rsi <- random_rsi(10)
rsi
#> Class 'rsi'
-#> [1] S S R I I R R R I S
+#> [1] I I I R R I I S R S
mean_amr_distance(rsi)
-#> [1] -0.7745967 -0.7745967 1.1618950 -0.7745967 -0.7745967 1.1618950
-#> [7] 1.1618950 1.1618950 -0.7745967 -0.7745967
+#> [1] -0.621059 -0.621059 -0.621059 1.449138 1.449138 -0.621059 -0.621059
+#> [8] -0.621059 1.449138 -0.621059
mic <- random_mic(10)
mic
#> Class 'mic'
-#> [1] 32 0.001 >=64 0.01 0.001 2 0.002 0.005 0.002 0.125
+#> [1] 64 2 0.25 0.002 0.125 256 8 16 32 0.005
mean_amr_distance(mic)
-#> [1] 1.5006685 -0.9103327 1.6617694 -0.3751671 -0.9103327 0.8562649
-#> [7] -0.7492318 -0.5362680 -0.7492318 0.2118614
+#> [1] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458
+#> [7] 0.42631669 0.59954827 0.77277985 -1.41753533
# equal to the Z-score of their log2:
(log2(mic) - mean(log2(mic))) / sd(log2(mic))
-#> [1] 1.5006685 -0.9103327 1.6617694 -0.3751671 -0.9103327 0.8562649
-#> [7] -0.7492318 -0.5362680 -0.7492318 0.2118614
+#> [1] 0.94601143 0.07985353 -0.43984121 -1.64653502 -0.61307279 1.29247458
+#> [7] 0.42631669 0.59954827 0.77277985 -1.41753533
disk <- random_disk(10)
disk
#> Class 'disk'
-#> [1] 50 50 42 10 25 25 24 41 14 46
+#> [1] 14 12 9 45 44 22 42 31 47 34
mean_amr_distance(disk)
-#> [1] 1.1634023 1.1634023 0.6254128 -1.5265452 -0.5178149 -0.5178149
-#> [7] -0.5850636 0.5581641 -1.2575504 0.8944075
+#> [1] -1.08531752 -1.22098221 -1.42447924 1.01748517 0.94965283 -0.54265876
+#> [7] 0.81398814 0.06783234 1.15314986 0.27132938
y <- data.frame(
id = LETTERS[1:10],
@@ -224,36 +224,36 @@
tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")
)
y
-#> id amox cipr gent tobr
-#> 1 A I 28 1 <=1
-#> 2 B S 18 2 8
-#> 3 C S 26 >=8 8
-#> 4 D R 28 >=8 8
-#> 5 E I 31 2 8
-#> 6 F R 23 1 8
-#> 7 G R 23 4 8
-#> 8 H I 31 4 <=1
-#> 9 I I 18 >=8 4
-#> 10 J I 17 2 2
+#> id amox cipr gent tobr
+#> 1 A S 27 4 2
+#> 2 B I 26 4 4
+#> 3 C R 29 16 <=1
+#> 4 D I 31 4 4
+#> 5 E I 29 8 2
+#> 6 F S 23 8 4
+#> 7 G I 25 <=0.5 2
+#> 8 H R 23 8 4
+#> 9 I S 25 4 2
+#> 10 J R 25 1 <=1
mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and
#> "tobr"
-#> [1] -0.7306638 -0.4034429 0.3974553 1.0087361 0.2058131 0.1354498
-#> [7] 0.5614212 -0.1640949 -0.1717694 -0.8389046
+#> [1] -0.15307753 0.07017847 0.57030268 0.53856269 0.20198126 -0.04314696
+#> [7] -0.84354651 0.47440221 -0.34043122 -0.47522509
y$amr_distance <- mean_amr_distance(y, where(is.mic))
#> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"
y[order(y$amr_distance), ]
-#> id amox cipr gent tobr amr_distance
-#> 1 A I 28 1 <=1 -1.49760542
-#> 10 J I 17 2 2 -0.68303823
-#> 8 H I 31 4 <=1 -0.64566267
-#> 6 F R 23 1 8 -0.33181796
-#> 2 B S 18 2 8 0.09415341
-#> 5 E I 31 2 8 0.09415341
-#> 7 G R 23 4 8 0.52012479
-#> 9 I I 18 >=8 4 0.55750034
-#> 3 C S 26 >=8 8 0.94609616
-#> 4 D R 28 >=8 8 0.94609616
+#> id amox cipr gent tobr amr_distance
+#> 10 J R 25 1 <=1 -1.43145922
+#> 7 G I 25 <=0.5 2 -1.13300373
+#> 1 A S 27 4 2 -0.12677314
+#> 9 I S 25 4 2 -0.12677314
+#> 3 C R 29 16 <=1 -0.08981844
+#> 5 E I 29 8 2 0.20863706
+#> 2 B I 26 4 4 0.50709255
+#> 4 D I 31 4 4 0.50709255
+#> 6 F S 23 8 4 0.84250275
+#> 8 H R 23 8 4 0.84250275
if (require("dplyr")) {
y %>%
@@ -265,17 +265,17 @@
}
#> 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 S 26 >=8 8 0.3974553 0.0000000
-#> 2 G R 23 4 8 0.5614212 0.1639659
-#> 3 E I 31 2 8 0.2058131 0.1916421
-#> 4 F R 23 1 8 0.1354498 0.2620054
-#> 5 H I 31 4 <=1 -0.1640949 0.5615502
-#> 6 I I 18 >=8 4 -0.1717694 0.5692247
-#> 7 D R 28 >=8 8 1.0087361 0.6112809
-#> 8 B S 18 2 8 -0.4034429 0.8008982
-#> 9 A I 28 1 <=1 -0.7306638 1.1281191
-#> 10 J I 17 2 2 -0.8389046 1.2363598
+#> id amox cipr gent tobr amr_distance check_id_C
+#> 1 C R 29 16 <=1 0.57030268 0.00000000
+#> 2 D I 31 4 4 0.53856269 0.03173999
+#> 3 H R 23 8 4 0.47440221 0.09590047
+#> 4 E I 29 8 2 0.20198126 0.36832142
+#> 5 B I 26 4 4 0.07017847 0.50012421
+#> 6 F S 23 8 4 -0.04314696 0.61344964
+#> 7 A S 27 4 2 -0.15307753 0.72338021
+#> 8 I S 25 4 2 -0.34043122 0.91073389
+#> 9 J R 25 1 <=1 -0.47522509 1.04552777
+#> 10 G I 25 <=0.5 2 -0.84354651 1.41384919
if (require("dplyr")) {
# support for groups
example_isolates %>%
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index 9d4f398d..fbcdacf4 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9081
+ 1.8.2.9082