R/sts.R
In meyera/riskscorer: An R Package for Calculating Surgical Risk Scores
webservice_url <- "http://riskcalc.sts.org/stswebriskcalc/v1/calculate/stsall"
do_sts_request <- function(queryList, verbose = FALSE) {
if (verbose) {
res <- httr::POST(webservice_url,
body = queryList,
encode = "json",
httr::verbose())
} else {
res <- httr::POST(webservice_url,
body = queryList,
encode = "json")
}
if (verbose) {
httr::http_status(res)
res$status_code
httr::stop_for_status(res)
}
httr::content(res)
}
#' Using the webservice from STS to calculate the Scores
#'
#' Service can also be used as a JSON webservice using plumber. Arguments that are
#' not given are automatically null, thus missing for the STS web service
#'
#' @param proc_cabg Was CABG performed? Valid values: 'TRUE', 'FALSE', '1', '0',
#' 'T', 'F', 'Y', 'N', 'Yes', 'No'
#'
#' @param proc_valve Specifies the type of valve procedure performed: 'AVR',
#' 'MVReplacement', 'MVRepair'
#'
#' @param age Age in years, must be within 20 and 100
#'
#' @param gender Gender of the patient, should be "Male" or "Female", 'F' or 'M',
#' plus in addition
#' all boolean FALSE strings --> Male
#' all boolean TRUE strings --> Female
#'
#' @param height_cm Patient's height in cm
#'
#' @param weight_kg Patient's height in kg
#'
#' @param lvef Patient's left ventricular ejection fraction (1-99%) measured before
#' induction of anesthesia
#'
#' @param chf_2w Indicate if there is physician documentation or report that the
#' patient has been in a state of heart failure within the past 2 weeks.
#' Valid values: "Yes", "No", "Unknown"; TRUE or FALSE
#'
#' @param race Following values are allowed: 'Undocumented', 'undisclosed',
#' 'black', 'asian', 'asianblack'
#'
#' @param hispanic_ethnicity Following values are allowed: 'No', 'Yes',
#' "Not Documented"
#'
#' @param dialysis Indicate whether the patient is currently (prior to surgery)
#' undergoing dialysis: boolean string or "Unknown"
#'
#' @param crea Indicate the creatinine level closest to the date and time prior
#' surgery but prior to anesthetic management (induction area or operating room)
#'
#' @param acs_type Type of Acute Coronary Syndrom at admission:
#' 'No Symptoms', 'Other', 'Angina equivalent', 'Stable Angina',
#' 'Unstable Angina', 'STEMI', 'NSTEMI'
#' This field is called in the STS web app "Cardiac Symptoms - At Time Of Surgery"
#' I do not think this is appropiate - it mixes symptoms with disease entities
#'
#' @param prior_mi Indicate if the patient has had at least one documented previous
#' myocardial infarction at any time prior to this surgery.
#' Values: '6h', '6-24h', '1-7d', '8-21d', 'longer', 'No', 'Unknown'
#'
#' @param arrhythmia Indicate whether the patient has a history of a cardiac rhythm
#' disturbance before the start of the operative procedure:
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param afib Afib before surgery? "None", "Paroxysmal", "Persistent"
#'
#' @param chrlungd Indicate whether the patient has chronic lung disease,
#' and the severity level according to the following classification:
#' No; Mild: FEV1 60% to 75% of predicted, and/or on chronic inhaled
#' or oral bronchodilator therapy. Moderate: FEV1 50% to 59% of predicted,
#' and/or on chronic steroid therapy aimed at lung disease.
#' Severe: FEV1 < 60 or Room Air pCO2 > 50.
#' For more details see the STS definition.
#' Values: 'no', 'unknown', 'yes-unknown', 'yes-mild', 'yes-moderate', 'yes-severe'
#'
#' @param cvd Cerebrovascular Disease; indicate whether the patient has a current
#' or previous history of any of the following:
#' a) Stroke - brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction lasts for greater than 24 hours
#' b) TIA - brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction resolves within 24 hours
#' c) Noninvasive or invasive arterial imaging test
#' demonstrating >=50% stenosis of any of the major
#' extracranial or intracranial vessels to the brain
#' d) Previous cervical or cerebral artery revascularization
#' surgery or percutaneous intervention This does not include
#' chronic (nonvascular) neurological diseases or other acute
#' neurological insults such as metabolic and anoxic ischemic
#' encephalopathy
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param stroke Explicit item for stroke (brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction lasts for greater than 24 hours)
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param pvd Peripheral Arterial Disease (history of peripheral arterial disease,
#' includes upper and lower extremity, renal, mesenteric, and
#' abdominal aortic systems)
#' 1. Claudication , either with exertion or at rest
#' 2. Amputation for arterial vascular insufficiency
#' 3. Vascular reconstruction, bypass surgery, or percutaneous intervention
#' to the extremities (excluding dialysis fistulas and vein stripping)
#' 4. Documented abdominal aortic aneurysm with or without repair
#' 5. Positive noninvasive test (e.g., ankle brachial index =< 0.9,
#' ultrasound, magnetic resonance or computed tomography
#' imaging of > 50% diameter stenosis in any peripheral artery,
#' i.e., renal, subclavian, femoral, iliac) or angiographic imaging
#' Peripheral arterial disease excludes disease in the carotid,
#' cerebrovascular arteries or thoracic aorta
#' PVD does not include DVT
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param diabetes History of diabetes diagnosed and/or treated by a healthcare
#' provider. See Def. STS website or 2013 ACCF/AHA Data Standards
#' Cannon et al. JACC Vol. 61, No. 9, 2013
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param diabetes_ctrl Indicate the patient’s diabetes control method as presented
#' on admission
#' Values: "diet", "oral", "insulin", "other", "other_subcutaneous",
#' "none", "unknown"
#'
#' @param htn Hypertension, see STS definition
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param immsupp Immunosuppression: Indicate whether immunocompromise is present
#' due to immunosuppressive medication therapy within 30 days
#' preceding the operative procedure or existing medical condition
#' (see training manual). This includes, but is not limited to
#' systemic steroid therapy, anti-rejection medications and chemotherapy.
#' This does not include topical steroid applications, one time systemic
#' therapy, inhaled steroid therapy or preprocedure protocol
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param endocarditis History of endocarditis: must meet at least 1 of the
#' following criteria:
#' 1. organisms cultured from valve or vegetation.
#' 2. 2 or more of the following signs or symptoms:
#' * fever (>38 degrees C)
#' * new or changing murmur*
#' * embolic phenomena*
#' * skin manifestations* (i.e., petechiae, splinter
#' hemorrhages, painful subcutaneous nodules)
#' * congestive heart failure*
#' * cardiac conduction abnormality*
#' With no other recognized cause and at least 1 of the following:
#' a. organisms cultured from 2 or more blood cultures
#' b. organisms seen on Gram’s stain of valve when culture
#' is negative or not done
#' c. valvular vegetation seen during an invasive procedure
#' or autopsy
#' d. positive laboratory test on blood or urine
#' (e.g., antigen tests for H influenzae, S pneumoniae,
#' N meningitidis, or Group B Streptococcus)
#' e. evidence of new vegetation seen on echocardiogram
#' and if diagnosis is made antemortem, physician institutes
#' appropriate antimicrobial therapy.
#' CDC, January 2013 Choose 'Yes' for patients with pre-operative
#' endocarditis who begin antibiotics post-op.
#' Code yes for patients who are diagnosed intraoperatively.
#' Values: "Yes", "No", or booleans string
#'
#' @param endocarditis_type Type of endocarditis the patient has. If the patient is
#' currently being treated for endocarditis, the disease
#' is considered active.
#' If no antibiotic medication (other than prophylactic
#' medication) is being given at the time of surgery,
#' then the infection is considered treated.
