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(v2.1.1.9267) update ATCs
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@ -30,7 +30,7 @@
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test_that("test-sir.R", {
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skip_on_cran()
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# Existing SIR ------------------------------------------------------------
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# Existing SIR ----------------------------------------------------------
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# we must only have EUCAST and CLSI, because otherwise the rules in as.sir() will fail
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expect_identical(
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@ -124,7 +124,7 @@ test_that("test-sir.R", {
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expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))
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# Human -------------------------------------------------------------------
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# Human -----------------------------------------------------------------
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# allow for guideline length > 1
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expect_equal(
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@ -345,7 +345,7 @@ test_that("test-sir.R", {
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)
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# Veterinary --------------------------------------------------------------
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# Veterinary ------------------------------------------------------------
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# multiple guidelines
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sir_history <- sir_interpretation_history(clean = TRUE)
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@ -390,7 +390,7 @@ test_that("test-sir.R", {
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)
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)
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# ECOFF -------------------------------------------------------------------
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# ECOFF -----------------------------------------------------------------
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expect_equal(
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suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF")),
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@ -398,4 +398,42 @@ test_that("test-sir.R", {
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)
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# old method
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expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
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# Parallel computing ----------------------------------------------------
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# MB 29 Apr 2025: I have run the code of AVC, PEI, Canada (dataset of 2854x65), and compared it like this:
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# system.time({
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# data_2022_2023_SIR_parallel <- data_2022_2023_clean |>
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# as.sir(amikacin:tiamulin,
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# col_mo = "mo",
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# guideline = "CLSI 2024",
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# host = "Species",
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# uti = "isUTI",
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# parallel = TRUE)
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# })
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# # user system elapsed
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# # 271.424 2.767 45.762
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#
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# history_parallel <- sir_interpretation_history(clean = TRUE)
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#
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# system.time({
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# data_2022_2023_SIR <- data_2022_2023_clean |>
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# as.sir(amikacin:tiamulin,
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# col_mo = "mo",
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# guideline = "CLSI 2024",
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# host = "Species",
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# uti = "isUTI")
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# })
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# # user system elapsed
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# # 120.637 5.406 128.835
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# history <- sir_interpretation_history()
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# and then got this:
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# identical(history[, -1], history_parallel[, -1])
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#> [1] TRUE
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# so parallel on Apple M2 is 2.8x faster, with identical history -> GREAT!
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})
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