R/CHDWilson.R
In Aidakazemi/CHDWilson: Coronary Heat Disease (CHD) Prediction Model using risk factor categories over 10 years based on <doi: 10.1161/01.cir.97.18.1837>
#' Predicting Coronary Heart Disease (CHD) over ten years using TChol and LDL categories
#'
#' @param age A number for age
#' @param gender A binary variables taking 1 for men and 0 for women
#' @param TChol A number for Total cholestrol in mg/dL
#' @param HDL A number for HDL cholesterol in mg/dL
#' @param LDL A number for LDL cholesterol in mg/dL
#' @param SBP A number for SBP Blood pressure in mm Hg without regard to the use of antihypertensive medication
#' @param DBP A number for DBP blood pressure in mm Hg without regard to the use of antihypertensive medication
#' @param diabetes A binary variable taking 1 if the participant was under treatment with insulin or oral hypoglycemic agents, if casual blood glucose determinations exceeded 150 mg/dL at two clinic visits in the original cohort, or if fasting blood glucose exceeded 140 mg/dL at the initial examination of the Offspring Study participants
#' @param smoker A binary variable taking 1 for person who smoked during the past 12 month and 0 therwise
#'
#' @examples
#'
#' predictchd (age = 55, gender = 1, TChol = 250, LDL = 120, HDL = 39,
#' SBP = 146, DBP = 88, diabetes = 0 , smoker =1)
#' predictchd (age = 30, gender = 0, TChol = 170, LDL = 120, HDL = 39,
#' SBP = 145, DBP = 88, diabetes = 0 , smoker =1)
#'
#' @source \url{https://www.ahajournals.org/doi/full/10.1161/01.CIR.97.18.1837}
#' @export
predictchd <- function (age, gender, TChol, LDL, HDL, SBP, DBP, diabetes, smoker) {
#categories of blood pressure SBP based on Joint National Committee (JNC-V) blood pressure
if (SBP < 120) {
#Normal blood pressure
BP_s = 1
} else if (SBP >= 120 & SBP < 130) {
#normal blood pressure (including optimal)
BP_s = 2
} else if (SBP >= 130 & SBP < 140) {
#High normal blood pressure
BP_s = 3
} else if (SBP >= 140 & SBP < 160) {
#Hypertension stage I blood pressure
BP_s = 4
} else if (SBP >= 160) {
#Hypertension stage II-IV
BP_s = 5
}
#categories of blood pressure DBP based on Joint National Committee (JNC-V) blood pressure
if (DBP < 80) {
#Normal blood pressure
BP_d = 1
} else if (DBP >= 80 & DBP < 85) {
#normal blood pressure (including optimal)
BP_d = 2
} else if (DBP >= 85 & DBP < 90) {
#High normal blood pressure
BP_d = 3
} else if (DBP >= 90 & DBP < 100) {
#Hypertension stage I blood pressure
BP_d = 4
} else if (DBP >= 100) {
#Hypertension stage II-IV
BP_d = 5
}
if (BP_s == BP_d) {
BP = BP_s
} else if (BP_s < BP_d) {
BP = BP_d
} else if (BP_s > BP_d) {
BP = BP_s
}
#================================================================ Men =======================================================================
if (gender == 1) {
#TCholl coefficient in range using TChol categories
if (TChol < 160) {
TChol_TCholcoef = -0.65945
} else if (TChol >= 160 & TChol <= 199) {
TChol_TCholcoef = 0
} else if (TChol >= 200 & TChol <= 239) {
TChol_TCholcoef = 0.17692
} else if (TChol >= 240 & TChol <= 279) {
TChol_TCholcoef = 0.50539
} else if (TChol >= 280) {
TChol_TCholcoef = 0.65713
}
#LDL coefficient in range using LDL categories
if (LDL < 100) {
LDL_ldlcoef = -0.69281
} else if (LDL >= 100 & LDL <= 129) {
LDL_ldlcoef = 0
} else if (LDL >= 130 & LDL <= 159) {
LDL_ldlcoef = 0.00389
} else if (LDL >= 160 & LDL <= 189) {
LDL_ldlcoef = 0.26755
} else if (LDL >= 190) {
LDL_ldlcoef = 0.56705
}
