P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-08-28 06:22:12 +02:00
Code Releases Activity

(v1.3.0.9033) skimr fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-28 11:00:59 +02:00
parent 519aada54f
commit 36ec8b0d81
27 changed files with 71 additions and 70 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
R/mo_matching_score.R
View File

@@ -25,7 +25,7 @@
#' @param x Any user input value(s)
#' @param n A full taxonomic name, that exists in [`microorganisms$fullname`][microorganisms]
#' @section Matching score for microorganisms:
#' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, ranging from 0 to 100%, is calculated as:
#' With ambiguous user input in [as.mo()] and all the [`mo_*`][mo_property()] functions, the returned results are chosen based on their matching score using [mo_matching_score()]. This matching score \eqn{m}, is calculated as:
#'
#' \deqn{m_{(x, n)} = \frac{l_{n} - 0.5 \cdot \min \begin{cases}l_{n} \\ \operatorname{lev}(x, n)\end{cases}}{l_{n} \cdot p_{n} \cdot k_{n}}}{m(x, n) = ( l_n * min(l_n, lev(x, n) ) ) / ( l_n * p_n * k_n )}
#'
@@ -66,7 +66,7 @@ mo_matching_score <- function(x, n) {
var_F <- nchar(n)
# L = modified Levenshtein distance
var_L <- levenshtein
# P = Prevalence (1 to 3)
# P = prevalence (1 to 3), see ?as.mo
var_P <- MO_lookup[match(n, MO_lookup$fullname), "prevalence", drop = TRUE]
# K = kingdom index (Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5)
var_K <- MO_lookup[match(n, MO_lookup$fullname), "kingdom_index", drop = TRUE]