#'
#' If a <i>endocarditis</i> type is set, endocarditis is automatically
#' set to "Yes"
#' Values: 'Active' or 'Treated'
#'
#' @param chd_known Indicate whether coronary artery anatomy and/or disease is documented
#' and available prior to surgery.
#' Values: "Yes", "No", or booleans string
#'
#' @param chd Indicate whether coronary artery anatomy and/or disease is documented
#' and available prior to
#'
#' If a valid <i>chd</i> type is set, chd_known is automatically
#' set to "Yes"
#' Values: "Yes", "No", or booleans string
#'
#' @param left_main_stenosis Any numeric string between 0 and 100, like "60%" or "45 %"
#'
#' @param urgency Indicate the clinical status of the patient prior to entering the operating room.
#' Indication urgency, accepts the following values:
#' "elective|elektiv", "urgent|dringlich",
#' "emergent|emergency|notfall|notfallindikation",
#' "salvage|emergent salvage"
#'
#' @param resuscitation Indicate whether the patient required cardiopulmonary
#' resuscitation before the start of the operative procedure
#' which includes the institution of anesthetic management.
#' Capture resuscitation timeframe: within 1 hour or 1-24 hours pre-op.
#' Allowed values:
#' - "yes-1h"
#' - "yes-1_24h"
#' - "no"
#'
#' @param cardiogenic_shock Indicate if the patient developed cardiogenic shock.
#' Cardiogenic shock is defined as a sustained (>30 min)
#' episode of hypoperfusion evidenced by systolic blood
#' pressure <90 mm Hg and/or, if available,
#' cardiac index <2.2 L/min per square meter determined to
#' be secondary to cardiac dysfunction and/or the requirement
#' for parenteral inotropic or vasopressor agents or
#' mechanical support (e.g., IABP, extracorporeal circulation, VADs)
#' to maintain blood pressure and cardiac index above those
#' specified levels. Note: Transient episodes of hypotension
#' reversed with IV fluid or atropine do not constitute
#' cardiogenic shock. The hemodynamic compromise
#' (with or without extraordinary supportive therapy) must persist
#' for at least 30 min. ACCF/AHA 2013
#' Accepted values:
#' - Boolean NO strings
#' - "yes-at_procedure"
#' - "yes-within_24h"
#' @param iabp Indicate whether the patient was placed on an Intra-Aortic Balloon Pump (IABP).
#' Values: "Yes", "No", or booleans string
#'
#' @param iabp_when Indicate when the IABP was inserted.
#' Accepted values:
#' - Boolean NO strings --> will set <i>iabp</i> to "No"
#' - "Preop" --> will set <i>iabp</i> to "Yes"
#' - "Intraop" --> will set <i>iabp</i> to "Yes"
#' - "Postop" --> will set <i>iabp</i> to "Yes"
#'
#' @param inotropes Indicate whether the patient received IV inotropic agents within
#' 48 hours preceding surgery.
#' Values: "Yes", "No", or booleans string
#'
#' @param pre_cv_intervention Indicate whether the patient has undergone any previous
#' cardiovascular intervention, either <b>surgical or non-surgical</b>,
#' which may include those done during the current admission.
#'
#' @param pre_pci Indicate whether a previous Percutaneous Coronary Intervention (PCI)
#' was performed any time prior to this surgical procedure. Percutaneous
#' coronary intervention (PCI) is the placement of an angioplasty guide
#' wire, balloon, or other device (e.g. stent, atherectomy, brachytherapy,
#' or thrombectomy catheter) into a native coronary artery or coronary
#' artery bypass graft for the purpose of mechanical coronary revascularization.
#' Values: "Yes", "No", or booleans string
#' --> will set the value of <i>pre_cv_intervention</i> accordingly
#'
#' @param pre_pci_interval Indicate the interval of time between the previous PCI
#' and the current surgical procedure.
#' Values: ">6h" or "<=6h"
#' --> will set the value of <i>pre_cv_intervention</i> and
#' <i>pre_pci</i> accordingly.
#'
#' @param vd_mitral Indicate whether Mitral valve disease is present.
#' Values: "Yes", "No", or booleans string
#'
#' @param vd_mitral_stenosis Indicate whether Mitral Stenosis is present.
#' Values: "Yes", "No", or booleans string
#' --> A boolean "Yes" value will also set <i>vd_mitral</i> to "Yes"
#'
#' @param vd_aortic Indicate whether Aortic valve disease is present.
#' Values: "Yes", "No", or booleans string
#'
#' @param vd_aortic_stenosis Indicate whether Aortic Stenosis is present.
#' Values: "Yes", "No", or booleans string
#' --> A boolean "Yes" value will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_aortic_regurg Indicate whether there is evidence of Aortic valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_mitral_regurg Indicate whether there is evidence of Mitral valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_tricuspid_regurg Indicate whether there is evidence of Tricuspid valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param no_cardiovascular_surgeries Incidence - Indicate if this is the patient's:
#' - 0 ==> first surgery
#' - 1 ==> first re-op surgery
#' - 2 ==> second re-op surgery
#' - 3 ==> third re-op surgery
#' - 4 ==> fourth or more re-op surgery.
#' Surgery is defined as cardiothoracic
#' operations (heart or great vessels) surgical
#' procedures performed with or without cardiopulmonary
#' bypass (CPB). Also include lung procedures
#' utilizing CPB or tracheal procedures utilizing CPB.
#' Reoperation increases risk due to the presence of
#' scar tissue and adhesions.
#'
#' @param return_query_list setting this on TRUE will return only the query list, but not
#' do the request to the STS web service. Useful for debugging.
#'
#' @param verbose prints detailed info about parameters and the http web service query
#'
#' @return a list of the predicted risks of the at the time of request current
#' STS risk model
#' @export
#' @examples
#' service <- plumber::plumb("R/sts.R")
#' service$run(port = 8080)
#
# Plumber decoration
#* @get /calc_sts
#* @post /calc_sts
calc_sts <- function(age,
gender,
proc_cabg,
proc_valve = NULL,
height_cm = NULL,
weight_kg = NULL,
lvef = NULL,
chf_2w = NULL,
race = NULL,
hispanic_ethnicity = NULL,
dialysis = NULL,
crea = NULL,
acs_type = NULL,
prior_mi = NULL,
arrhythmia = NULL,
afib = NULL,
chrlungd = NULL,
cvd = NULL,
stroke = NULL,
pvd = NULL,
diabetes = NULL,
diabetes_ctrl = NULL,
htn = NULL,
immsupp = NULL,
endocarditis = NULL,
endocarditis_type = NULL,
chd_known = NULL,
chd = NULL,
left_main_stenosis = NULL,
urgency = NULL,
resuscitation = NULL,
cardiogenic_shock = NULL,
iabp = NULL,
iabp_when = NULL,
inotropes = NULL,
pre_cv_intervention = NULL,
