x <- random_mic(10)
x
#> Class 'mic'
-#> [1] >=128 2 32 <=0.002 64 <=0.002 0.005 8 0.025
-#> [10] 64
+#> [1] 0.125 >=2 0.005 0.01 >=2 1 0.5 0.001 0.001 0.002
mean_amr_distance(x)
-#> [1] 1.0898120 0.1928148 0.7908130 -1.2970653 0.9403125 -1.2970653
-#> [7] -1.0994377 0.4918139 -0.7523105 0.9403125
+#> [1] 0.3309983 1.2029031 -0.6812519 -0.4632756 1.2029031 0.9849269
+#> [7] 0.7669507 -1.1873769 -1.1873769 -0.9694007
y <- data.frame(
id = LETTERS[1:10],
@@ -214,38 +213,38 @@
tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")
)
y
-#> id amox cipr gent tobr
-#> 1 A 16 <=0.0625 0.5 4
-#> 2 B 4 0.5 0.5 1
-#> 3 C 16 0.5 0.5 <=0.5
-#> 4 D 8 <=0.0625 0.5 <=0.5
-#> 5 E 4 0.25 0.25 >=16
-#> 6 F 16 0.5 4 4
-#> 7 G 8 <=0.0625 0.5 1
-#> 8 H >=32 0.5 1 2
-#> 9 I >=32 1 0.5 >=16
-#> 10 J 4 0.25 0.25 4
+#> id amox cipr gent tobr
+#> 1 A 32 0.25 <=0.5 4
+#> 2 B 4 >=1 1 4
+#> 3 C 2 >=1 <=0.5 <=1
+#> 4 D 8 0.5 1 <=1
+#> 5 E 32 0.5 1 <=1
+#> 6 F >=64 >=1 >=8 <=1
+#> 7 G 1 0.25 2 <=1
+#> 8 H 2 >=1 4 2
+#> 9 I 8 0.5 >=8 <=1
+#> 10 J 32 <=0.125 1 2
mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",
#> "id" and "tobr"
#> Warning: NAs introduced by coercion
-#> [1] -0.15596821 -0.35223027 -0.06296188 -0.77906287 -0.19333099 1.00776983
-#> [7] -0.64235988 0.64363737 1.00124386 -0.46673697
+#> [1] 0.12196526 0.40284317 -0.47762168 -0.30700434 -0.06650357 0.79277984
+#> [7] -0.73763891 0.32070406 0.19485787 -0.24438169
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
-#> 4 D 8 <=0.0625 0.5 <=0.5 -0.77906287
-#> 7 G 8 <=0.0625 0.5 1 -0.64235988
-#> 10 J 4 0.25 0.25 4 -0.46673697
-#> 2 B 4 0.5 0.5 1 -0.35223027
-#> 5 E 4 0.25 0.25 >=16 -0.19333099
-#> 1 A 16 <=0.0625 0.5 4 -0.15596821
-#> 3 C 16 0.5 0.5 <=0.5 -0.06296188
-#> 8 H >=32 0.5 1 2 0.64363737
-#> 9 I >=32 1 0.5 >=16 1.00124386
-#> 6 F 16 0.5 4 4 1.00776983
+#> id amox cipr gent tobr amr_distance
+#> 7 G 1 0.25 2 <=1 -0.73763891
+#> 3 C 2 >=1 <=0.5 <=1 -0.47762168
+#> 4 D 8 0.5 1 <=1 -0.30700434
+#> 10 J 32 <=0.125 1 2 -0.24438169
+#> 5 E 32 0.5 1 <=1 -0.06650357
+#> 1 A 32 0.25 <=0.5 4 0.12196526
+#> 9 I 8 0.5 >=8 <=1 0.19485787
+#> 8 H 2 >=1 4 2 0.32070406
+#> 2 B 4 >=1 1 4 0.40284317
+#> 6 F >=64 >=1 >=8 <=1 0.79277984
if (require("dplyr")) {
y %>%
@@ -257,17 +256,17 @@
}
#> 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 16 0.5 0.5 <=0.5 -0.06296188 0.00000000
-#> 2 A 16 <=0.0625 0.5 4 -0.15596821 0.09300632
-#> 3 E 4 0.25 0.25 >=16 -0.19333099 0.13036910
-#> 4 B 4 0.5 0.5 1 -0.35223027 0.28926839
-#> 5 J 4 0.25 0.25 4 -0.46673697 0.40377508
-#> 6 G 8 <=0.0625 0.5 1 -0.64235988 0.57939799
-#> 7 H >=32 0.5 1 2 0.64363737 0.70659925
-#> 8 D 8 <=0.0625 0.5 <=0.5 -0.77906287 0.71610098
-#> 9 I >=32 1 0.5 >=16 1.00124386 1.06420574
-#> 10 F 16 0.5 4 4 1.00776983 1.07073172
+#> id amox cipr gent tobr amr_distance check_id_C
+#> 1 C 2 >=1 <=0.5 <=1 -0.47762168 0.0000000
+#> 2 D 8 0.5 1 <=1 -0.30700434 0.1706173
+#> 3 J 32 <=0.125 1 2 -0.24438169 0.2332400
+#> 4 G 1 0.25 2 <=1 -0.73763891 0.2600172
+#> 5 E 32 0.5 1 <=1 -0.06650357 0.4111181
+#> 6 A 32 0.25 <=0.5 4 0.12196526 0.5995869
+#> 7 I 8 0.5 >=8 <=1 0.19485787 0.6724795
+#> 8 H 2 >=1 4 2 0.32070406 0.7983257
+#> 9 B 4 >=1 1 4 0.40284317 0.8804648
+#> 10 F >=64 >=1 >=8 <=1 0.79277984 1.2704015
if (require("dplyr")) {
# support for groups
example_isolates %>%
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index c609e644..4df3c3c2 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9058
+ 1.8.2.9059