x <- random_mic(10)
x
#> Class 'mic'
-#> [1] 16 0.25 8 0.025 128 4 0.0625 0.0625 <=0.002
-#> [10] 0.025
+#> [1] 0.125 4 0.025 32 <=0.001 128 0.002 16 <=0.001
+#> [10] 1
mean_amr_distance(x)
-#> [1] 1.0547374 -0.1257265 0.8579935 -0.7792959 1.6449694 0.6612495
-#> [7] -0.5192145 -0.5192145 -1.4962027 -0.7792959
+#> [1] -0.1673708 0.6088797 -0.5278503 1.0746300 -1.2488094 1.3851301
+#> [7] -1.0935593 0.9193799 -1.2488094 0.2983795
y <- data.frame(
id = LETTERS[1:10],
@@ -214,38 +214,38 @@
tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")
)
y
-#> id amox cipr gent tobr
-#> 1 A 16 0.5 4 1
-#> 2 B >=32 0.5 1 8
-#> 3 C 4 0.25 2 4
-#> 4 D 16 0.5 4 4
-#> 5 E 8 >=1 4 4
-#> 6 F 2 0.125 4 1
-#> 7 G 1 0.5 >=8 0.5
-#> 8 H 2 >=1 4 2
-#> 9 I 16 >=1 >=8 1
-#> 10 J 16 0.125 4 4
+#> id amox cipr gent tobr
+#> 1 A >=64 4 1 0.5
+#> 2 B 4 1 >=4 4
+#> 3 C 16 <=0.125 >=4 4
+#> 4 D 8 2 2 2
+#> 5 E 32 1 1 1
+#> 6 F 8 0.25 >=4 0.5
+#> 7 G >=64 0.5 2 4
+#> 8 H 4 0.5 >=4 1
+#> 9 I >=64 2 1 0.5
+#> 10 J 16 <=0.125 2 0.5
mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
#> "id" and "tobr"
#> Warning: NAs introduced by coercion
-#> [1] 0.036743946 0.196829201 -0.376851467 0.425339766 0.497315583
-#> [6] -0.848366515 -0.464960905 0.006554142 0.542471648 -0.015075399
+#> [1] 0.12023536 0.33318132 0.20872945 0.16343985 -0.14151184 -0.36277928
+#> [7] 0.52860021 -0.18662082 -0.02573319 -0.63754106
y$amr_distance <- mean_amr_distance(y, where(is.mic))
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and
#> "tobr"
y[order(y$amr_distance), ]
-#> id amox cipr gent tobr amr_distance
-#> 6 F 2 0.125 4 1 -0.848366515
-#> 7 G 1 0.5 >=8 0.5 -0.464960905
-#> 3 C 4 0.25 2 4 -0.376851467
-#> 10 J 16 0.125 4 4 -0.015075399
-#> 8 H 2 >=1 4 2 0.006554142
-#> 1 A 16 0.5 4 1 0.036743946
-#> 2 B >=32 0.5 1 8 0.196829201
-#> 4 D 16 0.5 4 4 0.425339766
-#> 5 E 8 >=1 4 4 0.497315583
-#> 9 I 16 >=1 >=8 1 0.542471648
+#> id amox cipr gent tobr amr_distance
+#> 10 J 16 <=0.125 2 0.5 -0.63754106
+#> 6 F 8 0.25 >=4 0.5 -0.36277928
+#> 8 H 4 0.5 >=4 1 -0.18662082
+#> 5 E 32 1 1 1 -0.14151184
+#> 9 I >=64 2 1 0.5 -0.02573319
+#> 1 A >=64 4 1 0.5 0.12023536
+#> 4 D 8 2 2 2 0.16343985
+#> 3 C 16 <=0.125 >=4 4 0.20872945
+#> 2 B 4 1 >=4 4 0.33318132
+#> 7 G >=64 0.5 2 4 0.52860021
if (require("dplyr")) {
y %>%
@@ -257,17 +257,17 @@
}
#> 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 4 0.25 2 4 -0.376851467 0.00000000
-#> 2 G 1 0.5 >=8 0.5 -0.464960905 0.08810944
-#> 3 J 16 0.125 4 4 -0.015075399 0.36177607
-#> 4 H 2 >=1 4 2 0.006554142 0.38340561
-#> 5 A 16 0.5 4 1 0.036743946 0.41359541
-#> 6 F 2 0.125 4 1 -0.848366515 0.47151505
-#> 7 B >=32 0.5 1 8 0.196829201 0.57368067
-#> 8 D 16 0.5 4 4 0.425339766 0.80219123
-#> 9 E 8 >=1 4 4 0.497315583 0.87416705
-#> 10 I 16 >=1 >=8 1 0.542471648 0.91932312
+#> id amox cipr gent tobr amr_distance check_id_C
+#> 1 C 16 <=0.125 >=4 4 0.20872945 0.00000000
+#> 2 D 8 2 2 2 0.16343985 0.04528960
+#> 3 A >=64 4 1 0.5 0.12023536 0.08849408
+#> 4 B 4 1 >=4 4 0.33318132 0.12445187
+#> 5 I >=64 2 1 0.5 -0.02573319 0.23446263
+#> 6 G >=64 0.5 2 4 0.52860021 0.31987077
+#> 7 E 32 1 1 1 -0.14151184 0.35024128
+#> 8 H 4 0.5 >=4 1 -0.18662082 0.39535027
+#> 9 F 8 0.25 >=4 0.5 -0.36277928 0.57150872
+#> 10 J 16 <=0.125 2 0.5 -0.63754106 0.84627050
if (require("dplyr")) {
# support for groups
example_isolates %>%
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index 3e653333..103e2265 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9061
+ 1.8.2.9062