Nothing
inst/extdata/config/concept-dict.R
In ricu: Intensive Care Unit Data with R
strip_ws <- function(x) gsub("\\s+", " ", x)
cfg <- list(
hr = list(
unit = c("bpm", "/min"),
min = 0,
max = 300,
description = "heart rate",
omopid = 4239408L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(211L, 220045L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "heartrate",
class = "col_itm")
),
hirid = list(
list(ids = 200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6640L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 220045L, table = "chartevents", sub_var = "itemid")
)
)
),
sbp = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 300,
description = "systolic blood pressure",
omopid = 4152194L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(51L, 455L, 6701L, 220050L, 220179L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicsystolic",
class = "col_itm")
),
hirid = list(
list(ids = 100L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6641L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220050L, 220179L), table = "chartevents",
sub_var = "itemid")
)
)
),
dbp = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 200,
description = "diastolic blood pressure",
omopid = 4154790L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(8368L, 8441L, 8555L, 220051L, 220180L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicdiastolic",
class = "col_itm")
),
hirid = list(
list(ids = 120L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6643L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220051L, 220180L), table = "chartevents",
sub_var = "itemid")
)
)
),
map = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 250,
description = "mean arterial pressure",
omopid = 4239021L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(52L, 443L, 456L, 6072L, 220052L, 220181L, 225312L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicmean",
class = "col_itm"),
list(table = "vitalaperiodic", val_var = "noninvasivemean",
class = "col_itm")
),
hirid = list(
list(ids = c(110L, 610L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = 6642L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220052L, 220181L, 225312L), table = "chartevents",
sub_var = "itemid")
)
)
),
resp = list(
unit = c("insp/min", "/min"),
min = 0,
max = 120,
description = "respiratory rate",
omopid = 4313591L,
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(618L, 619L, 220210L, 224688L, 224689L, 224690L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "respiration",
class = "col_itm")
),
hirid = list(
list(ids = c(300L, 310L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(8874L, 12266L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = c(220210L, 224688L, 224689L, 224690L),
table = "chartevents", sub_var = "itemid")
)
)
),
o2sat = list(
unit = c("%", "% Sat."),
min = 50,
max = 100,
description = "oxygen saturation",
omopid = 40483579L,
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(646L, 220277L, 226253L, 50817L), table = "chartevents",
sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "sao2", unit_val = "%",
class = "col_itm"),
list(ids = "O2 Sat (%)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(4000L, 8280L, 20000800L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6709L, 8903L), table = "numericitems",
sub_var = "itemid"),
list(ids = 12311L, table = "numericitems", sub_var = "itemid",
callback = "transform_fun(binary_op(`*`, 100))")
),
miiv = list(
list(ids = c(220277L, 226253L, 50817L), table = "chartevents",
sub_var = "itemid")
)
)
),
fio2 = list(
unit = "%",
min = 21,
max = 100,
description = "fraction of inspired oxygen",
omopid = 4353936L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = c(3420L, 223835L), table = "chartevents",
sub_var = "itemid"),
list(ids = 50816L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "FiO2", table = "respiratorycharting",
sub_var = "respchartvaluelabel",
callback = "transform_fun(percent_as_numeric)"),
list(ids = "FiO2", table = "lab", sub_var = "labname",
callback = "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')")
),
hirid = list(
list(ids = 2010L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 12279L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 223835L, table = "chartevents", sub_var = "itemid"),
list(ids = 50816L, table = "labevents", sub_var = "itemid")
)
)
),
tco2 = list(
unit = "mEq/L",
min = 5,
max = 60,
description = "totcal CO2",
omopid = 4193415L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50804L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Total CO2", table = "lab", sub_var = "labname",
callback = "convert_unit(set_val(NA), 'mEq/L', 'lpm')")
),
miiv = list(
list(ids = 50804L, table = "labevents", sub_var = "itemid")
)
)
),
alt = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "alanine aminotransferase",
omopid = 4146380L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50861L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "ALT (SGPT)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002600L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6800L, 11978L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50861L, table = "labevents", sub_var = "itemid")
)
)
),
ast = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "aspartate aminotransferase",
omopid = 4263457L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50878L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "AST (SGOT)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000330L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6806L, 11990L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50878L, table = "labevents", sub_var = "itemid")
)
)
),
phos = list(
unit = "mg/dL",
min = 0,
max = 40,
description = "phosphate",
omopid = 4017907L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50970L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "phosphate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002500L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6828L, 9935L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')")
),
miiv = list(
list(ids = 50970L, table = "labevents", sub_var = "itemid")
)
)
),
bun = list(
unit = "mg/dL",
min = 0,
max = 200,
description = "blood urea nitrogen",
omopid = 4017361L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51006L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "BUN", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004100L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6850L, 9943L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')")
),
miiv = list(
list(ids = 51006L, table = "labevents", sub_var = "itemid")
)
)
),
ph = list(
min = 6.8,
max = 8,
description = "pH of blood",
omopid = 4097822L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50820L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "pH", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6848L, 12310L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50820L, table = "labevents", sub_var = "itemid")
)
)
),
bili = list(
unit = "mg/dL",
min = 0,
max = 100,
description = "total bilirubin",
omopid = 4118986L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50885L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "total bilirubin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004300L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6813L, 9945L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 50885L, table = "labevents", sub_var = "itemid")
)
)
),
inr_pt = list(
description = "prothrombin time/international normalized ratio",
omopid = 4306239L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51237L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PT - INR", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000567L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11893L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51237L, table = "labevents", sub_var = "itemid")
)
)
),
plt = list(
unit = c("K/uL", "G/l"),
min = 5,
max = 1200,
description = "platelet count",
omopid = 4267147L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51265L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "platelets x 1000", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000110L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6797L, 9964L, 10409L, 14252L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51265L, table = "labevents", sub_var = "itemid")
)
)
),
lact = list(
unit = "mmol/L",
min = 0,
max = 50,
description = "lactate",
omopid = 4191725L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50813L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "lactate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000524L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6837L, 9580L, 10053L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50813L, table = "labevents", sub_var = "itemid")
)
)
),
lymph = list(
unit = "%",
min = 0,
max = 100,
description = "lymphocytes",
omopid = 4254663L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51244L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-lymphs", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000480L, table = "observations", sub_var = "variableid",
callback = "blood_cell_ratio", class = "hrd_itm")
),
aumc = list(
list(ids = 11846L, table = "numericitems", sub_var = "itemid"),
list(ids = 14258L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51244L, table = "labevents", sub_var = "itemid")
)
)
),
bicar = list(
unit = c("mEq/L", "mmol/l"),
min = 5,
max = 50,
description = "bicarbonate",
omopid = 4194291L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50882L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "bicarbonate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6810L, 9992L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50882L, table = "labevents", sub_var = "itemid")
)
)
),
crea = list(
unit = "mg/dL",
min = 0,
max = 15,
description = "creatinine",
omopid = 4013964L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50912L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "creatinine", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000600L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.011312), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6836L, 9941L, 14216L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.011309), 'mg/dL')")
),
miiv = list(
list(ids = 50912L, table = "labevents", sub_var = "itemid")
)
)
),
pt = list(
unit = "sec",
min = 0,
description = "prothrombine time",
omopid = 4245261L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51274L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PT", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 6789L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51274L, table = "labevents", sub_var = "itemid")
)
)
),
rdw = list(
unit = "%",
min = 0,
max = 100,
description = "erythrocyte distribution width",
omopid = 4281085L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51277L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "RDW", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 18952L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51277L, table = "labevents", sub_var = "itemid")
)
)
),
alp = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "alkaline phosphatase",
omopid = 4275206L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50863L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "alkaline phos.", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002700L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6803L, 11984L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50863L, table = "labevents", sub_var = "itemid")
)
)
),
wbc = list(
unit = c("K/uL", "G/l"),
min = 0,
description = "white blood cell count",
omopid = 4298431L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51301L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "WBC x 1000", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000700L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6779L, 9965L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51301L, table = "labevents", sub_var = "itemid")
)
)
),
hgb = list(
unit = "g/dL",
min = 4,
max = 18,
description = "hemoglobin",
omopid = 4118981L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51222L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Hgb", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(24000548L, 24000836L, 20000900L), table = "observations",
sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL', 'g/l')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6778L, 9553L, 9960L, 10286L, 19703L),
table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 1.611344), 'g/dL')")
),
miiv = list(
list(ids = 51222L, table = "labevents", sub_var = "itemid")
)
)
),
hct = list(
unit = "%",
min = 15,
max = 60,
description = "hematocrit",
omopid = 4151358L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51221L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Hct", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = c(6777L, 11423L, 11545L), table = "numericitems",
sub_var = "itemid",
callback = "transform_fun(binary_op(`*`, 100))")
),
miiv = list(
list(ids = 51221L, table = "labevents", sub_var = "itemid")
)
)
),
pco2 = list(
unit = c("mmHg", "mm Hg"),
min = 10,
max = 150,
description = "CO2 partial pressure",
omopid = 4097882L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50818L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "paCO2", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20001200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6846L, 9990L, 21213L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50818L, table = "labevents", sub_var = "itemid")
)
)
),
po2 = list(
unit = c("mmHg", "mm Hg"),
min = 40,
max = 600,
description = "O2 partial pressure",
omopid = 4094581L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50821L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "paO2", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(7433L, 9996L, 21214L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50821L, table = "labevents", sub_var = "itemid")
)
)
),
mch = list(
unit = "pg",
min = 0,
description = "mean corpuscular hemoglobin",
omopid = 4182871L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51248L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCH", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000160L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11679L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.016113), 'pg')")
),
miiv = list(
list(ids = 51248L, table = "labevents", sub_var = "itemid")
)
)
),
mchc = list(
unit = "%",
min = 20,
max = 50,
description = "mean corpuscular hemoglobin concentration",
omopid = 4290193L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51249L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCHC", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000170L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.16114), '%')",
class = "hrd_itm")
),
aumc = list(
list(ids = 18666L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 1.611), '%')")
),
miiv = list(
list(ids = 51249L, table = "labevents", sub_var = "itemid")
)
)
),
mcv = list(
unit = "fL",
min = 50,
max = 150,
description = "mean corpuscular volume",
omopid = 4016239L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51250L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCV", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000150L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 9968L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51250L, table = "labevents", sub_var = "itemid")
)
)
),
ptt = list(
unit = "sec",
min = 0,
description = "partial thromboplastin time",
omopid = 4175016L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51275L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PTT", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004410L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 17982L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51275L, table = "labevents", sub_var = "itemid")