pre_pci = NULL,
pre_pci_interval = NULL,
vd_mitral = NULL,
vd_mitral_stenosis = NULL,
vd_aortic = NULL,
vd_aortic_stenosis = NULL,
vd_aortic_regurg = NULL,
vd_mitral_regurg = NULL,
vd_tricuspid_regurg = NULL,
no_cardiovascular_surgeries = NULL,
return_query_list = FALSE,
verbose = FALSE
) {
queryList <- list()
age <- readr::parse_number(age)
queryList$age <- ensurer::ensure(age, is.numeric(.), . >= 1 , . <= 110)
queryList$gender <- parse_sex(gender)
if (!is.null(proc_cabg)) {
if (parse_bool(proc_cabg)) {
queryList$opcab <- "Yes, planned"
}
}
if (!is.null(proc_valve)) {
proc_valve <- stringr::str_to_lower(proc_valve)
if (proc_valve == "avr") {
queryList$opvalve <- "Yes"
queryList$vsav <- "Yes, planned"
queryList$vsavpr <- "Replacement"
} else if (proc_valve == "mvreplacement") {
queryList$opvalve <- "Yes"
queryList$vsmv <- "Yes, planned"
queryList$vsmvpr <- "Replacement"
} else if (proc_valve == "mvrepair") {
queryList$opvalve <- "Yes"
queryList$vsmv <- "Yes, planned"
queryList$vsmvpr <- "Repair"
} else if (proc_valve %in% c("none","no", "n", "false", "f", "0")) {
# do nothing, coding indicates no VALVE surgery
} else {
stop("'proc_valve' must be one of the following values: 'AVR',
'MVReplacement', 'MVRepair' or a boolean NO/FALSE string")
}
}
if (!is.null(height_cm)) {
queryList$heightcm <- ensurer::ensure(height_cm, is.numeric(.), . >= 20, . <= 251)
}
if (!is.null(weight_kg)) {
queryList$weightkg <- ensurer::ensure(weight_kg, is.numeric(.), . >= 10, . <= 250)
}
if (!is.null(lvef)) {
queryList$hdef <- ensurer::ensure(lvef, is.numeric(.), . >= 1, . <= 99)
queryList$hdefd <- "Yes"
}
if (!is.null(chf_2w)) {
queryList$chf <- parse_bool_and_add(stringr::str_to_title(chf_2w),
"Unknown")
}
if (!is.null(race)) {
race <- ensurer::ensure(stringr::str_to_title(race),
. %in% c("Undocumented", "Not Documented", "Undisclosed",
"Black", "Asian", "Asianblack"))
if (race %in% c("Undocumented", "Not Documented")) {
queryList$racedocumented = "No"
} else if (race == "Undisclosed") {
queryList$racedocumented = "Patient declined to disclose"
} else {
queryList$racedocumented = "Yes"
if (race %in% c("Black", "Asianblack")) {
queryList$raceblack = "Yes"
}
if (race %in% c("Asian", "Asianblack")) {
queryList$raceasian = "Yes"
}
}
}
if (!is.null(hispanic_ethnicity)) {
queryList$ethnicity <- parse_bool_and_add(stringr::str_to_title(hispanic_ethnicity),
additionals = "Not Documented")
}
if (!is.null(dialysis)) {
queryList$dialysis <- parse_bool_and_add(stringr::str_to_title(dialysis),
additionals = "Unknown")
}
if (!is.null(crea)) {
queryList$creatlst <- ensurer::ensure(crea, is.numeric(.), . > 0.1, . < 30)
}
if (!is.null(crea)) {
queryList$creatlst <- ensurer::ensure(crea, is.numeric(.), . > 0.1, . < 30)
}
if (!is.null(acs_type)) {
acs_type <- stringr::str_to_upper(acs_type)
if (acs_type == "OTHER") {
queryList$cardsymptimeofsurg <- "Other"
} else if (acs_type == "NO SYMPTOMS") {
queryList$cardsymptimeofsurg <- "No Symptoms"
} else if (acs_type == "ANGINA EQUIVALENT") {
queryList$cardsymptimeofsurg <- "Angina equivalent"
} else if (acs_type == "STABLE ANGINA") {
queryList$cardsymptimeofsurg <- "Stable Angina "
} else if (acs_type == "UNSTABLE ANGINA") {
queryList$cardsymptimeofsurg <- "Unstable Angina"
} else if (acs_type == "NSTEMI") {
queryList$cardsymptimeofsurg <- "Non-ST Elevation MI (Non-STEMI)"
} else if (acs_type == "STEMI") {
queryList$cardsymptimeofsurg <- "ST Elevation MI (STEMI)"
} else {
stop("ACS type or cardiac symptoms at time of surgery are not recognized.")
}
}
if (!is.null(prior_mi)) {
choices = c("6h" = " <=6 Hrs",
'6-24h' = " >6 Hrs but <24 Hrs",
'1-7d' = "1 to 7 Days",
'8-21d' = "8 to 21 Days",
'longer' = " >21 Days",
'No' = "No",
'Unknown' = "Unknown")
names(choices) <- stringr::str_to_upper(names(choices))
prior_mi <- stringr::str_to_upper(prior_mi)
prior_mi_bool <- parse_bool_and_add(prior_mi)
if (prior_mi %in% names(choices[1:5])) {
queryList$prevmi <- "Yes"
queryList$miwhen <- choices[prior_mi]
} else if (prior_mi %in% names(choices[6:7])) {
queryList$prevmi <- choices[prior_mi]
} else if (prior_mi_bool %in% c("Yes", "No")) {
queryList$prevmi <- prior_mi_bool
} else {
stop("Coding if of 'prior_mi' not recognized.")
}
}
if (!is.null(arrhythmia)) {
queryList$arrhythmia <- parse_bool_and_add(stringr::str_to_title(arrhythmia),
additionals = "Unknown")
}
if (!is.null(afib)) {
afib <- stringr::str_to_upper(afib)
if (afib %in% c("NONE","NO", "FALSE", "F", "0")) {
queryList$arrhythafib <- "None"
} else if (afib %in% c("PAROXYSMAL", "PAROX")) {
queryList$arrhythafib <- "Paroxysmal"
} else if (afib %in% c("CONT", "CONTINOUS", "PERSISTENT", "PERSI")) {
queryList$arrhythafib <- "Continuous / persistent"
} else {
stop("Coding if of 'afib' not recognized.")
}
}
# 'no', 'unknown', 'yes-unknown', 'yes-mild', 'yes-moderate', 'yes-severe'
if (!is.null(chrlungd)) {
chrlungd <- stringr::str_to_upper(chrlungd)
choices <- c("unknown" = "Unknown",
"yes-unknown" = "Lung disease documented, severity unknown",
"yes-mild" = "Mild",
"yes-moderate" = "Moderate",
"yes-severe" = "Severe")
names(choices) <- stringr::str_to_upper(names(choices))
if (chrlungd %in% c("NONE","NO", "N", "FALSE", "F", "0")) {
queryList$chrlungd <- "No"
} else if (chrlungd %in% names(choices)) {
queryList$chrlungd <- choices[chrlungd]
} else {
stop("Coding of 'chrlungd' not recognized.")
}
}
if (!is.null(cvd)) {
queryList$cvd <- parse_bool_and_add(stringr::str_to_title(cvd),
additionals = "Unknown")
}
if (!is.null(stroke)) {
queryList$cva <- parse_bool_and_add(stringr::str_to_title(stroke),
additionals = "Unknown")
if (queryList$cva == "Yes") {
queryList$cvd = "Yes"
}
}
if (!is.null(pvd)) {
queryList$pvd <- parse_bool_and_add(stringr::str_to_title(pvd),
additionals = "Unknown")
}
if (!is.null(diabetes)) {
queryList$diabetes <- parse_bool_and_add(stringr::str_to_title(diabetes),
additionals = "Unknown")
}
if (!is.null(diabetes_ctrl)) {
diabetes_ctrl <- stringr::str_to_upper(diabetes_ctrl)
choices <- c("unknown" = "Unknown",
"other_subcutaneous" = "Other subcutaneous medication",
"other" = "Other",
"insulin" = "Insulin",
"diet" = "Diet only",
"oral" = "Oral")
names(choices) <- stringr::str_to_upper(names(choices))
if (diabetes_ctrl %in% c("NONE","NO", "N", "FALSE", "F", "0")) {
queryList$diabctrl <- "None"
} else if (diabetes_ctrl %in% names(choices)) {
queryList$diabctrl <- choices[diabetes_ctrl]
queryList$diabetes <- "Yes"
} else {
stop("Coding of 'diabetes_ctrl' not recognized.")
