From 48896ee426434a2da167b11ec18bc1fe4afcb5fe Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 12 Feb 2023 10:30:57 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9119@c740967 --- 404.html | 2 +- LICENSE-text.html | 2 +- articles/AMR.html | 561 +-- .../AMR_files/figure-html/disk_plots-1.png | Bin 38129 -> 38779 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 52877 -> 56568 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28133 -> 28282 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 39044 -> 37530 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 37633 -> 37834 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50744 -> 51140 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 41884 -> 41787 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28491 -> 28456 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78257 -> 78268 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49868 -> 49897 bytes articles/EUCAST.html | 2 +- articles/MDR.html | 58 +- articles/PCA.html | 4 +- articles/SPSS.html | 4 +- articles/WHONET.html | 2 +- articles/datasets.html | 4 +- articles/index.html | 2 +- articles/resistance_predict.html | 2 +- articles/welcome_to_AMR.html | 2 +- authors.html | 2 +- index.html | 4 +- news/index.html | 26 +- pkgdown.yml | 2 +- reference/AMR-deprecated.html | 2 +- reference/AMR-options.html | 2 +- reference/AMR.html | 2 +- reference/Rplot005.png | Bin 12815 -> 13213 bytes reference/Rplot006.png | Bin 12472 -> 12855 bytes reference/Rplot007.png | Bin 13475 -> 13035 bytes reference/Rplot008.png | Bin 18478 -> 19987 bytes reference/Rplot009.png | Bin 8425 -> 8519 bytes reference/WHOCC.html | 2 +- reference/WHONET.html | 2 +- reference/ab_from_text.html | 2 +- reference/ab_property.html | 2 +- reference/add_custom_antimicrobials.html | 2 +- reference/add_custom_microorganisms.html | 2 +- reference/age.html | 22 +- reference/age_groups.html | 2 +- reference/antibiogram-1.png | Bin 21812 -> 24603 bytes reference/antibiogram-2.png | Bin 24672 -> 26492 bytes reference/antibiogram-3.png | Bin 29269 -> 32347 bytes reference/antibiogram-4.png | Bin 37811 -> 39648 bytes reference/antibiogram.html | 183 +- reference/antibiotic_class_selectors.html | 138 +- reference/antibiotics.html | 2 +- reference/as.ab.html | 2 +- reference/as.av.html | 2 +- reference/as.disk.html | 2 +- reference/as.mic.html | 2 +- reference/as.mo.html | 2 +- reference/as.sir.html | 22 +- reference/atc_online.html | 2 +- reference/av_from_text.html | 2 +- reference/av_property.html | 2 +- reference/availability.html | 2 +- reference/bug_drug_combinations.html | 3759 +---------------- reference/clinical_breakpoints.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 | 89 +- reference/ggplot_pca.html | 2 +- reference/ggplot_sir.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 | 69 +- reference/microorganisms.codes.html | 2 +- reference/microorganisms.html | 2 +- reference/mo_matching_score.html | 2 +- reference/mo_property.html | 2 +- reference/mo_source.html | 2 +- reference/pca.html | 2 +- reference/plot-1.png | Bin 27247 -> 26681 bytes reference/plot-2.png | Bin 27542 -> 27050 bytes reference/plot-3.png | Bin 28287 -> 28130 bytes reference/plot-4.png | Bin 39048 -> 38472 bytes reference/plot-5.png | Bin 39103 -> 38692 bytes reference/plot-6.png | Bin 38243 -> 37877 bytes reference/plot-7.png | Bin 37962 -> 38001 bytes reference/plot-8.png | Bin 55401 -> 58507 bytes reference/plot-9.png | Bin 26086 -> 26158 bytes reference/plot.html | 2 +- reference/proportion.html | 2 +- reference/random.html | 35 +- reference/resistance_predict.html | 2 +- reference/skewness.html | 4 +- reference/translate.html | 2 +- search.json | 2 +- 104 files changed, 630 insertions(+), 4476 deletions(-) diff --git a/404.html b/404.html index f4474448..810f0d11 100644 --- a/404.html +++ b/404.html @@ -36,7 +36,7 @@ AMR (for R) - 1.8.2.9118 + 1.8.2.9119
+generated on 12 February 2023.So only 61.5% is suitable for resistance analysis! We can now filter +
So only 61.2% is suitable for resistance analysis! We can now filter
on it with the filter()
function, also from the
dplyr
package:
So we end up with 12 300 isolates for analysis. Now our data looks +
So we end up with 12 241 isolates for analysis. Now our data looks like:
head(data_1st)
1 | +2011-02-07 | +G7 | +Hospital B | +B_ESCHR_COLI | +S | +S | +S | +R | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||
2 | -2017-01-11 | -D6 | -Hospital D | -B_STPHY_AURS | +2016-04-30 | +C8 | +Hospital B | +B_ESCHR_COLI | R | R | R | S | M | -Gram-positive | -Staphylococcus | -aureus | -TRUE | -||
10 | -2011-03-19 | -U9 | -Hospital D | -B_ESCHR_COLI | -S | -S | -R | -S | -F | Gram-negative | Escherichia | coli | TRUE | ||||||
11 | -2010-12-27 | -A2 | +3 | +2013-01-08 | +R7 | Hospital C | B_ESCHR_COLI | -R | -R | S | S | -M | +I | +S | +F | Gram-negative | Escherichia | coli | TRUE |
12 | -2012-12-11 | -I9 | -Hospital B | -B_KLBSL_PNMN | -R | -R | -R | -R | -M | -Gram-negative | -Klebsiella | -pneumoniae | -TRUE | -||||||
13 | -2015-07-02 | -Y10 | -Hospital D | +4 | +2010-01-11 | +Z6 | +Hospital A | B_STPHY_AURS | R | R | @@ -762,22 +746,38 @@ like:aureus | TRUE | |||||||
15 | -2015-08-12 | -V4 | -Hospital B | +||||||||||||||||
6 | +2017-06-05 | +C6 | +Hospital C | B_STPHY_AURS | -R | -I | -R | -I | -F | +S | +S | +S | +S | +M | Gram-positive | Staphylococcus | aureus | TRUE | |
7 | +2015-07-18 | +F7 | +Hospital B | +B_ESCHR_COLI | +S | +S | +R | +R | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +
Time for the analysis!