)
)
),
ca = list(
unit = "mg/dL",
min = 4,
max = 20,
description = "calcium",
omopid = 4216722L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50893L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "calcium", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`*`, 4), 'mg/dL', 'mmol/l')")
),
hirid = list(
list(ids = 20005100L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6817L, 9933L), table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')")
),
miiv = list(
list(ids = 50893L, table = "labevents", sub_var = "itemid")
)
)
),
cl = list(
unit = c("mEq/L", "mmol/l"),
min = 80,
max = 130,
description = "chloride",
omopid = 4188066L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50902L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "chloride", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(24000439L, 24000521L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = 9930L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50902L, table = "labevents", sub_var = "itemid")
)
)
),
mg = list(
unit = "mg/dL",
min = 0.5,
max = 5,
description = "magnesium",
omopid = 4243005L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50960L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "magnesium", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`/`, 1.215), 'mg/dL', 'mEq/L')"
)
),
hirid = list(
list(ids = 24000230L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6839L, 9952L), table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')")
),
miiv = list(
list(ids = 50960L, table = "labevents", sub_var = "itemid")
)
)
),
k = list(
unit = c("mEq/L", "mmol/l"),
min = 0,
max = 10,
description = "potassium",
omopid = 4207483L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50971L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "potassium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20000500L, 24000520L, 24000833L, 24000867L),
table = "observations", sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6835, 9556, 9927, 10285), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50971L, table = "labevents", sub_var = "itemid")
)
)
),
na = list(
unit = c("mEq/L", "mmol/l"),
min = 110,
max = 165,
description = "sodium",
omopid = 4208938L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50983L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "sodium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20000400L, 24000519L, 24000658L, 24000835L, 24000866L),
table = "observations", sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6840, 9555, 9924, 10284), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50983L, table = "labevents", sub_var = "itemid")
)
)
),
basos = list(
unit = "%",
min = 0,
max = 50,
description = "basophils",
omopid = 4172647L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51146L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-basos", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 11710L, table = "numericitems", sub_var = "itemid"),
list(ids = 14256L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51146L, table = "labevents", sub_var = "itemid")
)
)
),
eos = list(
unit = "%",
min = 0,
max = 50,
description = "eosinophils",
omopid = 4216098L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51200L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-eos", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 6773L, table = "numericitems", sub_var = "itemid"),
list(ids = 9967L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51200L, table = "labevents", sub_var = "itemid")
)
)
),
neut = list(
unit = "%",
min = 0,
max = 100,
description = "neutrophils",
omopid = 4148615L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51256L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-polys", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000550L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6786L, 11856L), table = "numericitems",
sub_var = "itemid"),
list(ids = 14254L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51256L, table = "labevents", sub_var = "itemid")
)
)
),
glu = list(
unit = "mg/dL",
min = 0,
max = 1000,
description = "glucose",
omopid = 4144235L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "glucose", table = "lab", sub_var = "labname"),
list(ids = "bedside glucose", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20005110L, 24000523L, 24000585L), table = "observations",
sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6833L, 9557L, 9947L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')")
),
miiv = list(
list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
)
)
),
cai = list(
unit = "mmol/L",
min = 0.5,
max = 2,
description = "calcium ionized",
omopid = 46272910L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50808L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "ionized calcium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000522L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6815L, 8915L, 9560L, 9561L, 10267L),
table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50808L, table = "labevents", sub_var = "itemid")
)
)
),
crp = list(
unit = "mg/L",
min = 0,
description = "C-reactive protein",
omopid = 4208414L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50889L, table = "labevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
),
eicu = list(
list(ids = "CRP", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
),
hirid = list(
list(ids = 20002200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6825L, 10079L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50889L, table = "labevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
)
)
),
esr = list(
unit = c("mm/hr", "mm/1h"),
min = 0,
max = 200,
description = "erythrocyte sedimentation rate",
omopid = 4212065L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51288L, table = "labevents", sub_var = "itemid")
),
hirid = list(
list(ids = 24000668L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6808L, 11902L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51288L, table = "labevents", sub_var = "itemid")
)
)
),
hbco = list(
description = "carboxyhemoglobin",
omopid = 4056787L,
category = "blood gas",
sources = list(
eicu = list(
list(ids = "Carboxyhemoglobin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000526L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11690L, table = "numericitems", sub_var = "itemid")
)
)
),
methb = list(
unit = "%",
min = 0,
max = 100,
description = "methemoglobin",
omopid = 4204561L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50814L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Methemoglobin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000549L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11692L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50814L, table = "labevents", sub_var = "itemid")
)
)
),
tnt = list(
unit = "ng/mL",
min = 0,
description = "troponin t",
omopid = 4005525L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51003L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "troponin - T", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000806L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`/`, 1000), 'ng/mL')",
class = "hrd_itm")
),
aumc = list(
list(ids = 10407L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51003L, table = "labevents", sub_var = "itemid")
)
)
),
alb = list(
unit = "g/dL",
min = 0,
max = 6,
description = "albumin",
omopid = 4017497L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50862L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "albumin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000605L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6801L, 9937L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')")
),
miiv = list(
list(ids = 50862L, table = "labevents", sub_var = "itemid")
)
)
),
fgn = list(
unit = "mg/dL",
min = 0,
max = 1500,
description = "fibrinogen",
omopid = 4094436L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51214L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "fibrinogen", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000536L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 100), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6776L, 9989L, 10175L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 51214L, table = "labevents", sub_var = "itemid")
)
)
),
be = list(
unit = c("mEq/L", "mmol/l"),
min = -25,
max = 25,
description = "base excess",
omopid = 4284393L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50802L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Base Excess", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20001300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6807L, 9994L), table = "numericitems",
sub_var = "itemid", dir_var = "tag", callback = "aumc_bxs")
),
miiv = list(
list(ids = 50802L, table = "labevents", sub_var = "itemid")
)
)
),
rbc = list(
unit = "m/uL",
min = 0,
max = 20,
description = "red blood cell count",
omopid = 4030871L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51279L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "RBC", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = c(6774L, 9962L), table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51279L, table = "labevents", sub_var = "itemid")
)
)
),
ck = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "creatine kinase",
omopid = 4265595L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50910L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "CPK", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000210L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6822L, 11998L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50910L, table = "labevents", sub_var = "itemid")
)
)
),
ckmb = list(
unit = "ng/mL",
min = 0,
description = "creatine kinase MB",
omopid = 4017058L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50911L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "CPK-MB", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000220L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6824L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50911L, table = "labevents", sub_var = "itemid")
)
)
),
egcs = list(
min = 1,
max = 4,
description = "GCS eye",
omopid = 4084277L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(184L, 220739L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Eyes", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6732L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Reactie op pijnprikkel` = 2,
`Reactie op verbale prikkel` = 3,
`Spontane reactie` = 4)
)")),
list(ids = 13077L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Niet` = 1,
`Op pijn` = 2,
`Op aanspreken` = 3,
`Spontaan` = 4)
)"))
),
miiv = list(
list(ids = 220739L, table = "chartevents", sub_var = "itemid")
)
)
),
vgcs = list(
min = 1,
max = 5,
description = "GCS verbal",
omopid = 4084912L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(723L, 223900L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Verbal", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000100L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6735L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie (geen zichtbare poging tot praten)` = 1,
`Onbegrijpelijke geluiden` = 2,
`Onduidelijke woorden (pogingen tot communicatie,
maar onduidelijk)` = 3,
`Verwarde conversatie` = 4,
`Helder en adequaat (communicatie mogelijk)` = 5)
)")),
list(ids = 13066L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen geluid` = 1,
`Onverstaanbare woorden` = 2,
`Onjuiste woorden` = 3,
`Verwarde taal` = 4,
`Georiënteerd` = 5)
)"))
),
miiv = list(
list(ids = 223900L, table = "chartevents", sub_var = "itemid")
)
)
),
mgcs = list(
min = 1,
max = 6,
description = "GCS motor",
omopid = 4083352L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(454L, 223901L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Motor", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6734L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Strekken` = 2,
`Decortatie reflex (abnormaal buigen)` = 3,
`Spastische reactie (terugtrekken)` = 4,
`Localiseert pijn` = 5,
`Volgt verbale commando's op` = 6)
)")),
list(ids = 13072L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Strekken op pijn` = 2,
`Abnormaal buigen bij pijn` = 3,
`Terugtrekken bij pijn` = 4,
`Localiseren pijn` = 5,
`Voert opdrachten uit` = 6)
)"))
),
miiv = list(
list(ids = 223901L, table = "chartevents", sub_var = "itemid")
)
)
),
tgcs = list(
min = 3,
max = 15,
description = "GCS total",
omopid = 4093836L,
category = "neurological",
sources = list(
mimic = list(
list(ids = 198L, table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "GCS Total", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
)
)
),
urine = list(
unit = "mL",
min = 0,
max = 2000,
aggregate = "sum",
description = "urine output",
omopid = 4264378L,
category = "output",
sources = list(
mimic = list(
list(ids = c(40055L, 40056L, 40057L, 40065L, 40069L, 40085L,
40086L, 40094L, 40096L, 40405L, 40428L, 40473L,
40715L, 43175L, 226557L, 226558L, 226559L, 226560L,
226561L, 226563L, 226564L, 226565L, 226566L, 226567L,
226584L, 227510L),
table = "outputevents", sub_var = "itemid")
),
eicu = list(
list(ids = c("Urine", "URINE CATHETER"), table = "intakeoutput",
sub_var = "celllabel"),
list(regex = c("catheter.+output|output.+catheter"),
table = "intakeoutput", sub_var = "celllabel", class = "rgx_itm")
),
hirid = list(
list(ids = 30005110L, table = "observations", sub_var = "variableid",
callback = "hirid_urine", class = "hrd_itm")
),
aumc = list(
list(ids = 8794L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(226557L, 226558L, 226559L, 226560L, 226561L, 226563L,
226564L, 226565L, 226566L, 226567L, 226584L, 227510L),
table = "outputevents", sub_var = "itemid")
)
)
),
dobu_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 50,
description = "dobutamine rate",
omopid = 1337720L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30042L, 30306L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^dobu.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 2000)", class = "rgx_itm")
),
hirid = list(
list(ids = 426L, table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 7178L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221653L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
dobu_dur = list(
description = "dobutamine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30042L, 30306L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^dobu", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = 426L, table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_duration")
),
aumc = list(
list(ids = 7178L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221653L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
dobu60 = list(
concepts = c("dobu_rate", "dobu_dur"),
description = "dobutamine administration for min 1h",
category = "medications",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
dopa_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 50,
description = "dopamine rate",
omopid = 1337860L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^dopa.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 1600)", class = "rgx_itm")
),
aumc = list(
list(ids = 7179L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221662L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
dopa_dur = list(
description = "dopamine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^dopa", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
aumc = list(
list(ids = 7179L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221662L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
dopa60 = list(
concepts = c("dopa_rate", "dopa_dur"),
description = "dopamine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
norepi_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 3,
description = "norepinephrine rate",
omopid = 1321341,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30047L, 30120L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^norepi.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 32)", class = "rgx_itm")
