Sepsis 3 label

The sepsis 3 label consists of a suspected infection combined with an acute increase in SOFA score.

sep3(
  ...,
  si_window = c("first", "last", "any"),
  delta_fun = delta_cummin,
  sofa_thresh = 2L,
  si_lwr = hours(48L),
  si_upr = hours(24L),
  keep_components = FALSE,
  interval = NULL
)

delta_cummin(x)

delta_start(x)

delta_min(x, shifts = seq.int(0L, 23L))

Arguments

...

Data objects

si_window

Switch that can be used to filter SI windows

delta_fun

Function used to determine the SOFA increase during an SI window

sofa_thresh

Required SOFA increase to trigger Sepsis 3

si_lwr, si_upr

Lower/upper extent of SI windows

keep_components

Logical flag indicating whether to return the individual components alongside the aggregated score

interval

Time series interval (only used for checking consistency of input data)

x

Vector of SOFA scores

shifts

Vector of time shifts (multiples of the current interval) over which base::pmin() is evaluated

Details

The Sepsis-3 Consensus (Singer et. al.) defines sepsis as an acute increase in the SOFA score (see sofa_score()) of 2 points or more within the suspected infection (SI) window (see susp_inf()):

A patient can potentially have multiple SI windows. The argument si_window is used to control which SI window we focus on (options are "first", "last", "any").

Further, although a 2 or more point increase in the SOFA score is defined, it is not perfectly clear to which value the increase refers. For this the delta_fun argument is used. If the increase is required to happen with respect to the minimal SOFA value (within the SI window) up to the current time, the delta_cummin function should be used. If, however, we are looking for an increase with respect to the start of the SI window, then the delta_start function should be used. Lastly, the increase might be defined with respect to values of the previous 24 hours, in which case the delta_min function is used.

References

Singer M, Deutschman CS, Seymour CW, et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). JAMA. 2016;315(8):801–810. doi:10.1001/jama.2016.0287