tests/testthat/test_sts.R
In meyera/riskscorer: An R Package for Calculating Surgical Risk Scores
library(testthat)
library(riskscorer)
context("STS Case Checking - Check against the database Version 2.81")
test_that("Case 1 gets correctly calculated (see PDF)", {
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "male",
age = 60,
lvef = 35,
weight_kg = 65,
height_cm = 185,
chf_2w = "yes")
expect_true(is.list(sts_res))
expect_equal(length(sts_res), 10)
expect_equal(sts_res$Procedure, "AV Replacement + CAB")
expect_equal(sts_res$Mortality, 0.01415)
expect_equal(sts_res$Renal_failure, 0.01895)
})
test_that("Iterative test case", {
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02363)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "NSTEMI",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02363)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02623)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.03138)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = "yes-severe",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.05223)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE)
expect_equal(sts_res$Mortality, 0.03797)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE)
expect_equal(sts_res$Mortality, 0.04831)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral")
expect_equal(sts_res$Mortality, 0.05366)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y")
expect_equal(sts_res$Mortality, 0.07087)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
endocarditis_type = "active")
expect_equal(sts_res$Mortality, 0.13469)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure"
)
expect_equal(sts_res$Mortality, 0.40422)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre"
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h"
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE
)
expect_equal(sts_res$Mortality, 0.51777)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE,
vd_aortic = TRUE,
vd_aortic_stenosis = FALSE
)
expect_equal(sts_res$Mortality, 0.51777)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE,
vd_aortic = TRUE,
vd_aortic_stenosis = FALSE,
vd_mitral_regurg = "undocumented",
vd_tricuspid_regurg = "severe",
vd_aortic_regurg = "moderate",
no_cardiovascular_surgeries = 2
)
expect_equal(sts_res$Mortality, 0.73026)
})
meyera/riskscorer documentation built on May 22, 2019, 7:54 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(testthat)
library(riskscorer)
context("STS Case Checking - Check against the database Version 2.81")
test_that("Case 1 gets correctly calculated (see PDF)", {
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "male",
age = 60,
lvef = 35,
weight_kg = 65,
height_cm = 185,
chf_2w = "yes")
expect_true(is.list(sts_res))
expect_equal(length(sts_res), 10)
expect_equal(sts_res$Procedure, "AV Replacement + CAB")
expect_equal(sts_res$Mortality, 0.01415)
expect_equal(sts_res$Renal_failure, 0.01895)
})
test_that("Iterative test case", {
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02363)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "NSTEMI",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02363)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.02623)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.03138)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = "yes-severe",
crea = 1.2)
expect_equal(sts_res$Mortality, 0.05223)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE)
expect_equal(sts_res$Mortality, 0.03797)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE)
expect_equal(sts_res$Mortality, 0.04831)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral")
expect_equal(sts_res$Mortality, 0.05366)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y")
expect_equal(sts_res$Mortality, 0.07087)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
endocarditis_type = "active")
expect_equal(sts_res$Mortality, 0.13469)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure"
)
expect_equal(sts_res$Mortality, 0.40422)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre"
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h"
)
expect_equal(sts_res$Mortality, 0.49308)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE
)
expect_equal(sts_res$Mortality, 0.51777)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE,
vd_aortic = TRUE,
vd_aortic_stenosis = FALSE
)
expect_equal(sts_res$Mortality, 0.51777)
sts_res <- calc_sts(proc_cabg = TRUE,
proc_valve = "avr",
gender = "f",
age = 75,
lvef = 50,
chf_2w = FALSE,
dialysis = FALSE,
acs_type = "Unstable Angina",
prior_mi = TRUE,
afib = "Paroxysmal",
chrlungd = FALSE,
crea = 1.2,
cvd = TRUE,
stroke = TRUE,
pvd = TRUE,
diabetes_ctrl = "oral",
immsupp = "Y",
chd = "KHK3",
urgency = "Notfall",
resuscitation = "yes-1h",
cardiogenic_shock = "yes-at_procedure",
iabp_when = "pre",
inotropes = TRUE,
pre_pci_interval = "<=6h",
vd_mitral_stenosis = TRUE,
vd_aortic = TRUE,
vd_aortic_stenosis = FALSE,
vd_mitral_regurg = "undocumented",
vd_tricuspid_regurg = "severe",
vd_aortic_regurg = "moderate",
no_cardiovascular_surgeries = 2
)
expect_equal(sts_res$Mortality, 0.73026)
})
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