),
hirid = list(
list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 7229L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221906L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
norepi_dur = list(
description = "norepinephrine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30047L, 30120L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^norepi", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_duration")
),
aumc = list(
list(ids = 7229L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221906L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
norepi60 = list(
concepts = c("norepi_rate", "norepi_dur"),
description = "norepinephrine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
epi_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 1.5,
description = "epinephrine rate",
omopid = 1343916L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^epi( |n).*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 40)", class = "rgx_itm")
),
hirid = list(
list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 6818L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221289L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
epi_dur = list(
description = "epinephrine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^epi( |n)", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_duration")
),
aumc = list(
list(ids = 6818L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221289L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
epi60 = list(
concepts = c("epi_rate", "epi_dur"),
description = "epinephrine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
vent_start = list(
class = "lgl_cncpt",
description = "ventilation start",
category = "respiratory",
sources = list(
mimic = list(
list(
ids = c(
1L, 60L, 218L, 221L, 223L, 436L, 437L,
444L, 445L, 448L, 449L, 450L, 459L, 501L,
502L, 503L, 505L, 506L, 535L, 543L, 639L,
654L, 667L, 668L, 669L, 670L, 671L, 672L,
681L, 682L, 683L, 684L, 686L, 1211L, 1340L,
1486L, 1600L, 1655L, 2000L, 3459L, 5865L, 5866L,
220339L, 223848L, 223849L, 224419L, 224684L, 224685L, 224686L,
224687L, 224695L, 224696L, 224697L, 224700L, 224701L, 224702L,
224703L, 224704L, 224705L, 224706L, 224707L, 224709L, 224738L,
224746L, 224747L, 224750L, 226873L, 227187L),
table = "chartevents", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
),
eicu = list(
list(table = "respiratorycare", val_var = "ventstartoffset",
callback = "vent_flag", class = "col_itm"),
list(table = "respiratorycare", val_var = "priorventstartoffset",
callback = "vent_flag", class = "col_itm"),
list(ids = c("Start", "Continued", "respFlowPtVentData"),
table = "respiratorycharting", sub_var = "respcharttypecat",
callback = "transform_fun(set_val(TRUE))")
)
)
),
vent_end = list(
class = "lgl_cncpt",
description = "ventilation end",
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(225468L, 225477L, 227194L), table = "procedureevents_mv",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))"),
list(ids = c(467L, 469L, 226732L), table = "chartevents",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
),
eicu = list(
list(table = "respiratorycare", val_var = "ventendoffset",
callback = "vent_flag", class = "col_itm"),
list(table = "respiratorycare", val_var = "priorventendoffset",
callback = "vent_flag", class = "col_itm"),
list(ids = c("off", "Off", "Suspended"), table = "respiratorycharting",
sub_var = "respchartvalue", val_var = "respchartvaluelabel",
callback = "transform_fun(set_val(TRUE))")
)
)
),
mech_vent = list(
class = "fct_cncpt",
target = "win_tbl",
levels = c("invasive", "noninvasive"),
description = "mechanical ventilation windows",
omopid = 4230167L,
category = "respiratory",
sources = list(
aumc = list(
list(ids = c(9328L, 10740L, 12635L), table = "processitems",
sub_var = "itemid", dur_var = "stop",
callback = "apply_map(c(`Beademen` = 'invasive',
`Beademen non-invasief` = 'noninvasive',
`Tracheostoma` = 'invasive'))"
)
),
miiv = list(
list(ids = c(225792L, 225794L), table = "procedureevents",
sub_var = "itemid", dur_var = "endtime",
callback = "apply_map(c(`225792` = 'invasive',
`225794` = 'noninvasive'),
var = 'sub_var')")
),
hirid = list(
list(ids = 15001552L, table = "observations", sub_var = "variableid",
target = "ts_tbl", interval = "00:01:00", class = "hrd_itm",
callback = "combine_callbacks(hirid_vent,
apply_map(c(`1` = 'invasive',
`2` = 'invasive',
`3` = 'noninvasive',
`4` = 'noninvasive',
`5` = 'noninvasive',
`6` = 'noninvasive')))")
)
)
),
ett_gcs = list(
class = "lgl_cncpt",
description = "tracheostomy",
omopid = 4097216L,
category = "respiratory",
target = "win_tbl",
sources = list(
mimic = list(
list(ids = c("1.0 ET/Trach", "No Response-ETT"), table = "chartevents",
sub_var = "value", target = "ts_tbl",
callback = "combine_callbacks(
transform_fun(set_val(TRUE)),
ts_to_win_tbl(mins(1L))
)")
),
hirid = list(
list(class = "fun_itm", callback = "combine_callbacks(
fwd_concept('mech_vent'),
transform_fun(comp_na(`==`, 'invasive'))
)")
),
aumc = list(
list(ids = 6735L, table = "listitems", sub_var = "itemid",
target = "ts_tbl", callback = "combine_callbacks(
transform_fun(comp_na(`==`, 'Geïntubeerd')),
ts_to_win_tbl(mins(1L))
)")
),
miiv = list(
list(ids = "No Response-ETT", table = "chartevents", sub_var = "value",
target = "ts_tbl", callback = "combine_callbacks(
transform_fun(set_val(TRUE)),
ts_to_win_tbl(mins(1L))
)")
),
eicu = list(
list(class = "fun_itm", callback = "combine_callbacks(
fwd_concept('rass'),
transform_fun(comp_na(`<=`, -3)),
ts_to_win_tbl(mins(360L))
)")
)
)
),
rass = list(
min = -5,
max = 4,
description = "Richmond agitation sedation scale",
omopid = 36684829L,
category = "neurological",
sources = list(
mimic = list(
list(ids = 228096L, table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Sedation Score", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 15001565L, table = "observations", sub_var = "variableid",
callback = "transform_fun(floor)", class = "hrd_itm")
),
aumc = list(
list(ids = 14444L, sub_var = "itemid", table = "listitems",
callback = "transform_fun(aumc_rass)")
),
miiv = list(
list(ids = 228096L, table = "chartevents", sub_var = "itemid")
)
)
),
abx = list(
class = "lgl_cncpt",
description = "antibiotics",
omopid = 4085730L,
category = "medications",
sources = list(
mimic = list(
list(regex = paste(
"aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
"flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
"rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
"gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
"peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
"clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
"tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
"uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
"ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
table = "prescriptions", sub_var = "drug", interval = "00:01:00",
callback = "mimic_abx_presc", class = "rgx_itm"
),
list(ids = c(
225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
227691L, 228003L), table = "inputevents_mv", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
),
eicu = list(
list(regex = paste(
"bactrim", "cipro", "flagyl", "metronidazole", "zithromax", "zosyn",
"(((amika", "cleo", "ofloxa)", "(azithro", "clinda", "tobra",
"vanco)my)c", "(ampi", "oxa", "peni", "pipera)cill", "cefazol",
"levaqu", "rifamp)in", sep = "|"), table = "infusiondrug",
sub_var = "drugname", callback = "transform_fun(set_val(TRUE))",
class = "rgx_itm"
),
list(regex = paste(
"cipro", "flagyl", "maxipime", "metronidazole", "tazobactam",
"zosyn", "cef(azolin", "epime)", "(((azithro", "clinda", "vanco)my",
"ofloxa", "vanco)c", "levaqu", "piperacill", "roceph)in", sep = "|"),
table = "medication", sub_var = "drugname",
callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
)
),
hirid = list(
list(ids = c(
163L, 176L, 181L, 186L, 189L, 300L, 326L,
331L, 351L, 405L, 1000234L, 1000272L, 1000273L, 1000274L,
1000284L, 1000299L, 1000300L, 1000302L, 1000304L, 1000305L, 1000306L,
1000315L, 1000317L, 1000318L, 1000320L, 1000321L, 1000322L, 1000335L,
1000348L, 1000352L, 1000363L, 1000365L, 1000390L, 1000407L, 1000408L,
1000424L, 1000425L, 1000426L, 1000437L, 1000483L, 1000507L, 1000508L,
1000518L, 1000519L, 1000549L, 1000601L, 1000648L, 1000666L, 1000670L,
1000671L, 1000760L, 1000781L, 1000791L, 1000797L, 1000812L, 1000825L,
1000829L, 1000830L, 1000837L, 1000838L, 1000854L, 1000855L, 1000893L,
1000894L, 1001005L, 1001068L, 1001075L, 1001079L, 1001084L, 1001086L,
1001095L, 1001096L, 1001097L, 1001098L, 1001168L, 1001169L, 1001170L,
1001171L, 1001173L, 1001193L, 1001198L), table = "pharma",
sub_var = "pharmaid", callback = "transform_fun(set_val(TRUE))")
),
aumc = list(
list(ids = c(
2L, 13L, 19L, 24L, 28L, 29L, 57L, 59L,
82L, 103L, 240L, 247L, 333L, 1133L, 1199L, 1300L,
1371L, 1795L, 2284L, 2834L, 3237L, 3741L, 5576L, 6834L,
6847L, 6871L, 6919L, 6948L, 6953L, 6958L, 7044L, 7064L,
7185L, 7187L, 7208L, 7227L, 7235L, 8064L, 8394L, 8942L,
9029L, 9030L, 9052L, 9070L, 9117L, 9128L, 9133L, 9142L,
9151L, 9152L, 12262L, 12389L, 12398L, 12956L, 12997L, 13057L,
13094L, 13102L, 15591L, 18860L, 19137L, 19773L, 20563L, 23166L,
24241L, 25776L, 27617L, 29321L), table = "drugitems",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
),
miiv = list(
list(regex = paste(
"aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
"flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
"rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
"gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
"peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
"clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
"tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
"uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
"ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
table = "prescriptions", sub_var = "drug",
callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
),
list(ids = c(
225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
227691L, 228003L), table = "inputevents", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
)
)
),
samp = list(
class = "lgl_cncpt",
category = "microbiology",
description = "body fluid sampling",
omopid = 4133843L,
sources = list(
mimic = list(
list(table = "microbiologyevents", val_var = "org_itemid",
callback = "mimic_sampling", aux_time = "charttime",
class = "col_itm")
),
eicu = list(
list(table = "microlab", val_var = "organism",
callback = "transform_fun(comp_na(`!=`, 'no growth'))",
class = "col_itm")
),
aumc = list(
list(ids = c(
8097L, 8418L, 8588L, 9189L, 9190L, 9191L, 9192L, 9193L, 9194L,
9195L, 9197L, 9198L, 9200L, 9202L, 9203L, 9204L, 9205L, 13024L,
19663L, 19664L), table = "procedureorderitems", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))")
),
miiv = list(
list(table = "microbiologyevents", val_var = "org_itemid",
callback = "mimic_sampling", aux_time = "charttime",
class = "col_itm")
)
)
),
tri = list(
unit = "ng/mL",
min = 0,
description = "troponin I",
omopid = 4007805L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51002L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "troponin - I", table = "lab", sub_var = "labname")
),
miiv = list(
list(ids = 51002L, table = "labevents", sub_var = "itemid")
)
)
),
bili_dir = list(
unit = "mg/dL",
min = 0,
max = 50,
description = "bilirubin direct",
omopid = 4216632L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50883L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "direct bilirubin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000560L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = 6812L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 50883L, table = "labevents", sub_var = "itemid")
)
)
),
temp = list(
unit = c("C", "°C"),
min = 32,
max = 42,
description = "temperature",
omopid = 4302666L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(676L, 677L, 223762L), table = "chartevents",
sub_var = "itemid"),
list(ids = c(678L, 679L, 223761L, 224027L), table = "chartevents",
sub_var = "itemid",
callback = "convert_unit(fahr_to_cels, 'C', 'f')")
),
eicu = list(
list(table = "vitalperiodic", val_var = "temperature",
class = "col_itm")
),
hirid = list(
list(ids = c(410L, 400L, 7100L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(8658L, 13952L, 16110L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 223762L, table = "chartevents", sub_var = "itemid"),
list(ids = c(223761L, 224027L), table = "chartevents",
sub_var = "itemid",
callback = "convert_unit(fahr_to_cels, 'C', 'f')")
)
)
),
etco2 = list(
unit = c("mmHg", "mm Hg"),
min = 10,
max = 60,
description = "endtidal CO2",
omopid = 4353940L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(1817L, 228640L), table = "chartevents",
sub_var = "itemid")
),
hirid = list(
list(ids = c(2200L, 8290L, 30010009L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(
ids = c(6707L, 8884L, 8885L, 9658L, 12805L, 12356L),
table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 7.6), 'mmHg', 'None|Geen')"
)
),
miiv = list(
list(ids = 228640L, table = "chartevents", sub_var = "itemid")
)
)
),
ins = list(
unit = "units/hr",
min = 0,
description = "insulin",
omopid = 42537007L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30045L, 30100L), table = "inputevents_cv",
sub_var = "itemid"),
list(ids = c(223258L, 223260L), table = "inputevents_mv",
sub_var = "itemid", val_var = "amount", end_var = "endtime",
callback = "distribute_amount")
),
eicu = list(
list(regex = "^insulin (250.+)?\\(((ml|units)/hr)?\\)$",
table = "infusiondrug", sub_var = "drugname", class = "rgx_itm")
),
hirid = list(
list(ids = c(15L, 1000724L), table = "pharma", sub_var = "pharmaid",
callback = "aggregate_fun('sum', 'units')")
),
aumc = list(
list(ids = c(7624L, 9014L, 19129L), sub_var = "itemid",
table = "drugitems")
),
miiv = list(
list(ids = c(223258L, 223260L), table = "inputevents",
sub_var = "itemid", val_var = "amount", end_var = "endtime",
callback = "distribute_amount")
)
)
),
sex = list(
target = "id_tbl",
levels = c("Female", "Male"),
class = "fct_cncpt",
description = "patient sex",
omopid = 37116947L,
category = "demographics",
sources = list(
mimic = list(
list(table = "patients", val_var = "gender",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
),
eicu = list(
list(table = "patient", val_var = "gender", class = "col_itm")
),
hirid = list(
list(table = "general", val_var = "sex",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
),
aumc = list(
list(val_var = "gender", table = "admissions",
callback = strip_ws("apply_map(c(Vrouw = 'Female',
Man = 'Male'))"),
class = "col_itm")
),
miiv = list(
list(table = "patients", val_var = "gender",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
)
)
),
age = list(
unit = "years",
min = 0,
max = 100,
target = "id_tbl",
description = "patient age",
omopid = 4314456L,
category = "demographics",
sources = list(
mimic = list(
list(table = "patients", val_var = "dob",
callback = "transform_fun(mimic_age)", class = "col_itm")
),
eicu = list(
list(table = "patient", val_var = "age",
callback = "transform_fun(eicu_age)", class = "col_itm")
),
hirid = list(
list(table = "general", val_var = "age", class = "col_itm")
),
aumc = list(
list(val_var = "agegroup", table = "admissions",
callback = strip_ws("apply_map(c(`18-39` = 30,
`40-49` = 45,
`50-59` = 55,
`60-69` = 65,
`70-79` = 75,
`80+` = 90))"),
class = "col_itm")
),
miiv = list(
list(table = "patients", val_var = "anchor_age", class = "col_itm")
)
)
),
weight = list(
unit = "kg",
min = 1,
max = 500,
target = "id_tbl",
description = "patient weight",
omopid = 4099154L,
category = "demographics",
sources = list(
mimic = list(
list(ids = c(762L, 4183L, 226512L), table = "chartevents",
sub_var = "itemid")
),
eicu = list(
list(table = "patient", val_var = "admissionweight",
class = "col_itm")
),
hirid = list(
list(ids = 10000400L, table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(val_var = "weightgroup", table = "admissions",
