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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
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parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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46
inst/tinytest/test-mo_property.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE 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. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -25,7 +29,7 @@
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
@ -55,7 +59,7 @@ expect_inherits(mo_synonyms(c("Candida albicans", "Escherichia coli")), "list")
expect_equal(names(mo_info("Escherichia coli")), c(
"kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies",
"synonyms", "gramstain", "url", "ref",
"status", "synonyms", "gramstain", "url", "ref",
"snomed"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
@ -64,31 +68,29 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
expect_equal(mo_year("Escherichia coli"), 1919)
expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
expect_true(mo_url("Candida albicans") %like% "gbif.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
MOs <- microorganisms
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en", keep_synonyms = TRUE))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
expect_stdout(print(mo_gramstain("Escherichia coli", language = "en")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "de")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "nl")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "es")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "pt")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
gr <- mo_gramstain("Escherichia coli", language = NULL)
for (l in AMR:::LANGUAGES_SUPPORTED[-1]) {
expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l))
}
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE) # should be transformable to English again
expect_identical(mo_name(dutch, language = NULL, keep_synonyms = TRUE),
microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names
# manual property function
expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
expect_identical(
mo_property("Escherichia coli", property = "fullname"),
@ -103,12 +105,16 @@ expect_identical(
mo_species("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "species_id"),
mo_property("Escherichia coli", property = "lpsn"),
mo_lpsn("Escherichia coli")
)
expect_identical(
mo_property("Escherichia coli", property = "gbif"),
mo_gbif("Escherichia coli")
)
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli"))
# old codes must throw a warning in mo_* family