P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 20:21:55 +02:00
Code Releases Activity

update mo algorithm

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-12-20 16:14:04 +01:00
parent b1b7534c78
commit f0a2cdbf5e
21 changed files with 48772 additions and 48747 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
R/mo_matching_score.R
View File

@ -52,14 +52,16 @@
#'
#' The grouping into human pathogenic prevalence (\eqn{p}) is based on recent work from Bartlett *et al.* (2022, \doi{10.1099/mic.0.001269}) who extensively studied medical-scientific literature to categorise all bacterial species into these groups:
#'
#' - **Established**, if a taxonomic species has infected at least three persons in three or more references. These records have `prevalence = 1.0` in the [microorganisms] data set.
#' - **Putative**, if a taxonomic species has fewer than three known cases. These records have `prevalence = 2.0` in the [microorganisms] data set.
#' - **Established**, if a taxonomic species has infected at least three persons in three or more references. These records have `prevalence = 1.0` in the [microorganisms] data set;
#' - **Putative**, if a taxonomic species has fewer than three known cases. These records have `prevalence = 1.25` in the [microorganisms] data set.
#'
#' Furthermore,
#'
#' - Any *other* bacterial genus, species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 2.5` in the [microorganisms] data set.
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, also has `prevalence = 2.5` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`.
#' - All other records have `prevalence = 3.0` in the [microorganisms] data set.
#' - Any genus present in the **established** list also has `prevalence = 1.0` in the [microorganisms] data set;
#' - Any other genus present in the **putative** list has `prevalence = 1.25` in the [microorganisms] data set;
#' - Any other species or subspecies of which the genus is present in the two aforementioned groups, has `prevalence = 1.5` in the [microorganisms] data set;
#' - Any *non-bacterial* genus, species or subspecies of which the genus is present in the following list, has `prevalence = 1.5` in the [microorganisms] data set: `r vector_or(MO_PREVALENT_GENERA, quotes = "*")`;
#' - All other records have `prevalence = 2.0` in the [microorganisms] data set.
#'
#' When calculating the matching score, all characters in \eqn{x} and \eqn{n} are ignored that are other than A-Z, a-z, 0-9, spaces and parentheses.
#'