Calculate 2020 Winther CACS-CL PTP model for obstructive CAD — calculate_winther_2020_cacs_cl

This function returns a patient's pre-test probability (PTP) of obstructive coronary artery disease (CAD) based on 2020 Winther et. al. Coronary Artery Calcium Score-Weighted Clinical Likelihood (CACS-CL) model. Obstructive CAD was defined as a stenosis causing $\geq$ 50% diameter stenosis on coronary CTA.

Usage

calculate_winther_2020_cacs_cl_ptp(
  age,
  sex,
  chest_pain_type,
  have_dyspnoea,
  have_family_history,
  have_smoking_history,
  have_dyslipidemia,
  have_hypertension,
  have_diabetes,
  coronary_calcium_score,
  allow_na_symptom_score = TRUE,
  max_na_num_of_rf = 0,
  label_sex_male = c("male"),
  label_sex_female = c("female"),
  label_sex_unknown = c(NA, NaN),
  label_have_dyspnoea_no = c("no"),
  label_have_dyspnoea_yes = c("yes"),
  label_have_dyspnoea_unknown = c(NA, NaN),
  label_cpt_no_chest_pain = c("no chest pain"),
  label_cpt_nonanginal = c("nonanginal"),
  label_cpt_atypical = c("atypical"),
  label_cpt_typical = c("typical"),
  label_cpt_unknown = c(NA, NaN),
  label_have_family_history_no = c("no"),
  label_have_family_history_yes = c("yes"),
  label_have_family_history_unknown = c(NA, NaN),
  label_have_smoking_history_no = c("no"),
  label_have_smoking_history_yes = c("yes"),
  label_have_smoking_history_unknown = c(NA, NaN),
  label_have_dyslipidemia_no = c("no"),
  label_have_dyslipidemia_yes = c("yes"),
  label_have_dyslipidemia_unknown = c(NA, NaN),
  label_have_hypertension_no = c("no"),
  label_have_hypertension_yes = c("yes"),
  label_have_hypertension_unknown = c(NA, NaN),
  label_have_diabetes_no = c("no"),
  label_have_diabetes_yes = c("yes"),
  label_have_diabetes_unknown = c(NA, NaN)
)

