Package 'possum'

CR-POSSUM predicted mortality

Description

Applies the colorectal POSSUM mortality equation (Tekkis and others, 2004):

$\mathrm{logit}(mortality) = -9.167 + 0.338 \times PS + 0.308 \times OS$

Usage

cr_possum(physiological_score, operative_score)

Arguments

physiological_score	CR-POSSUM physiological score (6-23), e.g. from cr_possum_physiology.
operative_score	CR-POSSUM operative score (4-22), e.g. from cr_possum_operative.

Value

Predicted probability of mortality (0-1).

Examples

cr_possum(physiological_score = 12, operative_score = 8)

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CR-POSSUM operative score

Description

Sums the four operative components of CR-POSSUM, all entered as their points. severity 1 (minor) / 3 (moderate) / 4 (major) / 8 (complex major); soiling 1 (none or serous) / 2 (local pus) / 3 (free pus, faeces or blood); cancer_staging 1 (none or Dukes A-B) / 2 (Dukes C) / 3 (Dukes D); urgency 1 (elective) / 3 (urgent) / 8 (emergency).

Usage

cr_possum_operative(severity, soiling, cancer_staging, urgency)

Arguments

severity	CR-POSSUM operative severity points (1, 3, 4 or 8).
soiling, cancer_staging	Points (1, 2 or 3).
urgency	Mode-of-surgery points (1, 3 or 8).

Value

Integer CR-POSSUM operative score (range 4-22).

Examples

cr_possum_operative(severity = 4, soiling = 1, cancer_staging = 2, urgency = 1)

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CR-POSSUM physiological score

Description

Sums the six physiological components of the colorectal POSSUM (CR-POSSUM) score. Age, systolic blood pressure, pulse, haemoglobin and urea are scored from raw clinical values; cardiac is entered as its points.

Usage

cr_possum_physiology(age, cardiac, systolic_bp, pulse, hb, urea)

Arguments

age, systolic_bp, pulse, hb, urea	Numeric raw clinical values, all non-negative.
cardiac	CR-POSSUM cardiac-failure points (1, 2 or 3).

Details

Cut-points and weights (Tekkis and others, 2004):

age (years)	$\le$60=1 / 61-80=3 or 4 / $\ge$81=8
systolic BP (mmHg)	100-170=1 / >170 or 90-99=2 / $\le$89=3
pulse (/min)	40-100=1 / 101-120=2 / >120 or <40=3
haemoglobin (g/dL)	13-16=1 / 10-12.9 or 16.1-18=2 / <10 or >18=3
urea (mmol/L)	$\le$10=1 / 10.1-15=2 / >15=3
cardiac failure	none/mild=1 / moderate=2 / severe=3 (entered as points)

Value

Integer CR-POSSUM physiological score (range 6-23).

Examples

cr_possum_physiology(age = 72, cardiac = 1, systolic_bp = 140, pulse = 88,
                     hb = 12, urea = 8)

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P-POSSUM predicted mortality

Description

Applies the Portsmouth (P-POSSUM) mortality equation (Prytherch and others, 1998), which recalibrates the POSSUM mortality prediction:

$\mathrm{logit}(mortality) = -9.065 + 0.1692 \times PS + 0.1550 \times OSS$

Usage

p_possum(physiological_score, operative_score)

Arguments

physiological_score	POSSUM physiological score (12-88).
operative_score	POSSUM operative severity score (6-48).

Value

Predicted probability of mortality (0-1).

Examples

p_possum(physiological_score = 20, operative_score = 10)

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POSSUM predicted morbidity and mortality

Description

Applies the original POSSUM logistic equations (Copeland and others, 1991) to a physiological and operative severity score:

$\mathrm{logit}(morbidity) = -5.91 + 0.16 \times PS + 0.19 \times OSS$

$\mathrm{logit}(mortality) = -7.04 + 0.13 \times PS + 0.16 \times OSS$

Usage

possum(physiological_score, operative_score)

Arguments

physiological_score	POSSUM physiological score (12-88), e.g. from possum_physiology.
operative_score	POSSUM operative severity score (6-48), e.g. from possum_operative.

