Transform Input to Minimum Inhibitory Concentrations (MIC)

This transforms vectors to a new class mic, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.

as.mic(x, na.rm = FALSE)

NA_mic_

is.mic(x)

# S3 method for mic
droplevels(
  x,
  exclude = if (any(is.na(levels(x)))) NULL else NA,
  as.mic = FALSE,
  ...
)

Arguments

x: a character or numeric vector
na.rm: a logical indicating whether missing values should be removed
exclude: factor levels which should be excluded from the result even if present, see droplevels()
as.mic: a logical to indicate whether the <mic> class should be kept, defaults to FALSE

Value

Ordered factor with additional class mic, that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a numeric value.

Details

To interpret MIC values as RSI values, use as.rsi() on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).

This class for MIC values is a quite a special data type: formally it is an ordered factor with valid MIC values as factor levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:

x <- random_mic(10)
x
#> Class <mic>
#>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16

is.factor(x)
#> [1] TRUE

x[1] * 2
#> [1] 32

median(x)
#> [1] 26

This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using numeric values in data analysis, e.g.:

x[x > 4]
#> Class <mic>
#> [1] 16    8     8     64    >=128 32    32    16

df <- data.frame(x, hospital = "A")
subset(df, x > 4) # or with dplyr: df %>% filter(x > 4)
#>        x hospital
#> 1     16        A
#> 5     64        A
#> 6  >=128        A
#> 8     32        A
#> 9     32        A
#> 10    16        A

The following generic functions are implemented for the MIC class: !, !=, %%, %/%, &, *, +, -, /, <, <=, ==, >, >=, ^, |, abs(), acos(), acosh(), all(), any(), asin(), asinh(), atan(), atanh(), ceiling(), cos(), cosh(), cospi(), cummax(), cummin(), cumprod(), cumsum(), digamma(), exp(), expm1(), floor(), gamma(), lgamma(), log(), log1p(), log2(), log10(), max(), mean(), min(), prod(), range(), round(), sign(), signif(), sin(), sinh(), sinpi(), sqrt(), sum(), tan(), tanh(), tanpi(), trigamma() and trunc(). Some functions of the stats package are also implemented: median(), quantile(), mad(), IQR(), fivenum(). Also, boxplot.stats() is supported. Since sd() and var() are non-generic functions, these could not be extended. Use mad() as an alternative, or use e.g. sd(as.numeric(x)) where x is your vector of MIC values.

Using as.double() or as.numeric() on MIC values will remove the operators and return a numeric vector. Do not use as.integer() on MIC values as by the R convention on factors, it will return the index of the factor levels (which is often useless for regular users).

Use droplevels() to drop unused levels. At default, it will return a plain factor. Use droplevels(..., as.mic = TRUE) to maintain the <mic> class.

NA_mic_ is a missing value of the new <mic> class, analogous to e.g. base R's NA_character_.

Stable Lifecycle

The lifecycle of this function is stable. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.

If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.

Examples

mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
is.mic(mic_data)

# this can also coerce combined MIC/RSI values:
as.mic("<=0.002; S") # will return <=0.002

# mathematical processing treats MICs as [numeric] values
fivenum(mic_data)
quantile(mic_data)
all(mic_data < 512)

# interpret MIC values
as.rsi(x = as.mic(2),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")
as.rsi(x = as.mic(4),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")

# plot MIC values, see ?plot
plot(mic_data)
plot(mic_data, mo = "E. coli", ab = "cipro")