}
}
if (!is.null(htn)) {
queryList$hypertn <- parse_bool_and_add(stringr::str_to_title(htn),
additionals = "Unknown")
}
if (!is.null(immsupp)) {
queryList$immsupp <- parse_bool_and_add(stringr::str_to_title(immsupp),
additionals = "Unknown")
}
if (!is.null(endocarditis)) {
queryList$infendo <- parse_bool_and_add(stringr::str_to_title(endocarditis))
}
if (!is.null(endocarditis_type)) {
endocarditis_type <- stringr::str_to_upper(endocarditis_type)
if (endocarditis_type %in% c("ACTIVE", "ACT")) {
queryList$infendty <- "Active"
queryList$infendo <- "Yes"
} else if (endocarditis_type %in% c("TREATED", "TRT", "TREAT")) {
queryList$infendty <- "Treated"
queryList$infendo <- "Yes"
} else {
stop("Coding of 'endocarditis_type' not recognized.")
}
}
if (!is.null(chd_known)) {
queryList$coranatdisknown <- parse_bool_and_add(stringr::str_to_title(chd_known))
}
if (!is.null(chd)) {
chd <- parseVesselsDisease(chd)
if (chd %in% c("None", "Three", "Two", "One")) {
queryList$numdisv <- chd
queryList$coranatdisknown <- "Yes"
} else {
stop("Coding of 'chd' not recognized.")
}
}
if (!is.null(left_main_stenosis) && chd %in% c("Three", "Two", "One")) {
stenosis <- readr::parse_number(left_main_stenosis)
queryList$pctstenlmain <- ensurer::ensure(stenosis, is.numeric(.), . >= 0, . <= 100)
queryList$pctstenknown <- "Yes"
}
if (!is.null(urgency)) {
urgency <- stringr::str_trim(stringr::str_to_lower(urgency))
if (urgency %in% c("elective", "elektiv")) {
queryList$status <- "Elective"
} else if (urgency %in% c("urgent", "dringlich")) {
queryList$status <- "Urgent"
} else if (urgency %in% c("emergent", "emergency", "notfall", "notfallindikation")) {
queryList$status <- "Emergent"
} else if (urgency %in% c("emergent salvage", "salvage")) {
queryList$status <- "Emergent Salvage"
} else {
stop("Coding of 'urgency' not recognized.")
}
}
if (!is.null(resuscitation)) {
resusc <- stringr::str_trim(stringr::str_to_lower(resuscitation))
if (resusc %in% c("none","no", "n", "false", "f", "0")) {
queryList$resusc <- "No"
} else if (resusc == "yes-1h") {
queryList$resusc <- "Yes - Within 1 hour of the start of the procedure"
} else if (resusc == "yes-1_24h") {
queryList$resusc <- "Yes - More than 1 hour but less than 24 hours of the start of the procedure"
} else {
stop("Coding of 'resuscitation' not recognized.")
}
}
if (!is.null(cardiogenic_shock)) {
carshock <- stringr::str_trim(stringr::str_to_lower(cardiogenic_shock))
if (carshock %in% c("none","no", "n", "false", "f", "0")) {
queryList$carshock <- "No"
} else if (carshock == "yes-at_procedure") {
queryList$carshock <- "Yes - At the time of the procedure"
} else if (carshock == "yes-within_24h") {
queryList$carshock <- "Yes, not at the time of the procedure but within prior 24 hours"
} else {
stop("Coding of 'cardiogenic_shock' not recognized.")
}
}
if (!is.null(iabp)) {
queryList$iabp <- parse_bool_and_add(stringr::str_to_title(iabp))
}
if (!is.null(iabp_when)) {
iabp_when <- stringr::str_trim(stringr::str_to_lower(iabp_when))
if (iabp_when %in% c("none","no", "n", "false", "f", "0")) {
queryList$iabp <- "No"
} else if (str_starts_with(iabp_when, "pre") ||
str_starts_with(iabp_when, "prae") ||
str_starts_with(iabp_when, "prä")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Preop"
} else if (str_starts_with(iabp_when, "intra")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Intraop"
} else if (str_starts_with(iabp_when, "post")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Postop"
} else {
stop("Coding of 'iabp_when' not recognized.")
}
}
if (!is.null(inotropes)) {
queryList$medinotr <- parse_bool_and_add(stringr::str_to_title(inotropes))
}
if (!is.null(pre_cv_intervention)) {
queryList$prcvint <- parse_bool_and_add(stringr::str_to_title(pre_cv_intervention),
additionals = "Unknown")
}
if (!is.null(pre_pci)) {
queryList$pocpci <- parse_bool_and_add(stringr::str_to_title(pre_pci))
if (queryList$pocpci == "Yes") {
queryList$prcvint <- "Yes"
}
}
if (!is.null(pre_pci_interval)) { #">6h" or "<=6h"
pre_pci_interval <- stringr::str_trim(stringr::str_to_lower(pre_pci_interval))
if (pre_pci_interval == ">6h") {
queryList$pocpciin <- " > 6 Hours"
queryList$prcvint <- "Yes"
queryList$pocpci <- "Yes"
} else if (pre_pci_interval == "<=6h") {
queryList$pocpciin <- " <= 6 Hours"
queryList$prcvint <- "Yes"
queryList$pocpci <- "Yes"
} else {
stop("Coding of 'pre_pci_interval' not recognized.")
}
}
if (!is.null(vd_mitral)) {
queryList$vdmit <- parse_bool_and_add(stringr::str_to_title(vd_mitral))
}
if (!is.null(vd_mitral_stenosis)) {
queryList$vdstenm <- parse_bool_and_add(stringr::str_to_title(vd_mitral_stenosis))
if (queryList$vdstenm == "Yes") {
queryList$vdmit <- "Yes"
}
}
if (!is.null(vd_aortic)) {
queryList$vdaort <- parse_bool_and_add(stringr::str_to_title(vd_aortic))
}
if (!is.null(vd_aortic_stenosis)) {
queryList$vdstena <- parse_bool_and_add(stringr::str_to_title(vd_aortic_stenosis))
if (queryList$vdstena == "Yes") {
queryList$vdaort <- "Yes"
}
}
if (!is.null(vd_aortic_regurg)) {
regurg <- parse_vd_regurg(vd_aortic_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsufa <- regurg
}
}
if (!is.null(vd_mitral_regurg)) {
regurg <- parse_vd_regurg(vd_mitral_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsufm <- regurg
}
}
if (!is.null(vd_tricuspid_regurg)) {
regurg <- parse_vd_regurg(vd_tricuspid_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsuft <- regurg
}
}
if (!is.null(no_cardiovascular_surgeries)) {
no_cardiovascular_surgeries <- readr::parse_number(no_cardiovascular_surgeries)
incidence <- ensurer::ensure(no_cardiovascular_surgeries,
is.numeric(.), . %in% c(0, 1, 2, 3, 4))
trans <- c("0"="First cardiovascular surgery",
"1"="First re-op cardiovascular surgery",
"2"="Second re-op cardiovascular surgery",
"3"="Third re-op cardiovascular surgery",
"4"="Fourth or more re-op cardiovascular surgery")
queryList$incidenc <- trans[as.character(incidence)]
}
#queryList <- as.list(match.call())[-1]
#queryList <- purrr::compact(queryList)
if (return_query_list) {
return(queryList)
}
res <- do_sts_request(queryList, verbose = verbose)
riskdf <- dplyr::as_data_frame(res)
dplyr::rename(riskdf,
Procedure = proceduretype,
Mortality = predmort,
Morbidity_Mortality = predmm,
DSW_Infection = preddeep,
Perm_Stroke = predstro,
Prolong_Vent = predvent,
Reoperation = predreop,
Renal_failure = predrenf,
Long_LOS = pred14d,
Short_LOS = pred6d
)
}
meyera/riskscorer documentation built on May 22, 2019, 7:54 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
webservice_url <- "http://riskcalc.sts.org/stswebriskcalc/v1/calculate/stsall"
do_sts_request <- function(queryList, verbose = FALSE) {
if (verbose) {
res <- httr::POST(webservice_url,
body = queryList,
encode = "json",
httr::verbose())
} else {
res <- httr::POST(webservice_url,
body = queryList,
encode = "json")
}
if (verbose) {
httr::http_status(res)
res$status_code
httr::stop_for_status(res)
}
httr::content(res)
}
#' Using the webservice from STS to calculate the Scores
#'
#' Service can also be used as a JSON webservice using plumber. Arguments that are
#' not given are automatically null, thus missing for the STS web service
#'
#' @param proc_cabg Was CABG performed? Valid values: 'TRUE', 'FALSE', '1', '0',
#' 'T', 'F', 'Y', 'N', 'Yes', 'No'
#'
#' @param proc_valve Specifies the type of valve procedure performed: 'AVR',
#' 'MVReplacement', 'MVRepair'
#'
#' @param age Age in years, must be within 20 and 100
#'
#' @param gender Gender of the patient, should be "Male" or "Female", 'F' or 'M',
#' plus in addition
#' all boolean FALSE strings --> Male
#' all boolean TRUE strings --> Female
#'
#' @param height_cm Patient's height in cm
#'
#' @param weight_kg Patient's height in kg
#'
#' @param lvef Patient's left ventricular ejection fraction (1-99%) measured before
#' induction of anesthesia
#'
#' @param chf_2w Indicate if there is physician documentation or report that the
#' patient has been in a state of heart failure within the past 2 weeks.
