From 59c39dc5d14cc0a69687e9641debda72abfc1a18 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 23 Jan 2023 19:14:37 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9099@eef0006 --- 404.html | 29 +- LICENSE-text.html | 29 +- articles/AMR.html | 557 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 39107 -> 38754 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 55128 -> 56475 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28168 -> 28324 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 39232 -> 37611 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 36941 -> 38328 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50186 -> 51436 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 41953 -> 41824 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28407 -> 28505 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78232 -> 78282 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49896 -> 49897 bytes articles/EUCAST.html | 29 +- articles/MDR.html | 87 +-- articles/PCA.html | 29 +- articles/SPSS.html | 29 +- articles/WHONET.html | 29 +- articles/datasets.html | 29 +- articles/index.html | 29 +- articles/resistance_predict.html | 29 +- articles/welcome_to_AMR.html | 29 +- authors.html | 29 +- index.html | 29 +- news/index.html | 51 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 29 +- reference/AMR-options.html | 71 ++- reference/AMR.html | 29 +- reference/Rplot005.png | Bin 12930 -> 13003 bytes reference/Rplot006.png | Bin 12462 -> 12528 bytes reference/Rplot007.png | Bin 12686 -> 12678 bytes reference/Rplot008.png | Bin 18894 -> 19061 bytes reference/Rplot009.png | Bin 8531 -> 8444 bytes reference/WHOCC.html | 29 +- reference/WHONET.html | 29 +- reference/ab_from_text.html | 29 +- reference/ab_property.html | 31 +- reference/add_custom_antimicrobials.html | 40 +- reference/add_custom_microorganisms.html | 31 +- reference/age.html | 49 +- reference/age_groups.html | 29 +- reference/antibiotic_class_selectors.html | 29 +- reference/antibiotics.html | 29 +- reference/as.ab.html | 29 +- reference/as.av.html | 29 +- reference/as.disk.html | 29 +- reference/as.mic.html | 29 +- reference/as.mo.html | 33 +- reference/as.sir.html | 60 +- reference/atc_online.html | 29 +- reference/av_from_text.html | 29 +- reference/av_property.html | 31 +- reference/availability.html | 29 +- reference/bug_drug_combinations.html | 31 +- reference/clinical_breakpoints.html | 29 +- reference/count.html | 31 +- reference/custom_eucast_rules.html | 29 +- reference/dosage.html | 29 +- reference/eucast_rules.html | 33 +- reference/example_isolates.html | 29 +- reference/example_isolates_unclean.html | 29 +- reference/first_isolate.html | 29 +- reference/g.test.html | 29 +- reference/get_episode.html | 180 +++--- reference/ggplot_pca.html | 29 +- reference/ggplot_sir.html | 31 +- reference/guess_ab_col.html | 29 +- reference/index.html | 45 +- reference/intrinsic_resistant.html | 29 +- reference/italicise_taxonomy.html | 29 +- reference/join.html | 29 +- reference/key_antimicrobials.html | 29 +- reference/kurtosis.html | 33 +- reference/like.html | 29 +- reference/mdro.html | 29 +- reference/mean_amr_distance.html | 118 ++-- reference/microorganisms.codes.html | 29 +- reference/microorganisms.html | 29 +- reference/mo_matching_score.html | 29 +- reference/mo_property.html | 31 +- reference/mo_source.html | 31 +- reference/pca.html | 29 +- reference/plot-1.png | Bin 25832 -> 26292 bytes reference/plot-2.png | Bin 26417 -> 26402 bytes reference/plot-3.png | Bin 28235 -> 27461 bytes reference/plot-4.png | Bin 37733 -> 38130 bytes reference/plot-5.png | Bin 38005 -> 38019 bytes reference/plot-6.png | Bin 36805 -> 36797 bytes reference/plot-7.png | Bin 36934 -> 36814 bytes reference/plot-8.png | Bin 56841 -> 56739 bytes reference/plot-9.png | Bin 26275 -> 26089 bytes reference/plot.html | 31 +- reference/proportion.html | 31 +- reference/random.html | 60 +- reference/resistance_predict.html | 29 +- reference/skewness.html | 31 +- reference/translate.html | 39 +- search.json | 2 +- 99 files changed, 1788 insertions(+), 1376 deletions(-) diff --git a/404.html b/404.html index eb7347f00..4c02e0c3e 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9098 + 1.8.2.9099
So only 61.2% is suitable for resistance analysis! We can now filter +
So only 61.6% is suitable for resistance analysis! We can now filter
on it with the filter()
function, also from the
dplyr
package:
@@ -635,7 +640,7 @@ on it with the data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
So we end up with 12,236 isolates for analysis. Now our data looks +
So we end up with 12,316 isolates for analysis. Now our data looks like:
head(data_1st)
Time for the analysis!