callback = strip_ws("apply_map(c(`59-` = 50,
`60-69` = 65,
`70-79` = 75,
`80-89` = 85,
`90-99` = 95,
`100-109` = 105,
`110+` = 120))"),
class = "col_itm")
),
miiv = list(
list(ids = 226512L, table = "chartevents", sub_var = "itemid")
)
)
),
height = list(
unit = "cm",
min = 10,
max = 230,
target = "id_tbl",
description = "patient height",
omopid = 607590L,
category = "demographics",
sources = list(
mimic = list(
list(ids = c(920L, 1394L, 3485L, 4187L, 4188L, 3486L, 226707L),
table = "chartevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
),
eicu = list(
list(table = "patient", val_var = "admissionheight",
class = "col_itm")
),
hirid = list(
list(ids = 10000450L, table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(val_var = "heightgroup", table = "admissions",
callback = strip_ws("apply_map(c(`159-` = 150,
`160-169` = 165,
`170-179` = 175,
`180-189` = 185,
`190+` = 200))"),
class = "col_itm")
),
miiv = list(
list(ids = 226707L, table = "chartevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
)
)
),
death = list(
class = "lgl_cncpt",
description = "in hospital mortality",
omopid = 4306655L,
category = "outcome",
sources = list(
mimic = list(
list(table = "admissions", index_var = "deathtime",
val_var = "hospital_expire_flag",
callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
),
eicu = list(
list(table = "patient", index_var = "unitdischargeoffset",
val_var = "hospitaldischargestatus",
callback = "transform_fun(comp_na(`==`, 'Expired'))",
class = "col_itm")
),
hirid = list(
list(ids = c(110L, 200L), table = "observations",
sub_var = "variableid", callback = "hirid_death",
class = "hrd_itm")
),
aumc = list(
list(table = "admissions", index_var = "dateofdeath",
val_var = "dischargedat", callback = "aumc_death",
class = "col_itm")
),
miiv = list(
list(table = "admissions", index_var = "deathtime",
val_var = "hospital_expire_flag",
callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
)
)
),
adm = list(
target = "id_tbl",
levels = c("med", "surg", "other"),
class = "fct_cncpt",
description = "patient admission type",
category = "demographics",
sources = list(
mimic = list(
list(table = "services", val_var = "curr_service",
callback = "apply_map(
c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
)",
class = "col_itm"
)
),
eicu = list(
list(table = "admissiondx", val_var = "admitdxpath",
callback = "eicu_adx", class = "col_itm")
),
aumc = list(
list(val_var = "specialty", table = "admissions",
callback = strip_ws("apply_map(
c(Cardiochirurgie = 'surg',
Cardiologie = 'med',
ders = 'other',
Gynaecologie = 'other',
`Heelkunde Gastro-enterologie` = 'surg',
`Heelkunde Longen/Oncologie` = 'surg',
`Heelkunde Oncologie` = 'surg',
Hematologie = 'med',
`Intensive Care Volwassenen` = 'other',
Inwendig = 'med',
`Keel, Neus & Oorarts` = 'surg',
Longziekte = 'med',
`Maag-,Darm-,Leverziekten` = 'med',
Mondheelkunde = 'surg',
Nefrologie = 'med',
Neurochirurgie = 'surg',
Neurologie = 'med',
Obstetrie = 'other',
`Oncologie Inwendig` = 'med',
Oogheelkunde = 'surg',
Orthopedie = 'surg',
`Plastische chirurgie` = 'surg',
Reumatologie = 'med',
Traumatologie = 'surg',
Urologie = 'surg',
Vaatchirurgie = 'surg',
Verloskunde = 'other'))"),
class = "col_itm")
),
miiv = list(
list(table = "services", val_var = "curr_service",
callback = "apply_map(
c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
)",
class = "col_itm"
)
)
)
),
los_icu = list(
unit = "days",
min = 0,
target = "id_tbl",
description = "ICU length of stay",
category = "outcome",
sources = list(
mimic = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
eicu = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
hirid = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
aumc = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
miiv = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
)
)
),
los_hosp = list(
unit = "days",
min = 0,
target = "id_tbl",
description = "hospital length of stay",
omopid = 462369952L,
category = "outcome",
sources = list(
mimic = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
),
eicu = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
),
miiv = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
)
)
),
pafi = list(
concepts = c("po2", "fio2"),
description = "Horowitz index",
omopid = 4233883L,
category = "respiratory",
aggregate = c("min", "max"),
callback = "pafi",
class = "rec_cncpt"
),
safi = list(
concepts = c("o2sat", "fio2"),
description = "SaO2/FiO2",
category = "respiratory",
aggregate = c("min", "max"),
callback = "safi",
class = "rec_cncpt"
),
vent_ind = list(
concepts = c("vent_start", "vent_end", "mech_vent"),
description = "ventilation durations",
omopid = 4230167L,
category = "respiratory",
interval = "00:01:00",
callback = "vent_ind",
target = "win_tbl",
class = "rec_cncpt"
),
vaso_ind = list(
concepts = c("dopa_dur", "norepi_dur", "dobu_dur", "epi_dur"),
description = "vasopressor indicator",
omopid = 3655896L,
category = "medications",
callback = "vaso_ind",
class = "rec_cncpt"
),
gcs = list(
concepts = c("egcs", "mgcs", "vgcs", "tgcs", "ett_gcs"),
description = "Glasgow coma scale (non-sedated)",
omopid = 4093836L,
category = "neurological",
aggregate = c("min", "min", "min", "min", "any"),
callback = "gcs",
class = "rec_cncpt"
),
urine24 = list(
concepts = "urine",
description = "urine output per 24h",
omopid = 4191836L,
category = "output",
callback = "urine24",
class = "rec_cncpt"
),
sofa_resp = list(
concepts = c("pafi", "vent_ind"),
description = "SOFA respiratory component",
omopid = 1616907L,
category = "outcome",
callback = "sofa_resp",
class = "rec_cncpt"
),
sofa_coag = list(
concepts = "plt",
description = "SOFA coagulation component",
omopid = 1616896L,
category = "outcome",
aggregate = "min",
callback = "sofa_coag",
class = "rec_cncpt"
),
sofa_liver = list(
concepts = "bili",
description = "SOFA liver component",
omopid = 1617043L,
category = "outcome",
aggregate = "max",
callback = "sofa_liver",
class = "rec_cncpt"
),
sofa_cardio = list(
concepts = c("map", "dopa60", "norepi60", "dobu60", "epi60"),
description = "SOFA cardiovascular component",
omopid = 1617534L,
category = "outcome",
aggregate = c("min", "max", "max", "max", "max"),
callback = "sofa_cardio",
class = "rec_cncpt"
),
sofa_cns = list(
concepts = "gcs",
description = "SOFA central nervous system component",
omopid = 1616439L,
category = "outcome",
callback = "sofa_cns",
class = "rec_cncpt"
),
sofa_renal = list(
concepts = c("crea", "urine24"),
description = "SOFA renal component",
omopid = 1616355L,
category = "outcome",
aggregate = c("max", NA),
callback = "sofa_renal",
class = "rec_cncpt"
),
sofa = list(
concepts = c("sofa_resp", "sofa_coag", "sofa_liver", "sofa_cardio",
"sofa_cns", "sofa_renal"),
description = "sequential organ failure assessment score",
omopid = 1616852L,
category = "outcome",
callback = "sofa_score",
class = "rec_cncpt"
),
qsofa = list(
concepts = c("gcs", "sbp", "resp"),
description = "quick SOFA score",
omopid = 1616732L,
category = "outcome",
callback = "qsofa_score",
class = "rec_cncpt"
),
susp_inf = list(
concepts = c("abx", "samp"),
description = "suspected infection",
omopid = 43021378L,
category = "outcome",
aggregate = lapply(list("sum", FALSE), list),
callback = "susp_inf",
class = "rec_cncpt"
),
sep3 = list(
concepts = c("sofa", "susp_inf"),
description = "sepsis-3 criterion",
omopid = 132797L,
category = "outcome",
callback = "sep3",
keep_components = c(FALSE, TRUE),
class = "rec_cncpt"
),
bnd = list(
unit = "%",
description = "band form neutrophils",
omopid = 4100147L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51144L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-bands", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000557L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6796L, 11586L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51144L, table = "labevents", sub_var = "itemid")
)
)
),
sirs = list(
concepts = c("temp", "hr", "resp", "pco2", "wbc", "bnd"),
description = "systemic inflammatory response syndrome score",
omopid = 4140444L,
category = "outcome",
callback = "sirs_score",
class = "rec_cncpt"
),
supp_o2 = list(
concepts = c("vent_ind", "fio2"),
description = "supplemental oxygen",
omopid = 36304401L,
category = "respiratory",
callback = "supp_o2",
class = "rec_cncpt"
),
avpu = list(
concepts = "gcs",
description = "AVPU scale",
omopid = 40493498L,
category = "neurological",
callback = "avpu",
class = "rec_cncpt"
),
news = list(
concepts = c("resp", "o2sat", "supp_o2", "temp", "sbp", "hr", "avpu"),
description = "national early warning score",
omopid = 44808550,
category = "outcome",
callback = "news_score",
class = "rec_cncpt"
),
mews = list(
concepts = c("sbp", "hr", "resp", "temp","avpu"),
description = "modified early warning score",
omopid = 40484211L,
category = "outcome",
callback = "mews_score",
class = "rec_cncpt"
),
hba1c = list(
unit = "%",
description = "Hemoglobin A1C",
omopid = 4184637L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 50852L, table = "labevents", sub_var = "itemid")
),
aumc = list(
list(ids = c(11812L, 16166L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50852L, table = "labevents", sub_var = "itemid")
)
)
),
bmi = list(
concepts = c("weight", "height"),
description = "patient body mass index",
omopid = 4245997L,
category = "demographics",
callback = "bmi",
target = "id_tbl",
class = "rec_cncpt"
),
adh_rate = list(
unit = c("units/min", "U/min"),
description = "vasopressin rate",
omopid = 1507835L,
category = "medications",
sources = list(
mimic = list(
list(ids = 30051L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),
mimic_rate_cv
)"),
list(ids = 222315L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
mimic_rate_mv
)")
),
eicu = list(
list(regex = "^vasopressin.*\\(.+/.+\\)$",
table = "infusiondrug", sub_var = "drugname",
callback = "eicu_rate_units(2.65, 0.53)",
class = "rgx_itm")
),
hirid = list(
list(ids = c(112L, 113L), table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate")
),
aumc = list(
list(ids = 12467L, table = "drugitems", sub_var = "itemid",
rate_uom = "doserateunit", stop_var = "stop",
callback = "aumc_rate_units(0.53)")
),
miiv = list(
list(ids = 222315L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
mimic_rate_mv
)")
)
)
),
phn_rate = list(
unit = "mcg/kg/min",
description = "phenylephrine rate",
omopid = 1135766L,
category = "medications",
sources = list(
mimic = list(
list(ids = 30127L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "combine_callbacks(
mimic_kg_rate, mimic_rate_cv)
"),
list(ids = 30128L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "mimic_rate_cv"),
list(ids = 221749L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^phenylephrine.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 200)", class = "rgx_itm")
),
miiv = list(
list(ids = 221749L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
norepi_equiv = list(
description = "norepinephrine equivalents",
category = "medications",
concepts = c("epi_rate", "norepi_rate", "dopa_rate", "adh_rate",
"phn_rate"),
callback = "norepi_equiv",
class = "rec_cncpt"
),
cort = list(
class = "lgl_cncpt",
description = "corticosteroids",
omopid = 304275008L,
category = "medications",
sources = list(
hirid = list(
list(ids = c( 146L, 151L, 1000325L, 1000383L, 1000431L,
1000432L, 1000433L, 1000434L, 1000435L, 1000486L,
1000487L, 1000488L, 1000769L, 1000770L, 1000929L),
table = "pharma", sub_var = "pharmaid",
callback = "transform_fun(set_val(TRUE))")
),
aumc = list(
list(ids = c(6922L, 6995L, 7106L, 8132L, 9042L, 9130L, 10628L),
table = "drugitems", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))")
)
)
),
dex = list(
min = 0,
unit = "ml/hr",
description = "dextrose (as D10)",
omopid = 4197597L,
category = "medications",
target = "win_tbl",
sources = list(
mimic = list(
list(ids = c(220950L, 228140L, 220952L), table = "inputevents_mv",
sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
auom_var = "amountuom", callback = "combine_callbacks(
mimv_rate,
dex_to_10(c(228140L, 220952L), c(2, 5))
)"),
list(ids = c(30016L, 30017L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid", val_var = "amount",
unit_var = "amountuom", target = "ts_tbl", interval = "00:01:00",
callback = "combine_callbacks(
grp_mount_to_rate(mins(1L), hours(1L)),
dex_to_10(30017L, 2)
)")
),
eicu = list(
list(regex = "(d50|dextrose.+50 ?%)", table = "medication",
sub_var = "drugname", dur_var = "drugstopoffset",
callback = "eicu_dex_med", class = "rgx_itm"),
list(regex = "(d10|dextrose.+10 ?%).+ml/hr", table = "infusiondrug",
sub_var = "drugname", callback = "eicu_dex_inf", target = "ts_tbl",
class = "rgx_itm")
),
hirid = list(
list(ids = c(1000022L, 1000690L, 1000689L, 1000544L, 1000746L,
1000835L, 1000060L, 1000545L, 1000567L),
table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
target = "ts_tbl", interval = "00:01:00",
callback = "combine_callbacks(
grp_mount_to_rate(mins(1L), hours(1L)),
dex_to_10(list(c(1000689L, 1000544L, 1000746L, 1000835L),
1000060L, 1000545L, 1000567L), c(2, 3, 4, 5))
)")
),
aumc = list(
list(ids = c(7254L, 7255L, 7256L, 8940L, 9571L), table = "drugitems",
sub_var = "itemid", dur_var = "stop", rate_var = "doserateunit",
callback = "combine_callbacks(
aumc_rate,
dex_to_10(list(7255L, 7256L, c(8940L, 9571L)),
c(2, 3, 4))
)"
)
),
miiv = list(
list(ids = c(220950L, 228140L, 220952L), table = "inputevents",
sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
auom_var = "amountuom", callback = "combine_callbacks(
mimv_rate,
dex_to_10(c(228140L, 220952L), c(2, 5))
)")
)
),
class = c("unt_cncpt", "num_cncpt")
)
)
cfg <- lapply(cfg, function(x) {
if ("sources" %in% names(x)) {
if ("mimic" %in% names(x[["sources"]]))
x[["sources"]] <- c(x[["sources"]],
mimic_demo = list(x[["sources"]][["mimic"]]))
if ("eicu" %in% names(x[["sources"]]))
x[["sources"]] <- c(x[["sources"]],
eicu_demo = list(x[["sources"]][["eicu"]]))
x[["sources"]] <- x[["sources"]][order(names(x[["sources"]]))]
}
x
})
pkg_dir <- rprojroot::find_root(rprojroot::is_r_package)
cfg_dir <- file.path(pkg_dir, "inst", "extdata", "config")
ricu::set_config(cfg[order(names(cfg))], "concept-dict", cfg_dir)
devtools::install(pkg_dir)
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strip_ws <- function(x) gsub("\\s+", " ", x)
cfg <- list(
hr = list(
unit = c("bpm", "/min"),
min = 0,
max = 300,
description = "heart rate",
omopid = 4239408L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(211L, 220045L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "heartrate",
class = "col_itm")
),
hirid = list(
list(ids = 200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6640L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 220045L, table = "chartevents", sub_var = "itemid")
)
)
),
sbp = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 300,
description = "systolic blood pressure",
omopid = 4152194L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(51L, 455L, 6701L, 220050L, 220179L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicsystolic",
class = "col_itm")
),
hirid = list(
list(ids = 100L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6641L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220050L, 220179L), table = "chartevents",
sub_var = "itemid")
)
)
),
dbp = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 200,
description = "diastolic blood pressure",
omopid = 4154790L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(8368L, 8441L, 8555L, 220051L, 220180L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicdiastolic",
class = "col_itm")
),
hirid = list(
list(ids = 120L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6643L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220051L, 220180L), table = "chartevents",
sub_var = "itemid")
)
)
),
map = list(
unit = c("mmHg", "mm Hg"),
min = 0,
max = 250,
description = "mean arterial pressure",
