MIC (version 1.1.0)

get_mic: Get MIC meta-data from feature database

Description

This function helps extract MICs from a database of results. It is compatible with the PATRIC meta data format when used on a tidy_patric_db object, created using tidy_patric_db().

If more than one MIC is present for a particular observation, the function can return the higher MIC by setting prefer_high_mic = TRUE. If prefer_high_mic = FALSE, the lower MIC will be returned.

Usage

get_mic(
  x,
  ids,
  ab_col,
  id_col = NULL,
  as_mic = TRUE,
  prefer_high_mic = TRUE,
  simplify = TRUE
)

Value

vector containing MICs, or dataframe of IDs and MICs

Arguments

x

dataframe containing meta-data

ids

vector of IDs to get meta-data for

ab_col

column name containing MIC results

id_col

column name containing IDs

as_mic

return as AMR::as.mic

prefer_high_mic

where multiple MIC results per ID, prefer the higher MIC

simplify

return as vector of MICs (vs dataframe)

Examples

df <- data.frame(genome_id = c("a_12", "b_42", "x_21", "x_21", "r_75"),
                 gentamicin = c(0.25, 0.125, 32.0, 16.0, "<0.0125"))
get_mic(df,
        ids = c("b_42", "x_21"),
        ab_col = "gentamicin",
        id_col = "genome_id",
        as_mic = FALSE,
        prefer_high_mic = TRUE,
        simplify = TRUE)