mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
64 lines
3.0 KiB
R
64 lines
3.0 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# CITE AS #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# doi:10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# 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 the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
vctr_disk <- as.disk(c(20:25))
|
|
vctr_mic <- as.mic(2^c(0:5))
|
|
vctr_sir <- as.sir(c("S", "S", "I", "I", "R", "R"))
|
|
|
|
expect_identical(
|
|
mean_amr_distance(vctr_disk),
|
|
(as.double(vctr_disk) - mean(as.double(vctr_disk))) / sd(as.double(vctr_disk))
|
|
)
|
|
|
|
expect_identical(
|
|
mean_amr_distance(vctr_mic),
|
|
(log2(vctr_mic) - mean(log2(vctr_mic))) / sd(log2(vctr_mic))
|
|
)
|
|
|
|
expect_identical(
|
|
mean_amr_distance(vctr_sir, combine_SI = FALSE),
|
|
(c(1, 1, 2, 2, 3, 3) - mean(c(1, 1, 2, 2, 3, 3))) / sd(c(1, 1, 2, 2, 3, 3))
|
|
)
|
|
expect_identical(
|
|
mean_amr_distance(vctr_sir, combine_SI = TRUE),
|
|
(c(1, 1, 1, 1, 3, 3) - mean(c(1, 1, 1, 1, 3, 3))) / sd(c(1, 1, 1, 1, 3, 3))
|
|
)
|
|
|
|
expect_equal(
|
|
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk)),
|
|
c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
|
|
tolerance = 0.00001
|
|
)
|
|
|
|
expect_equal(
|
|
mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_sir, TOB = vctr_disk), 2:3),
|
|
c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
|
|
tolerance = 0.00001
|
|
)
|