@@ -802,8 +807,8 @@ readable:data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 12,236
-Available: 12,236 (100%, NA: 0 = 0%)
+Length: 12,316
+Available: 12,316 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-# [1] 0.5813992
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1153,19 +1158,19 @@ own:Hospital A -0.5883615 +0.5650667 Hospital B -0.5790089 +0.5838028 Hospital C -0.5716704 +0.5864369 @@ -1190,23 +1195,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5820106 +0.5923414 Hospital A -0.5883615 -3729 +0.5650667 +3750 Hospital B -0.5790089 -4278 +0.5838028 +4260 Hospital C -0.5716704 -1772 +0.5864369 +1799 @@ -1231,27 +1236,27 @@ therapies very easily: Hospital D -0.5820106 -2457 +0.5923414 +2507 Escherichia -0.6688468 -0.6497418 -0.8898451 +0.6598423 +0.6524585 +0.8848800 Klebsiella -0.6378505 -0.6627726 -0.8777259 +0.6648308 +0.6396538 +0.8686074 Staphylococcus -0.6741369 -0.6556632 -0.8885524 +0.6738263 +0.6759742 +0.8922983 @@ -1279,23 +1284,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4766304 +0.4564860 0.0000000 -0.4766304 +0.4564860 Hospital A -58.8% -36.3% +56.5% +34.9% Hospital B -57.9% -35.7% +58.4% +37.2% Hospital C -57.2% -36.6% +58.6% +37.4% @@ -1411,16 +1416,18 @@ classes) Hospital D -58.2% -36.6% +59.2% +37.7% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 0.001 0.0625 32 0.0625 32 64 >=256 32 4 0.125 -# [11] 4 32 128 32 0.125 1 0.0625 >=256 16 64 -# [21] 0.025 64 16 16 >=256 128 0.025 0.005 0.25 1 -# [31] 0.5 32 0.0625 16 128 0.025 0.25 1 0.005 0.0625 -# [41] 0.025 0.025 0.25 0.002 0.001 2 8 32 0.0625 0.002 -# [51] 0.001 0.5 0.25 16 0.125 0.005 64 1 0.0625 0.001 -# [61] 0.025 32 16 >=256 0.005 0.002 16 >=256 1 0.125 -# [71] 2 0.125 16 16 64 64 0.0625 0.5 1 0.005 -# [81] 64 0.125 0.025 0.01 0.0625 0.5 0.002 0.25 0.25 128 -# [91] 4 16 0.002 0.25 32 32 128 128 0.125 0.25
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 18 29 23 17 30 20 29 20 17 19 22 25 29 30 24 22 29 29 24 17 30 19 25 23 26
-# [26] 20 25 17 20 23 27 19 26 19 26 19 21 19 24 20 18 19 30 17 27 29 21 22 29 21
-# [51] 22 30 20 23 27 30 27 19 24 24 21 24 24 17 21 20 31 27 31 20 22 26 25 29 31
-# [76] 31 18 20 18 17 26 25 24 31 20 18 25 26 19 18 23 31 27 18 18 28 30 26 30 27
+# [1] 29 26 20 20 26 31 29 17 28 21 27 17 30 23 21 19 23 23 20 23 19 27 23 20 23
+# [26] 25 22 25 28 31 19 31 20 31 19 19 28 31 20 29 23 25 28 27 18 24 26 21 30 23
+# [51] 22 31 27 26 27 26 23 22 17 19 18 24 31 25 29 21 29 19 27 20 31 23 23 25 18
+# [76] 31 18 27 31 20 21 23 25 22 31 26 28 21 30 17 31 29 19 25 24 17 19 19 21 21
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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