Derives the commonly reported blood-count and inflammation-based prognostic indices from routine complete-blood-count and biochemistry variables: the neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), lymphocyte-to-monocyte ratio (LMR), systemic immune-inflammation index (SII), Onodera's Prognostic Nutritional Index (PNI), the C-reactive-protein-to-albumin ratio (CAR), and the (modified) Glasgow Prognostic Score (GPS / mGPS). Each index is computed per patient, summarized across the cohort, optionally dichotomized at a literature or data-driven cutpoint, and optionally related to a survival outcome.
Usage
hematologicindices(
data,
neutrophils,
lymphocytes,
platelets,
monocytes = NULL,
albumin = NULL,
albuminUnit = "gdl",
crp = NULL,
indices = list("nlr", "plr", "sii", "pni"),
gpsType = "modified",
survivalTime = NULL,
survivalStatus = NULL,
eventLevel,
survivalIndex = "nlr",
splitMethod = "median",
showIndicesTable = TRUE,
showSurvival = FALSE,
showPlot = TRUE,
showSummary = FALSE,
showExplanation = FALSE
)Arguments
- data
The data as a data frame (one row per patient).
- neutrophils
Absolute neutrophil count (10^9/L).
- lymphocytes
Absolute lymphocyte count (10^9/L).
- platelets
Platelet count (10^9/L).
- monocytes
Absolute monocyte count (10^9/L), for LMR.
- albumin
Serum albumin in g/dL (for PNI). If your data are in g/L, set the albumin unit.
- albuminUnit
Unit of the albumin variable.
- crp
C-reactive protein in mg/L (for CAR and GPS).
- indices
Which indices to compute (subject to the required inputs being supplied).
- gpsType
Original GPS scores low albumin even with normal CRP; mGPS requires elevated CRP.
- survivalTime
Follow-up time, to relate an index to outcome.
- survivalStatus
Event indicator for the survival linkage.
- eventLevel
Level of the status variable representing the event.
- survivalIndex
Which continuous index to dichotomize for the survival comparison.
- splitMethod
How to dichotomize the chosen index for the survival split.
- showIndicesTable
Summary statistics for each computed index.
- showSurvival
Compare survival above vs below the cutpoint of the chosen index.
- showPlot
Plot the index distributions (or survival split).
- showSummary
Plain-language summary.
- showExplanation
Formulas and cut points.
Value
A results object containing:
results$todo | a html | ||||
results$indicesTable | a table | ||||
results$gpsTable | a table | ||||
results$survivalTable | a table | ||||
results$plot | an image | ||||
results$summary | a html | ||||
results$explanation | a html | ||||
results$addIndexToData | an output |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$indicesTable$asDF
as.data.frame(results$indicesTable)
Examples
# \donttest{
hematologicindices(
data = mydata,
neutrophils = "neut", lymphocytes = "lymph",
platelets = "plt", albumin = "alb", crp = "crp")
#> Error in hematologicindices(data = mydata, neutrophils = "neut", lymphocytes = "lymph", platelets = "plt", albumin = "alb", crp = "crp"): argument "eventLevel" is missing, with no default
# }