From a153eb26260db6eb4dc1942e8816cefff6ae499f Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 29 Nov 2022 18:45:20 +0000 Subject: [PATCH] Built site for AMR: 1.8.2.9054@6017f81 --- articles/AMR.html | 514 +++++++++--------- .../AMR_files/figure-html/disk_plots-1.png | Bin 38090 -> 39257 bytes .../figure-html/disk_plots_mo_ab-1.png | Bin 52875 -> 55217 bytes .../AMR_files/figure-html/mic_plots-1.png | Bin 28718 -> 27833 bytes .../AMR_files/figure-html/mic_plots-2.png | Bin 37435 -> 38507 bytes .../figure-html/mic_plots_mo_ab-1.png | Bin 38738 -> 37267 bytes .../figure-html/mic_plots_mo_ab-2.png | Bin 49533 -> 49948 bytes articles/AMR_files/figure-html/plot 1-1.png | Bin 43310 -> 42847 bytes articles/AMR_files/figure-html/plot 3-1.png | Bin 28398 -> 28454 bytes articles/AMR_files/figure-html/plot 4-1.png | Bin 78107 -> 78034 bytes articles/AMR_files/figure-html/plot 5-1.png | Bin 49896 -> 49877 bytes articles/MDR.html | 52 +- articles/SPSS.html | 2 +- articles/datasets.html | 2 +- pkgdown.yml | 2 +- reference/Rplot005.png | Bin 13167 -> 13172 bytes reference/Rplot006.png | Bin 12671 -> 12697 bytes reference/Rplot007.png | Bin 14225 -> 15662 bytes reference/Rplot008.png | Bin 20012 -> 17860 bytes reference/Rplot009.png | Bin 8970 -> 8473 bytes reference/age.html | 20 +- reference/as.rsi.html | 20 +- reference/get_episode.html | 143 +++-- reference/kurtosis.html | 4 +- reference/mean_amr_distance.html | 76 +-- reference/plot-1.png | Bin 26317 -> 26826 bytes reference/plot-2.png | Bin 27070 -> 26482 bytes reference/plot-3.png | Bin 28267 -> 28303 bytes reference/plot-4.png | Bin 38274 -> 38683 bytes reference/plot-5.png | Bin 38682 -> 38151 bytes reference/plot-6.png | Bin 37408 -> 36855 bytes reference/plot-7.png | Bin 39051 -> 41345 bytes reference/plot-8.png | Bin 58507 -> 54758 bytes reference/plot-9.png | Bin 27468 -> 26162 bytes reference/random.html | 32 +- reference/skewness.html | 2 +- search.json | 2 +- 37 files changed, 436 insertions(+), 435 deletions(-) diff --git a/articles/AMR.html b/articles/AMR.html index 053cd287..041d02a5 100644 --- a/articles/AMR.html +++ b/articles/AMR.html @@ -168,7 +168,7 @@
vignettes/AMR.Rmd
AMR.Rmd
Now, let’s start the cleaning and the analysis!
@@ -499,16 +499,16 @@ Longest: 1So only 53.2% is suitable for resistance analysis! We can now filter +
So only 53.5% is suitable for resistance analysis! We can now filter
on it with the filter()
function, also from the
dplyr
package:
@@ -634,12 +634,13 @@ on it with the data_1st <- data %>%
filter_first_isolate()
