From cfc4fd0c0ca2e91ea5d0eea0886672f78a4de51c Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 6 Oct 2022 10:25:44 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9007@b753b84 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 542 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 38143 -> 38752 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 52816 -> 56508 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 27882 -> 27842 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 41622 -> 38294 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 37183 -> 37603 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50374 -> 51289 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 43149 -> 43176 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28441 -> 28471 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78074 -> 78108 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49913 -> 49784 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 56 +- articles/PCA.html | 2 +- articles/SPSS.html | 2 +- articles/WHONET.html | 2 +- articles/datasets.html | 18 +- articles/index.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 2 +- news/index.html | 12 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR.html | 2 +- reference/Rplot005.png | Bin 13238 -> 12889 bytes reference/Rplot006.png | Bin 12736 -> 12410 bytes reference/Rplot007.png | Bin 13377 -> 13204 bytes reference/Rplot008.png | Bin 20099 -> 18872 bytes reference/Rplot009.png | Bin 8507 -> 8552 bytes reference/WHOCC.html | 2 +- reference/WHONET.html | 2 +- reference/ab_from_text.html | 2 +- reference/ab_property.html | 2 +- reference/age.html | 22 +- reference/age_groups.html | 2 +- reference/antibiotic_class_selectors.html | 2 +- reference/antibiotics.html | 2 +- reference/as.ab.html | 2 +- reference/as.disk.html | 2 +- reference/as.mic.html | 2 +- reference/as.mo.html | 2 +- reference/as.rsi.html | 22 +- reference/atc_online.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 2 +- reference/count.html | 2 +- reference/custom_eucast_rules.html | 2 +- reference/dosage.html | 2 +- reference/eucast_rules.html | 2 +- reference/example_isolates.html | 2 +- reference/example_isolates_unclean.html | 2 +- reference/first_isolate.html | 2 +- reference/g.test.html | 2 +- reference/get_episode.html | 131 +++-- reference/ggplot_pca.html | 2 +- reference/ggplot_rsi.html | 2 +- reference/guess_ab_col.html | 2 +- reference/index.html | 2 +- reference/intrinsic_resistant.html | 2 +- reference/italicise_taxonomy.html | 2 +- reference/join.html | 2 +- reference/key_antimicrobials.html | 2 +- reference/kurtosis.html | 6 +- reference/like.html | 2 +- reference/mdro.html | 2 +- reference/mean_amr_distance.html | 79 +-- reference/microorganisms.codes.html | 2 +- reference/microorganisms.html | 2 +- reference/mo_matching_score.html | 2 +- reference/mo_property.html | 100 ++-- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot-1.png | Bin 26904 -> 26893 bytes reference/plot-2.png | Bin 27065 -> 26439 bytes reference/plot-3.png | Bin 28358 -> 28264 bytes reference/plot-4.png | Bin 38618 -> 38716 bytes reference/plot-5.png | Bin 38726 -> 38027 bytes reference/plot-6.png | Bin 37456 -> 36822 bytes reference/plot-7.png | Bin 37459 -> 37285 bytes reference/plot-8.png | Bin 58572 -> 56741 bytes reference/plot-9.png | Bin 26202 -> 26284 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 34 +- reference/resistance_predict.html | 2 +- reference/rsi_translation.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 93 files changed, 570 insertions(+), 570 deletions(-) diff --git a/404.html b/404.html index ba91d953..9ea534d4 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9006 + 1.8.2.9007
As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (proportion_R()
, equal to resistance()
) and susceptibility as the proportion of S and I (proportion_SI()
, equal to susceptibility()
). These functions can be used on their own:
data_1st %>% resistance(AMX)
-# [1] 0.5456512
Or can be used in conjunction with group_by()
and summarise()
, both from the dplyr
package:
data_1st %>%
@@ -975,19 +975,19 @@ Longest: 24
Hospital A
-0.5437558
+0.5417823
Hospital B
-0.5492089
+0.5486465
Hospital C
-0.5465995
+0.5634971
Hospital D
-0.5415282
+0.5485369
@@ -1008,23 +1008,23 @@ Longest: 24
Hospital A
-0.5437558
-3211
+0.5417823
+3243
Hospital B
-0.5492089
-3729
+0.5486465
+3731
Hospital C
-0.5465995
-1588
+0.5634971
+1567
Hospital D
-0.5415282
-2107
+0.5485369
+2153
@@ -1047,27 +1047,27 @@ Longest: 24
Escherichia
-0.7712661
-0.8777608
-0.9748524
+0.7708831
+0.8791495
+0.9791712
Klebsiella
-0.8178808
-0.9097682
-0.9850993
+0.8193604
+0.9109767
+0.9783924
Staphylococcus
-0.7931785
-0.8809869
-0.9785922
+0.7871953
+0.8795926
+0.9770826
Streptococcus
-0.5371783
+0.5268472
0.0000000
-0.5371783
+0.5268472
@@ -1092,23 +1092,23 @@ Longest: 24
Hospital A
-54.4%
+54.2%
26.2%
Hospital B
54.9%
-26.7%
+27.0%
Hospital C
-54.7%
-26.6%
+56.3%
+28.1%
Hospital D
-54.2%
-25.9%
+54.9%
+27.1%
@@ -1206,18 +1206,16 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class <mic>
-# [1] 0.005 0.0625 <=0.001 0.0625 64 0.25 >=256 0.125 0.0625
-# [10] 0.01 4 2 32 0.25 0.0625 2 0.025 4
-# [19] 0.0625 >=256 0.125 0.5 64 0.0625 0.005 0.25 8
-# [28] 2 2 64 0.005 0.125 8 0.01 16 0.0625
-# [37] <=0.001 0.01 16 32 32 0.0625 0.5 32 64
-# [46] 0.025 4 2 1 <=0.001 128 32 0.002 <=0.001
-# [55] 0.5 128 128 <=0.001 >=256 32 0.5 0.01 64
-# [64] 1 64 0.0625 0.025 0.002 1 0.01 0.005 16
-# [73] 1 0.0625 0.125 1 <=0.001 0.0625 64 128 0.01
-# [82] 0.5 0.025 <=0.001 0.0625 0.005 64 1 0.25 32
-# [91] 0.025 16 0.005 128 0.01 0.005 0.005 64 32
-# [100] 0.5
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class <disk>
-# [1] 18 18 28 20 25 20 24 24 29 19 20 19 21 28 25 18 28 27 20 29 18 30 28 23 26
-# [26] 19 19 19 23 25 21 22 19 22 25 30 27 28 26 25 30 26 30 25 31 18 21 30 27 17
-# [51] 20 21 17 26 22 21 17 22 27 24 17 29 23 18 18 22 21 29 30 30 26 21 26 24 25
-# [76] 26 17 31 22 18 31 23 20 29 18 26 31 23 21 18 31 18 30 17 31 29 30 17 22 21
+# [1] 18 31 31 29 22 20 28 21 23 17 27 23 24 21 23 28 27 27 28 29 23 20 30 17 31
+# [26] 21 25 21 30 31 31 26 26 19 31 23 26 18 23 24 29 27 23 23 20 29 23 24 26 18
+# [51] 21 25 31 22 31 22 30 25 31 21 27 28 26 29 28 17 18 31 27 27 20 26 23 27 18
+# [76] 28 20 29 30 27 23 26 24 22 27 26 20 22 29 21 19 26 22 24 23 29 22 20 27 24
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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