Value

A list with elements morbidity and mortality, the predicted probabilities (0-1).

Examples

possum(physiological_score = 20, operative_score = 10)

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POSSUM operative severity score

Description

Sums the six operative components. n_procedures and blood_loss are scored from their raw values; severity, soiling, malignancy and urgency are entered as their POSSUM points.

Usage

possum_operative(
  severity,
  n_procedures,
  blood_loss,
  soiling,
  malignancy,
  urgency
)

Arguments

severity, soiling, malignancy	POSSUM points (1, 2, 4 or 8).
n_procedures	Number of procedures at this operation (at least 1).
blood_loss	Total blood loss in mL (non-negative).
urgency	POSSUM points for the mode of surgery (1, 4 or 8).

Details

Raw cut-points (points 1 / 2 / 4 / 8): number of procedures 1 / - / 2 / >2; blood loss (mL) $\le$100 / 101-500 / 501-999 / $\ge$1000. Graded, as points: severity 1 (minor) / 2 (moderate) / 4 (major) / 8 (major+); soiling 1 (none) / 2 (serous) / 4 (local pus) / 8 (free bowel content, pus or blood); malignancy 1 (none) / 2 (primary only) / 4 (nodal metastases) / 8 (distant metastases); urgency 1 (elective) / 4 (emergency, within 24 h) / 8 (emergency, within 2 h).

Value

Integer operative severity score (minimum 6).

Examples

possum_operative(severity = 4, n_procedures = 1, blood_loss = 200,
                 soiling = 1, malignancy = 2, urgency = 1)

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POSSUM physiological score

Description

Sums the twelve physiological components of the POSSUM score. The nine objective variables are scored from their raw clinical values; the three graded variables (cardiac, respiratory, ecg) are entered directly as their POSSUM points.

Usage

possum_physiology(
  age,
  systolic_bp,
  pulse,
  gcs,
  hb,
  wbc,
  urea,
  sodium,
  potassium,
  cardiac,
  respiratory,
  ecg
)

Arguments

age, systolic_bp, pulse, gcs, hb, wbc, urea, sodium, potassium	Numeric raw clinical values in the units above. All must be non-negative, and gcs must be 3-15, the range of the scale.
cardiac, respiratory	POSSUM points (1, 2, 4 or 8) for the cardiac and respiratory signs.
ecg	POSSUM points for the ECG (1, 4 or 8).

Details

Cut-points (points 1 / 2 / 4 / 8):

age (years)	$\le$60 / 61-70 / $\ge$71 / -
systolic BP (mmHg)	110-130 / 100-109 or 131-170 / 90-99 or $\ge$171 / $\le$89
pulse (/min)	50-80 / 40-49 or 81-100 / 101-120 / $\le$39 or $\ge$121
GCS	15 / 12-14 / 9-11 / $\le$8
haemoglobin (g/dL)	13-16 / 11.5-12.9 or 16.1-17 / 10-11.4 or 17.1-18 / <10 or >18
WCC (10^9/L)	4-10 / 3.1-3.9 or 10.1-20 / $\le$3 or $\ge$20.1 / -
urea (mmol/L)	$\le$7.5 / 7.6-10 / 10.1-15 / $\ge$15.1
sodium (mmol/L)	$\ge$136 / 131-135 / 126-130 / $\le$125
potassium (mmol/L)	3.5-5 / 3.2-3.4 or 5.1-5.3 / 2.9-3.1 or 5.4-5.9 / $\le$2.8 or $\ge$6

Graded variables, entered as points: cardiac and respiratory take 1, 2, 4 or 8; ecg takes 1 (normal), 4 (atrial fibrillation 60-90/min) or 8 (any other abnormality). Confirm the grading against the original tables before use.

Value

Integer physiological score (minimum 12).

Examples

possum_physiology(age = 65, systolic_bp = 120, pulse = 75, gcs = 15,
                  hb = 13.5, wbc = 8, urea = 6, sodium = 140, potassium = 4.2,
                  cardiac = 1, respiratory = 1, ecg = 1)

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POSSUM and P-POSSUM risk for a table of patients

Description

Convenience wrapper that scores a whole cohort in one call, rather than invoking possum_physiology, possum_operative and the risk functions separately. Each row of data is one patient.

