Title:	The Phoenix Pediatric Sepsis and Septic Shock Criteria
Version:	1.1.2
Description:	Implementation of the Phoenix and Phoenix-8 Sepsis Criteria as described in "Development and Validation of the Phoenix Criteria for Pediatric Sepsis and Septic Shock" by Sanchez-Pinto, Bennett, DeWitt, Russell et al. (2024) <doi:10.1001/jama.2024.0196> (Drs. Sanchez-Pinto and Bennett contributed equally to this manuscript; Dr. DeWitt and Mr. Russell contributed equally to the manuscript), "International Consensus Criteria for Pediatric Sepsis and Septic Shock" by Schlapbach, Watson, Sorce, Argent, et al. (2024) <doi:10.1001/jama.2024.0179> (Drs Schlapbach, Watson, Sorce, and Argent contributed equally) and the application note "phoenix: an R package and Python module for calculating the Phoenix pediatric sepsis score and criteria" by DeWitt, Russell, Rebull, Sanchez-Pinto, and Bennett (2024) <doi:10.1093/jamiaopen/ooae066>.
Depends:	R (≥ 3.5.0)
License:	MIT + file LICENSE
Encoding:	UTF-8
URL:	https://cu-dbmi-peds.github.io/phoenix/, https://github.com/CU-DBMI-Peds/phoenix/
BugReports:	https://github.com/CU-DBMI-Peds/phoenix/issues
Language:	en-us
LazyData:	true
Suggests:	knitr, ggplot2, qwraps2 (≥ 0.6.0), reticulate, rmarkdown
VignetteBuilder:	knitr
RoxygenNote:	7.3.2
Config/Needs/website:	rmarkdown
NeedsCompilation:	no
Packaged:	2025-05-02 20:12:49 UTC; peterdewitt
Author:	Peter DeWitt [aut, cre], Seth Russell [ctb], Meg Rebull [ctb], Tell Bennett [ctb], L. Nelson Sanchez-Pinto [ctb]
Maintainer:	Peter DeWitt <peter.dewitt@cuanschutz.edu>
Repository:	CRAN
Date/Publication:	2025-05-02 22:00:05 UTC

phoenix: Phoenix and Phoenix-8 Sepsis Criteria

Description

Implementation of the Phoenix and Phoenix-8 Sepsis Criteria as described in "Development and Validation of the Phoenix Criteria for Pediatric Sepsis and Septic Shock" by Sanchez-Pinto, Bennett, DeWitt, Russell et al. (2024) doi:10.1001/jama.2024.0196 and "International Consensus Criteria for Pediatric Sepsis and Septic Shock" by Schlapbach, Watson, Sorce, et al. (2024) doi:10.1001/jama.2024.0179.

How To Cite

When using this R package in your research please cite the Phoenix criteria and the package. You can get details more information via

citation('phoenix')

You can get bibtex entries for all the citations via

print(citation('phoenix'), bibtex = TRUE)

And you can get the up-to-date version and year information for the phoenix package via

print(citation('phoenix', auto = TRUE)) and print(citation('phoenix', auto = TRUE), bibtex = TRUE).

Author(s)

Maintainer: Peter DeWitt peter.dewitt@cuanschutz.edu (ORCID)

Other contributors:

• Seth Russell seth.russell@cuanschutz.edu (ORCID) [contributor]

• Meg Rebull meg.rebull@cuanschutz.edu (ORCID) [contributor]

• Tell Bennett tell.bennett@cuanschutz.edu (ORCID) [contributor]

• L. Nelson Sanchez-Pinto lsanchezpinto@luriechildrens.org (ORCID) [contributor]

References

There are two major publications to reference with respect to the development of the Phoenix criteria.

• L. Nelson Sanchez-Pinto, MD, MBI*; Tellen D. Bennett, MD, MS*; Peter E. DeWitt, PhD**; Seth Russell, MS**; Margaret N. Rebull, MA; Blake Martin, MD; Samuel Akech, MBChB, MMED; David J. Albers, PhD; Elizabeth R. Alpern, MD, MSCE; Fran Balamuth, MD, PhD, MSCE; Melania Bembea, MD, MPH, PhD; Mohammod Jobayer Chisti, MBBS, MMed, PhD; Idris Evans, MD, MSc; Christopher M. Horvat, MD, MHA; Juan Camilo Jaramillo-Bustamante, MD; Niranjan Kissoon, MD; Kusum Menon, MD, MSc; Halden F. Scott, MD, MSCS; Scott L. Weiss, MD; Matthew O. Wiens, PharmD, PhD; Jerry J. Zimmerman, MD, PhD; Andrew C. Argent, MD, MBBCh, MMed***; Lauren R. Sorce, PhD, RN, CPNP-AC/PC23***; Luregn J. Schlapbach, MD, PhD***; R. Scott Watson, MD, MPH***; and the Society of Critical Care Medicine Pediatric Sepsis Definition Task Force Development and Validation of the Phoenix Criteria for Pediatric Sepsis and Septic Shock. JAMA. 2024;331(8):675–686. Published online January 21, 2024. doi:10.1001/jama.2024.0196

