rsi <- random_rsi(10)
rsi
#> Class 'rsi'
-#> [1] S I S S R S S S I R
+#> [1] S I R S I I R I S I
mean_amr_distance(rsi)
-#> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666 -0.4743416
-#> [7] -0.4743416 -0.4743416 -0.4743416 1.8973666
+#> [1] -0.4743416 -0.4743416 1.8973666 -0.4743416 -0.4743416 -0.4743416
+#> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416
mic <- random_mic(10)
mic
#> Class 'mic'
-#> [1] >=64 0.25 16 0.001 0.125 32 0.125 0.001 0.002 8
+#> [1] 0.025 0.25 <=0.002 0.0625 0.005 >=256 0.25 0.01 0.01
+#> [10] 1
mean_amr_distance(mic)
-#> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686
-#> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097
+#> [1] -0.36458316 0.30826076 -1.10263240 -0.09683165 -0.83488088 2.33372278
+#> [7] 0.30826076 -0.63233468 -0.63233468 0.71335316
# equal to the Z-score of their log2:
(log2(mic) - mean(log2(mic))) / sd(log2(mic))
-#> [1] 1.26281480 -0.01764874 0.94269891 -1.29263579 -0.17770669 1.10275686
-#> [7] -0.17770669 -1.29263579 -1.13257785 0.78264097
+#> [1] -0.36458316 0.30826076 -1.10263240 -0.09683165 -0.83488088 2.33372278
+#> [7] 0.30826076 -0.63233468 -0.63233468 0.71335316
disk <- random_disk(10)
disk
#> Class 'disk'
-#> [1] 17 29 32 37 48 40 28 37 40 49
+#> [1] 12 41 32 36 28 23 7 49 36 37
mean_amr_distance(disk)
-#> [1] -1.9401430 -0.6951315 -0.3838786 0.1348763 1.2761369 0.4461291
-#> [7] -0.7988824 0.1348763 0.4461291 1.3798878
+#> [1] -1.3960299 0.8407031 0.1465446 0.4550595 -0.1619703 -0.5476139
+#> [7] -1.7816735 1.4577329 0.4550595 0.5321882
y <- data.frame(
id = LETTERS[1:10],
@@ -224,36 +225,36 @@
tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")
)
y
-#> id amox cipr gent tobr
-#> 1 A R 23 >=16 2
-#> 2 B I 24 1 4
-#> 3 C S 24 8 0.25
-#> 4 D R 18 2 4
-#> 5 E S 17 4 1
-#> 6 F S 22 8 2
-#> 7 G R 29 2 0.25
-#> 8 H S 28 >=16 1
-#> 9 I I 31 4 1
-#> 10 J S 20 >=16 0.5
+#> id amox cipr gent tobr
+#> 1 A R 20 <=0.5 2
+#> 2 B S 19 16 2
+#> 3 C R 25 8 0.5
+#> 4 D R 30 2 >=8
+#> 5 E R 28 1 >=8
+#> 6 F I 26 <=0.5 4
+#> 7 G I 21 1 2
+#> 8 H S 22 1 1
+#> 9 I S 25 2 >=8
+#> 10 J S 18 8 1
mean_amr_distance(y)
#> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and
#> "tobr"
-#> [1] 0.76502575 -0.22559420 -0.39112580 0.14405101 -0.59747772 0.01884049
-#> [7] 0.04569124 0.34391737 0.15560237 -0.25893050
+#> [1] -0.25809138 -0.09594429 0.26834683 1.00209109 0.73552766 -0.19144637
+#> [7] -0.53806425 -0.65193856 0.20590130 -0.47638203
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
-#> 7 G R 29 2 0.25 -1.2141339
-#> 3 C S 24 8 0.25 -0.5147553
-#> 2 B I 24 1 4 -0.1836920
-#> 5 E S 17 4 1 -0.1743790
-#> 9 I I 31 4 1 -0.1743790
-#> 4 D R 18 2 4 0.1659973
-#> 10 J S 20 >=16 0.5 0.1799668
-#> 6 F S 22 8 2 0.5203431
-#> 8 H S 28 >=16 1 0.5249996
-#> 1 A R 23 >=16 2 0.8700324
+#> id amox cipr gent tobr amr_distance
+#> 8 H S 22 1 1 -0.7418213
+#> 1 A R 20 <=0.5 2 -0.6727193
+#> 7 G I 21 1 2 -0.3892460
+#> 6 F I 26 <=0.5 4 -0.3201439
+#> 3 C R 25 8 0.5 -0.2439766
+#> 10 J S 18 8 1 0.1085987
+#> 5 E R 28 1 >=8 0.3159048
+#> 4 D R 30 2 >=8 0.5993781
+#> 9 I S 25 2 >=8 0.5993781
+#> 2 B S 19 16 2 0.7446475
if (require("dplyr")) {
y %>%
@@ -265,17 +266,17 @@
}
#> 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 24 8 0.25 -0.39112580 0.0000000
-#> 2 J S 20 >=16 0.5 -0.25893050 0.1321953
-#> 3 B I 24 1 4 -0.22559420 0.1655316
-#> 4 E S 17 4 1 -0.59747772 0.2063519
-#> 5 F S 22 8 2 0.01884049 0.4099663
-#> 6 G R 29 2 0.25 0.04569124 0.4368170
-#> 7 D R 18 2 4 0.14405101 0.5351768
-#> 8 I I 31 4 1 0.15560237 0.5467282
-#> 9 H S 28 >=16 1 0.34391737 0.7350432
-#> 10 A R 23 >=16 2 0.76502575 1.1561516
+#> id amox cipr gent tobr amr_distance check_id_C
+#> 1 C R 25 8 0.5 0.26834683 0.00000000
+#> 2 I S 25 2 >=8 0.20590130 0.06244553
+#> 3 B S 19 16 2 -0.09594429 0.36429112
+#> 4 F I 26 <=0.5 4 -0.19144637 0.45979320
+#> 5 E R 28 1 >=8 0.73552766 0.46718083
+#> 6 A R 20 <=0.5 2 -0.25809138 0.52643821
+#> 7 D R 30 2 >=8 1.00209109 0.73374426
+#> 8 J S 18 8 1 -0.47638203 0.74472886
+#> 9 G I 21 1 2 -0.53806425 0.80641108
+#> 10 H S 22 1 1 -0.65193856 0.92028539
if (require("dplyr")) {
# support for groups
example_isolates %>%
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index d746e7cb..4a9db40e 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -10,7 +10,7 @@
AMR (for R)
- 1.8.2.9078
+ 1.8.2.9079