# ==================================================================== #
# 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, 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.                 #
# 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/   #
# ==================================================================== #

unjoined <- example_isolates
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))

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"))