  *Drs Sanchez-Pinto and Bennett contributed equally. **Dr DeWitt and Mr Russell contributed equally. ***Drs Argent, Sorce, Schlapbach, and Watson contributed equally.

• Luregn J. Schlapbach, MD, PhD; R. Scott Watson, MD, MPH; Lauren R. Sorce, PhD, RN; Andrew C. Argent, MD, MBBCh, MMed; Kusum Menon, MD, MSc; Mark W. Hall, MD; Samuel Akech, MBChB, MMED, PhD; David J. Albers, PhD; Elizabeth R. Alpern, MD, MSCE; Fran Balamuth, MD, PhD, MSCE; Melania Bembea, MD, PhD; Paolo Biban, MD; Enitan D. Carrol, MBChB, MD; Kathleen Chiotos, MD; Mohammod Jobayer Chisti, MBBS, MMed, PhD; Peter E. DeWitt, PhD; Idris Evans, MD, MSc; Cláudio Flauzino de Oliveira, MD, PhD; Christopher M. Horvat, MD, MHA; David Inwald, MB, PhD; Paul Ishimine, MD31; Juan Camilo Jaramillo-Bustamante, MD; Michael Levin, MD, PhD; Rakesh Lodha, MD; Blake Martin, MD; Simon Nadel, MBBS; Satoshi Nakagawa, MD; Mark J. Peters, PhD; Adrienne G. Randolph, MD, MS; Suchitra Ranjit, MD; Margaret N. Rebull, MA; Seth Russell, MS; Halden F. Scott, MD; Daniela Carla de Souza, MD, PhD; Pierre Tissieres, MD, DSc; Scott L. Weiss, MD, MSCE; Matthew O. Wiens, PharmD, PhD; James L. Wynn, MD; Niranjan Kissoon, MD; Jerry J. Zimmerman, MD, PhD; L. Nelson Sanchez-Pinto, MD; Tellen D. Bennett, MD, MS; for the Society of Critical Care Medicine Pediatric Sepsis Definition Task Force International Consensus Criteria for Pediatric Sepsis and Septic Shock. JAMA. 2024;331(8):665–674. doi:10.1001/jama.2024.0179

  *Drs Schlapbach, Watson, Sorce, and Argent contributed equally. **Drs Sanchez-Pinto and Bennett contributed equally.

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Mean Arterial Pressure

Description

Estimate mean arterial pressure from systolic and diastolic blood pressures.

Usage

map(sbp, dbp)

Arguments

Details

Mean Arterial Pressure is approximated by: (DBP + (SBP - DBP) / 3) = (2/3) DBP + (1/3) SBP

Value

a numeric vector

Examples

DF <- expand.grid(
        sbp = 40:130, # expected units of mmHg
        dbp = 20:100  # expected units of mmHg
      )

DF$map <- with(DF, map(sbp, dbp))
with(DF, plot(sbp, dbp, col = map))
DF$map[DF$sbp < DF$dbp] <- NA

z <- matrix(DF$map, nrow = length(unique(DF$sbp)), ncol = length(unique(DF$dbp)))

image(
  x = unique(DF$sbp),
  y = unique(DF$dbp),
  z = z,
  col = hcl.colors(100, palette = "RdBu"),
  xlab = "SBP (mmHg)",
  ylab = "DBP (mmHg)",
  main = "Estimated Mean Arterial Pressue"
)
contour(x = unique(DF$sbp), y = unique(DF$dbp), z = z, add = TRUE)

The Phoenix Sepsis Score

Description

The diagnostic Phoenix Sepsis Criteria based on four organ dysfunction scores, respiratory, cardiovascular, coagulation, and neurologic. A score of 2 or more indicates sepsis.