#' Valid values: "Yes", "No", "Unknown"; TRUE or FALSE
#'
#' @param race Following values are allowed: 'Undocumented', 'undisclosed',
#' 'black', 'asian', 'asianblack'
#'
#' @param hispanic_ethnicity Following values are allowed: 'No', 'Yes',
#' "Not Documented"
#'
#' @param dialysis Indicate whether the patient is currently (prior to surgery)
#' undergoing dialysis: boolean string or "Unknown"
#'
#' @param crea Indicate the creatinine level closest to the date and time prior
#' surgery but prior to anesthetic management (induction area or operating room)
#'
#' @param acs_type Type of Acute Coronary Syndrom at admission:
#' 'No Symptoms', 'Other', 'Angina equivalent', 'Stable Angina',
#' 'Unstable Angina', 'STEMI', 'NSTEMI'
#' This field is called in the STS web app "Cardiac Symptoms - At Time Of Surgery"
#' I do not think this is appropiate - it mixes symptoms with disease entities
#'
#' @param prior_mi Indicate if the patient has had at least one documented previous
#' myocardial infarction at any time prior to this surgery.
#' Values: '6h', '6-24h', '1-7d', '8-21d', 'longer', 'No', 'Unknown'
#'
#' @param arrhythmia Indicate whether the patient has a history of a cardiac rhythm
#' disturbance before the start of the operative procedure:
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param afib Afib before surgery? "None", "Paroxysmal", "Persistent"
#'
#' @param chrlungd Indicate whether the patient has chronic lung disease,
#' and the severity level according to the following classification:
#' No; Mild: FEV1 60% to 75% of predicted, and/or on chronic inhaled
#' or oral bronchodilator therapy. Moderate: FEV1 50% to 59% of predicted,
#' and/or on chronic steroid therapy aimed at lung disease.
#' Severe: FEV1 < 60 or Room Air pCO2 > 50.
#' For more details see the STS definition.
#' Values: 'no', 'unknown', 'yes-unknown', 'yes-mild', 'yes-moderate', 'yes-severe'
#'
#' @param cvd Cerebrovascular Disease; indicate whether the patient has a current
#' or previous history of any of the following:
#' a) Stroke - brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction lasts for greater than 24 hours
#' b) TIA - brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction resolves within 24 hours
#' c) Noninvasive or invasive arterial imaging test
#' demonstrating >=50% stenosis of any of the major
#' extracranial or intracranial vessels to the brain
#' d) Previous cervical or cerebral artery revascularization
#' surgery or percutaneous intervention This does not include
#' chronic (nonvascular) neurological diseases or other acute
#' neurological insults such as metabolic and anoxic ischemic
#' encephalopathy
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param stroke Explicit item for stroke (brain, spinal cord, or retinal vascular injury as a
#' result of hemorrhage or infarction, where the neurological
#' dysfunction lasts for greater than 24 hours)
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param pvd Peripheral Arterial Disease (history of peripheral arterial disease,
#' includes upper and lower extremity, renal, mesenteric, and
#' abdominal aortic systems)
#' 1. Claudication , either with exertion or at rest
#' 2. Amputation for arterial vascular insufficiency
#' 3. Vascular reconstruction, bypass surgery, or percutaneous intervention
#' to the extremities (excluding dialysis fistulas and vein stripping)
#' 4. Documented abdominal aortic aneurysm with or without repair
#' 5. Positive noninvasive test (e.g., ankle brachial index =< 0.9,
#' ultrasound, magnetic resonance or computed tomography
#' imaging of > 50% diameter stenosis in any peripheral artery,
#' i.e., renal, subclavian, femoral, iliac) or angiographic imaging
#' Peripheral arterial disease excludes disease in the carotid,
#' cerebrovascular arteries or thoracic aorta
#' PVD does not include DVT
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param diabetes History of diabetes diagnosed and/or treated by a healthcare
#' provider. See Def. STS website or 2013 ACCF/AHA Data Standards
#' Cannon et al. JACC Vol. 61, No. 9, 2013
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param diabetes_ctrl Indicate the patient’s diabetes control method as presented
#' on admission
#' Values: "diet", "oral", "insulin", "other", "other_subcutaneous",
#' "none", "unknown"
#'
#' @param htn Hypertension, see STS definition
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param immsupp Immunosuppression: Indicate whether immunocompromise is present
#' due to immunosuppressive medication therapy within 30 days
#' preceding the operative procedure or existing medical condition
#' (see training manual). This includes, but is not limited to
#' systemic steroid therapy, anti-rejection medications and chemotherapy.
#' This does not include topical steroid applications, one time systemic
#' therapy, inhaled steroid therapy or preprocedure protocol
#' Values: "Yes", "No", or booleans string, "Unknown"
#'
#' @param endocarditis History of endocarditis: must meet at least 1 of the
#' following criteria:
#' 1. organisms cultured from valve or vegetation.
#' 2. 2 or more of the following signs or symptoms:
#' * fever (>38 degrees C)
#' * new or changing murmur*
#' * embolic phenomena*
#' * skin manifestations* (i.e., petechiae, splinter
#' hemorrhages, painful subcutaneous nodules)
#' * congestive heart failure*
#' * cardiac conduction abnormality*
#' With no other recognized cause and at least 1 of the following:
#' a. organisms cultured from 2 or more blood cultures
#' b. organisms seen on Gram’s stain of valve when culture
#' is negative or not done
#' c. valvular vegetation seen during an invasive procedure
#' or autopsy
#' d. positive laboratory test on blood or urine
#' (e.g., antigen tests for H influenzae, S pneumoniae,
#' N meningitidis, or Group B Streptococcus)
#' e. evidence of new vegetation seen on echocardiogram
#' and if diagnosis is made antemortem, physician institutes
#' appropriate antimicrobial therapy.
#' CDC, January 2013 Choose 'Yes' for patients with pre-operative
#' endocarditis who begin antibiotics post-op.
#' Code yes for patients who are diagnosed intraoperatively.
#' Values: "Yes", "No", or booleans string
#'
#' @param endocarditis_type Type of endocarditis the patient has. If the patient is
#' currently being treated for endocarditis, the disease
#' is considered active.
#' If no antibiotic medication (other than prophylactic
#' medication) is being given at the time of surgery,
#' then the infection is considered treated.
#'
#' If a <i>endocarditis</i> type is set, endocarditis is automatically
#' set to "Yes"
#' Values: 'Active' or 'Treated'
#'
#' @param chd_known Indicate whether coronary artery anatomy and/or disease is documented
#' and available prior to surgery.
