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(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

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dr. M.S. (Matthijs) Berends
2024-07-16 14:51:57 +02:00
parent 4f9db23684
commit 640888f408
191 changed files with 321091 additions and 89382 deletions
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13
inst/tinytest/test-mo_property.R
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@ -6,9 +6,9 @@
# 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. #
# 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 #
@ -76,8 +76,7 @@ current_grampos_classes <- c(
"Tepidiformia",
"Thermoflexia",
"Thermoleophilia",
"Thermolithobacteria",
"Tissierellia"
"Thermolithobacteria"
)
expect_identical(sort(unique(microorganisms[which(microorganisms$phylum %in% current_grampos_phyla), "class", drop = TRUE])),
current_grampos_classes)
@ -161,6 +160,10 @@ expect_identical(
mo_property("Escherichia coli", property = "gbif"),
mo_gbif("Escherichia coli")
)
expect_identical(
mo_property("Absidia abundans", property = "mycobank"),
mo_mycobank("Absidia abundans")
)
expect_true("Escherichia blattae" %in% mo_synonyms("Shimwellia blattae"))
expect_true(is.list(mo_synonyms(rep("Shimwellia blattae", 2))))