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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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35
inst/tinytest/test-data.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. #
@ -23,8 +27,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_true(AMR:::check_dataset_integrity()) # in misc.R
# IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
expect_identical(class(microorganisms$mo), c("mo", "character"))
@ -66,26 +68,14 @@ df <- AMR:::MO_lookup
expect_true(nrow(df[which(df$prevalence == 1), , drop = FALSE]) < nrow(df[which(df$prevalence == 2), , drop = FALSE]))
expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(df$prevalence == 3), , drop = FALSE]))
expect_true(all(c(
"mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "species_id", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species"
"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies", "rank", "ref", "source",
"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
) %in% colnames(df)))
expect_true(all(c(
"fullname", "fullname_new", "ref", "prevalence",
"fullname_lower", "g_species"
) %in% colnames(AMR:::MO.old_lookup)))
expect_inherits(AMR:::MO_CONS, "mo")
expect_identical(
class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list")
)
expect_stdout(print(catalogue_of_life_version()))
uncategorised <- subset(
microorganisms,
genus == "Staphylococcus" &
@ -97,7 +87,8 @@ expect_true(NROW(uncategorised) == 0,
"All staphylococcal species categorised as CoNS/CoPS.",
paste0(
"Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")"
uncategorised$species, " (", uncategorised$mo, ")",
collapse = "\n"
)
)
)