cleanse_urine_organism_names {MIMER} | R Documentation |
Cleanse organism names in Urine samples
Description
Function to preprocess organism names in urine samples. Removes specified strings, maps certain values to standard ones, and filters out unwanted values.
Usage
cleanse_urine_organism_names(
data,
column_name = "org_name",
strings_to_remove = NULL,
standard_mapping = NULL,
filter_values = NULL
)
Arguments
data |
The dataframe containing urine sample data. |
column_name |
The name of the column containing organism names. |
strings_to_remove |
A character vector of strings to be removed from the organism names. |
standard_mapping |
A named character vector specifying mappings of values to standard ones. |
filter_values |
A character vector of values to be filtered out from the organism names. |
Value
The preprocessed dataframe.
Examples
data <- data.frame(org_name = c("PRESUMPTIVELY Streptococcus",
"MODERATE Escherichia coli",
"S. AUREUS POSITIVE",
"CANCELLED Influenza A"))
data <- cleanse_urine_organism_names(data,
column_name = "org_name",
strings_to_remove = c("POSITIVE FOR",
"PRESUMPTIVELY","PRESUMPTIVE",
"PROBABLE", "IDENTIFICATION",
"RESEMBLING", "SEEN",
"MODERATE", "FEW", "BETA",
"METHICILLIN RESISTANT",
"NUTRITIONALLY VARIANT",
"NOT C. PERFRINGENS OR C. SEPTICUM",
"-LACTAMASE POSITIVE",
"-LACTAMASE NEGATIVE",
"VIRAL ANTIGEN",
"CANDIDA INCONSPICUA",
"/POSADASII",
"NOT FUMIGATUS, FLAVUS OR NIGER",
"MRSA POSITIVE", "MRSA NEGATIVE",
"HISTOLYTICA/DISPAR"),
standard_mapping = c(
"NON-FERMENTER" = "STREPTOCOCCUS",
"ABIOTROPHIA/GRANULICATELLA" =
"STREPTOCOCCUS",
"S. AUREUS POSITIVE" =
"STAPHYLOCOCCUS AUREUS",
"ASPERGILLUS FUMIGATUS COMPLEX" =
"ASPERGILLUS FUMIGATUS",
"(CRYPTOSPORIDIUM PARVUM OOCYSTS|
CUNNINGHAMELLA BERTHOLLETIAE|
EPIDERMOPHYTON FLOCCOSUM|
EXOPHIALA JEANSELMEI COMPLEX|
SCEDOSPORIUM|
NEOASCOCHYTA DESMAZIERI|
NEOSCYTALIDIUM DIMIDIATUM|
LOMENTOSPORA|NEUROSPORA|
PERONEUTYPA SCOPARIA|
SPOROTHRIX SCHENCKII COMPLEX|
ZYGOSACCHAROMYCES FERMENTATI)" =
"UNKNOWN FUNGUS"
),
filter_values = c('CANCELLED|VIRUS|SIMPLEX|PARAINFLUENZA|
INFLUENZA A|INFLUENZA B|TICK|
AFB GROWN|GRAM VARIABLE RODS|HYMENOLEPIS'))
[Package MIMER version 1.0.3 Index]