Usage

phoenix(
  pf_ratio,
  sf_ratio,
  imv,
  other_respiratory_support,
  vasoactives,
  lactate,
  map,
  platelets,
  inr,
  d_dimer,
  fibrinogen,
  gcs,
  fixed_pupils,
  age,
  data = parent.frame(),
  ...
)

Arguments

Details

The details of each of the four component scores are found in there respective help files.

Value

A data.frame with seven columns:

1. phoenix_respiratory_score

2. phoenix_cardiovascular_score

3. phoenix_coagulation_score

4. phoenix_neurologic_score

5. phoenix_sepsis_score

6. phoenix_sepsis An integer vector, 0 = not septic, 1 = septic (score greater or equal to 2)

7. phoenix_septic_shock An integer vector, 0 = not septic shock, 1 = septic shock (score greater or equal 2 and cardiovascular dysfunction)

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# Using the example sepsis data set, read more details in the vignette

phoenix_scores <-
  phoenix(
    # Respiratory
      pf_ratio = pao2 / fio2,
      sf_ratio = ifelse(spo2 <= 97, spo2 / fio2, NA_real_),
      imv = vent,
      other_respiratory_support = as.integer(fio2 > 0.21),
    # Cardiovascular
      vasoactives = dobutamine + dopamine + epinephrine + milrinone + norepinephrine + vasopressin,
      lactate = lactate,
      age = age,
      map = dbp + (sbp - dbp)/3,
    # Coagulation
      platelets = platelets,
      inr = inr,
      d_dimer = d_dimer,
      fibrinogen = fibrinogen,
    # Neurologic
      gcs = gcs_total,
      fixed_pupils = as.integer(pupil == "both-fixed"),
    data = sepsis
  )

str(phoenix_scores)

The Phoenix 8 Sepsis Score

Description

The extended Phoenix criteria using a total eight organ systems. This is intended mostly for research as an extension of the Phoenix Sepsis Criteria which is based on four organ systems.

Usage

phoenix8(
  pf_ratio,
  sf_ratio,
  imv,
  other_respiratory_support,
  vasoactives,
  lactate,
  map,
  platelets,
  inr,
  d_dimer,
  fibrinogen,
  gcs,
  fixed_pupils,
  glucose,
  anc,
  alc,
  creatinine,
  bilirubin,
  alt,
  age,
  data = parent.frame(),
  ...
)

Arguments

Details

The Phoenix Sepsis Criteria is based on the score form respiratory, cardiovascular, coagulation, and neurologic. Phoenix 8 uses these four an endocrine, immunologic, renal, and hepatic. Details on the scoring for each of the eight component organ systems are found in the respective manual files.

Value

a data.frame with 12 integer columns.

1. phoenix_respiratory_score

2. phoenix_cardiovascular_score

3. phoenix_coagulation_score

4. phoenix_neurologic_score

5. phoenix_sepsis_score

6. phoenix_sepsis 0 = not septic; 1 = septic (phoenix_sepsis_score greater or equal 2)

7. phoenix_septic_shock 0 = no septic shock; 1 = septic shock (sepsis with cardiovascular dysfunction)

8. phoenix_endocrine_score

9. phoenix_immunologic_score

10. phoenix_renal_score

11. phoenix_hepatic_score

12. phoenix8_sepsis_score

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# Using the example sepsis data set, read more details in the vignette

phoenix8_scores <-
  phoenix8(
    # Respiratory
      pf_ratio = pao2 / fio2,
      sf_ratio = ifelse(spo2 <= 97, spo2 / fio2, NA_real_),
      imv = vent,
      other_respiratory_support = as.integer(fio2 > 0.21),
    # Cardiovascular
      vasoactives = dobutamine + dopamine + epinephrine + milrinone + norepinephrine + vasopressin,
      lactate = lactate,
      age = age, # Also used in the renal assessment.
      map = dbp + (sbp - dbp)/3,
    # Coagulation
      platelets = platelets,
      inr = inr,
      d_dimer = d_dimer,
      fibrinogen = fibrinogen,
    # Neurologic
      gcs = gcs_total,
      fixed_pupils = as.integer(pupil == "both-fixed"),
    # Endocrine
      glucose = glucose,
    # Immunologic
      anc = anc,
      alc = alc,
    # Renal
      creatinine = creatinine,
      # no need to specify age again
    # Hepatic
      bilirubin = bilirubin,
      alt = alt,
    data = sepsis
  )

str(phoenix8_scores)

Phoenix Cardiovascular Score

Description

Generate the cardiovascular organ system dysfunction score as part of the diagnostic Phoenix Sepsis Criteria.

