AMR/inst/tinytest/test-mean_amr_distance.R

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R

# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/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
)