README.MD

In trentgillin/SepsisR: Data analysis for sepsis made easy

SepsisR

Sepsis can present in many different ways. Many professionals recognize sepsis’ presentation, but the literature is undecided when it comes to an exact clinical definition. The purpose of this package is to provide functions in order to make the process of identifying and analyzing sepsis patient data easier. assess_organ is the main function of this package; it allows you to assess organ failure using one of the three common organ failure scores, SIRS, SOFA, and qSOFA. Currently, all score vital thresholds are based off the MD Calc Website. Please view the description file to see MD Calc references for individual organ failure scores. This package also has a few helper functions including find_bx_window and find_qad, from the CDC (Centers for Disease and Control) definition of Sepsis. This package is not in anyway supported by the CDC or Emory Healthcare.

Installation

Get the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("trentgillin/Sepsis")

Example

This is a basic example which shows you how to solve a common problem:

library(SepsisR)

assess_organ(sirs_data, method = "SIRS",
                 patientid = Encounter, 
                time = Service_Timestamp, 
                vitals = c("RR" = "RR", 
                           "WBC" = "Wbc", 
                    "Temperature" = "Temperature",
                    "HR" = "HR"))
#> # A tibble: 9 × 7
#>   Encounter Service_Timestamp      HR Temperature    RR   Wbc sirs_total
#>       <dbl> <dttm>              <dbl>       <dbl> <dbl> <dbl>      <dbl>
#> 1         1 2018-12-11 08:00:00   120          31    20  5000          2
#> 2         1 2018-12-11 08:30:00    72          31    20  5000          1
#> 3         1 2018-12-11 09:00:00    85          33    21  5000          2
#> 4         1 2018-12-11 09:30:00    90          31    22  5000          2
#> 5         1 2018-12-11 10:00:00   111          31    20  5000          2
#> 6         1 2018-12-11 10:30:00    64          32    20  5000          1
#> 7         1 2018-12-11 11:00:00    70          38    20  5000          0
#> 8         1 2018-12-11 11:30:00    75          33    20  5000          1
#> 9         1 2018-12-11 12:00:00    81          31    20  5000          1

References

“Sequential Organ Failure Assessment (SOFA)” Vincent, https://www.mdcalc.com/sequential-organ-failure-assessment-sofa-score

“Quick Sequential Organ Failure Assessment (qSOFA)” Seymour, https://www.mdcalc.com/qsofa-quick-sofa-score-sepsis

“Systematic Inflammatory Response Syndrome (SIRS)” Balk, https://www.mdcalc.com/sirs-sepsis-septic-shock-criteria.

trentgillin/SepsisR documentation built on Nov. 26, 2022, 12:41 p.m.