# Including isolates from ICU.
So we end up with 10,638 isolates for analysis. Now our data looks +
So we end up with 10,709 isolates for analysis. Now our data looks like:
head(data_1st)
date | patient_id | hospital | @@ -671,90 +673,96 @@ like:||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2016-12-09 | -B5 | -Hospital A | +3 | +2010-12-27 | +U10 | +Hospital B | B_KLBSL_PNMN | R | S | -R | S | -M | +S | +F | Gram-negative | Klebsiella | pneumoniae | TRUE |
2013-12-22 | -V7 | -Hospital B | -B_ESCHR_COLI | -S | -S | -S | -S | -F | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||
2011-09-01 | -J7 | -Hospital B | -B_STRPT_PNMN | -R | -R | -S | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||||
2010-09-10 | -N5 | -Hospital A | -B_ESCHR_COLI | -S | -S | -S | -S | -M | -Gram-negative | -Escherichia | -coli | -TRUE | -||||||
2015-12-02 | -E9 | -Hospital B | +4 | +2013-08-11 | +H1 | +Hospital C | B_STPHY_AURS | -S | -S | R | S | +S | +S | M | Gram-positive | Staphylococcus | aureus | TRUE |
7 | +2013-10-25 | +I3 | +Hospital A | +B_ESCHR_COLI | +R | +S | +R | +S | +M | +Gram-negative | +Escherichia | +coli | +TRUE | +|||||
2012-01-20 | -V9 | -Hospital B | -B_STPHY_AURS | -R | +9 | +2011-08-23 | +Y10 | +Hospital A | +B_ESCHR_COLI | R | S | S | +S | F | +Gram-negative | +Escherichia | +coli | +TRUE | +
11 | +2012-08-03 | +U10 | +Hospital A | +B_KLBSL_PNMN | +R | +S | +S | +S | +F | +Gram-negative | +Klebsiella | +pneumoniae | +TRUE | +|||||
12 | +2013-12-31 | +L3 | +Hospital A | +B_STPHY_AURS | +R | +S | +S | +S | +M | Gram-positive | Staphylococcus | aureus | @@ -793,8 +801,8 @@ readable:||||||
1 | Escherichia coli | -4,646 | -43.67% | -4,646 | -43.67% | +4,635 | +43.28% | +4,635 | +43.28% | |||||||||
2 | Staphylococcus aureus | -2,743 | -25.78% | -7,389 | -69.46% | +2,757 | +25.74% | +7,392 | +69.03% | |||||||||
3 | Streptococcus pneumoniae | -2,065 | -19.41% | -9,454 | -88.87% | +2,115 | +19.75% | +9,507 | +88.78% | |||||||||
4 | Klebsiella pneumoniae | -1,184 | -11.13% | -10,638 | +1,202 | +11.22% | +10,709 | 100.00% | ||||||||||
2011-09-01 | -J7 | +2014-06-23 | +T5 | +Hospital B | +B_STRPT_PNMN | +S | +S | +S | +R | +F | +Gram-positive | +Streptococcus | +pneumoniae | +TRUE | +||||
2016-09-29 | +N9 | +Hospital A | +B_ESCHR_COLI | +S | +S | +S | +R | +F | +Gram-negative | +Escherichia | +coli | +TRUE | +||||||
2011-01-04 | +E8 | Hospital B | B_STRPT_PNMN | R | @@ -909,54 +947,24 @@ antibiotic class they are in:TRUE | |||||||||||||
2014-11-04 | -C7 | +2017-12-28 | +Z5 | Hospital C | B_STRPT_PNMN | -R | -R | S | -R | -M | -Gram-positive | -Streptococcus | -pneumoniae | -TRUE | -||||
2010-05-22 | -X1 | -Hospital C | -B_ESCHR_COLI | -R | -I | +S | S | R | F | -Gram-negative | -Escherichia | -coli | -TRUE | -|||||
2011-03-20 | -A1 | -Hospital C | -B_STRPT_PNMN | -R | -R | -S | -R | -M | Gram-positive | Streptococcus | pneumoniae | TRUE | ||||||
2016-05-13 | -K9 | -Hospital A | +2010-08-11 | +C6 | +Hospital C | B_STRPT_PNMN | S | S | @@ -969,9 +977,9 @@ antibiotic class they are in:TRUE | |||||||||
2014-01-21 | -Q10 | -Hospital D | +2012-08-24 | +Z9 | +Hospital A | B_STRPT_PNMN | S | S | @@ -1005,50 +1013,50 @@ different bug/drug combinations, you can use the||||||||||
