2019-01-11 20:37:23 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
# TITLE #
|
2021-02-02 23:57:35 +01:00
|
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
2019-01-11 20:37:23 +01:00
|
|
|
# #
|
|
|
|
|
# SOURCE #
|
2020-07-08 14:48:06 +02:00
|
|
|
# https://github.com/msberends/AMR #
|
2019-01-11 20:37:23 +01:00
|
|
|
# #
|
|
|
|
|
# LICENCE #
|
2020-12-27 00:30:28 +01:00
|
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
2020-10-08 11:16:03 +02:00
|
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
|
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
|
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
2019-01-11 20:37:23 +01:00
|
|
|
# #
|
|
|
|
|
# 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. #
|
2020-01-05 17:22:09 +01:00
|
|
|
# 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. #
|
2020-10-08 11:16:03 +02:00
|
|
|
# #
|
|
|
|
|
# Visit our website for the full manual and a complete tutorial about #
|
2021-02-02 23:57:35 +01:00
|
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
2019-01-11 20:37:23 +01:00
|
|
|
# ==================================================================== #
|
|
|
|
|
|
2021-05-15 21:36:22 +02:00
|
|
|
unjoined <- example_isolates
|
2021-05-16 09:25:36 +02:00
|
|
|
inner <- inner_join_microorganisms(example_isolates)
|
|
|
|
|
left <- left_join_microorganisms(example_isolates)
|
|
|
|
|
semi <- semi_join_microorganisms(example_isolates)
|
|
|
|
|
anti <- anti_join_microorganisms(example_isolates)
|
|
|
|
|
suppressWarnings(right <- right_join_microorganisms(example_isolates))
|
|
|
|
|
suppressWarnings(full <- full_join_microorganisms(example_isolates))
|
2021-05-15 21:36:22 +02:00
|
|
|
|
|
|
|
|
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"))
|