@@ -811,8 +811,8 @@ readable:data_1st %>% freq(genus, species)
Frequency table
Class: character
-Length: 12,300
-Available: 12,300 (100%, NA: 0 = 0%)
+Length: 12,241
+Available: 12,241 (100%, NA: 0 = 0%)
Unique: 4
Shortest: 16
Longest: 24
mo | ab | S | @@ -1021,52 +1022,58 @@ different bug/drug combinations, you can use the|||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
2 | E. coli | -S | -1489 | -1236 | -3101 | -5826 | -|||||
E. coli | -S1 | -2720 | +AMC | +2728 | 1160 | -1946 | -5826 | +1943 | +5831 | +||
1 | +E. coli | +AMX | +1490 | +1233 | +3108 | +5831 | |||||
3 | E. coli | -S2 | -1974 | -1845 | +CIP | 2007 | -5826 | +1763 | +2061 | +5831 | |
4 | E. coli | -S3 | -2027 | -1830 | -1969 | -5826 | +GEN | +1949 | +1853 | +2029 | +5831 |
6 | K. pneumoniae | -S | -0 | -0 | -1366 | -1366 | +AMC | +584 | +249 | +479 | +1312 |
5 | K. pneumoniae | -S1 | -570 | -310 | -486 | -1366 | +AMX | +0 | +0 | +1312 | +1312 |
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-# [1] 0.59
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1162,19 +1169,19 @@ own:Hospital A -0.5931973 +0.5864297 Hospital B -0.5891020 +0.5778776 Hospital C -0.5969416 +0.5783004 @@ -1199,23 +1206,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5818110 +0.5938144 Hospital A -0.5931973 -3675 +0.5864297 +3714 Hospital B -0.5891020 -4276 +0.5778776 +4231 Hospital C -0.5969416 -1831 +0.5783004 +1871 @@ -1240,27 +1247,27 @@ therapies very easily: Hospital D -0.5818110 -2518 +0.5938144 +2425 Escherichia -0.6659801 -0.6620323 -0.8884312 +0.6667810 +0.6520322 +0.8814955 Klebsiella -0.6442167 -0.6610542 -0.8755490 +0.6349085 +0.6692073 +0.8833841 Staphylococcus -0.6523353 -0.6640891 -0.8892669 +0.6599815 +0.6497994 +0.8707189 @@ -1288,23 +1295,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.4650667 +0.4787291 0.0000000 -0.4650667 +0.4787291 Hospital A -59.3% -37.6% +58.6% +36.7% Hospital B -58.9% -37.3% +57.8% +36.4% Hospital C -59.7% -36.4% +57.8% +37.7% @@ -1420,16 +1427,18 @@ classes) Hospital D -58.2% -36.3% +59.4% +36.5% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 4 0.5 0.0625 0.25 64 0.025 0.002 128 0.25 16 -# [11] 0.0625 0.002 32 32 64 >=256 0.005 0.25 32 2 -# [21] 4 0.002 0.01 128 >=256 0.0625 2 0.002 4 0.001 -# [31] 4 8 128 0.001 0.0625 32 0.01 0.002 64 16 -# [41] 8 16 0.25 0.25 0.001 64 128 0.025 0.01 2 -# [51] 0.01 1 0.0625 8 4 8 0.25 128 0.002 0.001 -# [61] 1 2 0.25 0.5 128 0.125 0.125 1 0.5 0.001 -# [71] 0.002 0.002 16 64 0.0625 2 0.0625 0.025 0.5 0.002 -# [81] 4 >=256 0.01 32 0.025 0.002 0.125 128 8 4 -# [91] 0.005 4 1 4 128 >=256 0.01 8 128 32
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 31 21 27 24 29 23 31 18 22 25 23 27 28 21 26 20 18 30 29 28 25 25 22 17 27
-# [26] 22 26 30 24 25 27 18 28 20 25 30 28 22 22 31 30 27 25 22 26 21 30 31 20 27
-# [51] 31 21 22 19 21 19 29 29 19 31 30 18 18 19 27 18 18 27 29 28 21 23 18 29 20
-# [76] 17 20 18 22 25 21 20 28 26 27 22 19 30 19 18 29 28 29 23 19 21 18 25 19 17
+# [1] 20 19 27 26 31 31 29 20 28 29 17 25 20 20 26 30 21 26 28 26 29 28 25 17 19
+# [26] 18 25 25 24 21 21 17 25 17 31 18 21 18 21 30 18 29 20 27 29 29 19 25 21 22
+# [51] 30 25 30 21 22 23 25 22 27 19 17 30 28 25 17 19 21 26 18 22 31 27 21 26 20
+# [76] 21 30 24 26 17 31 23 23 23 19 25 31 17 21 23 24 22 29 23 24 21 22 27 27 23
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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