#HDL-C coefficient in range using TChol categories
if (HDL < 35) {
HDL_TCholcoef = 0.49744
} else if (HDL >= 35 & HDL <= 44) {
HDL_TCholcoef = 0.24310
} else if (HDL >= 45 & HDL <= 49) {
HDL_TCholcoef = 0
} else if (HDL >= 50 & HDL <= 59) {
HDL_TCholcoef = -0.05107
} else if (HDL >= 60) {
HDL_TCholcoef = -0.48660
}
#HDL-C coefficient in range using LDL categories
if (HDL < 35) {
HDL_ldlcoef = 0.48598
} else if (HDL >= 35 & HDL <= 44) {
HDL_ldlcoef = 0.21643
} else if (HDL >= 45 & HDL <= 49) {
HDL_ldlcoef = 0
} else if (HDL >= 50 & HDL <= 59) {
HDL_ldlcoef = -0.04710
} else if (HDL >= 60) {
HDL_ldlcoef = -0.34190
}
#SBP coefficient in range using TChol categories
if (BP == 1) {
BP_TCholcoef = -0.00226
} else if (BP == 2) {
BP_TCholcoef = 0
} else if (BP == 3) {
BP_TCholcoef = 0.28320
} else if (BP == 4) {
BP_TCholcoef = 0.52168
} else if (BP == 5) {
BP_TCholcoef = 0.61859
}
#SBP coefficient in range using LDL categories
if (BP == 1) {
BP_ldlcoef = -0.02642
} else if (BP == 2) {
BP_ldlcoef = 0
} else if (BP == 3) {
BP_ldlcoef = 0.30104
} else if (BP == 4) {
BP_ldlcoef = 0.55714
} else if (BP == 5) {
BP_ldlcoef = 0.65107
}
#============================================================= Women ====================================================================
} else if (gender == 0) {
#TCholl coefficient in range using TChol categories
if (TChol < 160) {
TChol_TCholcoef = -0.26138
} else if (TChol >= 160 & TChol <= 199) {
TChol_TCholcoef = 0
} else if (TChol >= 200 & TChol <= 239) {
TChol_TCholcoef = 0.20771
} else if (TChol >= 240 & TChol <= 279) {
TChol_TCholcoef = 0.24385
} else if (TChol >= 280) {
TChol_TCholcoef = 0.53513
}
#LDL coefficient in range using LDL categories
if (LDL < 100) {
LDL_ldlcoef = -0.42616
} else if (LDL >= 100 & LDL <= 129) {
LDL_ldlcoef = 0
} else if (LDL >= 130 & LDL <= 159) {
LDL_ldlcoef = 0.01366
} else if (LDL >= 160 & LDL <= 189) {
LDL_ldlcoef = 0.26948
} else if (LDL >= 190) {
LDL_ldlcoef = 0.33251
}
#HDL-C coefficient in range using TChol categories
if (HDL < 35) {
HDL_TCholcoef = 0.84312
} else if (HDL >= 35 & HDL <= 44) {
HDL_TCholcoef = 0.37796
} else if (HDL >= 45 & HDL <= 49) {
HDL_TCholcoef = 0.19785
} else if (HDL >= 50 & HDL <= 59) {
HDL_TCholcoef = 0
} else if (HDL >= 60) {
HDL_TCholcoef = -0.42951
}
#HDL-C coefficient in range using LDL categories
if (HDL < 35) {
HDL_ldlcoef = 0.88121
} else if (HDL >= 35 & HDL <= 44) {
HDL_ldlcoef = 0.36312
} else if (HDL >= 45 & HDL <= 49) {
HDL_ldlcoef = 0.19247
} else if (HDL >= 50 & HDL <= 59) {
HDL_ldlcoef = 0
} else if (HDL >= 60) {
HDL_ldlcoef = -0.35404
}
#SBP coefficient in range using TChol categories
if (BP == 1) {
BP_TCholcoef = -0.53363
} else if (BP == 2) {
BP_TCholcoef = 0
} else if (BP == 3) {
BP_TCholcoef = 0.06773
} else if (BP == 4) {
BP_TCholcoef = 0.26288
} else if (BP == 5) {
BP_TCholcoef = 0.46573
}
#SBP coefficient in range using LDL categories
if (BP == 1) {
BP_ldlcoef = -0.51204
} else if (BP == 2) {
BP_ldlcoef = 0
} else if (BP == 3) {
BP_ldlcoef = -0.03484
} else if (BP == 4) {
BP_ldlcoef = 0.28533
} else if (BP == 5) {
BP_ldlcoef = 0.50403
}
}
#================================================== Prediction using TChol =========================================================
L_TChol_men <- 0.04826 * age + TChol_TCholcoef + HDL_TCholcoef + BP_TCholcoef + 0.42839 * diabetes + 0.52337 * smoker
#values of the means
G_TChol_men <- 3.0975
A_TChol_men <- L_TChol_men - G_TChol_men
B_TChol_men <- exp(A_TChol_men)
#Baseline survival function at 10 years for men:
s_TChol_men <- 0.90015
P_TChol_men <- round((1 - (s_TChol_men) ^ B_TChol_men) * 100, digits = 0)
L_TChol_women <- 0.33766 * age + (-0.00268) * age ^ 2 + TChol_TCholcoef + HDL_TCholcoef + BP_TCholcoef + 0.59626 * diabetes + 0.29246 * smoker
#values of the means
G_TChol_women <- 9.92545
A_TChol_women <- L_TChol_women - G_TChol_women
B_TChol_women <- exp(A_TChol_women)
#Baseline survival function at 10 years for women:
s_TChol_women <- 0.96246
P_TChol_women <- round((1 - (s_TChol_women) ^ B_TChol_women)* 100, digits = 0)
#================================================== Prediction using LDL =========================================================
L_ldl_men <- 0.04808 * age + LDL_ldlcoef + HDL_ldlcoef + BP_ldlcoef + 0.42146 * diabetes + 0.54377 * smoker
#values of the means
G_ldl_men <- 3.00069
A_ldl_men <- L_ldl_men - G_ldl_men
B_ldl_men <- exp(A_ldl_men)
#Baseline survival function at 10 years for men:
s_ldl_men <- 0.90017
P_ldl_men <- round((1 - (s_ldl_men) ^ B_ldl_men) * 100, digits = 0)
L_ldl_women <- 0.33994 * age + (-0.0027) * age ^ 2 + LDL_ldlcoef + HDL_ldlcoef + BP_ldlcoef + 0.61313 * diabetes + 0.29737 * smoker
#values of the means
G_ldl_women <- 9.914136
A_ldl_women <- L_ldl_women - G_ldl_women
B_ldl_women <- exp(A_ldl_women)
#Baseline survival function at 10 years for women:
s_ldl_women <- 0.96278
P_ldl_women <- round((1 - (s_ldl_women) ^ B_ldl_women)* 100, digits = 0)
results <- list()
if (gender == 1) {
results$CHDprediction_use_TChol <- P_TChol_men
results$CHDprediction_use_ldl <- P_ldl_men
return (results)
} else if (gender == 0) {
results$CHDprediction_use_TChol <- P_TChol_women
results$CHDprediction_use_ldl <- P_ldl_women
return (results)
}
}
Aidakazemi/CHDWilson documentation built on June 28, 2020, 7:14 p.m.
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#' Predicting Coronary Heart Disease (CHD) over ten years using TChol and LDL categories
#'
#' @param age A number for age
#' @param gender A binary variables taking 1 for men and 0 for women
#' @param TChol A number for Total cholestrol in mg/dL
#' @param HDL A number for HDL cholesterol in mg/dL
#' @param LDL A number for LDL cholesterol in mg/dL
#' @param SBP A number for SBP Blood pressure in mm Hg without regard to the use of antihypertensive medication
#' @param DBP A number for DBP blood pressure in mm Hg without regard to the use of antihypertensive medication
#' @param diabetes A binary variable taking 1 if the participant was under treatment with insulin or oral hypoglycemic agents, if casual blood glucose determinations exceeded 150 mg/dL at two clinic visits in the original cohort, or if fasting blood glucose exceeded 140 mg/dL at the initial examination of the Offspring Study participants
#' @param smoker A binary variable taking 1 for person who smoked during the past 12 month and 0 therwise
#'
#' @examples
#'
#' predictchd (age = 55, gender = 1, TChol = 250, LDL = 120, HDL = 39,
#' SBP = 146, DBP = 88, diabetes = 0 , smoker =1)
#' predictchd (age = 30, gender = 0, TChol = 170, LDL = 120, HDL = 39,
#' SBP = 145, DBP = 88, diabetes = 0 , smoker =1)
#'
#' @source \url{https://www.ahajournals.org/doi/full/10.1161/01.CIR.97.18.1837}
#' @export
predictchd <- function (age, gender, TChol, LDL, HDL, SBP, DBP, diabetes, smoker) {
#categories of blood pressure SBP based on Joint National Committee (JNC-V) blood pressure
if (SBP < 120) {
#Normal blood pressure
BP_s = 1
} else if (SBP >= 120 & SBP < 130) {
#normal blood pressure (including optimal)
BP_s = 2
} else if (SBP >= 130 & SBP < 140) {
#High normal blood pressure
BP_s = 3
} else if (SBP >= 140 & SBP < 160) {
#Hypertension stage I blood pressure
BP_s = 4
} else if (SBP >= 160) {
#Hypertension stage II-IV
BP_s = 5
}
#categories of blood pressure DBP based on Joint National Committee (JNC-V) blood pressure
if (DBP < 80) {
#Normal blood pressure
BP_d = 1
} else if (DBP >= 80 & DBP < 85) {
#normal blood pressure (including optimal)
BP_d = 2
} else if (DBP >= 85 & DBP < 90) {
#High normal blood pressure
BP_d = 3
} else if (DBP >= 90 & DBP < 100) {
#Hypertension stage I blood pressure
BP_d = 4
} else if (DBP >= 100) {
#Hypertension stage II-IV
BP_d = 5
}
if (BP_s == BP_d) {
BP = BP_s
} else if (BP_s < BP_d) {
BP = BP_d
} else if (BP_s > BP_d) {
BP = BP_s
}
#================================================================ Men =======================================================================
if (gender == 1) {
#TCholl coefficient in range using TChol categories
if (TChol < 160) {
TChol_TCholcoef = -0.65945
} else if (TChol >= 160 & TChol <= 199) {
TChol_TCholcoef = 0
} else if (TChol >= 200 & TChol <= 239) {
TChol_TCholcoef = 0.17692
} else if (TChol >= 240 & TChol <= 279) {
TChol_TCholcoef = 0.50539
} else if (TChol >= 280) {
TChol_TCholcoef = 0.65713
}
#LDL coefficient in range using LDL categories
if (LDL < 100) {
LDL_ldlcoef = -0.69281
} else if (LDL >= 100 & LDL <= 129) {
LDL_ldlcoef = 0
} else if (LDL >= 130 & LDL <= 159) {
LDL_ldlcoef = 0.00389
} else if (LDL >= 160 & LDL <= 189) {
LDL_ldlcoef = 0.26755
} else if (LDL >= 190) {
LDL_ldlcoef = 0.56705
}
#HDL-C coefficient in range using TChol categories
if (HDL < 35) {
HDL_TCholcoef = 0.49744
} else if (HDL >= 35 & HDL <= 44) {
HDL_TCholcoef = 0.24310
} else if (HDL >= 45 & HDL <= 49) {
HDL_TCholcoef = 0
} else if (HDL >= 50 & HDL <= 59) {
HDL_TCholcoef = -0.05107
} else if (HDL >= 60) {
HDL_TCholcoef = -0.48660
}
#HDL-C coefficient in range using LDL categories
if (HDL < 35) {
HDL_ldlcoef = 0.48598
} else if (HDL >= 35 & HDL <= 44) {
HDL_ldlcoef = 0.21643
} else if (HDL >= 45 & HDL <= 49) {
HDL_ldlcoef = 0
} else if (HDL >= 50 & HDL <= 59) {
HDL_ldlcoef = -0.04710
} else if (HDL >= 60) {
HDL_ldlcoef = -0.34190
}
#SBP coefficient in range using TChol categories
if (BP == 1) {
BP_TCholcoef = -0.00226
} else if (BP == 2) {
BP_TCholcoef = 0
} else if (BP == 3) {
BP_TCholcoef = 0.28320
} else if (BP == 4) {
BP_TCholcoef = 0.52168
} else if (BP == 5) {
BP_TCholcoef = 0.61859
}
#SBP coefficient in range using LDL categories
if (BP == 1) {
BP_ldlcoef = -0.02642
} else if (BP == 2) {
BP_ldlcoef = 0
} else if (BP == 3) {
BP_ldlcoef = 0.30104
} else if (BP == 4) {
BP_ldlcoef = 0.55714
} else if (BP == 5) {
BP_ldlcoef = 0.65107
}
#============================================================= Women ====================================================================
} else if (gender == 0) {
#TCholl coefficient in range using TChol categories
if (TChol < 160) {
TChol_TCholcoef = -0.26138
} else if (TChol >= 160 & TChol <= 199) {
TChol_TCholcoef = 0
} else if (TChol >= 200 & TChol <= 239) {
TChol_TCholcoef = 0.20771
} else if (TChol >= 240 & TChol <= 279) {
TChol_TCholcoef = 0.24385
} else if (TChol >= 280) {
TChol_TCholcoef = 0.53513
}
#LDL coefficient in range using LDL categories
if (LDL < 100) {
LDL_ldlcoef = -0.42616
} else if (LDL >= 100 & LDL <= 129) {
LDL_ldlcoef = 0
} else if (LDL >= 130 & LDL <= 159) {
LDL_ldlcoef = 0.01366
} else if (LDL >= 160 & LDL <= 189) {
LDL_ldlcoef = 0.26948
} else if (LDL >= 190) {
LDL_ldlcoef = 0.33251
}
#HDL-C coefficient in range using TChol categories
if (HDL < 35) {
HDL_TCholcoef = 0.84312
} else if (HDL >= 35 & HDL <= 44) {
HDL_TCholcoef = 0.37796
} else if (HDL >= 45 & HDL <= 49) {
HDL_TCholcoef = 0.19785
} else if (HDL >= 50 & HDL <= 59) {
HDL_TCholcoef = 0
} else if (HDL >= 60) {
HDL_TCholcoef = -0.42951
}
#HDL-C coefficient in range using LDL categories
if (HDL < 35) {
HDL_ldlcoef = 0.88121
} else if (HDL >= 35 & HDL <= 44) {
HDL_ldlcoef = 0.36312
} else if (HDL >= 45 & HDL <= 49) {
HDL_ldlcoef = 0.19247
} else if (HDL >= 50 & HDL <= 59) {
HDL_ldlcoef = 0
} else if (HDL >= 60) {
HDL_ldlcoef = -0.35404
}
#SBP coefficient in range using TChol categories
if (BP == 1) {
BP_TCholcoef = -0.53363
} else if (BP == 2) {
BP_TCholcoef = 0
} else if (BP == 3) {
BP_TCholcoef = 0.06773
} else if (BP == 4) {
BP_TCholcoef = 0.26288
} else if (BP == 5) {
BP_TCholcoef = 0.46573
}
#SBP coefficient in range using LDL categories
if (BP == 1) {
BP_ldlcoef = -0.51204
} else if (BP == 2) {
BP_ldlcoef = 0
} else if (BP == 3) {
BP_ldlcoef = -0.03484
} else if (BP == 4) {
BP_ldlcoef = 0.28533
} else if (BP == 5) {
BP_ldlcoef = 0.50403
}
}
#================================================== Prediction using TChol =========================================================
L_TChol_men <- 0.04826 * age + TChol_TCholcoef + HDL_TCholcoef + BP_TCholcoef + 0.42839 * diabetes + 0.52337 * smoker
#values of the means
G_TChol_men <- 3.0975
A_TChol_men <- L_TChol_men - G_TChol_men
B_TChol_men <- exp(A_TChol_men)
#Baseline survival function at 10 years for men:
s_TChol_men <- 0.90015
P_TChol_men <- round((1 - (s_TChol_men) ^ B_TChol_men) * 100, digits = 0)
L_TChol_women <- 0.33766 * age + (-0.00268) * age ^ 2 + TChol_TCholcoef + HDL_TCholcoef + BP_TCholcoef + 0.59626 * diabetes + 0.29246 * smoker
#values of the means
G_TChol_women <- 9.92545
A_TChol_women <- L_TChol_women - G_TChol_women
B_TChol_women <- exp(A_TChol_women)
#Baseline survival function at 10 years for women:
s_TChol_women <- 0.96246
P_TChol_women <- round((1 - (s_TChol_women) ^ B_TChol_women)* 100, digits = 0)
#================================================== Prediction using LDL =========================================================
L_ldl_men <- 0.04808 * age + LDL_ldlcoef + HDL_ldlcoef + BP_ldlcoef + 0.42146 * diabetes + 0.54377 * smoker
#values of the means
G_ldl_men <- 3.00069
A_ldl_men <- L_ldl_men - G_ldl_men
B_ldl_men <- exp(A_ldl_men)
#Baseline survival function at 10 years for men:
s_ldl_men <- 0.90017
P_ldl_men <- round((1 - (s_ldl_men) ^ B_ldl_men) * 100, digits = 0)
L_ldl_women <- 0.33994 * age + (-0.0027) * age ^ 2 + LDL_ldlcoef + HDL_ldlcoef + BP_ldlcoef + 0.61313 * diabetes + 0.29737 * smoker
#values of the means
G_ldl_women <- 9.914136
A_ldl_women <- L_ldl_women - G_ldl_women
B_ldl_women <- exp(A_ldl_women)
#Baseline survival function at 10 years for women:
s_ldl_women <- 0.96278
P_ldl_women <- round((1 - (s_ldl_women) ^ B_ldl_women)* 100, digits = 0)
results <- list()
if (gender == 1) {
results$CHDprediction_use_TChol <- P_TChol_men
results$CHDprediction_use_ldl <- P_ldl_men
return (results)
} else if (gender == 0) {
results$CHDprediction_use_TChol <- P_TChol_women
results$CHDprediction_use_ldl <- P_ldl_women
return (results)
}
}
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