epidm (version 1.0.6)

respeciate_generic: Respeciate unspecified samples

Description

Some samples within SGSS are submitted by laboratories as "GENUS SP" or "GENUS UNNAMED". However, they may also have a fully identified sample taken from the same site within a recent time period. This function captures species_col from another sample within X-days of an unspeciated isolate. Respeciation is restricted to organisms of the same genus; species will not be inferred from isolates belonging to a different genus. Trailing "UNNAMED" is normalised to "SP" before any processing.

Usage

respeciate_generic(
  x,
  group_vars,
  species_col,
  date_col,
  window = c(0:Inf),
  .forceCopy = FALSE
)

Value

a data.table with a recharacterised species_col column

Arguments

x

a data.frame or data.table object

group_vars

the minimum grouping set of variables for like samples in a character vector; suggest c('patient_id','specimen_type') - genus will automatically be included in the groupby. This is built from the species_col

species_col

a character containing the column with the organism species_col name

date_col

a character containing the column with the specimen/sample date_col

window

an integer representing the number of days for which you will allow a sample to be respeciated

.forceCopy

Logical (default FALSE). If FALSE, the input is converted to a data.table and modified by reference. If TRUE, the input must already be a data.table, and the function will create an explicit copy to avoid modifying the original object.

Examples

df <- data.frame(
ptid = c(round(runif(25,1,5))),
spec = sample(c("KLEBSIELLA SP",
                "KLEBSIELLA UNNAMED",
                "KLEBSIELLA PNEUMONIAE",
                "KLEBEIELLA OXYTOCA"),
              25,replace = TRUE),
type = "BLOOD",
specdate = sample(seq.Date(Sys.Date()-21,Sys.Date(),"day"),25,replace = TRUE)
)

respeciate_generic(x=df,
                   group_vars=c('ptid','type'),
                   species_col='spec',
                   date_col='specdate',
                   window = 14)[]