Usage

phoenix_cardiovascular(
  vasoactives = NA_integer_,
  lactate = NA_real_,
  age = NA_real_,
  map = NA_real_,
  data = parent.frame(),
  ...
)

Arguments

Details

There where six systemic vasoactive medications considered when the Phoenix criteria was developed: dobutamine, dopamine, epinephrine, milrinone, norepinephrine, and vasopressin.

During development, the values used for map were taken preferentially from arterial measurement, then cuff measures, and provided values before approximating the map from blood pressure values via DBP + 1/3 (SBP - DBP), where DBP is the diastolic blood pressure and SBP is the systolic blood pressure.

Value

a integer vector with values 0, 1, 2, 3, 4, 5, or 6.

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Cardiovascular Scoring

The Phoenix Cardiovascular score ranges from 0 to 6 points; 0, 1, or 2 points for each of systolic vasoactive medications, lactate, and MAP.

Systemic Vasoactive Medications

Lactate

MAP

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
phoenix_cardiovascular(
   vasoactives = dobutamine + dopamine + epinephrine + milrinone + norepinephrine + vasopressin,
   lactate = lactate,
   age = age,
   map = dbp + (sbp - dbp)/3,
   data = sepsis
)

# example data set to get all the possible scores
DF <-
  expand.grid(vasos = c(NA, 0:6),
              lactate = c(NA, 3.2, 5, 7.8, 11, 14), # units of mmol/L
              age = c(NA, 0.4, 1, 3, 12, 18, 24, 45, 60, 61, 144, 145), # months
              map = c(NA, 16:52)) # mmHg
DF$card <- phoenix_cardiovascular(vasos, lactate, age, map, DF)
head(DF)

# what if lactate is unknown for all records? - set the value either in the
# data object or the arguement value to NA
DF2 <-
  expand.grid(vasos = c(NA, 0:6),
              age = c(NA, 0.4, 1, 3, 12, 18, 24, 45, 60, 61, 144, 145), # months
              map = c(NA, 16:52)) # mmHg
DF2$card <- phoenix_cardiovascular(vasos, lactate = NA, age, map, DF2)

DF3 <-
  expand.grid(vasos = c(NA, 0:6),
              lactate = NA, # mmol/L
              age = c(NA, 0.4, 1, 3, 12, 18, 24, 45, 60, 61, 144, 145), # months
              map = c(NA, 16:52)) # mmHg
DF3$card <- phoenix_cardiovascular(vasos, lactate, age, map, DF3)

identical(DF2$card, DF3$card)

Phoenix Coagulation Score

Description

Applies the Phoenix coagulation organ dysfunction scoring to a set of inputs.

Usage

phoenix_coagulation(
  platelets = NA_real_,
  inr = NA_real_,
  d_dimer = NA_real_,
  fibrinogen = NA_real_,
  data = parent.frame(),
  ...
)

Arguments

Value

a integer vector with values 0, 1, or 2

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Coagulation Scoring

1 point each for platelets < 100 K/micro liter, INR > 1.3, D-dimer > 2 mg/L FEU, and fibrinogen < 100 mg/dL, with a max total score of 2.

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example data set
phoenix_coagulation(
  platelets = platelets,    # 1000/uL (thousand per microliter)
  inr = inr,                # unitless
  d_dimer = d_dimer,        # mg/L FEU
  fibrinogen = fibrinogen,  # mg/dL
  data = sepsis
)

# build a data.frame with values for all possible combationations of values
# leading to all possible coagulation scores.
DF <-
  expand.grid(plts = c(NA, 20, 100, 150),
              inr  = c(NA, 0.2, 1.3, 1.8),
              ddmr = c(NA, 1.7, 2.0, 2.8),
              fib  = c(NA, 88, 100, 120))

DF$coag <- phoenix_coagulation(plts, inr, ddmr, fib, DF)
DF

Phoenix Endocrine Score

Description

Assess the Phoenix endocrine organ dysfunction score. This score is not part of the Phoenix score, only part of the Phoenix-8 score.

Usage

phoenix_endocrine(glucose = NA_real_, data = parent.frame(), ...)

Arguments

Value

a integer vector with values 0 or 1

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Endocrine Scoring

The endocrine dysfunction score is based on blood glucose with one point for levels < 50 mg/dL or > 150 mg/dL.

