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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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29
inst/tinytest/test-antibiogram.R
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@ -99,17 +99,22 @@ expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikaci
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
# the data set could contain a filter for e.g. respiratory specimens
ab8 <- antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"),
ab_transform = NULL)
ab8 <- suppressWarnings(antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
wisca = TRUE))
expect_inherits(ab8, "antibiogram")
expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
expect_equal(colnames(ab8), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
# grouped tibbles
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
ab9 <- example_isolates %>%
group_by(ward, gender) %>%
wisca(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
expect_equal(colnames(ab9), c("ward", "gender", "Piperacillin/tazobactam", "Piperacillin/tazobactam + Gentamicin", "Piperacillin/tazobactam + Tobramycin"))
}
# Generate plots with ggplot2 or base R --------------------------------
@ -123,6 +128,9 @@ expect_silent(plot(ab5))
expect_silent(plot(ab6))
expect_silent(plot(ab7))
expect_silent(plot(ab8))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_silent(plot(ab9))
}
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(ab1), "gg")
@ -133,4 +141,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(ab6), "gg")
expect_inherits(ggplot2::autoplot(ab7), "gg")
expect_inherits(ggplot2::autoplot(ab8), "gg")
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_inherits(ggplot2::autoplot(ab9), "gg")
}
}

43
inst/tinytest/test-top_n_microorganisms.R Normal file
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@ -0,0 +1,43 @@
# ==================================================================== #
# 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/ #
# ==================================================================== #
out1 <- top_n_microorganisms(example_isolates, n = 3)
out2 <- top_n_microorganisms(example_isolates, n = 5, property = "genus")
out3 <- top_n_microorganisms(example_isolates, n = 5, property = "genus", n_for_each = 3)
expect_equal(NROW(out1), 1015, tolerance = 0.5)
expect_equal(NROW(out2), 1742, tolerance = 0.5)
expect_equal(NROW(out3), 1497, tolerance = 0.5)
expect_equal(length(table(out1$mo)), 3, tolerance = 0.5)
expect_equal(length(table(out2$mo)), 39, tolerance = 0.5)
expect_equal(length(table(out3$mo)), 13, tolerance = 0.5)
expect_equal(length(unique(mo_genus(out2$mo))), 5, tolerance = 0.5)
expect_equal(length(unique(mo_genus(out3$mo))), 5, tolerance = 0.5)