mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 11:26:11 +01:00
68 lines
3.2 KiB
R
Executable File
68 lines
3.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# 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 the full manual and a complete tutorial about #
|
|
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
context("join_microorganisms.R")
|
|
|
|
test_that("joins work", {
|
|
skip_on_cran()
|
|
unjoined <- example_isolates
|
|
inner <- example_isolates %>% inner_join_microorganisms()
|
|
left <- example_isolates %>% left_join_microorganisms()
|
|
semi <- example_isolates %>% semi_join_microorganisms()
|
|
anti <- example_isolates %>% anti_join_microorganisms()
|
|
suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
|
|
suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
|
|
|
|
expect_true(ncol(unjoined) < ncol(inner))
|
|
expect_true(nrow(unjoined) == nrow(inner))
|
|
|
|
expect_true(ncol(unjoined) < ncol(left))
|
|
expect_true(nrow(unjoined) == nrow(left))
|
|
|
|
expect_true(ncol(semi) == ncol(semi))
|
|
expect_true(nrow(semi) == nrow(semi))
|
|
|
|
expect_true(nrow(anti) == 0)
|
|
|
|
expect_true(nrow(unjoined) < nrow(right))
|
|
expect_true(nrow(unjoined) < nrow(full))
|
|
|
|
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
|
|
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
|
|
|
|
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
|
|
|
|
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
|
|
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
|
|
|
|
expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
|
|
expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
|
|
|
|
library(dplyr, warn.conflicts = FALSE)
|
|
x <- tibble(bact = as.mo("E.coli"))
|
|
expect_warning(left_join_microorganisms(x %>% group_by(bact), "bact"))
|
|
|
|
})
|