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rename pre-commit hook to pre-commit checks (no-check)
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@ -28,7 +28,7 @@
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# ==================================================================== #
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# Run this file to update the package using:
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# source("data-raw/_pre_commit_hook.R")
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# source("data-raw/_pre_commit_checks.R")
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library(dplyr, warn.conflicts = FALSE)
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try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like
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@ -251,7 +251,7 @@ taxonomy_gbif <- taxonomy_gbif.bak %>%
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kingdom %in% c("Archaea", "Bacteria", "Protozoa") |
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# include all of these fungal orders
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order %in% include_fungal_orders |
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# and all of these important genera (see "data-raw/_pre_commit_hook.R")
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# and all of these important genera (see "data-raw/_pre_commit_checks.R")
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# (they also contain bacteria and protozoa, but these will get prevalence = 2 later on)
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genus %in% AMR:::MO_PREVALENT_GENERA
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) %>%
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@ -1671,7 +1671,7 @@ if (!identical(example_isolates$mo, as.mo(example_isolates$mo, language = NULL))
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# load new data sets again
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devtools::load_all(".")
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source("data-raw/_pre_commit_hook.R")
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source("data-raw/_pre_commit_checks.R")
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devtools::load_all(".")
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if (!identical(intrinsic_resistant$mo, as.mo(intrinsic_resistant$mo, language = NULL))) {
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