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dr. M.S. (Matthijs) Berends 2022-09-18 16:35:45 +02:00
parent 835cf7c32d
commit a20293a0a3
3 changed files with 5 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.1.9055 Version: 1.8.1.9056
Date: 2022-09-18 Date: 2022-09-18
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

6
NEWS.md
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# AMR 1.8.1.9055 # AMR 1.8.1.9056
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!
@ -49,7 +49,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* An enormous lot of code cleaning, fixing some small bugs on the way * An enormous lot of code cleaning, fixing some small bugs on the way
# `AMR` 1.8.1 # AMR 1.8.1
### Changed ### Changed
* Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA` * Fix for using `as.rsi()` on values containing capped values (such as `>=`), sometimes leading to `NA`
@ -69,7 +69,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
* Fix for size of some image elements, as requested by CRAN * Fix for size of some image elements, as requested by CRAN
# `AMR` 1.8.0 # AMR 1.8.0
### Breaking changes ### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version

16
inst/tinytest/test-data.R
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@ -23,8 +23,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # 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 # IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo))) expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
expect_identical(class(microorganisms$mo), c("mo", "character")) expect_identical(class(microorganisms$mo), c("mo", "character"))
@ -68,24 +66,12 @@ expect_true(nrow(df[which(df$prevalence == 2), , drop = FALSE]) < nrow(df[which(
expect_true(all(c( expect_true(all(c(
"mo", "fullname", "mo", "fullname",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "species_id", "source", "prevalence", "snomed", "rank", "ref", "lpsn", "gbif", "status", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species" "kingdom_index", "fullname_lower", "g_species"
) %in% colnames(df))) ) %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_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( uncategorised <- subset(
microorganisms, microorganisms,
genus == "Staphylococcus" & genus == "Staphylococcus" &