#' Values: "Yes", "No", or booleans string
#'
#' @param chd Indicate whether coronary artery anatomy and/or disease is documented
#' and available prior to
#'
#' If a valid <i>chd</i> type is set, chd_known is automatically
#' set to "Yes"
#' Values: "Yes", "No", or booleans string
#'
#' @param left_main_stenosis Any numeric string between 0 and 100, like "60%" or "45 %"
#'
#' @param urgency Indicate the clinical status of the patient prior to entering the operating room.
#' Indication urgency, accepts the following values:
#' "elective|elektiv", "urgent|dringlich",
#' "emergent|emergency|notfall|notfallindikation",
#' "salvage|emergent salvage"
#'
#' @param resuscitation Indicate whether the patient required cardiopulmonary
#' resuscitation before the start of the operative procedure
#' which includes the institution of anesthetic management.
#' Capture resuscitation timeframe: within 1 hour or 1-24 hours pre-op.
#' Allowed values:
#' - "yes-1h"
#' - "yes-1_24h"
#' - "no"
#'
#' @param cardiogenic_shock Indicate if the patient developed cardiogenic shock.
#' Cardiogenic shock is defined as a sustained (>30 min)
#' episode of hypoperfusion evidenced by systolic blood
#' pressure <90 mm Hg and/or, if available,
#' cardiac index <2.2 L/min per square meter determined to
#' be secondary to cardiac dysfunction and/or the requirement
#' for parenteral inotropic or vasopressor agents or
#' mechanical support (e.g., IABP, extracorporeal circulation, VADs)
#' to maintain blood pressure and cardiac index above those
#' specified levels. Note: Transient episodes of hypotension
#' reversed with IV fluid or atropine do not constitute
#' cardiogenic shock. The hemodynamic compromise
#' (with or without extraordinary supportive therapy) must persist
#' for at least 30 min. ACCF/AHA 2013
#' Accepted values:
#' - Boolean NO strings
#' - "yes-at_procedure"
#' - "yes-within_24h"
#' @param iabp Indicate whether the patient was placed on an Intra-Aortic Balloon Pump (IABP).
#' Values: "Yes", "No", or booleans string
#'
#' @param iabp_when Indicate when the IABP was inserted.
#' Accepted values:
#' - Boolean NO strings --> will set <i>iabp</i> to "No"
#' - "Preop" --> will set <i>iabp</i> to "Yes"
#' - "Intraop" --> will set <i>iabp</i> to "Yes"
#' - "Postop" --> will set <i>iabp</i> to "Yes"
#'
#' @param inotropes Indicate whether the patient received IV inotropic agents within
#' 48 hours preceding surgery.
#' Values: "Yes", "No", or booleans string
#'
#' @param pre_cv_intervention Indicate whether the patient has undergone any previous
#' cardiovascular intervention, either <b>surgical or non-surgical</b>,
#' which may include those done during the current admission.
#'
#' @param pre_pci Indicate whether a previous Percutaneous Coronary Intervention (PCI)
#' was performed any time prior to this surgical procedure. Percutaneous
#' coronary intervention (PCI) is the placement of an angioplasty guide
#' wire, balloon, or other device (e.g. stent, atherectomy, brachytherapy,
#' or thrombectomy catheter) into a native coronary artery or coronary
#' artery bypass graft for the purpose of mechanical coronary revascularization.
#' Values: "Yes", "No", or booleans string
#' --> will set the value of <i>pre_cv_intervention</i> accordingly
#'
#' @param pre_pci_interval Indicate the interval of time between the previous PCI
#' and the current surgical procedure.
#' Values: ">6h" or "<=6h"
#' --> will set the value of <i>pre_cv_intervention</i> and
#' <i>pre_pci</i> accordingly.
#'
#' @param vd_mitral Indicate whether Mitral valve disease is present.
#' Values: "Yes", "No", or booleans string
#'
#' @param vd_mitral_stenosis Indicate whether Mitral Stenosis is present.
#' Values: "Yes", "No", or booleans string
#' --> A boolean "Yes" value will also set <i>vd_mitral</i> to "Yes"
#'
#' @param vd_aortic Indicate whether Aortic valve disease is present.
#' Values: "Yes", "No", or booleans string
#'
#' @param vd_aortic_stenosis Indicate whether Aortic Stenosis is present.
#' Values: "Yes", "No", or booleans string
#' --> A boolean "Yes" value will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_aortic_regurg Indicate whether there is evidence of Aortic valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_mitral_regurg Indicate whether there is evidence of Mitral valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param vd_tricuspid_regurg Indicate whether there is evidence of Tricuspid valve
#' insufficiency/regurgitation. Enter level of valve function
#' associated with highest risk (i.e., worst performance).
#' Enter the highest level recorded in the chart.
#' 'Moderately severe' should be coded as 'Severe'.
#' Values:
#' - "None" or Boolean NO strings
#' - "undocumented" | "not documented"
#' - "trivial/trace"
#' - "mild" | "1+" | "1"
#' - "moderate" | "2+" | "2" | "mittel" | "mittelgradig" | "mittelschwer"
#' - "severe" | "3+" | "3" | "schwer" | "schwergradig"
#' --> Any value >= 1+ will also set <i>vd_aortic</i> to "Yes"
#'
#' @param no_cardiovascular_surgeries Incidence - Indicate if this is the patient's:
#' - 0 ==> first surgery
#' - 1 ==> first re-op surgery
#' - 2 ==> second re-op surgery
#' - 3 ==> third re-op surgery
#' - 4 ==> fourth or more re-op surgery.
#' Surgery is defined as cardiothoracic
#' operations (heart or great vessels) surgical
#' procedures performed with or without cardiopulmonary
#' bypass (CPB). Also include lung procedures
#' utilizing CPB or tracheal procedures utilizing CPB.
#' Reoperation increases risk due to the presence of
#' scar tissue and adhesions.
#'
#' @param return_query_list setting this on TRUE will return only the query list, but not
#' do the request to the STS web service. Useful for debugging.
