Description Usage Arguments Value Converting to probability scale References Examples
This function will parse a dataframe and produce POSSUM scores to predict perioperative mortality and morbidity. To use the function, you will need to manipulate your dataframe to have columns with the structure detailed below.
1 | gen.POSSUM(x)
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x |
A dataframe or tbl where each row is a patient observation, and the columns are POSSUM predictor variables. x must contain the following column names (not necessarily in order):
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A dataframe (or tbl), which you can assign to an object, with the following variables:
The physiological score for POSSUM
The operative score for POSSUM
The log-odds for morbidity as calculated by POSSUM
The log-odds for mortatlity as calculated by pPOSSUM
The function will produce POSSUMLogit and pPOSSUMLogit values which are on the log-odds scale
To convert to probabilities (0 to 1 scale), use arm::invlogit()
. See: invlogit
.
Copeland GP, Jones D, Walters M. POSSUM: A scoring system for surgical audit. Br J Surg. 1991 Mar 1;78(3):355–60. http://onlinelibrary.wiley.com/doi/10.1002/bjs.1800780327/abstract.
Prytherch DR, Whiteley MS, Higgins B, Weaver PC, Prout WG, Powell SJ. POSSUM and Portsmouth POSSUM for predicting mortality. Br J Surg. 1998 Sep 1;85(9):1217–20. http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2168.1998.00840.x/abstract
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | ## Not run:
#Example of pre-processing to rename data variables to match expected column names
library(tidyverse)
test_data <- raw_data %>%
select(Age = S01Age,
JVP = S03ElevatedJugularVenousPressureJvp,
Cardiomegaly = S03RadiologicalFindingsCardiomegaly,
Oedema = S03PeripheralOedema,
Warfarin = S03DrugTreatmentWarfarin,
Diuretics = S03DrugTreatmentDiureticTreatment,
AntiAnginals = S03DrugTreatmentAntiAnginal,
Digoxin = S03DrugTreatmentDigoxinTherapy,
AntiHypertensives = S03DrugTreatmentAntiHypertensive,
Dyspnoea = S03Dyspnoea,
Consolidation = S03RadiologicalFindingsConsolidation,
PulmonaryFibrosis = S03PastMedicalHistoryPulmonaryFibrosis,
COPD = S03PastMedicalHistoryCOPD,
SysBP = S03SystolicBloodPressureBpAtPreAssessment,
HR = S03PulseRateAtPreoperativeAssessment,
GCS = S03GlasgowComaScaleGcsPreInductionOfAnaesthesia,
Hb = S03Hb,
WCC = S03WhiteCellCountWcc,
Ur = S03Urea,
Na = S03Na,
K = S03K,
ECG = S03EcgFindings,
OpSeverity = S02PlannedProcSeverity,
ProcedureCount = S04ProcedureCount,
EBL = S04BloodLoss,
PeritonealContamination = S04PeritonealContamination,
Malignancy = S04Malignancy,
OpUrgency = S02OperativeUrgency)
## End(Not run)
test_data <- patients
test_output <- gen.POSSUM(test_data)
head(test_output)
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