Usage

possum_risk(data)

Arguments

data	A data frame (one row per patient) containing the columns required by possum_physiology and possum_operative: age, systolic_bp, pulse, gcs, hb, wbc, urea, sodium, potassium, cardiac, respiratory, ecg, severity, n_procedures, blood_loss, soiling, malignancy and urgency.

Details

Rows are scored independently. A row with a missing or out-of-range value cannot be scored, so its five output columns are returned as NA and the rest of the cohort is scored as normal; a single missing laboratory value no longer aborts the whole call. A warning reports how many rows were left unscored.

Value

data with five columns added: physiological_score, operative_score, possum_morbidity, possum_mortality and p_possum_mortality. Rows that could not be scored carry NA in all five.

Examples

df <- data.frame(
  age = c(45, 82), systolic_bp = c(120, 95), pulse = c(70, 115),
  gcs = c(15, 13), hb = c(14, 9.5), wbc = c(7, 22), urea = c(5, 18),
  sodium = c(140, 128), potassium = c(4.2, 6.1), cardiac = c(1, 4),
  respiratory = c(1, 4), ecg = c(1, 8), severity = c(1, 8),
  n_procedures = c(1, 1), blood_loss = c(50, 1200), soiling = c(1, 8),
  malignancy = c(1, 4), urgency = c(1, 8))
possum_risk(df)

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RAAA-POSSUM predicted mortality (ruptured abdominal aortic aneurysm)

Description

Applies a POSSUM mortality equation specific to ruptured abdominal aortic aneurysm surgery, computed from the standard POSSUM physiological and operative severity scores. Two forms are provided:

$\mathrm{logit}(mortality) = -2.7569 + 0.0968 \times PS$

$\mathrm{logit}(mortality) = -4.9795 + 0.0913 \times PS + 0.0958 \times OS$

Usage

raaa_possum(
  physiological_score,
  operative_score = NULL,
  model = c("physiology", "full")
)

Arguments

physiological_score	Standard POSSUM physiological score (12-88), e.g. from possum_physiology.
operative_score	Standard POSSUM operative severity score (6-48), e.g. from possum_operative. Required when model = "full", and an error when model = "physiology", which cannot use it.
model	Which equation to use: "physiology" (default, physiology score only) or "full" (physiology plus operative score).

Details

RAAA-POSSUM (Prytherch and others, 2001) reuses the standard POSSUM scores. Both equations are as tabulated by Neary, Heather and Earnshaw (2003).

Value

Predicted probability of mortality (0-1).

Examples

raaa_possum(physiological_score = 30)
raaa_possum(physiological_score = 30, operative_score = 18, model = "full")

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V-POSSUM predicted mortality (vascular)

Description

Applies a vascular POSSUM (V-POSSUM) mortality equation, computed from the standard POSSUM physiological and operative severity scores (from possum_physiology and possum_operative). Two forms are provided:

$\mathrm{logit}(mortality) = -6.0386 + 0.1539 \times PS$

$\mathrm{logit}(mortality) = -8.0616 + 0.1552 \times PS + 0.1238 \times OS$

Usage

v_possum(
  physiological_score,
  operative_score = NULL,
  model = c("physiology", "full")
)

Arguments

physiological_score	Standard POSSUM physiological score (12-88), e.g. from possum_physiology.
operative_score	Standard POSSUM operative severity score (6-48), e.g. from possum_operative. Required when model = "full", and an error when model = "physiology", which cannot use it.
model	Which equation to use: "physiology" (default, physiology score only) or "full" (physiology plus operative score).

Details

V-POSSUM (Prytherch and others, 2001, for major arterial surgery) reuses the standard POSSUM scores. Both equations are as tabulated by Neary, Heather and Earnshaw (2003). No V-POSSUM morbidity equation has been published.

Value

Predicted probability of mortality (0-1).

Examples

v_possum(physiological_score = 25)
v_possum(physiological_score = 25, operative_score = 15, model = "full")

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