#'
#' @param verbose prints detailed info about parameters and the http web service query
#'
#' @return a list of the predicted risks of the at the time of request current
#' STS risk model
#' @export
#' @examples
#' service <- plumber::plumb("R/sts.R")
#' service$run(port = 8080)
#
# Plumber decoration
#* @get /calc_sts
#* @post /calc_sts
calc_sts <- function(age,
gender,
proc_cabg,
proc_valve = NULL,
height_cm = NULL,
weight_kg = NULL,
lvef = NULL,
chf_2w = NULL,
race = NULL,
hispanic_ethnicity = NULL,
dialysis = NULL,
crea = NULL,
acs_type = NULL,
prior_mi = NULL,
arrhythmia = NULL,
afib = NULL,
chrlungd = NULL,
cvd = NULL,
stroke = NULL,
pvd = NULL,
diabetes = NULL,
diabetes_ctrl = NULL,
htn = NULL,
immsupp = NULL,
endocarditis = NULL,
endocarditis_type = NULL,
chd_known = NULL,
chd = NULL,
left_main_stenosis = NULL,
urgency = NULL,
resuscitation = NULL,
cardiogenic_shock = NULL,
iabp = NULL,
iabp_when = NULL,
inotropes = NULL,
pre_cv_intervention = NULL,
pre_pci = NULL,
pre_pci_interval = NULL,
vd_mitral = NULL,
vd_mitral_stenosis = NULL,
vd_aortic = NULL,
vd_aortic_stenosis = NULL,
vd_aortic_regurg = NULL,
vd_mitral_regurg = NULL,
vd_tricuspid_regurg = NULL,
no_cardiovascular_surgeries = NULL,
return_query_list = FALSE,
verbose = FALSE
) {
queryList <- list()
age <- readr::parse_number(age)
queryList$age <- ensurer::ensure(age, is.numeric(.), . >= 1 , . <= 110)
queryList$gender <- parse_sex(gender)
if (!is.null(proc_cabg)) {
if (parse_bool(proc_cabg)) {
queryList$opcab <- "Yes, planned"
}
}
if (!is.null(proc_valve)) {
proc_valve <- stringr::str_to_lower(proc_valve)
if (proc_valve == "avr") {
queryList$opvalve <- "Yes"
queryList$vsav <- "Yes, planned"
queryList$vsavpr <- "Replacement"
} else if (proc_valve == "mvreplacement") {
queryList$opvalve <- "Yes"
queryList$vsmv <- "Yes, planned"
queryList$vsmvpr <- "Replacement"
} else if (proc_valve == "mvrepair") {
queryList$opvalve <- "Yes"
queryList$vsmv <- "Yes, planned"
queryList$vsmvpr <- "Repair"
} else if (proc_valve %in% c("none","no", "n", "false", "f", "0")) {
# do nothing, coding indicates no VALVE surgery
} else {
stop("'proc_valve' must be one of the following values: 'AVR',
'MVReplacement', 'MVRepair' or a boolean NO/FALSE string")
}
}
if (!is.null(height_cm)) {
queryList$heightcm <- ensurer::ensure(height_cm, is.numeric(.), . >= 20, . <= 251)
}
if (!is.null(weight_kg)) {
queryList$weightkg <- ensurer::ensure(weight_kg, is.numeric(.), . >= 10, . <= 250)
}
if (!is.null(lvef)) {
queryList$hdef <- ensurer::ensure(lvef, is.numeric(.), . >= 1, . <= 99)
queryList$hdefd <- "Yes"
}
if (!is.null(chf_2w)) {
queryList$chf <- parse_bool_and_add(stringr::str_to_title(chf_2w),
"Unknown")
}
if (!is.null(race)) {
race <- ensurer::ensure(stringr::str_to_title(race),
. %in% c("Undocumented", "Not Documented", "Undisclosed",
"Black", "Asian", "Asianblack"))
if (race %in% c("Undocumented", "Not Documented")) {
queryList$racedocumented = "No"
} else if (race == "Undisclosed") {
queryList$racedocumented = "Patient declined to disclose"
} else {
queryList$racedocumented = "Yes"
if (race %in% c("Black", "Asianblack")) {
queryList$raceblack = "Yes"
}
if (race %in% c("Asian", "Asianblack")) {
queryList$raceasian = "Yes"
}
}
}
if (!is.null(hispanic_ethnicity)) {
queryList$ethnicity <- parse_bool_and_add(stringr::str_to_title(hispanic_ethnicity),
additionals = "Not Documented")
}
if (!is.null(dialysis)) {
queryList$dialysis <- parse_bool_and_add(stringr::str_to_title(dialysis),
additionals = "Unknown")
}
if (!is.null(crea)) {
queryList$creatlst <- ensurer::ensure(crea, is.numeric(.), . > 0.1, . < 30)
}
if (!is.null(crea)) {
queryList$creatlst <- ensurer::ensure(crea, is.numeric(.), . > 0.1, . < 30)
}
if (!is.null(acs_type)) {
acs_type <- stringr::str_to_upper(acs_type)
if (acs_type == "OTHER") {
queryList$cardsymptimeofsurg <- "Other"
} else if (acs_type == "NO SYMPTOMS") {
queryList$cardsymptimeofsurg <- "No Symptoms"
} else if (acs_type == "ANGINA EQUIVALENT") {
queryList$cardsymptimeofsurg <- "Angina equivalent"
} else if (acs_type == "STABLE ANGINA") {
queryList$cardsymptimeofsurg <- "Stable Angina "
} else if (acs_type == "UNSTABLE ANGINA") {
queryList$cardsymptimeofsurg <- "Unstable Angina"
} else if (acs_type == "NSTEMI") {
queryList$cardsymptimeofsurg <- "Non-ST Elevation MI (Non-STEMI)"
} else if (acs_type == "STEMI") {
queryList$cardsymptimeofsurg <- "ST Elevation MI (STEMI)"
} else {
stop("ACS type or cardiac symptoms at time of surgery are not recognized.")
}
}
if (!is.null(prior_mi)) {
choices = c("6h" = " <=6 Hrs",
'6-24h' = " >6 Hrs but <24 Hrs",
'1-7d' = "1 to 7 Days",
'8-21d' = "8 to 21 Days",
'longer' = " >21 Days",
'No' = "No",
'Unknown' = "Unknown")
names(choices) <- stringr::str_to_upper(names(choices))
prior_mi <- stringr::str_to_upper(prior_mi)
prior_mi_bool <- parse_bool_and_add(prior_mi)
if (prior_mi %in% names(choices[1:5])) {
queryList$prevmi <- "Yes"
queryList$miwhen <- choices[prior_mi]
} else if (prior_mi %in% names(choices[6:7])) {
queryList$prevmi <- choices[prior_mi]
} else if (prior_mi_bool %in% c("Yes", "No")) {
queryList$prevmi <- prior_mi_bool
} else {
stop("Coding if of 'prior_mi' not recognized.")
}
}
if (!is.null(arrhythmia)) {
queryList$arrhythmia <- parse_bool_and_add(stringr::str_to_title(arrhythmia),
additionals = "Unknown")
}
if (!is.null(afib)) {
afib <- stringr::str_to_upper(afib)
if (afib %in% c("NONE","NO", "FALSE", "F", "0")) {
queryList$arrhythafib <- "None"
} else if (afib %in% c("PAROXYSMAL", "PAROX")) {
queryList$arrhythafib <- "Paroxysmal"
} else if (afib %in% c("CONT", "CONTINOUS", "PERSISTENT", "PERSI")) {
queryList$arrhythafib <- "Continuous / persistent"
} else {
stop("Coding if of 'afib' not recognized.")
}
}
# 'no', 'unknown', 'yes-unknown', 'yes-mild', 'yes-moderate', 'yes-severe'
if (!is.null(chrlungd)) {
chrlungd <- stringr::str_to_upper(chrlungd)
choices <- c("unknown" = "Unknown",
"yes-unknown" = "Lung disease documented, severity unknown",
"yes-mild" = "Mild",
"yes-moderate" = "Moderate",
"yes-severe" = "Severe")
names(choices) <- stringr::str_to_upper(names(choices))
if (chrlungd %in% c("NONE","NO", "N", "FALSE", "F", "0")) {
queryList$chrlungd <- "No"
} else if (chrlungd %in% names(choices)) {
queryList$chrlungd <- choices[chrlungd]
} else {
stop("Coding of 'chrlungd' not recognized.")
}
}
if (!is.null(cvd)) {
queryList$cvd <- parse_bool_and_add(stringr::str_to_title(cvd),
additionals = "Unknown")
}
if (!is.null(stroke)) {
queryList$cva <- parse_bool_and_add(stringr::str_to_title(stroke),
additionals = "Unknown")
if (queryList$cva == "Yes") {
queryList$cvd = "Yes"
}
}
if (!is.null(pvd)) {
queryList$pvd <- parse_bool_and_add(stringr::str_to_title(pvd),
additionals = "Unknown")
}
if (!is.null(diabetes)) {
queryList$diabetes <- parse_bool_and_add(stringr::str_to_title(diabetes),
additionals = "Unknown")
}
if (!is.null(diabetes_ctrl)) {
diabetes_ctrl <- stringr::str_to_upper(diabetes_ctrl)
choices <- c("unknown" = "Unknown",
"other_subcutaneous" = "Other subcutaneous medication",
"other" = "Other",
"insulin" = "Insulin",
"diet" = "Diet only",
"oral" = "Oral")
names(choices) <- stringr::str_to_upper(names(choices))
if (diabetes_ctrl %in% c("NONE","NO", "N", "FALSE", "F", "0")) {
queryList$diabctrl <- "None"
} else if (diabetes_ctrl %in% names(choices)) {
queryList$diabctrl <- choices[diabetes_ctrl]
queryList$diabetes <- "Yes"
} else {
stop("Coding of 'diabetes_ctrl' not recognized.")
