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2026-03-20 16:11:30 +00:00
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reference/mean_amr_distance.md
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@@ -131,8 +131,8 @@ y
#> 9 I R 28 16 2
#> 10 J S 22 16 4
mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
#> and "tobr"
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> "tobr"
#> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032
#> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366
y$amr_distance <- mean_amr_distance(y, is.mic(y))
@@ -158,8 +158,8 @@ if (require("dplyr")) {
) %>%
arrange(check_id_C)
}
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
#> and "tobr"
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent", and
#> "tobr"
#> id amox cipr gent tobr amr_distance check_id_C
#> 1 C S 27 16 32 0.34372779 0.00000000
#> 2 I R 28 16 2 0.36899264 0.02526485
@@ -180,8 +180,8 @@ if (require("dplyr")) {
mutate(dist = mean_amr_distance(.)) %>%
arrange(mo, dist)
}
#> ℹ Using column 'mo' as input for `mo_genus()`
#> ℹ Using column 'mo' as input for `mo_species()`
#> ℹ Using column 'mo' as input for `mo_genus()` (`?AMR::mo_genus()`)
#> ℹ Using column 'mo' as input for `mo_species()` (`?AMR::mo_species()`)
#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
#> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"
#> # A tibble: 63 × 5