From 49a33243404d21f2ab3179fae899ed2ec0e24ba6 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 21 Oct 2022 08:06:38 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9024@3102beb --- articles/AMR.html | 532 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 38189 -> 38759 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 52689 -> 56611 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 27424 -> 28131 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 37926 -> 39169 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 37606 -> 37202 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 50909 -> 50455 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 43120 -> 42887 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28407 -> 28447 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78023 -> 78123 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49914 -> 49919 bytes articles/MDR.html | 56 +- articles/SPSS.html | 2 +- articles/datasets.html | 18 +- pkgdown.yml | 2 +- reference/Rplot005.png | Bin 13255 -> 13197 bytes reference/Rplot006.png | Bin 12789 -> 12739 bytes reference/Rplot007.png | Bin 13592 -> 15720 bytes reference/Rplot008.png | Bin 16664 -> 16487 bytes reference/Rplot009.png | Bin 8560 -> 8127 bytes reference/age.html | 20 +- reference/as.rsi.html | 20 +- reference/get_episode.html | 138 ++--- reference/kurtosis.html | 4 +- reference/mean_amr_distance.html | 76 +-- reference/plot-1.png | Bin 26891 -> 26798 bytes reference/plot-2.png | Bin 27131 -> 27040 bytes reference/plot-3.png | Bin 27954 -> 28556 bytes reference/plot-4.png | Bin 38711 -> 38753 bytes reference/plot-5.png | Bin 38855 -> 38736 bytes reference/plot-6.png | Bin 37623 -> 37518 bytes reference/plot-7.png | Bin 37991 -> 41166 bytes reference/plot-8.png | Bin 52842 -> 52920 bytes reference/plot-9.png | Bin 26220 -> 24738 bytes reference/random.html | 33 +- reference/skewness.html | 2 +- search.json | 2 +- 37 files changed, 452 insertions(+), 453 deletions(-) diff --git a/articles/AMR.html b/articles/AMR.html index 9da4d567..57962d2c 100644 --- a/articles/AMR.html +++ b/articles/AMR.html @@ -162,7 +162,7 @@
vignettes/AMR.Rmd
AMR.Rmd
Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 20 October 2022.
+Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 21 October 2022.
So only 53.3% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
So only 53.1% is suitable for resistance analysis! We can now filter on it with the filter()
function, also from the dplyr
package:
data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
-So we end up with 10,663 isolates for analysis. Now our data looks like:
+So we end up with 10,623 isolates for analysis. Now our data looks like:
head(data_1st)
2 | -2014-02-09 | -T10 | -Hospital C | -B_STRPT_PNMN | -S | -S | -S | +2013-05-29 | +G1 | +Hospital A | +B_ESCHR_COLI | R | -F | -Gram-positive | -Streptococcus | -pneumoniae | +S | +S | +S | +M | +Gram-negative | +Escherichia | +coli | TRUE |
3 | -2017-03-28 | -P6 | -Hospital B | +2012-08-07 | +U2 | +Hospital A | B_ESCHR_COLI | -R | -R | +S | +S | S | S | F | @@ -569,64 +569,64 @@ Longest: 1TRUE | |||||||||
5 | -2016-10-13 | -F4 | +4 | +2012-05-20 | +V3 | Hospital D | -B_ESCHR_COLI | -R | -R | -S | -S | -M | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||||
6 | -2013-09-14 | -Y9 | -Hospital D | -B_STRPT_PNMN | -S | -S | -S | -R | -F | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -|||||||||||
7 | -2016-09-03 | -A7 | -Hospital B | B_STPHY_AURS | S | S | +R | S | -S | -M | +F | Gram-positive | Staphylococcus | aureus | TRUE | |||||||||
11 | -2012-12-21 | -O1 | -Hospital A | +5 | +2014-06-18 | +M1 | +Hospital D | +B_KLBSL_PNMN | +R | +S | +S | +S | +M | +Gram-negative | +Klebsiella | +pneumoniae | +TRUE | +|||||||
6 | +2016-02-29 | +V8 | +Hospital B | +B_STPHY_AURS | +R | +R | +S | +S | +F | +Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||||||||||
7 | +2010-05-10 | +B9 | +Hospital D | B_STRPT_PNMN | S | S | S | R | -F | +M | Gram-positive | Streptococcus | pneumoniae | @@ -653,8 +653,8 @@ Longest: 1|||||||||||
1 | Escherichia coli | -4,612 | -43.25% | -4,612 | -43.25% | +4,630 | +43.58% | +4,630 | +43.58% | |||||||||||||||