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
# recall glucose is expected to have units of mg/dL

endo_example       <- sepsis[c("pid", "glucose")]
endo_example$score <- phoenix_endocrine(glucose, data = sepsis)
endo_example

# example data set to get all the possible endocrine scores
# recall glucose is expected to have units of mg/dL

DF <- data.frame(glc = c(NA, 12, 50, 55, 100, 150, 178))
phoenix_endocrine(glucose = glc, data = DF)

Phoenix Hepatic Score

Description

Apply the Phoenix Hepatic scoring based on total bilirubin and ALT.

Usage

phoenix_hepatic(
  bilirubin = NA_real_,
  alt = NA_real_,
  data = parent.frame(),
  ...
)

Arguments

Value

a integer vector with values 0 or 1

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Hepatic Scoring

1 point for total bilirubin greater or equal to 4 mg/dL and/or ALT strictly greater than 102 IU/L.

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
# recall expected units:
#   (total) bilirubin: mg/dL
#   alt: IU/L

hep_example       <- sepsis[c("pid", "bilirubin", "alt")]
hep_example$score <- phoenix_hepatic(bilirubin, alt, sepsis)
hep_example

# example data set with all possilbe hepatic scores
DF <- expand.grid(bil = c(NA, 3.2, 4.0, 4.3), alt = c(NA, 99, 102, 106))
phoenix_hepatic(bilirubin = bil, alt = alt, data = DF)

Phoenix Immunologic Score

Description

Apply the Phoenix immunologic scoring based on ANC and ALC. This is only part of Phoenix-8 and not Phoenix.

Usage

phoenix_immunologic(anc = NA_real_, alc = NA_real_, data = parent.frame(), ...)

Arguments

Value

a integer vector with values 0 or 1

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Immunologic Scoring

1 point if ANC < 0.500 or ALC < 1.000 (units are 1000 cells per cubic millimeter).

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
# Expected units for ALC and ANC are 1000 cells per cubic millimeter

immu_example <- sepsis[c("pid", "anc", "alc")]
immu_example$score <- phoenix_immunologic(anc, alc, sepsis)
immu_example

# example data set with all possilbe immunologic scores
# Expected units for anc and alc are 1000 cells per cubic millimeter

DF <- expand.grid(anc = c(NA, 0.200, 0.500, 0.600),
                  alc = c(NA, 0.500, 1.000, 2.000))
phoenix_immunologic(anc = anc, alc = alc, data = DF)

Phoenix Sepsis Neurological Score

Description

Assessment of neurologic dysfunction based on Glasgow Coma Scale (GCS) and pupil reactivity. This score is part of the diagnostic Phoenix Sepsis criteria and Phoenix 8 Sepsis criteria.

Usage

phoenix_neurologic(
  gcs = NA_integer_,
  fixed_pupils = NA_real_,
  data = parent.frame(),
  ...
)

Arguments

Details

Missing values will map to a value of 0 as was done when developing the Phoenix criteria. Note that this is done on a input by input basis. That is, if pupil reactivity is missing but GCS (total) is 9, then the neurologic dysfunction score is 1.

GCS total is the sum of a score based on eyes, motor control, and verbal responsiveness.

Eye response:

1. no eye opening,

2. eye opening to pain,

3. eye opening to sound,

4. eyes open spontaneously.

Verbal response:

1. no verbal response,

2. incomprehensible sounds,

3. inappropriate words,

4. confused,

5. orientated

Motor response:

1. no motor response,

2. abnormal extension to pain,

3. abnormal flexion to pain,

4. withdrawal from pain,

5. localized pain,

6. obeys commands

Value

an integer vector with values 0, 1, or 2. As with all Phoenix organ dysfunction scores, missing input values map to scores of zero.

Phoenix Neurological Scoring

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
# Expected units:
#   GCS integer values from 3, 4, 5, ..., 15 
#   fixed_pupils: 1 if bilaterially fixed pupils, 0 otherwise

phoenix_neurologic(
  gcs = gcs_total, 
  fixed_pupils = as.integer(pupil == "both-fixed"),
  data = sepsis
)

# build an example data set with all possible neurologic scores
DF <- expand.grid(gcs = c(3:15, NA), pupils = c(0, 1, NA))
DF$target <- 0L
DF$target[DF$gcs <= 10] <- 1L
DF$target[DF$pupils == 1] <- 2L
DF$current <- phoenix_neurologic(gcs, pupils, DF)
stopifnot(identical(DF$target, DF$current))
DF

Phoenix Renal Score

Description

Apply the Phoenix renal organ dysfunction score based on age adjusted creatinine levels.