omopid = 4239021L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(52L, 443L, 456L, 6072L, 220052L, 220181L, 225312L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "systemicmean",
class = "col_itm"),
list(table = "vitalaperiodic", val_var = "noninvasivemean",
class = "col_itm")
),
hirid = list(
list(ids = c(110L, 610L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = 6642L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(220052L, 220181L, 225312L), table = "chartevents",
sub_var = "itemid")
)
)
),
resp = list(
unit = c("insp/min", "/min"),
min = 0,
max = 120,
description = "respiratory rate",
omopid = 4313591L,
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(618L, 619L, 220210L, 224688L, 224689L, 224690L),
table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "respiration",
class = "col_itm")
),
hirid = list(
list(ids = c(300L, 310L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(8874L, 12266L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = c(220210L, 224688L, 224689L, 224690L),
table = "chartevents", sub_var = "itemid")
)
)
),
o2sat = list(
unit = c("%", "% Sat."),
min = 50,
max = 100,
description = "oxygen saturation",
omopid = 40483579L,
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(646L, 220277L, 226253L, 50817L), table = "chartevents",
sub_var = "itemid")
),
eicu = list(
list(table = "vitalperiodic", val_var = "sao2", unit_val = "%",
class = "col_itm"),
list(ids = "O2 Sat (%)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(4000L, 8280L, 20000800L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6709L, 8903L), table = "numericitems",
sub_var = "itemid"),
list(ids = 12311L, table = "numericitems", sub_var = "itemid",
callback = "transform_fun(binary_op(`*`, 100))")
),
miiv = list(
list(ids = c(220277L, 226253L, 50817L), table = "chartevents",
sub_var = "itemid")
)
)
),
fio2 = list(
unit = "%",
min = 21,
max = 100,
description = "fraction of inspired oxygen",
omopid = 4353936L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = c(3420L, 223835L), table = "chartevents",
sub_var = "itemid"),
list(ids = 50816L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "FiO2", table = "respiratorycharting",
sub_var = "respchartvaluelabel",
callback = "transform_fun(percent_as_numeric)"),
list(ids = "FiO2", table = "lab", sub_var = "labname",
callback = "convert_unit(set_val(NA), '%', 'mm\\\\(hg\\\\)')")
),
hirid = list(
list(ids = 2010L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 12279L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 223835L, table = "chartevents", sub_var = "itemid"),
list(ids = 50816L, table = "labevents", sub_var = "itemid")
)
)
),
tco2 = list(
unit = "mEq/L",
min = 5,
max = 60,
description = "totcal CO2",
omopid = 4193415L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50804L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Total CO2", table = "lab", sub_var = "labname",
callback = "convert_unit(set_val(NA), 'mEq/L', 'lpm')")
),
miiv = list(
list(ids = 50804L, table = "labevents", sub_var = "itemid")
)
)
),
alt = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "alanine aminotransferase",
omopid = 4146380L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50861L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "ALT (SGPT)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002600L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6800L, 11978L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50861L, table = "labevents", sub_var = "itemid")
)
)
),
ast = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "aspartate aminotransferase",
omopid = 4263457L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50878L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "AST (SGOT)", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000330L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6806L, 11990L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50878L, table = "labevents", sub_var = "itemid")
)
)
),
phos = list(
unit = "mg/dL",
min = 0,
max = 40,
description = "phosphate",
omopid = 4017907L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50970L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "phosphate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002500L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6828L, 9935L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 3.097521), 'mg/dL')")
),
miiv = list(
list(ids = 50970L, table = "labevents", sub_var = "itemid")
)
)
),
bun = list(
unit = "mg/dL",
min = 0,
max = 200,
description = "blood urea nitrogen",
omopid = 4017361L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51006L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "BUN", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004100L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6850L, 9943L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.8), 'mg/dL')")
),
miiv = list(
list(ids = 51006L, table = "labevents", sub_var = "itemid")
)
)
),
ph = list(
min = 6.8,
max = 8,
description = "pH of blood",
omopid = 4097822L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50820L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "pH", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6848L, 12310L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50820L, table = "labevents", sub_var = "itemid")
)
)
),
bili = list(
unit = "mg/dL",
min = 0,
max = 100,
description = "total bilirubin",
omopid = 4118986L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50885L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "total bilirubin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004300L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6813L, 9945L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 50885L, table = "labevents", sub_var = "itemid")
)
)
),
inr_pt = list(
description = "prothrombin time/international normalized ratio",
omopid = 4306239L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51237L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PT - INR", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000567L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11893L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51237L, table = "labevents", sub_var = "itemid")
)
)
),
plt = list(
unit = c("K/uL", "G/l"),
min = 5,
max = 1200,
description = "platelet count",
omopid = 4267147L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51265L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "platelets x 1000", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000110L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6797L, 9964L, 10409L, 14252L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51265L, table = "labevents", sub_var = "itemid")
)
)
),
lact = list(
unit = "mmol/L",
min = 0,
max = 50,
description = "lactate",
omopid = 4191725L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50813L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "lactate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000524L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6837L, 9580L, 10053L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50813L, table = "labevents", sub_var = "itemid")
)
)
),
lymph = list(
unit = "%",
min = 0,
max = 100,
description = "lymphocytes",
omopid = 4254663L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51244L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-lymphs", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000480L, table = "observations", sub_var = "variableid",
callback = "blood_cell_ratio", class = "hrd_itm")
),
aumc = list(
list(ids = 11846L, table = "numericitems", sub_var = "itemid"),
list(ids = 14258L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51244L, table = "labevents", sub_var = "itemid")
)
)
),
bicar = list(
unit = c("mEq/L", "mmol/l"),
min = 5,
max = 50,
description = "bicarbonate",
omopid = 4194291L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50882L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "bicarbonate", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6810L, 9992L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50882L, table = "labevents", sub_var = "itemid")
)
)
),
crea = list(
unit = "mg/dL",
min = 0,
max = 15,
description = "creatinine",
omopid = 4013964L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50912L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "creatinine", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000600L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.011312), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6836L, 9941L, 14216L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.011309), 'mg/dL')")
),
miiv = list(
list(ids = 50912L, table = "labevents", sub_var = "itemid")
)
)
),
pt = list(
unit = "sec",
min = 0,
description = "prothrombine time",
omopid = 4245261L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51274L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PT", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 6789L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51274L, table = "labevents", sub_var = "itemid")
)
)
),
rdw = list(
unit = "%",
min = 0,
max = 100,
description = "erythrocyte distribution width",
omopid = 4281085L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51277L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "RDW", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 18952L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51277L, table = "labevents", sub_var = "itemid")
)
)
),
alp = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "alkaline phosphatase",
omopid = 4275206L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50863L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "alkaline phos.", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20002700L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6803L, 11984L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50863L, table = "labevents", sub_var = "itemid")
)
)
),
wbc = list(
unit = c("K/uL", "G/l"),
min = 0,
description = "white blood cell count",
omopid = 4298431L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51301L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "WBC x 1000", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000700L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6779L, 9965L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51301L, table = "labevents", sub_var = "itemid")
)
)
),
hgb = list(
unit = "g/dL",
min = 4,
max = 18,
description = "hemoglobin",
omopid = 4118981L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51222L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Hgb", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(24000548L, 24000836L, 20000900L), table = "observations",
sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL', 'g/l')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6778L, 9553L, 9960L, 10286L, 19703L),
table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 1.611344), 'g/dL')")
),
miiv = list(
list(ids = 51222L, table = "labevents", sub_var = "itemid")
)
)
),
hct = list(
unit = "%",
min = 15,
max = 60,
description = "hematocrit",
omopid = 4151358L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51221L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Hct", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = c(6777L, 11423L, 11545L), table = "numericitems",
sub_var = "itemid",
callback = "transform_fun(binary_op(`*`, 100))")
),
miiv = list(
list(ids = 51221L, table = "labevents", sub_var = "itemid")
)
)
),
pco2 = list(
unit = c("mmHg", "mm Hg"),
min = 10,
max = 150,
description = "CO2 partial pressure",
omopid = 4097882L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50818L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "paCO2", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20001200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6846L, 9990L, 21213L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50818L, table = "labevents", sub_var = "itemid")
)
)
),
po2 = list(
unit = c("mmHg", "mm Hg"),
min = 40,
max = 600,
description = "O2 partial pressure",
omopid = 4094581L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50821L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "paO2", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20000200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(7433L, 9996L, 21214L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50821L, table = "labevents", sub_var = "itemid")
)
)
),
mch = list(
unit = "pg",
min = 0,
description = "mean corpuscular hemoglobin",
omopid = 4182871L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51248L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCH", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000160L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11679L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.016113), 'pg')")
),
miiv = list(
list(ids = 51248L, table = "labevents", sub_var = "itemid")
)
)
),
mchc = list(
unit = "%",
min = 20,
max = 50,
description = "mean corpuscular hemoglobin concentration",
omopid = 4290193L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51249L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCHC", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000170L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.16114), '%')",
class = "hrd_itm")
),
aumc = list(
list(ids = 18666L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 1.611), '%')")
),
miiv = list(
list(ids = 51249L, table = "labevents", sub_var = "itemid")
)
)
),
mcv = list(
unit = "fL",
min = 50,
max = 150,
description = "mean corpuscular volume",
omopid = 4016239L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51250L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "MCV", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000150L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 9968L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51250L, table = "labevents", sub_var = "itemid")
)
)
),
ptt = list(
unit = "sec",
min = 0,
description = "partial thromboplastin time",
omopid = 4175016L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51275L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "PTT", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20004410L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 17982L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51275L, table = "labevents", sub_var = "itemid")
)
)
),
ca = list(
unit = "mg/dL",
min = 4,
max = 20,
description = "calcium",
omopid = 4216722L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50893L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "calcium", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`*`, 4), 'mg/dL', 'mmol/l')")
),
hirid = list(
list(ids = 20005100L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6817L, 9933L), table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 4.008), 'mg/dL')")
),
miiv = list(
list(ids = 50893L, table = "labevents", sub_var = "itemid")
)
)
),
cl = list(
unit = c("mEq/L", "mmol/l"),
min = 80,
max = 130,
description = "chloride",
omopid = 4188066L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50902L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "chloride", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(24000439L, 24000521L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = 9930L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50902L, table = "labevents", sub_var = "itemid")
)
)
),
mg = list(
unit = "mg/dL",
min = 0.5,
max = 5,
description = "magnesium",
omopid = 4243005L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50960L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "magnesium", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`/`, 1.215), 'mg/dL', 'mEq/L')"
)
),
hirid = list(
list(ids = 24000230L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6839L, 9952L), table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.431), 'mg/dL')")
),
miiv = list(
list(ids = 50960L, table = "labevents", sub_var = "itemid")
)
)
),
k = list(
unit = c("mEq/L", "mmol/l"),
min = 0,
