get_mic: Get MIC meta-data from feature database

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

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
)

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)

Value

vector containing MICs, or dataframe of IDs and MICs

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)

MIC documentation built on April 12, 2025, 2:26 a.m.