Usage

phoenix_renal(
  creatinine = NA_real_,
  age = NA_real_,
  data = parent.frame(),
  ...
)

Arguments

Value

a integer vector with values 0, 1, or 2

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Renal Scoring

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# using the example sepsis data set
# Expected units:
#   age: months
#   creatinine: mg/dL

renal_example <- sepsis[c("creatinine", "age")]
renal_example$score <- phoenix_renal(creatinine, age, sepsis)
renal_example

# build an example data set with all possible neurologic scores
DF <- expand.grid(age = c(NA, 0.4, 1, 3, 12, 18, 24, 45, 60, 61, 144, 145),
                  creatinine = c(NA, seq(0.0, 1.1, by = 0.1)))
DF$card <- phoenix_renal(age = age, creatinine = creatinine, data = DF)

head(DF)

Phoenix Respiratory Score

Description

Apply the Phoenix Respiratory Scoring rubric to a data set. The respiratory score is part of the diagnostic Phoenix Sepsis criteria and the diagnostic Phoenix 8 Sepsis criteria.

Usage

phoenix_respiratory(
  pf_ratio = NA_real_,
  sf_ratio = NA_real_,
  imv = NA_integer_,
  other_respiratory_support = NA_integer_,
  data = parent.frame(),
  ...
)

Arguments

Details

pf_ratio is the ratio of partial pressure of oxygen in arterial blood (PaO2) to the fraction of inspiratory oxygen concentration (FiO2).

sf_ratio is a non-invasive surrogate for pf_ratio using pulse oximetry (SpO2) instead of invasive PaO2.

Important Note: when the Phoenix Sepsis criteria was developed there is a requirement that SpO2 < 97 in order for the sf_ratio to be valid. That assumption is not checked in this code and it is left to the end user to account for this when building the sf_ratio vector.

imv Invasive mechanical ventilation - integer vector where 0 = not intubated and 1 = intubated.

other_respiratory_support other respiratory support such as receiving oxygen, high-flow, non-invasive positive pressure, or imv.

Value

a integer vector with values 0, 1, 2, or 3.

As with all other Phoenix organ system scores, missing values in the data set will map to a score of zero - this is consistent with the development of the criteria.

Phoenix Respiratory Scoring

References

See reference details in phoenix-package or by calling citation('phoenix').

See Also

• phoenix for generating the diagnostic Phoenix Sepsis score based on the four organ systems:

  • phoenix_cardiovascular,

  • phoenix_coagulation,

  • phoenix_neurologic,

  • phoenix_respiratory,

• phoenix8 for generating the diagnostic Phoenix 8 Sepsis criteria based on the four organ systems noted above and

  • phoenix_endocrine,

  • phoenix_immunologic,

  • phoenix_renal,

  • phoenix_hepatic,

vignette('phoenix') for more details and examples.

Examples

# Using the provided example data set:
# Expected units:
#   pf_ratio: PaO2 / FiO2
#     PaO2: mmHg
#     FiO2: decimal between 0.21 (room air) to 1.00 (pure oxygen)
#   sf_ratio: SpO2 / FiO2
#     SpO2: percentage, 0 to 100
#     FiO2: decimal between 0.21 (room air) to 1.00 (pure oxygen)
#   imv: (invasive mechanical ventilation) 1 for yes, 0 for no
#   other_respiratory_support: 1 for yes, 0 for no

phoenix_respiratory(
  pf_ratio = pao2 / fio2,
  sf_ratio = spo2 / fio2,
  imv      = vent,
  other_respiratory_support = as.integer(fio2 > 0.21),
  data = sepsis
)

# A set of values that will get all possible respiratory scores:
DF <- expand.grid(
  pfr = c(NA, 500, 400, 350, 200, 187, 100, 56),
  sfr = c(NA, 300, 292, 254, 220, 177, 148, 76),
  vent = c(NA, 0, 1),
  o2  = c(NA, 0, 1)
)

phoenix_respiratory(
  pf_ratio = pfr,
  sf_ratio = sfr,
  imv = vent,
  other_respiratory_support = o2,
  data = DF
)

sepsis

Description

A fully synthetic data set with variables need for examples and documentation of the Phoenix Sepsis Criteria.

Usage

sepsis

Format

a data.frame with 20 rows and 27 columns