max = 10,
description = "potassium",
omopid = 4207483L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50971L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "potassium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20000500L, 24000520L, 24000833L, 24000867L),
table = "observations", sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6835, 9556, 9927, 10285), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50971L, table = "labevents", sub_var = "itemid")
)
)
),
na = list(
unit = c("mEq/L", "mmol/l"),
min = 110,
max = 165,
description = "sodium",
omopid = 4208938L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50983L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "sodium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20000400L, 24000519L, 24000658L, 24000835L, 24000866L),
table = "observations", sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(6840, 9555, 9924, 10284), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50983L, table = "labevents", sub_var = "itemid")
)
)
),
basos = list(
unit = "%",
min = 0,
max = 50,
description = "basophils",
omopid = 4172647L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51146L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-basos", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 11710L, table = "numericitems", sub_var = "itemid"),
list(ids = 14256L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51146L, table = "labevents", sub_var = "itemid")
)
)
),
eos = list(
unit = "%",
min = 0,
max = 50,
description = "eosinophils",
omopid = 4216098L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51200L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-eos", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = 6773L, table = "numericitems", sub_var = "itemid"),
list(ids = 9967L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51200L, table = "labevents", sub_var = "itemid")
)
)
),
neut = list(
unit = "%",
min = 0,
max = 100,
description = "neutrophils",
omopid = 4148615L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51256L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-polys", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000550L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6786L, 11856L), table = "numericitems",
sub_var = "itemid"),
list(ids = 14254L, table = "numericitems", sub_var = "itemid",
callback = "blood_cell_ratio")
),
miiv = list(
list(ids = 51256L, table = "labevents", sub_var = "itemid")
)
)
),
glu = list(
unit = "mg/dL",
min = 0,
max = 1000,
description = "glucose",
omopid = 4144235L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "glucose", table = "lab", sub_var = "labname"),
list(ids = "bedside glucose", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = c(20005110L, 24000523L, 24000585L), table = "observations",
sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6833L, 9557L, 9947L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 18.016), 'mg/dL')")
),
miiv = list(
list(ids = c(50809L, 50931L), table = "labevents", sub_var = "itemid")
)
)
),
cai = list(
unit = "mmol/L",
min = 0.5,
max = 2,
description = "calcium ionized",
omopid = 46272910L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50808L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "ionized calcium", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000522L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6815L, 8915L, 9560L, 9561L, 10267L),
table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50808L, table = "labevents", sub_var = "itemid")
)
)
),
crp = list(
unit = "mg/L",
min = 0,
description = "C-reactive protein",
omopid = 4208414L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50889L, table = "labevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
),
eicu = list(
list(ids = "CRP", table = "lab", sub_var = "labname",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
),
hirid = list(
list(ids = 20002200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6825L, 10079L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50889L, table = "labevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 10), 'mg/L', 'mg/dl')")
)
)
),
esr = list(
unit = c("mm/hr", "mm/1h"),
min = 0,
max = 200,
description = "erythrocyte sedimentation rate",
omopid = 4212065L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51288L, table = "labevents", sub_var = "itemid")
),
hirid = list(
list(ids = 24000668L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6808L, 11902L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51288L, table = "labevents", sub_var = "itemid")
)
)
),
hbco = list(
description = "carboxyhemoglobin",
omopid = 4056787L,
category = "blood gas",
sources = list(
eicu = list(
list(ids = "Carboxyhemoglobin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000526L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11690L, table = "numericitems", sub_var = "itemid")
)
)
),
methb = list(
unit = "%",
min = 0,
max = 100,
description = "methemoglobin",
omopid = 4204561L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50814L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Methemoglobin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000549L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 11692L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50814L, table = "labevents", sub_var = "itemid")
)
)
),
tnt = list(
unit = "ng/mL",
min = 0,
description = "troponin t",
omopid = 4005525L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51003L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "troponin - T", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000806L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`/`, 1000), 'ng/mL')",
class = "hrd_itm")
),
aumc = list(
list(ids = 10407L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51003L, table = "labevents", sub_var = "itemid")
)
)
),
alb = list(
unit = "g/dL",
min = 0,
max = 6,
description = "albumin",
omopid = 4017497L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50862L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "albumin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000605L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6801L, 9937L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.1), 'g/dL')")
),
miiv = list(
list(ids = 50862L, table = "labevents", sub_var = "itemid")
)
)
),
fgn = list(
unit = "mg/dL",
min = 0,
max = 1500,
description = "fibrinogen",
omopid = 4094436L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51214L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "fibrinogen", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000536L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 100), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6776L, 9989L, 10175L), table = "numericitems",
sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 51214L, table = "labevents", sub_var = "itemid")
)
)
),
be = list(
unit = c("mEq/L", "mmol/l"),
min = -25,
max = 25,
description = "base excess",
omopid = 4284393L,
category = "blood gas",
sources = list(
mimic = list(
list(ids = 50802L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Base Excess", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 20001300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6807L, 9994L), table = "numericitems",
sub_var = "itemid", dir_var = "tag", callback = "aumc_bxs")
),
miiv = list(
list(ids = 50802L, table = "labevents", sub_var = "itemid")
)
)
),
rbc = list(
unit = "m/uL",
min = 0,
max = 20,
description = "red blood cell count",
omopid = 4030871L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51279L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "RBC", table = "lab", sub_var = "labname")
),
aumc = list(
list(ids = c(6774L, 9962L), table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 51279L, table = "labevents", sub_var = "itemid")
)
)
),
ck = list(
unit = c("IU/L", "U/l"),
min = 0,
description = "creatine kinase",
omopid = 4265595L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50910L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "CPK", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000210L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6822L, 11998L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50910L, table = "labevents", sub_var = "itemid")
)
)
),
ckmb = list(
unit = "ng/mL",
min = 0,
description = "creatine kinase MB",
omopid = 4017058L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50911L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "CPK-MB", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000220L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6824L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = 50911L, table = "labevents", sub_var = "itemid")
)
)
),
egcs = list(
min = 1,
max = 4,
description = "GCS eye",
omopid = 4084277L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(184L, 220739L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Eyes", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000300L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6732L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Reactie op pijnprikkel` = 2,
`Reactie op verbale prikkel` = 3,
`Spontane reactie` = 4)
)")),
list(ids = 13077L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Niet` = 1,
`Op pijn` = 2,
`Op aanspreken` = 3,
`Spontaan` = 4)
)"))
),
miiv = list(
list(ids = 220739L, table = "chartevents", sub_var = "itemid")
)
)
),
vgcs = list(
min = 1,
max = 5,
description = "GCS verbal",
omopid = 4084912L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(723L, 223900L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Verbal", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000100L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6735L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie (geen zichtbare poging tot praten)` = 1,
`Onbegrijpelijke geluiden` = 2,
`Onduidelijke woorden (pogingen tot communicatie,
maar onduidelijk)` = 3,
`Verwarde conversatie` = 4,
`Helder en adequaat (communicatie mogelijk)` = 5)
)")),
list(ids = 13066L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen geluid` = 1,
`Onverstaanbare woorden` = 2,
`Onjuiste woorden` = 3,
`Verwarde taal` = 4,
`Georiënteerd` = 5)
)"))
),
miiv = list(
list(ids = 223900L, table = "chartevents", sub_var = "itemid")
)
)
),
mgcs = list(
min = 1,
max = 6,
description = "GCS motor",
omopid = 4083352L,
category = "neurological",
sources = list(
mimic = list(
list(ids = c(454L, 223901L), table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Motor", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 10000200L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = 6734L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Strekken` = 2,
`Decortatie reflex (abnormaal buigen)` = 3,
`Spastische reactie (terugtrekken)` = 4,
`Localiseert pijn` = 5,
`Volgt verbale commando's op` = 6)
)")),
list(ids = 13072L, table = "listitems", sub_var = "itemid",
callback = strip_ws("apply_map(
c(`Geen reactie` = 1,
`Strekken op pijn` = 2,
`Abnormaal buigen bij pijn` = 3,
`Terugtrekken bij pijn` = 4,
`Localiseren pijn` = 5,
`Voert opdrachten uit` = 6)
)"))
),
miiv = list(
list(ids = 223901L, table = "chartevents", sub_var = "itemid")
)
)
),
tgcs = list(
min = 3,
max = 15,
description = "GCS total",
omopid = 4093836L,
category = "neurological",
sources = list(
mimic = list(
list(ids = 198L, table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "GCS Total", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
)
)
),
urine = list(
unit = "mL",
min = 0,
max = 2000,
aggregate = "sum",
description = "urine output",
omopid = 4264378L,
category = "output",
sources = list(
mimic = list(
list(ids = c(40055L, 40056L, 40057L, 40065L, 40069L, 40085L,
40086L, 40094L, 40096L, 40405L, 40428L, 40473L,
40715L, 43175L, 226557L, 226558L, 226559L, 226560L,
226561L, 226563L, 226564L, 226565L, 226566L, 226567L,
226584L, 227510L),
table = "outputevents", sub_var = "itemid")
),
eicu = list(
list(ids = c("Urine", "URINE CATHETER"), table = "intakeoutput",
sub_var = "celllabel"),
list(regex = c("catheter.+output|output.+catheter"),
table = "intakeoutput", sub_var = "celllabel", class = "rgx_itm")
),
hirid = list(
list(ids = 30005110L, table = "observations", sub_var = "variableid",
callback = "hirid_urine", class = "hrd_itm")
),
aumc = list(
list(ids = 8794L, table = "numericitems", sub_var = "itemid")
),
miiv = list(
list(ids = c(226557L, 226558L, 226559L, 226560L, 226561L, 226563L,
226564L, 226565L, 226566L, 226567L, 226584L, 227510L),
table = "outputevents", sub_var = "itemid")
)
)
),
dobu_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 50,
description = "dobutamine rate",
omopid = 1337720L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30042L, 30306L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^dobu.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 2000)", class = "rgx_itm")
),
hirid = list(
list(ids = 426L, table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 7178L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221653L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
dobu_dur = list(
description = "dobutamine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30042L, 30306L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221653L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^dobu", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = 426L, table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_duration")
),
aumc = list(
list(ids = 7178L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221653L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
dobu60 = list(
concepts = c("dobu_rate", "dobu_dur"),
description = "dobutamine administration for min 1h",
category = "medications",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
dopa_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 50,
description = "dopamine rate",
omopid = 1337860L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^dopa.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 1600)", class = "rgx_itm")
),
aumc = list(
list(ids = 7179L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221662L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
dopa_dur = list(
description = "dopamine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30043L, 30125L, 30307L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221662L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^dopa", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
aumc = list(
list(ids = 7179L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221662L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
dopa60 = list(
concepts = c("dopa_rate", "dopa_dur"),
description = "dopamine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
norepi_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 3,
description = "norepinephrine rate",
omopid = 1321341,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30047L, 30120L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^norepi.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 32)", class = "rgx_itm")
),
hirid = list(
list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 7229L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221906L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
norepi_dur = list(
description = "norepinephrine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30047L, 30120L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221906L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^norepi", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = c(1000462L, 1000656L, 1000657L, 1000658L), table = "pharma",
sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_duration")
),
aumc = list(
list(ids = 7229L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221906L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
norepi60 = list(
concepts = c("norepi_rate", "norepi_dur"),
description = "norepinephrine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
epi_rate = list(