}
}
if (!is.null(htn)) {
queryList$hypertn <- parse_bool_and_add(stringr::str_to_title(htn),
additionals = "Unknown")
}
if (!is.null(immsupp)) {
queryList$immsupp <- parse_bool_and_add(stringr::str_to_title(immsupp),
additionals = "Unknown")
}
if (!is.null(endocarditis)) {
queryList$infendo <- parse_bool_and_add(stringr::str_to_title(endocarditis))
}
if (!is.null(endocarditis_type)) {
endocarditis_type <- stringr::str_to_upper(endocarditis_type)
if (endocarditis_type %in% c("ACTIVE", "ACT")) {
queryList$infendty <- "Active"
queryList$infendo <- "Yes"
} else if (endocarditis_type %in% c("TREATED", "TRT", "TREAT")) {
queryList$infendty <- "Treated"
queryList$infendo <- "Yes"
} else {
stop("Coding of 'endocarditis_type' not recognized.")
}
}
if (!is.null(chd_known)) {
queryList$coranatdisknown <- parse_bool_and_add(stringr::str_to_title(chd_known))
}
if (!is.null(chd)) {
chd <- parseVesselsDisease(chd)
if (chd %in% c("None", "Three", "Two", "One")) {
queryList$numdisv <- chd
queryList$coranatdisknown <- "Yes"
} else {
stop("Coding of 'chd' not recognized.")
}
}
if (!is.null(left_main_stenosis) && chd %in% c("Three", "Two", "One")) {
stenosis <- readr::parse_number(left_main_stenosis)
queryList$pctstenlmain <- ensurer::ensure(stenosis, is.numeric(.), . >= 0, . <= 100)
queryList$pctstenknown <- "Yes"
}
if (!is.null(urgency)) {
urgency <- stringr::str_trim(stringr::str_to_lower(urgency))
if (urgency %in% c("elective", "elektiv")) {
queryList$status <- "Elective"
} else if (urgency %in% c("urgent", "dringlich")) {
queryList$status <- "Urgent"
} else if (urgency %in% c("emergent", "emergency", "notfall", "notfallindikation")) {
queryList$status <- "Emergent"
} else if (urgency %in% c("emergent salvage", "salvage")) {
queryList$status <- "Emergent Salvage"
} else {
stop("Coding of 'urgency' not recognized.")
}
}
if (!is.null(resuscitation)) {
resusc <- stringr::str_trim(stringr::str_to_lower(resuscitation))
if (resusc %in% c("none","no", "n", "false", "f", "0")) {
queryList$resusc <- "No"
} else if (resusc == "yes-1h") {
queryList$resusc <- "Yes - Within 1 hour of the start of the procedure"
} else if (resusc == "yes-1_24h") {
queryList$resusc <- "Yes - More than 1 hour but less than 24 hours of the start of the procedure"
} else {
stop("Coding of 'resuscitation' not recognized.")
}
}
if (!is.null(cardiogenic_shock)) {
carshock <- stringr::str_trim(stringr::str_to_lower(cardiogenic_shock))
if (carshock %in% c("none","no", "n", "false", "f", "0")) {
queryList$carshock <- "No"
} else if (carshock == "yes-at_procedure") {
queryList$carshock <- "Yes - At the time of the procedure"
} else if (carshock == "yes-within_24h") {
queryList$carshock <- "Yes, not at the time of the procedure but within prior 24 hours"
} else {
stop("Coding of 'cardiogenic_shock' not recognized.")
}
}
if (!is.null(iabp)) {
queryList$iabp <- parse_bool_and_add(stringr::str_to_title(iabp))
}
if (!is.null(iabp_when)) {
iabp_when <- stringr::str_trim(stringr::str_to_lower(iabp_when))
if (iabp_when %in% c("none","no", "n", "false", "f", "0")) {
queryList$iabp <- "No"
} else if (str_starts_with(iabp_when, "pre") ||
str_starts_with(iabp_when, "prae") ||
str_starts_with(iabp_when, "prä")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Preop"
} else if (str_starts_with(iabp_when, "intra")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Intraop"
} else if (str_starts_with(iabp_when, "post")) {
queryList$iabp <- "Yes"
queryList$iabpwhen <- "Postop"
} else {
stop("Coding of 'iabp_when' not recognized.")
}
}
if (!is.null(inotropes)) {
queryList$medinotr <- parse_bool_and_add(stringr::str_to_title(inotropes))
}
if (!is.null(pre_cv_intervention)) {
queryList$prcvint <- parse_bool_and_add(stringr::str_to_title(pre_cv_intervention),
additionals = "Unknown")
}
if (!is.null(pre_pci)) {
queryList$pocpci <- parse_bool_and_add(stringr::str_to_title(pre_pci))
if (queryList$pocpci == "Yes") {
queryList$prcvint <- "Yes"
}
}
if (!is.null(pre_pci_interval)) { #">6h" or "<=6h"
pre_pci_interval <- stringr::str_trim(stringr::str_to_lower(pre_pci_interval))
if (pre_pci_interval == ">6h") {
queryList$pocpciin <- " > 6 Hours"
queryList$prcvint <- "Yes"
queryList$pocpci <- "Yes"
} else if (pre_pci_interval == "<=6h") {
queryList$pocpciin <- " <= 6 Hours"
queryList$prcvint <- "Yes"
queryList$pocpci <- "Yes"
} else {
stop("Coding of 'pre_pci_interval' not recognized.")
}
}
if (!is.null(vd_mitral)) {
queryList$vdmit <- parse_bool_and_add(stringr::str_to_title(vd_mitral))
}
if (!is.null(vd_mitral_stenosis)) {
queryList$vdstenm <- parse_bool_and_add(stringr::str_to_title(vd_mitral_stenosis))
if (queryList$vdstenm == "Yes") {
queryList$vdmit <- "Yes"
}
}
if (!is.null(vd_aortic)) {
queryList$vdaort <- parse_bool_and_add(stringr::str_to_title(vd_aortic))
}
if (!is.null(vd_aortic_stenosis)) {
queryList$vdstena <- parse_bool_and_add(stringr::str_to_title(vd_aortic_stenosis))
if (queryList$vdstena == "Yes") {
queryList$vdaort <- "Yes"
}
}
if (!is.null(vd_aortic_regurg)) {
regurg <- parse_vd_regurg(vd_aortic_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsufa <- regurg
}
}
if (!is.null(vd_mitral_regurg)) {
regurg <- parse_vd_regurg(vd_mitral_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsufm <- regurg
}
}
if (!is.null(vd_tricuspid_regurg)) {
regurg <- parse_vd_regurg(vd_tricuspid_regurg)
if (!(is.null(regurg) || is.na(regurg))) {
queryList$vdinsuft <- regurg
}
}
if (!is.null(no_cardiovascular_surgeries)) {
no_cardiovascular_surgeries <- readr::parse_number(no_cardiovascular_surgeries)
incidence <- ensurer::ensure(no_cardiovascular_surgeries,
is.numeric(.), . %in% c(0, 1, 2, 3, 4))
trans <- c("0"="First cardiovascular surgery",
"1"="First re-op cardiovascular surgery",
"2"="Second re-op cardiovascular surgery",
"3"="Third re-op cardiovascular surgery",
"4"="Fourth or more re-op cardiovascular surgery")
queryList$incidenc <- trans[as.character(incidence)]
}
#queryList <- as.list(match.call())[-1]
#queryList <- purrr::compact(queryList)
if (return_query_list) {
return(queryList)
}
res <- do_sts_request(queryList, verbose = verbose)
riskdf <- dplyr::as_data_frame(res)
dplyr::rename(riskdf,
Procedure = proceduretype,
Mortality = predmort,
Morbidity_Mortality = predmm,
DSW_Infection = preddeep,
Perm_Stroke = predstro,
Prolong_Vent = predvent,
Reoperation = predreop,
Renal_failure = predrenf,
Long_LOS = pred14d,
Short_LOS = pred6d
)
}
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