Calculate the matching score for microorganisms — mo_matching

This helper function is used by as.mo() to determine the most probable match of taxonomic records, based on user input.

mo_matching_score(x, n)

Arguments

x	Any user input value(s)
n	A full taxonomic name, that exists in `microorganisms$fullname`
uncertainty	The level of uncertainty set in `as.mo()`, see `allow_uncertain` in that function (here, it defaults to 1, but is automatically determined in `as.mo()` based on the number of transformations needed to get to a result)

Matching score for microorganisms

With ambiguous user input in as.mo() and all the mo_* functions, the returned results are chosen based on their matching score using mo_matching_score(). This matching score $m$ is calculated as:

$$m_{(x, n)} = \frac{l_{n} - 0.5 \times \min \begin{cases}l_{n} \\ \operatorname{lev}(x, n)\end{cases}}{l_{n} p k}$$

where:

$x$ is the user input;
$n$ is a taxonomic name (genus, species and subspecies);
$l_{n}$ is the length of the taxonomic name;
$\operatorname{lev}$ is the Levenshtein distance function;
$p$ is the human pathogenic prevalence, categorised into group $1$, $2$ and $3$ (see Details in ?as.mo), meaning that $p = \{1, 2 , 3\}$;
$k$ is the kingdom index, set as follows: Bacteria = $1$, Fungi = $2$, Protozoa = $3$, Archaea = $4$, and all others = $5$, meaning that $k = \{1, 2 , 3, 4, 5\}$.

All matches are sorted descending on their matching score and for all user input values, the top match will be returned.

Examples

as.mo("E. coli")
mo_uncertainties()

mo_matching_score("E. coli", "Escherichia coli")