unit = c("mcg/kg/min", "mcgkgmin"),
min = 0,
max = 1.5,
description = "epinephrine rate",
omopid = 1343916L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_rate_cv"),
list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^epi( |n).*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 40)", class = "rgx_itm")
),
hirid = list(
list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate_kg")
),
aumc = list(
list(ids = 6818L, table = "drugitems", sub_var = "itemid",
rel_weight = "doserateperkg", rate_uom = "doserateunit",
stop_var = "stop", callback = "aumc_rate_kg")
),
miiv = list(
list(ids = 221289L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
epi_dur = list(
description = "epinephrine duration",
category = "medications",
aggregate = "max",
sources = list(
mimic = list(
list(ids = c(30044L, 30119L, 30309L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid",
callback = "mimic_dur_incv"),
list(ids = 221289L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
),
eicu = list(
list(regex = "^epi( |n)", table = "infusiondrug", sub_var = "drugname",
callback = "eicu_duration(gap_length = hours(5L))",
class = "rgx_itm")
),
hirid = list(
list(ids = c(71L, 1000649L, 1000650L, 1000655L, 1000750L),
table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
callback = "hirid_duration")
),
aumc = list(
list(ids = 6818L, table = "drugitems", sub_var = "itemid",
stop_var = "stop", grp_var = "orderid", callback = "aumc_dur")
),
miiv = list(
list(ids = 221289L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", grp_var = "linkorderid",
callback = "mimic_dur_inmv")
)
)
),
epi60 = list(
concepts = c("epi_rate", "epi_dur"),
description = "epinephrine administration for min 1h",
category = "outcome",
interval = "00:01:00",
callback = "vaso60",
class = "rec_cncpt"
),
vent_start = list(
class = "lgl_cncpt",
description = "ventilation start",
category = "respiratory",
sources = list(
mimic = list(
list(
ids = c(
1L, 60L, 218L, 221L, 223L, 436L, 437L,
444L, 445L, 448L, 449L, 450L, 459L, 501L,
502L, 503L, 505L, 506L, 535L, 543L, 639L,
654L, 667L, 668L, 669L, 670L, 671L, 672L,
681L, 682L, 683L, 684L, 686L, 1211L, 1340L,
1486L, 1600L, 1655L, 2000L, 3459L, 5865L, 5866L,
220339L, 223848L, 223849L, 224419L, 224684L, 224685L, 224686L,
224687L, 224695L, 224696L, 224697L, 224700L, 224701L, 224702L,
224703L, 224704L, 224705L, 224706L, 224707L, 224709L, 224738L,
224746L, 224747L, 224750L, 226873L, 227187L),
table = "chartevents", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
),
eicu = list(
list(table = "respiratorycare", val_var = "ventstartoffset",
callback = "vent_flag", class = "col_itm"),
list(table = "respiratorycare", val_var = "priorventstartoffset",
callback = "vent_flag", class = "col_itm"),
list(ids = c("Start", "Continued", "respFlowPtVentData"),
table = "respiratorycharting", sub_var = "respcharttypecat",
callback = "transform_fun(set_val(TRUE))")
)
)
),
vent_end = list(
class = "lgl_cncpt",
description = "ventilation end",
category = "respiratory",
sources = list(
mimic = list(
list(ids = c(225468L, 225477L, 227194L), table = "procedureevents_mv",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))"),
list(ids = c(467L, 469L, 226732L), table = "chartevents",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
),
eicu = list(
list(table = "respiratorycare", val_var = "ventendoffset",
callback = "vent_flag", class = "col_itm"),
list(table = "respiratorycare", val_var = "priorventendoffset",
callback = "vent_flag", class = "col_itm"),
list(ids = c("off", "Off", "Suspended"), table = "respiratorycharting",
sub_var = "respchartvalue", val_var = "respchartvaluelabel",
callback = "transform_fun(set_val(TRUE))")
)
)
),
mech_vent = list(
class = "fct_cncpt",
target = "win_tbl",
levels = c("invasive", "noninvasive"),
description = "mechanical ventilation windows",
omopid = 4230167L,
category = "respiratory",
sources = list(
aumc = list(
list(ids = c(9328L, 10740L, 12635L), table = "processitems",
sub_var = "itemid", dur_var = "stop",
callback = "apply_map(c(`Beademen` = 'invasive',
`Beademen non-invasief` = 'noninvasive',
`Tracheostoma` = 'invasive'))"
)
),
miiv = list(
list(ids = c(225792L, 225794L), table = "procedureevents",
sub_var = "itemid", dur_var = "endtime",
callback = "apply_map(c(`225792` = 'invasive',
`225794` = 'noninvasive'),
var = 'sub_var')")
),
hirid = list(
list(ids = 15001552L, table = "observations", sub_var = "variableid",
target = "ts_tbl", interval = "00:01:00", class = "hrd_itm",
callback = "combine_callbacks(hirid_vent,
apply_map(c(`1` = 'invasive',
`2` = 'invasive',
`3` = 'noninvasive',
`4` = 'noninvasive',
`5` = 'noninvasive',
`6` = 'noninvasive')))")
)
)
),
ett_gcs = list(
class = "lgl_cncpt",
description = "tracheostomy",
omopid = 4097216L,
category = "respiratory",
target = "win_tbl",
sources = list(
mimic = list(
list(ids = c("1.0 ET/Trach", "No Response-ETT"), table = "chartevents",
sub_var = "value", target = "ts_tbl",
callback = "combine_callbacks(
transform_fun(set_val(TRUE)),
ts_to_win_tbl(mins(1L))
)")
),
hirid = list(
list(class = "fun_itm", callback = "combine_callbacks(
fwd_concept('mech_vent'),
transform_fun(comp_na(`==`, 'invasive'))
)")
),
aumc = list(
list(ids = 6735L, table = "listitems", sub_var = "itemid",
target = "ts_tbl", callback = "combine_callbacks(
transform_fun(comp_na(`==`, 'Geïntubeerd')),
ts_to_win_tbl(mins(1L))
)")
),
miiv = list(
list(ids = "No Response-ETT", table = "chartevents", sub_var = "value",
target = "ts_tbl", callback = "combine_callbacks(
transform_fun(set_val(TRUE)),
ts_to_win_tbl(mins(1L))
)")
),
eicu = list(
list(class = "fun_itm", callback = "combine_callbacks(
fwd_concept('rass'),
transform_fun(comp_na(`<=`, -3)),
ts_to_win_tbl(mins(360L))
)")
)
)
),
rass = list(
min = -5,
max = 4,
description = "Richmond agitation sedation scale",
omopid = 36684829L,
category = "neurological",
sources = list(
mimic = list(
list(ids = 228096L, table = "chartevents", sub_var = "itemid")
),
eicu = list(
list(ids = "Sedation Score", table = "nursecharting",
sub_var = "nursingchartcelltypevalname")
),
hirid = list(
list(ids = 15001565L, table = "observations", sub_var = "variableid",
callback = "transform_fun(floor)", class = "hrd_itm")
),
aumc = list(
list(ids = 14444L, sub_var = "itemid", table = "listitems",
callback = "transform_fun(aumc_rass)")
),
miiv = list(
list(ids = 228096L, table = "chartevents", sub_var = "itemid")
)
)
),
abx = list(
class = "lgl_cncpt",
description = "antibiotics",
omopid = 4085730L,
category = "medications",
sources = list(
mimic = list(
list(regex = paste(
"aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
"flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
"rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
"gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
"peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
"clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
"tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
"uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
"ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
table = "prescriptions", sub_var = "drug", interval = "00:01:00",
callback = "mimic_abx_presc", class = "rgx_itm"
),
list(ids = c(
225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
227691L, 228003L), table = "inputevents_mv", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
),
eicu = list(
list(regex = paste(
"bactrim", "cipro", "flagyl", "metronidazole", "zithromax", "zosyn",
"(((amika", "cleo", "ofloxa)", "(azithro", "clinda", "tobra",
"vanco)my)c", "(ampi", "oxa", "peni", "pipera)cill", "cefazol",
"levaqu", "rifamp)in", sep = "|"), table = "infusiondrug",
sub_var = "drugname", callback = "transform_fun(set_val(TRUE))",
class = "rgx_itm"
),
list(regex = paste(
"cipro", "flagyl", "maxipime", "metronidazole", "tazobactam",
"zosyn", "cef(azolin", "epime)", "(((azithro", "clinda", "vanco)my",
"ofloxa", "vanco)c", "levaqu", "piperacill", "roceph)in", sep = "|"),
table = "medication", sub_var = "drugname",
callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
)
),
hirid = list(
list(ids = c(
163L, 176L, 181L, 186L, 189L, 300L, 326L,
331L, 351L, 405L, 1000234L, 1000272L, 1000273L, 1000274L,
1000284L, 1000299L, 1000300L, 1000302L, 1000304L, 1000305L, 1000306L,
1000315L, 1000317L, 1000318L, 1000320L, 1000321L, 1000322L, 1000335L,
1000348L, 1000352L, 1000363L, 1000365L, 1000390L, 1000407L, 1000408L,
1000424L, 1000425L, 1000426L, 1000437L, 1000483L, 1000507L, 1000508L,
1000518L, 1000519L, 1000549L, 1000601L, 1000648L, 1000666L, 1000670L,
1000671L, 1000760L, 1000781L, 1000791L, 1000797L, 1000812L, 1000825L,
1000829L, 1000830L, 1000837L, 1000838L, 1000854L, 1000855L, 1000893L,
1000894L, 1001005L, 1001068L, 1001075L, 1001079L, 1001084L, 1001086L,
1001095L, 1001096L, 1001097L, 1001098L, 1001168L, 1001169L, 1001170L,
1001171L, 1001173L, 1001193L, 1001198L), table = "pharma",
sub_var = "pharmaid", callback = "transform_fun(set_val(TRUE))")
),
aumc = list(
list(ids = c(
2L, 13L, 19L, 24L, 28L, 29L, 57L, 59L,
82L, 103L, 240L, 247L, 333L, 1133L, 1199L, 1300L,
1371L, 1795L, 2284L, 2834L, 3237L, 3741L, 5576L, 6834L,
6847L, 6871L, 6919L, 6948L, 6953L, 6958L, 7044L, 7064L,
7185L, 7187L, 7208L, 7227L, 7235L, 8064L, 8394L, 8942L,
9029L, 9030L, 9052L, 9070L, 9117L, 9128L, 9133L, 9142L,
9151L, 9152L, 12262L, 12389L, 12398L, 12956L, 12997L, 13057L,
13094L, 13102L, 15591L, 18860L, 19137L, 19773L, 20563L, 23166L,
24241L, 25776L, 27617L, 29321L), table = "drugitems",
sub_var = "itemid", callback = "transform_fun(set_val(TRUE))")
),
miiv = list(
list(regex = paste(
"aztreonam", "bactrim", "cephalexin", "chloramphenicol", "cipro",
"flagyl", "metronidazole", "nitrofurantoin", "tazobactam",
"rifampin", "sulfadiazine", "timentin", "trimethoprim", "(amika",
"gentami", "vanco)cin", "(amoxi", "ampi", "dicloxa", "naf", "oxa",
"peni", "pipera)cillin", "(azithro", "clarithro", "erythro",
"clinda", "strepto", "tobra", "vanco)mycin", "cef(azolin",
"tazidime", "adroxil", "epime", "otetan", "otaxime", "podoxime",
"uroxime)", "(doxy", "mino", "tetra)cycline", "(levofl", "moxifl",
"ofl)oxacin", "macro(bid", "dantin)", "(una", "zo)syn", sep = "|"),
table = "prescriptions", sub_var = "drug",
callback = "transform_fun(set_val(TRUE))", class = "rgx_itm"
),
list(ids = c(
225798L, 225837L, 225838L, 225840L, 225842L, 225843L, 225844L,
225845L, 225847L, 225848L, 225850L, 225851L, 225853L, 225855L,
225857L, 225859L, 225860L, 225862L, 225863L, 225865L, 225866L,
225868L, 225869L, 225871L, 225873L, 225875L, 225876L, 225877L,
225879L, 225881L, 225882L, 225883L, 225884L, 225885L, 225886L,
225888L, 225889L, 225890L, 225892L, 225893L, 225895L, 225896L,
225897L, 225898L, 225899L, 225900L, 225902L, 225903L, 225905L,
227691L, 228003L), table = "inputevents", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))"
)
)
)
),
samp = list(
class = "lgl_cncpt",
category = "microbiology",
description = "body fluid sampling",
omopid = 4133843L,
sources = list(
mimic = list(
list(table = "microbiologyevents", val_var = "org_itemid",
callback = "mimic_sampling", aux_time = "charttime",
class = "col_itm")
),
eicu = list(
list(table = "microlab", val_var = "organism",
callback = "transform_fun(comp_na(`!=`, 'no growth'))",
class = "col_itm")
),
aumc = list(
list(ids = c(
8097L, 8418L, 8588L, 9189L, 9190L, 9191L, 9192L, 9193L, 9194L,
9195L, 9197L, 9198L, 9200L, 9202L, 9203L, 9204L, 9205L, 13024L,
19663L, 19664L), table = "procedureorderitems", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))")
),
miiv = list(
list(table = "microbiologyevents", val_var = "org_itemid",
callback = "mimic_sampling", aux_time = "charttime",
class = "col_itm")
)
)
),
tri = list(
unit = "ng/mL",
min = 0,
description = "troponin I",
omopid = 4007805L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 51002L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "troponin - I", table = "lab", sub_var = "labname")
),
miiv = list(
list(ids = 51002L, table = "labevents", sub_var = "itemid")
)
)
),
bili_dir = list(
unit = "mg/dL",
min = 0,
max = 50,
description = "bilirubin direct",
omopid = 4216632L,
category = "chemistry",
sources = list(
mimic = list(
list(ids = 50883L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "direct bilirubin", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000560L, table = "observations", sub_var = "variableid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')",
class = "hrd_itm")
),
aumc = list(
list(ids = 6812L, table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 0.058467), 'mg/dL')")
),
miiv = list(
list(ids = 50883L, table = "labevents", sub_var = "itemid")
)
)
),
temp = list(
unit = c("C", "°C"),
min = 32,
max = 42,
description = "temperature",
omopid = 4302666L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(676L, 677L, 223762L), table = "chartevents",
sub_var = "itemid"),
list(ids = c(678L, 679L, 223761L, 224027L), table = "chartevents",
sub_var = "itemid",
callback = "convert_unit(fahr_to_cels, 'C', 'f')")
),
eicu = list(
list(table = "vitalperiodic", val_var = "temperature",
class = "col_itm")
),
hirid = list(
list(ids = c(410L, 400L, 7100L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(ids = c(8658L, 13952L, 16110L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 223762L, table = "chartevents", sub_var = "itemid"),
list(ids = c(223761L, 224027L), table = "chartevents",
sub_var = "itemid",
callback = "convert_unit(fahr_to_cels, 'C', 'f')")
)
)
),
etco2 = list(
unit = c("mmHg", "mm Hg"),
min = 10,
max = 60,
description = "endtidal CO2",
omopid = 4353940L,
category = "vitals",
sources = list(
mimic = list(
list(ids = c(1817L, 228640L), table = "chartevents",
sub_var = "itemid")
),
hirid = list(
list(ids = c(2200L, 8290L, 30010009L), table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(
ids = c(6707L, 8884L, 8885L, 9658L, 12805L, 12356L),
table = "numericitems", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 7.6), 'mmHg', 'None|Geen')"
)
),
miiv = list(
list(ids = 228640L, table = "chartevents", sub_var = "itemid")
)
)
),
ins = list(
unit = "units/hr",
min = 0,
description = "insulin",
omopid = 42537007L,
category = "medications",
sources = list(
mimic = list(
list(ids = c(30045L, 30100L), table = "inputevents_cv",
sub_var = "itemid"),
list(ids = c(223258L, 223260L), table = "inputevents_mv",
sub_var = "itemid", val_var = "amount", end_var = "endtime",
callback = "distribute_amount")
),
eicu = list(
list(regex = "^insulin (250.+)?\\(((ml|units)/hr)?\\)$",
table = "infusiondrug", sub_var = "drugname", class = "rgx_itm")
),
hirid = list(
list(ids = c(15L, 1000724L), table = "pharma", sub_var = "pharmaid",
callback = "aggregate_fun('sum', 'units')")
),
aumc = list(
list(ids = c(7624L, 9014L, 19129L), sub_var = "itemid",
table = "drugitems")
),
miiv = list(
list(ids = c(223258L, 223260L), table = "inputevents",
sub_var = "itemid", val_var = "amount", end_var = "endtime",
callback = "distribute_amount")
)
)
),
sex = list(
target = "id_tbl",
levels = c("Female", "Male"),
class = "fct_cncpt",
description = "patient sex",
omopid = 37116947L,
category = "demographics",
sources = list(
mimic = list(
list(table = "patients", val_var = "gender",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
),
eicu = list(
list(table = "patient", val_var = "gender", class = "col_itm")
),
hirid = list(
list(table = "general", val_var = "sex",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
),
aumc = list(
list(val_var = "gender", table = "admissions",
callback = strip_ws("apply_map(c(Vrouw = 'Female',
Man = 'Male'))"),
class = "col_itm")
),
miiv = list(
list(table = "patients", val_var = "gender",
callback = "apply_map(c(M = 'Male', F = 'Female'))",
class = "col_itm")
)
)
),
age = list(
unit = "years",
min = 0,
max = 100,
target = "id_tbl",
description = "patient age",
omopid = 4314456L,
category = "demographics",
sources = list(
mimic = list(
list(table = "patients", val_var = "dob",
callback = "transform_fun(mimic_age)", class = "col_itm")
),
eicu = list(
list(table = "patient", val_var = "age",
