cleanse_urine_organism_names: Cleanse organism names in Urine samples

In MIMER: Data Wrangling for Antimicrobial Resistance Studies

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'))

MIMER documentation built on June 22, 2024, 9:41 a.m.