Arguments

age: Input numeric value to indicate the age of the patient in years.
sex: The value of variable in the parameters label_sex_male,
label_sex_female and label_sex_unknown.
chest_pain_type: The value of variable in the parameters label_cpt_no_chest_pain,
label_cpt_nonanginal,
label_cpt_atypical,
label_cpt_typical,
and label_cpt_unknown.
have_dyspnoea: The value of variable in the parameters label_have_dyspnoea_no,
label_have_dyspnoea_yes and label_have_dyspnoea_unknown.
have_family_history: The value of variable in the parameters label_have_family_history_no,
label_have_family_history_yes
and label_have_family_history_unknown.
have_smoking_history: The value of variable in the parameters label_have_smoking_history_no,
label_have_smoking_history_yes,
and label_have_smoking_history_unknown.
have_dyslipidemia: The value of variable in the parameters label_have_dyslipidemia_no,
label_have_dyslipidemia_yes and label_have_dyslipidemia_unknown.
have_hypertension: The value of variable in the parameters label_have_hypertension_no,
label_have_hypertension_yes, and label_have_hypertension_unknown.
have_diabetes: The value of variable in the parameters label_have_diabetes_no,
label_have_diabetes_yes and label_have_diabetes_unknown.
coronary_calcium_score: Input non-negative numeric to indicate the total coronary calcium score of the patient.
allow_na_symptom_score: A logical evaluating to TRUE or FALSE
indicating whether we can allow chest_pain_type
or have_dyspnoea to be NA when calculating the score.
max_na_num_of_rf: Input integer 0 to 5 to indicate the maximum number of missing risk factors to tolerate before outputting an NA. Default: 0
label_sex_male: Label(s) for definition(s) of male sex. Default: c("male")
label_sex_female: Label(s) for definition(s) of female sex. Default: c("female")
label_sex_unknown: Label(s) for definition(s) of missing sex. Default: c(NA, NaN)
label_have_dyspnoea_no: Label(s) for patient having no dyspnoea symptoms. Default: c("no")
label_have_dyspnoea_yes: Label(s) for patient having dyspnoea symptoms. Default: c("yes")
label_have_dyspnoea_unknown: Label(s) for patient having unknown dyspnoea symptoms. Default: c(NA, NaN)
label_cpt_no_chest_pain: Label(s) for patient having no chest pain. Default: c("no chest pain")
label_cpt_nonanginal: Label(s) for patient having nonanginal or non-specific chest pain.
Default: c("nonanginal")
label_cpt_atypical: Label(s) for patient having atypical chest pain. Default: c("atypical")
label_cpt_typical: Label(s) for patient having typical chest pain. Default: c("typical")
label_cpt_unknown: Label(s) for patient having unknown chest pain type symptoms. Default: c(NA, NaN)
label_have_family_history_no: Label(s) for patient with no family history of CAD. Default: c("no")
label_have_family_history_yes: Label(s) for patient having family history of CAD. Default: c("yes")
label_have_family_history_unknown: Label(s) for patient having unknown family history of CAD. Default: c(NA, NaN)
label_have_smoking_history_no: Label(s) for patient with no smoking history (current or past). Default: c("no")
label_have_smoking_history_yes: Label(s) for patient having smoking history (current or past). Default: c("yes")
label_have_smoking_history_unknown: Label(s) for patient having unknown smoking history (current or past). Default: c(NA, NaN)
label_have_dyslipidemia_no: Label(s) for patient with no dyslipidemia. Default: c("no")
label_have_dyslipidemia_yes: Label(s) for patient having dyslipidemia. Default: c("yes")
label_have_dyslipidemia_unknown: Label(s) for patient having unknown dyslipidemia. Default: c(NA, NaN)
label_have_hypertension_no: Label(s) for patient with no hypertension. Default: c("no")
label_have_hypertension_yes: Label(s) for patient having hypertension. Default: c("yes")
label_have_hypertension_unknown: Label(s) for patient having unknown hypertension. Default: c(NA, NaN)
label_have_diabetes_no: Label(s) for patient with no diabetes. Default: c("no")
label_have_diabetes_yes: Label(s) for patient having diabetes. Default: c("yes")
label_have_diabetes_unknown: Label(s) for patient having unknown diabetes. Default: c(NA, NaN)

Value

A numeric value representing the patient's PTP for obstructive CAD based on the 2020 Winther et. al. Coronary Artery Calcium Score-Weighted Clinical Likelihood (CACS-CL) model.

Details

The predictive model is based on > 40000 symptomatic patients from 2008 to 2017 from 13 hospitals in Western Denmark. These patients are registered under the Western Denmark Heart Registry.

Model formula used is from Table S3.

It is of the form $$\frac{1}{(1 + e^{-F(x)})}$$ where $F(x)$ equals $$ \begin{array}{l} 0.0013\quad+ \\\\ (0.2021 * rf\_ptp)\quad+ \\\\ (0.0082 * cacs\_1\_to\_9)\quad+ \\\\ (0.0238 * cacs\_10\_to\_99)\quad+ \\\\ (0.1131 * cacs\_100\_to\_399)\quad+ \\\\ (0.2306 * cacs\_400\_to\_999)\quad+ \\\\ (0.4040 * cacs\_1000\_or\_more)\quad+ \\\\ (0.1311 * rf\_ptp * cacs\_1\_to\_9)\quad+ \\\\ (0.2909 * rf\_ptp * cacs\_10\_to\_99)\quad+ \\\\ (0.4077 * rf\_ptp * cacs\_100\_to\_399)\quad+ \\\\ (0.4658 * rf\_ptp * cacs\_400\_to\_999)\quad+ \\\\ (0.4489 * rf\_ptp * cacs\_1000\_or\_more) \end{array} $$

Examples

# 40 year old Male with nonanginal chest pain and coronary calcium score of 0
calculate_winther_2020_cacs_cl_ptp(
    age = 40,
    sex = "male",
    chest_pain_type = "no chest pain",
    have_dyspnoea = "no",
    have_family_history = "no",
    have_smoking_history = "no",
    have_dyslipidemia = "no",
    have_hypertension = "no",
    have_diabetes = "no",
    coronary_calcium_score = 0,
    allow_na_symptom_score = TRUE,
    max_na_num_of_rf = 0
)
#> [1] 0.004159686