callback = "transform_fun(eicu_age)", class = "col_itm")
),
hirid = list(
list(table = "general", val_var = "age", class = "col_itm")
),
aumc = list(
list(val_var = "agegroup", table = "admissions",
callback = strip_ws("apply_map(c(`18-39` = 30,
`40-49` = 45,
`50-59` = 55,
`60-69` = 65,
`70-79` = 75,
`80+` = 90))"),
class = "col_itm")
),
miiv = list(
list(table = "patients", val_var = "anchor_age", class = "col_itm")
)
)
),
weight = list(
unit = "kg",
min = 1,
max = 500,
target = "id_tbl",
description = "patient weight",
omopid = 4099154L,
category = "demographics",
sources = list(
mimic = list(
list(ids = c(762L, 4183L, 226512L), table = "chartevents",
sub_var = "itemid")
),
eicu = list(
list(table = "patient", val_var = "admissionweight",
class = "col_itm")
),
hirid = list(
list(ids = 10000400L, table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(val_var = "weightgroup", table = "admissions",
callback = strip_ws("apply_map(c(`59-` = 50,
`60-69` = 65,
`70-79` = 75,
`80-89` = 85,
`90-99` = 95,
`100-109` = 105,
`110+` = 120))"),
class = "col_itm")
),
miiv = list(
list(ids = 226512L, table = "chartevents", sub_var = "itemid")
)
)
),
height = list(
unit = "cm",
min = 10,
max = 230,
target = "id_tbl",
description = "patient height",
omopid = 607590L,
category = "demographics",
sources = list(
mimic = list(
list(ids = c(920L, 1394L, 3485L, 4187L, 4188L, 3486L, 226707L),
table = "chartevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
),
eicu = list(
list(table = "patient", val_var = "admissionheight",
class = "col_itm")
),
hirid = list(
list(ids = 10000450L, table = "observations",
sub_var = "variableid", class = "hrd_itm")
),
aumc = list(
list(val_var = "heightgroup", table = "admissions",
callback = strip_ws("apply_map(c(`159-` = 150,
`160-169` = 165,
`170-179` = 175,
`180-189` = 185,
`190+` = 200))"),
class = "col_itm")
),
miiv = list(
list(ids = 226707L, table = "chartevents", sub_var = "itemid",
callback = "convert_unit(binary_op(`*`, 2.54), 'cm', '^in')")
)
)
),
death = list(
class = "lgl_cncpt",
description = "in hospital mortality",
omopid = 4306655L,
category = "outcome",
sources = list(
mimic = list(
list(table = "admissions", index_var = "deathtime",
val_var = "hospital_expire_flag",
callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
),
eicu = list(
list(table = "patient", index_var = "unitdischargeoffset",
val_var = "hospitaldischargestatus",
callback = "transform_fun(comp_na(`==`, 'Expired'))",
class = "col_itm")
),
hirid = list(
list(ids = c(110L, 200L), table = "observations",
sub_var = "variableid", callback = "hirid_death",
class = "hrd_itm")
),
aumc = list(
list(table = "admissions", index_var = "dateofdeath",
val_var = "dischargedat", callback = "aumc_death",
class = "col_itm")
),
miiv = list(
list(table = "admissions", index_var = "deathtime",
val_var = "hospital_expire_flag",
callback = "transform_fun(comp_na(`==`, 1L))", class = "col_itm")
)
)
),
adm = list(
target = "id_tbl",
levels = c("med", "surg", "other"),
class = "fct_cncpt",
description = "patient admission type",
category = "demographics",
sources = list(
mimic = list(
list(table = "services", val_var = "curr_service",
callback = "apply_map(
c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
)",
class = "col_itm"
)
),
eicu = list(
list(table = "admissiondx", val_var = "admitdxpath",
callback = "eicu_adx", class = "col_itm")
),
aumc = list(
list(val_var = "specialty", table = "admissions",
callback = strip_ws("apply_map(
c(Cardiochirurgie = 'surg',
Cardiologie = 'med',
ders = 'other',
Gynaecologie = 'other',
`Heelkunde Gastro-enterologie` = 'surg',
`Heelkunde Longen/Oncologie` = 'surg',
`Heelkunde Oncologie` = 'surg',
Hematologie = 'med',
`Intensive Care Volwassenen` = 'other',
Inwendig = 'med',
`Keel, Neus & Oorarts` = 'surg',
Longziekte = 'med',
`Maag-,Darm-,Leverziekten` = 'med',
Mondheelkunde = 'surg',
Nefrologie = 'med',
Neurochirurgie = 'surg',
Neurologie = 'med',
Obstetrie = 'other',
`Oncologie Inwendig` = 'med',
Oogheelkunde = 'surg',
Orthopedie = 'surg',
`Plastische chirurgie` = 'surg',
Reumatologie = 'med',
Traumatologie = 'surg',
Urologie = 'surg',
Vaatchirurgie = 'surg',
Verloskunde = 'other'))"),
class = "col_itm")
),
miiv = list(
list(table = "services", val_var = "curr_service",
callback = "apply_map(
c(MED = 'med', SURG = 'surg', CMED = 'med', CSURG = 'surg',
VSURG = 'surg', NSURG = 'surg', NB = 'other', NMED = 'med',
ORTHO = 'surg', TRAUM = 'surg', OMED = 'med', GU = 'other',
NBB = 'other', TSURG = 'surg', GYN = 'other', PSURG = 'surg',
OBS = 'other', ENT = 'surg', DENT = 'surg', PSYCH = 'other')
)",
class = "col_itm"
)
)
)
),
los_icu = list(
unit = "days",
min = 0,
target = "id_tbl",
description = "ICU length of stay",
category = "outcome",
sources = list(
mimic = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
eicu = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
hirid = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
aumc = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
),
miiv = list(
list(callback = "los_callback", win_type = "icustay",
class = "fun_itm")
)
)
),
los_hosp = list(
unit = "days",
min = 0,
target = "id_tbl",
description = "hospital length of stay",
omopid = 462369952L,
category = "outcome",
sources = list(
mimic = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
),
eicu = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
),
miiv = list(
list(callback = "los_callback", win_type = "hadm", class = "fun_itm")
)
)
),
pafi = list(
concepts = c("po2", "fio2"),
description = "Horowitz index",
omopid = 4233883L,
category = "respiratory",
aggregate = c("min", "max"),
callback = "pafi",
class = "rec_cncpt"
),
safi = list(
concepts = c("o2sat", "fio2"),
description = "SaO2/FiO2",
category = "respiratory",
aggregate = c("min", "max"),
callback = "safi",
class = "rec_cncpt"
),
vent_ind = list(
concepts = c("vent_start", "vent_end", "mech_vent"),
description = "ventilation durations",
omopid = 4230167L,
category = "respiratory",
interval = "00:01:00",
callback = "vent_ind",
target = "win_tbl",
class = "rec_cncpt"
),
vaso_ind = list(
concepts = c("dopa_dur", "norepi_dur", "dobu_dur", "epi_dur"),
description = "vasopressor indicator",
omopid = 3655896L,
category = "medications",
callback = "vaso_ind",
class = "rec_cncpt"
),
gcs = list(
concepts = c("egcs", "mgcs", "vgcs", "tgcs", "ett_gcs"),
description = "Glasgow coma scale (non-sedated)",
omopid = 4093836L,
category = "neurological",
aggregate = c("min", "min", "min", "min", "any"),
callback = "gcs",
class = "rec_cncpt"
),
urine24 = list(
concepts = "urine",
description = "urine output per 24h",
omopid = 4191836L,
category = "output",
callback = "urine24",
class = "rec_cncpt"
),
sofa_resp = list(
concepts = c("pafi", "vent_ind"),
description = "SOFA respiratory component",
omopid = 1616907L,
category = "outcome",
callback = "sofa_resp",
class = "rec_cncpt"
),
sofa_coag = list(
concepts = "plt",
description = "SOFA coagulation component",
omopid = 1616896L,
category = "outcome",
aggregate = "min",
callback = "sofa_coag",
class = "rec_cncpt"
),
sofa_liver = list(
concepts = "bili",
description = "SOFA liver component",
omopid = 1617043L,
category = "outcome",
aggregate = "max",
callback = "sofa_liver",
class = "rec_cncpt"
),
sofa_cardio = list(
concepts = c("map", "dopa60", "norepi60", "dobu60", "epi60"),
description = "SOFA cardiovascular component",
omopid = 1617534L,
category = "outcome",
aggregate = c("min", "max", "max", "max", "max"),
callback = "sofa_cardio",
class = "rec_cncpt"
),
sofa_cns = list(
concepts = "gcs",
description = "SOFA central nervous system component",
omopid = 1616439L,
category = "outcome",
callback = "sofa_cns",
class = "rec_cncpt"
),
sofa_renal = list(
concepts = c("crea", "urine24"),
description = "SOFA renal component",
omopid = 1616355L,
category = "outcome",
aggregate = c("max", NA),
callback = "sofa_renal",
class = "rec_cncpt"
),
sofa = list(
concepts = c("sofa_resp", "sofa_coag", "sofa_liver", "sofa_cardio",
"sofa_cns", "sofa_renal"),
description = "sequential organ failure assessment score",
omopid = 1616852L,
category = "outcome",
callback = "sofa_score",
class = "rec_cncpt"
),
qsofa = list(
concepts = c("gcs", "sbp", "resp"),
description = "quick SOFA score",
omopid = 1616732L,
category = "outcome",
callback = "qsofa_score",
class = "rec_cncpt"
),
susp_inf = list(
concepts = c("abx", "samp"),
description = "suspected infection",
omopid = 43021378L,
category = "outcome",
aggregate = lapply(list("sum", FALSE), list),
callback = "susp_inf",
class = "rec_cncpt"
),
sep3 = list(
concepts = c("sofa", "susp_inf"),
description = "sepsis-3 criterion",
omopid = 132797L,
category = "outcome",
callback = "sep3",
keep_components = c(FALSE, TRUE),
class = "rec_cncpt"
),
bnd = list(
unit = "%",
description = "band form neutrophils",
omopid = 4100147L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 51144L, table = "labevents", sub_var = "itemid")
),
eicu = list(
list(ids = "-bands", table = "lab", sub_var = "labname")
),
hirid = list(
list(ids = 24000557L, table = "observations", sub_var = "variableid",
class = "hrd_itm")
),
aumc = list(
list(ids = c(6796L, 11586L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 51144L, table = "labevents", sub_var = "itemid")
)
)
),
sirs = list(
concepts = c("temp", "hr", "resp", "pco2", "wbc", "bnd"),
description = "systemic inflammatory response syndrome score",
omopid = 4140444L,
category = "outcome",
callback = "sirs_score",
class = "rec_cncpt"
),
supp_o2 = list(
concepts = c("vent_ind", "fio2"),
description = "supplemental oxygen",
omopid = 36304401L,
category = "respiratory",
callback = "supp_o2",
class = "rec_cncpt"
),
avpu = list(
concepts = "gcs",
description = "AVPU scale",
omopid = 40493498L,
category = "neurological",
callback = "avpu",
class = "rec_cncpt"
),
news = list(
concepts = c("resp", "o2sat", "supp_o2", "temp", "sbp", "hr", "avpu"),
description = "national early warning score",
omopid = 44808550,
category = "outcome",
callback = "news_score",
class = "rec_cncpt"
),
mews = list(
concepts = c("sbp", "hr", "resp", "temp","avpu"),
description = "modified early warning score",
omopid = 40484211L,
category = "outcome",
callback = "mews_score",
class = "rec_cncpt"
),
hba1c = list(
unit = "%",
description = "Hemoglobin A1C",
omopid = 4184637L,
category = "hematology",
sources = list(
mimic = list(
list(ids = 50852L, table = "labevents", sub_var = "itemid")
),
aumc = list(
list(ids = c(11812L, 16166L), table = "numericitems",
sub_var = "itemid")
),
miiv = list(
list(ids = 50852L, table = "labevents", sub_var = "itemid")
)
)
),
bmi = list(
concepts = c("weight", "height"),
description = "patient body mass index",
omopid = 4245997L,
category = "demographics",
callback = "bmi",
target = "id_tbl",
class = "rec_cncpt"
),
adh_rate = list(
unit = c("units/min", "U/min"),
description = "vasopressin rate",
omopid = 1507835L,
category = "medications",
sources = list(
mimic = list(
list(ids = 30051L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'Uhr'),
mimic_rate_cv
)"),
list(ids = 222315L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
mimic_rate_mv
)")
),
eicu = list(
list(regex = "^vasopressin.*\\(.+/.+\\)$",
table = "infusiondrug", sub_var = "drugname",
callback = "eicu_rate_units(2.65, 0.53)",
class = "rgx_itm")
),
hirid = list(
list(ids = c(112L, 113L), table = "pharma", sub_var = "pharmaid",
grp_var = "infusionid", callback = "hirid_rate")
),
aumc = list(
list(ids = 12467L, table = "drugitems", sub_var = "itemid",
rate_uom = "doserateunit", stop_var = "stop",
callback = "aumc_rate_units(0.53)")
),
miiv = list(
list(ids = 222315L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "combine_callbacks(
convert_unit(binary_op(`/`, 60), 'units/min', 'units/hour'),
mimic_rate_mv
)")
)
)
),
phn_rate = list(
unit = "mcg/kg/min",
description = "phenylephrine rate",
omopid = 1135766L,
category = "medications",
sources = list(
mimic = list(
list(ids = 30127L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "combine_callbacks(
mimic_kg_rate, mimic_rate_cv)
"),
list(ids = 30128L, table = "inputevents_cv", sub_var = "itemid",
grp_var = "linkorderid", callback = "mimic_rate_cv"),
list(ids = 221749L, table = "inputevents_mv", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
),
eicu = list(
list(regex = "^phenylephrine.*\\(.+\\)$", table = "infusiondrug",
sub_var = "drugname", weight_var = "patientweight",
callback = "eicu_rate_kg(ml_to_mcg = 200)", class = "rgx_itm")
),
miiv = list(
list(ids = 221749L, table = "inputevents", sub_var = "itemid",
stop_var = "endtime", callback = "mimic_rate_mv")
)
)
),
norepi_equiv = list(
description = "norepinephrine equivalents",
category = "medications",
concepts = c("epi_rate", "norepi_rate", "dopa_rate", "adh_rate",
"phn_rate"),
callback = "norepi_equiv",
class = "rec_cncpt"
),
cort = list(
class = "lgl_cncpt",
description = "corticosteroids",
omopid = 304275008L,
category = "medications",
sources = list(
hirid = list(
list(ids = c( 146L, 151L, 1000325L, 1000383L, 1000431L,
1000432L, 1000433L, 1000434L, 1000435L, 1000486L,
1000487L, 1000488L, 1000769L, 1000770L, 1000929L),
table = "pharma", sub_var = "pharmaid",
callback = "transform_fun(set_val(TRUE))")
),
aumc = list(
list(ids = c(6922L, 6995L, 7106L, 8132L, 9042L, 9130L, 10628L),
table = "drugitems", sub_var = "itemid",
callback = "transform_fun(set_val(TRUE))")
)
)
),
dex = list(
min = 0,
unit = "ml/hr",
description = "dextrose (as D10)",
omopid = 4197597L,
category = "medications",
target = "win_tbl",
sources = list(
mimic = list(
list(ids = c(220950L, 228140L, 220952L), table = "inputevents_mv",
sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
auom_var = "amountuom", callback = "combine_callbacks(
mimv_rate,
dex_to_10(c(228140L, 220952L), c(2, 5))
)"),
list(ids = c(30016L, 30017L), table = "inputevents_cv",
sub_var = "itemid", grp_var = "linkorderid", val_var = "amount",
unit_var = "amountuom", target = "ts_tbl", interval = "00:01:00",
callback = "combine_callbacks(
grp_mount_to_rate(mins(1L), hours(1L)),
dex_to_10(30017L, 2)
)")
),
eicu = list(
list(regex = "(d50|dextrose.+50 ?%)", table = "medication",
sub_var = "drugname", dur_var = "drugstopoffset",
callback = "eicu_dex_med", class = "rgx_itm"),
list(regex = "(d10|dextrose.+10 ?%).+ml/hr", table = "infusiondrug",
sub_var = "drugname", callback = "eicu_dex_inf", target = "ts_tbl",
class = "rgx_itm")
),
hirid = list(
list(ids = c(1000022L, 1000690L, 1000689L, 1000544L, 1000746L,
1000835L, 1000060L, 1000545L, 1000567L),
table = "pharma", sub_var = "pharmaid", grp_var = "infusionid",
target = "ts_tbl", interval = "00:01:00",
callback = "combine_callbacks(
grp_mount_to_rate(mins(1L), hours(1L)),
dex_to_10(list(c(1000689L, 1000544L, 1000746L, 1000835L),
1000060L, 1000545L, 1000567L), c(2, 3, 4, 5))
)")
),
aumc = list(
list(ids = c(7254L, 7255L, 7256L, 8940L, 9571L), table = "drugitems",
sub_var = "itemid", dur_var = "stop", rate_var = "doserateunit",
callback = "combine_callbacks(
aumc_rate,
dex_to_10(list(7255L, 7256L, c(8940L, 9571L)),
c(2, 3, 4))
)"
)
),
miiv = list(
list(ids = c(220950L, 228140L, 220952L), table = "inputevents",
sub_var = "itemid", dur_var = "endtime", amount_var = "amount",
auom_var = "amountuom", callback = "combine_callbacks(
mimv_rate,
dex_to_10(c(228140L, 220952L), c(2, 5))
)")
)
),
class = c("unt_cncpt", "num_cncpt")
)
)
cfg <- lapply(cfg, function(x) {
if ("sources" %in% names(x)) {
if ("mimic" %in% names(x[["sources"]]))
x[["sources"]] <- c(x[["sources"]],
mimic_demo = list(x[["sources"]][["mimic"]]))
if ("eicu" %in% names(x[["sources"]]))
x[["sources"]] <- c(x[["sources"]],
eicu_demo = list(x[["sources"]][["eicu"]]))
x[["sources"]] <- x[["sources"]][order(names(x[["sources"]]))]
}
x
})
pkg_dir <- rprojroot::find_root(rprojroot::is_r_package)
cfg_dir <- file.path(pkg_dir, "inst", "extdata", "config")
ricu::set_config(cfg[order(names(cfg))], "concept-dict", cfg_dir)
devtools::install(pkg_dir)
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