E. coli | AMX | -2171 | -147 | -2328 | -4646 | +2204 | +121 | +2310 | +4635 | |||||||||
E. coli | AMC | -3429 | -157 | -1060 | -4646 | +3389 | +150 | +1096 | +4635 | |||||||||
E. coli | CIP | -3354 | +3408 | 0 | -1292 | -4646 | +1227 | +4635 | ||||||||||
E. coli | GEN | -4083 | +4065 | 0 | -563 | -4646 | +570 | +4635 | ||||||||||
K. pneumoniae | AMX | 0 | 0 | -1184 | -1184 | +1202 | +1202 | |||||||||||
K. pneumoniae | AMC | -936 | -42 | -206 | -1184 | +927 | +50 | +225 | +1202 |
proportion_SI()
, equa
own:
data_1st %>% resistance(AMX)
-# [1] 0.5455913
Or can be used in conjunction with group_by()
and
summarise()
, both from the dplyr
package:
@@ -1144,19 +1152,19 @@ own:Hospital A -0.5382918 +0.5461974 Hospital B -0.5347408 +0.5343758 Hospital C -0.5776965 +0.5487149 @@ -1181,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R): Hospital D -0.5509126 +0.5482517 Hospital A -0.5382918 -3173 +0.5461974 +3182 Hospital B -0.5347408 -3742 +0.5343758 +3709 Hospital C -0.5776965 -1641 +0.5487149 +1673 @@ -1222,27 +1230,27 @@ therapies very easily: Hospital D -0.5509126 -2082 +0.5482517 +2145 Escherichia -0.7718467 -0.8788205 -0.9750323 +0.7635383 +0.8770227 +0.9766990 Klebsiella -0.8260135 -0.9062500 -0.9873311 +0.8128120 +0.9109817 +0.9833611 Staphylococcus -0.7907401 -0.8877142 -0.9817718 +0.7972434 +0.8734131 +0.9818643 @@ -1270,23 +1278,23 @@ classes, use a antibiotic class selector such as Streptococcus -0.5438257 +0.5399527 0.0000000 -0.5438257 +0.5399527 Hospital A -53.8% -25.3% +54.6% +27.7% Hospital B -53.5% -25.1% +53.4% +26.4% Hospital C -57.8% -30.1% +54.9% +25.2% @@ -1402,18 +1410,16 @@ classes) Hospital D -55.1% -26.3% +54.8% +26.7% <mic>
and<disk>
:mic_values <- random_mic(size = 100) mic_values # Class 'mic' -# [1] 8 0.01 0.025 32 0.01 16 32 >=256 0.125 -# [10] 128 0.5 0.125 128 0.005 4 2 0.01 0.0625 -# [19] 0.025 4 <=0.001 0.025 0.002 0.125 0.0625 0.0625 0.01 -# [28] 0.025 <=0.001 16 8 0.005 0.0625 2 2 0.002 -# [37] 0.0625 64 0.025 0.005 0.125 0.002 2 16 0.005 -# [46] 4 16 >=256 0.25 64 128 1 8 0.0625 -# [55] 4 0.002 32 0.0625 8 128 0.0625 64 0.0625 -# [64] 8 0.125 1 <=0.001 128 0.002 8 1 0.002 -# [73] 0.002 64 0.125 0.005 0.5 8 0.025 0.125 0.005 -# [82] 0.005 0.002 <=0.001 0.0625 2 0.125 2 0.25 64 -# [91] 0.25 4 <=0.001 0.125 0.005 0.5 4 0.0625 64 -# [100] 2
# base R:
plot(mic_values)
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
# Class 'disk'
-# [1] 31 26 24 18 17 18 27 18 28 19 17 23 30 18 22 25 28 27 19 21 27 31 27 20 31
-# [26] 20 18 24 17 17 30 18 24 25 29 29 17 25 18 18 17 31 20 29 30 18 24 29 23 27
-# [51] 17 19 29 17 29 24 22 17 19 19 28 25 25 25 31 30 30 23 28 29 27 20 18 31 28
-# [76] 24 30 22 27 20 20 28 23 31 25 19 30 20 19 19 21 28 27 19 31 21 28 30 17 18
+# [1] 31 26 18 31 23 20 17 17 28 29 27 20 23 19 19 24 23 29 20 17 24 26 31 21 20
+# [26] 26 19 20 18 31 18 17 31 19 26 20 19 27 20 22 17 25 24 29 19 24 28 25 20 22
+# [51] 30 23 18 28 29 22 18 23 30 18 18 22 24 29 26 23 31 31 21 20 31 21 26 23 25
+# [76] 23 26 25 29 22 26 18 23 29 26 31 25 17 30 23 21 28 31 26 30 29 29 25 28 27
# base R:
plot(disk_values, mo = "E. coli", ab = "cipro")
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