2 | Staphylococcus aureus | -2,732 | -25.62% | -7,344 | -68.87% | +2,710 | +25.51% | +7,340 | +69.10% | |||||||||||||||
3 | Streptococcus pneumoniae | -2,151 | -20.17% | -9,495 | -89.05% | +2,057 | +19.36% | +9,397 | +88.46% | |||||||||||||||
4 | Klebsiella pneumoniae | -1,168 | -10.95% | -10,663 | +1,226 | +11.54% | +10,623 | 100.00% | ||||||||||||||||
2014-02-09 | -T10 | +2010-05-10 | +B9 | +Hospital D | +B_STRPT_PNMN | +S | +S | +S | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||||||
2017-02-28 | +B6 | +Hospital D | +B_STRPT_PNMN | +S | +S | +S | +R | +M | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||||||||||
2016-03-07 | +L6 | Hospital C | -B_STRPT_PNMN | -S | +B_ESCHR_COLI | +R | S | S | R | -F | -Gram-positive | -Streptococcus | -pneumoniae | +M | +Gram-negative | +Escherichia | +coli | TRUE | ||||||
2013-09-14 | -Y9 | +2011-02-04 | +J2 | Hospital D | B_STRPT_PNMN | -S | -S | +R | +R | S | R | -F | +M | Gram-positive | Streptococcus | pneumoniae | TRUE | |||||||
2012-12-21 | -O1 | +2015-07-22 | +X8 | Hospital A | -B_STRPT_PNMN | +B_STPHY_AURS | S | S | S | R | F | Gram-positive | +Staphylococcus | +aureus | +TRUE | +|||||||||
2017-03-20 | +P7 | +Hospital D | +B_STRPT_PNMN | +R | +R | +R | +R | +F | +Gram-positive | Streptococcus | pneumoniae | TRUE | ||||||||||||
2011-07-03 | -S2 | -Hospital B | -B_ESCHR_COLI | -S | -S | -S | -R | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||||||||
2010-04-27 | -Y1 | -Hospital A | -B_ESCHR_COLI | -S | -S | -S | -R | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||||||||
2017-06-16 | -V4 | -Hospital D | -B_ESCHR_COLI | -R | -S | -S | -R | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -
If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the bug_drug_combinations()
function:
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] 0.5430929
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
-0.5517885
+0.5565721
Hospital B
-0.5364807
+0.5457235
Hospital C
-0.5249089
+0.5533546
Hospital D
-0.5559306
+0.5385735
@@ -1008,23 +1008,23 @@ Longest: 24
Hospital A
-0.5517885
-3215
+0.5565721
+3279
Hospital B
-0.5364807
-3728
+0.5457235
+3718
Hospital C
-0.5249089
-1646
+0.5533546
+1565
Hospital D
-0.5559306
-2074
+0.5385735
+2061
@@ -1047,27 +1047,27 @@ Longest: 24
Escherichia
-0.7708153
-0.8751084
-0.9754987
+0.7723542
+0.8753780
+0.9790497
Klebsiella
-0.8176370
-0.8921233
-0.9803082
+0.8083197
+0.8907015
+0.9787928
Staphylococcus
-0.7877013
-0.8905564
-0.9802343
+0.7911439
+0.8856089
+0.9833948
Streptococcus
-0.5281265
+0.5333009
0.0000000
-0.5281265
+0.5333009
@@ -1092,23 +1092,23 @@ Longest: 24
Hospital A
-55.2%
+55.7%
28.5%
Hospital B
-53.6%
-25.4%
+54.6%
+25.6%
Hospital C
-52.5%
-26.3%
+55.3%
+26.5%
Hospital D
-55.6%
-27.4%
+53.9%
+24.8%
@@ -1206,18 +1206,16 @@ Longest: 24
mic_values <- random_mic(size = 100)
mic_values
# Class 'mic'
-# [1] 32 0.025 4 0.01 32 <=0.001 0.0625 0.002 0.125
-# [10] 4 64 64 0.01 0.005 64 0.125 8 1
-# [19] 0.25 0.002 0.01 16 0.01 256 32 2 0.005
-# [28] 8 0.002 0.125 0.025 0.005 1 0.025 4 0.005
-# [37] 4 <=0.001 64 32 0.025 0.125 1 64 0.002
-# [46] 0.005 0.5 0.005 0.0625 0.5 0.125 1 0.25 0.025
-# [55] 1 0.005 0.002 0.0625 2 32 0.01 0.0625 16
-# [64] 0.005 0.125 0.01 4 0.5 4 2 0.01 0.25
-# [73] 16 <=0.001 0.0625 0.0625 64 16 0.0625 0.25 0.01
-# [82] 256 128 64 16 0.25 8 64 0.002 <=0.001
-# [91] 256 <=0.001 32 0.5 16 <=0.001 0.5 16 0.5
-# [100] 16
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 28 27 22 29 26 26 28 22 31 20 23 18 26 31 28 18 17 19 17 23 19 21 27 28 24
-# [26] 30 27 22 21 24 28 28 24 18 31 31 17 17 30 30 17 30 26 27 21 17 28 20 21 27
-# [51] 31 28 23 24 30 19 27 30 24 29 23 26 22 24 17 17 31 20 27 20 22 29 27 28 30
-# [76] 20 31 25 29 20 29 27 28 29 20 30 27 21 23 24 24 26 18 26 27 19 25 26 28 24
+# [1] 22 18 29 23 26 26 22 22 17 28 29 31 25 28 22 27 28 30 27 26 28 29 31 19 26
+# [26] 25 25 24 25 30 17 21 25 21 18 17 30 23 30 19 18 29 25 29 27 23 28 21 17 25
+# [51] 27 23 17 29 28 25 30 23 21 22 20 21 28 25 23 31 29 25 31 17 22 20 21 17 19
+# [76] 17 21 21 18 18 20 29 30 21 18 23 18 29 25 22 27 22 22 24 24 25 27 31 26 18
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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