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Lookup table switch handler

Source: R/lookup_recode.R
lookup_recode.Rd

[Stable] A function to call an epidm lookup table and recode where we are aware of a new value.

Built in are the organism re-classifications and specimen_type groupings and a manual mode.

Usage

lookup_recode(
  src,
  type = c("species", "specimen", "inpatient_admission_method",
    "inpatient_discharge_destination", "ecds_destination_code", "manual"),
  .import = NULL
)

Arguments

src

a character, vector or column containing the value(s) to be referenced

type

a character value to denote the lookup table used

.import

a list in the order list(new,old) containing the values for another lookup table existing in the environment

Value

a list object of the recoded field

Examples

df <- data.frame(
  spec = c(
    sample(grep(")",
                respeciate_organism$previous_organism_name,
                value=TRUE,
                invert = TRUE),
           9),
    "ESCHERICHIA COLI","SARS-COV-2","CANDIDA AUREUS"),
  type = sample(specimen_type_grouping$specimen_type,12),
  date = sample(seq.Date(from = Sys.Date()-365,
                         to = Sys.Date(),
                         by = "day"),12)
)
df <- df[order(df$date),]

# show the data before the changes
df
#>                                     spec              type       date
#> 8                   CORYNEBACTERIUM EQUI         BRONCHIAL 2023-09-20
#> 7  ALCALIGENES XYLOSOXIDANS XYLOSOXIDANS              BURN 2023-10-01
#> 9                  RHIZOBIUM RADIOBACTER             WOUND 2023-10-28
#> 11                            SARS-COV-2             PENIS 2024-01-16
#> 3                   CITROBACTER DIVERSUS   IV CATHETER TIP 2024-01-28
#> 4                    PANTOEA AGGLOMERANS ARTERIAL LINE TIP 2024-01-29
#> 6        CALYMMATOBACTERIUM GRANULOMATIS        SKIN ULCER 2024-03-20
#> 5                  ANAEROCOCCUS PREVOTII    DENTAL ABSCESS 2024-03-23
#> 2                 STREPTOCOCCUS FAECALIS  PERITONEAL FLUID 2024-04-15
#> 1                       STOMATOCOCCUS SP              BONE 2024-05-05
#> 10                      ESCHERICHIA COLI           TRACHEA 2024-05-10
#> 12                        CANDIDA AUREUS        BIOPSY-NOS 2024-05-11

# check the lookup tables
# observe the changes
head(respeciate_organism[1:2])
#>                  previous_organism_name       organism_species_name
#> 1             ALCALIGENES DENITRIFICANS ACHROMOBACTER DENITRIFICANS
#> 2                ALCALIGENES PIECHAUDII    ACHROMOBACTER PIECHAUDII
#> 3              ALCALIGENES XYLOSOXIDANS  ACHROMOBACTER XYLOSOXIDANS
#> 4 ALCALIGENES XYLOSOXIDANS XYLOSOXIDANS  ACHROMOBACTER XYLOSOXIDANS
#> 5                ACTINOBACULUM SCHAALII       ACTINOTIGNUM SCHAALII
#> 6          TETRATHIOBACTER KASHMIRENSIS      ADVENELLA KASHMIRENSIS
df$species <- lookup_recode(df$spec,'species')
df[,c('spec','species','date')]
#>                                     spec                     species       date
#> 8                   CORYNEBACTERIUM EQUI            RHODOCOCCUS EQUI 2023-09-20
#> 7  ALCALIGENES XYLOSOXIDANS XYLOSOXIDANS  ACHROMOBACTER XYLOSOXIDANS 2023-10-01
#> 9                  RHIZOBIUM RADIOBACTER   AGROBACTERIUM TUMEFACIENS 2023-10-28
#> 11                            SARS-COV-2                  SARS-COV-2 2024-01-16
#> 3                   CITROBACTER DIVERSUS          CITROBACTER KOSERI 2024-01-28
#> 4                    PANTOEA AGGLOMERANS         PANTOEA AGGLOMERANS 2024-01-29
#> 6        CALYMMATOBACTERIUM GRANULOMATIS    KLEBSIELLA GRANULOMATIS  2024-03-20
#> 5                  ANAEROCOCCUS PREVOTII PEPTOSTREPTOCOCCUS PREVOTII 2024-03-23
#> 2                 STREPTOCOCCUS FAECALIS       ENTEROCOCCUS FAECALIS 2024-04-15
#> 1                       STOMATOCOCCUS SP                   ROTHIA SP 2024-05-05
#> 10                      ESCHERICHIA COLI            ESCHERICHIA COLI 2024-05-10
#> 12                        CANDIDA AUREUS              CANDIDA AUREUS 2024-05-11

head(specimen_type_grouping)
#>      specimen_type specimen_group
#> 1            BLOOD          Blood
#> 2       CORD BLOOD          Blood
#> 3            JOINT Bones & Joints
#> 4   SYNOVIAL FLUID Bones & Joints
#> 5             BONE Bones & Joints
#> 6 JOINT PROSTHESIS Bones & Joints
df$grp <- lookup_recode(df$type,'specimen')
df[,c('species','type','grp','date')]
#>                        species              type                     grp
#> 8             RHODOCOCCUS EQUI         BRONCHIAL Lower Respiratory Tract
#> 7   ACHROMOBACTER XYLOSOXIDANS              BURN           Swabs-General
#> 9    AGROBACTERIUM TUMEFACIENS             WOUND             Wound Swabs
#> 11                  SARS-COV-2             PENIS                 Genital
#> 3           CITROBACTER KOSERI   IV CATHETER TIP            Tips & Lines
#> 4          PANTOEA AGGLOMERANS ARTERIAL LINE TIP            Tips & Lines
#> 6     KLEBSIELLA GRANULOMATIS         SKIN ULCER           Swabs-General
#> 5  PEPTOSTREPTOCOCCUS PREVOTII    DENTAL ABSCESS           URT/Mouth/Ear
#> 2        ENTEROCOCCUS FAECALIS  PERITONEAL FLUID                  Fluids
#> 1                    ROTHIA SP              BONE          Bones & Joints
#> 10            ESCHERICHIA COLI           TRACHEA Lower Respiratory Tract
#> 12              CANDIDA AUREUS        BIOPSY-NOS           Swabs-General
#>          date
#> 8  2023-09-20
#> 7  2023-10-01
#> 9  2023-10-28
#> 11 2024-01-16
#> 3  2024-01-28
#> 4  2024-01-29
#> 6  2024-03-20
#> 5  2024-03-23
#> 2  2024-04-15
#> 1  2024-05-05
#> 10 2024-05-10
#> 12 2024-05-11

# for a tidyverse use
# df %>% mutate(spec=lookup_recode(spec,'species))

# manual input of your own lookup
# .import=list(new,old)
lookup_recode(
  "ALCALIGENES DENITRIFICANS",
  type = 'manual',
  .import=list(respeciate_organism$organism_species_name,
               respeciate_organism$previous_organism_name)
  )
#> [1] "ACHROMOBACTER DENITRIFICANS"