male            other 0.05378606

A picky estimator

predict_10yr_ascvd_risk() is a picky estimator that will throw hard stops at you if it doesn’t like the data you give it. In particular, if the input data has continuous variables with values outside the range of recommended values for the Pooled Cohort equations, you will get an error message.


predict_10yr_ascvd_risk(
  sex = 'male',
  race = 'black',
  age_years = 35, # age recommendation: 40-79
  chol_total_mgdl = 213,
  chol_hdl_mgdl = 55,
  bp_sys_mmhg = 120,
  bp_meds = 'no',
  smoke_current = 'no',
  diabetes = 'no'
)
#> Error: min(age_years) is 35 but should be >= 40

This is meant to help you avoid mis-use of the Pooled Cohort Risk equations. However, if you must go outside the range of recommended values, you can set the argument override_boundary_errors to TRUE.


predict_10yr_ascvd_risk(
  sex = 'male',
  race = 'black',
  age_years = 35,
  chol_total_mgdl = 213,
  chol_hdl_mgdl = 55,
  bp_sys_mmhg = 120,
  bp_meds = 'no',
  smoke_current = 'no',
  diabetes = 'no',
  override_boundary_errors = TRUE
)
#> [1] 0.01969643