P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 12:31:58 +02:00
Code Releases Activity

(v1.4.0) matching score update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-10-08 11:16:03 +02:00
parent c04dc852cf
commit 28e77680c5
261 changed files with 1488 additions and 1171 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
R/zzz.R
View File

@ -1,22 +1,26 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# Antimicrobial Resistance (AMR) Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
.onLoad <- function(libname, pkgname) {
@ -49,14 +53,14 @@
# developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("tibble::type_sum", "ab")
s3_register("pillar::pillar_shaft", "mo")
s3_register("tibble::type_sum", "mo")
s3_register("pillar::pillar_shaft", "rsi")
s3_register("tibble::type_sum", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("tibble::type_sum", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "ab")
s3_register("tibble::type_sum", "mo")
s3_register("tibble::type_sum", "rsi")
s3_register("tibble::type_sum", "mic")
s3_register("tibble::type_sum", "disk")
# Support for frequency tables from the cleaner package
s3_register("cleaner::freq", "mo")
@ -81,8 +85,8 @@
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
# Determination of which staphylococcal species are CoNS/CoPS according to Becker et al.:
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
# returns class <mo>
# https://cmr.asm.org/content/cmr/27/4/870/F6.large.jpg
# this function returns class <mo>
MO_staph <- AMR::microorganisms
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {