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2026-02-09 12:53:52 +00:00
parent 8b71d0eb99
commit c149bb1f65
92 changed files with 154 additions and 22838 deletions
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12
reference/key_antimicrobials.md
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@@ -195,14 +195,10 @@ strainB <- "SSSIRSSSRSSS"
# those strings can be compared with:
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] TRUE
# TRUE, because I is ignored (as well as missing values)
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] FALSE
# FALSE, because I is not ignored and so the 4th [character] differs
@@ -222,14 +218,6 @@ if (require("dplyr")) {
sum(my_patients$first_regular, na.rm = TRUE)
sum(my_patients$first_weighted, na.rm = TRUE)
}
#> Warning: There were 823 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `first_weighted = first_isolate(col_keyantimicrobials =
#> "keyab")`.
#> Caused by warning:
#> ! in `as.sir()`: 1 result in column 'first_weighted' truncated (8%) that were
#> invalid antimicrobial interpretations: "."
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 822 remaining warnings.
#> [1] 1383
# }
```